From 500a140603e9eb95baa9bc43b5a68eeaff73e05b Mon Sep 17 00:00:00 2001
From: pavan-kumar-s <138394293+pavan-kumar-s@users.noreply.github.com>
Date: Sat, 16 Dec 2023 22:14:56 +0530
Subject: [PATCH 1/4] Update printFunctionIO.m
This function can handle no output case. Also, it can print inputs, outputs, notes, authors, example.
---
src/base/codeConsistency/printFunctionIO.m | 342 ++++++++++++++-------
1 file changed, 239 insertions(+), 103 deletions(-)
diff --git a/src/base/codeConsistency/printFunctionIO.m b/src/base/codeConsistency/printFunctionIO.m
index 5d7d3a75c6..a991b318ad 100644
--- a/src/base/codeConsistency/printFunctionIO.m
+++ b/src/base/codeConsistency/printFunctionIO.m
@@ -7,8 +7,6 @@
%
% INPUTS:
% functionName: name of the function to print io for
-%
-% OPTIONAL INPUTS:
% derivedInputNames: name of a variable derived from an input variable
% or a cell array of variable names
% printLevel: if >0 then print to terminal (default 1)
@@ -19,43 +17,104 @@
%
% NOTE:
%
-% Author(s): Ronan Fleming
-
-% EXAMPLE:
-% [inputs,outputs] = printFunctionInputsAndOutputs('solveCobraLP',{},1);
-%
-% Returns the following:
-% INPUTS:
-% LPproblem.A:
-% LPproblem.S:
-% LPproblem.csense:
-% LPproblem.b:
-% LPproblem.osense:
-% LPproblem.modelID:
-% LPproblem.c:
-% LPproblem.lb:
-% LPproblem.ub:
-% LPproblem.basis:
-% LPproblem.LPBasis:
-% varargin:
-%
-% OUTPUTS:
-% solution.basis:
-% solution.solver:
-% solution.algorithm:
-% solution.slack:
-% solution.obj:
-% solution.rcost:
-% solution.dual:
-% solution.stat:
-% solution.origStat:
-% solution.origStatText:
+% Author(s):
+% - Ronan Fleming
+% - Pavan, BiSECt Lab
%
% EXAMPLE:
-%
-% NOTE:
-%
-% Author(s):
+%
+% [inputs,outputs] = printFunctionIO('solveCobraLP',{},1);
+%
+% Returns the following:
+% USAGE:
+% solution = solveCobraLP(LPproblem, varargin)
+%
+% INPUTS:
+% LPproblem.mat:
+% LPproblem.A :* .A - m x n linear constraint matrix
+% LPproblem.S:
+% LPproblem.csense :* .csense - m x 1 character array of constraint senses, one for each row in A
+% must be either ('E', equality, 'G' greater than, 'L' less than).
+% LPproblem.b :* .b - m x 1 right hand sider vector for constraint A*x = b
+% LPproblem.osense :* .osense - scalar objective sense (-1 means maximise (default), 1 means minimise)
+% LPproblem.modelID:
+% LPproblem.c :* .c - n x 1 linear objective coefficient vector
+% LPproblem.lb :* .lb - n x 1 lower bound vector for lb <= x
+% LPproblem.ub :* .ub - n x 1 upper bound vector for x <= ub
+% LPproblem.basis:
+% LPproblem.LPBasis:
+% LPproblem.solve:
+% LPproblem.Solution:
+% LPproblem.Model:
+% LPproblem.Param:
+% varargin : Additional parameters either as parameter struct, or as
+% parameter/value pairs. A combination is possible, if
+% the parameter struct is either at the beginning or the
+% end of the optional input.
+% All fields of the struct which are not COBRA parameters
+% (see `getCobraSolverParamsOptionsForType`) for this
+% problem type will be passed on to the solver in a
+% solver specific manner. Some optional parameters which
+% can be passed to the function as parameter value pairs,
+% or as part of the options struct are listed below:
+%
+% OUTPUTS:
+% solution.basis :* .basis: (optional) LP basis corresponding to solution
+% solution.solver :* .solver: Solver used to solve LP problem
+% solution.algorithm :* .algorithm: Algorithm used by solver to solve LP problem
+% solution.slack:
+% solution.obj :* .obj: Objective value
+% solution.rcost :* .rcost: Reduced costs, dual solution to :math:`lb <= v <= ub`
+% solution.dual :* .dual: dual solution to `A*v ('E' | 'G' | 'L') b`
+% solution.stat :* .stat: Solver status in standardized form
+% solution.origStat :* .origStat: Original status returned by the specific solver
+% solution.origStatText:* .origStatText: Original status text returned by the specific solver
+%
+% EXAMPLE:
+%
+%
+% %Optional parameters can be entered in three different ways {A,B,C}
+%
+% %A) as a problem specific parameter followed by parameter value:
+% [solution] = solveCobraLP(LP, 'printLevel', 1);
+% [solution] = solveCobraLP(LP, 'printLevel', 1, 'feasTol', 1e-8);
+%
+% %B) as a parameters structure with field names specific to a specific solver
+% [solution] = solveCobraLP(LPCoupled, parameters);
+%
+% %C) as parameter followed by parameter value, with a parameter structure
+% %with field names specific to a particular solvers internal parameter,
+% %fields as the LAST argument
+% [solution] = solveCobraLP(LPCoupled, 'printLevel', 1, 'feasTol', 1e-6, parameters);
+%
+%
+% NOTE:
+%
+% Optional parameters can also be set through the
+% solver can be set through `changeCobraSolver('LP', value)`;
+% `changeCobraSolverParams('LP', 'parameter', value)` function. This
+% includes the minNorm and the `printLevel` flags.
+%
+%
+% Author(s):
+%
+% - Markus Herrgard, 08/29/06
+% - Ronan Fleming, 11/12/08 'cplex_direct' allows for more refined control
+% of cplex than tomlab tomrun
+% - Ronan Fleming, 04/25/09 Option to minimise the Euclidean Norm of internal
+% fluxes using either 'cplex_direct' solver or 'pdco'
+% - Jan Schellenberger, 09/28/09 Changed header to be much simpler. All parameters
+% now accessed through changeCobraSolverParams(LP, parameter,value)
+% - Richard Que, 11/30/09 Changed handling of optional parameters to use
+% getCobraSolverParams().
+% - Ronan Fleming, 12/07/09 Commenting of input/output
+% - Ronan Fleming, 21/01/10 Not having second input, means use the parameters as specified in the
+% global paramerer variable, rather than 'default' parameters
+% - Steinn Gudmundsson, 03/03/10 Added support for the Gurobi solver
+% - Ronan Fleming, 01/24/01 Now accepts an optional parameter structure with nonstandard
+% solver specific parameter options
+% - Tim Harrington, 05/18/12 Added support for the Gurobi 5.0 solver
+% - Ronan Fleming, 07/04/13 Reinstalled support for optional parameter structure
if ~exist('functionName','var')
functionName = 'solveCobraLP.m';
@@ -70,6 +129,13 @@
str = fileread(which(functionName));
C = regexp(str, '\r\n|\r|\n', 'split')';
+% to get the function descriptors
+temp = find(~(startsWith(C,'%')|cellfun(@isempty,C)));
+idS = temp(1);
+idE = temp(2);
+funcDes = C(idS+1:idE-1);
+[inpDes,outDes,noteDes,authDes,exDes,opInpDes] = getDescriptors(funcDes);
+
boolHeader = contains(C,strrep(functionName,'.m',''));
if any(boolHeader)
header = C{boolHeader};
@@ -89,52 +155,29 @@
inputNames = [inputNames;derivedInputNames];
end
-for i=1:length(inputNames)
- inputNames{i} = strtrim(inputNames{i});
-end
n=1;
for i=1:length(inputNames)
%https://nl.mathworks.com/help/matlab/ref/alphanumericspattern.html
- pat = pattern([sprintf(inputNames{i})]) + '.' + alphanumericsPattern;
+ pat = pattern(sprintf(inputNames{i})) + '.' + alphanumericsPattern;
inputInds = find(contains(C,pat));
if isempty(inputInds)
- inputs{n,1}=inputNames{i};
+ inputs{n,1}=strtrim(inputNames{i});
n=n+1;
else
for j=1:length(inputInds)
extractedText = extract(C{inputInds(j)},pat);
- if any(contains(extractedText,'LPproblem.Solution')) || 0
- disp(extractedText)
- end
extractedField = extract(extractedText,'.' + alphanumericsPattern);
for k=1:length(extractedField)
inputs{n,1} = strtrim([inputNames{i} extractedField{k}]);
%disp(inputs{n,1})
n=n+1;
-
- %one level deeper
- pat2 = pattern((sprintf(inputNames{i}))) + extractedField{k} + '.' + alphanumericsPattern;
- outputInds2 = find(contains(C,pat2));
- if ~isempty(outputInds2)
- for j2=1:length(outputInds2)
- extractedText2 = extract(C{outputInds2(j2)},pat2);
- extractedField2 = extract(extractedText2,'.' + alphanumericsPattern);
- for k2=1:length(extractedField2)
- inputs{n,1} = strtrim([inputNames{i} extractedField{k} extractedField2{k2}]);
- n=n+1;
- end
- end
- end
-
end
end
end
end
inputs = unique(inputs,'stable');
-
-
%outputs
indL = strfind(header,'[');
indR = strfind(header,']');
@@ -151,50 +194,45 @@
outputNames = strtrim(outputNames);
end
n=1;
-if isempty(outputNames)
- outputs = [];
-else
- for i=1:length(outputNames)
- %https://nl.mathworks.com/help/matlab/ref/alphanumericspattern.html
- pat = pattern((sprintf(outputNames{i}))) + '.' + alphanumericsPattern;
- outputInds = find(contains(C,pat));
- if isempty(outputInds)
- outputs{n,1}=strtrim(outputNames{i});
- n=n+1;
- else
- for j=1:length(outputInds)
- extractedText = extract(C{outputInds(j)},pat);
- if any(strcmp(extractedText,'LPproblem.Solution')) || 0
- disp(extractedText)
- end
- extractedField = extract(extractedText,'.' + alphanumericsPattern);
- for k=1:length(extractedField)
-
- outputs{n,1} = strtrim([outputNames{i} extractedField{k}]);
- n=n+1;
-
- %one level deeper
- pat2 = pattern((sprintf(outputNames{i}))) + extractedField{k} + '.' + alphanumericsPattern;
- outputInds2 = find(contains(C,pat2));
- if ~isempty(outputInds2)
- for j2=1:length(outputInds2)
- extractedText2 = extract(C{outputInds2(j2)},pat2);
- extractedField2 = extract(extractedText2,'.' + alphanumericsPattern);
- for k2=1:length(extractedField2)
- outputs{n,1} = strtrim([outputNames{i} extractedField{k} extractedField2{k2}]);
- n=n+1;
- end
- end
- end
- end
+for i=1:length(outputNames)
+ %https://nl.mathworks.com/help/matlab/ref/alphanumericspattern.html
+ pat = pattern([' ' sprintf(outputNames{i})]) + '.' + alphanumericsPattern;
+ outputInds = find(contains(C,pat));
+ if isempty(outputInds)
+ outputs{n,1}=strtrim(outputNames{i});
+ n=n+1;
+ else
+ for j=1:length(outputInds)
+ extractedText = extract(C{outputInds(j)},pat);
+ extractedField = extract(extractedText,'.' + alphanumericsPattern);
+ for k=1:length(extractedField)
+ outputs{n,1} = strtrim([outputNames{i} extractedField{k}]);
+ %disp(inputs{n,1})
+ n=n+1;
end
end
end
- outputs = unique(outputs,'stable');
end
-
+if ~exist('outputs','var')
+ outputs = {};
+end
+outputs = unique(outputs,'stable');
maxLength=max(cellfun('length',[outputs;inputs]));
-maxLength = maxLength +8;
+
+InpVar = {};
+for i=1:numel(inputs)
+ var = getVariableDescriptor(inputs{i},inpDes,maxLength);
+ if strcmp(['% ',inputs{i},':'],var)
+ var = getVariableDescriptor(inputs{i},opInpDes,maxLength);
+ end
+ InpVar{i} = var;
+end
+
+OutVar = {};
+for i=1:numel(outputs)
+ var = getVariableDescriptor(outputs{i},outDes,maxLength);
+ OutVar{i} = var;
+end
if printLevel>0
fprintf('%s\n','%');
@@ -204,21 +242,119 @@
fprintf('%s\n','%');
fprintf('%s\n','% INPUTS:')
for i=1:length(inputs)
- fprintf('%s\n',pad(['% ' inputs{i} ':'],maxLength - length(inputs{i}) - 3))
+ fprintf('%s\n',InpVar{i})
end
fprintf('%s\n','%');
fprintf('%s\n','% OUTPUTS:')
for i=1:length(outputs)
- fprintf('%s\n',pad(['% ' outputs{i} ':'],maxLength - length(outputs{i}) - 3))
+ fprintf('%s\n',OutVar{i})
end
fprintf('%s\n','%');
fprintf('%s\n','% EXAMPLE:')
+ fprintf('%s\n',' % ', strjoin(exDes,'\n '))
fprintf('%s\n','%');
fprintf('%s\n','% NOTE:');
+ fprintf('%s\n','%', strjoin(noteDes,'\n'))
fprintf('%s\n','%');
fprintf('%s\n','% Author(s):');
+ fprintf('%s\n','%', strjoin(authDes,'\n'))
end
end
+
+function var = getVariableDescriptor(a,des,maxLength)
+des = strrep(des,'%','');
+if contains(a,'.')
+ % if the variable is a field
+ t = split(a,'.');
+ pa = pattern('*')+(" "|"")+("."|"")+pattern(t{2});
+ id = find(contains(des,pa));
+ if numel(id)>1 % what if the same field is present twice
+ pa2 = whitespacePattern+pattern(t{1});
+ id2 = find(contains(des,pa2));
+ id = id(id >id2(1));
+ id = id(1);
+ end
+ field =1;
+else
+ pa = whitespacePattern +pattern(a);
+ id = find(contains(des,pa));
+ field =0;
+end
+
+if isempty(id)
+ var = ['% ',a,':'];
+ return
+end
+ % to count number of leading spaces in des
+ des2 = des(id:end);
+ spaceCount = cellfun(@(x) numel(regexp(x, '^\s*', 'match', 'once')), des2);
+ id2 = find(spaceCount<=spaceCount(1));
+ id2 = id2(2)-1;
+ var = des2(1:id2);
+ if field
+ var{1} = ['% ',pad(a,maxLength),':',strtrim(var{1})];
+ for i =2:numel(var)
+ var{i}= ['% ',pad('',maxLength),strtrim(var{i})];
+ end
+ else
+ var{1} = ['% ',strtrim(strrep(var{1},[a,':'],[pad(a,maxLength),':']))];
+ for i =2:numel(var)
+ var{i}= ['% ',pad('',maxLength),strtrim(var{i})];
+ end
+ end
+ if ischar(var)
+ var = var;
+ else
+ var =strjoin(var,'\n');
+ end
+
+end
+
+
+
+function [inpDes,outDes,noteDes,authDes,exDes,opInpDes] = getDescriptors(funcDes)
+ % to get the input, output, notes, author, example descriptions
+ inpPat = pattern("%")+(" "|"")+("INPUT"|"INPUTS");
+ outPat = pattern("%")+(" "|"")+("OUTPUT"|"OUTPUTS");
+ notePat = pattern("%")+(" "|"")+("NOTE");
+ authPat = pattern("%")+(" "|""|" .. ")+("Author"|"AUTHOR");
+ exPat = pattern("%")+(" "|"")+("EXAMPLE");
+ optInpPat = pattern("%")+(" "|"")+("OPTIONAL INPUTS");
+
+ inpID = find(contains(funcDes,inpPat));
+ outID = find(contains(funcDes,outPat));
+ noteID = find(contains(funcDes,notePat));
+ authID = find(contains(funcDes,authPat));
+ exID = find(contains(funcDes,exPat));
+ optInpID = find(contains(funcDes,optInpPat));
+
+ temp = ~cellfun(@isempty,{inpID;outID;noteID;authID;exID;optInpID});
+
+ ids=[];
+ temp2 = {'inpID','outID','noteID','authID','exID','optInpID'};
+ for i=1:numel(temp2)
+ if eval(['~isempty(',temp2{i},')'])
+ eval(['temp3 =',temp2{i},';'])
+ ids = [ids;temp3(1)];
+ end
+ end
+ [ids,B] = sort(ids);
+ Names ={'inpDes','outDes','noteDes','authDes','exDes','opInpDes'};
+ noNames = Names(temp==0);
+ for i=1:numel(noNames)
+ eval([noNames{i},'={};'])
+ end
+ Names = Names(temp~=0);
+ Names = Names(B);
+
+ for i=1:numel(ids)
+ if i==numel(ids)
+ eval([Names{i},'=funcDes(ids(i)+1:end);']);
+ else
+ eval([Names{i},'=funcDes(ids(i)+1:ids(i+1)-1);']);
+ end
+ end
+end
From 336e0e848511b6525c648a167a07d782c9c37e5a Mon Sep 17 00:00:00 2001
From: pavan-kumar-s <138394293+pavan-kumar-s@users.noreply.github.com>
Date: Wed, 20 Dec 2023 17:09:21 +0530
Subject: [PATCH 2/4] Add files via upload
---
docs/COBRA.bib | 53789 +++++++++++++++++++++++++++++++++++++++
docs/requirements.txt | 10 +-
docs/requirements2.txt | 9 +
3 files changed, 53805 insertions(+), 3 deletions(-)
create mode 100644 docs/COBRA.bib
create mode 100644 docs/requirements2.txt
diff --git a/docs/COBRA.bib b/docs/COBRA.bib
new file mode 100644
index 0000000000..905355e5b6
--- /dev/null
+++ b/docs/COBRA.bib
@@ -0,0 +1,53789 @@
+
+@article{ WOS:000391972600020,
+Author = {Yuan, Qianqian and Huang, Teng and Li, Peishun and Hao, Tong and Li,
+ Feiran and Ma, Hongwu and Wang, Zhiwen and Zhao, Xueming and Chen, Tao
+ and Goryanin, Igor},
+Title = {Pathway-Consensus Approach to Metabolic Network Reconstruction for
+ Pseudomonas putida KT2440 by Systematic Comparison of Published
+ Models},
+Journal = {PLOS ONE},
+Year = {2017},
+Volume = {12},
+Number = {1},
+Month = {JAN 13},
+Type = {Article},
+DOI = {10.1371/journal.pone.0169437},
+Article-Number = {e0169437},
+ISSN = {1932-6203},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GLUCOSE CATABOLISM; GENOTYPE; ENZYMES; YEAST},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Li, Feiran/GNP-2168-2022
+ Goryanin, Igor/J-1913-2015
+ Goryanin, Igor/AAB-1400-2022
+ Zhao, Xueming/W-4891-2019
+ CHEN, Tao/N-1817-2015
+ },
+ORCID-Numbers = {Li, Feiran/0000-0001-9155-5260
+ Goryanin, Igor/0000-0002-8293-774X
+ CHEN, Tao/0000-0001-9588-1821
+ ?, ?/0000-0001-8323-6163
+ Li, Peishun/0000-0003-4200-0474},
+Times-Cited = {27},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000391972600020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000391499900001,
+Author = {Demidenko, Aleksandr and Akberdin, Ilya R. and Allemann, Marco and
+ Allen, Eric E. and Kalyuzhnaya, Marina G.},
+Title = {Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense
+ 5G(B1)},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2017},
+Volume = {7},
+Month = {JAN 10},
+Type = {Article},
+DOI = {10.3389/fmicb.2016.02167},
+Article-Number = {2167},
+ISSN = {1664-302X},
+Keywords = {methane valorization; methanotrophs; fatty acid metabolism; farE; fatty
+ acid elongation},
+Keywords-Plus = {ACYL CARRIER PROTEIN; ESCHERICHIA-COLI; METHANOL DEHYDROGENASE;
+ MEMBRANE; LIPIDS; EXPRESSION; MODELS; STEROL; TOOLS; FABF},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Akberdin, Ilya/J-3172-2018
+ },
+ORCID-Numbers = {Akberdin, Ilya/0000-0003-0010-8620
+ Allemann, Marco/0000-0002-9290-7296},
+Times-Cited = {38},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000391499900001},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000400925200011,
+Author = {Anne, Jozef and Economou, Anastassios and Bernaerts, Kristel},
+Editor = {Bagnoli, F and Rappuoli, R},
+Title = {Protein Secretion in Gram-Positive Bacteria: From Multiple Pathways to
+ Biotechnology},
+Booktitle = {PROTEIN AND SUGAR EXPORT AND ASSEMBLY IN GRAM-POSITIVE BACTERIA},
+Series = {Current Topics in Microbiology and Immunology},
+Year = {2017},
+Volume = {404},
+Pages = {267-308},
+Type = {Review; Book Chapter},
+DOI = {10.1007/82\_2016\_49},
+ISSN = {0070-217X},
+EISSN = {2196-9965},
+ISBN = {978-3-319-56014-4; 978-3-319-56012-0},
+Keywords-Plus = {ARGININE TRANSLOCATION PATHWAY; I SIGNAL PEPTIDASES; CONTROLLED
+ GENE-EXPRESSION; SEC-INDEPENDENT PROTEIN; METABOLIC FLUX ANALYSIS;
+ LARGE-SCALE PRODUCTION; HIGH-LEVEL SECRETION; BACILLUS-SUBTILIS;
+ STREPTOMYCES-LIVIDANS; RECOMBINANT PROTEIN},
+Research-Areas = {Immunology; Microbiology},
+Web-of-Science-Categories = {Immunology; Microbiology},
+ResearcherID-Numbers = {Economou, Anastassios/P-8292-2017
+ ANNE, Jozef/H-7983-2019
+ },
+ORCID-Numbers = {Economou, Anastassios/0000-0002-1770-507X
+ ANNE, Jozef/0000-0002-0493-2644
+ Bernaerts, Kristel/0000-0001-6211-7042},
+Times-Cited = {38},
+Journal-ISO = {Curr.Top.Microbiol.Immunol.},
+Unique-ID = {WOS:000400925200011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000396840500004,
+Author = {Asghari, Arvand and Marashi, Sayed-Amir and Ansari-Pour, Naser},
+Title = {A sperm-specific proteome-scale metabolic network model identifies
+ non-glycolytic genes for energy deficiency in asthenozoospermia},
+Journal = {SYSTEMS BIOLOGY IN REPRODUCTIVE MEDICINE},
+Year = {2017},
+Volume = {63},
+Number = {2},
+Pages = {100-112},
+Type = {Article},
+DOI = {10.1080/19396368.2016.1263367},
+ISSN = {1939-6368},
+EISSN = {1939-6376},
+Keywords = {Asthenozoospermia; ATP production; energy metabolism; male infertility;
+ model reconstruction; sperm motility},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; IDIOPATHIC ASTHENOZOOSPERMIA;
+ OXIDATIVE-PHOSPHORYLATION; GLOBAL RECONSTRUCTION; INFERTILE MEN;
+ DOUBLE-BLIND; MOTILITY; CARNITINE; MITOCHONDRION; SPERMATOZOA},
+Research-Areas = {Endocrinology \& Metabolism; Reproductive Biology},
+Web-of-Science-Categories = {Andrology; Reproductive Biology},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008
+ Asghari, Arvand/C-7005-2019
+ },
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Asghari, Arvand/0000-0001-6184-0861
+ Ansari-Pour, Naser/0000-0003-0908-0484},
+Times-Cited = {28},
+Journal-ISO = {Syst. Biol. Reprod. Med.},
+Unique-ID = {WOS:000396840500004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000400684700004,
+Author = {Carbonell, Pablo and Lopez, Oriol and Amberg, Alexander and Pastor,
+ Manuel and Sanz, Ferran},
+Title = {Hepatotoxicity Prediction by Systems Biology Modeling of Disturbed
+ Metabolic Pathways Using Gene Expression Data},
+Journal = {ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION},
+Year = {2017},
+Volume = {34},
+Number = {2},
+Pages = {219-234},
+Type = {Article},
+DOI = {10.14573/altex.1602071},
+ISSN = {1868-596X},
+EISSN = {1868-8551},
+Keywords = {systems biology; predictive modeling; drug toxicity; hepatotoxicity;
+ gene regulation},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; INDUCED LIVER-INJURY; IN-SILICO; TOXICITY;
+ RECONSTRUCTION; NETWORK; QSAR; ROSUVASTATIN; MECHANISMS; CHALLENGES},
+Research-Areas = {Research \& Experimental Medicine},
+Web-of-Science-Categories = {Medicine, Research \& Experimental},
+ResearcherID-Numbers = {López-Massaguer, Oriol/C-3053-2014
+ Sanz, Ferran/B-3852-2009
+ Pastor, Manuel/A-1566-2010
+ Carbonell, Pablo/A-3572-2011},
+ORCID-Numbers = {López-Massaguer, Oriol/0000-0003-0148-1101
+ Sanz, Ferran/0000-0002-7534-7661
+ Pastor, Manuel/0000-0001-8850-1341
+ Carbonell, Pablo/0000-0002-0993-5625},
+Times-Cited = {14},
+Journal-ISO = {ALTEX-Altern. Anim. Exp.},
+Unique-ID = {WOS:000400684700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459648000035,
+Author = {Chakrabarti, Anirikh and Membrez, Mathieu and Morin-Rivron, Delphine and
+ Siddharth, Jay and Chou, Chieh Jason and Henry, Hugues and Bruce,
+ Stephen and Metairon, Sylviane and Raymond, Frederic and Betrisey,
+ Bertrand and Loyer, Carole and Parkinson, Scott J. and Masoodi, Mojgan},
+Title = {Transcriptomics-driven lipidomics (TDL) identifies the
+ microbiome-regulated targets of ileal lipid metabolism},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2017},
+Volume = {3},
+Type = {Article},
+DOI = {10.1038/s41540-017-0033-0},
+Article-Number = {33},
+EISSN = {2056-7189},
+Keywords-Plus = {INFLAMMATORY-BOWEL-DISEASE; HIGH-THROUGHPUT; GUT MICROBIOTA; LIPOPROTEIN
+ PROFILES; SHOTGUN LIPIDOMICS; ESCHERICHIA-COLI; EXPRESSION DATA; ACID;
+ DYSLIPIDEMIA; INTEGRATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {MASOODI, MOJGAN/P-1499-2019
+ },
+ORCID-Numbers = {MASOODI, MOJGAN/0000-0001-9840-1731
+ Chakrabarti, Anirikh/0000-0001-7804-209X
+ Raymond, Frederic/0000-0002-6148-6898},
+Times-Cited = {11},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000459648000035},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000414555900007,
+Author = {Dahal, Sanjeev and Poudel, Suresh and Thompson, R. Adam},
+Editor = {Nookaew, I},
+Title = {Genome-Scale Modeling of Thermophilic Microorganisms},
+Booktitle = {NETWORK BIOLOGY},
+Series = {Advances in Biochemical Engineering-Biotechnology},
+Year = {2017},
+Volume = {160},
+Pages = {103-119},
+Type = {Article; Book Chapter},
+DOI = {10.1007/10\_2016\_45},
+ISSN = {0724-6145},
+EISSN = {1616-8542},
+ISBN = {978-3-319-56460-9; 978-3-319-56459-3},
+Keywords = {Draft reconstruction; Flux balance analysis; Flux variability analysis;
+ Gap-filling; Genome-scale models; Stoichiometric matrix},
+Keywords-Plus = {CLOSTRIDIUM-THERMOCELLUM; ANAEROBIC-DIGESTION; THERMOTOGA-MARITIMA;
+ THERMOBIFIDA-FUSCA; SOLID-WASTE; SEQUENCE; BACTERIA; METABOLISM;
+ PHYSIOLOGY; LIFE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Poudel, Suresh/AAG-4383-2021
+ },
+ORCID-Numbers = {Dahal, Sanjeev/0000-0003-4636-7732},
+Times-Cited = {6},
+Journal-ISO = {Adv. Biochem. Eng. Biotechnol.},
+Unique-ID = {WOS:000414555900007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392565200002,
+Author = {Gonzalez, Jacqueline E. and Long, Christopher P. and Antoniewicz, Maciek
+ R.},
+Title = {Comprehensive analysis of glucose and xylose metabolism in
+ Escherichia coli under aerobic and anaerobic conditions by
+ 13C metabolic flux analysis},
+Journal = {METABOLIC ENGINEERING},
+Year = {2017},
+Volume = {39},
+Pages = {9-18},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2016.11.003},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Parallel labeling experiments; Metabolism; Model validation; Flux
+ estimation; Co-factor balances},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; GAS CHROMATOGRAPHY/MASS SPECTROMETRY;
+ MASS ISOTOPOMER DISTRIBUTIONS; SACCHAROMYCES-CEREVISIAE; NETWORK MODEL;
+ UNITS EMU; PATHWAY; FERMENTATION; STRAIN; SYSTEM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009},
+Times-Cited = {83},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000392565200002},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000414555900006,
+Author = {Klanchui, Amornpan and Raethong, Nachon and Prommeenate, Peerada and
+ Vongsangnak, Wanwipa and Meechai, Asawin},
+Editor = {Nookaew, I},
+Title = {Cyanobacterial Biofuels: Strategies and Developments on Network and
+ Modeling},
+Booktitle = {NETWORK BIOLOGY},
+Series = {Advances in Biochemical Engineering-Biotechnology},
+Year = {2017},
+Volume = {160},
+Pages = {75-102},
+Type = {Article; Book Chapter},
+DOI = {10.1007/10\_2016\_42},
+ISSN = {0724-6145},
+EISSN = {1616-8542},
+ISBN = {978-3-319-56460-9; 978-3-319-56459-3},
+Keywords = {Biofuels; Cyanobacteria; Genome-scale metabolic model; Metabolic network
+ reconstruction; Systems metabolic engineering},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FATTY-ACID PRODUCTION; FLUX BALANCE ANALYSIS;
+ GENOME-SCALE MODELS; SP PCC 6803; HYDROGEN-PRODUCTION; METABOLIC
+ NETWORK; CARBON-DIOXIDE; PHOTOSYNTHETIC PRODUCTION; UNICELLULAR
+ MICROALGAE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Raethong, Nachon/E-3130-2016
+ },
+ORCID-Numbers = {Raethong, Nachon/0000-0003-4442-3411
+ Prommeenate, Peerada/0000-0003-0421-0243},
+Times-Cited = {7},
+Journal-ISO = {Adv. Biochem. Eng. Biotechnol.},
+Unique-ID = {WOS:000414555900006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000408193500008,
+Author = {Levering, Jennifer and Dupont, Christopher L. and Allen, Andrew E. and
+ Palsson, Bernhard O. and Zengler, Karsten},
+Title = {Integrated Regulatory and Metabolic Networks of the Marine Diatom
+ Phaeodactylum tricornutum Predict the Response to Rising
+ CO2 Levels},
+Journal = {MSYSTEMS},
+Year = {2017},
+Volume = {2},
+Number = {1},
+Month = {JAN-FEB},
+Type = {Article},
+DOI = {10.1128/mSystems.00142-16},
+Article-Number = {e00142-16},
+ISSN = {2379-5077},
+Keywords = {Phaeodactylum tricornutum; coregulated genes; genome-scale metabolic
+ network reconstruction; integrated network modeling; regulatory network
+ inference},
+Keywords-Plus = {GENOMES; CARBON; OCEAN},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Allen, Andrew E/C-4896-2012
+ },
+ORCID-Numbers = {Allen, Andrew E/0000-0001-5911-6081
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {27},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000408193500008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392460800026,
+Author = {Magnusdottir, Stefania and Heinken, Almut and Kutt, Laura and Ravcheev,
+ Dmitry A. and Bauer, Eugen and Noronha, Alberto and Greenhalgh, Kacy and
+ Jager, Christian and Baginska, Joanna and Wilmes, Paul and Fleming,
+ Ronan M. T. and Thiele, Ines},
+Title = {Generation of genome-scale metabolic reconstructions for 773 members of
+ the human gut microbiota},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2017},
+Volume = {35},
+Number = {1},
+Pages = {81-89},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1038/nbt.3703},
+ISSN = {1087-0156},
+EISSN = {1546-1696},
+Keywords-Plus = {BUTYRATE-PRODUCING BACTERIA; CELLULAR-METABOLISM; SYSTEMS BIOLOGY;
+ COMPETITION; ANNOTATION; PREDICTION; NETWORKS; ECOLOGY; MODELS; HEALTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ravcheev, Dmitry A/M-6877-2015
+ Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ Wilmes, Paul/B-1707-2017
+ Bauer, Eugen/L-1837-2019
+ Magnusdottir, Stefania/ABA-2212-2021
+ },
+ORCID-Numbers = {Ravcheev, Dmitry A/0000-0002-8435-5516
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Wilmes, Paul/0000-0002-6478-2924
+ Noronha, Alberto/0000-0002-0935-4599
+ Heinken, Almut/0000-0001-6938-8072
+ Baginska, Joanna/0000-0001-5182-7575},
+Times-Cited = {399},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000392460800026},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394135800038,
+Author = {Malatinszky, David and Steuer, Ralf and Jones, Patrik R.},
+Title = {A Comprehensively Curated Genome-Scale Two-Cell Model for the
+ Heterocystous Cyanobacterium Anabaena sp PCC 7120},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2017},
+Volume = {173},
+Number = {1},
+Pages = {509-523},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1104/pp.16.01487},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {NITROGEN-FIXATION; PHOSPHOENOLPYRUVATE CARBOXYLASE;
+ CELLULAR-DIFFERENTIATION; DIAZOTROPHIC GROWTH; METABOLIC RECONSTRUCTION;
+ BIOSYNTHETIC-PATHWAY; STRAIN PCC7120; SP PCC-7120; EXPRESSION; SUCROSE},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Steuer, Ralf/E-7482-2017
+ },
+ORCID-Numbers = {Steuer, Ralf/0000-0003-2217-1655
+ Jones, Patrik/0000-0001-7618-8204
+ Malatinszky, David/0000-0002-4155-2085},
+Times-Cited = {28},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000394135800038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403796900002,
+Author = {Mienda, Bashir Sajo},
+Title = {Genome-scale metabolic models as platforms for strain design and
+ biological discovery},
+Journal = {JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS},
+Year = {2017},
+Volume = {35},
+Number = {9},
+Pages = {1863-1873},
+Type = {Review},
+DOI = {10.1080/07391102.2016.1197153},
+ISSN = {0739-1102},
+EISSN = {1538-0254},
+Keywords = {genome-scale metabolic models; strain design; biological discovery;
+ integrated workflow; superior strains},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; GENE KNOCKOUT; SUCCINATE
+ PRODUCTION; SACCHAROMYCES-CEREVISIAE; QUANTITATIVE PREDICTION; ANAEROBIC
+ FERMENTATION; CELLULAR-METABOLISM; ACID; GLYCEROL},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ResearcherID-Numbers = {Mienda, Bashir Sajo/N-8908-2017},
+ORCID-Numbers = {Mienda, Bashir Sajo/0000-0002-7205-2753},
+Times-Cited = {17},
+Journal-ISO = {J. Biomol. Struct. Dyn.},
+Unique-ID = {WOS:000403796900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403796900003,
+Author = {Miklossy, Ildiko and Bodor, Zsolt and Sinkler, Reka and Orban, Kalman
+ Csongor and Lanyi, Szabolcs and Albert, Beata},
+Title = {In silico and in vivo stability analysis of a heterologous
+ biosynthetic pathway for 1,4-butanediol production in metabolically
+ engineered E-coli},
+Journal = {JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS},
+Year = {2017},
+Volume = {35},
+Number = {9},
+Pages = {1874-1889},
+Type = {Article},
+DOI = {10.1080/07391102.2016.1198721},
+ISSN = {0739-1102},
+EISSN = {1538-0254},
+Keywords = {FBA; metabolic engineering; E. coli; fermentation; 1,4-butanediol},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GENOME-SCALE MODEL; SUCCINIC ACID; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; N-BUTANOL; GENE; GLYCEROL; STRATEGIES;
+ CHEMICALS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ResearcherID-Numbers = {Orban, Csongor/AAP-4611-2021
+ Bodor, Zsolt/ABE-2182-2020
+ },
+ORCID-Numbers = {Orban, Kalman-Csongor/0000-0002-7509-748X
+ Bodor, Zsolt/0000-0003-1386-6957},
+Times-Cited = {8},
+Journal-ISO = {J. Biomol. Struct. Dyn.},
+Unique-ID = {WOS:000403796900003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000393681000019,
+Author = {Ribaudo, Nicholas and Li, Xianhua and Davis, Brett and Wood, Thomas K.
+ and Huang, Zuyi (Jacky)},
+Title = {A Genome-Scale Modeling Approach to Quantify Biofilm Component Growth of
+ Salmonella Typhimurium},
+Journal = {JOURNAL OF FOOD SCIENCE},
+Year = {2017},
+Volume = {82},
+Number = {1},
+Pages = {154-166},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1111/1750-3841.13565},
+ISSN = {0022-1147},
+EISSN = {1750-3841},
+Keywords = {biofilm formation; genome-scale metabolic model; Salmonella Typhimurium},
+Keywords-Plus = {ENTERICA SEROVAR TYPHIMURIUM; CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI;
+ LIPID-A; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; ACID
+ BIOSYNTHESIS; SYSTEMS BIOLOGY; LIPOPOLYSACCHARIDE; EXPRESSION},
+Research-Areas = {Food Science \& Technology},
+Web-of-Science-Categories = {Food Science \& Technology},
+ResearcherID-Numbers = {Wood, Thomas/GWZ-2481-2022},
+ORCID-Numbers = {Wood, Thomas/0000-0001-8962-8571},
+Times-Cited = {6},
+Journal-ISO = {J. Food Sci.},
+Unique-ID = {WOS:000393681000019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394841100003,
+Author = {Sanchez, Borja and Delgado, Susana and Blanco-Miguez, Aitor and
+ Lourenco, Analia and Gueimonde, Miguel and Margolles, Abelardo},
+Title = {Probiotics, gut microbiota, and their influence on host health and
+ disease},
+Journal = {MOLECULAR NUTRITION \& FOOD RESEARCH},
+Year = {2017},
+Volume = {61},
+Number = {1},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1002/mnfr.201600240},
+Article-Number = {1600240},
+ISSN = {1613-4125},
+EISSN = {1613-4133},
+Keywords = {Gut microbiota; Health effects; Molecular mechanisms bioinformatics;
+ Probiotics},
+Keywords-Plus = {ANTIBIOTIC-ASSOCIATED DIARRHEA; INFLAMMATORY-BOWEL-DISEASE; INTESTINAL
+ MICROBIOTA; FAECALIBACTERIUM-PRAUSNITZII; FECAL MICROBIOTA; BACTERIAL;
+ METABOLISM; PREVENTION; DIVERSITY; BIFIDOBACTERIA},
+Research-Areas = {Food Science \& Technology},
+Web-of-Science-Categories = {Food Science \& Technology},
+ResearcherID-Numbers = {Gueimonde, Miguel/A-2106-2008
+ Lourenço, Anália/G-8879-2013
+ Blanco-Míguez, Aitor/AAN-2149-2020
+ Margolles, Abelardo/H-3871-2012
+ Lourenço, Anália/Y-9447-2019
+ Blanco-Míguez, Aitor ABM/H-3628-2017
+ Delgado, Susana/H-9844-2012
+ Duarte, Graziela Biude Silva/Q-7728-2016},
+ORCID-Numbers = {Gueimonde, Miguel/0000-0002-0192-901X
+ Lourenço, Anália/0000-0001-8401-5362
+ Blanco-Míguez, Aitor/0000-0001-7386-5572
+ Margolles, Abelardo/0000-0003-2278-1816
+ Lourenço, Anália/0000-0001-8401-5362
+ Blanco-Míguez, Aitor ABM/0000-0001-7386-5572
+ Delgado, Susana/0000-0002-1081-2614
+ },
+Times-Cited = {579},
+Journal-ISO = {Mol. Nutr. Food Res.},
+Unique-ID = {WOS:000394841100003},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392060500021,
+Author = {Sannino, F. and Giuliani, M. and Salvatore, U. and Apuzzo, G. A. and de
+ Pascale, D. and Fani, R. and Fondi, M. and Marino, G. and Tutino, M. L.
+ and Parrilli, E.},
+Title = {A novel synthetic medium and expression system for subzero growth and
+ recombinant protein production in Pseudoalteromonas haloplanktis
+ TAC125},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2017},
+Volume = {101},
+Number = {2},
+Pages = {725-734},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1007/s00253-016-7942-5},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {P. haloplanktis TAC125; Subzero growth temperature; Recombinant protein
+ production; Cold-adapted bacteria; Synthetic medium},
+Keywords-Plus = {ANTI-BIOFILM ACTIVITY; ESCHERICHIA-COLI; OXIDATIVE STRESS;
+ PSEUDOMONAS-PUTIDA; GAL REPRESSOR; BACTERIUM; GALACTOSIDASE;
+ TRANSCRIPTION; TEMPERATURES; ADAPTATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {TUTINO, MARIA LUISA/L-1834-2013
+ parrilli, ermenegilda/K-4616-2016
+ },
+ORCID-Numbers = {parrilli, ermenegilda/0000-0002-9002-5409
+ Tutino, Maria Luisa/0000-0002-4978-6839},
+Times-Cited = {19},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000392060500021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000399116500001,
+Author = {Thor, ShengShee and Peterson, Joseph R. and Luthey-Schulten, Zaida},
+Title = {Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity
+ of Metabolic Function},
+Journal = {ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL},
+Year = {2017},
+Volume = {2017},
+Type = {Review},
+DOI = {10.1155/2017/9763848},
+Article-Number = {9763848},
+ISSN = {1472-3646},
+EISSN = {1472-3654},
+Keywords-Plus = {METHANOL METHYLTRANSFERASE ISOZYMES; CONSTRAINT-BASED MODELS;
+ METHANOSARCINA-ACETIVORANS; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; ESCHERICHIA-COLI; GENETIC-ANALYSIS;
+ CARBON-MONOXIDE; RECONSTRUCTION; BACTERIA},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Luthey-Schulten, Zaida/0000-0001-9749-8367},
+Times-Cited = {17},
+Journal-ISO = {Archaea},
+Unique-ID = {WOS:000399116500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000390044900015,
+Author = {Broddrick, Jared T. and Rubin, Benjamin E. and Welkie, David G. and Du,
+ Niu and Mih, Nathan and Diamond, Spencer and Lee, Jenny J. and Golden,
+ Susan S. and Palsson, Bernhard O.},
+Title = {Unique attributes of cyanobacterial metabolism revealed by improved
+ genome-scale metabolic modeling and essential gene analysis},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2016},
+Volume = {113},
+Number = {51},
+Pages = {E8344-E8353},
+Month = {DEC 20},
+Type = {Article},
+DOI = {10.1073/pnas.1613446113},
+ISSN = {0027-8424},
+Keywords = {cyanobacteria; constraint-based modeling; TCA cycle; photosynthesis;
+ Synechococcus elongatus},
+Keywords-Plus = {TRICARBOXYLIC-ACID CYCLE; SP PCC 6803; DEPENDENT PHOSPHOGLYCERATE
+ MUTASE; INORGANIC CARBON LIMITATION; CONSTRAINT-BASED MODELS; FLUX
+ BALANCE ANALYSIS; SP STRAIN PCC-7942; ESCHERICHIA-COLI;
+ ELECTRON-TRANSPORT; BIOFUEL PRODUCTION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Diamond, Spencer/M-6492-2019
+ Diamond, Spencer/A-9122-2017
+ },
+ORCID-Numbers = {Diamond, Spencer/0000-0003-4131-341X
+ Diamond, Spencer/0000-0003-4131-341X
+ Welkie, David/0000-0003-0173-1457
+ Broddrick, Jared/0000-0003-4871-4822
+ Mih, Nathan/0000-0002-4302-9052},
+Times-Cited = {83},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000390044900015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000389300400001,
+Author = {Koehorst, Jasper J. and van Dam, Jesse C. J. and van Heck, Ruben G. A.
+ and Saccenti, Edoardo and dos Santos, Vitor A. P. Martins and
+ Suarez-Diez, Maria and Schaap, Peter J.},
+Title = {Comparison of 432 Pseudomonas strains through integration of
+ genomic, functional, metabolic and expression data},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2016},
+Volume = {6},
+Month = {DEC 6},
+Type = {Article},
+DOI = {10.1038/srep38699},
+Article-Number = {38699},
+ISSN = {2045-2322},
+Keywords-Plus = {SEQUENCE; PUTIDA; RECONSTRUCTION; PHYLOGENY; GENES; TOOL},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Koehorst, Jasper Jan/Z-1697-2019
+ Koehorst, Jasper/G-3595-2013
+ Diez, Maria Suarez/AAI-1354-2020
+ },
+ORCID-Numbers = {Koehorst, Jasper Jan/0000-0001-8172-8981
+ Koehorst, Jasper/0000-0001-8172-8981
+ Suarez-Diez, Maria/0000-0001-5845-146X
+ Van Heck, Ruben/0000-0001-6787-6830
+ van Dam, Jesse/0000-0001-9395-5559
+ Saccenti, Edoardo/0000-0001-8284-4829
+ Schaap, Peter/0000-0002-4346-6084},
+Times-Cited = {34},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000389300400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392486100009,
+Author = {Fu, Weiqi and Chaiboonchoe, Amphun and Khraiwesh, Basel and Nelson,
+ David R. and Al-Khairy, Dina and Mystikou, Alexandra and Alzahmi, Amnah
+ and Salehi-Ashtiani, Kourosh},
+Title = {Algal Cell Factories: Approaches, Applications, and Potentials},
+Journal = {MARINE DRUGS},
+Year = {2016},
+Volume = {14},
+Number = {12},
+Month = {DEC},
+Type = {Review},
+DOI = {10.3390/md14120225},
+Article-Number = {225},
+EISSN = {1660-3397},
+Keywords = {algae; bioactive compound; cell factory; genetic engineering;
+ mutagenesis; systems biology},
+Keywords-Plus = {DIATOM PHAEODACTYLUM-TRICORNUTUM; STABLE NUCLEAR TRANSFORMATION;
+ METABOLIC NETWORK MODEL; HIGH LIGHT ACCLIMATION; SP PCC 6803;
+ CHLAMYDOMONAS-REINHARDTII; PHYSCOMITRELLA-PATENS; LIPID-ACCUMULATION;
+ ADAPTIVE EVOLUTION; SYSTEMS BIOLOGY},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Chemistry, Medicinal; Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {FU, WEIQI/E-4167-2019
+ Khraiwesh, Basel/G-7509-2015
+ Chaiboonchoe, Amphun/H-2873-2016
+ },
+ORCID-Numbers = {FU, WEIQI/0000-0002-7368-383X
+ Khraiwesh, Basel/0000-0001-7026-1263
+ Mystikou, Alexandra/0000-0002-7961-3015
+ Nelson, David/0000-0001-8868-5734
+ Chaiboonchoe, Amphun/0000-0002-0009-0806
+ Salehi-Ashtiani, Kourosh/0000-0002-6521-5243},
+Times-Cited = {55},
+Journal-ISO = {Mar. Drugs},
+Unique-ID = {WOS:000392486100009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392946900048,
+Author = {Hunt, Kristopher A. and Jennings, Ryan deM. and Inskeep, William P. and
+ Carlson, Ross P.},
+Title = {Stoichiometric modelling of assimilatory and dissimilatory biomass
+ utilisation in a microbial community},
+Journal = {ENVIRONMENTAL MICROBIOLOGY},
+Year = {2016},
+Volume = {18},
+Number = {12},
+Pages = {4946-4960},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1111/1462-2920.13444},
+ISSN = {1462-2912},
+EISSN = {1462-2920},
+Keywords-Plus = {METABOLIC PATHWAY ANALYSIS; ESCHERICHIA-COLI; IRON; TEMPERATURE; GROWTH;
+ SEDIMENTS; FIXATION; ARCHAEA; MASS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+Times-Cited = {10},
+Journal-ISO = {Environ. Microbiol.},
+Unique-ID = {WOS:000392946900048},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000387597600008,
+Author = {Li, Xianhua and Liu, Yanhong and Jia, Qian and LaMacchia, Virginia and
+ O'Donoghue, Kathryn and Huang, Zuyi},
+Title = {A systems biology approach to investigate the antimicrobial activity of
+ oleuropein},
+Journal = {JOURNAL OF INDUSTRIAL MICROBIOLOGY \& BIOTECHNOLOGY},
+Year = {2016},
+Volume = {43},
+Number = {12},
+Pages = {1705-1717},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1007/s10295-016-1841-8},
+ISSN = {1367-5435},
+EISSN = {1476-5535},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; STAPHYLOCOCCUS-AUREUS; PHENOLIC-COMPOUNDS;
+ ESCHERICHIA-COLI; METABOLIC NETWORK; TRANSPORTER PROP; MODEL MEMBRANES;
+ OLEA-EUROPAEA; DEHYDROGENASE; HYDROLYSIS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Liu, Yanhong/L-7093-2019
+ },
+ORCID-Numbers = {Liu, Yanhong/0000-0002-0759-7597
+ O'Donoghue, Keelin/0000-0002-4616-2887},
+Times-Cited = {15},
+Journal-ISO = {J. Ind. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000387597600008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394176200001,
+Author = {Panichkin, V. B. and Livshits, V. A. and Biryukova, I. V. and Mashko, S.
+ V.},
+Title = {Metabolic Engineering of Escherichia coli for L-Tryptophan
+ Production},
+Journal = {APPLIED BIOCHEMISTRY AND MICROBIOLOGY},
+Year = {2016},
+Volume = {52},
+Number = {9},
+Pages = {783-809},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1134/S0003683816090052},
+ISSN = {0003-6838},
+EISSN = {1608-3024},
+Keywords = {metabolic engineering; producer; L-tryptophan; stress resistance;
+ Escherichia coli},
+Keywords-Plus = {3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE; AMINO-ACID
+ BIOSYNTHESIS; VITREOSCILLA-HEMOGLOBIN; L-PHENYLALANINE; D-GLUCOSE;
+ CHORISMATE SYNTHASE; SHIKIMIC ACID; L-THREONINE;
+ CORYNEBACTERIUM-GLUTAMICUM; PHOSPHOTRANSFERASE SYSTEM},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+Times-Cited = {13},
+Journal-ISO = {Appl. Biochem. Microbiol.},
+Unique-ID = {WOS:000394176200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000388824500015,
+Author = {Richards, Matthew A. and Lie, Thomas J. and Zhang, Juan and Ragsdale,
+ Stephen W. and Leigh, John A. and Price, Nathan D.},
+Title = {Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic
+ Reconstruction of Methanococcus maripaludis},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2016},
+Volume = {198},
+Number = {24},
+Pages = {3379-3390},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1128/JB.00571-16},
+ISSN = {0021-9193},
+EISSN = {1098-5530},
+Keywords-Plus = {ELECTRON BIFURCATION; DATABASE; FORMATE; PATHWAY; MODELS; GROWTH; H-2;
+ BIOSYNTHESIS; ASSIMILATION; DISRUPTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Zhang, Juan/GRX-2638-2022
+ },
+ORCID-Numbers = {Price, Nathan/0000-0002-4157-0267
+ Ragsdale, Stephen/0000-0003-3938-8906},
+Times-Cited = {28},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000388824500015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000388773300006,
+Author = {Fondi, Marco and Bosi, Emanuele and Presta, Luana and Natoli, Diletta
+ and Fani, Renato},
+Title = {Modelling microbial metabolic rewiring during growth in a complex medium},
+Journal = {BMC GENOMICS},
+Year = {2016},
+Volume = {17},
+Month = {NOV 24},
+Type = {Article},
+DOI = {10.1186/s12864-016-3311-0},
+Article-Number = {970},
+ISSN = {1471-2164},
+Keywords = {Flux balance analysis; Pseudoalteromonas haloplanktis TAC125; Antarctic
+ bacteria; Metabolic modelling},
+Keywords-Plus = {TRANSCRIPTIONAL REGULATION; GENOME; DATABASE; SWITCH; RECONSTRUCTION;
+ RESOURCE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ORCID-Numbers = {Presta, Luana/0000-0001-6482-6758
+ Fondi, Marco/0000-0001-9291-5467
+ Bosi, Emanuele/0000-0002-4769-8667},
+Times-Cited = {10},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000388773300006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000395782200008,
+Author = {Hefzi, Hooman and Ang, Kok Siong and Hanscho, Michael and Bordbar,
+ Aarash and Ruckerbauer, David and Lakshmanan, Meiyappan and Orellana,
+ Camila A. and Baycin-Hizal, Deniz and Huang, Yingxiang and Ley, Daniel
+ and Martinez, Veronica S. and Kyriakopoulos, Sarantos and Jimenez,
+ Natalia E. and Zielinski, Daniel C. and Quek, Lake-Ee and Wulff, Tune
+ and Arnsdorf, Johnny and Li, Shangzhong and Lee, Jae Seong and Paglia,
+ Giuseppe and Loira, Nicolas and Spahn, Philipp N. and Pedersen, Lasse E.
+ and Gutierrez, Jahir M. and King, Zachary A. and Lund, Anne Mathilde and
+ Nagarajan, Harish and Thomas, Alex and Abdel-Haleem, Alyaa M. and
+ Zanghellini, Juergen and Kildegaard, Helene F. and Voldborg, Bjorn G.
+ and Gerdtzen, Ziomara P. and Betenbaugh, Michael J. and Palsson,
+ Bernhard O. and Andersen, Mikael R. and Nielsen, Lars K. and Borth,
+ Nicole and Lee, Dong-Yup and Lewis, Nathan E.},
+Title = {A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell
+ Metabolism},
+Journal = {CELL SYSTEMS},
+Year = {2016},
+Volume = {3},
+Number = {5},
+Pages = {434+},
+Month = {NOV 23},
+Type = {Article},
+DOI = {10.1016/j.cels.2016.10.020},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {CHO-CELLS; FLUX ANALYSIS; GLOBAL RECONSTRUCTION; ANTIBODY-PRODUCTION;
+ ESCHERICHIA-COLI; MOUSE HYBRIDOMA; AMINO-ACID; OMICS DATA; GROWTH;
+ CULTURE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/ABC-7628-2020
+ King, Zachary/V-3402-2019
+ Orellana, Camila A/AAN-4060-2021
+ Li, Shangzhong/Y-6882-2019
+ Lewis, Nathan/ABE-7290-2020
+ Zanghellini, Jürgen/A-4635-2017
+ Pedersen, Lasse Ebdrup/F-9848-2018
+ Nielsen, Lars K/A-5519-2011
+ /AAG-5264-2021
+ Li, Shangzhong/HHD-1335-2022
+ Lee, Dong-Yup/D-6650-2011
+ Gerdtzen, Ziomara P/H-2711-2013
+ Ang, Kok Siong/M-2674-2019
+ Andersen, Mikael Rørdam/P-6743-2019
+ Paglia, Giuseppe/H-2012-2018
+ Andersen, Mikael R/F-9377-2013
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Li, Shangzhong/HHD-1393-2022
+ },
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ King, Zachary/0000-0003-1238-1499
+ Orellana, Camila A/0000-0002-6828-6071
+ Li, Shangzhong/0000-0003-0272-3942
+ Lewis, Nathan/0000-0001-7700-3654
+ Zanghellini, Jürgen/0000-0002-1964-2455
+ Pedersen, Lasse Ebdrup/0000-0002-6064-919X
+ Nielsen, Lars K/0000-0001-8191-3511
+ /0000-0001-6460-6771
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Gerdtzen, Ziomara P/0000-0002-7486-8537
+ Andersen, Mikael Rørdam/0000-0003-4794-6808
+ Paglia, Giuseppe/0000-0003-4724-6801
+ Andersen, Mikael R/0000-0003-4794-6808
+ Martinez, Veronica/0000-0003-2729-5278
+ Arnsdorf, Johnny/0000-0002-2738-0811
+ Quek, Lake-Ee/0000-0002-9313-8740
+ Abdel-haleem, Alyaa/0000-0002-3114-1100
+ Lee, Jae Seong/0000-0002-3291-2093
+ Borth, Nicole/0000-0001-6324-9338
+ Zielinski, Daniel/0000-0001-6452-483X
+ Voldborg, Bjorn Gunnar/0000-0002-7005-1642
+ Hefzi, Hooman/0009-0003-4067-6224
+ Wulff, Tune/0000-0002-8822-1048
+ Ruckerbauer, David/0000-0003-3374-8456
+ Jimenez, Natalia/0000-0003-2084-1256
+ Kildegaard, Helene Faustrup/0000-0003-3727-5721},
+Times-Cited = {159},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000395782200008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000388119800002,
+Author = {Castillo, Sandra and Barth, Dorothee and Arvas, Mikko and Pakula, Tiina
+ M. and Pitkanen, Esa and Blomberg, Peter and Seppanen-Laakso, Tuulikki
+ and Nygren, Heli and Sivasiddarthan, Dhinakaran and Penttila, Merja and
+ Oja, Merja},
+Title = {Whole-genome metabolic model of Trichoderma reesei built by
+ comparative reconstruction},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2016},
+Volume = {9},
+Month = {NOV 21},
+Type = {Article},
+DOI = {10.1186/s13068-016-0665-0},
+Article-Number = {252},
+ISSN = {1754-6834},
+Keywords-Plus = {RECOMBINANT PROTEIN-PRODUCTION; SACCHAROMYCES-CEREVISIAE; SCALE
+ RECONSTRUCTION; PICHIA-PASTORIS; SYSTEMS BIOLOGY; GENE; ANNOTATION;
+ EXPRESSION; SEQUENCE; NETWORK},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Penttilä, Merja E/A-4710-2013
+ Barth, Dorothee/S-2158-2016
+ Arvas, Mikko/AAA-7438-2021
+ Pitkanen, Esa/H-2435-2018
+ },
+ORCID-Numbers = {Arvas, Mikko/0000-0002-6902-8488
+ Pitkanen, Esa/0000-0002-9818-6370
+ Barth, Dorothee/0000-0001-9575-905X
+ Castillo, Sandra/0000-0003-1968-4820
+ Nygren, Heli/0000-0002-6498-7567
+ Penttila, Merja/0000-0002-6929-1032},
+Times-Cited = {8},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000388119800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000385471800001,
+Author = {Fleming, Ronan M. T. and Vlassis, Nikos and Thiele, Ines and Saunders,
+ Michael A.},
+Title = {Conditions for duality between fluxes and concentrations in biochemical
+ networks},
+Journal = {JOURNAL OF THEORETICAL BIOLOGY},
+Year = {2016},
+Volume = {409},
+Pages = {1-10},
+Month = {NOV 21},
+Type = {Article},
+DOI = {10.1016/j.jtbi.2016.06.033},
+ISSN = {0022-5193},
+EISSN = {1095-8541},
+Keywords = {Biochemical network; Flux; Concentration; Duality; Kinetics},
+Keywords-Plus = {MINIMAL CUT SETS; TOOLBOX; RECONSTRUCTION; MODELS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Saunders, Michael A/D-1083-2012
+ Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Saunders, Michael/0000-0003-3800-4982},
+Times-Cited = {14},
+Journal-ISO = {J. Theor. Biol.},
+Unique-ID = {WOS:000385471800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000387984600038,
+Author = {Chen, Jin and Henson, Michael A.},
+Title = {In silico metabolic engineering of Clostridium ljungdahlii
+ for synthesis gas fermentation},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {38},
+Pages = {389-400},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2016.10.002},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Gas fermentation; Clostridium ljungdahlii; In silico metabolic
+ engineering; OptKnock; Spatiotemporal metabolic modeling},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; BIOLOGICAL PRODUCTION; MICROBIAL-PRODUCTION;
+ ENERGY-CONSERVATION; ANAEROBIC BACTERIUM; LACTIC-ACID; SP-NOV; ETHANOL;
+ BIOMASS; SYNGAS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {34},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000387984600038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000391230900001,
+Author = {Haraldsdottir, Hulda S. and Fleming, Ronan M. T.},
+Title = {Identification of Conserved Moieties in Metabolic Networks by Graph
+ Theoretical Analysis of Atom Transition Networks},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2016},
+Volume = {12},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004999},
+Article-Number = {e1004999},
+EISSN = {1553-7358},
+Keywords-Plus = {BIDIRECTIONAL REACTION STEPS; CHEMICAL-REACTION SYSTEMS; BIOCHEMICAL
+ NETWORKS; MODELS; INFORMATION; DEFINITION; PATHWAYS; KINETICS; DATABASE;
+ MATRIX},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021},
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812},
+Times-Cited = {17},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000391230900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000389841300006,
+Author = {Lechner, Anna and Brunk, Elizabeth and Keasling, Jay D.},
+Title = {The Need for Integrated Approaches in Metabolic Engineering},
+Journal = {COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY},
+Year = {2016},
+Volume = {8},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1101/cshperspect.a023903},
+Article-Number = {a023903},
+ISSN = {1943-0264},
+Keywords-Plus = {DELTA-SELINENE SYNTHASE; CONSTRAINT-BASED MODELS; DE-NOVO DESIGN;
+ ESCHERICHIA-COLI; DIRECTED EVOLUTION; CODON USAGE; GENE-EXPRESSION;
+ SESQUITERPENE SYNTHASES; PATHWAY OPTIMIZATION; TRANSLATION RATES},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Keasling, Jay D/J-9162-2012
+ Keasling, Jay/HPG-6073-2023},
+ORCID-Numbers = {Keasling, Jay D/0000-0003-4170-6088
+ },
+Times-Cited = {32},
+Journal-ISO = {Cold Spring Harbor Perspect. Biol.},
+Unique-ID = {WOS:000389841300006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392716500013,
+Author = {Pfau, Thomas and Pacheco, Maria Pires and Sauter, Thomas},
+Title = {Towards improved genome-scale metabolic network reconstructions:
+ unification, transcript specificity and beyond},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2016},
+Volume = {17},
+Number = {6},
+Pages = {1060-1069},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1093/bib/bbv100},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {metabolic network reconstruction; gene-protein-reaction association;
+ unification},
+Keywords-Plus = {ALTERNATIVE SPLICING DATABASE; SACCHAROMYCES-CEREVISIAE;
+ ESCHERICHIA-COLI; GLOBAL RECONSTRUCTION; SOFTWARE APPLICATIONS; HUMAN
+ TISSUES; ANNOTATION; PROTEIN; MODELS; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Pfau, Thomas/0000-0001-5048-2923
+ Sauter, Thomas/0000-0001-8225-2954},
+Times-Cited = {16},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000392716500013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000384711900045,
+Author = {Wallenius, Janne and Maaheimo, Hannu and Eerikainen, Tero},
+Title = {Carbon 13-Metabolic Flux Analysis derived constraint-based metabolic
+ modelling of Clostridium acetobutylicum in stressed chemostat
+ conditions},
+Journal = {BIORESOURCE TECHNOLOGY},
+Year = {2016},
+Volume = {219},
+Pages = {378-386},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.biortech.2016.07.137},
+ISSN = {0960-8524},
+EISSN = {1873-2976},
+Keywords = {C-13 Metabolic Flux Analysis; Butanol stress; C. acetobutylicum;
+ Exopolysaccharide; COBRA},
+Keywords-Plus = {QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; BUTANOL; BIOBUTANOL;
+ BUTYRATE},
+Research-Areas = {Agriculture; Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Agricultural Engineering; Biotechnology \& Applied Microbiology; Energy
+ \& Fuels},
+ORCID-Numbers = {Wallenius, Janne/0000-0003-1786-4027},
+Times-Cited = {11},
+Journal-ISO = {Bioresour. Technol.},
+Unique-ID = {WOS:000384711900045},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000387984600034,
+Author = {Wang, Zhihao and Chan, Siu Hung Joshua and Sudarsan, Suresh and Blank,
+ Lars M. and Jensen, Peter Ruhdal and Solem, Christian},
+Title = {Elucidation of the regulatory role of the fructose operon reveals a
+ novel target for enhancing the NADPH supply in Corynebacterium
+ glutamicum},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {38},
+Pages = {344-357},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2016.08.004},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Corynebacterium glutamicum; Fructose operon; Convergent evolution;
+ Transcriptomics; Hexose phosphates; NADPH},
+Keywords-Plus = {BACTERIUM ESCHERICHIA-COLI; METABOLIC FLUX ANALYSIS; L-LYSINE
+ PRODUCTION; PHOSPHOTRANSFERASE SYSTEM; RNA-SEQ; PROTEIN-PHOSPHORYLATION;
+ EXPRESSION ANALYSIS; LACTOCOCCUS-LACTIS; SUGAR-TRANSPORT; CARBON-SOURCES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Chan, Siu Hung Joshua/N-9777-2016
+ jensen, Peter Ruhdal/AAC-4891-2019
+ Blank, Lars M./A-6761-2012
+ },
+ORCID-Numbers = {Jensen, Peter Ruhdal/0000-0003-2080-2070
+ Sudarsan, Suresh/0000-0002-2985-1728
+ Blank, Lars M./0000-0003-0961-4976
+ Chan, Siu Hung Joshua/0000-0002-7707-656X
+ Solem, Christian/0000-0002-3898-280X},
+Times-Cited = {16},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000387984600034},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000388431500006,
+Author = {Zielinski, Lukasz P. and Smith, Anthony C. and Smith, Alexander G. and
+ Robinson, Alan J.},
+Title = {Metabolic flexibility of mitochondrial respiratory chain disorders
+ predicted by computer modelling},
+Journal = {MITOCHONDRION},
+Year = {2016},
+Volume = {31},
+Pages = {45-55},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.mito.2016.09.003},
+ISSN = {1567-7249},
+EISSN = {1872-8278},
+Keywords = {Flux balance analysis; Electron transport chain; Mitochondrial disease;
+ Metabolism},
+Keywords-Plus = {COMPLEX-III DEFICIENCY; CYTOCHROME-C-OXIDASE; I DEFICIENCY;
+ SUCCINATE-DEHYDROGENASE; TTC19 MUTATION; DISEASE; CHILDREN; FUMARATE;
+ MYOPATHY; ORIGIN},
+Research-Areas = {Cell Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Cell Biology; Genetics \& Heredity},
+ResearcherID-Numbers = {Smith, Anthony C/B-1891-2009},
+ORCID-Numbers = {Smith, Anthony C/0000-0003-0141-0434},
+Times-Cited = {34},
+Journal-ISO = {Mitochondrion},
+Unique-ID = {WOS:000388431500006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000385760100001,
+Author = {Hosseini, Sayed-Rzgar and Wagner, Andreas},
+Title = {The potential for non-adaptive origins of evolutionary innovations in
+ central carbon metabolism},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2016},
+Volume = {10},
+Month = {OCT 21},
+Type = {Article},
+DOI = {10.1186/s12918-016-0343-7},
+Article-Number = {97},
+ISSN = {1752-0509},
+Keywords = {Exaptation; Innovation; Central carbon metabolism; Exhaustive
+ genotype-phenotype mapping},
+Keywords-Plus = {COLI K-12 MG1655; ESCHERICHIA-COLI; ADAPTIVE EVOLUTION; GENOTYPE
+ NETWORKS; RECONSTRUCTIONS; EXAPTATION; BACTERIA; SYSTEMS; CAPABILITIES;
+ DEGRADATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Hosseini, Sayed-Rzgar/0000-0002-2308-6754},
+Times-Cited = {10},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000385760100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000388613200016,
+Author = {Belda, Eugeni and van Heck, Ruben G. A. and Lopez-Sanchez, Maria Jose
+ and Cruveiller, Stephane and Barbe, Valerie and Fraser, Claire and
+ Klenk, Hans-Peter and Petersen, Joern and Morgat, Anne and Nikel, Pablo
+ I. and Vallenet, David and Rouy, Zoe and Sekowska, Agnieszka and dos
+ Santos, Vitor A. P. Martins and de Lorenzo, Victor and Danchin, Antoine
+ and Medigue, Claudine},
+Title = {The revisited genome of Pseudomonas putida KT2440 enlightens its
+ value as a robust metabolic chassis},
+Journal = {ENVIRONMENTAL MICROBIOLOGY},
+Year = {2016},
+Volume = {18},
+Number = {10, SI},
+Pages = {3403-3424},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1111/1462-2920.13230},
+ISSN = {1462-2912},
+EISSN = {1462-2920},
+Keywords-Plus = {AROMATIC CATABOLIC PATHWAYS; ACID DEGRADATION PATHWAY; ESCHERICHIA-COLI;
+ NA+/H+ ANTIPORTER; MOLECULAR CHARACTERIZATION; GENETIC ANALYSES;
+ IDENTIFICATION; TREHALOSE; EXPRESSION; CLONING},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Danchin, Antoine/F-3745-2018
+ Nikel, Pablo Ivan/L-4146-2014
+ Belda, Eugeni/ABI-1349-2020
+ },
+ORCID-Numbers = {Danchin, Antoine/0000-0002-6350-5001
+ Nikel, Pablo Ivan/0000-0002-9313-7481
+ Belda, Eugeni/0000-0003-4307-5072
+ Morgat, Anne/0000-0002-1216-2969
+ Van Heck, Ruben/0000-0001-6787-6830
+ Claudine, MEDIGUE/0000-0002-3905-1054
+ martins dos santos, vitor/0000-0002-2352-9017
+ Barbe, Valerie/0000-0002-8162-3343
+ de Lorenzo, Victor/0000-0002-6041-2731},
+Times-Cited = {205},
+Journal-ISO = {Environ. Microbiol.},
+Unique-ID = {WOS:000388613200016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000387660200024,
+Author = {Machado, Daniel and Herrgard, Markus J. and Rocha, Isabel},
+Title = {Stoichiometric Representation of Gene-Protein-Reaction Associations
+ Leverages Constraint-Based Analysis from Reaction to Gene-Level
+ Phenotype Prediction},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2016},
+Volume = {12},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1005140},
+Article-Number = {e1005140},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ELEMENTARY MODE ANALYSIS; SCALE METABOLIC MODELS; ESCHERICHIA-COLI;
+ QUANTITATIVE PREDICTION; FLUX MODES; OPTIMIZATION; GENERATION;
+ EVOLUTION; TOOLBOX; DESIGN},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Machado, Daniel/O-5493-2015
+ Rocha, Isabel/A-4279-2013
+ },
+ORCID-Numbers = {Machado, Daniel/0000-0002-2063-5383
+ Rocha, Isabel/0000-0001-9494-3410
+ Herrgard, Markus/0000-0003-2377-9929},
+Times-Cited = {33},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000387660200024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000391147700052,
+Author = {Schwahn, Kevin and Kuken, Anika and Kliebenstein, Daniel J. and Fernie,
+ Alisdair R. and Nikoloski, Zoran},
+Title = {Observability of Plant Metabolic Networks Is Reflected in the
+ Correlation of Metabolic Profiles},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2016},
+Volume = {172},
+Number = {2},
+Pages = {1324-1333},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1104/pp.16.00900},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {FLUX ANALYSIS; ARABIDOPSIS; SCALE; CYCLE},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Küken, Anika/AAA-7991-2020
+ fernie, alisdair/IWD-9278-2023
+ },
+ORCID-Numbers = {Küken, Anika/0000-0003-1367-0719
+ Nikoloski, Zoran/0000-0003-2671-6763},
+Times-Cited = {3},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000391147700052},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392913700002,
+Author = {Shen, Fangzhou and Li, Jian and Zhu, Ying and Wang, Zhuo},
+Title = {Systematic investigation of metabolic reprogramming in different cancers
+ based on tissue-specific metabolic models},
+Journal = {JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY},
+Year = {2016},
+Volume = {14},
+Number = {5, SI},
+Month = {OCT},
+Note = {27th International Conference on Genome Informatics (GIW) - Systems
+ Biology, Fudan Univ, Shanghai, PEOPLES R CHINA, OCT 03-05, 2016},
+Type = {Article; Proceedings Paper},
+DOI = {10.1142/S0219720016440017},
+Article-Number = {1644001},
+ISSN = {0219-7200},
+EISSN = {1757-6334},
+Keywords = {Metabolic programming; cancer; metabolic network; tissue-specific model;
+ flux balance analysis},
+Keywords-Plus = {GLUTATHIONE; GLYCINE; TARGETS},
+Research-Areas = {Biochemistry \& Molecular Biology; Computer Science; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Computer Science, Interdisciplinary
+ Applications; Mathematical \& Computational Biology},
+Times-Cited = {6},
+Journal-ISO = {J. Bioinform. Comput. Biol.},
+Unique-ID = {WOS:000392913700002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000383750400001,
+Author = {Yang, Laurence and Ma, Ding and Ebrahim, Ali and Lloyd, Colton J. and
+ Saunders, Michael A. and Palsson, Bernhard O.},
+Title = {solveME: fast and reliable solution of nonlinear ME models},
+Journal = {BMC BIOINFORMATICS},
+Year = {2016},
+Volume = {17},
+Month = {SEP 22},
+Type = {Article},
+DOI = {10.1186/s12859-016-1240-1},
+Article-Number = {391},
+ISSN = {1471-2105},
+Keywords = {Nonlinear optimization; Constraint-based modeling; Metabolism; Proteome;
+ Quasiconvex},
+Keywords-Plus = {GENOME-SCALE MODELS; ESCHERICHIA-COLI; ALGORITHM; METABOLISM;
+ RECONSTRUCTION; EXPRESSION; PROTEOME},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Saunders, Michael A/D-1083-2012
+ },
+ORCID-Numbers = {MA, Ding/0000-0002-5503-2945
+ Yang, Laurence/0000-0001-6663-7643
+ Ebrahim, Ali/0000-0002-4009-2128
+ Saunders, Michael/0000-0003-3800-4982},
+Times-Cited = {29},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000383750400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000383016700001,
+Author = {Thompson, R. Adam and Dahal, Sanjeev and Garcia, Sergio and Nookaew,
+ Intawat and Trinh, Cong T.},
+Title = {Exploring complex cellular phenotypes and model-guided strain design
+ with a novel genome-scale metabolic model of Clostridium
+ thermocellum DSM 1313 implementing an adjustable cellulosome},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2016},
+Volume = {9},
+Month = {SEP 6},
+Type = {Article},
+DOI = {10.1186/s13068-016-0607-x},
+Article-Number = {194},
+EISSN = {1754-6834},
+Keywords = {Clostridium thermocellum; Genome-scale model; Consolidated
+ bioprocessing; Biofuels; Bioenergetics; Elementary mode analysis; Flux
+ balance analysis; Rational strain design; Minimal cut sets},
+Keywords-Plus = {ATCC 27405; HYDROGEN-PRODUCTION; PROTEIN EXPRESSION; MAINTENANCE ENERGY;
+ ETHANOL-PRODUCTION; ENZYME-ACTIVITIES; ELECTRON FLUX; FERMENTATION;
+ GROWTH; PATHWAYS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Trinh, Cong T/H-5300-2012
+ },
+ORCID-Numbers = {Thompson, R. Adam/0000-0002-9862-4801
+ Garcia, Sergio/0000-0002-3998-986X
+ Dahal, Sanjeev/0000-0003-4636-7732},
+Times-Cited = {22},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000383016700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000382833000001,
+Author = {Mendes-Soares, Helena and Mundy, Michael and Soares, Luis Mendes and
+ Chia, Nicholas},
+Title = {MMinte: an application for predicting metabolic interactions among the
+ microbial species in a community},
+Journal = {BMC BIOINFORMATICS},
+Year = {2016},
+Volume = {17},
+Month = {SEP 2},
+Type = {Article},
+DOI = {10.1186/s12859-016-1230-3},
+Article-Number = {343},
+ISSN = {1471-2105},
+Keywords = {Metabolic network reconstruction; Network; Microbiome; 16S rDNA;
+ Predictive community modeling},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ HYDROGEN-SULFIDE; HOST-MICROBE; GUT; BACTERIA; TOOLS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Mundy, Michael/0000-0002-9936-0406
+ Chia, Nicholas/0000-0001-9652-691X
+ Mendes Soares, Helena/0000-0002-6727-4327},
+Times-Cited = {45},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000382833000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000386971500012,
+Author = {Karp, Peter D. and Latendresse, Mario and Paley, Suzanne M. and
+ Krummenacker, Markus and Ong, Quang D. and Billington, Richard and
+ Kothari, Anamika and Weaver, Daniel and Lee, Thomas and Subhraveti,
+ Pallavi and Spaulding, Aaron and Fulcher, Carol and Keseler, Ingrid M.
+ and Caspi, Ron},
+Title = {Pathway Tools version 19.0 update: software for pathway/genome
+ informatics and systems biology},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2016},
+Volume = {17},
+Number = {5},
+Pages = {877-890},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1093/bib/bbv079},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {metabolic pathways; metabolic models; systems biology; computational
+ genomics},
+Keywords-Plus = {DATABASE; RESOURCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Paley, Suzanne Mercer/HII-3163-2022
+ Caspi, Ron/HII-3060-2022},
+ORCID-Numbers = {Paley, Suzanne Mercer/0000-0001-5763-8935
+ Caspi, Ron/0000-0002-6113-3590},
+Times-Cited = {161},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000386971500012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000377983400010,
+Author = {Long, Christopher P. and Gonzalez, Jacqueline E. and Sandoval, Nicholas
+ R. and Antoniewicz, Maciek R.},
+Title = {Characterization of physiological responses to 22 gene knockouts in
+ Escherichia coli central carbon metabolism},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {37},
+Pages = {102-113},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2016.05.006},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Escherichia coli; Gene knockout; Cell physiology; Metabolism; COBRA
+ modeling},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; FLUX ANALYSIS; BIOMASS COMPOSITION;
+ HIGH-THROUGHPUT; GROWTH; MODEL; OPTIMALITY; STRAIN},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009
+ Sandoval, Nicholas R./Y-5605-2019
+ },
+ORCID-Numbers = {Sandoval, Nicholas R./0000-0002-1743-3975
+ Long, Christopher/0000-0003-1007-417X
+ Antoniewicz, Maciek/0000-0002-0087-2875},
+Times-Cited = {42},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000377983400010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000377983400005,
+Author = {Savoglidis, Georgios and dos Santos, Aline Xavier da Silveira and
+ Riezman, Isabelle and Angelino, Paolo and Riezman, Howard and
+ Hatzimanikatis, Vassily},
+Title = {A method for analysis and design of metabolism using metabolomics data
+ and kinetic models: Application on lipidomics using a novel kinetic
+ model of sphingolipid metabolism},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {37},
+Pages = {46-62},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2016.04.002},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Inverse metabolic engineering; Strain design; Nonlinear kinetic models;
+ Lipid metabolism; Sphingolipid regulation; Lipidomics},
+Keywords-Plus = {PROTEIN EXPRESSION PATTERNS; ACETYL-COA METABOLISM;
+ SACCHAROMYCES-CEREVISIAE; MESSENGER-RNA; GENE NETWORKS;
+ BIOLOGICAL-MEMBRANES; CERAMIDE SYNTHESIS; STRESS-RESPONSE; KEY
+ REGULATOR; HEAT-STRESS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Hatzimanikatis, Vassily/G-6505-2010
+ },
+ORCID-Numbers = {Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Riezman, Howard/0000-0003-4680-9422},
+Times-Cited = {31},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000377983400005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000382418000001,
+Author = {Vivek-Ananth, R. P. and Samal, Areejit},
+Title = {Advances in the integration of transcriptional regulatory information
+ into genome-scale metabolic models},
+Journal = {BIOSYSTEMS},
+Year = {2016},
+Volume = {147},
+Pages = {1-10},
+Month = {SEP},
+Type = {Review},
+DOI = {10.1016/j.biosystems.2016.06.001},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Flux balance analysis; Metabolic networks; Transcriptional regulatory
+ networks; Data integration; Integrated regulatory-metabolic models},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GENE-EXPRESSION; ESCHERICHIA-COLI; GLOBAL
+ RECONSTRUCTION; CELLULAR-METABOLISM; HIGH-THROUGHPUT; OMICS DATA;
+ NETWORK; SYSTEM; TISSUE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Samal, Areejit/E-5422-2011
+ Samal, Areejit/AAC-2485-2020
+ },
+ORCID-Numbers = {R.P., Vivek Ananth/0000-0002-3232-3299
+ Samal, Areejit/0000-0002-6796-9604},
+Times-Cited = {32},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000382418000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000388451900044,
+Author = {Zuniga, Cristal and Li, Chien-Ting and Huelsman, Tyler and Levering,
+ Jennifer and Zielinski, Daniel C. and McConnell, Brian O. and Long,
+ Christopher P. and Knoshaug, Eric P. and Guarnieri, Michael T. and
+ Antoniewicz, Maciek R. and Betenbaugh, Michael J. and Zengler, Karsten},
+Title = {Genome-Scale Metabolic Model for the Green Alga Chlorella
+ vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic,
+ Heterotrophic, and Mixotrophic Growth Conditions},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2016},
+Volume = {172},
+Number = {1},
+Pages = {589-602},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1104/pp.16.00593},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; BIODIESEL PRODUCTION; CARBONIC-ANHYDRASE;
+ RECONSTRUCTION; MICROALGAE; LIGHT; PROTOTHECOIDES; CYANOBACTERIA;
+ ACCUMULATION; FERMENTATION},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Li, Chien-Ting/I-7080-2019
+ Zuniga, Cristal/CAA-0015-2022
+ Antoniewicz, Maciek R/D-4015-2009
+ },
+ORCID-Numbers = {Levering, Jennifer/0000-0001-8491-9337
+ Zengler, Karsten/0000-0002-8062-3296
+ Antoniewicz, Maciek/0000-0002-0087-2875
+ Zielinski, Daniel/0000-0001-6452-483X
+ Guarnieri, Michael/0000-0003-1403-9689
+ Long, Christopher/0000-0003-1007-417X},
+Times-Cited = {69},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000388451900044},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000381830600001,
+Author = {Chitale, Meghana and Khan, Ishita K. and Kihara, Daisuke},
+Title = {Missing gene identification using functional coherence scores},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2016},
+Volume = {6},
+Month = {AUG 24},
+Type = {Article},
+DOI = {10.1038/srep31725},
+Article-Number = {31725},
+ISSN = {2045-2322},
+Keywords-Plus = {PROTEIN FUNCTION PREDICTION; ORPHAN ENZYME-ACTIVITIES; GENOME-SCALE;
+ METABOLIC RECONSTRUCTIONS; PATHWAYS; ONTOLOGY; ANNOTATION; EXPRESSION;
+ SIMILARITY; NETWORKS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Kihara, Daisuke/0000-0003-4091-6614},
+Times-Cited = {2},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000381830600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000381814400001,
+Author = {Grosskopf, Tobias and Consuegra, Jessika and Gaffe, Joel and Willison,
+ John C. and Lenski, Richard E. and Soyer, Orkun S. and Schneider,
+ Dominique},
+Title = {Metabolic modelling in a dynamic evolutionary framework predicts
+ adaptive diversification of bacteria in a long-term evolution experiment},
+Journal = {BMC EVOLUTIONARY BIOLOGY},
+Year = {2016},
+Volume = {16},
+Month = {AUG 20},
+Type = {Article},
+DOI = {10.1186/s12862-016-0733-x},
+Article-Number = {163},
+ISSN = {1471-2148},
+Keywords = {Adaptive diversification; Experimental evolution; FBA; In silico
+ evolution; Tradeoffs},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GENOME-SCALE MODELS; ESCHERICHIA-COLI;
+ TRANSCRIPTIONAL REGULATION; MICROBIAL-METABOLISM; OVERFLOW METABOLISM;
+ SYSTEMS-BIOLOGY; GENE-EXPRESSION; GROWTH; POLYMORPHISM},
+Research-Areas = {Evolutionary Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Evolutionary Biology; Genetics \& Heredity},
+ResearcherID-Numbers = {Consuegra, Jessika/F-7473-2013
+ Soyer, Orkun S/I-4863-2014
+ },
+ORCID-Numbers = {Consuegra, Jessika/0000-0002-3185-803X
+ Soyer, Orkun S/0000-0002-9504-3796
+ Lenski, Richard/0000-0002-1064-8375},
+Times-Cited = {42},
+Journal-ISO = {BMC Evol. Biol.},
+Unique-ID = {WOS:000381814400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000381381100039,
+Author = {Wu, Xudong and Li, Guohui},
+Title = {Prevalent Accumulation of Non-Optimal Codons through Somatic Mutations
+ in Human Cancers},
+Journal = {PLOS ONE},
+Year = {2016},
+Volume = {11},
+Number = {8},
+Month = {AUG 11},
+Type = {Article},
+DOI = {10.1371/journal.pone.0160463},
+Article-Number = {e0160463},
+ISSN = {1932-6203},
+Keywords-Plus = {PREDICTION; PROTEINS; RESOURCE; RECONSTRUCTION; SUBSTITUTION; EVOLUTION;
+ ONCOGENES; PATTERNS; NETWORK; REGIONS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {5},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000381381100039},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000381226100008,
+Author = {Edirisinghe, Janaka N. and Weisenhorn, Pamela and Conrad, Neal and Xia,
+ Fangfang and Overbeek, Ross and Stevens, Rick L. and Henry, Christopher
+ S.},
+Title = {Modeling central metabolism and energy biosynthesis across microbial
+ life},
+Journal = {BMC GENOMICS},
+Year = {2016},
+Volume = {17},
+Month = {AUG 8},
+Type = {Article},
+DOI = {10.1186/s12864-016-2887-8},
+Article-Number = {568},
+ISSN = {1471-2164},
+Keywords-Plus = {ESCHERICHIA-COLI; BACILLUS-SUBTILIS; PARACOCCUS-DENITRIFICANS; TERMINAL
+ OXIDASES; QUINOL OXIDASE; CYTOCHROME BD; GROWTH; OPTIMIZATION;
+ CAPABILITIES; GENERATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Times-Cited = {22},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000381226100008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000380790300002,
+Author = {Aurich, Maike K. and Fleming, Ronan M. T. and Thiele, Ines},
+Title = {MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale
+ Metabolic Models},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2016},
+Volume = {7},
+Month = {AUG 3},
+Type = {Article},
+DOI = {10.3389/fphys.2016.00327},
+Article-Number = {327},
+ISSN = {1664-042X},
+Keywords = {constraint-based reconstruction and analysis (COBRA); metabolomics;
+ metabolism; metabolic modeling; metabolic phenotypes; protocol; model
+ analysis},
+Keywords-Plus = {CELLULAR-METABOLISM; SYSTEMS BIOLOGY; NETWORK; DRIVEN; RECONSTRUCTION;
+ STATES; INTEGRATION; MACROPHAGE; PREDICTION; DATABASE},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {29},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000380790300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000381018000004,
+Author = {Cuperlovic-Culf, M. and Culf, A. S.},
+Title = {Applied metabolomics in drug discovery},
+Journal = {EXPERT OPINION ON DRUG DISCOVERY},
+Year = {2016},
+Volume = {11},
+Number = {8},
+Pages = {759-770},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1080/17460441.2016.1195365},
+ISSN = {1746-0441},
+EISSN = {1746-045X},
+Keywords = {Metabolomics; metabonomics; metabolic profiling; drug discovery; natural
+ products; chemical libraries; metabolic network},
+Keywords-Plus = {NATURAL-PRODUCT; MASS-SPECTROMETRY; UNTARGETED METABOLOMICS; H-1-NMR
+ SPECTROSCOPY; NMR METABOLOMICS; MIXTURE ANALYSIS; LC-MS/MS;
+ IDENTIFICATION; NETWORK; PREDICTION},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Cuperlovic-Culf, Miroslava/C-7876-2016},
+ORCID-Numbers = {Cuperlovic-Culf, Miroslava/0000-0002-9483-8159},
+Times-Cited = {20},
+Journal-ISO = {Expert. Opin. Drug Discov.},
+Unique-ID = {WOS:000381018000004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000383346100012,
+Author = {Hartleb, Daniel and Jarre, Florian and Lercher, Martin J.},
+Title = {Improved Metabolic Models for E. coli and Mycoplasma
+ genitalium from GlobalFit, an Algorithm That Simultaneously Matches
+ Growth and Non-Growth Data Sets},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2016},
+Volume = {12},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1005036},
+Article-Number = {e1005036},
+EISSN = {1553-7358},
+Keywords-Plus = {ADAPTIVE EVOLUTION; GLYCEROL KINASE; NETWORKS; RECONSTRUCTION;
+ OPTIMIZATION; TARGETS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Lercher, Martin J/K-7939-2013},
+ORCID-Numbers = {Lercher, Martin J/0000-0003-3940-1621},
+Times-Cited = {17},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000383346100012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000377935200027,
+Author = {Hendry, John I. and Prasannan, Charulata B. and Joshi, Aditi and
+ Dasgupta, Santanu and Wangikar, Pramod P.},
+Title = {Metabolic model of Synechococcus sp PCC 7002: Prediction of flux
+ distribution and network modification for enhanced biofuel production},
+Journal = {BIORESOURCE TECHNOLOGY},
+Year = {2016},
+Volume = {213},
+Pages = {190-197},
+Month = {AUG},
+Note = {International Conference on New Horizons in Biotechnology (NHBT-2015),
+ Trivandrum, INDIA, NOV 22-25, 2015},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.biortech.2016.02.128},
+ISSN = {0960-8524},
+EISSN = {1873-2976},
+Keywords = {Cyanobacteria; Synechococcus sp PCC 7002; Genome scale metabolic model;
+ Flux Balance Analysis; Minimization of Metabolic Adjustments (MOMA)},
+Keywords-Plus = {CYANOBACTERIA; CAROTENOIDS; OPTIMALITY; GENES},
+Research-Areas = {Agriculture; Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Agricultural Engineering; Biotechnology \& Applied Microbiology; Energy
+ \& Fuels},
+ORCID-Numbers = {Hendry, John/0000-0001-6949-7404},
+Times-Cited = {61},
+Journal-ISO = {Bioresour. Technol.},
+Unique-ID = {WOS:000377935200027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000377935200016,
+Author = {Juneja, Ankita and Chaplen, Frank W. R. and Murthy, Ganti S.},
+Title = {Genome scale metabolic reconstruction of Chlorella
+ variabilis for exploring its metabolic potential for biofuels},
+Journal = {BIORESOURCE TECHNOLOGY},
+Year = {2016},
+Volume = {213},
+Pages = {103-110},
+Month = {AUG},
+Note = {International Conference on New Horizons in Biotechnology (NHBT-2015),
+ Trivandrum, INDIA, NOV 22-25, 2015},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.biortech.2016.02.118},
+ISSN = {0960-8524},
+EISSN = {1873-2976},
+Keywords = {Algae; Chlorella variabilis; Genome scale reconstruction; Flux balance
+ analysis; Metabolic reconstruction},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CHLAMYDOMONAS-REINHARDTII;
+ SUBCELLULAR-LOCALIZATION; GREEN-ALGA; CELL-WALL; ANNOTATION; VULGARIS;
+ PROTEINS; HOMOLOGY; VIRUSES},
+Research-Areas = {Agriculture; Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Agricultural Engineering; Biotechnology \& Applied Microbiology; Energy
+ \& Fuels},
+ResearcherID-Numbers = {Juneja, Ankita/HJY-7942-2023
+ },
+ORCID-Numbers = {Juneja, Ankita/0000-0002-6784-7906
+ Chaplen, Frank/0000-0002-6631-9247},
+Times-Cited = {26},
+Journal-ISO = {Bioresour. Technol.},
+Unique-ID = {WOS:000377935200016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000383605900015,
+Author = {Peterson, Eliza J. R. and Ma, Shuyi and Sherman, David R. and Baliga,
+ Nitin S.},
+Title = {Network analysis identifies Rv0324 and Rv0880 as regulators of
+ bedaquiline tolerance in Mycobacterium tuberculosis},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2016},
+Volume = {1},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1038/NMICROBIOL.2016.78},
+Article-Number = {16078},
+ISSN = {2058-5276},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; BACTERICIDAL ACTIVITY;
+ CELLULAR-METABOLISM; PERSISTER CELLS; DIARYLQUINOLINES; PYRAZINAMIDE;
+ COMBINATIONS; MECHANISMS; RESISTANCE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {baliga, nitin/0000-0001-9157-5974
+ Ma, Shuyi/0000-0003-0783-1328},
+Times-Cited = {50},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000383605900015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000383184500012,
+Author = {Saa, Pedro A. and Nielsen, Lars K.},
+Title = {ll-ACHRB: a scalable algorithm for sampling the feasible solution space
+ of metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2016},
+Volume = {32},
+Number = {15},
+Pages = {2330-2337},
+Month = {AUG 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btw132},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {ESCHERICHIA-COLI; MONTE-CARLO; STATES; RECONSTRUCTION; MODELS; VOLUME},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Nielsen, Lars K/A-5519-2011
+ Saa, Pedro Andrés/X-1987-2018},
+ORCID-Numbers = {Nielsen, Lars K/0000-0001-8191-3511
+ Saa, Pedro Andrés/0000-0002-1659-9041},
+Times-Cited = {24},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000383184500012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000383346100037,
+Author = {van Heck, Ruben G. A. and Ganter, Mathias and dos Santos, Vitor A. P.
+ Martins and Stelling, Joerg},
+Title = {Efficient Reconstruction of Predictive Consensus Metabolic Network
+ Models},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2016},
+Volume = {12},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1005085},
+Article-Number = {e1005085},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE;
+ GENOME; GENES; IDENTIFICATION; VALIDATION; DATABASES; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Stelling, Joerg/F-7499-2010
+ },
+ORCID-Numbers = {Stelling, Joerg/0000-0002-1145-891X
+ Van Heck, Ruben/0000-0001-6787-6830
+ martins dos santos, vitor/0000-0002-2352-9017},
+Times-Cited = {14},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000383346100037},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379748600015,
+Author = {Yang, Xiaoyan and Yuan, Qianqian and Zheng, Yangyang and Ma, Hongwu and
+ Chen, Tao and Zhao, Xueming},
+Title = {An engineered non-oxidative glycolysis pathway for acetone production in
+ Escherichia coli},
+Journal = {BIOTECHNOLOGY LETTERS},
+Year = {2016},
+Volume = {38},
+Number = {8},
+Pages = {1359-1365},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1007/s10529-016-2115-2},
+ISSN = {0141-5492},
+EISSN = {1573-6776},
+Keywords = {Acetone; Escherichia coli; Non-oxidative glycolysis; Phosphoketolase},
+Keywords-Plus = {ISOPROPANOL PRODUCTION; SYNTHETIC PATHWAY; METABOLISM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ma, Hongwu/I-5263-2013
+ Zhao, Xueming/W-4891-2019
+ CHEN, Tao/N-1817-2015},
+ORCID-Numbers = {Ma, Hongwu/0000-0001-5325-2314
+ CHEN, Tao/0000-0001-9588-1821},
+Times-Cited = {16},
+Journal-ISO = {Biotechnol. Lett.},
+Unique-ID = {WOS:000379748600015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379846200001,
+Author = {Jouhten, Paula and Boruta, Tomasz and Andrejev, Sergej and Pereira,
+ Filipa and Rocha, Isabel and Patil, Kiran Raosaheb},
+Title = {Yeast metabolic chassis designs for diverse biotechnological products},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2016},
+Volume = {6},
+Month = {JUL 19},
+Type = {Article},
+DOI = {10.1038/srep29694},
+Article-Number = {29694},
+ISSN = {2045-2322},
+Keywords-Plus = {DE-NOVO PRODUCTION; SACCHAROMYCES-CEREVISIAE; KNOCKOUT STRATEGIES;
+ ESCHERICHIA-COLI; SCALE; STRAIN; PLATFORM; MODELS; PRECURSOR; ETHANOL},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Boruta, Tomasz/L-9558-2018
+ Patil, Kiran R/B-9709-2009
+ Rocha, Isabel/A-4279-2013
+ },
+ORCID-Numbers = {Boruta, Tomasz/0000-0002-8807-878X
+ Patil, Kiran R/0000-0002-6166-8640
+ Rocha, Isabel/0000-0001-9494-3410
+ Jouhten, Paula/0000-0003-1075-7448
+ Pereira, Filipa/0000-0002-0557-8480
+ Andrejev, Sergej/0000-0002-7875-0261},
+Times-Cited = {23},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000379846200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000380839600001,
+Author = {diCenzo, George C. and Checcucci, Alice and Bazzicalupo, Marco and
+ Mengoni, Alessio and Viti, Carlo and Dziewit, Lukasz and Finan, Turlough
+ M. and Galardini, Marco and Fondi, Marco},
+Title = {Metabolic modelling reveals the specialization of secondary replicons
+ for niche adaptation in Sinorhizobium meliloti},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2016},
+Volume = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1038/ncomms12219},
+Article-Number = {12219},
+ISSN = {2041-1723},
+Keywords-Plus = {TRANSPORT-SYSTEM; RHIZOBIUM-LEGUMINOSARUM; NITROGEN-FIXATION;
+ ESCHERICHIA-COLI; BACTERIAL GENOME; GENE-EXPRESSION; BIOSYNTHESIS;
+ MEGAPLASMID; SYMBIOSIS; IDENTIFICATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {checcucci, alice/AAF-7869-2021
+ Dziewit, Lukasz/L-1131-2016
+ Galardini, Marco/H-6413-2019
+ Checcucci, Alice/ISR-8746-2023
+ Mengoni, Alessio/G-5336-2013
+ diCenzo, George C C/M-1876-2017
+ },
+ORCID-Numbers = {Dziewit, Lukasz/0000-0002-5057-2811
+ Galardini, Marco/0000-0003-2018-8242
+ Mengoni, Alessio/0000-0002-1265-8251
+ diCenzo, George C C/0000-0003-3889-6570
+ VITI, CARLO/0000-0001-7188-549X
+ Fondi, Marco/0000-0001-9291-5467},
+Times-Cited = {64},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000380839600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379098100001,
+Author = {Jian, Xingxing and Zhou, Shengguo and Zhang, Cheng and Hua, Qiang},
+Title = {In silico identification of gene amplification targets based on
+ analysis of production and growth coupling},
+Journal = {BIOSYSTEMS},
+Year = {2016},
+Volume = {145},
+Pages = {1-8},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2016.05.002},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Analysis of production and growth coupling; Gene amplification target;
+ Constraint-based flux analysis; Genome-scale metabolic modeling;
+ Metabolic engineering strategy},
+Keywords-Plus = {ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; LYCOPENE PRODUCTION;
+ PATHWAY; KNOCKOUT; FLUX; OVERPRODUCTION; BIOSYNTHESIS; EXPRESSION;
+ DEHYDROGENASE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zhang, Cheng/L-7906-2016
+ },
+ORCID-Numbers = {Zhang, Cheng/0000-0002-3721-8586
+ Jian, Xingxing/0000-0003-3587-662X},
+Times-Cited = {7},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000379098100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379508500001,
+Author = {Swainston, Neil and Smallbone, Kieran and Hefzi, Hooman and Dobson, Paul
+ D. and Brewer, Judy and Hanscho, Michael and Zielinski, Daniel C. and
+ Ang, Kok Siong and Gardiner, Natalie J. and Gutierrez, Jahir M. and
+ Kyriakopoulos, Sarantos and Lakshmanan, Meiyappan and Li, Shangzhong and
+ Liu, Joanne K. and Martinez, Veronica S. and Orellana, Camila A. and
+ Quek, Lake-Ee and Thomas, Alex and Zanghellini, Juergen and Borth,
+ Nicole and Lee, Dong-Yup and Nielsen, Lars K. and Kell, Douglas B. and
+ Lewis, Nathan E. and Mendes, Pedro},
+Title = {Recon 2.2: from reconstruction to model of human metabolism},
+Journal = {METABOLOMICS},
+Year = {2016},
+Volume = {12},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1007/s11306-016-1051-4},
+Article-Number = {109},
+ISSN = {1573-3882},
+EISSN = {1573-3890},
+Keywords = {Human; Metabolism; Modelling; Reconstruction; Model; Systems biology},
+Keywords-Plus = {GENOME-SCALE MODELS; GLOBAL RECONSTRUCTION; NETWORK; PREDICTION; CHEBI},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Li, Shangzhong/HHD-1393-2022
+ Liu, Joanne/JRY-7564-2023
+ Nielsen, Lars K/A-5519-2011
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Li, Shangzhong/Y-6882-2019
+ Ang, Kok Siong/M-2674-2019
+ Lee, Dong-Yup/D-6650-2011
+ Zanghellini, Jürgen/A-4635-2017
+ Lewis, Nathan/ABE-7290-2020
+ Li, Shangzhong/HHD-1335-2022
+ Orellana, Camila/C-2979-2017
+ Orellana, Camila A/AAN-4060-2021
+ Kell, Douglas/E-8318-2011
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ },
+ORCID-Numbers = {Nielsen, Lars K/0000-0001-8191-3511
+ Li, Shangzhong/0000-0003-0272-3942
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Zanghellini, Jürgen/0000-0002-1964-2455
+ Lewis, Nathan/0000-0001-7700-3654
+ Orellana, Camila/0000-0002-6828-6071
+ Orellana, Camila A/0000-0002-6828-6071
+ Kell, Douglas/0000-0001-5838-7963
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Borth, Nicole/0000-0001-6324-9338
+ Mendes, Pedro/0000-0001-6507-9168
+ Martinez, Veronica/0000-0003-2729-5278
+ Quek, Lake-Ee/0000-0002-9313-8740
+ Hefzi, Hooman/0009-0003-4067-6224
+ Gardiner, Natalie/0000-0001-8287-1181
+ Zielinski, Daniel/0000-0001-6452-483X},
+Times-Cited = {190},
+Journal-ISO = {Metabolomics},
+Unique-ID = {WOS:000379508500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379761500011,
+Author = {Tobalina, Luis and Pey, Jon and Planes, Francisco J.},
+Title = {Direct calculation of minimal cut sets involving a specific reaction
+ knock-out},
+Journal = {BIOINFORMATICS},
+Year = {2016},
+Volume = {32},
+Number = {13},
+Pages = {2001-2007},
+Month = {JUL 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btw072},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {ELEMENTARY FLUX MODES; SYNTHETIC LETHALITY; ALGORITHM; NETWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Planes, Francisco J/H-3341-2013
+ },
+ORCID-Numbers = {Planes, Francisco J/0000-0003-1155-3105
+ Tobalina, Luis/0000-0002-1947-8309},
+Times-Cited = {10},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000379761500011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000378725700036,
+Author = {Wang, Xi and Xiong, Xiaochao and Sa, Na and Roje, Sanja and Chen, Shulin},
+Title = {Metabolic engineering of enhanced glycerol-3-phosphate synthesis to
+ increase lipid production in Synechocystis sp PCC 6803},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2016},
+Volume = {100},
+Number = {13},
+Pages = {6091-6101},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1007/s00253-016-7521-9},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Metabolic engineering; Synechocystis sp PCC6803; Glycerol-3-phosphate;
+ Lipid synthesis; FBA},
+Keywords-Plus = {YEAST YARROWIA-LIPOLYTICA; BIOFUEL PRODUCTION; ESCHERICHIA-COLI;
+ FATTY-ACIDS; SACCHAROMYCES-CEREVISIAE; LACTIC-ACID; SP PCC-6803;
+ CYANOBACTERIUM; PATHWAY; FLUX},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Roje, Sanja/0000-0002-6302-5382},
+Times-Cited = {20},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000378725700036},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000377960100001,
+Author = {Cuevas, Daniel A. and Edirisinghe, Janaka and Henry, Chris S. and
+ Overbeek, Ross and O'Connell, Taylor G. and Edwards, Robert A.},
+Title = {From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2016},
+Volume = {7},
+Month = {JUN 17},
+Type = {Article},
+DOI = {10.3389/fmicb.2016.00907},
+Article-Number = {907},
+ISSN = {1664-302X},
+Keywords = {metabolic modeling; metabolic reconstruction; in silico modeling;
+ flux-balance analysis; model SEED; genome annotation},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; SYSTEMS BIOLOGY; ANNOTATION;
+ RECONSTRUCTION; CAPABILITIES; INFORMATION; CHALLENGES; NETWORKS;
+ SOFTWARE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Edwards, Robert/Q-1691-2019},
+ORCID-Numbers = {Edwards, Robert/0000-0001-8383-8949},
+Times-Cited = {32},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000377960100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000377271100002,
+Author = {Du, Bin and Zielinski, Daniel C. and Kavvas, Erol S. and Draeger,
+ Andreas and Tan, Justin and Zhang, Zhen and Ruggiero, Kayla E. and
+ Arzumanyan, Garri A. and Palsson, Bernhard O.},
+Title = {Evaluation of rate law approximations in bottom-up kinetic models of
+ metabolism},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2016},
+Volume = {10},
+Month = {JUN 6},
+Type = {Article},
+DOI = {10.1186/s12918-016-0283-2},
+Article-Number = {40},
+EISSN = {1752-0509},
+Keywords = {Metabolic modeling; Kinetic modeling; Approximate rate laws;
+ Michaelis-Menten kinetics; Mass action kinetics},
+Keywords-Plus = {STEADY-STATE ASSUMPTION; CELL; SIMULATION; DYNAMICS; NETWORKS; REDESIGN;
+ VALIDITY},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Dräger, Andreas/F-5620-2015
+ },
+ORCID-Numbers = {Dräger, Andreas/0000-0002-1240-5553
+ Zielinski, Daniel/0000-0001-6452-483X},
+Times-Cited = {21},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000377271100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379349700023,
+Author = {Choudhary, Kumari Sonal and Rohatgi, Neha and Halldorsson, Skarphedinn
+ and Briem, Eirikur and Gudjonsson, Thorarinn and Gudmundsson, Steinn and
+ Rolfsson, Ottar},
+Title = {EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in
+ EMT},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2016},
+Volume = {12},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004924},
+Article-Number = {e1004924},
+EISSN = {1553-7358},
+Keywords-Plus = {EPITHELIAL-MESENCHYMAL TRANSITION; UP-REGULATION; CELL-GROWTH; CANCER;
+ AKT; PATHWAY; PHOSPHORYLATION; EXPRESSION; PROTEIN; TARGET},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Kumari, Sonal/AAW-7588-2020
+ Gudjonsson, Thorkell/K-5361-2014
+ Halldórsson, Skarphéðinn/AAD-7217-2019
+ Choudhary, Kumari Sonal/M-4517-2017
+ },
+ORCID-Numbers = {Choudhary, Kumari Sonal/0000-0001-9527-7958
+ Gudjonsson, Thorarinn/0000-0001-9645-9665
+ Rolfsson, Ottar/0000-0003-4258-6057
+ Halldorsson, Skarphedinn/0000-0003-4337-9252
+ Rohatgi, Neha/0000-0003-1103-0259},
+Times-Cited = {35},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000379349700023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000378178400007,
+Author = {Di Filippo, Marzia and Colombo, Riccardo and Damiani, Chiara and
+ Pescini, Dario and Gaglio, Daniela and Vanoni, Marco and Alberghina,
+ Lilia and Mauri, Giancarlo},
+Title = {Zooming-in on cancer metabolic rewiring with tissue specific
+ constraint-based models},
+Journal = {COMPUTATIONAL BIOLOGY AND CHEMISTRY},
+Year = {2016},
+Volume = {62},
+Pages = {60-69},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1016/j.compbiolchem.2016.03.002},
+ISSN = {1476-9271},
+EISSN = {1476-928X},
+Keywords = {Cancer metabolic rewiring; Network reconstruction; Core metabolic model;
+ Flux Balance Analysis},
+Keywords-Plus = {QUANTITATIVE PREDICTION; GLOBAL RECONSTRUCTION; GLUTAMINE-METABOLISM;
+ CELLULAR-METABOLISM; ESCHERICHIA-COLI; SYSTEMS BIOLOGY; NETWORK; HMDB;
+ CAPABILITIES; GLYCOLYSIS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications},
+ResearcherID-Numbers = {Vanoni, Marco/AAA-3699-2021
+ Gaglio, Daniela/AEZ-3835-2022
+ Mauri, Giancarlo/M-3258-2013
+ Pescini, Dario/H-4866-2017
+ },
+ORCID-Numbers = {Vanoni, Marco/0000-0002-8690-2587
+ Mauri, Giancarlo/0000-0003-3520-4022
+ Pescini, Dario/0000-0002-3090-4823
+ Alberghina, Lilia/0000-0003-1694-931X
+ Damiani, Chiara/0000-0002-5742-8302
+ COLOMBO, RICCARDO/0000-0002-9499-0126},
+Times-Cited = {28},
+Journal-ISO = {Comput. Biol. Chem.},
+Unique-ID = {WOS:000378178400007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379349700019,
+Author = {Mori, Matteo and Hwa, Terence and Martin, Olivier C. and De Martino,
+ Andrea and Marinari, Enzo},
+Title = {Constrained Allocation Flux Balance Analysis},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2016},
+Volume = {12},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004913},
+Article-Number = {e1004913},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI; INTRACELLULAR FLUXES; RESOURCE-ALLOCATION; OVERFLOW
+ METABOLISM; RIBOSOMAL-RNA; GROWTH LAWS; EXPRESSION; PROTEOME; MODELS;
+ DEPENDENCY},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Mori, Matteo/Q-6717-2018
+ Hwa, Terence/J-4012-2013
+ Martin, Olivier C/B-6656-2012
+ De Martino, Andrea/AAY-4120-2020
+ Hwa, Terry/GOJ-9904-2022
+ },
+ORCID-Numbers = {Mori, Matteo/0000-0002-6263-8021
+ Hwa, Terence/0000-0003-1837-6842
+ Martin, Olivier C/0000-0002-5295-5963
+ De Martino, Andrea/0000-0001-7590-6542},
+Times-Cited = {95},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000379349700019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000374609300005,
+Author = {Vongsangnak, Wanwipa and Klanchui, Amornpan and Tawornsamretkit, Iyarest
+ and Tatiyaborwornchai, Witthawin and Laoteng, Kobkul and Meechai, Asawin},
+Title = {Genome-scale metabolic modeling of Mucor circinelloides and
+ comparative analysis with other oleaginous species},
+Journal = {GENE},
+Year = {2016},
+Volume = {583},
+Number = {2},
+Pages = {121-129},
+Month = {JUN 1},
+Type = {Article},
+DOI = {10.1016/j.gene.2016.02.028},
+ISSN = {0378-1119},
+EISSN = {1879-0038},
+Keywords = {Lipid; Mucor circinelloides; Genome-scale metabolic modeling; Oleaginous
+ species; Metabolic engineering},
+Keywords-Plus = {LIPID-ACCUMULATION; ACID PRODUCTION; OIL PRODUCTION; PREDICTION;
+ PHYSIOLOGY; RACEMOSUS},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+Times-Cited = {17},
+Journal-ISO = {Gene},
+Unique-ID = {WOS:000374609300005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000381316600011,
+Author = {Waschina, Silvio and D'Souza, Glen and Kost, Christian and Kaleta,
+ Christoph},
+Title = {Metabolic network architecture and carbon source determine metabolite
+ production costs},
+Journal = {FEBS JOURNAL},
+Year = {2016},
+Volume = {283},
+Number = {11},
+Pages = {2149-2163},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1111/febs.13727},
+ISSN = {1742-464X},
+EISSN = {1742-4658},
+Keywords = {amino acid auxotrophies; biosynthetic cost; Escherichia coli; flux
+ balance analysis; metabolic trade-off; resource allocation problem},
+Keywords-Plus = {ESCHERICHIA-COLI K-12; GROWTH-RATE; EVOLUTION; EXPRESSION; PROTEOME;
+ ACETATE; FITNESS; GENES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Waschina, Silvio/AAE-2908-2021
+ },
+ORCID-Numbers = {Waschina, Silvio/0000-0002-6290-3593
+ Kost, Christian/0000-0002-7870-7343
+ Kaleta, Christoph/0000-0001-8004-9514
+ D'Souza, Glen Gerald/0000-0002-9123-101X},
+Times-Cited = {33},
+Journal-ISO = {FEBS J.},
+Unique-ID = {WOS:000381316600011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000376787300001,
+Author = {Li, Ying and Wang, Xi and Ge, Xizhen and Tian, Pingfang},
+Title = {High Production of 3-Hydroxypropionic Acid in Klebsiella
+ pneumoniae by Systematic Optimization of Glycerol Metabolism},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2016},
+Volume = {6},
+Month = {MAY 27},
+Type = {Article},
+DOI = {10.1038/srep26932},
+Article-Number = {26932},
+ISSN = {2045-2322},
+Keywords-Plus = {ALDEHYDE DEHYDROGENASE-ACTIVITY; ESCHERICHIA-COLI; TAC PROMOTER;
+ CONTROLLED-EXPRESSION; RESTING CELLS; 1,3-PROPANEDIOL; DISSIMILATION;
+ COPRODUCTION; BIOSYNTHESIS; PATHWAY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Li, Ying/0000-0001-8321-022X},
+Times-Cited = {66},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000376787300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394360100006,
+Author = {Gebauer, Juliane and Gentsch, Christoph and Mansfeld, Johannes and
+ Schmeisser, Kathrin and Waschina, Silvio and Brandes, Susanne and
+ Klimmasch, Lukas and Zamboni, Nicola and Zarse, Kim and Schuster, Stefan
+ and Ristow, Michael and Schaeuble, Sascha and Kaleta, Christoph},
+Title = {A Genome-Scale Database and Reconstruction of Caenorhabditis
+ elegans Metabolism},
+Journal = {CELL SYSTEMS},
+Year = {2016},
+Volume = {2},
+Number = {5},
+Pages = {312-322},
+Month = {MAY 25},
+Type = {Article},
+DOI = {10.1016/j.cels.2016.04.017},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {LIFE-SPAN REGULATION; LIVED CLK-1 MUTANTS; CALORIC RESTRICTION; GLOBAL
+ RECONSTRUCTION; DIETARY RESTRICTION; OXIDATIVE STRESS; GENE-EXPRESSION;
+ QUINOLINIC ACID; PROTEIN; BIOSYNTHESIS},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Ristow, Michael/O-9858-2014
+ Zarse, Kim/D-2133-2016
+ Schäuble, Sascha/AAF-7809-2021
+ Waschina, Silvio/AAE-2908-2021
+ Zamboni, Nicola/K-3042-2012
+ },
+ORCID-Numbers = {Ristow, Michael/0000-0003-2109-2453
+ Zarse, Kim/0000-0003-2542-6123
+ Waschina, Silvio/0000-0002-6290-3593
+ Zamboni, Nicola/0000-0003-1271-1021
+ Kaleta, Christoph/0000-0001-8004-9514},
+Times-Cited = {26},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000394360100006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000376155700001,
+Author = {Ferrarini, Mariana G. and Siqueira, Franciele M. and Mucha, Scheila G.
+ and Palama, Tony L. and Jobard, Elodie and Elena-Herrmann, Benedicte and
+ Vasconcelos, Ana T. R. and Tardy, Florence and Schrank, Irene S. and
+ Zaha, Arnaldo and Sagot, Marie-France},
+Title = {Insights on the virulence of swine respiratory tract mycoplasmas through
+ genome-scale metabolic modeling},
+Journal = {BMC GENOMICS},
+Year = {2016},
+Volume = {17},
+Month = {MAY 13},
+Type = {Article},
+DOI = {10.1186/s12864-016-2644-z},
+Article-Number = {353},
+ISSN = {1471-2164},
+Keywords = {Mycoplasma; Mollicutes; Metabolic network; Metabolism; Whole-genome
+ metabolic reconstruction; Hydrogen peroxide},
+Keywords-Plus = {HYOPNEUMONIAE INFECTION; GROWTH-RATE; FLOCCULARE; HYORHINIS; STRAIN;
+ SEQUENCE; SUIPNEUMONIAE; PNEUMONIAE; GLYCEROL; PIGS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {PALAMA, Tony L./GQZ-0761-2022
+ Zaha, Arnaldo/D-3165-2013
+ Elodie, Jobard/B-8059-2015
+ Elena-Herrmann, Bénédicte/B-9965-2008
+ Vasconcelos, Ana Carolina Souza de/GXW-3453-2022
+ Vasconcelos, Ana Tereza R/I-1011-2012
+ Siqueira, Franciele M/K-4043-2014
+ },
+ORCID-Numbers = {PALAMA, Tony L./0000-0002-4519-4502
+ Elena-Herrmann, Bénédicte/0000-0002-0230-1590
+ Vasconcelos, Ana Tereza R/0000-0002-4632-2086
+ Siqueira, Franciele M/0000-0001-7282-6117
+ TARDY, Florence/0000-0003-3968-4801
+ Galvao Ferrarini, Mariana/0000-0002-9574-9991
+ Mucha, Scheila/0000-0001-8686-6857
+ /0000-0002-5933-9960
+ Zaha, Arnaldo/0000-0001-6336-474X},
+Times-Cited = {25},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000376155700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000375677000062,
+Author = {Levering, Jennifer and Broddrick, Jared and Dupont, Christopher L. and
+ Peers, Graham and Beeri, Karen and Mayers, Joshua and Gallina,
+ Alessandra A. and Allen, Andrew E. and Palsson, Bernhard O. and Zengler,
+ Karsten},
+Title = {Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a
+ Model Diatom},
+Journal = {PLOS ONE},
+Year = {2016},
+Volume = {11},
+Number = {5},
+Month = {MAY 6},
+Type = {Article},
+DOI = {10.1371/journal.pone.0155038},
+Article-Number = {e0155038},
+ISSN = {1932-6203},
+Keywords-Plus = {PHAEODACTYLUM-TRICORNUTUM; FUNCTIONAL-CHARACTERIZATION;
+ EXTRACELLULAR-MATRIX; SIGNAL PEPTIDES; MARINE DIATOMS; AMINO-ACID;
+ PROTEIN; NITROGEN; RECONSTRUCTION; LOCALIZATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Allen, Andrew E/C-4896-2012
+ },
+ORCID-Numbers = {Allen, Andrew E/0000-0001-5911-6081
+ Levering, Jennifer/0000-0001-8491-9337
+ Zengler, Karsten/0000-0002-8062-3296
+ Broddrick, Jared/0000-0003-4871-4822
+ Peers, Graham/0000-0002-3590-7820},
+Times-Cited = {69},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000375677000062},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000375676400055,
+Author = {Tobalina, Luis and Pey, Jon and Rezola, Alberto and Planes, Francisco J.},
+Title = {Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast
+ Context-Specific Network Reconstruction Method},
+Journal = {PLOS ONE},
+Year = {2016},
+Volume = {11},
+Number = {5},
+Month = {MAY 4},
+Type = {Article},
+DOI = {10.1371/journal.pone.0154583},
+Article-Number = {e0154583},
+ISSN = {1932-6203},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; EXPRESSION DATA; PROLIFERATION; INTEGRATION;
+ PREDICTION; REDUCTASE; INVASION; CELLS; COLI},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Planes, Francisco J/H-3341-2013
+ Rezola, Alberto/L-5631-2014
+ },
+ORCID-Numbers = {Planes, Francisco J/0000-0003-1155-3105
+ Rezola, Alberto/0000-0001-9942-5487
+ Tobalina, Luis/0000-0002-1947-8309},
+Times-Cited = {9},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000375676400055},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373167900017,
+Author = {Andreozzi, Stefano and Chakrabarti, Anirikh and Soh, Keng Cher and
+ Burgard, Anthony and Yang, Tae Hoon and Van Dien, Stephen and Miskovic,
+ Ljubisa and Hatzimanikatis, Vassily},
+Title = {Identification of metabolic engineering targets for the enhancement of
+ 1,4-butanediol production in recombinant E. coli using
+ large-scale kinetic models},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {35},
+Pages = {148-159},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2016.01.009},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {ORACLE; 1,4-butanediol; Metabolic control analysis; Kinetic models;
+ Thermodynamics; Flux balance analysis; Uncertainty},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE;
+ QUANTITATIVE PREDICTION; THERMODYNAMIC ANALYSIS; CELLULAR-METABOLISM;
+ FRAMEWORK; STRAIN; UNCERTAINTY; EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Hatzimanikatis, Vassily/G-6505-2010
+ Andreozzi, Stefano/JEP-4511-2023
+ Miskovic, Ljubisa/E-8927-2012
+ },
+ORCID-Numbers = {Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Miskovic, Ljubisa/0000-0001-7333-8211
+ Chakrabarti, Anirikh/0000-0001-7804-209X},
+Times-Cited = {56},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000373167900017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000374834900004,
+Author = {Ho, Wei-Chin and Zhang, Jianzhi},
+Title = {Adaptive Genetic Robustness of Escherichia coli Metabolic Fluxes},
+Journal = {MOLECULAR BIOLOGY AND EVOLUTION},
+Year = {2016},
+Volume = {33},
+Number = {5},
+Pages = {1164-1176},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1093/molbev/msw002},
+ISSN = {0737-4038},
+EISSN = {1537-1719},
+Keywords = {environmental robustness; metabolic network; flux balance analysis;
+ evolution; natural selection},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; SACCHAROMYCES-CEREVISIAE; FITNESS;
+ CANALIZATION; EVOLUTION; SELECTION; INNOVATION; BALANCE; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Evolutionary Biology; Genetics \&
+ Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Evolutionary Biology; Genetics \&
+ Heredity},
+Times-Cited = {14},
+Journal-ISO = {Mol. Biol. Evol.},
+Unique-ID = {WOS:000374834900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379684200008,
+Author = {Morin, Manon and Ropers, Delphine and Letisse, Fabien and Laguerre,
+ Sandrine and Portais, Jean-Charles and Cocaign-Bousquet, Muriel and
+ Enjalbert, Brice},
+Title = {The post-transcriptional regulatory system CSR controls the balance of
+ metabolic pools in upper glycolysis of Escherichia coli},
+Journal = {MOLECULAR MICROBIOLOGY},
+Year = {2016},
+Volume = {100},
+Number = {4},
+Pages = {686-700},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1111/mmi.13343},
+ISSN = {0950-382X},
+EISSN = {1365-2958},
+Keywords-Plus = {CENTRAL CARBON METABOLISM; GENE-EXPRESSION; MESSENGER-RNA; GLYCOGEN
+ BIOSYNTHESIS; FLUX ANALYSIS; PRODUCT; YEAST; ACCUMULATION; CATABOLISM;
+ STABILITY},
+Research-Areas = {Biochemistry \& Molecular Biology; Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Microbiology},
+ResearcherID-Numbers = {Morin, Manon/AAB-4837-2021
+ Enjalbert, Brice/JFJ-8505-2023
+ Cocaign-Bousquet, Muriel/ISV-5020-2023
+ },
+ORCID-Numbers = {Enjalbert, Brice/0000-0003-1291-1373
+ Cocaign-Bousquet, Muriel/0000-0003-2033-9901
+ Portais, Jean-Charles/0000-0002-3480-0933
+ Fabien, Letisse/0000-0002-1490-0152
+ Ropers, Delphine/0000-0003-2659-3003
+ Morin, Manon/0000-0003-2158-0473},
+Times-Cited = {32},
+Journal-ISO = {Mol. Microbiol.},
+Unique-ID = {WOS:000379684200008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373476700021,
+Author = {Perez-Garcia, Octavio and Chandran, Kartik and Villas-Boas, Silas G. and
+ Singhal, Naresh},
+Title = {Assessment of nitric oxide (NO) redox reactions contribution to nitrous
+ oxide (N2O) formation during nitrification using a
+ multispecies metabolic network model},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2016},
+Volume = {113},
+Number = {5},
+Pages = {1124-1136},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/bit.25880},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {metabolic modeling; nitrous oxide emission; nitrification; oxidreductase
+ enzymes; AOB; NOB},
+Keywords-Plus = {AMMONIA-OXIDIZING BACTERIUM; COMPLETE GENOME SEQUENCE; WASTE-WATER
+ TREATMENT; FLUX BALANCE ANALYSIS; NITROSOMONAS-EUROPAEA;
+ ESCHERICHIA-COLI; EMISSIONS; COMMUNITIES; MECHANISMS; GENERATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Villas-Boas, Silas Granato/HLQ-1860-2023
+ Villas-Boas, Silas/AAR-6748-2020
+ Singhal, Naresh/C-2769-2008
+ Villas-Boas, Silas/AAS-5888-2020
+ },
+ORCID-Numbers = {Singhal, Naresh/0000-0002-9461-688X
+ Villas-Boas, Silas/0000-0003-0148-5882
+ Perez-Garcia, Octavio/0000-0002-5900-1310},
+Times-Cited = {8},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000373476700021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000376654200007,
+Author = {Robaina-Estevez, Semidan and Nikoloski, Zoran},
+Title = {Metabolic Network Constrains Gene Regulation of C4
+ Photosynthesis: The Case of Maize},
+Journal = {PLANT AND CELL PHYSIOLOGY},
+Year = {2016},
+Volume = {57},
+Number = {5},
+Pages = {933-943},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1093/pcp/pcw034},
+ISSN = {0032-0781},
+EISSN = {1471-9053},
+Keywords = {C4 metabolism; Gene regulation; Metabolic networks; Systems biology},
+Keywords-Plus = {DEVELOPMENTAL DYNAMICS; LEAF; DIFFERENTIATION; EVOLUTION; MODEL; RICE;
+ PHOTORESPIRATION; TRANSCRIPTOME; EXPRESSION; PREDICTION},
+Research-Areas = {Plant Sciences; Cell Biology},
+Web-of-Science-Categories = {Plant Sciences; Cell Biology},
+ORCID-Numbers = {Robaina Estevez, Semidan/0000-0003-0781-1677
+ Nikoloski, Zoran/0000-0003-2671-6763},
+Times-Cited = {5},
+Journal-ISO = {Plant Cell Physiol.},
+Unique-ID = {WOS:000376654200007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373167900008,
+Author = {Zhang, Xiaolin and Tervo, Christopher J. and Reed, Jennifer L.},
+Title = {Metabolic assessment of E. coli as a Biofactory for commercial products},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {35},
+Pages = {64-74},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2016.01.007},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic engineering; Flux balance analysis; Constraint-based analysis;
+ Path finding; Metabolic model; Metabolic network analysis},
+Keywords-Plus = {HIGH-YIELD PRODUCTION; ESCHERICHIA-COLI; ACRYLIC-ACID; PATHWAYS;
+ PREDICTION; MESO-2,3-BUTANEDIOL; TRANSCRIPTION; BIOSYNTHESIS;
+ TRANSLATION; CONVERSION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Tervo, Christopher J/E-5919-2012
+ Reed, Jennifer L/E-5137-2011
+ Zhang, Xiaolin/N-7139-2017},
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220
+ Zhang, Xiaolin/0000-0003-4745-0810},
+Times-Cited = {33},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000373167900008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000374732300001,
+Author = {Yuan, Huili and Cheung, C. Y. Maurice and Hilbers, Peter A. J. and van
+ Riel, Natal A. W.},
+Title = {Flux Balance Analysis of Plant Metabolism: The Effect of Biomass
+ Composition and Model Structure on Model Predictions},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2016},
+Volume = {7},
+Month = {APR 26},
+Type = {Article},
+DOI = {10.3389/fpls.2016.00537},
+Article-Number = {537},
+ISSN = {1664-462X},
+Keywords = {biomass composition; model structure; sensitivity; flux balance
+ analysis; central carbon metabolism; Arabidopsis; large-scale metabolic
+ model},
+Keywords-Plus = {NETWORK RECONSTRUCTION; CHEMICAL-COMPOSITION; WINTER BARLEY;
+ ARABIDOPSIS; GROWTH; TOMATO; CARBON; ALLOCATION; EFFICIENCY; STABILITY},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {van Riel, Natal/J-5319-2013
+ },
+ORCID-Numbers = {van Riel, Natal/0000-0001-9375-4730
+ Cheung, C. Y. Maurice/0000-0002-5531-7895},
+Times-Cited = {26},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000374732300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000374447400001,
+Author = {Ozcan, Emrah and Cakir, Tunahan},
+Title = {Reconstructed Metabolic Network Models Predict Flux-Level Metabolic
+ Reprogramming in Glioblastoma},
+Journal = {FRONTIERS IN NEUROSCIENCE},
+Year = {2016},
+Volume = {10},
+Month = {APR 18},
+Type = {Article},
+DOI = {10.3389/fnins.2016.00156},
+Article-Number = {156},
+ISSN = {1662-453X},
+Keywords = {aerobic glycolysis; glutaminolysis; constraint-based models; omics data;
+ tumor subtypes; GBM-specific metabolic model},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GENE-EXPRESSION; AMINO-ACIDS; HUMAN BRAIN;
+ GROWTH; ADULT; CELLS; INTEGRATION; GLIOMAS; STATES},
+Research-Areas = {Neurosciences \& Neurology},
+Web-of-Science-Categories = {Neurosciences},
+ResearcherID-Numbers = {Cakir, Tunahan/F-4523-2011
+ ÖZCAN, EMRAH/HZH-6141-2023
+ },
+ORCID-Numbers = {Cakir, Tunahan/0000-0001-8262-4420
+ OZCAN, EMRAH/0000-0001-9036-9909},
+Times-Cited = {26},
+Journal-ISO = {Front. Neurosci.},
+Unique-ID = {WOS:000374447400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373676200001,
+Author = {Kunjapur, Aditya M. and Hyun, Jason C. and Prather, Kristala L. J.},
+Title = {Deregulation of S-adenosylmethionine biosynthesis and
+ regeneration improves methylation in the E-coli de novo vanillin
+ biosynthesis pathway},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2016},
+Volume = {15},
+Month = {APR 11},
+Type = {Article},
+DOI = {10.1186/s12934-016-0459-x},
+Article-Number = {61},
+ISSN = {1475-2859},
+Keywords = {E. coli; Vanillin; Methylation; S-adenosylmethionine; SAM; AdoMet;
+ Methionine; Deregulation; Metabolic engineering},
+Keywords-Plus = {CATECHOL-O-METHYLTRANSFERASE; METHIONINE SYNTHASE METE; CONSTRAINT-BASED
+ MODELS; BAKERS-YEAST; SACCHAROMYCES-CEREVISIAE; QUANTITATIVE PREDICTION;
+ HOMOCYSTEINE TOXICITY; CELLULAR-METABOLISM; COBRA TOOLBOX; INHIBITION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Kunjapur, Aditya Mohan/HKM-6296-2023
+ },
+ORCID-Numbers = {Kunjapur, Aditya Mohan/0000-0001-6869-9530
+ Hyun, Jason/0000-0002-3263-3860},
+Times-Cited = {56},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000373676200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373656300058,
+Author = {McCloskey, Douglas and Young, Jamey D. and Xu, Sibei and Palsson,
+ Bernhard O. and Feist, Adam M.},
+Title = {Modeling Method for Increased Precision and Scope of Directly Measurable
+ Fluxes at a Genome-Scale},
+Journal = {ANALYTICAL CHEMISTRY},
+Year = {2016},
+Volume = {88},
+Number = {7},
+Pages = {3844-3852},
+Month = {APR 5},
+Type = {Article},
+DOI = {10.1021/acs.analchem.5b04914},
+ISSN = {0003-2700},
+EISSN = {1520-6882},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; CONSTRAINT-BASED MODELS;
+ ESCHERICHIA-COLI; CORYNEBACTERIUM-GLUTAMICUM; MEVALONATE PATHWAY;
+ ISOPRENOID PATHWAY; MASS-SPECTROMETRY; RECONSTRUCTION; PRECURSOR;
+ METABOLITES},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Analytical},
+ResearcherID-Numbers = {Young, Jamey/A-5857-2012},
+Times-Cited = {23},
+Journal-ISO = {Anal. Chem.},
+Unique-ID = {WOS:000373656300058},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373675900001,
+Author = {Nidelet, Thibault and Brial, Pascale and Camarasa, Carole and Dequin,
+ Sylvie},
+Title = {Diversity of flux distribution in central carbon metabolism of S.
+ cerevisiae strains from diverse environments},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2016},
+Volume = {15},
+Month = {APR 5},
+Type = {Article},
+DOI = {10.1186/s12934-016-0456-0},
+Article-Number = {58},
+EISSN = {1475-2859},
+Keywords = {Diversity; Flux balance analysis; Metabolic flux; Modeling; S.
+ cerevisiae},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; POPULATION-STRUCTURE; OBJECTIVE FUNCTIONS;
+ NETWORK ANALYSIS; WINE; GLYCEROL; DEHYDROGENASE; GLUCOSE; CONSEQUENCES;
+ STRATEGIES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {20},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000373675900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000374343900023,
+Author = {Bordbar, Aarash and Johansson, Par I. and Paglia, Giuseppe and Harrison,
+ Scott J. and Wichuk, Kristine and Magnusdottir, Manuela and
+ Valgeirsdottir, Soley and Gybel-Brask, Mikkel and Ostrowski, Sisse R.
+ and Palsson, Sirus and Rolfsson, Ottar and Sigurjonsson, Olafur E. and
+ Hansen, Morten B. and Gudmundsson, Sveinn and Palsson, Bernhard O.},
+Title = {Identified metabolic signature for assessing red blood cell unit quality
+ is associated with endothelial damage markers and clinical outcomes},
+Journal = {TRANSFUSION},
+Year = {2016},
+Volume = {56},
+Number = {4},
+Pages = {852-862},
+Month = {APR},
+Type = {Article},
+DOI = {10.1111/trf.13460},
+ISSN = {0041-1132},
+EISSN = {1537-2995},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; STORAGE DURATION; TRANSFUSED BLOOD; PLASMA;
+ MORTALITY; AGE; DIMETHYLGLYCINE; 5-OXOPROLINURIA; HOMOCYSTEINE;
+ GLUTATHIONE},
+Research-Areas = {Hematology},
+Web-of-Science-Categories = {Hematology},
+ResearcherID-Numbers = {Ostrowski, Sisse Rye/E-7423-2011
+ /AAG-5264-2021
+ Paglia, Giuseppe/H-2012-2018
+ Johansson, Pär/GQB-1032-2022
+ Sigurjonsson, Olafur/T-8190-2019
+ },
+ORCID-Numbers = {Ostrowski, Sisse Rye/0000-0001-5288-3851
+ /0000-0001-6460-6771
+ Paglia, Giuseppe/0000-0003-4724-6801
+ Johansson, Pär/0000-0001-9778-5964
+ Sigurjonsson, Olafur/0000-0002-4968-842X
+ Gybel-Brask, Mikkel/0000-0002-5716-5899
+ Rolfsson, Ottar/0000-0003-4258-6057},
+Times-Cited = {80},
+Journal-ISO = {Transfusion},
+Unique-ID = {WOS:000374343900023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373709900010,
+Author = {Meng, Hai-Lin and Xiong, Zhi-Qiang and Song, Shu-Jie and Wang, Jianfeng
+ and Wang, Yong},
+Title = {Construction of polyketide overproducing Escherichia coli strains
+ via synthetic antisense RNAs based on in silico fluxome analysis and
+ comparative transcriptome analysis},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2016},
+Volume = {11},
+Number = {4},
+Pages = {530-541},
+Month = {APR},
+Type = {Article},
+DOI = {10.1002/biot.201500351},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Antisense RNA; Comparative transcriptome analysis; In silico fluxome
+ analysis; Metabolic module interactions; Polyketides},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ZWF GENE-KNOCKOUT; 6-DEOXYERYTHRONOLIDE B; E.
+ COLI; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; BACILLUS-SUBTILIS;
+ COBRA TOOLBOX; FATTY-ACIDS; BIOSYNTHESIS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {LI, QI/IUM-8577-2023
+ },
+ORCID-Numbers = {Xiong, Zhi-Qiang/0000-0002-7984-3662},
+Times-Cited = {10},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000373709900010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373308200007,
+Author = {Sohrabi-Jahromi, Salma and Marashi, Sayed-Amir and Kalantari, Shiva},
+Title = {A kidney-specific genome-scale metabolic network model for analyzing
+ focal segmental glomerulosclerosis},
+Journal = {MAMMALIAN GENOME},
+Year = {2016},
+Volume = {27},
+Number = {3-4},
+Pages = {158-167},
+Month = {APR},
+Type = {Article},
+DOI = {10.1007/s00335-016-9622-2},
+ISSN = {0938-8990},
+EISSN = {1432-1777},
+Keywords-Plus = {DRUG TARGETS; RECONSTRUCTION; SULFATE; BIOLOGY; PREDICTION; CANCER; CELL},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008
+ },
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Sohrabi-Jahromi, Salma/0000-0002-8417-8230
+ Kalantari, Shiva/0000-0001-7690-141X},
+Times-Cited = {13},
+Journal-ISO = {Mamm. Genome},
+Unique-ID = {WOS:000373308200007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373922700003,
+Author = {Zhao, Yuqi and Wang, Yanjie and Zou, Lei and Huang, Jingfei},
+Title = {Reconstruction and applications of consensus yeast metabolic network
+ based on RNA sequencing},
+Journal = {FEBS OPEN BIO},
+Year = {2016},
+Volume = {6},
+Number = {4},
+Pages = {264-275},
+Month = {APR},
+Type = {Article},
+DOI = {10.1002/2211-5463.12033},
+ISSN = {2211-5463},
+Keywords = {metabolic engineering; metabolic network; RNA sequencing; Saccharomyces
+ species},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ TRANSCRIPTOME; IDENTIFICATION; ANNOTATION; STRATEGIES; PROTEOME;
+ DISEASE; BIOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Zhao, Yuqi/L-5639-2016
+ huang, jing/JDC-2548-2023
+ },
+ORCID-Numbers = {Zhao, Yuqi/0000-0003-0730-5854
+ Zhao, Yuqi/0000-0002-4256-4512},
+Times-Cited = {3},
+Journal-ISO = {FEBS Open Bio},
+Unique-ID = {WOS:000373922700003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000372531700002,
+Author = {Puniya, Bhanwar Lal and Kulshreshtha, Deepika and Mittal, Inna and
+ Mobeen, Ahmed and Ramachandran, Srinivasan},
+Title = {Integration of Metabolic Modeling with Gene Co-expression Reveals
+ Transcriptionally Programmed Reactions Explaining Robustness in
+ Mycobacterium tuberculosis},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2016},
+Volume = {6},
+Month = {MAR 22},
+Type = {Article},
+DOI = {10.1038/srep23440},
+Article-Number = {23440},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; NETWORK ANALYSIS; EXPRESSION; SYSTEMS;
+ RECONSTRUCTION; CAPABILITIES; MACROPHAGES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Puniya, Bhanwar Lal/K-6295-2016
+ },
+ORCID-Numbers = {Puniya, Bhanwar Lal/0000-0001-7528-3568
+ MOBEEN, AHMED/0000-0002-2218-6120},
+Times-Cited = {5},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000372531700002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000372582800091,
+Author = {Bogart, Eli and Myers, Christopher R.},
+Title = {Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear
+ Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves},
+Journal = {PLOS ONE},
+Year = {2016},
+Volume = {11},
+Number = {3},
+Month = {MAR 18},
+Type = {Article},
+DOI = {10.1371/journal.pone.0151722},
+Article-Number = {e0151722},
+ISSN = {1932-6203},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; C-4 PHOTOSYNTHESIS; BUNDLE-SHEATH; DEVELOPMENTAL
+ DYNAMICS; MESSENGER-RNA; PATHWAY; EVOLUTION; DATABASE; DECARBOXYLATION;
+ PROTEOMICS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Myers, Christopher R/I-8516-2017},
+Times-Cited = {29},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000372582800091},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000372975000010,
+Author = {Biggs, Matthew B. and Papin, Jason A.},
+Title = {Metabolic network-guided binning of metagenomic sequence fragments},
+Journal = {BIOINFORMATICS},
+Year = {2016},
+Volume = {32},
+Number = {6},
+Pages = {867-874},
+Month = {MAR 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btv671},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {UNCULTURED BACTERIA; GENOME ANNOTATION; SYSTEMS BIOLOGY; MICROBIOME;
+ REVEALS; RECONSTRUCTIONS; IDENTIFICATION; COVERAGE; DISEASE; SHIFTS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Biggs, Matthew/0000-0001-6492-8180},
+Times-Cited = {7},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000372975000010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000371779400001,
+Author = {Brunk, Elizabeth and Mih, Nathan and Monk, Jonathan and Zhang, Zhen and
+ O'Brien, Edward J. and Bliven, Spencer E. and Chen, Ke and Chang, Roger
+ L. and Bourne, Philip E. and Palsson, Bernhard O.},
+Title = {Systems biology of the structural proteome},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2016},
+Volume = {10},
+Month = {MAR 11},
+Type = {Article},
+DOI = {10.1186/s12918-016-0271-6},
+Article-Number = {26},
+EISSN = {1752-0509},
+Keywords-Plus = {COMPLETE GENOME SEQUENCE; I-TASSER; STRUCTURE PREDICTION; METABOLIC
+ NETWORK; PROTEINS; EVOLUTION; DATABASE; RECONSTRUCTION; RECOGNITION;
+ EFFICIENT},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Bourne, Philip/ABG-8967-2021
+ Bliven, Spencer/ABA-3249-2021
+ },
+ORCID-Numbers = {Bourne, Philip/0000-0002-7618-7292
+ Bliven, Spencer/0000-0002-1200-1698
+ Chang, Roger/0000-0003-1630-6584
+ Mih, Nathan/0000-0002-4302-9052
+ Monk, Jonathan M./0000-0002-3895-8949},
+Times-Cited = {39},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000371779400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000383604600004,
+Author = {Alam, Mohammad Tauqeer and Zelezniak, Aleksej and Mulleder, Michael and
+ Shliaha, Pavel and Schwarz, Roland and Capuano, Floriana and Vowinckel,
+ Jakob and Radmaneshfar, Elahe and Krueger, Antje and Calvani, Enrica and
+ Michel, Steve and Boerno, Stefan and Christen, Stefan and Patil, Kiran
+ Raosaheb and Timmermann, Bernd and Lilley, Kathryn S. and Ralser, Markus},
+Title = {The metabolic background is a global player in Saccharomyces gene
+ expression epistasis},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2016},
+Volume = {1},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1038/NMICROBIOL.2015.30},
+Article-Number = {15030},
+ISSN = {2058-5276},
+Keywords-Plus = {MESSENGER-RNA; YEAST STRAINS; PROTEIN; GENOME; DATABASE; TRANSCRIPTION;
+ BIOSYNTHESIS; NETWORKS; COMPLEX; CEREVISIAE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Schwarz, Roland/B-6451-2009
+ Patil, Kiran R/B-9709-2009
+ Lilley, Kathryn/ABF-5787-2020
+ alam, mohammed/GXH-3645-2022
+ },
+ORCID-Numbers = {Patil, Kiran R/0000-0002-6166-8640
+ Lilley, Kathryn/0000-0003-0594-6543
+ Alam, Mohammad Tauqeer/0000-0002-6872-0691
+ Mulleder, Michael/0000-0001-9792-3861
+ Calvani, Enrica/0009-0004-6408-1054
+ Zelezniak, Aleksej/0000-0002-3098-9441
+ Kruger, Antje/0000-0002-8155-0682
+ Ralser, Markus/0000-0001-9535-7413
+ Schwarz, Roland/0000-0001-9155-4268
+ Shliaha, Pavel/0000-0003-3092-0724
+ Vowinckel, Jakob/0000-0002-4343-4058},
+Times-Cited = {50},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000383604600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000369520200001,
+Author = {Dersch, Lisa Maria and Beckers, Veronique and Wittmann, Christoph},
+Title = {Green pathways: Metabolic network analysis of plant systems},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {34},
+Pages = {1-24},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1016/j.ymben.2015.12.001},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Plant network; Arabidopsis; Flux balance analysis; Elementary flux mode
+ analysis; C-13 metabolic flux analysis; Isotopically non-stationary;
+ NMR; GC/MS; Compartment},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; HETEROTROPHIC ARABIDOPSIS CELLS;
+ PENTOSE-PHOSPHATE PATHWAY; NEUTRAL INVERTASE ACTIVITY; CENTRAL CARBON
+ METABOLISM; ESSENTIAL OIL COMPOSITION; FATTY-ACID SYNTHESIS; IN-VIVO
+ C-13; MASS-SPECTROMETRY; STEADY-STATE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Wittmann, Christoph/0000-0002-7952-985X},
+Times-Cited = {18},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000369520200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000369015100020,
+Author = {Kim, Minsuk and Yi, Jeong Sang and Lakshmanan, Meiyappan and Lee,
+ Dong-Yup and Kim, Byung-Gee},
+Title = {Transcriptomics-based strain optimization tool for designing secondary
+ metabolite overproducing strains of Streptomyces coelicolor},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2016},
+Volume = {113},
+Number = {3},
+Pages = {651-660},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1002/bit.25830},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {strain design; transcriptomics; genome-scale model of metabolism;
+ metabolic engineering; Streptomyces coelicolor; antibiotics},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ANTIBIOTIC PRODUCTION; EXPRESSION DATA;
+ INTEGRATION; FLUX; OVEREXPRESSION; RECONSTRUCTION; IDENTIFICATION;
+ PREDICTION; NETWORKS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/ABC-7628-2020
+ kim, byung-gee/AAR-1933-2020
+ Lee, Dong-Yup/D-6650-2011
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ },
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Kim, Minsuk/0000-0001-9958-0380},
+Times-Cited = {29},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000369015100020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000376583800037,
+Author = {Schultz, Andre and Qutub, Amina A.},
+Title = {Reconstruction of Tissue-Specific Metabolic Networks Using CORDA},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2016},
+Volume = {12},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004808},
+Article-Number = {e1004808},
+EISSN = {1553-7358},
+Keywords-Plus = {ADENOSINE-DEAMINASE ACTIVITY; TYROSINE KINASE INHIBITOR;
+ CONSTRAINT-BASED MODELS; HUMAN CANCER-CELLS; PROSTATE-CANCER;
+ CHONDROITIN SULFATE; GLOBAL RECONSTRUCTION; CELLULAR-METABOLISM;
+ SQUALENE SYNTHASE; ELEVATED LEVELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Qutub, Amina/0000-0003-1737-9208},
+Times-Cited = {82},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000376583800037},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368723100009,
+Author = {Gallardo, Roberto and Acevedo, Alejandro and Quintero, Julian and
+ Paredes, Ivan and Conejeros, Raul and Aroca, German},
+Title = {In silico analysis of Clostridium acetobutylicum ATCC 824
+ metabolic response to an external electron supply},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2016},
+Volume = {39},
+Number = {2},
+Pages = {295-305},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1007/s00449-015-1513-5},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {Clostridium acetobutylicum; Butanol; Available reducing capacity;
+ Electron supply; Flux balance analysis},
+Keywords-Plus = {GENOME-SCALE MODEL; BUTANOL PRODUCTION; METHYL VIOLOGEN; TRANSCRIPTIONAL
+ ANALYSIS; SOLVENT PRODUCTION; CHEMOSTAT CULTURE; BUTYRATE; ACID;
+ FERMENTATION; MODULATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Gallardo, Roberto/AAN-6510-2021
+ Quintero, Julián/I-6335-2016
+ Conejeros, Raul/A-2466-2011
+ Conejeros, Raul/ABG-5517-2020
+ Aroca, German/ABG-6714-2020},
+ORCID-Numbers = {Quintero, Julián/0000-0003-1224-5649
+ Conejeros, Raul/0000-0002-1273-535X
+ Aroca, German/0000-0003-1376-7940},
+Times-Cited = {6},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000368723100009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000370888100347,
+Author = {Salazar, Diego A. and Rodriguez-Lopez, Alexander and Herreno, Angelica
+ and Barbosa, Hector and Herrera, Juliana and Ardila, Andrea and Barreto,
+ George E. and Gonzalez, Janneth and Almeciga-Diaz, Carlos J.},
+Title = {Systems biology study of mucopolysaccharidosis using a human metabolic
+ reconstruction network},
+Journal = {MOLECULAR GENETICS AND METABOLISM},
+Year = {2016},
+Volume = {117},
+Number = {2},
+Pages = {129-139},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1016/j.ymgme.2015.08.001},
+ISSN = {1096-7192},
+EISSN = {1096-7206},
+Keywords = {Systems biology; Lysosomal storage disease; Disease biomarkers; Flux
+ balance analysis; Diagnostic},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; OXIDATIVE STRESS; GLOBAL RECONSTRUCTION;
+ PATHOGENIC CASCADES; DISEASE; BIOMARKERS; MECHANISM; MORQUIO; CANCER;
+ INFLAMMATION},
+Research-Areas = {Endocrinology \& Metabolism; Genetics \& Heredity; Research \&
+ Experimental Medicine},
+Web-of-Science-Categories = {Endocrinology \& Metabolism; Genetics \& Heredity; Medicine, Research \&
+ Experimental},
+ResearcherID-Numbers = {Barreto, George E./B-5747-2014
+ Barreto, George E./AAD-7420-2020
+ Almeciga-Diaz, Carlos J/A-2494-2017
+ Rodriguez-Lopez, Edwin Alexander/E-6650-2015
+ GONZALEZ, JANNETH/AAB-9948-2020
+ },
+ORCID-Numbers = {Barreto, George E./0000-0002-6644-1971
+ Barreto, George E./0000-0002-6644-1971
+ Almeciga-Diaz, Carlos J/0000-0001-6484-1173
+ Rodriguez-Lopez, Edwin Alexander/0000-0001-5409-3466
+ GONZALEZ, JANNETH/0000-0003-4482-256X
+ ARDILA GOMEZ, YUDY ANDREA/0000-0003-0508-6168},
+Times-Cited = {21},
+Journal-ISO = {Mol. Genet. Metab.},
+Unique-ID = {WOS:000370888100347},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000372751100007,
+Author = {Sauls, John T. and Li, Dongyang and Jun, Suckjoon},
+Title = {Adder and a coarse-grained approach to cell size homeostasis in bacteria},
+Journal = {CURRENT OPINION IN CELL BIOLOGY},
+Year = {2016},
+Volume = {38},
+Pages = {38-44},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1016/j.ceb.2016.02.004},
+ISSN = {0955-0674},
+EISSN = {1879-0410},
+Keywords-Plus = {ESCHERICHIA-COLI; SINGLE CELLS; CHROMOSOME-REPLICATION; GROWTH-RATE;
+ DIVISION; CYCLE; DYNAMICS; YEAST; TIMES; LAWS},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Li, Dongyang/IZE-7642-2023
+ Jun, Suckjoon/K-9008-2015},
+ORCID-Numbers = {Li, Dongyang/0000-0003-2728-4843
+ Jun, Suckjoon/0000-0002-0139-4297},
+Times-Cited = {70},
+Journal-ISO = {Curr. Opin. Cell Biol.},
+Unique-ID = {WOS:000372751100007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000370458800019,
+Author = {Shi, Hai and Schwender, Joerg},
+Title = {Mathematical models of plant metabolism},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2016},
+Volume = {37},
+Pages = {143-152},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1016/j.copbio.2015.10.008},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; OILSEED RAPE; COMPARATIVE
+ GENOMICS; VARIABILITY ANALYSIS; STORAGE SYNTHESIS; LEAF METABOLISM;
+ MAIZE LEAF; ARABIDOPSIS; RECONSTRUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Schwender, Jorg/P-2282-2014},
+ORCID-Numbers = {Schwender, Jorg/0000-0003-1350-4171},
+Times-Cited = {15},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000370458800019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367673500019,
+Author = {Zavrel, Tomas and Knoop, Henning and Steuer, Ralf and Jones, Patrik R.
+ and Cerveny, Jan and Trtilek, Martin},
+Title = {A quantitative evaluation of ethylene production in the recombinant
+ cyanobacterium Synechocystis sp PCC 6803 harboring the
+ ethylene-forming enzyme by membrane inlet mass spectrometry},
+Journal = {BIORESOURCE TECHNOLOGY},
+Year = {2016},
+Volume = {202},
+Pages = {142-151},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1016/j.biortech.2015.11.062},
+ISSN = {0960-8524},
+EISSN = {1873-2976},
+Keywords = {Biofuels; Cyanobacteria; Photobioreactor; MIMS; Biotechnology},
+Keywords-Plus = {HETEROLOGOUS EXPRESSION; PHOTOBIOREACTOR SYSTEM; CULTIVATION;
+ PREDICTION; METABOLISM; GROWTH; MODELS; GENE; CO2},
+Research-Areas = {Agriculture; Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Agricultural Engineering; Biotechnology \& Applied Microbiology; Energy
+ \& Fuels},
+ResearcherID-Numbers = {Zavrel, Tomas/H-4263-2014
+ Steuer, Ralf/E-7482-2017
+ Červený, Jan/J-1911-2012
+ Zavřel, Tomáš/L-5814-2019},
+ORCID-Numbers = {Zavrel, Tomas/0000-0002-0849-3503
+ Steuer, Ralf/0000-0003-2217-1655
+ Červený, Jan/0000-0002-5046-3105
+ Zavřel, Tomáš/0000-0002-0849-3503},
+Times-Cited = {27},
+Journal-ISO = {Bioresour. Technol.},
+Unique-ID = {WOS:000367673500019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368587200001,
+Author = {Bjornson, Elias and Boren, Jan and Mardinoglu, Adil},
+Title = {Personalized Cardiovascular Disease Prediction and Treatment-A Review of
+ Existing Strategies and Novel Systems Medicine Tools},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2016},
+Volume = {7},
+Month = {JAN 26},
+Type = {Review},
+DOI = {10.3389/fphys.2016.00002},
+Article-Number = {2},
+ISSN = {1664-042X},
+Keywords = {patient stratification; risk estimation; metabolism; systems medicine;
+ systems biology; network medicine},
+Keywords-Plus = {GENOME-SCALE MODELS; NEED EXACT SOLVERS; HEPATOCELLULAR-CARCINOMA;
+ METABOLIC NETWORK; HUMAN GUT; RISK; IDENTIFICATION; VALIDATION;
+ DISCOVERY; PROTEOME},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {Mardinoglu, Adil/AAS-6360-2021
+ },
+ORCID-Numbers = {Bjornson, Elias/0000-0002-0003-6463},
+Times-Cited = {28},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000368587200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000369528000071,
+Author = {Tomas-Gamisans, Marius and Ferrer, Pau and Albiol, Joan},
+Title = {Integration and Validation of the Genome-Scale Metabolic Models of
+ Pichia pastoris: A Comprehensive Update of Protein Glycosylation
+ Pathways, Lipid and Energy Metabolism},
+Journal = {PLOS ONE},
+Year = {2016},
+Volume = {11},
+Number = {1},
+Month = {JAN 26},
+Type = {Article},
+DOI = {10.1371/journal.pone.0148031},
+Article-Number = {e0148031},
+ISSN = {1932-6203},
+Keywords-Plus = {CYANIDE-RESISTANT RESPIRATION; FATTY-ACID SYNTHESIS; YEAST
+ SACCHAROMYCES-CEREVISIAE; N-LINKED OLIGOSACCHARIDES; ACYL-COA
+ SYNTHETASE; METHYLOTROPHIC YEAST; KLUYVEROMYCES-LACTIS; FLUX ANALYSIS;
+ HETEROLOGOUS PROTEINS; PRODUCTION HOST},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Albiol, Joan/Z-5173-2019
+ Sala, Joan Albiol/A-8280-2008
+ Tomàs-Gamisans, Màrius/B-4136-2016
+ Tomàs-Gamisans, Màrius/AAG-8539-2020
+ Ferrer, Pau/A-4147-2009},
+ORCID-Numbers = {Albiol, Joan/0000-0001-5626-429X
+ Sala, Joan Albiol/0000-0001-5626-429X
+ Tomàs-Gamisans, Màrius/0000-0002-6076-6716
+ Tomàs-Gamisans, Màrius/0000-0002-6076-6716
+ Ferrer, Pau/0000-0002-5287-4127},
+Times-Cited = {43},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000369528000071},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368586900001,
+Author = {Pacheco, Maria P. and Pfau, Thomas and Sauter, Thomas},
+Title = {Benchmarking Procedures for High-Throughput Context Specific
+ Reconstruction Algorithms},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2016},
+Volume = {6},
+Month = {JAN 22},
+Type = {Article},
+DOI = {10.3389/fphys.2015.00410},
+Article-Number = {410},
+ISSN = {1664-042X},
+Keywords = {metabolic networks and pathways; metabolic reconstruction;
+ constraint-based modeling; tissue specific networks; benchmarking;
+ validation},
+Keywords-Plus = {GENE-EXPRESSION; METABOLIC MODELS; GLOBAL RECONSTRUCTION; INTEGRATION},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Pfau, Thomas/0000-0001-5048-2923
+ Sauter, Thomas/0000-0001-8225-2954},
+Times-Cited = {20},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000368586900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368123100001,
+Author = {Nazem-Bokaee, Hadi and Gopalakrishnan, Saratram and Ferry, James G. and
+ Wood, Thomas K. and Maranas, Costas D.},
+Title = {Assessing methanotrophy and carbon fixation for biofuel production by
+ Methanosarcina acetivorans},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2016},
+Volume = {15},
+Month = {JAN 17},
+Type = {Article},
+DOI = {10.1186/s12934-015-0404-4},
+Article-Number = {10},
+EISSN = {1475-2859},
+Keywords = {Methanosarcina acetivorans; Genome-scale metabolic model; Methane
+ utilization},
+Keywords-Plus = {ANAEROBIC OXIDATION; METHANE OXIDATION; ELECTRON-TRANSPORT; METABOLIC
+ RECONSTRUCTION; DEPENDENT GROWTH; GENETIC-ANALYSIS; ACETATE;
+ METHANOGENESIS; CONVERSION; ARCHAEA},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Wood, Thomas/GWZ-2481-2022
+ Maranas, Costas D/A-4774-2011
+ },
+ORCID-Numbers = {Wood, Thomas/0000-0001-8962-8571
+ Maranas, Costas D/0000-0002-1508-1398
+ Nazem-Bokaee, Hadi/0000-0002-4246-1804
+ Gopalakrishnan, Saratram/0000-0002-3254-0584},
+Times-Cited = {33},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000368123100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000366537700004,
+Author = {Mei, Jie and Xu, Nan and Ye, Chao and Liu, Liming and Wu, Jianrong},
+Title = {Reconstruction and analysis of a genome-scale metabolic network of
+ Corynebacterium glutamicum S9114},
+Journal = {GENE},
+Year = {2016},
+Volume = {575},
+Number = {2, 3},
+Pages = {615-622},
+Month = {JAN 10},
+Type = {Article},
+DOI = {10.1016/j.gene.2015.09.038},
+ISSN = {0378-1119},
+EISSN = {1879-0038},
+Keywords = {Corynebacterium glutamicum S9114; Genome-scale metabolic model;
+ L-Glutamate production; gamma-Aminobutyrate production; L-Isoleucine
+ production},
+Keywords-Plus = {L-ISOLEUCINE PRODUCTION; ANAPLEROTIC PATHWAYS; GLUTAMATE PRODUCTION;
+ FLUX DISTRIBUTION; ACID PRODUCTION; CARBON-FLUX; SYNTHASE; GENE;
+ PREDICTION; DATABASE},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Ye, Chao/HGD-3564-2022
+ Ye, Chao/M-3689-2019
+ Wu, Jian-Rong/ISV-3861-2023
+ Ye, Chao/H-7623-2014
+ Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Ye, Chao/0000-0002-6671-7819
+ Wu, Jian-Rong/0000-0002-9337-3548
+ Ye, Chao/0000-0002-6671-7819
+ Liu, Liming/0000-0003-3022-936X
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {21},
+Journal-ISO = {Gene},
+Unique-ID = {WOS:000366537700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000371261700071,
+Author = {King, Zachary A. and Lu, Justin and Draeger, Andreas and Miller, Philip
+ and Federowicz, Stephen and Lerman, Joshua A. and Ebrahim, Ali and
+ Palsson, Bernhard O. and Lewis, Nathan E.},
+Title = {BiGG Models: A platform for integrating, standardizing and sharing
+ genome-scale models},
+Journal = {NUCLEIC ACIDS RESEARCH},
+Year = {2016},
+Volume = {44},
+Number = {D1},
+Pages = {D515-D522},
+Month = {JAN 4},
+Type = {Article},
+DOI = {10.1093/nar/gkv1049},
+ISSN = {0305-1048},
+EISSN = {1362-4962},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; RECONSTRUCTION; DATABASE; GENERATION;
+ METABOLISM; KNOWLEDGE; BIOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ King, Zachary/V-3402-2019
+ Dräger, Andreas/F-5620-2015
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ King, Zachary/0000-0003-1238-1499
+ Dräger, Andreas/0000-0002-1240-5553
+ Ebrahim, Ali/0000-0002-4009-2128},
+Times-Cited = {462},
+Journal-ISO = {Nucleic Acids Res.},
+Unique-ID = {WOS:000371261700071},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368103200038,
+Author = {Alff-Tuomala, Susanne and Salusjarvi, Laura and Barth, Dorothee and Oja,
+ Merja and Penttila, Merja and Pitkanen, Juha-Pekka and Ruohonen, Laura
+ and Jouhten, Paula},
+Title = {Xylose-induced dynamic effects on metabolism and gene expression in
+ engineered Saccharomyces cerevisiae in anaerobic glucose-xylose
+ cultures},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2016},
+Volume = {100},
+Number = {2},
+Pages = {969-985},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1007/s00253-015-7038-7},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Metabolic modelling; Saccharomyces cerevisiae; Xylose; Gene expression;
+ Anaerobic},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; FLUX BALANCE ANALYSIS; TRANSCRIPTIONAL
+ REGULATION; ETHANOL-PRODUCTION; FUNCTIONAL EXPRESSION;
+ XYLITOL-DEHYDROGENASE; FERMENTATION; RECOMBINANT; GROWTH; REDUCTASE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Penttilä, Merja E/A-4710-2013
+ Pitkänen, Juha-Pekka/K-4658-2013
+ Barth, Dorothee/S-2158-2016
+ },
+ORCID-Numbers = {Pitkänen, Juha-Pekka/0000-0002-4006-0302
+ Barth, Dorothee/0000-0001-9575-905X
+ Penttila, Merja/0000-0002-6929-1032
+ Jouhten, Paula/0000-0003-1075-7448},
+Times-Cited = {23},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000368103200038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459646200005,
+Author = {Ben Guebila, Marouen and Thiele, Ines},
+Title = {Model-based dietary optimization for late-stage, levodopa-treated,
+ Parkinson's disease patients},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2016},
+Volume = {2},
+Type = {Article},
+DOI = {10.1038/npjsba.2016.13},
+Article-Number = {16013},
+EISSN = {2056-7189},
+Keywords-Plus = {AMINO-ACIDS; GLOBAL RECONSTRUCTION; MOTOR SYMPTOMS; ABSORPTION;
+ PHARMACOKINETICS; PROTEIN; BALANCE; METABOLISM; INGESTION; MECHANISM},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {24},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000459646200005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379873100007,
+Author = {Chaiboonchoe, Amphun and Ghamsari, Lila and Dohai, Bushra and Ng,
+ Patrick and Khraiwesh, Basel and Jaiswal, Ashish and Jijakli, Kenan and
+ Koussa, Joseph and Nelson, David R. and Cai, Hong and Yang, Xinping and
+ Chang, Roger L. and Papin, Jason and Yu, Haiyuan and Balaji, Santhanam
+ and Salehi-Ashtiani, Kourosh},
+Title = {Systems level analysis of the Chlamydomonas reinhardtii
+ metabolic network reveals variability in evolutionary co-conservation},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2016},
+Volume = {12},
+Number = {8},
+Pages = {2394-2407},
+Type = {Article},
+DOI = {10.1039/c6mb00237d},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {FITNESS LANDSCAPES; EXPRESSION; EPISTASIS; ORGANIZATION; COEVOLUTION;
+ ANNOTATION; MODULARITY; PHYLOGENY; NECESSITY; GENOMICS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Jaiswal, Ashish Kumar k/H-8692-2016
+ Khraiwesh, Basel/G-7509-2015
+ },
+ORCID-Numbers = {Jaiswal, Ashish Kumar k/0000-0002-6193-1824
+ Salehi-Ashtiani, Kourosh/0000-0002-6521-5243
+ Nelson, David/0000-0001-8868-5734
+ Dohai, Bushra/0000-0001-8179-8883
+ Khraiwesh, Basel/0000-0001-7026-1263
+ Chang, Roger/0000-0003-1630-6584},
+Times-Cited = {9},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000379873100007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000371039800030,
+Author = {Chaudhary, Neha and Tondel, Kristin and Bhatnagar, Rakesh and dos
+ Santos, Vitor A. P. Martins and Puchalka, Jacek},
+Title = {Characterizing the optimal flux space of genomescale metabolic
+ reconstructions through modified latin-hypercube sampling},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2016},
+Volume = {12},
+Number = {3},
+Pages = {994-1005},
+Type = {Article},
+DOI = {10.1039/c5mb00457h},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {KNOCKOUT STRATEGIES; COUPLING ANALYSIS; ESCHERICHIA-COLI; MODELS;
+ NETWORK; PATHWAYS; FRAMEWORK; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {1},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000371039800030},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000372106600012,
+Author = {Conway, Max and Angione, Claudio and Lio, Pietro},
+Title = {Iterative Multi Level Calibration of Metabolic Networks},
+Journal = {CURRENT BIOINFORMATICS},
+Year = {2016},
+Volume = {11},
+Number = {1},
+Pages = {93-105},
+Type = {Article},
+DOI = {10.2174/1574893611666151203222505},
+ISSN = {1574-8936},
+EISSN = {2212-392X},
+Keywords = {Meta-analysis; gene expression engineering; multi-scale model; metabolic
+ network exploration},
+Keywords-Plus = {GEOBACTER-SULFURREDUCENS; PARETO OPTIMALITY; MODELS; FRAMEWORK; DESIGN},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {P. Lió, Pietro Lio/AAV-3358-2021
+ },
+ORCID-Numbers = {P. Lió, Pietro Lio/0000-0002-0540-5053
+ Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {4},
+Journal-ISO = {Curr. Bioinform.},
+Unique-ID = {WOS:000372106600012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459646200002,
+Author = {Fard, Atefeh Taherian and Srihari, Sriganesh and Mar, Jessica C. and
+ Ragan, Mark A.},
+Title = {Not just a colourful metaphor: modelling the landscape of cellular
+ development using Hopfield networks},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2016},
+Volume = {2},
+Type = {Article},
+DOI = {10.1038/npjsba.2016.1},
+Article-Number = {16001},
+EISSN = {2056-7189},
+Keywords-Plus = {WADDINGTON; CANCER; FIBROBLASTS; ATTRACTORS; ENRICHMENT; GENES; PATHS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ragan, Mark A/A-9825-2014
+ Srihari, Sriganesh/H-1740-2013
+ Fard, Ati/AAX-4092-2021
+ },
+ORCID-Numbers = {Ragan, Mark A/0000-0003-1672-7020
+ Srihari, Sriganesh/0000-0002-0713-6723
+ Taherian Fard, Atefeh/0000-0002-9126-4540
+ Mar, Jessica/0000-0002-5147-9299},
+Times-Cited = {17},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000459646200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368858900013,
+Author = {Han, Feifei and Li, Gonghua and Dai, Shaoxing and Huang, Jingfei},
+Title = {Genome-wide metabolic model to improve understanding of CD4+
+ T cell metabolism, immunometabolism and application in drug design},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2016},
+Volume = {12},
+Number = {2},
+Pages = {431-443},
+Type = {Article},
+DOI = {10.1039/c5mb00480b},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {FATTY-ACID-METABOLISM; REGULATORY T; GLOBAL RECONSTRUCTION;
+ GLUCOSE-METABOLISM; CANCER; PTEN; ACTIVATION; GLUTAMINE; INFLAMMATION;
+ DEFICIENCY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Dai, shaoxing/ABA-8699-2020
+ huang, jing/JDC-2548-2023
+ },
+ORCID-Numbers = {Li, Gong-Hua/0000-0002-9311-6613
+ HAN, FEIFEI/0000-0003-4373-8753},
+Times-Cited = {11},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000368858900013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000386669400023,
+Author = {Jamialahmadi, Oveis and Motamedian, Ehsan and Hashemi-Najafabadi,
+ Sameereh},
+Title = {BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG
+ databases},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2016},
+Volume = {12},
+Number = {11},
+Pages = {3459-3466},
+Type = {Article},
+DOI = {10.1039/c6mb00532b},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ ESCHERICHIA-COLI; RECONSTRUCTION; VISUALIZATION; GENERATION; NETWORK},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Motamedian, Ehsan/GPK-8344-2022
+ Hashemi-Najafabadi, Sameereh/JSB-1968-2023
+ },
+ORCID-Numbers = {Hashemi-Najafabadi, Sameereh/0000-0001-7826-6325
+ , Ehsan/0000-0001-8750-2879},
+Times-Cited = {9},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000386669400023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000382073300001,
+Author = {Kawasaki, Regiane and Barauna, Rafael A. and Silva, Artur and Carepo,
+ Marta S. P. and Oliveira, Rui and Marques, Rodolfo and Ramos, Rommel T.
+ J. and Schneider, Andmaria P. C.},
+Title = {Reconstruction of the Fatty Acid Biosynthetic Pathway of
+ Exiguobacterium antarcticum B7 Based on Genomic and
+ Bibliomic Data},
+Journal = {BIOMED RESEARCH INTERNATIONAL},
+Year = {2016},
+Volume = {2016},
+Type = {Article},
+DOI = {10.1155/2016/7863706},
+Article-Number = {7863706},
+ISSN = {2314-6133},
+EISSN = {2314-6141},
+Keywords-Plus = {IN-SILICO; GLOBAL RECONSTRUCTION; MODELS; ANNOTATION; METABOLISM;
+ PREDICTION; NETWORKS; SEQUENCE; BIOLOGY; SERVER},
+Research-Areas = {Biotechnology \& Applied Microbiology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Medicine, Research \&
+ Experimental},
+ResearcherID-Numbers = {Carepo, Marta S.P./D-7196-2013
+ Luiz Silva, Artur da Costa da/AAI-3516-2021
+ FCT/UNL, REQUIMTE Biological Chemistry at/V-8183-2017
+ Oliveira, Rui/D-8815-2013
+ Ramos, Rommel Thiago Juca/L-9329-2013},
+ORCID-Numbers = {Carepo, Marta S.P./0000-0003-3222-8141
+ Luiz Silva, Artur da Costa da/0000-0002-4082-1132
+ Oliveira, Rui/0000-0001-8077-4177
+ Ramos, Rommel Thiago Juca/0000-0002-8032-1474},
+Times-Cited = {3},
+Journal-ISO = {Biomed Res. Int.},
+Unique-ID = {WOS:000382073300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367731700001,
+Author = {Liu, Lin and Shen, Fangzhou and Xin, Changpeng and Wang, Zhuo},
+Title = {Multi-scale modeling of Arabidopsis thaliana response to
+ different CO2 conditions: From gene expression to metabolic
+ flux},
+Journal = {JOURNAL OF INTEGRATIVE PLANT BIOLOGY},
+Year = {2016},
+Volume = {58},
+Number = {1},
+Pages = {2-11},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1111/jipb.12370},
+ISSN = {1672-9072},
+EISSN = {1744-7909},
+Keywords = {Metabolic model; gene expression; multi-scale analysis; low; elevated
+ CO2; post-transcriptional regulation},
+Keywords-Plus = {ELEVATED CO2; COLD-ACCLIMATION; PROFILES; DATABASE; PLANTS;
+ PHOTOSYNTHESIS; PRODUCTIVITY; RESPIRATION; PREDICTION; PATTERNS},
+Research-Areas = {Biochemistry \& Molecular Biology; Plant Sciences},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Plant Sciences},
+ORCID-Numbers = {Liu, Lin/0009-0004-5093-2516},
+Times-Cited = {11},
+Journal-ISO = {J. Integr. Plant Biol.},
+Unique-ID = {WOS:000367731700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000376082400015,
+Author = {Marcellin, Esteban and Behrendorff, James B. and Nagaraju, Shilpa and
+ DeTissera, Sashini and Segovia, Simon and Palfreyman, Robin W. and
+ Daniell, James and Licona-Cassani, Cuauhtemoc and Quek, Lake-ee and
+ Speight, Robert and Hodson, Mark P. and Simpson, Sean D. and Mitchell,
+ Wayne P. and Kopke, Michael and Nielsen, Lars K.},
+Title = {Low carbon fuels and commodity chemicals from waste gases - systematic
+ approach to understand energy metabolism in a model acetogen},
+Journal = {GREEN CHEMISTRY},
+Year = {2016},
+Volume = {18},
+Number = {10},
+Pages = {3020-3028},
+Type = {Article},
+DOI = {10.1039/c5gc02708j},
+ISSN = {1463-9262},
+EISSN = {1463-9270},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; CLOSTRIDIUM-AUTOETHANOGENUM; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; SP-NOV; GENOME; ETHANOL; LJUNGDAHLII;
+ RECONSTRUCTION; BIOFUELS},
+Research-Areas = {Chemistry; Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary; Green \& Sustainable Science \& Technology},
+ResearcherID-Numbers = {Palfreyman, Robin W/V-8516-2017
+ Köpke, Michael/I-3963-2019
+ Behrendorff, James/M-5452-2019
+ Nielsen, Lars K/A-5519-2011
+ Behrendorff, James B Y H/G-1601-2010
+ Speight, Robert/AAY-4466-2020
+ Hodson, Mark/J-7609-2013
+ },
+ORCID-Numbers = {Palfreyman, Robin W/0000-0002-1088-7069
+ Köpke, Michael/0000-0003-0642-1415
+ Behrendorff, James/0000-0003-4130-6252
+ Nielsen, Lars K/0000-0001-8191-3511
+ Behrendorff, James B Y H/0000-0003-4130-6252
+ Speight, Robert/0000-0003-4161-8272
+ Hodson, Mark/0000-0002-5436-1886
+ Quek, Lake-Ee/0000-0002-9313-8740
+ Licona-Cassani, Cuauhtemoc/0000-0002-0360-3945
+ Marcellin, Esteban/0000-0003-3173-7956},
+Times-Cited = {107},
+Journal-ISO = {Green Chem.},
+Unique-ID = {WOS:000376082400015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368321600013,
+Author = {Marinkovic, Tijana and Oresic, Matej},
+Title = {Modeling strategies to study metabolic pathways in progression to type 1
+ diabetes - Challenges and opportunities},
+Journal = {ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS},
+Year = {2016},
+Volume = {589},
+Number = {SI},
+Pages = {131-137},
+Month = {JAN 1},
+Type = {Review},
+DOI = {10.1016/j.abb.2015.08.011},
+ISSN = {0003-9861},
+EISSN = {1096-0384},
+Keywords = {Autoimmunity; Lipidomics; Metabolic modeling; Metabolomics; Type 1
+ diabetes},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ISLET AUTOIMMUNITY; PROTECTIVE AUTOIMMUNITY;
+ GLOBAL RECONSTRUCTION; HUMAN TISSUES; AMINO-ACID; T-CELLS; CHILDREN;
+ NETWORK; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ResearcherID-Numbers = {Oresic, Matej/AAV-3978-2020
+ Oresic, Matej/K-7673-2016},
+ORCID-Numbers = {Oresic, Matej/0000-0002-2856-9165},
+Times-Cited = {12},
+Journal-ISO = {Arch. Biochem. Biophys.},
+Unique-ID = {WOS:000368321600013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000379873100021,
+Author = {Mohammadi, Reza and Fallah-Mehrabadi, Jalil and Bidkhori, Gholamreza and
+ Zahiri, Javad and Niroomand, Mohammad Javad and Masoudi-Nejad, Ali},
+Title = {A systems biology approach to reconcile metabolic network models with
+ application to Synechocystis sp PCC 6803 for biofuel production},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2016},
+Volume = {12},
+Number = {8},
+Pages = {2552-2561},
+Type = {Article},
+DOI = {10.1039/c6mb00119j},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {KNOCKOUT STRATEGIES; CYANOBACTERIA; RECONSTRUCTION; PREDICTION;
+ PHENOTYPE; ALGORITHM; FRAMEWORK; GENOMICS; DATABASE; GENES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Masoudi-Nejad, Ali/ABH-2078-2021
+ Mohammadi, Reza/AAS-6539-2021
+ },
+ORCID-Numbers = {Mohammadi, Reza/0000-0001-5445-2991
+ Masoudi-Nejad, Ali/0000-0003-0659-5183
+ Zahiri, Javad/0000-0002-8360-2458},
+Times-Cited = {15},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000379873100021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000372612600019,
+Author = {Motamedian, E. and Saeidi, M. and Shojaosadati, S. A.},
+Title = {Reconstruction of a charge balanced genome-scale metabolic model to
+ study the energy-uncoupled growth of Zymomonas mobilis ZM1},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2016},
+Volume = {12},
+Number = {4},
+Pages = {1241-1249},
+Type = {Article},
+DOI = {10.1039/c5mb00588d},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {HOPANOID BIOSYNTHESIS; ETHANOL-PRODUCTION; BACILLUS-SUBTILIS;
+ ESCHERICHIA-COLI; PERFORMANCE; SEQUENCE; TOOLBOX; NETWORK; GLUCOSE;
+ OXYGEN},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Shojaosadati, Seyed Abbas/A-7565-2010
+ Shojaosadati, Seyed Abbas/ABE-1178-2021
+ Motamedian, Ehsan/GPK-8344-2022
+ },
+ORCID-Numbers = {Shojaosadati, Seyed Abbas/0000-0002-8561-2414
+ , Ehsan/0000-0001-8750-2879},
+Times-Cited = {19},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000372612600019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367323000014,
+Author = {Moura, Matthew and Finkle, Justin and Stainbrook, Sarah and Greene,
+ Jennifer and Broadbelt, Linda J. and Tyo, Keith E. J.},
+Title = {Evaluating enzymatic synthesis of small molecule drugs},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {33},
+Pages = {138-147},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2015.11.006},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic engineering; Computational biology; Predictive biochemistry;
+ Pharmaceutical production; Drug synthesis},
+Keywords-Plus = {ESCHERICHIA-COLI; METABOLIC PATHWAYS; PREDICTION; DESIGN; PROMISCUITY;
+ BIOSYNTHESIS; COMPLEX; TOOLS; ACID; DECARBOXYLATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Tyo, Keith/H-6227-2012
+ Broadbelt, Linda/B-7640-2009
+ Tyo, Keith/AAM-4543-2020
+ },
+ORCID-Numbers = {Finkle, Justin/0000-0001-7296-9855
+ Tyo, Keith/0000-0002-2342-0687
+ Stainbrook, Sarah/0000-0002-0124-8230},
+Times-Cited = {10},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000367323000014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368973600031,
+Author = {Phaiphinit, Suthat and Pattaradilokrat, Sittiporn and Lursinsap,
+ Chidchanok and Plaimas, Kitipom},
+Title = {In silico multiple-targets identification for heme detoxification in the
+ human malaria parasite Plasmodium falciparum},
+Journal = {INFECTION GENETICS AND EVOLUTION},
+Year = {2016},
+Volume = {37},
+Pages = {237-244},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.meegid.2015.11.025},
+ISSN = {1567-1348},
+EISSN = {1567-7257},
+Keywords = {Antimalarial drug targets; Flux balance analysis; Plasmodium falciparum;
+ Red blood cell; Metabolic network; Multiple drug targets; Drug
+ resistance},
+Keywords-Plus = {BETA-HEMATIN FORMATION; FLUX-BALANCE ANALYSIS; METABOLIC NETWORK; DRUG
+ TARGET; ANTIMALARIAL-DRUGS; COPROPORPHYRINOGEN OXIDASE; INHIBITORS;
+ DEHYDROGENASE; TRANSPORTER; PREDICTION},
+Research-Areas = {Infectious Diseases},
+Web-of-Science-Categories = {Infectious Diseases},
+ResearcherID-Numbers = {Plaimas, Kitiporn/GLV-3478-2022
+ },
+ORCID-Numbers = {Plaimas, Kitiporn/0000-0002-0416-8316
+ Pattaradilokrat, Sittiporn/0000-0002-1516-1961},
+Times-Cited = {5},
+Journal-ISO = {Infect. Genet. Evol.},
+Unique-ID = {WOS:000368973600031},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367323000006,
+Author = {Spahn, Philipp N. and Hansen, Anders H. and Hansen, Henning G. and
+ Arnsdorf, Johnny and Kildegaard, Helene F. and Lewis, Nathan E.},
+Title = {A Markov chain model for N-linked protein glycosylation - towards a
+ low-parameter tool for model-driven glycoengineering},
+Journal = {METABOLIC ENGINEERING},
+Year = {2016},
+Volume = {33},
+Pages = {52-66},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2015.10.007},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Glycosylation; Glycoengineering; Markov chains; Flux-balance analysis},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; MATHEMATICAL-MODEL; QUANTITATIVE PREDICTION;
+ SYSTEMS GLYCOBIOLOGY; CELLULAR-METABOLISM; GLYCAN STRUCTURES; KIN
+ RECOGNITION; GOLGI ENZYMES; CHO-CELLS; GLYCOSYLTRANSFERASES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Kildegaard, Helene Faustrup/0000-0003-3727-5721
+ Arnsdorf, Johnny/0000-0002-2738-0811
+ Hansen, Anders Holmgaard/0000-0002-6007-4787
+ Hansen, Henning Gram/0000-0002-2832-730X},
+Times-Cited = {68},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000367323000006},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000383715400012,
+Author = {Toogood, H. S. and Tait, S. and Jervis, A. and Cheallaigh, A. Ni and
+ Humphreys, L. and Takano, E. and Gardiner, J. M. and Scrutton, N. S.},
+Editor = {OConnor, SE},
+Title = {Natural Product Biosynthesis in Escherichia coli: Mentha
+ Monoterpenoids},
+Booktitle = {SYNTHETIC BIOLOGY AND METABOLIC ENGINEERING IN PLANTS AND MICROBES, PT
+ A: METABOLISM IN MICROBES},
+Series = {Methods in Enzymology},
+Year = {2016},
+Volume = {575},
+Pages = {247-270},
+Type = {Review; Book Chapter},
+DOI = {10.1016/bs.mie.2016.02.020},
+ISSN = {0076-6879},
+ISBN = {978-0-12-804616-6; 978-0-12-804584-8},
+Keywords-Plus = {SYNTHETIC BIOLOGY; PATHWAY; LIMONENE; METABOLOMICS; CONSTRUCTION;
+ METABOLISM; EXPRESSION; PEPPERMINT; PREDICTION; DISCOVERY},
+Research-Areas = {Biochemistry \& Molecular Biology; Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biochemistry \& Molecular Biology;
+ Microbiology},
+ResearcherID-Numbers = {Gardiner, John M/Q-7268-2017
+ },
+ORCID-Numbers = {Gardiner, John M/0000-0003-1827-6817
+ Takano, Eriko/0000-0002-6791-3256
+ Tait, Shirley/0000-0002-3053-9547
+ Toogood, Helen/0000-0003-4797-0293},
+Times-Cited = {0},
+Journal-ISO = {Methods Enzymol.},
+Unique-ID = {WOS:000383715400012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367200100023,
+Author = {Wang, Bin and Ning, Qianji and Hao, Tong and Yu, Ailing and Sun,
+ Jinsheng},
+Title = {Reconstruction and analysis of a genome-scale metabolic model for
+ Eriocheir sinensis eyestalks},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2016},
+Volume = {12},
+Number = {1},
+Pages = {246-252},
+Type = {Article},
+DOI = {10.1039/c5mb00571j},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {NETWORK RECONSTRUCTION; BIOGENIC-AMINES; BOW-TIES; COMPARTMENTALIZATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {11},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000367200100023},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000396056900006,
+Author = {Weiner, Michael and Troendle, Julia and Albermann, Christoph and
+ Sprenger, Georg A. and Weuster-Botz, Dirk},
+Editor = {Bao, J and Ye, Q and Zhong, JJ},
+Title = {Perturbation Experiments: Approaches for Metabolic Pathway Analysis in
+ Bioreactors},
+Booktitle = {BIOREACTOR ENGINEERING RESEARCH AND INDUSTRIAL APPLICATIONS II},
+Series = {Advances in Biochemical Engineering-Biotechnology},
+Year = {2016},
+Volume = {152},
+Pages = {91-136},
+Type = {Article; Book Chapter},
+DOI = {10.1007/10\_2015\_326},
+ISSN = {0724-6145},
+EISSN = {1616-8542},
+ISBN = {978-3-662-48347-3; 978-3-662-48346-6},
+Keywords = {Perturbation experiments; Steady-state experiments; Metabolic flux
+ analysis; Constraint-based approaches; Metabolome quantification;
+ L-phenylalanine; Escherichia coli; Glycerol},
+Keywords-Plus = {RECOMBINANT ESCHERICHIA-COLI; IN-VIVO KINETICS; L-PHENYLALANINE
+ PRODUCTION; GENOME-SCALE RECONSTRUCTION; CONSTRAINT-BASED MODELS; FLUX
+ BALANCE ANALYSIS; SACCHAROMYCES-CEREVISIAE; MASS-SPECTROMETRY;
+ QUANTITATIVE PREDICTION; CELLULAR-METABOLISM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sprenger, Georg A./E-2384-2011
+ },
+ORCID-Numbers = {Sprenger, Georg A./0000-0002-7879-8978
+ Weuster-Botz, Dirk/0000-0002-1171-4194},
+Times-Cited = {6},
+Journal-ISO = {Adv. Biochem. Eng. Biotechnol.},
+Unique-ID = {WOS:000396056900006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000388516000007,
+Author = {Yadav, Kamlesh K. and Shameer, Khader and Readhead, Ben and Yadav,
+ Shalini S. and Li, Li and Kasarskis, Andrew and Tewari, Ashutosh K. and
+ Dudley, Joel T.},
+Title = {Systems Medicine Approaches to Improving Understanding, Treatment, and
+ Clinical Management of Neuroendocrine Prostate Cancer},
+Journal = {CURRENT PHARMACEUTICAL DESIGN},
+Year = {2016},
+Volume = {22},
+Number = {34},
+Pages = {5234-5248},
+Type = {Review},
+DOI = {10.2174/1381612822666160513145924},
+ISSN = {1381-6128},
+EISSN = {1873-4286},
+Keywords = {Prostate cacner; precision medicine; systems biology; neuroendocrine
+ prostate cancer},
+Keywords-Plus = {SMALL-CELL CARCINOMA; RANDOMIZED CONTROLLED-TRIAL; TMPRSS2-ERG GENE
+ FUSION; FLUX BALANCE ANALYSIS; DRUG DISCOVERY; GROWTH-FACTOR; MOLECULAR
+ CHARACTERIZATION; TRANSCRIPTION FACTOR; TUMOR-CELLS; ALLERGIC
+ RHINOCONJUNCTIVITIS},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Khader, Shameer/J-2564-2016
+ },
+ORCID-Numbers = {Li, Li/0000-0001-6746-4297},
+Times-Cited = {7},
+Journal-ISO = {Curr. Pharm. Design},
+Unique-ID = {WOS:000388516000007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367250300001,
+Author = {Yurkovich, James T. and Palsson, Bernhard O.},
+Title = {Solving Puzzles With Missing Pieces: The Power of Systems Biology},
+Journal = {PROCEEDINGS OF THE IEEE},
+Year = {2016},
+Volume = {104},
+Number = {1, SI},
+Pages = {2-7},
+Month = {JAN},
+Type = {Editorial Material},
+DOI = {10.1109/JPROC.2015.2505338},
+ISSN = {0018-9219},
+EISSN = {1558-2256},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; PHENOTYPE},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Electrical \& Electronic},
+Times-Cited = {10},
+Journal-ISO = {Proc. IEEE},
+Unique-ID = {WOS:000367250300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000360920400002,
+Author = {Ruckerbauer, David E. and Jungreuthmayer, Christian and Zanghellini,
+ Juergen},
+Title = {Predicting genetic engineering targets with Elementary Flux Mode
+ Analysis: a review of four current methods},
+Journal = {NEW BIOTECHNOLOGY},
+Year = {2015},
+Volume = {32},
+Number = {6},
+Pages = {534-546},
+Month = {DEC 25},
+Note = {16th European Congress on Biotechnology, Edinburgh, SCOTLAND, JUL 13-16,
+ 2014},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.nbt.2015.03.017},
+ISSN = {1871-6784},
+EISSN = {1876-4347},
+Keywords-Plus = {MINIMAL CUT SETS; SCALE METABOLIC NETWORKS; ESCHERICHIA-COLI; CELL
+ FACTORIES; PATHWAY ANALYSIS; DESIGN; CONSTRUCTION; OPTIMIZATION;
+ PRODUCTIVITY; COMPUTATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Zanghellini, Jürgen/A-4635-2017
+ },
+ORCID-Numbers = {Zanghellini, Jürgen/0000-0002-1964-2455
+ Ruckerbauer, David/0000-0003-3374-8456},
+Times-Cited = {8},
+Journal-ISO = {New Biotech.},
+Unique-ID = {WOS:000360920400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367048100001,
+Author = {He, Lian and Wu, Stephen G. and Wan, Ni and Reding, Adrienne C. and
+ Tang, Yinjie J.},
+Title = {Simulating cyanobacterial phenotypes by integrating flux balance
+ analysis, kinetics, and a light distribution function},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2015},
+Volume = {14},
+Month = {DEC 24},
+Type = {Article},
+DOI = {10.1186/s12934-015-0396-0},
+Article-Number = {206},
+EISSN = {1475-2859},
+Keywords = {Glycogen; Multiple-scale modeling; Photobioreactors; Photosynthesis
+ efficiency; Self-shading; Synechocystis 6803},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; SYNECHOCYSTIS SP PCC6803; PHOTOSYNTHETIC
+ PRODUCTION; MARINE CYANOBACTERIUM; SOLAR-ENERGY; ALGAE GROWTH;
+ LACTIC-ACID; METABOLISM; PHOTOBIOREACTORS; PRODUCTIVITIES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Tang, Yinjie/AAI-5584-2020},
+Times-Cited = {5},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000367048100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000366274200001,
+Author = {Marmiesse, Lucas and Peyraud, Remi and Cottret, Ludovic},
+Title = {FlexFlux: combining metabolic flux and regulatory network analyses},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {9},
+Month = {DEC 15},
+Type = {Article},
+DOI = {10.1186/s12918-015-0238-z},
+Article-Number = {93},
+ISSN = {1752-0509},
+Keywords = {Metabolism; Regulatory network; Flux balance analysis; Genome-scale
+ models; Logical models; Steady-state; Multi-state; Java},
+Keywords-Plus = {OPEN-SOURCE SOFTWARE; ESCHERICHIA-COLI; SYSTEMS BIOLOGY; TRANSCRIPTIONAL
+ REGULATION; SIGNALING NETWORKS; BALANCE ANALYSIS; MODELS;
+ RECONSTRUCTION; SBML; REPRESENTATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Peyraud, Rémi/G-5226-2010
+ /AAD-2293-2020
+ },
+ORCID-Numbers = {Peyraud, Rémi/0000-0002-7580-042X
+ /0000-0001-7418-7750
+ Marmiesse, Lucas/0000-0002-7931-930X},
+Times-Cited = {38},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000366274200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000365926300074,
+Author = {Ponce-de-Leon, Miguel and Calle-Espinosa, Jorge and Pereto, Juli and
+ Montero, Francisco},
+Title = {Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A
+ Metamodel Approach},
+Journal = {PLOS ONE},
+Year = {2015},
+Volume = {10},
+Number = {12},
+Month = {DEC 2},
+Type = {Article},
+DOI = {10.1371/journal.pone.0143626},
+Article-Number = {e0143626},
+ISSN = {1932-6203},
+Keywords-Plus = {FLUX COUPLING ANALYSIS; NETWORK RECONSTRUCTION; PATHWAY DATABASES;
+ ORPHAN ENZYMES; SYSTEMS; ANNOTATION; OPTIMIZATION; GENERATION;
+ PREDICTION; BALANCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Montero, Francisco/G-9850-2015
+ Peretó, Juli/G-5969-2015
+ Ponce-de-Leon, Miguel/AAB-8124-2020
+ },
+ORCID-Numbers = {Montero, Francisco/0000-0003-2366-3635
+ Peretó, Juli/0000-0002-5756-1517
+ Ponce-de-Leon, Miguel/0000-0002-7496-844X
+ Calle-Espinosa, Jorge/0000-0003-2090-2768},
+Times-Cited = {5},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000365926300074},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368445300007,
+Author = {Henson, Michael A.},
+Title = {Genome-scale modelling of microbial metabolism with temporal and spatial
+ resolution},
+Journal = {BIOCHEMICAL SOCIETY TRANSACTIONS},
+Year = {2015},
+Volume = {43},
+Number = {6},
+Pages = {1164-1171},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1042/BST20150146},
+ISSN = {0300-5127},
+EISSN = {1470-8752},
+Keywords = {biofilms; genome-scale reconstructions; metabolic modelling; microbial
+ communities; spatiotemporal models},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; SACCHAROMYCES-CEREVISIAE; ETHANOL-PRODUCTION;
+ OPTIMIZATION; FERMENTATION; FRAMEWORK; NETWORKS; GROWTH; RECONSTRUCTION;
+ INDUSTRIAL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {17},
+Journal-ISO = {Biochem. Soc. Trans.},
+Unique-ID = {WOS:000368445300007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367487500001,
+Author = {Kopriva, Stanislav and Calderwood, Alexander and Weckopp, Silke C. and
+ Koprivova, Anna},
+Title = {Plant sulfur and Big Data},
+Journal = {PLANT SCIENCE},
+Year = {2015},
+Volume = {241},
+Pages = {1-10},
+Month = {DEC},
+Type = {Review},
+DOI = {10.1016/j.plantsci.2015.09.014},
+ISSN = {0168-9452},
+Keywords = {Sulfate assimilation; Systems biology; Genome wide association;
+ Glucosinolates; Glutathione},
+Keywords-Plus = {GENOME-WIDE ASSOCIATION; ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE;
+ ARABIDOPSIS-THALIANA; SULFATE ASSIMILATION; NATURAL VARIATION; SYSTEMS
+ BIOLOGY; GLUCOSINOLATE BIOSYNTHESIS; TRANSCRIPTOME ANALYSIS; DEFICIENCY
+ RESPONSE; METABOLIC NETWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Plant Sciences},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Plant Sciences},
+ResearcherID-Numbers = {Kopriva, Stanislav/C-7401-2013
+ },
+ORCID-Numbers = {Kopriva, Stanislav/0000-0002-7416-6551
+ Gerlich, Silke Christine/0000-0003-3043-5657},
+Times-Cited = {40},
+Journal-ISO = {Plant Sci.},
+Unique-ID = {WOS:000367487500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368472700048,
+Author = {Lakshmanan, Meiyappan and Lim, Sun-Hyung and Mohanty, Bijayalaxmi and
+ Kim, Jae Kwang and Ha, Sun-Hwa and Lee, Dong-Yup},
+Title = {Unraveling the Light-Specific Metabolic and Regulatory Signatures of
+ Rice through Combined in Silico Modeling and Multiomics Analysis},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2015},
+Volume = {169},
+Number = {4},
+Pages = {3002-3020},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1104/pp.15.01379},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {RED LIGHT; TRANSCRIPTIONAL REGULATION; CHLAMYDOMONAS-REINHARDTII; GENOME
+ EXPRESSION; ABSCISIC-ACID; BZIP PROTEIN; ARABIDOPSIS; NETWORK;
+ RECONSTRUCTION; DATABASE},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/AAM-1171-2020
+ Mohanty, Bijayalaxmi/AAY-7386-2020
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Lee, Dong-Yup/D-6650-2011
+ },
+ORCID-Numbers = {Mohanty, Bijayalaxmi/0000-0002-8226-2367
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Lim, Sun-Hyung/0009-0008-5269-3589},
+Times-Cited = {53},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000368472700048},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000363040600003,
+Author = {Ren, Sheng and Hinzman, Anna A. and Kang, Emily L. and Szczesniak,
+ Rhonda D. and Lu, Long Jason},
+Title = {Computational and statistical analysis of metabolomics data},
+Journal = {METABOLOMICS},
+Year = {2015},
+Volume = {11},
+Number = {6},
+Pages = {1492-1513},
+Month = {DEC},
+Type = {Review},
+DOI = {10.1007/s11306-015-0823-6},
+ISSN = {1573-3882},
+EISSN = {1573-3890},
+Keywords = {Computational; Statistical; Unsupervised learning; Supervised learning;
+ Pathway analysis; Time course data},
+Keywords-Plus = {PARTIAL LEAST-SQUARES; CHROMATOGRAPHY-MASS SPECTROMETRY; BIOMARKER
+ DISCOVERY; COMPONENT ANALYSIS; PATHWAY ANALYSIS; DISCRIMINANT-ANALYSIS;
+ FUNCTIONAL GENOMICS; EXPERIMENTAL-DESIGN; PEAK DETECTION; LARGE-SCALE},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {lu, lu/HII-7530-2022
+ lu, lu/HGA-0894-2022
+ LU, LU/JEZ-4760-2023
+ Kang, Emily/HDL-6550-2022
+ },
+ORCID-Numbers = {Kang, Emily/0000-0001-9433-6223},
+Times-Cited = {126},
+Journal-ISO = {Metabolomics},
+Unique-ID = {WOS:000363040600003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000366354400001,
+Author = {Bauer, Eugen and Laczny, Cedric Christian and Magnusdottir, Stefania and
+ Wilmes, Paul and Thiele, Ines},
+Title = {Phenotypic differentiation of gastrointestinal microbes is reflected in
+ their encoded metabolic repertoires},
+Journal = {MICROBIOME},
+Year = {2015},
+Volume = {3},
+Month = {NOV 30},
+Type = {Article},
+DOI = {10.1186/s40168-015-0121-6},
+Article-Number = {55},
+ISSN = {2049-2618},
+Keywords = {Genome-scale metabolic reconstructions; Metabolic modeling;
+ Metagenomics; Intestinal microbiota; Evolution; Ecology},
+Keywords-Plus = {GUT MICROBIOTA; BACTERIA; PHYLOGENY; NETWORK; FERMENTATION;
+ OPTIMIZATION; ANNOTATION; PREDICTION; DIVERSITY; GENOTYPE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Bauer, Eugen/L-1837-2019
+ Magnusdottir, Stefania/ABA-2212-2021
+ Laczny, Cedric/B-2589-2019
+ Thiele, Ines/A-7629-2014
+ Wilmes, Paul/B-1707-2017
+ },
+ORCID-Numbers = {Laczny, Cedric/0000-0002-1100-1282
+ Thiele, Ines/0000-0002-8071-7110
+ Wilmes, Paul/0000-0002-6478-2924
+ Magnusdottir, Stefania/0000-0001-6506-8696},
+Times-Cited = {30},
+Journal-ISO = {Microbiome},
+Unique-ID = {WOS:000366354400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000365654300002,
+Author = {Abedpour, Nima and Kollmann, Markus},
+Title = {Resource constrained flux balance analysis predicts selective pressure
+ on the global structure of metabolic networks},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {9},
+Month = {NOV 23},
+Type = {Article},
+DOI = {10.1186/s12918-015-0232-5},
+Article-Number = {88},
+EISSN = {1752-0509},
+Keywords = {Metabolic networks; Evolution; Bacterial metabolism; Mathematical
+ modeling},
+Keywords-Plus = {ESCHERICHIA-COLI; OPTIMALITY; EVOLUTION; EXPRESSION; GENE; SEQUENCE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {/0000-0002-2933-8035},
+Times-Cited = {3},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000365654300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000365269100001,
+Author = {Lin, Zhenquan and Zhang, Yan and Yuan, Qianqian and Liu, Qiaojie and Li,
+ Yifan and Wang, Zhiwen and Ma, Hongwu and Chen, Tao and Zhao, Xueming},
+Title = {Metabolic engineering of Escherichia coli for
+ poly(3-hydroxybutyrate) production via threonine bypass},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2015},
+Volume = {14},
+Month = {NOV 20},
+Type = {Article},
+DOI = {10.1186/s12934-015-0369-3},
+Article-Number = {185},
+ISSN = {1475-2859},
+Keywords = {Genome-scale metabolic network; Threonine bypass; Strain optimization;
+ Poly(3-hydroxybutyrate)},
+Keywords-Plus = {ONE-CARBON METABOLISM; L-SERINE; POLYHYDROXYALKANOATES; DEHYDROGENASE;
+ BIOSYNTHESIS; FERMENTATION; DEGRADATION; DEFICIENCY; PATHWAYS; MUTANTS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Li, Yifan/HGA-6843-2022
+ Ma, Hongwu/I-5263-2013
+ Zhao, Xueming/W-4891-2019
+ CHEN, Tao/N-1817-2015},
+ORCID-Numbers = {Li, Yifan/0000-0002-3249-1778
+ Ma, Hongwu/0000-0001-5325-2314
+ CHEN, Tao/0000-0001-9588-1821},
+Times-Cited = {35},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000365269100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000361981800007,
+Author = {Mienda, Bashir Sajo and Shamsir, Mohd Shahir},
+Title = {In silico deletion of PtsG gene in Escherichia coli
+ genome-scale model predicts increased succinate production from glycerol},
+Journal = {JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS},
+Year = {2015},
+Volume = {33},
+Number = {11},
+Pages = {2380-2389},
+Month = {NOV 2},
+Type = {Article},
+DOI = {10.1080/07391102.2015.1036461},
+ISSN = {0739-1102},
+EISSN = {1538-0254},
+Keywords = {Phosphatetransferase system (ptsG); Escherichia coli genome-scale model;
+ succinate production; gene deletion; OptFlux; prediction; glycerol},
+Keywords-Plus = {METABOLICALLY ENGINEERED STRAINS; CONSTRAINT-BASED MODELS;
+ PYRUVATE-CARBOXYLASE; ANAEROBIC FERMENTATION; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; ACID PRODUCTION; PLATFORM; GLUCOSE; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ResearcherID-Numbers = {Shamsir, Mohd Shahir/AAG-1097-2021
+ Shamsir, Mohd Shahir/H-7100-2012
+ Mienda, Bashir Sajo/N-8908-2017},
+ORCID-Numbers = {Shamsir, Mohd Shahir/0000-0002-1191-1294
+ Mienda, Bashir Sajo/0000-0002-7205-2753},
+Times-Cited = {13},
+Journal-ISO = {J. Biomol. Struct. Dyn.},
+Unique-ID = {WOS:000361981800007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000362881400006,
+Author = {Contador, C. A. and Rodriguez, V. and Andrews, B. A. and Asenjo, J. A.},
+Title = {Genome-scale reconstruction of Salinispora tropica CNB-440
+ metabolism to study strain-specific adaptation},
+Journal = {ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR
+ MICROBIOLOGY},
+Year = {2015},
+Volume = {108},
+Number = {5},
+Pages = {1075-1090},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1007/s10482-015-0561-9},
+ISSN = {0003-6072},
+EISSN = {1572-9699},
+Keywords = {Salinispora tropica; Metabolic capabilities; Strain adaptation;
+ Genome-scale metabolic reconstruction},
+Keywords-Plus = {SALINOSPORAMIDE-A; SP NOV.; PROTEASOME INHIBITOR; CHEMICAL PRODUCTION;
+ ESCHERICHIA-COLI; MARINE-SEDIMENTS; NATURAL-PRODUCTS; SULFUR GLOBULES;
+ HIGH-THROUGHPUT; DRUG DISCOVERY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Asenjo, Juan JAA/L-8336-2013
+ Contador, Carolina A./K-4101-2019
+ Andrews, Barbara/J-5070-2016},
+ORCID-Numbers = {Asenjo, Juan JAA/0000-0002-3475-7664
+ Contador, Carolina A./0000-0003-0761-3101
+ },
+Times-Cited = {9},
+Journal-ISO = {Antonie Van Leeuwenhoek},
+Unique-ID = {WOS:000362881400006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000365801600018,
+Author = {Heavner, Benjamin D. and Price, Nathan D.},
+Title = {Comparative Analysis of Yeast Metabolic Network Models Highlights
+ Progress, Opportunities for Metabolic Reconstruction},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2015},
+Volume = {11},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004530},
+Article-Number = {e1004530},
+EISSN = {1553-7358},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; GENE DELETION; SCALE;
+ GENOME; FLUX; OPTIMIZATION; TOOLBOX; VALIDATION; REPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Heavner, Benjamin/0000-0003-2898-9044
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {48},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000365801600018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000365753100002,
+Author = {Izard, Jerome and Balderas, Cindy D. C. Gomez and Ropers, Delphine and
+ Lacour, Stephan and Song, Xiaohu and Yang, Yifan and Lindner, Ariel B.
+ and Geiselmann, Johannes and de Jong, Hidde},
+Title = {A synthetic growth switch based on controlled expression of RNA
+ polymerase},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {11},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.15252/msb.20156382},
+Article-Number = {840},
+ISSN = {1744-4292},
+Keywords = {bacterial physiology; growth; RNA polymerase; synthetic biology;
+ biotechnology},
+Keywords-Plus = {DYNAMIC PATHWAY REGULATION; ESCHERICHIA-COLI; GENE-EXPRESSION;
+ PROTEIN-SYNTHESIS; TRANSCRIPTIONAL REGULATION; LACTOSE OPERON; IN-VIVO;
+ METABOLISM; PHENOTYPE; SUBUNITS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Lindner, Ariel B/I-8503-2016
+ Yang, Yifan/JOK-1420-2023
+ Geiselmann, Hans/GVT-8876-2022
+ },
+ORCID-Numbers = {Lindner, Ariel B/0000-0001-5015-6511
+ Yang, Yifan/0000-0001-6697-0198
+ Geiselmann, Hans/0000-0002-1329-7558
+ Lacour, Stephan/0000-0002-6066-4189
+ Ropers, Delphine/0000-0003-2659-3003
+ de Jong, Hidde/0000-0002-2226-650X},
+Times-Cited = {60},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000365753100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000368366700013,
+Author = {Lee, Na-Rae and Yun, Ji-Yeong and Lee, Sun-Mee and Park, Jin-Byung},
+Title = {Cyclohexanone-induced stress metabolism of Escherichia coli and
+ Corynebacterium glutamicum},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2015},
+Volume = {20},
+Number = {6},
+Pages = {1088-1098},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1007/s12257-015-0607-x},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {Escherichia coli; Corynebacterium glutamicum; cyclohexanone; solvent
+ stress; constraints-based flux analysis},
+Keywords-Plus = {EPSILON-CAPROLACTONE; MICROBIAL SYNTHESIS; CARBON METABOLISM;
+ FATTY-ACIDS; MONOOXYGENASE; EPOXIDATION; BIOTRANSFORMATION; BIOCATALYST;
+ INHIBITION; MECHANISMS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {5},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:000368366700013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000365801600022,
+Author = {Ma, Shuyi and Minch, Kyle J. and Rustad, Tige R. and Hobbs, Samuel and
+ Zhou, Suk-Lin and Sherman, David R. and Price, Nathan D.},
+Title = {Integrated Modeling of Gene Regulatory and Metabolic Networks in
+ Mycobacterium tuberculosis},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2015},
+Volume = {11},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004543},
+Article-Number = {e1004543},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; TRANSCRIPTIONAL REGULATION; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; HIGH-THROUGHPUT; EXPRESSION; TB},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Hobbs, Samuel/0000-0002-4282-8813
+ Ma, Shuyi/0000-0003-0783-1328
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {43},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000365801600022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000365708700015,
+Author = {Ravikrishnan, Aarthi and Raman, Karthik},
+Title = {Critical assessment of genome-scale metabolic networks: the need for a
+ unified standard},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2015},
+Volume = {16},
+Number = {6},
+Pages = {1057-1068},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1093/bib/bbv003},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {genome-scale metabolic networks; reconstruction; blocked reactions;
+ standards; SBML},
+Keywords-Plus = {OPEN-SOURCE SOFTWARE; IN-SILICO ANALYSIS; SACCHAROMYCES-CEREVISIAE;
+ ESCHERICHIA-COLI; COMPUTATIONAL MODELS; FLUX ANALYSIS; RECONSTRUCTION;
+ DATABASE; COMMUNITY; YEAST},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019
+ Ravikrishnan, Aarthi/ABG-9476-2020
+ },
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ Ravikrishnan, Aarthi/0000-0003-2391-0202},
+Times-Cited = {47},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000365708700015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000365279000002,
+Author = {Varga, John J. and Barbier, Mariette and Mulet, Xavier and Bielecki,
+ Piotr and Bartell, Jennifer A. and Owings, Joshua P. and Martinez-Ramos,
+ Inmaculada and Hittle, Lauren E. and Davis, Jr., Michael R. and Damron,
+ F. Heath and Liechti, George W. and Puchalka, Jacek and dos Santos,
+ Vitor A. P. Martins and Ernst, Robert K. and Papin, Jason A. and
+ Alberti, Sebastian and Oliver, Antonio and Goldberg, Joanna B.},
+Title = {Genotypic and phenotypic analyses of a Pseudomonas aeruginosa
+ chronic bronchiectasis isolate reveal differences from cystic fibrosis
+ and laboratory strains},
+Journal = {BMC GENOMICS},
+Year = {2015},
+Volume = {16},
+Month = {OCT 30},
+Type = {Article},
+DOI = {10.1186/s12864-015-2069-0},
+Article-Number = {883},
+ISSN = {1471-2164},
+Keywords = {Pseudomonas aeruginosa; Metabolic model; Transcriptome; Comparative
+ genomics; Cystic fibrosis; Bronchiectasis},
+Keywords-Plus = {VI-SECRETION-SYSTEM; COMPLETE GENOME SEQUENCE; CHRONIC LUNG INFECTIONS;
+ PATHOGEN CLOSTRIDIUM-PERFRINGENS; CHRONIC PULMONARY INFECTION;
+ BETA-LACTAM RESISTANCE; IV PILI; GENETIC ADAPTATION; BIOFILM FORMATION;
+ SIGMA-FACTOR},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Oliver, Antonio/V-5541-2019
+ Liechti, George/C-3129-2015
+ Alberti, Sebastian/H-2490-2013
+ Ernst, Robert/H-9513-2013
+ Varga, John J/I-8130-2012
+ Oliver, Antonio/E-4048-2012
+ },
+ORCID-Numbers = {Oliver, Antonio/0000-0001-9327-1894
+ Liechti, George/0000-0003-3028-8474
+ Alberti, Sebastian/0000-0003-0020-6861
+ Varga, John J/0000-0002-4868-1971
+ Oliver, Antonio/0000-0001-9327-1894
+ Damron, Fredrick/0000-0002-3140-402X
+ Bartell, Jennifer/0000-0003-2750-9678
+ Ernst, Robert/0000-0001-5016-8694
+ Barbier, Mariette/0000-0002-3250-3636},
+Times-Cited = {25},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000365279000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000209926000008,
+Author = {Bordbar, Aarash and McCloskey, Douglas and Zielinski, Daniel C. and
+ Sonnenschein, Nikolaus and Jamshidi, Neema and Palsson, Bernhard O.},
+Title = {Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in
+ Genomics and Pharmacodynamics},
+Journal = {CELL SYSTEMS},
+Year = {2015},
+Volume = {1},
+Number = {4},
+Pages = {283-292},
+Month = {OCT 28},
+Type = {Article},
+DOI = {10.1016/j.cels.2015.10.003},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {SINGLE-NUCLEOTIDE POLYMORPHISMS; CONSTRAINT-BASED MODELS; INBORN-ERRORS;
+ ANEMIA; FLUX; GLYCOLYSIS; NETWORKS; DRIVEN; RECONSTRUCTION; TRANSPORT},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {/AAG-5264-2021
+ Sonnenschein, Nikolaus/F-6853-2012
+ },
+ORCID-Numbers = {/0000-0001-6460-6771
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Jamshidi, Neema/0000-0003-3857-9735
+ Zielinski, Daniel/0000-0001-6452-483X},
+Times-Cited = {68},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000209926000008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000209926000007,
+Author = {Gerosa, Luca and van Rijsewijk, Bart R. B. Haverkorn and Christodoulou,
+ Dimitris and Kochanowski, Karl and Schmidt, Thomas S. B. and Noor, Elad
+ and Sauer, Uwe},
+Title = {Pseudo-transition Analysis Identifies the Key Regulators of Dynamic
+ Metabolic Adaptations from Steady-State Data},
+Journal = {CELL SYSTEMS},
+Year = {2015},
+Volume = {1},
+Number = {4},
+Pages = {270-282},
+Month = {OCT 28},
+Type = {Article},
+DOI = {10.1016/j.cels.2015.09.008},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Sauer, Uwe/Y-3556-2019
+ Kochanowski, Karl/ABE-7236-2021
+ Noor, Elad/AAN-9042-2020
+ Schmidt, Thomas/F-3022-2014
+ },
+ORCID-Numbers = {Noor, Elad/0000-0001-8776-4799
+ Gerosa, Luca/0000-0001-6805-9410
+ Schmidt, Thomas/0000-0001-8587-4177
+ Christodoulou, Dimitris/0000-0002-0646-6181},
+Times-Cited = {94},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000209926000007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000363507000001,
+Author = {Kavscek, Martin and Bhutada, Govindprasad and Madl, Tobias and Natter,
+ Klaus},
+Title = {Optimization of lipid production with a genome-scale model of
+ Yarrowia lipolytica},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {9},
+Month = {OCT 26},
+Type = {Article},
+DOI = {10.1186/s12918-015-0217-4},
+Article-Number = {72},
+EISSN = {1752-0509},
+Keywords = {Flux balance analysis; Citrate; Oleaginous yeast; Oxygen limitation;
+ Fed-batch fermentation},
+Keywords-Plus = {METABOLIC MODEL; MALIC ENZYME; YEAST; RECONSTRUCTION; ACID;
+ ACCUMULATION; EXPRESSION; MUTANTS; STRAINS; NADPH},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Madl, Tobias/B-1682-2012
+ },
+ORCID-Numbers = {Madl, Tobias/0000-0002-9725-5231
+ Natter, Klaus/0000-0002-4483-9321
+ Bhutada, Govindprasad/0000-0002-3945-9527
+ Kavscek, Martin/0000-0002-0109-565X},
+Times-Cited = {77},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000363507000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000363029200001,
+Author = {Angione, Claudio and Lio, Pietro},
+Title = {Predictive analytics of environmental adaptability in multi-omic network
+ models},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2015},
+Volume = {5},
+Month = {OCT 20},
+Type = {Article},
+DOI = {10.1038/srep15147},
+Article-Number = {15147},
+ISSN = {2045-2322},
+Keywords-Plus = {GENE-EXPRESSION; ESCHERICHIA-COLI; CODON USAGE; ADAPTIVE EVOLUTION;
+ PROTEIN ABUNDANCE; MESSENGER-RNA; TRANSLATION; INTEGRATION; FRAMEWORK;
+ DESIGN},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {P. Lió, Pietro Lio/AAV-3358-2021
+ },
+ORCID-Numbers = {P. Lió, Pietro Lio/0000-0002-0540-5053
+ Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {42},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000363029200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000362875500001,
+Author = {Anfelt, Josefine and Kaczmarzyk, Danuta and Shabestary, Kiyan and
+ Renberg, Bjorn and Rockberg, Johan and Nielsen, Jens and Uhlen, Mathias
+ and Hudson, Elton P.},
+Title = {Genetic and nutrient modulation of acetyl-CoA levels in
+ Synechocystis for n-butanol production},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2015},
+Volume = {14},
+Month = {OCT 16},
+Type = {Article},
+DOI = {10.1186/s12934-015-0355-9},
+Article-Number = {167},
+EISSN = {1475-2859},
+Keywords = {Cyanobacteria; Butanol; Biofuel; Metabolic engineering; Phosphoketolase;
+ Starvation},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; NITROGEN-STARVATION; PHOTOSYNTHETIC
+ PRODUCTION; ENGINEERING CYANOBACTERIA; SYNTHETIC BIOLOGY;
+ CARBON-DIOXIDE; ACID; PHOSPHOKETOLASE; OVEREXPRESSION; METABOLISM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Uhlen, Mathias/B-3262-2016
+ Nielsen, Jens Bo/C-7632-2015
+ Uhlen, Mathias/HPB-8445-2023
+ Hudson, Paul/ABH-8177-2020
+ Shabestary, Kiyan/JCE-6866-2023
+ Uhlen, Mathias/AAV-8746-2021
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Uhlen, Mathias/0000-0002-4858-8056
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Uhlen, Mathias/0000-0002-4858-8056
+ Shabestary, Kiyan/0000-0002-4207-0547
+ Hudson, Elton/0000-0003-1899-7649
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {74},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000362875500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000362866400001,
+Author = {Ye, Chao and Qiao, Weihua and Yu, Xiaobin and Ji, Xiaojun and Huang, He
+ and Collier, Jackie L. and Liu, Liming},
+Title = {Reconstruction and analysis of the genome-scale metabolic model of
+ schizochytrium limacinum SR21 for docosahexaenoic acid production},
+Journal = {BMC GENOMICS},
+Year = {2015},
+Volume = {16},
+Month = {OCT 16},
+Type = {Article},
+DOI = {10.1186/s12864-015-2042-y},
+Article-Number = {799},
+ISSN = {1471-2164},
+Keywords = {Schizochytrium limacinum SR21; Docosahexaenoic acid; Genome-scale
+ metabolic model; Polyketide synthase system; Minimization of metabolic
+ adjustment algorithm},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; CRUDE GLYCEROL; FATTY-ACIDS; BIOSYNTHESIS; DHA;
+ LOCALIZATION; OPTIMIZATION; STRATEGY; DATABASE; BIOMASS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009
+ Ye, Chao/M-3689-2019
+ Collier, Jackie/AFF-7928-2022
+ Ye, Chao/H-7623-2014
+ Ji, Xiao-Jun/E-6447-2012
+ Ye, Chao/HGD-3564-2022},
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X
+ Ye, Chao/0000-0002-6671-7819
+ Collier, Jackie/0000-0001-8774-5715
+ Ye, Chao/0000-0002-6671-7819
+ Ji, Xiao-Jun/0000-0002-6450-0229
+ Ye, Chao/0000-0002-6671-7819},
+Times-Cited = {31},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000362866400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000363184600010,
+Author = {Mannan, Ahmad A. and Toya, Yoshihiro and Shimizu, Kazuyuki and McFadden,
+ Johnjoe and Kierzek, Andrzej M. and Rocco, Andrea},
+Title = {Integrating Kinetic Model of E. coli with Genome Scale
+ Metabolic Fluxes Overcomes Its Open System Problem and Reveals
+ Bistability in Central Metabolism},
+Journal = {PLOS ONE},
+Year = {2015},
+Volume = {10},
+Number = {10},
+Month = {OCT 15},
+Type = {Article},
+DOI = {10.1371/journal.pone.0139507},
+Article-Number = {e0139507},
+ISSN = {1932-6203},
+Keywords-Plus = {CENTRAL CARBON METABOLISM; ESCHERICHIA-COLI; MYCOBACTERIUM-TUBERCULOSIS;
+ ISOCITRATE DEHYDROGENASE; BALANCE ANALYSIS; GROWTH; ACETATE; GLYOXYLATE;
+ MECHANISM; TOOLBOX},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Mannan, Ahmad/AAT-1820-2021
+ Rocco, Andrea/N-7076-2017
+ Shimizu, Kazuyuki/GVT-4698-2022
+ },
+ORCID-Numbers = {Mannan, Ahmad/0000-0001-7628-8416
+ Rocco, Andrea/0000-0002-0974-5522
+ Shimizu, Kazuyuki/0000-0002-4847-0197
+ McFadden, Johnjoe/0000-0003-2145-0046
+ Kierzek, Andrzej/0000-0002-2605-9057
+ Toya, Yoshihiro/0000-0001-9670-6961},
+Times-Cited = {19},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000363184600010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000362846600009,
+Author = {Pratapa, Aditya and Balachandran, Shankar and Raman, Karthik},
+Title = {Fast-SL: an efficient algorithm to identify synthetic lethal sets in
+ metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2015},
+Volume = {31},
+Number = {20},
+Pages = {3299-3305},
+Month = {OCT 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btv352},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {FLUX-BALANCE ANALYSIS; CONSTRAINT-BASED ANALYSIS;
+ SALMONELLA-TYPHIMURIUM; RECONSTRUCTION; MODELS; IDENTIFICATION;
+ ROBUSTNESS; TOOLBOX; TARGETS; SINGLE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019
+ Pratapa, Aditya/HNR-3125-2023},
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ Pratapa, Aditya/0000-0002-3323-6250},
+Times-Cited = {30},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000362846600009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000373895800001,
+Author = {Quandt, Erik M. and Gollihar, Jimmy and Blount, Zachary D. and
+ Ellington, Andrew D. and Georgiou, George and Barrick, Jeffrey E.},
+Title = {Fine-tuning citrate synthase flux potentiates and refines metabolic
+ innovation in the Lenski evolution experiment},
+Journal = {ELIFE},
+Year = {2015},
+Volume = {4},
+Month = {OCT 14},
+Type = {Article},
+DOI = {10.7554/eLife.09696},
+Article-Number = {e09696},
+ISSN = {2050-084X},
+Keywords-Plus = {NICOTINAMIDE-ADENINE-DINUCLEOTIDE; NADH BINDING-SITE; ESCHERICHIA-COLI;
+ ALLOSTERIC PROPERTIES; GENE-EXPRESSION; KEY INNOVATION; OPTIMAL-GROWTH;
+ GENOME; ADAPTATION; POPULATION},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Blount, Zachary/L-3130-2019
+ },
+ORCID-Numbers = {Quandt, Erik/0000-0002-3287-7777
+ Barrick, Jeffrey/0000-0003-0888-7358
+ Blount, Zachary/0000-0001-5153-0034
+ Gollihar, Jimmy/0000-0003-3957-2092},
+Times-Cited = {53},
+Journal-ISO = {eLife},
+Unique-ID = {WOS:000373895800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000361865000022,
+Author = {Zamora, Maria A. and Pinzon, Andres and Zambrano, Maria M. and Restrepo,
+ Silvia and Broadbelte, Linda J. and Moura, Matthew and Husserl Orjuela,
+ Johana and Gonzalez Barrios, Andres F.},
+Title = {A comparison between functional frequency and metabolic flows framed by
+ biogeochemical cycles in metagenomes: The case of ``El Coquito{''} hot
+ spring located at Colombia's national Nevados park},
+Journal = {ECOLOGICAL MODELLING},
+Year = {2015},
+Volume = {313},
+Pages = {259-265},
+Month = {OCT 10},
+Type = {Article},
+DOI = {10.1016/j.ecolmodel.2015.06.041},
+ISSN = {0304-3800},
+EISSN = {1872-7026},
+Keywords = {Metabolic reconstruction; Network topology analysis in ecosystems;
+ Ecosystem FBA},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; THERMODYNAMIC ANALYSIS; SYSTEMS BIOLOGY;
+ COMMUNITY; RECONSTRUCTION; VISUALIZATION; NETWORKS; GENES},
+Research-Areas = {Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Ecology},
+ResearcherID-Numbers = {Zambrano, Maria Mercedes/AAD-2805-2019
+ },
+ORCID-Numbers = {Zambrano, Maria Mercedes/0000-0002-0796-4473
+ Gonzalez Barrios, Andres Fernando/0000-0003-2517-2020
+ Husserl, Johana/0000-0002-1390-1583
+ Restrepo, Silvia/0000-0001-9016-1040},
+Times-Cited = {3},
+Journal-ISO = {Ecol. Model.},
+Unique-ID = {WOS:000361865000022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000363379900001,
+Author = {Jamshidi, Neema and Raghunathan, Anu},
+Title = {Cell scale host-pathogen modeling: another branch in the evolution of
+ constraint-based methods},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2015},
+Volume = {6},
+Month = {OCT 6},
+Type = {Article},
+DOI = {10.3389/fmicb.2015.01032},
+Article-Number = {1032},
+ISSN = {1664-302X},
+Keywords = {constraint-based model; host-pathogen; optimization methods;
+ mathematical models; omics-technologies; tuberculosis; salmonella
+ typhimurium; flux balance analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GENOME-SCALE; METABOLIC NETWORK;
+ ESCHERICHIA-COLI; SYSTEMS BIOLOGY; MYCOBACTERIUM-TUBERCULOSIS;
+ BIOCHEMICAL NETWORKS; IRON-METABOLISM; RECONSTRUCTION; GENE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Jamshidi, Neema/0000-0003-3857-9735},
+Times-Cited = {10},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000363379900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358968000093,
+Author = {De Bhowmick, Goldy and Koduru, Lokanand and Sen, Ramkrishna},
+Title = {Metabolic pathway engineering towards enhancing microalgal lipid
+ biosynthesis for biofuel application-A review},
+Journal = {RENEWABLE \& SUSTAINABLE ENERGY REVIEWS},
+Year = {2015},
+Volume = {50},
+Pages = {1239-1253},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1016/j.rser.2015.04.131},
+ISSN = {1364-0321},
+Keywords = {Microalgal biodiesel; Triacylglycerol biosynthesis; Metabolic pathway
+ engineering; Flux analysis; Systems biology; Integrated approach},
+Keywords-Plus = {RECOMBINANT PROTEIN EXPRESSION; FATTY-ACID-COMPOSITION; FLUX BALANCE
+ ANALYSIS; CHLAMYDOMONAS-REINHARDTII; TUBULAR PHOTOBIOREACTORS; NETWORK
+ RECONSTRUCTION; GENE-EXPRESSION; GREEN-ALGA; THALASSIOSIRA-PSEUDONANA;
+ SACCHAROMYCES-CEREVISIAE},
+Research-Areas = {Science \& Technology - Other Topics; Energy \& Fuels},
+Web-of-Science-Categories = {Green \& Sustainable Science \& Technology; Energy \& Fuels},
+ResearcherID-Numbers = {Sen, Ramkrishna/C-8772-2014
+ Koduru, Lokanand/AAY-3079-2020
+ },
+ORCID-Numbers = {Sen, Ramkrishna/0000-0002-6207-3307
+ Koduru, Lokanand/0000-0001-9223-8742
+ De Bhowmick, Goldy/0000-0001-7166-2579},
+Times-Cited = {78},
+Journal-ISO = {Renew. Sust. Energ. Rev.},
+Unique-ID = {WOS:000358968000093},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000364315500003,
+Author = {Ebrahim, Ali and Almaas, Eivind and Bauer, Eugen and Bordbar, Aarash and
+ Burgard, Anthony P. and Chang, Roger L. and Draeger, Andreas and Famili,
+ Iman and Feist, Adam M. and Fleming, Ronan M. T. and Fong, Stephen S.
+ and Hatzimanikatis, Vassily and Herrgard, Markus J. and Holder, Allen
+ and Hucka, Michael and Hyduke, Daniel and Jamshidi, Neema and Lee, Sang
+ Yup and Le Novere, Nicolas and Lerman, Joshua A. and Lewis, Nathan E.
+ and Ma, Ding and Mahadevan, Radhakrishnan and Maranas, Costas and
+ Nagarajan, Harish and Navid, Ali and Nielsen, Jens and Nielsen, Lars K.
+ and Nogales, Juan and Noronha, Alberto and Pal, Csaba and Palsson,
+ Bernhard O. and Papin, Jason A. and Patil, Kiran R. and Price, Nathan D.
+ and Reed, Jennifer L. and Saunders, Michael and Senger, Ryan S. and
+ Sonnenschein, Nikolaus and Sun, Yuekai and Thiele, Ines},
+Title = {Do genome-scale models need exact solvers or clearer standards?},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {11},
+Number = {10},
+Month = {OCT},
+Type = {Letter},
+DOI = {10.15252/msb.20156157},
+Article-Number = {831},
+ISSN = {1744-4292},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; TOOLBOX},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ Navid, Ali/A-1336-2013
+ Hatzimanikatis, Vassily/G-6505-2010
+ Thiele, Ines/A-7629-2014
+ Lee, Sang Yup/C-1526-2011
+ Maranas, Costas D/A-4774-2011
+ /AAG-5264-2021
+ Lewis, Nathan/ABE-7290-2020
+ Le Novère, Nicolas/F-9973-2010
+ Reed, Jennifer L/E-5137-2011
+ Dräger, Andreas/F-5620-2015
+ Nielsen, Jens Bo/C-7632-2015
+ Bauer, Eugen/L-1837-2019
+ Sonnenschein, Nikolaus/F-6853-2012
+ Saunders, Michael A/D-1083-2012
+ Patil, Kiran R/B-9709-2009
+ Fleming, Ronan MT/ABC-4093-2021
+ Nielsen, Lars K/A-5519-2011
+ Hucka, Michael/B-1896-2012
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Navid, Ali/0000-0003-2560-6984
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Thiele, Ines/0000-0002-8071-7110
+ Lee, Sang Yup/0000-0003-0599-3091
+ Maranas, Costas D/0000-0002-1508-1398
+ /0000-0001-6460-6771
+ Lewis, Nathan/0000-0001-7700-3654
+ Le Novère, Nicolas/0000-0002-6309-7327
+ Reed, Jennifer L/0000-0001-7854-6220
+ Dräger, Andreas/0000-0002-1240-5553
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Patil, Kiran R/0000-0002-6166-8640
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Nielsen, Lars K/0000-0001-8191-3511
+ Hucka, Michael/0000-0001-9105-5960
+ Nogales, Juan/0000-0002-4961-0833
+ Chang, Roger/0000-0003-1630-6584
+ MA, Ding/0000-0002-5503-2945
+ Price, Nathan/0000-0002-4157-0267
+ Ebrahim, Ali/0000-0002-4009-2128
+ Nielsen, Jens/0000-0002-9955-6003
+ Almaas, Eivind/0000-0002-9125-326X
+ Noronha, Alberto/0000-0002-0935-4599
+ Saunders, Michael/0000-0003-3800-4982},
+Times-Cited = {38},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000364315500003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000361941600057,
+Author = {Megchelenbrink, Wout and Katzir, Rotem and Lu, Xiaowen and Ruppin, Eytan
+ and Notebaart, Richard A.},
+Title = {Synthetic dosage lethality in the human metabolic network is highly
+ predictive of tumor growth and cancer patient survival},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2015},
+Volume = {112},
+Number = {39},
+Pages = {12217-12222},
+Month = {SEP 29},
+Type = {Article},
+DOI = {10.1073/pnas.1508573112},
+ISSN = {0027-8424},
+Keywords = {systems biology; synthetic dosage lethality; human metabolism; cancer;
+ genetic interactions},
+Keywords-Plus = {GENOME-SCALE; GENETIC INTERACTIONS; OVARIAN-CANCER; DRUG TARGETS; GLOBAL
+ RECONSTRUCTION; ESCHERICHIA-COLI; YEAST METABOLISM; BREAST-CANCER;
+ MODELS; CELLS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Wang, Jing/IQW-3496-2023
+ Notebaart, Richard A./A-1459-2014
+ Ruppin, Eytan/R-9698-2017
+ yang, qing/JBR-8440-2023},
+ORCID-Numbers = {Wang, Jing/0000-0002-8296-2961
+ Ruppin, Eytan/0000-0002-7862-3940
+ },
+Times-Cited = {33},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000361941600057},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000361601100191,
+Author = {Subramanian, Abhishek and Jhawar, Jitesh and Sarkar, Ram Rup},
+Title = {Dissecting Leishmania infantum Energy Metabolism - A Systems
+ Perspective},
+Journal = {PLOS ONE},
+Year = {2015},
+Volume = {10},
+Number = {9},
+Month = {SEP 14},
+Type = {Article},
+DOI = {10.1371/journal.pone.0137976},
+Article-Number = {e0137976},
+ISSN = {1932-6203},
+Keywords-Plus = {SUBSTRATE LEVEL PHOSPHORYLATION; PROCYCLIC TRYPANOSOMA-BRUCEI;
+ CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS; CARBOHYDRATE-METABOLISM;
+ ENZYME-ACTIVITIES; KREBS CYCLE; MEXICANA; PROTEINS; COMPARTMENTATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Subramanian, Abhishek/AAN-1302-2020
+ Jhawar, Jitesh/IXW-4971-2023
+ },
+ORCID-Numbers = {Subramanian, Abhishek/0000-0002-4601-5991
+ Jhawar, Jitesh/0000-0002-8774-2351
+ SARKAR, RAM RUP/0000-0001-7115-163X},
+Times-Cited = {17},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000361601100191},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000361601100093,
+Author = {Whitmore, Leanne S. and Ye, Ping},
+Title = {Dissecting Germ Cell Metabolism through Network Modeling},
+Journal = {PLOS ONE},
+Year = {2015},
+Volume = {10},
+Number = {9},
+Month = {SEP 14},
+Type = {Article},
+DOI = {10.1371/journal.pone.0137607},
+Article-Number = {e0137607},
+ISSN = {1932-6203},
+Keywords-Plus = {RETINOIC ACID METABOLISM; BINDING-PROTEIN-I; SERTOLI-CELLS; GLOBAL
+ RECONSTRUCTION; TARGETED DISRUPTION; INSULIN-RESISTANCE; SPERMATOGENIC
+ WAVE; MICE; DIFFERENTIATION; EXPRESSION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {7},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000361601100093},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000361797000006,
+Author = {Biggs, Matthew B. and Medlock, Gregory L. and Kolling, Glynis L. and
+ Papin, Jason A.},
+Title = {Metabolic network modeling of microbial communities},
+Journal = {WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE},
+Year = {2015},
+Volume = {7},
+Number = {5},
+Pages = {317-334},
+Month = {SEP-OCT},
+Type = {Review},
+DOI = {10.1002/wsbm.1308},
+ISSN = {1939-5094},
+EISSN = {1939-005X},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; SYSTEMS BIOLOGY; GUT MICROBIOME; SCALE
+ RECONSTRUCTION; EXPRESSION DATA; S. CEREVISIAE; GENOME; HOST; GROWTH;
+ INTEGRATION},
+Research-Areas = {Research \& Experimental Medicine},
+Web-of-Science-Categories = {Medicine, Research \& Experimental},
+ORCID-Numbers = {Kolling, Glynis/0000-0001-8871-8129
+ Medlock, Gregory/0000-0002-1571-0801
+ Biggs, Matthew/0000-0001-6492-8180},
+Times-Cited = {72},
+Journal-ISO = {Wiley Interdiscip. Rev.-Syst. Biol},
+Unique-ID = {WOS:000361797000006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000361000500021,
+Author = {La Rosa, Ruggero and Nogales, Juan and Rojo, Fernando},
+Title = {The Crc/CrcZ-CrcY global regulatory system helps the integration of
+ gluconeogenic and glycolytic metabolism in Pseudomonas putida},
+Journal = {ENVIRONMENTAL MICROBIOLOGY},
+Year = {2015},
+Volume = {17},
+Number = {9},
+Pages = {3362-3378},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1111/1462-2920.12812},
+ISSN = {1462-2912},
+EISSN = {1462-2920},
+Keywords-Plus = {CARBON CATABOLITE REPRESSION; TOLUENE DEGRADATION PATHWAY; GENOME-SCALE
+ MODELS; ESCHERICHIA-COLI; TOL PLASMID; TRANSCRIPTIONAL REGULATOR;
+ MICROBIAL-METABOLISM; INHIBITS TRANSLATION; AERUGINOSA PAO1; PU PROMOTER},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {La Rosa, Ruggero/AAR-8197-2021
+ Rojo, Fernando/A-7038-2008
+ Nogales, Juan/Y-8829-2019
+ },
+ORCID-Numbers = {La Rosa, Ruggero/0000-0002-6705-3989
+ Rojo, Fernando/0000-0003-1848-7745
+ Nogales, Juan/0000-0002-4961-0833},
+Times-Cited = {36},
+Journal-ISO = {Environ. Microbiol.},
+Unique-ID = {WOS:000361000500021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000362266400008,
+Author = {Martin, Hector Garcia and Kumar, Vinay Satish and Weaver, Daniel and
+ Ghosh, Amit and Chubukov, Victor and Mukhopadhyay, Aindrila and Arkin,
+ Adam and Keasling, Jay D.},
+Title = {A Method to Constrain Genome-Scale Models with 13C Labeling
+ Data},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2015},
+Volume = {11},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004363},
+Article-Number = {e1004363},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {METABOLIC FLUX ANALYSIS; CENTRAL CARBON METABOLISM; ESCHERICHIA-COLI;
+ AMINO-ACIDS; IN-VIVO; FERMENTATION; ISOTOPOMER; OPTIMALITY; PHENOTYPE;
+ CULTURE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Mukhopadhyay, Aindrila/AAW-7257-2021
+ Keasling, Jay D/J-9162-2012
+ Arkin, Adam/M-9941-2019
+ Keasling, Jay/HPG-6073-2023
+ Ghosh, Amit/AAA-3490-2021
+ Martin, Hector Garcia/B-5357-2009
+ Ghosh, Amit/AAB-3140-2019
+ Arkin, Adam P/A-6751-2008},
+ORCID-Numbers = {Keasling, Jay D/0000-0003-4170-6088
+ Arkin, Adam/0000-0002-4999-2931
+ Ghosh, Amit/0000-0003-3514-885X
+ Martin, Hector Garcia/0000-0002-4556-9685
+ Arkin, Adam P/0000-0002-4999-2931},
+Times-Cited = {42},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000362266400008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000360018600060,
+Author = {Reimers, Arne C.},
+Title = {Obstructions to Sampling Qualitative Properties},
+Journal = {PLOS ONE},
+Year = {2015},
+Volume = {10},
+Number = {8},
+Month = {AUG 19},
+Type = {Article},
+DOI = {10.1371/journal.pone.0135636},
+Article-Number = {e0135636},
+ISSN = {1932-6203},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; METABOLIC NETWORK; THERMODYNAMIC CONSTRAINTS;
+ VOLUME; DISTRIBUTIONS; MODELS; STATES; SPACE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {3},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000360018600060},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000359048300001,
+Author = {Tajparast, Mohammad and Frigon, Dominic},
+Title = {Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174)
+ to study the accumulation of storage compounds during nitrogen-limited
+ condition},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {9},
+Month = {AUG 7},
+Type = {Article},
+DOI = {10.1186/s12918-015-0190-y},
+Article-Number = {43},
+EISSN = {1752-0509},
+Keywords-Plus = {BIOCYC COLLECTION; CATABOLIC GENES; DEGRADER; BIOSYNTHESIS; DATABASE;
+ ENZYMES},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+Times-Cited = {14},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000359048300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358783300005,
+Author = {Erlmeier, Franziska and Feuchtinger, Annette and Borgmann, Daniela and
+ Rudelius, Martina and Autenrieth, Michael and Walch, Axel Karl and
+ Weirich, Gregor},
+Title = {Supremacy of modern morphometry in typing renal oncocytoma and malignant
+ look-alikes},
+Journal = {HISTOCHEMISTRY AND CELL BIOLOGY},
+Year = {2015},
+Volume = {144},
+Number = {2},
+Pages = {147-156},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1007/s00418-015-1324-4},
+ISSN = {0948-6143},
+EISSN = {1432-119X},
+Keywords = {Morphometry; Renal oncocytoma; Chromophobe renal cell carcinoma; Clear
+ cell renal cell carcinoma},
+Keywords-Plus = {PLASMA-MASS SPECTROMETRY; FORMALIN-FIXED TISSUES; CELL CARCINOMA;
+ NUCLEAR MORPHOMETRY; CLASSIFICATION; FEATURES; CANCER; GRADE;
+ EXTRACTION; SECTIONS},
+Research-Areas = {Cell Biology; Microscopy},
+Web-of-Science-Categories = {Cell Biology; Microscopy},
+ResearcherID-Numbers = {Erlmeier, Franziska/AAS-7234-2020
+ Feuchtinger, Annette/O-4569-2014
+ Walch, Axel/B-4554-2012},
+ORCID-Numbers = {Walch, Axel/0000-0001-5578-4023},
+Times-Cited = {12},
+Journal-ISO = {Histochem. Cell Biol.},
+Unique-ID = {WOS:000358783300005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000357680600010,
+Author = {Fouladiha, H. and Marashi, S. -A. and Shokrgozar, M. A.},
+Title = {Reconstruction and validation of a constraint-based metabolic network
+ model for bone marrow-derived mesenchymal stem cells},
+Journal = {CELL PROLIFERATION},
+Year = {2015},
+Volume = {48},
+Number = {4},
+Pages = {475-485},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1111/cpr.12197},
+ISSN = {0960-7722},
+EISSN = {1365-2184},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; THERAPEUTIC APPLICATION; GLOBAL
+ RECONSTRUCTION; GENE-THERAPY; CANCER; GROWTH; BIOLOGY; PROLIFERATION;
+ EXPRESSION},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Shokrgozar, Mohammad Ali/HDM-1639-2022
+ shokrgozar, mohammad ali/L-4149-2017
+ Marashi, Sayed-Amir/A-5384-2008},
+ORCID-Numbers = {shokrgozar, mohammad ali/0000-0001-5123-4155
+ Marashi, Sayed-Amir/0000-0001-9801-7449},
+Times-Cited = {14},
+Journal-ISO = {Cell Prolif.},
+Unique-ID = {WOS:000357680600010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000360824500009,
+Author = {Hosseini, Sayed-Rzgar and Barve, Aditya and Wagner, Andreas},
+Title = {Exhaustive Analysis of a Genotype Space Comprising 1015
+ Central Carbon Metabolisms Reveals an Organization Conducive to
+ Metabolic Innovation},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2015},
+Volume = {11},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004329},
+Article-Number = {e1004329},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {COLI K-12 MG1655; MYCOBACTERIUM-TUBERCULOSIS; ADAPTIVE EVOLUTION;
+ GLUCOSE-METABOLISM; NETWORKS; RECONSTRUCTION; OPTIMIZATION;
+ CAPABILITIES; DEGRADATION; GLYCOLYSIS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Hosseini, Sayed-Rzgar/0000-0002-2308-6754},
+Times-Cited = {11},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000360824500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358278600021,
+Author = {Latif, Haythem and Sahin, Merve and Tarasova, Janna and Tarasova,
+ Yekaterina and Portnoy, Vasiliy A. and Nogales, Juan and Zengler,
+ Karsten},
+Title = {Adaptive Evolution of Thermotoga maritima Reveals Plasticity of
+ the ABC Transporter Network},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2015},
+Volume = {81},
+Number = {16},
+Pages = {5477-5485},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1128/AEM.01365-15},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords-Plus = {LABORATORY EVOLUTION; ESCHERICHIA-COLI; GENE-EXPRESSION; MALTOSE
+ TRANSPORT; MICROBIAL GENOMES; REP SEQUENCES; MESSENGER-RNA; BACTERIA;
+ PREDICTION; DATABASE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Sahin, Merve/U-7144-2017
+ Nogales, Juan/Y-8829-2019
+ },
+ORCID-Numbers = {Sahin, Merve/0000-0003-3858-8332
+ Nogales, Juan/0000-0002-4961-0833
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {9},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000358278600021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000369759200010,
+Author = {Marashi, Sayed-Amir and Hosseini, Zhaleh},
+Title = {On correlated reaction sets and coupled reaction sets in metabolic
+ networks},
+Journal = {JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY},
+Year = {2015},
+Volume = {13},
+Number = {4},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1142/S0219720015710031},
+Article-Number = {1571003},
+ISSN = {0219-7200},
+EISSN = {1757-6334},
+Keywords = {Co-sets; flux coupling analysis (FCA); Monte Carlo sampling; uniform
+ sampling; flux cone},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GENOME-SCALE; RECONSTRUCTION; BIOLOGY; STATES},
+Research-Areas = {Biochemistry \& Molecular Biology; Computer Science; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Computer Science, Interdisciplinary
+ Applications; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008
+ },
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Hosseini, Zhaleh/0000-0003-4724-0637},
+Times-Cited = {1},
+Journal-ISO = {J. Bioinform. Comput. Biol.},
+Unique-ID = {WOS:000369759200010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000361878400007,
+Author = {Salleh, Abdul Hakim Mohamed and Mohamad, Mohd Saberi and Deris, Safaai
+ and Omatu, Sigeru and Fdez-Riverola, Florentino and Manuel Corchado,
+ Juan},
+Title = {Gene knockout identification for metabolite production improvement using
+ a hybrid of genetic ant colony optimization and flux balance analysis},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2015},
+Volume = {20},
+Number = {4},
+Pages = {685-693},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1007/s12257-015-0276-9},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {gene knockout; metabolites production; flux balance analysis; genetic
+ ant colony optimization; hybrid algorithm},
+Keywords-Plus = {IN-SILICO MODELS; ESCHERICHIA-COLI; SUCCINIC ACID; EXPRESSION;
+ ALGORITHM; OXYGEN},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Corchado Rodríguez, Juan/D-3229-2013
+ Mohamad, Mohd Saberi/J-3201-2014
+ Fdez-Riverola, Florentino/G-1411-2011
+ SALLEH, ABDUL HAKIM/D-2869-2018},
+ORCID-Numbers = {Corchado Rodríguez, Juan/0000-0002-2829-1829
+ Mohamad, Mohd Saberi/0000-0002-1079-4559
+ Fdez-Riverola, Florentino/0000-0002-3943-8013
+ SALLEH, ABDUL HAKIM/0000-0003-1332-6176},
+Times-Cited = {9},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:000361878400007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358781100034,
+Author = {Krumholz, Elias W. and Libourel, Igor G. L.},
+Title = {Sequence-based Network Completion Reveals the Integrality of Missing
+ Reactions in Metabolic Networks},
+Journal = {JOURNAL OF BIOLOGICAL CHEMISTRY},
+Year = {2015},
+Volume = {290},
+Number = {31},
+Pages = {19197-19207},
+Month = {JUL 31},
+Type = {Article},
+DOI = {10.1074/jbc.M114.634121},
+ISSN = {0021-9258},
+EISSN = {1083-351X},
+Keywords-Plus = {ESCHERICHIA-COLI; ESSENTIAL GENES; RAST SERVER; RECONSTRUCTION; MODEL;
+ PHENOTYPE; OPTIMIZATION; GENERATION; ENZYMES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Libourel, Igor/0000-0001-9408-3270},
+Times-Cited = {11},
+Journal-ISO = {J. Biol. Chem.},
+Unique-ID = {WOS:000358781100034},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358173500012,
+Author = {Zhang, Cheng and Ji, Boyang and Mardinoglu, Adil and Nielsen, Jens and
+ Hua, Qiang},
+Title = {Logical transformation of genome-scale metabolic models for gene level
+ applications and analysis},
+Journal = {BIOINFORMATICS},
+Year = {2015},
+Volume = {31},
+Number = {14},
+Pages = {2324-2331},
+Month = {JUL 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btv134},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; SYNTHETIC LETHALITY; MICROBIAL
+ STRAINS; YEAST METABOLISM; CANCER; OPTIMIZATION; IDENTIFICATION;
+ CONSTRAINT; NETWORKS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Mardinoglu, Adil/AAS-6360-2021
+ Ji, Boyang/HMV-6662-2023
+ Zhang, Cheng/L-7906-2016
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Ji, Boyang/0000-0002-7269-4342
+ Zhang, Cheng/0000-0002-3721-8586
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {30},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000358173500012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000357738900004,
+Author = {Gutierrez, Jahir M. and Lewis, Nathan E.},
+Title = {Optimizing eukaryotic cell hosts for protein production through systems
+ biotechnology and genome-scale modeling},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2015},
+Volume = {10},
+Number = {7, SI},
+Pages = {939-949},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1002/biot.201400647},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Eukaryotic cell engineering; Genome-scale models; Metabolic networks;
+ Recombinant protein production; Systems Biology},
+Keywords-Plus = {METABOLIC FLUX ANALYSIS; CONSTRAINT-BASED MODELS; YEAST PICHIA-PASTORIS;
+ IN-SILICO ANALYSIS; FED-BATCH CULTURE; CHINESE-HAMSTER; CHO-CELLS;
+ LACTATE CONSUMPTION; ESCHERICHIA-COLI; HYBRIDOMA CELLS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020},
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654},
+Times-Cited = {38},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000357738900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000360620100029,
+Author = {Hamilton, Joshua J. and Contreras, Montserrat Calixto and Reed, Jennifer
+ L.},
+Title = {Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic
+ Community},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2015},
+Volume = {11},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1004364},
+Article-Number = {e1004364},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {SYNTROPHOBACTER-FUMAROXIDANS; ELECTRON-TRANSFER; IN-SILICO; METABOLIC
+ INTERACTIONS; PROPIONATE OXIDATION; FORMATE; BUTYRATE; BACTERIA; GROWTH;
+ DEHYDROGENASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Reed, Jennifer L/E-5137-2011
+ },
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220
+ Hamilton, Joshua/0000-0001-9790-3609},
+Times-Cited = {20},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000360620100029},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000355948400004,
+Author = {Heinken, Almut and Thiele, Ines},
+Title = {Systems biology of host-microbe metabolomics},
+Journal = {WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE},
+Year = {2015},
+Volume = {7},
+Number = {4},
+Pages = {195-219},
+Month = {JUL-AUG},
+Type = {Review},
+DOI = {10.1002/wsbm.1301},
+ISSN = {1939-5094},
+EISSN = {1939-005X},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; P-CRESYL SULFATE; GUT MICROBIOTA;
+ FAECALIBACTERIUM-PRAUSNITZII; BACTERIAL METABOLITES; GLOBAL
+ RECONSTRUCTION; SCALE RECONSTRUCTION; CELLULAR-METABOLISM;
+ MASS-SPECTROMETRY; ANALYSIS REVEALS},
+Research-Areas = {Research \& Experimental Medicine},
+Web-of-Science-Categories = {Medicine, Research \& Experimental},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Heinken, Almut/0000-0001-6938-8072},
+Times-Cited = {63},
+Journal-ISO = {Wiley Interdiscip. Rev.-Syst. Biol},
+Unique-ID = {WOS:000355948400004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358707200001,
+Author = {Currie, Devin H. and Raman, Babu and Gowen, Christopher M. and
+ Tschaplinski, Timothy J. and Land, Miriam L. and Brown, Steven D. and
+ Covalla, Sean F. and Klingeman, Dawn M. and Yang, Zamin K. and Engle,
+ Nancy L. and Johnson, Courtney M. and Rodriguez, Miguel and Shaw, A. Joe
+ and Kenealy, William R. and Lynd, Lee R. and Fong, Stephen S. and
+ Mielenz, Jonathan R. and Davison, Brian H. and Hogsett, David A. and
+ Herring, Christopher D.},
+Title = {Genome-scale resources for Thermoanaerobacterium saccharolyticum},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {9},
+Month = {JUN 26},
+Type = {Article},
+DOI = {10.1186/s12918-015-0159-x},
+Article-Number = {30},
+ISSN = {1752-0509},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; CLOSTRIDIUM-THERMOCELLUM;
+ BIOCHEMICAL-CHARACTERIZATION; QUANTITATIVE PREDICTION; THERMOPHILIC
+ ANAEROBES; CELLULAR-METABOLISM; ETHANOL-PRODUCTION; GENE; STRATEGIES;
+ SEQUENCE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Klingeman, Dawn M/B-9415-2012
+ Davison, Brian h/D-7617-2013
+ Tschaplinski, Timothy J/D-6382-2018
+ Brown, Steven D/A-6792-2011
+ Lynd, Lee R/N-1260-2013
+ Land, Miriam L/A-6200-2011
+ Engle, Nancy L/D-6494-2018},
+ORCID-Numbers = {Klingeman, Dawn M/0000-0002-4307-2560
+ Davison, Brian h/0000-0002-7408-3609
+ Tschaplinski, Timothy J/0000-0002-9540-6622
+ Brown, Steven D/0000-0002-9281-3898
+ Lynd, Lee R/0000-0002-5642-668X
+ Land, Miriam L/0000-0001-7102-0031
+ Engle, Nancy L/0000-0003-0290-7987},
+Times-Cited = {14},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000358707200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000357212700001,
+Author = {Wang, Yali and Xu, Nan and Ye, Chao and Liu, Liming and Shi, Zhongping
+ and Wu, Jing},
+Title = {Reconstruction and in silico analysis of an Actinoplanes
+ sp SE50/110 genome-scale metabolic model for acarbose production},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2015},
+Volume = {6},
+Month = {JUN 25},
+Type = {Article},
+DOI = {10.3389/fmicb.2015.00632},
+Article-Number = {632},
+ISSN = {1664-302X},
+Keywords = {Actinoplanes sp SE50/110; genome-scale metabolic model; acarbose
+ production; amino acids; oxygen uptake rate},
+Keywords-Plus = {GLUCOSIDASE INHIBITOR ACARBOSE; FED-BATCH FERMENTATION; COMPONENT-C; SP
+ A56; SP SE-50/110; BIOSYNTHESIS; PROTEIN; IDENTIFICATION; OSMOLALITY;
+ TREHALOSE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Ye, Chao/M-3689-2019
+ Liu, Liming/B-1972-2009
+ Ye, Chao/H-7623-2014
+ Wu, Jing/GZK-5063-2022
+ Shi, Zhongping/K-9884-2019
+ Ye, Chao/HGD-3564-2022
+ },
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Liu, Liming/0000-0003-3022-936X
+ Ye, Chao/0000-0002-6671-7819
+ Ye, Chao/0000-0002-6671-7819
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {5},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000357212700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000353008000001,
+Author = {Irani, Zahra Azimzadeh and Maghsoudi, Amir and Shojaosadati, Seyed Abbas
+ and Motamedian, Ehsan},
+Title = {Development and in silico analysis of a new nitrogen-limited
+ feeding strategy for fed-batch cultures of Pichia pastoris based
+ on a simple pH-control system},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2015},
+Volume = {98},
+Pages = {1-9},
+Month = {JUN 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2015.02.016},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Control; Fed-batch culture; Fermentation; Protein; Nitrogen-limitation;
+ Metabolic model},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; PROTEIN-PRODUCTION; METABOLIC RECONSTRUCTION;
+ FLUX ANALYSIS; METHANOL; GROWTH; YEAST; FERMENTATION; STRAIN; MODEL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Maghsoudi, Amir/E-8711-2010
+ Shojaosadati, Seyed Abbas/A-7565-2010
+ Shojaosadati, Seyed Abbas/ABE-1178-2021
+ Motamedian, Ehsan/GPK-8344-2022
+ irani, zahra azimzadeh/G-7900-2017
+ },
+ORCID-Numbers = {Maghsoudi, Amir/0000-0002-8094-4620
+ Shojaosadati, Seyed Abbas/0000-0002-8561-2414
+ , Ehsan/0000-0001-8750-2879},
+Times-Cited = {13},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000353008000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000356090900001,
+Author = {Chen, Haiqin and Hao, Guangfei and Wang, Lei and Wang, Hongchao and Gu,
+ Zhennan and Liu, Liming and Zhang, Hao and Chen, Wei and Chen, Yong Q.},
+Title = {Identification of a critical determinant that enables efficient fatty
+ acid synthesis in oleaginous fungi},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2015},
+Volume = {5},
+Month = {JUN 10},
+Type = {Article},
+DOI = {10.1038/srep11247},
+Article-Number = {11247},
+ISSN = {2045-2322},
+Keywords-Plus = {MALIC ENZYME; LIPID-ACCUMULATION; OVER-EXPRESSION; MICROORGANISMS;
+ METABOLISM; YEASTS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Wang, Lei/C-5176-2009
+ Liu, Liming/B-1972-2009
+ Chen, Yong Q/AAI-9864-2021},
+ORCID-Numbers = {Wang, Lei/0000-0003-4427-0881
+ Liu, Liming/0000-0003-3022-936X
+ Chen, Yong Q/0000-0003-4747-4708},
+Times-Cited = {74},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000356090900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000354137100009,
+Author = {Aurich, Maike K. and Paglia, Giuseppe and Rolfsson, Ottar and
+ Hrafnsdottir, Sigrun and Magnusdottir, Manuela and Stefaniak, Magdalena
+ M. and Palsson, Bernhard O. and Fleming, Ronan M. T. and Thiele, Ines},
+Title = {Prediction of intracellular metabolic states from extracellular
+ metabolomic data},
+Journal = {METABOLOMICS},
+Year = {2015},
+Volume = {11},
+Number = {3},
+Pages = {603-619},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1007/s11306-014-0721-3},
+ISSN = {1573-3882},
+EISSN = {1573-3890},
+Keywords = {Constraint-based modeling; Metabolomics; Multi-omics; Metabolic network;
+ Transcriptomics},
+Keywords-Plus = {PERFORMANCE LIQUID-CHROMATOGRAPHY; GENOME-SCALE MODELS; GLOBAL
+ RECONSTRUCTION; CELLULAR-METABOLISM; ENERGY-METABOLISM; FREE-RADICALS;
+ DRUG TARGETS; CANCER; CELLS; NETWORK},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ Paglia, Giuseppe/H-2012-2018
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Paglia, Giuseppe/0000-0003-4724-6801
+ Palsson, Bernhard/0000-0003-2357-6785
+ Rolfsson, Ottar/0000-0003-4258-6057},
+Times-Cited = {48},
+Journal-ISO = {Metabolomics},
+Unique-ID = {WOS:000354137100009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000354498900002,
+Author = {Brandl, Julian and Andersen, Mikael R.},
+Title = {Current state of genome-scale modeling in filamentous fungi},
+Journal = {BIOTECHNOLOGY LETTERS},
+Year = {2015},
+Volume = {37},
+Number = {6},
+Pages = {1131-1139},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1007/s10529-015-1782-8},
+ISSN = {0141-5492},
+EISSN = {1573-6776},
+Keywords = {Filamentous fungi; Genome-scale models; Metabolic engineering;
+ Metabolism; Systems biology},
+Keywords-Plus = {ASPERGILLUS-NIDULANS; GENE-EXPRESSION; METABOLISM; RECONSTRUCTION;
+ NIGER; INFORMATION; INTEGRATION; ANNOTATION; SEQUENCE; PATHWAY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Andersen, Mikael Rørdam/P-6743-2019
+ Andersen, Mikael R/F-9377-2013
+ },
+ORCID-Numbers = {Andersen, Mikael Rørdam/0000-0003-4794-6808
+ Andersen, Mikael R/0000-0003-4794-6808
+ Brandl, Julian/0000-0002-3479-8642},
+Times-Cited = {21},
+Journal-ISO = {Biotechnol. Lett.},
+Unique-ID = {WOS:000354498900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000353981400019,
+Author = {Damiani, Andrew L. and He, Q. Peter and Jeffries, Thomas W. and Wang,
+ Jin},
+Title = {Comprehensive Evaluation of Two Genome-Scale Metabolic Network Models
+ for Scheffersomyces Stipitis},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2015},
+Volume = {112},
+Number = {6},
+Pages = {1250-1262},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/bit.25535},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Scheffersomyces stipitis; metabolic network models; genome-scale; flux
+ balance analysis; system identification; principal component analysis},
+Keywords-Plus = {YEAST PICHIA-STIPITIS; PHASE PLANE ANALYSIS; SACCHAROMYCES-CEREVISIAE;
+ XYLOSE FERMENTATION; ETHANOL-PRODUCTION; PHENOTYPE; RECONSTRUCTION;
+ RESPIRATION; CULTURES; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Jeffries, Thomas William/AAH-7675-2021
+ },
+ORCID-Numbers = {Jeffries, Thomas William/0000-0001-7408-4065
+ Wang, Jin/0000-0002-7638-8537
+ He, Qinghua/0000-0002-2474-5950},
+Times-Cited = {15},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000353981400019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000355714900002,
+Author = {Hala, David and Petersen, Lene H. and Martinovic, Dalma and Huggett,
+ Duane B.},
+Title = {In Silico analysis of perturbed steroidogenesis and gonad growth
+ in fathead minnows (P. promelas) exposed to
+ 17α-ethynylestradiol},
+Journal = {SYSTEMS BIOLOGY IN REPRODUCTIVE MEDICINE},
+Year = {2015},
+Volume = {61},
+Number = {3},
+Pages = {122-138},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3109/19396368.2015.1035817},
+ISSN = {1939-6368},
+EISSN = {1939-6376},
+Keywords = {17 alpha-ethynylestradiol; fathead minnows; flux balance analysis; gonad
+ growth; steroid hormones},
+Keywords-Plus = {ADVERSE OUTCOME PATHWAYS; ENDOCRINE DISRUPTING CHEMICALS; RELATIVE
+ BINDING AFFINITIES; CONSTRAINT-BASED MODELS; GENE-EXPRESSION;
+ ESCHERICHIA-COLI; HORMONE NEURONS; RAINBOW-TROUT;
+ REPRODUCTIVE-PERFORMANCE; QUANTITATIVE PREDICTION},
+Research-Areas = {Endocrinology \& Metabolism; Reproductive Biology},
+Web-of-Science-Categories = {Andrology; Reproductive Biology},
+ORCID-Numbers = {Martinovic-Weigelt, Dalma/0000-0002-9973-4965},
+Times-Cited = {3},
+Journal-ISO = {Syst. Biol. Reprod. Med.},
+Unique-ID = {WOS:000355714900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000354864000015,
+Author = {Heinken, Almut and Thiele, Ines},
+Title = {Anoxic Conditions Promote Species-Specific Mutualism between Gut
+ Microbes In Silico},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2015},
+Volume = {81},
+Number = {12},
+Pages = {4049-4061},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1128/AEM.00101-15},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords-Plus = {METABOLIC INTERACTIONS; LACTOCOCCUS-LACTIS; COMMUNITY; MODEL; OXYGEN;
+ DIET; RECONSTRUCTION; FERMENTATION; PREDICTION; BACTERIA},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Heinken, Almut/0000-0001-6938-8072},
+Times-Cited = {71},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000354864000015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000360113800005,
+Author = {Montagud, Arnau and Gamermann, Daniel and Fernandez de Cordoba, Pedro
+ and Urchueguia, Javier F.},
+Title = {Synechocystis sp PCC6803 metabolic models for the enhanced
+ production of hydrogen},
+Journal = {CRITICAL REVIEWS IN BIOTECHNOLOGY},
+Year = {2015},
+Volume = {35},
+Number = {2},
+Pages = {184-198},
+Month = {JUN},
+Type = {Review},
+DOI = {10.3109/07388551.2013.829799},
+ISSN = {0738-8551},
+EISSN = {1549-7801},
+Keywords = {Cyanobacteria; hydrogen; metabolic engineering; photon-fuelled
+ production; production strategies; systems biology},
+Keywords-Plus = {SP STRAIN PCC-6803; DNA MICROARRAY ANALYSIS; FLUX BALANCE MODELS;
+ ESCHERICHIA-COLI; GENE-EXPRESSION; CHLAMYDOMONAS-REINHARDTII;
+ MULTIORGANISM DATABASE; FEFE-HYDROGENASES; H-2 PRODUCTION; GENOME},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Montagud, Arnau/B-8001-2008
+ Gamermann, Daniel/K-7387-2013
+ Urchueguia, Javier F./AAD-7469-2021
+ de Cordoba, Pedro Fernandez/L-2645-2015
+ },
+ORCID-Numbers = {Montagud, Arnau/0000-0002-7696-1241
+ de Cordoba, Pedro Fernandez/0000-0002-0347-7280
+ Gamermann, Daniel/0000-0002-3492-264X},
+Times-Cited = {5},
+Journal-ISO = {Crit. Rev. Biotechnol.},
+Unique-ID = {WOS:000360113800005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000354889100005,
+Author = {Rolfsson, Ottar and Palsson, Bernhard O.},
+Title = {Decoding the jargon of bottom-up metabolic systems biology},
+Journal = {BIOESSAYS},
+Year = {2015},
+Volume = {37},
+Number = {6},
+Pages = {588-591},
+Month = {JUN},
+Type = {Editorial Material},
+DOI = {10.1002/bies.201400187},
+ISSN = {0265-9247},
+EISSN = {1521-1878},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; NETWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Life Sciences \& Biomedicine - Other
+ Topics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biology},
+ORCID-Numbers = {Rolfsson, Ottar/0000-0003-4258-6057
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {7},
+Journal-ISO = {Bioessays},
+Unique-ID = {WOS:000354889100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000357164700001,
+Author = {Zielinski, Daniel C. and Filipp, Fabian V. and Bordbar, Aarash and
+ Jensen, Kasper and Smith, Jeffrey W. and Herrgard, Markus J. and Mo,
+ Monica L. and Palsson, Bernhard O.},
+Title = {Pharmacogenomic and clinical data link non-pharmacokinetic metabolic
+ dysregulation to drug side effect pathogenesis},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2015},
+Volume = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1038/ncomms8101},
+Article-Number = {7101},
+ISSN = {2041-1723},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; NITRIC-OXIDE; GLOBAL RECONSTRUCTION;
+ FOLIC-ACID; GENE; EXPRESSION; NETWORK; IDENTIFICATION; PREDICTION;
+ TRANSPORT},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {/AAG-5264-2021
+ Filipp, Fabian Volker/X-5425-2018
+ },
+ORCID-Numbers = {/0000-0001-6460-6771
+ Filipp, Fabian Volker/0000-0001-9889-5727
+ Zielinski, Daniel/0000-0001-6452-483X
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {30},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000357164700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000356234900001,
+Author = {Gold, Nicholas D. and Gowen, Christopher M. and Lussier, Francois-Xavier
+ and Cautha, Sarat C. and Mahadevan, Radhakrishnan and Martin, Vincent J.
+ J.},
+Title = {Metabolic engineering of a tyrosine-overproducing yeast platform using
+ targeted metabolomics},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2015},
+Volume = {14},
+Month = {MAY 28},
+Type = {Article},
+DOI = {10.1186/s12934-015-0252-2},
+Article-Number = {73},
+ISSN = {1475-2859},
+Keywords = {L-tyrosine; Saccharomyces cerevisiae; Metabolic engineering; Targeted
+ metabolomics; Glucose-6-phosphate dehydrogenase; Pyruvate kinase;
+ Prephenate dehydrogenase; Cyclohexadienyl dehydrogenase; Phenylpyruvate
+ decarboxylase; Aromatic amino acids},
+Keywords-Plus = {AMINO-ACID BIOSYNTHESIS; SACCHAROMYCES-CEREVISIAE; PYRUVATE
+ DECARBOXYLASE; STRUCTURAL GENE; IDENTIFICATION; EXPRESSION; PATHWAY;
+ DEHYDROGENASE; RESVERATROL; ISOENZYMES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Mahadevan, Radhakrishnan/A-8502-2008},
+ORCID-Numbers = {Mahadevan, Radhakrishnan/0000-0002-1270-9063},
+Times-Cited = {91},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000356234900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000355235700003,
+Author = {Bayer, Thomas and Milker, Sofia and Wiesinger, Thomas and Rudroff,
+ Florian and Mihovilovic, Marko. D.},
+Title = {Designer Microorganisms for Optimized Redox Cascade Reactions -
+ Challenges and Future Perspectives},
+Journal = {ADVANCED SYNTHESIS \& CATALYSIS},
+Year = {2015},
+Volume = {357},
+Number = {8, SI},
+Pages = {1587-1618},
+Month = {MAY 26},
+Type = {Review},
+DOI = {10.1002/adsc.201500202},
+ISSN = {1615-4150},
+EISSN = {1615-4169},
+Keywords = {biotransformations; knock-in/knock-out; metabolic engineering; redox
+ biocatalysis; synthetic biology},
+Keywords-Plus = {ESCHERICHIA-COLI STRAINS; METABOLIC FLUX ANALYSIS; RECOMBINANT PROTEIN
+ EXPRESSION; LIGATION-INDEPENDENT CLONING; SYNTHETIC BIOLOGY PLATFORM;
+ MESSENGER-RNA SEQUENCES; RIBOSOME BINDING-SITES; ONE-STEP INACTIVATION;
+ GROUP-II INTRONS; SACCHAROMYCES-CEREVISIAE},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Applied; Chemistry, Organic},
+ORCID-Numbers = {Bayer, Thomas/0000-0002-0656-3280
+ Mihovilovic, Marko D./0000-0002-5438-8368
+ Rudroff, Florian/0000-0002-6680-8200},
+Times-Cited = {46},
+Journal-ISO = {Adv. Synth. Catal.},
+Unique-ID = {WOS:000355235700003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000355152600007,
+Author = {O'Brien, Edward J. and Monk, Jonathan M. and Palsson, Bernhard O.},
+Title = {Using Genome-scale Models to Predict Biological Capabilities},
+Journal = {CELL},
+Year = {2015},
+Volume = {161},
+Number = {5},
+Pages = {971-987},
+Month = {MAY 21},
+Type = {Article},
+DOI = {10.1016/j.cell.2015.05.019},
+ISSN = {0092-8674},
+EISSN = {1097-4172},
+Keywords-Plus = {ALTERNATE OPTIMAL-SOLUTIONS; CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI;
+ METABOLIC NETWORK; GLOBAL RECONSTRUCTION; CELLULAR-METABOLISM; ADAPTIVE
+ EVOLUTION; HIGH-THROUGHPUT; EXPRESSION; PHENOTYPE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785
+ Monk, Jonathan M./0000-0002-3895-8949},
+Times-Cited = {428},
+Journal-ISO = {Cell},
+Unique-ID = {WOS:000355152600007},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000354123900003,
+Author = {Adolfsen, Kristin J. and Brynildsen, Mark P.},
+Title = {Futile cycling increases sensitivity toward oxidative stress in
+ Escherichia coli},
+Journal = {METABOLIC ENGINEERING},
+Year = {2015},
+Volume = {29},
+Pages = {26-35},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2015.02.006},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Reactive oxygen species; Oxidative stress; Futile cycle; Hydrogen
+ peroxide; Metabolism},
+Keywords-Plus = {ALKYL HYDROPEROXIDE REDUCTASE; NEUTROPHIL NADPH OXIDASE; ENDOGENOUS
+ HYDROGEN-PEROXIDE; SITE-DIRECTED MUTAGENESIS; SUPEROXIDE-DISMUTASE;
+ MYCOBACTERIUM-TUBERCULOSIS; CATALASE KATA; REPAIR; DNA; METABOLISM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {49},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000354123900003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000353672000001,
+Author = {Tan, Justin and Zuniga, Cristal and Zengler, Karsten},
+Title = {Unraveling interactions in microbial communities - from co-cultures to
+ microbiomes},
+Journal = {JOURNAL OF MICROBIOLOGY},
+Year = {2015},
+Volume = {53},
+Number = {5},
+Pages = {295-305},
+Month = {MAY},
+Type = {Review},
+DOI = {10.1007/s12275-015-5060-1},
+ISSN = {1225-8873},
+EISSN = {1976-3794},
+Keywords = {synthetic communities; system biology; co-cultures; metabolic models},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS; HUMAN GUT MICROBES;
+ GENE-EXPRESSION; CONSORTIA; COOPERATION; METABOLISM; PREDICTION; CELL;
+ COMPETITION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Zuniga, Cristal/CAA-0015-2022
+ },
+ORCID-Numbers = {Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {45},
+Journal-ISO = {J. Microbiol.},
+Unique-ID = {WOS:000353672000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000352477800156,
+Author = {De Martino, Daniele and Mori, Matteo and Parisi, Valerio},
+Title = {Uniform Sampling of Steady States in Metabolic Networks: Heterogeneous
+ Scales and Rounding},
+Journal = {PLOS ONE},
+Year = {2015},
+Volume = {10},
+Number = {4},
+Month = {APR 7},
+Type = {Article},
+DOI = {10.1371/journal.pone.0122670},
+Article-Number = {e0122670},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; RECONSTRUCTION; MODELS; SPACES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {de martino, daniele/L-6519-2017
+ Mori, Matteo/Q-6717-2018
+ De Martino, Daniele/GQA-9589-2022
+ Parisi, Valerio/B-1492-2008
+ },
+ORCID-Numbers = {Mori, Matteo/0000-0002-6263-8021
+ De Martino, Daniele/0000-0002-5214-4706},
+Times-Cited = {33},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000352477800156},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000353951800004,
+Author = {Ferrer Valenzuela, Javier and Andres Pinuer, Luis and Garcia Cancino,
+ Apolinaria and Borquez Yanez, Rodrigo},
+Title = {Metabolic Fluxes in Lactic Acid Bacteria-A Review},
+Journal = {FOOD BIOTECHNOLOGY},
+Year = {2015},
+Volume = {29},
+Number = {2},
+Pages = {185-217},
+Month = {APR 3},
+Type = {Review},
+DOI = {10.1080/08905436.2015.1027913},
+ISSN = {0890-5436},
+EISSN = {1532-4249},
+Keywords = {food quality biotechnology; fermentation; food ingredient biotechnology;
+ metabolic food biotechnology; lactic acid bacteria},
+Keywords-Plus = {IN-SILICO ANALYSIS; LACTOCOCCUS-LACTIS; LACTOBACILLUS-PLANTARUM;
+ HYDROGEN-PRODUCTION; GENE-EXPRESSION; SUBSP LACTIS;
+ LACTATE-DEHYDROGENASE; MANNITOL PRODUCTION; NETWORK; MODEL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {borquez, rodrigo/R-9639-2017
+ },
+ORCID-Numbers = {borquez, rodrigo/0000-0003-3601-5557
+ Garcia, Apolinaria/0000-0003-3909-9733},
+Times-Cited = {9},
+Journal-ISO = {Food Biotechnol.},
+Unique-ID = {WOS:000353951800004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000352740400027,
+Author = {Fontanarosa, Gabriele and Menichetti, Giulia and Giampieri, Enrico and
+ Castellani, Gastone and Martinelli, Giovanni and Remondini, Daniel},
+Title = {NETWORK APPROACHES FOR ANALYSIS AND MODELING OF THE HUMAN METABOLISM},
+Journal = {JOURNAL OF MECHANICS IN MEDICINE AND BIOLOGY},
+Year = {2015},
+Volume = {15},
+Number = {2, SI},
+Month = {APR},
+Note = {19th International Conference on Mechanics in Medicine and Biology,
+ Bologna, ITALY, SEP 03-05, 2014},
+Type = {Article; Proceedings Paper},
+DOI = {10.1142/S0219519415400266},
+Article-Number = {1540026},
+ISSN = {0219-5194},
+EISSN = {1793-6810},
+Keywords = {Metabolic network; pathway analysis; graph visualization; Markov models},
+Keywords-Plus = {GLOBAL RECONSTRUCTION},
+Research-Areas = {Biophysics; Engineering},
+Web-of-Science-Categories = {Biophysics; Engineering, Biomedical},
+ResearcherID-Numbers = {Remondini, Daniel/ABA-9971-2020
+ Castellani, Gastone c/L-3333-2017
+ Giampieri, Enrico/AAC-7354-2022
+ Martinelli, Giovanni/AAK-9211-2020
+ },
+ORCID-Numbers = {Castellani, Gastone c/0000-0003-4892-925X
+ Giampieri, Enrico/0000-0003-2269-2338
+ Martinelli, Giovanni/0000-0002-1025-4210
+ Menichetti, Giulia/0000-0001-5201-6774
+ Remondini, Daniel/0000-0003-3185-7456},
+Times-Cited = {0},
+Journal-ISO = {J. Mech. Med. Biol.},
+Unique-ID = {WOS:000352740400027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000369755400006,
+Author = {Loira, Nicolas and Zhukova, Anna and Sherman, David James},
+Title = {Pantograph: A template-based method for genome-scale metabolic model
+ reconstruction},
+Journal = {JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY},
+Year = {2015},
+Volume = {13},
+Number = {2},
+Month = {APR},
+Type = {Article},
+DOI = {10.1142/S0219720015500067},
+Article-Number = {1550006},
+ISSN = {0219-7200},
+EISSN = {1757-6334},
+Keywords = {Metabolic modeling; genome-scale reconstruction; model validation},
+Keywords-Plus = {NETWORK RECONSTRUCTION; SBML; ANNOTATION; GENES; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology; Computer Science; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Computer Science, Interdisciplinary
+ Applications; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zhukova, Anna/AET-0798-2022
+ },
+ORCID-Numbers = {Zhukova, Anna/0000-0003-2200-7935
+ Sherman, David James/0000-0002-2316-1005},
+Times-Cited = {19},
+Journal-ISO = {J. Bioinform. Comput. Biol.},
+Unique-ID = {WOS:000369755400006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000351880000012,
+Author = {Gavai, Anand K. and Supandi, Farahaniza and Hettling, Hannes and
+ Murrell, Paul and Leunissen, Jack A. M. and van Beek, Johannes H. G. M.},
+Title = {Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on
+ Gene Expression Changes in Brain},
+Journal = {PLOS ONE},
+Year = {2015},
+Volume = {10},
+Number = {3},
+Month = {MAR 25},
+Type = {Article},
+DOI = {10.1371/journal.pone.0119016},
+Article-Number = {e0119016},
+ISSN = {1932-6203},
+Keywords-Plus = {ALZHEIMERS-DISEASE; ENERGY-METABOLISM; GLUCOSE; BIOLOGY; OXYGEN},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Supandi, Farahaniza/B-8486-2010
+ /GOP-0313-2022},
+ORCID-Numbers = {Supandi, Farahaniza/0000-0001-5671-5986
+ /0000-0002-4738-190X},
+Times-Cited = {16},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000351880000012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000352433000002,
+Author = {Shi, Chao and Yin, Jian and Liu, Zhe and Wu, Jian-Xin and Zhao, Qi and
+ Ren, Jian and Yao, Nan},
+Title = {A systematic simulation of the effect of salicylic acid on sphingolipid
+ metabolism},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2015},
+Volume = {6},
+Month = {MAR 25},
+Type = {Article},
+DOI = {10.3389/fpls.2015.00186},
+Article-Number = {186},
+ISSN = {1664-462X},
+Keywords = {ceramides; salicylic acid; sphingolipid},
+Keywords-Plus = {PROGRAMMED CELL-DEATH; FLUX ANALYSIS; ACQUIRED-RESISTANCE; ARABIDOPSIS
+ MUTANTS; DISEASE RESISTANCE; DEFENSE; NETWORK; PATHWAY; RECONSTRUCTION;
+ TOOLBOX},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Ren, Jian/D-3270-2011
+ Zhao, Qi/M-4830-2016
+ Yao, Nan/H-2423-2011
+ Zhao, Qi/X-7899-2019},
+ORCID-Numbers = {Ren, Jian/0000-0002-4161-1292
+ Zhao, Qi/0000-0002-8683-6145
+ Yao, Nan/0000-0002-4081-1495
+ Zhao, Qi/0000-0002-8683-6145},
+Times-Cited = {16},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000352433000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000595396600001,
+Author = {Stanford, Natalie J. and Millard, Pierre and Swainston, Neil},
+Title = {RobOKoD: microbial strain design for (over)production of target
+ compounds},
+Journal = {FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY},
+Year = {2015},
+Volume = {3},
+Month = {MAR 24},
+Type = {Article},
+DOI = {10.3389/fcell.2015.00017},
+Article-Number = {17},
+ISSN = {2296-634X},
+Keywords = {synthetic biology; systems biology; metabolic engineering; strain
+ design; constraint-based modeling},
+Research-Areas = {Cell Biology; Developmental Biology},
+Web-of-Science-Categories = {Cell Biology; Developmental Biology},
+ORCID-Numbers = {Millard, Pierre/0000-0002-8136-9963
+ Stanford, Natalie J/0000-0003-4958-0184},
+Times-Cited = {13},
+Journal-ISO = {Front. Cell. Dev. Biol.},
+Unique-ID = {WOS:000595396600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000351986300001,
+Author = {Cole, John A. and Kohler, Lars and Hedhli, Jamila and Luthey-Schulten,
+ Zaida},
+Title = {Spatially-resolved metabolic cooperativity within dense bacterial
+ colonies},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {9},
+Month = {MAR 18},
+Type = {Article},
+DOI = {10.1186/s12918-015-0155-1},
+Article-Number = {15},
+EISSN = {1752-0509},
+Keywords = {Flux balance analysis; Reaction-diffusion modeling; Metabolic
+ cooperativity; Crossfeeding; Colony modeling},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; GROWTH; DIFFUSION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Luthey-Schulten, Zaida/0000-0001-9749-8367},
+Times-Cited = {65},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000351986300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000352420800001,
+Author = {Hillje, Anna-Lena and Beckmann, Elisabeth and Pavlou, Maria A. S. and
+ Jaeger, Christian and Pacheco, Maria P. and Sauter, Thomas and
+ Schwamborn, Jens C. and Lewejohann, Lars},
+Title = {The neural stem cell fate determinant TRIM32 regulates complex
+ behavioral traits},
+Journal = {FRONTIERS IN CELLULAR NEUROSCIENCE},
+Year = {2015},
+Volume = {9},
+Month = {MAR 18},
+Type = {Article},
+DOI = {10.3389/fncel.2015.00075},
+Article-Number = {75},
+EISSN = {1662-5102},
+Keywords = {adult neurogenesis; cell fate determinant; neural stem cells; olfactory
+ behavior; brain metabolism},
+Keywords-Plus = {ADULT OLFACTORY-BULB; E3 UBIQUITIN LIGASE; DYSTROPHY TYPE 2H; NEWBORN
+ NEURONS; SELF-RENEWAL; MOUSE MODEL; NEUROGENESIS; INHIBITION; ANXIETY;
+ BRAIN},
+Research-Areas = {Neurosciences \& Neurology},
+Web-of-Science-Categories = {Neurosciences},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ Lewejohann, Lars/H-3717-2013
+ Schwamborn, Jens C/F-9395-2011
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Lewejohann, Lars/0000-0002-0202-4351
+ Schwamborn, Jens C/0000-0003-4496-0559
+ PAVLOU, Maria Angeliki/0000-0002-4753-163X
+ Sauter, Thomas/0000-0001-8225-2954},
+Times-Cited = {16},
+Journal-ISO = {Front. Cell. Neurosci.},
+Unique-ID = {WOS:000352420800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000351972500032,
+Author = {Folch-Fortuny, A. and Tortajada, M. and Prats-Montalban, J. M. and
+ Llaneras, F. and Pico, J. and Ferrer, A.},
+Title = {MCR-ALS on metabolic networks: Obtaining more meaningful pathways},
+Journal = {CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS},
+Year = {2015},
+Volume = {142},
+Pages = {293-303},
+Month = {MAR 15},
+Note = {3rd European Conference on Process Analytics and Control Technology,
+ Barcelona, SPAIN, MAY 06-09, 2014},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.chemolab.2014.10.004},
+ISSN = {0169-7439},
+EISSN = {1873-3239},
+Keywords = {Pichia pastoris; Metabolic network; Grey modelling; Multivariate Curve
+ Resolution-Alternating; Least Squares},
+Keywords-Plus = {MULTIVARIATE CURVE RESOLUTION; PRINCIPAL COMPONENT ANALYSIS; RECOMBINANT
+ PICHIA-PASTORIS; CONSTRAINT-BASED MODELS; GENE-EXPRESSION DATA;
+ CONTINUOUS-CULTURE; ESCHERICHIA-COLI; HIGH-THROUGHPUT; CELL-DENSITY;
+ BALANCE},
+Research-Areas = {Automation \& Control Systems; Chemistry; Computer Science; Instruments
+ \& Instrumentation; Mathematics},
+Web-of-Science-Categories = {Automation \& Control Systems; Chemistry, Analytical; Computer Science,
+ Artificial Intelligence; Instruments \& Instrumentation; Mathematics,
+ Interdisciplinary Applications; Statistics \& Probability},
+ResearcherID-Numbers = {Picó, Jesús/A-5347-2011
+ Llaneras, Francisco/B-8133-2008
+ Ferrer, Alberto/AAA-9418-2020
+ Prats-Montalban, Jose Manuel/H-5951-2015
+ },
+ORCID-Numbers = {Picó, Jesús/0000-0003-4144-3521
+ Ferrer, Alberto/0000-0001-7244-5947
+ Prats-Montalban, Jose Manuel/0000-0001-6294-4486
+ Llaneras, Francisco/0000-0002-5299-1737
+ Folch-Fortuny, Abel/0000-0001-6845-0807},
+Times-Cited = {10},
+Journal-ISO = {Chemometrics Intell. Lab. Syst.},
+Unique-ID = {WOS:000351972500032},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000351435600020,
+Author = {Fondi, Marco and Maida, Isabel and Perrin, Elena and Mellera, Alessandra
+ and Mocali, Stefano and Parrilli, Ermenegilda and Tutino, Maria Luisa
+ and Lio, Pietro and Fani, Renato},
+Title = {Genome-scale metabolic reconstruction and constraint-based modelling of
+ the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.},
+Journal = {ENVIRONMENTAL MICROBIOLOGY},
+Year = {2015},
+Volume = {17},
+Number = {3},
+Pages = {751-766},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1111/1462-2920.12513},
+ISSN = {1462-2912},
+EISSN = {1462-2920},
+Keywords-Plus = {COLD SHOCK RESPONSE; ESCHERICHIA-COLI; LOW-TEMPERATURE; MARINE
+ BACTERIUM; PROTEOMIC ANALYSIS; CELL-GROWTH; ADAPTATION; EXPRESSION;
+ NETWORK; DATABASE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {P. Lió, Pietro Lio/AAV-3358-2021
+ Mocali, Stefano/ABE-2918-2020
+ TUTINO, MARIA LUISA/L-1834-2013
+ parrilli, ermenegilda/K-4616-2016
+ Perrin, Elena/AAX-2762-2020
+ },
+ORCID-Numbers = {P. Lió, Pietro Lio/0000-0002-0540-5053
+ parrilli, ermenegilda/0000-0002-9002-5409
+ Fondi, Marco/0000-0001-9291-5467
+ Perrin, Elena/0000-0001-5148-3178
+ Mocali, Stefano/0000-0002-1173-7206
+ Tutino, Maria Luisa/0000-0002-4978-6839},
+Times-Cited = {33},
+Journal-ISO = {Environ. Microbiol.},
+Unique-ID = {WOS:000351435600020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000351402300004,
+Author = {Kim, Byoungjin and Kim, Won Jun and Kim, Dong In and Lee, Sang Yup},
+Title = {Applications of genome-scale metabolic network model in metabolic
+ engineering},
+Journal = {JOURNAL OF INDUSTRIAL MICROBIOLOGY \& BIOTECHNOLOGY},
+Year = {2015},
+Volume = {42},
+Number = {3, SI},
+Pages = {339-348},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1007/s10295-014-1554-9},
+ISSN = {1367-5435},
+EISSN = {1476-5535},
+Keywords = {Genome-scale metabolic network; Systems metabolic engineering; Gene
+ knock-out prediction; Gene amplification prediction; Metabolic pathway
+ prediction; Integrated genome-scale model},
+Keywords-Plus = {IN-SILICO ANALYSIS; ESCHERICHIA-COLI; KNOCKOUT STRATEGIES; CHEMICAL
+ PRODUCTION; PICHIA-PASTORIS; EXPRESSION DATA; RECONSTRUCTION; FLUX;
+ DESIGN; PREDICTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lee, Sang Yup/C-1526-2011},
+ORCID-Numbers = {Lee, Sang Yup/0000-0003-0599-3091},
+Times-Cited = {64},
+Journal-ISO = {J. Ind. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000351402300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000352980700009,
+Author = {Motamedian, Ehsan and Ghavami, Ghazaleh and Sardari, Soroush},
+Title = {Investigation on metabolism of cisplatin resistant ovarian cancer using
+ a genome scale metabolic model and microarray data},
+Journal = {IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES},
+Year = {2015},
+Volume = {18},
+Number = {3},
+Pages = {267-276},
+Month = {MAR},
+Type = {Article},
+ISSN = {2008-3866},
+EISSN = {2008-3874},
+Keywords = {Cisplatin resistance; Drug target; Lactate; Metabolism; Microarray;
+ Warburg effect},
+Keywords-Plus = {RAT-LIVER MITOCHONDRIA; GLOBAL RECONSTRUCTION; EXPRESSION DATA;
+ BREAST-CANCER; NETWORK; PREDICTION; GROWTH; PROLIFERATION; INTEGRATION;
+ TARGETS},
+Research-Areas = {Research \& Experimental Medicine; Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Medicine, Research \& Experimental; Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Sardari, Soroush/AGY-3278-2022
+ Motamedian, Ehsan/GPK-8344-2022
+ Sardari, Soroush/L-6448-2017
+ },
+ORCID-Numbers = {Sardari, Soroush/0000-0003-2080-7402
+ , Ehsan/0000-0001-8750-2879},
+Times-Cited = {17},
+Journal-ISO = {Iran. J. Basic Med. Sci.},
+Unique-ID = {WOS:000352980700009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000350862600019,
+Author = {Sekar, Karthik and Tyo, Keith E. J.},
+Title = {Regulatory effects on central carbon metabolism from
+ poly-3-hydroxybutryate synthesis},
+Journal = {METABOLIC ENGINEERING},
+Year = {2015},
+Volume = {28},
+Pages = {180-189},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ymben.2015.01.003},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic engineering; Poly-3-hydroxybutyrate; Chemostat; Escherichia
+ coli; Flux balance analysis},
+Keywords-Plus = {RECOMBINANT ESCHERICHIA-COLI; POLY-BETA-HYDROXYBUTYRATE;
+ ALCALIGENES-EUTROPHUS; GENE-EXPRESSION; LACTATE-DEHYDROGENASE;
+ 2-COMPONENT SYSTEM; REDOX STATE; POLY(3-HYDROXYBUTYRATE); BIOSYNTHESIS;
+ PHOSPHATE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Tyo, Keith/H-6227-2012
+ Tyo, Keith/AAM-4543-2020
+ },
+ORCID-Numbers = {Sekar, Karthik/0000-0003-2045-9364
+ Tyo, Keith/0000-0002-2342-0687},
+Times-Cited = {13},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000350862600019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000351402300003,
+Author = {Simeonidis, Evangelos and Price, Nathan D.},
+Title = {Genome-scale modeling for metabolic engineering},
+Journal = {JOURNAL OF INDUSTRIAL MICROBIOLOGY \& BIOTECHNOLOGY},
+Year = {2015},
+Volume = {42},
+Number = {3, SI},
+Pages = {327-338},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1007/s10295-014-1576-3},
+ISSN = {1367-5435},
+EISSN = {1476-5535},
+Keywords = {Flux balance analysis; Metabolic engineering; Metabolic reconstructions;
+ Automated network reconstruction; Gene regulatory networks},
+Keywords-Plus = {FLUX BALANCE MODELS; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; NETWORK
+ RECONSTRUCTION; KNOCKOUT STRATEGIES; CHEMICAL PRODUCTION; INVIVO
+ MEASUREMENT; OPTIMAL SELECTION; SYSTEMS; PATHWAY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Price, Nathan/0000-0002-4157-0267
+ Simeonidis, Vangelis/0000-0001-6153-4493},
+Times-Cited = {69},
+Journal-ISO = {J. Ind. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000351402300003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000350369900001,
+Author = {Binns, Michael and de Atauri, Pedro and Vlysidis, Anestis and Cascante,
+ Marta and Theodoropoulos, Constantinos},
+Title = {Sampling with poling-based flux balance analysis: optimal versus
+ sub-optimal flux space analysis of Actinobacillus succinogenes},
+Journal = {BMC BIOINFORMATICS},
+Year = {2015},
+Volume = {16},
+Month = {FEB 18},
+Type = {Article},
+DOI = {10.1186/s12859-015-0476-5},
+Article-Number = {49},
+ISSN = {1471-2105},
+Keywords = {Flux sampling; Optimisation; Flux balance analysis},
+Keywords-Plus = {COMPLEX METABOLIC NETWORKS; SUCCINIC ACID PRODUCTION; CONSTRAINT-BASED
+ MODELS; QUANTITATIVE PREDICTION; FRAMEWORK DEVELOPMENT;
+ CELLULAR-METABOLISM; ESCHERICHIA-COLI; COBRA TOOLBOX; PATHWAYS;
+ UNCERTAINTY},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {CASCANTE, MARTA/AAG-4355-2022
+ CASCANTE, MARTA/AFK-5991-2022
+ de Atauri, Pedro Ramón/R-3957-2019
+ de Atauri, Pedro/AAG-2384-2020
+ },
+ORCID-Numbers = {CASCANTE, MARTA/0000-0002-2062-4633
+ CASCANTE, MARTA/0000-0002-2062-4633
+ de Atauri, Pedro Ramón/0000-0002-7754-7851
+ Theodoropoulos, Constantinos/0000-0003-3249-0422},
+Times-Cited = {8},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000350369900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000352782200006,
+Author = {Kerkhoven, Eduard J. and Lahtvee, Petri-Jaan and Nielsen, Jens},
+Title = {Applications of computational modeling in metabolic engineering of yeast},
+Journal = {FEMS YEAST RESEARCH},
+Year = {2015},
+Volume = {15},
+Number = {1},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1111/1567-1364.12199},
+ISSN = {1567-1356},
+EISSN = {1567-1364},
+Keywords = {genome-scale model; kinetic model; biotechnology; synthetic biology},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; HIGH-THROUGHPUT;
+ TRANSCRIPTIONAL REGULATION; GLYCOLYTIC-ENZYMES; ETHANOL-PRODUCTION;
+ SILICON CELL; RATE LAW; NETWORK; PATHWAY},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+ResearcherID-Numbers = {Lahtvee, Petri-Jaan/G-5257-2016
+ Nielsen, Jens Bo/C-7632-2015
+ Kerkhoven, Eduard/P-2469-2019
+ Kerkhoven, Eduard/H-2072-2014
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Lahtvee, Petri-Jaan/0000-0002-3327-3190
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {40},
+Journal-ISO = {FEMS Yeast Res.},
+Unique-ID = {WOS:000352782200006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347778100010,
+Author = {Lee, Hae Woo and Christie, Andrew and Starkey, Jason A. and Read, Erik
+ K. and Yoon, Seongkyu},
+Title = {Intracellular metabolic flux analysis of CHO cells supplemented with
+ wheat hydrolysates for improved mAb production and cell-growth},
+Journal = {JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY},
+Year = {2015},
+Volume = {90},
+Number = {2, SI},
+Pages = {291-302},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1002/jctb.4523},
+ISSN = {0268-2575},
+EISSN = {1097-4660},
+Keywords = {flux balance analysis; metabolic flux analysis; CHO cell culture; raw
+ materials; wheat hydrolysates},
+Keywords-Plus = {RECOMBINANT PROTEIN THERAPEUTICS; PRINCIPAL COMPONENT ANALYSIS;
+ CULTURE-MEDIA; LACTATE-DEHYDROGENASE; MALATE-DEHYDROGENASE; HYBRIDOMA
+ CELLS; AMMONIA; DISTRIBUTIONS; CHEMOMETRICS; GLUTAMINE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Chemistry; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Chemistry, Multidisciplinary;
+ Engineering, Environmental; Engineering, Chemical},
+Times-Cited = {12},
+Journal-ISO = {J. Chem. Technol. Biotechnol.},
+Unique-ID = {WOS:000347778100010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000348771400007,
+Author = {Liu, Yanfeng and Shin, Hyun-dong and Li, Jianghua and Liu, Long},
+Title = {Toward metabolic engineering in the context of system biology and
+ synthetic biology: advances and prospects},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2015},
+Volume = {99},
+Number = {3},
+Pages = {1109-1118},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1007/s00253-014-6298-y},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {System metabolic engineering; Modular pathway engineering; Synthetic
+ biology; Genome-scale metabolic model; Spatial engineering},
+Keywords-Plus = {IN-VITRO RECONSTITUTION; FATTY-ACIDS PRODUCTION; ESCHERICHIA-COLI;
+ 2-KETO-L-GULONIC ACID; BACILLUS-SUBTILIS; CANDIDA-GLABRATA; PATHWAY;
+ OVERPRODUCTION; MODEL; RECONSTRUCTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Liu, Long/D-6112-2013
+ li, jianghua/GXG-4735-2022
+ },
+ORCID-Numbers = {Liu, Yanfeng/0000-0002-0562-9647},
+Times-Cited = {26},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000348771400007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000348086900004,
+Author = {Masoudi-Nejad, Ali and Asgari, Yazdan},
+Title = {Metabolic Cancer Biology: Structural-based analysis of cancer as a
+ metabolic disease, new sights and opportunities for disease treatment},
+Journal = {SEMINARS IN CANCER BIOLOGY},
+Year = {2015},
+Volume = {30},
+Pages = {21-29},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1016/j.semcancer.2014.01.007},
+ISSN = {1044-579X},
+EISSN = {1096-3650},
+Keywords = {Cancer; Metabolic networks; Topological analysis; Flux balance analysis;
+ Warburg effect; Genome-scale modeling; Cancer treatment},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; SYSTEMS BIOLOGY; EXPRESSION DATA; TRANSCRIPTIONAL
+ REGULATION; GLOBAL RECONSTRUCTION; NUCLEOSIDE ANALOGS; CELL METABOLISM;
+ GENOME; NETWORKS; MODELS},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ResearcherID-Numbers = {Masoudi-Nejad, Ali/ABH-2078-2021
+ asgari, yazdan/AAL-9037-2020
+ },
+ORCID-Numbers = {asgari, yazdan/0000-0001-6993-6956
+ Masoudi-Nejad, Ali/0000-0003-0659-5183},
+Times-Cited = {31},
+Journal-ISO = {Semin. Cancer Biol.},
+Unique-ID = {WOS:000348086900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000349403300002,
+Author = {Wang, Cheng and Deng, Zhi-Luo and Xie, Zhi-Ming and Chu, Xin-Yi and
+ Chang, Ji-Wei and Kong, De-Xin and Li, Bao-Ju and Zhang, Hong-Yu and
+ Chen, Ling-Ling},
+Title = {Construction of a genome-scale metabolic network of the plant pathogen
+ Pectobacterium carotovorum provides new strategies for
+ bactericide discovery},
+Journal = {FEBS LETTERS},
+Year = {2015},
+Volume = {589},
+Number = {3},
+Pages = {285-294},
+Month = {JAN 30},
+Type = {Article},
+DOI = {10.1016/j.febslet.2014.12.010},
+ISSN = {0014-5793},
+EISSN = {1873-3468},
+Keywords = {Metabolic network; Flux balance analysis; Phenotype microarray; Virtual
+ screening; Pectobacterium carotovorum subsp.; carotovorum PC1},
+Keywords-Plus = {ALKALINE-PHOSPHATASE; DATABASE; RECONSTRUCTION; ENZYMES; CLASSIFICATION;
+ IDENTIFICATION; PREDICTION; VIRULENCE; MG1655; GENE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+ResearcherID-Numbers = {Kong, De-Xin/E-5630-2012
+ Deng, Zhi-Luo/AGK-6758-2022
+ Chen, Ling-Ling/AAY-3547-2021
+ Chen, Lingling/JCD-4631-2023
+ },
+ORCID-Numbers = {Kong, De-Xin/0000-0003-0744-116X
+ Deng, Zhi-Luo/0000-0003-1242-7557
+ Wang, Cheng/0000-0003-4823-1484},
+Times-Cited = {14},
+Journal-ISO = {FEBS Lett.},
+Unique-ID = {WOS:000349403300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000350210400095,
+Author = {Shameer, Sanu and Logan-Klumpler, Flora J. and Vinson, Florence and
+ Cottret, Ludovic and Merlet, Benjamin and Achcar, Fiona and Boshart,
+ Michael and Berriman, Matthew and Breitling, Rainer and Bringaud,
+ Fredrric and Butikofer, Peter and Cattanach, Amy M. and
+ Bannerman-Chukualim, Bridget and Creek, Darren J. and Crouch, Kathryn
+ and de Koning, Harry P. and Denise, Hubert and Ebikeme, Charles and
+ Fairlamb, Alan H. and Ferguson, Michael A. J. and Ginger, Michael L. and
+ Hertz-Fowler, Christiane and Kerkhoven, Eduard J. and Maeser, Pascal and
+ Michels, Paul A. M. and Nayak, Archana and Nes, David W. and Nolan,
+ Derek P. and Olsen, Christian and Silva-Franco, Fatima and Smith, Terry
+ K. and Taylor, Martin C. and Tielens, Aloysius G. M. and Urbaniak,
+ Michael D. and van Hellemond, Jaap J. and Vincent, Isabel M. and
+ Wilkinson, Shane R. and Wyllie, Susan and Opperdoes, Fred R. and
+ Barrett, Michael P. and Jourdan, Fabien},
+Title = {TrypanoCyc: a community-led biochemical pathways database for
+ Trypanosoma brucei},
+Journal = {NUCLEIC ACIDS RESEARCH},
+Year = {2015},
+Volume = {43},
+Number = {D1},
+Pages = {D637-D644},
+Month = {JAN 28},
+Type = {Article},
+DOI = {10.1093/nar/gku944},
+ISSN = {0305-1048},
+EISSN = {1362-4962},
+Keywords-Plus = {METABOLIC PATHWAYS; GENOME; PREDICTION; NETWORKS; ENZYMES;
+ RECONSTRUCTION; LOCALIZATION; RESOURCE; PROGRESS; METACYC},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Opperdoes, Frederik R/C-8897-2018
+ Kerkhoven, Eduard/H-2072-2014
+ /AAD-2293-2020
+ Crouch, Kathryn/HDO-6240-2022
+ Ferguson, Michael A. J./F-7829-2010
+ van Hellemond, Jaap/T-7555-2019
+ Boshart, Michael/A-2700-2011
+ Berriman, Matthew/A-7618-2011
+ Opperdoes, Fred/N-9922-2019
+ Fairlamb, Alan/A-5272-2009
+ Jourdan, Fabien/AAW-5075-2021
+ Michels, Paul A/A-5637-2009
+ Kerkhoven, Eduard/P-2469-2019
+ Wyllie, Susan/AAI-4430-2021
+ },
+ORCID-Numbers = {Opperdoes, Frederik R/0000-0003-1984-3764
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ /0000-0001-7418-7750
+ Crouch, Kathryn/0000-0001-9310-4762
+ Ferguson, Michael A. J./0000-0003-1321-8714
+ van Hellemond, Jaap/0000-0003-4862-7796
+ Boshart, Michael/0000-0002-5070-2663
+ Berriman, Matthew/0000-0002-9581-0377
+ Opperdoes, Fred/0000-0003-1984-3764
+ Fairlamb, Alan/0000-0001-5134-0329
+ Jourdan, Fabien/0000-0001-9401-2894
+ Michels, Paul A/0000-0003-3726-6104
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Maser, Pascal/0000-0003-3122-1941
+ Vincent, Isabel/0000-0003-2663-4389
+ Hertz-Fowler, Christiane/0000-0002-0729-6479
+ Nolan, Derek/0000-0002-3742-4304
+ Silva-Franco, Fatima/0000-0002-2900-027X
+ De Koning, Harry/0000-0002-9963-1827
+ Ginger, Michael/0000-0002-9643-8482
+ Denise, Hubert/0000-0001-9862-5890
+ Creek, Darren/0000-0001-7497-7082
+ Breitling, Rainer/0000-0001-7173-0922
+ Tielens, Aloysius/0000-0002-5485-1105
+ Achcar, Fiona/0000-0001-8792-7615
+ Taylor, Martin/0000-0003-4147-0693
+ Ebikeme, Charles/0000-0002-9989-6489
+ Wyllie, Susan/0000-0001-8810-5605
+ Urbaniak, Michael/0000-0003-2745-9420
+ Barrett, Mike/0000-0001-9447-3519},
+Times-Cited = {19},
+Journal-ISO = {Nucleic Acids Res.},
+Unique-ID = {WOS:000350210400095},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000348821400004,
+Author = {Barker, Brandon and Xu, Lin and Gu, Zhenglong},
+Title = {Dynamic Epistasis under Varying Environmental Perturbations},
+Journal = {PLOS ONE},
+Year = {2015},
+Volume = {10},
+Number = {1},
+Month = {JAN 27},
+Type = {Article},
+DOI = {10.1371/journal.pone.0114911},
+Article-Number = {e0114911},
+ISSN = {1932-6203},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX BALANCE MODELS; SACCHAROMYCES-CEREVISIAE;
+ ESCHERICHIA-COLI; QUANTITATIVE PREDICTION; SPONTANEOUS MUTATIONS;
+ CELLULAR-METABOLISM; FITNESS; LOAD; BIOLOGY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {xu, lin/H-8560-2016
+ },
+ORCID-Numbers = {Barker, Brandon/0000-0001-5732-9550},
+Times-Cited = {4},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000348821400004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000348217500001,
+Author = {Dal'Molin, Cristiana Gomes de Oliveira and Quek, Lake-Ee and Saa, Pedro
+ A. and Nielsen, Lars K.},
+Title = {A multi-tissue genome-scale metabolic modeling framework for the
+ analysis of whole plant systems},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2015},
+Volume = {6},
+Month = {JAN 22},
+Type = {Article},
+DOI = {10.3389/fpls.2015.00004},
+Article-Number = {4},
+ISSN = {1664-462X},
+Keywords = {multi-tissue; genome-scale; modeling; plant metabolism; AraGEM},
+Keywords-Plus = {DIURNAL CHANGES; ARABIDOPSIS; PHLOEM; RECONSTRUCTION; SUCROSE;
+ ASSIMILATION; SYMPORTER; NETWORK},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Saa, Pedro Andrés/X-1987-2018
+ Nielsen, Lars K/A-5519-2011
+ Palfreyman, Robin/V-8516-2017
+ Hodson, Mark/J-7609-2013
+ Orellana, Camila/C-2979-2017},
+ORCID-Numbers = {Saa, Pedro Andrés/0000-0002-1659-9041
+ Nielsen, Lars K/0000-0001-8191-3511
+ Quek, Lake-Ee/0000-0002-9313-8740
+ Steen, Jennifer/0000-0002-4760-9492
+ Palfreyman, Robin/0000-0002-1088-7069
+ Gebbie, Leigh/0000-0002-9137-3413
+ Hodson, Mark/0000-0002-5436-1886
+ Orellana, Camila/0000-0002-6828-6071},
+Times-Cited = {79},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000348217500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347721700008,
+Author = {Quartermana, Josh and Kim, Soo Rin and Kim, Pan-Jun and Jin, Yong-Su},
+Title = {Enhanced hexose fermentation by Saccharomyces cerevisiae through
+ integration of stoichiometric modeling and genetic screening},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2015},
+Volume = {194},
+Pages = {48-57},
+Month = {JAN 20},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2014.11.017},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Saccharomyces cerevisiae; Constraint-based flux analysis; Genome-scale
+ model; Cytochrome c oxidase; Ubiquinol cytochrome c reductasea},
+Keywords-Plus = {CYTOCHROME-C-OXIDASE; YEAST; COMPLEX; PHENOTYPES; EFFICIENCY; DELETION;
+ MUTANTS; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Jin, Yong-Su/L-4530-2013
+ Kim, Soo Rin/X-2192-2019
+ },
+ORCID-Numbers = {Kim, Soo Rin/0000-0001-5855-643X
+ Jin, Yong-Su/0000-0002-4464-9536
+ Kim, Pan-Jun/0000-0002-9329-4997},
+Times-Cited = {6},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000347721700008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347810300046,
+Author = {Plata, German and Henry, Christopher S. and Vitkup, Dennis},
+Title = {Long-term phenotypic evolution of bacteria},
+Journal = {NATURE},
+Year = {2015},
+Volume = {517},
+Number = {7534},
+Pages = {369-U498},
+Month = {JAN 15},
+Type = {Article},
+DOI = {10.1038/nature13827},
+ISSN = {0028-0836},
+EISSN = {1476-4687},
+Keywords-Plus = {GENETIC INTERACTION NETWORKS; GENERATION; CONSERVATION; STRAINS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Plata, German/GXG-8357-2022
+ },
+ORCID-Numbers = {Plata, German/0000-0002-6470-7748},
+Times-Cited = {52},
+Journal-ISO = {Nature},
+Unique-ID = {WOS:000347810300046},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347582200026,
+Author = {Voges, Raphael and Corsten, Stephanie and Wiechert, Wolfgang and Noack,
+ Stephan},
+Title = {Absolute quantification of Corynebacterium glutamicum glycolytic
+ and anaplerotic enzymes by QconCAT},
+Journal = {JOURNAL OF PROTEOMICS},
+Year = {2015},
+Volume = {113},
+Pages = {366-377},
+Month = {JAN 15},
+Type = {Article},
+DOI = {10.1016/j.jprot.2014.10.008},
+ISSN = {1874-3919},
+EISSN = {1876-7737},
+Keywords = {Selected reaction monitoring; Mass spectrometry; Protein quantification;
+ QconCAT; Corynebacterium glutamicum},
+Keywords-Plus = {QUANTITATIVE-ANALYSIS; MEMBRANE PROTEOME; LYSINE PRODUCTION;
+ PYRUVATE-KINASE; AMINO-ACIDS; PROTEINS; METABOLISM; PEPTIDES;
+ STOICHIOMETRY; ADAPTATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ORCID-Numbers = {Wiechert, Wolfgang/0000-0001-8501-0694
+ Noack, Stephan/0000-0001-9784-3626},
+Times-Cited = {11},
+Journal-ISO = {J. Proteomics},
+Unique-ID = {WOS:000347582200026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000350597400001,
+Author = {Ye, Chao and Xu, Nan and Chen, Haiqin and Chen, Yong Q. and Chen, Wei
+ and Liu, Liming},
+Title = {Reconstruction and analysis of a genome-scale metabolic model of the
+ oleaginous fungus Mortierella alpina},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2015},
+Volume = {9},
+Month = {JAN 13},
+Type = {Article},
+DOI = {10.1186/s12918-014-0137-8},
+Article-Number = {1},
+EISSN = {1752-0509},
+Keywords = {Mortierella alpina; Arachidonic acid; Genome-scale metabolic model;
+ Polyunsaturated fatty acids; Malic enzyme},
+Keywords-Plus = {ARACHIDONIC-ACID PRODUCTION; POLYUNSATURATED FATTY-ACIDS; RATE-LIMITING
+ STEP; SUBCELLULAR-LOCALIZATION; EICOSAPENTAENOIC ACID;
+ FUNCTIONAL-ANALYSIS; DESATURASE GENES; MUTATION SITES; 1S-4;
+ IDENTIFICATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ye, Chao/H-7623-2014
+ Chen, Yong Q/AAI-9864-2021
+ Ye, Chao/M-3689-2019
+ Ye, Chao/HGD-3564-2022
+ Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Chen, Yong Q/0000-0003-4747-4708
+ Ye, Chao/0000-0002-6671-7819
+ Ye, Chao/0000-0002-6671-7819
+ Liu, Liming/0000-0003-3022-936X
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {48},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000350597400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347127500002,
+Author = {Xu, Nan and Liu, Jie and Ai, Lianzhong and Liu, Liming},
+Title = {Reconstruction and analysis of the genome-scale metabolic model of
+ Lactobacillus casei LC2W},
+Journal = {GENE},
+Year = {2015},
+Volume = {554},
+Number = {2},
+Pages = {140-147},
+Month = {JAN 10},
+Type = {Article},
+DOI = {10.1016/j.gene.2014.10.034},
+ISSN = {0378-1119},
+EISSN = {1879-0038},
+Keywords = {Lactobacillus casei; Genome-scale metabolic model; Lactic acid bacteria},
+Keywords-Plus = {EXOPOLYSACCHARIDE PRODUCTION; PHOSPHOTRANSFERASE SYSTEM;
+ CARBOHYDRATE-METABOLISM; PREDICTION; TRANSPORT; ENZYME; REQUIREMENTS;
+ STRATEGIES; SEQUENCE; DIACETYL},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {23},
+Journal-ISO = {Gene},
+Unique-ID = {WOS:000347127500002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000362950000019,
+Author = {Babaei, Parizad and Marashi, Sayed-Amir and Asad, Sedigheh},
+Title = {Genome-scale reconstruction of the metabolic network in Pseudomonas
+ stutzeri A1501},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2015},
+Volume = {11},
+Number = {11},
+Pages = {3022-3032},
+Type = {Article},
+DOI = {10.1039/c5mb00086f},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; NITROGEN-FIXATION; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; PUTIDA KT2440; WHOLE CELLS; IN-VIVO; DEGRADATION;
+ NAPHTHALENE; BACTERIAL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008
+ },
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Babaei, Parizad/0000-0001-9411-0427},
+Times-Cited = {7},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000362950000019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345897600004,
+Author = {Beld, Joris and Lee, D. John and Burkart, Michael D.},
+Title = {Fatty acid biosynthesis revisited: structure elucidation and metabolic
+ engineering},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2015},
+Volume = {11},
+Number = {1},
+Pages = {38-59},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1039/c4mb00443d},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {ACYL-CARRIER-PROTEIN; MALONYL-COENZYME-A; SYNTHASE III FABH; COA-ACP
+ TRANSACYLASE; X-RAY-STRUCTURE; ESCHERICHIA-COLI; CRYSTAL-STRUCTURE;
+ STREPTOMYCES-COELICOLOR; CHAIN-LENGTH; PLASMODIUM-FALCIPARUM},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Beld, Joris/JMA-9778-2023
+ },
+ORCID-Numbers = {Lee, David/0000-0002-5132-3243},
+Times-Cited = {122},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000345897600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000346649000007,
+Author = {Borodina, Irina and Kildegaard, Kanchana R. and Jensen, Niels B. and
+ Blicher, Thomas H. and Maury, Jerome and Sherstyk, Svetlana and
+ Schneider, Konstantin and Lamosa, Pedro and Herrgard, Markus J. and
+ Rosenstand, Inger and Oberg, Fredrik and Forster, Jochen and Nielsen,
+ Jens},
+Title = {Establishing a synthetic pathway for high-level production of
+ 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine},
+Journal = {METABOLIC ENGINEERING},
+Year = {2015},
+Volume = {27},
+Pages = {57-64},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2014.10.003},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Biosustainable acrylics; 3-hydroxypropionic acid; Saccharomyces
+ cerevisiae; beta-alanine; beta-alanine-pyruvate aminotransferase},
+Keywords-Plus = {METABOLISM; DEHYDROGENASE; BIOSYNTHESIS; REDUCTASE; YEAST},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Borodina, Irina/G-5587-2013
+ Jensen, Betina W/J-2207-2015
+ Öberg, Fredrik Kryh/B-1241-2011
+ Lamosa, Pedro/B-2271-2009
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Öberg, Fredrik Kryh/0000-0002-7089-2118
+ Borodina, Irina/0000-0002-8452-1393
+ Lamosa, Pedro/0000-0002-3003-1516
+ Kildegaard, Kanchana Rueksomtawin/0000-0001-9885-380X
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {147},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000346649000007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358915500009,
+Author = {Gawand, Pratish and Abukar, Fatumina Said and Venayak, Naveen and
+ Partow, Siavash and Motter, Adilson E. and Mahadevan, Radhakrishnan},
+Title = {Sub-optimal phenotypes of double-knockout mutants of Escherichia
+ coli depend on the order of gene deletions},
+Journal = {INTEGRATIVE BIOLOGY},
+Year = {2015},
+Volume = {7},
+Number = {8},
+Pages = {930-939},
+Type = {Article},
+DOI = {10.1039/c5ib00096c},
+ISSN = {1757-9694},
+EISSN = {1757-9708},
+Keywords-Plus = {METABOLIC NETWORKS; SYNTHETIC RESCUES; RECONSTRUCTION; OPTIMALITY},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Mahadevan, Radhakrishnan/A-8502-2008
+ },
+ORCID-Numbers = {Mahadevan, Radhakrishnan/0000-0002-1270-9063
+ Motter, Adilson E./0000-0003-1794-4828},
+Times-Cited = {4},
+Journal-ISO = {Integr. Biol.},
+Unique-ID = {WOS:000358915500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000457443200005,
+Author = {Heinken, Almut and Thiele, Ines},
+Title = {Systematic prediction of health-relevant human-microbial co-metabolism
+ through a computational framework},
+Journal = {GUT MICROBES},
+Year = {2015},
+Volume = {6},
+Number = {2},
+Pages = {120-130},
+Type = {Article},
+DOI = {10.1080/19490976.2015.1023494},
+ISSN = {1949-0976},
+EISSN = {1949-0984},
+Keywords = {human gut microbiome; in silico; metabolome; metabolic modeling},
+Keywords-Plus = {GUT MICROBIOTA; HOST; BACTERIA; BIOLOGY; RECONSTRUCTION; METABOLOMICS;
+ MICROFLORA; PHYSIOLOGY; GROWTH; MODEL},
+Research-Areas = {Gastroenterology \& Hepatology; Microbiology},
+Web-of-Science-Categories = {Gastroenterology \& Hepatology; Microbiology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Heinken, Almut/0000-0001-6938-8072},
+Times-Cited = {73},
+Journal-ISO = {Gut Microbes},
+Unique-ID = {WOS:000457443200005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358915500004,
+Author = {Islam, M. Ahsanul and Zengler, Karsten and Edwards, Elizabeth A. and
+ Mahadevan, Radhakrishnan and Stephanopoulos, Gregory},
+Title = {Investigating Moorella thermoacetica metabolism with a
+ genome-scale constraint-based metabolic model},
+Journal = {INTEGRATIVE BIOLOGY},
+Year = {2015},
+Volume = {7},
+Number = {8},
+Pages = {869-882},
+Type = {Article},
+DOI = {10.1039/c5ib00095e},
+ISSN = {1757-9694},
+EISSN = {1757-9708},
+Keywords-Plus = {DEPENDENT FORMATE DEHYDROGENASE; WOOD-LJUNGDAHL PATHWAY;
+ CLOSTRIDIUM-THERMOACETICUM; FUMARATE RESPIRATION; ACETOGENIC BACTERIA;
+ ENERGY-CONSERVATION; RECONSTRUCTION; ELECTRON; PROTEIN; LIFE},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Edwards, Elizabeth Anne/GXV-2307-2022
+ Mahadevan, Radhakrishnan/A-8502-2008
+ },
+ORCID-Numbers = {Mahadevan, Radhakrishnan/0000-0002-1270-9063
+ Edwards, Elizabeth/0000-0002-8071-338X
+ Islam, M. Ahsanul/0000-0001-9585-6263
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {27},
+Journal-ISO = {Integr. Biol.},
+Unique-ID = {WOS:000358915500004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000536548500045,
+Author = {Knoop, Henning and Steuer, Ralf},
+Title = {A computational analysis of stoichiometric constraints and trade-offs in
+ cyanobacterial biofuel production},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2015},
+Volume = {3},
+Type = {Article},
+DOI = {10.3389/fbioe.2015.00047},
+Article-Number = {47},
+ISSN = {2296-4185},
+Keywords = {flux-balance analysis; metabolic modeling; cyanobacteria; Synechocystis
+ sp. PCC 6803; microbial cell factories; photosynthesis},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Steuer, Ralf/E-7482-2017},
+ORCID-Numbers = {Steuer, Ralf/0000-0003-2217-1655},
+Times-Cited = {30},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000536548500045},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000365223100015,
+Author = {Li, Yi and Zhang, Guojian and Pfeifer, Blaine A.},
+Editor = {Schrader, J and Bohlmann, J},
+Title = {Current and Emerging Options for Taxol Production},
+Booktitle = {BIOTECHNOLOGY OF ISOPRENOIDS},
+Series = {Advances in Biochemical Engineering-Biotechnology},
+Year = {2015},
+Volume = {148},
+Pages = {405-425},
+Type = {Article; Book Chapter},
+DOI = {10.1007/10\_2014\_292},
+ISSN = {0724-6145},
+EISSN = {1616-8542},
+ISBN = {978-3-319-20107-8; 978-3-319-20106-1},
+Keywords = {Paclitaxel; Taxus; Metabolic engineering; E. coli; Yeast; Fungi},
+Keywords-Plus = {HETEROLOGOUS PROTEIN-PRODUCTION; CELL-SUSPENSION CULTURES;
+ CONSTRAINT-BASED MODELS; BACCATIN-III PRODUCTION; 1ST OXYGENATION STEP;
+ ESCHERICHIA-COLI; ISOPRENOID PATHWAY; SYNTHETIC BIOLOGY;
+ TAXUS-CUSPIDATA; GERANYLGERANYL DIPHOSPHATE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Times-Cited = {21},
+Journal-ISO = {Adv. Biochem. Eng. Biotechnol.},
+Unique-ID = {WOS:000365223100015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367752600056,
+Author = {Mao, Longfei and Nicolae, Averina and Oliveira, Miguel A. P. and He,
+ Feng and Hachi, Siham and Fleming, Ronan M. T.},
+Title = {A constraint-based modelling approach to metabolic dysfunction in
+ Parkinson's disease},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2015},
+Volume = {13},
+Pages = {484-491},
+Type = {Review},
+DOI = {10.1016/j.csbj.2015.08.002},
+ISSN = {2001-0370},
+Keywords = {Dopaminergic neurons; Constraint-based modelling; Metabolic
+ reconstruction; Energy metabolism; Parkinson's disease},
+Keywords-Plus = {PLURIPOTENT STEM-CELLS; HUMAN BRAIN; BIOCHEMICAL NETWORKS;
+ GENDER-DIFFERENCES; NEURODEGENERATION; NEUROINFLAMMATION;
+ RECONSTRUCTION; PATHOGENESIS; PRINCIPLE; NEURONS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Oliveira, Miguel/AAB-2753-2022
+ HeFeng, Feng/HGC-3025-2022
+ Fleming, Ronan MT/ABC-4093-2021
+ },
+ORCID-Numbers = {Oliveira, Miguel/0000-0001-6808-2389
+ HeFeng, Feng/0000-0003-2657-7361
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Mao, Longfei/0000-0003-0759-0501},
+Times-Cited = {4},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000367752600056},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345517800013,
+Author = {Pasztor, Andras and Kallio, Pauli and Malatinszky, David and Akhtar, M.
+ Kalim and Jones, Patrik R.},
+Title = {A Synthetic O2-Tolerant Butanol Pathway Exploiting Native
+ Fatty Acid Biosynthesis in Escherichia coli},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2015},
+Volume = {112},
+Number = {1},
+Pages = {120-128},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1002/bit.25324},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {butanol; Escherichia coli; synthetic pathway; fatty acid biosynthesis;
+ biofuel},
+Keywords-Plus = {STRAIN PCC 6803; CLOSTRIDIUM-ACETOBUTYLICUM; FERMENTATION; ACETONE;
+ MICROALGAE; EXPRESSION; 1-BUTANOL; REDUCTASE; ETHANOL; MODELS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Akhtar, M. Kalim/HMP-2523-2023
+ Kallio, Pauli/T-8149-2017
+ },
+ORCID-Numbers = {Akhtar, M. Kalim/0000-0002-8805-0373
+ Kallio, Pauli/0000-0003-3590-9882
+ Malatinszky, David/0000-0002-4155-2085
+ Jones, Patrik/0000-0001-7618-8204},
+Times-Cited = {19},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000345517800013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000536548500131,
+Author = {Petzold, Christopher J. and Chan, Leanne Jade G. and Nhan, Melissa and
+ Adams, Paul D.},
+Title = {Analytics for metabolic engineering},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2015},
+Volume = {3},
+Type = {Review},
+DOI = {10.3389/fbioe.2015.00135},
+Article-Number = {135},
+ISSN = {2296-4185},
+Keywords = {metabolic engineering; RNA-seq; proteomics; metabolomics;
+ high-throughput screening; microfluidics},
+Keywords-Plus = {HIGH-THROUGHPUT; PATHWAY OPTIMIZATION; MASS-SPECTROMETRY;
+ ESCHERICHIA-COLI; SYNTHETIC BIOLOGY; GENE-EXPRESSION; IN-VIVO; DESIGN;
+ QUANTIFICATION; TRANSCRIPTION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Adams, Paul David/A-1977-2013
+ },
+ORCID-Numbers = {Adams, Paul David/0000-0001-9333-8219
+ Petzold, Christopher/0000-0002-8270-5228},
+Times-Cited = {55},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000536548500131},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358915500003,
+Author = {Ryu, Jae Yong and Kim, Hyun Uk and Lee, Sang Yup},
+Title = {Reconstruction of genome-scale human metabolic models using omics data},
+Journal = {INTEGRATIVE BIOLOGY},
+Year = {2015},
+Volume = {7},
+Number = {8},
+Pages = {859-868},
+Type = {Article},
+DOI = {10.1039/c5ib00002e},
+ISSN = {1757-9694},
+EISSN = {1757-9708},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; CELLULAR-METABOLISM; NETWORK; INTEGRATION;
+ PREDICTION; FLUX; EXPRESSION; GENERATION; PROTEOME},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Kim, Hyun Uk/F-4509-2018
+ Lee, Sang Yup/C-1526-2011},
+ORCID-Numbers = {Kim, Hyun Uk/0000-0001-7224-642X
+ Lee, Sang Yup/0000-0003-0599-3091},
+Times-Cited = {44},
+Journal-ISO = {Integr. Biol.},
+Unique-ID = {WOS:000358915500003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000348517400007,
+Author = {Sahoo, Swagatika and Haraldsdottir, Hulda S. and Fleming, Ronan M. T.
+ and Thiele, Ines},
+Title = {Modeling the effects of commonly used drugs on human metabolism},
+Journal = {FEBS JOURNAL},
+Year = {2015},
+Volume = {282},
+Number = {2},
+Pages = {297-317},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1111/febs.13128},
+ISSN = {1742-464X},
+EISSN = {1742-4658},
+Keywords = {constraint-based modeling; drug metabolism; genome-scale metabolic
+ network reconstruction; inborn errors of metabolism; reconstruction
+ module},
+Keywords-Plus = {HMG-COA REDUCTASE; HUMAN LIVER-MICROSOMES; IN-VITRO METABOLISM; CLINICAL
+ PHARMACOKINETICS; INBORN-ERRORS; INTESTINAL-ABSORPTION; GLOBAL
+ RECONSTRUCTION; PHARMACEUTICAL DRUGS; CYTOCHROME-P450 3A4; LACTONE FORMS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Sahoo, Swagatika/0000-0003-3773-8597},
+Times-Cited = {25},
+Journal-ISO = {FEBS J.},
+Unique-ID = {WOS:000348517400007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000348188400014,
+Author = {Santos, Nadine Castelhano and Pereira, Maria Olivia and Lourenco, Analia},
+Title = {Pathogenicity phenomena in three model systems: from network mining to
+ emerging system-level properties},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2015},
+Volume = {16},
+Number = {1},
+Pages = {169-182},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1093/bib/bbt071},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {pathogenicity; biofilm-associated infections; drug therapeutics; network
+ reconstruction; in silico tools},
+Keywords-Plus = {RESISTANT STAPHYLOCOCCUS-AUREUS; PROTEIN-PROTEIN INTERACTIONS;
+ PSEUDOMONAS-AERUGINOSA PAO1; CONSTRAINT-BASED MODELS; FLUX BALANCE
+ ANALYSIS; III SECRETION SYSTEM; CANDIDA-ALBICANS; GLOBAL REGULATOR;
+ QUANTITATIVE PREDICTION; ANTIBIOTIC-RESISTANCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Lourenço, Anália/G-8879-2013
+ Pereira, Maria O/O-4859-2015
+ Lourenço, Anália/Y-9447-2019
+ },
+ORCID-Numbers = {Lourenço, Anália/0000-0001-8401-5362
+ Pereira, Maria O/0000-0002-4307-3985
+ Lourenço, Anália/0000-0001-8401-5362
+ Castelhano, Nadine/0000-0002-6181-6471},
+Times-Cited = {1},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000348188400014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000367752600045,
+Author = {Tamura, Takeyuki and Lu, Wei and Akutsu, Tatsuya},
+Title = {Computational Methods for Modification of Metabolic Networks},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2015},
+Volume = {13},
+Pages = {376-381},
+Type = {Review},
+DOI = {10.1016/j.csbj.2015.05.004},
+ISSN = {2001-0370},
+Keywords = {Metabolic network; Constraint-based programming; Flux balance analysis;
+ Elementary mode; Boolean model; Overfitting},
+Keywords-Plus = {MINIMAL CUT SETS; INTERVENTION STRATEGIES; KNOCKOUT STRATEGIES;
+ OPTIMIZATION; FRAMEWORK; PATHWAYS; DEFINITION; SYSTEMS; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Tamura, Takeyuki/AGG-2853-2022
+ Tamura, Takeyuki/ABI-2627-2020
+ },
+ORCID-Numbers = {Tamura, Takeyuki/0000-0003-1596-901X
+ Akutsu, Tatsuya/0000-0001-9763-797X},
+Times-Cited = {4},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000367752600045},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000358915500010,
+Author = {Tummler, Katja and Kuhn, Clemens and Klipp, Edda},
+Title = {Dynamic metabolic models in context: biomass backtracking},
+Journal = {INTEGRATIVE BIOLOGY},
+Year = {2015},
+Volume = {7},
+Number = {8},
+Pages = {940-951},
+Type = {Article},
+DOI = {10.1039/c5ib00050e},
+ISSN = {1757-9694},
+EISSN = {1757-9708},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS;
+ MYCOBACTERIUM-TUBERCULOSIS; SACCHAROMYCES-CEREVISIAE; REDUCTION;
+ NETWORKS; YEAST},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Kühn, Clemens/C-2139-2017},
+ORCID-Numbers = {Kühn, Clemens/0000-0002-9853-5307},
+Times-Cited = {2},
+Journal-ISO = {Integr. Biol.},
+Unique-ID = {WOS:000358915500010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000353493000001,
+Author = {Xu, Zhaobin and Islam, Sabina and Wood, Thomas K. and Huang, Zuyi},
+Title = {An Integrated Modeling and Experimental Approach to Study the Influence
+ of Environmental Nutrients on Biofilm Formation of Pseudomonas
+ aeruginosa},
+Journal = {BIOMED RESEARCH INTERNATIONAL},
+Year = {2015},
+Volume = {2015},
+Type = {Article},
+DOI = {10.1155/2015/506782},
+Article-Number = {506782},
+ISSN = {2314-6133},
+EISSN = {2314-6141},
+Keywords-Plus = {METABOLIC NETWORK ANALYSIS; IRON; MODULATION; PHOSPHATE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Medicine, Research \&
+ Experimental},
+ResearcherID-Numbers = {Islam, Saiful/AAJ-1513-2021
+ Wood, Thomas/GWZ-2481-2022
+ },
+ORCID-Numbers = {Islam, Saiful/0000-0003-1953-6908
+ Wood, Thomas/0000-0001-8962-8571
+ Wood, Thomas/0000-0002-6258-529X
+ xu, zhaobin/0000-0002-1136-5684},
+Times-Cited = {21},
+Journal-ISO = {Biomed Res. Int.},
+Unique-ID = {WOS:000353493000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000359458000008,
+Author = {Yukihira, Daichi and Fujimura, Yoshinori and Wariishi, Hiroyuki and
+ Miura, Daisuke},
+Title = {Bacterial metabolism in immediate response to nutritional perturbation
+ with temporal and network view of metabolites},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2015},
+Volume = {11},
+Number = {9},
+Pages = {2473-2482},
+Type = {Article},
+DOI = {10.1039/c5mb00182j},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {ESCHERICHIA-COLI; GROWTH-RATE; SYSTEMS; MODELS; POOLS; FLUX},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Fujimura, Yoshinori/AAG-4403-2019
+ Miura, Daisuke/H-1517-2019
+ },
+ORCID-Numbers = {Fujimura, Yoshinori/0000-0003-0798-0649},
+Times-Cited = {3},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000359458000008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000348814700001,
+Author = {Noronha, Alberto and Vilaca, Paulo and Rocha, Miguel},
+Title = {An integrated network visualization framework towards metabolic
+ engineering applications},
+Journal = {BMC BIOINFORMATICS},
+Year = {2014},
+Volume = {15},
+Month = {DEC 30},
+Type = {Article},
+DOI = {10.1186/s12859-014-0420-0},
+Article-Number = {420},
+ISSN = {1471-2105},
+Keywords = {Metabolic network visualization; Metabolic engineering; Open-source
+ software},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; BIOLOGICAL NETWORKS; COBRA TOOLBOX;
+ QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; SOFTWARE; REPRESENTATION;
+ SBML},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Rocha, Miguel/B-9404-2011
+ },
+ORCID-Numbers = {Rocha, Miguel/0000-0001-8439-8172
+ Vilaca, Paulo/0000-0002-1098-5849
+ Noronha, Alberto/0000-0002-0935-4599},
+Times-Cited = {6},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000348814700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345970600003,
+Author = {Fernandez-Castane, Alfered and Feher, Tamas and Carbonell, Pablo and
+ Pauthenier, Cyrille and Faulon, Jean-Loup},
+Title = {Computer-aided design for metabolic engineering},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2014},
+Volume = {192},
+Number = {B},
+Pages = {302-313},
+Month = {DEC 20},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2014.03.029},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Metabolic engineering; Computer-aided design; Retrosynthesis; Synthetic
+ biology},
+Keywords-Plus = {SIGNATURE MOLECULAR DESCRIPTOR; ESCHERICHIA-COLI; GENE-EXPRESSION;
+ SACCHAROMYCES-CEREVISIAE; PATHWAY RECONSTRUCTION; NETWORK ANALYSIS;
+ RECOMBINANT-DNA; ONLINE TOOL; IN-VITRO; CLONING},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Fernandez-Castane, Alfred/K-8199-2017
+ Carbonell, Pablo/A-3572-2011
+ Feher, Tamas/AAH-4479-2019
+ },
+ORCID-Numbers = {Fernandez-Castane, Alfred/0000-0002-2572-7797
+ Carbonell, Pablo/0000-0002-0993-5625
+ Feher, Tamas/0000-0001-9318-3640
+ Faulon, Jean-Loup/0000-0003-4274-2953},
+Times-Cited = {20},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000345970600003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347780900001,
+Author = {Hay, Jordan O. and Shi, Hai and Heinzel, Nicolas and Hebbelmann, Inga
+ and Rolletschek, Hardy and Schwender, Jorg},
+Title = {Integration of a constraint-based metabolic model of Brassica
+ napus developing seeds with 13C-metabolic flux analysis},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2014},
+Volume = {5},
+Month = {DEC 19},
+Type = {Article},
+DOI = {10.3389/fpls.2014.00724},
+Article-Number = {724},
+ISSN = {1664-462X},
+Keywords = {loopless flux balance analysis; C-13-metabolic flux analysis; central
+ metabolism; carbon partitioning; constraint-based reconstruction and
+ analysis},
+Keywords-Plus = {DEPENDENT MALATE-DEHYDROGENASE; CENTRAL CARBON METABOLISM; VARIABILITY
+ ANALYSIS; BALANCE ANALYSIS; STORAGE SYNTHESIS; EXPRESSION DATA;
+ RECONSTRUCTION; ARABIDOPSIS; NETWORK; PREDICTION},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Schwender, Jorg/P-2282-2014},
+ORCID-Numbers = {Schwender, Jorg/0000-0003-1350-4171},
+Times-Cited = {29},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000347780900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347650700001,
+Author = {Gomez, Jose A. and Hoffner, Kai and Barton, Paul I.},
+Title = {DFBAlab: a fast and reliable MATLAB code for dynamic flux balance
+ analysis},
+Journal = {BMC BIOINFORMATICS},
+Year = {2014},
+Volume = {15},
+Month = {DEC 18},
+Type = {Article},
+DOI = {10.1186/s12859-014-0409-8},
+Article-Number = {409},
+ISSN = {1471-2105},
+Keywords = {Dynamic flux balance analysis; Nonsmooth dynamic systems; Linear
+ programming; Lexicographic optimization},
+Keywords-Plus = {ESCHERICHIA-COLI; METABOLIC MODEL; CHLAMYDOMONAS; RECONSTRUCTION;
+ GROWTH; BATCH},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {/0000-0001-8964-8433},
+Times-Cited = {91},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000347650700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000346375400038,
+Author = {Sridhara, Viswanadham and Meyer, Austin G. and Rai, Piyush and Barrick,
+ Jeffrey E. and Ravikumar, Pradeep and Segre, Daniel and Wilke, Claus O.},
+Title = {Predicting Growth Conditions from Internal Metabolic Fluxes in an
+ In-Silico Model of E. coli},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {12},
+Month = {DEC 12},
+Type = {Article},
+DOI = {10.1371/journal.pone.0114608},
+Article-Number = {e114608},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; GENE-EXPRESSION; ASSOCIATION; ADAPTATION; SELECTION;
+ NUTRIENT; MUTANTS; MG1655},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Wilke, Claus O./B-4643-2008
+ Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Wilke, Claus O./0000-0002-7470-9261
+ Segrè, Daniel/0000-0003-4859-1914
+ Sridhara, Viswanadham/0000-0003-0688-6140
+ Meyer, Austin/0000-0002-0581-800X},
+Times-Cited = {14},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000346375400038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347561800001,
+Author = {Narang, Pankaj and Khan, Shawez and Hemrom, Anmol Jaywant and Lynn,
+ Andrew Michael and Open Source Drug Discovery},
+Title = {MetaNET - a web-accessible interactive platform for biological metabolic
+ network analysis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {8},
+Month = {DEC 5},
+Type = {Article},
+DOI = {10.1186/s12918-014-0130-2},
+Article-Number = {130},
+EISSN = {1752-0509},
+Keywords = {Flux balance analysis; Metabolic network; Systems biology; in silico
+ gene knock-out; Perturbation analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; MODELS; RECONSTRUCTION;
+ KNOWLEDGEBASE; PATHWAYS; TOOLBOX; GSM/GPR; GROWTH; KEGG},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Khan, Shawez/0000-0003-1682-4824},
+Times-Cited = {9},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000347561800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347559900001,
+Author = {Carreira, Rafael and Evangelista, Pedro and Maia, Paulo and Vilaca,
+ Paulo and Pont, Marcellinus and Tomb, Jean-Francois and Rocha, Isabel
+ and Rocha, Miguel},
+Title = {CBFA: phenotype prediction integrating metabolic models with constraints
+ derived from experimental data},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {8},
+Month = {DEC 3},
+Type = {Article},
+DOI = {10.1186/s12918-014-0123-1},
+Article-Number = {123},
+ISSN = {1752-0509},
+Keywords = {Constraint-based modeling; Metabolic Flux analysis; Metabolic
+ engineering; Open-source software},
+Keywords-Plus = {CENTRAL CARBON METABOLISM; OPEN-SOURCE SOFTWARE; ESCHERICHIA-COLI; FLUX
+ ANALYSIS; IN-SILICO; NETWORKS; ROBUSTNESS; CONSISTENT; GENOMICS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Rocha, Isabel/A-4279-2013
+ Rocha, Miguel/B-9404-2011
+ Maia, Paulo/AAM-1025-2021
+ Maia, Paulo/F-9148-2010
+ },
+ORCID-Numbers = {Rocha, Isabel/0000-0001-9494-3410
+ Rocha, Miguel/0000-0001-8439-8172
+ Maia, Paulo/0000-0002-0848-8683
+ Carreira, Rafael/0000-0003-4102-4204
+ Vilaca, Paulo/0000-0002-1098-5849},
+Times-Cited = {6},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000347559900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345090800001,
+Author = {Florez Parra, Daniela Carolina and Ramirez Tovar, Vanessa and Gonzalez
+ Barrios, Andres Fernando},
+Title = {ELUCIDATING THE ROLE OF METABOLITES AS QUORUM SENSING SIGNALS USING
+ PHASE PLANE ANALYSIS: THE CASE OF INDOLE IN ESCHERICHIA COLI},
+Journal = {JOURNAL OF BIOLOGICAL SYSTEMS},
+Year = {2014},
+Volume = {22},
+Number = {4},
+Pages = {523-531},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1142/S0218339014500193},
+ISSN = {0218-3390},
+EISSN = {1793-6470},
+Keywords = {Escherichia coli; Indole; Flux-Balance Analysis; Phenotype Phase Plane;
+ Quorum Sensing},
+Keywords-Plus = {BIOFILM FORMATION},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ORCID-Numbers = {Gonzalez Barrios, Andres Fernando/0000-0003-2517-2020},
+Times-Cited = {0},
+Journal-ISO = {J. Biol. Syst.},
+Unique-ID = {WOS:000345090800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000209583100020,
+Author = {Olavarria, K. and De Ingeniis, J. and Zielinski, D. C. and Fuentealba,
+ M. and Munoz, R. and McCloskey, D. and Feist, A. M. and Cabrera, R.},
+Title = {Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase
+ in Escherichia coli},
+Journal = {MICROBIOLOGY-SGM},
+Year = {2014},
+Volume = {160},
+Number = {12},
+Pages = {2780-2793},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1099/mic.0.082180-0},
+ISSN = {1350-0872},
+EISSN = {1465-2080},
+Keywords-Plus = {LEUCONOSTOC-MESENTEROIDES GLUCOSE-6-PHOSPHATE-DEHYDROGENASE; GLUCOSE
+ CATABOLISM; DEHYDROGENASE; PURIFICATION; ENZYME; GENE; PHOSPHORYLATION;
+ CONSTRUCTION; INACTIVATION; OPTIMALITY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Gamez, Karel Olavarria/L-7765-2014
+ Gamez, Karel Olavarria/I-8125-2012
+ Cabrera, Ricardo M/H-8132-2014
+ },
+ORCID-Numbers = {Gamez, Karel Olavarria/0000-0003-0435-7640
+ Cabrera, Ricardo/0000-0002-8896-3172
+ Fuentealba, Matias/0000-0001-7353-4394
+ Zielinski, Daniel/0000-0001-6452-483X
+ Munoz-Gonzalez, Rodrigo/0000-0003-2266-5014},
+Times-Cited = {15},
+Journal-ISO = {Microbiology-(UK)},
+Unique-ID = {WOS:000209583100020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000344385500009,
+Author = {Parambil, Lisha K. and Sarkar, Debasis},
+Title = {Probing the bioethanol production potential of Scheffersomyces
+ (Pichia) stipitis using validated genome-scale model},
+Journal = {BIOTECHNOLOGY LETTERS},
+Year = {2014},
+Volume = {36},
+Number = {12},
+Pages = {2443-2451},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1007/s10529-014-1629-8},
+ISSN = {0141-5492},
+EISSN = {1573-6776},
+Keywords = {Community-culture; Dynamic flux balance modelling; Ethanol production;
+ Pichia stipitis; Scheffersomyces stipitis; Xylose uptake},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GLUCOSE/XYLOSE MIXTURES; ETHANOL-PRODUCTION;
+ SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; NRRL Y-7124; CONVERSION;
+ XYLOSE; RECONSTRUCTION; FERMENTATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {3},
+Journal-ISO = {Biotechnol. Lett.},
+Unique-ID = {WOS:000344385500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000346330900017,
+Author = {Rienksma, Rienk A. and Suarez-Diez, Maria and Spina, Lucie and Schaap,
+ Peter J. and dos Santos, Vitor A. P. Martins},
+Title = {Systems-level modeling of mycobacterial metabolism for the
+ identification of new (multi-)drug targets},
+Journal = {SEMINARS IN IMMUNOLOGY},
+Year = {2014},
+Volume = {26},
+Number = {6},
+Pages = {610-622},
+Month = {DEC},
+Type = {Review},
+DOI = {10.1016/j.smim.2014.09.013},
+ISSN = {1044-5323},
+EISSN = {1096-3618},
+Keywords = {Mycobacterium tuberculosis; Metabolic model; Constraint-based metabolic
+ model; Gene essentiality; Metabolic state; Systems biology},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; GLOBAL RECONSTRUCTION;
+ TUBERCULOSIS; NETWORK; GROWTH; INSIGHTS; BIOSYNTHESIS; INTEGRATION;
+ MECHANISMS},
+Research-Areas = {Immunology},
+Web-of-Science-Categories = {Immunology},
+ResearcherID-Numbers = {Diez, Maria Suarez/AAI-1354-2020
+ },
+ORCID-Numbers = {Suarez-Diez, Maria/0000-0001-5845-146X
+ Schaap, Peter/0000-0002-4346-6084
+ Rienksma, Rienk/0000-0002-8670-5559
+ martins dos santos, vitor/0000-0002-2352-9017},
+Times-Cited = {28},
+Journal-ISO = {Semin. Immunol.},
+Unique-ID = {WOS:000346330900017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347580700009,
+Author = {Shellman, Erin R. and Chen, Yu and Lin, Xiaoxia and Burant, Charles F.
+ and Schnell, Santiago},
+Title = {Metabolic network motifs can provide novel insights into evolution: The
+ evolutionary origin of Eukaryotic organelles as a case study},
+Journal = {COMPUTATIONAL BIOLOGY AND CHEMISTRY},
+Year = {2014},
+Volume = {53},
+Number = {B},
+Pages = {242-250},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1016/j.compbiolchem.2014.09.006},
+ISSN = {1476-9271},
+EISSN = {1476-928X},
+Keywords = {Metabolism; Eukaryotic cell; Evolution; Phylogenies; Network motifs;
+ Enzyme classification},
+Keywords-Plus = {LATERAL GENE-TRANSFER; GENOME SEQUENCE; PROTEOBACTERIA; MITOCHONDRIA;
+ CONNECTION; PEROXISOME; HYPOTHESIS; PHYLOGENY; ALIGNMENT; ARCHAEAL},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications},
+ResearcherID-Numbers = {Schnell, Santiago/B-8682-2008
+ Burant, Charles/GPC-5690-2022},
+ORCID-Numbers = {Schnell, Santiago/0000-0002-9477-3914
+ Burant, Charles/0000-0001-9189-5003},
+Times-Cited = {4},
+Journal-ISO = {Comput. Biol. Chem.},
+Unique-ID = {WOS:000347580700009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345899700067,
+Author = {Erickson, Keesha E. and Gill, Ryan T. and Chatterjee, Anushree},
+Title = {CONSTRICTOR: Constraint Modification Provides Insight into Design of
+ Biochemical Networks},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {11},
+Month = {NOV 25},
+Type = {Article},
+DOI = {10.1371/journal.pone.0113820},
+Article-Number = {e113820},
+ISSN = {1932-6203},
+Keywords-Plus = {ETHYLENE-FORMING ENZYME; FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI;
+ ETHANOL-PRODUCTION; GENE; STRAIN; BIOSYNTHESIS; OPTIMIZATION;
+ METABOLISM; FRAMEWORK},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Erickson, Keesha/0000-0001-7482-457X},
+Times-Cited = {5},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000345899700067},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345770600050,
+Author = {Chouchani, Edward T. and Pell, Victoria R. and Gaude, Edoardo and
+ Aksentijevic, Dunja and Sundier, Stephanie Y. and Robb, Ellen L. and
+ Logan, Angela and Nadtochiy, Sergiy M. and Ord, Emily N. J. and Smith,
+ Anthony C. and Eyassu, Filmon and Shirley, Rachel and Hu, Chou-Hui and
+ Dare, Anna J. and James, Andrew M. and Rogatti, Sebastian and Hartley,
+ Richard C. and Eaton, Simon and Costa, Ana S. H. and Brookes, Paul S.
+ and Davidson, Sean M. and Duchen, Michael R. and Saeb-Parsy, Kourosh and
+ Shattock, Michael J. and Robinson, Alan J. and Work, Lorraine M. and
+ Frezza, Christian and Krieg, Thomas and Murphy, Michael P.},
+Title = {Ischaemic accumulation of succinate controls reperfusion injury through
+ mitochondrial ROS},
+Journal = {NATURE},
+Year = {2014},
+Volume = {515},
+Number = {7527},
+Pages = {431+},
+Month = {NOV 20},
+Type = {Article},
+DOI = {10.1038/nature13909},
+ISSN = {0028-0836},
+EISSN = {1476-4687},
+Keywords-Plus = {PURINE NUCLEOTIDE CYCLE; COMPLEX-I; SUPEROXIDE-PRODUCTION;
+ HYPOXIA-ISCHEMIA; MECHANISM; CARDIOPROTECTION; DEHYDROGENASE;
+ CONSEQUENCES; INHIBITION; PROTECTION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Costa, Ana/HDL-9297-2022
+ Hartley, Richard/AAT-7834-2020
+ Hartley, Richard/E-3489-2010
+ Eaton, Simon/C-4942-2008
+ Costa, Ana SH/H-2852-2012
+ Frezza, Christian/G-2174-2010
+ Davidson, Sean M/F-5275-2010
+ Smith, Anthony C/B-1891-2009
+ James, Andrew M/A-2639-2015
+ Chouchani, Edward T./HCH-3775-2022
+ duchen, michael/A-2116-2009
+ Lorkiewicz, Pawel/A-2126-2011
+ Murphy, Michael P/C-2120-2009
+ },
+ORCID-Numbers = {Hartley, Richard/0000-0003-1033-5405
+ Hartley, Richard/0000-0003-1033-5405
+ Eaton, Simon/0000-0003-0892-9204
+ Costa, Ana SH/0000-0001-8932-6370
+ Frezza, Christian/0000-0002-3293-7397
+ Davidson, Sean M/0000-0001-5182-4980
+ Smith, Anthony C/0000-0003-0141-0434
+ James, Andrew M/0000-0002-0515-9649
+ duchen, michael/0000-0003-2548-4294
+ Lorkiewicz, Pawel/0000-0002-1755-9826
+ Murphy, Michael P/0000-0003-1115-9618
+ Work, Lorraine/0000-0002-6462-4109
+ Ord, Emily/0000-0001-8564-7724
+ Gaude, Edoardo/0000-0001-8523-7792
+ Aksentijevic, Dunja/0000-0002-8480-6727
+ Krieg, Thomas/0000-0002-5192-580X
+ Shattock, Michael/0000-0001-6242-7585
+ Brookes, Paul/0000-0002-8639-8413
+ Saeb-Parsy, Kourosh/0000-0002-0633-3696},
+Times-Cited = {1686},
+Journal-ISO = {Nature},
+Unique-ID = {WOS:000345770600050},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345250400072,
+Author = {Sun, Zhiqiang and Meng, Hailin and Li, Jing and Wang, Jianfeng and Li,
+ Qian and Wang, Yong and Zhang, Yansheng},
+Title = {Identification of Novel Knockout Targets for Improving Terpenoids
+ Biosynthesis in Saccharomyces cerevisiae},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {11},
+Month = {NOV 11},
+Type = {Article},
+DOI = {10.1371/journal.pone.0112615},
+Article-Number = {e112615},
+ISSN = {1932-6203},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; COBRA TOOLBOX; BUDDING YEAST; EXPRESSION; GENE;
+ MITOCHONDRIAL; PATHWAY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {LI, QI/IUM-8577-2023
+ Jiang, Tao/IWM-7503-2023},
+Times-Cited = {27},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000345250400072},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000344402000018,
+Author = {Tsai, Kevin J. and Chang, Chuan-Hsiung},
+Title = {Diagnostics for Stochastic Genome-Scale Modeling via Model Slicing and
+ Debugging},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {11},
+Month = {NOV 4},
+Type = {Article},
+DOI = {10.1371/journal.pone.0110380},
+Article-Number = {e110380},
+ISSN = {1932-6203},
+Keywords-Plus = {SIMULATION; NETWORKS; TOOLBOX; BIOLOGY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Tsai, Kevin/GQR-1990-2022},
+Times-Cited = {0},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000344402000018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345558100106,
+Author = {Salehzadeh-Yazdi, Ali and Asgari, Yazdan and Saboury, Ali Akbar and
+ Masoudi-Nejad, Ali},
+Title = {Computational Analysis of Reciprocal Association of Metabolism and
+ Epigenetics in the Budding Yeast: A Genome-Scale Metabolic Model (GSMM)
+ Approach},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {11},
+Month = {NOV 3},
+Type = {Article},
+DOI = {10.1371/journal.pone.0111686},
+Article-Number = {e111686},
+ISSN = {1932-6203},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; TRANSCRIPTIONAL REGULATION; EXPRESSION DATA;
+ AMINO TERMINI; HISTONE H2A; NETWORK; RECONSTRUCTION; INTEGRATION;
+ VALIDATION; OPTIMALITY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Salehzadeh-Yazdi, Ali/J-9510-2019
+ Masoudi-Nejad, Ali/ABH-2078-2021
+ asgari, yazdan/AAL-9037-2020
+ Saboury, Ali Akbar/L-6136-2019
+ },
+ORCID-Numbers = {Salehzadeh-Yazdi, Ali/0000-0002-1678-0051
+ asgari, yazdan/0000-0001-6993-6956
+ Masoudi-Nejad, Ali/0000-0003-0659-5183},
+Times-Cited = {11},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000345558100106},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345433500002,
+Author = {Aguilar-Pontes, Maria Victoria and de Vries, Ronald P. and Zhou,
+ Miaomiao},
+Title = {(Post-)Genomics approaches in fungal research},
+Journal = {BRIEFINGS IN FUNCTIONAL GENOMICS},
+Year = {2014},
+Volume = {13},
+Number = {6, SI},
+Pages = {424-439},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1093/bfgp/elu028},
+ISSN = {2041-2649},
+EISSN = {2041-2657},
+Keywords = {fungal genomes; next-generation sequencing; fungal bioinformatics;
+ -omics data analysis; post-genomic analysis},
+Keywords-Plus = {IDENTIFYING DIFFERENTIAL EXPRESSION; NATURAL ANTISENSE TRANSCRIPTS;
+ TANDEM MASS-SPECTROMETRY; RNA-SEQ; GENE-EXPRESSION; METABOLIC
+ RECONSTRUCTION; FUNCTIONAL GENOMICS; STATISTICAL-METHODS;
+ TRICHODERMA-REESEI; MAMMALIAN GENOMES},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {de Vries, Ronald/JQJ-0061-2023
+ de Vries, Ronald P./F-8125-2011
+ Aguilar Pontes, Maria Victoria/AAU-1093-2021},
+ORCID-Numbers = {de Vries, Ronald P./0000-0002-4363-1123
+ Aguilar Pontes, Maria Victoria/0000-0002-3174-8834},
+Times-Cited = {11},
+Journal-ISO = {Brief. Funct. Genomics},
+Unique-ID = {WOS:000345433500002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347141300014,
+Author = {Mao, Longfei and Verwoerd, Wynand S.},
+Title = {Computational comparison of mediated current generation capacity of
+ Chlamydomonas reinhardtii in photosynthetic and respiratory
+ growth modes},
+Journal = {JOURNAL OF BIOSCIENCE AND BIOENGINEERING},
+Year = {2014},
+Volume = {118},
+Number = {5},
+Pages = {565-574},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.jbiosc.2014.04.021},
+ISSN = {1389-1723},
+EISSN = {1347-4421},
+Keywords = {Microbial fuel cell; Chlamydomonas reinhardtii; Bioelectricity; Flux
+ balance analysis; Flux variability analysis; Flux minimization; Flux
+ variability analysis with target flux minimization},
+Keywords-Plus = {MICROBIAL FUEL-CELLS; ELECTRICITY-GENERATION; METABOLIC NETWORK;
+ GEOBACTER-SULFURREDUCENS; SYSTEMS BIOLOGY; RECONSTRUCTION;
+ SYNECHOCYSTIS; ESSENTIALITY; BACTERIA; ACETATE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Verwoerd, Wynand/A-8320-2010
+ },
+ORCID-Numbers = {Verwoerd, Wynand/0000-0001-5489-9101
+ Mao, Longfei/0000-0003-0759-0501},
+Times-Cited = {5},
+Journal-ISO = {J. Biosci. Bioeng.},
+Unique-ID = {WOS:000347141300014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000357670400007,
+Author = {Senger, Ryan S. and Yen, Jiun Y. and Fong, Stephen S.},
+Title = {A review of genome-scale metabolic flux modeling of anaerobiosis in
+ biotechnology},
+Journal = {CURRENT OPINION IN CHEMICAL ENGINEERING},
+Year = {2014},
+Volume = {6},
+Pages = {33-42},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.coche.2014.08.003},
+ISSN = {2211-3398},
+Keywords-Plus = {IN-SILICO ANALYSIS; SACCHAROMYCES-CEREVISIAE; KLEBSIELLA-OXYTOCA;
+ ESCHERICHIA-COLI; RECONSTRUCTION; ACID; GENERATION; CONVERSION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+Times-Cited = {10},
+Journal-ISO = {Curr. Opin. Chem. Eng.},
+Unique-ID = {WOS:000357670400007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347742300001,
+Author = {Wu, Pei-Jung and Wu, Wu-Hsiung and Chen, Tzu-Chi and Lin, Kuan-Ting and
+ Lai, Jin-Mei and Huang, Chi-Ying F. and Wang, Feng-Sheng},
+Title = {Reconstruction and analysis of a signal transduction network using HeLa
+ cell protein-protein interaction data},
+Journal = {JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS},
+Year = {2014},
+Volume = {45},
+Number = {6},
+Pages = {2835-2842},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.jtice.2014.07.006},
+ISSN = {1876-1070},
+EISSN = {1876-1089},
+Keywords = {Protein-protein interaction; Signal transduction network; Systems
+ biology; HeLa cell; In situ proximity ligation assay},
+Keywords-Plus = {PROXIMITY LIGATION ASSAY; ANTITUMOR-ACTIVITY; IN-VIVO; ACTIVATION;
+ PATHWAYS; PHOSPHORYLATION; APOPTOSIS; GROWTH; PHARMACOGENOMICS;
+ METABOLISM},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Huang, Chi-Ying/AAG-7672-2022
+ Huang, Chi-Ying/AFL-7729-2022},
+ORCID-Numbers = {Huang, Chi-Ying/0000-0003-4898-4937
+ Huang, Chi-Ying/0000-0003-4898-4937},
+Times-Cited = {0},
+Journal-ISO = {J. Taiwan Inst. Chem. Eng.},
+Unique-ID = {WOS:000347742300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347558300001,
+Author = {Larocque, Mathieu and Chenard, Thierry and Najmanovich, Rafael},
+Title = {A curated C-difficile strain 630 metabolic network: prediction of
+ essential targets and inhibitors},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {8},
+Month = {OCT 15},
+Type = {Article},
+DOI = {10.1186/s12918-014-0117-z},
+Article-Number = {117},
+EISSN = {1752-0509},
+Keywords = {Essential genes; Flux balance analysis; Manual curation; Reconstructed
+ metabolic network; Synthetic accessibility; Inhibitors; Cross-reactivity
+ targets},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; COMPREHENSIVE DATABASE; BIOCYC COLLECTION;
+ ESSENTIAL GENES; GROWTH; ACETOBUTYLICUM; INFECTION; MECHANISM; SYSTEMS;
+ MODELS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Najmanovich, Rafael J/B-7100-2009
+ },
+ORCID-Numbers = {Najmanovich, Rafael/0000-0002-6971-7224
+ LAROCQUE, MELISSA/0000-0001-8109-9222},
+Times-Cited = {33},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000347558300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000343083600026,
+Author = {Vieira, Gilles and Carnicer, Marc and Portais, Jean-Charles and Heux,
+ Stephanie},
+Title = {FindPath: a Matlab solution for in silico design of synthetic
+ metabolic pathways},
+Journal = {BIOINFORMATICS},
+Year = {2014},
+Volume = {30},
+Number = {20},
+Pages = {2986-2988},
+Month = {OCT 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btu422},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {PREDICTION; CEREVISIAE; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Heras, Marc Carnicer/AAU-7304-2021
+ Carnicer, Marc/F-4065-2016
+ },
+ORCID-Numbers = {Heras, Marc Carnicer/0000-0003-4459-5969
+ Carnicer, Marc/0000-0003-4459-5969
+ Heux, Stephanie/0000-0003-1312-3002
+ Portais, Jean-Charles/0000-0002-3480-0933},
+Times-Cited = {13},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000343083600026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345920900008,
+Author = {Baghalian, Kambiz and Hajirezaei, Mohammad-Reza and Schreiber, Falk},
+Title = {Plant Metabolic Modeling: Achieving New Insight into Metabolism and
+ Metabolic Engineering},
+Journal = {PLANT CELL},
+Year = {2014},
+Volume = {26},
+Number = {10},
+Pages = {3847-3866},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1105/tpc.114.130328},
+ISSN = {1040-4651},
+EISSN = {1532-298X},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CRASSULACEAN ACID METABOLISM; SYSTEMS BIOLOGY
+ APPROACH; CARBON METABOLISM; PATHWAY ANALYSIS; OILSEED RAPE;
+ PHOTORESPIRATORY METABOLISM; SECONDARY METABOLISM; BIOCHEMICAL NETWORKS;
+ VARIABILITY ANALYSIS},
+Research-Areas = {Biochemistry \& Molecular Biology; Plant Sciences; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Plant Sciences; Cell Biology},
+ResearcherID-Numbers = {Hajirezaei, Mohammad-Reza/O-1217-2017
+ },
+ORCID-Numbers = {Hajirezaei, Mohammad-Reza/0000-0002-9537-0121
+ Baghalian, Kambiz/0000-0002-0813-7111},
+Times-Cited = {43},
+Journal-ISO = {Plant Cell},
+Unique-ID = {WOS:000345920900008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000344547900035,
+Author = {Benedict, Matthew N. and Mundy, Michael B. and Henry, Christopher S. and
+ Chia, Nicholas and Price, Nathan D.},
+Title = {Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment
+ in Genome-Scale Metabolic Models},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2014},
+Volume = {10},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003882},
+Article-Number = {e1003882},
+EISSN = {1553-7358},
+Keywords-Plus = {TRANSPOSON MUTANT LIBRARY; ADAPTIVE EVOLUTION; RECONSTRUCTION;
+ IDENTIFICATION; NETWORKS; MEVALONATE; GENERATION; BIOSYNTHESIS;
+ OPTIMIZATION; ISOPRENOIDS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Chia, Nicholas/0000-0001-9652-691X
+ Mundy, Michael/0000-0002-9936-0406
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {47},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000344547900035},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000342072500009,
+Author = {Blazeck, John and Miller, Jarrett and Pan, Anny and Gengler, Jon and
+ Holden, Clinton and Jamoussi, Mariam and Alper, Hal S.},
+Title = {Metabolic engineering of Saccharomyces cerevisiae for itaconic
+ acid production},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2014},
+Volume = {98},
+Number = {19},
+Pages = {8155-8164},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1007/s00253-014-5895-0},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Itaconic acid; Metabolic engineering; Saccharomyces cerevisiae; Flux
+ balance analysis; Genome-scale metabolic engineering},
+Keywords-Plus = {FUNCTIONAL-CHARACTERIZATION; ASPERGILLUS-TERREUS; YEAST; GENE; GENOME;
+ BIOSYNTHESIS; OPTIMIZATION; EXPRESSION; PATHWAYS; PROTEINS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Blazeck, John/0000-0002-6110-2938},
+Times-Cited = {64},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000342072500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000343934100001,
+Author = {Chindelevitch, Leonid and Trigg, Jason and Regev, Aviv and Berger,
+ Bonnie},
+Title = {An exact arithmetic toolbox for a consistent and reproducible structural
+ analysis of metabolic network models},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2014},
+Volume = {5},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1038/ncomms5893},
+Article-Number = {4893},
+ISSN = {2041-1723},
+Keywords-Plus = {MINIMAL CUT SETS; ELEMENTARY MODES; CONSTRAINTS; PREDICTION; SYSTEMS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Chindelevitch, Leonid/0000-0002-6619-6013},
+Times-Cited = {28},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000343934100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345709300003,
+Author = {Henson, Michael A. and Hanly, Timothy J.},
+Title = {Dynamic flux balance analysis for synthetic microbial communities},
+Journal = {IET SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {8},
+Number = {5},
+Pages = {214-229},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1049/iet-syb.2013.0021},
+ISSN = {1751-8849},
+EISSN = {1751-8857},
+Keywords-Plus = {SCALE METABOLIC MODELS; CONSTRAINT-BASED MODELS;
+ SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; ETHANOL-PRODUCTION;
+ BIOETHANOL PRODUCTION; PICHIA-STIPITIS; GLUCOSE/XYLOSE MIXTURES; XYLOSE
+ FERMENTATION; COCULTURE},
+Research-Areas = {Cell Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Cell Biology; Mathematical \& Computational Biology},
+Times-Cited = {49},
+Journal-ISO = {IET Syst. Biol.},
+Unique-ID = {WOS:000345709300003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000342809300015,
+Author = {Jayasinghe, Nadeera and Franks, Ashley and Nevin, Kelly P. and
+ Mahadevan, Radhakrishnan},
+Title = {Metabolic modeling of spatial heterogeneity of biofilms in microbial
+ fuel cells reveals substrate limitations in electrical current
+ generation},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2014},
+Volume = {9},
+Number = {10},
+Pages = {1350-1361},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1002/biot.201400068},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Biofilms; Genome-scale modeling; Mass transfer; Microbial growth;
+ Spatial heterogeneity},
+Keywords-Plus = {GEOBACTER-SULFURREDUCENS; ANODE; CONDUCTIVITY; EFFICIENCIES; NANOWIRES;
+ TRANSPORT; CAPACITY; STRAIN; GROWTH; POWER},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nevin, Kelly/AAA-4626-2019
+ Mahadevan, Radhakrishnan/A-8502-2008
+ },
+ORCID-Numbers = {Mahadevan, Radhakrishnan/0000-0002-1270-9063
+ Franks, Ashley/0000-0003-1664-6060},
+Times-Cited = {36},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000342809300015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000343378100006,
+Author = {Kim, Joonhoon and Reed, Jennifer L.},
+Title = {Refining metabolic models and accounting for regulatory effects},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2014},
+Volume = {29},
+Pages = {34-38},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1016/j.copbio.2014.02.009},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {TRANSCRIPTIONAL REGULATION; ESCHERICHIA-COLI; HIGH-THROUGHPUT; NETWORK
+ MODEL; OMIC DATA; GENOME; RECONSTRUCTION; EXPRESSION; GENE; DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Kim, Joonhoon/E-6253-2012
+ Reed, Jennifer L/E-5137-2011},
+ORCID-Numbers = {Kim, Joonhoon/0000-0002-7425-1828
+ Reed, Jennifer L/0000-0001-7854-6220},
+Times-Cited = {18},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000343378100006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000343859600001,
+Author = {Estevez, Semidan Robaina and Nikoloski, Zoran},
+Title = {Generalized framework for context-specific metabolic model extraction
+ methods},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2014},
+Volume = {5},
+Month = {SEP 19},
+Type = {Review},
+DOI = {10.3389/fpls.2014.00491},
+Article-Number = {491},
+ISSN = {1664-462X},
+Keywords = {genome-scale models; high-throughput data; data integration;
+ context-specific models; mathematical programming},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS; EXPRESSION DATA;
+ GENE-EXPRESSION; SACCHAROMYCES-CEREVISIAE; CELLULAR-METABOLISM;
+ PLANT-METABOLISM; NETWORK MODELS; OMICS DATA; SCALE},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ORCID-Numbers = {Robaina Estevez, Semidan/0000-0003-0781-1677
+ Nikoloski, Zoran/0000-0003-2671-6763},
+Times-Cited = {61},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000343859600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000340989800015,
+Author = {Badsha, Md Bahadur and Tsuboi, Ryo and Kurata, Hiroyuki},
+Title = {Complementary elementary modes for fast and efficient analysis of
+ metabolic networks},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2014},
+Volume = {90},
+Pages = {121-130},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2014.05.022},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Bioreactors; Elementary mode; Metabolic network; Metabolite over
+ production; Microbial growth; Modelling},
+Keywords-Plus = {FLUX MODES; PATHWAY ANALYSIS; STEADY-STATE; DISTRIBUTIONS; COMPUTATION;
+ DEFINITION; PREDICTION; SPACE; TOOL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ORCID-Numbers = {Kurata, Hiroyuki/0000-0003-4254-2214
+ Badsha, Md/0000-0002-6379-1554},
+Times-Cited = {7},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000340989800015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000347675900001,
+Author = {Taffi, Marianna and Paoletti, Nicola and Angione, Claudio and
+ Pucciarelli, Sandra and Marini, Mauro and Lio, Pietro},
+Title = {Bioremediation in marine ecosystems: a computational study combining
+ ecological modeling and flux balance analysis},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2014},
+Volume = {5},
+Month = {SEP 12},
+Type = {Article},
+DOI = {10.3389/fgene.2014.00319},
+Article-Number = {319},
+EISSN = {1664-8021},
+Keywords-Plus = {POLYCHLORINATED-BIPHENYLS; METABOLISM; PCBS; DECHLORINATION;
+ DEGRADATION; ORGANISMS; FRAMEWORK; TISSUES},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {P. Lió, Pietro Lio/AAV-3358-2021
+ Marini, Mauro/A-6477-2012
+ Paoletti, Nicola/D-8120-2018
+ Paoletti, Nicola/AAM-2322-2020
+ Marini, Mauro/AAE-9399-2020
+ CNR, Ismar/P-1247-2014
+ },
+ORCID-Numbers = {P. Lió, Pietro Lio/0000-0002-0540-5053
+ Marini, Mauro/0000-0002-9674-7197
+ Paoletti, Nicola/0000-0002-4723-5363
+ Marini, Mauro/0000-0002-9674-7197
+ CNR, Ismar/0000-0001-5351-1486
+ Pucciarelli, Sandra/0000-0003-4178-2689
+ Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {10},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000347675900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341312200015,
+Author = {Campodonico, Miguel A. and Andrews, Barbara A. and Asenjo, Juan A. and
+ Palsson, Bernhard O. and Feist, Adam M.},
+Title = {Generation of an atlas for commodity chemical production in
+ Escherichia coli and a novel pathway prediction algorithm,
+ GEM-Path},
+Journal = {METABOLIC ENGINEERING},
+Year = {2014},
+Volume = {25},
+Pages = {140-158},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2014.07.009},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Systems biology; Pathway predictions; Escherichia coli; Strain design},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; MICROBIAL-PRODUCTION; METABOLIC PATHWAYS;
+ 2,3-BUTANEDIOL PRODUCTION; ADAPTIVE EVOLUTION; K-12 MG1655; DESIGN;
+ SYSTEMS; RECONSTRUCTION; BIOFUELS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Andrews, Barbara/J-5070-2016
+ Asenjo, Juan JAA/L-8336-2013
+ },
+ORCID-Numbers = {Asenjo, Juan JAA/0000-0002-3475-7664
+ Palsson, Bernhard/0000-0003-2357-6785
+ Angel Campodonico Alt, Miguel/0000-0003-4105-9976},
+Times-Cited = {114},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000341312200015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341312200019,
+Author = {Cardenas, Javier and Da Silva, Nancy A.},
+Title = {Metabolic engineering of Saccharomyces cerevisiae for the
+ production of triacetic acid lactone},
+Journal = {METABOLIC ENGINEERING},
+Year = {2014},
+Volume = {25},
+Pages = {194-203},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2014.07.008},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Saccharomyces cerevisiae; Triacetic acid lactone; 2-pyrone synthase;
+ Biorenewable chemicals; Metabolic engineering; Central carbon metabolism},
+Keywords-Plus = {POLYKETIDE SYNTHASES; YEAST-CELLS; VECTOR SET; PATHWAY; GENE;
+ TRANSFORMATION; BIOSYNTHESIS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Cardenas, Javier/C-6837-2015},
+ORCID-Numbers = {Cardenas, Javier/0000-0002-9229-5082},
+Times-Cited = {67},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000341312200019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341233500009,
+Author = {Heinken, Almut and Khan, M. Tanweer and Paglia, Giuseppe and Rodionov,
+ Dmitry A. and Harmsen, Hermie J. M. and Thiele, Ines},
+Title = {Functional Metabolic Map of Faecalibacterium prausnitzii, a
+ Beneficial Human Gut Microbe},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2014},
+Volume = {196},
+Number = {18},
+Pages = {3289-3302},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1128/JB.01780-14},
+ISSN = {0021-9193},
+EISSN = {1098-5530},
+Keywords-Plus = {FUSOBACTERIUM-PRAUSNITZII; SYSTEMS BIOLOGY; HIGH-THROUGHPUT; GENOME;
+ FERMENTATION; MODEL; RECONSTRUCTION; ASSOCIATION; METAGENOME; DIVERSITY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Paglia, Giuseppe/H-2012-2018
+ Rodionov, Dmitry/V-2688-2018
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Paglia, Giuseppe/0000-0003-4724-6801
+ Rodionov, Dmitry/0000-0002-0939-390X
+ Heinken, Almut/0000-0001-6938-8072},
+Times-Cited = {131},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000341233500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341694200010,
+Author = {Kim, Minsuk and Yi, Jeong Sang and Kim, Joonwon and Kim, Ji-Nu and Kim,
+ Min Woo and Kim, Byung-Gee},
+Title = {Reconstruction of a high-quality metabolic model enables the
+ identification of gene overexpression targets for enhanced antibiotic
+ production in Streptomyces coelicolor A3(2)},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2014},
+Volume = {9},
+Number = {9, SI},
+Pages = {1185-1194},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1002/biot.201300539},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Antibiotics; BCDH; Genome-scale model; Metabolic engineering;
+ Streptomyces coelicolor},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GENOME-SCALE ANALYSIS; CELLULAR-METABOLISM;
+ SYSTEMS BIOLOGY; DEHYDROGENASE; BIOSYNTHESIS; ACTINORHODIN; SEQUENCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {kim, byung-gee/AAR-1933-2020
+ },
+ORCID-Numbers = {Kim, Minsuk/0000-0001-9958-0380},
+Times-Cited = {45},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000341694200010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000345340300015,
+Author = {Lisha, K. P. and Sarkar, Debasis},
+Title = {In silico analysis of bioethanol production from glucose/xylose
+ mixtures during fed-batch fermentation of co-culture and mono-culture
+ systems},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2014},
+Volume = {19},
+Number = {5},
+Pages = {879-891},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1007/s12257-014-0320-1},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {bioethanol; bioreactors; fermentation; metabolic engineering;
+ optimization},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; SACCHAROMYCES-CEREVISIAE; ETHANOL-PRODUCTION;
+ ESCHERICHIA-COLI; XYLOSE; OPTIMIZATION; RECONSTRUCTION; METABOLISM;
+ GROWTH; STATE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {1},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:000345340300015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000343011700034,
+Author = {Nam, Hojung and Campodonico, Miguel and Bordbar, Aarash and Hyduke,
+ Daniel R. and Kim, Sangwoo and Zielinski, Daniel C. and Palsson,
+ Bernhard O.},
+Title = {A Systems Approach to Predict Oncometabolites via Context-Specific
+ Genome-Scale Metabolic Networks},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2014},
+Volume = {10},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003837},
+Article-Number = {e1003837},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI; GLOBAL RECONSTRUCTION; DRUG TARGETS; CANCER;
+ MUTATIONS; FUMARATE; 2-HYDROXYGLUTARATE; ACCUMULATION; INHIBITION;
+ EXPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {/AAG-5264-2021
+ Nam, Hojung/AAR-4065-2020
+ Kim, Sangwoo/I-7348-2015
+ },
+ORCID-Numbers = {/0000-0001-6460-6771
+ Nam, Hojung/0000-0002-5109-9114
+ Kim, Sangwoo/0000-0001-5356-0827
+ Palsson, Bernhard/0000-0003-2357-6785
+ Zielinski, Daniel/0000-0001-6452-483X
+ Angel Campodonico Alt, Miguel/0000-0003-4105-9976},
+Times-Cited = {49},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000343011700034},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000337861600025,
+Author = {Perez-Garcia, Octavio and Villas-Boas, Silas G. and Swift, Simon and
+ Chandran, Kartik and Singhal, Naresh},
+Title = {Clarifying the regulation of NO/N2O production in
+ Nitrosomonas europaea during anoxic-oxic transition via flux
+ balance analysis of a metabolic network model},
+Journal = {WATER RESEARCH},
+Year = {2014},
+Volume = {60},
+Pages = {267-277},
+Month = {SEP 1},
+Type = {Article},
+DOI = {10.1016/j.watres.2014.04.049},
+ISSN = {0043-1354},
+Keywords = {Nitrous oxide production; Ammonia oxidizing bacteria; Nitrosomonas
+ europaea metabolism; Metabolic network modelling; Flux balance analysis;
+ Nitrifier denitrification},
+Keywords-Plus = {WASTE-WATER TREATMENT; CONSTRAINT-BASED MODELS; NITROUS-OXIDE;
+ NITRIC-OXIDE; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; AMMONIA;
+ N2O; GENERATION; REMOVAL},
+Research-Areas = {Engineering; Environmental Sciences \& Ecology; Water Resources},
+Web-of-Science-Categories = {Engineering, Environmental; Environmental Sciences; Water Resources},
+ResearcherID-Numbers = {Villas-Boas, Silas/AAS-5888-2020
+ Villas-Boas, Silas Granato/HLQ-1860-2023
+ Singhal, Naresh/C-2769-2008
+ Swift, Simon/H-3072-2019
+ Villas-Boas, Silas/AAR-6748-2020
+ },
+ORCID-Numbers = {Villas-Boas, Silas/0000-0003-0148-5882
+ Singhal, Naresh/0000-0002-9461-688X
+ Swift, Simon/0000-0001-7352-1112
+ Perez-Garcia, Octavio/0000-0002-5900-1310},
+Times-Cited = {37},
+Journal-ISO = {Water Res.},
+Unique-ID = {WOS:000337861600025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341312200016,
+Author = {Sanchez, Benjamin J. and Perez-Correa, Jose R. and Agosin, Eduardo},
+Title = {Construction of robust dynamic genome-scale metabolic model structures
+ of Saccharomyces cerevisiae through iterative re-parameterization},
+Journal = {METABOLIC ENGINEERING},
+Year = {2014},
+Volume = {25},
+Pages = {159-173},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2014.07.004},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Genome-scale metabolic models; Dynamic flux balance analysis;
+ Metaheuristic optimization; Yeast; Parameter estimation; Sensitivity
+ analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI;
+ ETHANOL-PRODUCTION; GENE-EXPRESSION; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; CARBON-SUFFICIENT; HIGH-THROUGHPUT; OPTIMIZATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Perez-Correa, Jose Ricardo/I-5565-2012
+ Sánchez, Benjamín/D-2151-2015
+ Agosin, Eduardo/D-1411-2014
+ Sánchez, Benjamín J./O-6859-2019},
+ORCID-Numbers = {Perez-Correa, Jose Ricardo/0000-0002-1278-7782
+ Sánchez, Benjamín/0000-0001-6093-4110
+ Agosin, Eduardo/0000-0003-1656-150X
+ Sánchez, Benjamín J./0000-0001-6093-4110},
+Times-Cited = {19},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000341312200016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000340837600002,
+Author = {Sandstrom, Anders G. and Almqvist, Henrik and Portugal-Nunes, Diogo and
+ Neves, Dario and Liden, Gunnar and Gorwa-Grauslund, Marie F.},
+Title = {Saccharomyces cerevisiae: a potential host for carboxylic acid
+ production from lignocellulosic feedstock?},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2014},
+Volume = {98},
+Number = {17},
+Pages = {7299-7318},
+Month = {SEP},
+Type = {Review},
+DOI = {10.1007/s00253-014-5866-5},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Saccharomyces cerevisiae; Carboxylic acid; Metabolic engineering;
+ Lignocellulosic biomass},
+Keywords-Plus = {YEAST ARTIFICIAL CHROMOSOMES; ALPHA-KETOGLUTARIC ACID; FUMARIC-ACID;
+ ACETIC-ACID; BIOTECHNOLOGICAL PRODUCTION; LACTIC-ACID;
+ GLYCEROL-3-PHOSPHATE DEHYDROGENASE; 3-HYDROXYPROPIONIC ACID;
+ ALCOHOL-DEHYDROGENASE; BIOSYNTHETIC PATHWAYS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Gorwa-Grauslund, Marie/AAD-4225-2020
+ },
+ORCID-Numbers = {Gorwa-Grauslund, Marie F/0000-0002-4810-4082
+ Neves, Dario/0000-0002-9808-6476
+ Liden, Gunnar/0000-0002-1494-8201
+ Almqvist, Henrik/0000-0003-2835-1817},
+Times-Cited = {17},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000340837600002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000342912400069,
+Author = {Thiele, Ines and Vlassis, Nikos and Fleming, Ronan M. T.},
+Title = {FASTGAPFILL: efficient gap filling in metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2014},
+Volume = {30},
+Number = {17},
+Pages = {2529-2531},
+Month = {SEP 1},
+Note = {13th European Conference on Computational Biology (ECCB), Strasbourg,
+ FRANCE, SEP 07-10, 2014},
+Type = {Article; Proceedings Paper},
+DOI = {10.1093/bioinformatics/btu321},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {RECONSTRUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Fleming, Ronan MT/ABC-4093-2021},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Fleming, Ronan MT/0000-0001-5346-9812},
+Times-Cited = {75},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000342912400069},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000343011700040,
+Author = {Yang, Hong and Krumholz, Elias W. and Brutinel, Evan D. and Palani,
+ Nagendra P. and Sadowsky, Michael J. and Odlyzko, Andrew M. and
+ Gralnick, Jeffrey A. and Libourel, Igor G. L.},
+Title = {Genome-Scale Metabolic Network Validation of Shewanella
+ oneidensis Using Transposon Insertion Frequency Analysis},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2014},
+Volume = {10},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003848},
+Article-Number = {e1003848},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {HIDDEN MARKOV MODEL; BACTERIAL GENOMES; MUTANT LIBRARY; TN-SEQ;
+ RECONSTRUCTION; GROWTH; GENES; IDENTIFICATION; FITNESS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Sadowsky, Michael/J-2507-2016
+ },
+ORCID-Numbers = {Sadowsky, Michael/0000-0001-8779-2781
+ Gralnick, Jeffrey/0000-0001-9250-7770
+ Palani, Nagendra Prasad/0000-0001-7701-8901},
+Times-Cited = {19},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000343011700040},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000340306700022,
+Author = {Quek, Lake-Ee and Dietmair, Stefanie and Hanscho, Michael and Martinez,
+ Veronica S. and Borth, Nicole and Nielsen, Lars K.},
+Title = {Reducing Recon 2 for steady-state flux analysis of HEK cell culture},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2014},
+Volume = {184},
+Pages = {172-178},
+Month = {AUG 20},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2014.05.021},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Genome-scale model; Mammalian cell culture; Flux analysis; Human
+ metabolism; Model reduction},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; METABOLIC FLUXES; GLUTAMINE; GLUCOSE; GROWTH;
+ MEDIA},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nielsen, Lars K/A-5519-2011
+ },
+ORCID-Numbers = {Nielsen, Lars K/0000-0001-8191-3511
+ Borth, Nicole/0000-0001-6324-9338
+ Martinez, Veronica/0000-0003-2729-5278
+ Quek, Lake-Ee/0000-0002-9313-8740},
+Times-Cited = {45},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000340306700022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000340648000001,
+Author = {Costa, Rafael S. and Verissimo, Andre and Vinga, Susana},
+Title = {KiMoSys: a web-based repository of experimental data for KInetic
+ MOdels of biological SYStems},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {8},
+Month = {AUG 13},
+Type = {Article},
+DOI = {10.1186/s12918-014-0085-3},
+Article-Number = {85},
+EISSN = {1752-0509},
+Keywords = {Dynamic modeling; Repository; Data sharing; Accessible dynamic data;
+ Associated kinetic models},
+Keywords-Plus = {CENTRAL CARBON METABOLISM; ESCHERICHIA-COLI; PATHWAY; NETWORKS;
+ DYNAMICS; LIMITATIONS; SIMULATION; REDUCTION; PLATFORM},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Vinga, Susana/B-8450-2008
+ Costa, RS/ABB-5507-2020
+ Verissimo, Andre/H-7446-2017},
+ORCID-Numbers = {Vinga, Susana/0000-0002-1954-5487
+ Costa, RS/0000-0002-7539-488X
+ Verissimo, Andre/0000-0002-2212-339X},
+Times-Cited = {18},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000340648000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000338812100008,
+Author = {Ye, Chao and Zou, Wei and Xu, Nan and Liu, Liming},
+Title = {Metabolic model reconstruction and analysis of an artificial microbial
+ ecosystem for vitamin C production},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2014},
+Volume = {182},
+Pages = {61-67},
+Month = {JUL 20},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2014.04.027},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Artificial microbial ecosystem; Ketogulonicigenium vulgare; Bacillus
+ megaterium; Genome-scale metabolic models; Vitamin C},
+Keywords-Plus = {KETOGULONICIGENIUM-VULGARE; KETOGULONIGENIUM-VULGARE;
+ BACILLUS-MEGATERIUM; MIXED CULTURE; FERMENTATIONS; COMMUNITY; FOLATE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ye, Chao/M-3689-2019
+ Ye, Chao/HGD-3564-2022
+ Liu, Liming/B-1972-2009
+ Ye, Chao/H-7623-2014
+ },
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Ye, Chao/0000-0002-6671-7819
+ Liu, Liming/0000-0003-3022-936X
+ Ye, Chao/0000-0002-6671-7819
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {29},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000338812100008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341306600062,
+Author = {Kumar, Amit and Harrelson, Thomas and Lewis, Nathan E. and Gallagher,
+ Emily J. and LeRoith, Derek and Shiloach, Joseph and Betenbaugh, Michael
+ J.},
+Title = {Multi-Tissue Computational Modeling Analyzes Pathophysiology of Type 2
+ Diabetes in MKR Mice},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {7},
+Month = {JUL 16},
+Type = {Article},
+DOI = {10.1371/journal.pone.0102319},
+Article-Number = {e102319},
+ISSN = {1932-6203},
+Keywords-Plus = {PROTEIN REFERENCE DATABASE; HUMAN METABOLIC NETWORK;
+ FATTY-ACID-METABOLISM; INSULIN-RESISTANCE; MOLECULAR-CLONING;
+ MENDELIAN-INHERITANCE; COA SYNTHETASE; AMINO-ACIDS; MOUSE MODEL; ENZYME},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Harrelson, Thomas/0000-0002-8689-4273
+ Kumar, Amit/0000-0003-2140-5130},
+Times-Cited = {12},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000341306600062},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341354100039,
+Author = {De Martino, Andrea and De Martino, Daniele and Mulet, Roberto and
+ Pagnani, Andrea},
+Title = {Identifying All Moiety Conservation Laws in Genome-Scale Metabolic
+ Networks},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {7},
+Month = {JUL 2},
+Type = {Article},
+DOI = {10.1371/journal.pone.0100750},
+Article-Number = {e100750},
+ISSN = {1932-6203},
+Keywords-Plus = {CHEMICAL-REACTION SYSTEMS; ESCHERICHIA-COLI; BIOCHEMICAL NETWORKS; NULL
+ SPACE; ALGORITHM; RECONSTRUCTION; ESSENTIALITY; ORGANIZATION; SIZE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {de martino, daniele/L-6519-2017
+ Pagnani, Andrea/J-2363-2015
+ De Martino, Andrea/AAY-4120-2020
+ De Martino, Daniele/GQA-9589-2022
+ },
+ORCID-Numbers = {Pagnani, Andrea/0000-0002-6509-0807
+ De Martino, Daniele/0000-0002-5214-4706
+ Mulet, Roberto/0000-0001-5168-5116
+ De Martino, Andrea/0000-0001-7590-6542},
+Times-Cited = {9},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000341354100039},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341970300019,
+Author = {Bodor, Zsolt and Fazakas, Andrea (Iuhasz) and Kovacs, Erika and Lanyi,
+ Szabolcs and Albert, Beata},
+Title = {Systems biology and metabolic engineering for obtaining E.
+ coli mutants capable to produce succinate from renewable
+ resources},
+Journal = {ROMANIAN BIOTECHNOLOGICAL LETTERS},
+Year = {2014},
+Volume = {19},
+Number = {4},
+Pages = {9625-9636},
+Month = {JUL-AUG},
+Type = {Article},
+ISSN = {1224-5984},
+Keywords = {systems biology; biotechnology; succinate; Escherichia coli; metabolic
+ engineering; modelling; glycerol},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; GLYCEROL; STRAINS; OVERPRODUCTION; STRATEGIES;
+ GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Bodor, Zsolt/ABE-2182-2020
+ },
+ORCID-Numbers = {Bodor, Zsolt/0000-0003-1386-6957},
+Times-Cited = {6},
+Journal-ISO = {Rom. Biotech. Lett.},
+Unique-ID = {WOS:000341970300019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000340295800007,
+Author = {Bordbar, Aarash and Nagarajan, Harish and Lewis, Nathan E. and Latif,
+ Haythem and Ebrahim, Ali and Federowicz, Stephen and Schellenberger, Jan
+ and Palsson, Bernhard O.},
+Title = {Minimal metabolic pathway structure is consistent with associated
+ biomolecular interactions},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {10},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.15252/msb.20145243},
+Article-Number = {737},
+ISSN = {1744-4292},
+Keywords = {constraint-based modeling; genetic interactions; pathway analysis;
+ protein-protein interactions; transcriptional regulatory networks},
+Keywords-Plus = {FUNCTIONAL-CHARACTERIZATION; EXTREME PATHWAYS; GENE ONTOLOGY;
+ RECONSTRUCTION; NETWORKS; DATABASE; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ /AAG-5264-2021
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ /0000-0001-6460-6771
+ Palsson, Bernhard/0000-0003-2357-6785
+ Ebrahim, Ali/0000-0002-4009-2128},
+Times-Cited = {33},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000340295800007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000340295800002,
+Author = {Carrera, Javier and Estrela, Raissa and Luo, Jing and Rai, Navneet and
+ Tsoukalas, Athanasios and Tagkopoulos, Ilias},
+Title = {An integrative, multi-scale, genome-wide model reveals the phenotypic
+ landscape of Escherichia coli},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {10},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.15252/msb.20145108},
+Article-Number = {735},
+ISSN = {1744-4292},
+Keywords = {genome engineering; genome-scale model; model-driven experimentation;
+ predictive modeling and integration; systems and synthetic biology},
+Keywords-Plus = {SCALE METABOLIC RECONSTRUCTIONS; GENE NETWORK INFERENCE; WHOLE-CELL
+ SIMULATION; REGULATORY NETWORKS; COMPUTATIONAL MODEL; EXPRESSION;
+ ENVIRONMENTS; VARIABILITY; ANNOTATION; VALIDATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Rai, Navneet/H-4669-2019
+ Tagkopoulos, Ilias/B-3468-2009},
+ORCID-Numbers = {Rai, Navneet/0000-0002-2321-2378
+ },
+Times-Cited = {56},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000340295800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341588100027,
+Author = {Eilam, Omer and Zarecki, Raphy and Oberhardt, Matthew and Ursell, Luke
+ K. and Kupiec, Martin and Knight, Rob and Gophna, Uri and Ruppin, Eytan},
+Title = {Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota
+ Abundance and Host Diet-Specific Adaptations},
+Journal = {MBIO},
+Year = {2014},
+Volume = {5},
+Number = {4},
+Month = {JUL-AUG},
+Type = {Article},
+DOI = {10.1128/mBio.01526-14},
+Article-Number = {e01526-14},
+ISSN = {2150-7511},
+Keywords-Plus = {FUNCTIONAL INTERACTIONS; SYSTEMS BIOLOGY; METABOLISM; COMMUNITY;
+ ASSOCIATION; MODELS; HEALTH; IMPACT; COLON},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Gophna, Uri/AAS-8376-2020
+ Knight, Rob/D-1299-2010
+ Ruppin, Eytan/R-9698-2017
+ },
+ORCID-Numbers = {Gophna, Uri/0000-0001-5129-5652
+ Ruppin, Eytan/0000-0002-7862-3940
+ Knight, Rob/0000-0002-0975-9019},
+Times-Cited = {34},
+Journal-ISO = {mBio},
+Unique-ID = {WOS:000341588100027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000342206100002,
+Author = {Jing, Lu Shi and Shah, Farah Fathiah Muzaffar and Mohamad, Mohd Saberi
+ and Hamran, Nur Laily and Salleh, Abdul Hakim Mohamed and Deris, Safaai
+ and Alashwal, Hany},
+Title = {Database and tools for metabolic network analysis},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2014},
+Volume = {19},
+Number = {4},
+Pages = {568-585},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1007/s12257-014-0172-8},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {metabolic network analysis tools; metabolic network reconstruction;
+ Kyoto Encyclopedia of Genes and Genomes (KEGG); flux balance analysis
+ (FBA); OptFlux; MetaFluxNet},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; PATHWAY DATABASES; JATROPHA-CURCAS;
+ HIGH-THROUGHPUT; PLATFORM; SOFTWARE; METACYC; MODELS; KEGG;
+ VISUALIZATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {SALLEH, ABDUL HAKIM/D-2869-2018
+ Mohamad, Mohd Saberi/J-3201-2014
+ },
+ORCID-Numbers = {SALLEH, ABDUL HAKIM/0000-0003-1332-6176
+ Mohamad, Mohd Saberi/0000-0002-1079-4559
+ Alashwal, Hany/0000-0002-5721-5104},
+Times-Cited = {13},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:000342206100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000338934300012,
+Author = {King, Zachary A. and Feist, Adam M.},
+Title = {Optimal cofactor swapping can increase the theoretical yield for
+ chemical production in Escherichia coli and Saccharomyces
+ cerevisiae},
+Journal = {METABOLIC ENGINEERING},
+Year = {2014},
+Volume = {24},
+Pages = {117-128},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2014.05.009},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Cofactor balancing; Escherichia coli; Saccharomyces cerevisiae;
+ Constraint-based modeling; MILP; Theoretical yield; Metabolic
+ engineering},
+Keywords-Plus = {NADH AVAILABILITY; 3-HYDROXYPROPIONIC ACID; MALIC ENZYME; N-BUTANOL;
+ OVEREXPRESSION; PATHWAY; TRANSHYDROGENASE; FERMENTATION; METABOLISM;
+ EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {King, Zachary/V-3402-2019},
+ORCID-Numbers = {King, Zachary/0000-0003-1238-1499},
+Times-Cited = {32},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000338934300012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000339365700005,
+Author = {Sarria, Stephen and Wong, Betty and Martin, Hector Garcia and Keasling,
+ Jay D. and Peralta-Yahya, Pamela},
+Title = {Microbial Synthesis of Pinene},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2014},
+Volume = {3},
+Number = {7},
+Pages = {466-475},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1021/sb4001382},
+ISSN = {2161-5063},
+Keywords = {advanced biofuels; tactical fuels; isoprenoids; terpene synthase; pinene},
+Keywords-Plus = {GERANYL DIPHOSPHATE SYNTHASE; CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI;
+ ABIES-GRANDIS; FUNCTIONAL EXPRESSION; ADVANCED BIOFUELS; CDNA ISOLATION;
+ QUANTITATIVE PREDICTION; PYROPHOSPHATE SYNTHASE; MONOTERPENE SYNTHASES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Keasling, Jay D/J-9162-2012
+ Keasling, Jay/HPG-6073-2023
+ Martin, Hector Garcia/B-5357-2009},
+ORCID-Numbers = {Keasling, Jay D/0000-0003-4170-6088
+ Martin, Hector Garcia/0000-0002-4556-9685},
+Times-Cited = {162},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000339365700005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000338118900071,
+Author = {Seaver, Samuel M. D. and Gerdes, Svetlana and Frelin, Oceane and
+ Lerma-Ortiz, Claudia and Bradbury, Louis M. T. and Zallot, Remi and
+ Hasnain, Ghulam and Niehaus, Thomas D. and El Yacoubi, Basma and
+ Pasternak, Shiran and Olson, Robert and Pusch, Gordon and Overbeek, Ross
+ and Stevens, Rick and de Crecy-Lagard, Valerie and Ware, Doreen and
+ Hanson, Andrew D. and Henry, Christopher S.},
+Title = {High-throughput comparison, functional annotation, and metabolic
+ modeling of plant genomes using the PlantSEED resource},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2014},
+Volume = {111},
+Number = {26},
+Pages = {9645-9650},
+Month = {JUL 1},
+Type = {Article},
+DOI = {10.1073/pnas.1401329111},
+ISSN = {0027-8424},
+Keywords = {systems biology; computational biochemistry; plant metabolism; plant
+ genomics},
+Keywords-Plus = {PATHWAY DATABASE; NETWORK; RECONSTRUCTION; ARABIDOPSIS; GENERATION;
+ PROTEOMICS; OPTIMIZATION; COLLECTION; CURATION; ONLINE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Yacoubi keyhani, basma/HLH-3840-2023
+ Seaver, Samuel M. D./C-2614-2008
+ ZALLOT, Rémi/D-3933-2014
+ de Crecy-Lagard, Valerie/AAN-8995-2020
+ Zallot, Rémi Gilles/J-9645-2019
+ },
+ORCID-Numbers = {Seaver, Samuel M. D./0000-0002-7674-5194
+ ZALLOT, Rémi/0000-0002-7317-1578
+ Zallot, Rémi Gilles/0000-0002-7317-1578
+ Niehaus, Thomas/0000-0002-3575-8001},
+Times-Cited = {58},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000338118900071},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000337580000014,
+Author = {Weiner, Michael and Troendle, Julia and Albermann, Christoph and
+ Sprenger, Georg A. and Weuster-Botz, Dirk},
+Title = {Improvement of constraint-based flux estimation during L-phenylalanine
+ production with Escherichia coli using targeted knock-out mutants},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2014},
+Volume = {111},
+Number = {7},
+Pages = {1406-1416},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/bit.25195},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {constraint-based flux estimation; Flux Variability Analysis;
+ L-phenylalanine; glycerol; malic enzymes},
+Keywords-Plus = {GENOME-SCALE; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; GLYCEROL;
+ MODELS; RECONSTRUCTIONS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sprenger, Georg A./E-2384-2011
+ },
+ORCID-Numbers = {Sprenger, Georg A./0000-0002-7879-8978
+ Weuster-Botz, Dirk/0000-0002-1171-4194},
+Times-Cited = {14},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000337580000014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000338583000001,
+Author = {Weaver, Daniel S. and Keseler, Ingrid M. and Mackie, Amanda and Paulsen,
+ Ian T. and Karp, Peter D.},
+Title = {A genome-scale metabolic flux model of Escherichia coli K-12
+ derived from the EcoCyc database},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {8},
+Month = {JUN 30},
+Type = {Article},
+DOI = {10.1186/1752-0509-8-79},
+Article-Number = {79},
+EISSN = {1752-0509},
+Keywords = {Escherichia coli; Flux balance analysis; Constraint-based modeling;
+ Metabolic network reconstruction; Metabolic modeling; Genome-scale
+ model; Gene essentiality; Systems biology; EcoCyc; Pathway Tools},
+Keywords-Plus = {ETHANOLAMINE AMMONIA-LYASE; PHENOTYPIC CHARACTERIZATION;
+ LIPOPOLYSACCHARIDE CORE; SOFTWARE APPLICATIONS; PROTON TRANSLOCATION;
+ SERINE BIOSYNTHESIS; PHYSIOLOGICAL-ROLE; MOLECULAR-CLONING; ANAEROBIC
+ GROWTH; CITRATE SYNTHASE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Paulsen, Ian T/K-3832-2012
+ Karp, Peter/C-3514-2012},
+ORCID-Numbers = {Paulsen, Ian T/0000-0001-9015-9418
+ Karp, Peter/0000-0002-5876-6418},
+Times-Cited = {34},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000338583000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000338733600001,
+Author = {Latendresse, Mario},
+Title = {Efficiently gap-filling reaction networks},
+Journal = {BMC BIOINFORMATICS},
+Year = {2014},
+Volume = {15},
+Month = {JUN 28},
+Type = {Article},
+DOI = {10.1186/1471-2105-15-225},
+Article-Number = {225},
+ISSN = {1471-2105},
+Keywords = {Flux Balance Analysis (FBA); Gap-filling; Systems biology; Reaction
+ network; Linear Programming (LP); Mixed-Integer Linear Programming
+ (MILP)},
+Keywords-Plus = {OPTIMIZATION; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+Times-Cited = {21},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000338733600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000338430700072,
+Author = {Rohatgi, Neha and Nielsen, Tine Kragh and Bjorn, Sara Petersen and
+ Axelsson, Ivar and Paglia, Giuseppe and Voldborg, Bjorn Gunnar and
+ Palsson, Bernhard O. and Rolfsson, Ottar},
+Title = {Biochemical Characterization of Human Gluconokinase and the Proposed
+ Metabolic Impact of Gluconic Acid as Determined by Constraint Based
+ Metabolic Network Analysis},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {6},
+Month = {JUN 4},
+Type = {Article},
+DOI = {10.1371/journal.pone.0098760},
+Article-Number = {e98760},
+ISSN = {1932-6203},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; CELL; RECONSTRUCTION; GENES; GNTK},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Paglia, Giuseppe/H-2012-2018
+ },
+ORCID-Numbers = {Paglia, Giuseppe/0000-0003-4724-6801
+ Rolfsson, Ottar/0000-0003-4258-6057
+ Palsson, Bernhard/0000-0003-2357-6785
+ Voldborg, Bjorn Gunnar/0000-0002-7005-1642
+ Rohatgi, Neha/0000-0003-1103-0259},
+Times-Cited = {28},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000338430700072},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000342868000003,
+Author = {Bodor, Zsolt and Fazakas (Iuhasz), Andrea and Kovacs, Erika and Lanyi,
+ Szabolcs and Abraham, Beata},
+Title = {BIOTECHNOLOGICAL PRODUCTION OF SUCCINIC ACID FROM GLYCEROL; THE ROLE OF
+ CO-SUBSTRATES},
+Journal = {STUDIA UNIVERSITATIS BABES-BOLYAI CHEMIA},
+Year = {2014},
+Volume = {59},
+Number = {2},
+Pages = {33-50},
+Month = {JUN},
+Type = {Article},
+ISSN = {1224-7154},
+Keywords = {Glycerol; Succinic acid; Escherichia coli; Metabolic engineering -
+ Modelling},
+Keywords-Plus = {ESCHERICHIA-COLI; MODELS},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary},
+ResearcherID-Numbers = {Bodor, Zsolt/ABE-2182-2020
+ },
+ORCID-Numbers = {Bodor, Zsolt/0000-0003-1386-6957},
+Times-Cited = {1},
+Journal-ISO = {Stud. Univ. Babes-Bolyai Chem.},
+Unique-ID = {WOS:000342868000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000337700000008,
+Author = {Dias, Oscar and Pereira, Rui and Gombert, Andreas K. and Ferreira,
+ Eugenio C. and Rocha, Isabel},
+Title = {iOD907, the first genome-scale metabolic model for the milk yeast
+ Kluyveromyces lactis},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2014},
+Volume = {9},
+Number = {6, SI},
+Pages = {776-790},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/biot.201300242},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Bioinformatics; Fungi; Genome-scale metabolic model; Metabolic
+ engineering; Systems biology},
+Keywords-Plus = {IN-SILICO ANALYSIS; SACCHAROMYCES-CEREVISIAE; PICHIA-PASTORIS;
+ MOLECULAR-GENETICS; ANAEROBIC GROWTH; RECONSTRUCTION; DATABASE; GLUCOSE;
+ GENERATION; NETWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Rocha, Isabel/A-4279-2013
+ Ferreira, Eugénio Campos/B-5417-2009
+ Dias, Oscar/A-4359-2010
+ Gombert, Andreas K/F-3764-2010},
+ORCID-Numbers = {Rocha, Isabel/0000-0001-9494-3410
+ Ferreira, Eugénio Campos/0000-0002-5400-3333
+ Dias, Oscar/0000-0002-1765-7178
+ Gombert, Andreas K/0000-0001-9557-3773},
+Times-Cited = {34},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000337700000008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000335436000034,
+Author = {Nilsson, Robert and Bauer, Fredric and Mesfun, Sennai and Hulteberg,
+ Christian and Lundgren, Joakim and Wannstrom, Sune and Rova, Ulrika and
+ Berglund, Kris Arvid},
+Title = {Techno-economics of carbon preserving butanol production using a
+ combined fermentative and catalytic approach},
+Journal = {BIORESOURCE TECHNOLOGY},
+Year = {2014},
+Volume = {161},
+Pages = {263-269},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1016/j.biortech.2014.03.055},
+ISSN = {0960-8524},
+EISSN = {1873-2976},
+Keywords = {Process integration; Butanol; Succinic acid; Fermentation;
+ Lignocellulose},
+Keywords-Plus = {SUCCINIC ACID PRODUCTION; RENEWABLE RESOURCES; ESCHERICHIA-COLI;
+ N-BUTANOL; BIOMASS; 1,4-BUTANEDIOL; DEHYDRATION; HYDROLYSATE;
+ BIOREACTOR; CHEMICALS},
+Research-Areas = {Agriculture; Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Agricultural Engineering; Biotechnology \& Applied Microbiology; Energy
+ \& Fuels},
+ResearcherID-Numbers = {Lundgren, Joakim/T-6693-2019
+ Hulteberg, Christian/G-5628-2011
+ Bauer, Fredric/C-1805-2014
+ },
+ORCID-Numbers = {Bauer, Fredric/0000-0001-8231-2099
+ Hulteberg, Christian/0000-0002-3502-5529
+ Nilsson, Robert/0000-0001-8373-244X
+ Mesfun, Sennai/0000-0002-4909-6643},
+Times-Cited = {9},
+Journal-ISO = {Bioresour. Technol.},
+Unique-ID = {WOS:000335436000034},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000336828100010,
+Author = {Gonzalez-Martinez, J. M. and Folch-Fortuny, A. and Llaneras, F. and
+ Tortajada, M. and Pico, J. and Ferrer, A.},
+Title = {Metabolic flux understanding of Pichia pastoris grown on
+ heterogenous culture media},
+Journal = {CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS},
+Year = {2014},
+Volume = {134},
+Pages = {89-99},
+Month = {MAY 15},
+Type = {Article},
+DOI = {10.1016/j.chemolab.2014.02.003},
+ISSN = {0169-7439},
+EISSN = {1873-3239},
+Keywords = {Metabolic network; Possibilistic consistency analysis; Monte Carlo
+ sampling; Principal Component Analysis; Missing-data methods for
+ Exploratory Data Analysis},
+Keywords-Plus = {PRINCIPAL COMPONENT ANALYSIS; CONSTRAINT-BASED MODELS; GENE-EXPRESSION;
+ ESCHERICHIA-COLI; CELL-DENSITY; IDENTIFICATION; DISTRIBUTIONS;
+ INFORMATION; TEMPERATURE; PERFORMANCE},
+Research-Areas = {Automation \& Control Systems; Chemistry; Computer Science; Instruments
+ \& Instrumentation; Mathematics},
+Web-of-Science-Categories = {Automation \& Control Systems; Chemistry, Analytical; Computer Science,
+ Artificial Intelligence; Instruments \& Instrumentation; Mathematics,
+ Interdisciplinary Applications; Statistics \& Probability},
+ResearcherID-Numbers = {Picó, Jesús/A-5347-2011
+ Llaneras, Francisco/B-8133-2008
+ Ferrer, Alberto/AAA-9418-2020
+ },
+ORCID-Numbers = {Picó, Jesús/0000-0003-4144-3521
+ Ferrer, Alberto/0000-0001-7244-5947
+ Llaneras, Francisco/0000-0002-5299-1737
+ Folch-Fortuny, Abel/0000-0001-6845-0807},
+Times-Cited = {15},
+Journal-ISO = {Chemometrics Intell. Lab. Syst.},
+Unique-ID = {WOS:000336828100010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000336680100001,
+Author = {Ling, Maurice H. T. and Poh, Chueh Loo},
+Title = {A predictor for predicting Escherichia coli transcriptome and the
+ effects of gene perturbations},
+Journal = {BMC BIOINFORMATICS},
+Year = {2014},
+Volume = {15},
+Month = {MAY 13},
+Type = {Article},
+DOI = {10.1186/1471-2105-15-140},
+Article-Number = {140},
+ISSN = {1471-2105},
+Keywords-Plus = {NATURAL ANTISENSE TRANSCRIPTS; COEXPRESSION NETWORK ANALYSIS; REGULATORY
+ NETWORKS; OVER-EXPRESSION; SKELETAL-MUSCLE; REPRODUCIBILITY;
+ MICROARRAYS; METABOLISM; TOLERANCE; VIRULENCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Poh, Chueh Loo/AAG-9907-2021
+ Poh, Chueh Loo/G-6211-2010
+ },
+ORCID-Numbers = {Ling, Maurice/0000-0001-7868-1238},
+Times-Cited = {1},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000336680100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000335770500005,
+Author = {Borodina, Irina and Nielsen, Jens},
+Title = {Advances in metabolic engineering of yeast Saccharomyces cerevisiae for
+ production of chemicals},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2014},
+Volume = {9},
+Number = {5, SI},
+Pages = {609-620},
+Month = {MAY},
+Type = {Review},
+DOI = {10.1002/biot.201300445},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Industrial biotechnology; Metabolic engineering; Saccharomyces
+ cerevisiae; Synthetic biology; Yeast},
+Keywords-Plus = {PYRUVATE-DECARBOXYLASE; GENE-EXPRESSION; SUCCINIC ACID; BAKERS-YEAST;
+ GENOME; BIOSYNTHESIS; VERSATILE; PATHWAY; GLUCOSE; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Borodina, Irina/G-5587-2013
+ Nielsen, Jens Bo/C-7632-2015
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Borodina, Irina/0000-0002-8452-1393
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {175},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000335770500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000334846500010,
+Author = {Chubukov, Victor and Gerosa, Luca and Kochanowski, Karl and Sauer, Uwe},
+Title = {Coordination of microbial metabolism},
+Journal = {NATURE REVIEWS MICROBIOLOGY},
+Year = {2014},
+Volume = {12},
+Number = {5},
+Pages = {327-340},
+Month = {MAY},
+Type = {Review},
+DOI = {10.1038/nrmicro3238},
+ISSN = {1740-1526},
+EISSN = {1740-1534},
+Keywords-Plus = {CARBON CATABOLITE REPRESSION; SIGNAL-TRANSDUCTION PROTEINS; GENOME-SCALE
+ RECONSTRUCTION; ESCHERICHIA-COLI; BACILLUS-SUBTILIS; PYRUVATE-KINASE;
+ TRANSCRIPTIONAL REGULATION; GENE-EXPRESSION; IN-VIVO; NITROGEN
+ ASSIMILATION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Sauer, Uwe/Y-3556-2019
+ Kochanowski, Karl/ABE-7236-2021
+ },
+ORCID-Numbers = {Gerosa, Luca/0000-0001-6805-9410},
+Times-Cited = {336},
+Journal-ISO = {Nat. Rev. Microbiol.},
+Unique-ID = {WOS:000334846500010},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000335385500011,
+Author = {Cintolesi, Angela and Clomburg, James M. and Gonzalez, Ramon},
+Title = {In silico assessment of the metabolic capabilities of an
+ engineered functional reversal of the β-oxidation cycle for the
+ synthesis of longer-chain (C ≥ 4) products},
+Journal = {METABOLIC ENGINEERING},
+Year = {2014},
+Volume = {23},
+Pages = {100-115},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2014.02.011},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {beta-Oxidation reversal; In silico analysis; Systems biology; Fuels and
+ chemicals},
+Keywords-Plus = {ESCHERICHIA-COLI; FATTY-ACIDS; BIOSYNTHESIS; PATHWAYS; FUELS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Gonzalez, Ramon/B-1961-2010},
+Times-Cited = {28},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000335385500011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000336095100030,
+Author = {Jensen, Paul A. and Papin, Jason A.},
+Title = {MetDraw: automated visualization of genome-scale metabolic network
+ reconstructions and high-throughput data},
+Journal = {BIOINFORMATICS},
+Year = {2014},
+Volume = {30},
+Number = {9},
+Pages = {1327-1328},
+Month = {MAY 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btt758},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {23},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000336095100030},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000335346100001,
+Author = {Lee, Na-Rae and Lakshmanan, Meiyappan and Aggarwal, Shilpi and Song,
+ Ji-Won and Karimi, Iftekhar A. and Lee, Dong-Yup and Park, Jin-Byung},
+Title = {Genome-scale metabolic network reconstruction and in silico flux
+ analysis of the thermophilic bacterium Thermus thermophilus HB27},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2014},
+Volume = {13},
+Month = {APR 28},
+Type = {Article},
+DOI = {10.1186/1475-2859-13-61},
+Article-Number = {61},
+EISSN = {1475-2859},
+Keywords = {Thermus thermophilus; Thermophile; Genome-scale metabolic model;
+ Constraints-based flux analysis; Ethanol},
+Keywords-Plus = {EXTREME THERMOPHILE; ESCHERICHIA-COLI; GROWTH TEMPERATURE; BALANCE
+ ANALYSIS; ENZYMES; ACID; BIOSYNTHESIS; FATTY; RNA},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/H-1267-2014
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Lee, Dong-Yup/D-6650-2011
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Karimi, Iftekhar/D-4607-2009},
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Karimi, Iftekhar/0000-0001-7122-0578},
+Times-Cited = {16},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000335346100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000335001000015,
+Author = {Wu, Ming and Chan, Christina},
+Title = {Prediction of therapeutic microRNA based on the human metabolic network},
+Journal = {BIOINFORMATICS},
+Year = {2014},
+Volume = {30},
+Number = {8},
+Pages = {1163-1171},
+Month = {APR 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btt751},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX ANALYSIS; CELLULAR-METABOLISM;
+ QUANTITATIVE PREDICTION; CANCER METABOLISM; EXPRESSION; RECONSTRUCTION;
+ GENES; TRANSFORMATION; INTEGRATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Wu, Ming/K-4074-2014},
+Times-Cited = {4},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000335001000015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000335344500001,
+Author = {Li, Shubo and Gao, Xiang and Xu, Nan and Liu, Liming and Chen, Jian},
+Title = {Enhancement of acetoin production in Candida glabrata by in
+ silico-aided metabolic engineering},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2014},
+Volume = {13},
+Month = {APR 13},
+Type = {Article},
+DOI = {10.1186/1475-2859-13-55},
+Article-Number = {55},
+ISSN = {1475-2859},
+Keywords = {Acetoin; Candida glabrata; Cofactor engineering; Heterologous pathway;
+ In silico; Metabolic engineering},
+Keywords-Plus = {TORULOPSIS-GLABRATA; ESCHERICHIA-COLI; 2,3-BUTANEDIOL; RECONSTRUCTION;
+ DEHYDROGENASE; MODELS; ACID},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {19},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000335344500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000334804300001,
+Author = {El-Semman, Ibrahim E. and Karlsson, Fredrik H. and Shoaie, Saeed and
+ Nookaew, Intawat and Soliman, Taysir H. and Nielsen, Jens},
+Title = {Genome-scale metabolic reconstructions of Bifidobacterium
+ adolescentis L2-32 and Faecalibacterium prausnitzii A2-165
+ and their interaction},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {8},
+Month = {APR 3},
+Type = {Article},
+DOI = {10.1186/1752-0509-8-41},
+Article-Number = {41},
+EISSN = {1752-0509},
+Keywords = {Bifidobacterium adolescentis L2-32; Faecalibacterium prausnitzii A2-165;
+ Genome-scale metabolic model; Metabolic modeling of gut microbiota},
+Keywords-Plus = {SYSTEMS BIOLOGY; GUT MICROBIOTA; BACTEROIDES-THETAIOTAOMICRON; FLUX
+ ANALYSIS; DATABASE; MODELS; CONSTRAINT; BUTYRATE; BACTERIA; GROWTH},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Shoaie, Saeed/0000-0001-5834-4533
+ Karlsson, Fredrik/0000-0003-4377-6514
+ Elsemman, Ibrahim/0000-0002-2720-8245
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {70},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000334804300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000335499600004,
+Author = {Federowicz, Stephen and Kim, Donghyuk and Ebrahim, Ali and Lerman,
+ Joshua and Nagarajan, Harish and Cho, Byung-kwan and Zengler, Karsten
+ and Palsson, Bernhard},
+Title = {Determining the Control Circuitry of Redox Metabolism at the
+ Genome-Scale},
+Journal = {PLOS GENETICS},
+Year = {2014},
+Volume = {10},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.pgen.1004264},
+Article-Number = {e1004264},
+ISSN = {1553-7404},
+Keywords-Plus = {ESCHERICHIA-COLI; RNA-POLYMERASE; ADAPTATION; TRANSITION; ARCA;
+ PHYSIOLOGY; NETWORK; BIOMASS; SYSTEM; SENSOR},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Cho, Byung-Kwan/C-1830-2011
+ Kim, Donghyuk/AAS-9141-2020
+ },
+ORCID-Numbers = {Ebrahim, Ali/0000-0002-4009-2128
+ Zengler, Karsten/0000-0002-8062-3296
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {48},
+Journal-ISO = {PLoS Genet.},
+Unique-ID = {WOS:000335499600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000336507500008,
+Author = {Feist, Adam M. and Nagarajan, Harish and Rotaru, Amelia-Elena and
+ Tremblay, Pier-Luc and Zhang, Tian and Nevin, Kelly P. and Lovley, Derek
+ R. and Zengler, Karsten},
+Title = {Constraint-Based Modeling of Carbon Fixation and the Energetics of
+ Electron Transfer in Geobacter metallireducens},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2014},
+Volume = {10},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003575},
+Article-Number = {e1003575},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {SCALE METABOLIC RECONSTRUCTION; COMMODITY CHEMICALS; EXPRESSION DATA;
+ IN-SILICO; GENOME; OXIDATION; SULFURREDUCENS; REDUCTION; IRON;
+ PHYSIOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Nevin, Kelly/AAA-4626-2019
+ Zhang, Tian/N-4696-2015
+ Rotaru, Amelia-Elena/C-4782-2014
+ },
+ORCID-Numbers = {Zhang, Tian/0000-0003-3840-4839
+ Rotaru, Amelia-Elena/0000-0003-2415-8585
+ Zengler, Karsten/0000-0002-8062-3296
+ Tremblay, Pier-Luc/0000-0002-0230-7837},
+Times-Cited = {24},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000336507500008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000335111500028,
+Author = {Junker, Bjoern H.},
+Title = {Flux analysis in plant metabolic networks: increasing throughput and
+ coverage},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2014},
+Volume = {26},
+Pages = {183-188},
+Month = {APR},
+Type = {Review},
+DOI = {10.1016/j.copbio.2014.01.016},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {BALANCE ANALYSIS; ARABIDOPSIS; MODEL; RECONSTRUCTION; STRATEGIES;
+ REVEALS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+Times-Cited = {22},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000335111500028},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000334930800004,
+Author = {Lisha, K. P. and Sarkar, Debasis},
+Title = {Dynamic flux balance analysis of batch fermentation: effect of genetic
+ manipulations on ethanol production},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2014},
+Volume = {37},
+Number = {4},
+Pages = {617-627},
+Month = {APR},
+Type = {Article},
+DOI = {10.1007/s00449-013-1027-y},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {Dynamic flux balance modeling; Batch fermentation; Ethanol;
+ Mono-culture; Co-culture; Mixed substrate},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; METABOLISM; GLUCOSE; OPTIMIZATION; COCULTURES;
+ KINETICS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+Times-Cited = {15},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000334930800004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000336507500016,
+Author = {Machado, Daniel and Herrgard, Markus},
+Title = {Systematic Evaluation of Methods for Integration of Transcriptomic Data
+ into Constraint-Based Models of Metabolism},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2014},
+Volume = {10},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003580},
+Article-Number = {e1003580},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; CELLULAR-METABOLISM; ESCHERICHIA-COLI;
+ EXPRESSION DATA; SCALE MODELS; FLUXES; RECONSTRUCTION; METABOLOMICS;
+ OPTIMALITY; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Machado, Daniel/O-5493-2015},
+ORCID-Numbers = {Machado, Daniel/0000-0002-2063-5383},
+Times-Cited = {251},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000336507500016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000334078300030,
+Author = {Sauls, John T. and Buescher, Joerg M.},
+Title = {Assimilating genome-scale metabolic reconstructions with modelBorgifier},
+Journal = {BIOINFORMATICS},
+Year = {2014},
+Volume = {30},
+Number = {7},
+Pages = {1036-1038},
+Month = {APR 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btt747},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {OPTIMIZATION; MODELS; SBML},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Buescher, Joerg/0000-0002-6547-0076},
+Times-Cited = {8},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000334078300030},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000333119500001,
+Author = {Wang, Xiaoyang and Zhang, Chuanbo and Wang, Meiling and Lu, Wenyu},
+Title = {Genome-scale metabolic network reconstruction of Saccharopolyspora
+ spinosa for Spinosad Production improvement},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2014},
+Volume = {13},
+Month = {MAR 15},
+Type = {Article},
+DOI = {10.1186/1475-2859-13-41},
+Article-Number = {41},
+EISSN = {1475-2859},
+Keywords = {Saccharopolyspora spinosa; Genome-scale metabolic network
+ reconstruction; Target prediction; Strain engineering},
+Keywords-Plus = {BIOSYNTHETIC GENE-CLUSTER; ESCHERICHIA-COLI; ALCOHOL-DEHYDROGENASE;
+ CONJUGAL TRANSFER; AMINO-ACIDS; TRANSHYDROGENASE; RHAMNOSE; MODELS;
+ YIELD; CELLS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {16},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000333119500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000346839300002,
+Author = {Sahoo, Swagatika and Aurich, Maike K. and Jonsson, Jon J. and Thiele,
+ Ines},
+Title = {Membrane transporters in a human genonne-scale metabolic knowledgebase
+ and their implications for disease},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2014},
+Volume = {5},
+Month = {MAR 11},
+Type = {Review},
+DOI = {10.3389/fphys.2014.00091},
+Article-Number = {91},
+EISSN = {1664-042X},
+Keywords = {human metabolism; transport mechanisms; constraint-based modeling;
+ inborn errors of metabolism; cancer; metabolic networks and pathways},
+Keywords-Plus = {AMINO-ACID TRANSPORTER; GLUCOSE-TRANSPORTER; INTESTINAL-ABSORPTION;
+ CACO-2 CELLS; FUNCTIONAL-CHARACTERIZATION; BINDING PROTEINS;
+ PLASMA-MEMBRANE; GLOBAL RECONSTRUCTION; AQUAPORIN EXPRESSION; COUPLED
+ TRANSPORT},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Sahoo, Swagatika/0000-0003-3773-8597},
+Times-Cited = {68},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000346839300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000332416200005,
+Author = {Li, Shubo and Xu, Nan and Liu, Liming and Chen, Jian},
+Title = {Engineering of carboligase activity reaction in Candida glabrata
+ for acetoin production},
+Journal = {METABOLIC ENGINEERING},
+Year = {2014},
+Volume = {22},
+Pages = {32-39},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ymben.2013.12.005},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Acetoin; Candida glabrata; Metabolic engineering; In silico; Cofactor
+ engineering},
+Keywords-Plus = {PYRUVATE-DEHYDROGENASE BYPASS; SACCHAROMYCES-CEREVISIAE;
+ TORULOPSIS-GLABRATA; ESCHERICHIA-COLI; NADH OXIDASE; 2,3-BUTANEDIOL;
+ DECARBOXYLASE; GLYCEROL; STRAINS; FERMENTATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {25},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000332416200005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000332475000001,
+Author = {Maarleveld, Timo R. and Boele, Joost and Bruggeman, Frank J. and
+ Teusink, Bas},
+Title = {A Data Integration and Visualization Resource for the Metabolic Network
+ of Synechocystis sp PCC 6803},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2014},
+Volume = {164},
+Number = {3},
+Pages = {1111-1121},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1104/pp.113.224394},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {RNA-SEQ; MODELS; CYANOBACTERIA; BALANCE; SYSTEMS; KNOWLEDGEBASE;
+ TRANSCRIPTOME; GENES},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Maarleveld, Timo/I-5838-2013
+ Bruggeman, Frank/C-4356-2015
+ Bruggeman, Frank/AAS-8371-2020
+ },
+ORCID-Numbers = {Maarleveld, Timo/0000-0002-3947-134X
+ Bruggeman, Frank/0000-0002-0255-4766
+ Bruggeman, Frank/0000-0002-0255-4766
+ Teusink, Bas/0000-0003-3929-0423
+ Boele, Joost/0000-0002-7183-9650},
+Times-Cited = {20},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000332475000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000333873000002,
+Author = {Wu, Xinsen and Wang, Xiaoyang and Lu, Wenyu},
+Title = {Genome-scale reconstruction of a metabolic network for Gluconobacter
+ oxydans 621H},
+Journal = {BIOSYSTEMS},
+Year = {2014},
+Volume = {117},
+Pages = {10-14},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2014.01.001},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Gluconobacter oxydans; Genome-scale metabolic network; Flux balance
+ analysis; Flux variability analysis; Gene essentiality analysis},
+Keywords-Plus = {GLYCEROL; BIOCHEMISTRY; GROWTH},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Yan, Miaochen/JLL-5061-2023
+ zhang, luyu/JJC-4227-2023},
+Times-Cited = {14},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000333873000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000331882900001,
+Author = {Kubacka, Anna and Diez, Maria Suarez and Rojo, David and Bargiela,
+ Rafael and Ciordia, Sergio and Zapico, Ines and Albar, Juan P. and
+ Barbas, Coral and dos Santos, Vitor A. P. Martins and Fernandez-Garcia,
+ Marcos and Ferrer, Manuel},
+Title = {Understanding the antimicrobial mechanism of TiO2-based
+ nanocomposite films in a pathogenic bacterium},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2014},
+Volume = {4},
+Month = {FEB 19},
+Type = {Article},
+DOI = {10.1038/srep04134},
+Article-Number = {4134},
+ISSN = {2045-2322},
+Keywords-Plus = {PSEUDOMONAS-AERUGINOSA; PHOTOCATALYTIC DISINFECTION; ESCHERICHIA-COLI;
+ MUTANT LIBRARY; GENES; METABOLISM; EXPRESSION; SYSTEM; SILVER; HEME},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Diez, Maria Suarez/AAI-1354-2020
+ Barbas, Coral/K-3871-2014
+ Bargiela, Rafael/K-6783-2014
+ Kubacka, Anna/B-8054-2015
+ Rojo, David/K-3365-2015
+ Bargiela Bargiela, Rafael María/HGU-3420-2022
+ Fernandez-Garcia, Marcos/A-8122-2014
+ Ferrer, Manuel/K-4535-2014
+ },
+ORCID-Numbers = {Barbas, Coral/0000-0003-4722-491X
+ Bargiela, Rafael/0000-0003-1442-3269
+ Kubacka, Anna/0000-0002-3504-0032
+ Bargiela Bargiela, Rafael María/0000-0003-1442-3269
+ Fernandez-Garcia, Marcos/0000-0002-9987-0289
+ martins dos santos, vitor/0000-0002-2352-9017
+ Ciordia, Sergio/0000-0002-5726-853X
+ Ferrer, Manuel/0000-0003-4962-4714
+ Suarez-Diez, Maria/0000-0001-5845-146X},
+Times-Cited = {288},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000331882900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000332032100022,
+Author = {Mao, Longfei and Verwoerd, Wynand S.},
+Title = {ORCA: a COBRA toolbox extension for model-driven discovery and analysis},
+Journal = {BIOINFORMATICS},
+Year = {2014},
+Volume = {30},
+Number = {4},
+Pages = {584-585},
+Month = {FEB 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btt723},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Verwoerd, Wynand/A-8320-2010
+ },
+ORCID-Numbers = {Verwoerd, Wynand/0000-0001-5489-9101
+ Mao, Longfei/0000-0003-0759-0501},
+Times-Cited = {11},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000332032100022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000334796500001,
+Author = {Lindfors, Erno and Jouhten, Paula and Oja, Merja and Rintala, Eija and
+ Oresic, Matej and Penttila, Merja},
+Title = {Integration of transcription and flux data reveals molecular paths
+ associated with differences in oxygen-dependent phenotypes of
+ Saccharomyces cerevisiae},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2014},
+Volume = {8},
+Month = {FEB 14},
+Type = {Article},
+DOI = {10.1186/1752-0509-8-16},
+Article-Number = {16},
+EISSN = {1752-0509},
+Keywords = {Saccharomyces cerevisiae; Network biology; Molecular path finding; Data
+ integration; Oxygen; Constraint-based modeling},
+Keywords-Plus = {REGULATORY ASSOCIATIONS; INTERACTION NETWORK; PROTEIN; METABOLISM;
+ RECONSTRUCTION; CLASSIFICATION; INTERACTOME; COENZYME; ACETATE; KINASE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Penttilä, Merja E/A-4710-2013
+ Oresic, Matej/K-7673-2016
+ Oresic, Matej/AAV-3978-2020
+ },
+ORCID-Numbers = {Oresic, Matej/0000-0002-2856-9165
+ Lindfors, Erno/0000-0002-7314-5927
+ Jouhten, Paula/0000-0003-1075-7448
+ Penttila, Merja/0000-0002-6929-1032},
+Times-Cited = {2},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000334796500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000331737200001,
+Author = {Kalnenieks, Uldis and Pentjuss, Agris and Rutkis, Reinis and Stalidzans,
+ Egils and Fell, David A.},
+Title = {Modeling of Zymomonas mobilis central metabolism for novel
+ metabolic engineering strategies},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2014},
+Volume = {5},
+Month = {FEB 5},
+Type = {Article},
+DOI = {10.3389/fmicb.2014.00042},
+Article-Number = {42},
+ISSN = {1664-302X},
+Keywords = {stoichiometric modeling; elementary flux modes; kinetic modeling;
+ systems biology; metabolic engineering; Entner Doudoroff pathway;
+ central metabolism; Zymomonas mobilis},
+Keywords-Plus = {GENOME SEQUENCE; ETHANOL-PRODUCTION; ESCHERICHIA-COLI; FUEL ETHANOL;
+ DEHYDROGENASE; IDENTIFICATION; GLUCOSE; PATHWAYS; GROWTH; CELL},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Stalidzans, Egils/G-5883-2010
+ Fell, David A/B-2109-2009
+ },
+ORCID-Numbers = {Stalidzans, Egils/0000-0001-6063-0184
+ Fell, David A/0000-0001-6669-2247
+ Pentjuss, Agris/0000-0001-7880-5130},
+Times-Cited = {25},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000331737200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000332626700016,
+Author = {Chokkathukalam, Achuthanunni and Kim, Dong-Hyun and Barrett, Michael P.
+ and Breitling, Rainer and Creek, Darren J.},
+Title = {Stable isotope- labeling studies in metabolomics: new insights into
+ structure and dynamics of metabolic networks},
+Journal = {BIOANALYSIS},
+Year = {2014},
+Volume = {6},
+Number = {4},
+Pages = {511-524},
+Month = {FEB},
+Type = {Article},
+DOI = {10.4155/bio.13.348},
+ISSN = {1757-6180},
+EISSN = {1757-6199},
+Keywords-Plus = {DILUTION MASS-SPECTROMETRY; RELATIVE QUANTIFICATION; ESCHERICHIA-COLI;
+ FLUX ANALYSIS; RESOLVED METABOLOMICS; ABSOLUTE QUANTITATION;
+ GAS-CHROMATOGRAPHY; PATHWAY ANALYSIS; C-13; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology; Chemistry},
+Web-of-Science-Categories = {Biochemical Research Methods; Chemistry, Analytical},
+ResearcherID-Numbers = {Kim, Dong-Hyun/AAT-3953-2021
+ },
+ORCID-Numbers = {Kim, Dong-Hyun/0000-0002-3689-2130
+ Breitling, Rainer/0000-0001-7173-0922
+ Creek, Darren/0000-0001-7497-7082
+ Barrett, Mike/0000-0001-9447-3519},
+Times-Cited = {138},
+Journal-ISO = {Bioanalysis},
+Unique-ID = {WOS:000332626700016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000330969300014,
+Author = {Unthan, Simon and Gruenberger, Alexander and van Ooyen, Jan and
+ Gaetgens, Jochem and Heinrich, Johanna and Paczia, Nicole and Wiechert,
+ Wolfgang and Kohlheyer, Dietrich and Noack, Stephan},
+Title = {Beyond Growth Rate 0.6: What Drives Corynebacterium glutamicum to
+ Higher Growth Rates in Defined Medium},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2014},
+Volume = {111},
+Number = {2},
+Pages = {359-371},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1002/bit.25103},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {growth rate; Corynebacterium glutamicum; microfluidics; single cell
+ growth; protocatechuic acid; biphasic growth},
+Keywords-Plus = {METABOLISM; BIOSYNTHESIS; BACTERIA; EXPRESSION; GLUCOSE; GENES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Kohlheyer, Dietrich/A-9645-2012
+ van Ooyen, Jan/C-7068-2013
+ },
+ORCID-Numbers = {Kohlheyer, Dietrich/0000-0001-6215-1857
+ Paczia, Nicole/0000-0003-3859-8186
+ Noack, Stephan/0000-0001-9784-3626
+ Wiechert, Wolfgang/0000-0001-8501-0694
+ Grunberger, Alexander/0000-0002-7564-4957},
+Times-Cited = {88},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000330969300014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000331922400001,
+Author = {Xu Zi-Xiang and Zheng Ping and Sun Ji-Bin},
+Title = {Reconstruction of Whole Cell Network and Design of Cell Factory},
+Journal = {PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS},
+Year = {2014},
+Volume = {41},
+Number = {2},
+Pages = {105-114},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3724/SP.J.1206.2012.00530},
+ISSN = {1000-3282},
+Keywords = {cell integral network; systems biology; synthetic biology;
+ bioinformatics; cell factory; metabolic engineering},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; GENE KNOCKOUT STRATEGIES; ESCHERICHIA-COLI
+ K-12; METABOLIC NETWORK; REGULATORY NETWORK; ASPERGILLUS-NIGER;
+ OPTIMIZATION; MODELS; FRAMEWORK; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ORCID-Numbers = {Sun, Jibin/0000-0002-0208-504X},
+Times-Cited = {0},
+Journal-ISO = {Prog. Biochem. Biophys.},
+Unique-ID = {WOS:000331922400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000330570000153,
+Author = {Acevedo, Alejandro and Aroca, German and Conejeros, Raul},
+Title = {Genome-Scale NAD(H/+) Availability Patterns as a
+ Differentiating Feature between Saccharomyces cerevisiae and
+ Scheffersomyces stipitis in Relation to Fermentative Metabolism},
+Journal = {PLOS ONE},
+Year = {2014},
+Volume = {9},
+Number = {1},
+Month = {JAN 29},
+Type = {Article},
+DOI = {10.1371/journal.pone.0087494},
+Article-Number = {e87494},
+ISSN = {1932-6203},
+Keywords-Plus = {YEAST PICHIA-STIPITIS; OXYGEN AVAILABILITY; ETHANOL-PRODUCTION; NADH
+ AVAILABILITY; ESCHERICHIA-COLI; RESPIRATION; XYLOSE; MODELS;
+ RECONSTRUCTION; IDENTIFICATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Conejeros, Raul/ABG-5517-2020
+ Aroca, German/ABG-6714-2020
+ Conejeros, Raul/A-2466-2011},
+ORCID-Numbers = {Conejeros, Raul/0000-0002-1273-535X
+ Aroca, German/0000-0003-1376-7940
+ },
+Times-Cited = {4},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000330570000153},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000329614900002,
+Author = {Benedict, Matthew N. and Henriksen, James R. and Metcalf, William W. and
+ Whitaker, Rachel J. and Price, Nathan D.},
+Title = {ITEP: An integrated toolkit for exploration of microbial pan-genomes},
+Journal = {BMC GENOMICS},
+Year = {2014},
+Volume = {15},
+Month = {JAN 3},
+Type = {Article},
+DOI = {10.1186/1471-2164-15-8},
+Article-Number = {8},
+ISSN = {1471-2164},
+Keywords = {Comparative genomics; Clustering; Curation; Database; Metabolic
+ networks; Orthologs; Pan-genome; Phylogenetics},
+Keywords-Plus = {MAXIMUM-LIKELIHOOD; SCALE MODEL; GENE; CLOSTRIDIUM; RECONSTRUCTION;
+ ALIGNMENTS; ORTHOLOGS; DATABASE; PROJECT; METABOLISM},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ORCID-Numbers = {Price, Nathan/0000-0002-4157-0267
+ Henriksen, James/0000-0003-2485-0889},
+Times-Cited = {79},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000329614900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000332577300001,
+Author = {Babaei, Parizad and Ghasemi-Kahrizsangi, Tahereh and Marashi, Sayed-Amir},
+Title = {Modeling the Differences in Biochemical Capabilities of
+ Pseudomonas Species by Flux Balance Analysis: How Good Are
+ Genome-Scale Metabolic Networks at Predicting the Differences?},
+Journal = {SCIENTIFIC WORLD JOURNAL},
+Year = {2014},
+Type = {Article},
+DOI = {10.1155/2014/416289},
+Article-Number = {416289},
+ISSN = {1537-744X},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; AMINO-ACIDS; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; RECONSTRUCTION; AERUGINOSA; CATABOLISM; NITROGEN;
+ BENZENE; CARBON},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008},
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449},
+Times-Cited = {9},
+Journal-ISO = {Sci. World J.},
+Unique-ID = {WOS:000332577300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000332624300002,
+Author = {Bartell, Jennifer A. and Yen, Phillip and Varga, John J. and Goldberg,
+ Joanna B. and Papin, Jason A.},
+Title = {Comparative Metabolic Systems Analysis of Pathogenic Burkholderia},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2014},
+Volume = {196},
+Number = {2},
+Pages = {210-226},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1128/JB.00997-13},
+ISSN = {0021-9193},
+EISSN = {1098-5530},
+Keywords-Plus = {CYSTIC-FIBROSIS; CEPACIA COMPLEX; PSEUDOMONAS-AERUGINOSA;
+ ANTIBIOTIC-RESISTANCE; CENOCEPACIA J2315; EPIDEMIC PATHOGEN; NETWORK
+ ANALYSIS; GENOME; GENE; VIRULENCE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Varga, John J/I-8130-2012
+ },
+ORCID-Numbers = {Varga, John J/0000-0002-4868-1971
+ Bartell, Jennifer/0000-0003-2750-9678
+ Yen, Phillip/0000-0002-0234-7791
+ Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {33},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000332624300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000330834800008,
+Author = {Dandekar, Thomas and Fieselmann, Astrid and Majeed, Saman and Ahmed,
+ Zeeshan},
+Title = {Software applications toward quantitative metabolic flux analysis and
+ modeling},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2014},
+Volume = {15},
+Number = {1},
+Pages = {91-107},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1093/bib/bbs065},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {metabolism; flux modes; metabolites; metabolic network},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; LISTERIA-MONOCYTOGENES; CELLULAR-METABOLISM;
+ CARBON METABOLISM; ELEMENTARY MODES; PATHWAY ANALYSIS; GENE-EXPRESSION;
+ NETWORKS; PREDICTION; ALGORITHM},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ahmed, Zeeshan/C-1668-2014
+ Zeeshan, Saman/AAQ-3401-2021
+ Ahmed, Zeeshan/AAN-3205-2021
+ Zeeshan, Saman/C-2298-2014
+ Dandekar, Thomas/A-4431-2017},
+ORCID-Numbers = {Ahmed, Zeeshan/0000-0002-7065-1699
+ Zeeshan, Saman/0000-0001-9278-6204
+ Ahmed, Zeeshan/0000-0002-7065-1699
+ Zeeshan, Saman/0000-0001-9278-6204
+ Dandekar, Thomas/0000-0003-1886-7625},
+Times-Cited = {35},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000330834800008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000346694600007,
+Author = {de Mas, Igor Marin and Aguilar, Esther and Jayaraman, Anusha and Polat,
+ Ibrahim H. and Martin-Bernabe, Alfonso and Bharat, Rohit and Foguet,
+ Carles and Mila, Enric and Papp, Balazs and Centelles, Josep J. and
+ Cascante, Marta},
+Title = {Cancer cell metabolism as new targets for novel designed therapies},
+Journal = {FUTURE MEDICINAL CHEMISTRY},
+Year = {2014},
+Volume = {6},
+Number = {16},
+Pages = {1791-1810},
+Type = {Review},
+DOI = {10.4155/FMC.14.119},
+ISSN = {1756-8919},
+EISSN = {1756-8927},
+Keywords-Plus = {EPITHELIAL-MESENCHYMAL TRANSITION; GENOME-SCALE RECONSTRUCTION;
+ IN-SILICO ANALYSIS; OXIDATIVE STRESS; PYRUVATE-KINASE;
+ HEPATOCELLULAR-CARCINOMA; LACTATE-DEHYDROGENASE; GLOBAL RECONSTRUCTION;
+ ESCHERICHIA-COLI; ANTICANCER DRUGS},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Chemistry, Medicinal},
+ResearcherID-Numbers = {Foguet, Carles/W-4864-2018
+ CASCANTE, MARTA/AFK-5991-2022
+ CASCANTE, MARTA/AAG-4355-2022
+ Centelles, Josep J./K-2972-2014
+ Polat, Ibrahim Halil/W-2678-2018
+ Polat, Ibrahim Halil/R-3739-2017
+ },
+ORCID-Numbers = {Foguet, Carles/0000-0001-8494-9595
+ CASCANTE, MARTA/0000-0002-2062-4633
+ CASCANTE, MARTA/0000-0002-2062-4633
+ Centelles, Josep J./0000-0002-6289-9678
+ Polat, Ibrahim Halil/0000-0003-2196-6667
+ Polat, Ibrahim Halil/0000-0003-2196-6667
+ Martin-Bernabe, Alfonso/0000-0002-8885-6043
+ Mila Vilalta, Enric/0000-0002-3708-1022
+ Aguilar Fado, Esther/0000-0001-6304-1983
+ Papp, Balazs/0000-0003-3093-8852
+ Marin de Mas, Igor/0000-0003-2925-8155
+ Jayaraman, Anusha/0000-0001-8548-155X},
+Times-Cited = {16},
+Journal-ISO = {Future Med. Chem.},
+Unique-ID = {WOS:000346694600007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341360200005,
+Author = {Fang, Xin and Reifman, Jaques and Wallqvist, Anders},
+Title = {Modeling metabolism and stage-specific growth of Plasmodium
+ falciparum HB3 during the intraerythrocytic developmental cycle},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2014},
+Volume = {10},
+Number = {10},
+Pages = {2526-2537},
+Type = {Article},
+DOI = {10.1039/c4mb00115j},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {MALARIA PARASITE; GENE-EXPRESSION; DRUG TARGETS; PHOSPHATE-PATHWAY;
+ HOST-CELL; BIOSYNTHESIS; NETWORK; TRANSCRIPTOME; REVEALS; ERYTHROCYTES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {wallqvist, anders/W-2584-2019},
+ORCID-Numbers = {wallqvist, anders/0000-0002-9775-7469},
+Times-Cited = {16},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000341360200005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000339749000001,
+Author = {Gao, Yue-Dong and Zhao, Yuqi and Huang, Jingfei},
+Title = {Metabolic Modeling of Common Escherichia coli Strains in Human
+ Gut Microbiome},
+Journal = {BIOMED RESEARCH INTERNATIONAL},
+Year = {2014},
+Volume = {2014},
+Type = {Article},
+DOI = {10.1155/2014/694967},
+Article-Number = {694967},
+ISSN = {2314-6133},
+EISSN = {2314-6141},
+Keywords-Plus = {E. COLI; RECONSTRUCTION; DIVERSITY; HEALTH; TRANSCRIPTOME; RESISTANT;
+ BACTERIA},
+Research-Areas = {Biotechnology \& Applied Microbiology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Medicine, Research \&
+ Experimental},
+ResearcherID-Numbers = {huang, jing/JDC-2548-2023
+ },
+ORCID-Numbers = {Zhao, Yuqi/0000-0002-4256-4512},
+Times-Cited = {21},
+Journal-ISO = {Biomed Res. Int.},
+Unique-ID = {WOS:000339749000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000330801200008,
+Author = {Golberg, Alexander and Vitkin, Edward and Linshiz, Gregory and Khan,
+ Sabaa Ahmad and Hillson, Nathan J. and Yakhini, Zohar and Yarmush,
+ Martin L.},
+Title = {Proposed design of distributed macroalgal biorefineries: thermodynamics,
+ bioconversion technology, and sustainability implications for developing
+ economies},
+Journal = {BIOFUELS BIOPRODUCTS \& BIOREFINING-BIOFPR},
+Year = {2014},
+Volume = {8},
+Number = {1},
+Pages = {67-82},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1002/bbb.1438},
+ISSN = {1932-104X},
+EISSN = {1932-1031},
+Keywords = {biorefinery design; thermodynamic modeling; biorefinery optimization;
+ fermentation modeling; metabolic modeling; biofuel sustainability;
+ biofuel policy},
+Keywords-Plus = {LIGNOCELLULOSIC BIOMASS; FUNCTIONAL-PROPERTIES; MICROBIAL-PRODUCTION;
+ CONSTRUCTAL DESIGN; SEAWEED; RECONSTRUCTION; ETHANOL; POLYSACCHARIDE;
+ CULTIVATION; CHALLENGES},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Golberg, Alexander/M-9563-2017
+ },
+ORCID-Numbers = {Golberg, Alexander/0000-0001-8782-8879
+ Yarmush, Martin/0000-0003-4986-8444},
+Times-Cited = {40},
+Journal-ISO = {Biofuels Bioprod. Biorefining},
+Unique-ID = {WOS:000330801200008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000342760300029,
+Author = {Hadi, Mahdieh and Marashi, Sayed-Amir},
+Title = {Reconstruction of a generic metabolic network model of cancer cells},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2014},
+Volume = {10},
+Number = {11},
+Pages = {3014-3021},
+Type = {Article},
+DOI = {10.1039/c4mb00300d},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {PATHWAY; FLUX; RESOURCE; SURVIVAL; SERINE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008
+ },
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Hadi, Mahdieh/0000-0003-0159-3277
+ Hadi, Mahdieh/0000-0002-8947-7168},
+Times-Cited = {19},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000342760300029},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000329293700005,
+Author = {Hamilton, Joshua J. and Reed, Jennifer L.},
+Title = {Software platforms to facilitate reconstructing genome-scale metabolic
+ networks},
+Journal = {ENVIRONMENTAL MICROBIOLOGY},
+Year = {2014},
+Volume = {16},
+Number = {1, SI},
+Pages = {49-59},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1111/1462-2920.12312},
+ISSN = {1462-2912},
+EISSN = {1462-2920},
+Keywords-Plus = {IN-SILICO; SYSTEMS-BIOLOGY; GLOBAL RECONSTRUCTION; MODELS; DATABASE;
+ BALANCE; OPTIMIZATION; INTEGRATION; PREDICTION; TOOLS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Reed, Jennifer L/E-5137-2011
+ },
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220
+ Hamilton, Joshua/0000-0001-9790-3609},
+Times-Cited = {51},
+Journal-ISO = {Environ. Microbiol.},
+Unique-ID = {WOS:000329293700005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341360200010,
+Author = {Joshi, Chintan Jagdishchandra and Prasad, Ashok},
+Title = {Epistatic interactions among metabolic genes depend upon environmental
+ conditions},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2014},
+Volume = {10},
+Number = {10},
+Pages = {2578-2589},
+Type = {Article},
+DOI = {10.1039/c4mb00181h},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {ESCHERICHIA-COLI; FLUX ANALYSIS; HIGH LIGHT; OPTIMALITY; EVOLUTION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Prasad, Ashok/HDN-5956-2022
+ },
+ORCID-Numbers = {Joshi, Chintan/0000-0002-9339-2511},
+Times-Cited = {6},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000341360200010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000346707500001,
+Author = {Koussa, Joseph and Chaiboonchoe, Amphun and Salehi-Ashtiani, Kourosh},
+Title = {Computational Approaches for Microalgal Biofuel Optimization: A Review},
+Journal = {BIOMED RESEARCH INTERNATIONAL},
+Year = {2014},
+Volume = {2014},
+Type = {Review},
+DOI = {10.1155/2014/649453},
+Article-Number = {649453},
+ISSN = {2314-6133},
+EISSN = {2314-6141},
+Keywords-Plus = {COBRA TOOLBOX EXTENSION; CONSTRAINT-BASED MODELS; METABOLIC MODELS;
+ BIOCYC COLLECTION; METACYC DATABASE; EXPRESSION DATA;
+ SACCHAROMYCES-CEREVISIAE; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ SOFTWARE PLATFORM},
+Research-Areas = {Biotechnology \& Applied Microbiology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Medicine, Research \&
+ Experimental},
+Times-Cited = {14},
+Journal-ISO = {Biomed Res. Int.},
+Unique-ID = {WOS:000346707500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000344242100001,
+Author = {Lakshmanan, Meiyappan and Mohanty, Bijayalaxmi and Lim, Sun-Hyung and
+ Ha, Sun-Hwa and Lee, Dong-Yup},
+Title = {Metabolic and transcriptional regulatory mechanisms underlying the
+ anoxic adaptation of rice coleoptile},
+Journal = {AOB PLANTS},
+Year = {2014},
+Volume = {6},
+Type = {Article},
+DOI = {10.1093/aobpla/plu026},
+Article-Number = {plu026},
+ISSN = {2041-2851},
+Keywords = {Anoxia; cis-elements; flux sampling; rice; systems biology;
+ transcription factors; transcriptional regulation},
+Keywords-Plus = {CARBOHYDRATE-METABOLISM; EXPRESSION ANALYSIS; GENE; GERMINATION;
+ DEHYDROGENASE; PREDICTION; SEEDLINGS; PATTERNS; DATABASE; GROWTH},
+Research-Areas = {Plant Sciences; Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Plant Sciences; Ecology},
+ResearcherID-Numbers = {Mohanty, Bijayalaxmi/AAY-7386-2020
+ Lee, Dong-Yup/D-6650-2011
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Lakshmanan, Meiyappan/H-1267-2014
+ },
+ORCID-Numbers = {Mohanty, Bijayalaxmi/0000-0002-8226-2367
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lim, Sun-Hyung/0009-0008-5269-3589},
+Times-Cited = {9},
+Journal-ISO = {Aob Plants},
+Unique-ID = {WOS:000344242100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000330834800009,
+Author = {Lakshmanan, Meiyappan and Koh, Geoffrey and Chung, Bevan K. S. and Lee,
+ Dong-Yup},
+Title = {Software applications for flux balance analysis},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2014},
+Volume = {15},
+Number = {1},
+Pages = {108-122},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1093/bib/bbs069},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {systems biology; flux balance analysis (FBA); FBA tools; genome-scale
+ model reconstruction; web applications},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; METABOLIC MODELS; QUANTITATIVE PREDICTION;
+ KNOCKOUT STRATEGIES; CELLULAR-METABOLISM; ESCHERICHIA-COLI; NETWORK
+ MODEL; GENOME; RECONSTRUCTION; PLATFORM},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/H-1267-2014
+ Lee, Dong-Yup/D-6650-2011
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Lakshmanan, Meiyappan/AAM-1171-2020},
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ },
+Times-Cited = {62},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000330834800009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000329529600006,
+Author = {Liang, Meng and Damiani, Andrew and He, Q. Peter and Wang, Jin},
+Title = {Elucidating Xylose Metabolism of Scheffersomyces stipitis for
+ Lignocellulosic Ethanol Production},
+Journal = {ACS SUSTAINABLE CHEMISTRY \& ENGINEERING},
+Year = {2014},
+Volume = {2},
+Number = {1, SI},
+Pages = {38-48},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1021/sc400265g},
+ISSN = {2168-0485},
+Keywords = {Scheffersoinyces stipitis; Xylose metabolism; Redox balance; Principal
+ component analysis; Cofactor engineering; Systems biology},
+Keywords-Plus = {RECOMBINANT SACCHAROMYCES-CEREVISIAE; YEAST PICHIA-STIPITIS; PHASE PLANE
+ ANALYSIS; GENOME-SCALE; XYLITOL DEHYDROGENASE; COENZYME SPECIFICITY;
+ OXYGEN-TRANSFER; FERMENTATION; REDUCTASE; RECONSTRUCTION},
+Research-Areas = {Chemistry; Science \& Technology - Other Topics; Engineering},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary; Green \& Sustainable Science \&
+ Technology; Engineering, Chemical},
+ORCID-Numbers = {He, Qinghua/0000-0002-2474-5950},
+Times-Cited = {20},
+Journal-ISO = {ACS Sustain. Chem. Eng.},
+Unique-ID = {WOS:000329529600006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000346607300005,
+Author = {Rustad, Tige R. and Minch, Kyle J. and Ma, Shuyi and Winkler, Jessica K.
+ and Hobbs, Samuel and Hickey, Mark and Brabant, William and Turkarslan,
+ Serdar and Price, Nathan D. and Baliga, Nitin S. and Sherman, David R.},
+Title = {Mapping and manipulating the Mycobacterium tuberculosis
+ transcriptome using a transcription factor overexpression-derived
+ regulatory network},
+Journal = {GENOME BIOLOGY},
+Year = {2014},
+Volume = {15},
+Number = {11},
+Type = {Article},
+DOI = {10.1186/s13059-014-0502-3},
+Article-Number = {502},
+ISSN = {1474-760X},
+Keywords-Plus = {HYPOXIC RESPONSE; VIRULENCE; EXPRESSION; PREDICTION; REPRESSOR; OPERON;
+ FAMILY; FURA},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ORCID-Numbers = {baliga, nitin/0000-0001-9157-5974
+ Hobbs, Samuel/0000-0002-4282-8813
+ Price, Nathan/0000-0002-4157-0267
+ Ma, Shuyi/0000-0003-0783-1328},
+Times-Cited = {96},
+Journal-ISO = {Genome Biol.},
+Unique-ID = {WOS:000346607300005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000341360200018,
+Author = {Schatschneider, Sarah and Huber, Claudia and Neuweger, Heiko and Watt,
+ Tony Francis and Puehler, Alfred and Eisenreich, Wolfgang and Wittmann,
+ Christoph and Niehaus, Karsten and Vorhoelter, Frank-Joerg},
+Title = {Metabolic flux pattern of glucose utilization by Xanthomonas
+ campestris pv. campestris: prevalent role of the Entner-Doudoroff
+ pathway and minor fluxes through the pentose phosphate pathway and
+ glycolysis},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2014},
+Volume = {10},
+Number = {10},
+Pages = {2663-2676},
+Type = {Article},
+DOI = {10.1039/c4mb00198b},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {ACID METHYL-ESTERS; ESCHERICHIA-COLI; CORYNEBACTERIUM-GLUTAMICUM;
+ XANTHAN GUM; C-13-LABELING EXPERIMENTS; CATABOLITE REPRESSION; LABELING
+ EXPERIMENTS; CARBON METABOLISM; NETWORK ANALYSIS; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Eisenreich, Wolfgang/A-1258-2013
+ },
+ORCID-Numbers = {Eisenreich, Wolfgang/0000-0002-9832-8279
+ Puhler, Alfred/0000-0003-4723-2960
+ Wittmann, Christoph/0000-0002-7952-985X},
+Times-Cited = {23},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000341360200018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000338981500010,
+Author = {VanderSluis, Benjamin and Hess, David C. and Pesyna, Colin and Krumholz,
+ Elias W. and Syed, Tahin and Szappanos, Balazs and Nislow, Corey and
+ Papp, Balazs and Troyanskaya, Olga G. and Myers, Chad L. and Caudy, Amy
+ A.},
+Title = {Broad metabolic sensitivity profiling of a prototrophic yeast deletion
+ collection},
+Journal = {GENOME BIOLOGY},
+Year = {2014},
+Volume = {15},
+Number = {4},
+Type = {Article},
+DOI = {10.1186/gb-2014-15-4-r64},
+Article-Number = {R64},
+ISSN = {1465-6906},
+EISSN = {1474-760X},
+Keywords-Plus = {AMINO-ACID PERMEASE; NONNEGATIVE MATRIX FACTORIZATION;
+ SACCHAROMYCES-CEREVISIAE; GENOME-SCALE; GENETIC INTERACTIONS; SECRETORY
+ PATHWAY; ESCHERICHIA-COLI; DUPLICATE GENES; BUDDING YEAST; NETWORKS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Szappanos, Balázs/D-1937-2013
+ },
+ORCID-Numbers = {Papp, Balazs/0000-0003-3093-8852
+ Nislow, Corey/0000-0002-4016-8874
+ Troyanskaya, Olga/0000-0002-5676-5737
+ Caudy, Amy/0000-0001-6307-8137
+ Szappanos, Balazs/0000-0002-5075-1799},
+Times-Cited = {41},
+Journal-ISO = {Genome Biol.},
+Unique-ID = {WOS:000338981500010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000337948500024,
+Author = {Vlassis, Nikos and Pacheco, Maria Pires and Sauter, Thomas},
+Title = {Fast Reconstruction of Compact Context-Specific Metabolic Network Models},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2014},
+Volume = {10},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003424},
+Article-Number = {e1003424},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {CELLULAR-METABOLISM; ESCHERICHIA-COLI; EXPRESSION DATA; DRUG TARGETS;
+ GENOME; CANCER; INTEGRATION; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Sauter, Thomas/0000-0001-8225-2954},
+Times-Cited = {152},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000337948500024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000328730300002,
+Author = {Xu, Zixiang and Zheng, Ping and Sun, Jibin and Ma, Yanhe},
+Title = {ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain
+ Optimization Based on Genome-Scale Metabolic Network},
+Journal = {PLOS ONE},
+Year = {2013},
+Volume = {8},
+Number = {12},
+Month = {DEC 11},
+Type = {Article},
+DOI = {10.1371/journal.pone.0072150},
+Article-Number = {e72150},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; KNOCKOUT STRATEGIES; LINEAR BILEVEL; RECONSTRUCTION;
+ FRAMEWORK; MODELS; GSM/GPR},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {MA, YAN/HHN-2912-2022
+ },
+ORCID-Numbers = {Sun, Jibin/0000-0002-0208-504X},
+Times-Cited = {7},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000328730300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000329781700001,
+Author = {Ghosh, Soma and Baloni, Priyanka and Mukherjee, Sumanta and Anand,
+ Praveen and Chandra, Nagasuma},
+Title = {A multi-level multi-scale approach to study essential genes in
+ Mycobacterium tuberculosis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {7},
+Month = {DEC 5},
+Type = {Article},
+DOI = {10.1186/1752-0509-7-132},
+Article-Number = {132},
+EISSN = {1752-0509},
+Keywords = {Essential genes; Multi-scale analysis; Mycobacterium tuberculosis;
+ Protein structure},
+Keywords-Plus = {PROTEIN-PROTEIN INTERACTION; FLUX BALANCE ANALYSIS; LIGAND-BINDING
+ SITES; GENOME-WIDE; TARGET IDENTIFICATION; METABOLIC NETWORK; DRUG
+ TARGET; IN-VIVO; EXPRESSION; BIOLOGY},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ghosh, Soma/IWM-2427-2023
+ Baloni, Priyanka/J-9180-2019
+ Ghosh, Soma/T-7185-2019},
+ORCID-Numbers = {Baloni, Priyanka/0000-0002-3382-4941
+ Chandra, Nagasuma/0000-0002-9939-8439
+ Anand, Praveen/0000-0002-2478-7042
+ Ghosh, Soma/0000-0002-6729-4838},
+Times-Cited = {12},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000329781700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000329364800019,
+Author = {Chandrasekaran, Sriram and Price, Nathan D.},
+Title = {Metabolic Constraint-Based Refinement of Transcriptional Regulatory
+ Networks},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2013},
+Volume = {9},
+Number = {12},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003370},
+Article-Number = {e1003370},
+EISSN = {1553-7358},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; EXPRESSION PROFILES;
+ HIGH-THROUGHPUT; MODELS; GENOME; YEAST; RECONSTRUCTION; INFERENCE;
+ STATES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Chandrasekaran, Sriram/AAD-9774-2019
+ Chandrasekaran, Sriram/AAF-4731-2019
+ },
+ORCID-Numbers = {Chandrasekaran, Sriram/0000-0002-8405-5708
+ Chandrasekaran, Sriram/0000-0002-8405-5708
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {23},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000329364800019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327126300004,
+Author = {Kell, Douglas B.},
+Title = {Finding novel pharmaceuticals in the systems biology era using multiple
+ effective drug targets, phenotypic screening and knowledge of
+ transporters: where drug discovery went wrong and how to fix it},
+Journal = {FEBS JOURNAL},
+Year = {2013},
+Volume = {280},
+Number = {23},
+Pages = {5957-5980},
+Month = {DEC},
+Type = {Review},
+DOI = {10.1111/febs.12268},
+ISSN = {1742-464X},
+EISSN = {1742-4658},
+Keywords = {drug discovery; drug resistance; drug transporters; enzyme kinetics;
+ expression profiling; genomics; polypharmacology; promiscuity;
+ robustness},
+Keywords-Plus = {EQUILIBRATIVE NUCLEOSIDE TRANSPORTER-1; HUMAN METABOLIC NETWORK;
+ SELECTIVE MONOAMINE-OXIDASE; LEVELS PREDICT RESPONSE; PRODUCT-LIKENESS
+ SCORE; IN-VIVO EXTRAPOLATION; NATURAL-PRODUCTS; HIGH-THROUGHPUT; SMALL
+ MOLECULES; FLOW-CYTOMETRY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Kell, Douglas/E-8318-2011},
+ORCID-Numbers = {Kell, Douglas/0000-0001-5838-7963},
+Times-Cited = {78},
+Journal-ISO = {FEBS J.},
+Unique-ID = {WOS:000327126300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000326631100010,
+Author = {Tabe-Bordbar, Shayan and Marashi, Sayed-Amir},
+Title = {Finding elementary flux modes in metabolic networks based on flux
+ balance analysis and flux coupling analysis: application to the analysis
+ of Escherichia coli metabolism},
+Journal = {BIOTECHNOLOGY LETTERS},
+Year = {2013},
+Volume = {35},
+Number = {12},
+Pages = {2039-2044},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1007/s10529-013-1328-x},
+ISSN = {0141-5492},
+EISSN = {1573-6776},
+Keywords = {Constraint-based modeling; Elementary flux modes; Flux balancing
+ analysis; Flux coupling analysis; Metabolic networks; Metabolic
+ pathways; Random sampling},
+Keywords-Plus = {GENOME-SCALE; PATHWAY ANALYSIS; COMPUTATION; SUBNETWORKS; TOOL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008},
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449},
+Times-Cited = {16},
+Journal-ISO = {Biotechnol. Lett.},
+Unique-ID = {WOS:000326631100010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000329902700001,
+Author = {Facchetti, Giuseppe and Altafini, Claudio},
+Title = {Partial inhibition and bilevel optimization in flux balance analysis},
+Journal = {BMC BIOINFORMATICS},
+Year = {2013},
+Volume = {14},
+Month = {NOV 29},
+Type = {Article},
+DOI = {10.1186/1471-2105-14-344},
+Article-Number = {344},
+ISSN = {1471-2105},
+Keywords-Plus = {METABOLIC NETWORK; DRUG TARGETS; PLASMODIUM-FALCIPARUM; SYSTEMS;
+ IDENTIFICATION; FRAMEWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Altafini, Claudio/AAL-4235-2020},
+ORCID-Numbers = {Altafini, Claudio/0000-0003-4142-6502},
+Times-Cited = {4},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000329902700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000328950000002,
+Author = {Nagarajan, Harish and Sahin, Merve and Nogales, Juan and Latif, Haythem
+ and Lovley, Derek R. and Ebrahim, Ali and Zengler, Karsten},
+Title = {Characterizing acetogenic metabolism using a genome-scale metabolic
+ reconstruction of Clostridium ljungdahlii},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2013},
+Volume = {12},
+Month = {NOV 25},
+Type = {Article},
+DOI = {10.1186/1475-2859-12-118},
+Article-Number = {118},
+EISSN = {1475-2859},
+Keywords-Plus = {ESCHERICHIA-COLI; NITRATE REDUCTION; NETWORK; COMPLEX; MODEL;
+ GENERATION; PATHWAY; GLUCOSE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ Sahin, Merve/U-7144-2017
+ },
+ORCID-Numbers = {Sahin, Merve/0000-0003-3858-8332
+ Nogales, Juan/0000-0002-4961-0833
+ Ebrahim, Ali/0000-0002-4009-2128
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {115},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000328950000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000329781500001,
+Author = {Yousofshahi, Mona and Ullah, Ehsan and Stern, Russell and Hassoun, Soha},
+Title = {MC3: a steady-state model and constraint consistency checker
+ for biochemical networks},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {7},
+Month = {NOV 21},
+Type = {Article},
+DOI = {10.1186/1752-0509-7-129},
+Article-Number = {129},
+EISSN = {1752-0509},
+Keywords = {Constraint-based modeling; Pathway analysis; Model validation;
+ Consistency checking; Model reuse},
+Keywords-Plus = {METABOLIC NETWORKS; FLUX ANALYSIS; OPTIMIZATION; FRAMEWORK; BALANCE;
+ SBML; CELL},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ullah, Ehsan/J-3669-2019
+ },
+ORCID-Numbers = {Ullah, Ehsan/0000-0002-9881-6731
+ ULLAH, EHSAN/0000-0002-5269-9568},
+Times-Cited = {8},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000329781500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000325945800002,
+Author = {Crook, Nathan and Alper, Hal S.},
+Title = {Model-based design of synthetic, biological systems},
+Journal = {CHEMICAL ENGINEERING SCIENCE},
+Year = {2013},
+Volume = {103},
+Pages = {2-11},
+Month = {NOV 15},
+Type = {Article},
+DOI = {10.1016/j.ces.2012.12.022},
+ISSN = {0009-2509},
+EISSN = {1873-4405},
+Keywords = {Cellular biology and engineering; Mathematical modeling; Biological and
+ biomolecular engineering; Metabolism; Molecular biology; Synthetic
+ biology},
+Keywords-Plus = {CELL-CELL COMMUNICATION; RIBOSOME BINDING-SITES; SCALE METABOLIC MODEL;
+ COMPUTATIONAL DESIGN; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE;
+ DIRECTED EVOLUTION; POSITIVE FEEDBACK; AUTOMATIC DESIGN; GENE-EXPRESSION},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ORCID-Numbers = {Crook, Nathan/0000-0001-6165-1972},
+Times-Cited = {13},
+Journal-ISO = {Chem. Eng. Sci.},
+Unique-ID = {WOS:000325945800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327505300001,
+Author = {Gelius-Dietrich, Gabriel and Desouki, Abdelmoneim Amer and Fritzemeier,
+ Claus Jonathan and Lercher, Martin J.},
+Title = {sybil - Efficient constraint-based modelling in R},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {7},
+Month = {NOV 13},
+Type = {Article},
+DOI = {10.1186/1752-0509-7-125},
+Article-Number = {125},
+ISSN = {1752-0509},
+Keywords = {Constraint-based modelling; Flux-balance analysis; FBA; MOMA; ROOM; GNU
+ R},
+Keywords-Plus = {FLUX BALANCE MODELS; ESCHERICHIA-COLI; GENE-EXPRESSION; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; RECONSTRUCTION; NETWORKS; COMPUTATION;
+ SOFTWARE; TOOLBOX},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Lercher, Martin J/K-7939-2013
+ },
+ORCID-Numbers = {Lercher, Martin J/0000-0003-3940-1621
+ Fritzemeier, Claus Jonathan/0000-0003-2218-2020
+ Desouki, Abdelmoneim Amer/0000-0003-2083-1277},
+Times-Cited = {77},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000327505300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000329427000001,
+Author = {Buechel, Finja and Saliger, Sandra and Draeger, Andreas and Hoffmann,
+ Stephanie and Wrzodek, Clemens and Zell, Andreas and Kahle, Philipp J.},
+Title = {Parkinson's disease: dopaminergic nerve cell model is consistent with
+ experimental finding of increased extracellular transport of α-synuclein},
+Journal = {BMC NEUROSCIENCE},
+Year = {2013},
+Volume = {14},
+Month = {NOV 6},
+Type = {Article},
+DOI = {10.1186/1471-2202-14-136},
+Article-Number = {136},
+ISSN = {1471-2202},
+Keywords = {Parkinson's disease; Dopaminergic nerve cell model; SBML model; Flux
+ balance analysis},
+Keywords-Plus = {IMPAIRED MITOCHONDRIAL DYNAMICS; OXIDATIVE STRESS; MUTATIONS; DATABASE;
+ BIOLOGY; PATHOGENESIS; INHIBITION; METABOLISM; PREDICTION; RESOURCE},
+Research-Areas = {Neurosciences \& Neurology},
+Web-of-Science-Categories = {Neurosciences},
+ResearcherID-Numbers = {Dräger, Andreas/F-5620-2015
+ },
+ORCID-Numbers = {Dräger, Andreas/0000-0002-1240-5553
+ Wrzodek, Finja/0000-0001-5031-1016
+ Wrzodek, Clemens/0000-0003-4995-780X},
+Times-Cited = {12},
+Journal-ISO = {BMC Neurosci.},
+Unique-ID = {WOS:000329427000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327503900001,
+Author = {Buechel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek,
+ Clemens and Czauderna, Tobias and Keller, Roland and Mittag, Florian and
+ Schubert, Michael and Glont, Mihai and Golebiewski, Martin and van
+ Iersel, Martijn and Keating, Sarah and Rall, Matthias and Wybrow,
+ Michael and Hermjakob, Henning and Hucka, Michael and Kell, Douglas B.
+ and Mueller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya,
+ Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe,
+ Camille and Draeger, Andreas and Le Novere, Nicolas},
+Title = {Path2Models: large-scale generation of computational models from
+ biochemical pathway maps},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {7},
+Month = {NOV 1},
+Type = {Article},
+DOI = {10.1186/1752-0509-7-116},
+Article-Number = {116},
+EISSN = {1752-0509},
+Keywords = {Modular rate law; Constraint based models; Logical models; SBGN; SBML},
+Keywords-Plus = {RECONSTRUCTION; KEGG; INTEGRATION; NETWORKS; DATABASE; LIBRARY; SBML;
+ KNOWLEDGEBASE; ANNOTATION; LAYOUT},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {van Iersel, Martijn P/E-9105-2010
+ Kell, Douglas/E-8318-2011
+ Saez-Rodriguez, Julio/H-7114-2019
+ Hucka, Michael/B-1896-2012
+ Hermjakob, Henning/AFM-3497-2022
+ Chaouiya, Claudine/F-8560-2012
+ Dräger, Andreas/F-5620-2015
+ Le Novère, Nicolas/F-9973-2010
+ },
+ORCID-Numbers = {van Iersel, Martijn P/0000-0002-5877-4338
+ Kell, Douglas/0000-0001-5838-7963
+ Saez-Rodriguez, Julio/0000-0002-8552-8976
+ Hucka, Michael/0000-0001-9105-5960
+ Hermjakob, Henning/0000-0001-8479-0262
+ Chaouiya, Claudine/0000-0003-2350-0756
+ Dräger, Andreas/0000-0002-1240-5553
+ Le Novère, Nicolas/0000-0002-6309-7327
+ Mendes, Pedro/0000-0001-6507-9168
+ Laibe, Camille/0000-0002-4625-743X
+ Rodriguez, Nicolas/0000-0002-9290-7894
+ Czauderna, Tobias/0000-0002-1788-9593
+ Wrzodek, Clemens/0000-0003-4995-780X
+ Golebiewski, Martin/0000-0002-8683-7084
+ Wybrow, Michael/0000-0001-5536-7780
+ Glont, Mihai/0000-0002-8211-7581
+ Wrzodek, Finja/0000-0001-5031-1016
+ Schubert, Michael/0000-0002-6862-5221
+ Mittag, Florian/0000-0002-6472-0221
+ Keating, Sarah/0000-0002-3356-3542},
+Times-Cited = {102},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000327503900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000324352700014,
+Author = {Lo, Tat-Ming and Teo, Wei Suong and Ling, Hua and Chen, Binbin and Kang,
+ Aram and Chang, Matthew Wook},
+Title = {Microbial engineering strategies to improve cell viability for
+ biochemical production},
+Journal = {BIOTECHNOLOGY ADVANCES},
+Year = {2013},
+Volume = {31},
+Number = {6, SI},
+Pages = {903-914},
+Month = {NOV 1},
+Type = {Review},
+DOI = {10.1016/j.biotechadv.2013.02.001},
+ISSN = {0734-9750},
+EISSN = {1873-1899},
+Keywords = {Microbial production; Bio-catalyst; Viability; Growth rates;
+ Productivity; Metabolic engineering; Synthetic biology},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE;
+ METABOLIC PATHWAYS; GENE-EXPRESSION; QUANTITATIVE PREDICTION;
+ TRANSCRIPTION MACHINERY; SPATIAL-ORGANIZATION; VANILLIN PRODUCTION;
+ DIRECTED EVOLUTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Chang, Matthew Wook/G-6220-2010
+ },
+ORCID-Numbers = {Chang, Matthew Wook/0000-0001-6448-6319
+ Ling, Hua/0000-0002-0680-6422},
+Times-Cited = {50},
+Journal-ISO = {Biotechnol. Adv.},
+Unique-ID = {WOS:000324352700014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327567100012,
+Author = {Lule, Ivan and D'Huys, Pieter-Jan and Van Mellaert, Lieve and Anne,
+ Jozef and Bernaerts, Kristel and Van Impe, Jan},
+Title = {Metabolic impact assessment for heterologous protein production in
+ Streptomyces lividans based on genome-scale metabolic network
+ modeling},
+Journal = {MATHEMATICAL BIOSCIENCES},
+Year = {2013},
+Volume = {246},
+Number = {1},
+Pages = {113-121},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.mbs.2013.08.006},
+ISSN = {0025-5564},
+EISSN = {1879-3134},
+Keywords = {Streptomyces lividans; (geometric) Flux balance analysis; Mouse tumor
+ necrosis factor (mTNF-alpha); Heterologous proteins; Genome-scale
+ metabolic network},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; NECROSIS-FACTOR-ALPHA; ESCHERICHIA-COLI;
+ SECRETION; OVEREXPRESSION; COELICOLOR},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {ANNE, Jozef/H-7983-2019
+ Van Mellaert, Lieve/Q-4975-2017
+ },
+ORCID-Numbers = {ANNE, Jozef/0000-0002-0493-2644
+ Van Mellaert, Lieve/0000-0002-8584-8160
+ Van Impe, Jan/0000-0002-5904-1638
+ Bernaerts, Kristel/0000-0001-6211-7042},
+Times-Cited = {7},
+Journal-ISO = {Math. Biosci.},
+Unique-ID = {WOS:000327567100012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000336905300018,
+Author = {Mao, Longfei and Verwoerd, Wynand S.},
+Title = {Exploration and comparison of inborn capacity of aerobic and anaerobic
+ metabolisms of Saccharomyces cerevisiae for microbial electrical
+ current production},
+Journal = {BIOENGINEERED},
+Year = {2013},
+Volume = {4},
+Number = {6},
+Pages = {420-430},
+Month = {NOV-DEC},
+Type = {Article},
+DOI = {10.4161/bioe.26222},
+ISSN = {2165-5979},
+EISSN = {2165-5987},
+Keywords = {MFC; microbial fuel cell; Saccharomyces cerevisiae; bioelectricity; flux
+ balance analysis; flux variability analysis; flux minimization; FATMIN},
+Keywords-Plus = {FUEL-CELLS; YEAST; GENERATION; ESSENTIALITY; ELECTRODE; HOMOLOGS;
+ MODELS; GROWTH; ANODE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Verwoerd, Wynand/A-8320-2010
+ },
+ORCID-Numbers = {Verwoerd, Wynand/0000-0001-5489-9101
+ Mao, Longfei/0000-0003-0759-0501},
+Times-Cited = {4},
+Journal-ISO = {Bioengineered},
+Unique-ID = {WOS:000336905300018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000328025800006,
+Author = {Nagarajan, Harish and Embree, Mallory and Rotaru, Amelia-Elena and
+ Shrestha, Pravin M. and Feist, Adam M. and Palsson, Bernhard O. and
+ Lovley, Derek R. and Zengler, Karsten},
+Title = {Characterization and modelling of interspecies electron transfer
+ mechanisms and microbial community dynamics of a syntrophic association},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2013},
+Volume = {4},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1038/ncomms3809},
+Article-Number = {2809},
+ISSN = {2041-1723},
+Keywords-Plus = {IN-SILICO; PELOBACTER-CARBINOLICUS; GEOBACTER-SULFURREDUCENS;
+ PROPIONATE; METABOLISM; RNA; OPTIMIZATION; COOPERATION; EVOLUTION;
+ OXIDATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Rotaru, Amelia-Elena/C-4782-2014
+ Shrestha, Pravin Malla/I-8025-2014
+ },
+ORCID-Numbers = {Rotaru, Amelia-Elena/0000-0003-2415-8585
+ Palsson, Bernhard/0000-0003-2357-6785
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {60},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000328025800006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000328084500006,
+Author = {Song, Carl and Chiasson, Melissa A. and Nursimulu, Nirvana and Hung,
+ Stacy S. and Wasmuth, James and Grigg, Michael E. and Parkinson, John},
+Title = {Metabolic reconstruction identifies strain-specific regulation of
+ virulence in Toxoplasma gondii},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {9},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1038/msb.2013.62},
+Article-Number = {708},
+ISSN = {1744-4292},
+Keywords = {flux balance analysis; metabolic reconstruction; strain differences;
+ Toxoplasma gondii},
+Keywords-Plus = {FLUX-BALANCE ANALYSIS; BIOCHEMICAL-CHARACTERIZATION; PLASMODIUM;
+ BIOSYNTHESIS; PURIFICATION; INHIBITORS; EVOLUTION; GROWTH; ACID;
+ RESISTANCE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Parkinson, John/A-4424-2008
+ },
+ORCID-Numbers = {Parkinson, John/0000-0001-9815-1189
+ Wasmuth, James/0000-0002-9516-212X
+ Nursimulu, Nirvana/0000-0001-5962-5863
+ Chiasson, Melissa/0000-0002-1880-3181},
+Times-Cited = {32},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000328084500006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327503700004,
+Author = {Ponce-de-Leon, Miguel and Montero, Francisco and Pereto, Juli},
+Title = {Solving gap metabolites and blocked reactions in genome-scale models:
+ application to the metabolic network of Blattabacterium cuenoti},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {7},
+Month = {OCT 31},
+Type = {Article},
+DOI = {10.1186/1752-0509-7-114},
+Article-Number = {114},
+EISSN = {1752-0509},
+Keywords-Plus = {ESCHERICHIA-COLI; PATHWAY; RECONSTRUCTION; SYSTEMS; GENES;
+ IDENTIFICATION; OPTIMIZATION; DEFINITION; GENERATION; PREDICTION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Montero, Francisco/G-9850-2015
+ Peretó, Juli/G-5969-2015
+ Ponce-de-Leon, Miguel/AAB-8124-2020},
+ORCID-Numbers = {Montero, Francisco/0000-0003-2366-3635
+ Peretó, Juli/0000-0002-5756-1517
+ Ponce-de-Leon, Miguel/0000-0002-7496-844X},
+Times-Cited = {16},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000327503700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000326022200093,
+Author = {Biggs, Matthew B. and Papin, Jason A.},
+Title = {Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa
+ Biofilm Formation},
+Journal = {PLOS ONE},
+Year = {2013},
+Volume = {8},
+Number = {10},
+Month = {OCT 17},
+Type = {Article},
+DOI = {10.1371/journal.pone.0078011},
+Article-Number = {e78011},
+ISSN = {1932-6203},
+Keywords-Plus = {METABOLIC NETWORK ANALYSIS; FLUX BALANCE ANALYSIS; ADAPTATION; GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Papin, Jason/0000-0002-2769-5805
+ Biggs, Matthew/0000-0001-6492-8180},
+Times-Cited = {50},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000326022200093},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327502600001,
+Author = {Chang, Roger L. and Xie, Lei and Bourne, Philip E. and Palsson, Bernhard
+ O.},
+Title = {Antibacterial mechanisms identified through structural systems
+ pharmacology},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {7},
+Month = {OCT 10},
+Type = {Article},
+DOI = {10.1186/1752-0509-7-102},
+Article-Number = {102},
+EISSN = {1752-0509},
+Keywords = {Structural systems pharmacology; Antibacterial; Metabolic model; Ligand
+ binding; Escherichia coli},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; WEB SERVICE; PROTEIN; RECONSTRUCTION; PREDICTION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Bourne, Philip/ABG-8967-2021
+ },
+ORCID-Numbers = {Bourne, Philip/0000-0002-7618-7292
+ Palsson, Bernhard/0000-0003-2357-6785
+ Chang, Roger/0000-0003-1630-6584},
+Times-Cited = {22},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000327502600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000324552500030,
+Author = {Flahaut, Nicolas A. L. and Wiersma, Anne and van de Bunt, Bert and
+ Martens, Dirk E. and Schaap, Peter J. and Sijtsma, Lolke and dos Santos,
+ Vitor A. Martins and de Vos, Willem M.},
+Title = {Genome-scale metabolic model for Lactococcus lactis MG1363 and
+ its application to the analysis of flavor formation},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2013},
+Volume = {97},
+Number = {19},
+Pages = {8729-8739},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1007/s00253-013-5140-2},
+ISSN = {0175-7598},
+Keywords = {Genome-scale; Constraint-based model; Metabolic network; Lactococcus
+ lactis; Flavors; Chemostat culture},
+Keywords-Plus = {AMINO-ACID CATABOLISM; STREPTOCOCCUS-LACTIS; CREMORIS MG1363;
+ STEADY-STATE; BACTERIA; GROWTH; RECONSTRUCTION; NETWORKS; SYSTEMS;
+ CHEESE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Schaap, Peter/0000-0002-4346-6084},
+Times-Cited = {81},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000324552500030},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000324234100008,
+Author = {Mao, Longfei and Verwoerd, Wynand S.},
+Title = {Genome-scale stoichiometry analysis to elucidate the innate capability
+ of the cyanobacterium Synechocystis for electricity generation},
+Journal = {JOURNAL OF INDUSTRIAL MICROBIOLOGY \& BIOTECHNOLOGY},
+Year = {2013},
+Volume = {40},
+Number = {10},
+Pages = {1161-1180},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1007/s10295-013-1308-0},
+ISSN = {1367-5435},
+EISSN = {1476-5535},
+Keywords = {Microbial fuel cell (MFC); Synechocystis sp PCC 6803; Bioelectricity;
+ Flux balance analysis; Flux; variability analysis},
+Keywords-Plus = {MICROBIAL FUEL-CELLS; EXTRACELLULAR ELECTRON-TRANSFER; NEUTRAL RED;
+ GEOBACTER-SULFURREDUCENS; ENERGY; LIGHT; BALANCE; METABOLISM;
+ CHALLENGES; MEDIATORS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Verwoerd, Wynand/A-8320-2010
+ },
+ORCID-Numbers = {Verwoerd, Wynand/0000-0001-5489-9101
+ Mao, Longfei/0000-0003-0759-0501},
+Times-Cited = {8},
+Journal-ISO = {J. Ind. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000324234100008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000324652500011,
+Author = {Mitra, Koyel and Carvunis, Anne-Ruxandra and Ramesh, Sanath Kumar and
+ Ideker, Trey},
+Title = {Integrative approaches for finding modular structure in biological
+ networks},
+Journal = {NATURE REVIEWS GENETICS},
+Year = {2013},
+Volume = {14},
+Number = {10},
+Pages = {719-732},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1038/nrg3552},
+ISSN = {1471-0056},
+EISSN = {1471-0064},
+Keywords-Plus = {PROTEIN-INTERACTION NETWORKS; IDENTIFYING FUNCTIONAL MODULES;
+ GENE-EXPRESSION; TRANSCRIPTIONAL REGULATION; REGULATORY NETWORKS;
+ INTERACTION MAP; YEAST; REVEALS; IDENTIFICATION; COMPLEXES},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ORCID-Numbers = {Carvunis, Anne-Ruxandra/0000-0002-6474-6413
+ Ramesh, Sanath Kumar/0000-0002-9793-7742
+ Ideker, Trey/0000-0002-1708-8454},
+Times-Cited = {368},
+Journal-ISO = {Nat. Rev. Genet.},
+Unique-ID = {WOS:000324652500011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000324176900006,
+Author = {Wang, Yi and Li, Xiangzhen and Milne, Caroline B. and Janssen, Holger
+ and Lin, Weiyin and Phan, Gloria and Hu, Huiying and Jin, Yong-Su and
+ Price, Nathan D. and Blaschek, Hans P.},
+Title = {Development of a Gene Knockout System Using Mobile Group II Introns
+ (Targetron) and Genetic Disruption of Acid Production Pathways in
+ Clostridium beijerinckii},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2013},
+Volume = {79},
+Number = {19},
+Pages = {5853-5863},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1128/AEM.00971-13},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords-Plus = {GENOME-SCALE MODEL; ACETOBUTYLICUM ATCC 824; NCIMB 8052; SOLVENT
+ PRODUCTION; METABOLIC NETWORK; ACETATE; SOLVENTOGENESIS; INACTIVATION;
+ MANIPULATION; FERMENTATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Jin, Yong-Su/L-4530-2013
+ },
+ORCID-Numbers = {Jin, Yong-Su/0000-0002-4464-9536
+ Wang, Yi/0000-0002-0192-3195
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {50},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000324176900006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000324523100015,
+Author = {Wu, Wei and Jamshidi, Neema and Eraly, Satish A. and Liu, Henry C. and
+ Bush, Kevin T. and Palsson, Bernhard O. and Nigam, Sanjay K.},
+Title = {Multispecific Drug Transporter Slc22a8 (Oat3) Regulates
+ Multiple Metabolic and Signaling Pathways},
+Journal = {DRUG METABOLISM AND DISPOSITION},
+Year = {2013},
+Volume = {41},
+Number = {10},
+Pages = {1825-1834},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1124/dmd.113.052647},
+ISSN = {0090-9556},
+EISSN = {1521-009X},
+Keywords-Plus = {ORGANIC ANION TRANSPORTERS; CONSTRAINT-BASED MODELS; CATION
+ TRANSPORTERS; QUANTITATIVE PREDICTION; MEMBRANE TRANSPORTERS;
+ CELLULAR-METABOLISM; MOLECULAR-CLONING; KNOCKOUT MICE; IN-VITRO; KIDNEY},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785
+ Jamshidi, Neema/0000-0003-3857-9735},
+Times-Cited = {52},
+Journal-ISO = {Drug Metab. Dispos.},
+Unique-ID = {WOS:000324523100015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000324408400040,
+Author = {Meng, Jing and Xu, Zixiang and Guo, Jing and Yue, Yunxia and Sun, Xiao},
+Title = {Analysis of Enhanced Current-Generating Mechanism of Geobacter
+ sulfurreducens Strain via Model-Driven Metabolism Simulation},
+Journal = {PLOS ONE},
+Year = {2013},
+Volume = {8},
+Number = {9},
+Month = {SEP 13},
+Type = {Article},
+DOI = {10.1371/journal.pone.0073907},
+Article-Number = {e73907},
+ISSN = {1932-6203},
+Keywords-Plus = {MICROBIAL FUEL-CELLS; FLUX BALANCE ANALYSIS; C-TYPE CYTOCHROME;
+ ELECTRON-TRANSFER; EVOLUTION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {12},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000324408400040},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327590100009,
+Author = {Chakrabarti, Anirikh and Miskovic, Ljubisa and Soh, Keng Cher and
+ Hatzimanikatis, Vassily},
+Title = {Towards kinetic modeling of genome-scale metabolic networks without
+ sacrificing stoichiometric, thermodynamic and physiological constraints},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2013},
+Volume = {8},
+Number = {9, SI},
+Pages = {1043-U105},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1002/biot.201300091},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Elasticity; Mass action; Saturation; Stability; Thermodynamics},
+Keywords-Plus = {ESCHERICHIA-COLI; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; ENZYMES;
+ RECONSTRUCTION; UNCERTAINTY; INTEGRATION; DESIGN},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Miskovic, Ljubisa/E-8927-2012
+ Hatzimanikatis, Vassily/G-6505-2010
+ },
+ORCID-Numbers = {Miskovic, Ljubisa/0000-0001-7333-8211
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Chakrabarti, Anirikh/0000-0001-7804-209X},
+Times-Cited = {104},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000327590100009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327590100011,
+Author = {Gonnerman, Matthew C. and Benedict, Matthew N. and Feist, Adam M. and
+ Metcalf, William W. and Price, Nathan D.},
+Title = {Genomically and biochemically accurate metabolic reconstruction of
+ Methanosarcina barkeri Fusaro, iMG746},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2013},
+Volume = {8},
+Number = {9, SI},
+Pages = {1070-U129},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1002/biot.201200266},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Metabolic flux analysis; Metabolic network; Modeling; Microbiology;
+ Systems biology},
+Keywords-Plus = {THERMODYNAMIC ANALYSIS; REDUCTIVE DECHLORINATION; AMMONIA ASSIMILATION;
+ GENOME; GROWTH; METHANOGENESIS; BIOSYNTHESIS; REVEALS; PATHWAY;
+ 1,2-DICHLOROETHANE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {34},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000327590100011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000327590100003,
+Author = {Zhuang, Kai and Bakshi, Bhavik R. and Herrgard, Markus J.},
+Title = {Multi-scale modeling for sustainable chemical production},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2013},
+Volume = {8},
+Number = {9, SI},
+Pages = {973+},
+Month = {SEP},
+Type = {Review},
+DOI = {10.1002/biot.201200272},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Biochemicals; Life cycle analysis; Metabolic modeling; Multi-scale
+ modeling; Sustainability},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; QUANTITATIVE PREDICTION;
+ MICROBIAL-PRODUCTION; CELLULAR-METABOLISM; OPTIMIZATION; DESIGN;
+ RECONSTRUCTION; INDUSTRY; ENERGY},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Bakshi, Bhavik/G-3878-2012},
+ORCID-Numbers = {Bakshi, Bhavik/0000-0002-6604-8408},
+Times-Cited = {11},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000327590100003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000323271400073,
+Author = {Labhsetwar, Piyush and Cole, John Andrew and Roberts, Elijah and Price,
+ Nathan D. and Luthey-Schulten, Zaida A.},
+Title = {Heterogeneity in protein expression induces metabolic variability in a
+ modeled Escherichia coli population},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2013},
+Volume = {110},
+Number = {34},
+Pages = {14006-14011},
+Month = {AUG 20},
+Type = {Article},
+DOI = {10.1073/pnas.1222569110},
+ISSN = {0027-8424},
+Keywords = {protein noise; pathway utilization; metabolism; aerobic regulation;
+ systems biology},
+Keywords-Plus = {NETWORK RECONSTRUCTION; GENE-EXPRESSION; PHENOTYPE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Labhsetwar, Piyush/K-3285-2013
+ Labhsetwar, Piyush/P-3227-2019
+ },
+ORCID-Numbers = {Labhsetwar, Piyush/0000-0001-5933-3609
+ Labhsetwar, Piyush/0000-0001-5933-3609
+ Price, Nathan/0000-0002-4157-0267
+ Luthey-Schulten, Zaida/0000-0001-9749-8367},
+Times-Cited = {76},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000323271400073},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000323809600007,
+Author = {Schatschneider, Sarah and Persicke, Marcus and Watt, Steven Alexander
+ and Hublik, Gerd and Puehler, Alfred and Niehaus, Karsten and
+ Vorhoelter, Frank-Joerg},
+Title = {Establishment, in silico analysis, and experimental verification
+ of a large-scale metabolic network of the xanthan producing
+ Xanthomonas campestris pv. campestris strain B100},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2013},
+Volume = {167},
+Number = {2, SI},
+Pages = {123-134},
+Month = {AUG 20},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2013.01.023},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Central carbon metabolism; Plant pathogen; Phosphogluconate
+ dehydrogenase; Transketolase; Phosphofructokinase; Phosphoglucose
+ isomerase},
+Keywords-Plus = {PSEUDOMONAS-PUTIDA KT2440; CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI;
+ GUM PRODUCTION; QUANTITATIVE PREDICTION; ENERGY-REQUIREMENTS;
+ CELLULAR-METABOLISM; GLUCOSE-METABOLISM; GENOME; RECONSTRUCTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Hublik, Gerd/0000-0003-2408-0343
+ Puhler, Alfred/0000-0003-4723-2960},
+Times-Cited = {33},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000323809600007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000323104400001,
+Author = {Heavner, Benjamin D. and Smallbone, Kieran and Price, Nathan D. and
+ Walker, Larry P.},
+Title = {Version 6 of the consensus yeast metabolic network refines biochemical
+ coverage and improves model performance},
+Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
+Year = {2013},
+Month = {AUG 9},
+Type = {Article},
+DOI = {10.1093/database/bat059},
+Article-Number = {bat059},
+ISSN = {1758-0463},
+Keywords-Plus = {GENOME; RECONSTRUCTION; PREDICTION; ACCURACY},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Smallbone, Kieran/0000-0003-2815-7045
+ Heavner, Benjamin/0000-0003-2898-9044
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {71},
+Journal-ISO = {Database},
+Unique-ID = {WOS:000323104400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000323121200001,
+Author = {Ebrahim, Ali and Lerman, Joshua A. and Palsson, Bernhard O. and Hyduke,
+ Daniel R.},
+Title = {COBRApy: COnstraints-Based Reconstruction and Analysis for Python},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {7},
+Month = {AUG 8},
+Type = {Article},
+DOI = {10.1186/1752-0509-7-74},
+Article-Number = {74},
+ISSN = {1752-0509},
+Keywords = {Genome-scale; Network reconstruction; Metabolism; Gene expression;
+ Constraint-based modeling},
+Keywords-Plus = {TRANSCRIPTIONAL REGULATION; METABOLISM; MODEL; SYSTEMS; NETWORKS;
+ PRODUCT; LIBRARY; GROWTH},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785
+ Ebrahim, Ali/0000-0002-4009-2128
+ Lerman, Joshua/0000-0003-0377-2674},
+Times-Cited = {596},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000323121200001},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000323455900004,
+Author = {Sharma, Ashwini Kumar and Koenig, Rainer},
+Title = {Metabolic network modeling approaches for investigating the ``hungry
+ cancer{''}},
+Journal = {SEMINARS IN CANCER BIOLOGY},
+Year = {2013},
+Volume = {23},
+Number = {4},
+Pages = {227-234},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1016/j.semcancer.2013.05.001},
+ISSN = {1044-579X},
+EISSN = {1096-3650},
+Keywords = {Cancer; Metabolism; Networks; Regulation; Flux balance analysis;
+ Metabolic flux analysis; Pattern analysis},
+Keywords-Plus = {ENRICHMENT ANALYSIS; TUMOR-SUPPRESSOR; FLUX; GENOME; PATHWAY; CELLS;
+ GLYCOLYSIS; PREDICTION; HALLMARKS; FRAMEWORK},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ORCID-Numbers = {Sharma, Ashwini Kumar/0000-0001-7883-7888},
+Times-Cited = {11},
+Journal-ISO = {Semin. Cancer Biol.},
+Unique-ID = {WOS:000323455900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000322292800081,
+Author = {Wallenius, Janne and Viikila, Matti and Survase, Shrikant and Ojamo,
+ Heikki and Eerikainen, Tero},
+Title = {Constraint-based genome-scale metabolic modeling of Clostridium
+ acetobutylicum behavior in an immobilized column},
+Journal = {BIORESOURCE TECHNOLOGY},
+Year = {2013},
+Volume = {142},
+Pages = {603-610},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1016/j.biortech.2013.05.085},
+ISSN = {0960-8524},
+EISSN = {1873-2976},
+Keywords = {Genome-scale metabolic modeling; Flux balance analysis; Clostridia;
+ Continuous fermentation; Cell immobilization},
+Keywords-Plus = {ACETONE-BUTANOL-ETHANOL; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM},
+Research-Areas = {Agriculture; Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Agricultural Engineering; Biotechnology \& Applied Microbiology; Energy
+ \& Fuels},
+ResearcherID-Numbers = {Survase, Shrikant A/F-8840-2012
+ Eerikäinen, Tero/F-5201-2015
+ },
+ORCID-Numbers = {Eerikäinen, Tero/0000-0002-6796-3712
+ Wallenius, Janne/0000-0003-1786-4027},
+Times-Cited = {8},
+Journal-ISO = {Bioresour. Technol.},
+Unique-ID = {WOS:000322292800081},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000322915900001,
+Author = {Sun, Yuekai and Fleming, Ronan M. T. and Thiele, Ines and Saunders,
+ Michael A.},
+Title = {Robust flux balance analysis of multiscale biochemical reaction networks},
+Journal = {BMC BIOINFORMATICS},
+Year = {2013},
+Volume = {14},
+Month = {JUL 30},
+Type = {Article},
+DOI = {10.1186/1471-2105-14-240},
+Article-Number = {240},
+ISSN = {1471-2105},
+Keywords-Plus = {OPTIMIZATION; METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Saunders, Michael A/D-1083-2012
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Saunders, Michael/0000-0003-3800-4982},
+Times-Cited = {16},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000322915900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000331367000001,
+Author = {Misra, Ashish and Conway, Matthew F. and Johnnie, Joseph and Qureshi,
+ Tabish M. and Lige, Bao and Derrick, Anne M. and Agbo, Eddy C. and
+ Sriram, Ganesh},
+Title = {Metabolic analyses elucidate non-trivial gene targets for amplifying
+ dihydroartemisinic acid production in yeast},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2013},
+Volume = {4},
+Month = {JUL 26},
+Type = {Article},
+DOI = {10.3389/fmicb.2013.00200},
+Article-Number = {200},
+ISSN = {1664-302X},
+Keywords = {artemisinin; metabolic engineering; metabolic pathway; extreme pathway;
+ isotope labeling; metabolic flux analysis; flux balance analysis;
+ minimization of metabolic adjustment},
+Keywords-Plus = {ARTEMISIA-ANNUA; LABELING EXPERIMENTS; MOLECULAR-CLONING; FLUX ANALYSIS;
+ BIOSYNTHESIS; PATHWAY; MALARIA; PRECURSORS; FRAMEWORK; REDUCTASE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Sriram, Ganesh/A-5154-2010
+ },
+ORCID-Numbers = {Sriram, Ganesh/0000-0002-6303-1328},
+Times-Cited = {6},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000331367000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000322599400001,
+Author = {Vital-Lopez, Francisco G. and Wallqvist, Anders and Reifman, Jaques},
+Title = {Bridging the gap between gene expression and metabolic phenotype via
+ kinetic models},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {7},
+Month = {JUL 22},
+Type = {Article},
+DOI = {10.1186/1752-0509-7-63},
+Article-Number = {63},
+ISSN = {1752-0509},
+Keywords = {Gene expression; Kinetic models; Metabolic networks; S. cerevisiae;
+ Transcriptomics; Fluxomics; Metabolomics},
+Keywords-Plus = {TRANSCRIPTIONAL REGULATION; BIOCHEMICAL NETWORKS; CELLULAR-METABOLISM;
+ YEAST; SYSTEMS; SENSITIVITIES; CONSTRAINTS; PREDICTION; CELLS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {wallqvist, anders/W-2584-2019},
+ORCID-Numbers = {wallqvist, anders/0000-0002-9775-7469},
+Times-Cited = {14},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000322599400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000322320200014,
+Author = {Dreyfuss, Jonathan M. and Zucker, Jeremy D. and Hood, Heather M. and
+ Ocasio, Linda R. and Sachs, Matthew S. and Galagan, James E.},
+Title = {Reconstruction and Validation of a Genome-Scale Metabolic Model for the
+ Filamentous Fungus Neurospora crassa Using FARM},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2013},
+Volume = {9},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003126},
+Article-Number = {e1003126},
+EISSN = {1553-7358},
+Keywords-Plus = {FLUX-BALANCE ANALYSIS; MAGNETIC-RESONANCE-SPECTROSCOPY;
+ ACETATE-NONUTILIZING MUTANTS; CONSTRAINT-BASED MODELS; GENETIC-CONTROL;
+ PATHWAY/GENOME DATABASES; QUANTITATIVE PREDICTION; BIOCHEMICAL
+ REACTIONS; CELLULAR-METABOLISM; BIOCYC COLLECTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zucker, Jeremy/M-3643-2016
+ },
+ORCID-Numbers = {Zucker, Jeremy/0000-0002-7276-9009
+ Sachs, Matthew/0000-0001-9891-9223
+ Galagan, James/0000-0003-0542-3291
+ Dreyfuss, Jonathan/0000-0001-7242-3991},
+Times-Cited = {44},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000322320200014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000322321100022,
+Author = {Hottes, Alison K. and Freddolino, Peter L. and Khare, Anupama and
+ Donnell, Zachary N. and Liu, Julia C. and Tavazoie, Saeed},
+Title = {Bacterial Adaptation through Loss of Function},
+Journal = {PLOS GENETICS},
+Year = {2013},
+Volume = {9},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1371/journal.pgen.1003617},
+Article-Number = {e1003617},
+ISSN = {1553-7404},
+Keywords-Plus = {ESCHERICHIA-COLI; STATIONARY-PHASE; PSEUDOMONAS-AERUGINOSA; EVOLUTION;
+ MUTATIONS; GENES; RESISTANCE; PLCR; VIRULENCE; SELECTION},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Khare, Anupama/N-9220-2018
+ Freddolino, Peter L/C-2288-2008
+ },
+ORCID-Numbers = {Khare, Anupama/0000-0003-1231-670X
+ Liu, Julia/0000-0002-8604-1633},
+Times-Cited = {152},
+Journal-ISO = {PLoS Genet.},
+Unique-ID = {WOS:000322321100022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000320478800005,
+Author = {Kim, Hyun Ju and Hou, Bo Kyeng and Lee, Sung Gun and Kim, Joong Su and
+ Lee, Dong-Woo and Lee, Sang Jun},
+Title = {Genome-wide analysis of redox reactions reveals metabolic engineering
+ targets for D-lactate overproduction in Escherichia coli},
+Journal = {METABOLIC ENGINEERING},
+Year = {2013},
+Volume = {18},
+Pages = {44-52},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2013.03.004},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Anaerobic; D-Lactate; Escherichia coli; Metabolic engineering; Redox},
+Keywords-Plus = {D-LACTIC ACID; HOMOFERMENTATIVE PRODUCTION; SACCHAROMYCES-CEREVISIAE;
+ SUCCINIC ACID; DEHYDROGENASE; GENES; FERMENTATION; K-12; NETWORKS;
+ PATHWAY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Kim, Mi Jin/GXH-9639-2022
+ Lee, Sang Jun/GPT-4187-2022
+ },
+ORCID-Numbers = {Lee, Sang Jun/0000-0002-2803-753X
+ Hou, Bo Kyeng/0000-0002-9324-5263},
+Times-Cited = {28},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000320478800005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000322320200001,
+Author = {Noor, Elad and Haraldsdottir, Hulda S. and Milo, Ron and Fleming, Ronan
+ M. T.},
+Title = {Consistent Estimation of Gibbs Energy Using Component Contributions},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2013},
+Volume = {9},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003098},
+Article-Number = {e1003098},
+EISSN = {1553-7358},
+Keywords-Plus = {METABOLIC RECONSTRUCTION; THERMODYNAMIC PROPERTIES; BIOCHEMICAL
+ NETWORKS; ADDITIVITY RULES; TOOLBOX; MODELS; THERMOCHEMISTRY; ACCURACY;
+ DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Noor, Elad/AAN-9042-2020
+ Milo, Hilla/C-8767-2016
+ Fleming, Ronan MT/ABC-4093-2021
+ },
+ORCID-Numbers = {Noor, Elad/0000-0001-8776-4799
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Milo, Ron/0000-0003-1641-2299},
+Times-Cited = {170},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000322320200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000320125100014,
+Author = {Sahoo, Swagatika and Thiele, Ines},
+Title = {Predicting the impact of diet and enzymopathies on human small
+ intestinal epithelial cells},
+Journal = {HUMAN MOLECULAR GENETICS},
+Year = {2013},
+Volume = {22},
+Number = {13},
+Pages = {2705-2722},
+Month = {JUL 1},
+Type = {Article},
+DOI = {10.1093/hmg/ddt119},
+ISSN = {0964-6906},
+EISSN = {1460-2083},
+Keywords-Plus = {ACUTE INTERMITTENT PORPHYRIA; CENTRAL-NERVOUS-SYSTEM; METABOLIC
+ SYNDROME; CARBON-MONOXIDE; CELIAC-DISEASE; INBORN-ERRORS; MOUSE MODEL;
+ DEFICIENCY; RECONSTRUCTION; BOWEL},
+Research-Areas = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Sahoo, Swagatika/0000-0003-3773-8597},
+Times-Cited = {45},
+Journal-ISO = {Hum. Mol. Genet.},
+Unique-ID = {WOS:000320125100014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000321241600005,
+Author = {Knoop, Henning and Gruendel, Marianne and Zilliges, Yvonne and Lehmann,
+ Robert and Hoffmann, Sabrina and Lockau, Wolfgang and Steuer, Ralf},
+Title = {Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic
+ Network of Synechocystis sp PCC 6803},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2013},
+Volume = {9},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1003081},
+Article-Number = {e1003081},
+EISSN = {1553-7358},
+Keywords-Plus = {RECONSTRUCTION; PATHWAY; CARBON; MODEL; PHOTORESPIRATION; DEHYDROGENASE;
+ OPTIMALITY; EXPRESSION; PROTEINS; DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Steuer, Ralf/E-7482-2017
+ },
+ORCID-Numbers = {Steuer, Ralf/0000-0003-2217-1655
+ Lehmann, Robert/0000-0001-7071-4226},
+Times-Cited = {189},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000321241600005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000319032500001,
+Author = {Tomar, Namrata and De, Rajat K.},
+Title = {Comparing methods for metabolic network analysis and an application to
+ metabolic engineering},
+Journal = {GENE},
+Year = {2013},
+Volume = {521},
+Number = {1},
+Pages = {1-14},
+Month = {MAY 25},
+Type = {Review},
+DOI = {10.1016/j.gene.2013.03.017},
+ISSN = {0378-1119},
+EISSN = {1879-0038},
+Keywords = {Systems Biology; Flux balance analysis; Elementary flux mode analysis;
+ Metabolic pathway modeling; Strain optimization},
+Keywords-Plus = {ESCHERICHIA-COLI; PATHWAY ANALYSIS; OPTIMIZATION FRAMEWORK;
+ STEADY-STATES; CELL; SYSTEMS; MODEL; DATABASE; OVERPRODUCTION;
+ REPRESENTATION},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+Times-Cited = {39},
+Journal-ISO = {Gene},
+Unique-ID = {WOS:000319032500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000320177000001,
+Author = {Huang, Di and Li, Shanshan and Xia, Menglei and Wen, Jianping and Jia,
+ Xiaoqiang},
+Title = {Genome-scale metabolic network guided engineering of Streptomyces
+ tsukubaensis for FK506 production improvement},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2013},
+Volume = {12},
+Month = {MAY 24},
+Type = {Article},
+DOI = {10.1186/1475-2859-12-52},
+Article-Number = {52},
+ISSN = {1475-2859},
+Keywords = {Streptomyces tsukubaensis; FK506; Genome-scale metabolic model; Target
+ prediction; Metabolic engineering; Combinatorial modification},
+Keywords-Plus = {BIOSYNTHETIC GENE-CLUSTER; ESCHERICHIA-COLI; PHOSPHOENOLPYRUVATE
+ CARBOXYLASE; CORYNEBACTERIUM-GLUTAMICUM; TRANSPLANT RECIPIENTS; KNOCKOUT
+ STRATEGIES; CARBON FLUX; ACID; TACROLIMUS; EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Li, Shanshan/HLH-7747-2023
+ Wen, Jianping/A-1866-2015
+ Huang, Di/JBJ-3541-2023},
+ORCID-Numbers = {Huang, Di/0000-0001-7877-7301},
+Times-Cited = {60},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000320177000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000319330200030,
+Author = {Chaudhury, Sidhartha and Abdulhameed, Mohamed Diwan M. and Singh,
+ Narender and Tawa, Gregory J. and D'haeseleer, Patrik M. and Zemla, Adam
+ T. and Navid, Ali and Zhou, Carol E. and Franklin, Matthew C. and
+ Cheung, Jonah and Rudolph, Michael J. and Love, James and Graf, John F.
+ and Rozak, David A. and Dankmeyer, Jennifer L. and Amemiya, Kei and
+ Daefler, Simon and Wallqvist, Anders},
+Title = {Rapid Countermeasure Discovery against Francisella tularensis
+ Based on a Metabolic Network Reconstruction},
+Journal = {PLOS ONE},
+Year = {2013},
+Volume = {8},
+Number = {5},
+Month = {MAY 21},
+Type = {Article},
+DOI = {10.1371/journal.pone.0063369},
+Article-Number = {e63369},
+ISSN = {1932-6203},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; MYCOBACTERIUM-TUBERCULOSIS; ACCURATE DOCKING;
+ SYSTEMS BIOLOGY; DRUG DISCOVERY; INHIBITORS; DATABASE; ENZYME;
+ PREDICTION; TULAREMIA},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {wallqvist, anders/W-2584-2019
+ AbdulHameed, Mohamed Diwan M/O-3088-2015
+ Navid, Ali/A-1336-2013
+ },
+ORCID-Numbers = {wallqvist, anders/0000-0002-9775-7469
+ AbdulHameed, Mohamed Diwan M/0000-0003-1483-4084
+ Navid, Ali/0000-0003-2560-6984
+ Graf, John/0000-0002-0396-9867},
+Times-Cited = {11},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000319330200030},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000317572800001,
+Author = {Pentjuss, Agris and Odzina, Ilona and Kostromins, Andrejs and Fell,
+ David A. and Stalidzans, Egils and Kalnenieks, Uldis},
+Title = {Biotechnological potential of respiring Zymomonas mobilis: A
+ stoichiometric analysis of its central metabolism},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2013},
+Volume = {165},
+Number = {1},
+Pages = {1-10},
+Month = {MAY 10},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2013.02.014},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Zymomonas mobilis; Stoichiometric model; Central metabolism; Redox
+ balance; Respiration; Metabolic engineering},
+Keywords-Plus = {COBRA TOOLBOX EXTENSION; ESCHERICHIA-COLI; RESPIRATORY-CHAIN; BIOCYC
+ COLLECTION; FUEL ETHANOL; GLUCOSE; GROWTH; ENZYME; DEHYDROGENASE;
+ PATHWAYS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Stalidzans, Egils/G-5883-2010
+ Kostromins, Andrejs/G-5855-2012
+ Kalnenieks, Uldis/I-3301-2013
+ Fell, David A/B-2109-2009
+ },
+ORCID-Numbers = {Stalidzans, Egils/0000-0001-6063-0184
+ Fell, David A/0000-0001-6669-2247
+ Pentjuss, Agris/0000-0001-7880-5130},
+Times-Cited = {40},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000317572800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000319055600069,
+Author = {Ray, Debjit and Ye, Ping},
+Title = {Characterization of the Metabolic Requirements in Yeast Meiosis},
+Journal = {PLOS ONE},
+Year = {2013},
+Volume = {8},
+Number = {5},
+Month = {MAY 8},
+Type = {Article},
+DOI = {10.1371/journal.pone.0063707},
+Article-Number = {e63707},
+ISSN = {1932-6203},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; MITOCHONDRIAL TRANSPORTER;
+ GLYCOGEN-PHOSPHORYLASE; CELLULAR-METABOLISM; ESCHERICHIA-COLI;
+ SPORULATION; GENOME; GENE; IDENTIFICATION; GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Ray, Debjit/J-9302-2016},
+ORCID-Numbers = {Ray, Debjit/0000-0002-7192-9859},
+Times-Cited = {6},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000319055600069},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000317608100009,
+Author = {Fong, Nicole L. and Lerman, Joshua A. and Lam, Irene and Palsson,
+ Bernhard O. and Charusanti, Pep},
+Title = {Reconciling a Salmonella enterica metabolic model with experimental data
+ confirms that overexpression of the glyoxylate shunt can rescue a lethal
+ ppc deletion mutant},
+Journal = {FEMS MICROBIOLOGY LETTERS},
+Year = {2013},
+Volume = {342},
+Number = {1},
+Pages = {62-69},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1111/1574-6968.12109},
+ISSN = {0378-1097},
+EISSN = {1574-6968},
+Keywords = {systems biology; metabolic reconstruction; gap filling; mathematical
+ modeling},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; ESCHERICHIA-COLI; GENE-EXPRESSION; BYPASS
+ OPERON; NETWORKS; DEHYDROGENASE; ACID; PREDICTION; KNOWLEDGE; SELECTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Charusanti, Pep/0000-0003-0009-6615
+ Lerman, Joshua/0000-0003-0377-2674
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {11},
+Journal-ISO = {FEMS Microbiol. Lett.},
+Unique-ID = {WOS:000317608100009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000318589600021,
+Author = {Thiele, Ines and Swainston, Neil and Fleming, Ronan M. T. and Hoppe,
+ Andreas and Sahoo, Swagatika and Aurich, Maike K. and Haraldsdottir,
+ Hulda and Mo, Monica L. and Rolfsson, Ottar and Stobbe, Miranda D. and
+ Thorleifsson, Stefan G. and Agren, Rasmus and Boelling, Christian and
+ Bordel, Sergio and Chavali, Arvind K. and Dobson, Paul and Dunn, Warwick
+ B. and Endler, Lukas and Hala, David and Hucka, Michael and Hull, Duncan
+ and Jameson, Daniel and Jamshidi, Neema and Jonsson, Jon J. and Juty,
+ Nick and Keating, Sarah and Nookaew, Intawat and Le Novere, Nicolas and
+ Malys, Naglis and Mazein, Alexander and Papin, Jason A. and Price,
+ Nathan D. and Selkov, Sr., Evgeni and Sigurdsson, Martin I. and
+ Simeonidis, Evangelos and Sonnenschein, Nikolaus and Smallbone, Kieran
+ and Sorokin, Anatoly and van Beek, Johannes H. G. M. and Weichart,
+ Dieter and Goryanin, Igor and Nielsen, Jens and Westerhoff, Hans V. and
+ Kell, Douglas B. and Mendes, Pedro and Palsson, Bernhard O.},
+Title = {A community-driven global reconstruction of human metabolism},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2013},
+Volume = {31},
+Number = {5},
+Pages = {419+},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1038/nbt.2488},
+ISSN = {1087-0156},
+EISSN = {1546-1696},
+Keywords-Plus = {SYSTEMS BIOLOGY; INBORN-ERRORS; NETWORK; MODELS; KNOWLEDGEBASE;
+ ANNOTATION; PREDICTION; CANCER; SBML},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sigurdsson, Martin Ingi/I-9655-2016
+ Mazein, Alexander/C-1369-2013
+ Hull, Duncan/HGB-6116-2022
+ damiani, chiara/R-4256-2016
+ Bordel, Sergio/A-3325-2017
+ Goryanin, Igor/J-1913-2015
+ Le Novère, Nicolas/F-9973-2010
+ Chavali, Arvind/L-7157-2016
+ Jameson, Daniel/G-7386-2014
+ Westerhoff, Hans V/I-5762-2012
+ Malys, Naglis/Y-6961-2018
+ Nielsen, Jens Bo/C-7632-2015
+ Fleming, Ronan MT/ABC-4093-2021
+ Kell, Douglas/E-8318-2011
+ Lukas, Endler/ABD-2002-2021
+ Sorokin, Anatoly/A-9090-2008
+ Hucka, Michael/B-1896-2012
+ Sonnenschein, Nikolaus/F-6853-2012
+ Goryanin, Igor/AAB-1400-2022
+ Dunn, Warwick/CAJ-1648-2022
+ Thiele, Ines/A-7629-2014
+ Agren, Rasmus/I-1434-2012
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Sigurdsson, Martin Ingi/0000-0001-7054-0844
+ Mazein, Alexander/0000-0001-7137-4171
+ Hull, Duncan/0000-0003-2387-503X
+ Bordel, Sergio/0000-0001-6162-6478
+ Goryanin, Igor/0000-0002-8293-774X
+ Le Novère, Nicolas/0000-0002-6309-7327
+ Jameson, Daniel/0000-0003-1183-2825
+ Westerhoff, Hans V/0000-0002-0443-6114
+ Malys, Naglis/0000-0002-5010-310X
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Kell, Douglas/0000-0001-5838-7963
+ Lukas, Endler/0000-0002-9115-8756
+ Hucka, Michael/0000-0001-9105-5960
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Dunn, Warwick/0000-0001-6924-0027
+ Thiele, Ines/0000-0002-8071-7110
+ Agren, Rasmus/0000-0002-9814-2191
+ Price, Nathan/0000-0002-4157-0267
+ Mendes, Pedro/0000-0001-6507-9168
+ Sorokin, Anatoly/0000-0002-0047-0606
+ Keating, Sarah/0000-0002-3356-3542
+ Juty, Navtej/0000-0002-2036-8350
+ Nielsen, Jens/0000-0002-9955-6003
+ Rolfsson, Ottar/0000-0003-4258-6057
+ Sahoo, Swagatika/0000-0003-3773-8597
+ Papin, Jason/0000-0002-2769-5805
+ Simeonidis, Vangelis/0000-0001-6153-4493
+ Smallbone, Kieran/0000-0003-2815-7045
+ Palsson, Bernhard/0000-0003-2357-6785
+ Hoppe, Andreas/0000-0001-5181-6411},
+Times-Cited = {683},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000318589600021},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000318352900009,
+Author = {Yen, Jiun Y. and Nazem-Bokaee, Hadi and Freedman, Benjamin G. and
+ Athamneh, Ahmad I. M. and Senger, Ryan S.},
+Title = {Deriving metabolic engineering strategies from genome-scale modeling
+ with flux ratio constraints},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2013},
+Volume = {8},
+Number = {5, SI},
+Pages = {581-594},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/biot.201200234},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Bio-based fuels and chemicals; Flux ratio; Genome-scale model; Microbial
+ cell factory; Systems metabolic engineering},
+Keywords-Plus = {FORMATE-HYDROGEN LYASE; SACCHAROMYCES-CEREVISIAE; COA-TRANSFERASE;
+ RECONSTRUCTION; NETWORK; BINDING; DESIGN; GENERATION; ALCOHOL; ACETONE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Nazem-Bokaee, Hadi/0000-0002-4246-1804},
+Times-Cited = {12},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000318352900009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000317187800009,
+Author = {Zou, Wei and Zhou, Maoda and Liu, Liming and Chen, Jian},
+Title = {Reconstruction and analysis of the industrial strain Bacillus
+ megaterium WSH002 genome-scale in silico metabolic model},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2013},
+Volume = {164},
+Number = {4},
+Pages = {503-509},
+Month = {APR 15},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2013.01.019},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Bacillus megaterium; Flux balance analysis; Genome-scale metabolic
+ model; Vitamin C},
+Keywords-Plus = {KETOGULONICIGENIUM-VULGARE; SUBTILIS; NETWORKS; DATABASE; FLUXES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009},
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X},
+Times-Cited = {19},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000317187800009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000316830700023,
+Author = {Dal'Molin, Cristiana Gomes de Oliveira and Nielsen, Lars Keld},
+Title = {Plant genome-scale metabolic reconstruction and modelling},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2013},
+Volume = {24},
+Number = {2},
+Pages = {271-277},
+Month = {APR},
+Type = {Review},
+DOI = {10.1016/j.copbio.2012.08.007},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; BUNDLE-SHEATH; SYSTEMS BIOLOGY; NETWORK;
+ ARABIDOPSIS; PREDICTION; MESOPHYLL; DIFFERENTIATION; ANNOTATION;
+ GENERATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nielsen, Lars K/A-5519-2011},
+ORCID-Numbers = {Nielsen, Lars K/0000-0001-8191-3511},
+Times-Cited = {49},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000316830700023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000316695700011,
+Author = {Mueller, Arne C. and Bockmayr, Alexander},
+Title = {Fast thermodynamically constrained flux variability analysis},
+Journal = {BIOINFORMATICS},
+Year = {2013},
+Volume = {29},
+Number = {7},
+Pages = {903-909},
+Month = {APR 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btt059},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {SCALE METABOLIC NETWORK; BALANCE ANALYSIS; PATHWAYS; MODELS;
+ RECONSTRUCTION; DEFINITION; PREDICTION; STATES},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Bockmayr, Alexander/0000-0002-5074-1347},
+Times-Cited = {33},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000316695700011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000318872100112,
+Author = {Qiu, Yu and Nagarajan, Harish and Embree, Mallory and Shieu, Wendy and
+ Abate, Elisa and Juarez, Katy and Cho, Byung-Kwan and Elkins, James G.
+ and Nevin, Kelly P. and Barrett, Christian L. and Lovley, Derek R. and
+ Palsson, Bernhard O. and Zengler, Karsten},
+Title = {Characterizing the interplay between multiple levels of organization
+ within bacterial sigma factor regulatory networks},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2013},
+Volume = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1038/ncomms2743},
+Article-Number = {1755},
+ISSN = {2041-1723},
+Keywords-Plus = {GENOME-WIDE ANALYSIS; GEOBACTER-SULFURREDUCENS; ESCHERICHIA-COLI;
+ STRESS-RESPONSE; SP-NOV; GENES; IDENTIFICATION; MICROORGANISM;
+ ARCHITECTURE; METABOLISM},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Elkins, James/A-6199-2011
+ Nevin, Kelly/AAA-4626-2019
+ Cho, Byung-Kwan/C-1830-2011
+ },
+ORCID-Numbers = {Elkins, James/0000-0002-8052-5688
+ Palsson, Bernhard/0000-0003-2357-6785
+ JUAREZ, KATY/0000-0002-4400-4674
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {34},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000318872100112},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000318072700042,
+Author = {Steeb, Benjamin and Claudi, Beatrice and Burton, Neil A. and Tienz,
+ Petra and Schmidt, Alexander and Farhan, Hesso and Maze, Alain and
+ Bumann, Dirk},
+Title = {Parallel Exploitation of Diverse Host Nutrients Enhances
+ Salmonella Virulence},
+Journal = {PLOS PATHOGENS},
+Year = {2013},
+Volume = {9},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.ppat.1003301},
+Article-Number = {e1003301},
+ISSN = {1553-7366},
+EISSN = {1553-7374},
+Keywords-Plus = {ESCHERICHIA-COLI; MYCOBACTERIUM-TUBERCULOSIS; CARBON METABOLISM;
+ ABSOLUTE QUANTIFICATION; BACTERIAL PATHOGENS; VACCINE EFFICACY; OMIC
+ DATA; TYPHIMURIUM; GROWTH; MODEL},
+Research-Areas = {Microbiology; Parasitology; Virology},
+Web-of-Science-Categories = {Microbiology; Parasitology; Virology},
+ResearcherID-Numbers = {Farhan, Hesso/C-7997-2012
+ },
+ORCID-Numbers = {Farhan, Hesso/0000-0002-0889-8463
+ Bumann, Dirk/0000-0003-3636-4239
+ Maze, Alain/0000-0003-0873-3690},
+Times-Cited = {123},
+Journal-ISO = {PLoS Pathog.},
+Unique-ID = {WOS:000318072700042},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000318693000011,
+Author = {Wodke, Judith A. H. and Puchalka, Jacek and Lluch-Senar, Maria and
+ Marcos, Josep and Yus, Eva and Godinho, Miguel and Gutierrez-Gallego,
+ Ricardo and dos Santos, Vitor A. P. Martins and Serrano, Luis and Klipp,
+ Edda and Maier, Tobias},
+Title = {Dissecting the energy metabolism in Mycoplasma pneumoniae through
+ genome-scale metabolic modeling},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2013},
+Volume = {9},
+Month = {APR},
+Type = {Article},
+DOI = {10.1038/msb.2013.6},
+Article-Number = {653},
+ISSN = {1744-4292},
+Keywords = {biomass composition; energy metabolism; in silico knock-outs; metabolic
+ modeling; Mycoplasma pneumonia},
+Keywords-Plus = {COBRA TOOLBOX EXTENSION; FLUX BALANCE MODELS; ESCHERICHIA-COLI; INVIVO
+ MEASUREMENT; OPTIMAL SELECTION; GENETIC-ANALYSIS; MEMBRANE-LIPIDS;
+ RECONSTRUCTION; PROTEIN; PHOSPHORYLATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Lluch, Maria/ABF-8435-2021
+ Senar, Maria Lluch/K-7848-2018
+ Serrano, Luis/B-3355-2013
+ Marcos, Josep/F-3545-2015
+ },
+ORCID-Numbers = {Senar, Maria Lluch/0000-0001-7568-4353
+ Serrano, Luis/0000-0002-5276-1392
+ Marcos, Josep/0000-0002-3624-108X
+ Gutierrez Gallego, Ricardo/0000-0001-9639-2181},
+Times-Cited = {56},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000318693000011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000316830700025,
+Author = {Yonekura-Sakakibara, Keiko and Fukushima, Atsushi and Saito, Kazuki},
+Title = {Transcriptome data modeling for targeted plant metabolic engineering},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2013},
+Volume = {24},
+Number = {2},
+Pages = {285-290},
+Month = {APR},
+Type = {Review},
+DOI = {10.1016/j.copbio.2012.10.018},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {INDEPENDENT COMPONENT ANALYSIS; ZINC-FINGER NUCLEASES; GENE-EXPRESSION
+ DATA; ARABIDOPSIS-THALIANA; COEXPRESSION ANALYSIS; NUTRITIONAL CUES;
+ HYPOTHESIS GENERATION; NETWORK BIOLOGY; SYSTEMS BIOLOGY; DATA SETS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Fukushima, Atsushi/C-9279-2017
+ Yonekura-Sakakibara, Keiko/J-8749-2014
+ Saito, Kazuki/D-2670-2009},
+ORCID-Numbers = {Fukushima, Atsushi/0000-0001-9015-1694
+ Yonekura-Sakakibara, Keiko/0000-0002-0409-1523
+ Saito, Kazuki/0000-0001-6310-5342},
+Times-Cited = {30},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000316830700025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000316270400026,
+Author = {Ganter, Mathias and Bernard, Thomas and Moretti, Sebastien and Stelling,
+ Joerg and Pagni, Marco},
+Title = {MetaNetX.org: a website and repository for accessing, analysing and
+ manipulating metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2013},
+Volume = {29},
+Number = {6},
+Pages = {815-816},
+Month = {MAR 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btt036},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {MODELS; KNOWLEDGEBASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Stelling, Joerg/F-7499-2010
+ },
+ORCID-Numbers = {Stelling, Joerg/0000-0002-1145-891X
+ Moretti, Sebastien/0000-0003-3947-488X
+ Bernard, Thomas/0000-0003-3736-1507
+ Pagni, Marco/0000-0001-9292-9463},
+Times-Cited = {64},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000316270400026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000316864200050,
+Author = {Agren, Rasmus and Liu, Liming and Shoaie, Saeed and Vongsangnak, Wanwipa
+ and Nookaew, Intawat and Nielsen, Jens},
+Title = {The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic
+ Model for Penicillium chrysogenum},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2013},
+Volume = {9},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1002980},
+Article-Number = {e1002980},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {HIGH-YIELDING STRAIN; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE;
+ BIOCHEMICAL NETWORKS; RECONSTRUCTION; PREDICTION; SEQUENCE; PATHWAY;
+ IDENTIFICATION; BIOSYNTHESIS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009
+ Nielsen, Jens Bo/C-7632-2015
+ Agren, Rasmus/I-1434-2012
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Agren, Rasmus/0000-0002-9814-2191
+ Nielsen, Jens/0000-0002-9955-6003
+ Shoaie, Saeed/0000-0001-5834-4533},
+Times-Cited = {262},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000316864200050},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000315343600006,
+Author = {Angel Medina, Miguel},
+Title = {Systems biology for molecular life sciences and its impact in
+ biomedicine},
+Journal = {CELLULAR AND MOLECULAR LIFE SCIENCES},
+Year = {2013},
+Volume = {70},
+Number = {6},
+Pages = {1035-1053},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1007/s00018-012-1109-z},
+ISSN = {1420-682X},
+EISSN = {1420-9071},
+Keywords = {Complexity; Disease-ome; Holism; Network; Reductionism; Systems biology},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; IN-VIVO MAP; METABOLIC NETWORK; INTERACTOME
+ NETWORK; MATHEMATICAL-MODEL; CANCER; MEDICINE; PHARMACOLOGY;
+ INTEGRATION; REVEALS},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Medina, Miguel/HPF-3857-2023
+ Medina, Miguel Ángel/K-1763-2014},
+ORCID-Numbers = {Medina, Miguel Ángel/0000-0001-7275-6462},
+Times-Cited = {23},
+Journal-ISO = {Cell. Mol. Life Sci.},
+Unique-ID = {WOS:000315343600006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000314836600006,
+Author = {Chung, Bevan Kai-Sheng and Lakshmanan, Meiyappan and Klement, Maximilian
+ and Ching, Chi Bun and Lee, Dong-Yup},
+Title = {Metabolic reconstruction and flux analysis of industrial Pichia
+ yeasts},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2013},
+Volume = {97},
+Number = {5},
+Pages = {1865-1873},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1007/s00253-013-4702-7},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Genome-scale metabolic modeling; Constraints-based flux analysis; Pichia
+ pastoris; Pichia stipitis; Microbial cell factories; Systems
+ biotechnology},
+Keywords-Plus = {XYLOSE-FERMENTING YEAST; CENTRAL CARBON METABOLISM; CONSTRAINT-BASED
+ MODELS; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; QUANTITATIVE
+ PREDICTION; RECOMBINANT PROTEINS; CELLULAR-METABOLISM;
+ MATHEMATICAL-MODEL; ETHANOL-PRODUCTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/H-1267-2014
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Lee, Dong-Yup/D-6650-2011},
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X},
+Times-Cited = {12},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000314836600006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000316427000003,
+Author = {Kell, Douglas B. and Dobson, Paul D. and Bilsland, Elizabeth and Oliver,
+ Stephen G.},
+Title = {The promiscuous binding of pharmaceutical drugs and their
+ transporter-mediated uptake into cells: what we (need to) know and how
+ we can do so},
+Journal = {DRUG DISCOVERY TODAY},
+Year = {2013},
+Volume = {18},
+Number = {5-6},
+Pages = {218-239},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1016/j.drudis.2012.11.008},
+ISSN = {1359-6446},
+EISSN = {1878-5832},
+Keywords-Plus = {BLOOD-BRAIN-BARRIER; ORGANIC ANION TRANSPORTERS; NONSTEROIDAL
+ ANTIINFLAMMATORY DRUGS; METABOLIC NETWORK RECONSTRUCTION; QT INTERVAL
+ PROLONGATION; AMINO-ACID TRANSPORTERS; CENTRAL-NERVOUS-SYSTEM; IN-VITRO;
+ P-GLYCOPROTEIN; CATION TRANSPORTERS},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Bilsland, Elizabeth/H-3523-2014
+ Oliver, Stephen/AAQ-5992-2021
+ Kell, Douglas/E-8318-2011
+ },
+ORCID-Numbers = {Oliver, Stephen/0000-0003-3410-6439
+ Kell, Douglas/0000-0001-5838-7963
+ Bilsland, Elizabeth/0000-0002-8697-3553},
+Times-Cited = {105},
+Journal-ISO = {Drug Discov. Today},
+Unique-ID = {WOS:000316427000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000315494700004,
+Author = {Mukherjee, Sumanta and Sambarey, Awanti and Prashanthi, Karyala and
+ Chandra, Nagasuma},
+Title = {Current trends in modeling hostpathogen interactions},
+Journal = {WILEY INTERDISCIPLINARY REVIEWS-DATA MINING AND KNOWLEDGE DISCOVERY},
+Year = {2013},
+Volume = {3},
+Number = {2},
+Pages = {109-128},
+Month = {MAR-APR},
+Type = {Review},
+DOI = {10.1002/widm.1085},
+ISSN = {1942-4787},
+EISSN = {1942-4795},
+Keywords-Plus = {HOST-PATHOGEN INTERACTIONS; HUMAN METABOLIC NETWORK; GENE-EXPRESSION;
+ SOFTWARE ENVIRONMENT; GRANULOMA-FORMATION; CELLULAR NETWORKS; SYSTEMS;
+ DATABASE; RECONSTRUCTION; RESOURCE},
+Research-Areas = {Computer Science},
+Web-of-Science-Categories = {Computer Science, Artificial Intelligence; Computer Science, Theory \&
+ Methods},
+ResearcherID-Numbers = {Karyala, Prashanthi/AAP-5229-2020
+ Sambarey, Awanti/ABI-2566-2020
+ },
+ORCID-Numbers = {Sambarey, Awanti/0000-0002-6561-720X
+ Karyala, Prashanthi/0000-0002-1099-5262
+ Chandra, Nagasuma/0000-0002-9939-8439},
+Times-Cited = {7},
+Journal-ISO = {Wiley Interdiscip. Rev.-Data Mining Knowl. Discov.},
+Unique-ID = {WOS:000315494700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000316658800066,
+Author = {Xu, Zhaobin and Fang, Xin and Wood, Thomas K. and Huang, Zuyi Jacky},
+Title = {A Systems-Level Approach for Investigating Pseudomonas aeruginosa
+ Biofilm Formation},
+Journal = {PLOS ONE},
+Year = {2013},
+Volume = {8},
+Number = {2},
+Month = {FEB 22},
+Type = {Article},
+DOI = {10.1371/journal.pone.0057050},
+Article-Number = {e57050},
+ISSN = {1932-6203},
+Keywords-Plus = {STAPHYLOCOCCUS-AUREUS BIOFILMS; METABOLIC NETWORK ANALYSIS;
+ CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; QUANTITATIVE PREDICTION;
+ STREPTOCOCCUS-MUTANS; CELLULAR-METABOLISM; GENE-EXPRESSION; COBRA
+ TOOLBOX; RESISTANCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Wood, Thomas/GWZ-2481-2022
+ },
+ORCID-Numbers = {Wood, Thomas/0000-0001-8962-8571
+ xu, zhaobin/0000-0002-1136-5684
+ Wood, Thomas/0000-0002-6258-529X},
+Times-Cited = {27},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000316658800066},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000315017000003,
+Author = {Schmidt, Brian J. and Papin, Jason A. and Musante, Cynthia J.},
+Title = {Mechanistic systems modeling to guide drug discovery and development},
+Journal = {DRUG DISCOVERY TODAY},
+Year = {2013},
+Volume = {18},
+Number = {3-4},
+Pages = {116-127},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1016/j.drudis.2012.09.003},
+ISSN = {1359-6446},
+EISSN = {1878-5832},
+Keywords-Plus = {SCALE METABOLIC NETWORK; FLUX BALANCE ANALYSIS; GENOME-SCALE; EXPRESSION
+ DATA; PREDICTIVE BIOSIMULATION; MATHEMATICAL-MODEL; SEPSIS PATIENTS;
+ HIGH-RISK; RECONSTRUCTION; BIOLOGY},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy},
+ORCID-Numbers = {Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {37},
+Journal-ISO = {Drug Discov. Today},
+Unique-ID = {WOS:000315017000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000314487200002,
+Author = {Thiele, Ines and Heinken, Almut and Fleming, Ronan M. T.},
+Title = {A systems biology approach to studying the role of microbes in human
+ health},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2013},
+Volume = {24},
+Number = {1},
+Pages = {4-12},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1016/j.copbio.2012.10.001},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {HUMAN METABOLIC NETWORK; GUT MICROBES; MODELS; RECONSTRUCTION; BALANCE;
+ FERMENTATION; ENERGY},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Heinken, Almut/0000-0001-6938-8072},
+Times-Cited = {68},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000314487200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000315563800118,
+Author = {Xu, Zixiang and Sun, Xiao and Sun, Jibin},
+Title = {Construction and Analysis of the Model of Energy Metabolism in E.
+ coli},
+Journal = {PLOS ONE},
+Year = {2013},
+Volume = {8},
+Number = {1},
+Month = {JAN 30},
+Type = {Article},
+DOI = {10.1371/journal.pone.0055137},
+Article-Number = {e55137},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; THERMODYNAMIC ANALYSIS; RECONSTRUCTION; NETWORKS;
+ CONSTRAINTS; PREDICTION; GSM/GPR},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Sun, Jibin/0000-0002-0208-504X},
+Times-Cited = {5},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000315563800118},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000313088100011,
+Author = {Rolfsson, Ottar and Paglia, Giuseppe and Magnusdottir, Manuela and
+ Palsson, Bernhard O. and Thiele, Ines},
+Title = {Inferring the metabolism of human orphan metabolites from their
+ metabolic network context affirms human gluconokinase activity},
+Journal = {BIOCHEMICAL JOURNAL},
+Year = {2013},
+Volume = {449},
+Number = {2},
+Pages = {427-435},
+Month = {JAN 15},
+Type = {Article},
+DOI = {10.1042/BJ20120980},
+ISSN = {0264-6021},
+EISSN = {1470-8728},
+Keywords = {gap filling; human metabolism; metabolic network; RECON 1},
+Keywords-Plus = {ESCHERICHIA-COLI; GENOME ANNOTATION; ENZYME; RECONSTRUCTION; ACID;
+ GENERATION; EXCRETION; PROTEINS; DATABASE; PATHWAYS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Paglia, Giuseppe/H-2012-2018
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Paglia, Giuseppe/0000-0003-4724-6801
+ Thiele, Ines/0000-0002-8071-7110
+ Rolfsson, Ottar/0000-0003-4258-6057
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {20},
+Journal-ISO = {Biochem. J.},
+Unique-ID = {WOS:000313088100011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000313882500006,
+Author = {Curran, Kathleen A. and Leavitt, Johnm. and Karim, AshtyS. and Alper,
+ Hal S.},
+Title = {Metabolic engineering of muconic acid production in Saccharomyces
+ cerevisiae},
+Journal = {METABOLIC ENGINEERING},
+Year = {2013},
+Volume = {15},
+Pages = {55-66},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2012.10.003},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Muconic acid; Muconate; Terephthalic acid; Adipic acid; Saccharomyces
+ cerevisiae},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; L-TYROSINE PRODUCTION; ESCHERICHIA-COLI;
+ QUANTITATIVE PREDICTION; TRANSCRIPTION MACHINERY; CELLULAR-METABOLISM;
+ SYSTEMS BIOLOGY; GENE KNOCKOUT; BAKERS-YEAST; BIOSYNTHESIS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Karim, Ashty/0000-0002-5789-7715
+ Curran, Kathleen/0000-0002-5117-4831},
+Times-Cited = {193},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000313882500006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000321199100006,
+Author = {Hao, Tong and Han, Binbin and Ma, Hongwu and Fu, Jing and Wang, Hui and
+ Wang, Zhiwen and Tang, Bincai and Chen, Tao and Zhao, Xueming},
+Title = {In silico metabolic engineering of Bacillus subtilis for
+ improved production of riboflavin, Egl-237, (R,R)-2,3-butanediol
+ and isobutanol},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2013},
+Volume = {9},
+Number = {8},
+Pages = {2034-2044},
+Type = {Article},
+DOI = {10.1039/c3mb25568a},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {CARBON FLUXES; GROWTH; RECONSTRUCTION; SEQUENCE; MODEL; BIOSYNTHESIS;
+ PROTEINS; DATABASE; NETWORK; CLONING},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Ma, Hongwu/I-5263-2013
+ CHEN, Tao/N-1817-2015
+ Zhao, Xueming/W-4891-2019
+ },
+ORCID-Numbers = {Ma, Hongwu/0000-0001-5325-2314
+ CHEN, Tao/0000-0001-9588-1821
+ Jing, Fu/0000-0001-8651-0658},
+Times-Cited = {34},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000321199100006},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000329255800004,
+Author = {Harwood, Colin R. and Pohl, Susanne and Smith, Wendy and Wipat, Anil},
+Editor = {Harwood, C and Wipat, A},
+Title = {Bacillus subtilis: Model Gram-Positive Synthetic Biology Chassis},
+Booktitle = {MICROBIAL SYNTHETIC BIOLOGY},
+Series = {Methods in Microbiology},
+Year = {2013},
+Volume = {40},
+Pages = {87-117},
+Type = {Review; Book Chapter},
+DOI = {10.1016/B978-0-12-417029-2.00004-2},
+ISSN = {0580-9517},
+ISBN = {978-0-12-417029-2},
+Keywords-Plus = {SIGMA-FACTOR; METABOLIC NETWORK; ESCHERICHIA-COLI; GENOME SEQUENCE;
+ GENE-EXPRESSION; PLASMID PLS20; CELL; TRANSFORMATION; TRANSCRIPTION;
+ REPLICATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Microbiology},
+ResearcherID-Numbers = {Harwood, Colin Robert/AGF-0120-2022
+ },
+ORCID-Numbers = {Harwood, Colin/0000-0002-3624-0001},
+Times-Cited = {12},
+Journal-ISO = {Methods Microbiol.},
+Unique-ID = {WOS:000329255800004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000525686600008,
+Author = {Heinken, Almut and Sahoo, Swagatika and Fleming, Ronan M. T. and Thiele,
+ Ines},
+Title = {Systems-level characterization of a host-microbe metabolic symbiosis in
+ the mammalian gut},
+Journal = {GUT MICROBES},
+Year = {2013},
+Volume = {4},
+Number = {1},
+Pages = {28-40},
+Type = {Article},
+DOI = {10.4161/gmic.22370},
+ISSN = {1949-0976},
+EISSN = {1949-0984},
+Keywords = {systems biology; computational modeling; metabolism; host-microbe
+ interactions; Bacteroides thetaiotaomicron; constraint-based modeling;
+ Mus musculus},
+Research-Areas = {Gastroenterology \& Hepatology; Microbiology},
+Web-of-Science-Categories = {Gastroenterology \& Hepatology; Microbiology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Heinken, Almut/0000-0001-6938-8072
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Sahoo, Swagatika/0000-0003-3773-8597},
+Times-Cited = {144},
+Journal-ISO = {Gut Microbes},
+Unique-ID = {WOS:000525686600008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000346773600005,
+Author = {Hernandez Patino, Claudia E. and Jaime-Munoz, Gustavo and
+ Resendis-Antonio, Osbaldo},
+Title = {Systems biology of cancer: moving toward the integrative study of the
+ metabolic alterations in cancer cells},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2013},
+Volume = {3},
+Type = {Review},
+DOI = {10.3389/fphys.2012.00481},
+Article-Number = {481},
+ISSN = {1664-042X},
+Keywords = {computational modeling of metabolism; cancer metabolic phenotype;
+ constraint-based modeling; genome scale metabolic reconstruction; high
+ throughput biology},
+Keywords-Plus = {TUMOR; MODELS; DEHYDROGENASE; INHIBITION; GLYCOLYSIS; PHENOTYPE; HYPOXIA},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {RESENDIS, OSBALDO/ADE-5280-2022},
+ORCID-Numbers = {RESENDIS, OSBALDO/0000-0001-5220-541X},
+Times-Cited = {11},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000346773600005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000318557100044,
+Author = {Kim, Young-Mo and Schmidt, Brian J. and Kidwai, Afshan S. and Jones,
+ Marcus B. and Kaiser, Brooke L. Deatherage and Brewer, Heather M. and
+ Mitchell, Hugh D. and Palsson, Bernhard O. and McDermott, Jason E. and
+ Heffron, Fred and Smith, Richard D. and Peterson, Scott N. and Ansong,
+ Charles and Hyduke, Daniel R. and Metz, Thomas O. and Adkins, Joshua N.},
+Title = {Salmonella modulates metabolism during growth under conditions
+ that induce expression of virulence genes},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2013},
+Volume = {9},
+Number = {6},
+Pages = {1522-1534},
+Type = {Article},
+DOI = {10.1039/c3mb25598k},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {ENTERICA SEROVAR TYPHIMURIUM; PROTEOMIC ANALYSIS; INTRACELLULAR
+ SURVIVAL; ESCHERICHIA-COLI; METABOLOMICS; MODELS; PROTEIN;
+ IDENTIFICATION; ARCHITECTURE; COMPONENTS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Schmidt, Brian J/A-3805-2009
+ Kim, Young-Mo/D-3282-2009
+ Smith, Richard/HMD-4857-2023
+ Smith, Richard D/J-3664-2012
+ Kim, Young-Mo/AAG-2866-2019
+ Adkins, Joshua N/B-9881-2013
+ },
+ORCID-Numbers = {Kim, Young-Mo/0000-0002-8972-7593
+ Smith, Richard D/0000-0002-2381-2349
+ Kim, Young-Mo/0000-0002-8972-7593
+ Adkins, Joshua N/0000-0003-0399-0700
+ Metz, Tom/0000-0001-6049-3968
+ Mitchell, Hugh/0000-0003-0143-8461
+ Palsson, Bernhard/0000-0003-2357-6785
+ Schmidt, Brian/0000-0001-6015-9636
+ McDermott, Jason/0000-0003-2961-2572},
+Times-Cited = {42},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000318557100044},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000332675300009,
+Author = {Krauser, Steffen and Weyler, Christian and Blass, Lisa Katharina and
+ Heinzle, Elmar},
+Editor = {Zeng, AP},
+Title = {Directed Multistep Biocatalysis Using Tailored Permeabilized Cells},
+Booktitle = {FUNDAMENTALS AND APPLICATION OF NEW BIOPRODUCTION SYSTEMS},
+Series = {Advances in Biochemical Engineering-Biotechnology},
+Year = {2013},
+Volume = {137},
+Pages = {185-234},
+Type = {Article; Book Chapter},
+DOI = {10.1007/10\_2013\_240},
+ISSN = {0724-6145},
+EISSN = {1616-8542},
+ISBN = {978-3-642-41521-0; 978-3-642-41520-3},
+Keywords = {Biocatalysis; In situ biocatalysis; Metabolic engineering; Network
+ design; One-pot synthesis; Permeabilization},
+Keywords-Plus = {BIOSYNTHETIC GENE-CLUSTER; LARGE-SCALE PRODUCTION; CONSTRAINT-BASED
+ MODELS; ANTARCTICA LIPASE-B; AMINO-ACID OXIDASE; NONRIBOSOMAL PEPTIDE;
+ ESCHERICHIA-COLI; IN-SITU; CORYNEBACTERIUM-GLUTAMICUM; METABOLIC
+ PATHWAYS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Krauser, Steffen/C-5541-2011
+ },
+ORCID-Numbers = {Weyler, Christian/0000-0002-6997-0799},
+Times-Cited = {18},
+Journal-ISO = {Adv. Biochem. Eng. Biotechnol.},
+Unique-ID = {WOS:000332675300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000319882200039,
+Author = {Liu, Jie and Gao, Qian and Xu, Nan and Liu, Liming},
+Title = {Genome-scale reconstruction and in silico analysis of
+ Aspergillus terreus metabolism},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2013},
+Volume = {9},
+Number = {7},
+Pages = {1939-1948},
+Type = {Article},
+DOI = {10.1039/c3mb70090a},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {ITACONIC ACID PRODUCTION; BIOSYNTHESIS; LOVASTATIN; IDENTIFICATION;
+ ANNOTATION; PREDICTION; AUTOLYSIS; FUMIGATUS; DATABASE; NIGER},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {20},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000319882200039},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000334096700013,
+Author = {Mao, Longfei and Verwoerd, Wynand S.},
+Title = {Model-driven elucidation of the inherent capacity of Geobacter
+ sulfurreducens for electricity generation},
+Journal = {JOURNAL OF BIOLOGICAL ENGINEERING},
+Year = {2013},
+Volume = {7},
+Number = {1},
+Type = {Article},
+DOI = {10.1186/1754-1611-7-14},
+Article-Number = {14},
+ISSN = {1754-1611},
+Keywords = {MFC; Microbial fuel cell; Geobacter sulfurreducens; Bioelectricity; Flux
+ balance analysis; Flux variability analysis; Flux minimization; FATMIN},
+Keywords-Plus = {MICROBIAL FUEL-CELLS; EXTRACELLULAR ELECTRON-TRANSFER; ALTERNATE
+ OPTIMAL-SOLUTIONS; FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; NEUTRAL RED;
+ EXTREME PATHWAYS; OPTIMIZATION; METABOLISM; FRAMEWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Verwoerd, Wynand/A-8320-2010
+ },
+ORCID-Numbers = {Verwoerd, Wynand/0000-0001-5489-9101
+ Mao, Longfei/0000-0003-0759-0501},
+Times-Cited = {17},
+Journal-ISO = {J. Biol. Eng.},
+Unique-ID = {WOS:000334096700013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000314473500004,
+Author = {Shellman, Erin R. and Burant, Charles F. and Schnell, Santiago},
+Title = {Network motifs provide signatures that characterize metabolism},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2013},
+Volume = {9},
+Number = {3},
+Pages = {352-360},
+Type = {Article},
+DOI = {10.1039/c2mb25346a},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; TOPOLOGICAL MOTIFS; EVOLUTION;
+ ORGANIZATION; AGGREGATION; MODULARITY; BIOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Burant, Charles/GPC-5690-2022
+ Schnell, Santiago/B-8682-2008},
+ORCID-Numbers = {Burant, Charles/0000-0001-9189-5003
+ Schnell, Santiago/0000-0002-9477-3914},
+Times-Cited = {21},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000314473500004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311822100014,
+Author = {Shen, Tie and Rui, Bin and Zhou, Hong and Zhang, Ximing and Yi, Yin and
+ Wen, Han and Zheng, Haoran and Wu, Jihui and Shi, Yunyu},
+Title = {Metabolic flux ratio analysis and multi-objective optimization revealed
+ a globally conserved and coordinated metabolic response of E.
+ coli to paraquat-induced oxidative stress},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2013},
+Volume = {9},
+Number = {1},
+Pages = {121-132},
+Type = {Article},
+DOI = {10.1039/c2mb25285f},
+ISSN = {1742-206X},
+Keywords-Plus = {CENTRAL CARBON METABOLISM; MUTANT ESCHERICHIA-COLI; CONSTRAINT-BASED
+ MODELS; SACCHAROMYCES-CEREVISIAE; SERINE HYDROXYMETHYLTRANSFERASE;
+ PHOSPHOGLUCOSE ISOMERASE; QUANTITATIVE PREDICTION;
+ ENVIRONMENTAL-CHANGES; ADAPTIVE PREDICTION; CELLULAR-METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Shen, Tie/A-6579-2015
+ Zhang, Ximing/HSB-3985-2023},
+Times-Cited = {11},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000311822100014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000315194500002,
+Author = {Tajparast, Mohammad and Frigon, Dominic},
+Title = {Genome-scale metabolic modeling to provide insight into the production
+ of storage compounds during feast-famine cycles of activated sludge},
+Journal = {WATER SCIENCE AND TECHNOLOGY},
+Year = {2013},
+Volume = {67},
+Number = {3},
+Pages = {469-476},
+Type = {Article},
+DOI = {10.2166/wst.2012.569},
+ISSN = {0273-1223},
+EISSN = {1996-9732},
+Keywords = {biomaterials; Escherichia coli strain K-12; genome-scale flux balance
+ analysis; Rhodococcus jostii RHA1; storage metabolism; wastewater
+ treatment operation},
+Research-Areas = {Engineering; Environmental Sciences \& Ecology; Water Resources},
+Web-of-Science-Categories = {Engineering, Environmental; Environmental Sciences; Water Resources},
+ResearcherID-Numbers = {Frigon, Dominic/P-7898-2018},
+ORCID-Numbers = {Frigon, Dominic/0000-0003-1587-8943},
+Times-Cited = {5},
+Journal-ISO = {Water Sci. Technol.},
+Unique-ID = {WOS:000315194500002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000315908800021,
+Author = {Tong, Wei and Chen, Zhen and Cao, Zhe and Wang, Quanhui and Zhang,
+ Jiyuan and Bai, Xue and Wang, Rong and Liu, Siqi},
+Title = {Robustness analysis of a constraint-based metabolic model links cell
+ growth and proteomics of Thermoanaerobacter tengcongensis under
+ temperature perturbation},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2013},
+Volume = {9},
+Number = {4},
+Pages = {713-722},
+Type = {Article},
+DOI = {10.1039/c3mb25278g},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {SYSTEMS BIOLOGY; PATHWAYS; RECONSTRUCTION; NETWORK; STRAIN},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Wang, Rong/A-8721-2009},
+Times-Cited = {5},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000315908800021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000313651700006,
+Author = {Xu, Chuan and Liu, Lili and Zhang, Zhao and Jin, Danfeng and Qiu,
+ Juanping and Chen, Ming},
+Title = {Genome-scale metabolic model in guiding metabolic engineering of
+ microbial improvement},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2013},
+Volume = {97},
+Number = {2},
+Pages = {519-539},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1007/s00253-012-4543-9},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Genome-scale metabolic model; Systems biology; Metabolic engineering;
+ Microbial improvement; Industrial application},
+Keywords-Plus = {IN-SILICO ANALYSIS; PSEUDOMONAS-PUTIDA KT2440; ACINETOBACTER-BAYLYI
+ ADP1; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; SYSTEMS BIOLOGY;
+ GEOBACTER-SULFURREDUCENS; NETWORK RECONSTRUCTION; PLASMODIUM-FALCIPARUM;
+ BACILLUS-SUBTILIS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Chen, Ming/AAV-3682-2020
+ Liu, Lili/I-7619-2019
+ Zhang, Zhao/U-4742-2019
+ },
+ORCID-Numbers = {Chen, Ming/0000-0002-9677-1699
+ Liu, Lili/0000-0002-2622-9669
+ Zhang, Zhao/0000-0002-3679-8945},
+Times-Cited = {43},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000313651700006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000312945700005,
+Author = {Xu, Nan and Liu, Liming and Zou, Wei and Liu, Jie and Hua, Qiang and
+ Chen, Jian},
+Title = {Reconstruction and analysis of the genome-scale metabolic network of
+ Candida glabrata},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2013},
+Volume = {9},
+Number = {2},
+Pages = {205-216},
+Type = {Article},
+DOI = {10.1039/c2mb25311a},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {ENHANCED PYRUVATE PRODUCTION; TORULOPSIS-GLABRATA;
+ SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; GLYCOLYTIC FLUX;
+ OXIDATIVE-PHOSPHORYLATION; MULTIDRUG TRANSPORTERS; AUXOTROPHIC YEAST;
+ CARBON FLUX; CELL-WALL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {37},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000312945700005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000325582800001,
+Author = {Zhang, Ai-Di and Dai, Shao-Xing and Huang, Jing-Fei},
+Title = {Reconstruction and Analysis of Human Kidney-Specific Metabolic Network
+ Based on Omics Data},
+Journal = {BIOMED RESEARCH INTERNATIONAL},
+Year = {2013},
+Volume = {2013},
+Type = {Article},
+DOI = {10.1155/2013/187509},
+Article-Number = {187509},
+ISSN = {2314-6133},
+EISSN = {2314-6141},
+Keywords-Plus = {DRUG DISCOVERY; GENE; DISEASE; TRANSCRIPTOME},
+Research-Areas = {Biotechnology \& Applied Microbiology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Medicine, Research \&
+ Experimental},
+ResearcherID-Numbers = {zhang, aidi/JDC-4289-2023
+ huang, jing/JDC-2548-2023
+ Dai, shaoxing/ABA-8699-2020
+ },
+ORCID-Numbers = {Dai, Shao-Xing/0000-0002-6919-2034},
+Times-Cited = {14},
+Journal-ISO = {Biomed Res. Int.},
+Unique-ID = {WOS:000325582800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311642000020,
+Author = {Chiewchankaset, Porntip and Srimarut, Yanee and Klanchui, Amornpan and
+ Kurdi, Peter and Plengvidhya, Vethachai and Meechai, Asawin},
+Title = {Systematic identification of Lactobacillus plantarum auxotrophs
+ for fermented Nham using genome-scale metabolic model},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2012},
+Volume = {162},
+Number = {2-3},
+Pages = {327-335},
+Month = {DEC 31},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2012.08.019},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Auxotroph; Essential gene; Genome-scale metabolic model; Lactobacillus
+ plantarum; Phenotypic characteristics},
+Keywords-Plus = {RECONSTRUCTION; GENE; GROWTH; SCOPE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Srimarut, Yanee/0000-0002-6782-2565},
+Times-Cited = {1},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000311642000020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000313618800047,
+Author = {Xu, Guoqiang and Zou, Wei and Chen, Xiulai and Xu, Nan and Liu, Liming
+ and Chen, Jian},
+Title = {Fumaric Acid Production in Saccharomyces cerevisiae by In
+ Silico Aided Metabolic Engineering},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {12},
+Month = {DEC 26},
+Type = {Article},
+DOI = {10.1371/journal.pone.0052086},
+Article-Number = {e52086},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; YEAST; RECONSTRUCTION; EXPRESSION; MODELS; GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Chen, Xiulai/AAB-8395-2020
+ Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Chen, Xiulai/0000-0002-5154-3860
+ Liu, Liming/0000-0003-3022-936X
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {38},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000313618800047},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000312386800049,
+Author = {Zakrzewski, Piotr and Medema, Marnix H. and Gevorgyan, Albert and
+ Kierzek, Andrzej M. and Breitling, Rainer and Takano, Eriko},
+Title = {MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale
+ Metabolic Models},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {12},
+Month = {DEC 14},
+Type = {Article},
+DOI = {10.1371/journal.pone.0051511},
+Article-Number = {e51511},
+ISSN = {1932-6203},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; STREPTOMYCES-COELICOLOR; IN-SILICO; CLAVULANIC
+ ACID; QUANTITATIVE PREDICTION; HETEROLOGOUS EXPRESSION;
+ CELLULAR-METABOLISM; NETWORK ANALYSIS; COBRA TOOLBOX; GENE-CLUSTER},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Medema, Marnix H./AAR-3138-2021
+ },
+ORCID-Numbers = {Medema, Marnix H./0000-0002-2191-2821
+ Takano, Eriko/0000-0002-6791-3256
+ Kierzek, Andrzej/0000-0002-2605-9057
+ Breitling, Rainer/0000-0001-7173-0922},
+Times-Cited = {28},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000312386800049},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000315260900001,
+Author = {Wang, Yuliang and Eddy, James A. and Price, Nathan D.},
+Title = {Reconstruction of genome-scale metabolic models for 126 human tissues
+ using mCADRE},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {DEC 13},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-153},
+Article-Number = {153},
+ISSN = {1752-0509},
+Keywords = {Automated metabolic network reconstruction; Brain; Cancer metabolism;
+ Tissue-specific metabolic model; Constraint-based modeling},
+Keywords-Plus = {FATTY-ACID SYNTHESIS; RNA-SEQ; HEPATOCELLULAR-CARCINOMA; CANCER
+ PATHOGENESIS; IN-VITRO; EXPRESSION; NETWORK; PHYSIOLOGY; PREDICTION;
+ CELLS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Wang, Yuliang/H-9070-2012
+ Shao, Zhifeng/B-6075-2013
+ },
+ORCID-Numbers = {Wang, Yuliang/0000-0002-3788-5477
+ Hao, Pei/0000-0002-1498-7059
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {187},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000315260900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000312991400009,
+Author = {Wang, Chuanli and Guo, Longyun and Li, Yixue and Wang, Zhuo},
+Title = {Systematic Comparison of C3 and C4 Plants Based on Metabolic Network
+ Analysis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Number = {2},
+Month = {DEC 12},
+Note = {23rd International Conference on Genome Informatics (GIW), Tainan,
+ TAIWAN, DEC 12-14, 2012},
+Type = {Article; Proceedings Paper},
+DOI = {10.1186/1752-0509-6-S2-S9},
+Article-Number = {S9},
+ISSN = {1752-0509},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; PHOTOSYNTHETIC PATHWAY; GENOME; GROWTH; MODEL;
+ NITROGEN; BIOLOGY; RICE; ARABIDOPSIS; RUBISCO},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {zhang, shuai/IVU-7877-2023
+ liu, xiao/HKE-9880-2023},
+Times-Cited = {56},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000312991400009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000312064100130,
+Author = {Pan, Pengcheng and Hua, Qiang},
+Title = {Reconstruction and In Silico Analysis of Metabolic Network for an
+ Oleaginous Yeast, Yarrowia lipolytica},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {12},
+Month = {DEC 7},
+Type = {Article},
+DOI = {10.1371/journal.pone.0051535},
+Article-Number = {e51535},
+ISSN = {1932-6203},
+Keywords-Plus = {LIPID PRODUCTION; ACETYL-COENZYME; MODEL; BIOFUELS; CARBOXYLASE; ACID},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {28},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000312064100130},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000312589700007,
+Author = {Aurich, Maike K. and Thiele, Ines},
+Title = {Contextualization Procedure and Modeling of Monocyte Specific TLR
+ Signaling},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {12},
+Month = {DEC 6},
+Type = {Article},
+DOI = {10.1371/journal.pone.0049978},
+Article-Number = {e49978},
+ISSN = {1932-6203},
+Keywords-Plus = {TOLL-LIKE RECEPTORS; NOD-LIKE RECEPTOR; NF-KAPPA-B; GENE-EXPRESSION;
+ BINDING-PROTEIN; MESSENGER-RNAS; NETWORK; ACTIVATION; CELL; INTEGRATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {4},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000312589700007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000314923600001,
+Author = {Navid, Ali and Almaas, Eivind},
+Title = {Genome-level transcription data of Yersinia pestis analyzed with
+ a New metabolic constraint-based approach},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {DEC 6},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-150},
+Article-Number = {150},
+EISSN = {1752-0509},
+Keywords = {Flux balance analysis; Gene-expression; Yersinia pestis; Stress
+ response; Metabolism},
+Keywords-Plus = {GENE-EXPRESSION; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; OXIDATIVE
+ STRESS; HIGH-THROUGHPUT; SCALE; RECONSTRUCTION; NETWORK; MODELS;
+ LIPOPOLYSACCHARIDE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Navid, Ali/A-1336-2013
+ },
+ORCID-Numbers = {Navid, Ali/0000-0003-2560-6984
+ Almaas, Eivind/0000-0002-9125-326X},
+Times-Cited = {49},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000314923600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311019700009,
+Author = {Kamarainen, Jari and Knoop, Henning and Stanford, Natalie J. and
+ Guerrero, Fernando and Akhtar, M. Kalim and Aro, Eva-Mari and Steuer,
+ Ralf and Jones, Patrik R.},
+Title = {Physiological tolerance and stoichiometric potential of cyanobacteria
+ for hydrocarbon fuel production},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2012},
+Volume = {162},
+Number = {1, SI},
+Pages = {67-74},
+Month = {NOV 30},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2012.07.193},
+ISSN = {0168-1656},
+Keywords = {Cyanobacteria; Hydrocarbon; Fuel; Toxicity; Stoichiometric potential},
+Keywords-Plus = {BLUE-GREEN-ALGAE; ORGANIC-SOLVENTS; METABOLISM; MODELS; GROWTH;
+ MICROORGANISMS; TOXICITY; BIOFUELS; NETWORK; BALANCE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Aro, Eva-Mari/Q-8664-2017
+ Akhtar, M. Kalim/HMP-2523-2023
+ Steuer, Ralf/E-7482-2017
+ },
+ORCID-Numbers = {Aro, Eva-Mari/0000-0002-2922-1435
+ Akhtar, M. Kalim/0000-0002-8805-0373
+ Steuer, Ralf/0000-0003-2217-1655
+ Stanford, Natalie J/0000-0003-4958-0184
+ Guerrero, Fernando/0000-0003-2215-3115},
+Times-Cited = {43},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000311019700009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311141300009,
+Author = {Jerby, Livnat and Wolf, Lior and Denkert, Carsten and Stein, Gideon Y.
+ and Hilvo, Mika and Oresic, Matej and Geiger, Tamar and Ruppin, Eytan},
+Title = {Metabolic Associations of Reduced Proliferation and Oxidative Stress in
+ Advanced Breast Cancer},
+Journal = {CANCER RESEARCH},
+Year = {2012},
+Volume = {72},
+Number = {22},
+Pages = {5712-5720},
+Month = {NOV 15},
+Type = {Article},
+DOI = {10.1158/0008-5472.CAN-12-2215},
+ISSN = {0008-5472},
+EISSN = {1538-7445},
+Keywords-Plus = {GENE-EXPRESSION; NETWORK; INTEGRATION; RECONSTRUCTION; PREDICTION;
+ APOPTOSIS; MIGRATION; INVASION; MARKERS; CELLS},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ResearcherID-Numbers = {Denkert, Carsten/AHE-2675-2022
+ Oresic, Matej/K-7673-2016
+ Geiger, Tamar/C-2349-2014
+ Ruppin, Eytan/R-9698-2017
+ Hilvo, Mika/AAC-7468-2020
+ Oresic, Matej/AAV-3978-2020
+ },
+ORCID-Numbers = {Oresic, Matej/0000-0002-2856-9165
+ Ruppin, Eytan/0000-0002-7862-3940
+ Hilvo, Mika/0000-0003-0663-5843
+ Denkert, Carsten/0000-0002-2249-0982
+ Geiger, Tamar/0000-0002-9526-197X},
+Times-Cited = {91},
+Journal-ISO = {Cancer Res.},
+Unique-ID = {WOS:000311141300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311151900205,
+Author = {Bekaert, Michael},
+Title = {Reconstruction of Danio rerio Metabolic Model Accounting for
+ Subcellular Compartmentalisation},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {11},
+Month = {NOV 14},
+Type = {Article},
+DOI = {10.1371/journal.pone.0049903},
+Article-Number = {e49903},
+ISSN = {1932-6203},
+Keywords-Plus = {NETWORK; GENERATION; PREDICTION; ZEBRAFISH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Bekaert, Michael/0000-0002-1206-7654},
+Times-Cited = {9},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000311151900205},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311642700012,
+Author = {Borenstein, Elhanan},
+Title = {Computational systems biology and in silico modeling of the human
+ microbiome},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2012},
+Volume = {13},
+Number = {6, SI},
+Pages = {769-780},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1093/bib/bbs022},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {systems biology; metabolic models; human microbiome; metagenomics;
+ reverse ecology; ecosystomics},
+Keywords-Plus = {LARGE-SCALE ORGANIZATION; INTERSPECIES INTERACTIONS; COOCCURRENCE
+ PATTERNS; ECOSYSTEMS BIOLOGY; METABOLIC NETWORKS; GUT MICROBIOTA; RAST
+ SERVER; RECONSTRUCTION; METAGENOMICS; DIVERSITY},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+Times-Cited = {56},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000311642700012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311897100017,
+Author = {Brochado, Ana Rita and Andrejev, Sergej and Maranas, Costas D. and
+ Patil, Kiran R.},
+Title = {Impact of Stoichiometry Representation on Simulation of
+ Genotype-Phenotype Relationships in Metabolic Networks},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2012},
+Volume = {8},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1002758},
+Article-Number = {e1002758},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI; MODELS; ESSENTIALITY; GROWTH; YEAST; RECONSTRUCTION;
+ ROBUSTNESS; OPTIMALITY},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Maranas, Costas D/A-4774-2011
+ Patil, Kiran R/B-9709-2009
+ },
+ORCID-Numbers = {Maranas, Costas D/0000-0002-1508-1398
+ Patil, Kiran R/0000-0002-6166-8640
+ Brochado, Ana Rita/0000-0003-1703-383X
+ Andrejev, Sergej/0000-0002-7875-0261},
+Times-Cited = {28},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000311897100017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000310924400008,
+Author = {Zomorrodi, Ali R. and Suthers, Patrick F. and Ranganathan, Sridhar and
+ Maranas, Costas D.},
+Title = {Mathematical optimization applications in metabolic networks},
+Journal = {METABOLIC ENGINEERING},
+Year = {2012},
+Volume = {14},
+Number = {6},
+Pages = {672-686},
+Month = {NOV},
+Type = {Review},
+DOI = {10.1016/j.ymben.2012.09.005},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Mathematical optimization; Metabolic model; Metabolic network analysis;
+ Metabolic network redesign},
+Keywords-Plus = {FLUX COUPLING ANALYSIS; BIDIRECTIONAL REACTION STEPS; ESCHERICHIA-COLI
+ METABOLISM; ALTERNATE OPTIMAL-SOLUTIONS; GENE KNOCKOUT STRATEGIES;
+ CONSTRAINT-BASED MODELS; GENOME-SCALE MODEL; SACCHAROMYCES-CEREVISIAE;
+ MICROBIAL-PRODUCTION; GLOBAL OPTIMIZATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Maranas, Costas D/A-4774-2011
+ },
+ORCID-Numbers = {Maranas, Costas D/0000-0002-1508-1398
+ Suthers, Patrick/0000-0002-5560-9986
+ Ranganathan, Sridhar/0000-0003-0535-7634},
+Times-Cited = {99},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000310924400008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000307885000007,
+Author = {Setoodeh, P. and Jahanmiri, A. and Eslamloueyan, R.},
+Title = {Hybrid neural modeling framework for simulation and optimization of
+ diauxie-involved fed-batch fermentative succinate production},
+Journal = {CHEMICAL ENGINEERING SCIENCE},
+Year = {2012},
+Volume = {81},
+Pages = {57-76},
+Month = {OCT 22},
+Type = {Article},
+DOI = {10.1016/j.ces.2012.06.031},
+ISSN = {0009-2509},
+EISSN = {1873-4405},
+Keywords = {Mathematical modeling; Fermentation; Dynamic simulation; Optimization;
+ Diauxie phenomenon; Succinate production},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE STRAIN; FLUX BALANCE ANALYSIS; DYNAMIC
+ OPTIMIZATION; ESCHERICHIA-COLI; DIFFERENTIAL EVOLUTION;
+ ETHANOL-PRODUCTION; YEAST FERMENTATION; GENOME-SCALE; RENEWABLE
+ RESOURCES; METHANOL SYNTHESIS},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+Times-Cited = {10},
+Journal-ISO = {Chem. Eng. Sci.},
+Unique-ID = {WOS:000307885000007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000307735500020,
+Author = {Bujara, Matthias and Panke, Sven},
+Title = {In silico assessment of cell-free systems},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2012},
+Volume = {109},
+Number = {10},
+Pages = {2620-2629},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1002/bit.24534},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {cell-free systems; multi-enzyme catalysis; biocatalysis; genome scale
+ model},
+Keywords-Plus = {FREE PROTEIN-SYNTHESIS; ESCHERICHIA-COLI; INTRACELLULAR FLUXES; GROWTH;
+ METABOLISM; BIOLOGY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Panke, Sven/0000-0002-9368-539X},
+Times-Cited = {14},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000307735500020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000309973900047,
+Author = {Thiele, Ines and Fleming, Ronan M. T. and Que, Richard and Bordbar,
+ Aarash and Diep, Dinh and Palsson, Bernhard O.},
+Title = {Multiscale Modeling of Metabolism and Macromolecular Synthesis in
+ E. coli and Its Application to the Evolution of Codon
+ Usage},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {9},
+Month = {SEP 28},
+Type = {Article},
+DOI = {10.1371/journal.pone.0045635},
+Article-Number = {e45635},
+ISSN = {1932-6203},
+Keywords-Plus = {IN-SILICO MODELS; ESCHERICHIA-COLI; SALMONELLA-TYPHIMURIUM;
+ HIGH-THROUGHPUT; TRANSFER-RNAS; RECONSTRUCTION; NETWORK; EXPRESSION;
+ GENOMES; CONSEQUENCES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ /AAG-5264-2021
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ /0000-0001-6460-6771
+ Thiele, Ines/0000-0002-8071-7110
+ Que, Richard/0000-0003-1076-4357
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {81},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000309973900047},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311485800001,
+Author = {Liu, Ting and Zou, Wei and Liu, Liming and Chen, Jian},
+Title = {A constraint-based model of Scheffersomyces stipitis for improved
+ ethanol production},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2012},
+Volume = {5},
+Month = {SEP 21},
+Type = {Article},
+DOI = {10.1186/1754-6834-5-72},
+Article-Number = {72},
+EISSN = {1754-6834},
+Keywords = {Scheffersomyces stipitis; Genome-scale metabolic model; Constraint-based
+ simulation; Xylose utilization; Ethanol production},
+Keywords-Plus = {XYLOSE-FERMENTING YEAST; PICHIA-STIPITIS; METABOLIC RECONSTRUCTION;
+ PHYLOGENETIC ANALYSIS; D-XYLULOKINASE; FERMENTATION; GENOME; GLUCOSE;
+ OXYGENATION; FRAMEWORK},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009},
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X},
+Times-Cited = {22},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000311485800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306662800001,
+Author = {D'Huys, Pieter-Jan and Lule, Ivan and Vercammen, Dominique and Anne,
+ Jozef and Van Impe, Jan F. and Bernaerts, Kristel},
+Title = {Genome-scale metabolic flux analysis of Streptomyces lividans
+ growing on a complex medium},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2012},
+Volume = {161},
+Number = {1},
+Pages = {1-13},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2012.04.010},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Streptomyces lividans; Constraint-based metabolic modeling; Genome-scale
+ metabolic model; Flux balance analysis; Flux variability analysis;
+ Complex medium; Heterologous protein},
+Keywords-Plus = {ESCHERICHIA-COLI; COELICOLOR A3(2); NETWORK; MODELS; GROWTH;
+ OPTIMIZATION; MINIMIZATION; EXPRESSION; PREDICTION; PRINCIPLE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {ANNE, Jozef/H-7983-2019
+ },
+ORCID-Numbers = {ANNE, Jozef/0000-0002-0493-2644
+ Bernaerts, Kristel/0000-0001-6211-7042
+ Van Impe, Jan/0000-0002-5904-1638},
+Times-Cited = {36},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000306662800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306662800006,
+Author = {Zou, Wei and Liu, Liming and Zhang, Jing and Yang, Haoru and Zhou, Maoda
+ and Hua, Qiang and Chen, Jian},
+Title = {Reconstruction and analysis of a genome-scale metabolic model of the
+ vitamin C producing industrial strain Ketogulonicigenium vulgare
+ WSH-001},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2012},
+Volume = {161},
+Number = {1},
+Pages = {42-48},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2012.05.015},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Genome-scale metabolic model; Ketogulonicigenium vulgare;
+ 2-keto-L-Gulonic acid; Sulfate metabolism; Vitamin C},
+Keywords-Plus = {L-ASCORBIC-ACID; 2-KETO-L-GULONIC ACID; L-SORBOSE; BACILLUS-MEGATERIUM;
+ DEHYDROGENASE; ANNOTATION; SEQUENCE; DATABASE; SERVER},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Liu, Liming/B-1972-2009},
+ORCID-Numbers = {Liu, Liming/0000-0003-3022-936X},
+Times-Cited = {27},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000306662800006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000309510900025,
+Author = {Fang, Xin and Wallqvist, Anders and Reifman, Jaques},
+Title = {Modeling Phenotypic Metabolic Adaptations of Mycobacterium
+ tuberculosis H37Rv under Hypoxia},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2012},
+Volume = {8},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1002688},
+Article-Number = {e1002688},
+EISSN = {1553-7358},
+Keywords-Plus = {GENE-EXPRESSION; SACCHAROMYCES-CEREVISIAE; SYSTEMS BIOLOGY; LATENT
+ TUBERCULOSIS; PROTEIN EXPRESSION; DRUG DISCOVERY; TRANSCRIPTIONAL
+ REGULATION; MACROMOLECULAR-COMPOSITION; STATIONARY-PHASE;
+ ALPHA-CRYSTALLIN},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {wallqvist, anders/W-2584-2019},
+ORCID-Numbers = {wallqvist, anders/0000-0002-9775-7469},
+Times-Cited = {48},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000309510900025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000308299200005,
+Author = {Jouhten, Paula and Wiebe, Marilyn and Penttila, Merja},
+Title = {Dynamic flux balance analysis of the metabolism of Saccharomyces
+ cerevisiae during the shift from fully respirative or
+ respirofermentative metabolic states to anaerobiosis},
+Journal = {FEBS JOURNAL},
+Year = {2012},
+Volume = {279},
+Number = {18},
+Pages = {3338-3354},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1111/j.1742-4658.2012.08649.x},
+ISSN = {1742-464X},
+EISSN = {1742-4658},
+Keywords = {dynamic flux balance analysis; metabolism; modelling; oxygen;
+ Saccharomyces cerevisiae},
+Keywords-Plus = {ETHANOL-PRODUCTION; STEADY-STATE; GROWTH-RATE; TRANSCRIPTIONAL RESPONSE;
+ ELECTRON-TRANSFER; GENE-EXPRESSION; NADH METABOLISM; YEAST; OXYGEN;
+ GLUCOSE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Penttilä, Merja E/A-4710-2013
+ },
+ORCID-Numbers = {Penttila, Merja/0000-0002-6929-1032
+ Jouhten, Paula/0000-0003-1075-7448
+ Wiebe, Marilyn/0000-0002-4535-2427},
+Times-Cited = {21},
+Journal-ISO = {FEBS J.},
+Unique-ID = {WOS:000308299200005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000314920300001,
+Author = {Karlstaedt, Anja and Fliegner, Daniela and Kararigas, Georgios and
+ Ruderisch, Hugo Sanchez and Regitz-Zagrosek, Vera and Holzhuetter,
+ Hermann-Georg},
+Title = {CardioNet: A human metabolic network suited for the study of
+ cardiomyocyte metabolism},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {AUG 29},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-114},
+Article-Number = {114},
+EISSN = {1752-0509},
+Keywords = {Computational biology; Flux balance; Heart; Cardiomyocyte; Efficency;
+ Metabolism},
+Keywords-Plus = {FATTY-ACID-COMPOSITION; RAT-HEART; OXIDATIVE STRESS;
+ FUNCTIONAL-CHARACTERIZATION; MITOCHONDRIAL DYSFUNCTION;
+ CARDIAC-FUNCTION; BETA-OXIDATION; ISCHEMIC-HEART; FLUX; RECONSTRUCTION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Karlstaedt, Anja/N-6557-2019
+ },
+ORCID-Numbers = {Karlstaedt, Anja/0000-0001-5689-3571
+ Sanchez Ruderisch, Hugo/0000-0001-9315-4508
+ Holzhutter, Hermann-Georg/0000-0002-5054-6023
+ Kararigas, Georgios/0000-0002-8187-0176
+ Regitz-Zagrosek, Vera/0000-0002-3566-3467},
+Times-Cited = {49},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000314920300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000308139500001,
+Author = {Kelk, Steven M. and Olivier, Brett G. and Stougie, Leen and Bruggeman,
+ Frank J.},
+Title = {Optimal flux spaces of genome-scale stoichiometric models are determined
+ by a few subnetworks},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2012},
+Volume = {2},
+Month = {AUG 15},
+Type = {Article},
+DOI = {10.1038/srep00580},
+Article-Number = {580},
+ISSN = {2045-2322},
+Keywords-Plus = {METABOLIC NETWORK; ESCHERICHIA-COLI; STATE; PATHWAYS; DEFINITION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Olivier, Brett G/A-2800-2008
+ Bruggeman, Frank/AAS-8371-2020
+ Bruggeman, Frank/C-4356-2015},
+ORCID-Numbers = {Olivier, Brett G/0000-0002-5293-5321
+ Bruggeman, Frank/0000-0002-0255-4766
+ Bruggeman, Frank/0000-0002-0255-4766},
+Times-Cited = {55},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000308139500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000307378500036,
+Author = {Garcia Sanchez, Carlos Eduardo and Vargas Garcia, Cesar Augusto and
+ Torres Saez, Rodrigo Gonzalo},
+Title = {Predictive Potential of Flux Balance Analysis of Saccharomyces
+ cerevisiae Using as Optimization Function Combinations of Cell
+ Compartmental Objectives},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {8},
+Month = {AUG 9},
+Type = {Article},
+DOI = {10.1371/journal.pone.0043006},
+Article-Number = {e43006},
+ISSN = {1932-6203},
+Keywords-Plus = {METABOLIC FLUXES; GROWTH; MODEL; IDENTIFICATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Torres, Rodrigo/HSG-8535-2023
+ Vargas-Garcia, Cesar/J-8090-2017
+ },
+ORCID-Numbers = {Torres, Rodrigo/0000-0003-1113-3020
+ Vargas-Garcia, Cesar/0000-0002-4286-8882
+ Garcia Sanchez, Carlos Eduardo/0000-0003-1543-1498},
+Times-Cited = {10},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000307378500036},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000307437900018,
+Author = {Fearnley, Liam G. and Nielsen, Lars K.},
+Title = {PATHLOGIC-S: A Scalable Boolean Framework for Modelling Cellular
+ Signalling},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {8},
+Month = {AUG 7},
+Type = {Article},
+DOI = {10.1371/journal.pone.0041977},
+Article-Number = {e41977},
+ISSN = {1932-6203},
+Keywords-Plus = {FUNCTIONAL-ANALYSIS; ACTIVATION; PATHWAYS; RECEPTOR; NETWORKS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Nielsen, Lars K/A-5519-2011},
+ORCID-Numbers = {Nielsen, Lars K/0000-0001-8191-3511},
+Times-Cited = {5},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000307437900018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306105900010,
+Author = {Macdonald, Sandy J. and Lin, George G. and Russell, Calum W. and Thomas,
+ Gavin H. and Douglas, Angela E.},
+Title = {The central role of the host cell in symbiotic nitrogen metabolism},
+Journal = {PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
+Year = {2012},
+Volume = {279},
+Number = {1740},
+Pages = {2965-2973},
+Month = {AUG 7},
+Type = {Article},
+DOI = {10.1098/rspb.2012.0414},
+ISSN = {0962-8452},
+EISSN = {1471-2954},
+Keywords = {Acyrthosiphon pisum; Buchnera; flux balance analysis; metabolic
+ modelling; nitrogen recycling; symbiosis},
+Keywords-Plus = {ACYRTHOSIPHON-PISUM; PEA APHID; BACTERIAL SYMBIONT; GENOME;
+ ASSIMILATION; COOPERATION; GLUTAMATE; INSECT},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Environmental Sciences \&
+ Ecology; Evolutionary Biology},
+Web-of-Science-Categories = {Biology; Ecology; Evolutionary Biology},
+ResearcherID-Numbers = {Thomas, Gavin H/E-5753-2011
+ },
+ORCID-Numbers = {Thomas, Gavin H/0000-0002-9763-1313
+ Macdonald, Sandy/0000-0002-4112-0987},
+Times-Cited = {69},
+Journal-ISO = {Proc. R. Soc. B-Biol. Sci.},
+Unique-ID = {WOS:000306105900010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000309121800001,
+Author = {Feng, Xueyang and Xu, You and Chen, Yixin and Tang, Yinjie J.},
+Title = {MicrobesFlux: a web platform for drafting metabolic models from the KEGG
+ database},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {AUG 2},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-94},
+Article-Number = {94},
+EISSN = {1752-0509},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; FLUX BALANCE ANALYSIS; IN-SILICO;
+ CLOSTRIDIUM; NETWORK; GROWTH},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {chen, yu-cheng/IQT-1648-2023
+ Chen, Yi/HPD-0595-2023
+ Feng, Xueyang/G-1295-2015
+ Chen, Yi/HIR-2608-2022
+ Chen, Yu/Y-3292-2019
+ Tang, Yinjie/AAI-5584-2020
+ },
+ORCID-Numbers = {Feng, Xueyang/0000-0003-4426-5732},
+Times-Cited = {43},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000309121800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306255800007,
+Author = {Collakova, Eva and Yen, Jiun Y. and Senger, Ryan S.},
+Title = {Are we ready for genome-scale modeling in plants?},
+Journal = {PLANT SCIENCE},
+Year = {2012},
+Volume = {191},
+Pages = {53-70},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1016/j.plantsci.2012.04.010},
+ISSN = {0168-9452},
+Keywords = {AraGEM; C4GEM; Flux balance analysis; Genome-scale model; Metabolic
+ network reconstruction; Photorespiration; Photosynthesis; Plant primary
+ and secondary metabolism},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; HETEROTROPHIC ARABIDOPSIS CELLS; CONSTRAINT-BASED
+ ANALYSIS; CENTRAL METABOLIC FLUXES; ESCHERICHIA-COLI; IN-SILICO;
+ QUANTITATIVE PREDICTION; THERMODYNAMIC ANALYSIS; VARIABILITY ANALYSIS;
+ CELLULAR-METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology; Plant Sciences},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Plant Sciences},
+ORCID-Numbers = {Collakova, Eva/0000-0003-3476-6701},
+Times-Cited = {46},
+Journal-ISO = {Plant Sci.},
+Unique-ID = {WOS:000306255800007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000308266100020,
+Author = {de Jong, Bouke and Siewers, Verena and Nielsen, Jens},
+Title = {Systems biology of yeast: enabling technology for development of cell
+ factories for production of advanced biofuels},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2012},
+Volume = {23},
+Number = {4},
+Pages = {624-630},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1016/j.copbio.2011.11.021},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {ESCHERICHIA-COLI; HIGH-THROUGHPUT; QUANTITATIVE METABOLOMICS;
+ SACCHAROMYCES-CEREVISIAE; EXPRESSION; METABOLISM; BIOSYNTHESIS;
+ TOLERANCE; SELECTION; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Siewers, Verena/AAV-4902-2020
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Siewers, Verena/0000-0002-9502-9804
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {59},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000308266100020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306721800019,
+Author = {Kostromins, Andrejs and Stalidzans, Egils},
+Title = {Paint4Net: COBRA Toolbox extension for visualization of stoichiometric
+ models of metabolism},
+Journal = {BIOSYSTEMS},
+Year = {2012},
+Volume = {109},
+Number = {2},
+Pages = {233-239},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2012.03.002},
+ISSN = {0303-2647},
+Keywords = {Automatic visualization; COBRA Toolbox; Stoichiometric models;
+ Metabolism; Flux balance analysis},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Stalidzans, Egils/G-5883-2010
+ Kostromins, Andrejs/G-5855-2012},
+ORCID-Numbers = {Stalidzans, Egils/0000-0001-6063-0184
+ },
+Times-Cited = {25},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000306721800019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302349300013,
+Author = {Lee, Joo Sang and Nishikawa, Takashi and Motter, Adilson E.},
+Title = {WHY OPTIMAL STATES RECRUIT FEWER REACTIONS IN METABOLIC NETWORKS},
+Journal = {DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS},
+Year = {2012},
+Volume = {32},
+Number = {8, SI},
+Pages = {2937-2950},
+Month = {AUG},
+Type = {Article},
+DOI = {10.3934/dcds.2012.32.2937},
+ISSN = {1078-0947},
+EISSN = {1553-5231},
+Keywords = {Network modeling; cellular metabolism; duality principle; flux balance
+ analysis; optimization},
+Keywords-Plus = {SYNTHETIC RESCUES; DISPENSABILITY; EVOLUTION},
+Research-Areas = {Mathematics},
+Web-of-Science-Categories = {Mathematics, Applied; Mathematics},
+ResearcherID-Numbers = {Nishikawa, Takashi/B-3752-2010
+ },
+ORCID-Numbers = {Nishikawa, Takashi/0000-0002-2147-0242
+ Motter, Adilson E./0000-0003-1794-4828},
+Times-Cited = {1},
+Journal-ISO = {Discret. Contin. Dyn. Syst.},
+Unique-ID = {WOS:000302349300013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000308553500042,
+Author = {Reed, Jennifer L.},
+Title = {Shrinking the Metabolic Solution Space Using Experimental Datasets},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2012},
+Volume = {8},
+Number = {8},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1371/journal.pcbi.1002662},
+Article-Number = {e1002662},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {TRANSCRIPTIONAL REGULATION; ESCHERICHIA-COLI; REGULATORY NETWORKS;
+ HIGH-THROUGHPUT; GENOME; MODELS; CONSTRAINT; RECONSTRUCTION;
+ OPTIMIZATION; INTEGRATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Reed, Jennifer L/E-5137-2011},
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220},
+Times-Cited = {73},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000308553500042},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306492900005,
+Author = {Shahzad, Khuram and Loor, Juan J.},
+Title = {Application of Top-Down and Bottom-up Systems Approaches in Ruminant
+ Physiology and Metabolism},
+Journal = {CURRENT GENOMICS},
+Year = {2012},
+Volume = {13},
+Number = {5},
+Pages = {379-394},
+Month = {AUG},
+Type = {Article},
+DOI = {10.2174/138920212801619269},
+ISSN = {1389-2029},
+EISSN = {1875-5488},
+Keywords = {Bioinformatics; dairy cow; nutrigenomics; microarray},
+Keywords-Plus = {GENE-EXPRESSION PROFILES; NEGATIVE-ENERGY BALANCE; BOVINE MAMMARY-GLAND;
+ CONSTRAINT-BASED MODELS; RNA-SEQ ANALYSIS; DAIRY-COWS; ADIPOSE-TISSUE;
+ LACTATING COW; QUANTITATIVE PREDICTION; LONGISSIMUS-LUMBORUM},
+Research-Areas = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
+ResearcherID-Numbers = {Shahzad, Khuram/AAC-8884-2019
+ Loor, Juan J./H-3760-2012
+ },
+ORCID-Numbers = {Loor, Juan J./0000-0003-1586-4365
+ Shahzad, Dr Khuram/0000-0002-2333-1684},
+Times-Cited = {31},
+Journal-ISO = {Curr. Genomics},
+Unique-ID = {WOS:000306492900005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306751300089,
+Author = {Barat, Somedutta and Steeb, Benjamin and Maze, Alain and Bumann, Dirk},
+Title = {Extensive In Vivo Resilience of Persistent Salmonella},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {7},
+Month = {JUL 24},
+Type = {Article},
+DOI = {10.1371/journal.pone.0042007},
+Article-Number = {e42007},
+ISSN = {1932-6203},
+Keywords-Plus = {MYCOBACTERIUM-TUBERCULOSIS PERSISTENCE; ESCHERICHIA-COLI; TYPHIMURIUM;
+ VIRULENCE; REPLICATION; INFECTION; METABOLISM; DYNAMICS; MUTANTS; DUBLIN},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Maze, Alain/0000-0003-0873-3690},
+Times-Cited = {18},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000306751300089},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306195300005,
+Author = {Carinhas, Nuno and Oliveira, Rui and Alves, Paula Marques and Carrondo,
+ Manuel J. T. and Teixeira, Ana P.},
+Title = {Systems biotechnology of animal cells: the road to prediction},
+Journal = {TRENDS IN BIOTECHNOLOGY},
+Year = {2012},
+Volume = {30},
+Number = {7},
+Pages = {377-385},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1016/j.tibtech.2012.03.004},
+ISSN = {0167-7799},
+EISSN = {1879-3096},
+Keywords = {systems biotechnology; mathematical modeling; computational prediction;
+ animal cell culture; recombinant protein; bioprocess improvement},
+Keywords-Plus = {METABOLIC-FLUX ANALYSIS; MONOCLONAL-ANTIBODY PRODUCTION; C-13 LABELING
+ EXPERIMENTS; LOW CULTURE TEMPERATURE; HAMSTER OVARY CELLS; CHO-CELLS;
+ QUANTITATIVE-ANALYSIS; MASS-SPECTROMETRY; ENZYME-ACTIVITIES;
+ MAMMALIAN-CELLS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Teixeira, Ana P/JND-7641-2023
+ Teixeira, Ana/F-5594-2011
+ Carrondo, Manuel JT/C-8155-2011
+ Alves, Paula M/C-1070-2008
+ Oliveira, Rui/D-8815-2013
+ Alves, Ana/JGM-1495-2023
+ },
+ORCID-Numbers = {Teixeira, Ana/0000-0002-9208-8737
+ Alves, Paula M/0000-0003-1445-3556
+ Oliveira, Rui/0000-0001-8077-4177
+ Carrondo, Manuel/0000-0002-4550-4574
+ Carinhas, Nuno/0000-0002-3321-1221},
+Times-Cited = {34},
+Journal-ISO = {Trends Biotechnol.},
+Unique-ID = {WOS:000306195300005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000305825600012,
+Author = {Liao, Yu-Chieh and Tsai, Ming-Hsin and Chen, Feng-Chi and Hsiung, Chao
+ A.},
+Title = {GEMSiRV: a software platform for GEnome-scale metabolic model
+ simulation, reconstruction and visualization},
+Journal = {BIOINFORMATICS},
+Year = {2012},
+Volume = {28},
+Number = {13},
+Pages = {1752-1758},
+Month = {JUL 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/bts267},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {IN-SILICO; NETWORKS; TOOLBOX; SYSTEM; SBML},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Liao, Yu-Chieh/L-5113-2019
+ Chen, Feng-Chi/E-3841-2010
+ Liao, Yu-Chieh/E-5031-2011
+ Hsiung, Chao Agnes/E-3994-2010},
+ORCID-Numbers = {Liao, Yu-Chieh/0000-0002-4360-7932
+ },
+Times-Cited = {31},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000305825600012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000305565000002,
+Author = {Vital-Lopez, Francisco G. and Memisevic, Vesna and Dutta, Bhaskar},
+Title = {Tutorial on biological networks},
+Journal = {WILEY INTERDISCIPLINARY REVIEWS-DATA MINING AND KNOWLEDGE DISCOVERY},
+Year = {2012},
+Volume = {2},
+Number = {4},
+Pages = {298-325},
+Month = {JUL-AUG},
+Type = {Review},
+DOI = {10.1002/widm.1061},
+ISSN = {1942-4787},
+EISSN = {1942-4795},
+Keywords-Plus = {PROTEIN-INTERACTION NETWORKS; ONLINE MENDELIAN INHERITANCE; GENETIC
+ INTERACTION NETWORKS; SCALE-FREE NETWORKS; SYSTEMS BIOLOGY; INTERACTION
+ MAP; SACCHAROMYCES-CEREVISIAE; COMPUTATIONAL METHODS; REGULATORY
+ NETWORK; SIGNALING NETWORKS},
+Research-Areas = {Computer Science},
+Web-of-Science-Categories = {Computer Science, Artificial Intelligence; Computer Science, Theory \&
+ Methods},
+Times-Cited = {8},
+Journal-ISO = {Wiley Interdiscip. Rev.-Data Mining Knowl. Discov.},
+Unique-ID = {WOS:000305565000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000306291400068,
+Author = {Xu, Lin and Barker, Brandon and Gu, Zhenglong},
+Title = {Dynamic epistasis for different alleles of the same gene},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2012},
+Volume = {109},
+Number = {26},
+Pages = {10420-10425},
+Month = {JUN 26},
+Type = {Article},
+DOI = {10.1073/pnas.1121507109},
+ISSN = {0027-8424},
+Keywords-Plus = {FLUX-BALANCE ANALYSIS; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE;
+ ADAPTIVE EVOLUTION; METABOLIC NETWORKS; DELETERIOUS MUTATIONS; SEXUAL
+ REPRODUCTION; POSITIVE EPISTASIS; GENOMIC COMPLEXITY; YEAST METABOLISM},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {xu, lin/H-8560-2016
+ },
+ORCID-Numbers = {Barker, Brandon/0000-0001-5732-9550},
+Times-Cited = {18},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000306291400068},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000310442000001,
+Author = {Lee, Dave and Smallbone, Kieran and Dunn, Warwick B. and Murabito,
+ Ettore and Winder, Catherine L. and Kell, Douglas B. and Mendes, Pedro
+ and Swainston, Neil},
+Title = {Improving metabolic flux predictions using absolute gene expression data},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {JUN 19},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-73},
+Article-Number = {73},
+ISSN = {1752-0509},
+Keywords = {Flux balance analysis; Metabolic flux; Metabolic networks;
+ Transcriptomics; RNA-Seq; Exometabolomics},
+Keywords-Plus = {SYSTEMS BIOLOGY; RNA-SEQ; ESCHERICHIA-COLI; BALANCE ANALYSIS; NETWORK;
+ MODELS; RECONSTRUCTION; GROWTH; REVEALS; PROTEIN},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Dunn, Warwick/CAJ-1648-2022
+ Kell, Douglas/E-8318-2011
+ },
+ORCID-Numbers = {Dunn, Warwick/0000-0001-6924-0027
+ Kell, Douglas/0000-0001-5838-7963
+ Lee, Dave/0000-0003-3367-5808
+ Mendes, Pedro/0000-0001-6507-9168
+ Smallbone, Kieran/0000-0003-2815-7045},
+Times-Cited = {110},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000310442000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000308104200001,
+Author = {Klanchui, Amornpan and Khannapho, Chiraphan and Phodee, Atchara and
+ Cheevadhanarak, Supapon and Meechai, Asawin},
+Title = {iAK692: A genome-scale metabolic model of Spirulina platensis
+ C1},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {JUN 15},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-71},
+Article-Number = {71},
+EISSN = {1752-0509},
+Keywords = {Spirulina platensis C1; Cyanobacteria; Metabolic network reconstruction;
+ Genome-scale metabolic model; Flux balance analysis},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; SPIRULINA-PLATENSIS; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; RECONSTRUCTION; DATABASE; GROWTH; PATHWAYS;
+ TOOLBOX; CELLS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Khannapho, Chiraphan/JAN-8333-2023
+ },
+ORCID-Numbers = {Khannapho, Chiraphan/0000-0003-4709-5257},
+Times-Cited = {30},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000308104200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000307248200001,
+Author = {Heavner, Benjamin D. and Smallbone, Kieran and Barker, Brandon and
+ Mendes, Pedro and Walker, Larry P.},
+Title = {Yeast 5-an expanded reconstruction of the Saccharomyces
+ cerevisiae metabolic network},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {JUN 4},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-55},
+Article-Number = {55},
+EISSN = {1752-0509},
+Keywords = {Metabolic; Reconstruction; Yeast; Flux balance analysis; GEM; GENRE;
+ Model},
+Keywords-Plus = {COMMUNITY APPROACH; SYSTEMS BIOLOGY; GENE DELETION; GENOME; MODEL;
+ BALANCE; REPRESENTATION; ROBUSTNESS; ANNOTATION; VALIDATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Mendes, Pedro/0000-0001-6507-9168
+ Barker, Brandon/0000-0001-5732-9550
+ Smallbone, Kieran/0000-0003-2815-7045
+ Heavner, Benjamin/0000-0003-2898-9044},
+Times-Cited = {97},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000307248200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000305110200003,
+Author = {Fontana, Judith M. and Alexander, Elizabeth and Salvatore, Mirella},
+Title = {Translational research in infectious disease: current paradigms and
+ challenges ahead},
+Journal = {TRANSLATIONAL RESEARCH},
+Year = {2012},
+Volume = {159},
+Number = {6},
+Pages = {430-453},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1016/j.trsl.2011.12.009},
+ISSN = {1931-5244},
+EISSN = {1878-1810},
+Keywords-Plus = {RESPIRATORY-TRACT INFECTIONS; CONSTRAINT-BASED MODELS; YELLOW-FEVER
+ VACCINE; HEPATITIS-C VIRUS; INFLUENZA-A VIRUS; MASS-SPECTROMETRY;
+ QUANTITATIVE PROTEOMICS; SYSTEMS BIOLOGY; VIRAL PATHOGENS;
+ MYCOBACTERIUM-TUBERCULOSIS},
+Research-Areas = {Medical Laboratory Technology; General \& Internal Medicine; Research \&
+ Experimental Medicine},
+Web-of-Science-Categories = {Medical Laboratory Technology; Medicine, General \& Internal; Medicine,
+ Research \& Experimental},
+ResearcherID-Numbers = {Salvatore, Mirella/K-6691-2016
+ },
+ORCID-Numbers = {Salvatore, Mirella/0000-0002-8296-0376
+ Minkoff, Judith/0000-0002-7379-2753},
+Times-Cited = {32},
+Journal-ISO = {Transl. Res.},
+Unique-ID = {WOS:000305110200003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000308752400001,
+Author = {Ng, Chiam Yu and Jung, Moo-Young and Lee, Jinwon and Oh, Min-Kyu},
+Title = {Production of 2,3-butanediol in Saccharomyces cerevisiae
+ by in silico aided metabolic engineering},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2012},
+Volume = {11},
+Month = {MAY 28},
+Type = {Article},
+DOI = {10.1186/1475-2859-11-68},
+Article-Number = {68},
+ISSN = {1475-2859},
+Keywords = {2,3-Butanediol; Saccharomyces cerevisiae; Metabolic engineering; Flux
+ balance analysis; Alcohol dehydrogenase; OptKnock},
+Keywords-Plus = {YEAST PYRUVATE DECARBOXYLASE; LACTATE-DEHYDROGENASE GENE; BREWERS-YEAST;
+ ESCHERICHIA-COLI; LACTIC-ACID; FLUX; RECONSTRUCTION; FERMENTATION;
+ ACETALDEHYDE; ACETOIN},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lee, Jae-ung/I-1815-2017
+ Oh, Min-Kyu/F-6933-2013
+ },
+ORCID-Numbers = {Lee, Jae-ung/0000-0002-6699-2335
+ Oh, Min-Kyu/0000-0001-6406-3930
+ Lee, Jinwon/0000-0003-4153-0609
+ Ng, Chiam Yu/0000-0002-1567-517X},
+Times-Cited = {117},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000308752400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000309402800001,
+Author = {Bergdahl, Basti and Heer, Dominik and Sauer, Uwe and Hahn-Hagerdal,
+ Barbel and van Niel, Ed W. J.},
+Title = {Dynamic metabolomics differentiates between carbon and energy starvation
+ in recombinant Saccharomyces cerevisiae fermenting xylose},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2012},
+Volume = {5},
+Month = {MAY 15},
+Type = {Article},
+DOI = {10.1186/1754-6834-5-34},
+Article-Number = {34},
+ISSN = {1754-6834},
+Keywords = {Metabolomics; Yeast metabolism; Xylose fermentation; Metabolic status;
+ Starvation; Bioethanol},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; ANAEROBIC FERMENTATION; THERMODYNAMIC
+ ANALYSIS; GUANINE-NUCLEOTIDES; ETHANOL-PRODUCTION; PROTEIN-SYNTHESIS;
+ CO-FERMENTATION; FLUX ANALYSIS; CURRENT STATE; CELL-CYCLE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Sauer, Uwe/Y-3556-2019
+ van Niel, Ed/GQQ-1220-2022
+ },
+ORCID-Numbers = {Heer, Dominik/0009-0003-2089-4339},
+Times-Cited = {45},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000309402800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000305339400043,
+Author = {Brandes, Aaron and Lun, Desmond S. and Ip, Kuhn and Zucker, Jeremy and
+ Colijn, Caroline and Weiner, Brian and Galagan, James E.},
+Title = {Inferring Carbon Sources from Gene Expression Profiles Using Metabolic
+ Flux Models},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {5},
+Month = {MAY 14},
+Type = {Article},
+DOI = {10.1371/journal.pone.0036947},
+Article-Number = {e36947},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; PROTEIN EXPRESSION; GROWTH; OPTIMIZATION;
+ TUBERCULOSIS; CONSTRAINTS; INFORMATION; NETWORKS; MG1655},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Zucker, Jeremy/M-3643-2016
+ Lun, Desmond S/A-4943-2010
+ },
+ORCID-Numbers = {Zucker, Jeremy/0000-0002-7276-9009
+ Weiner, Brian/0000-0002-7285-4385
+ Galagan, James/0000-0003-0542-3291},
+Times-Cited = {23},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000305339400043},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311224300001,
+Author = {McAnulty, Michael J. and Yen, Jiun Y. and Freedman, Benjamin G. and
+ Senger, Ryan S.},
+Title = {Genome-scale modeling using flux ratio constraints to enable metabolic
+ engineering of clostridial metabolism in silico},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {MAY 14},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-42},
+Article-Number = {42},
+EISSN = {1752-0509},
+Keywords = {Genome-scale model; clostridia; flux ratio; flux balance analysis;
+ metabolic engineering; systems biology},
+Keywords-Plus = {ACID-FORMATION PATHWAYS; ESCHERICHIA-COLI; DOWN-REGULATION; RECOMBINANT
+ STRAINS; CONTINUOUS CULTURES; SOLVENT PRODUCTION; ACETOBUTYLICUM;
+ RECONSTRUCTION; FERMENTATIONS; INACTIVATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {McAnulty, Michael/0000-0002-1926-196X},
+Times-Cited = {57},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000311224300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000309120500001,
+Author = {Loira, Nicolas and Dulermo, Thierry and Nicaud, Jean-Marc and Sherman,
+ David James},
+Title = {A genome-scale metabolic model of the lipid-accumulating yeast
+ Yarrowia lipolytica},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {MAY 4},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-35},
+Article-Number = {35},
+EISSN = {1752-0509},
+Keywords-Plus = {GENE; PATHWAY; GROWTH; RECONSTRUCTION; VALIDATION; DISRUPTION; ORTHOLOGS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Nicaud, jean marc/G-4204-2016
+ NICAUD, Jean-marc/ABA-9076-2021
+ },
+ORCID-Numbers = {Nicaud, jean marc/0000-0002-6679-972X
+ Sherman, David James/0000-0002-2316-1005},
+Times-Cited = {81},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000309120500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302876000011,
+Author = {Copeland, Wilbert B. and Bartley, Bryan A. and Chandran, Deepak and
+ Galdzicki, Michal and Kim, Kyung H. and Sleight, Sean C. and Maranas,
+ Costas D. and Sauro, Herbert M.},
+Title = {Computational tools for metabolic engineering},
+Journal = {METABOLIC ENGINEERING},
+Year = {2012},
+Volume = {14},
+Number = {3},
+Pages = {270-280},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2012.03.001},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic engineering; Software; Genome-scale metabolic networks;
+ Network visualization},
+Keywords-Plus = {KYOTO ENCYCLOPEDIA; BIOCYC COLLECTION; SOFTWARE PLATFORM;
+ ESCHERICHIA-COLI; METACYC DATABASE; SYSTEMS; DESIGN; NETWORKS; MODELS;
+ GENES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Maranas, Costas D/A-4774-2011
+ Galdzicki, Michal/F-5682-2010
+ },
+ORCID-Numbers = {Maranas, Costas D/0000-0002-1508-1398
+ Galdzicki, Michal/0000-0002-8392-8183
+ Kim, Kyung/0000-0001-9304-0201
+ Kim, Kyung/0000-0002-7191-9917
+ Sauro, Herbert/0000-0002-3659-6817},
+Times-Cited = {72},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000302876000011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000303828900022,
+Author = {Hala, David and Petersen, Lene H. and Martinovic, Dalma and Huggett,
+ Duane B.},
+Title = {Constraints-based stoichiometric analysis of hypoxic stress on
+ steroidogenesis in fathead minnows, Pimephales promelas},
+Journal = {JOURNAL OF EXPERIMENTAL BIOLOGY},
+Year = {2012},
+Volume = {215},
+Number = {10},
+Pages = {1753-1765},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1242/jeb.066027},
+ISSN = {0022-0949},
+EISSN = {1477-9145},
+Keywords = {constraints based; genome scale; steroidogenesis; in silico; in vivo;
+ hypoxia; fathead minnow},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; ESCHERICHIA-COLI; METABOLIC NETWORK;
+ COMPUTATIONAL MODEL; FISH; EXPRESSION; BALANCE; RESPONSES; CELLS; SEX},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ORCID-Numbers = {Martinovic-Weigelt, Dalma/0000-0002-9973-4965},
+Times-Cited = {16},
+Journal-ISO = {J. Exp. Biol.},
+Unique-ID = {WOS:000303828900022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000307894100001,
+Author = {Orth, Jeffrey D. and Palsson, Bernhard O.},
+Title = {Gap-filling analysis of the iJO1366 Escherichia coli
+ metabolic network reconstruction for discovery of metabolic functions},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {MAY 1},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-30},
+Article-Number = {30},
+EISSN = {1752-0509},
+Keywords = {Constraint-based modeling; Metabolic network reconstruction; Escherichia
+ coli; Gap-filling; Gene annotation},
+Keywords-Plus = {CITRATE SYNTHASE; GENES; IDENTIFICATION; PURIFICATION; MODELS; ENZYME},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {45},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000307894100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000311931100001,
+Author = {Larhlimi, Abdelhalim and David, Laszlo and Selbig, Joachim and Bockmayr,
+ Alexander},
+Title = {F2C2: a fast tool for the computation of flux coupling in genome-scale
+ metabolic networks},
+Journal = {BMC BIOINFORMATICS},
+Year = {2012},
+Volume = {13},
+Month = {APR 23},
+Type = {Article},
+DOI = {10.1186/1471-2105-13-57},
+Article-Number = {57},
+ISSN = {1471-2105},
+Keywords-Plus = {BALANCE ANALYSIS; RECONSTRUCTION; PATHWAYS; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Larhlimi, Abdelhalim/0000-0002-1709-2648
+ Bockmayr, Alexander/0000-0002-5074-1347},
+Times-Cited = {49},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000311931100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000303003300003,
+Author = {Haraldsdottir, H. S. and Thiele, I. and Fleming, R. M. T.},
+Title = {Quantitative Assignment of Reaction Directionality in a
+ Multicompartmental Human Metabolic Reconstruction},
+Journal = {BIOPHYSICAL JOURNAL},
+Year = {2012},
+Volume = {102},
+Number = {8},
+Pages = {1703-1711},
+Month = {APR 18},
+Type = {Article},
+DOI = {10.1016/j.bpj.2012.02.032},
+ISSN = {0006-3495},
+Keywords-Plus = {ESCHERICHIA-COLI; THERMODYNAMIC ANALYSIS; FLUX ANALYSIS; NETWORKS;
+ MODELS; CONSTRAINTS; CHORISMATE; CONVERSION; REDUCTASE; KINETICS},
+Research-Areas = {Biophysics},
+Web-of-Science-Categories = {Biophysics},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {36},
+Journal-ISO = {Biophys. J.},
+Unique-ID = {WOS:000303003300003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000305345000018,
+Author = {Sigurdsson, Gunnar and Fleming, Ronan M. T. and Heinken, Almut and
+ Thiele, Ines},
+Title = {A Systems Biology Approach to Drug Targets in Pseudomonas
+ aeruginosa Biofilm},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {4},
+Month = {APR 16},
+Type = {Article},
+DOI = {10.1371/journal.pone.0034337},
+Article-Number = {e34337},
+ISSN = {1932-6203},
+Keywords-Plus = {METABOLIC NETWORK ANALYSIS; CONSTRAINT-BASED MODELS; FLUX BALANCE
+ ANALYSIS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; MUTANT LIBRARY;
+ RECONSTRUCTION; PAO1; INFECTIONS; GENE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Fleming, Ronan MT/ABC-4093-2021
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Heinken, Almut/0000-0001-6938-8072},
+Times-Cited = {32},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000305345000018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000303440400012,
+Author = {Blair, Rachael Hageman and Kliebenstein, Daniel J. and Churchill, Gary
+ A.},
+Title = {What Can Causal Networks Tell Us about Metabolic Pathways?},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2012},
+Volume = {8},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1002458},
+Article-Number = {e1002458},
+EISSN = {1553-7358},
+Keywords-Plus = {GENE REGULATORY NETWORKS; GLUCOSINOLATE METABOLISM; BIOCHEMICAL SYSTEMS;
+ SLOPPY MODELS; INFERENCE; BIOLOGY; TRANSCRIPTION; FLUCTUATIONS;
+ PROPAGATION; PREDICTIONS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Churchill, Gary/AAY-7496-2020
+ },
+ORCID-Numbers = {Churchill, Gary/0000-0001-9190-9284
+ Kliebenstein, Daniel/0000-0001-5759-3175},
+Times-Cited = {18},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000303440400012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000305757400001,
+Author = {van Hoek, Milan J. A. and Merks, Roeland M. H.},
+Title = {Redox balance is key to explaining full vs. partial switching to
+ low-yield metabolism},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {MAR 24},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-22},
+Article-Number = {22},
+EISSN = {1752-0509},
+Keywords = {Metabolic switching; Genome-scale metabolic model; Flux Balance Analysis
+ with Molecular Crowding; Overflow metabolism; Redox balance; Escherichia
+ coli; Lactococcus lactis; Saccharomyces cerevisiae},
+Keywords-Plus = {ESCHERICHIA-COLI; OVERFLOW METABOLISM; GROWTH; EVOLUTION; MODELS;
+ COMPETITION; GLYCOLYSIS; CONSTRAINT; ENERGETICS; EFFICIENCY},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Merks, Roeland MH/A-2249-2008},
+ORCID-Numbers = {Merks, Roeland MH/0000-0002-6152-687X},
+Times-Cited = {79},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000305757400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000301023700042,
+Author = {Klier, Christine},
+Title = {Use of an Uncertainty Analysis for Genome-Scale Models as a Prediction
+ Tool for Microbial Growth Processes in Subsurface Environments},
+Journal = {ENVIRONMENTAL SCIENCE \& TECHNOLOGY},
+Year = {2012},
+Volume = {46},
+Number = {5},
+Pages = {2790-2798},
+Month = {MAR 6},
+Type = {Article},
+DOI = {10.1021/es203461u},
+ISSN = {0013-936X},
+EISSN = {1520-5851},
+Keywords-Plus = {STABLE-ISOTOPE FRACTIONATION; PSEUDOMONAS-PUTIDA KT2440;
+ GEOBACTER-SULFURREDUCENS; IN-SILICO; BIOAVAILABILITY RESTRICTIONS;
+ METABOLIC RECONSTRUCTION; BIODEGRADATION KINETICS; CATABOLITE
+ REPRESSION; ESCHERICHIA-COLI; TRANSPORT},
+Research-Areas = {Engineering; Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Engineering, Environmental; Environmental Sciences},
+Times-Cited = {7},
+Journal-ISO = {Environ. Sci. Technol.},
+Unique-ID = {WOS:000301023700042},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000300657900025,
+Author = {Boghigian, Brett A. and Armando, John and Salas, Daniel and Pfeifer,
+ Blaine A.},
+Title = {Computational identification of gene over-expression targets for
+ metabolic engineering of taxadiene production},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2012},
+Volume = {93},
+Number = {5},
+Pages = {2063-2073},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1007/s00253-011-3725-1},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Taxol; Taxadiene; Taxadiene synthase; Over-expression; E. coli;
+ Heterologous biosynthesis; Metabolic engineering},
+Keywords-Plus = {ESCHERICHIA-COLI; ISOPRENOID PATHWAY; BACILLUS-SUBTILIS; FLUX ANALYSIS;
+ BIOSYNTHESIS; OVERPRODUCTION; SYNTHASE; OPPORTUNITIES; OPTIMIZATION;
+ DIPHOSPHATE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {38},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000300657900025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302455600003,
+Author = {Chavali, Arvind K. and D'Auria, Kevin M. and Hewlett, Erik L. and
+ Pearson, Richard D. and Papin, Jason A.},
+Title = {A metabolic network approach for the identification and prioritization
+ of antimicrobial drug targets},
+Journal = {TRENDS IN MICROBIOLOGY},
+Year = {2012},
+Volume = {20},
+Number = {3},
+Pages = {113-123},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1016/j.tim.2011.12.004},
+ISSN = {0966-842X},
+EISSN = {1878-4380},
+Keywords-Plus = {FLUX-BALANCE ANALYSIS; GENOME-SCALE RECONSTRUCTION;
+ HAEMOPHILUS-INFLUENZAE RD; ESCHERICHIA-COLI; MYCOBACTERIUM-TUBERCULOSIS;
+ PSEUDOMONAS-AERUGINOSA; SALMONELLA-TYPHIMURIUM; MODEL; HOST;
+ CAPABILITIES},
+Research-Areas = {Biochemistry \& Molecular Biology; Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Microbiology},
+ResearcherID-Numbers = {Chavali, Arvind/L-7157-2016
+ },
+ORCID-Numbers = {Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {71},
+Journal-ISO = {Trends Microbiol.},
+Unique-ID = {WOS:000302455600003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302304400008,
+Author = {Chen, Xuewen and Shachar-Hill, Yair},
+Title = {Insights into metabolic efficiency from flux analysis},
+Journal = {JOURNAL OF EXPERIMENTAL BOTANY},
+Year = {2012},
+Volume = {63},
+Number = {6, SI},
+Pages = {2343-2351},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1093/jxb/ers057},
+ISSN = {0022-0957},
+EISSN = {1460-2431},
+Keywords = {Carbon conversion efficiency; efficiency; metabolic flux analysis; plant
+ metabolism},
+Keywords-Plus = {BALANCE ANALYSIS; VARIABILITY ANALYSIS; DEVELOPING EMBRYOS; STORAGE
+ SYNTHESIS; ARABIDOPSIS; NETWORK; YIELD; MODEL; RECONSTRUCTION; SEEDS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Shachar-Hill, Yair/B-6165-2013},
+ORCID-Numbers = {Shachar-Hill, Yair/0000-0001-8793-5084},
+Times-Cited = {39},
+Journal-ISO = {J. Exp. Bot.},
+Unique-ID = {WOS:000302304400008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302736900004,
+Author = {Ding, De-Wu and Ying, Long},
+Title = {REVISITING MODULES (AND CENTERS) IN STAPHYLOCOCCUS AUREUS
+ METABOLIC NETWORK WITH LINK CLUSTERING},
+Journal = {JOURNAL OF BIOLOGICAL SYSTEMS},
+Year = {2012},
+Volume = {20},
+Number = {1},
+Pages = {57-66},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1142/S021833901150032X},
+ISSN = {0218-3390},
+EISSN = {1793-6470},
+Keywords = {Centrality; Community Structure; Metabolic Network; Link Clustering},
+Keywords-Plus = {COMMUNITY STRUCTURE; RECONSTRUCTION; MODEL},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+Times-Cited = {0},
+Journal-ISO = {J. Biol. Syst.},
+Unique-ID = {WOS:000302736900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000301280500004,
+Author = {Fernie, Alisdair R. and Stitt, Mark},
+Title = {On the Discordance of Metabolomics with Proteomics and Transcriptomics:
+ Coping with Increasing Complexity in Logic, Chemistry, and Network
+ Interactions},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2012},
+Volume = {158},
+Number = {3},
+Pages = {1139-1145},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1104/pp.112.193235},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {HETEROTROPHIC ARABIDOPSIS CELLS; MASS-SPECTROMETRY; ENZYME-ACTIVITIES;
+ DIURNAL CYCLES; CALVIN CYCLE; METABOLITE; SUCROSE; INTEGRATION;
+ THALIANA; REVEALS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Stitt, Mark/GVT-1242-2022
+ fernie, alisdair/IWD-9278-2023
+ },
+ORCID-Numbers = {Stitt, Mark/0000-0002-4900-1763},
+Times-Cited = {151},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000301280500004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000300500100010,
+Author = {Kim, Il-Kwon and Roldao, Antonio and Siewers, Verena and Nielsen, Jens},
+Title = {A systems-level approach for metabolic engineering of yeast cell
+ factories},
+Journal = {FEMS YEAST RESEARCH},
+Year = {2012},
+Volume = {12},
+Number = {2},
+Pages = {228-248},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1111/j.1567-1364.2011.00779.x},
+ISSN = {1567-1356},
+EISSN = {1567-1364},
+Keywords = {metabolic engineering; systems biology; synthetic biology; omics'
+ technologies; Saccharomyces cerevisiae; in silico strain optimization},
+Keywords-Plus = {RIBOSOME ENTRY SITE; IN-VIVO KINETICS; SACCHAROMYCES-CEREVISIAE;
+ GENE-EXPRESSION; DIRECTED EVOLUTION; XYLOSE FERMENTATION; FUNCTIONAL
+ GENOMICS; GLUCOSE REPRESSION; ETHANOL-PRODUCTION; MASS-SPECTROMETRY},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+ResearcherID-Numbers = {Siewers, Verena/AAV-4902-2020
+ Roldao, Antonio/J-2396-2013
+ Nielsen, Jens Bo/C-7632-2015
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Siewers, Verena/0000-0002-9502-9804
+ Roldao, Antonio/0000-0003-0414-4899
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Nielsen, Jens/0000-0002-9955-6003
+ Kim, Il-Kwon/0000-0002-6946-3375},
+Times-Cited = {78},
+Journal-ISO = {FEMS Yeast Res.},
+Unique-ID = {WOS:000300500100010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302304400009,
+Author = {Krumholz, Elias W. and Yang, Hong and Weisenhorn, Pamela and Henry,
+ Christopher S. and Libourel, Igor G. L.},
+Title = {Genome-wide metabolic network reconstruction of the picoalga
+ Ostreococcus},
+Journal = {JOURNAL OF EXPERIMENTAL BOTANY},
+Year = {2012},
+Volume = {63},
+Number = {6, SI},
+Pages = {2353-2362},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1093/jxb/err407},
+ISSN = {0022-0957},
+Keywords = {Gap-filling; metabolic network; network reconstruction; Ostreococcus},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CHLAMYDOMONAS-REINHARDTII; ARABIDOPSIS;
+ ANNOTATION; GENERATION; FEATURES; TOOLBOX; MODELS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+Times-Cited = {32},
+Journal-ISO = {J. Exp. Bot.},
+Unique-ID = {WOS:000302304400009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000300620100011,
+Author = {Medema, Marnix H. and van Raaphorst, Renske and Takano, Eriko and
+ Breitling, Rainer},
+Title = {Computational tools for the synthetic design of biochemical pathways},
+Journal = {NATURE REVIEWS MICROBIOLOGY},
+Year = {2012},
+Volume = {10},
+Number = {3},
+Pages = {191-202},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1038/nrmicro2717},
+ISSN = {1740-1526},
+EISSN = {1740-1534},
+Keywords-Plus = {NOVO BIOSYNTHETIC PATHWAYS; RIBOSOME BINDING-SITES; GENOME-SCALE MODELS;
+ METABOLIC PATHWAYS; GENE SYNTHESIS; ESCHERICHIA-COLI; WEB SERVER;
+ MICROBIAL-PRODUCTION; PROTEIN; BIOLOGY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Medema, Marnix H./AAR-3138-2021
+ },
+ORCID-Numbers = {Medema, Marnix H./0000-0002-2191-2821
+ van Raaphorst, Renske/0000-0001-7778-5289
+ Breitling, Rainer/0000-0001-7173-0922
+ Takano, Eriko/0000-0002-6791-3256},
+Times-Cited = {161},
+Journal-ISO = {Nat. Rev. Microbiol.},
+Unique-ID = {WOS:000300620100011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302607100002,
+Author = {Munro, Sarah A. and Choe, Leila and Zinder, Stephen H. and Lee, Kelvin
+ H. and Walker, Larry P.},
+Title = {Proteomic and physiological experiments to test Thermotoga neapolitana
+ constraint-based model hypotheses of carbon source utilization},
+Journal = {BIOTECHNOLOGY PROGRESS},
+Year = {2012},
+Volume = {28},
+Number = {2},
+Pages = {312-318},
+Month = {MAR-APR},
+Type = {Article},
+DOI = {10.1002/btpr.735},
+ISSN = {8756-7938},
+Keywords = {Thermotoga neapolitana; proteomics; two-dimensional protein
+ electrophoresis; constraint-based model; flux balance analysis; ATP
+ conservation; cellotetraose},
+Keywords-Plus = {CLOSTRIDIUM-THERMOCELLUM; BACTERIUM THERMOTOGA; MARITIMA; TOOLBOX;
+ ARCHAEA},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Lee, Kelvin H./A-4673-2010
+ Crozier, Laura/C-2170-2011},
+ORCID-Numbers = {Lee, Kelvin H./0000-0003-0908-2981
+ },
+Times-Cited = {2},
+Journal-ISO = {Biotechnol. Prog.},
+Unique-ID = {WOS:000302607100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302304400003,
+Author = {Steuer, Ralf and Knoop, Henning and Machne, Rainer},
+Title = {Modelling cyanobacteria: from metabolism to integrative models of
+ phototrophic growth},
+Journal = {JOURNAL OF EXPERIMENTAL BOTANY},
+Year = {2012},
+Volume = {63},
+Number = {6, SI},
+Pages = {2259-2274},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1093/jxb/ers018},
+ISSN = {0022-0957},
+EISSN = {1460-2431},
+Keywords = {Ecosystems biology; flux balance analysis (FBA); network reconstruction;
+ photosynthesis; quantitative modelling; systems biology},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS; SYSTEMS BIOLOGY;
+ CIRCADIAN CLOCK; IN-SILICO; PHOTOAUTOTROPHIC METABOLISM; THERMODYNAMIC
+ CONSTRAINTS; QUANTITATIVE PREDICTION; NETWORK RECONSTRUCTION;
+ BIOCHEMICAL NETWORKS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Machne, Rainer/AAY-2159-2020
+ Machne, Rainer/G-6753-2014
+ Steuer, Ralf/E-7482-2017},
+ORCID-Numbers = {Machne, Rainer/0000-0002-1274-5099
+ Steuer, Ralf/0000-0003-2217-1655},
+Times-Cited = {44},
+Journal-ISO = {J. Exp. Bot.},
+Unique-ID = {WOS:000302304400003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302224200001,
+Author = {Balagurunathan, Balaji and Jonnalagadda, Sudhakar and Tan, Lily and
+ Srinivasan, Rajagopalan},
+Title = {Reconstruction and analysis of a genome-scale metabolic model for
+ Scheffersomyces stipitis},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2012},
+Volume = {11},
+Month = {FEB 23},
+Type = {Article},
+DOI = {10.1186/1475-2859-11-27},
+Article-Number = {27},
+EISSN = {1475-2859},
+Keywords = {Genome scale metabolic models; Scheffersomyces stipitis; Metabolic flux
+ analysis; Xylose utilization; Anaerobic growth},
+Keywords-Plus = {YEAST PICHIA-STIPITIS; CONSTRAINT-BASED MODELS;
+ SACCHAROMYCES-CEREVISIAE; ETHANOL-PRODUCTION; XYLOSE FERMENTATION;
+ HEMICELLULOSE HYDROLYSATE; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ CYTOSOLIC NADPH; GENE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Balagurunathan, Balaji/GXZ-8736-2022
+ Srinivasan, Rajagopalan/B-5322-2010
+ Balagurunathan, Balaji/Q-4282-2016},
+ORCID-Numbers = {Balagurunathan, Balaji/0000-0003-0003-3040
+ Srinivasan, Rajagopalan/0000-0002-8790-4349
+ Balagurunathan, Balaji/0000-0003-0003-3040},
+Times-Cited = {45},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000302224200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000300489200099,
+Author = {Nogales, Juan and Gudmundsson, Steinn and Knight, Eric M. and Palsson,
+ Bernhard O. and Thiele, Ines},
+Title = {Detailing the optimality of photosynthesis in cyanobacteria through
+ systems biology analysis},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2012},
+Volume = {109},
+Number = {7},
+Pages = {2678-2683},
+Month = {FEB 14},
+Type = {Article},
+DOI = {10.1073/pnas.1117907109},
+ISSN = {0027-8424},
+Keywords = {constraint-based modeling; photobioenergetic; metabolic engineering;
+ biosustainability; metabolic robustness},
+Keywords-Plus = {SP STRAIN PCC-6803; SP PCC 6803; NITRATE ASSIMILATION; PHOTOSYSTEM-I;
+ SYNECHOCYSTIS; METABOLISM; BALANCE; PREDICTION; EVOLUTION; PATHWAYS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Nogales, Juan/0000-0002-4961-0833},
+Times-Cited = {221},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000300489200099},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000299966000011,
+Author = {Benedict, Matthew N. and Gonnerman, Matthew C. and Metcalf, William W.
+ and Price, Nathan D.},
+Title = {Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the
+ Methanogenic Archaeon Methanosarcina acetivorans C2A},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2012},
+Volume = {194},
+Number = {4},
+Pages = {855-865},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1128/JB.06040-11},
+ISSN = {0021-9193},
+EISSN = {1098-5530},
+Keywords-Plus = {GENETIC-ANALYSIS; CARBON-MONOXIDE; ENERGY-CONSERVATION;
+ KINETIC-PROPERTIES; NA+/H+ ANTIPORTER; ECH HYDROGENASE; METHANE;
+ BARKERI; GROWTH; REVEALS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {58},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000299966000011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000299157900004,
+Author = {Bordbar, A. and Palsson, B. O.},
+Title = {Using the reconstructed genome-scale human metabolic network to study
+ physiology and pathology},
+Journal = {JOURNAL OF INTERNAL MEDICINE},
+Year = {2012},
+Volume = {271},
+Number = {2},
+Pages = {131-141},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1111/j.1365-2796.2011.02494.x},
+ISSN = {0954-6820},
+EISSN = {1365-2796},
+Keywords = {constraints-based modelling; human metabolism; systems biology},
+Keywords-Plus = {IN-SILICO; SALMONELLA-TYPHIMURIUM; MATHEMATICAL-MODEL; COMMUNITY
+ APPROACH; GENE-EXPRESSION; CONSTRAINT; CELL; PREDICTION; CANCER;
+ ANNOTATION},
+Research-Areas = {General \& Internal Medicine},
+Web-of-Science-Categories = {Medicine, General \& Internal},
+ResearcherID-Numbers = {/AAG-5264-2021
+ },
+ORCID-Numbers = {/0000-0001-6460-6771
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {80},
+Journal-ISO = {J. Intern. Med.},
+Unique-ID = {WOS:000299157900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000300043200013,
+Author = {Latendresse, Mario and Krummenacker, Markus and Trupp, Miles and Karp,
+ Peter D.},
+Title = {Construction and completion of flux balance models from pathway
+ databases},
+Journal = {BIOINFORMATICS},
+Year = {2012},
+Volume = {28},
+Number = {3},
+Pages = {388-396},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btr681},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {OPTIMIZATION; METABOLISM; GENERATION; SOFTWARE; CHOLINE; BETAINE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Latendresse, Mario/C-9192-2014
+ Karp, Peter/C-3514-2012},
+ORCID-Numbers = {Latendresse, Mario/0000-0002-6292-0158
+ Karp, Peter/0000-0002-5876-6418},
+Times-Cited = {59},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000300043200013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000300041600011,
+Author = {Vardi, Liram and Ruppin, Eytan and Sharan, Roded},
+Title = {A Linearized Constraint-Based Approach for Modeling Signaling Networks},
+Journal = {JOURNAL OF COMPUTATIONAL BIOLOGY},
+Year = {2012},
+Volume = {19},
+Number = {2, SI},
+Pages = {232-240},
+Month = {FEB},
+Note = {Joint RECOMB Conference on Systems Biology, Regulatory Genomics/DREAM
+ Challenges, Barcelona, SPAIN, OCT 14-19, 2011},
+Type = {Article; Proceedings Paper},
+DOI = {10.1089/cmb.2011.0277},
+ISSN = {1066-5277},
+EISSN = {1557-8666},
+Keywords = {biochemical networks; linear programming},
+Keywords-Plus = {TOPOLOGICAL ANALYSIS; RECONSTRUCTION; FRAMEWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Ruppin, Eytan/R-9698-2017},
+ORCID-Numbers = {Ruppin, Eytan/0000-0002-7862-3940},
+Times-Cited = {9},
+Journal-ISO = {J. Comput. Biol.},
+Unique-ID = {WOS:000300041600011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000301977500033,
+Author = {Zhao, Hansheng and Li, Mao and Fang, Kechi and Chen, Wenfeng and Wang,
+ Jing},
+Title = {In Silico Insights into the Symbiotic Nitrogen Fixation in
+ Sinorhizobium meliloti via Metabolic Reconstruction},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {2},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1371/journal.pone.0031287},
+Article-Number = {e31287},
+ISSN = {1932-6203},
+Keywords-Plus = {RHIZOBIUM-MELILOTI; FUNCTIONAL-CHARACTERIZATION; NUCLEOTIDE-SEQUENCE;
+ ROOT-NODULE; LEGUME; GENES; ALFALFA; TRANSPORT; DATABASE; MUTANTS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Zhang, Liqun/JDN-3523-2023
+ zhao, hansheng/GRS-2764-2022
+ Fang, Kechi/D-9994-2011},
+Times-Cited = {21},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000301977500033},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000302645600001,
+Author = {Boele, Joost and Olivier, Brett G. and Teusink, Bas},
+Title = {FAME, the Flux Analysis and Modeling Environment},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2012},
+Volume = {6},
+Month = {JAN 30},
+Type = {Article},
+DOI = {10.1186/1752-0509-6-8},
+Article-Number = {8},
+EISSN = {1752-0509},
+Keywords-Plus = {BIDIRECTIONAL REACTION STEPS; ISOTOPOMER DISTRIBUTIONS; METABOLIC
+ NETWORKS; HIGH-THROUGHPUT; SCALE MODELS; IDENTIFICATION; ELUCIDATION;
+ FRAMEWORK; PROTOCOL},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Reed, Jennifer L/E-5137-2011
+ Olivier, Brett G/A-2800-2008
+ },
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220
+ Olivier, Brett G/0000-0002-5293-5321
+ Teusink, Bas/0000-0003-3929-0423
+ Boele, Joost/0000-0002-7183-9650},
+Times-Cited = {58},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000302645600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000301639600043,
+Author = {Belda, Eugeni and Silva, Francisco J. and Pereto, Juli and Moya, Andres},
+Title = {Metabolic Networks of Sodalis glossinidius: A Systems Biology
+ Approach to Reductive Evolution},
+Journal = {PLOS ONE},
+Year = {2012},
+Volume = {7},
+Number = {1},
+Month = {JAN 24},
+Type = {Article},
+DOI = {10.1371/journal.pone.0030652},
+Article-Number = {e30652},
+ISSN = {1932-6203},
+Keywords-Plus = {MINIMAL-GENE-SET; ESCHERICHIA-COLI; GENOME SEQUENCE; SECONDARY
+ ENDOSYMBIONT; MICROBIAL GENOME; SCALE; SYMBIONT; ENZYME; DNA;
+ RECONSTRUCTION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Silva, Francisco/ABF-7144-2021
+ Belda, Eugeni/ABI-1349-2020
+ Peretó, Juli/G-5969-2015
+ Moya, Andrés/A-8190-2008},
+ORCID-Numbers = {Silva, Francisco/0000-0002-6911-6541
+ Belda, Eugeni/0000-0003-4307-5072
+ Peretó, Juli/0000-0002-5756-1517
+ Moya, Andrés/0000-0002-2867-1119},
+Times-Cited = {20},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000301639600043},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000304083500005,
+Author = {Maria Gonzalez-Domenech, Carmen and Belda, Eugeni and Patino-Navarrete,
+ Rafael and Moya, Andres and Pereto, Juli and Latorre, Amparo},
+Title = {Metabolic stasis in an ancient symbiosis: genome-scale metabolic
+ networks from two Blattabacterium cuenoti strains, primary
+ endosymbionts of cockroaches},
+Journal = {BMC MICROBIOLOGY},
+Year = {2012},
+Volume = {12},
+Number = {1},
+Month = {JAN 18},
+Type = {Article},
+DOI = {10.1186/1471-2180-12-S1-S5},
+Article-Number = {S5},
+ISSN = {1471-2180},
+Keywords-Plus = {NITROGEN-EXCRETION; AMERICAN COCKROACH; FAT-BODY; RECONSTRUCTION;
+ EVOLUTION; MODELS; SMART},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Patiño-Navarrete, Rafael/AAD-6682-2019
+ Latorre, Amparo/E-4997-2015
+ Domenech, Carmen Maria Gonzalez/F-6068-2019
+ Belda, Eugeni/ABI-1349-2020
+ Peretó, Juli/G-5969-2015
+ Moya, Andrés/A-8190-2008},
+ORCID-Numbers = {Patiño-Navarrete, Rafael/0000-0003-4226-8374
+ Latorre, Amparo/0000-0002-9146-7284
+ Domenech, Carmen Maria Gonzalez/0000-0001-8248-3904
+ Belda, Eugeni/0000-0003-4307-5072
+ Peretó, Juli/0000-0002-5756-1517
+ Moya, Andrés/0000-0002-2867-1119},
+Times-Cited = {26},
+Journal-ISO = {BMC Microbiol.},
+Unique-ID = {WOS:000304083500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000299913800009,
+Author = {Metris, Aline and George, Susan and Baranyi, Jozsef},
+Title = {Modelling osmotic stress by Flux Balance Analysis at the genomic scale},
+Journal = {INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY},
+Year = {2012},
+Volume = {152},
+Number = {3, SI},
+Pages = {123-128},
+Month = {JAN 16},
+Note = {22nd Symposium of the International Committee on Food Microbiology and
+ Hygiene (ICFMH) on Microbial Behaviour in the Food Chain (Food Micro),
+ Copenhagen, DENMARK, AUG 30-SEP 03, 2010},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.ijfoodmicro.2011.06.016},
+ISSN = {0168-1605},
+EISSN = {1879-3460},
+Keywords = {Food safety; Predictive microbiology; Flux Balance Analysis; Osmotic
+ stress; Growth rate},
+Keywords-Plus = {ESCHERICHIA-COLI; GENE-EXPRESSION; GLYCINE BETAINE; GROWTH;
+ OSMOREGULATION; BIOSYNTHESIS; WATER; CELL},
+Research-Areas = {Food Science \& Technology; Microbiology},
+Web-of-Science-Categories = {Food Science \& Technology; Microbiology},
+ResearcherID-Numbers = {George, Susan/W-7494-2019
+ Baranyi, Jozsef/A-7531-2008
+ },
+ORCID-Numbers = {Baranyi, Jozsef/0000-0001-8360-6021
+ Metris, Aline/0000-0002-9725-5178},
+Times-Cited = {9},
+Journal-ISO = {Int. J. Food Microbiol.},
+Unique-ID = {WOS:000299913800009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000297450100008,
+Author = {Fleming, R. M. T. and Maes, C. M. and Saunders, M. A. and Ye, Y. and
+ Palsson, B. O.},
+Title = {A variational principle for computing nonequilibrium fluxes and
+ potentials in genome-scale biochemical networks},
+Journal = {JOURNAL OF THEORETICAL BIOLOGY},
+Year = {2012},
+Volume = {292},
+Pages = {71-77},
+Month = {JAN 7},
+Type = {Article},
+DOI = {10.1016/j.jtbi.2011.09.029},
+ISSN = {0022-5193},
+Keywords = {Constraint-based modeling; Flux balance analysis; Thermodynamics; Convex
+ optimization; Entropy function},
+Keywords-Plus = {COMPLEX METABOLIC NETWORKS; THERMODYNAMIC ANALYSIS; ESCHERICHIA-COLI;
+ KINETIC-MODELS; OPTIMIZATION; BALANCE; ENERGY; PREDICTION; PATHWAYS;
+ SYSTEMS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Saunders, Michael A/D-1083-2012
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Palsson, Bernhard/0000-0003-2357-6785
+ Saunders, Michael/0000-0003-3800-4982},
+Times-Cited = {24},
+Journal-ISO = {J. Theor. Biol.},
+Unique-ID = {WOS:000297450100008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000298756500013,
+Author = {Assary, Rajeev Surendran and Broadbelt, Linda J. and Curtiss, Larry A.},
+Title = {Bronsted-Evans-Polanyi relationships for C-C bond forming and C-C bond
+ breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids
+ using density functional theory},
+Journal = {JOURNAL OF MOLECULAR MODELING},
+Year = {2012},
+Volume = {18},
+Number = {1},
+Pages = {145-150},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1007/s00894-011-1062-z},
+ISSN = {1610-2940},
+EISSN = {0948-5023},
+Keywords = {Enzyme catalysis; BEP relationship; Density functional theory},
+Keywords-Plus = {GENOME-SCALE MODEL; THERMODYNAMIC ANALYSIS; ENERGIES; RECONSTRUCTION;
+ NETWORKS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Chemistry; Computer
+ Science},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics; Chemistry,
+ Multidisciplinary; Computer Science, Interdisciplinary Applications},
+ResearcherID-Numbers = {Assary, Rajeev Surendran/E-6833-2012
+ Broadbelt, Linda/B-7640-2009},
+ORCID-Numbers = {Assary, Rajeev Surendran/0000-0002-9571-3307
+ },
+Times-Cited = {5},
+Journal-ISO = {J. Mol. Model.},
+Unique-ID = {WOS:000298756500013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000208863600214,
+Author = {Dandekar, Thomas and Fieselmann, Astrid and Popp, Jasmin and Hensel,
+ Michael},
+Title = {Salmonella enterica: a surprisingly well-adapted intracellular
+ lifestyle},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2012},
+Volume = {3},
+Type = {Review},
+DOI = {10.3389/fmicb.2012.00164},
+Article-Number = {164},
+EISSN = {1664-302X},
+Keywords = {metabolism; Salmonella-containing vacuole; regulation; virulence},
+Keywords-Plus = {CARBON METABOLISM; SEROVAR TYPHIMURIUM; ESCHERICHIA-COLI; VIRULENCE;
+ GENOME; INFECTION; GENE; MUTANTS; GLUCOSE; METHYLGLYOXAL},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Dandekar, Thomas/A-4431-2017
+ },
+ORCID-Numbers = {Dandekar, Thomas/0000-0003-1886-7625
+ Hensel, Michael/0000-0001-6604-6253},
+Times-Cited = {45},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000208863600214},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000321104000005,
+Author = {Gerdtzen, Ziomara P.},
+Editor = {Hu, WS and Zeng, AP},
+Title = {Modeling Metabolic Networks for Mammalian Cell Systems: General
+ Considerations, Modeling Strategies, and Available Tools},
+Booktitle = {GENOMICS AND SYSTEMS BIOLOGY OF MAMMALIAN CELL CULTURE},
+Series = {Advances in Biochemical Engineering-Biotechnology},
+Year = {2012},
+Volume = {127},
+Pages = {71-108},
+Type = {Article; Book Chapter},
+DOI = {10.1007/10\_2011\_120},
+ISSN = {0724-6145},
+EISSN = {1616-8542},
+ISBN = {978-3-642-28350-5; 978-3-642-28349-9},
+Keywords = {Mammalian cell models; Metabolic networks; Systems biology},
+Keywords-Plus = {FLUX ANALYSIS; CHO-CELLS; SACCHAROMYCES-CEREVISIAE; DYNAMIC SIMULATION;
+ BIOCYC COLLECTION; MARKUP LANGUAGE; GENOME; DATABASE; GROWTH; BIOLOGY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Gerdtzen, Ziomara P/H-2711-2013},
+ORCID-Numbers = {Gerdtzen, Ziomara P/0000-0002-7486-8537},
+Times-Cited = {9},
+Journal-ISO = {Adv. Biochem. Eng. Biotechnol.},
+Unique-ID = {WOS:000321104000005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000313182600007,
+Author = {Kim, Joonhoon and Reed, Jennifer L.},
+Title = {RELATCH: relative optimality in metabolic networks explains robust
+ metabolic and regulatory responses to perturbations},
+Journal = {GENOME BIOLOGY},
+Year = {2012},
+Volume = {13},
+Number = {9},
+Type = {Article},
+DOI = {10.1186/gb-2012-13-9-r78},
+Article-Number = {R78},
+ISSN = {1474-7596},
+Keywords-Plus = {ESCHERICHIA-COLI K-12; GENOME-SCALE RECONSTRUCTION; BACILLUS-SUBTILIS;
+ HIGH-THROUGHPUT; SACCHAROMYCES-CEREVISIAE; OPTIMAL-GROWTH; GENE
+ KNOCKOUT; EXPRESSION; FLUXES; PREDICTION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Reed, Jennifer L/E-5137-2011
+ Kim, Joonhoon/E-6253-2012},
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220
+ Kim, Joonhoon/0000-0002-7425-1828},
+Times-Cited = {64},
+Journal-ISO = {Genome Biol.},
+Unique-ID = {WOS:000313182600007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000301124600026,
+Author = {Ma, Jing and Zhang, Xun and Ung, Choong Yong and Chen, Yu Zong and Li,
+ Baowen},
+Title = {Metabolic network analysis revealed distinct routes of deletion effects
+ between essential and non-essential genes},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2012},
+Volume = {8},
+Number = {4},
+Pages = {1179-1186},
+Type = {Article},
+DOI = {10.1039/c2mb05376d},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {KNOCKOUT ESCHERICHIA-COLI; ROBUSTNESS; EXPRESSION; IDENTIFICATION;
+ CONSTRUCTION; EPISTASIS; GENOMICS; PATHWAY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {chen, yu-cheng/IQT-1648-2023
+ Li, Baowen/G-3003-2011
+ Chen, Yu-Cheng/ISS-5682-2023
+ Ung, Choong Yong/D-4525-2012
+ },
+ORCID-Numbers = {Li, Baowen/0000-0002-8728-520X
+ Chen, Yu-Cheng/0000-0003-1696-4667
+ Chen, Yu Zong/0000-0002-5473-8022},
+Times-Cited = {5},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000301124600026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000308098600011,
+Author = {Sahoo, Swagatika and Franzson, Leifur and Jonsson, Jon J. and Thiele,
+ Ines},
+Title = {A compendium of inborn errors of metabolism mapped onto the human
+ metabolic network},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2012},
+Volume = {8},
+Number = {10},
+Pages = {2545-2558},
+Type = {Article},
+DOI = {10.1039/c2mb25075f},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {GLYCOGEN-SYNTHASE DEFICIENCY; PEROXISOMAL BETA-OXIDATION; COBRA TOOLBOX
+ EXTENSION; RENAL TUBULAR-ACIDOSIS; SYRUP-URINE-DISEASE; ACIDURIA TYPE-I;
+ MASS-SPECTROMETRY; TAY-SACHS; BIOCHEMICAL NETWORKS; CELLULAR-METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Sahoo, Swagatika/0000-0003-3773-8597},
+Times-Cited = {50},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000308098600011},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000333844000003,
+Author = {Wagner, Andreas},
+Editor = {Soyer, OS},
+Title = {Metabolic Networks and Their Evolution},
+Booktitle = {EVOLUTIONARY SYSTEMS BIOLOGY},
+Series = {Advances in Experimental Medicine and Biology},
+Year = {2012},
+Volume = {751},
+Pages = {29-52},
+Type = {Article; Book Chapter},
+DOI = {10.1007/978-1-4614-3567-9\_2},
+ISSN = {0065-2598},
+EISSN = {2214-8019},
+ISBN = {978-1-4614-3566-2; 978-1-4614-3567-9},
+Keywords-Plus = {HORIZONTAL GENE-TRANSFER; CITRIC-ACID CYCLE; ESCHERICHIA-COLI; MOLECULAR
+ EVOLUTION; ADAPTIVE EVOLUTION; GENOME SEQUENCE; FLUX ANALYSIS; PATHWAY;
+ ROBUSTNESS; GENOTYPE},
+Research-Areas = {Evolutionary Biology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Evolutionary Biology; Medicine, Research \& Experimental},
+Times-Cited = {26},
+Journal-ISO = {Adv.Exp.Med.Biol.},
+Unique-ID = {WOS:000333844000003},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000301839600018,
+Author = {Xie, Lei and Xie, Li and Kinnings, Sarah L. and Bourne, Philip E.},
+Editor = {Insel, PA and Amara, SG and Blaschke, TF},
+Title = {Novel Computational Approaches to Polypharmacology as a Means to Define
+ Responses to Individual Drugs},
+Booktitle = {ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 52},
+Series = {Annual Review of Pharmacology and Toxicology},
+Year = {2012},
+Volume = {52},
+Pages = {361+},
+Type = {Review; Book Chapter},
+DOI = {10.1146/annurev-pharmtox-010611-134630},
+ISSN = {0362-1642},
+EISSN = {1545-4304},
+ISBN = {978-0-8243-0452-2},
+Keywords = {protein-ligand interaction; drug-target network; in vivo efficacy;
+ dynamic simulation; metabolic modeling},
+Keywords-Plus = {PROTEIN-LIGAND-BINDING; MOLECULAR-DYNAMICS SIMULATIONS; ULTRAFAST
+ SHAPE-RECOGNITION; TARGET INTERACTION NETWORKS; IN-SILICO PREDICTION;
+ GENE-EXPRESSION; FREE-ENERGY; INTERACTION FINGERPRINT; QUANTITATIVE
+ PREDICTION; STRUCTURAL GENOMICS},
+Research-Areas = {Pharmacology \& Pharmacy; Toxicology},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy; Toxicology},
+ResearcherID-Numbers = {Bourne, Philip/ABG-8967-2021},
+ORCID-Numbers = {Bourne, Philip/0000-0002-7618-7292},
+Times-Cited = {163},
+Journal-ISO = {Annu. Rev. Pharmacol. Toxicol.},
+Unique-ID = {WOS:000301839600018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000298121600021,
+Author = {Assary, Rajeev S. and Broadbelt, Linda J.},
+Title = {2-Keto acids to branched-chain alcohols as biofuels: Application of
+ reaction network analysis and high-level quantum chemical methods to
+ understand thermodynamic landscapes},
+Journal = {COMPUTATIONAL AND THEORETICAL CHEMISTRY},
+Year = {2011},
+Volume = {978},
+Number = {1-3},
+Pages = {160-165},
+Month = {DEC 30},
+Type = {Article},
+DOI = {10.1016/j.comptc.2011.10.009},
+ISSN = {2210-271X},
+EISSN = {1872-7999},
+Keywords = {Reaction network; ABE fermentation; Ehrlich's pathways; Thermochemistry;
+ G3B3},
+Keywords-Plus = {GENOME-SCALE MODEL; RECONSTRUCTION; GENERATION; ENERGIES; PATHWAYS;
+ DESIGN},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Physical},
+ResearcherID-Numbers = {Assary, Rajeev Surendran/E-6833-2012
+ Broadbelt, Linda/B-7640-2009},
+ORCID-Numbers = {Assary, Rajeev Surendran/0000-0002-9571-3307
+ },
+Times-Cited = {3},
+Journal-ISO = {Comput. Theor. Chem.},
+Unique-ID = {WOS:000298121600021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000303921800005,
+Author = {Dal'Molin, Cristiana Gomes de Oliveira and Quek, Lake-Ee and Palfreyman,
+ Robin W. and Nielsen, Lars K.},
+Title = {AlgaGEM - a genome-scale metabolic reconstruction of algae based on the
+ Chlamydomonas reinhardtii genome},
+Journal = {BMC GENOMICS},
+Year = {2011},
+Volume = {12},
+Number = {4},
+Month = {DEC 22},
+Note = {6th International Conference of the
+ Brazilian-Association-for-Bioinformatics-and-Computational-Biology
+ (X-meeting), Ouro Preto, BRAZIL, NOV 15-18, 2010},
+Type = {Article; Proceedings Paper},
+DOI = {10.1186/1471-2164-12-S4-S5},
+Article-Number = {S5},
+ISSN = {1471-2164},
+Keywords-Plus = {HYDROGEN-PRODUCTION; GLYCOLATE DEHYDROGENASE; GREEN-ALGAE; SYSTEMS
+ BIOLOGY; NETWORK; FLUX; LOCALIZATION; PATHWAYS; DATABASE; GENE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Palfreyman, Robin W/V-8516-2017
+ Nielsen, Lars K/A-5519-2011
+ },
+ORCID-Numbers = {Palfreyman, Robin W/0000-0002-1088-7069
+ Nielsen, Lars K/0000-0001-8191-3511
+ Quek, Lake-Ee/0000-0002-9313-8740},
+Times-Cited = {93},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000303921800005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000301741200001,
+Author = {Jamshidi, Neema and Miller, Franklin J. and Mandel, Jess and Evans,
+ Timothy and Kuo, Michael D.},
+Title = {Individualized therapy of HHT driven by network analysis of metabolomic
+ profiles},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {DEC 20},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-200},
+Article-Number = {200},
+ISSN = {1752-0509},
+Keywords-Plus = {ENDOTHELIAL GROWTH-FACTOR; HEREDITARY HEMORRHAGIC TELANGIECTASIA; FLUX
+ BALANCE ANALYSIS; GENOME-SCALE; ESCHERICHIA-COLI; MODELS;
+ RECONSTRUCTION; BIOLOGY},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Mandel, Jess/0000-0002-2658-6025
+ Jamshidi, Neema/0000-0003-3857-9735},
+Times-Cited = {15},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000301741200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000297958600005,
+Author = {Zhao, Yuqi and Huang, Jingfei},
+Title = {Reconstruction and analysis of human heart-specific metabolic network
+ based on transcriptome and proteome data},
+Journal = {BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS},
+Year = {2011},
+Volume = {415},
+Number = {3},
+Pages = {450-454},
+Month = {NOV 25},
+Type = {Article},
+DOI = {10.1016/j.bbrc.2011.10.090},
+ISSN = {0006-291X},
+EISSN = {1090-2104},
+Keywords = {Metabolic network; Heart-specific model; Flux balance analysis;
+ Biomarkers for cardiovascular disease; Selective drug targets},
+Keywords-Plus = {DISEASE; RISK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ResearcherID-Numbers = {huang, jing/JDC-2548-2023
+ Zhao, Yuqi/L-5639-2016
+ },
+ORCID-Numbers = {Zhao, Yuqi/0000-0003-0730-5854
+ Zhao, Yuqi/0000-0002-4256-4512},
+Times-Cited = {22},
+Journal-ISO = {Biochem. Biophys. Res. Commun.},
+Unique-ID = {WOS:000297958600005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000297198200064,
+Author = {Ghosh, Amit and Zhao, Huimin and Price, Nathan D.},
+Title = {Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose
+ Utilization Pathways in Saccharomyces cerevisiae},
+Journal = {PLOS ONE},
+Year = {2011},
+Volume = {6},
+Number = {11},
+Month = {NOV 4},
+Type = {Article},
+DOI = {10.1371/journal.pone.0027316},
+Article-Number = {e27316},
+ISSN = {1932-6203},
+Keywords-Plus = {XYLOSE ISOMERASE PATHWAYS; METABOLIC NETWORK; XYLITOL DEHYDROGENASE;
+ ESCHERICHIA-COLI; SYSTEMS BIOLOGY; PICHIA-STIPITIS; FERMENTATION;
+ ETHANOL; ARABINOSE; REDUCTASE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Ghosh, Amit/AAA-3490-2021
+ },
+ORCID-Numbers = {Ghosh, Amit/0000-0003-3514-885X
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {40},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000297198200064},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000296128300034,
+Author = {Leppavuori, Juha T. and Domach, Michael M. and Biegler, Lorenz T.},
+Title = {Parameter Estimation in Batch Bioreactor Simulation Using Metabolic
+ Models: Sequential Solution with Direct Sensitivities},
+Journal = {INDUSTRIAL \& ENGINEERING CHEMISTRY RESEARCH},
+Year = {2011},
+Volume = {50},
+Number = {21},
+Pages = {12080-12091},
+Month = {NOV 2},
+Type = {Article},
+DOI = {10.1021/ie201020g},
+ISSN = {0888-5885},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ETHANOL-PRODUCTION; NETWORKS; FERMENTATION;
+ OPTIMIZATION; GROWTH; STATE},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ORCID-Numbers = {Biegler, Lorenz/0000-0003-3875-4441},
+Times-Cited = {16},
+Journal-ISO = {Ind. Eng. Chem. Res.},
+Unique-ID = {WOS:000296128300034},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000297698400001,
+Author = {Baumler, David J. and Peplinski, Roman G. and Reed, Jennifer L. and
+ Glasner, Jeremy D. and Perna, Nicole T.},
+Title = {The evolution of metabolic networks of E. coli},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {NOV 1},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-182},
+Article-Number = {182},
+EISSN = {1752-0509},
+Keywords-Plus = {COMPLETE GENOME SEQUENCE; PHENYLACETIC ACID DEGRADATION;
+ ESCHERICHIA-COLI; MENAQUINONE BIOSYNTHESIS; SALMONELLA-TYPHIMURIUM;
+ CRYSTAL-STRUCTURE; HIGH-THROUGHPUT; GENE; RECONSTRUCTION; IDENTIFICATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Reed, Jennifer L/E-5137-2011
+ },
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220
+ Perna, Nicole/0000-0001-8208-0929},
+Times-Cited = {51},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000297698400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000296821900003,
+Author = {Fernandes, R. Lencastre and Nierychlo, M. and Lundin, L. and Pedersen,
+ A. E. and Tellez, P. E. Puentes and Dutta, A. and Carlquist, M. and
+ Bolic, A. and Schapper, D. and Brunetti, A. C. and Helmark, S. and
+ Heins, A. -L and Jensen, A. D. and Nopens, I. and Rottwitt, K. and
+ Szita, N. and van Elsas, J. D. and Nielsen, P. H. and Martinussen, J.
+ and Sorensen, S. J. and Lantz, A. E. and Gernaey, K. V.},
+Title = {Experimental methods and modeling techniques for description of cell
+ population heterogeneity},
+Journal = {BIOTECHNOLOGY ADVANCES},
+Year = {2011},
+Volume = {29},
+Number = {6},
+Pages = {575-599},
+Month = {NOV-DEC},
+Type = {Review},
+DOI = {10.1016/j.biotechadv.2011.03.007},
+ISSN = {0734-9750},
+EISSN = {1873-1899},
+Keywords = {Cell heterogeneity; Reporter systems; Flow cytometry; Microscopy; Raman
+ spectroscopy; Microbioreactors; Population balance models; Computational
+ fluid dynamics},
+Keywords-Plus = {GREEN-FLUORESCENT PROTEIN; IN-SITU HYBRIDIZATION; COMPUTATIONAL
+ FLUID-DYNAMICS; TETRAZOLIUM CHLORIDE REDUCTION; TRANSIENT MICROBIAL
+ PROCESSES; DIFFERENTIAL GENE-EXPRESSION; FLOW-CYTOMETRIC TECHNIQUES;
+ FED-BATCH FERMENTATIONS; PROBE-DEFINED BACTERIA; ESCHERICHIA-COLI},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sørensen, Søren Johannes/N-2120-2019
+ Lantz, Anna Eliasson/G-8569-2012
+ Dutta, Abhishek/ABB-7958-2020
+ Gernaey, Krist V./J-1759-2018
+ Dutta, Abhishek/HHS-7245-2022
+ Martinussen, Jan/I-4738-2013
+ Rottwitt, Karsten/D-5466-2009
+ nopens, ingmar/H-5614-2011
+ Dutta, Abhishek/A-7039-2010
+ Nielsen, Per Halkjær/T-6796-2018
+ Sørensen, Søren J/J-5015-2014
+ },
+ORCID-Numbers = {Sørensen, Søren Johannes/0000-0001-6227-9906
+ Lantz, Anna Eliasson/0000-0003-1547-9299
+ Dutta, Abhishek/0000-0002-0714-1119
+ Gernaey, Krist V./0000-0002-0364-1773
+ Martinussen, Jan/0000-0001-6223-9322
+ Rottwitt, Karsten/0000-0001-6738-5847
+ nopens, ingmar/0000-0001-6670-3700
+ Dutta, Abhishek/0000-0002-0714-1119
+ Nielsen, Per Halkjær/0000-0002-6402-1877
+ Sørensen, Søren J/0000-0001-6227-9906
+ Nierychlo, Marta/0000-0003-1756-3726
+ Carlquist, Magnus/0000-0001-8881-8197
+ Jensen, Anker Degn/0000-0002-7341-4859},
+Times-Cited = {86},
+Journal-ISO = {Biotechnol. Adv.},
+Unique-ID = {WOS:000296821900003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000297666400001,
+Author = {Metris, Aline and Reuter, Mark and Gaskin, Duncan J. H. and Baranyi,
+ Jozsef and van Vliet, Arnoud H. M.},
+Title = {In vivo and in silico determination of essential genes of
+ Campylobacter jejuni},
+Journal = {BMC GENOMICS},
+Year = {2011},
+Volume = {12},
+Month = {NOV 1},
+Type = {Article},
+DOI = {10.1186/1471-2164-12-535},
+Article-Number = {535},
+ISSN = {1471-2164},
+Keywords-Plus = {SCALE METABOLIC RECONSTRUCTION; SIGNATURE-TAGGED MUTAGENESIS;
+ PROTEIN-INTERACTION MAP; ANTIMICROBIAL RESISTANCE; GENOME ANNOTATION;
+ RETAIL CHICKEN; ACID; GROWTH; REVEALS; PATHWAY},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Baranyi, Jozsef/A-7531-2008
+ van Vliet, Arnoud HM/B-5155-2013
+ },
+ORCID-Numbers = {Baranyi, Jozsef/0000-0001-8360-6021
+ Metris, Aline/0000-0002-9725-5178
+ van Vliet, Arnoud/0000-0003-0203-1305},
+Times-Cited = {35},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000297666400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000298387100005,
+Author = {Navid, Ali},
+Title = {Applications of system-level models of metabolism for analysis of
+ bacterial physiology and identification of new drug targets},
+Journal = {BRIEFINGS IN FUNCTIONAL GENOMICS},
+Year = {2011},
+Volume = {10},
+Number = {6, SI},
+Pages = {354-364},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1093/bfgp/elr034},
+ISSN = {2041-2649},
+EISSN = {2041-2657},
+Keywords = {flux balance analysis; systems biology; drug target identification;
+ bacterial metabolism; constraint-based modeling},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; HAEMOPHILUS-INFLUENZAE RD; FLUX-BALANCE
+ ANALYSIS; ESCHERICHIA-COLI; PSEUDOMONAS-AERUGINOSA; OPTIMIZATION
+ FRAMEWORK; NETWORK RECONSTRUCTION; BIOMASS COMPOSITION; OVERPRODUCTION;
+ CAPABILITIES},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Navid, Ali/A-1336-2013},
+ORCID-Numbers = {Navid, Ali/0000-0003-2560-6984},
+Times-Cited = {8},
+Journal-ISO = {Brief. Funct. Genomics},
+Unique-ID = {WOS:000298387100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000297122500001,
+Author = {Bordbar, Aarash and Feist, Adam M. and Usaite-Black, Renata and
+ Woodcock, Joseph and Palsson, Bernhard O. and Famili, Iman},
+Title = {A multi-tissue type genome-scale metabolic network for analysis of
+ whole-body systems physiology},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {OCT 31},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-180},
+Article-Number = {180},
+EISSN = {1752-0509},
+Keywords-Plus = {RECONSTRUCTION; OBESITY; MUSCLE; MODEL; PREDICTION; TAURINE; PLASMA;
+ RISK; MASS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {/AAG-5264-2021
+ },
+ORCID-Numbers = {/0000-0001-6460-6771
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {130},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000297122500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000296693500001,
+Author = {Tzamali, Eleftheria and Poirazi, Panayiota and Tollis, Ioannis G. and
+ Reczko, Martin},
+Title = {A computational exploration of bacterial metabolic diversity identifying
+ metabolic interactions and growth-efficient strain communities},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {OCT 18},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-167},
+Article-Number = {167},
+EISSN = {1752-0509},
+Keywords-Plus = {ESCHERICHIA-COLI; EVOLUTIONARY DYNAMICS; COOPERATION; MODELS; GAME;
+ FLUXES; MAINTENANCE; COEXISTENCE; CHEMOSTAT; NETWORKS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Reczko, Martin/O-8935-2019
+ },
+ORCID-Numbers = {Reczko, Martin/0000-0002-0005-8718
+ Poirazi, Panayiota/0000-0001-6152-595X},
+Times-Cited = {33},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000296693500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000297165700001,
+Author = {Charusanti, Pep and Chauhan, Sadhana and McAteer, Kathleen and Lerman,
+ Joshua A. and Hyduke, Daniel R. and Motin, Vladimir L. and Ansong,
+ Charles and Adkins, Joshua N. and Palsson, Bernhard O.},
+Title = {An experimentally-supported genome-scale metabolic network
+ reconstruction for Yersinia pestis CO92},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {OCT 13},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-163},
+Article-Number = {163},
+EISSN = {1752-0509},
+Keywords-Plus = {LOW-CALCIUM RESPONSE; PHYSIOLOGICAL-BASIS; PLAGUE OUTBREAK; SEQUENCE;
+ LIPOPOLYSACCHARIDE; BIOSYNTHESIS; TEMPERATURE; MUTATIONS; DIVERSITY;
+ DATABASE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Adkins, Joshua N/B-9881-2013
+ Motin, Vladimir L/O-1535-2013
+ },
+ORCID-Numbers = {Adkins, Joshua N/0000-0003-0399-0700
+ Lerman, Joshua/0000-0003-0377-2674
+ Charusanti, Pep/0000-0003-0009-6615
+ Palsson, Bernhard/0000-0003-2357-6785
+ Motin, Vladimir/0000-0002-4762-457X
+ Chauhan, Sadhana/0000-0002-6461-0313},
+Times-Cited = {31},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000297165700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000297105100001,
+Author = {Pandit, Aditya V. and Mahadevan, Radhakrishnan},
+Title = {In silico characterization of microbial electrosynthesis for
+ metabolic engineering of biochemicals},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2011},
+Volume = {10},
+Month = {OCT 3},
+Type = {Article},
+DOI = {10.1186/1475-2859-10-76},
+Article-Number = {76},
+EISSN = {1475-2859},
+Keywords-Plus = {ESCHERICHIA-COLI; NEUTRAL RED; REDUCTION; AVAILABILITY; FERMENTATION;
+ MODULATION; MODELS; GROWTH; CELLS; BC(1)},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Mahadevan, Radhakrishnan/A-8502-2008},
+ORCID-Numbers = {Mahadevan, Radhakrishnan/0000-0002-1270-9063},
+Times-Cited = {36},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000297105100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000294878000007,
+Author = {Henry, Christopher S. and Overbeek, Ross and Xia, Fangfang and Best,
+ Aaron A. and Glass, Elizabeth and Gilbert, Jack and Larsen, Peter and
+ Edwards, Rob and Disz, Terry and Meyer, Folker and Vonstein, Veronika
+ and DeJongh, Matthew and Bartels, Daniela and Desai, Narayan and
+ D'Souza, Mark and Devoid, Scott and Keegan, Kevin P. and Olson, Robert
+ and Wilke, Andreas and Wilkening, Jared and Stevens, Rick L.},
+Title = {Connecting genotype to phenotype in the era of high-throughput
+ sequencing},
+Journal = {BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS},
+Year = {2011},
+Volume = {1810},
+Number = {10, SI},
+Pages = {967-977},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1016/j.bbagen.2011.03.010},
+ISSN = {0304-4165},
+EISSN = {1872-8006},
+Keywords = {SEED; RAST; MG-RAST; Metagenomics; Genome-scale metabolic models;
+ Assembly},
+Keywords-Plus = {ESCHERICHIA-COLI; GENOME ANNOTATION; METABOLIC CAPABILITIES; MICROBIAL
+ GENOMES; RAST SERVER; PROTEIN; RESOURCE; DATABASE; RECONSTRUCTION; KEGG},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ResearcherID-Numbers = {Gilbert, Jack/AAF-3270-2019
+ Edwards, Robert/Q-1691-2019
+ Best, Aaron A/IXN-1453-2023
+ Wilke, Andreas/F-1816-2018
+ },
+ORCID-Numbers = {Edwards, Robert/0000-0001-8383-8949
+ Wilke, Andreas/0000-0002-7699-2267
+ Meyer, Folker/0000-0003-1112-2284},
+Times-Cited = {23},
+Journal-ISO = {Biochim. Biophys. Acta-Gen. Subj.},
+Unique-ID = {WOS:000294878000007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000296902100005,
+Author = {Motamedian, Ehsan and Naeimpoor, Fereshteh},
+Title = {Prediction of Proton Exchange and Bacterial Growth on Various Substrates
+ Using Constraint-based Modeling Approach},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2011},
+Volume = {16},
+Number = {5},
+Pages = {875-884},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1007/s12257-011-0115-6},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {culture pH; flux balance analysis; genome-scale model; Bacillus
+ subtilis; carbon and nitrogen sources},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; BACILLUS-SUBTILIS; SURFACTIN PRODUCTION;
+ ESCHERICHIA-COLI; NITROGEN-SOURCES; BATCH CULTURE; PH; CARBON;
+ TEMPERATURE; NETWORK},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Motamedian, Ehsan/GPK-8344-2022
+ Naeimpoor, Fereshteh/S-9872-2018
+ },
+ORCID-Numbers = {Naeimpoor, Fereshteh/0000-0002-0802-001X
+ , Ehsan/0000-0001-8750-2879},
+Times-Cited = {4},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:000296902100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000296652600001,
+Author = {Orth, Jeffrey D. and Conrad, Tom M. and Na, Jessica and Lerman, Joshua
+ A. and Nam, Hojung and Feist, Adam M. and Palsson, Bernhard O.},
+Title = {A comprehensive genome-scale reconstruction of Escherichia coli
+ metabolism-2011},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {7},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1038/msb.2011.65},
+Article-Number = {535},
+ISSN = {1744-4292},
+Keywords = {constraint-based modeling; Escherichia coli; metabolic network
+ reconstruction; metabolism; phenotypic screening},
+Keywords-Plus = {HIGH-THROUGHPUT; E.-COLI; GENERATION; SEQUENCE; MODELS; MG1655; K-12;
+ OPTIMIZATION; NETWORKS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Nam, Hojung/AAR-4065-2020
+ },
+ORCID-Numbers = {Nam, Hojung/0000-0002-5109-9114
+ Lerman, Joshua/0000-0003-0377-2674
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {724},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000296652600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000296442800001,
+Author = {Rolfsson, Ottar and Palsson, Bernhard O. and Thiele, Ines},
+Title = {The human metabolic reconstruction Recon 1 directs hypotheses of novel
+ human metabolic functions},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {OCT 1},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-155},
+Article-Number = {155},
+EISSN = {1752-0509},
+Keywords-Plus = {SIALIC-ACID; NETWORK RECONSTRUCTION; EXPRESSION; PREDICTION; CONSTRAINT;
+ TRANSPORT; PROTEINS; CLONING; GENES; MOUSE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Rolfsson, Ottar/0000-0003-4258-6057
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {53},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000296442800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000296438900001,
+Author = {Jensen, Paul A. and Lutz, Kyla A. and Papin, Jason A.},
+Title = {TIGER: Toolbox for integrating genome-scale metabolic models, expression
+ data, and transcriptional regulatory networks},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {SEP 23},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-147},
+Article-Number = {147},
+ISSN = {1752-0509},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; PREDICTION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {69},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000296438900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000294014100004,
+Author = {Cvijovic, Marija and Bordel, Sergio and Nielsen, Jens},
+Title = {Mathematical models of cell factories: moving towards the core of
+ industrial biotechnology},
+Journal = {MICROBIAL BIOTECHNOLOGY},
+Year = {2011},
+Volume = {4},
+Number = {5},
+Pages = {572-584},
+Month = {SEP},
+Type = {Review},
+DOI = {10.1111/j.1751-7915.2010.00233.x},
+ISSN = {1751-7915},
+Keywords-Plus = {BIOCHEMICAL SYSTEMS ANALYSIS; COMPLEX METABOLIC NETWORKS; POWER-LAW
+ APPROXIMATION; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; PATHWAY
+ ANALYSIS; OSMOTIC-STRESS; FISSION YEAST; CORYNEBACTERIUM-GLUTAMICUM;
+ THERMODYNAMIC FEASIBILITY},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Bordel, Sergio/A-3325-2017
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Bordel, Sergio/0000-0001-6162-6478
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {20},
+Journal-ISO = {Microb. Biotechnol.},
+Unique-ID = {WOS:000294014100004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000295362900003,
+Author = {Schellenberger, Jan and Que, Richard and Fleming, Ronan M. T. and
+ Thiele, Ines and Orth, Jeffrey D. and Feist, Adam M. and Zielinski,
+ Daniel C. and Bordbar, Aarash and Lewis, Nathan E. and Rahmanian, Sorena
+ and Kang, Joseph and Hyduke, Daniel R. and Palsson, Bernhard O.},
+Title = {Quantitative prediction of cellular metabolism with constraint-based
+ models: the COBRA Toolbox v2.0},
+Journal = {NATURE PROTOCOLS},
+Year = {2011},
+Volume = {6},
+Number = {9},
+Pages = {1290-1307},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1038/nprot.2011.308},
+ISSN = {1754-2189},
+EISSN = {1750-2799},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; ALTERNATE OPTIMAL-SOLUTIONS;
+ ESCHERICHIA-COLI; HIGH-THROUGHPUT; 2-DIMENSIONAL ANNOTATION; NETWORK;
+ GENES; IDENTIFICATION; OPTIMIZATION; TUBERCULOSIS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ damiani, chiara/R-4256-2016
+ Lewis, Nathan/ABE-7290-2020
+ Fleming, Ronan MT/ABC-4093-2021
+ /AAG-5264-2021
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Lewis, Nathan/0000-0001-7700-3654
+ Fleming, Ronan MT/0000-0001-5346-9812
+ /0000-0001-6460-6771
+ Zielinski, Daniel/0000-0001-6452-483X
+ Palsson, Bernhard/0000-0003-2357-6785
+ Que, Richard/0000-0003-1076-4357},
+Times-Cited = {974},
+Journal-ISO = {Nat. Protoc.},
+Unique-ID = {WOS:000295362900003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000295457600003,
+Author = {Milne, Caroline B. and Eddy, James A. and Raju, Ravali and Ardekani,
+ Soroush and Kim, Pan-Jun and Senger, Ryan S. and Jin, Yong-Su and
+ Blaschek, Hans P. and Price, Nathan D.},
+Title = {Metabolic network reconstruction and genome-scale model of
+ butanol-producing strain Clostridium beijerinckii NCIMB 8052},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {AUG 16},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-130},
+Article-Number = {130},
+EISSN = {1752-0509},
+Keywords-Plus = {CARBON-MONOXIDE; FERMENTATION; CARBOHYDRATE; PATHWAYS; DATABASE; GROWTH;
+ BA101},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Jin, Yong-Su/L-4530-2013
+ },
+ORCID-Numbers = {Jin, Yong-Su/0000-0002-4464-9536
+ Price, Nathan/0000-0002-4157-0267
+ Kim, Pan-Jun/0000-0002-9329-4997},
+Times-Cited = {78},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000295457600003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293620800012,
+Author = {Chan, Siu Hung Joshua and Ji, Ping},
+Title = {Decomposing flux distributions into elementary flux modes in
+ genome-scale metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2011},
+Volume = {27},
+Number = {16},
+Pages = {2256-2262},
+Month = {AUG 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btr367},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {ESCHERICHIA-COLI MG1655; PATHWAY ANALYSIS; MONITORING UTILIZATION;
+ FUNCTIONAL-ANALYSIS; EXTREME PATHWAYS; STEADY-STATE; LB MEDIUM;
+ COMPUTATION; SYSTEMS; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Ji, Ping/F-3535-2011
+ Chan, Siu Hung Joshua/N-9777-2016
+ },
+ORCID-Numbers = {Ji, Ping/0000-0002-7841-6677
+ Chan, Siu Hung Joshua/0000-0002-7707-656X},
+Times-Cited = {24},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000293620800012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000294440200001,
+Author = {Carbonell, Pablo and Planson, Anne-Gaelle and Fichera, Davide and
+ Faulon, Jean-Loup},
+Title = {A retrosynthetic biology approach to metabolic pathway design for
+ therapeutic production},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {AUG 5},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-122},
+Article-Number = {122},
+EISSN = {1752-0509},
+Keywords-Plus = {FUNCTIONAL EXPRESSION; COMBINATORIAL BIOSYNTHESIS; MOLECULAR-CLONING;
+ ESCHERICHIA-COLI; PRECURSOR; NETWORK; CDNA; PREDICTION; SYNTHASE; TAXUS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Planson, Anne-Gaëlle/AAK-9595-2021
+ Carbonell, Pablo/A-3572-2011
+ },
+ORCID-Numbers = {Carbonell, Pablo/0000-0002-0993-5625
+ Planson, Anne-Gaelle/0000-0003-4343-3386
+ Faulon, Jean-Loup/0000-0003-4274-2953},
+Times-Cited = {71},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000294440200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000294537800002,
+Author = {Chang, Roger L. and Ghamsari, Lila and Manichaikul, Ani and Hom, Erik F.
+ Y. and Balaji, Santhanam and Fu, Weiqi and Shen, Yun and Hao, Tong and
+ Palsson, Bernhard O. and Salehi-Ashtiani, Kourosh and Papin, Jason A.},
+Title = {Metabolic network reconstruction of Chlamydomonas offers insight
+ into light-driven algal metabolism},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {7},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1038/msb.2011.52},
+Article-Number = {518},
+ISSN = {1744-4292},
+Keywords = {Chlamydomonas reinhardtii; lipid metabolism; metabolic engineering;
+ photobioreactor},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; PROTOCHLOROPHYLLIDE REDUCTASE;
+ CARBONIC-ANHYDRASE; FATTY-ACIDS; REINHARDTII; MODELS; MUTANT;
+ BIOSYNTHESIS; EFFICIENCY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Manichaikul, Ani W/B-7726-2009
+ FU, WEIQI/E-4167-2019
+ Hom, Erik/B-3889-2008
+ },
+ORCID-Numbers = {FU, WEIQI/0000-0002-7368-383X
+ Chang, Roger/0000-0003-1630-6584
+ Papin, Jason/0000-0002-2769-5805
+ Hom, Erik/0000-0003-0964-0031
+ Salehi-Ashtiani, Kourosh/0000-0002-6521-5243
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {220},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000294537800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293868800002,
+Author = {Faust, Karoline and Croes, Didier and van Helden, Jacques},
+Title = {Prediction of metabolic pathways from genome-scale metabolic networks},
+Journal = {BIOSYSTEMS},
+Year = {2011},
+Volume = {105},
+Number = {2, SI},
+Pages = {109-121},
+Month = {AUG},
+Note = {Workshop on Integration of OMICS Datasets into Metabolic Pathway
+ Analysis (IOMPA 2010), Edinburgh, SCOTLAND, OCT 15, 2010},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.biosystems.2011.05.004},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Metabolic pathway definition; Metabolic pathway prediction; Metabolic
+ network representation; Subgraph extraction},
+Keywords-Plus = {ELEMENTARY FLUX MODES; SMALL-WORLD; MEANINGFUL PATHWAYS;
+ ESCHERICHIA-COLI; RECONSTRUCTION; TOOL; EXPRESSION; DATABASES; PATHS;
+ SET},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Faust, Karoline/P-7578-2017
+ van Helden, Jacques/D-8590-2013},
+ORCID-Numbers = {Faust, Karoline/0000-0001-7129-2803
+ van Helden, Jacques/0000-0002-8799-8584},
+Times-Cited = {23},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000293868800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293176600011,
+Author = {Hay, Jordan and Schwender, Joerg},
+Title = {Computational analysis of storage synthesis in developing Brassica
+ napus L. (oilseed rape) embryos: flux variability analysis in
+ relation to 13C metabolic flux analysis},
+Journal = {PLANT JOURNAL},
+Year = {2011},
+Volume = {67},
+Number = {3},
+Pages = {513-525},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1111/j.1365-313X.2011.04611.x},
+ISSN = {0960-7412},
+Keywords = {flux balance analysis; carbon partitioning; constraint-based model;
+ linear program; stoichiometric model},
+Keywords-Plus = {CENTRAL CARBOHYDRATE-METABOLISM; DEVELOPING SOYBEAN COTYLEDONS;
+ NUCLEAR-MAGNETIC-RESONANCE; SUSPENSION CELL-CULTURES; BALANCE ANALYSIS;
+ GLUTAMATE-DEHYDROGENASE; NITROGEN ASSIMILATION; ESCHERICHIA-COLI;
+ DEVELOPING SEEDS; PLANT},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Schwender, Jorg/P-2282-2014},
+ORCID-Numbers = {Schwender, Jorg/0000-0003-1350-4171},
+Times-Cited = {68},
+Journal-ISO = {Plant J.},
+Unique-ID = {WOS:000293176600011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293176600012,
+Author = {Hay, Jordan and Schwender, Joerg},
+Title = {Metabolic network reconstruction and flux variability analysis of
+ storage synthesis in developing oilseed rape (Brassica napus L.)
+ embryos},
+Journal = {PLANT JOURNAL},
+Year = {2011},
+Volume = {67},
+Number = {3},
+Pages = {526-541},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1111/j.1365-313X.2011.04613.x},
+ISSN = {0960-7412},
+Keywords = {flux balance analysis; carbon partitioning; constraint-based model;
+ linear program; stoichiometric model},
+Keywords-Plus = {FATTY-ACID SYNTHESIS; ESCHERICHIA-COLI; BALANCE ANALYSIS; SYSTEMIC
+ PROPERTIES; CARBON METABOLISM; SCALE; MODEL; ARABIDOPSIS; SEEDS; PATHWAY},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Schwender, Jorg/P-2282-2014},
+ORCID-Numbers = {Schwender, Jorg/0000-0003-1350-4171},
+Times-Cited = {57},
+Journal-ISO = {Plant J.},
+Unique-ID = {WOS:000293176600012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293868800008,
+Author = {Klamt, Steffen and von Kamp, Axel},
+Title = {An application programming interface for CellNetAnalyzer},
+Journal = {BIOSYSTEMS},
+Year = {2011},
+Volume = {105},
+Number = {2, SI},
+Pages = {162-168},
+Month = {AUG},
+Note = {Workshop on Integration of OMICS Datasets into Metabolic Pathway
+ Analysis (IOMPA 2010), Edinburgh, SCOTLAND, OCT 15, 2010},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.biosystems.2011.02.002},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Constraint-based modeling; Elementary modes; Metabolic networks; Network
+ analysis; Systems biology; Signaling networks},
+Keywords-Plus = {MINIMAL CUT SETS; REGULATORY NETWORKS; FUNCTIONAL-ANALYSIS; CELLULAR
+ NETWORKS; SYSTEMS BIOLOGY; MODES; TOOLBOX; MATLAB},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ORCID-Numbers = {Klamt, Steffen/0000-0003-2563-7561},
+Times-Cited = {35},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000293868800008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293487900002,
+Author = {Toya, Yoshihiro and Kono, Nobuaki and Arakawa, Kazuharu and Tomita,
+ Masaru},
+Title = {Metabolic Flux Analysis and Visualization},
+Journal = {JOURNAL OF PROTEOME RESEARCH},
+Year = {2011},
+Volume = {10},
+Number = {8},
+Pages = {3313-3323},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1021/pr2002885},
+ISSN = {1535-3893},
+EISSN = {1535-3907},
+Keywords = {C-13-Metabolic Flux Analysis; Flux Balance Analysis; Pathway Projector;
+ genome-scale model},
+Keywords-Plus = {BIDIRECTIONAL REACTION STEPS; CENTRAL CARBON METABOLISM; GENOME-SCALE
+ MODELS; ESCHERICHIA-COLI; C-13-LABELING EXPERIMENTS; BIOCHEMICAL
+ NETWORKS; BIOCYC COLLECTION; BACILLUS-SUBTILIS; BALANCE ANALYSIS; BATCH
+ CULTURE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ORCID-Numbers = {Toya, Yoshihiro/0000-0001-9670-6961
+ Kono, Nobuaki/0000-0001-5960-7956
+ Arakawa, Kazuharu/0000-0002-2893-4919},
+Times-Cited = {23},
+Journal-ISO = {J. Proteome Res.},
+Unique-ID = {WOS:000293487900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293868800009,
+Author = {Xavier, Daniela and Vazquez, Sara and Higuera, Clara and Moran, Federico
+ and Montero, Francisco},
+Title = {Tools-4-Metatool (T4M): Online suite of web-tools to process
+ stoichiometric network analysis data from Metatool},
+Journal = {BIOSYSTEMS},
+Year = {2011},
+Volume = {105},
+Number = {2, SI},
+Pages = {169-172},
+Month = {AUG},
+Note = {Workshop on Integration of OMICS Datasets into Metabolic Pathway
+ Analysis (IOMPA 2010), Edinburgh, SCOTLAND, OCT 15, 2010},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.biosystems.2011.04.004},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Metabolic networks; Stoichiometric analysis},
+Keywords-Plus = {GENOME; MODES},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Moran, Federico/L-1297-2014
+ Montero, Francisco/G-9850-2015},
+ORCID-Numbers = {Moran, Federico/0000-0003-3992-8829
+ Montero, Francisco/0000-0003-2366-3635},
+Times-Cited = {3},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000293868800009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000294440100002,
+Author = {Resendis-Antonio, Osbaldo and Hernandez, Magdalena and Salazar, Emmanuel
+ and Contreras, Sandra and Martinez Batallar, Gabriel and Mora, Yolanda
+ and Encarnacion, Sergio},
+Title = {Systems biology of bacterial nitrogen fixation: High-throughput
+ technology and its integrative description with constraint-based
+ modeling},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {JUL 29},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-120},
+Article-Number = {120},
+EISSN = {1752-0509},
+Keywords-Plus = {GLOBAL PROTEIN EXPRESSION; AMINO-ACID PERMEASE; RHIZOBIUM-ETLI;
+ GENE-EXPRESSION; METABOLISM; SYMBIOSIS; GENOME; RECONSTRUCTION;
+ LEGUMINOSARUM; ACCUMULATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {RESENDIS, OSBALDO/ADE-5280-2022
+ },
+ORCID-Numbers = {RESENDIS, OSBALDO/0000-0001-5220-541X
+ Encarnacion Guevara, Sergio/0000-0001-7889-1681},
+Times-Cited = {35},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000294440100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000292772800043,
+Author = {Alam, Mohammad Tauqeer and Medema, Marnix H. and Takano, Eriko and
+ Breitling, Rainer},
+Title = {Comparative genome-scale metabolic modeling of actinomycetes: The
+ topology of essential core metabolism},
+Journal = {FEBS LETTERS},
+Year = {2011},
+Volume = {585},
+Number = {14},
+Pages = {2389-2394},
+Month = {JUL 21},
+Type = {Article},
+DOI = {10.1016/j.febslet.2011.06.014},
+ISSN = {1873-3468},
+Keywords = {Flux balance analysis; Constraint-based metabolic model; Systems
+ biology; Streptomyces; Secondary metabolite},
+Keywords-Plus = {CORYNEBACTERIUM-GLUTAMICUM; STREPTOMYCES-COELICOLOR; ESSENTIAL GENES;
+ NETWORKS; SEQUENCE; STRAIN; ACTINOBACTERIA; RECONSTRUCTION; PHYLOGENY;
+ BIOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+ResearcherID-Numbers = {Alam, Mohammad Tauqeer/A-5304-2013
+ Medema, Marnix H./AAR-3138-2021
+ },
+ORCID-Numbers = {Medema, Marnix H./0000-0002-2191-2821
+ Alam, Mohammad Tauqeer/0000-0002-6872-0691
+ Takano, Eriko/0000-0002-6791-3256
+ Breitling, Rainer/0000-0001-7173-0922},
+Times-Cited = {27},
+Journal-ISO = {FEBS Lett.},
+Unique-ID = {WOS:000292772800043},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000294012700001,
+Author = {Bordbar, Aarash and Jamshidi, Neema and Palsson, Bernhard O.},
+Title = {iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte
+ metabolism that can be used to simulate its physiological and
+ patho-physiological states},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {JUL 12},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-110},
+Article-Number = {110},
+EISSN = {1752-0509},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; RECONSTRUCTION; CELL; MEMBRANE; NETWORK;
+ MODEL; LIVER; GLYCOLYSIS; TURNOVER},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {/AAG-5264-2021
+ },
+ORCID-Numbers = {/0000-0001-6460-6771
+ Jamshidi, Neema/0000-0003-3857-9735
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {67},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000294012700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000291473700010,
+Author = {Noack, Stephan and Noeh, Katharina and Moch, Matthias and Oldiges, Marco
+ and Wiechert, Wolfgang},
+Title = {Stationary versus non-stationary 13C-MFA: A comparison using
+ a consistent dataset},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2011},
+Volume = {154},
+Number = {2-3},
+Pages = {179-190},
+Month = {JUL 10},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2010.07.008},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Metabolic flux analysis; Isotopic labeling; C-13-MFA},
+Keywords-Plus = {METABOLIC-FLUX ANALYSIS; CHROMATOGRAPHY-MASS SPECTROMETRY; SENSOR
+ REACTOR APPROACH; L-LYSINE PRODUCTION; BIDIRECTIONAL REACTION STEPS;
+ NUCLEAR-MAGNETIC-RESONANCE; PENTOSE-PHOSPHATE PATHWAY; IN-VIVO FLUX;
+ CORYNEBACTERIUM-GLUTAMICUM; LABELING EXPERIMENTS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Oldiges, Marco/0000-0003-0704-5597
+ Noh, Katharina/0000-0002-5407-2275
+ Noack, Stephan/0000-0001-9784-3626
+ Wiechert, Wolfgang/0000-0001-8501-0694},
+Times-Cited = {53},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000291473700010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293351900007,
+Author = {Conrad, Tom M. and Lewis, Nathan E. and Palsson, Bernhard O.},
+Title = {Microbial laboratory evolution in the era of genome-scale science},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {7},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1038/msb.2011.42},
+Article-Number = {509},
+ISSN = {1744-4292},
+Keywords = {epistasis; flux-balance analysis; metabolic engineering; mutation;
+ regulatory hub},
+Keywords-Plus = {ESCHERICHIA-COLI POPULATIONS; TERM EXPERIMENTAL EVOLUTION; HIGH
+ MUTATION-RATES; ADAPTIVE EVOLUTION; SACCHAROMYCES-CEREVISIAE;
+ OPTIMAL-GROWTH; BACTERIAL-POPULATIONS; REGULATORY MUTATIONS; CONSTANT
+ ENVIRONMENT; RPOS MUTATIONS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Zheng, Yanqing/B-5557-2012
+ Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {188},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000293351900007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000208589400006,
+Author = {Moore, J. Bernadette and Weeks, Mark E.},
+Title = {Proteomics and Systems Biology: Current and Future Applications in the
+ Nutritional Sciences},
+Journal = {ADVANCES IN NUTRITION},
+Year = {2011},
+Volume = {2},
+Number = {4},
+Pages = {355-364},
+Month = {JUL},
+Type = {Review},
+DOI = {10.3945/an.111.000554},
+ISSN = {2161-8313},
+EISSN = {2156-5376},
+Keywords-Plus = {2-DIMENSIONAL GEL-ELECTROPHORESIS; SPECTROMETRY-BASED PROTEOMICS;
+ MASS-SPECTROMETRY; QUANTITATIVE PROTEOMICS; URINE PROTEOME;
+ CEREBROSPINAL-FLUID; PROTEINS; BIOMARKERS; ORBITRAP; IDENTIFICATION},
+Research-Areas = {Nutrition \& Dietetics},
+Web-of-Science-Categories = {Nutrition \& Dietetics},
+ResearcherID-Numbers = {Moore, Justin B/B-9357-2012
+ weeks, Mark/AAT-7258-2021
+ Moore, J Bernadette/D-5258-2012
+ /C-2531-2011
+ },
+ORCID-Numbers = {Moore, Justin B/0000-0003-4059-0538
+ /0000-0002-6576-8809
+ Moore, J Bernadette/0000-0003-4750-1550
+ , mark/0000-0002-2936-2860},
+Times-Cited = {28},
+Journal-ISO = {Adv. Nutr.},
+Unique-ID = {WOS:000208589400006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000291467600019,
+Author = {Pilalis, Eleftherios and Chatziioannou, Aristotelis and Thomasset,
+ Brigitte and Kolisis, Fragiskos},
+Title = {An In Silico Compartmentalized Metabolic Model of Brassica Napus
+ Enables the Systemic Study of Regulatory Aspects of Plant Central
+ Metabolism},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2011},
+Volume = {108},
+Number = {7},
+Pages = {1673-1682},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/bit.23107},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {metabolic engineering; regulatory analysis; in silico cellular modeling;
+ systems biotechnology; plant central metabolism models; network
+ plasticity},
+Keywords-Plus = {FLUX-BALANCE ANALYSIS; ESCHERICHIA-COLI; RECONSTRUCTION; PATHWAY; ARACYC},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {KOLISIS, FRAGKISKOS/GSN-7219-2022
+ },
+ORCID-Numbers = {Kolisis, Frangiskos/0000-0001-7656-3975
+ Pilalis, Eleftherios/0000-0002-5253-5256
+ Chatziioannou, Aristotelis/0000-0003-2078-0844},
+Times-Cited = {44},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000291467600019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000291471500009,
+Author = {Yousofshahi, Mona and Lee, Kyongbum and Hassoun, Soha},
+Title = {Probabilistic pathway construction},
+Journal = {METABOLIC ENGINEERING},
+Year = {2011},
+Volume = {13},
+Number = {4},
+Pages = {435-444},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2011.01.006},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Pathway construction; Pathway inference; Connectivity; Probabilistic
+ synthesis; Yield diversity},
+Keywords-Plus = {METABOLIC PATHWAYS; MICROBIAL-PRODUCTION; MEVALONATE PATHWAY;
+ ESCHERICHIA-COLI; STRAIN; BIOSYNTHESIS; PREDICTION; ACID; POLYKETIDES;
+ NETWORKS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lee, Kyongbum/D-9230-2013
+ },
+ORCID-Numbers = {Lee, Kyongbum/0000-0002-0699-8057},
+Times-Cited = {28},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000291471500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293689100001,
+Author = {Smith, Anthony C. and Robinson, Alan J.},
+Title = {A metabolic model of the mitochondrion and its use in modelling diseases
+ of the tricarboxylic acid cycle},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {JUN 29},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-102},
+Article-Number = {102},
+EISSN = {1752-0509},
+Keywords-Plus = {COMPLEX-II; DEHYDROGENASE-DEFICIENCY; FUMARASE DEFICIENCY;
+ SKELETAL-MUSCLE; 2 SIBLINGS; SUCCINATE; HEART; MUTATION; GENOME; GENE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Smith, Anthony C/B-1891-2009},
+ORCID-Numbers = {Smith, Anthony C/0000-0003-0141-0434},
+Times-Cited = {49},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000293689100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000292204700003,
+Author = {Meng, Hailin and Lu, Zhiguo and Wang, Yong and Wang, Xiaoning and Zhang,
+ Siliang},
+Title = {In silico improvement of heterologous biosynthesis of erythromycin
+ precursor 6-deoxyerythronolide B in Escherichia coli},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2011},
+Volume = {16},
+Number = {3},
+Pages = {445-456},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1007/s12257-010-0321-7},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {6-deoxyerythronolide B (6dEB); heterologous biosynthesis; in silico
+ strain improvement; gene targets},
+Keywords-Plus = {METABOLIC CAPABILITIES; LYCOPENE PRODUCTION; RECONSTRUCTION;
+ POLYKETIDES; NETWORK; MODELS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {11},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:000292204700003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000290801000017,
+Author = {Weckwerth, Wolfram},
+Title = {Unpredictability of metabolism-the key role of metabolomics science in
+ combination with next-generation genome sequencing},
+Journal = {ANALYTICAL AND BIOANALYTICAL CHEMISTRY},
+Year = {2011},
+Volume = {400},
+Number = {7},
+Pages = {1967-1978},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1007/s00216-011-4948-9},
+ISSN = {1618-2642},
+EISSN = {1618-2650},
+Keywords = {Genotype-phenotype relationship; Systems biology; Metabolomics;
+ Proteomics; Genome annotation; Gene models; Metabolic modelling; Flux
+ balance analysis; Dynamic modelling; Stochastic differential equations;
+ Covariance; Principal components analysis; Phenotypic plasticity},
+Keywords-Plus = {IN-VIVO; PATTERN-RECOGNITION; PLANT METABOLOMICS; MASS-SPECTROMETRY;
+ SYSTEMS; PROTEOMICS; MODELS; NETWORK; REVEAL; C-13},
+Research-Areas = {Biochemistry \& Molecular Biology; Chemistry},
+Web-of-Science-Categories = {Biochemical Research Methods; Chemistry, Analytical},
+ResearcherID-Numbers = {Weckwerth, Wolfram/G-5811-2010
+ },
+ORCID-Numbers = {Weckwerth, Wolfram/0000-0002-9719-6358},
+Times-Cited = {57},
+Journal-ISO = {Anal. Bioanal. Chem.},
+Unique-ID = {WOS:000290801000017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000291602500001,
+Author = {Santala, Suvi and Efimova, Elena and Kivinen, Virpi and Larjo, Antti and
+ Aho, Tommi and Karp, Matti and Santala, Ville},
+Title = {Improved Triacylglycerol Production in Acinetobacter baylyi ADP1
+ by Metabolic Engineering},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2011},
+Volume = {10},
+Month = {MAY 18},
+Type = {Article},
+DOI = {10.1186/1475-2859-10-36},
+Article-Number = {36},
+ISSN = {1475-2859},
+Keywords-Plus = {ESCHERICHIA-COLI; WAX ESTER; MUTANTS; ACETATE; MICROORGANISMS;
+ BIOSYNTHESIS; PROKARYOTES; BACTERIUM; BIOLOGY; MODEL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Karp, Matti T/G-4227-2014
+ },
+ORCID-Numbers = {Karp, Matti T/0000-0001-6686-4416
+ Santala, Suvi Maarit/0000-0002-0047-5319
+ Santala, Ville/0000-0002-9084-931X},
+Times-Cited = {64},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000291602500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000291544000004,
+Author = {Cogne, Guillaume and Ruegen, Marco and Bockmayr, Alexander and Titica,
+ Mariana and Dussap, Claude-Gilles and Cornet, Jean-Francois and Legrand,
+ Jack},
+Title = {A Model-Based Method for Investigating Bioenergetic Processes in
+ Autotrophically Growing Eukaryotic Microalgae: Application to the Green
+ Algae Chlamydomonas reinhardtii},
+Journal = {BIOTECHNOLOGY PROGRESS},
+Year = {2011},
+Volume = {27},
+Number = {3},
+Pages = {631-640},
+Month = {MAY-JUN},
+Type = {Article},
+DOI = {10.1002/btpr.596},
+ISSN = {8756-7938},
+EISSN = {1520-6033},
+Keywords = {metabolic modeling; eukaryotic microalgae; thermodynamic constraints;
+ mixed integer programming},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CHLOROPLAST DNA; CELL-WALL; GENOME;
+ THERMODYNAMICS; METABOLISM; EFFICIENCY; CONVERSION; SEQUENCE; BEHAVIOR},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {DUSSAP, Claude-Gilles/JPC-6972-2023
+ },
+ORCID-Numbers = {DUSSAP, Claude-Gilles/0000-0002-6461-6264
+ Bockmayr, Alexander/0000-0002-5074-1347
+ Titica, Mariana/0000-0002-5704-0439},
+Times-Cited = {49},
+Journal-ISO = {Biotechnol. Prog.},
+Unique-ID = {WOS:000291544000004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000290659800007,
+Author = {Hopkins, Andrew L. and Bickerton, G. Richard and Carruthers, Ian M. and
+ Boyer, Stephen K. and Rubin, Harvey and Overington, John P.},
+Title = {Rapid Analysis of Pharmacology for Infectious Diseases},
+Journal = {CURRENT TOPICS IN MEDICINAL CHEMISTRY},
+Year = {2011},
+Volume = {11},
+Number = {10},
+Pages = {1292-1300},
+Month = {MAY},
+Type = {Review},
+ISSN = {1568-0266},
+EISSN = {1873-5294},
+Keywords = {Chemogenomics; target identification; druggable genome},
+Keywords-Plus = {DRUG DISCOVERY; CHEMOGENOMICS; TARGETS; MODELS; METABOLISM;
+ PRIORITIZATION; RECONSTRUCTION; ESSENTIALITY; MECHANISMS; INHIBITORS},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Chemistry, Medicinal},
+ResearcherID-Numbers = {Overington, John P/G-8607-2015
+ Hopkins, Andrew/H-5138-2011},
+ORCID-Numbers = {Overington, John P/0000-0002-5859-1064
+ /0000-0001-6426-0598
+ Hopkins, Andrew/0000-0003-1977-018X},
+Times-Cited = {18},
+Journal-ISO = {Curr. Top. Med. Chem.},
+Unique-ID = {WOS:000290659800007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000290168900005,
+Author = {MacDonald, S. J. and Thomas, G. H. and Douglas, A. E.},
+Title = {Genetic and metabolic determinants of nutritional phenotype in an
+ insect-bacterial symbiosis},
+Journal = {MOLECULAR ECOLOGY},
+Year = {2011},
+Volume = {20},
+Number = {10},
+Pages = {2073-2084},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1111/j.1365-294X.2011.05031.x},
+ISSN = {0962-1083},
+Keywords = {Acyrthosiphon pisum; amino acid nutrition; aphid; Buchnera; flux balance
+ analysis; nutritional phenotype; symbiosis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; PEA APHID; ACYRTHOSIPHON-PISUM;
+ BUCHNERA-APHIDICOLA; THERMAL TOLERANCE; AMINO-ACIDS; GENOME; MICROBIOME;
+ TRYPTOPHAN; DYNAMICS},
+Research-Areas = {Biochemistry \& Molecular Biology; Environmental Sciences \& Ecology;
+ Evolutionary Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Ecology; Evolutionary Biology},
+ResearcherID-Numbers = {MacDonald, Steven J/B-6173-2015
+ Thomas, Gavin H/E-5753-2011
+ },
+ORCID-Numbers = {Thomas, Gavin H/0000-0002-9763-1313
+ Macdonald, Sandy/0000-0002-4112-0987},
+Times-Cited = {50},
+Journal-ISO = {Mol. Ecol.},
+Unique-ID = {WOS:000290168900005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000289680400005,
+Author = {Wang, Zhi and Zhang, Jianzhi},
+Title = {Impact of gene expression noise on organismal fitness and the efficacy
+ of natural selection},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2011},
+Volume = {108},
+Number = {16},
+Pages = {E67-E76},
+Month = {APR 19},
+Type = {Article},
+DOI = {10.1073/pnas.1100059108},
+ISSN = {0027-8424},
+Keywords = {flux balance analysis; metabolic network},
+Keywords-Plus = {ESCHERICHIA-COLI; CELLULAR HETEROGENEITY; ADAPTIVE EVOLUTION; METABOLIC
+ NETWORKS; VARIABILITY; CONSEQUENCES; CONSTRAINT; STOCHASTICITY;
+ SENSITIVITY; ORIGINS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {145},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000289680400005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000288314400023,
+Author = {Liao, Yu-Chieh and Huang, Tzu-Wen and Chen, Feng-Chi and Charusanti, Pep
+ and Hong, Jay S. J. and Chang, Hwan-You and Tsai, Shih-Feng and Palsson,
+ Bernhard O. and Hsiung, Chao A.},
+Title = {An Experimentally Validated Genome-Scale Metabolic Reconstruction of
+ Klebsiella pneumoniae MGH 78578, iYL1228},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2011},
+Volume = {193},
+Number = {7},
+Pages = {1710-1717},
+Month = {APR},
+Type = {Article},
+DOI = {10.1128/JB.01218-10},
+ISSN = {0021-9193},
+EISSN = {1098-5530},
+Keywords-Plus = {GLYCEROL METABOLISM; ESCHERICHIA-COLI; GENES; PATHWAY; ASSIMILATION;
+ CATABOLISM; PHENOTYPE; HYDROLASE; FLUX},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Liao, Yu-Chieh/E-5031-2011
+ Liao, Yu-Chieh/L-5113-2019
+ Hsiung, Chao Agnes/E-3994-2010
+ Tsai, Shih-Feng/E-3997-2010
+ Chen, Feng-Chi/E-3841-2010
+ },
+ORCID-Numbers = {Liao, Yu-Chieh/0000-0002-4360-7932
+ Charusanti, Pep/0000-0003-0009-6615
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {81},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000288314400023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000288049700013,
+Author = {Assary, Rajeev S. and Broadbelt, Linda J.},
+Title = {Computational screening of novel thiamine-catalyzed decarboxylation
+ reactions of 2-keto acids},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2011},
+Volume = {34},
+Number = {3},
+Pages = {375-388},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1007/s00449-010-0481-z},
+ISSN = {1615-7591},
+Keywords = {Novel biochemical transformations; Molecular modeling; Enzyme screening},
+Keywords-Plus = {PYRUVATE-FERREDOXIN OXIDOREDUCTASE; POLARIZABLE CONTINUUM MODEL; COMPLEX
+ METABOLIC NETWORKS; GENOME-SCALE MODEL; THERMODYNAMIC ANALYSIS;
+ REACTION-MECHANISMS; DIPHOSPHATE CATALYSIS; RADICAL INTERMEDIATE;
+ ACCURATE DOCKING; DFT CALCULATIONS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Broadbelt, Linda/B-7640-2009
+ Assary, Rajeev Surendran/E-6833-2012},
+ORCID-Numbers = {Assary, Rajeev Surendran/0000-0002-9571-3307},
+Times-Cited = {8},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000288049700013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000290070800001,
+Author = {Meng, Hailin and Wang, Yong and Hua, Qiang and Zhang, Siliang and Wang,
+ Xiaoning},
+Title = {In silico Analysis and Experimental Improvement of Taxadiene
+ Heterologous Biosynthesis in Escherichia coli},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2011},
+Volume = {16},
+Number = {2},
+Pages = {205-215},
+Month = {MAR-APR},
+Type = {Article},
+DOI = {10.1007/s12257-010-0329-z},
+ISSN = {1226-8372},
+Keywords = {taxadiene; isopentenyl pyrophosphate; heterologous biosynthesis; in
+ silico analysis; pathway engineering},
+Keywords-Plus = {E. COLI; METABOLIC CAPABILITIES; TAXOL; PRECURSOR; PATHWAY; GENES;
+ YEAST; RECONSTRUCTION; PERSPECTIVES; TERPENOIDS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {27},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:000290070800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000288995500023,
+Author = {Oberhardt, Matthew A. and Puchalka, Jacek and dos Santos, Vitor A. P.
+ Martins and Papin, Jason A.},
+Title = {Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative
+ Systems Analysis},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2011},
+Volume = {7},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1001116},
+Article-Number = {e1001116},
+EISSN = {1553-7358},
+Keywords-Plus = {PSEUDOMONAS-AERUGINOSA PAO1; FLUX BALANCE ANALYSIS; CYSTIC-FIBROSIS;
+ OPPORTUNISTIC PATHOGEN; PUTIDA KT2440; ANAEROBIC SURVIVAL; NETWORK
+ ANALYSIS; MUTANT LIBRARY; GENES; ANNOTATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {90},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000288995500023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000287989200014,
+Author = {Vilaca, Paulo and Rocha, Isabel and Rocha, Miguel},
+Title = {A computational tool for the simulation and optimization of microbial
+ strains accounting integrated metabolic/regulatory information},
+Journal = {BIOSYSTEMS},
+Year = {2011},
+Volume = {103},
+Number = {3},
+Pages = {435-441},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2010.11.012},
+ISSN = {0303-2647},
+Keywords = {Metabolic engineering; Integrated models; Metabolic models; Regulatory
+ models; Software tool; Open-source},
+Keywords-Plus = {NETWORKS; PERTURBATIONS; METABOLISM; MODELS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Rocha, Isabel/A-4279-2013
+ Rocha, Miguel/B-9404-2011
+ },
+ORCID-Numbers = {Rocha, Isabel/0000-0001-9494-3410
+ Rocha, Miguel/0000-0001-8439-8172
+ Vilaca, Paulo/0000-0002-1098-5849},
+Times-Cited = {17},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000287989200014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000288799300005,
+Author = {Xi, Yanping and Chen, Yi-Ping Phoebe and Qian, Chen and Wang, Fei},
+Title = {Comparative study of computational methods to detect the correlated
+ reaction sets in biochemical networks},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2011},
+Volume = {12},
+Number = {2},
+Pages = {132-150},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1093/bib/bbp068},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {correlated reaction set; enzyme subset; hard-coupled reaction set;
+ linear optimization; Monte Carlo sampling; network-based pathway
+ analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; POLYNOMIAL-TIME ALGORITHM; IN-SILICO MODELS;
+ GENOME-SCALE; PATHWAY ANALYSIS; METABOLIC NETWORK; SIGNALING NETWORKS;
+ ESCHERICHIA-COLI; EXTREME PATHWAYS; SYSTEMS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {qian, chen/HSG-9475-2023
+ Chen, Yi-Ping Phoebe/B-8844-2008},
+ORCID-Numbers = {Chen, Yi-Ping Phoebe/0000-0002-4122-3767},
+Times-Cited = {8},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000288799300005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000291875300002,
+Author = {Sorokina, Oksana and Corellou, Florence and Dauvillee, David and
+ Sorokin, Anatoly and Goryanin, Igor and Ball, Steven and Bouget,
+ Francois-Yves and Millar, Andrew J.},
+Title = {Microarray data can predict diurnal changes of starch content in the
+ picoalga Ostreococcus},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {FEB 26},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-36},
+Article-Number = {36},
+EISSN = {1752-0509},
+Keywords-Plus = {FREE-LIVING EUKARYOTE; REDOX REGULATION; ORCHESTRATED TRANSCRIPTION;
+ ESCHERICHIA-COLI; CIRCADIAN CLOCK; CELL-DIVISION; ARABIDOPSIS;
+ METABOLISM; CHLAMYDOMONAS; ENZYMES},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Bouget, Francois-Yves/A-5217-2011
+ Dauvillée, David/A-2174-2009
+ Millar, Andrew J/G-2423-2012
+ Goryanin, Igor/J-1913-2015
+ Goryanin, Igor/AAB-1400-2022
+ Sorokin, Anatoly/A-9090-2008
+ Corellou, Florence/E-1378-2011
+ Sorokina, Oksana V/B-1800-2010
+ },
+ORCID-Numbers = {Dauvillée, David/0000-0002-0751-9193
+ Millar, Andrew J/0000-0003-1756-3654
+ Goryanin, Igor/0000-0002-8293-774X
+ Sorokina, Oksana V/0000-0002-6786-9945
+ Corellou, Florence/0000-0001-8026-2120
+ Sorokin, Anatoly/0000-0002-0047-0606
+ Ball, Steven/0000-0003-1629-1650},
+Times-Cited = {36},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000291875300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000287580400014,
+Author = {Cornelius, Sean P. and Lee, Joo Sang and Motter, Adilson E.},
+Title = {Dispensability of Escherichia coli's latent pathways},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2011},
+Volume = {108},
+Number = {8},
+Pages = {3124-3129},
+Month = {FEB 22},
+Type = {Article},
+DOI = {10.1073/pnas.1009772108},
+ISSN = {0027-8424},
+Keywords = {complex networks; flux balance analysis; metabolic networks; gene
+ dispensability; synthetic rescues},
+Keywords-Plus = {ADAPTIVE EVOLUTION; GENETIC ROBUSTNESS; HIGH-THROUGHPUT; METABOLISM;
+ GROWTH; YEAST; EXPRESSION; MUTATIONS; PHENOTYPE; RESPONSES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Cornelius, Sean/L-9468-2014
+ },
+ORCID-Numbers = {Cornelius, Sean/0000-0001-8697-791X
+ Motter, Adilson E./0000-0003-1794-4828},
+Times-Cited = {20},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000287580400014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000291873400001,
+Author = {Pabinger, Stephan and Rader, Robert and Agren, Rasmus and Nielsen, Jens
+ and Trajanoski, Zlatko},
+Title = {MEMOSys: Bioinformatics platform for genome-scale metabolic models},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2011},
+Volume = {5},
+Month = {JAN 31},
+Type = {Article},
+DOI = {10.1186/1752-0509-5-20},
+Article-Number = {20},
+EISSN = {1752-0509},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; SYSTEMS BIOLOGY; RECONSTRUCTION; ANNOTATION;
+ DATABASE; PREDICTION; VALIDATION; PATHWAYS; LANGUAGE; SBML},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Trajanoski, Zlatko/AAT-6703-2021
+ Agren, Rasmus/I-1434-2012
+ },
+ORCID-Numbers = {Agren, Rasmus/0000-0002-9814-2191
+ Pabinger, Stephan/0000-0001-9876-5965},
+Times-Cited = {21},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000291873400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000287231200001,
+Author = {Hoppe, Andreas and Hoffmann, Sabrina and Gerasch, Andreas and Gille,
+ Christoph and Holzhuetter, Hermann-Georg},
+Title = {FASIMU: flexible software for flux-balance computation series in large
+ metabolic networks},
+Journal = {BMC BIOINFORMATICS},
+Year = {2011},
+Volume = {12},
+Month = {JAN 22},
+Type = {Article},
+DOI = {10.1186/1471-2105-12-28},
+Article-Number = {28},
+ISSN = {1471-2105},
+Keywords-Plus = {ESCHERICHIA-COLI; MODELS; MINIMIZATION; RECONSTRUCTION; PREDICTION;
+ CONSISTENT},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Hoppe, Andreas/0000-0001-5181-6411
+ Holzhutter, Hermann-Georg/0000-0002-5054-6023},
+Times-Cited = {42},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000287231200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000287081300001,
+Author = {Archer, Colin T. and Kim, Jihyun F. and Jeong, Haeyoung and Park, Jin
+ Hwan and Vickers, Claudia E. and Lee, Sang Yup and Nielsen, Lars K.},
+Title = {The genome sequence of E. coli W (ATCC 9637): comparative genome
+ analysis and an improved genome-scale reconstruction of E. coli},
+Journal = {BMC GENOMICS},
+Year = {2011},
+Volume = {12},
+Month = {JAN 6},
+Type = {Article},
+DOI = {10.1186/1471-2164-12-9},
+Article-Number = {9},
+ISSN = {1471-2164},
+Keywords-Plus = {ENTEROPATHOGENIC ESCHERICHIA-COLI; PROTEIN SECRETION SYSTEM; FLAGELLAR
+ GENE SYSTEM; LONG POLAR FIMBRIAE; INCI1 PLASMID R64; II SECRETION;
+ METABOLIC EVOLUTION; NUCLEOTIDE-SEQUENCE; ETHANOL-PRODUCTION; TRANSFER
+ REGION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Kim, Jihyun F./B-6286-2013
+ Lee, Sang Yup/C-1526-2011
+ Nielsen, Lars K/A-5519-2011
+ Vickers, Claudia E/A-1288-2009
+ },
+ORCID-Numbers = {Lee, Sang Yup/0000-0003-0599-3091
+ Nielsen, Lars K/0000-0001-8191-3511
+ Vickers, Claudia E/0000-0002-0792-050X
+ Jeong, Haeyoung/0000-0002-4479-4573},
+Times-Cited = {132},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000287081300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000285651100005,
+Author = {Chen, Xuewen and Alonso, Ana P. and Allen, Doug K. and Reed, Jennifer L.
+ and Shachar-Hill, Yair},
+Title = {Synergy between 13C-metabolic flux analysis and flux balance
+ analysis for understanding metabolic adaption to anaerobiosis in
+ E. coli},
+Journal = {METABOLIC ENGINEERING},
+Year = {2011},
+Volume = {13},
+Number = {1},
+Pages = {38-48},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2010.11.004},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {E. coli; Metabolic flux analysis; Flux balance analysis; Maintenance ATP
+ utilization; Formate hydrogen lyase; Incomplete TCA cycle},
+Keywords-Plus = {BIDIRECTIONAL REACTION STEPS; ESCHERICHIA-COLI; MASS-SPECTROMETRY;
+ BIOCHEMICAL NETWORKS; HYDROGEN-PRODUCTION; EVOLUTION; MODELS; RESPONSES;
+ KNOCKOUT; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Shachar-Hill, Yair/B-6165-2013
+ Reed, Jennifer L/E-5137-2011
+ Allen, Doug K/M-2836-2013
+ Alonso, Ana Paula/W-4283-2019},
+ORCID-Numbers = {Shachar-Hill, Yair/0000-0001-8793-5084
+ Reed, Jennifer L/0000-0001-7854-6220
+ Allen, Doug K/0000-0001-8599-8946
+ Alonso, Ana Paula/0000-0003-4696-1811},
+Times-Cited = {110},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000285651100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000299432000001,
+Author = {Eslamloueyan, Reza and Setoodeh, Payam},
+Title = {Optimization of Fed-Batch Recombinant Yeast Fermentation for Ethanol
+ Production Using a Reduced Dynamic Flux Balance Model Based on
+ Artificial Neural Networks},
+Journal = {CHEMICAL ENGINEERING COMMUNICATIONS},
+Year = {2011},
+Volume = {198},
+Number = {11},
+Pages = {1309-1338},
+Type = {Article},
+DOI = {10.1080/00986445.2011.560512},
+ISSN = {0098-6445},
+EISSN = {1563-5201},
+Keywords = {Dynamic flux balance analysis; Dynamic optimization; Fed-batch ethanol
+ production; Hybrid neural modeling; Model reduction},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; DIFFERENTIAL EVOLUTION; SIMULTANEOUS
+ SACCHARIFICATION; ESCHERICHIA-COLI; METHANOL SYNTHESIS; XYLOSE;
+ BIOREACTOR; CULTIVATION; GROWTH; BIOPROCESSES},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+Times-Cited = {16},
+Journal-ISO = {Chem. Eng. Commun.},
+Unique-ID = {WOS:000299432000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000293648300012,
+Author = {Fang, Xin and Wallqvist, Anders and Reifman, Jaques},
+Title = {Modeling synergistic drug inhibition of Mycobacterium
+ tuberculosis growth in murine macrophages},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2011},
+Volume = {7},
+Number = {9},
+Pages = {2622-2636},
+Type = {Article},
+DOI = {10.1039/c1mb05106g},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {CONSTRAINT-BASED ANALYSIS; FLUX BALANCE ANALYSIS;
+ SALMONELLA-TYPHIMURIUM; INTRACELLULAR GROWTH; BIOCHEMICAL NETWORKS;
+ ISOCITRATE LYASE-1; METABOLIC MODEL; RECONSTRUCTION; PHARMACOKINETICS;
+ PHARMACODYNAMICS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {wallqvist, anders/W-2584-2019},
+ORCID-Numbers = {wallqvist, anders/0000-0002-9775-7469},
+Times-Cited = {11},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000293648300012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000285626300023,
+Author = {Fleming, Ronan M. T. and Thiele, Ines},
+Title = {von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically
+ constrain metabolic models},
+Journal = {BIOINFORMATICS},
+Year = {2011},
+Volume = {27},
+Number = {1},
+Pages = {142-143},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btq607},
+ISSN = {1367-4803},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {38},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000285626300023},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000295816800021,
+Author = {Haggart, Charles R. and Bartell, Jennifer A. and Saucerman, Jeffrey J.
+ and Papin, Jason A.},
+Editor = {Jameson, D and Verma, M and Westerhoff, HV},
+Title = {WHOLE-GENOME METABOLIC NETWORK RECONSTRUCTION AND CONSTRAINT-BASED
+ MODELING},
+Booktitle = {METHODS IN ENZYMOLOGY, VOL 500: METHODS IN SYSTEMS BIOLOGY},
+Series = {Methods in Enzymology},
+Year = {2011},
+Volume = {500},
+Pages = {411-433},
+Type = {Review; Book Chapter},
+DOI = {10.1016/B978-0-12-385118-5.00021-9},
+ISSN = {0076-6879},
+ISBN = {978-0-12-385118-5},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; TRANSPOSON MUTANT LIBRARY; ESCHERICHIA-COLI;
+ PSEUDOMONAS-AERUGINOSA; OBJECTIVE FUNCTIONS; SCALE MODELS; SYSTEMS
+ BIOLOGY; FRAMEWORK; OPTIMIZATION; GENE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Saucerman, Jeffrey/0000-0001-9464-8374
+ Bartell, Jennifer/0000-0003-2750-9678
+ Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {22},
+Journal-ISO = {Methods Enzymol.},
+Unique-ID = {WOS:000295816800021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000301178900009,
+Author = {Mendum, Tom A. and Newcombe, Jane and Mannan, Ahmad A. and Kierzek,
+ Andrzej M. and McFadden, Johnjoe},
+Title = {Interrogation of global mutagenesis data with a genome scale model of
+ Neisseria meningitidis to assess gene fitness in vitro and
+ in sera},
+Journal = {GENOME BIOLOGY},
+Year = {2011},
+Volume = {12},
+Number = {12},
+Type = {Article},
+DOI = {10.1186/gb-2011-12-12-r127},
+Article-Number = {R127},
+ISSN = {1474-760X},
+Keywords-Plus = {IDENTIFICATION; METABOLISM; PROTEINS; GROWTH; ACQUISITION; RESISTANCE;
+ LACTATE; BINDING; CELLS; DSBA},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Mannan, Ahmad/AAT-1820-2021
+ },
+ORCID-Numbers = {Mannan, Ahmad/0000-0001-7628-8416
+ Kierzek, Andrzej/0000-0002-2605-9057
+ McFadden, Johnjoe/0000-0003-2145-0046},
+Times-Cited = {25},
+Journal-ISO = {Genome Biol.},
+Unique-ID = {WOS:000301178900009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000286094400001,
+Author = {Kozhenkov, Sergey and Dubinina, Yulia and Sedova, Mayya and Gupta,
+ Amarnath and Ponomarenko, Julia and Baitaluk, Michael},
+Title = {BiologicalNetworks 2.0-an integrative view of genome biology data},
+Journal = {BMC BIOINFORMATICS},
+Year = {2010},
+Volume = {11},
+Month = {DEC 29},
+Type = {Article},
+DOI = {10.1186/1471-2105-11-610},
+Article-Number = {610},
+ISSN = {1471-2105},
+Keywords-Plus = {REGULATORY NETWORKS; GENES; COMMUNITY; MODELS; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Gallardo, Julie/H-8878-2013
+ Ponomarenko, Julia/K-8105-2015
+ Sedova, Mayya/L-5528-2016
+ },
+ORCID-Numbers = {Sedova, Mayya/0000-0002-1121-2661
+ Ponomarenko, Julia/0000-0002-1477-9444},
+Times-Cited = {17},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000286094400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000285479700001,
+Author = {Fang, Xin and Wallqvist, Anders and Reifman, Jaques},
+Title = {Development and analysis of an in vivo-compatible
+ metabolic network of Mycobacterium tuberculosis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2010},
+Volume = {4},
+Month = {NOV 23},
+Type = {Article},
+DOI = {10.1186/1752-0509-4-160},
+Article-Number = {160},
+EISSN = {1752-0509},
+Keywords-Plus = {NITRIC-OXIDE; RECONSTRUCTION; GROWTH; GENE; MACROPHAGES; EXPRESSION;
+ RESPIRATION; PREDICTION; PATHOGENS; VIRULENCE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {wallqvist, anders/W-2584-2019},
+ORCID-Numbers = {wallqvist, anders/0000-0002-9775-7469},
+Times-Cited = {31},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000285479700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000284585400038,
+Author = {Kinnings, Sarah L. and Xie, Li and Fung, Kingston H. and Jackson,
+ Richard M. and Xie, Lei and Bourne, Philip E.},
+Title = {The Mycobacterium tuberculosis Drugome and Its
+ Polypharmacological Implications},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2010},
+Volume = {6},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1000976},
+Article-Number = {e1000976},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {PROTEIN-KINASE-G; ANTIBIOTIC-RESISTANCE; STRUCTURAL GENOMICS;
+ CONNECTIVITY MAP; TARGET; LIGAND; PREDICTION; SEQUENCE; SYSTEMS; GENE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Bourne, Philip/ABG-8967-2021},
+ORCID-Numbers = {Bourne, Philip/0000-0002-7618-7292},
+Times-Cited = {80},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000284585400038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000284585400015,
+Author = {Klitgord, Niels and Segre, Daniel},
+Title = {Environments that Induce Synthetic Microbial Ecosystems},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2010},
+Volume = {6},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1001002},
+Article-Number = {e1001002},
+EISSN = {1553-7358},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; METABOLIC NETWORKS;
+ METHANOCOCCUS-MARIPALUDIS; METHANOGENIC BACTERIA; HUMAN GUT; GENOME;
+ COOPERATION; RECONSTRUCTION; METHANE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Segrè, Daniel/A-1993-2009},
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914},
+Times-Cited = {218},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000284585400015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000284464100001,
+Author = {Dobson, Paul D. and Smallbone, Kieran and Jameson, Daniel and
+ Simeonidis, Evangelos and Lanthaler, Karin and Pir, Pinar and Lu, Chuan
+ and Swainston, Neil and Dunn, Warwick B. and Fisher, Paul and Hull,
+ Duncan and Brown, Marie and Oshota, Olusegun and Stanford, Natalie J.
+ and Kell, Douglas B. and King, Ross D. and Oliver, Stephen G. and
+ Stevens, Robert D. and Mendes, Pedro},
+Title = {Further developments towards a genome-scale metabolic model of yeast},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2010},
+Volume = {4},
+Month = {OCT 28},
+Type = {Article},
+DOI = {10.1186/1752-0509-4-145},
+Article-Number = {145},
+EISSN = {1752-0509},
+Keywords-Plus = {SACCHAROMYCES; RECONSTRUCTION; PROMISCUITY; INFORMATION; MARKUP; GENES},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Oliver, Stephen/AAQ-5992-2021
+ Jameson, Daniel/G-7386-2014
+ Pir, Pinar/AAA-5103-2022
+ Hull, Duncan/HGB-6116-2022
+ Dunn, Warwick/CAJ-1648-2022
+ Fisher, Paul/K-6012-2019
+ Kell, Douglas/E-8318-2011
+ },
+ORCID-Numbers = {Oliver, Stephen/0000-0003-3410-6439
+ Jameson, Daniel/0000-0003-1183-2825
+ Hull, Duncan/0000-0003-2387-503X
+ Dunn, Warwick/0000-0001-6924-0027
+ Fisher, Paul/0000-0003-1983-9204
+ Kell, Douglas/0000-0001-5838-7963
+ Simeonidis, Vangelis/0000-0001-6153-4493
+ King, Ross/0000-0001-7208-4387
+ Stanford, Natalie J/0000-0003-4958-0184
+ Pir, Pinar/0000-0002-0078-4904
+ Lu, Chuan/0000-0002-4898-6679
+ Mendes, Pedro/0000-0001-6507-9168
+ Smallbone, Kieran/0000-0003-2815-7045},
+Times-Cited = {79},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000284464100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000284088900001,
+Author = {Sigurdsson, Martin I. and Jamshidi, Neema and Steingrimsson, Eirikur and
+ Thiele, Ines and Palsson, Bernhard O.},
+Title = {A detailed genome-wide reconstruction of mouse metabolism based on human
+ Recon 1},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2010},
+Volume = {4},
+Month = {OCT 19},
+Type = {Article},
+DOI = {10.1186/1752-0509-4-140},
+Article-Number = {140},
+EISSN = {1752-0509},
+Keywords-Plus = {EMBRYONIC LETHALITY; NETWORK ANALYSIS; KNOCKOUT MICE; GENE; MODELS;
+ LIPOPROTEIN; EXPRESSION; PREDICTION; HOMOLOGY; DISRUPTION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Sigurdsson, Martin Ingi/I-9655-2016
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Sigurdsson, Martin Ingi/0000-0001-7054-0844
+ Steingrimsson, Eirikur/0000-0001-5826-7486
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {115},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000284088900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000282809700072,
+Author = {Chandrasekaran, Sriram and Price, Nathan D.},
+Title = {Probabilistic integrative modeling of genome-scale metabolic and
+ regulatory networks in Escherichia coli and
+ Mycobacterium tuberculosis},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2010},
+Volume = {107},
+Number = {41},
+Pages = {17845-17850},
+Month = {OCT 12},
+Type = {Article},
+DOI = {10.1073/pnas.1005139107},
+ISSN = {0027-8424},
+Keywords = {constraint-based modeling; flux balance analysis; metabolic networks;
+ transcriptional regulation; probabilistic regulation of metabolism},
+Keywords-Plus = {TRANSCRIPTIONAL REGULATION; GENE-EXPRESSION; SACCHAROMYCES-CEREVISIAE;
+ SINGLE-CELL; MECHANISMS; PREDICTION; DATABASE; RECONSTRUCTION;
+ CONSTRAINTS; MUTAGENESIS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Chandrasekaran, Sriram/AAD-9774-2019
+ Chandrasekaran, Sriram/AAF-4731-2019
+ },
+ORCID-Numbers = {Chandrasekaran, Sriram/0000-0002-8405-5708
+ Chandrasekaran, Sriram/0000-0002-8405-5708
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {274},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000282809700072},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000283434700001,
+Author = {Li, Limin and Zhou, Xiaobo and Ching, Wai-Ki and Wang, Ping},
+Title = {Predicting enzyme targets for cancer drugs by profiling human Metabolic
+ reactions in NCI-60 cell lines},
+Journal = {BMC BIOINFORMATICS},
+Year = {2010},
+Volume = {11},
+Month = {OCT 8},
+Type = {Article},
+DOI = {10.1186/1471-2105-11-501},
+Article-Number = {501},
+ISSN = {1471-2105},
+Keywords-Plus = {RECONSTRUCTION; IDENTIFICATION; OPINION; EFFLUX; MRP},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ching, Wai Ki/D-3062-2009},
+Times-Cited = {51},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000283434700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000283934000001,
+Author = {Bordbar, Aarash and Lewis, Nathan E. and Schellenberger, Jan and
+ Palsson, Bernhard O. and Jamshidi, Neema},
+Title = {Insight into human alveolar macrophage and M. tuberculosis
+ interactions via metabolic reconstructions},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2010},
+Volume = {6},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1038/msb.2010.68},
+Article-Number = {422},
+ISSN = {1744-4292},
+Keywords = {computational biology; host-pathogen; Mycobacterium tuberculosis;
+ systems biology; macrophage},
+Keywords-Plus = {MYCOBACTERIUM-TUBERCULOSIS; GENE-EXPRESSION; STATIONARY-PHASE;
+ CELL-LINE; ADAPTATION; PROTEIN; BIOSYNTHESIS; PERSISTENCE; PREDICTION;
+ TRANSPORT},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ /AAG-5264-2021
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ /0000-0001-6460-6771
+ Jamshidi, Neema/0000-0003-3857-9735
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {205},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000283934000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000282281000027,
+Author = {Oberhardt, Matthew A. and Goldberg, Joanna B. and Hogardt, Michael and
+ Papin, Jason A.},
+Title = {Metabolic Network Analysis of Pseudomonas aeruginosa during
+ Chronic Cystic Fibrosis Lung Infection},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2010},
+Volume = {192},
+Number = {20},
+Pages = {5534-5548},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1128/JB.00900-10},
+ISSN = {0021-9193},
+Keywords-Plus = {CHRONIC PULMONARY INFECTION; TRANSCRIPTIONAL REGULATION; OPPORTUNISTIC
+ PATHOGEN; GROWTH PHENOTYPES; ESCHERICHIA-COLI; MODELS; RECONSTRUCTION;
+ MICROARRAYS; ADAPTATION; PREDICTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {71},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000282281000027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000282595100025,
+Author = {Woo, Han Min and Noack, Stephan and Seibold, Gerd M. and Willbold,
+ Sabine and Eikmanns, Bernhard J. and Bott, Michael},
+Title = {Link between Phosphate Starvation and Glycogen Metabolism in
+ Corynebacterium glutamicum, Revealed by Metabolomics},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2010},
+Volume = {76},
+Number = {20},
+Pages = {6910-6919},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1128/AEM.01375-10},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords-Plus = {ESCHERICHIA-COLI; REGULATOR SUGR; EXPRESSION; TREHALOSE; SYSTEM; GROWTH;
+ DEHYDROGENASE; MALTODEXTRIN; ENCODES; MODELS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Seibold, Gerd/F-9617-2011
+ Woo, Han Min/J-1847-2015
+ Bott, Michael/E-8004-2011
+ },
+ORCID-Numbers = {Seibold, Gerd/0000-0002-9823-8134
+ Woo, Han Min/0000-0002-8797-0477
+ Bott, Michael/0000-0002-4701-8254
+ Eikmanns, Bernhard/0000-0002-3069-431X
+ Noack, Stephan/0000-0001-9784-3626
+ Willbold, Sabine/0000-0002-8335-9478},
+Times-Cited = {28},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000282595100025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000283434500001,
+Author = {Gudmundsson, Steinn and Thiele, Ines},
+Title = {Computationally efficient flux variability analysis},
+Journal = {BMC BIOINFORMATICS},
+Year = {2010},
+Volume = {11},
+Month = {SEP 29},
+Type = {Article},
+DOI = {10.1186/1471-2105-11-489},
+Article-Number = {489},
+ISSN = {1471-2105},
+Keywords-Plus = {METABOLIC NETWORK; RECONSTRUCTION; OPTIMIZATION; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {206},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000283434500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000282372600008,
+Author = {Chang, Roger L. and Xie, Li and Xie, Lei and Bourne, Philip E. and
+ Palsson, Bernhard O.},
+Title = {Drug Off-Target Effects Predicted Using Structural Analysis in the
+ Context of a Metabolic Network Model},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2010},
+Volume = {6},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1000938},
+Article-Number = {e1000938},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ESTER TRANSFER PROTEIN; BLOOD-PRESSURE; FUMARASE DEFICIENCY; DIETARY
+ CALCIUM; MESSENGER-RNA; RAT-KIDNEY; MITOCHONDRIAL; HYPERTENSION; SODIUM;
+ GENE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Bourne, Philip/ABG-8967-2021
+ },
+ORCID-Numbers = {Bourne, Philip/0000-0002-7618-7292
+ Palsson, Bernhard/0000-0003-2357-6785
+ Chang, Roger/0000-0003-1630-6584},
+Times-Cited = {160},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000282372600008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000281714100061,
+Author = {Forth, Thomas and McConkey, Glenn A. and Westhead, David R.},
+Title = {MetNetMaker: a free and open-source tool for the creation of novel
+ metabolic networks in SBML format},
+Journal = {BIOINFORMATICS},
+Year = {2010},
+Volume = {26},
+Number = {18},
+Pages = {2352-2353},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btq425},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {McConkey, Glenn A./I-4062-2019
+ },
+ORCID-Numbers = {McConkey, Glenn/0000-0001-6529-794X
+ Westhead, David/0000-0002-0519-3820},
+Times-Cited = {12},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000281714100061},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000283629300007,
+Author = {Hala, D. and Amin, A. and Mikler, A. and Huggett, D. B.},
+Title = {A CONSTRAINT-BASED STOICHIOMETRIC MODEL OF THE STEROIDOGENIC NETWORK OF
+ ZEBRAFISH (DANIO RERIO)},
+Journal = {JOURNAL OF BIOLOGICAL SYSTEMS},
+Year = {2010},
+Volume = {18},
+Number = {3},
+Pages = {669-685},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1142/S0218339010003469},
+ISSN = {0218-3390},
+EISSN = {1793-6470},
+Keywords = {Zebrafish; Steroidogenesis; Network; Stoichiometric; Reconstruction},
+Keywords-Plus = {AROMATASE INHIBITOR FADROZOLE; ESCHERICHIA-COLI; RECONSTRUCTION;
+ METABOLISM; VITELLOGENESIS; OPTIMIZATION; PATHWAY; SYSTEMS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ORCID-Numbers = {Mikler, Armin/0000-0002-5253-144X},
+Times-Cited = {3},
+Journal-ISO = {J. Biol. Syst.},
+Unique-ID = {WOS:000283629300007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000281570000033,
+Author = {Knoop, Henning and Zilliges, Yvonne and Lockau, Wolfgang and Steuer,
+ Ralf},
+Title = {The Metabolic Network of Synechocystis sp. PCC 6803: Systemic
+ Properties of Autotrophic Growth},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2010},
+Volume = {154},
+Number = {1},
+Pages = {410-422},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1104/pp.110.157198},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; NATURAL-PRODUCTS; CYANOBACTERIA; DATABASE;
+ GENOME; IDENTIFICATION; INFORMATION; CYANOBASE; MODELS; CYCLE},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Steuer, Ralf/E-7482-2017},
+ORCID-Numbers = {Steuer, Ralf/0000-0003-2217-1655},
+Times-Cited = {158},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000281570000033},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000282226900027,
+Author = {Kschischo, M.},
+Title = {A gentle introduction to the thermodynamics of biochemical
+ stoichiometric networks in steady state},
+Journal = {EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS},
+Year = {2010},
+Volume = {187},
+Number = {1},
+Pages = {255-274},
+Month = {SEP},
+Type = {Review},
+DOI = {10.1140/epjst/e2010-01290-3},
+ISSN = {1951-6355},
+EISSN = {1951-6401},
+Keywords-Plus = {GENOME-SCALE MODELS; FLUCTUATION THEOREM; METABOLIC NETWORKS;
+ RECONSTRUCTION; CONSTRAINT; BALANCE; ENERGY; PREDICTION; SYSTEMS;
+ OPTIMIZATION},
+Research-Areas = {Physics},
+Web-of-Science-Categories = {Physics, Multidisciplinary},
+Times-Cited = {7},
+Journal-ISO = {Eur. Phys. J.-Spec. Top.},
+Unique-ID = {WOS:000282226900027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000282766200002,
+Author = {Plata, German and Hsiao, Tzu-Lin and Olszewski, Kellen L. and Llinas,
+ Manuel and Vitkup, Dennis},
+Title = {Reconstruction and flux-balance analysis of the Plasmodium
+ falciparum metabolic network},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2010},
+Volume = {6},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1038/msb.2010.60},
+Article-Number = {408},
+ISSN = {1744-4292},
+Keywords = {flux-balance analysis; Plasmodium falciparum metabolism; systems biology},
+Keywords-Plus = {HUMAN RED-CELL; 2-CYS PEROXIREDOXIN TPX-1; HUMAN MALARIA PARASITES;
+ IN-VITRO; SACCHAROMYCES-CEREVISIAE; BIOCHEMICAL-CHARACTERIZATION;
+ TRANSCRIPTIONAL REGULATION; ANTIMALARIAL ACTIVITY; ERYTHROCYTIC STAGES;
+ POLYAMINE SYNTHESIS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Plata, German/GXG-8357-2022
+ Califano, Andrea/F-7239-2012
+ },
+ORCID-Numbers = {Plata, German/0000-0002-6470-7748},
+Times-Cited = {97},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000282766200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000281234700013,
+Author = {Resendis-Antonio, Osbaldo and Checa, Alberto and Encarnacion, Sergio},
+Title = {Modeling Core Metabolism in Cancer Cells: Surveying the Topology
+ Underlying the Warburg Effect},
+Journal = {PLOS ONE},
+Year = {2010},
+Volume = {5},
+Number = {8},
+Month = {AUG 25},
+Type = {Article},
+DOI = {10.1371/journal.pone.0012383},
+Article-Number = {e12383},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; AEROBIC GLYCOLYSIS; TUMOR SUPPRESSORS;
+ DRUG-RESISTANCE; GROWTH; RECONSTRUCTION; CONSTRAINTS; INHIBITION;
+ NETWORKS; BALANCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {RESENDIS, OSBALDO/ADE-5280-2022
+ },
+ORCID-Numbers = {RESENDIS, OSBALDO/0000-0001-5220-541X
+ Encarnacion Guevara, Sergio/0000-0001-7889-1681},
+Times-Cited = {53},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000281234700013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000282259600001,
+Author = {Raghunathan, Anu and Shin, Sookil and Daefler, Simon},
+Title = {Systems approach to investigating host-pathogen interactions in
+ infections with the biothreat agent Francisella.
+ Constraints-based model of Francisella tularensis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2010},
+Volume = {4},
+Month = {AUG 23},
+Type = {Article},
+DOI = {10.1186/1752-0509-4-118},
+Article-Number = {118},
+ISSN = {1752-0509},
+Keywords-Plus = {SCALE METABOLIC RECONSTRUCTION; CHEMICALLY DEFINED MEDIUM; LIVE VACCINE
+ STRAIN; PASTEURELLA-TULARENSIS; ESCHERICHIA-COLI; ATTENUATED VIRULENCE;
+ PROTEIN EXPRESSION; GROWTH; IDENTIFICATION; RESISTANCE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+Times-Cited = {36},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000282259600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000280968100002,
+Author = {Barton, Michael D. and Delneri, Daniela and Oliver, Stephen G. and
+ Rattray, Magnus and Bergman, Casey M.},
+Title = {Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast},
+Journal = {PLOS ONE},
+Year = {2010},
+Volume = {5},
+Number = {8},
+Month = {AUG 17},
+Type = {Article},
+DOI = {10.1371/journal.pone.0011935},
+Article-Number = {e11935},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; PROTEIN EVOLUTION; GENE-EXPRESSION; SELECTION;
+ RECONSTRUCTION; MINIMIZATION; MODEL; RATES; USAGE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Oliver, Stephen/AAQ-5992-2021
+ Bergman, Casey/F-7854-2010
+ Rattray, Magnus/AAE-3297-2021
+ Rattray, Magnus/B-4393-2009
+ Zeef, Leo/D-6922-2011
+ },
+ORCID-Numbers = {Oliver, Stephen/0000-0003-3410-6439
+ Bergman, Casey/0000-0002-5462-9854
+ Rattray, Magnus/0000-0001-8196-5565
+ Rattray, Magnus/0000-0001-8196-5565
+ Barton, Michael/0000-0002-0064-2279
+ Delneri, Daniela/0000-0001-8070-411X},
+Times-Cited = {49},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000280968100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000280374100006,
+Author = {Koschuetzki, Dirk and Junker, Bjoern H. and Schwender, Joerg and
+ Schreiber, Falk},
+Title = {Structural analysis of metabolic networks based on flux centrality},
+Journal = {JOURNAL OF THEORETICAL BIOLOGY},
+Year = {2010},
+Volume = {265},
+Number = {3},
+Pages = {261-269},
+Month = {AUG 7},
+Type = {Article},
+DOI = {10.1016/j.jtbi.2010.05.009},
+ISSN = {0022-5193},
+EISSN = {1095-8541},
+Keywords = {Network centralities; Metabolism; Network analysis; Flux balance
+ analysis},
+Keywords-Plus = {ESCHERICHIA-COLI; CONNECTIVITY STRUCTURE; SMALL WORLD; ORGANIZATION;
+ RECONSTRUCTION; PREDICTION; GROWTH; MG1655},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Schwender, Jorg/P-2282-2014},
+ORCID-Numbers = {Schwender, Jorg/0000-0003-1350-4171},
+Times-Cited = {11},
+Journal-ISO = {J. Theor. Biol.},
+Unique-ID = {WOS:000280374100006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000280808100001,
+Author = {Chen Qi and Wang Zhuo and Wei DongQing},
+Title = {Progress in the applications of flux analysis of metabolic networks},
+Journal = {CHINESE SCIENCE BULLETIN},
+Year = {2010},
+Volume = {55},
+Number = {22},
+Pages = {2315-2322},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1007/s11434-010-3022-x},
+ISSN = {1001-6538},
+EISSN = {1861-9541},
+Keywords = {metabolic network; flux balance analysis; minimization of metabolic
+ adjustment; gene regulation; topological property},
+Keywords-Plus = {BALANCE ANALYSIS; PATHWAY ANALYSIS; GENE-EXPRESSION; MODELS;
+ ORGANIZATION; DEFINITION; PREDICTION; TARGETS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {4},
+Journal-ISO = {Chin. Sci. Bull.},
+Unique-ID = {WOS:000280808100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000281389500019,
+Author = {Islam, M. Ahsanul and Edwards, Elizabeth A. and Mahadevan, Radhakrishnan},
+Title = {Characterizing the Metabolism of Dehalococcoides with a
+ Constraint-Based Model},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2010},
+Volume = {6},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1000887},
+Article-Number = {e1000887},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {DEHALOGENASE-HOMOLOGOUS GENES; VINYL-CHLORIDE REDUCTASE; SP STRAIN;
+ ENERGY-CONSERVATION; ELECTRON-TRANSPORT; MAINTENANCE ENERGY;
+ CIS-DICHLOROETHENE; BACTERIAL-GROWTH; GENOME SEQUENCE; PAN-GENOME},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Mahadevan, Radhakrishnan/A-8502-2008
+ Edwards, Elizabeth Anne/GXV-2307-2022
+ },
+ORCID-Numbers = {Mahadevan, Radhakrishnan/0000-0002-1270-9063
+ Edwards, Elizabeth/0000-0002-8071-338X
+ Islam, M. Ahsanul/0000-0001-9585-6263},
+Times-Cited = {41},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000281389500019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000282256000001,
+Author = {Veeramani, Balaji and Bader, Joel S.},
+Title = {Predicting functional associations from metabolism using bi-partite
+ network algorithms},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2010},
+Volume = {4},
+Month = {JUL 14},
+Type = {Article},
+DOI = {10.1186/1752-0509-4-95},
+Article-Number = {95},
+EISSN = {1752-0509},
+Keywords-Plus = {GENETIC INTERACTIONS; SEMANTIC SIMILARITY; MODELS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Bader, Joel S/A-1818-2009},
+ORCID-Numbers = {Bader, Joel S/0000-0002-6020-4625},
+Times-Cited = {5},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000282256000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000280622500002,
+Author = {Blazeck, John and Alper, Hal},
+Title = {Systems metabolic engineering: Genome-scale models and beyond},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2010},
+Volume = {5},
+Number = {7},
+Pages = {647-659},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1002/biot.200900247},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Genome-scale modeling; Metabolic engineering; Systems biology},
+Keywords-Plus = {IMPROVED ETHANOL TOLERANCE; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE;
+ TRANSCRIPTIONAL REGULATION; LYCOPENE BIOSYNTHESIS; MICROBIAL-PRODUCTION;
+ BIOCYC COLLECTION; DATABASE; RECONSTRUCTION; SEQUENCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Blazeck, John/0000-0002-6110-2938},
+Times-Cited = {90},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000280622500002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000280528300028,
+Author = {Bordel, Sergio and Agren, Rasmus and Nielsen, Jens},
+Title = {Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals
+ Transcriptional Regulation in Key Enzymes},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2010},
+Volume = {6},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1000859},
+Article-Number = {e1000859},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; FLUXES; PROTEIN; INTEGRATION; BIOLOGY; MODELS;
+ STRAIN; STATES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {damiani, chiara/R-4256-2016
+ Bordel, Sergio/A-3325-2017
+ Agren, Rasmus/I-1434-2012
+ Nielsen, Jens Bo/C-7632-2015
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Bordel, Sergio/0000-0001-6162-6478
+ Agren, Rasmus/0000-0002-9814-2191
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {128},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000280528300028},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000284148900024,
+Author = {Cvijovic, Marija and Olivares-Hernandez, Roberto and Agren, Rasmus and
+ Dahr, Niklas and Vongsangnak, Wanwipa and Nookaew, Intawat and Patil,
+ Kiran Raosaheb and Nielsen, Jens},
+Title = {BioMet Toolbox: genome-wide analysis of metabolism},
+Journal = {NUCLEIC ACIDS RESEARCH},
+Year = {2010},
+Volume = {38},
+Number = {2},
+Pages = {W144-W149},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1093/nar/gkq404},
+ISSN = {0305-1048},
+EISSN = {1362-4962},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; SYSTEMS BIOLOGY; TRANSCRIPTIONAL REGULATION;
+ NETWORK; MODELS; RECONSTRUCTION; FLUXES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Patil, Kiran R/B-9709-2009
+ Agren, Rasmus/I-1434-2012
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Patil, Kiran R/0000-0002-6166-8640
+ Agren, Rasmus/0000-0002-9814-2191
+ Nielsen, Jens/0000-0002-9955-6003
+ Olivares-Hernandez, Roberto/0000-0002-8431-4052},
+Times-Cited = {67},
+Journal-ISO = {Nucleic Acids Res.},
+Unique-ID = {WOS:000284148900024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000280622500009,
+Author = {Salimi, Fahimeh and Zhuang, Kai and Mahadevan, Radhakrishnan},
+Title = {Genome-scale metabolic modeling of a clostridial co-culture for
+ consolidated bioprocessing},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2010},
+Volume = {5},
+Number = {7},
+Pages = {726-738},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/biot.201000159},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Clostridial co-culture; Clostridium acetobutylicum; Clostridium
+ cellulolyticum; Genome-scale metabolic modeling; Systems biology},
+Keywords-Plus = {ACETONE-BUTANOL FERMENTATION; CHEMICALLY-DEFINED MEDIUM; STATE
+ CONTINUOUS CULTURES; FLUX BALANCE ANALYSIS; SYNTHETIC MEDIUM;
+ ACETOBUTYLICUM ATCC-824; CELLULOSE FERMENTATION; ESCHERICHIA-COLI;
+ CELLULOLYTICUM; KINETICS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Mahadevan, Radhakrishnan/A-8502-2008},
+ORCID-Numbers = {Mahadevan, Radhakrishnan/0000-0002-1270-9063},
+Times-Cited = {84},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000280622500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000280622500003,
+Author = {Schmidt, Brian J. and Lin-Schmidt, Xiefan and Chamberlin, Austin and
+ Salehi-Ashtiani, Kourosh and Papin, Jason A.},
+Title = {Metabolic systems analysis to advance algal biotechnology},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2010},
+Volume = {5},
+Number = {7},
+Pages = {660-670},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1002/biot.201000129},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Algae; Biofuels; Chlamydomonas reinhardtii; Flux balance analysis;
+ Metabolic network},
+Keywords-Plus = {ROBUST SYNTHETIC BIOLOGY; FLUX BALANCE ANALYSIS; IN-SILICO;
+ CHLAMYDOMONAS-REINHARDTII; ESCHERICHIA-COLI;
+ MANNHEIMIA-SUCCINICIPRODUCENS; SACCHAROMYCES-CEREVISIAE; BIOETHANOL
+ PRODUCTION; MITOCHONDRIAL-DNA; GENOME SEQUENCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Schmidt, Brian J/A-3805-2009
+ },
+ORCID-Numbers = {Salehi-Ashtiani, Kourosh/0000-0002-6521-5243
+ Papin, Jason/0000-0002-2769-5805
+ Lin-Schmidt, Xiefan/0000-0001-8292-3930
+ Schmidt, Brian/0000-0001-6015-9636},
+Times-Cited = {22},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000280622500003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000278031800009,
+Author = {Liu, Liming and Agren, Rasmus and Bordel, Sergio and Nielsen, Jens},
+Title = {Use of genome-scale metabolic models for understanding microbial
+ physiology},
+Journal = {FEBS LETTERS},
+Year = {2010},
+Volume = {584},
+Number = {12, SI},
+Pages = {2556-2564},
+Month = {JUN 18},
+Type = {Review},
+DOI = {10.1016/j.febslet.2010.04.052},
+ISSN = {0014-5793},
+EISSN = {1873-3468},
+Keywords = {Genome-scale metabolic model; Reconstruction; Algorithm; Microbial
+ physiology},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; ESSENTIAL GENES;
+ TRANSCRIPTIONAL REGULATION; OPTIMIZATION FRAMEWORK;
+ INFORMATION-RETRIEVAL; SYSTEM; CELL; STRESS; OVERPRODUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+ResearcherID-Numbers = {Agren, Rasmus/I-1434-2012
+ Liu, Liming/B-1972-2009
+ Nielsen, Jens Bo/C-7632-2015
+ Bordel, Sergio/A-3325-2017
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Agren, Rasmus/0000-0002-9814-2191
+ Liu, Liming/0000-0003-3022-936X
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Bordel, Sergio/0000-0001-6162-6478
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {71},
+Journal-ISO = {FEBS Lett.},
+Unique-ID = {WOS:000278031800009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000278689000031,
+Author = {Yizhak, Keren and Benyamini, Tomer and Liebermeister, Wolfram and
+ Ruppin, Eytan and Shlomi, Tomer},
+Title = {Integrating quantitative proteomics and metabolomics with a genome-scale
+ metabolic network model},
+Journal = {BIOINFORMATICS},
+Year = {2010},
+Volume = {26},
+Number = {12},
+Pages = {i255-i260},
+Month = {JUN 15},
+Note = {18th Annual International Conference on Intelligent Systems for
+ Molecular Biology (ISMB), Boston, MA, JUL 11-13, 2010},
+Type = {Article; Proceedings Paper},
+DOI = {10.1093/bioinformatics/btq183},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {ESCHERICHIA-COLI; GENE-EXPRESSION; SACCHAROMYCES-CEREVISIAE; FLUX;
+ RECONSTRUCTION; CONSTRAINTS; PREDICTION; FRAMEWORK; TISSUE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Liebermeister, Wolfram/AAC-7326-2020
+ Ruppin, Eytan/R-9698-2017},
+ORCID-Numbers = {Liebermeister, Wolfram/0000-0002-2568-2381
+ Ruppin, Eytan/0000-0002-7862-3940},
+Times-Cited = {176},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000278689000031},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000276821400001,
+Author = {Feist, Adam M. and Zielinski, Daniel C. and Orth, Jeffrey D. and
+ Schellenberger, Jan and Herrgard, Markus J. and Palsson, Bernhard O.},
+Title = {Model-driven evaluation of the production potential for growth-coupled
+ products of Escherichia coli},
+Journal = {METABOLIC ENGINEERING},
+Year = {2010},
+Volume = {12},
+Number = {3},
+Pages = {173-186},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2009.10.003},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Systems biology; Escherichia coli; Metabolism; OptGene; OptKnock},
+Keywords-Plus = {IN-SILICO MODELS; MICROBIAL-PRODUCTION; ADAPTIVE EVOLUTION; SYSTEMS
+ BIOLOGY; AMINO-ACIDS; FRAMEWORK; DESIGN; RECONSTRUCTION; STRATEGIES;
+ GLYCEROL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785
+ Zielinski, Daniel/0000-0001-6452-483X},
+Times-Cited = {165},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000276821400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000278360800001,
+Author = {Schellenberger, Jan and Park, Junyoung O. and Conrad, Tom M. and
+ Palsson, Bernhard O.},
+Title = {BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale
+ metabolic reconstructions},
+Journal = {BMC BIOINFORMATICS},
+Year = {2010},
+Volume = {11},
+Month = {APR 29},
+Type = {Article},
+DOI = {10.1186/1471-2105-11-213},
+Article-Number = {213},
+ISSN = {1471-2105},
+Keywords-Plus = {KINETIC-MODEL; NETWORK; ANNOTATION; EXPANSION; CELL},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Park, Junyoung/AAL-8090-2020
+ },
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785
+ Park, Jun/0000-0001-9869-8993},
+Times-Cited = {384},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000278360800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000277360800001,
+Author = {Rocha, Isabel and Maia, Paulo and Evangelista, Pedro and Vilaca, Paulo
+ and Soares, Simao and Pinto, Jose P. and Nielsen, Jens and Patil, Kiran
+ R. and Ferreira, Eugenio C. and Rocha, Miguel},
+Title = {OptFlux: an open-source software platform for in silico metabolic
+ engineering},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2010},
+Volume = {4},
+Month = {APR 19},
+Type = {Article},
+DOI = {10.1186/1752-0509-4-45},
+Article-Number = {45},
+EISSN = {1752-0509},
+Keywords-Plus = {KNOCKOUT STRATEGIES; ESCHERICHIA-COLI; RECONSTRUCTION; REPRESENTATION;
+ BIOTECHNOLOGY; COMPUTATION; NETWORKS; PATHWAYS; MODELS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ferreira, Eugénio Campos/B-5417-2009
+ Nielsen, Jens Bo/C-7632-2015
+ Maia, Paulo/AAM-1025-2021
+ Patil, Kiran R/B-9709-2009
+ Rocha, Isabel/A-4279-2013
+ Maia, Paulo/F-9148-2010
+ Rocha, Miguel/B-9404-2011
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Ferreira, Eugénio Campos/0000-0002-5400-3333
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Patil, Kiran R/0000-0002-6166-8640
+ Rocha, Isabel/0000-0001-9494-3410
+ Maia, Paulo/0000-0002-0848-8683
+ Rocha, Miguel/0000-0001-8439-8172
+ Nielsen, Jens/0000-0002-9955-6003
+ Basto Gouveia Pereira Pinto, Jose Pedro/0000-0002-8762-8030
+ Vilaca, Paulo/0000-0002-1098-5849
+ Evangelista, Pedro Tiago/0000-0002-8408-0989},
+Times-Cited = {249},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000277360800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000276787300011,
+Author = {Dietz, Sven and Panke, Sven},
+Title = {Microbial systems engineering: First successes and the way ahead},
+Journal = {BIOESSAYS},
+Year = {2010},
+Volume = {32},
+Number = {4, SI},
+Pages = {356-362},
+Month = {APR},
+Type = {Review},
+DOI = {10.1002/bies.200900174},
+ISSN = {0265-9247},
+EISSN = {1521-1878},
+Keywords = {biological chassis; biotechnology; genome engineering; minimal genomes;
+ synthetic biology},
+Keywords-Plus = {ESCHERICHIA-COLI GENOME; MINIMAL-GENE-SET; REDUCED-GENOME;
+ MYCOPLASMA-GENITALIUM; METABOLIC NETWORKS; BACILLUS-SUBTILIS; AUTOMATIC
+ DESIGN; EXPRESSION; BACTERIUM; CELL},
+Research-Areas = {Biochemistry \& Molecular Biology; Life Sciences \& Biomedicine - Other
+ Topics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biology},
+ORCID-Numbers = {Panke, Sven/0000-0002-9368-539X},
+Times-Cited = {12},
+Journal-ISO = {Bioessays},
+Unique-ID = {WOS:000276787300011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000276565100001,
+Author = {Alam, Mohammad T. and Merlo, Maria E. and Hodgson, David A. and
+ Wellington, Elizabeth M. H. and Takano, Eriko and Breitling, Rainer and
+ STREAM Consortium},
+Title = {Metabolic modeling and analysis of the metabolic switch in
+ Streptomyces coelicolor},
+Journal = {BMC GENOMICS},
+Year = {2010},
+Volume = {11},
+Month = {MAR 26},
+Type = {Article},
+DOI = {10.1186/1471-2164-11-202},
+Article-Number = {202},
+ISSN = {1471-2164},
+Keywords-Plus = {GENOME-SCALE MODELS; GENE-EXPRESSION; A3(2); CONSTRAINTS; EVOLUTION;
+ RECONSTRUCTION; BIOSYNTHESIS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Gaze, William/HCH-3571-2022
+ Moore, Jonathan D/D-1796-2013
+ Dijkhuizen, Lubbert/E-9454-2014
+ Alam, Mohammad Tauqeer/A-5304-2013
+ },
+ORCID-Numbers = {Moore, Jonathan D/0000-0002-5486-0407
+ Alam, Mohammad Tauqeer/0000-0002-6872-0691
+ Merlo, Maria Elena/0000-0003-2208-9467
+ Wellington, ELizabeth/0000-0002-4329-0699
+ Breitling, Rainer/0000-0001-7173-0922
+ Takano, Eriko/0000-0002-6791-3256
+ Omara, Walid/0000-0001-5086-8260
+ Battke, Florian/0000-0001-6021-5837
+ Krabben, Preben/0000-0003-3105-6173},
+Times-Cited = {69},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000276565100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000274909200022,
+Author = {Ramsey, J. S. and MacDonald, S. J. and Jander, G. and Nakabachi, A. and
+ Thomas, G. H. and Douglas, A. E.},
+Title = {Genomic evidence for complementary purine metabolism in the pea aphid,
+ Acyrthosiphon pisum, and its symbiotic bacterium Buchnera
+ aphidicola},
+Journal = {INSECT MOLECULAR BIOLOGY},
+Year = {2010},
+Volume = {19},
+Number = {2},
+Pages = {241-248},
+Month = {MAR 10},
+Type = {Article},
+DOI = {10.1111/j.1365-2583.2009.00945.x},
+ISSN = {0962-1075},
+Keywords = {Acyrthosiphon pisum; Buchnera aphidicola; insect; nucleotide synthesis;
+ purine salvage; pea aphid; symbiosis},
+Keywords-Plus = {POLYAMINE COMPOSITION; NITROGEN; EXCRETION; INSECT;
+ PHOSPHORIBOSYLTRANSFERASE; EXPRESSION; STRESS; ACID; GENE},
+Research-Areas = {Biochemistry \& Molecular Biology; Entomology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Entomology},
+ResearcherID-Numbers = {Jander, Georg/E-7101-2012
+ Thomas, Gavin H/E-5753-2011
+ Nakabachi, Atsushi/H-1661-2011
+ },
+ORCID-Numbers = {Thomas, Gavin H/0000-0002-9763-1313
+ Nakabachi, Atsushi/0000-0003-0281-1723
+ Macdonald, Sandy/0000-0002-4112-0987},
+Times-Cited = {41},
+Journal-ISO = {Insect Mol. Biol.},
+Unique-ID = {WOS:000274909200022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000275581900006,
+Author = {Acuna, Vicente and Marchetti-Spaccamela, Alberto and Sagot, Marie-France
+ and Stougie, Leen},
+Title = {A note on the complexity of finding and enumerating elementary modes},
+Journal = {BIOSYSTEMS},
+Year = {2010},
+Volume = {99},
+Number = {3},
+Pages = {210-214},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2009.11.004},
+ISSN = {0303-2647},
+Keywords = {Metabolic networks; Computational complexity; Elementary modes;
+ Enumeration},
+Keywords-Plus = {GENOME-SCALE MODEL; METABOLIC NETWORKS; STRATEGIES; ALGORITHM; SYSTEMS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ORCID-Numbers = {/0000-0002-5933-9960},
+Times-Cited = {37},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000275581900006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000274860200001,
+Author = {Boghigian, Brett A. and Seth, Gargi and Kiss, Robert and Pfeifer, Blaine
+ A.},
+Title = {Metabolic flux analysis and pharmaceutical production},
+Journal = {METABOLIC ENGINEERING},
+Year = {2010},
+Volume = {12},
+Number = {2},
+Pages = {81-95},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ymben.2009.10.004},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {MFA; FBA; Escherichia coli; CHO; Hybridoma; C-13 labeling},
+Keywords-Plus = {COMPLETE GENOME SEQUENCE; HUMAN RED-CELL; BIOCHEMICAL SYSTEMS-ANALYSIS;
+ ESCHERICHIA-COLI STRAINS; NATURAL-PRODUCTS; SCALE RECONSTRUCTION;
+ LYCOPENE PRODUCTION; PATHWAY ANALYSIS; BALANCE MODELS; WILD-TYPE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {80},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000274860200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000275288300022,
+Author = {Orth, Jeffrey D. and Thiele, Ines and Palsson, Bernhard O.},
+Title = {What is flux balance analysis?},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2010},
+Volume = {28},
+Number = {3},
+Pages = {245-248},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1038/nbt.1614},
+ISSN = {1087-0156},
+Keywords-Plus = {SCALE METABOLIC RECONSTRUCTIONS; ESCHERICHIA-COLI; IN-SILICO; MODELS;
+ NETWORKS; OPTIMIZATION; CAPABILITIES; INFORMATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {damiani, chiara/R-4256-2016
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {2278},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000275288300022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000275524400005,
+Author = {Heino, Jenni and Calvetti, Daniela and Somersalo, Erkki},
+Title = {METABOLICA: A statistical research tool for analyzing metabolic networks},
+Journal = {COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE},
+Year = {2010},
+Volume = {97},
+Number = {2},
+Pages = {151-167},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1016/j.cmpb.2009.07.007},
+ISSN = {0169-2607},
+EISSN = {1872-7565},
+Keywords = {Cellular metabolism; Steady state; Bayesian; Flux balance analysis;
+ Markov Chain Monte Carlo},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; PARAMETER-ESTIMATION; SKELETAL-MUSCLE;
+ CELLULAR-METABOLISM; SYSTEMS BIOLOGY; MODEL},
+Research-Areas = {Computer Science; Engineering; Medical Informatics},
+Web-of-Science-Categories = {Computer Science, Interdisciplinary Applications; Computer Science,
+ Theory \& Methods; Engineering, Biomedical; Medical Informatics},
+ORCID-Numbers = {Somersalo, Erkki/0000-0001-5099-3512
+ Calvetti, Daniela/0000-0001-5696-718X},
+Times-Cited = {18},
+Journal-ISO = {Comput. Meth. Programs Biomed.},
+Unique-ID = {WOS:000275524400005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000274646700001,
+Author = {Boghigian, Brett A. and Lee, Kyongbum and Pfeifer, Blaine A.},
+Title = {Computational analysis of phenotypic space in heterologous polyketide
+ biosynthesis-Applications to Escherichia coli, Bacillus
+ subtilis, and Saccharomyces cerevisiae},
+Journal = {JOURNAL OF THEORETICAL BIOLOGY},
+Year = {2010},
+Volume = {262},
+Number = {2},
+Pages = {197-207},
+Month = {JAN 21},
+Type = {Article},
+DOI = {10.1016/j.jtbi.2009.10.006},
+ISSN = {0022-5193},
+EISSN = {1095-8541},
+Keywords = {FBA; MoMA; Polyketide; Metabolic engineering},
+Keywords-Plus = {SYSTEMS BIOLOGY; STRAIN IMPROVEMENT; DRUG DISCOVERY; TRANSCRIPTION
+ MACHINERY; OBJECTIVE FUNCTIONS; METABOLIC NETWORK; NATURAL-PRODUCT; FLUX
+ ANALYSIS; K-12 MG1655; WILD-TYPE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Lee, Kyongbum/D-9230-2013
+ },
+ORCID-Numbers = {Lee, Kyongbum/0000-0002-0699-8057},
+Times-Cited = {11},
+Journal-ISO = {J. Theor. Biol.},
+Unique-ID = {WOS:000274646700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000275201000001,
+Author = {Srinivasan, Karthikeyan and Mahadevan, Radhakrishnan},
+Title = {Characterization of proton production and consumption associated with
+ microbial metabolism},
+Journal = {BMC BIOTECHNOLOGY},
+Year = {2010},
+Volume = {10},
+Month = {JAN 20},
+Type = {Article},
+DOI = {10.1186/1472-6750-10-2},
+Article-Number = {2},
+EISSN = {1472-6750},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; IN-SILICO MODELS; ESCHERICHIA-COLI;
+ GEOBACTER-SULFURREDUCENS; DNA MICROARRAY; REDUCTION; EXTRUSION;
+ SUBSTRATE; GROWTH; PH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Mahadevan, Radhakrishnan/A-8502-2008},
+ORCID-Numbers = {Mahadevan, Radhakrishnan/0000-0002-1270-9063},
+Times-Cited = {34},
+Journal-ISO = {BMC Biotechnol.},
+Unique-ID = {WOS:000275201000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000287870200001,
+Author = {Feng, Xueyang and Page, Lawrence and Rubens, Jacob and Chircus, Lauren
+ and Colletti, Peter and Pakrasi, Himadri B. and Tang, Yinjie J.},
+Title = {Bridging the Gap between Fluxomics and Industrial Biotechnology},
+Journal = {JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY},
+Year = {2010},
+Type = {Review},
+DOI = {10.1155/2010/460717},
+Article-Number = {460717},
+ISSN = {1110-7243},
+EISSN = {1110-7251},
+Keywords-Plus = {METABOLIC-FLUX ANALYSIS; ENGINEERED SACCHAROMYCES-CEREVISIAE;
+ SHEWANELLA-ONEIDENSIS MR-1; C-13 LABELING EXPERIMENTS; HIGH-LEVEL
+ PRODUCTION; FED-BATCH CULTURE; IN-SILICO DESIGN; ESCHERICHIA-COLI;
+ BACILLUS-SUBTILIS; BALANCE ANALYSIS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Medicine, Research \&
+ Experimental},
+ResearcherID-Numbers = {Feng, Xueyang/G-1295-2015
+ Tang, Yinjie/AAI-5584-2020
+ },
+ORCID-Numbers = {/0000-0003-1304-0151
+ Chircus, Lauren/0000-0003-3082-605X
+ Feng, Xueyang/0000-0003-4426-5732},
+Times-Cited = {18},
+Journal-ISO = {J. Biomed. Biotechnol.},
+Unique-ID = {WOS:000287870200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000274973400001,
+Author = {Link, Hannes and Anselment, Bernd and Weuster-Botz, Dirk},
+Title = {Rapid Media Transition: An Experimental Approach for Steady State
+ Analysis of Metabolic Pathways},
+Journal = {BIOTECHNOLOGY PROGRESS},
+Year = {2010},
+Volume = {26},
+Number = {1},
+Pages = {1-10},
+Month = {JAN-FEB},
+Type = {Article},
+DOI = {10.1002/btpr.290},
+ISSN = {8756-7938},
+EISSN = {1520-6033},
+Keywords = {steady state perturbation; metabolome analysis; metabolic flux analysis;
+ fed-batch process},
+Keywords-Plus = {ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; DETERMINING ELASTICITIES;
+ MULTIPLE MEASUREMENTS; FLUX RATES; GLUCOSE; GLYCOLYSIS; PHYSIOLOGY;
+ RESPONSES; DYNAMICS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Link, Hannes/K-1932-2015
+ },
+ORCID-Numbers = {Weuster-Botz, Dirk/0000-0002-1171-4194},
+Times-Cited = {20},
+Journal-ISO = {Biotechnol. Prog.},
+Unique-ID = {WOS:000274973400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000280480000019,
+Author = {Medema, Marnix H. and Trefzer, Axel and Kovalchuk, Andriy and van den
+ Berg, Marco and Muller, Ulrike and Heijne, Wilbert and Wu, Liang and
+ Alam, Mohammad T. and Ronning, Catherine M. and Nierman, William C. and
+ Bovenberg, Roel A. L. and Breitling, Rainer and Takano, Eriko},
+Title = {The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich
+ Evolutionary Reservoir of Secondary Metabolic Pathways},
+Journal = {GENOME BIOLOGY AND EVOLUTION},
+Year = {2010},
+Volume = {2},
+Pages = {212-224},
+Type = {Article},
+DOI = {10.1093/gbe/evq013},
+ISSN = {1759-6653},
+Keywords = {genome sequence; chromosomal evolution; natural products; Streptomyces
+ clavuligerus},
+Keywords-Plus = {COMPLETE GENOME SEQUENCE; STREPTOMYCES-COELICOLOR; CLAVULANIC ACID;
+ GENE-CLUSTER; ANTIBIOTIC PRODUCTION; REPLICATION ORIGIN; BIOSYNTHETIC
+ GENES; CHROMOSOMES; CLONING; SYSTEM},
+Research-Areas = {Evolutionary Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Evolutionary Biology; Genetics \& Heredity},
+ResearcherID-Numbers = {Medema, Marnix H./AAR-3138-2021
+ Alam, Mohammad Tauqeer/A-5304-2013
+ },
+ORCID-Numbers = {Medema, Marnix H./0000-0002-2191-2821
+ Kovalchuk, Andriy/0000-0001-8704-4644
+ Alam, Mohammad Tauqeer/0000-0002-6872-0691
+ Takano, Eriko/0000-0002-6791-3256
+ Breitling, Rainer/0000-0001-7173-0922},
+Times-Cited = {147},
+Journal-ISO = {Genome Biol. Evol.},
+Unique-ID = {WOS:000280480000019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000274246500009,
+Author = {Thiele, Ines and Palsson, Bernhard O.},
+Title = {A protocol for generating a high-quality genome-scale metabolic
+ reconstruction},
+Journal = {NATURE PROTOCOLS},
+Year = {2010},
+Volume = {5},
+Number = {1},
+Pages = {93-121},
+Type = {Article},
+DOI = {10.1038/nprot.2009.203},
+ISSN = {1754-2189},
+EISSN = {1750-2799},
+Keywords-Plus = {IN-SILICO MODELS; ESCHERICHIA-COLI; NETWORK ANALYSIS;
+ SUBCELLULAR-LOCALIZATION; INFORMATION-SYSTEM; DATABASE RESOURCES;
+ HIGH-THROUGHPUT; NATIONAL-CENTER; ANNOTATION; BACTERIAL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {1097},
+Journal-ISO = {Nat. Protoc.},
+Unique-ID = {WOS:000274246500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000273208000005,
+Author = {Palsson, Bernhard},
+Title = {Metabolic systems biology},
+Journal = {FEBS LETTERS},
+Year = {2009},
+Volume = {583},
+Number = {24, SI},
+Pages = {3900-3904},
+Month = {DEC 17},
+Note = {146th Nobel Symposium on Systems Biology, Drobak, NORWAY, JUN 25-27,
+ 2009},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.febslet.2009.09.031},
+ISSN = {1873-3468},
+Keywords = {Systems biology; Metabolism},
+Keywords-Plus = {HAEMOPHILUS-INFLUENZAE RD; GENOME-SCALE MODELS; ESCHERICHIA-COLI;
+ RECONSTRUCTION; ANNOTATION; PREDICTION; NETWORK; PHOSPHOPROTEOMICS;
+ MICROORGANISMS; EVOLUTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {71},
+Journal-ISO = {FEBS Lett.},
+Unique-ID = {WOS:000273208000005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000272254400074,
+Author = {Perez-Escudero, Alfonso and Rivera-Alba, Marta and de Polavieja, Gonzalo
+ G.},
+Title = {Structure of deviations from optimality in biological systems},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2009},
+Volume = {106},
+Number = {48},
+Pages = {20544-20549},
+Month = {DEC 1},
+Type = {Article},
+DOI = {10.1073/pnas.0905336106},
+ISSN = {0027-8424},
+Keywords = {Caenorhabditis elegans; Escherichia coli; evolution; neuroanatomy;
+ optimization},
+Keywords-Plus = {INTRACELLULAR FLUXES; WIRING OPTIMIZATION; NERVOUS-SYSTEM; EVOLUTION;
+ NEURONS; MODELS; GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Pérez-Escudero, Alfonso/B-2837-2017
+ },
+ORCID-Numbers = {Pérez-Escudero, Alfonso/0000-0002-4782-6139
+ Rivera-Alba, Marta/0000-0002-8069-385X
+ de Polavieja, Gonzalo/0000-0001-5359-3426},
+Times-Cited = {24},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000272254400074},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000272190400006,
+Author = {Warren, P. B. and Queiros, S. M. Duarte and Jones, J. L.},
+Title = {Flux networks in metabolic graphs},
+Journal = {PHYSICAL BIOLOGY},
+Year = {2009},
+Volume = {6},
+Number = {4},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1088/1478-3975/6/4/046006},
+Article-Number = {046006},
+ISSN = {1478-3967},
+EISSN = {1478-3975},
+Keywords-Plus = {ESCHERICHIA-COLI; GLOBAL ORGANIZATION; RECONSTRUCTION; PREDICTION;
+ CAPABILITIES; VALIDATION; FRAMEWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ResearcherID-Numbers = {Queirós, Sílvio M. Duarte/L-1170-2016
+ Warren, Patrick B/D-1682-2009},
+ORCID-Numbers = {Queirós, Sílvio M. Duarte/0000-0001-6915-1892
+ Warren, Patrick B/0000-0002-0189-2704},
+Times-Cited = {5},
+Journal-ISO = {Phys. Biol.},
+Unique-ID = {WOS:000272190400006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000271106800020,
+Author = {Jung, Tae-Sung and Yeo, Hock Chuan and Reddy, Satty G. and Cho, Wan-Sup
+ and Lee, Dong-Yup},
+Title = {WEbcoli: an interactive and asynchronous web application for in
+ silico design and analysis of genome-scale E.coli
+ model},
+Journal = {BIOINFORMATICS},
+Year = {2009},
+Volume = {25},
+Number = {21},
+Pages = {2850-2852},
+Month = {NOV 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btp496},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Lee, Dong-Yup/D-6650-2011
+ },
+ORCID-Numbers = {Lee, Dong-Yup/0000-0003-0901-708X
+ Yeo, Hock Chuan/0000-0001-5176-8800},
+Times-Cited = {11},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000271106800020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000272308900002,
+Author = {Oberhardt, Matthew A. and Palsson, Bernhard O. and Papin, Jason A.},
+Title = {Applications of genome-scale metabolic reconstructions},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2009},
+Volume = {5},
+Month = {NOV},
+Type = {Review},
+DOI = {10.1038/msb.2009.77},
+Article-Number = {320},
+ISSN = {1744-4292},
+Keywords = {computational biology; metabolic model; modeling; network; systems
+ biology},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; HAEMOPHILUS-INFLUENZAE RD; CONSTRAINT-BASED
+ ANALYSIS; NETWORK-BASED PREDICTION; SACCHAROMYCES-CEREVISIAE;
+ STAPHYLOCOCCUS-AUREUS; MYCOBACTERIUM-TUBERCULOSIS; SYSTEMS-ANALYSIS;
+ TRANSCRIPTIONAL REGULATION; GEOBACTER-SULFURREDUCENS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785
+ Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {587},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000272308900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000271422300004,
+Author = {van Hoek, Milan J. A. and Hogeweg, Paulien},
+Title = {Metabolic Adaptation after Whole Genome Duplication},
+Journal = {MOLECULAR BIOLOGY AND EVOLUTION},
+Year = {2009},
+Volume = {26},
+Number = {11},
+Pages = {2441-2453},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1093/molbev/msp160},
+ISSN = {0737-4038},
+EISSN = {1537-1719},
+Keywords = {evolutionary systems biology; whole genome duplication; metabolic
+ network; flux balance analysis; Saccharomyces cerevisiae},
+Keywords-Plus = {RECIPROCAL GENE LOSS; SACCHAROMYCES-CEREVISIAE; INTEGRATED ANALYSIS;
+ YEAST GENOME; EVOLUTION; SCALE; EXPRESSION; NETWORK; GROWTH;
+ RECONSTRUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Evolutionary Biology; Genetics \&
+ Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Evolutionary Biology; Genetics \&
+ Heredity},
+ResearcherID-Numbers = {Hogeweg, paulien/D-1242-2011},
+Times-Cited = {52},
+Journal-ISO = {Mol. Biol. Evol.},
+Unique-ID = {WOS:000271422300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000270685200026,
+Author = {Grafahrend-Belau, Eva and Klukas, Christian and Junker, Bjoern H. and
+ Schreiber, Falk},
+Title = {FBA-SimVis: interactive visualization of constraint-based metabolic
+ models},
+Journal = {BIOINFORMATICS},
+Year = {2009},
+Volume = {25},
+Number = {20},
+Pages = {2755-2757},
+Month = {OCT 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btp408},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Grafahrend-Belau, Eva/0000-0002-1938-3908},
+Times-Cited = {35},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000270685200026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000270755600001,
+Author = {Fang, Xin and Wallqvist, Anders and Reifman, Jaques},
+Title = {A systems biology framework for modeling metabolic enzyme inhibition of
+ Mycobacterium tuberculosis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2009},
+Volume = {3},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1186/1752-0509-3-92},
+Article-Number = {92},
+ISSN = {1752-0509},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; DRUG TARGETS; SIDEROPHORE
+ BIOSYNTHESIS; ISOCITRATE LYASE-1; PATHWAY ANALYSIS; GENOME; NETWORK;
+ RECONSTRUCTION; GROWTH},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {wallqvist, anders/W-2584-2019},
+ORCID-Numbers = {wallqvist, anders/0000-0002-9775-7469},
+Times-Cited = {31},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000270755600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000270755500001,
+Author = {Feala, Jacob D. and Coquin, Laurence and Zhou, Dan and Haddad, Gabriel
+ G. and Paternostro, Giovanni and McCulloch, Andrew D.},
+Title = {Metabolism as means for hypoxia adaptation: metabolic profiling and flux
+ balance analysis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2009},
+Volume = {3},
+Month = {SEP 9},
+Type = {Article},
+DOI = {10.1186/1752-0509-3-91},
+Article-Number = {91},
+ISSN = {1752-0509},
+Keywords-Plus = {INSECT FLIGHT MUSCLE; DROSOPHILA-MELANOGASTER; ENERGY-METABOLISM;
+ MYOCARDIAL-ISCHEMIA; RAT-HEART; HYPERTROPHY; ANAPLEROSIS; TOLERANCE;
+ RESPONSES; DECLINE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zhou, Dan/T-7203-2017
+ },
+ORCID-Numbers = {Zhou, Dan/0000-0001-6401-9040
+ Brander, Luke/0000-0002-5862-4030},
+Times-Cited = {50},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000270755500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000278693200006,
+Author = {Ding, Dewu and He, Xiaoqing and Lu, Kezhong and Wu, Pu and Huang,
+ Haisheng},
+Title = {Application of Constraint-based Methods in Staphylococcus aureus
+ Metabolic Network},
+Journal = {RIVISTA DI BIOLOGIA-BIOLOGY FORUM},
+Year = {2009},
+Volume = {102},
+Number = {3},
+Pages = {385-397},
+Month = {SEP-DEC},
+Type = {Article},
+ISSN = {0035-6050},
+EISSN = {1825-6538},
+Keywords = {Constraint-based modeling; flux balance analysis; metabolic network;
+ systems biology},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; GIANT STRONG COMPONENT; FLUX BALANCE
+ ANALYSIS; FUNCTIONAL-ANALYSIS; PATHWAY ANALYSIS; MODELS; ROBUSTNESS;
+ BIOLOGY},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {xiaoqing, he/ABF-8047-2021},
+Times-Cited = {2},
+Journal-ISO = {Riv. Biol.-Biol. Forum},
+Unique-ID = {WOS:000278693200006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000270456400003,
+Author = {Nakahigashi, Kenji and Toya, Yoshihiro and Ishii, Nobuyoshi and Soga,
+ Tomoyoshi and Hasegawa, Miki and Watanabe, Hisami and Takai, Yuki and
+ Honma, Masayuki and Mori, Hirotada and Tomita, Masaru},
+Title = {Systematic phenome analysis of Escherichia coli multiple-knockout
+ mutants reveals hidden reactions in central carbon metabolism},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2009},
+Volume = {5},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1038/msb.2009.65},
+Article-Number = {306},
+ISSN = {1744-4292},
+Keywords = {genetic interaction; metabolic flux; metabolomics; system biology;
+ transaldolase},
+Keywords-Plus = {GENOME-WIDE ANALYSIS; GENETIC INTERACTIONS; HIGH-THROUGHPUT; EXPRESSION;
+ PENTOSE; PATHWAY; RECONSTRUCTION; ROBUSTNESS; RESPONSES; HEXOSE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Mori, Hirotada/B-4934-2011
+ Soga, Tomoyoshi/B-8105-2014
+ },
+ORCID-Numbers = {Soga, Tomoyoshi/0000-0001-9502-2509
+ Toya, Yoshihiro/0000-0001-9670-6961},
+Times-Cited = {124},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000270456400003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000268107100029,
+Author = {Le Fevre, F. and Smidtas, S. and Combe, C. and Durot, M. and
+ d'Alche-Buc, Florence and Schachter, V.},
+Title = {CycSim-an online tool for exploring and experimenting with genome-scale
+ metabolic models},
+Journal = {BIOINFORMATICS},
+Year = {2009},
+Volume = {25},
+Number = {15},
+Pages = {1987-1988},
+Month = {AUG 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btp268},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; RECONSTRUCTION; INFORMATION;
+ ANNOTATION; DATABASE; SYSTEMS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+Times-Cited = {15},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000268107100029},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000268493700018,
+Author = {Manichaikul, Ani and Ghamsari, Lila and Hom, Erik F. Y. and Lin, Chenwei
+ and Murray, Ryan R. and Chang, Roger L. and Balaji, S. and Hao, Tong and
+ Shen, Yun and Chavali, Arvind K. and Thiele, Ines and Yang, Xinping and
+ Fan, Changyu and Mello, Elizabeth and Hill, David E. and Vidal, Marc and
+ Salehi-Ashtiani, Kourosh and Papin, Jason A.},
+Title = {Metabolic network analysis integrated with transcript verification for
+ sequenced genomes},
+Journal = {NATURE METHODS},
+Year = {2009},
+Volume = {6},
+Number = {8},
+Pages = {589-U53},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1038/NMETH.1348},
+ISSN = {1548-7091},
+EISSN = {1548-7105},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CHLAMYDOMONAS-REINHARDTII; RECONSTRUCTION; SCALE;
+ PREDICTION; PROTEINS; GATEWAY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Manichaikul, Ani W/B-7726-2009
+ Chavali, Arvind/L-7157-2016
+ Hill, David E/B-6617-2011
+ Yang, Xinping/HGA-6104-2022
+ Hom, Erik/B-3889-2008
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Manichaikul, Ani/0000-0002-5998-795X
+ Salehi-Ashtiani, Kourosh/0000-0002-6521-5243
+ Yang, Xinping/0000-0003-4086-4180
+ Hom, Erik/0000-0003-0964-0031
+ Chang, Roger/0000-0003-1630-6584
+ Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {66},
+Journal-ISO = {Nat. Methods},
+Unique-ID = {WOS:000268493700018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000266953900009,
+Author = {Raman, Karthik and Chandra, Nagasuma},
+Title = {Flux balance analysis of biological systems: applications and challenges},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2009},
+Volume = {10},
+Number = {4},
+Pages = {435-449},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1093/bib/bbp011},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {network reconstruction; metabolic network analysis; objective functions;
+ genome scale modelling; reactome modelling},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; METABOLIC OBJECTIVE FUNCTIONS;
+ HAEMOPHILUS-INFLUENZAE RD; ESCHERICHIA-COLI; IN-SILICO;
+ SACCHAROMYCES-CEREVISIAE; MYCOBACTERIUM-TUBERCULOSIS; BACILLUS-SUBTILIS;
+ PATHWAY ANALYSIS; HIGH-THROUGHPUT},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019
+ },
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ Chandra, Nagasuma/0000-0002-9939-8439},
+Times-Cited = {254},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000266953900009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000269365200011,
+Author = {Verouden, Maikel P. H. and Notebaart, Richard A. and Westerhuis, Johan
+ A. and van der Werf, Mariet J. and Teusink, Bas and Smilde, Age K.},
+Title = {Multi-way analysis of flux distributions across multiple conditions},
+Journal = {JOURNAL OF CHEMOMETRICS},
+Year = {2009},
+Volume = {23},
+Number = {7-8, SI},
+Pages = {406-420},
+Month = {JUL-AUG},
+Type = {Article},
+DOI = {10.1002/cem.1238},
+ISSN = {0886-9383},
+EISSN = {1099-128X},
+Keywords = {PARAFAC; PCA; correlation; flux distributions; genome-scale network},
+Keywords-Plus = {PARALLEL FACTOR-ANALYSIS; METABOLIC NETWORK; MODELS; BACTERIUM; GROWTH},
+Research-Areas = {Automation \& Control Systems; Chemistry; Computer Science; Instruments
+ \& Instrumentation; Mathematics},
+Web-of-Science-Categories = {Automation \& Control Systems; Chemistry, Analytical; Computer Science,
+ Artificial Intelligence; Instruments \& Instrumentation; Mathematics,
+ Interdisciplinary Applications; Statistics \& Probability},
+ResearcherID-Numbers = {Notebaart, Richard A./A-1459-2014
+ },
+ORCID-Numbers = {Verouden, Maikel/0000-0002-4893-3323
+ Smilde, Age/0000-0002-3052-4644
+ Teusink, Bas/0000-0003-3929-0423},
+Times-Cited = {11},
+Journal-ISO = {J. Chemometr.},
+Unique-ID = {WOS:000269365200011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000268436100018,
+Author = {Teusink, Bas and Wiersma, Anne and Jacobs, Leo and Notebaart, Richard A.
+ and Smid, Eddy J.},
+Title = {Understanding the Adaptive Growth Strategy of Lactobacillus
+ plantarum by In Silico Optimisation},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2009},
+Volume = {5},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1000410},
+Article-Number = {e1000410},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI; METABOLIC NETWORKS; EVOLUTION; MODELS; PHENOTYPES;
+ PATHWAYS; GENE; POPULATIONS; PREDICTIONS; EXPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Notebaart, Richard A./A-1459-2014
+ },
+ORCID-Numbers = {Jacobs, Leo/0000-0002-6635-5440
+ Teusink, Bas/0000-0003-3929-0423},
+Times-Cited = {90},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000268436100018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000266130100008,
+Author = {Fatumo, Segun and Plaimas, Kitiporn and Mallm, Jan-Philipp and Schramm,
+ Gunnar and Adebiyi, Ezekiel and Oswald, Marcus and Eils, Roland and
+ Koenig, Rainer},
+Title = {Estimating novel potential drug targets of Plasmodium falciparum
+ by analysing the metabolic network of knock-out strains in silico},
+Journal = {INFECTION GENETICS AND EVOLUTION},
+Year = {2009},
+Volume = {9},
+Number = {3},
+Pages = {351-358},
+Month = {MAY},
+Note = {Conference on Bioinformatics of African Pathogens and Vectors, Nairobi,
+ KENYA, MAY 28-JUN 02, 2007},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.meegid.2008.01.007},
+ISSN = {1567-1348},
+EISSN = {1567-7257},
+Keywords = {Knock-out; Drug targets; Metabolic network; Plasmodium; Breadth first
+ search; Malaria},
+Keywords-Plus = {GLUTATHIONE-S-TRANSFERASE; ISOPRENYLCYSTEINE CARBOXYL METHYLTRANSFERASE;
+ FATTY-ACID BIOSYNTHESIS; MALARIA PARASITE; DIHYDROOROTATE DEHYDROGENASE;
+ PYRIMIDINE BIOSYNTHESIS; ERYTHROCYTIC STAGES; ANTIMALARIAL-DRUGS;
+ INHIBITION; SYNTHASE},
+Research-Areas = {Infectious Diseases},
+Web-of-Science-Categories = {Infectious Diseases},
+ResearcherID-Numbers = {Fatumo, Segun/W-5880-2019
+ Plaimas, Kitiporn/GLV-3478-2022
+ Fatumo, Segun/AAI-8845-2021
+ Eils, Roland/B-6121-2009
+ },
+ORCID-Numbers = {Plaimas, Kitiporn/0000-0002-0416-8316
+ Eils, Roland/0000-0002-0034-4036
+ Mallm, Jan-Philipp/0000-0002-7059-4030},
+Times-Cited = {59},
+Journal-ISO = {Infect. Genet. Evol.},
+Unique-ID = {WOS:000266130100008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000266001800001,
+Author = {Mo, Monica L. and Palsson, Bernhard O. and Herrgard, Markus J.},
+Title = {Connecting extracellular metabolomic measurements to intracellular flux
+ states in yeast},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2009},
+Volume = {3},
+Month = {MAR 25},
+Type = {Article},
+DOI = {10.1186/1752-0509-3-37},
+Article-Number = {37},
+ISSN = {1752-0509},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; SYSTEMS BIOLOGY; AMMONIUM
+ ASSIMILATION; INTERACTION NETWORKS; FUNCTIONAL GENOMICS; RECONSTRUCTION;
+ MODELS; IDENTIFICATION; CONSTRAINTS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {311},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000266001800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000265498800015,
+Author = {Resendis-Antonio, Osbaldo},
+Title = {Filling Kinetic Gaps: Dynamic Modeling of Metabolism Where Detailed
+ Kinetic Information Is Lacking},
+Journal = {PLOS ONE},
+Year = {2009},
+Volume = {4},
+Number = {3},
+Month = {MAR 23},
+Type = {Article},
+DOI = {10.1371/journal.pone.0004967},
+Article-Number = {e4967},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; HIGH-THROUGHPUT; ROBUSTNESS; SIMULATION;
+ RECONSTRUCTION; METABOLOMICS; CELLS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {RESENDIS, OSBALDO/ADE-5280-2022},
+ORCID-Numbers = {RESENDIS, OSBALDO/0000-0001-5220-541X},
+Times-Cited = {14},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000265498800015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000265069100001,
+Author = {Barrett, Christian L. and Herrgard, Markus J. and Palsson, Bernhard},
+Title = {Decomposing complex reaction networks using random sampling, principal
+ component analysis and basis rotation},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2009},
+Volume = {3},
+Month = {MAR 6},
+Type = {Article},
+DOI = {10.1186/1752-0509-3-30},
+Article-Number = {30},
+EISSN = {1752-0509},
+Keywords-Plus = {GENE-EXPRESSION; METABOLISM; MODELS; ORGANIZATION; MODULARITY; BALANCE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {38},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000265069100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000264357300004,
+Author = {Mallavarapu, Aneil and Thomson, Matthew and Ullian, Benjamin and
+ Gunawardena, Jeremy},
+Title = {Programming with models: modularity and abstraction provide powerful
+ capabilities for systems biology},
+Journal = {JOURNAL OF THE ROYAL SOCIETY INTERFACE},
+Year = {2009},
+Volume = {6},
+Number = {32},
+Pages = {257-270},
+Month = {MAR 6},
+Type = {Article},
+DOI = {10.1098/rsif.2008.0205},
+ISSN = {1742-5689},
+EISSN = {1742-5662},
+Keywords = {model building; systems biology; modularity; abstraction},
+Keywords-Plus = {PROCESSIVE PHOSPHORYLATION; MULTISITE PHOSPHORYLATION;
+ PROTEIN-PHOSPHORYLATION; DUAL PHOSPHORYLATION; SCAFFOLD PROTEINS;
+ KINASE; NETWORKS; REPRESENTATION; THRESHOLD; MECHANISM},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {49},
+Journal-ISO = {J. R. Soc. Interface},
+Unique-ID = {WOS:000264357300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000263560600007,
+Author = {Schellenberger, Jan and Palsson, Bernhard O.},
+Title = {Use of Randomized Sampling for Analysis of Metabolic Networks},
+Journal = {JOURNAL OF BIOLOGICAL CHEMISTRY},
+Year = {2009},
+Volume = {284},
+Number = {9},
+Pages = {5457-5461},
+Month = {FEB 27},
+Type = {Review},
+DOI = {10.1074/jbc.R800048200},
+EISSN = {1083-351X},
+Keywords-Plus = {ESCHERICHIA-COLI; STEADY-STATE; INVIVO MEASUREMENT; OPTIMAL SELECTION;
+ SCALE; PATHWAYS; MODELS; FLUXES; CAPABILITIES; CONSTRAINTS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {damiani, chiara/R-4256-2016
+ },
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {171},
+Journal-ISO = {J. Biol. Chem.},
+Unique-ID = {WOS:000263560600007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000264393000001,
+Author = {Thomas, Gavin H. and Zucker, Jeremy and Macdonald, Sandy J. and Sorokin,
+ Anatoly and Goryanin, Igor and Douglas, Angela E.},
+Title = {A fragile metabolic network adapted for cooperation in the symbiotic
+ bacterium Buchnera aphidicola},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2009},
+Volume = {3},
+Month = {FEB 21},
+Type = {Article},
+DOI = {10.1186/1752-0509-3-24},
+Article-Number = {24},
+EISSN = {1752-0509},
+Keywords-Plus = {ESCHERICHIA-COLI K-12; GENOME-SCALE; RESOURCE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Thomas, Gavin H/E-5753-2011
+ Sorokin, Anatoly/A-9090-2008
+ Zucker, Jeremy/M-3643-2016
+ Goryanin, Igor/AAB-1400-2022
+ Goryanin, Igor/J-1913-2015
+ },
+ORCID-Numbers = {Thomas, Gavin H/0000-0002-9763-1313
+ Zucker, Jeremy/0000-0002-7276-9009
+ Goryanin, Igor/0000-0002-8293-774X
+ Sorokin, Anatoly/0000-0002-0047-0606
+ Macdonald, Sandy/0000-0002-4112-0987},
+Times-Cited = {78},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000264393000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000263090900012,
+Author = {Feist, Adam M. and Herrgard, Markus J. and Thiele, Ines and Reed, Jennie
+ L. and Palsson, Bernhard O.},
+Title = {Reconstruction of biochemical networks in microorganisms},
+Journal = {NATURE REVIEWS MICROBIOLOGY},
+Year = {2009},
+Volume = {7},
+Number = {2},
+Pages = {129-143},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1038/nrmicro1949},
+ISSN = {1740-1526},
+EISSN = {1740-1534},
+Keywords-Plus = {SMALL NONCODING RNAS; ESCHERICHIA-COLI METABOLISM; TRANSCRIPTION FACTOR;
+ SYSTEMS-APPROACH; GENE-EXPRESSION; IN-VITRO; SACCHAROMYCES-CEREVISIAE;
+ PLASMODIUM-FALCIPARUM; BIOMASS COMPOSITION; HIGH-THROUGHPUT},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Reed, Jennifer L/E-5137-2011
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220
+ Thiele, Ines/0000-0002-8071-7110
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {639},
+Journal-ISO = {Nat. Rev. Microbiol.},
+Unique-ID = {WOS:000263090900012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000263924500007,
+Author = {Li, Fan and Thiele, Ines and Jamshidi, Neema and Palsson, Bernhard O.},
+Title = {Identification of Potential Pathway Mediation Targets in Toll-like
+ Receptor Signaling},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2009},
+Volume = {5},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1000292},
+Article-Number = {e1000292},
+EISSN = {1553-7358},
+Keywords-Plus = {NF-KAPPA-B; METABOLIC NETWORKS; IMMUNE-RESPONSES; DISEASE; PROTEIN;
+ ACTIVATION; RECONSTRUCTION; COMPLEX; MODELS; MYD88},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Li, Fan/D-1975-2009
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Palsson, Bernhard/0000-0003-2357-6785
+ Li, Fan/0000-0002-2400-9021
+ Jamshidi, Neema/0000-0003-3857-9735},
+Times-Cited = {48},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000263924500007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000263057400014,
+Author = {Veeramani, Balaji and Bader, Joel S.},
+Title = {Metabolic Flux Correlations, Genetic Interactions, and Disease},
+Journal = {JOURNAL OF COMPUTATIONAL BIOLOGY},
+Year = {2009},
+Volume = {16},
+Number = {2},
+Pages = {291-302},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1089/cmb.2008.14TT},
+ISSN = {1066-5277},
+EISSN = {1557-8666},
+Keywords = {flux balance analysis; metabolic network; OMIM; synthetic lethal genetic
+ interactions; systems biology},
+Keywords-Plus = {RECONSTRUCTION; MODELS; ORGANIZATION; PATHWAY},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Bader, Joel S/A-1818-2009},
+ORCID-Numbers = {Bader, Joel S/0000-0002-6020-4625},
+Times-Cited = {9},
+Journal-ISO = {J. Comput. Biol.},
+Unique-ID = {WOS:000263057400014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000262100800015,
+Author = {Yu, Chenggang and Zavaijevski, Nela and Desai, Valmik and Reifman,
+ Jaques},
+Title = {Genome-wide enzyme annotation with precision control: Catalytic families
+ {[}CatFam] databases},
+Journal = {PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS},
+Year = {2009},
+Volume = {74},
+Number = {2},
+Pages = {449-460},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1002/prot.22167},
+ISSN = {0887-3585},
+EISSN = {1097-0134},
+Keywords = {catalytic function; automated annotation; Enzyme Commission number;
+ profile method; protein function prediction},
+Keywords-Plus = {PROTEIN FUNCTION; SEQUENCE ANNOTATION; PREDICTION; PROFILES; PRORULE;
+ EFICAZ; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+Times-Cited = {55},
+Journal-ISO = {Proteins},
+Unique-ID = {WOS:000262100800015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000265601900058,
+Author = {Xi, Yanping and Chen, Yi-Ping Phoebe and Cao, Ming and Wang, Weirong and
+ Wang, Fei},
+Title = {Analysis on relationship between extreme pathways and correlated
+ reaction sets},
+Journal = {BMC BIOINFORMATICS},
+Year = {2009},
+Volume = {10},
+Number = {1},
+Month = {JAN 30},
+Note = {9th Asia Pacific Bioinformatics Conference, Tsinghua Univ, Beijing,
+ PEOPLES R CHINA, JAN 13-16, 2009},
+Type = {Article; Proceedings Paper},
+DOI = {10.1186/1471-2105-10-S1-S58},
+Article-Number = {S58},
+ISSN = {1471-2105},
+Keywords-Plus = {BIOCHEMICAL REACTION NETWORKS; IN-SILICO MODELS; HUMAN RED-CELL;
+ METABOLIC NETWORKS; ESCHERICHIA-COLI; ORGANIZATION; CONSTRAINTS;
+ DEFINITION; DYNAMICS; SYSTEMS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Chen, Yi-Ping Phoebe/B-8844-2008
+ },
+ORCID-Numbers = {Chen, Yi-Ping Phoebe/0000-0002-4122-3767
+ Li, Wei/0000-0001-9931-5990},
+Times-Cited = {589},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000265601900058},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000265601900062,
+Author = {Xu, Zixiang and Sun, Xiao and Yu, Shihai},
+Title = {Genome-scale analysis to the impact of gene deletion on the metabolism
+ of E-coli: constraint-based simulation approach},
+Journal = {BMC BIOINFORMATICS},
+Year = {2009},
+Volume = {10},
+Number = {1},
+Month = {JAN 30},
+Note = {9th Asia Pacific Bioinformatics Conference, Tsinghua Univ, Beijing,
+ PEOPLES R CHINA, JAN 13-16, 2009},
+Type = {Article; Proceedings Paper},
+DOI = {10.1186/1471-2105-10-S1-S62},
+Article-Number = {S62},
+ISSN = {1471-2105},
+Keywords-Plus = {NETWORK; RECONSTRUCTION; MODELS; ESSENTIALITY; PREDICTION; GSM/GPR},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+Times-Cited = {6},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000265601900062},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000261621600011,
+Author = {Durot, Maxime and Bourguignon, Pierre-Yves and Schachter, Vincent},
+Title = {Genome-scale models of bacterial metabolism: reconstruction and
+ applications},
+Journal = {FEMS MICROBIOLOGY REVIEWS},
+Year = {2009},
+Volume = {33},
+Number = {1},
+Pages = {164-190},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1111/j.1574-6976.2008.00146.x},
+ISSN = {0168-6445},
+EISSN = {1574-6976},
+Keywords = {metabolic network; systems biology; computational methods; genome-scale
+ metabolic models; metabolic engineering; omics data integration},
+Keywords-Plus = {AB-INITIO PREDICTION; FLUX BALANCE MODELS; IN-SILICO MODELS;
+ ESCHERICHIA-COLI; HIGH-THROUGHPUT; GENE-EXPRESSION; ADAPTIVE EVOLUTION;
+ SYSTEMS BIOLOGY; TRANSCRIPTIONAL REGULATION; THERMODYNAMIC CONSTRAINTS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Bourguignon, Pierre-Yves/A-9962-2009},
+ORCID-Numbers = {Bourguignon, Pierre-Yves/0000-0001-9334-0845},
+Times-Cited = {210},
+Journal-ISO = {Fems Microbiol. Rev.},
+Unique-ID = {WOS:000261621600011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000262261500057,
+Author = {Grafahrend-Belau, Eva and Schreiber, Falk and Koschuetzki, Dirk and
+ Junker, Bjoern H.},
+Title = {Flux Balance Analysis of Barley Seeds: A Computational Approach to Study
+ Systemic Properties of Central Metabolism},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2009},
+Volume = {149},
+Number = {1},
+Pages = {585-598},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1104/pp.108.129635},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {ADP-GLUCOSE PYROPHOSPHORYLASE; STRONGLY DECREASED EXPRESSION;
+ ORTHO-PHOSPHATE DIKINASE; PHOSPHOENOLPYRUVATE CARBOXYLASE; STARCH
+ SYNTHESIS; ORTHOPHOSPHATE DIKINASE; GENE-EXPRESSION;
+ PYROPHOSPHATE-FRUCTOSE-6-PHOSPHATE PHOSPHOTRANSFERASE; MOLECULAR
+ CHARACTERIZATION; DEVELOPING GRAINS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ORCID-Numbers = {Grafahrend-Belau, Eva/0000-0002-1938-3908},
+Times-Cited = {120},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000262261500057},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000261628100007,
+Author = {Mazumdar, Varun and Snitkin, Evan S. and Amar, Salomon and Segre, Daniel},
+Title = {Metabolic Network Model of a Human Oral Pathogen},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2009},
+Volume = {191},
+Number = {1},
+Pages = {74-90},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1128/JB.01123-08},
+ISSN = {0021-9193},
+EISSN = {1098-5530},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; PORPHYROMONAS-GINGIVALIS INFECTION; AORTIC
+ ENDOTHELIAL-CELLS; GENE-DELETION MUTANTS; FLUX BALANCE ANALYSIS;
+ PERIODONTAL-DISEASE; ESCHERICHIA-COLI; BACTEROIDES-GINGIVALIS; BONE
+ LOSS; TREPONEMA MICRODENTIUM},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914
+ Snitkin, Evan/0000-0001-8409-278X
+ Amar, Salomon/0000-0002-0017-5930},
+Times-Cited = {55},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000261628100007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000262604200008,
+Author = {Mo, Monica L. and Palsson, Bernhard O.},
+Title = {Understanding human metabolic physiology: a genome-to-systems approach},
+Journal = {TRENDS IN BIOTECHNOLOGY},
+Year = {2009},
+Volume = {27},
+Number = {1},
+Pages = {37-44},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1016/j.tibtech.2008.09.007},
+ISSN = {0167-7799},
+EISSN = {1879-3096},
+Keywords-Plus = {ESCHERICHIA-COLI; NETWORK RECONSTRUCTION; NUCLEOSIDE ANALOGS; SIGNALING
+ NETWORKS; PATHWAY ANALYSIS; FLUX ANALYSIS; ANNOTATION; DISEASE; SCALE;
+ GENE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {35},
+Journal-ISO = {Trends Biotechnol.},
+Unique-ID = {WOS:000262604200008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000271727600032,
+Author = {Raman, Karthik and Vashisht, Rohit and Chandra, Nagasuma},
+Title = {Strategies for efficient disruption of metabolism in Mycobacterium
+ tuberculosis from network analysis},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2009},
+Volume = {5},
+Number = {12},
+Pages = {1740-1751},
+Type = {Article},
+DOI = {10.1039/b905817f},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {PROTEIN FUNCTION; RESISTANCE; DATABASE; BIOLOGY; TARGET; CAPABILITIES;
+ PREDICTION; MODELS; GENES; INHA},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019
+ Vashisht, Rohit/K-6181-2019
+ Vashisht, Rohit/JEP-0023-2023
+ },
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ Vashisht, Rohit/0000-0002-2938-7259
+ Chandra, Nagasuma/0000-0002-9939-8439},
+Times-Cited = {23},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000271727600032},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000263517400009,
+Author = {Sigurdsson, Martin I. and Jamshidi, Neema and Jonsson, Jon J. and
+ Palsson, Bernhard O.},
+Title = {Genome-scale network analysis of imprinted human metabolic genes},
+Journal = {EPIGENETICS},
+Year = {2009},
+Volume = {4},
+Number = {1},
+Pages = {43-46},
+Month = {JAN},
+Type = {Review},
+DOI = {10.4161/epi.4.1.7603},
+ISSN = {1559-2294},
+EISSN = {1559-2308},
+Keywords = {systems biology; human reconstruction; epigenetics; obesity; ATP10A},
+Keywords-Plus = {ANGELMAN-SYNDROME; PREDICTION; PHENOTYPE; MODELS; MOUSE},
+Research-Areas = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
+ResearcherID-Numbers = {Sigurdsson, Martin Ingi/I-9655-2016},
+ORCID-Numbers = {Sigurdsson, Martin Ingi/0000-0001-7054-0844},
+Times-Cited = {18},
+Journal-ISO = {Epigenetics},
+Unique-ID = {WOS:000263517400009},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000266543800003,
+Author = {Steuer, Ralf and Junker, Bjoern H.},
+Editor = {Rice, SA},
+Title = {COMPUTATIONAL MODELS OF METABOLISM: STABILITY AND REGULATION IN
+ METABOLIC NETWORKS},
+Booktitle = {ADVANCES IN CHEMICAL PHYSICS, VOL 142},
+Series = {Advances in Chemical Physics},
+Year = {2009},
+Volume = {142},
+Pages = {105-251},
+Type = {Review},
+DOI = {10.1002/9780470475935.ch3},
+ISSN = {0065-2385},
+EISSN = {1934-4791},
+ISBN = {978-0-470-46499-1},
+Keywords-Plus = {ENZYME-CATALYZED REACTIONS; BIDIRECTIONAL REACTION STEPS;
+ TRICARBOXYLIC-ACID CYCLE; RED-BLOOD-CELL; BIOCHEMICAL SYSTEMS-ANALYSIS;
+ PENTOSE-PHOSPHATE PATHWAY; CENTRAL CARBON METABOLISM; MULTIPLE
+ STEADY-STATES; IN-SILICO BIOLOGY; MINIMAL CUT SETS},
+Research-Areas = {Physics},
+Web-of-Science-Categories = {Physics, Atomic, Molecular \& Chemical},
+ResearcherID-Numbers = {Steuer, Ralf/E-7482-2017},
+ORCID-Numbers = {Steuer, Ralf/0000-0003-2217-1655},
+Times-Cited = {36},
+Journal-ISO = {Adv. Chem. Phys.},
+Unique-ID = {WOS:000266543800003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000275269200004,
+Author = {Wang, Zhi and Zhang, Jianzhi},
+Title = {Abundant Indispensable Redundancies in Cellular Metabolic Networks},
+Journal = {GENOME BIOLOGY AND EVOLUTION},
+Year = {2009},
+Volume = {1},
+Pages = {23-33},
+Type = {Article},
+DOI = {10.1093/gbe/evp002},
+ISSN = {1759-6653},
+Keywords = {systems biology; redundancy; metabolic network; yeast; E. coli},
+Keywords-Plus = {ESCHERICHIA-COLI; ADAPTIVE EVOLUTION; DUPLICATE GENES; NULL MUTATIONS;
+ YEAST; ROBUSTNESS; PATHWAY; MODELS; CONSTRAINTS; PLASTICITY},
+Research-Areas = {Evolutionary Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Evolutionary Biology; Genetics \& Heredity},
+Times-Cited = {60},
+Journal-ISO = {Genome Biol. Evol.},
+Unique-ID = {WOS:000275269200004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000266221100012,
+Author = {Wang, Zhi and Zhang, Jianzhi},
+Title = {Why Is the Correlation between Gene Importance and Gene Evolutionary
+ Rate So Weak?},
+Journal = {PLOS GENETICS},
+Year = {2009},
+Volume = {5},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1371/journal.pgen.1000329},
+Article-Number = {e1000329},
+ISSN = {1553-7390},
+Keywords-Plus = {PROTEIN EVOLUTION; YEAST; DISPENSABILITY; GENOME; SEQUENCE;
+ DETERMINANTS; CEREVISIAE; PHENOTYPES; CONSTRAINT; MUTATIONS},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+Times-Cited = {51},
+Journal-ISO = {PLoS Genet.},
+Unique-ID = {WOS:000266221100012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000264388800001,
+Author = {Raman, Karthik and Yeturu, Kalidas and Chandra, Nagasuma},
+Title = {targetTB: A target identification pipeline for Mycobacterium
+ tuberculosis through an interactome, reactome and genome-scale
+ structural analysis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2008},
+Volume = {2},
+Month = {DEC 19},
+Type = {Review},
+DOI = {10.1186/1752-0509-2-109},
+Article-Number = {109},
+EISSN = {1752-0509},
+Keywords-Plus = {WALL ARABINAN BIOSYNTHESIS; MYCOLIC ACID BIOSYNTHESIS; LIGAND-BINDING
+ SITES; CRYSTAL-STRUCTURE; GENE-EXPRESSION; FUNCTIONAL-CHARACTERIZATION;
+ STATIONARY-PHASE; PROTEIN NETWORKS; ESSENTIAL ENZYME; SYSTEMS BIOLOGY},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019
+ },
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ Chandra, Nagasuma/0000-0002-9939-8439},
+Times-Cited = {182},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000264388800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000262180900003,
+Author = {Coquin, Laurence and Feala, Jacob D. and McCulloch, Andrew D. and
+ Paternostro, Giovanni},
+Title = {Metabolomic and flux-balance analysis of age-related decline of hypoxia
+ tolerance in Drosophila muscle tissue},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2008},
+Volume = {4},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1038/msb.2008.71},
+Article-Number = {233},
+ISSN = {1744-4292},
+Keywords = {aging; constraint-based model; Drosophila melanogaster; hypoxia;
+ metabolomics},
+Keywords-Plus = {OXIDATIVE STRESS; ENERGY-METABOLISM; NMR-SPECTROSCOPY; FLIGHT-MUSCLE;
+ MELANOGASTER; RESPONSES; OXYGEN; METABONOMICS; TREHALOSE; GLYCOGEN},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {48},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000262180900003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000261513700014,
+Author = {Portnoy, Vasiliy A. and Herrgard, Markus J. and Palsson, Bernhard O.},
+Title = {Aerobic Fermentation of D-Glucose by an Evolved Cytochrome
+ Oxidase-Deficient Escherichia coli Strain},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2008},
+Volume = {74},
+Number = {24},
+Pages = {7561-7569},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1128/AEM.00880-08},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; TERMINAL OXIDASES; GENES; PURIFICATION; OXYGEN;
+ METABOLISM; COMPLEX; ACID},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {47},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000261513700014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000261246900002,
+Author = {Bumann, Dirk},
+Title = {Has nature already identified all useful antibacterial targets?},
+Journal = {CURRENT OPINION IN MICROBIOLOGY},
+Year = {2008},
+Volume = {11},
+Number = {5},
+Pages = {387-392},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1016/j.mib.2008.08.002},
+ISSN = {1369-5274},
+Keywords-Plus = {DISCOVERY; GENES; DRUGS; ANTIMICROBIALS; ANTIBIOTICS; METABOLISM;
+ CHALLENGES; INHIBITOR; BACILLUS; GENOME},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+Times-Cited = {35},
+Journal-ISO = {Curr. Opin. Microbiol.},
+Unique-ID = {WOS:000261246900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000260755600025,
+Author = {Jones, Patrik R.},
+Title = {Improving fermentative biomass-derived H2-production by
+ engineering microbial metabolism},
+Journal = {INTERNATIONAL JOURNAL OF HYDROGEN ENERGY},
+Year = {2008},
+Volume = {33},
+Number = {19, SI},
+Pages = {5122-5130},
+Month = {OCT},
+Note = {2nd Asian Bio-Hydrogen Symposium, Daejeon, SOUTH KOREA, NOV, 2007},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.ijhydene.2008.05.004},
+ISSN = {0360-3199},
+Keywords = {Review; Hydrogen production; Biomass; Fermentation; Engineering of
+ microbial metabolism},
+Keywords-Plus = {ENHANCED HYDROGEN-PRODUCTION; ESCHERICHIA-COLI STRAINS;
+ CALDICELLULOSIRUPTOR-SACCHAROLYTICUS; ENTEROBACTER-AEROGENES;
+ CHLAMYDOMONAS-REINHARDTII; BIOHYDROGEN PRODUCTION; EXTREME THERMOPHILE;
+ BIOFUELS PRODUCTION; CELLULOSIC ETHANOL; ELECTRON-ACCEPTORS},
+Research-Areas = {Chemistry; Electrochemistry; Energy \& Fuels},
+Web-of-Science-Categories = {Chemistry, Physical; Electrochemistry; Energy \& Fuels},
+Times-Cited = {40},
+Journal-ISO = {Int. J. Hydrog. Energy},
+Unique-ID = {WOS:000260755600025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000260333700001,
+Author = {Nogales, Juan and Palsson, Bernhard O. and Thiele, Ines},
+Title = {A genome-scale metabolic reconstruction of Pseudomonas putida
+ KT2440: iJN746 as a cell factory},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2008},
+Volume = {2},
+Month = {SEP 16},
+Type = {Review},
+DOI = {10.1186/1752-0509-2-79},
+Article-Number = {79},
+EISSN = {1752-0509},
+Keywords-Plus = {AROMATIC CATABOLIC PATHWAYS; FLUX-BALANCE ANALYSIS; TOL PLASMID;
+ ESCHERICHIA-COLI; 2-DIMENSIONAL ANNOTATION; LYSINE CATABOLISM; NETWORK;
+ STRAIN; EXPRESSION; SYSTEMS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Nogales, Juan/Y-8829-2019
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Palsson, Bernhard/0000-0003-2357-6785
+ Nogales, Juan/0000-0002-4961-0833},
+Times-Cited = {169},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000260333700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000258870500001,
+Author = {Plaimas, Kitiporn and Mallm, Jan-Phillip and Oswald, Marcus and Svara,
+ Fabian and Sourjik, Victor and Eils, Roland and Koenig, Rainer},
+Title = {Machine learning based analyses on metabolic networks supports
+ high-throughput knockout screens},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2008},
+Volume = {2},
+Month = {JUL 24},
+Type = {Article},
+DOI = {10.1186/1752-0509-2-67},
+Article-Number = {67},
+ISSN = {1752-0509},
+Keywords-Plus = {ESCHERICHIA-COLI; GENOMIC INFORMATION; DRUG DISCOVERY; PATHWAYS;
+ RECONSTRUCTION; ESSENTIALITY; ORGANIZATION; DATABASE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Eils, Roland/B-6121-2009
+ Plaimas, Kitiporn/GLV-3478-2022
+ },
+ORCID-Numbers = {Eils, Roland/0000-0002-0034-4036
+ Plaimas, Kitiporn/0000-0002-0416-8316
+ Mallm, Jan-Philipp/0000-0002-7059-4030},
+Times-Cited = {37},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000258870500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000257558500001,
+Author = {Wright, Jeremiah and Wagner, Andreas},
+Title = {The Systems Biology Research Tool: evolvable open-source software},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2008},
+Volume = {2},
+Month = {JUN 29},
+Type = {Article},
+DOI = {10.1186/1752-0509-2-55},
+Article-Number = {55},
+EISSN = {1752-0509},
+Keywords-Plus = {MODELS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+Times-Cited = {32},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000257558500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000256611900025,
+Author = {Feist, Adam M. and Palsson, Bernhard O.},
+Title = {The growing scope of applications of genome-scale metabolic
+ reconstructions using Escherichia coli},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2008},
+Volume = {26},
+Number = {6},
+Pages = {659-667},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1038/nbt1401},
+ISSN = {1087-0156},
+EISSN = {1546-1696},
+Keywords-Plus = {OPTIMIZATION FRAMEWORK; ADAPTIVE EVOLUTION; BIOMASS COMPOSITION;
+ REGULATORY NETWORK; ESSENTIAL GENES; CONSTRAINT; MODELS; SEQUENCE;
+ BALANCE; FLUXES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {404},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000256611900025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000255682100004,
+Author = {Alves, Rui and Vilaprinyo, Ester and Sorribas, Albert},
+Title = {Integrating bioinformatics and computational biology:: Perspectives and
+ possibilities for in silico network reconstruction in molecular
+ systems biology},
+Journal = {CURRENT BIOINFORMATICS},
+Year = {2008},
+Volume = {3},
+Number = {2},
+Pages = {98-129},
+Month = {MAY},
+Type = {Review},
+DOI = {10.2174/157489308784340694},
+ISSN = {1574-8936},
+EISSN = {2212-392X},
+Keywords-Plus = {GENOME DATABASE SGD; METABOLIC-CONTROL ANALYSIS; PROTEIN-PROTEIN
+ DOCKING; GENE-EXPRESSION DATA; FACTOR-BINDING SITES; STOCHASTIC
+ SIMULATION ALGORITHM; CLUSTER ASSEMBLY METABOLISM; PENTOSE-PHOSPHATE
+ PATHWAYS; DNA MICROARRAY EXPERIMENTS; TEXT-MINING ALGORITHMS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Alves, Rui/C-5920-2009
+ Vilaprinyo, Ester/A-6702-2010
+ Sorribas, Albert/A-2181-2009},
+ORCID-Numbers = {Alves, Rui/0000-0002-8112-5184
+ Vilaprinyo, Ester/0000-0002-5787-5890
+ Sorribas, Albert/0000-0002-7407-4075},
+Times-Cited = {12},
+Journal-ISO = {Curr. Bioinform.},
+Unique-ID = {WOS:000255682100004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000256866400016,
+Author = {Becker, Scott A. and Palsson, Bernhard O.},
+Title = {Context-specific metabolic networks are consistent with experiments},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2008},
+Volume = {4},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1000082},
+Article-Number = {e1000082},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {OLIGONUCLEOTIDE ARRAY DATA; ESCHERICHIA-COLI; ADAPTIVE EVOLUTION;
+ MODELS; RECONSTRUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {405},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000256866400016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000253864700001,
+Author = {Becker, Scott A. and Palsson, Bernhard O.},
+Title = {Three factors underlying incorrect in silico predictions of essential
+ metabolic genes},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2008},
+Volume = {2},
+Month = {FEB 4},
+Type = {Article},
+DOI = {10.1186/1752-0509-2-14},
+Article-Number = {14},
+ISSN = {1752-0509},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; SACCHAROMYCES-CEREVISIAE;
+ STAPHYLOCOCCUS-AUREUS; HELICOBACTER-PYLORI; ESCHERICHIA-COLI; NETWORK;
+ IDENTIFICATION; ANNOTATION; OPTIMIZATION; VALIDATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {22},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000253864700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000255407500006,
+Author = {Notebaart, Richard A. and Teusink, Bas and Siezen, Roland J. and Papp,
+ Balazs},
+Title = {Co-regulation of metabolic genes is better explained by flux coupling
+ than by network distance},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2008},
+Volume = {4},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.0040026},
+Article-Number = {e26},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI; TRANSCRIPTIONAL REGULATION; PREDICTION; EXPRESSION;
+ DESIGN; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Notebaart, Richard A./A-1459-2014
+ Siezen, Roland J/P-5745-2015
+ },
+ORCID-Numbers = {Papp, Balazs/0000-0003-3093-8852
+ Teusink, Bas/0000-0003-3929-0423},
+Times-Cited = {72},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000255407500006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000259526300006,
+Author = {Okumoto, Sakiko and Takanaga, Hitomi and Frommer, Wolf B.},
+Title = {Quantitative imaging for discovery and assembly of the metabo-regulome},
+Journal = {NEW PHYTOLOGIST},
+Year = {2008},
+Volume = {180},
+Number = {2},
+Pages = {271-295},
+Type = {Review},
+DOI = {10.1111/j.1469-8137.2008.02611.x},
+ISSN = {0028-646X},
+EISSN = {1469-8137},
+Keywords = {fluorescence resonance energy transfer (FRET); fluxomics; metabolomics;
+ metabolic signaling; metabolic pathways; sugar signaling},
+Keywords-Plus = {RESONANCE ENERGY-TRANSFER; GENETICALLY ENCODED INDICATORS; GREEN
+ FLUORESCENT PROTEIN; LIVING CELLS; PLASMA-MEMBRANE; INOSITOL
+ 1,4,5-TRISPHOSPHATE; SPATIOTEMPORAL DYNAMICS; ENDOPLASMIC-RETICULUM;
+ FRET-SENSOR; GUARD-CELLS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Frommer, Wolf B/A-8256-2008
+ Frommer, Wolf B/K-5042-2017},
+ORCID-Numbers = {Frommer, Wolf B/0000-0001-6465-0115
+ Frommer, Wolf B/0000-0001-6465-0115},
+Times-Cited = {42},
+Journal-ISO = {New Phytol.},
+Unique-ID = {WOS:000259526300006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000260586900010,
+Author = {Snitkin, Evan S. and Dudley, Aimee M. and Janse, Daniel M. and Wong,
+ Kaisheen and Church, George M. and Segre, Daniel},
+Title = {Model-driven analysis of experimentally determined growth phenotypes for
+ 465 yeast gene deletion mutants under 16 different conditions},
+Journal = {GENOME BIOLOGY},
+Year = {2008},
+Volume = {9},
+Number = {9},
+Type = {Article},
+DOI = {10.1186/gb-2008-9-9-r140},
+Article-Number = {R140},
+ISSN = {1474-7596},
+Keywords-Plus = {METABOLIC OBJECTIVE FUNCTIONS; SACCHAROMYCES-CEREVISIAE;
+ ESCHERICHIA-COLI; ADAPTIVE EVOLUTION; FLUX-MINIMIZATION; NETWORKS;
+ GENOME; RECONSTRUCTION; STRAINS; OPTIMIZATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Segrè, Daniel/A-1993-2009
+ Dudley, Aimee/K-3163-2019
+ },
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914
+ Dudley, Aimee/0000-0003-3644-0625
+ Snitkin, Evan/0000-0001-8409-278X
+ church, george/0000-0001-6232-9969},
+Times-Cited = {42},
+Journal-ISO = {Genome Biol.},
+Unique-ID = {WOS:000260586900010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000247907700001,
+Author = {Feist, Adam M. and Henry, Christopher S. and Reed, Jennifer L. and
+ Krummenacker, Markus and Joyce, Andrew R. and Karp, Peter D. and
+ Broadbelt, Linda J. and Hatzimanikatis, Vassily and Palsson, Bernhard O.},
+Title = {A genome-scale metabolic reconstruction for Escherichia coli K-12
+ MG1655 that accounts for 1260 ORFs and thermodynamic information},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2007},
+Volume = {3},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1038/msb4100155},
+Article-Number = {121},
+ISSN = {1744-4292},
+Keywords = {computational biology; group contribution method; systems biology;
+ thermodynamics},
+Keywords-Plus = {ADAPTIVE EVOLUTION; BIOMASS COMPOSITION; HIGH-THROUGHPUT; MODELS;
+ ENERGY; CAPABILITIES; NETWORK; CONSTRAINTS; ANNOTATION; EFFICIENCY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Reed, Jennifer L/E-5137-2011
+ Broadbelt, Linda/B-7640-2009
+ Hatzimanikatis, Vassily/B-7646-2009
+ Hatzimanikatis, Vassily/G-6505-2010
+ Karp, Peter/C-3514-2012},
+ORCID-Numbers = {Reed, Jennifer L/0000-0001-7854-6220
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Palsson, Bernhard/0000-0003-2357-6785
+ Karp, Peter/0000-0002-5876-6418},
+Times-Cited = {1035},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000247907700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000248731500003,
+Author = {Mo, Monica L. and Jamshidi, Neema and Palsson, Bernhard O.},
+Title = {A genome-scale, constraint-based approach to systems biology of human
+ metabolism},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2007},
+Volume = {3},
+Number = {9},
+Pages = {598-603},
+Type = {Article},
+DOI = {10.1039/b705597h},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {ESCHERICHIA-COLI; ADAPTIVE EVOLUTION; SKELETAL-MUSCLE; NETWORK;
+ RECONSTRUCTION; MODEL; ANNOTATION; OBESITY; NUTRIGENOMICS; GENOTYPE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {47},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000248731500003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001027246000001,
+Author = {Basile, Arianna and Heinken, Almut and Hertel, Johannes and Smarr, Larry
+ and Li, Weizhong and Treu, Laura and Valle, Giorgio and Campanaro,
+ Stefano and Thiele, Ines},
+Title = {Longitudinal flux balance analyses of a patient with episodic colonic
+ inflammation reveals microbiome metabolic dynamics},
+Journal = {GUT MICROBES},
+Year = {2023},
+Volume = {15},
+Number = {1},
+Month = {DEC 31},
+Type = {Article},
+DOI = {10.1080/19490976.2023.2226921},
+Article-Number = {2226921},
+ISSN = {1949-0976},
+EISSN = {1949-0984},
+Keywords = {Flux balance analysis; longitudinal data; inflammatory bowel diseases;
+ colonic inflammation; metagenomics; microbiota; metabolic modeling;
+ bioinformatics; constraint-based modeling; personalized medicine},
+Keywords-Plus = {CROHNS-DISEASE; GUT MICROBIOTA; ACID-METABOLISM; SYSTEMS BIOLOGY;
+ COLITIS; SEROTONIN; LIPOPOLYSACCHARIDE; MECHANISMS; DYSBIOSIS; RESPONSES},
+Research-Areas = {Gastroenterology \& Hepatology; Microbiology},
+Web-of-Science-Categories = {Gastroenterology \& Hepatology; Microbiology},
+ResearcherID-Numbers = {Basile, Arianna/IXW-5482-2023
+ Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Basile, Arianna/0000-0003-2461-5221
+ Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {1},
+Journal-ISO = {Gut Microbes},
+Unique-ID = {WOS:001027246000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001118692900001,
+Author = {Lee, Dae-Hee and Kim, Haseong and Sung, Bong-Hyun and Cho, Byung Kwan
+ and Lee, Seung-Goo},
+Title = {Biofoundries: Bridging Automation and Biomanufacturing in Synthetic
+ Biology},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2023},
+Month = {2023 DEC 11},
+Type = {Review; Early Access},
+DOI = {10.1007/s12257-023-0226-x},
+EarlyAccessDate = {DEC 2023},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {biofoundry; DBTL cycle; synthetic biology; biomanufacturing; automation},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; DNA; STRATEGIES; MOLECULES; DESIGN; GENES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:001118692900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001090445500001,
+Author = {Olavarria, Karel and Becker, Marco V. and Sousa, Diana Z. and van
+ Loosdrecht, Mark C. M. and Wahl, S. Aljoscha},
+Title = {Design and thermodynamic analysis of a pathway enabling anaerobic
+ production of poly-3-hydroxybutyrate in Escherichia coli},
+Journal = {SYNTHETIC AND SYSTEMS BIOTECHNOLOGY},
+Year = {2023},
+Volume = {8},
+Number = {4},
+Pages = {629-639},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1016/j.synbio.2023.09.005},
+ISSN = {2405-805X},
+Keywords = {Pathway feasibility analysis; Protein cost; Anaerobic metabolism;
+ Engineered pathways; Metabolite concentrations},
+Keywords-Plus = {PYRUVATE-DEHYDROGENASE COMPLEX; TRANSPORTERS; FERMENTATION; EXPRESSION;
+ MECHANISM; DATABASE; CLONING; GLUCOSE; MODELS; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Wahl, Sebastian Aljoscha/B-1839-2013
+ Sousa, Diana Z./K-5558-2012
+ Olavarria Gamez, Karel/I-8125-2012},
+ORCID-Numbers = {Wahl, Sebastian Aljoscha/0000-0003-2120-1859
+ Sousa, Diana Z./0000-0003-3569-1545
+ Olavarria Gamez, Karel/0000-0003-0435-7640},
+Times-Cited = {0},
+Journal-ISO = {Synth. Syst. Biotechnol.},
+Unique-ID = {WOS:001090445500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001107351700001,
+Author = {Yuan, Qianqian and Wei, Fan and Deng, Xiaogui and Li, Aonan and Shi,
+ Zhenkun and Mao, Zhitao and Li, Feiran and Ma, Hongwu},
+Title = {Reconstruction and metabolic profiling of the genome-scale metabolic
+ network model of Pseudomonas stutzeri A1501},
+Journal = {SYNTHETIC AND SYSTEMS BIOTECHNOLOGY},
+Year = {2023},
+Volume = {8},
+Number = {4},
+Pages = {688-696},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1016/j.synbio.2023.10.001},
+ISSN = {2405-805X},
+Keywords-Plus = {BIOLOGY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ma, Hongwu/I-5263-2013},
+ORCID-Numbers = {Li, Feiran/0000-0001-9155-5260
+ Ma, Hongwu/0000-0001-5325-2314},
+Times-Cited = {0},
+Journal-ISO = {Synth. Syst. Biotechnol.},
+Unique-ID = {WOS:001107351700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001111044800001,
+Author = {Malci, Koray and Santibanez, Rodrigo and Jonguitud-Borrego, Nestor and
+ Santoyo-Garcia, Jorge H. and Kerkhoven, Eduard J. and Rios-Solis,
+ Leonardo},
+Title = {Improved production of Taxol® precursors in S. cerevisiae using
+ combinatorial in silico design and metabolic engineering},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2023},
+Volume = {22},
+Number = {1},
+Month = {NOV 29},
+Type = {Article},
+DOI = {10.1186/s12934-023-02251-7},
+Article-Number = {243},
+EISSN = {1475-2859},
+Keywords = {Computational metabolic engineering; Genome-scale modelling; in silico
+ design; Synthetic biology; Systems biology; Mevalonate pathway;
+ Saccharomyces cerevisiae; Taxadiene; Taxol},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; YEAST; PATHWAY; SYNTHASE; GENES; ACID;
+ OVERPRODUCTION; EXPRESSION; MEMBRANE; GENOME},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:001111044800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001106780700001,
+Author = {Kaste, Joshua A. M. and Shachar-Hill, Yair},
+Title = {Model validation and selection in metabolic flux analysis and flux
+ balance analysis},
+Journal = {BIOTECHNOLOGY PROGRESS},
+Year = {2023},
+Month = {2023 NOV 24},
+Type = {Review; Early Access},
+DOI = {10.1002/btpr.3413},
+EarlyAccessDate = {NOV 2023},
+ISSN = {8756-7938},
+EISSN = {1520-6033},
+Keywords = {constraint-based modeling; flux balance analysis; metabolic flux
+ analysis; metabolic modeling; model selection; model validation},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; KNOCKOUT STRATEGIES; ESCHERICHIA-COLI;
+ SCALE; SYSTEMS; MINIMIZATION; FRAMEWORK; SOFTWARE; TRACERS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Shachar-Hill, Yair/B-6165-2013},
+ORCID-Numbers = {Kaste, Joshua/0000-0003-1942-0315
+ Shachar-Hill, Yair/0000-0001-8793-5084},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Prog.},
+Unique-ID = {WOS:001106780700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001112631700001,
+Author = {Plante, Mirco},
+Title = {Epistemology of synthetic biology: a new theoretical framework based on
+ its potential objects and objectives},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2023},
+Volume = {11},
+Month = {NOV 20},
+Type = {Article},
+DOI = {10.3389/fbioe.2023.1266298},
+Article-Number = {1266298},
+ISSN = {2296-4185},
+Keywords = {synthetic biology; philosophy of biology; epistemology; natural;
+ non-natural; artificial; virtual; living},
+Keywords-Plus = {GREEN FLUORESCENT PROTEIN; CHEMICAL-SYNTHESIS; SUBJECT-MATTER; CELL;
+ DNA; INTERDISCIPLINARITY; CLASSIFICATION; REDUCTION; MODELS; DEFINITIONS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+Times-Cited = {0},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:001112631700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001112938100001,
+Author = {Arora, Garhima and Banerjee, Mallar and Langthasa, Jimpi and Bhat,
+ Ramray and Chatterjee, Samrat},
+Title = {Article Targeting metabolic fluxes reverts metastatic transitions in
+ ovarian cancer},
+Journal = {ISCIENCE},
+Year = {2023},
+Volume = {26},
+Number = {11},
+Month = {NOV 17},
+Type = {Article},
+DOI = {10.1016/j.isci.2023.108081},
+Article-Number = {108081},
+EISSN = {2589-0042},
+Keywords-Plus = {DRUG-SENSITIVITY; EXPRESSION; DISCOVERY; SIALIDASE; RESOURCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {0},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:001112938100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001107260700001,
+Author = {Avila-Cabre, Silvia and Perez-Trujillo, Miriam and Albiol, Joan and
+ Ferrer, Pau},
+Title = {Engineering the synthetic β-alanine pathway in Komagataella phaffii for
+ conversion of methanol into 3-hydroxypropionic acid},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2023},
+Volume = {22},
+Number = {1},
+Month = {NOV 17},
+Type = {Article},
+DOI = {10.1186/s12934-023-02241-9},
+Article-Number = {237},
+EISSN = {1475-2859},
+Keywords = {3-Hydroxypropionic acid; Pichia pastoris; Komagataella phaffii;
+ Methanol; beta-Alanine pathway; Metabolic engineering},
+Keywords-Plus = {MALONYL-COA PATHWAY; ORYZAE LIPASE PRODUCTION; PICHIA-PASTORIS;
+ OPERATIONAL STRATEGIES; METHYLOTROPHIC YEAST; CLASSIFICATION;
+ METABOLISM; PREDICTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ferrer, Pau/A-4147-2009},
+Times-Cited = {0},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:001107260700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001106626200002,
+Author = {Gao, Le and Meng, Jiao and Dai, Wuling and Zhang, Zhaokun and Dong,
+ Haofan and Yuan, Qianqian and Zhang, Wuyuan and Liu, Shuguang and Wu,
+ Xin},
+Title = {Deciphering cell wall sensors enabling the construction of robust P.
+ pastoris for single-cell protein production},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS},
+Year = {2023},
+Volume = {16},
+Number = {1},
+Month = {NOV 17},
+Type = {Article},
+DOI = {10.1186/s13068-023-02428-7},
+Article-Number = {178},
+EISSN = {2731-3654},
+Keywords = {Single-cell protein; Pichia pastoris; Cell wall sensor; Signal
+ perturbations; Space-time productivity},
+Keywords-Plus = {SYNTHETIC BIOLOGY; SACCHAROMYCES-CEREVISIAE; YEAST; STRESS; ACID;
+ MYCOBACTERIUM; COMBINATION; PERFORMANCE; OSMOLARITY; GLYCEROL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Biofuels Bioprod.},
+Unique-ID = {WOS:001106626200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001113604300001,
+Author = {Kim, Won Jun and Lee, Youngjoon and Kim, Hyun Uk and Ryu, Jae Yong and
+ Yang, Jung Eun and Lee, Sang Yup},
+Title = {Genome-wide identification of overexpression and downregulation gene
+ targets based on the sum of covariances of the outgoing reaction fluxes},
+Journal = {CELL SYSTEMS},
+Year = {2023},
+Volume = {14},
+Number = {11},
+Pages = {990+},
+Month = {NOV 15},
+Type = {Article},
+DOI = {10.1016/j.cels.2023.10.005},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {CARBOXYLIC-ACID REDUCTASE; ESCHERICHIA-COLI; CORYNEBACTERIUM-GLUTAMICUM;
+ DESIGN; EXPRESSION; STRATEGIES; PLATFORM; STRAINS; YIELD},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Lee, Sang Yup/C-1526-2011},
+ORCID-Numbers = {Lee, Sang Yup/0000-0003-0599-3091},
+Times-Cited = {0},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:001113604300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001105486000001,
+Author = {Yu, Jing and Wang, Xiaowei and Yuan, Qianqian and Shi, Jiaxin and Cai,
+ Jingyi and Li, Zhichao and Ma, Hongwu},
+Title = {Elucidating the impact of in vitro cultivation on Nicotiana
+ tabacum metabolism through combined in silico modeling and
+ multiomics analysis},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2023},
+Volume = {14},
+Month = {NOV 3},
+Type = {Article},
+DOI = {10.3389/fpls.2023.1281348},
+Article-Number = {1281348},
+ISSN = {1664-462X},
+Keywords = {genome-scale metabolic model; tobacco; flux balance analysis; in vitro
+ cultivation; multiomics analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; LIGHT-INTENSITY; GROWTH; PHOTOSYNTHESIS;
+ PLANTLETS; RICE; RECONSTRUCTION; MICROPROPAGATION; ACCLIMATION;
+ GENERATION},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+Times-Cited = {0},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:001105486000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001094448600026,
+Author = {Bay, Omer F. and Hayes, Kelly S. and Schwartz, Jean-Marc and Grencis,
+ Richard K. and Roberts, Ian S.},
+Title = {A genome-scale metabolic model of parasitic whipworm},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2023},
+Volume = {14},
+Number = {1},
+Month = {OCT 31},
+Type = {Article},
+DOI = {10.1038/s41467-023-42552-4},
+Article-Number = {6937},
+EISSN = {2041-1723},
+Keywords-Plus = {THIOREDOXIN GLUTATHIONE-REDUCTASE; KNOWLEDGEBASE; MANSONI; DRUG},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Bay, Ömer Faruk/JMQ-0565-2023
+ },
+ORCID-Numbers = {Bay, Ömer Faruk/0000-0002-1142-2204
+ Schwartz, Jean-Marc/0000-0002-6472-0184
+ Roberts, Ian/0000-0002-0662-0214},
+Times-Cited = {0},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:001094448600026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001099106500001,
+Author = {Castaneda, Maria Teresita and Nunez, Sebastian and Jamilis, Martin and
+ De Battista, Hernan},
+Title = {Computational assessment of lipid production in Rhodosporidium
+ toruloides in two-stage and one-stage batch bioprocesses},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2023},
+Month = {2023 OCT 30},
+Type = {Article; Early Access},
+DOI = {10.1002/bit.28579},
+EarlyAccessDate = {OCT 2023},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {bioprocess performance metrics; designed strains; dynamic flux balance
+ analysis; metabolic model; Rhodosporidium toruloides},
+Keywords-Plus = {BIODIESEL PRODUCTION; GROWTH; CULTIVATION; KINETICS; OIL; Y4},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:001099106500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001108504900001,
+Author = {Mazat, Jean-Pierre},
+Title = {The metabolic control theory: Its development and its application to
+ mitochondrial oxidative phosphorylation},
+Journal = {BIOSYSTEMS},
+Year = {2023},
+Volume = {234},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2023.105038},
+EarlyAccessDate = {OCT 2023},
+Article-Number = {105038},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Metabolic control theory; Metabolic control analysis; Oxidative
+ phoshorylation; Mitochondrial diseases},
+Keywords-Plus = {FLUX-CONTROL COEFFICIENTS; ADENINE-NUCLEOTIDE TRANSLOCATOR; GENERAL
+ SENSITIVITY THEORY; ENZYME-ENZYME INTERACTIONS; BIOCHEMICAL
+ SYSTEMS-THEORY; STEADY-STATE TREATMENT; TOP-DOWN APPROACH; MUSCLE
+ MITOCHONDRIA; ADDITIONAL THEOREM; RESPIRATORY-CHAIN},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+Times-Cited = {0},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:001108504900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001088803500001,
+Author = {Liu, Yanhua and Westerhoff, Hans V.},
+Title = {`Social' versus `asocial' cells-dynamic competition flux balance
+ analysis},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2023},
+Volume = {9},
+Number = {1},
+Month = {OCT 28},
+Type = {Article},
+DOI = {10.1038/s41540-023-00313-5},
+Article-Number = {53},
+EISSN = {2056-7189},
+Keywords-Plus = {CANCER; HALLMARKS; GROWTH; METABOLISM; COMPLEX; MYC},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Westerhoff, Hans/I-5762-2012},
+ORCID-Numbers = {Westerhoff, Hans/0000-0002-0443-6114},
+Times-Cited = {0},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:001088803500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001091723000001,
+Author = {Casini, Isabella and Mccubbin, Tim and Esquivel-Elizondo, Sofia and
+ Luque, Guillermo G. and Evseeva, Daria and Fink, Christian and Beblawy,
+ Sebastian and Youngblut, Nicholas D. and Aristilde, Ludmilla and Huson,
+ Daniel H. and Draeger, Andreas and Ley, Ruth E. and Marcellin, Esteban
+ and Angenent, Largus T. and Molitor, Bastian},
+Title = {An integrated systems biology approach reveals differences in formate
+ metabolism in the genus Methanothermobacter},
+Journal = {ISCIENCE},
+Year = {2023},
+Volume = {26},
+Number = {10},
+Month = {OCT 20},
+Type = {Article},
+DOI = {10.1016/j.isci.2023.108016},
+Article-Number = {108016},
+EISSN = {2589-0042},
+Keywords-Plus = {COMPLETE GENOME SEQUENCE; METHANOSARCINA-BARKERI; METHANOGENIC ARCHAEON;
+ RECONSTRUCTION; DEHYDROGENASE; GROWTH; THERMAUTOTROPHICUS; MODEL;
+ QUANTIFICATION; MARBURGENSIS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Angenent, Largus T/A-6219-2018},
+ORCID-Numbers = {Angenent, Largus T/0000-0003-0180-1865},
+Times-Cited = {0},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:001091723000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001091166300001,
+Author = {Hou, Chengjie and Song, Xin and Xiong, Zhiqiang and Wang, Guangqiang and
+ Xia, Yongjun and Ai, Lianzhong},
+Title = {Genome-scale reconstruction of the metabolic network in Streptococcus
+ thermophilus S-3 and assess urea metabolism},
+Journal = {JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE},
+Year = {2023},
+Month = {2023 OCT 18},
+Type = {Article; Early Access},
+DOI = {10.1002/jsfa.13026},
+EarlyAccessDate = {OCT 2023},
+ISSN = {0022-5142},
+EISSN = {1097-0010},
+Keywords = {Streptococcus thermophilus; genome-scale metabolic network model;
+ urease; metabolic flux distribution},
+Keywords-Plus = {GROWTH; MODEL; ANNOTATION; BIOLOGY; MILK; ATP},
+Research-Areas = {Agriculture; Chemistry; Food Science \& Technology},
+Web-of-Science-Categories = {Agriculture, Multidisciplinary; Chemistry, Applied; Food Science \&
+ Technology},
+ORCID-Numbers = {hou, chengjie/0000-0003-1399-2814},
+Times-Cited = {0},
+Journal-ISO = {J. Sci. Food Agric.},
+Unique-ID = {WOS:001091166300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001085320000001,
+Author = {Elkasaby, Taghreed and Hanh, Dao Duy and Kawaguchi, Hideo and Toyoshima,
+ Masakazu and Kondo, Akihiko and Ogino, Chiaki},
+Title = {Co-utilization of Maltose and Sodium Acetate via Engineered
+ Corynebacterium glutamicum for Improved Itaconic Acid Production},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2023},
+Month = {2023 OCT 17},
+Type = {Article; Early Access},
+DOI = {10.1007/s12257-023-0091-7},
+EarlyAccessDate = {OCT 2023},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {itaconic acid Corynebacterium glutamicum; sodium acetate; monophasic
+ growth; flux balance analysis},
+Keywords-Plus = {GROWTH; METABOLISM; KINETICS; STRAIN; FLUX},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:001085320000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001088325400001,
+Author = {Jin, Qusheng},
+Title = {Building microbial kinetic models for environmental application: A
+ theoretical perspective},
+Journal = {APPLIED GEOCHEMISTRY},
+Year = {2023},
+Volume = {158},
+Month = {NOV},
+Type = {Review},
+DOI = {10.1016/j.apgeochem.2023.105782},
+EarlyAccessDate = {OCT 2023},
+Article-Number = {105782},
+ISSN = {0883-2927},
+EISSN = {1872-9134},
+Keywords = {Trait-based microbial kinetic model; Microbial kinetics; Rate laws;
+ Functional group; Microbial parameter; Internal consistency},
+Keywords-Plus = {REACTIVE TRANSPORT MODEL; GENOME-SCALE MODELS; BACTERIAL-GROWTH;
+ WATER-ACTIVITY; MARINE-SEDIMENTS; ORGANIC-MATTER; MASS-TRANSFER;
+ THERMODYNAMIC PROPERTIES; METHANOSARCINA-BARKERI; URANIUM BIOREMEDIATION},
+Research-Areas = {Geochemistry \& Geophysics},
+Web-of-Science-Categories = {Geochemistry \& Geophysics},
+Times-Cited = {0},
+Journal-ISO = {Appl. Geochem.},
+Unique-ID = {WOS:001088325400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001089610400002,
+Author = {Ferreira, Mauricio Alexander de Moura and Silveira, Wendel Batista da
+ and Nikoloski, Zoran},
+Title = {PARROT: Prediction of enzyme abundances using protein-constrained
+ metabolic models},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Volume = {19},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1011549},
+Article-Number = {e1011549},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI; GROWTH; RATES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ferreira, Mauricio/O-3900-2017
+ },
+ORCID-Numbers = {Silveira, Wendel/0000-0001-7869-8144
+ Ferreira, Mauricio/0000-0002-6545-6813
+ Nikoloski, Zoran/0000-0003-2671-6763},
+Times-Cited = {0},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:001089610400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001099895500001,
+Author = {Neal, Maxwell and Thiruppathy, Deepan and Zengler, Karsten},
+Title = {Genome-scale metabolic modeling of the human gut bacterium
+ Bacteroides fragilis strain 638R},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Volume = {19},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1011594},
+Article-Number = {e1011594},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI; GROWTH; MICROBIOTA},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+Times-Cited = {0},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:001099895500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001075130900001,
+Author = {Chen, Ke-Lin and Wang, Feng-Sheng},
+Title = {Cell-specific genome-scale metabolic modeling of SARS-CoV-2-infected
+ lung to identify antiviral enzymes},
+Journal = {FEBS OPEN BIO},
+Year = {2023},
+Month = {2023 SEP 30},
+Type = {Article; Early Access},
+DOI = {10.1002/2211-5463.13710},
+EarlyAccessDate = {SEP 2023},
+ISSN = {2211-5463},
+Keywords = {antiviral target design; constraint-based model; fuzzy optimization;
+ genome-scale metabolic model; hybrid differential evolution; multilevel
+ optimization},
+Keywords-Plus = {OPTIMIZATION; STRATEGIES; FRAMEWORK; NETWORK; DESIGN},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {0},
+Journal-ISO = {FEBS Open Bio},
+Unique-ID = {WOS:001075130900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001075479000002,
+Author = {Wang, Xia and Teng, Ying and Wang, Xiaomi and Xu, Yongfeng and Li, Ran
+ and Sun, Yi and Dai, Shixiang and Hu, Wenbo and Wang, Hongzhe and Li,
+ Yanning and Fang, Yan and Luo, Yongming},
+Title = {Nitrogen transfer and cross-feeding between Azotobacter
+ chroococcum and Paracoccus aminovorans promotes pyrene
+ degradation},
+Journal = {ISME JOURNAL},
+Year = {2023},
+Month = {2023 SEP 29},
+Type = {Article; Early Access},
+DOI = {10.1038/s41396-023-01522-w},
+EarlyAccessDate = {SEP 2023},
+ISSN = {1751-7362},
+EISSN = {1751-7370},
+Keywords-Plus = {POLYCYCLIC AROMATIC-HYDROCARBONS; METABOLITES; CONSORTIUM;
+ BIODEGRADATION; PERFORMANCE; PATHWAYS; FIXATION; BACTERIA},
+Research-Areas = {Environmental Sciences \& Ecology; Microbiology},
+Web-of-Science-Categories = {Ecology; Microbiology},
+Times-Cited = {0},
+Journal-ISO = {ISME J.},
+Unique-ID = {WOS:001075479000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001087778000061,
+Author = {Pentjuss, Agris and Bolmanis, Emils and Suleiko, Anastasija and
+ Didrihsone, Elina and Suleiko, Arturs and Dubencovs, Konstantins and
+ Liepins, Janis and Kazaks, Andris and Vanags, Juris},
+Title = {Pichia pastoris growth-coupled heme biosynthesis analysis using
+ metabolic modelling},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2023},
+Volume = {13},
+Number = {1},
+Month = {SEP 22},
+Type = {Article},
+DOI = {10.1038/s41598-023-42865-w},
+Article-Number = {15816},
+ISSN = {2045-2322},
+Keywords-Plus = {ESCHERICHIA-COLI; RECOMBINANT PROTEINS; EXPRESSION; HEMOGLOBIN;
+ STRATEGIES; BALANCE; BIOLOGY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Bolmanis, Emils/0000-0002-5087-2179},
+Times-Cited = {1},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:001087778000061},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001087778000079,
+Author = {Zangene, Ehsan and Marashi, Sayed-Amir and Montazeri, Hesam},
+Title = {SL-scan identifies synthetic lethal interactions in cancer using
+ metabolic networks},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2023},
+Volume = {13},
+Number = {1},
+Month = {SEP 22},
+Type = {Article},
+DOI = {10.1038/s41598-023-42992-4},
+Article-Number = {15763},
+ISSN = {2045-2322},
+Keywords-Plus = {CAPECITABINE; MUTANTS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {0},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:001087778000079},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001083895600001,
+Author = {Sridhar, Subasree and Bhalla, Prerna and Kullu, Justin and Veerapaneni,
+ Sriya and Sahoo, Swagatika and Bhatt, Nirav and Suraishkumar, G. K.},
+Title = {A reactive species reactions module for integration into genome-scale
+ metabolic models for improved insights: Application to cancer},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {80},
+Pages = {78-93},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2023.08.006},
+EarlyAccessDate = {SEP 2023},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Reactive species; Genome-scale metabolic models; Cancer metabolism;
+ Ferroptosis},
+Keywords-Plus = {OXIDATIVE STRESS; OXYGEN; PROGRESSION; GENERATION; IMPACT; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Suraishkumar, GK/0000-0002-6521-4494},
+Times-Cited = {0},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:001083895600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001076955100001,
+Author = {Wang, Bo and Zuniga, Cristal and Guarnieri, Michael T. and Zengler,
+ Karsten and Betenbaugh, Michael and Young, Jamey D.},
+Title = {Metabolic engineering of Synechococcus elongatus 7942 for
+ enhanced sucrose biosynthesis},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {80},
+Pages = {12-24},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2023.09.002},
+EarlyAccessDate = {SEP 2023},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords-Plus = {C-13 FLUX ANALYSIS; CARBON-DIOXIDE; CYANOBACTERIA; PHOSPHATE;
+ PHOTOSYNTHESIS; EXPRESSION; PLASTICITY; EFFICIENCY; SYNTHASE; RHYTHMS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Young, Jamey/0000-0002-0871-1494},
+Times-Cited = {0},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:001076955100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001075917400001,
+Author = {Eng, Thomas and Banerjee, Deepanwita and Menasalvas, Javier and Chen,
+ Yan and Gin, Jennifer and Choudhary, Hemant and Baidoo, Edward and Chen,
+ Jian Hua and Ekman, Axel and Kakumanu, Ramu and Diercks, Yuzhong Liu and
+ Codik, Alex and Larabell, Carolyn and Gladden, John and Simmons, Blake
+ A. and Keasling, Jay D. and Petzold, Christopher J. and Mukhopadhyay,
+ Aindrila},
+Title = {Maximizing microbial bioproduction from sustainable carbon sources using
+ iterative systems engineering},
+Journal = {CELL REPORTS},
+Year = {2023},
+Volume = {42},
+Number = {9},
+Month = {SEP 26},
+Type = {Article},
+DOI = {10.1016/j.celrep.2023.113087},
+EarlyAccessDate = {SEP 2023},
+Article-Number = {113087},
+ISSN = {2211-1247},
+Keywords-Plus = {PSEUDOMONAS-PUTIDA; ESCHERICHIA-COLI; FUMARATE REDUCTASE;
+ HYDROGEN-PEROXIDE; ACID PRODUCTION; EVOLUTION; CHEMICALS; PRODUCTS;
+ BIOFUELS; ENZYME},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+Times-Cited = {1},
+Journal-ISO = {Cell Reports},
+Unique-ID = {WOS:001075917400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001064259700001,
+Author = {Fleming, Ronan M. T. and Haraldsdottir, Hulda S. and Minh, Le Hoai and
+ Vuong, Phan Tu and Hankemeier, Thomas and Thiele, Ines},
+Title = {Cardinality optimization in constraint-based modelling: application to
+ human metabolism},
+Journal = {BIOINFORMATICS},
+Year = {2023},
+Volume = {39},
+Number = {9},
+Month = {SEP 2},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btad450},
+Article-Number = {btad450},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; PRINCIPLE; SELECTION; FLUXES},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Phan, Vuong/E-3833-2017
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Phan, Vuong/0000-0002-1474-994X
+ Hankemeier, Thomas/0000-0001-7871-2073
+ Thiele, Ines/0000-0002-8071-7110
+ Fleming, Ronan MT/0000-0001-5346-9812},
+Times-Cited = {0},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:001064259700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001072620900001,
+Author = {Griesemer, Marc and Navid, Ali},
+Title = {Uses of Multi-Objective Flux Analysis for Optimization of Microbial
+ Production of Secondary Metabolites},
+Journal = {MICROORGANISMS},
+Year = {2023},
+Volume = {11},
+Number = {9},
+Month = {SEP},
+Type = {Review},
+DOI = {10.3390/microorganisms11092149},
+Article-Number = {2149},
+EISSN = {2076-2607},
+Keywords = {secondary metabolism; flux balance analysis; COBRA; multi-objective flux
+ optimization; systems biology; metabolic engineering; synthesis
+ optimization},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; STREPTOMYCES-COELICOLOR;
+ RHODOPSEUDOMONAS-PALUSTRIS; QUANTITATIVE PREDICTION; ANTIBIOTIC
+ PRODUCTION; KNOCKOUT STRATEGIES; CELLULAR-METABOLISM; SYSTEMS BIOLOGY;
+ GENOME},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+Times-Cited = {1},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:001072620900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001077459700020,
+Author = {Healy, David and Wang, Shuo and Grimaud, Ghjuvan and Warda, Alicja
+ Katarzyna and Ross, Paul and Stanton, Catherine and Dempsey, Eugene M.},
+Title = {Longitudinal observational study protocol - Preterm Infants: Microbiome
+ Establishment, Neuro-CrossTalk and Origins (PIMENTO)},
+Journal = {BMJ OPEN},
+Year = {2023},
+Volume = {13},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1136/bmjopen-2023-075060},
+Article-Number = {e075060},
+ISSN = {2044-6055},
+Keywords = {Microbiology; Neonatal intensive \& critical care; NEONATOLOGY},
+Keywords-Plus = {PREVENT NECROTIZING ENTEROCOLITIS; GUT MICROBIOME; SEPSIS},
+Research-Areas = {General \& Internal Medicine},
+Web-of-Science-Categories = {Medicine, General \& Internal},
+ResearcherID-Numbers = {Ross, Paul/A-7584-2015
+ },
+ORCID-Numbers = {Ross, Paul/0000-0003-4876-8839
+ Healy, Dave/0000-0002-7627-4409},
+Times-Cited = {0},
+Journal-ISO = {BMJ Open},
+Unique-ID = {WOS:001077459700020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001075910200001,
+Author = {Sneha, Nela Pragathi and Dharshini, S. Akila Parvathy and Taguchi, Y. -H
+ and Gromiha, M. Michael},
+Title = {Investigating Neuron Degeneration in Huntington's Disease Using RNA-Seq
+ Based Transcriptome Study},
+Journal = {GENES},
+Year = {2023},
+Volume = {14},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.3390/genes14091801},
+Article-Number = {1801},
+EISSN = {2073-4425},
+Keywords = {Huntington's disease; Brodmann area 4; tissue-specific network analysis;
+ variant effect; function interaction network},
+Keywords-Plus = {ASTROCYTE ELEVATED GENE-1; PROTEIN-COUPLED RECEPTORS; GENOME-WIDE
+ ASSOCIATION; SUBUNIT; COMPLEX; IDENTIFICATION; PATHWAY; REVEALS;
+ ANGIOGENESIS; METABOLISM},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Taguchi, Y-h./E-1474-2011},
+ORCID-Numbers = {Michael, Gromiha/0000-0002-1776-4096
+ Taguchi, Y-h./0000-0003-0867-8986},
+Times-Cited = {0},
+Journal-ISO = {Genes},
+Unique-ID = {WOS:001075910200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001069368500001,
+Author = {Vera-Siguenza, Elias and Escribano-Gonzalez, Cristina and
+ Serrano-Gonzalo, Irene and Eskla, Kattri-Liis and Spill, Fabian and
+ Tennant, Daniel},
+Title = {Mathematical reconstruction of the metabolic network in an in-vitro
+ multiple myeloma model},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Volume = {19},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1011374},
+Article-Number = {e1011374},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {MESENCHYMAL STEM-CELLS; TUMOR MICROENVIRONMENT; CANCER; EXPRESSION;
+ PROLIFERATION; COCULTURE; INSIGHTS; LINES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Tennant, Daniel/0000-0003-0499-2732
+ Siguenza, Elias/0000-0003-4090-3557},
+Times-Cited = {0},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:001069368500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001064621000001,
+Author = {Holland, Bethany L. and Matthews, Megan L. and Bota, Pedro and
+ Sweetlove, Lee J. and Long, Stephen P. and Dicenzo, George C.},
+Title = {A genome-scale metabolic reconstruction of soybean and Bradyrhizobium
+ diazoefficiens reveals the cost-benefit of nitrogen fixation},
+Journal = {NEW PHYTOLOGIST},
+Year = {2023},
+Volume = {240},
+Number = {2},
+Pages = {744-756},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1111/nph.19203},
+EarlyAccessDate = {AUG 2023},
+ISSN = {0028-646X},
+EISSN = {1469-8137},
+Keywords = {carbon costs; mathematical model; nitrogen fixation; nitrogen
+ metabolism; root nodule; soybean},
+Keywords-Plus = {CARBON-DIOXIDE CONCENTRATION; GLOMUS-RHIZOBIUM SYMBIOSIS;
+ ACETYLENE-REDUCTION ASSAY; PERIBACTEROID MEMBRANE; DINITROGEN FIXATION;
+ GLYCINE MAXMERR.; GRAIN PRODUCTION; ATPASE ACTIVITY; USE EFFICIENCY; N-2
+ FIXATION},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {diCenzo, George C/M-1876-2017
+ Long, Stephen/AAA-1741-2019
+ },
+ORCID-Numbers = {Holland, Bethany/0000-0002-6660-606X
+ diCenzo, George C/0000-0003-3889-6570
+ Matthews, Megan/0000-0002-5513-9320
+ Bota, Pedro/0000-0003-0889-9789
+ Long, Stephen/0000-0002-8501-7164
+ Sweetlove, Lee/0000-0002-2461-4133},
+Times-Cited = {0},
+Journal-ISO = {New Phytol.},
+Unique-ID = {WOS:001064621000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001057775600001,
+Author = {Nonaka, Kyoshiro and Osamura, Tatsuya and Takahashi, Fumikazu},
+Title = {A 4-hydroxybenzoate 3-hydroxylase mutant enables
+ 4-amino-3-hydroxybenzoic acid production from glucose in
+ Corynebacterium glutamicum},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2023},
+Volume = {22},
+Number = {1},
+Month = {AUG 29},
+Type = {Article},
+DOI = {10.1186/s12934-023-02179-y},
+Article-Number = {168},
+EISSN = {1475-2859},
+Keywords = {4-Amino-3-hydroxybenzoic acid; 4-Aminobenzoic acid; Polybenzoxazole;
+ Artificial biosynthetic pathway; Shikimate pathway; Corynebacterium
+ glutamicum; Flavoprotein monooxygenases; 4-Hydroxybenzoate
+ 3-hydroxylase; Enzyme engineering; Genome-scale metabolic modeling},
+Keywords-Plus = {P-HYDROXYBENZOATE HYDROXYLASE; HIGH-PERFORMANCE; LYASE; SITE;
+ EXPRESSION; SUBSTRATE; SEQUENCE; PATHWAY; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:001057775600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001119048600001,
+Author = {Park, Seo-Young and Choi, Dong-Hyuk and Song, Jinsung and Park, Uiseon
+ and Cho, Hyeran and Hong, Bee Hak and Silberberg, Yaron R. and Lee,
+ Dong-Yup},
+Title = {Debottlenecking and reformulating feed media for improved CHO cell
+ growth and titer by data-driven and model-guided analyses},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2023},
+Month = {2023 AUG 27},
+Type = {Article; Early Access},
+DOI = {10.1002/biot.202300126},
+EarlyAccessDate = {AUG 2023},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {biopharmaceutical processes; Chinese hamster ovary cells; feed
+ reformulation; flux balance analysis; monoclonal antibody; multivariate
+ data analysis},
+Keywords-Plus = {PROTEIN-PRODUCTION; OPTIMIZATION; DESIGN},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lee, Dong-Yup/D-6650-2011},
+ORCID-Numbers = {Park, Seo-Young/0000-0001-6140-412X
+ Lee, Dong-Yup/0000-0003-0901-708X},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:001119048600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001067868800001,
+Author = {Puig-Castellvi, Francesc and Pacheco-Tapia, Romina and Deslande, Maxime
+ and Jia, Manyi and Andrikopoulos, Petros and Chechi, Kanta and
+ Bonnefond, Amelie and Froguel, Philippe and Dumas, Marc-Emmanuel},
+Title = {Advances in the integration of metabolomics and metagenomics for human
+ gut microbiome and their clinical applications},
+Journal = {TRAC-TRENDS IN ANALYTICAL CHEMISTRY},
+Year = {2023},
+Volume = {167},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1016/j.trac.2023.117248},
+EarlyAccessDate = {AUG 2023},
+Article-Number = {117248},
+ISSN = {0165-9936},
+EISSN = {1879-3142},
+Keywords = {Gut microbiome; Clinical metabolomics; metagenomics; Data fusion;
+ Knowledge integration; Biosynthetic gene clusters; Multi-omic analyses},
+Keywords-Plus = {UNTARGETED MASS-SPECTROMETRY; NATURAL-PRODUCTS; GENE CLUSTERS;
+ NONRIBOSOMAL PEPTIDE; LATENT STRUCTURES; WIDE ASSOCIATION; DISCOVERY;
+ REVEALS; METABOLITES; DATABASE},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Analytical},
+ResearcherID-Numbers = {Puig-Castellví, Francesc/ABA-2909-2020
+ Dumas, Marc-Emmanuel/C-1736-2008
+ },
+ORCID-Numbers = {Puig-Castellví, Francesc/0000-0003-1064-9586
+ Andrikopoulos, Petros/0000-0002-1555-3498
+ Dumas, Marc-Emmanuel/0000-0001-9523-7024
+ Jia, Manyi/0000-0001-9467-1494},
+Times-Cited = {0},
+Journal-ISO = {Trac-Trends Anal. Chem.},
+Unique-ID = {WOS:001067868800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001069306800001,
+Author = {Gelbach, Patrick E. and Finley, Stacey D.},
+Title = {Genome-scale modeling predicts metabolic differences between macrophage
+ subtypes in colorectal cancer},
+Journal = {ISCIENCE},
+Year = {2023},
+Volume = {26},
+Number = {9},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1016/j.isci.2023.107569},
+EarlyAccessDate = {AUG 2023},
+Article-Number = {107569},
+EISSN = {2589-0042},
+Keywords-Plus = {FATTY-ACID OXIDATION; TUMOR-ASSOCIATED MACROPHAGES; MICROENVIRONMENT;
+ POLARIZATION; ACTIVATION; EXPRESSION; CELLS; IMMUNOMETABOLISM;
+ DIFFERENTIATION; REQUIREMENTS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Finley, Stacey/0000-0001-6901-3692},
+Times-Cited = {0},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:001069306800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001058398700001,
+Author = {Povo-Retana, Adrian and Farinas, Marco and Landauro-Vera, Rodrigo and
+ Mojena, Marina and Alvarez-Lucena, Carlota and Fernandez-Moreno, Miguel
+ A. and Castrillo, Antonio and de la Rosa Medina, Juan Vladimir and
+ Sanchez-Garcia, Sergio and Foguet, Carles and Mas, Francesc and Marin,
+ Silvia and Cascante, Marta and Bosca, Lisardo},
+Title = {Immunometabolic actions of trabectedin and lurbinectedin on human
+ macrophages: relevance for their anti-tumor activity},
+Journal = {FRONTIERS IN IMMUNOLOGY},
+Year = {2023},
+Volume = {14},
+Month = {AUG 22},
+Type = {Article},
+DOI = {10.3389/fimmu.2023.1211068},
+Article-Number = {1211068},
+ISSN = {1664-3224},
+Keywords = {macrophages; immunometabolism; trabectedin; lurbinectedin; ROS},
+Keywords-Plus = {TUMOR-ASSOCIATED MACROPHAGES; CELLULAR-METABOLISM; CELLS; CANCER;
+ POLARIZATION; ACTIVATION; SYSTEM},
+Research-Areas = {Immunology},
+Web-of-Science-Categories = {Immunology},
+ResearcherID-Numbers = {Foguet Coll, Carles/W-4864-2018},
+ORCID-Numbers = {Foguet Coll, Carles/0000-0001-8494-9595},
+Times-Cited = {0},
+Journal-ISO = {Front. Immunol.},
+Unique-ID = {WOS:001058398700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001055176800012,
+Author = {Velasco-Alvarez, Juan Ricardo and Torres, Nimbe Torres y and Chairez,
+ Isaac and Castrejon-Flores, Jose Luis},
+Title = {Microbiome distribution modeling using gradient descent strategies for
+ mock, in vitro and clinical community distributions},
+Journal = {PLOS ONE},
+Year = {2023},
+Volume = {18},
+Number = {8},
+Month = {AUG 21},
+Type = {Article},
+DOI = {10.1371/journal.pone.0290082},
+ISSN = {1932-6203},
+Keywords-Plus = {GUT MICROBIOTA; HOMEOSTASIS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Castrejon, Luis/0000-0002-2808-2808},
+Times-Cited = {0},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:001055176800012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001049314000008,
+Author = {Cordoba, Sandra Correa and Tong, Hao and Burgos, Asdrubal and Zhu, Feng
+ and Alseekh, Saleh and Fernie, Alisdair R. and Nikoloski, Zoran},
+Title = {Identification of gene function based on models capturing natural
+ variability of Arabidopsis thaliana lipid metabolism},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2023},
+Volume = {14},
+Number = {1},
+Month = {AUG 14},
+Type = {Article},
+DOI = {10.1038/s41467-023-40644-9},
+Article-Number = {4897},
+EISSN = {2041-1723},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FATTY-ACID SYNTHESIS; BETA-OXIDATION;
+ COMPUTATIONAL ANALYSIS; CARBON; EXPRESSION; GROWTH; LIGHT;
+ TRIACYLGLYCEROL; ACYLTRANSFERASE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Nikoloski, Zoran/0000-0003-2671-6763
+ Alseekh, Saleh/0000-0003-2067-5235
+ Tong, Hao/0000-0003-4856-1336},
+Times-Cited = {0},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:001049314000008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001048553800026,
+Author = {Arend, Marius and Zimmer, David and Xu, Rudan and Sommer, Frederik and
+ Muehlhaus, Timo and Nikoloski, Zoran},
+Title = {Proteomics and constraint-based modelling reveal enzyme kinetic
+ properties of Chlamydomonas reinhardtii on a genome scale},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2023},
+Volume = {14},
+Number = {1},
+Month = {AUG 8},
+Type = {Article},
+DOI = {10.1038/s41467-023-40498-1},
+EISSN = {2041-1723},
+Keywords-Plus = {RESOURCE; DATABASE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Nikoloski, Zoran/0000-0003-2671-6763
+ Sommer, Frederik/0000-0003-0247-4907
+ Arend, Marius/0000-0002-9608-4960},
+Times-Cited = {0},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:001048553800026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001063039700001,
+Author = {de Atauri, Pedro and Foguet, Carles and Cascante, Marta},
+Title = {Control analysis in the identification of key enzymes driving metabolic
+ adaptations: Towards drug target discovery},
+Journal = {BIOSYSTEMS},
+Year = {2023},
+Volume = {231},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2023.104984},
+EarlyAccessDate = {AUG 2023},
+Article-Number = {104984},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Metabolic control analysis; Control coefficients; Metabolic adaptations},
+Keywords-Plus = {GENERAL SENSITIVITY THEORY; ACHIEVING INCREASES; SYSTEMATIC-APPROACH;
+ IMPLICIT METHODS; LINEAR TREATMENT; MATRIX-METHOD; RESPONSES; FLUXES;
+ HEXOKINASE; EFFECTORS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Foguet Coll, Carles/W-4864-2018},
+ORCID-Numbers = {de Atauri, Pedro/0000-0002-7754-7851
+ CASCANTE, MARTA/0000-0002-2062-4633
+ Foguet Coll, Carles/0000-0001-8494-9595},
+Times-Cited = {0},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:001063039700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001042595000001,
+Author = {Neves, Dario and Meinen, Daniel and Alter, Tobias B. B. and Blank, Lars
+ M. M. and Ebert, Birgitta E. E.},
+Title = {Expanding Pseudomonas taiwanensis VLB120's acyl-CoA portfolio:
+ Propionate production in mineral salt medium},
+Journal = {MICROBIAL BIOTECHNOLOGY},
+Year = {2023},
+Month = {2023 AUG 3},
+Type = {Article; Early Access},
+DOI = {10.1111/1751-7915.14309},
+EarlyAccessDate = {AUG 2023},
+ISSN = {1751-7915},
+Keywords-Plus = {ENGINEERING ESCHERICHIA-COLI; GRAM-NEGATIVE BACTERIA; PUTIDA;
+ BIOSYNTHESIS; METABOLISM; STRAIN; CONSTRUCTION; EXPRESSION; PATHWAYS;
+ OXIDE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Ebert, Birgitta Elisabeth/B-7845-2014
+ Blank, Lars M./A-6761-2012
+ },
+ORCID-Numbers = {Meinen, Daniel/0000-0003-3032-2695
+ Ebert, Birgitta Elisabeth/0000-0001-9425-7509
+ Blank, Lars M./0000-0003-0961-4976
+ Alter, Tobias Benedikt/0000-0002-9593-4388},
+Times-Cited = {0},
+Journal-ISO = {Microb. Biotechnol.},
+Unique-ID = {WOS:001042595000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001049460700001,
+Author = {Suyama, Hiroki and Luu, Laurence Don Wai and Zhong, Ling and Raftery,
+ Mark J. and Lan, Ruiting},
+Title = {Integrating proteomic data with metabolic modeling provides insight into
+ key pathways of Bordetella pertussis biofilms},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2023},
+Volume = {14},
+Month = {AUG 3},
+Type = {Article},
+DOI = {10.3389/fmicb.2023.1169870},
+Article-Number = {1169870},
+EISSN = {1664-302X},
+Keywords = {Bordetella pertussis; proteomics; metabolic model; infectious disease;
+ label free quantification (LFQ); mass spectrometry; whooping cough},
+Keywords-Plus = {CHANGING EPIDEMIOLOGY; GLYOXYLATE SHUNT; DIFFUSION; COLONIZATION;
+ SALMONELLA; INFECTION; VIRULENCE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Luu, Laurence/0000-0003-2516-2121},
+Times-Cited = {0},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:001049460700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001049682200001,
+Author = {Murali, Sarayu and Ibrahim, Maziya and Rajendran, Hemalatha and Shagun,
+ Shagun and Masakapalli, Shyam Kumar and Raman, Karthik and Srivastava,
+ Smita},
+Title = {Genome-scale metabolic model led engineering of Nothapodytes
+ nimmoniana plant cells for high camptothecin production},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2023},
+Volume = {14},
+Month = {AUG 2},
+Type = {Article},
+DOI = {10.3389/fpls.2023.1207218},
+Article-Number = {1207218},
+ISSN = {1664-462X},
+Keywords = {camptothecin yield; metabolic engineering; genome-scale metabolic model;
+ enzyme overexpression; Agrobacterium tumefaciens transformation;
+ strictosidine synthase},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; STRICTOSIDINE SYNTHASE; ALKALOID PRODUCTION;
+ OVER-EXPRESSION; RECONSTRUCTION; ARABIDOPSIS; NETWORK; TISSUE; GENES;
+ BIOSYNTHESIS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Masakapalli, Shyam/ABD-9712-2020},
+ORCID-Numbers = {Masakapalli, Shyam/0000-0003-1988-5569},
+Times-Cited = {0},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:001049682200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000999684000003,
+Author = {Cesur, Mueberra Fatma and Basile, Arianna and Patil, Kiran Raosaheb and
+ Cakir, Tunahan},
+Title = {A new metabolic model of Drosophila melanogaster and the
+ integrative analysis of Parkinson's disease},
+Journal = {LIFE SCIENCE ALLIANCE},
+Year = {2023},
+Volume = {6},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.26508/lsa.202201695},
+Article-Number = {e202201695},
+EISSN = {2575-1077},
+Keywords-Plus = {JUVENILE PARKINSONISM; ENRICHMENT ANALYSIS; BIOCYC COLLECTION; METACYC
+ DATABASE; GUT MICROBIOTA; WEB SERVER; GENE; PROTEIN; HOMEOSTASIS;
+ FLYBASE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Basile, Arianna/IXW-5482-2023
+ Cesur, Müberra Fatma/AHC-2805-2022
+ Patil, Kiran Raosaheb/B-9709-2009
+ Cakir, Tunahan/F-4523-2011},
+ORCID-Numbers = {Basile, Arianna/0000-0003-2461-5221
+ Cesur, Müberra Fatma/0000-0003-2993-0634
+ Patil, Kiran Raosaheb/0000-0002-6166-8640
+ Cakir, Tunahan/0000-0001-8262-4420},
+Times-Cited = {0},
+Journal-ISO = {Life Sci. Alliance},
+Unique-ID = {WOS:000999684000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001057928100003,
+Author = {Cunha, Emanuel and Lagoa, Davide and Faria, Jose P. and Liu, Filipe and
+ Henry, Christopher S. and Dias, Oscar},
+Title = {TranSyT, an innovative framework for identifying transport
+ systems},
+Journal = {BIOINFORMATICS},
+Year = {2023},
+Volume = {39},
+Number = {8},
+Month = {AUG 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btad466},
+Article-Number = {btad466},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {MEMBRANE; DATABASE; HOMEOSTASIS; ANNOTATION; RESOURCE; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+Times-Cited = {0},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:001057928100003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001051688600003,
+Author = {Jadebeck, Johann. F. F. and Wiechert, Wolfgang and Noeh, Katharina},
+Title = {Practical sampling of constraint-based models: Optimized thinning boosts
+ CHRR performance},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Volume = {19},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1011378},
+Article-Number = {e1011378},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {HIT-AND-RUN; SCALE METABOLIC MODELS; RECONSTRUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+Times-Cited = {0},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:001051688600003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001082879404138,
+Author = {Luo, X. and Liu, Y. J. and Balck, A. and Klein, C. and Fleming, R.},
+Title = {Identification of Reproducible Metabolites for Parkinson's Disease
+ Diagnosis using Clinical Data and Computational Modelling},
+Journal = {MOVEMENT DISORDERS},
+Year = {2023},
+Volume = {38},
+Number = {1},
+Meeting = {1484},
+Pages = {S647-S648},
+Month = {AUG},
+Note = {International Congress of Parkinson's Disease and Movement Disorders,
+ Copenhagen, DENMARK, AUG 27-31, 2023},
+Type = {Meeting Abstract},
+ISSN = {0885-3185},
+EISSN = {1531-8257},
+Research-Areas = {Neurosciences \& Neurology},
+Web-of-Science-Categories = {Clinical Neurology},
+Times-Cited = {0},
+Journal-ISO = {Mov. Disord.},
+Unique-ID = {WOS:001082879404138},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001108527600001,
+Author = {Qiu, Sizhe and Yang, Aidong and Zeng, Hong},
+Title = {Flux balance analysis-based metabolic modeling of microbial secondary
+ metabolism: Current status and outlook},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Volume = {19},
+Number = {8},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1371/journal.pcbi.1011391},
+Article-Number = {e1011391},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {LACTIC-ACID BACTERIA; SYNTHETIC BIOLOGY; ESCHERICHIA-COLI;
+ EXOPOLYSACCHARIDE PRODUCTION; COMPUTATIONAL TOOLS; GENOME;
+ RECONSTRUCTION; BIOSYNTHESIS; INTEGRATION; RIBOFLAVIN},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Qiu, Sizhe/0000-0002-1936-1223},
+Times-Cited = {0},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:001108527600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001050842200005,
+Author = {Scott Jr, William T. R. and Benito-Vaquerizo, Sara and Zimmermann,
+ Johannes R. and Bajic, Djordje and Heinken, Almut R. and Suarez-Diez,
+ Maria and Schaap, Peter R.},
+Title = {A structured evaluation of genome-scale constraint-based modeling tools
+ for microbial consortia},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Volume = {19},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1011363},
+Article-Number = {e1011363},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {RECONSTRUCTION; DESIGN; BIOREMEDIATION; COCULTURES; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zimmermann, Johannes/HTP-7711-2023
+ },
+ORCID-Numbers = {Zimmermann, Johannes/0000-0002-5041-1954
+ Heinken, Almut/0000-0001-6938-8072
+ Suarez-Diez, Maria/0000-0001-5845-146X
+ Schaap, Peter/0000-0002-4346-6084
+ Scott, William/0000-0002-4029-2998},
+Times-Cited = {1},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:001050842200005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001050820800001,
+Author = {Tec-Campos, Diego and Posadas, Camila and Tibocha-Bonilla, Juan D. and
+ Thiruppathy, Deepan and Glonek, Nathan and Zuniga, Cristal and Zepeda,
+ Alejandro and Zengler, Karsten},
+Title = {The genome-scale metabolic model for the purple non-sulfur bacterium
+ Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes
+ under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and
+ photoautotrophic growth conditions},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Volume = {19},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1011371},
+Article-Number = {e1011371},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {AROMATIC-COMPOUNDS; CAROTENOID PRODUCTION; HYDROGEN-PRODUCTION;
+ WASTE-WATER; LIGHT; OPTIMIZATION; PHOTOSYNTHESIS; CONVERSION; SEQUENCE;
+ CGA010},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {1},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:001050820800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001054786900001,
+Author = {Choi, Yoon-Mi and Choi, Dong-Hyuk and Lee, Yi Qing and Koduru, Lokanand
+ and Lewis, Nathan E. and Lakshmanan, Meiyappan and Lee, Dong-Yup},
+Title = {Mitigating biomass composition uncertainties in flux balance analysis
+ using ensemble representations},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2023},
+Volume = {21},
+Pages = {3736-3745},
+Type = {Article},
+DOI = {10.1016/j.csbj.2023.07.025},
+EarlyAccessDate = {JUL 2023},
+ISSN = {2001-0370},
+Keywords = {Flux balance analysis (FBA); Parsimonious flux balance analysis (pFBA);
+ Biomass equation; Ensemble modeling; Macromolecular composition},
+Keywords-Plus = {SCALE METABOLIC MODEL; IN-SILICO ANALYSIS; ESCHERICHIA-COLI;
+ ACID-COMPOSITION; GENE-EXPRESSION; STRESSES; GROWTH; CHO},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/H-1267-2014
+ Lee, Dong-Yup/D-6650-2011
+ },
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Lee, Yi Qing/0000-0002-8970-0729
+ Koduru, Lokanand/0000-0001-9223-8742},
+Times-Cited = {1},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:001054786900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001038744000001,
+Author = {Tong, Hao and Laitinen, Roosa A. E. and Nikoloski, Zoran},
+Title = {Predicting plasticity of rosette growth and metabolic fluxes in
+ Arabidopsis thaliana},
+Journal = {NEW PHYTOLOGIST},
+Year = {2023},
+Volume = {240},
+Number = {1},
+Pages = {426-438},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1111/nph.19154},
+EarlyAccessDate = {JUL 2023},
+ISSN = {0028-646X},
+EISSN = {1469-8137},
+Keywords = {genomic prediction; genotype-by-environment interaction; metabolic
+ network; phenotypic plasticity; plant growth; reaction flux},
+Keywords-Plus = {PHENOTYPIC PLASTICITY; GENETICS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ORCID-Numbers = {Laitinen, Roosa/0000-0003-3317-4667
+ Nikoloski, Zoran/0000-0003-2671-6763
+ Tong, Hao/0000-0003-4856-1336},
+Times-Cited = {0},
+Journal-ISO = {New Phytol.},
+Unique-ID = {WOS:001038744000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001054229600001,
+Author = {Gao, Xiaoxiang and Zhao, Jianxin and Chen, Wei and Zhai, Qixiao},
+Title = {Food and drug design for gut microbiota-directed regulation: Current
+ experimental landscape and future innovation},
+Journal = {PHARMACOLOGICAL RESEARCH},
+Year = {2023},
+Volume = {194},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1016/j.phrs.2023.106867},
+EarlyAccessDate = {JUL 2023},
+Article-Number = {106867},
+ISSN = {1043-6618},
+EISSN = {1096-1186},
+Keywords = {Microbiota-directed foods and drugs; Simulated cultivation; Specific
+ physiological characteristics; Microbial model; Germ-free animal;
+ Precision nutrition},
+Keywords-Plus = {INTERSPECIES COMPETITION; HOST GENETICS; HEALTH; INHIBITORS; BACTERIA;
+ DATABASE},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {liang, liang/IAO-8518-2023},
+Times-Cited = {0},
+Journal-ISO = {Pharmacol. Res.},
+Unique-ID = {WOS:001054229600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001037767700004,
+Author = {Bintener, Tamara and Pacheco, Maria Pires and Philippidou, Demetra and
+ Margue, Christiane and Kishk, Ali and Del Mistro, Greta and Di Leo, Luca
+ and Moscardo Garcia, Maria and Halder, Rashi and Sinkkonen, Lasse and De
+ Zio, Daniela and Kreis, Stephanie and Kulms, Dagmar and Sauter, Thomas},
+Title = {Metabolic modelling-based in silico drug target prediction identifies
+ six novel repurposable drugs for melanoma},
+Journal = {CELL DEATH \& DISEASE},
+Year = {2023},
+Volume = {14},
+Number = {7},
+Month = {JUL 26},
+Type = {Article},
+DOI = {10.1038/s41419-023-05955-1},
+Article-Number = {468},
+ISSN = {2041-4889},
+Keywords-Plus = {FATTY-ACID SYNTHASE; SQUAMOUS-CELL CARCINOMA; BREAST-CANCER CELLS;
+ COLON-CANCER; DOUBLE-BLIND; GEMCITABINE; INHIBITOR; GROWTH; FLUVASTATIN;
+ LOVASTATIN},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Sinkkonen, Lasse/AAL-7906-2021
+ Pires Pacheco, Maria/C-4494-2014},
+ORCID-Numbers = {Sinkkonen, Lasse/0000-0002-4223-3027
+ Sauter, Thomas/0000-0001-8225-2954
+ HALDER, Rashi/0000-0002-1402-1254
+ Pires Pacheco, Maria/0000-0001-7956-8093},
+Times-Cited = {0},
+Journal-ISO = {Cell Death Dis.},
+Unique-ID = {WOS:001037767700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001033794300001,
+Author = {Mirveis, Zohreh and Howe, Orla and Cahill, Paul and Patil, Nitin and
+ Byrne, Hugh J. J.},
+Title = {Monitoring and modelling the glutamine metabolic pathway: a review and
+ future perspectives},
+Journal = {METABOLOMICS},
+Year = {2023},
+Volume = {19},
+Number = {8},
+Month = {JUL 23},
+Type = {Review},
+DOI = {10.1007/s11306-023-02031-9},
+Article-Number = {67},
+ISSN = {1573-3882},
+EISSN = {1573-3890},
+Keywords = {Metabolic pathways analysis; Glutaminolysis; Flux analysis;
+ Computational modelling; Vibrational spectroscopy; Chemometrics},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; CHROMATOGRAPHY-MASS SPECTROMETRY;
+ TRANSFORM-INFRARED-SPECTROSCOPY; RAMAN MICRO SPECTROSCOPY; FLUX
+ ANALYSIS; CANCER-CELLS; SAMPLE PREPARATION; ION SUPPRESSION; SYSTEMS
+ BIOLOGY; KINETIC-MODELS},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Byrne, Hugh James/AAD-9713-2020
+ },
+ORCID-Numbers = {Byrne, Hugh James/0000-0002-1735-8610
+ Patil, Nitin/0000-0001-7113-5111},
+Times-Cited = {0},
+Journal-ISO = {Metabolomics},
+Unique-ID = {WOS:001033794300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001074497900001,
+Author = {Watanabe, Kengo and Wilmanski, Tomasz and Baloni, Priyanka and Robinson,
+ Max and Garcia, Gonzalo G. and Hoopmann, Michael R. and Midha, Mukul K.
+ and Baxter, David H. and Maes, Michal and Morrone, Seamus R. and Crebs,
+ Kelly M. and Kapil, Charu and Kusebauch, Ulrike and Wiedrick, Jack and
+ Lapidus, Jodi and Pflieger, Lance and Lausted, Christopher and Roach,
+ Jared C. and Glusman, Gwenlyn and Cummings, Steven R. and Schork,
+ Nicholas J. and Price, Nathan D. and Hood, Leroy and Miller, Richard A.
+ and Moritz, Robert L. and Rappaport, Noa},
+Title = {Lifespan-extending interventions induce consistent patterns of fatty
+ acid oxidation in mouse livers},
+Journal = {COMMUNICATIONS BIOLOGY},
+Year = {2023},
+Volume = {6},
+Number = {1},
+Month = {JUL 22},
+Type = {Article},
+DOI = {10.1038/s42003-023-05128},
+Article-Number = {768},
+EISSN = {2399-3642},
+Keywords-Plus = {NORDIHYDROGUAIARETIC ACID; CALORIE RESTRICTION; STATISTICAL-MODEL;
+ RAPAMYCIN; MTOR; 17-ALPHA-ESTRADIOL; METABOLISM; LONGEVITY; DATABASE;
+ MICE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Science \& Technology -
+ Other Topics},
+Web-of-Science-Categories = {Biology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Watanabe, Kengo/ABB-2216-2020
+ },
+ORCID-Numbers = {Watanabe, Kengo/0000-0002-0348-1634
+ Glusman, Gwenlyn/0000-0001-8060-5955
+ Midha, Mukul/0000-0003-4053-0682},
+Times-Cited = {0},
+Journal-ISO = {Commun. Biol.},
+Unique-ID = {WOS:001074497900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001109924100001,
+Author = {Watanabe, Kengo and Wilmanski, Tomasz and Baloni, Priyanka and Robinson,
+ Max and Garcia, Gonzalo G. and Hoopmann, Michael R. and Midha, Mukul K.
+ and Baxter, David H. and Maes, Michal and Morrone, Seamus R. and Crebs,
+ Kelly M. and Kapil, Charu and Kusebauch, Ulrike and Wiedrick, Jack and
+ Lapidus, Jodi and Pflieger, Lance and Lausted, Christopher and Roach,
+ Jared C. and Glusman, Gwenlyn and Cummings, Steven R. and Schork,
+ Nicholas J. and Price, Nathan D. and Hood, Leroy and Miller, Richard A.
+ and Moritz, Robert L. and Rappaport, Noa},
+Title = {Lifespan-extending interventions induce consistent patterns of fatty
+ acid oxidation in mouse livers},
+Journal = {COMMUNICATIONS BIOLOGY},
+Year = {2023},
+Volume = {6},
+Number = {1},
+Month = {JUL 22},
+Type = {Article},
+DOI = {10.1038/s42003-023-05128-y},
+Article-Number = {768},
+EISSN = {2399-3642},
+Keywords-Plus = {NORDIHYDROGUAIARETIC ACID; CALORIE RESTRICTION; STATISTICAL-MODEL;
+ RAPAMYCIN; MTOR; 17-ALPHA-ESTRADIOL; METABOLISM; LONGEVITY; DATABASE;
+ MICE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Science \& Technology -
+ Other Topics},
+Web-of-Science-Categories = {Biology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Watanabe, Kengo/ABB-2216-2020
+ },
+ORCID-Numbers = {Watanabe, Kengo/0000-0002-0348-1634
+ Glusman, Gwenlyn/0000-0001-8060-5955
+ Midha, Mukul/0000-0003-4053-0682},
+Times-Cited = {0},
+Journal-ISO = {Commun. Biol.},
+Unique-ID = {WOS:001109924100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001029148100001,
+Author = {Barrena, Naroa and Valcarcel, Luis V. V. and Olaverri-Mendizabal, Danel
+ and Apaolaza, Inigo and Planes, Francisco J. J.},
+Title = {Synthetic lethality in large-scale integrated metabolic and regulatory
+ network models of human cells},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2023},
+Volume = {9},
+Number = {1},
+Month = {JUL 15},
+Type = {Article},
+DOI = {10.1038/s41540-023-00296-3},
+Article-Number = {32},
+EISSN = {2056-7189},
+Keywords-Plus = {CANCER; ESSENTIALITY},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Planes, Francisco J/H-3341-2013},
+ORCID-Numbers = {Barrena, Naroa/0000-0003-4324-3371
+ Olaverri Mendizabal, Danel/0000-0003-1740-6616
+ Planes, Francisco J/0000-0003-1155-3105},
+Times-Cited = {0},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:001029148100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001024548200001,
+Author = {Fan, Xingcun and Cao, Lingfeng and Yan, Xuefeng},
+Title = {Sensitivity analysis and adaptive mutation strategy differential
+ evolution algorithm for optimizing enzymes' turnover numbers in
+ metabolic models},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2023},
+Volume = {120},
+Number = {8},
+Pages = {2301-2313},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1002/bit.28493},
+EarlyAccessDate = {JUL 2023},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {adaptive mutation strategy; enzyme-constrained genome-scale metabolic
+ network model; Saccharomyces cerevisiae; sensitivity analysis},
+Keywords-Plus = {NETWORK; CONSTRAINTS; PARAMETERS; PHENOTYPE; KINETICS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:001024548200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001037085900001,
+Author = {Kim, Su-Kyung and Lee, Minouk and Lee, Yi Qing and Lee, Hyun Jun and
+ Rho, Mina and Kim, Yunkwan and Seo, Jung Yeon and Youn, Sung Hun and
+ Hwang, Seung Jin and Kang, Nae Gyu and Lee, Choong-Hwan and Park,
+ Seo-Young and Lee, Dong-Yup},
+Title = {Genome-scale metabolic modeling and in silico analysis of
+ opportunistic skin pathogen Cutibacterium acnes},
+Journal = {FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY},
+Year = {2023},
+Volume = {13},
+Month = {JUL 13},
+Type = {Article},
+DOI = {10.3389/fcimb.2023.1099314},
+Article-Number = {1099314},
+ISSN = {2235-2988},
+Keywords = {skin microbiome; skin pathogen; Cutibacterium acnes; acne vulgaris;
+ genome-scale metabolic model; Wood-Werkman cycle},
+Keywords-Plus = {PROPIONIC-ACID PRODUCTION; GLYCEROL/GLUCOSE CO-FERMENTATION;
+ PROPIONIBACTERIUM-ACNES; DATABASE; GENERATION; STRAINS; VALIDATION;
+ TRACT; KEGG},
+Research-Areas = {Immunology; Microbiology},
+Web-of-Science-Categories = {Immunology; Microbiology},
+ORCID-Numbers = {Park, Seo-Young/0000-0001-6140-412X
+ Seo, Jung Yeon/0000-0003-2016-2974},
+Times-Cited = {1},
+Journal-ISO = {Front. Cell. Infect. Microbiol.},
+Unique-ID = {WOS:001037085900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001030999200001,
+Author = {Schafer, Martin and Pacheco, Alan R. and Kunzler, Rahel and
+ Bortfeld-Miller, Miriam and Field, Christopher M. and Vayena, Evangelia
+ and Hatzimanikatis, Vassily and Vorholt, Julia A.},
+Title = {Metabolic interaction models recapitulate leaf microbiota ecology},
+Journal = {SCIENCE},
+Year = {2023},
+Volume = {381},
+Number = {6653},
+Pages = {42+},
+Month = {JUL 7},
+Type = {Article},
+DOI = {10.1126/science.adf5121},
+Article-Number = {eadf5121},
+ISSN = {0036-8075},
+EISSN = {1095-9203},
+Keywords-Plus = {ARABIDOPSIS-THALIANA; OVERLAP; STRAINS; DEGRADATION; COMMUNITIES;
+ PHENOTYPE; QUALITY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Pacheco, Alan R/IUQ-5711-2023
+ Schafer, Martin/HNS-3105-2023
+ Vorholt, Julia A./K-3514-2016
+ Hatzimanikatis, Vassily/G-6505-2010
+ },
+ORCID-Numbers = {Pacheco, Alan R/0000-0002-1128-3232
+ Schafer, Martin/0000-0002-7875-0819
+ Vayena, Evangelia/0000-0001-8536-4505
+ Vorholt, Julia A./0000-0002-6011-4910
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Field, Christopher/0000-0002-6434-3745},
+Times-Cited = {4},
+Journal-ISO = {Science},
+Unique-ID = {WOS:001030999200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001058411100001,
+Author = {Li, Peishun and Roos, Stefan and Luo, Hao and Ji, Boyang and Nielsen,
+ Jens},
+Title = {Metabolic engineering of human gut microbiome: Recent developments and
+ future perspectives},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {79},
+Pages = {1-13},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2023.06.006},
+EarlyAccessDate = {JUL 2023},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Gut microbiome; Probiotics; Microbial consortia; Metabolic modeling;
+ Engineered microbes},
+Keywords-Plus = {LACTOCOCCUS-LACTIS; SYSTEMS BIOLOGY; ORAL DELIVERY; MULTI-OMICS;
+ LONG-TERM; MODELS; RECONSTRUCTION; METAGENOME; BACTERIA; CATALOG},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Roos, Stefan/JPX-3809-2023
+ },
+ORCID-Numbers = {Ji, Boyang/0000-0002-7269-4342
+ Li, Peishun/0000-0003-4200-0474
+ Roos, Stefan/0000-0002-1606-1794},
+Times-Cited = {0},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:001058411100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001027855100003,
+Author = {Karlsen, Signe T. and Rau, Martin H. and Sanchez, Benjamin J. and
+ Jensen, Kristian and Zeidan, Ahmad A.},
+Title = {From genotype to phenotype: computational approaches for inferring
+ microbial traits relevant to the food industry},
+Journal = {FEMS MICROBIOLOGY REVIEWS},
+Year = {2023},
+Volume = {47},
+Number = {4},
+Month = {JUL 5},
+Type = {Review},
+DOI = {10.1093/femsre/fuad030},
+Article-Number = {fuad030},
+ISSN = {0168-6445},
+EISSN = {1574-6976},
+Keywords = {genotype; microbial phenotype; food fermentations; mechanistic models;
+ machine Learning},
+Keywords-Plus = {GENOME-WIDE ASSOCIATION; CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS;
+ LACTIC-ACID BACTERIA; LACTOCOCCUS-LACTIS; METABOLIC MODELS; SELECTION
+ METHODS; SYSTEMS BIOLOGY; SCALE; DATABASE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Zeidan, Ahmad/A-7845-2012},
+ORCID-Numbers = {Zeidan, Ahmad/0000-0001-9984-5625},
+Times-Cited = {1},
+Journal-ISO = {Fems Microbiol. Rev.},
+Unique-ID = {WOS:001027855100003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001020492900001,
+Author = {Zhang, Yang and Yang, Menglei and Bao, Yangyang and Tao, Weihua and Tuo,
+ Jinyou and Liu, Boya and Gan, Luxi and Fu, Shuilin and Gong, Heng},
+Title = {A genome-scale metabolic model of the effect of dissolved oxygen on
+ 1,3-propanediol fermentation by Klebsiella pneumoniae},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2023},
+Volume = {46},
+Number = {9},
+Pages = {1319-1330},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1007/s00449-023-02899-w},
+EarlyAccessDate = {JUL 2023},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {1; 3-Propanediol; Flux balance analysis; Genome-scale metabolic model;
+ Klebsiella pneumoniae; Microaerobic culture},
+Keywords-Plus = {GLYCEROL; GENERATION; CONVERSION; BALANCE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+Times-Cited = {0},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:001020492900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001021358600002,
+Author = {Balazs, Marta and Bartos, Hunor and Lanyi, Szabolcs and Bodor, Zsolt and
+ Miklossy, Ildiko},
+Title = {Substrate type and CO2 addition significantly influence
+ succinic acid production of Basfia succiniciproducens},
+Journal = {BIOTECHNOLOGY LETTERS},
+Year = {2023},
+Volume = {45},
+Number = {9},
+Pages = {1133-1145},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1007/s10529-023-03406-7},
+EarlyAccessDate = {JUL 2023},
+ISSN = {0141-5492},
+EISSN = {1573-6776},
+Keywords = {Basfia succiniciproducens; Fermentation; Gene expression; Substrate
+ utilization; Succinic acid; Systems biology},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; MANNHEIMIA-SUCCINICIPRODUCENS; BIOTECHNOLOGICAL
+ PRODUCTION; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; FERMENTATION;
+ BACTERIUM; GLYCEROL; COLI},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Bodor, Zsolt/0000-0003-1386-6957},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Lett.},
+Unique-ID = {WOS:001021358600002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001038856400001,
+Author = {Camargo, Fidias D. Gonzalez and Santamaria-Torres, Mary and Cala, Monica
+ P. and Guevara-Suarez, Marcela and Restrepo, Silvia Restrepo and
+ Sanchez-Camargo, Andrea and Fernandez-Nino, Miguel and Corujo, Maria and
+ Gallo Molina, Ada Carolina and Cifuentes, Javier and Serna, Julian A.
+ and Cruz, Juan C. and Munoz-Camargo, Carolina and Gonzalez Barrios,
+ Andres F.},
+Title = {Genome-Scale Metabolic Reconstruction, Non-Targeted LC-QTOF-MS Based
+ Metabolomics Data, and Evaluation of Anticancer Activity of Cannabis
+ sativa Leaf Extracts},
+Journal = {METABOLITES},
+Year = {2023},
+Volume = {13},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.3390/metabo13070788},
+Article-Number = {788},
+EISSN = {2218-1989},
+Keywords = {Cannabis sativa; plant genome-scale metabolic reconstruction;
+ metabolomic validation; secondary metabolism; anticancer activity},
+Keywords-Plus = {CHEMICAL-COMPOSITION; BIOSYNTHESIS; INHIBITION; PLANTS; GENE; KEGG},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Sánchez-Camargo, Andrea del Pilar/D-8105-2014
+ },
+ORCID-Numbers = {Sánchez-Camargo, Andrea del Pilar/0000-0002-5172-7096
+ , Carolina/0000-0001-6238-9021
+ Cifuentes, Javier/0000-0003-0916-3909
+ SANTAMARIA, MARY/0009-0008-9136-9626
+ Restrepo, Silvia/0000-0001-9016-1040
+ Corujo Besga, Maria/0000-0003-0708-684X},
+Times-Cited = {0},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:001038856400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001073418900001,
+Author = {Sen, Partho and Oresic, Matej},
+Title = {Integrating Omics Data in Genome-Scale Metabolic Modeling: A
+ Methodological Perspective for Precision Medicine},
+Journal = {METABOLITES},
+Year = {2023},
+Volume = {13},
+Number = {7},
+Month = {JUL},
+Type = {Review},
+DOI = {10.3390/metabo13070855},
+Article-Number = {855},
+EISSN = {2218-1989},
+Keywords = {constraint-based modeling; host microbiome; human metabolism; human
+ metabolic networks; metabolic reconstructions; metabolic modeling;
+ multi-omics},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; NORMALIZATION METHODS; QUANTITATIVE PREDICTION;
+ GLOBAL RECONSTRUCTION; CELLULAR-METABOLISM; EXPRESSION DATA; NETWORK
+ MODEL; PATHWAYS; OPTIMIZATION; INFORMATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Oresic, Matej/K-7673-2016
+ Sen, Partho/L-8471-2019},
+ORCID-Numbers = {Oresic, Matej/0000-0002-2856-9165
+ Sen, Partho/0000-0003-0475-2763},
+Times-Cited = {0},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:001073418900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001033464300001,
+Author = {Yasemi, Mohammadreza and Jolicoeur, Mario},
+Title = {A genome-scale dynamic constraint-based modelling (gDCBM) framework
+ predicts growth dynamics, medium composition and intracellular flux
+ distributions in CHO clonal variations},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {78},
+Pages = {209-222},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2023.06.005},
+EarlyAccessDate = {JUN 2023},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Mathematical modelling; Genome-scale dynamic constraint-based;
+ modelling; Flux distribution; Chinese hamster ovary; Mammalian cell
+ culture},
+Keywords-Plus = {METABOLIC NETWORKS; ESCHERICHIA-COLI; BALANCE ANALYSIS; CELLS;
+ RECONSTRUCTION; PRODUCTIVITY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:001033464300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001022393900001,
+Author = {Fina, Albert and Millard, Pierre and Albiol, Joan and Ferrer, Pau and
+ Heux, Stephanie},
+Title = {High throughput 13C-metabolic flux analysis of
+ 3-hydroxypropionic acid producing Pichia pastoris reveals limited
+ availability of acetyl-CoA and ATP due to tight control of the
+ glycolytic flux},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2023},
+Volume = {22},
+Number = {1},
+Month = {JUN 29},
+Type = {Article},
+DOI = {10.1186/s12934-023-02123-0},
+Article-Number = {117},
+EISSN = {1475-2859},
+Keywords = {Fluxomics; C-13-Metabolic flux analysis; Pichia pastoris; Komagataella
+ phaffii; High throughput; 3-hydroxypropionic acid; acetyl-CoA},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; HIGH-LEVEL PRODUCTION;
+ SACCHAROMYCES-CEREVISIAE; METABOLIC NETWORKS; OVERPRODUCTION;
+ PREDICTION; SOFTWARE; RECOVERY; GROWTH; BRANCH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ferrer, Pau/A-4147-2009
+ },
+ORCID-Numbers = {Fina Romero, Albert/0000-0001-7949-0484},
+Times-Cited = {0},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:001022393900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001054272800001,
+Author = {Sarmah, Dipanka Tanu and Paul, Abhijit and Kumar, Shivam and Bairagi,
+ Nandadulal and Chatterjee, Samrat},
+Title = {A data-driven multilayer approach for the identification of potential
+ therapeutic targets in non-alcoholic steatohepatitis},
+Journal = {PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS},
+Year = {2023},
+Volume = {624},
+Month = {AUG 15},
+Type = {Article},
+DOI = {10.1016/j.physa.2023.128955},
+EarlyAccessDate = {JUN 2023},
+Article-Number = {128955},
+ISSN = {0378-4371},
+EISSN = {1873-2119},
+Keywords = {Non-alcoholic steatohepatitis; Protein-protein interaction network;
+ Machine learning; Random walk with restart; Network controllability;
+ Metabolic network},
+Keywords-Plus = {GENES; NETWORKS; RESOURCE; WALKING},
+Research-Areas = {Physics},
+Web-of-Science-Categories = {Physics, Multidisciplinary},
+Times-Cited = {0},
+Journal-ISO = {Physica A},
+Unique-ID = {WOS:001054272800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001009377500001,
+Author = {Li, Zhongcai and Liu, Qian and Sun, Jiahui and Sun, Jianjian and Li,
+ Mingjie and Zhang, Yun and Deng, Aihua and Liu, Shuwen and Wen, Tingyi},
+Title = {Multivariate modular metabolic engineering for enhanced
+ L-methionine biosynthesis in Escherichia coli},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS},
+Year = {2023},
+Volume = {16},
+Number = {1},
+Month = {JUN 13},
+Type = {Article},
+DOI = {10.1186/s13068-023-02347-7},
+Article-Number = {101},
+EISSN = {2731-3654},
+Keywords = {(L)-Methionine; Escherichia coli; Metabolic engineering; Multivariate
+ modular; Cystathionine gamma-synthase},
+Keywords-Plus = {CORYNEBACTERIUM-GLUTAMICUM; L-METHIONINE; L-CYSTEINE; SERINE
+ ACETYLTRANSFERASE; PATHWAY; OVERPRODUCTION; MUTAGENESIS; STRATEGIES;
+ MECHANISM; STRAINS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Times-Cited = {1},
+Journal-ISO = {Biotechnol. Biofuels Bioprod.},
+Unique-ID = {WOS:001009377500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001003347800001,
+Author = {Romero, Sandra Gomez and Boyle, Nanette},
+Title = {Systems biology and metabolic modeling for cultivated meat: A promising
+ approach for cell culture media optimization and cost reduction},
+Journal = {COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY},
+Year = {2023},
+Volume = {22},
+Number = {4},
+Pages = {3422-3443},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1111/1541-4337.13193},
+EarlyAccessDate = {JUN 2023},
+ISSN = {1541-4337},
+Keywords = {biotechnology; fermentation; mathematical modeling; meat science;
+ cultivated meat; metabolism},
+Keywords-Plus = {EMBRYONIC STEM-CELLS; FLUX ANALYSIS; SERUM-FREE; CHO-CELLS; GROWTH;
+ NETWORKS; DIFFERENTIATION; RECONSTRUCTION; LINES},
+Research-Areas = {Food Science \& Technology},
+Web-of-Science-Categories = {Food Science \& Technology},
+ResearcherID-Numbers = {Boyle, Nanette/AFM-1806-2022
+ },
+ORCID-Numbers = {Boyle, Nanette/0000-0002-9103-0007
+ Gomez Romero, Sandra Itzel/0000-0001-7530-0380},
+Times-Cited = {0},
+Journal-ISO = {Compr. Rev. Food. Sci. Food Saf.},
+Unique-ID = {WOS:001003347800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001026289800013,
+Author = {Chowdhury, Sourav and Zielinski, Daniel C. and Dalldorf, Christopher and
+ Rodrigues, Joao V. and Palsson, Bernhard O. and Shakhnovich, Eugene I.},
+Title = {Empowering drug off-target discovery with metabolic and structural
+ analysis},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2023},
+Volume = {14},
+Number = {1},
+Month = {JUN 9},
+Type = {Article},
+DOI = {10.1038/s41467-023-38859-x},
+Article-Number = {3390},
+EISSN = {2041-1723},
+Keywords-Plus = {ESCHERICHIA-COLI; BINDING; LIMITATION; INHIBITORS; BACTERIA; PATHWAY;
+ SYSTEMS; HPPK},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Zielinski, Daniel/0000-0001-6452-483X
+ Shakhnovich, Eugene/0000-0002-4769-2265},
+Times-Cited = {1},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:001026289800013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001026279100001,
+Author = {Fakih, Ibrahim and Got, Jeanne and Robles-Rodriguez, Carlos Eduardo and
+ Siegel, Anne and Forano, Evelyne and Munoz-Tamayo, Rafael},
+Title = {Dynamic genome-based metabolic modeling of the predominant cellulolytic
+ rumen bacterium Fibrobacter succinogenes S85},
+Journal = {MSYSTEMS},
+Year = {2023},
+Volume = {8},
+Number = {3},
+Month = {JUN 29},
+Type = {Article},
+DOI = {10.1128/msystems.01027-22},
+EarlyAccessDate = {JUN 2023},
+ISSN = {2379-5077},
+Keywords = {dynamic model; elementary flux mode analysis; genome-scale metabolic
+ model; fiber degradation; network reconstruction; rumen fermentation},
+Keywords-Plus = {PRACTICAL IDENTIFIABILITY; METHANE PRODUCTION; SYSTEMS BIOLOGY;
+ WHEAT-STRAW; GROWTH; RECONCILIATION; RECONSTRUCTION; DEGRADATION;
+ RUMINICOLA; KINETICS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Muñoz-Tamayo, Rafael/K-1884-2019
+ },
+ORCID-Numbers = {Muñoz-Tamayo, Rafael/0000-0002-9266-4132
+ Got, Jeanne/0000-0002-2310-0843
+ ROBLES RODRIGUEZ, Carlos Eduardo/0000-0002-2436-3653
+ Siegel, Anne/0000-0001-6542-1568
+ FAKIH, Ibrahim/0000-0001-6202-062X},
+Times-Cited = {0},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:001026279100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001026954400001,
+Author = {Gralka, Matti},
+Title = {Searching for Principles of Microbial Ecology Across Levels of
+ Biological Organization},
+Journal = {INTEGRATIVE AND COMPARATIVE BIOLOGY},
+Year = {2023},
+Month = {2023 JUN 6},
+Type = {Article; Early Access},
+DOI = {10.1093/icb/icad060},
+EarlyAccessDate = {JUN 2023},
+ISSN = {1540-7063},
+EISSN = {1557-7023},
+Keywords-Plus = {FUNCTIONAL REDUNDANCY; COMMUNITY ECOLOGY; METABOLIC THEORY; TEMPERATURE;
+ DIVERSITY; DYNAMICS; PHYTOPLANKTON; ORGANISMS; GROWTH; WILL},
+Research-Areas = {Zoology},
+Web-of-Science-Categories = {Zoology},
+ORCID-Numbers = {Gralka, Matti/0000-0003-4599-1859},
+Times-Cited = {0},
+Journal-ISO = {Integr. Comp. Biol.},
+Unique-ID = {WOS:001026954400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001020440000005,
+Author = {Chalkis, Apostolos and Fisikopoulos, Vissarion and Papachristou, Marios
+ and Tsigaridas, Elias},
+Title = {Truncated Log-concave Sampling for Convex Bodies with Reflective
+ Hamiltonian Monte Carlo},
+Journal = {ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE},
+Year = {2023},
+Volume = {49},
+Number = {2},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1145/3589505},
+Article-Number = {16},
+ISSN = {0098-3500},
+EISSN = {1557-7295},
+Keywords = {Statistical software; truncated sampling; geometric random walks;
+ experiments; mixing time},
+Keywords-Plus = {HIT-AND-RUN; LANGEVIN; MODELS; VOLUME; MCMC},
+Research-Areas = {Computer Science; Mathematics},
+Web-of-Science-Categories = {Computer Science, Software Engineering; Mathematics, Applied},
+ResearcherID-Numbers = {Papachristou, Marios/HQD-5282-2023
+ Fisikopoulos, Vissarion/A-1564-2018},
+ORCID-Numbers = {Papachristou, Marios/0000-0002-1728-0729
+ Fisikopoulos, Vissarion/0000-0002-0780-666X},
+Times-Cited = {1},
+Journal-ISO = {ACM Trans. Math. Softw.},
+Unique-ID = {WOS:001020440000005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001014912700001,
+Author = {Grausa, Kristina and Siddiqui, Shahida A. and Lameyer, Norbert and
+ Wiesotzki, Karin and Smetana, Sergiy and Pentjuss, Agris},
+Title = {Metabolic Modeling of Hermetia illucens Larvae Resource
+ Allocation for High-Value Fatty Acid Production},
+Journal = {METABOLITES},
+Year = {2023},
+Volume = {13},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3390/metabo13060724},
+Article-Number = {724},
+EISSN = {2218-1989},
+Keywords = {metabolic modeling; insects; fatty acids; Hermetia illucens; resource
+ allocation},
+Keywords-Plus = {FEED; FOOD},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Siddiqui, Shahida Anusha/AAI-1551-2021
+ },
+ORCID-Numbers = {Siddiqui, Shahida Anusha/0000-0001-6942-4408
+ Pentjuss, Agris/0000-0001-7880-5130},
+Times-Cited = {0},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:001014912700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001017396000001,
+Author = {Muiznieks, Reinis and Dace, Elina and Stalidzans, Egils},
+Title = {Integrated Sustainability Score Implementation as an Objective Function
+ in Sustainable Metabolic Engineering},
+Journal = {FERMENTATION-BASEL},
+Year = {2023},
+Volume = {9},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3390/fermentation9060548},
+Article-Number = {548},
+EISSN = {2311-5637},
+Keywords = {economic sustainability; environmental sustainability; social
+ sustainability; genome-scale metabolic model; growth coupled production},
+Keywords-Plus = {GENOME-SCALE MODELS; OPTIMIZATION; DESIGN; IMPACT},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Stalidzans, Egils/G-5883-2010
+ Dace, Elina/H-5824-2019},
+ORCID-Numbers = {Stalidzans, Egils/0000-0001-6063-0184
+ Dace, Elina/0000-0002-7880-0820},
+Times-Cited = {0},
+Journal-ISO = {FERMENTATION},
+Unique-ID = {WOS:001017396000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001015017800001,
+Author = {Stikane, Anna and Baumanis, Matiss Ricards and Muiznieks, Reinis and
+ Stalidzans, Egils},
+Title = {Impact of Waste as a Substrate on Biomass Formation, and Optimization of
+ Spent Microbial Biomass Re-Use by Sustainable Metabolic Engineering},
+Journal = {FERMENTATION-BASEL},
+Year = {2023},
+Volume = {9},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3390/fermentation9060531},
+Article-Number = {531},
+EISSN = {2311-5637},
+Keywords = {bioprocess waste; waste fermentation; resource circulation; biomass
+ residues; constraint-based stoichiometric modeling; amino acids; strain
+ design; bio-based products},
+Keywords-Plus = {GLUCOSE; PROTEIN; GROWTH; XYLOSE; MODELS; ACID},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Stalidzans, Egils/G-5883-2010},
+ORCID-Numbers = {Stalidzans, Egils/0000-0001-6063-0184},
+Times-Cited = {1},
+Journal-ISO = {FERMENTATION},
+Unique-ID = {WOS:001015017800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001014072100001,
+Author = {Wang, Xueting and Mohsin, Ali and Sun, Yifei and Li, Chao and Zhuang,
+ Yingping and Wang, Guan},
+Title = {From Spatial-Temporal Multiscale Modeling to Application: Bridging the
+ Valley of Death in Industrial Biotechnology},
+Journal = {BIOENGINEERING-BASEL},
+Year = {2023},
+Volume = {10},
+Number = {6},
+Month = {JUN},
+Type = {Review},
+DOI = {10.3390/bioengineering10060744},
+Article-Number = {744},
+EISSN = {2306-5354},
+Keywords = {bioeconomy; hybrid modeling; intelligent biomanufacturing; machine
+ learning; industrial biotechnology; mechanistic model; data-driven model},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Biomedical},
+ResearcherID-Numbers = {wang, xueting/JPY-2782-2023
+ },
+ORCID-Numbers = {WANG, XUETING/0000-0002-0023-7468},
+Times-Cited = {0},
+Journal-ISO = {Bioengineering-Basel},
+Unique-ID = {WOS:001014072100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001004929700001,
+Author = {Germann, Anna T. and Nakielski, Andreas and Dietsch, Maximilian and
+ Petzel, Tim and Moser, Daniel and Triesch, Sebastian and Westhoff,
+ Philipp and Axmann, Ilka M.},
+Title = {A systematic overexpression approach reveals native targets to increase
+ squalene production in Synechocystis sp. PCC 6803},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2023},
+Volume = {14},
+Month = {MAY 30},
+Type = {Article},
+DOI = {10.3389/fpls.2023.1024981},
+Article-Number = {1024981},
+ISSN = {1664-462X},
+Keywords = {Synechocystis; squalene; MEP pathway; FBA; metabolic engineering;
+ metabolic modeling},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CYANOBACTERIUM SYNECHOCYSTIS; INHIBITION;
+ METABOLISM; ISOPRENE; PATHWAY; MODELS; 1-DEOXY-D-XYLULOSE; CANCER; OIL},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Westhoff, Philipp/AAV-1542-2020
+ },
+ORCID-Numbers = {Westhoff, Philipp/0000-0002-3494-9420
+ Nakielski, Andreas/0000-0001-5069-4387},
+Times-Cited = {0},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:001004929700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000994620700001,
+Author = {Molversmyr, Havard and Oyas, Ove and Rotnes, Filip and Vik, Jon Olav},
+Title = {Extracting functionally accurate context-specific models of Atlantic
+ salmon metabolism},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2023},
+Volume = {9},
+Number = {1},
+Month = {MAY 27},
+Type = {Article},
+DOI = {10.1038/s41540-023-00280-x},
+Article-Number = {19},
+EISSN = {2056-7189},
+Keywords-Plus = {FISH},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Vik, Jon Olav/B-9350-2008
+ },
+ORCID-Numbers = {Oyas, Ove/0000-0001-6990-0339
+ Rotnes, Filip/0000-0002-1702-7379
+ Vik, Jon Olav/0000-0002-7778-4515
+ Molversmyr, Havard/0000-0001-5257-3335},
+Times-Cited = {0},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000994620700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001009464600001,
+Author = {Vo, Chi Hung and Goyal, Nishu and Kraft, Markus and Karimi, Iftekhar A.},
+Title = {Carbon conversion by Methanococcus maripaludis S2 under
+ diazotrophy and a revised genome-scale metabolic model},
+Journal = {CHEMICAL ENGINEERING SCIENCE},
+Year = {2023},
+Volume = {278},
+Month = {AUG 15},
+Type = {Article},
+DOI = {10.1016/j.ces.2023.118910},
+EarlyAccessDate = {MAY 2023},
+Article-Number = {118910},
+ISSN = {0009-2509},
+EISSN = {1873-4405},
+Keywords = {Methanococcus maripaludis; Diazotrophy; Methanogenesis; CO 2
+ utilization; Genome-scale metabolic model},
+Keywords-Plus = {NITROGEN-FIXATION; MOLECULAR NITROGEN; METHANOGEN; CO2;
+ THERMOLITHOTROPHICUS; MUTAGENESIS; RESISTANCE; REPRESSOR; GENE; GLNA},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Kraft, Markus/D-7243-2016},
+ORCID-Numbers = {Kraft, Markus/0000-0002-4293-8924},
+Times-Cited = {0},
+Journal-ISO = {Chem. Eng. Sci.},
+Unique-ID = {WOS:001009464600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000994546800001,
+Author = {Henriques, David and Minebois, Romain and dos Santos, David and Barrio,
+ Eladio and Querol, Amparo and Balsa-Canto, Eva},
+Title = {A Dynamic Genome-Scale Model Identifies Metabolic Pathways Associated
+ with Cold Tolerance in Saccharomyces kudriavzevii},
+Journal = {MICROBIOLOGY SPECTRUM},
+Year = {2023},
+Volume = {11},
+Number = {3},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1128/spectrum.03519-22},
+EarlyAccessDate = {MAY 2023},
+ISSN = {2165-0497},
+Keywords = {Saccharomyces kudriavzevii; wine fermentation; cold tolerance; dFBA;
+ genome-scale metabolic model; nonconventional yeasts; proteolysis;
+ sympatry},
+Keywords-Plus = {CEREVISIAE; OPTIMIZATION; POPULATIONS; EXPRESSION; SUCCINATE; BACTERIA;
+ HYBRIDS; ACID},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Henriques, David/AAF-9525-2021
+ Querol, Amparo/AAW-7469-2020
+ Barrio, Eladio/G-8969-2015
+ Balsa-Canto, Eva/A-9339-2008},
+ORCID-Numbers = {Henriques, David/0000-0002-9477-292X
+ Querol, Amparo/0000-0002-6478-6845
+ Barrio, Eladio/0000-0003-1024-954X
+ MINEBOIS, ROMAIN/0000-0001-6959-1572
+ Balsa-Canto, Eva/0000-0002-1978-2626},
+Times-Cited = {0},
+Journal-ISO = {Microbiol. Spectr.},
+Unique-ID = {WOS:000994546800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000998397300001,
+Author = {Wang, Lvjing and Wang, Xiaoyu and Wu, Hao and Wang, Haixia and Wang,
+ Yihan and Lu, Zhenmei},
+Title = {Metabolic modeling of synthetic microbial communities for bioremediation},
+Journal = {CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY},
+Year = {2023},
+Volume = {53},
+Number = {24},
+Pages = {2092-2111},
+Month = {DEC 17},
+Type = {Review},
+DOI = {10.1080/10643389.2023.2212569},
+EarlyAccessDate = {MAY 2023},
+ISSN = {1064-3389},
+EISSN = {1547-6537},
+Keywords = {Genome-scale metabolic models (GEMs); microbial interactions; synthetic
+ microbial community; biodegradation; multi-omics analysis; machine
+ learning; Eakalak Khan and Lena Q; Ma},
+Keywords-Plus = {HIGHER-ORDER INTERACTIONS; RECONSTRUCTION; ANNOTATION; DYNAMICS;
+ DATABASE},
+Research-Areas = {Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Environmental Sciences},
+ResearcherID-Numbers = {zhang, lin/IZQ-4870-2023},
+Times-Cited = {0},
+Journal-ISO = {Crit. Rev. Environ. Sci. Technol.},
+Unique-ID = {WOS:000998397300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000994402400001,
+Author = {de Mas, Igor Marin and Herand, Helena and Carrasco, Jorge and Nielsen,
+ Lars K. and Johansson, Par I.},
+Title = {A Protocol for the Automatic Construction of Highly Curated Genome-Scale
+ Models of Human Metabolism},
+Journal = {BIOENGINEERING-BASEL},
+Year = {2023},
+Volume = {10},
+Number = {5},
+Month = {MAY 10},
+Type = {Article},
+DOI = {10.3390/bioengineering10050576},
+Article-Number = {576},
+EISSN = {2306-5354},
+Keywords = {genome-scale metabolic model; human metabolism; model construction;
+ constraints-based modeling},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Biomedical},
+ResearcherID-Numbers = {Nielsen, Lars K/A-5519-2011
+ },
+ORCID-Numbers = {Nielsen, Lars K/0000-0001-8191-3511
+ Herand, Helena/0000-0003-0351-2848
+ Carrasco Muriel, Jorge/0000-0001-7365-0299
+ Johansson, Par Ingemar/0000-0001-9778-5964},
+Times-Cited = {0},
+Journal-ISO = {Bioengineering-Basel},
+Unique-ID = {WOS:000994402400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000984673900001,
+Author = {Mao, Zhitao and Yuan, Qianqian and Li, Haoran and Zhang, Yue and Huang,
+ Yuanyuan and Yang, Chunhe and Wang, Ruoyu and Yang, Yongfu and Wu, Yalun
+ and Yang, Shihui and Liao, Xiaoping and Ma, Hongwu},
+Title = {CAVE: a cloud-based platform for analysis and visualization of metabolic
+ pathways},
+Journal = {NUCLEIC ACIDS RESEARCH},
+Year = {2023},
+Volume = {51},
+Number = {W1},
+Pages = {W70-W77},
+Month = {JUL 5},
+Type = {Article},
+DOI = {10.1093/nar/gkad360},
+EarlyAccessDate = {MAY 2023},
+ISSN = {0305-1048},
+EISSN = {1362-4962},
+Keywords-Plus = {MODELS; RECONSTRUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Yang, Shihui/AAE-4100-2020
+ },
+ORCID-Numbers = {Yang, Shihui/0000-0002-9394-9148
+ mao, zhi tao/0000-0002-8160-2585},
+Times-Cited = {1},
+Journal-ISO = {Nucleic Acids Res.},
+Unique-ID = {WOS:000984673900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000992866600001,
+Author = {Punyasu, Nattharat and Kalapanulak, Saowalak and Saithong, Treenut},
+Title = {CO2 recycling by phosphoenolpyruvate carboxylase
+ enables cassava leaf metabolism to tolerate low water availability},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2023},
+Volume = {14},
+Month = {MAY 9},
+Type = {Article},
+DOI = {10.3389/fpls.2023.1159247},
+Article-Number = {1159247},
+ISSN = {1664-462X},
+Keywords = {carbon metabolism; genome-scale metabolic modeling; cassava leaf;
+ cassava (Manhiot esculenta); drought response; phosphoenolpyruvate
+ carboxylase; CO2 recycling; PEPC},
+Keywords-Plus = {MANIHOT-ESCULENTA CRANTZ; INTERMEDIATE PHOTOSYNTHETIC CHARACTERISTICS;
+ DROUGHT STRESSES; CELL-METABOLISM; CRUCIAL ROLE; CARBON;
+ PHOTORESPIRATION; PREDICTION; DEFICITS; PLAYS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ORCID-Numbers = {Punyasu, Nattharat/0009-0005-9365-4605},
+Times-Cited = {1},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000992866600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000985070800001,
+Author = {Scott, William T. and Henriques, David and Smid, Eddy J. and Notebaart,
+ Richard A. and Balsa-Canto, Eva},
+Title = {Dynamic genome-scale modeling of Saccharomyces cerevisiae
+ unravels mechanisms for ester formation during alcoholic fermentation},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2023},
+Volume = {120},
+Number = {7},
+Pages = {1998-2012},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/bit.28421},
+EarlyAccessDate = {MAY 2023},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {dynamic flux balance analysis (dFBA); esters; fermentation; metabolic
+ modeling; systems biology; wine; yeast},
+Keywords-Plus = {NITROGEN STARVATION; ETHANOL-PRODUCTION; ESCHERICHIA-COLI; AROMA
+ FORMATION; KINETIC-MODEL; AMINO-ACIDS; YEAST; METABOLISM; GROWTH;
+ RECONSTRUCTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Henriques, David/AAF-9525-2021
+ Balsa-Canto, Eva/A-9339-2008
+ },
+ORCID-Numbers = {Henriques, David/0000-0002-9477-292X
+ Smid, Eddy J./0000-0002-6687-5083
+ Balsa-Canto, Eva/0000-0002-1978-2626
+ Scott, William/0000-0002-4029-2998},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000985070800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000982242300007,
+Author = {Kaste, Joshua A. M. and Shachar-Hill, Yair},
+Title = {Accurate flux predictions using tissue-specific gene expression in plant
+ metabolic modeling},
+Journal = {BIOINFORMATICS},
+Year = {2023},
+Volume = {39},
+Number = {5},
+Month = {MAY 4},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btad186},
+Article-Number = {btad186},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {ESCHERICHIA-COLI; KNOCKOUT STRATEGIES; ARABIDOPSIS; RECONSTRUCTION;
+ TRANSCRIPTOME; COSTS; NETWORK; CARBON},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Shachar-Hill, Yair/B-6165-2013
+ },
+ORCID-Numbers = {Shachar-Hill, Yair/0000-0001-8793-5084
+ Kaste, Joshua/0000-0003-1942-0315},
+Times-Cited = {3},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000982242300007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000993159100004,
+Author = {Noecker, Cecilia and Sanchez, Juan and Bisanz, Jordan E. and Escalante,
+ Veronica and Alexander, Margaret and Trepka, Kai and Heinken, Almut and
+ Liu, Yuanyuan and Dodd, Dylan and Thiele, Ines and DeFelice, Brian C.
+ and Turnbaugh, Peter J.},
+Title = {Systems biology elucidates the distinctive metabolic niche filled by the
+ human gut microbe Eggerthella lenta},
+Journal = {PLOS BIOLOGY},
+Year = {2023},
+Volume = {21},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1371/journal.pbio.3002125},
+Article-Number = {e3002125},
+ISSN = {1544-9173},
+EISSN = {1545-7885},
+Keywords-Plus = {TEICHOIC-ACIDS; GENOME; BACTERIA; ARGININE; PATHWAY; GROWTH; CYCLE; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology; Life Sciences \& Biomedicine - Other
+ Topics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biology},
+ORCID-Numbers = {Dodd, Dylan/0000-0001-6210-6239},
+Times-Cited = {2},
+Journal-ISO = {PLoS. Biol.},
+Unique-ID = {WOS:000993159100004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000990433700001,
+Author = {Lee, GaRyoung and Lee, Sang Mi and Kim, Hyun Uk},
+Title = {A contribution of metabolic engineering to addressing medical problems:
+ Metabolic flux analysis},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {77},
+Pages = {283-293},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2023.04.008},
+EarlyAccessDate = {APR 2023},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic engineering; Metabolic flux analysis; Constraint-based
+ reconstruction and analysis; Genome-scale metabolic model; Isotope-based
+ metabolic flux analysis; Medical problem},
+Keywords-Plus = {CITRIC-ACID CYCLE; HAEMOPHILUS-INFLUENZAE RD; ESCHERICHIA-COLI;
+ GENE-EXPRESSION; GLOBAL RECONSTRUCTION; MASS ISOTOPOMER; BALANCE MODELS;
+ NETWORK MODEL; GENOME; LIVER},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Kim, Hyun Uk/F-4509-2018
+ },
+ORCID-Numbers = {Kim, Hyun Uk/0000-0001-7224-642X
+ Lee, Sang Mi/0000-0002-0043-4269
+ Lee, GaRyoung/0000-0001-7084-1663},
+Times-Cited = {0},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000990433700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000989385600001,
+Author = {Walakira, Andrew and Skubic, Cene and Nadizar, Nejc and Rozman, Damjana
+ and Rezen, Tadeja and Mraz, Miha and Moskon, Miha},
+Title = {Integrative computational modeling to unravel novel potential biomarkers
+ in hepatocellular carcinoma},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2023},
+Volume = {159},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2023.106957},
+EarlyAccessDate = {APR 2023},
+Article-Number = {106957},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Hepatocellular carcinoma; Meta-analysis; Genome-scale metabolic
+ modeling; Network analysis; Enriched pathways; Enriched reactions;
+ Enriched subsystems},
+Keywords-Plus = {PROGNOSTIC BIOMARKER; SARCOSINE METABOLISM; ACTIVATION; BREAST;
+ METASTASIS; MARKER; GABRP},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ORCID-Numbers = {Rezen, Tadeja/0000-0001-6210-7370
+ Walakira, Andrew/0000-0002-3651-2679
+ Moskon, Miha/0000-0003-4600-1730},
+Times-Cited = {0},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000989385600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001025469900004,
+Author = {Libby, Eric and Kempes, Christopher P. and Okie, Jordan G.},
+Title = {Metabolic compatibility and the rarity of prokaryote endosymbioses},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2023},
+Volume = {120},
+Number = {17},
+Month = {APR 25},
+Type = {Article},
+DOI = {10.1073/pnas.2206527120},
+Article-Number = {e2206527120},
+ISSN = {0027-8424},
+EISSN = {1091-6490},
+Keywords = {endosymbiosis; eukaryogenesis; metabolic model; prokaryote; evolution},
+Keywords-Plus = {BACTERIAL ENDOSYMBIONTS; ORIGIN; EVOLUTION; MODELS; ENERGY;
+ RECONSTRUCTION; MICROBES; ARCHAEA; BIOLOGY; BENEFIT},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Kempes, Christopher/0000-0002-1622-9761
+ Okie, Jordan G./0000-0002-7884-7688
+ Libby, Eric/0000-0002-6569-5793},
+Times-Cited = {0},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:001025469900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000981957100001,
+Author = {Carranza-Saavedra, Darwin and Torres-Bacete, Jesus and Blazquez, Blas
+ and Henao, Claudia Patricia Sanchez and Montoya, Jose Edgar Zapata and
+ Nogales, Juan},
+Title = {System metabolic engineering of Escherichia coli W for the
+ production of 2-ketoisovalerate using unconventional feedstock},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2023},
+Volume = {11},
+Month = {APR 20},
+Type = {Article},
+DOI = {10.3389/fbioe.2023.1176445},
+Article-Number = {1176445},
+ISSN = {2296-4185},
+Keywords = {dairy by-products; L-valine; bioeconomy; feedback inhibition;
+ non-conventional microbial factories; systems biotechnology},
+Keywords-Plus = {DEHYDROGENASE COMPLEX-DEFICIENT; L-VALINE PRODUCTION;
+ CORYNEBACTERIUM-GLUTAMICUM; GROWTH; ISOBUTANOL; PATHWAY; GLUCOSE;
+ LACTOSE; SUGARS; ACIDS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ },
+ORCID-Numbers = {Carranza Saavedra, Darwin/0000-0001-5697-6107
+ Nogales, Juan/0000-0002-4961-0833
+ Torres-Bacete, Jesus/0009-0001-8997-7592
+ Blazquez, Blas/0000-0003-4099-6909
+ Sanchez Henao, Claudia Patricia/0000-0003-2282-4994},
+Times-Cited = {0},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000981957100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000990606400001,
+Author = {Bjune, Mona Synnove and Lawrence-Archer, Laurence and Laupsa-Borge,
+ Johnny and Sommersten, Cathrine Horn and McCann, Adrian and Glastad,
+ Robert Clay and Johnston, Iain George and Kern, Matthias and Blueher,
+ Matthias and Mellgren, Gunnar and Dankel, Simon N.},
+Title = {Metabolic role of the hepatic valine/3-hydroxyisobutyrate (3-HIB)
+ pathway in fatty liver disease},
+Journal = {EBIOMEDICINE},
+Year = {2023},
+Volume = {91},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ebiom.2023.104569},
+EarlyAccessDate = {APR 2023},
+Article-Number = {104569},
+ISSN = {2352-3964},
+Keywords = {Branched-chain amino acids (BCAA); NAFLD; NASH; Insulin resistance;
+ Lipid metabolism},
+Keywords-Plus = {CHAIN AMINO-ACIDS; INSULIN-RESISTANCE; OXIDATIVE STRESS; PLASMA;
+ 3-HYDROXYISOBUTYRATE; PATHOGENESIS; SUBSTRATE; DEFECTS; LIPIDS},
+Research-Areas = {General \& Internal Medicine; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Medicine, General \& Internal; Medicine, Research \& Experimental},
+ResearcherID-Numbers = {Mellgren, Gunnar/N-8314-2015},
+ORCID-Numbers = {Bjune, Mona Synnove/0000-0003-2680-8465
+ Mellgren, Gunnar/0000-0001-6282-4986},
+Times-Cited = {1},
+Journal-ISO = {EBioMedicine},
+Unique-ID = {WOS:000990606400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000964881700001,
+Author = {Zhang, Yiming and Su, Mo and Chen, Yu and Wang, Zheng and Nielsen, Jens
+ and Liu, Zihe},
+Title = {Engineering yeast mitochondrial metabolism for 3-hydroxypropionate
+ production},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS},
+Year = {2023},
+Volume = {16},
+Number = {1},
+Month = {APR 8},
+Type = {Article},
+DOI = {10.1186/s13068-023-02309-z},
+Article-Number = {64},
+EISSN = {2731-3654},
+Keywords = {Yeast mitochondrion; Malonyl-CoA reductase; 3-Hydroxypropionate; Redox
+ factor engineering; Acetyl-CoA carboxylase},
+Keywords-Plus = {ACETYL-COA CARBOXYLASE; NADH KINASE; ACID; EXPRESSION; PATHWAY; GENE;
+ BALANCE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916},
+Times-Cited = {2},
+Journal-ISO = {Biotechnol. Biofuels Bioprod.},
+Unique-ID = {WOS:000964881700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000983953600001,
+Author = {Liu, Yanhua and Westerhoff, Hans V.},
+Title = {Competitive, multi-objective, and compartmented Flux Balance Analysis
+ for addressing tissue-specific inborn errors of metabolism},
+Journal = {JOURNAL OF INHERITED METABOLIC DISEASE},
+Year = {2023},
+Volume = {46},
+Number = {4},
+Pages = {573-585},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/jimd.12603},
+EarlyAccessDate = {APR 2023},
+ISSN = {0141-8955},
+EISSN = {1573-2665},
+Keywords = {competitive flux balance analysis; inborn errors of metabolism;
+ multiple-compartment model; phenylketonuria; systems biology},
+Keywords-Plus = {AMINO-ACID TRANSPORTER; GENETIC MOUSE MODEL; BLOOD-BRAIN-BARRIER;
+ PROTEIN-SYNTHESIS; GLOBAL RECONSTRUCTION; TYROSINE-HYDROXYLASE; ACUTE
+ EXERCISE; PHENYLKETONURIA; PHENYLALANINE; EXPRESSION},
+Research-Areas = {Endocrinology \& Metabolism; Genetics \& Heredity; Research \&
+ Experimental Medicine},
+Web-of-Science-Categories = {Endocrinology \& Metabolism; Genetics \& Heredity; Medicine, Research \&
+ Experimental},
+ResearcherID-Numbers = {Westerhoff, Hans/I-5762-2012
+ },
+ORCID-Numbers = {Westerhoff, Hans/0000-0002-0443-6114
+ Liu, Yanhua/0000-0001-8282-7404},
+Times-Cited = {3},
+Journal-ISO = {J. Inherit. Metab. Dis.},
+Unique-ID = {WOS:000983953600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000969635700001,
+Author = {Qian, Jinyi and Wang, Yuzhou and Liu, Xiner and Hu, Zijian and Xu, Nan
+ and Wang, Yuetong and Shi, Tianqiong and Ye, Chao},
+Title = {Improving acetoin production through construction of a genome-scale
+ metabolic model},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2023},
+Volume = {158},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2023.106833},
+EarlyAccessDate = {APR 2023},
+Article-Number = {106833},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Acetoin; Bacillus amyloliquefaciens; Genome-scale metabolic network
+ model; Potential targets},
+Keywords-Plus = {BACILLUS-AMYLOLIQUEFACIENS; ENTEROBACTER-AEROGENES; 1-DEOXYNOJIRIMYCIN;
+ RECONSTRUCTION; FERMENTATION; EXPRESSION; GENES},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ye, Chao/HGD-3564-2022
+ },
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Wang, Yuetong/0000-0003-4984-1647},
+Times-Cited = {1},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000969635700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000977779100001,
+Author = {Blazquez, Blas and San Leon, David and Rojas, Antonia and Tortajada,
+ Marta and Nogales, Juan},
+Title = {New Insights on Metabolic Features of Bacillus subtilis Based on
+ Multistrain Genome-Scale Metabolic Modeling},
+Journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
+Year = {2023},
+Volume = {24},
+Number = {8},
+Month = {APR},
+Type = {Article},
+DOI = {10.3390/ijms24087091},
+Article-Number = {7091},
+EISSN = {1422-0067},
+Keywords = {Bacillus subtilis; genome-scale metabolic model; flux balance analysis;
+ multistrain modeling; panphenome},
+Keywords-Plus = {NETWORK; RIBOFLAVIN; SECRETION; DATABASE; GROWTH; SEED},
+Research-Areas = {Biochemistry \& Molecular Biology; Chemistry},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Chemistry, Multidisciplinary},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ },
+ORCID-Numbers = {Nogales, Juan/0000-0002-4961-0833
+ San Leon Granado, David/0000-0001-8138-500X
+ Blazquez, Blas/0000-0003-4099-6909},
+Times-Cited = {1},
+Journal-ISO = {Int. J. Mol. Sci.},
+Unique-ID = {WOS:000977779100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000958788400001,
+Author = {Jung, Heewon and Song, Hyun-Seob and Meile, Christof},
+Title = {CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry,
+ microbial metabolism, and biofilm dynamics},
+Journal = {GEOSCIENTIFIC MODEL DEVELOPMENT},
+Year = {2023},
+Volume = {16},
+Number = {6},
+Pages = {1683-1696},
+Month = {MAR 27},
+Type = {Article},
+DOI = {10.5194/gmd-16-1683-2023},
+ISSN = {1991-959X},
+EISSN = {1991-9603},
+Keywords-Plus = {GEOBACTER-METALLIREDUCENS; PERMEABILITY; CARBON},
+Research-Areas = {Geology},
+Web-of-Science-Categories = {Geosciences, Multidisciplinary},
+ResearcherID-Numbers = {Song, Hyun-Seob/IAQ-0503-2023
+ },
+ORCID-Numbers = {Jung, Heewon/0000-0002-6113-2002
+ Meile, Christof/0000-0002-0825-4596},
+Times-Cited = {0},
+Journal-ISO = {Geosci. Model Dev.},
+Unique-ID = {WOS:000958788400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000956563100001,
+Author = {Lo, Jonathan and Wu, Chao and Humphreys, Jonathan R. and Yang, Bin and
+ Jiang, Zhenxiong and Wang, Xin and Maness, PinChing and Tsesmetzis,
+ Nicolas and Xiong, Wei},
+Title = {Thermodynamic and Kinetic Modeling Directs Pathway Optimization for
+ Isopropanol Production in a Gas-Fermenting Bacterium},
+Journal = {MSYSTEMS},
+Year = {2023},
+Volume = {8},
+Number = {2},
+Month = {APR 27},
+Type = {Article},
+DOI = {10.1128/msystems.01274-22},
+EarlyAccessDate = {MAR 2023},
+ISSN = {2379-5077},
+Keywords = {Clostridium ljungdahlii; flux control index; isopropanol; gas
+ fermentation; metabolic robustness analysis; protein cost analysis;
+ thermodynamic analysis},
+Keywords-Plus = {BIOCHEMICAL THERMODYNAMICS; ESCHERICHIA-COLI; EXPRESSION; DATABASE;
+ ACETONE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+Times-Cited = {0},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000956563100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000962064300001,
+Author = {Miyoshi, Kenta and Kawai, Ryutaro and Niide, Teppei and Toya, Yoshihiro
+ and Shimizu, Hiroshi},
+Title = {Functional evaluation of non-oxidative glycolysis in
+ Escherichia coli in the stationary phase under microaerobic
+ conditions},
+Journal = {JOURNAL OF BIOSCIENCE AND BIOENGINEERING},
+Year = {2023},
+Volume = {135},
+Number = {4},
+Pages = {291-297},
+Month = {APR},
+Type = {Article},
+DOI = {10.1016/j.jbiosc.2023.01.002},
+EarlyAccessDate = {MAR 2023},
+ISSN = {1389-1723},
+EISSN = {1347-4421},
+Keywords = {Non-oxidative glycolysis; Flux estimation; Flux variability analysis;
+ Flux balance analysis; Stationary phase; Acetyl-CoA; Escherichia coli]},
+Keywords-Plus = {ISOPROPYL-ALCOHOL; PHOSPHOKETOLASE; RNA; DEHYDRATION; 6-PHOSPHATE;
+ ENABLES},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Shimizu, Hiroshi/C-3688-2017
+ Niide, Teppei/IUQ-2183-2023
+ },
+ORCID-Numbers = {Shimizu, Hiroshi/0000-0002-8986-0861
+ Toya, Yoshihiro/0000-0001-9670-6961
+ Miyoshi, Kenta/0000-0001-7800-1036},
+Times-Cited = {1},
+Journal-ISO = {J. Biosci. Bioeng.},
+Unique-ID = {WOS:000962064300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000957762100001,
+Author = {Shahbazinia, Amirhossein and Salehkaleybar, Saber and Hashemi, Matin},
+Title = {ParaLiNGAM: Parallel causal structure learning for linear non-Gaussian
+ acyclic models},
+Journal = {JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING},
+Year = {2023},
+Volume = {176},
+Pages = {114-127},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1016/j.jpdc.2023.01.007},
+EarlyAccessDate = {MAR 2023},
+ISSN = {0743-7315},
+EISSN = {1096-0848},
+Keywords = {Causal discovery; GPU acceleration; Machine learning; Parallel
+ processing; DirectLiNGAM algorithm},
+Keywords-Plus = {NETWORKS},
+Research-Areas = {Computer Science},
+Web-of-Science-Categories = {Computer Science, Theory \& Methods},
+Times-Cited = {0},
+Journal-ISO = {J. Parallel Distrib. Comput.},
+Unique-ID = {WOS:000957762100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000952182200001,
+Author = {Strain, Benjamin and Morrissey, James and Antonakoudis, Athanasios and
+ Kontoravdi, Cleo},
+Title = {How reliable are Chinese hamster ovary (CHO) cell genome-scale metabolic
+ models?},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2023},
+Month = {2023 MAR 18},
+Type = {Article; Early Access},
+DOI = {10.1002/bit.28366},
+EarlyAccessDate = {MAR 2023},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {bioprocessing; Chinese hamster ovary cells; flux analysis; metabolic
+ network; recombinant protein production},
+Keywords-Plus = {THERMODYNAMICALLY INFEASIBLE LOOPS; FED-BATCH; SYSTEMATIC EVALUATION;
+ PRODUCTIVITY; EXPRESSION; PATHWAYS; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Kontoravdi, Cleo/0000-0003-0213-4830},
+Times-Cited = {1},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000952182200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001040483800023,
+Author = {Wendering, Philipp and Arend, Marius and Razaghi-Moghadam, Zahra and
+ Nikoloski, Zoran},
+Title = {Data integration across conditions improves turnover number estimates
+ and metabolic predictions},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2023},
+Volume = {14},
+Number = {1},
+Month = {MAR 17},
+Type = {Article},
+DOI = {10.1038/s41467-023-37151-2},
+Article-Number = {1485},
+EISSN = {2041-1723},
+Keywords-Plus = {ESCHERICHIA-COLI; ALLOCATION; PROTEIN; GROWTH; RATES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Wendering, Philipp/0000-0002-0155-6217
+ Arend, Marius/0000-0002-9608-4960
+ Nikoloski, Zoran/0000-0003-2671-6763},
+Times-Cited = {3},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:001040483800023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000955284100001,
+Author = {Correia, Goncalo D. S. and Marchesi, Julian R. and MacIntyre, David A.},
+Title = {Moving beyond DNA: towards functional analysis of the vaginal microbiome
+ by non-sequencing-based methods},
+Journal = {CURRENT OPINION IN MICROBIOLOGY},
+Year = {2023},
+Volume = {73},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1016/j.mib.2023.102292},
+EarlyAccessDate = {MAR 2023},
+Article-Number = {102292},
+ISSN = {1369-5274},
+EISSN = {1879-0364},
+Keywords-Plus = {IONIZATION MASS-SPECTROMETRY; SCALE METABOLIC MODELS;
+ LACTOBACILLUS-INERS; SYSTEMS BIOLOGY; EXPRESSION; NETWORK;
+ METAPROTEOMICS; RECONSTRUCTION; VALIDATION; TARGET},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {dos Santos Correia, Goncalo/0000-0001-8271-9294},
+Times-Cited = {2},
+Journal-ISO = {Curr. Opin. Microbiol.},
+Unique-ID = {WOS:000955284100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000959374200001,
+Author = {Santos-Merino, Maria and Gargantilla-Becerra, Alvaro and de la Cruz,
+ Fernando and Nogales, Juan},
+Title = {Highlighting the potential of Synechococcus elongatus PCC 7942 as
+ platform to produce α-linolenic acid through an updated genome-scale
+ metabolic modeling},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2023},
+Volume = {14},
+Month = {MAR 14},
+Type = {Article},
+DOI = {10.3389/fmicb.2023.1126030},
+Article-Number = {1126030},
+EISSN = {1664-302X},
+Keywords = {cyanobacteria; Synechococcus elongatus PCC 7942; genome-scale metabolic
+ model; strain-designing algorithms; alpha-linolenic acid},
+Keywords-Plus = {POLY-BETA-HYDROXYBUTYRATE; CYANOBACTERIA; ACCUMULATION; ENHANCEMENT;
+ PHENOTYPE; GROWTH; LIPIDS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ },
+ORCID-Numbers = {GARGANTILLA-BECERRA, ALVARO/0000-0003-0429-2365
+ Nogales, Juan/0000-0002-4961-0833},
+Times-Cited = {1},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000959374200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000952803800001,
+Author = {Jamshidi, Neema and Nigam, Kabir B. and Nigam, Sanjay K.},
+Title = {Loss of the Kidney Urate Transporter, Urat1, Leads to Disrupted Redox
+ Homeostasis in Mice},
+Journal = {ANTIOXIDANTS},
+Year = {2023},
+Volume = {12},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.3390/antiox12030780},
+Article-Number = {780},
+EISSN = {2076-3921},
+Keywords = {metabolic network reconstruction; genome-scale; constraint-based
+ optimization; flux simulation; remote sensing and signaling theory;
+ ABCG2; SLC22 transporter},
+Keywords-Plus = {HUMAN METABOLIC NETWORK; ORGANIC ANION; HYPERURICEMIA; TOOLBOX; SLC22A8},
+Research-Areas = {Biochemistry \& Molecular Biology; Pharmacology \& Pharmacy; Food
+ Science \& Technology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Chemistry, Medicinal; Food Science \&
+ Technology},
+ORCID-Numbers = {Jamshidi, Neema/0000-0003-3857-9735},
+Times-Cited = {1},
+Journal-ISO = {Antioxidants},
+Unique-ID = {WOS:000952803800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000967472600002,
+Author = {Leonidou, Nantia and Renz, Alina and Mostolizadeh, Reihaneh and Draeger,
+ Andreas},
+Title = {New workflow predicts drug targets against SARS-CoV-2 via metabolic
+ changes in infected cells},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Volume = {19},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1010903},
+Article-Number = {e1010903},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {CYCLOPENTENYL CYTOSINE CPEC; IN-VITRO; CARBOCYCLIC NUCLEOSIDE; ANTIVIRAL
+ ACTIVITY; VIRUS; CORONAVIRUS; MECHANISM; SPECTRUM; REPLICATION;
+ INHIBITION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Leonidou, Nantia/ACL-1405-2022
+ Dräger, Andreas/F-5620-2015
+ },
+ORCID-Numbers = {Leonidou, Nantia/0000-0002-0248-6679
+ Dräger, Andreas/0000-0002-1240-5553
+ Renz, Alina/0000-0003-3851-9978},
+Times-Cited = {1},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000967472600002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000965674700068,
+Author = {Tamura, Takeyuki},
+Title = {Trimming Gene Deletion Strategies for Growth-Coupled Production in
+ Constraint-Based Metabolic Networks: TrimGdel},
+Journal = {IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS},
+Year = {2023},
+Volume = {20},
+Number = {2},
+Pages = {1540-1549},
+Month = {MAR-APR},
+Type = {Article},
+DOI = {10.1109/TCBB.2022.3185221},
+ISSN = {1545-5963},
+EISSN = {1557-9964},
+Keywords = {Biology and genetics; chemistry; combinatorial algorithms; graphs and
+ network; linear programming},
+Keywords-Plus = {KNOCKOUT STRATEGIES; FRAMEWORK; ENABLES},
+Research-Areas = {Biochemistry \& Molecular Biology; Computer Science; Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Computer Science, Interdisciplinary
+ Applications; Mathematics, Interdisciplinary Applications; Statistics \&
+ Probability},
+Times-Cited = {0},
+Journal-ISO = {IEEE-ACM Trans. Comput. Biol. Bioinform.},
+Unique-ID = {WOS:000965674700068},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000939721500001,
+Author = {Riccardi, Christopher and Calvanese, Marzia and Ghini, Veronica and
+ Alonso-Vasquez, Tania and Perrin, Elena and Turano, Paola and Giurato,
+ Giorgio and Weisz, Alessandro and Parrilli, Ermenegilda and Tutino,
+ Maria Luisa and Fondi, Marco},
+Title = {Metabolic Robustness to Growth Temperature of a Cold- Adapted Marine
+ Bacterium},
+Journal = {MSYSTEMS},
+Year = {2023},
+Volume = {8},
+Number = {2},
+Month = {APR 27},
+Type = {Article},
+DOI = {10.1128/msystems.01124-22},
+EarlyAccessDate = {FEB 2023},
+ISSN = {2379-5077},
+Keywords = {cold-adaptation; genome-scale modeling; metabolomics; transcriptomics},
+Keywords-Plus = {ESCHERICHIA-COLI; ANTARCTIC BACTERIUM; CSPA-FAMILY; EXPRESSION;
+ ADAPTATION; DELETION; GENOME},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Weisz, Alessandro/A-1317-2014
+ Giurato, Giorgio/K-3859-2018
+ TUTINO, MARIA LUISA/L-1834-2013
+ parrilli, ermenegilda/K-4616-2016
+ Turano, Paola/F-9089-2011
+ },
+ORCID-Numbers = {Weisz, Alessandro/0000-0003-0455-2083
+ Giurato, Giorgio/0000-0002-0538-8978
+ Perrin, Elena/0000-0001-5148-3178
+ Alonso-Vasquez, Tania/0000-0003-0194-8736
+ parrilli, ermenegilda/0000-0002-9002-5409
+ Riccardi, Christopher/0000-0002-5310-6437
+ Turano, Paola/0000-0002-7683-8614
+ Calvanese, Marzia/0000-0002-7554-0680
+ Tutino, Maria Luisa/0000-0002-4978-6839},
+Times-Cited = {2},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000939721500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000934522400001,
+Author = {Tamura, Takeyuki and Muto-fujita, Ai and Tohsato, Yukako and Kosaka,
+ Tomoyuki},
+Title = {Gene Deletion Algorithms for Minimum Reaction Network Design by
+ Mixed-Integer Linear Programming for Metabolite Production in
+ Constraint-Based Models: gDel\_minRN},
+Journal = {JOURNAL OF COMPUTATIONAL BIOLOGY},
+Year = {2023},
+Month = {2023 FEB 17},
+Type = {Article; Early Access},
+DOI = {10.1089/cmb.2022.0352},
+EarlyAccessDate = {FEB 2023},
+ISSN = {1066-5277},
+EISSN = {1557-8666},
+Keywords = {flux balance analysis; gene deletions; growth-coupled production;
+ metabolic networks; mixed-integer linear programming},
+Keywords-Plus = {KNOCKOUT STRATEGIES; FRAMEWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Tamura, Takeyuki/AGG-2853-2022
+ },
+ORCID-Numbers = {Tamura, Takeyuki/0000-0003-1596-901X
+ Kosaka, Tomoyuki/0000-0002-8181-9127},
+Times-Cited = {0},
+Journal-ISO = {J. Comput. Biol.},
+Unique-ID = {WOS:000934522400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000943016500001,
+Author = {Zhang, Zhidong and Guo, Qi and Qian, Jinyi and Ye, Chao and Huang, He},
+Title = {Construction and application of the genome-scale metabolic model of
+ Streptomyces radiopugnans},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2023},
+Volume = {11},
+Month = {FEB 17},
+Type = {Article},
+DOI = {10.3389/fbioe.2023.1108412},
+Article-Number = {1108412},
+ISSN = {2296-4185},
+Keywords = {geosmin; Streptomyces radiopugnans; genome-scale metabolic model;
+ culture condition optimization; metabolic engineering},
+Keywords-Plus = {SP NOV.; GEOSMIN; BIOSYNTHESIS; 2-METHYLISOBORNEOL; RECONSTRUCTION;
+ GENERATION; SOIL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Ye, Chao/HGD-3564-2022},
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819},
+Times-Cited = {0},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000943016500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000944145100001,
+Author = {Weston, Bronson R. and Thiele, Ines},
+Title = {A nutrition algorithm to optimize feed and medium composition using
+ genome-scale metabolic models},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {76},
+Pages = {167-178},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ymben.2023.01.010},
+EarlyAccessDate = {FEB 2023},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Linear programming; Metabolic modeling; COBRA; Genome-scale metabolic
+ model; Chinese hamster ovary cells; Aquaculture; Nutrition},
+Keywords-Plus = {SALMON SALMO-SALAR; FLUX BALANCE ANALYSIS; FED-BATCH CULTURE; ATLANTIC
+ SALMON; DIGESTIBILITY; AMMONIA; UREA; AQUACULTURE; GROWTH; CELLS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {0},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000944145100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000932018300003,
+Author = {Borer, Benedict and Magnusdottir, Stefania},
+Title = {The media composition as a crucial element in high-throughput metabolic
+ network reconstruction},
+Journal = {INTERFACE FOCUS},
+Year = {2023},
+Volume = {13},
+Number = {2},
+Month = {FEB 10},
+Type = {Article},
+DOI = {10.1098/rsfs.2022.0070},
+Article-Number = {20220070},
+ISSN = {2042-8898},
+EISSN = {2042-8901},
+Keywords = {metagenome-assembled genomes; genome-scale metabolic networks; automated
+ gap filling; KBase; high-throughput reconstruction; amino acid
+ auxotrophies},
+Keywords-Plus = {DIVERSITY; QUALITY; MODELS; STATES},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Magnusdottir, Stefania/ABA-2212-2021
+ Borer, Benedict/ABB-1914-2021
+ },
+ORCID-Numbers = {Borer, Benedict/0000-0002-1801-1088
+ Magnusdottir, Stefania/0000-0001-6506-8696},
+Times-Cited = {1},
+Journal-ISO = {Interface Focus},
+Unique-ID = {WOS:000932018300003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000992322400001,
+Author = {Clasen, Frederick and Nunes, Patricia M. and Bidkhori, Gholamreza and
+ Bah, Nourdine and Boeing, Stefan and Shoaie, Saeed and Anastasiou,
+ Dimitrios},
+Title = {Systematic diet composition swap in a mouse genome-scale metabolic model
+ reveals determinants of diet metabolism in liver cancer},
+Journal = {ISCIENCE},
+Year = {2023},
+Volume = {26},
+Number = {2},
+Month = {FEB 17},
+Type = {Article},
+DOI = {10.1016/j.isci.2023.106040},
+EarlyAccessDate = {FEB 2023},
+Article-Number = {106040},
+EISSN = {2589-0042},
+Keywords = {Western diet increases; Western diet amplifies; metabolic differences;
+ Dietary carbohydrates; Dietary nutrient availability and gene
+ expression; together; influence tissue},
+Keywords-Plus = {HIGH-FAT DIET; GLOBAL RECONSTRUCTION; QUALITY-CONTROL; GLUCONEOGENESIS;
+ FRUCTOSE; GLUCOSE; STRATEGIES; ENRICHMENT; LIPOLYSIS; GLYCEROL},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {1},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000992322400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000964051100001,
+Author = {Zampieri, Guido and Efthimiou, Georgios and Angione, Claudio},
+Title = {Multi-dimensional experimental and computational exploration of
+ metabolism pinpoints complex probiotic interactions},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {76},
+Pages = {120-132},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ymben.2023.01.008},
+EarlyAccessDate = {FEB 2023},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Probiotics; Metabolic modelling; Biofilms; Microbial interactions;
+ Multivariate analysis},
+Keywords-Plus = {EXTRACELLULAR-MATRIX; AMINO-ACID; MICROBIOME; MODELS; PREVENTION;
+ PREBIOTICS; CONSORTIA; BIOFILMS; RULES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Angione, Claudio/0000-0002-3140-7909
+ ZAMPIERI, GUIDO/0000-0002-4518-5913},
+Times-Cited = {2},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000964051100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000964018900001,
+Author = {Gurdo, Nicolas and Volke, Daniel C. and McCloskey, Douglas and Nikel,
+ Pablo Ivan},
+Title = {Automating the design-build-test-learn cycle towards next-generation
+ bacterial cell factories},
+Journal = {NEW BIOTECHNOLOGY},
+Year = {2023},
+Volume = {74},
+Pages = {1-15},
+Month = {MAY 25},
+Type = {Article},
+DOI = {10.1016/j.nbt.2023.01.002},
+EarlyAccessDate = {FEB 2023},
+ISSN = {1871-6784},
+EISSN = {1876-4347},
+Keywords = {Synthetic biology; Biofoundry; DBTL cycle; Automation; Machine learning;
+ Metabolic engineering; Synthetic metabolism; Bacteria},
+Keywords-Plus = {METABOLIC FLUX ANALYSIS; ESCHERICHIA-COLI METABOLISM; CONSTRAINT-BASED
+ MODELS; QUANTITATIVE-ANALYSIS; HIGH-THROUGHPUT; MICROBIAL-PRODUCTION;
+ MASS-SPECTROMETRY; SYNTHETIC BIOLOGY; CORYNEBACTERIUM-GLUTAMICUM;
+ ABSOLUTE QUANTIFICATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nikel, Pablo Ivan/L-4146-2014
+ },
+ORCID-Numbers = {Nikel, Pablo Ivan/0000-0002-9313-7481
+ Volke, Daniel Christoph/0000-0003-0244-2534},
+Times-Cited = {4},
+Journal-ISO = {New Biotech.},
+Unique-ID = {WOS:000964018900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000938861300001,
+Author = {Esvap, Elif and Ulgen, Kutlu O.},
+Title = {Neuroinflammation, Energy and Sphingolipid Metabolism Biomarkers Are
+ Revealed by Metabolic Modeling of Autistic Brains},
+Journal = {BIOMEDICINES},
+Year = {2023},
+Volume = {11},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/biomedicines11020583},
+Article-Number = {583},
+EISSN = {2227-9059},
+Keywords = {autism spectrum disorder; genome-scale metabolic modeling;
+ neuroinflammation; oxidative stress; mitochondrial dysfunction;
+ sphingolipid},
+Keywords-Plus = {ESSENTIAL FATTY-ACIDS; OXIDATIVE STRESS; ANTIOXIDANT ENZYMES;
+ GLUCOSE-METABOLISM; PREFRONTAL CORTEX; CHILDREN; MITOCHONDRIAL;
+ INFLAMMATION; ABNORMALITIES; TOMOGRAPHY},
+Research-Areas = {Biochemistry \& Molecular Biology; Research \& Experimental Medicine;
+ Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Medicine, Research \& Experimental;
+ Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Esvap, Elif/AAR-4483-2020
+ },
+ORCID-Numbers = {Esvap, Elif/0000-0002-7915-2618
+ Ulgen, Kutlu/0000-0003-3668-3467},
+Times-Cited = {1},
+Journal-ISO = {Biomedicines},
+Unique-ID = {WOS:000938861300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000940546200001,
+Author = {Shen, Qiu and Yang, Hua and Kong, Qing-Peng and Li, Gong-Hua and Li, Li},
+Title = {Metabolic Modeling Identifies a Novel Molecular Type of Glioblastoma
+ Associated with Good Prognosis},
+Journal = {METABOLITES},
+Year = {2023},
+Volume = {13},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/metabo13020172},
+Article-Number = {172},
+EISSN = {2218-1989},
+Keywords = {metabolic modeling; metabolic pathway; GPMM; glioblastoma; cancer
+ prognosis},
+Keywords-Plus = {CARBON METABOLISM; CANCER; ATP; ADENOSINE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Li, Gong-Hua/0000-0002-9311-6613
+ Kong, Qingpeng/0000-0002-6046-4494},
+Times-Cited = {0},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000940546200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000996456400001,
+Author = {Sevrin, Thomas and Strasser, Lisa and Ternet, Camille and Junk, Philipp
+ and Caffarini, Miriam and Prins, Stella and D'Arcy, Cian and Catozzi,
+ Simona and Oliviero, Giorgio and Wynne, Kieran and Kiel, Christina and
+ Luthert, Philip J.},
+Title = {Whole-cell energy modeling reveals quantitative changes of predicted
+ energy flows in RAS mutant cancer cell lines},
+Journal = {ISCIENCE},
+Year = {2023},
+Volume = {26},
+Number = {2},
+Month = {FEB 17},
+Type = {Article},
+DOI = {10.1016/j.isci.2023.105931},
+EarlyAccessDate = {JAN 2023},
+Article-Number = {105931},
+EISSN = {2589-0042},
+Keywords-Plus = {MUTATIONS; BALANCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {WYNNE, KIERAN/0000-0001-5759-5285
+ Junk, Philipp/0000-0002-5228-3896
+ D'Arcy, Cian/0000-0002-1890-3211},
+Times-Cited = {1},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000996456400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000916149200003,
+Author = {Heinken, Almut and Hertel, Johannes and Acharya, Geeta and Ravcheev,
+ Dmitry A. A. and Nyga, Malgorzata and Okpala, Onyedika Emmanuel and
+ Hogan, Marcus and Magnusdottir, Stefania and Martinelli, Filippo and
+ Nap, Bram and Preciat, German and Edirisinghe, Janaka N. N. and Henry,
+ Christopher S. S. and Fleming, Ronan M. T. and Thiele, Ines},
+Title = {Genome-scale metabolic reconstruction of 7,302 human microorganisms for
+ personalized medicine},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2023},
+Volume = {41},
+Number = {9},
+Pages = {1320+},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1038/s41587-022-01628-0},
+EarlyAccessDate = {JAN 2023},
+ISSN = {1087-0156},
+EISSN = {1546-1696},
+Keywords-Plus = {MULTIPLE SEQUENCE ALIGNMENT; BACTERIAL; MICROBIOME; DATABASE;
+ INHIBITION; GENERATION; PATHWAYS; VIEW},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Hertel, Johannes/HZJ-3685-2023
+ Magnusdottir, Stefania/ABA-2212-2021
+ },
+ORCID-Numbers = {Hertel, Johannes/0000-0002-7641-0132
+ Preciat Gonzalez, German Andres/0000-0003-4903-9515
+ Magnusdottir, Stefania/0000-0001-6506-8696
+ Nap, Bram/0000-0003-2910-9109
+ OKPALA, ONYEDIKA EMMANUEL/0000-0002-3007-6730
+ Heinken, Almut/0000-0001-6938-8072},
+Times-Cited = {18},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000916149200003},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000913297700001,
+Author = {Yao, Haoyang and Dahal, Sanjeev and Yang, Laurence},
+Title = {Novel context-specific genome-scale modelling explores the potential of
+ triacylglycerol production by Chlamydomonas reinhardtii},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2023},
+Volume = {22},
+Number = {1},
+Month = {JAN 17},
+Type = {Article},
+DOI = {10.1186/s12934-022-02004-y},
+Article-Number = {13},
+EISSN = {1475-2859},
+Keywords = {Genome-scale modelling; C; reinhardtii; Metabolic engineering;
+ Optimization; Systems biology},
+Keywords-Plus = {METABOLISM; STARCH; CARBON; LIPIDS; OIL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Yao, Haoyang/0000-0002-7989-6529},
+Times-Cited = {2},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000913297700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000920211000001,
+Author = {Zhao, Yunpeng and Feng, Yiming and Zhou, Jianhang and Zhang, Kuo and
+ Sun, Jingqi and Wang, Lina and Liu, Sitong},
+Title = {Potential bacterial isolation by dosing metabolites in cross-feedings},
+Journal = {WATER RESEARCH},
+Year = {2023},
+Volume = {231},
+Month = {MAR 1},
+Type = {Article},
+DOI = {10.1016/j.watres.2023.119589},
+EarlyAccessDate = {JAN 2023},
+Article-Number = {119589},
+ISSN = {0043-1354},
+EISSN = {1879-2448},
+Keywords = {Cross-feedings; Bacterial abundance; Bacterial activity; Anammox
+ consortia},
+Keywords-Plus = {UNCULTIVABLE MICROORGANISMS; PSEUDOMONAS-AERUGINOSA;
+ SPATIAL-ORGANIZATION; ANAMMOX; GROWTH; CULTIVATION; EVOLUTION; IMPACT;
+ TIME},
+Research-Areas = {Engineering; Environmental Sciences \& Ecology; Water Resources},
+Web-of-Science-Categories = {Engineering, Environmental; Environmental Sciences; Water Resources},
+ResearcherID-Numbers = {Zhao, Yunpeng/AAQ-8398-2020
+ Liu, Si/JBJ-5042-2023},
+Times-Cited = {5},
+Journal-ISO = {Water Res.},
+Unique-ID = {WOS:000920211000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000922747900001,
+Author = {Muthulakshmi, M. Vidya and Srinivasan, Aparajitha and Srivastava, Smita},
+Title = {Antioxidant Green Factories: Toward Sustainable Production of Vitamin E
+ in Plant In Vitro Cultures},
+Journal = {ACS OMEGA},
+Year = {2023},
+Month = {2023 JAN 13},
+Type = {Article; Early Access},
+DOI = {10.1021/acsomega.2c05819},
+EarlyAccessDate = {JAN 2023},
+ISSN = {2470-1343},
+Keywords-Plus = {GAMMA-TOCOPHEROL METHYLTRANSFERASE; SCALE METABOLIC MODEL; TINCTORIUS L.
+ CELL; ALPHA-TOCOPHEROL; HELIANTHUS-ANNUUS; HOMOGENTISATE
+ PHYTYLTRANSFERASE; OXIDATIVE STRESS; GROWTH; ARABIDOPSIS; PATHWAY},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary},
+ORCID-Numbers = {M, Vidya Muthulakshmi/0000-0002-0067-8722},
+Times-Cited = {2},
+Journal-ISO = {ACS Omega},
+Unique-ID = {WOS:000922747900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000913115100006,
+Author = {Kindschuh, William F. F. and Baldini, Federico and Liu, Martin C. C. and
+ Liao, Jingqiu and Meydan, Yoli and Lee, Harry H. H. and Heinken, Almut
+ and Thiele, Ines and Thaiss, Christoph A. A. and Levy, Maayan and Korem,
+ Tal},
+Title = {Preterm birth is associated with xenobiotics and predicted by the
+ vaginal metabolome},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2023},
+Volume = {8},
+Number = {2},
+Pages = {246+},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1038/s41564-022-01293-8},
+EarlyAccessDate = {JAN 2023},
+ISSN = {2058-5276},
+Keywords-Plus = {BACTERIAL VAGINOSIS; SAFETY ASSESSMENT; GESTATIONAL-AGE; GUT MICROBIOTA;
+ CHOLINE; DIETHANOLAMINE; NUTRIENT; IDENTIFICATION; NUTRITION; CHEMICALS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Korem, Tal/D-4155-2018
+ Kindschuh, William/JFK-7820-2023
+ Levy, Maayan/HCJ-0551-2022
+ Liao, Jingqiu/AAW-2093-2021
+ Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Korem, Tal/0000-0002-0609-0858
+ Liao, Jingqiu/0000-0002-2579-8157
+ Meydan, Yoli/0009-0003-4597-3340
+ Levy, Maayan/0000-0002-7149-9422
+ Heinken, Almut/0000-0001-6938-8072
+ Kindschuh, William/0000-0002-7433-7808
+ Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {9},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000913115100006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000911959300001,
+Author = {Vikromvarasiri, Nunthaphan and Noda, Shuhei and Shirai, Tomokazu and
+ Kondo, Akihiko},
+Title = {Investigation of two metabolic engineering approaches for
+ (R,R)-2,3-butanediol production from glycerol in Bacillus
+ subtilis},
+Journal = {JOURNAL OF BIOLOGICAL ENGINEERING},
+Year = {2023},
+Volume = {17},
+Number = {1},
+Month = {JAN 10},
+Type = {Article},
+DOI = {10.1186/s13036-022-00320-w},
+ISSN = {1754-1611},
+Keywords = {Glycerol; 2,3-Butanediol; Bacillus subtilis; Flux balance analysis;
+ OptKnock; Genome-scale metabolic model},
+Keywords-Plus = {GENOME; FRAMEWORK; YIELD},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Shirai, Tomokazu/C-7986-2017
+ Noda, Shuhei/D-4815-2017
+ },
+ORCID-Numbers = {Vikromvarasiri, Nunthaphan/0000-0002-0665-6882},
+Times-Cited = {2},
+Journal-ISO = {J. Biol. Eng.},
+Unique-ID = {WOS:000911959300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000945553800001,
+Author = {Karlsen, Emil and Gylseth, Marianne and Schulz, Christian and Almaas,
+ Eivind},
+Title = {A study of a diauxic growth experiment using an expanded dynamic flux
+ balance framework},
+Journal = {PLOS ONE},
+Year = {2023},
+Volume = {18},
+Number = {1},
+Month = {JAN 6},
+Type = {Article},
+DOI = {10.1371/journal.pone.0280077},
+Article-Number = {e0280077},
+ISSN = {1932-6203},
+Keywords-Plus = {CONTROLLED METABOLIC NETWORKS; ESCHERICHIA-COLI; DATABASE; HMDB;
+ PHENOTYPE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Karlsen, Emil/0000-0002-6626-8697},
+Times-Cited = {1},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000945553800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000922026600001,
+Author = {Correia-Melo, Clara and Kamrad, Stephan and Tengoelics, Roland and
+ Messner, Christoph B. and Trebulle, Pauline and Townsend, StJohn and
+ Varma, Sreejith Jayasree and Freiwald, Anja and Heineike, Benjamin M.
+ and Campbell, Kate and Herrera-Dominguez, Lucia and Aulakh, Simran Kaur
+ and Szyrwiel, Lukasz and Yu, Jason S. L. and Zelezniak, Aleksej and
+ Demichev, Vadim and Muelleder, Michael and Papp, Balazs and Alam,
+ Mohammad Tauqeer and Rasler, Markus},
+Title = {Cell-cell metabolite exchange creates a pro-survival metabolic
+ environment that extends lifespan},
+Journal = {CELL},
+Year = {2023},
+Volume = {186},
+Number = {1},
+Pages = {63+},
+Month = {JAN 5},
+Type = {Article},
+DOI = {10.1016/j.cell.2022.12.007},
+EarlyAccessDate = {JAN 2023},
+ISSN = {0092-8674},
+EISSN = {1097-4172},
+Keywords-Plus = {MASS-SPECTROMETRY; HYDROGEN-SULFIDE; STATIONARY-PHASE; TOR PATHWAY;
+ YEAST; GROWTH; MODEL; GENE; COOPERATION; RESOURCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Messner, Christoph/IUP-2898-2023
+ Alam, Mohammad Tauqeer/A-5304-2013
+ },
+ORCID-Numbers = {Messner, Christoph/0000-0001-7217-0867
+ Szyrwiel, Lukasz/0000-0003-1983-2950
+ Mulleder, Michael/0000-0001-9792-3861
+ Zelezniak, Aleksej/0000-0002-3098-9441
+ Correia-Melo, Clara/0000-0001-6062-1472
+ Ralser, Markus/0000-0001-9535-7413
+ Demichev, Vadim/0000-0002-2424-9412},
+Times-Cited = {4},
+Journal-ISO = {Cell},
+Unique-ID = {WOS:000922026600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000932732000025,
+Author = {Fernandes, Philip and Sharma, Yash and Zulqarnain, Fatima and McGrew,
+ Brooklyn and Shrivastava, Aman and Ehsan, Lubaina and Payne, Dawson and
+ Dillard, Lillian and Powers, Deborah and Aldridge, Isabelle and
+ Matthews, Jason and Kugathasan, Subra and Fernandez, Facundo M. and
+ Gaul, David and Papin, Jason A. and Syed, Sana},
+Title = {Identifying metabolic shifts in Crohn's disease using' omics-driven
+ contextualized computational metabolic network models},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2023},
+Volume = {13},
+Number = {1},
+Month = {JAN 5},
+Type = {Article},
+DOI = {10.1038/s41598-022-26816-5},
+Article-Number = {203},
+ISSN = {2045-2322},
+Keywords-Plus = {INFLAMMATORY-BOWEL-DISEASE; MEVALONATE KINASE-DEFICIENCY; FLUX-BALANCE
+ ANALYSIS; NECROSIS-FACTOR-ALPHA; CHILDREN; ENERGY; MANAGEMENT; CERAMIDE;
+ STRESS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Shrivastava, Aman/AAF-6144-2021
+ Fernandez, Facundo Martin/B-7015-2008},
+ORCID-Numbers = {Fernandez, Facundo Martin/0000-0002-0302-2534},
+Times-Cited = {0},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000932732000025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001101105500001,
+Author = {Viana, Romeu and Carreiro, Tiago and Couceiro, Diogo and Dias, Oscar and
+ Rocha, Isabel and Teixeira, Miguel Cacho},
+Title = {Metabolic reconstruction of the human pathogen Candida auris: using a
+ cross-species approach for drug target prediction},
+Journal = {FEMS YEAST RESEARCH},
+Year = {2023},
+Volume = {23},
+Month = {JAN 4},
+Type = {Article},
+DOI = {10.1093/femsyr/foad045},
+Article-Number = {foad045},
+ISSN = {1567-1356},
+EISSN = {1567-1364},
+Keywords = {C. auris; Global stoichiometric model; gene essentiality; drug target;
+ metabolic features},
+Keywords-Plus = {DATABASE; MODELS; HAEMULONII; TROPICALIS; ALBICANS; STEROL; NOV.},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+ResearcherID-Numbers = {Teixeira, Miguel/A-3870-2008},
+ORCID-Numbers = {Teixeira, Miguel/0000-0002-5676-6174},
+Times-Cited = {0},
+Journal-ISO = {FEMS Yeast Res.},
+Unique-ID = {WOS:001101105500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000918617500001,
+Author = {Moskon, Miha and Rezen, Tadeja},
+Title = {Context-Specific Genome-Scale Metabolic Modelling and Its Application to
+ the Analysis of COVID-19 Metabolic Signatures},
+Journal = {METABOLITES},
+Year = {2023},
+Volume = {13},
+Number = {1},
+Month = {JAN},
+Type = {Review},
+DOI = {10.3390/metabo13010126},
+Article-Number = {126},
+EISSN = {2218-1989},
+Keywords = {context-specific genome scale metabolic modelling; constraint-based
+ modelling; omics data integration; model extraction method;
+ computational pipeline; metabolic fluxes; context-specific model;
+ COVID-19},
+Keywords-Plus = {GENE-EXPRESSION; INTEGRATION; RECONSTRUCTION; BALANCE; PHENOTYPE;
+ RESOURCE; PLATFORM; ENABLES; ARCHIVE; TARGET},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Moskon, Miha/0000-0003-4600-1730
+ Rezen, Tadeja/0000-0001-6210-7370},
+Times-Cited = {3},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000918617500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000916944200001,
+Author = {Gopalakrishnan, Saratram and Joshi, Chintan J. and Valderrama-Gomez,
+ Miguel A. and Icten, Elcin and Rolandi, Pablo and Johnson, William and
+ Kontoravdi, Cleo and Lewis, Nathan E.},
+Title = {Guidelines for extracting biologically relevant context-specific
+ metabolic models using gene expression data},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {75},
+Pages = {181-191},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2022.12.003},
+EarlyAccessDate = {DEC 2022},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Systems biology; Metabolic modeling; Constraint -based models; Context
+ -specific models; Model extraction methods},
+Keywords-Plus = {SYSTEMATIC EVALUATION; RECONSTRUCTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Kontoravdi, Cleo/0000-0003-0213-4830},
+Times-Cited = {4},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000916944200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000905027700001,
+Author = {Tibocha-Bonilla, Juan D. and Zuniga, Cristal and Lekbua, Asama and
+ Lloyd, Colton and Rychel, Kevin and Short, Katie and Zengler, Karsten},
+Title = {Predicting stress response and improved protein overproduction in
+ Bacillus subtilis},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2022},
+Volume = {8},
+Number = {1},
+Month = {DEC 27},
+Type = {Article},
+DOI = {10.1038/s41540-022-00259-0},
+Article-Number = {50},
+EISSN = {2056-7189},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Short, Katie/JGM-1493-2023
+ },
+ORCID-Numbers = {Lekbua, Asama/0000-0002-6641-1385
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {2},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000905027700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000917907400003,
+Author = {Diaz-Tang, Gabriela and Meneses, Estefania Marin and Patel, Kavish and
+ Mirkin, Sophia and Garcia-Dieguez, Laura and Pajon, Camryn and Barraza,
+ Ivana and Patel, Vijay and Ghali, Helana and Tracey, Angelica P. and
+ Blanar, Christopher A. and Lopatkin, Allison J. and Smith, Robert P.},
+Title = {Growth productivity as a determinant of the inoculum effect for
+ bactericidal antibiotics},
+Journal = {SCIENCE ADVANCES},
+Year = {2022},
+Volume = {8},
+Number = {50},
+Month = {DEC 14},
+Type = {Article},
+DOI = {10.1126/sciadv.add0924},
+Article-Number = {eadd0924},
+ISSN = {2375-2548},
+Keywords-Plus = {ESCHERICHIA-COLI; STAPHYLOCOCCUS-AUREUS; OVERFLOW METABOLISM; SIZE;
+ MAINTENANCE; INFECTIONS; EXPRESSION; EFFICIENCY; MECHANISM; EFFICACY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Mirkin, Sophia/0000-0001-5083-3498
+ Diaz-Tang, Gabriela/0000-0003-3002-3046
+ Garcia-Dieguez, Lau/0000-0003-4535-0138
+ Marin Meneses, Estefania/0000-0002-4785-9184
+ Tracey, Angelica/0000-0002-2733-0216},
+Times-Cited = {4},
+Journal-ISO = {Sci. Adv.},
+Unique-ID = {WOS:000917907400003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000901453900001,
+Author = {Koduru, Lokanand and Lakshmanan, Meiyappan and Lee, Yi Qing and Ho,
+ Pooi-Leng and Lim, Pei-Yu and Ler, Wei Xuan and Ng, Say Kong and Kim,
+ Dongseok and Park, Doo-Sang and Banu, Mazlina and Ow, Dave Siak Wei and
+ Lee, Dong-Yup},
+Title = {Systematic evaluation of genome-wide metabolic landscapes in lactic acid
+ bacteria reveals diet- and strain-specific probiotic idiosyncrasies},
+Journal = {CELL REPORTS},
+Year = {2022},
+Volume = {41},
+Number = {10},
+Month = {DEC 6},
+Type = {Article},
+DOI = {10.1016/j.celrep.2022.111735},
+EarlyAccessDate = {DEC 2022},
+Article-Number = {111735},
+ISSN = {2211-1247},
+Keywords-Plus = {REGULATORY T-CELLS; LACTOBACILLUS-CASEI; ESCHERICHIA-COLI; RNA-SEQ;
+ OXIDATIVE STRESS; CYTOKINE PROFILE; SEQUENCE; PLANTARUM; MODEL;
+ HOMEOSTASIS},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/H-1267-2014
+ },
+ORCID-Numbers = {seong-gyungwandaehaggyo, gimdongseog/0000-0003-0096-7767
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Yi Qing/0000-0002-8970-0729
+ Lim, Pei Yu/0009-0002-0834-787X},
+Times-Cited = {3},
+Journal-ISO = {Cell Reports},
+Unique-ID = {WOS:000901453900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000904513500001,
+Author = {Castillo-Alfonso, Freddy and Quintana-Menendez, Alejandro and
+ Vigueras-Ramirez, Gabriel and Sales-Cruz, Alfonso Mauricio and
+ Rosales-Colunga, Luis Manuel and Olivares-Hernandez, Roberto},
+Title = {Analysis of the Propionate Metabolism in Bacillus subtilis during
+ 3-Indolacetic Production},
+Journal = {MICROORGANISMS},
+Year = {2022},
+Volume = {10},
+Number = {12},
+Month = {DEC},
+Type = {Article},
+DOI = {10.3390/microorganisms10122352},
+Article-Number = {2352},
+EISSN = {2076-2607},
+Keywords = {Bacillus subtilis; propionate metabolism; 3-indole acetic acid; flux
+ balance analysis},
+Keywords-Plus = {FLUX-BALANCE ANALYSIS; ROBUSTNESS ANALYSIS; OPTIMIZATION;
+ OVERPRODUCTION; FRAMEWORK; GLUCOSE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Castillo Alfonso, Freddy/0000-0001-6043-5776},
+Times-Cited = {1},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000904513500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000902549500001,
+Author = {Francine, Piubeli},
+Title = {Systems Biology: New Insight into Antibiotic Resistance},
+Journal = {MICROORGANISMS},
+Year = {2022},
+Volume = {10},
+Number = {12},
+Month = {DEC},
+Type = {Review},
+DOI = {10.3390/microorganisms10122362},
+Article-Number = {2362},
+EISSN = {2076-2607},
+Keywords = {antibiotic resistance; omics approches; system biology; mathematical
+ models; genome-scale metabolic models},
+Keywords-Plus = {GENOME-SCALE MODELS; EPIDEMIOLOGY; EMERGENCE; RECONSTRUCTION;
+ SUSCEPTIBILITY; SURVEILLANCE; BACTERIA; REVEALS; GENES},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Piubeli, Francine/H-1991-2015},
+ORCID-Numbers = {Piubeli, Francine/0000-0002-5065-5297},
+Times-Cited = {3},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000902549500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000902692900001,
+Author = {Pacheco, Maria Pires and Ji, Jimmy and Prohaska, Tessy and Garcia, Maria
+ Moscardo and Sauter, Thomas},
+Title = {scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic
+ Multi-Cell Population Models from Single-Cell RNAseq Data},
+Journal = {METABOLITES},
+Year = {2022},
+Volume = {12},
+Number = {12},
+Month = {DEC},
+Type = {Article},
+DOI = {10.3390/metabo12121211},
+Article-Number = {1211},
+EISSN = {2218-1989},
+Keywords = {single-cell RNAseq; metabolism; metabolic modelling; algorithm},
+Keywords-Plus = {CANCER; EXPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Sauter, Thomas/0000-0001-8225-2954
+ Moscardo Garcia, Maria Isabel/0000-0001-9352-4097},
+Times-Cited = {1},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000902692900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000890398000003,
+Author = {Foguet, Carles and Xu, Yu and Ritchie, Scott C. and Lambert, Samuel A.
+ and Persyn, Elodie and Nath, Artika P. and Davenport, Emma E. and
+ Roberts, David J. and Paul, Dirk S. and Di Angelantonio, Emanuele and
+ Danesh, John and Butterworth, Adam S. and Yau, Christopher and Inouye,
+ Michael},
+Title = {Genetically personalised organ-specific metabolic models in health and
+ disease},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2022},
+Volume = {13},
+Number = {1},
+Month = {NOV 29},
+Type = {Article},
+DOI = {10.1038/s41467-022-35017-7},
+Article-Number = {7356},
+EISSN = {2041-1723},
+Keywords-Plus = {FATTY-ACID OXIDATION; HEPATIC LIPASE; ARACHIDONIC-ACID; SKELETAL-MUSCLE;
+ GENE; ASSOCIATION; GENOME; RISK; ACYLTRANSFERASE; TARGETS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Ritchie, Scott/AAX-1020-2020
+ Foguet, Carles/W-4864-2018
+ Butterworth, Adam/JOZ-2470-2023
+ },
+ORCID-Numbers = {Ritchie, Scott/0000-0002-8454-9548
+ Foguet, Carles/0000-0001-8494-9595
+ Paul, Dirk/0000-0002-8230-0116
+ Inouye, Michael/0000-0001-9413-6520
+ Lambert, Samuel/0000-0001-8222-008X},
+Times-Cited = {3},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000890398000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000891352200001,
+Author = {Han, Bin and Dai, Zeyu and Li, Zhimin},
+Title = {Computer-Based Design of a Cell Factory for High-Yield Cytidine
+ Production},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2022},
+Volume = {11},
+Number = {12},
+Pages = {4123-4133},
+Month = {DEC 16},
+Type = {Article},
+DOI = {10.1021/acssynbio.2c00431},
+EarlyAccessDate = {NOV 2022},
+ISSN = {2161-5063},
+Keywords = {cytidine; metabolic network model; flux coupling analysis; chassis cells},
+Keywords-Plus = {ESCHERICHIA-COLI; BIOSYNTHESIS; INHIBITION; ROBUSTNESS; METABOLISM;
+ GENES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ORCID-Numbers = {han, bin/0000-0002-8811-7910},
+Times-Cited = {2},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000891352200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000933800700001,
+Author = {Loganathan, Tamizhini and Doss C, George Priya},
+Title = {The influence of machine learning technologies in gut microbiome
+ research and cancer studies - A review},
+Journal = {LIFE SCIENCES},
+Year = {2022},
+Volume = {311},
+Month = {DEC 15},
+Type = {Review},
+DOI = {10.1016/j.lfs.2022.121118},
+EarlyAccessDate = {NOV 2022},
+Article-Number = {121118},
+ISSN = {0024-3205},
+EISSN = {1879-0631},
+Keywords = {Human gut microbiome; Cancer; Machine learning},
+Keywords-Plus = {IRRITABLE-BOWEL-SYNDROME; HELICOBACTER-PYLORI; HEALTHY INFANTS;
+ BACTERIAL; IMMUNITY; DATABASE; METABOLISM; DYSBIOSIS; TUMORIGENESIS;
+ METAGENOMICS},
+Research-Areas = {Research \& Experimental Medicine; Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Medicine, Research \& Experimental; Pharmacology \& Pharmacy},
+ORCID-Numbers = {LOGANATHAN, TAMIZHINI/0000-0002-7736-7885},
+Times-Cited = {3},
+Journal-ISO = {Life Sci.},
+Unique-ID = {WOS:000933800700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000975856900001,
+Author = {Bujdos, Dalimil and Popelarova, Barbora and Volke, Daniel C. and Nikel,
+ Pablo I. and Sonnenschein, Nikolaus and Dvorak, Pavel},
+Title = {Engineering of Pseudomonas putida for accelerated
+ co-utilization of glucose and cellobiose yields aerobic overproduction
+ of pyruvate explained by an upgraded metabolic model},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {75},
+Pages = {29-46},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2022.10.011},
+EarlyAccessDate = {NOV 2022},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Pseudomonas putida; Metabolic engineering; Glucose; Cellobiose;
+ Co-utilization of sugars; Pyruvate; Metabolic model},
+Keywords-Plus = {ESCHERICHIA-COLI; BETA-GLUCOSIDASE; KT2440; PATHWAYS; ENZYMES; ACID;
+ BIODEGRADATION; DEHYDROGENASE; DEGRADATION; AERUGINOSA},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nikel, Pablo Ivan/L-4146-2014
+ Dvorak, Pavel/AAO-7902-2020
+ Sonnenschein, Nikolaus/F-6853-2012
+ },
+ORCID-Numbers = {Nikel, Pablo Ivan/0000-0002-9313-7481
+ Dvorak, Pavel/0000-0002-3215-4763
+ Volke, Daniel Christoph/0000-0003-0244-2534
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Popelarova, Barbora/0000-0003-3760-0539},
+Times-Cited = {2},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000975856900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000995351200009,
+Author = {Vayena, Evangelia and Chiappino-Pepe, Anush and MohammadiPeyhani, Homa
+ and Francioli, Yannick and Hadadi, Noushin and Ataman, Meric and Hafner,
+ Jasmin and Pavlou, Stavros and Hatzimanikatis, Vassily},
+Title = {A workflow for annotating the knowledge gaps in metabolic
+ reconstructions using known and hypothetical reactions},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2022},
+Volume = {119},
+Number = {46},
+Month = {NOV 15},
+Type = {Article},
+DOI = {10.1073/pnas.2211197119},
+Article-Number = {e2211197119},
+ISSN = {0027-8424},
+EISSN = {1091-6490},
+Keywords = {hypothetical biochemistry; gap-filling; missing annotation; metabolic
+ model; genome annotation},
+Keywords-Plus = {ESCHERICHIA-COLI; IDENTIFICATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Chiappino Pepe, Anush/AAY-8830-2021
+ Pavlou, Stavros/F-5771-2013
+ Hatzimanikatis, Vassily/G-6505-2010},
+ORCID-Numbers = {Chiappino Pepe, Anush/0000-0002-3993-907X
+ Pavlou, Stavros/0000-0002-5146-2390
+ Vayena, Evangelia/0000-0001-8536-4505
+ Hatzimanikatis, Vassily/0000-0001-6432-4694},
+Times-Cited = {6},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000995351200009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000978697600001,
+Author = {Cao, Xuan and Yu, Wei and Chen, Yu and Yang, Shan and Zhao, Zongbao K.
+ and Nielsen, Jens and Luan, Hongwei and Zhou, Yongjin J.},
+Title = {Engineering yeast for high-level production of diterpenoid sclareol},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {75},
+Pages = {19-28},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2022.11.002},
+EarlyAccessDate = {NOV 2022},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords-Plus = {BIOSYNTHETIC PATHWAYS; SYNTHETIC BIOLOGY; OVERPRODUCTION; MILTIRADIENE;
+ EXPRESSION; SYNTHASES; RIGIDITY; ENZYMES; PROTEIN; CARBON},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Cao, Xuan/JMB-2654-2023
+ Chen, Yu/AAL-3329-2020
+ Zhou, Yongjin/D-5911-2018},
+ORCID-Numbers = {Chen, Yu/0000-0003-3326-9068
+ Zhou, Yongjin/0000-0002-2369-3079},
+Times-Cited = {5},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000978697600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000975874600001,
+Author = {Li, Zhendong and Gao, Cong and Ye, Chao and Guo, Liang and Liu, Jia and
+ Chen, Xiulai and Song, Wei and Wu, Jing and Liu, Liming},
+Title = {Systems engineering of Escherichia coli for high-level shikimate
+ production},
+Journal = {METABOLIC ENGINEERING},
+Year = {2023},
+Volume = {75},
+Pages = {1-11},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2022.10.010},
+EarlyAccessDate = {NOV 2022},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Shikimate; Escherichia coli; Model simulation; Metabolic and protein
+ engineering; Dynamic tolerance engineering},
+Keywords-Plus = {SCALE METABOLIC MODELS; SACCHAROMYCES-CEREVISIAE; DYNAMIC REGULATION;
+ GENE; DEHYDROGENASE; BIOSYNTHESIS; ACID; EXPRESSION; TOLERANCE; BACTERIA},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ye, Chao/HGD-3564-2022
+ Gao, Cong/AAB-4849-2022},
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Gao, Cong/0000-0001-8505-2026},
+Times-Cited = {8},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000975874600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000900186300007,
+Author = {Magazzu, Giuseppe and Zampieri, Guido and Angione, Claudio},
+Title = {Clinical stratification improves the diagnostic accuracy of small omics
+ datasets within machine learning and genome-scale metabolic modelling
+ methods?},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2022},
+Volume = {151},
+Number = {A},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2022.106244},
+EarlyAccessDate = {NOV 2022},
+Article-Number = {106244},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Machine learning; Metabolic modelling; Hepatoblastoma; Clinical
+ stratification; Multi-omics; Cancer; Systems biology},
+Keywords-Plus = {SYSTEMS BIOLOGY; HEPATOBLASTOMA; EXPRESSION; CANCER},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ORCID-Numbers = {ZAMPIERI, GUIDO/0000-0002-4518-5913
+ Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {3},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000900186300007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000862258600012,
+Author = {Sawant, Kaustubh R. and Sarnaik, Aditya P. and Savvashe, Prashant and
+ Hajinajaf, Nima and Poole, Parker and Varman, Arul M. and Lali, Arvind
+ and Pandit, Reena},
+Title = {One cell-two wells bio-refinery: Demonstrating cyanobacterial chassis
+ for co-production of heterologous and natural hydrocarbons},
+Journal = {BIORESOURCE TECHNOLOGY},
+Year = {2022},
+Volume = {363},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.biortech.2022.127921},
+Article-Number = {127921},
+ISSN = {0960-8524},
+EISSN = {1873-2976},
+Keywords = {Bicarbonate -integrated system; Cyanobacterial Outdoor scale -up
+ cultivation; Flux balance analysis; Ethylene; Carotenoids},
+Keywords-Plus = {INTEGRATED CARBON CAPTURE; ELONGATUS PCC 7942; METABOLISM; CO2;
+ EFFICIENCY; BIOMASS; FLUX; PH},
+Research-Areas = {Agriculture; Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Agricultural Engineering; Biotechnology \& Applied Microbiology; Energy
+ \& Fuels},
+Times-Cited = {1},
+Journal-ISO = {Bioresour. Technol.},
+Unique-ID = {WOS:000862258600012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000883767400029,
+Author = {Warda, Alicja K. and Dempsey, Eugene M. and Forssten, Sofia D. and Ryan,
+ C. Anthony and Cryan, John F. and Patterson, Elaine and O'Riordan,
+ Mairead N. and O'Shea, Carol-Anne and Keohane, Finola and Meehan,
+ Grainne and O'Connor, Orlagh and Ross, R. Paul and Stanton, Catherine},
+Title = {Cross-sectional observational study protocol: missing microbes in
+ infants born by caesarean section (MiMIC): antenatal antibiotics and
+ mode of delivery},
+Journal = {BMJ OPEN},
+Year = {2022},
+Volume = {12},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1136/bmjopen-2022-064398},
+Article-Number = {e064398},
+ISSN = {2044-6055},
+Keywords = {MICROBIOLOGY; PAEDIATRICS; OBSTETRICS},
+Keywords-Plus = {DEPRESSION; PREGNANCY},
+Research-Areas = {General \& Internal Medicine},
+Web-of-Science-Categories = {Medicine, General \& Internal},
+ResearcherID-Numbers = {Ross, Paul/A-7584-2015
+ Cryan, John F./A-6950-2013},
+ORCID-Numbers = {Ross, Paul/0000-0003-4876-8839
+ Cryan, John F./0000-0001-5887-2723},
+Times-Cited = {1},
+Journal-ISO = {BMJ Open},
+Unique-ID = {WOS:000883767400029},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000877140500058,
+Author = {Jamshidi, Neema and Nigam, Sanjay K.},
+Title = {Drug transporters OAT1 and OAT3 have specific effects on multiple organs
+ and gut microbiome as revealed by contextualized metabolic network
+ reconstructions},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2022},
+Volume = {12},
+Number = {1},
+Month = {OCT 31},
+Type = {Article},
+DOI = {10.1038/s41598-022-21091-w},
+Article-Number = {18308},
+ISSN = {2045-2322},
+Keywords-Plus = {GENOME-SCALE; ANION TRANSPORTERS; SYSTEMS BIOLOGY; UREMIC TOXINS;
+ EXPRESSION; SLC22A8; FAMILY; ACID; MECHANISMS; PHYLOGENY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {6},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000877140500058},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000877010200001,
+Author = {Ford, Kathryne C. and Kaste, Joshua A. M. and Shachar-Hill, Yair and
+ TerAvest, Michaela A.},
+Title = {Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a
+ Conditionally Essential Gene in Shewanella oneidensis MR-1},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2022},
+Volume = {11},
+Number = {10},
+Pages = {3405-3413},
+Month = {OCT 21},
+Type = {Article},
+DOI = {10.1021/acssynbio.2c003233405},
+ISSN = {2161-5063},
+Keywords = {Shewanella oneidensis; genetic engineering; CRISPRi; synthetic biology;
+ carbon metabolism; flux-balance analysis},
+Keywords-Plus = {CARBON FIXATION; MICROBIAL ELECTROSYNTHESIS; ESCHERICHIA-COLI; LACTATE;
+ RESPIRATION; METABOLISM; PATHWAYS; IDENTIFICATION; FERMENTATION;
+ EXPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Shachar-Hill, Yair/B-6165-2013
+ },
+ORCID-Numbers = {Shachar-Hill, Yair/0000-0001-8793-5084
+ Ford, Kathryne Caldwell/0000-0002-6357-9318
+ TerAvest, Michaela/0000-0002-5435-3587
+ Kaste, Joshua/0000-0003-1942-0315},
+Times-Cited = {1},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000877010200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000879895400001,
+Author = {Ciurans, Carles and Guerrero, Josep M. and Martinez-Mongue, Ivan and
+ Dussap, Claude G. and de Mas, Igor Marin and Godia, Francesc},
+Title = {Enhancing control systems of higher plant culture chambers via
+ multilevel structural mechanistic modelling},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2022},
+Volume = {13},
+Month = {OCT 20},
+Type = {Article},
+DOI = {10.3389/fpls.2022.970410},
+Article-Number = {970410},
+ISSN = {1664-462X},
+Keywords = {closed ecological life support systems; higher plant chambers;
+ functional-structural modelling; model predictive control; FBA; Melissa},
+Keywords-Plus = {PREDICTIVE CONTROL; ACID METABOLISM; PHOTOSYNTHESIS; LEAVES; FLUX;
+ LIGHT; C-3; ASSIMILATION; RESPIRATION; CHLOROPLAST},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Guerrero, Josep M./D-5519-2014
+ DUSSAP, Claude-Gilles/JPC-6972-2023},
+ORCID-Numbers = {Guerrero, Josep M./0000-0001-5236-4592
+ DUSSAP, Claude-Gilles/0000-0002-6461-6264},
+Times-Cited = {1},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000879895400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000868469100001,
+Author = {Ramos, Joao R. C. and Oliveira, Gil P. and Dumas, Patrick and Oliveira,
+ Rui},
+Title = {Genome-scale modeling of Chinese hamster ovary cells by hybrid
+ semi-parametric flux balance analysis},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2022},
+Volume = {45},
+Number = {11},
+Pages = {1889-1904},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1007/s00449-022-02795-9},
+EarlyAccessDate = {OCT 2022},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {Genome-scale modeling; CHO-K1 cells; Flux balance analysis; Hybrid
+ semi-parametric systems; Machine learning; Culture media design},
+Keywords-Plus = {CHO; RECONSTRUCTION; MEDIA; ERA},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Poiares-Oliveira, Gil/AAE-9440-2021
+ Ramos, João/IVV-2419-2023
+ Oliveira, Rui/D-8815-2013},
+ORCID-Numbers = {Poiares-Oliveira, Gil/0000-0003-4638-2879
+ Oliveira, Rui/0000-0001-8077-4177},
+Times-Cited = {8},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000868469100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000868094500001,
+Author = {Karakurt, Hamza Umut and Pir, Pinar},
+Title = {In silico analysis of metabolic effects of bipolar disorder on
+ prefrontal cortex identified altered GABA, glutamate-glutamine cycle,
+ energy metabolism and amino acid synthesis pathways},
+Journal = {INTEGRATIVE BIOLOGY},
+Year = {2022},
+Volume = {14},
+Number = {6},
+Pages = {127-136},
+Month = {OCT 21},
+Type = {Article},
+DOI = {10.1093/intbio/zyac012},
+EarlyAccessDate = {OCT 2022},
+ISSN = {1757-9694},
+EISSN = {1757-9708},
+Keywords = {bioinformatics; genome-scale metabolic models; systems biology;
+ transcriptome; bipolar disorder},
+Keywords-Plus = {BRAIN; MANIA; ABNORMALITIES; METAANALYSIS; INHIBITION},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ORCID-Numbers = {Karakurt, Hamza Umut/0000-0002-4072-3065
+ Pir, Pinar/0000-0002-0078-4904},
+Times-Cited = {0},
+Journal-ISO = {Integr. Biol.},
+Unique-ID = {WOS:000868094500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000867889200040,
+Author = {Venkatraghavan, Sankalpa and Anantakrishnan, Sathvik and Raman, Karthik},
+Title = {Probing patterning in microbial consortia with a cellular automaton for
+ spatial organisation},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2022},
+Volume = {12},
+Number = {1},
+Month = {OCT 13},
+Type = {Article},
+DOI = {10.1038/s41598-022-20705-7},
+Article-Number = {17159},
+ISSN = {2045-2322},
+Keywords-Plus = {GROWTH; DIFFUSION; BACTERIA; BIOLOGY; MODELS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019},
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093},
+Times-Cited = {0},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000867889200040},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000866302900001,
+Author = {Mekanik, Mahsa and Fotovat, Reza and Motamedian, Ehsan and Jafarian,
+ Vahab},
+Title = {Improvement of Lutein Production in Auxenochlorella
+ protothecoides Using Its Genome-Scale Metabolic Model and a
+ System-Oriented Approach},
+Journal = {APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY},
+Year = {2023},
+Volume = {195},
+Number = {2},
+Pages = {889-904},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1007/s12010-022-04186-y},
+EarlyAccessDate = {OCT 2022},
+ISSN = {0273-2289},
+EISSN = {1559-0291},
+Keywords = {Microalgae; Activator; Metabolite; Metabolic flux analysis; Multiple
+ optimal solutions; Sodium citrate},
+Keywords-Plus = {CHLORELLA-PROTOTHECOIDES; OUTDOOR CULTIVATION; CULTURE-CONDITIONS;
+ MICROALGAE; BIOSYNTHESIS; OPTIMIZATION; CAROTENOIDS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Appl. Biochem. Biotechnol.},
+Unique-ID = {WOS:000866302900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000869102400001,
+Author = {Ford, Kathryne C. and Kaste, Joshua A. M. and Shachar-Hill, Yair and
+ TerAvest, Michaela A.},
+Title = {Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a
+ Conditionally Essential Gene in Shewanella oneidensis MR-1},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2022},
+Month = {2022 OCT 11},
+Type = {Article; Early Access},
+DOI = {10.1021/acssynbio.2c00323},
+EarlyAccessDate = {OCT 2022},
+ISSN = {2161-5063},
+Keywords = {Shewanella oneidensis; genetic engineering; CRISPRi; synthetic biology;
+ carbon metabolism; flux-balance analysis},
+Keywords-Plus = {CARBON FIXATION; MICROBIAL ELECTROSYNTHESIS; ESCHERICHIA-COLI; LACTATE;
+ RESPIRATION; METABOLISM; PATHWAYS; IDENTIFICATION; FERMENTATION;
+ EXPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Shachar-Hill, Yair/B-6165-2013
+ },
+ORCID-Numbers = {Shachar-Hill, Yair/0000-0001-8793-5084
+ Ford, Kathryne Caldwell/0000-0002-6357-9318
+ TerAvest, Michaela/0000-0002-5435-3587
+ Kaste, Joshua/0000-0003-1942-0315},
+Times-Cited = {1},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000869102400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000865175700001,
+Author = {Baloni, Priyanka and Arnold, Matthias and Buitrago, Luna and Nho,
+ Kwangsik and Moreno, Herman and Huynh, Kevin and Brauner, Barbara and
+ Louie, Gregory and Kueider-Paisley, Alexandra and Suhre, Karsten and
+ Saykin, Andrew J. and Ekroos, Kim and Meikle, Peter J. and Hood, Leroy
+ and Price, Nathan D. and Doraiswamy, P. Murali and Funk, Cory C. and
+ Hernandez, A. Ivan and Kastenmueller, Gabi and Baillie, Rebecca and Han,
+ Xianlin and Kaddurah-Daouk, Rima and Alzheimer's Dis Metabolomics Conso},
+Title = {Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a
+ therapeutic target in Alzheimer's disease},
+Journal = {COMMUNICATIONS BIOLOGY},
+Year = {2022},
+Volume = {5},
+Number = {1},
+Month = {OCT 8},
+Type = {Article},
+DOI = {10.1038/s42003-022-04011-6},
+Article-Number = {1074},
+EISSN = {2399-3642},
+Keywords-Plus = {CENTRAL-NERVOUS-SYSTEM; AMYLOID-BETA; PRECURSOR PROTEIN;
+ CLINICAL-TRIALS; METABOLISM; CERAMIDE; MICROGLIA; NEURODEGENERATION;
+ CHOLESTEROL; MODULATION},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Science \& Technology -
+ Other Topics},
+Web-of-Science-Categories = {Biology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Suhre, Karsten/AAF-1778-2020
+ baillie, rebecca/AAQ-3400-2020
+ Meikle, Peter J/B-4023-2009
+ },
+ORCID-Numbers = {Suhre, Karsten/0000-0001-9638-3912
+ baillie, rebecca/0000-0003-3966-6320
+ Meikle, Peter/0000-0002-2593-4665
+ Arnold, Matthias/0000-0002-4666-0923},
+Times-Cited = {11},
+Journal-ISO = {Commun. Biol.},
+Unique-ID = {WOS:000865175700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000865046000001,
+Author = {Kim, Jungyeon and Cheong, Yu Eun and Yu, Sora and Jin, Yong-Su and Kim,
+ Kyoung Heon},
+Title = {Strain engineering and metabolic flux analysis of a probiotic yeast
+ Saccharomyces boulardii for metabolizing l-fucose, a mammalian
+ mucin component},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2022},
+Volume = {21},
+Number = {1},
+Month = {OCT 7},
+Type = {Article},
+DOI = {10.1186/s12934-022-01926-x},
+Article-Number = {204},
+EISSN = {1475-2859},
+Keywords = {l-Fucose; Saccharomyces boulardii; Saccharomyces cerevisiae;
+ Genome-scale metabolic model analysis; Elementary flux mode analysis},
+Keywords-Plus = {GUT MICROBIOTA; CAMPYLOBACTER; SALMONELLA; PREVENTION; EFFICACY;
+ DIARRHEA; MODEL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Kim, Kyoung Heon/F-1059-2013
+ },
+ORCID-Numbers = {Kim, Kyoung Heon/0000-0003-4600-8668
+ Kim, Jungyeon/0000-0003-1193-0919},
+Times-Cited = {3},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000865046000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000864277100059,
+Author = {Granados, Jeffry C. and Falah, Kian and Koo, Imhoi and Morgan, Ethan W.
+ and Perdew, Gary H. and Patterson, Andrew D. and Jamshidi, Neema and
+ Nigam, Sanjay K.},
+Title = {AHR is a master regulator of diverse pathways in endogenous metabolism},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2022},
+Volume = {12},
+Number = {1},
+Month = {OCT 5},
+Type = {Article},
+DOI = {10.1038/s41598-022-20572-2},
+Article-Number = {16625},
+ISSN = {2045-2322},
+Keywords-Plus = {ARYL-HYDROCARBON RECEPTOR; BILE-ACID HOMEOSTASIS; ORGANIC ANION;
+ 2,3,7,8-TETRACHLORODIBENZO-P-DIOXIN; ACTIVATION; EXPRESSION; TOOLBOX;
+ AGONIST; COMPLEX; LIVER},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Koo, Imhoi/E-5759-2011
+ Patterson, Andrew/ABF-1575-2020
+ },
+ORCID-Numbers = {Koo, Imhoi/0000-0002-5816-0627
+ Patterson, Andrew/0000-0003-2073-0070
+ Granados, Jeffry/0000-0003-0393-7141},
+Times-Cited = {11},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000864277100059},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000965685900005,
+Author = {Gencturk, Elif and Ulgen, Kutlu O.},
+Title = {Understanding HMF inhibition on yeast growth coupled with ethanol
+ production for the improvement of bio-based industrial processes},
+Journal = {PROCESS BIOCHEMISTRY},
+Year = {2022},
+Volume = {121},
+Pages = {425-438},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1016/j.procbio.2022.07.015},
+ISSN = {1359-5113},
+EISSN = {1873-3298},
+Keywords = {COBRA; HMF; Yeast; Modelling; Bioethanol; Microfluidics},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS; CHAIN AMINO-ACIDS;
+ SACCHAROMYCES-CEREVISIAE; TRANSCRIPTIONAL REGULATION;
+ OXIDATIVE-PHOSPHORYLATION; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ BIOMASS YIELD; GENES},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Engineering},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Engineering, Chemical},
+Times-Cited = {3},
+Journal-ISO = {Process Biochem.},
+Unique-ID = {WOS:000965685900005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000864259800001,
+Author = {Jouhten, Paula and Konstantinidis, Dimitrios and Pereira, Filipa and
+ Andrejev, Sergej and Grkovska, Kristina and Castillo, Sandra and
+ Ghiachi, Payam and Beltran, Gemma and Almaas, Eivind and Mas, Albert and
+ Warringer, Jonas and Gonzalez, Ramon and Morales, Pilar and Patil, Kiran
+ R.},
+Title = {Predictive evolution of metabolic phenotypes using model-designed
+ environments},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2022},
+Volume = {18},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.15252/msb.202210980},
+Article-Number = {e10980},
+ISSN = {1744-4292},
+Keywords = {adaptive evolution; genome-scale metabolic model; predictive evolution;
+ Saccharomyces cerevisiae; wine aroma},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; YEAST; GROWTH;
+ RECONSTRUCTION; IDENTIFICATION; COVARIANCES; SELECTION; PROTEOME;
+ STRAINS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Patil, Kiran R/B-9709-2009
+ Mas, Albert/C-9812-2010
+ Beltran, Gemma/C-6416-2015
+ },
+ORCID-Numbers = {Patil, Kiran R/0000-0002-6166-8640
+ Konstantinidis, Dimitrios/0000-0002-2134-6823
+ Jouhten, Paula/0000-0003-1075-7448
+ Mas, Albert/0000-0002-0763-1679
+ Ghiaci, Payam/0000-0003-1914-5130
+ Beltran, Gemma/0000-0002-7071-205X
+ Pereira, Filipa/0000-0002-0557-8480},
+Times-Cited = {7},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000864259800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000861949100001,
+Author = {Gosselin, Maxime R. F. and Mournetas, Virginie and Borczyk, Malgorzata
+ and Verma, Suraj and Occhipinti, Annalisa and Rog, Justyna and Bozycki,
+ Lukasz and Korostynski, Michal and Robson, Samuel C. and Angione,
+ Claudio and Pinset, Christian and Gorecki, Dariusz C.},
+Title = {Loss of full-length dystrophin expression results in major
+ cell-autonomous abnormalities in proliferating myoblasts},
+Journal = {ELIFE},
+Year = {2022},
+Volume = {11},
+Month = {SEP 27},
+Type = {Article},
+DOI = {10.7554/eLife.75521},
+Article-Number = {e75521},
+ISSN = {2050-084X},
+Keywords = {DMD; dystrophin; myoblast; transcriptomics; mdx; Mouse; Human},
+Keywords-Plus = {DUCHENNE MUSCULAR-DYSTROPHY; EMBRYONIC STEM-CELLS; MDX MOUSE; IN-VITRO;
+ MUSCLE HISTOLOGY; SATELLITE CELLS; NITRIC-OXIDE; DIFFERENTIATION; MODEL;
+ MICE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Korostynski, Michal/AAS-2626-2021
+ Róg, Justyna/HKV-2221-2023
+ Verma, Suraj/JPA-2789-2023
+ Mournetas, Virginie/H-7336-2013
+ },
+ORCID-Numbers = {Korostynski, Michal/0000-0002-4273-7401
+ Róg, Justyna/0000-0001-5718-2536
+ Verma, Suraj/0000-0002-9684-0885
+ Occhipinti, Annalisa/0000-0001-6075-1496
+ Gosselin, Maxime Raymond Fernand/0000-0002-8916-0953
+ Gorecki, Dariusz/0000-0003-3584-1654
+ Pikula, Slawomir/0000-0003-4640-3094
+ Mournetas, Virginie/0000-0002-6557-4190
+ Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {7},
+Journal-ISO = {eLife},
+Unique-ID = {WOS:000861949100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000875635000002,
+Author = {Subramanian, Abhishek and Zakeri, Pooya and Mousa, Mira and Alnaqbi,
+ Halima and Alshamsi, Fatima Yousif and Bettoni, Leo and Damiani, Ernesto
+ and Alsafar, Habiba and Saeys, Yvan and Carmeliet, Peter},
+Title = {Angiogenesis goes computational - The future way forward to discover new
+ angiogenic targets?},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2022},
+Volume = {20},
+Pages = {5235-5255},
+Type = {Review},
+DOI = {10.1016/j.csbj.2022.09.019},
+EarlyAccessDate = {SEP 2022},
+ISSN = {2001-0370},
+Keywords = {Angiogenesis; Single-cell multi-omics; Functional enrichment; Biological
+ networks; Unsupervised and supervised data fusion; Gene prioritization},
+Keywords-Plus = {ENDOTHELIAL-CELL HETEROGENEITY; GENE PRIORITIZATION; ENRICHMENT
+ ANALYSIS; WEB SERVER; PROTEOGENOMIC CHARACTERIZATION; REVEALS;
+ METABOLISM; NETWORKS; ASSOCIATIONS; MECHANISMS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Saeys, Yvan/C-1311-2009
+ Carmeliet, Peter/AAQ-5140-2020
+ Alsafar, Habiba/P-2003-2016
+ },
+ORCID-Numbers = {Saeys, Yvan/0000-0002-0415-1506
+ Carmeliet, Peter/0000-0001-7961-1821
+ Alsafar, Habiba/0000-0001-7141-1438
+ Yousif Alshamsi, Fatima/0000-0002-4378-6598
+ Mousa, Mira/0000-0002-5676-3221
+ Subramanian, Abhishek/0000-0002-4601-5991},
+Times-Cited = {2},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000875635000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000856009500004,
+Author = {Achreja, Abhinav and Yu, Tao and Mittal, Anjali and Choppara, Srinadh
+ and Animasahun, Olamide and Nenwani, Minal and Wuchu, Fulei and Meurs,
+ Noah and Mohan, Aradhana and Jeon, Jin Heon and Sarangi, Itisam and
+ Jayaraman, Anusha and Owen, Sarah and Kulkarni, Reva and Cusato, Michele
+ and Weinberg, Frank and Kweon, Hye Kyong and Subramanian, Chitra and
+ Wicha, Max S. and Merajver, Sofia D. and Nagrath, Sunitha and Cho,
+ Kathleen R. and DiFeo, Analisa and Lu, Xiongbin and Nagrath, Deepak},
+Title = {Metabolic collateral lethal target identification reveals MTHFD2
+ paralogue dependency in ovarian cancer},
+Journal = {NATURE METABOLISM},
+Year = {2022},
+Volume = {4},
+Number = {9},
+Pages = {1119+},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1038/s42255-022-00636-3},
+EarlyAccessDate = {SEP 2022},
+EISSN = {2522-5812},
+Keywords-Plus = {FLUX ANALYSIS; MITOCHONDRIA; INHIBITOR; PROLIFERATION; RESPIRATION;
+ DELETION; 19P13.3; TUMOR},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Mittal, Anjali/ITU-6127-2023
+ },
+ORCID-Numbers = {Nagrath, Sunitha/0000-0002-1497-7977
+ Achreja, Abhinav/0000-0002-1773-6490
+ Mittal, Anjali/0000-0001-5670-032X
+ Yu, Tao/0000-0002-1903-7589
+ Animasahun, Olamide/0000-0002-4032-3619
+ Jeon, Jin Heon/0000-0002-8427-8514},
+Times-Cited = {4},
+Journal-ISO = {Nat. Metab.},
+Unique-ID = {WOS:000856009500004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000874916800001,
+Author = {Ruan, Zhepu and Xu, Mengjun and Xing, Youwen and Jiang, Qi and Yang,
+ Bingang and Jiang, Jiandong and Xu, Xihui},
+Title = {Interspecies Metabolic Interactions in a Synergistic Consortium Drive
+ Efficient Degradation of the Herbicide Bromoxynil Octanoate},
+Journal = {JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY},
+Year = {2022},
+Volume = {70},
+Number = {37},
+Pages = {11613-11622},
+Month = {SEP 21},
+Type = {Article},
+DOI = {10.1021/acs.jafc.2c03057},
+ISSN = {0021-8561},
+EISSN = {1520-5118},
+Keywords = {microbial degradation; bromoxynil octanoate; synergistic consortium;
+ metabolic modeling; interspecies interaction},
+Keywords-Plus = {GENOME; BENZONITRILE; RESIDUES},
+Research-Areas = {Agriculture; Chemistry; Food Science \& Technology},
+Web-of-Science-Categories = {Agriculture, Multidisciplinary; Chemistry, Applied; Food Science \&
+ Technology},
+ORCID-Numbers = {Jiang, Jiandong/0000-0003-4877-5756
+ Xu, Xihui/0000-0003-2092-9987},
+Times-Cited = {5},
+Journal-ISO = {J. Agric. Food Chem.},
+Unique-ID = {WOS:000874916800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000860100500001,
+Author = {Schneider, Philipp and Bekiaris, Pavlos Stephanos and von Kamp, Axel and
+ Klamt, Steffen},
+Title = {StrainDesign: a comprehensive Python package for computational design of
+ metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Volume = {38},
+Number = {21},
+Pages = {4981-4983},
+Month = {OCT 31},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btac632},
+EarlyAccessDate = {SEP 2022},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {KNOCKOUT STRATEGIES},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Schneider, Philipp/GYU-8053-2022
+ },
+ORCID-Numbers = {Schneider, Philipp/0000-0001-8858-428X
+ Klamt, Steffen/0000-0003-2563-7561},
+Times-Cited = {4},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000860100500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000852278800001,
+Author = {Behravan, Aidin and Hashemi, Atieh and Marashi, Sayed-Amir and
+ Fouladiha, Hamideh},
+Title = {Genome-scale metabolic model-based engineering of Escherichia
+ coli enhances recombinant single-chain antibody fragment production},
+Journal = {BIOTECHNOLOGY LETTERS},
+Year = {2022},
+Volume = {44},
+Number = {10},
+Pages = {1231-1242},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1007/s10529-022-03301-7},
+EarlyAccessDate = {SEP 2022},
+ISSN = {0141-5492},
+EISSN = {1573-6776},
+Keywords = {AntiEpEX-scFv; Escherichia coli; FVSEOF; Genome-scale metabolic model;
+ glk; Glucokinase},
+Keywords-Plus = {EXPRESSION; TRANSPORT; STRESS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008},
+ORCID-Numbers = {Fouladiha, Hamideh/0000-0002-5522-8809
+ behravan, aidin/0000-0002-7218-4262
+ Marashi, Sayed-Amir/0000-0001-9801-7449},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Lett.},
+Unique-ID = {WOS:000852278800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000851930300005,
+Author = {Keller, Philipp and Reiter, Michael A. and Kiefer, Patrick and Gassler,
+ Thomas and Hemmerle, Lucas and Christen, Philipp and Noor, Elad and
+ Vorholt, Julia A.},
+Title = {Generation of an Escherichia coli strain growing on methanol via
+ the ribulose monophosphate cycle},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2022},
+Volume = {13},
+Number = {1},
+Month = {SEP 6},
+Type = {Article},
+DOI = {10.1038/s41467-022-32744-9},
+Article-Number = {5243},
+EISSN = {2041-1723},
+Keywords-Plus = {BACILLUS-METHANOLICUS; DIRECT CONVERSION; METHYLOTROPHY; GENOME; CO2;
+ DEHYDROGENASE; ASSIMILATION; METABOLISM; EXPRESSION; STRATEGIES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Vorholt, Julia A/K-3514-2016
+ Kiefer, Patrick/G-5138-2010
+ },
+ORCID-Numbers = {Vorholt, Julia A/0000-0002-6011-4910
+ Christen, Philipp/0000-0002-3139-2874
+ Gassler, Thomas/0000-0003-1873-8807
+ Keller, Philipp/0000-0003-3962-5078},
+Times-Cited = {14},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000851930300005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000858046100001,
+Author = {Du, Yuan-Hang and Wang, Min-Yu and Yang, Lin-Hui and Tong, Ling-Ling and
+ Guo, Dong-Sheng and Ji, Xiao-Jun},
+Title = {Optimization and Scale-Up of Fermentation Processes Driven by Models},
+Journal = {BIOENGINEERING-BASEL},
+Year = {2022},
+Volume = {9},
+Number = {9},
+Month = {SEP},
+Type = {Review},
+DOI = {10.3390/bioengineering9090473},
+Article-Number = {473},
+EISSN = {2306-5354},
+Keywords = {mechanistic modeling; data-driven; hybrid modeling; scale-up;
+ computational fluid dynamics},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Biomedical},
+ResearcherID-Numbers = {Ji, Xiao-Jun/E-6447-2012
+ },
+ORCID-Numbers = {Ji, Xiao-Jun/0000-0002-6450-0229
+ Yuan-Hang, Du/0000-0003-2223-2972},
+Times-Cited = {12},
+Journal-ISO = {Bioengineering-Basel},
+Unique-ID = {WOS:000858046100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000933363400003,
+Author = {Nursimulu, Nirvana and Moses, Alan M. and Parkinson, John},
+Title = {Architect: A tool for aiding the reconstruction of high-quality
+ metabolic models through improved enzyme annotation},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2022},
+Volume = {18},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1010452},
+Article-Number = {e1010452},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {GENOME; DATABASE; BRENDA},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Parkinson, John/A-4424-2008
+ },
+ORCID-Numbers = {Parkinson, John/0000-0001-9815-1189
+ Nursimulu, Nirvana/0000-0001-5962-5863},
+Times-Cited = {1},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000933363400003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000854224400001,
+Author = {Thiele, Ines and Preciat, German and Fleming, Ronan M. T.},
+Title = {MetaboAnnotator: an efficient toolbox to annotate metabolites in
+ genome-scale metabolic reconstructions},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Volume = {38},
+Number = {20},
+Pages = {4831-4832},
+Month = {OCT 14},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btac596},
+EarlyAccessDate = {SEP 2022},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Preciat Gonzalez, German Andres/0000-0003-4903-9515
+ Fleming, Ronan MT/0000-0001-5346-9812},
+Times-Cited = {2},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000854224400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000863292100007,
+Author = {Beura, Satyajit and Kundu, Pritam and Das, Amit Kumar and Ghosh, Amit},
+Title = {Metagenome-scale community metabolic modelling for understanding the
+ role of gut microbiota in human health},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2022},
+Volume = {149},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2022.105997},
+EarlyAccessDate = {AUG 2022},
+Article-Number = {105997},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Microbial communities; Human gut microbiota; Metabolic disorders;
+ Systems biology; Community metabolic model; Metagenome-scale community
+ metabolic\ model},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; IN-VITRO; FUSOBACTERIUM-NUCLEATUM;
+ PSEUDOMONAS-AERUGINOSA; STAPHYLOCOCCUS-AUREUS; DIETARY PATTERNS;
+ RECONSTRUCTION; ECOSYSTEM; INTEGRATION; CONSORTIA},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ORCID-Numbers = {Ghosh, Amit/0000-0003-3514-885X
+ KUNDU, PRITAM/0000-0001-6129-4506
+ Beura, Satyajit/0000-0002-8052-2962},
+Times-Cited = {3},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000863292100007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000846845500001,
+Author = {Hirmas, Belen and Gasaly, Naschla and Orellana, Guillermo and
+ Vega-Sagardia, Marco and Saa, Pedro and Gotteland, Martin and Garrido,
+ Daniel},
+Title = {Metabolic Modeling and Bidirectional Culturing of Two Gut Microbes
+ Reveal Cross-Feeding Interactions and Protective Effects on Intestinal
+ Cells},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {5},
+Month = {OCT 26},
+Type = {Article},
+DOI = {10.1128/msystems.00646-22},
+EarlyAccessDate = {AUG 2022},
+ISSN = {2379-5077},
+Keywords = {cross-feeding; genome-scale metabolic models; butyrate; prebiotics},
+Keywords-Plus = {CHAIN FATTY-ACIDS; BUTYRATE-PRODUCING BACTERIA; SODIUM-BUTYRATE; DIETARY
+ FIBER; INULIN; ECOLOGY; BIFIDOBACTERIA; FERMENTATION; MECHANISM;
+ EVOLUTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Saa, Pedro Andrés/X-1987-2018
+ GARRIDO, DANIEL/F-8229-2013},
+ORCID-Numbers = {Saa, Pedro Andrés/0000-0002-1659-9041
+ Gasaly, Naschla/0000-0002-2951-7527
+ Vega-Sagardia, Marco/0000-0002-1254-4748
+ GARRIDO, DANIEL/0000-0002-4982-134X},
+Times-Cited = {7},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000846845500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000846845500002,
+Author = {Pacheco, Alan R. and Pauvert, Charlie and Kishore, Dileep and Segre,
+ Daniel},
+Title = {Toward FAIR Representations of Microbial Interactions},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {5},
+Month = {OCT 26},
+Type = {Article},
+DOI = {10.1128/msystems.00659-22},
+EarlyAccessDate = {AUG 2022},
+ISSN = {2379-5077},
+Keywords = {microbiome; microbial interactions; microbial ecology; data sharing;
+ accessibility; reproducibility; FAIR; metadata; co-occurrence; microbial
+ networks},
+Keywords-Plus = {MINIMUM INFORMATION; BACTERIAL; NETWORKS; ECOLOGY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Pacheco, Alan R/IUQ-5711-2023
+ Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Pacheco, Alan R/0000-0002-1128-3232
+ Segrè, Daniel/0000-0003-4859-1914
+ Kishore, Dileep/0000-0003-4859-8681
+ PAUVERT, Charlie/0000-0001-9832-2507},
+Times-Cited = {4},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000846845500002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000844051100002,
+Author = {Ambikan, Anoop T. and Yang, Hong and Krishnan, Shuba and Akusjarvi, Sara
+ Svensson and Gupta, Soham and Lourda, Magda and Sperk, Maike and Arif,
+ Muhammad and Zhang, Chenq and Nordqvist, Hampus and Ponnan, Sivasankaran
+ Munusamy and Sonnerborg, Anders and Treutiger, Carl Johan and O'Mahony,
+ Liam and Mardinoglu, Adil and Benfeitas, Rui and Neogi, Ujjwal},
+Title = {Multi-omics personalized network analyses highlight progressive
+ disruption of central metabolism associated with COVID-19 severity},
+Journal = {CELL SYSTEMS},
+Year = {2022},
+Volume = {13},
+Number = {8},
+Pages = {665+},
+Month = {AUG 17},
+Type = {Article},
+DOI = {10.1016/j.cels.2022.06.006},
+EarlyAccessDate = {AUG 2022},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {GENE-EXPRESSION; BUTYRATE; GLUCOSE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Arif, Muhammad/AFQ-6409-2022
+ Munusamy Ponnan, Sivasankaran/HKN-4841-2023
+ O'Mahony, Liam/AAG-5838-2019
+ Zhang, Cheng/L-7906-2016},
+ORCID-Numbers = {Arif, Muhammad/0000-0003-2261-0881
+ Munusamy Ponnan, Sivasankaran/0000-0001-6705-4474
+ O'Mahony, Liam/0000-0003-4705-3583
+ Zhang, Cheng/0000-0002-3721-8586},
+Times-Cited = {10},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000844051100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000860671500005,
+Author = {John, J. Ashwini and Samuel, Melvin S. and Govarthanan, Muthusamy and
+ Selvarajan, Ethiraj},
+Title = {A comprehensive review on strategic study of cellulase producing marine
+ actinobacteria for biofuel applications},
+Journal = {ENVIRONMENTAL RESEARCH},
+Year = {2022},
+Volume = {214},
+Number = {3},
+Month = {NOV},
+Type = {Review},
+DOI = {10.1016/j.envres.2022.114018},
+EarlyAccessDate = {AUG 2022},
+Article-Number = {114018},
+ISSN = {0013-9351},
+EISSN = {1096-0953},
+Keywords = {Biofuel; Cellulase; Genetic engineering; Genomic mining; Lignocellulosic
+ biomass; Marine actinobacteria},
+Keywords-Plus = {COMPLETE GENOME SEQUENCE; ENZYMATIC-HYDROLYSIS; LIGNOCELLULOSIC BIOMASS;
+ ENZYMES; EVOLUTION; SACCHARIFICATION; BIOCONVERSION; EXTREMOZYMES;
+ PURIFICATION; PRETREATMENT},
+Research-Areas = {Environmental Sciences \& Ecology; Public, Environmental \& Occupational
+ Health},
+Web-of-Science-Categories = {Environmental Sciences; Public, Environmental \& Occupational Health},
+ResearcherID-Numbers = {Muthusamy, Govarthanan/C-1491-2014
+ E, Selvarajan/K-6947-2013},
+ORCID-Numbers = {Muthusamy, Govarthanan/0000-0001-8725-3059
+ John, Ashwini/0000-0001-6172-5425
+ E, Selvarajan/0000-0002-3447-6432},
+Times-Cited = {8},
+Journal-ISO = {Environ. Res.},
+Unique-ID = {WOS:000860671500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000880816000008,
+Author = {Murugan, Raja and Sundararaghavan, Archanaa and Dhami, Navdeep K. and
+ Mukherjee, Abhijit and Suraishkumar, G. K.},
+Title = {Importance of carbon to nitrogen ratio in microbial cement production:
+ Insights through experiments and genome-scale metabolic modelling},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2022},
+Volume = {186},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1016/j.bej.2022.108573},
+EarlyAccessDate = {AUG 2022},
+Article-Number = {108573},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {MICP; Sporosarcina pasteurii; C/N ratio; Intracellular urease activity;
+ GSMM},
+Keywords-Plus = {CALCIUM-CARBONATE; PRECIPITATION; GROWTH; PASTEURII; UREOLYSIS;
+ BIOMINERALIZATION; TEMPERATURE; MORPHOLOGY; UREASE; SIZE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+Times-Cited = {2},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000880816000008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000836490900001,
+Author = {Kawai, Ryutaro and Toya, Yoshihiro and Shimizu, Hiroshi},
+Title = {Metabolic pathway design for growth-associated phenylalanine production
+ using synthetically designed mutualism},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2022},
+Volume = {45},
+Number = {9},
+Pages = {1539-1546},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1007/s00449-022-02762-4},
+EarlyAccessDate = {AUG 2022},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {Metabolic engineering; Flux balance analysis; Mutualistic co-culture},
+Keywords-Plus = {ESCHERICHIA-COLI; KNOCKOUT STRATEGIES; EVOLUTION; MODELS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Shimizu, Hiroshi/C-3688-2017
+ },
+ORCID-Numbers = {Shimizu, Hiroshi/0000-0002-8986-0861
+ Toya, Yoshihiro/0000-0001-9670-6961},
+Times-Cited = {4},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000836490900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000836651200072,
+Author = {Carlsen, J. and Henriksen, H. H. and de Mas, I. Marin and Johansson, I,
+ P.},
+Title = {An explorative metabolomic analysis of the endothelium in pulmonary
+ hypertension},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2022},
+Volume = {12},
+Number = {1},
+Month = {AUG 2},
+Type = {Article},
+DOI = {10.1038/s41598-022-17374-x},
+Article-Number = {13284},
+ISSN = {2045-2322},
+Keywords-Plus = {SIGNALING CONTRIBUTES; DYSFUNCTION; MODELS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Johansson, Pär/GQB-1032-2022
+ },
+ORCID-Numbers = {Johansson, Pär/0000-0001-9778-5964
+ Hee Henriksen, Hanne/0000-0003-1323-9718},
+Times-Cited = {2},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000836651200072},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000834667600001,
+Author = {Cetin, Handan and Cakar, Zeynep Petek and Ulgen, Kutlu O.},
+Title = {Understanding the adaptive laboratory evolution of multiple
+ stress-resistant yeast strains by genome-scale modeling},
+Journal = {YEAST},
+Year = {2022},
+Volume = {39},
+Number = {8},
+Pages = {449-465},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1002/yea.3806},
+EarlyAccessDate = {AUG 2022},
+ISSN = {0749-503X},
+EISSN = {1097-0061},
+Keywords = {differential expression analysis; evolutionary engineering; flux balance
+ analysis; genome-scale metabolic modeling; Saccharomyces cerevisiae;
+ systems biology},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE;
+ GENE; RECONSTRUCTION; EXPRESSION; BIOSYNTHESIS; LOCALIZATION;
+ MAINTENANCE; INTEGRATION; IMPROVEMENT},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Microbiology; Mycology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Microbiology; Mycology},
+ResearcherID-Numbers = {Cakar, Z. Petek/A-6152-2019},
+ORCID-Numbers = {Cakar, Z. Petek/0000-0002-2278-3670},
+Times-Cited = {0},
+Journal-ISO = {Yeast},
+Unique-ID = {WOS:000834667600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000846649200001,
+Author = {Cheawchanlertfa, Pattsarun and Chitcharoen, Suwalak and Raethong, Nachon
+ and Liu, Qing and Chumnanpuen, Pramote and Soommat, Panyawarin and Song,
+ Yuanda and Koffas, Mattheos and Laoteng, Kobkul and Vongsangnak, Wanwipa},
+Title = {Enhancing Genome-Scale Model by Integrative Exometabolome and
+ Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid
+ Biosynthetic Capability of Cordyceps militaris},
+Journal = {JOURNAL OF FUNGI},
+Year = {2022},
+Volume = {8},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.3390/jof8080887},
+Article-Number = {887},
+EISSN = {2309-608X},
+Keywords = {Cordyceps militaris; genome-scale metabolic model; sphingolipid;
+ metabolic footprinting; metabolic responses; transcriptome},
+Keywords-Plus = {MEDICINAL MUSHROOM; METABOLITES; METLIN},
+Research-Areas = {Microbiology; Mycology},
+Web-of-Science-Categories = {Microbiology; Mycology},
+ResearcherID-Numbers = {Raethong, Nachon/E-3130-2016
+ },
+ORCID-Numbers = {Raethong, Nachon/0000-0003-4442-3411
+ Cheawchanlertfa, Pattsarun/0000-0002-0157-4255
+ Koffas, Mattheos/0000-0002-1405-0565
+ Song, Yuanda/0000-0002-8565-6724
+ laoteng, kobkul/0000-0002-7263-4892
+ Chumnanpuen, Pramote/0000-0003-3072-1733},
+Times-Cited = {1},
+Journal-ISO = {J. Fungi},
+Unique-ID = {WOS:000846649200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000847801200009,
+Author = {Choudhury, Subham and Moret, Michael and Salvy, Pierre and Weilandt,
+ Daniel and Hatzimanikatis, Vassily and Miskovic, Ljubisa},
+Title = {Reconstructing Kinetic Models for Dynamical Studies of Metabolism using
+ Generative Adversarial Networks},
+Journal = {NATURE MACHINE INTELLIGENCE},
+Year = {2022},
+Volume = {4},
+Number = {8},
+Pages = {710+},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1038/s42256-022-00519-y},
+EISSN = {2522-5839},
+Keywords-Plus = {UNCERTAINTY; CONSTRAINT; COLI},
+Research-Areas = {Computer Science},
+Web-of-Science-Categories = {Computer Science, Artificial Intelligence; Computer Science,
+ Interdisciplinary Applications},
+ResearcherID-Numbers = {Hatzimanikatis, Vassily/G-6505-2010
+ Miskovic, Ljubisa/E-8927-2012
+ },
+ORCID-Numbers = {Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Miskovic, Ljubisa/0000-0001-7333-8211
+ Moret, Michael/0000-0002-8672-3386
+ Weilandt, Daniel Robert/0000-0002-0556-8485},
+Times-Cited = {6},
+Journal-ISO = {Nat. Mach. Intell.},
+Unique-ID = {WOS:000847801200009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000859901800003,
+Author = {Dvoretsky, D. S. and Temnov, M. S. and Markin, V, I. and Ustinskaya, V,
+ Ya and Es'kova, M. A.},
+Title = {Problems in the Development of Efficient Biotechnology for the Synthesis
+ of Valuable Components from Microalgae Biomass},
+Journal = {THEORETICAL FOUNDATIONS OF CHEMICAL ENGINEERING},
+Year = {2022},
+Volume = {56},
+Number = {4},
+Pages = {425-439},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1134/S0040579522040224},
+ISSN = {0040-5795},
+EISSN = {1608-3431},
+Keywords = {microalgae; process intensification; energy- and resource-saving
+ technologies; computer modeling; bioeconomics},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; BIODIESEL PRODUCTION; LIPID EXTRACTION; CELL
+ DISRUPTION; FATTY-ACIDS; RECOVERY; GROWTH; CYANOBACTERIAL; OILS},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Temnov, Mikhail Sergeevich/K-5320-2015
+ Dvoretsky, Dmitry/L-5613-2015},
+ORCID-Numbers = {Temnov, Mikhail Sergeevich/0000-0003-2110-1305
+ Ustinskaa, Ana/0000-0001-8642-8558
+ Dvoretsky, Dmitry/0000-0002-4352-810X},
+Times-Cited = {0},
+Journal-ISO = {Theor. Found. Chem. Eng.},
+Unique-ID = {WOS:000859901800003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000847011500001,
+Author = {Kishk, Ali and Pacheco, Maria Pires and Heurtaux, Tony and Sinkkonen,
+ Lasse and Pang, Jun and Fritah, Sabrina and Niclou, Simone P. and
+ Sauter, Thomas},
+Title = {Review of Current Human Genome-Scale Metabolic Models for Brain Cancer
+ and Neurodegenerative Diseases},
+Journal = {CELLS},
+Year = {2022},
+Volume = {11},
+Number = {16},
+Month = {AUG},
+Type = {Review},
+DOI = {10.3390/cells11162486},
+Article-Number = {2486},
+EISSN = {2073-4409},
+Keywords = {brain metabolism; metabolic modelling; glioma; neurodegenerative
+ diseases; astrocyte; neuron},
+Keywords-Plus = {CENTRAL-NERVOUS-SYSTEM; GLOBAL RECONSTRUCTION; NETWORK; MICROGLIA;
+ ENERGY; CELLS; OLIGODENDROCYTES; PHYSIOLOGY; EXPRESSION; LANDSCAPE},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ Sinkkonen, Lasse/AAL-7906-2021
+ Niclou, Simone/P-2304-2018},
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Sinkkonen, Lasse/0000-0002-4223-3027
+ Pang, Jun/0000-0002-4521-4112
+ Sauter, Thomas/0000-0001-8225-2954
+ Niclou, Simone/0000-0002-3417-9534},
+Times-Cited = {1},
+Journal-ISO = {Cells},
+Unique-ID = {WOS:000847011500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000828817300001,
+Author = {Huss, Sebastian and Judd, Rika Siedah and Koper, Kaan and Maeda, Hiroshi
+ A. and Nikoloski, Zoran},
+Title = {An automated workflow that generates atom mappings for large-scale
+ metabolic models and its application to Arabidopsis thaliana},
+Journal = {PLANT JOURNAL},
+Year = {2022},
+Volume = {111},
+Number = {5},
+Pages = {1486-1500},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1111/tpj.15903},
+EarlyAccessDate = {JUL 2022},
+ISSN = {0960-7412},
+EISSN = {1365-313X},
+Keywords = {atom mapping; genome-scale metabolic model; isotopic labeling; metabolic
+ flux analysis; technical advance},
+Keywords-Plus = {FLUX ANALYSIS; NETWORKS; CONSISTENT; RESOURCE; CELLS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ORCID-Numbers = {Maeda, Hiroshi/0000-0003-0246-694X
+ Nikoloski, Zoran/0000-0003-2671-6763
+ Huss, Sebastian/0000-0003-0712-2986},
+Times-Cited = {5},
+Journal-ISO = {Plant J.},
+Unique-ID = {WOS:000828817300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000824243700001,
+Author = {Ye, Chao and Wei, Xinyu and Shi, Tianqiong and Sun, Xiaoman and Xu, Nan
+ and Gao, Cong and Zou, Wei},
+Title = {Genome-scale metabolic network models: from first-generation to
+ next-generation},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2022},
+Volume = {106},
+Number = {13-16},
+Pages = {4907-4920},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1007/s00253-022-12066-y},
+EarlyAccessDate = {JUL 2022},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Genome-scale metabolic model; Phenotype prediction; Metabolic
+ engineering; Biological mechanisms; Biomarkers; Drug targets},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; KNOCKOUT STRATEGIES; GLOBAL RECONSTRUCTION;
+ FRAMEWORK; OPTIMIZATION; CONSTRAINTS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ye, Chao/HGD-3564-2022
+ Gao, Cong/AAB-4849-2022},
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Gao, Cong/0000-0001-8505-2026},
+Times-Cited = {8},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000824243700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000824697600001,
+Author = {Balzerani, Francesco and Hinojosa-Nogueira, Daniel and Cendoya, Xabier
+ and Blasco, Telmo and Perez-Burillo, Sergio and Apaolaza, Inigo and
+ Francino, M. Pilar and Rufian-Henares, Jose Angel and Planes, Francisco
+ J.},
+Title = {Prediction of degradation pathways of phenolic compounds in the human
+ gut microbiota through enzyme promiscuity methods},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2022},
+Volume = {8},
+Number = {1},
+Month = {JUL 12},
+Type = {Article},
+DOI = {10.1038/s41540-022-00234-9},
+Article-Number = {24},
+EISSN = {2056-7189},
+Keywords-Plus = {ANTIOXIDANT ACTIVITY; DIETARY POLYPHENOLS; METABOLISM; CHEMISTRY;
+ DESIGN; FRUITS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Apaolaza, Iñigo/T-6236-2017
+ Francino, M.Pilar/H-9090-2015
+ Perez-Burillo, Sergio/F-4048-2018
+ Planes, Francisco J/H-3341-2013
+ Rufian-Henares, Jose Angel/K-4935-2014
+ },
+ORCID-Numbers = {Apaolaza, Iñigo/0000-0002-8961-4513
+ Francino, M.Pilar/0000-0002-4510-5653
+ Perez-Burillo, Sergio/0000-0001-6398-7496
+ Blasco, Telmo/0000-0001-7819-8668
+ Planes, Francisco J/0000-0003-1155-3105
+ Rufian-Henares, Jose Angel/0000-0002-1428-4353
+ Balzerani, Francesco/0000-0002-5608-5766
+ Hinojosa-Nogueira, Daniel/0000-0002-2604-3303},
+Times-Cited = {5},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000824697600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000827502800002,
+Author = {Hong, Jong Kwang and Choi, Dong-Hyuk and Park, Seo-Young and Silberberg,
+ Yaron R. and Shozui, Fumi and Nakamura, Eiji and Kayahara, Takashi and
+ Lee, Dong-Yup},
+Title = {Data-driven and model-guided systematic framework for media development
+ in CHO cell culture},
+Journal = {METABOLIC ENGINEERING},
+Year = {2022},
+Volume = {73},
+Pages = {114-123},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2022.07.003},
+EarlyAccessDate = {JUL 2022},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Media development; CHO cells; Multivariate data analysis; Coenzyme q10;
+ Genome-scale metabolic model; Mammalian systems biotechnology},
+Keywords-Plus = {OPTIMIZATION; METABOLISM; QUALITY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Choi, Donghyuk/ABA-4685-2021
+ Lee, Dong-Yup/D-6650-2011
+ },
+ORCID-Numbers = {Lee, Dong-Yup/0000-0003-0901-708X
+ Park, Seo-Young/0000-0001-6140-412X},
+Times-Cited = {6},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000827502800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000829832300001,
+Author = {Ng, Rachel H. and Lee, Jihoon W. and Baloni, Priyanka and Diener,
+ Christian and Heath, James R. and Su, Yapeng},
+Title = {Constraint-Based Reconstruction and Analyses of Metabolic Models:
+ Open-Source Python Tools and Applications to Cancer},
+Journal = {FRONTIERS IN ONCOLOGY},
+Year = {2022},
+Volume = {12},
+Month = {JUL 7},
+Type = {Review},
+DOI = {10.3389/fonc.2022.914594},
+Article-Number = {914594},
+ISSN = {2234-943X},
+Keywords = {cancer; metabolism; constraint-based modeling; genome-scale metabolic
+ models; systems biology; omics; python; single-cell analysis},
+Keywords-Plus = {THERMODYNAMICALLY INFEASIBLE LOOPS; FLUX BALANCE ANALYSIS; HIT-AND-RUN;
+ GLOBAL RECONSTRUCTION; SIGNALING DYNAMICS; ESCHERICHIA-COLI; NETWORK;
+ EXPRESSION; PREDICTION; PATHWAYS},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ResearcherID-Numbers = {Diener, Christian/X-9574-2019},
+ORCID-Numbers = {Diener, Christian/0000-0002-7476-0868},
+Times-Cited = {0},
+Journal-ISO = {Front. Oncol.},
+Unique-ID = {WOS:000829832300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000827436100002,
+Author = {Baez, Antonino and Sharma, Ashish K. and Bryukhanov, Andrey and
+ Anderson, Eric D. and Rudack, Leba and Olivares-Hernandez, Roberto and
+ Quan, David and Shiloach, Joseph},
+Title = {Iron availability enhances the cellular energetics of aerobic
+ Escherichia coli cultures while upregulating anaerobic respiratory
+ chains},
+Journal = {NEW BIOTECHNOLOGY},
+Year = {2022},
+Volume = {71},
+Pages = {11-20},
+Month = {NOV 25},
+Type = {Article},
+DOI = {10.1016/j.nbt.2022.06.004},
+EarlyAccessDate = {JUL 2022},
+ISSN = {1871-6784},
+EISSN = {1876-4347},
+Keywords = {Iron limitation; Carbon flux distribution; Chemostat; Over oxygenation},
+Keywords-Plus = {RYHB SMALL RNA; HYDROGEN-PEROXIDE; GROWTH-RATE; EXPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Brioukhanov, Andrey L/B-3746-2013},
+ORCID-Numbers = {Brioukhanov, Andrey L/0000-0003-1807-297X},
+Times-Cited = {1},
+Journal-ISO = {New Biotech.},
+Unique-ID = {WOS:000827436100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000819858600043,
+Author = {Tomi-Andrino, Claudio and Pandele, Alina and Winzer, Klaus and King,
+ John and Rahman, Ruman and Kim, Dong-Hyun},
+Title = {Metabolic modeling-based drug repurposing in Glioblastoma},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2022},
+Volume = {12},
+Number = {1},
+Month = {JUL 1},
+Type = {Article},
+DOI = {10.1038/s41598-022-14721-w},
+Article-Number = {11189},
+ISSN = {2045-2322},
+Keywords-Plus = {CELL; PROLIFERATION; CANCER; DISCOVERY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {King, John/0000-0002-6228-8375
+ Rahman, Ruman/0000-0002-6541-9983},
+Times-Cited = {4},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000819858600043},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001043210000001,
+Author = {Domenzain, Ivan and Sanchez, Benjamin and Anton, Mihail and Kerkhoven,
+ Eduard J. and Millan-Oropeza, Aaron and Henry, Celine and Siewers,
+ Verena and Morrissey, John P. and Sonnenschein, Nikolaus and Nielsen,
+ Jens},
+Title = {Reconstruction of a catalogue of genome-scale metabolic models with
+ enzymatic constraints using GECKO 2.0},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2022},
+Volume = {13},
+Number = {1},
+Month = {JUN 30},
+Type = {Article},
+DOI = {10.1038/s41467-022-31421-1},
+Article-Number = {3766},
+EISSN = {2041-1723},
+Keywords-Plus = {ESCHERICHIA-COLI; ACID PRODUCTION; BALANCE; RESOURCE; SEQUENCE; PROTEIN;
+ YEAST},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Anton, Mihail/GXH-0002-2022
+ Domenzain, Ivan/HCI-9542-2022
+ Nielsen, Jens Bo/C-7632-2015
+ Sonnenschein, Nikolaus/F-6853-2012
+ Nielsen, Jens/Q-1347-2017
+ Kerkhoven, Eduard/H-2072-2014},
+ORCID-Numbers = {Anton, Mihail/0000-0002-7753-9042
+ Domenzain, Ivan/0000-0002-5322-2040
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Siewers, Verena/0000-0002-9502-9804
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Henry, Celine/0000-0002-2355-1791
+ Nielsen, Jens/0000-0002-9955-6003
+ Morrissey, John/0000-0001-7960-2001
+ Sanchez, Benjamin/0000-0001-6093-4110
+ Kerkhoven, Eduard/0000-0002-3593-5792},
+Times-Cited = {26},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:001043210000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000817857100001,
+Author = {Wagner, Andreas},
+Title = {Competition for nutrients increases invasion resistance during assembly
+ of microbial communities},
+Journal = {MOLECULAR ECOLOGY},
+Year = {2022},
+Volume = {31},
+Number = {15},
+Pages = {4188-4203},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1111/mec.16565},
+EarlyAccessDate = {JUN 2022},
+ISSN = {0962-1083},
+EISSN = {1365-294X},
+Keywords = {assembly network; attractor; community assembly; competition;
+ cross-feeding; invasion resistance},
+Keywords-Plus = {CONTINUOUS-CULTURE SYSTEM; PLANT INVASIONS; TROPHIC INTERACTIONS;
+ IN-VITRO; METABOLISM; PATTERNS; DIVERSITY; GRASSLAND; MODELS; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Environmental Sciences \& Ecology;
+ Evolutionary Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Ecology; Evolutionary Biology},
+Times-Cited = {3},
+Journal-ISO = {Mol. Ecol.},
+Unique-ID = {WOS:000817857100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000823152500046,
+Author = {Cesur, Muberra Fatma and Cakir, Tunahan and Pir, Pinar},
+Title = {Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network
+ Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {3},
+Month = {JUN 28},
+Type = {Article},
+DOI = {10.1128/msystems.01347-21},
+Article-Number = {01347-21},
+ISSN = {2379-5077},
+Keywords = {RNA-seq; ATAC-seq; genome-scale metabolic network; flux balance
+ analysis; Saccharomyces cerevisiae; yeast metabolic cycle},
+Keywords-Plus = {CELL-CYCLE; SACCHAROMYCES-CEREVISIAE; CHROMATIN; TRANSCRIPTION; GROWTH;
+ ENTRY; RECONSTRUCTION; EPIGENOME; PHASE; STATE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Cesur, Müberra Fatma/AHC-2805-2022
+ Cakir, Tunahan/F-4523-2011},
+ORCID-Numbers = {Cesur, Müberra Fatma/0000-0003-2993-0634
+ Cakir, Tunahan/0000-0001-8262-4420},
+Times-Cited = {1},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000823152500046},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000819031500002,
+Author = {Li, Jingjing and Gou, Yifei and Yang, Jiarui and Zhao, Lingxuan and
+ Wang, Bin and Hao, Tong and Sun, Jinsheng},
+Title = {Genome-scale metabolic network model of Eriocheir sinensis
+ icrab4665 and nutritional requirement analysis},
+Journal = {BMC GENOMICS},
+Year = {2022},
+Volume = {23},
+Number = {1},
+Month = {JUN 28},
+Type = {Article},
+DOI = {10.1186/s12864-022-08698-z},
+Article-Number = {475},
+ISSN = {1471-2164},
+Keywords = {Genome-scale metabolic network(1); network analysis(2); biomass(3);
+ nutrient requirement(4); Eriocheir sinensis(5)},
+Keywords-Plus = {CHINESE MITTEN CRAB; AEROMONAS-HYDROPHILA; ERIOCHEIR-SINENSIS;
+ BACILLUS-SUBTILIS; GROWTH; GENE; RECONSTRUCTION; HEPATOPANCREAS;
+ RESISTANCE; EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Times-Cited = {0},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000819031500002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000817196600001,
+Author = {Suthers, Patrick F. and Maranas, Costas D.},
+Title = {Examining organic acid production potential and growth-coupled
+ strategies in Issatchenkia orientalis using constraint-based
+ modeling},
+Journal = {BIOTECHNOLOGY PROGRESS},
+Year = {2022},
+Volume = {38},
+Number = {5},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1002/btpr.3276},
+EarlyAccessDate = {JUN 2022},
+Article-Number = {e3276},
+ISSN = {8756-7938},
+EISSN = {1520-6033},
+Keywords = {constraint-based modeling; metabolic engineering; nonmodel yeast},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; KNOCKOUT STRATEGIES;
+ CHEMICAL PRODUCTION; GENERATION; LIGNOCELLULOSE; FERMENTATION;
+ OPTIMIZATION; FEASIBILITY; CONVERSION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Maranas, Costas D/A-4774-2011
+ },
+ORCID-Numbers = {Maranas, Costas D/0000-0002-1508-1398
+ Suthers, Patrick/0000-0002-5560-9986},
+Times-Cited = {2},
+Journal-ISO = {Biotechnol. Prog.},
+Unique-ID = {WOS:000817196600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000817299700003,
+Author = {Xia, Menglei and Wang, Di and Xia, Yiming and Shi, Haijiao and Tian,
+ Zhongyu and Zheng, Yu and Wang, Min},
+Title = {Oxidoreduction potential controlling for increasing the fermentability
+ of enzymatically hydrolyzed steam-exploded corn stover for butanol
+ production},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2022},
+Volume = {21},
+Number = {1},
+Month = {JUN 27},
+Type = {Article},
+DOI = {10.1186/s12934-022-01824-2},
+Article-Number = {130},
+EISSN = {1475-2859},
+Keywords = {Clostridium acetobutylicum; Steam-explosion; Fermentability;
+ Oxidoreduction potential controlling; Mechanism analysis},
+Keywords-Plus = {CLOSTRIDIUM-ACETOBUTYLICUM; N-BUTANOL; ETHANOL FERMENTATION;
+ ESCHERICHIA-COLI; SYSTEMS-ANALYSIS; ACETONE; TOLERANCE; MECHANISMS;
+ BUTYRATE; CULTURE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {0},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000817299700003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000815631000001,
+Author = {Feng, Jun and Guo, Xiaolong and Cai, Feifei and Fu, Hongxin and Wang,
+ Jufang},
+Title = {Model-based driving mechanism analysis for butyric acid production in
+ Clostridium tyrobutyricum},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS},
+Year = {2022},
+Volume = {15},
+Number = {1},
+Month = {JUN 25},
+Type = {Article},
+DOI = {10.1186/s13068-022-02169-z},
+Article-Number = {71},
+EISSN = {2731-3654},
+Keywords = {Clostridium tyrobutyricum; Butyrate; Genome-scale metabolic model;
+ Metabolic driving forces; Energy conversion; Hydrogenase},
+Keywords-Plus = {DELETED MUTANT; FERMENTATION; GENOME; ACETOBUTYLICUM; CONSTRUCTION;
+ TOLERANCE; PH},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Wang, Jufang/AAH-8068-2019},
+Times-Cited = {2},
+Journal-ISO = {Biotechnol. Biofuels Bioprod.},
+Unique-ID = {WOS:000815631000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000812063200003,
+Author = {Li, Feiran and Yuan, Le and Lu, Hongzhong and Li, Gang and Chen, Yu and
+ Engqvist, Martin K. M. and Kerkhoven, Eduard J. and Nielsen, Jens},
+Title = {Deep learning-based kcat prediction enables improved
+ enzyme-constrained model reconstruction},
+Journal = {NATURE CATALYSIS},
+Year = {2022},
+Volume = {5},
+Number = {8},
+Pages = {662+},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1038/s41929-022-00798-z},
+EarlyAccessDate = {JUN 2022},
+ISSN = {2520-1158},
+Keywords-Plus = {EVOLUTIONARY; METABOLISM; PERSPECTIVE; MUTAGENESIS; CAPACITY; CONTEXT;
+ FLUX},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Physical},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Kerkhoven, Eduard/P-2469-2019
+ Chen, Yu/AAL-3329-2020
+ Li, Feiran/GNP-2168-2022
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Chen, Yu/0000-0003-3326-9068
+ Li, Feiran/0000-0001-9155-5260
+ Nielsen, Jens/0000-0002-9955-6003
+ Yuan, Le/0000-0003-3317-9011},
+Times-Cited = {53},
+Journal-ISO = {Nat. Catal.},
+Unique-ID = {WOS:000812063200003},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000824457000003,
+Author = {Proffitt, Ceri and Bidkhori, Gholamreza and Lee, Sunjae and Tebani,
+ Abdellah and Mardinoglu, Adil and Uhlen, Mathias and Moyes, David L. and
+ Shoaie, Saeed},
+Title = {Genome-scale metabolic modelling of the human gut microbiome reveals
+ changes in the glyoxylate and dicarboxylate metabolism in metabolic
+ disorders},
+Journal = {ISCIENCE},
+Year = {2022},
+Volume = {25},
+Number = {7},
+Month = {JUL 15},
+Type = {Article},
+DOI = {10.1016/j.isci.2022.104513},
+EarlyAccessDate = {JUN 2022},
+Article-Number = {104513},
+EISSN = {2589-0042},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; CHAIN FATTY-ACIDS; SYSTEMS BIOLOGY; TARTARIC
+ ACID; DIET; METAGENOME; TARTRATE; ACETATE; PATHWAY; RISK},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Lee, Sunjae/H-9815-2019
+ Uhlen, Mathias/HPB-8445-2023
+ TEBANI, Abdellah/ABE-5140-2021
+ },
+ORCID-Numbers = {Lee, Sunjae/0000-0002-6428-5936
+ Uhlen, Mathias/0000-0002-4858-8056
+ TEBANI, Abdellah/0000-0002-8901-2678
+ Proffitt, Ceri/0000-0003-3820-735X
+ Shoaie, Saeed/0000-0001-5834-4533},
+Times-Cited = {5},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000824457000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000809346000002,
+Author = {Thanamit, Kulwadee and Hoerhold, Franziska and Oswald, Marcus and
+ Koenig, Rainer},
+Title = {Linear programming based gene expression model (LPM-GEM) predicts the
+ carbon source for Bacillus subtilis},
+Journal = {BMC BIOINFORMATICS},
+Year = {2022},
+Volume = {23},
+Number = {1},
+Month = {JUN 10},
+Type = {Article},
+DOI = {10.1186/s12859-022-04742-7},
+Article-Number = {226},
+ISSN = {1471-2105},
+Keywords = {Flux balance analysis; Mixed-integer linear programming; Bacillus
+ subtilis; Carbon source; Transcriptomics; Constraint-based modeling;
+ Thermodynamically infeasible loops},
+Keywords-Plus = {METABOLIC FLUX ANALYSIS; NETWORK; KEGG; PATHWAYS; REVEALS; BALANCE;
+ MALATE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+Times-Cited = {0},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000809346000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000824505000005,
+Author = {Islam, Mohammad Mazharul and Goertzen, Andrea and Singh, Pankaj K. and
+ Saha, Rajib},
+Title = {Exploring the metabolic landscape of pancreatic ductal adenocarcinoma
+ cells using genome-scale metabolic modeling},
+Journal = {ISCIENCE},
+Year = {2022},
+Volume = {25},
+Number = {6},
+Month = {JUN 17},
+Type = {Article},
+DOI = {10.1016/j.isci.2022.104483},
+EarlyAccessDate = {JUN 2022},
+Article-Number = {104483},
+EISSN = {2589-0042},
+Keywords-Plus = {GLUT1 GLUCOSE-TRANSPORTER; CONSTRAINT-BASED MODELS; GEMCITABINE
+ RESISTANCE; BETA-OXIDATION; ANNEXIN A3; TROGLITAZONE DERIVATIVES;
+ QUANTITATIVE PREDICTION; GLOBAL RECONSTRUCTION; GLUTAMINE-METABOLISM;
+ CELLULAR-METABOLISM},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Islam, Mohammad Mazharul/GWV-6127-2022
+ },
+ORCID-Numbers = {Islam, Mohammad Mazharul/0000-0002-9745-0344
+ Singh, Pankaj/0000-0001-8903-0131},
+Times-Cited = {2},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000824505000005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000805202900013,
+Author = {Wu, Shengbo and Feng, Jie and Liu, Chunjiang and Wu, Hao and Qiu, Zekai
+ and Ge, Jianjun and Sun, Shuyang and Hong, Xia and Li, Yukun and Wang,
+ Xiaona and Yang, Aidong and Guo, Fei and Qiao, Jianjun},
+Title = {Machine learning aided construction of the quorum sensing communication
+ network for human gut microbiota},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2022},
+Volume = {13},
+Number = {1},
+Month = {JUN 2},
+Type = {Article},
+DOI = {10.1038/s41467-022-30741-6},
+Article-Number = {3079},
+EISSN = {2041-1723},
+Keywords-Plus = {PSEUDOMONAS-AERUGINOSA; PROTEIN-STRUCTURE; BACTERIA; DATABASE; INDOLE;
+ SIGNAL; REGULATORS; DIVERSITY; SYSTEMS; MOTIFS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Li, Yukun/J-2135-2015
+ Yang, Aidong/M-2887-2013
+ Wu, Shengbo/GRK-0088-2022
+ LI, Xiang/JBJ-8387-2023
+ },
+ORCID-Numbers = {Yang, Aidong/0000-0001-7771-6777
+ Wu, Shengbo/0000-0001-7497-2935
+ xiaona, wang/0000-0001-9064-3349},
+Times-Cited = {19},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000805202900013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000911874300021,
+Author = {Law, Richard C. and Lakhani, Aliya and O'Keeffe, Samantha and Ersan,
+ Sevcan and Park, Junyoung O.},
+Title = {Integrative metabolic flux analysis reveals an indispensable dimension
+ of phenotypes},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2022},
+Volume = {75},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1016/j.copbio.2022.102701},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {MITOCHONDRIAL-FUNCTION; TOOLS; DIET},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Erşan, Sevcan/I-1404-2019
+ },
+ORCID-Numbers = {Erşan, Sevcan/0000-0002-5334-1955
+ Park, Jun/0000-0001-9869-8993
+ Law, Richard/0000-0002-4944-9306
+ O'Keeffe, Samantha/0009-0009-8884-6708},
+Times-Cited = {3},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000911874300021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000809611300001,
+Author = {Legon, Laurence and Corre, Christophe and Bates, Declan G. and Mannan,
+ Ahmad A.},
+Title = {gcFront: a tool for determining a Pareto front of growth-coupled cell
+ factory designs},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Month = {2022 JUN 1},
+Type = {Article; Early Access},
+DOI = {10.1093/bioinformatics/btac376},
+EarlyAccessDate = {JUN 2022},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {KNOCKOUT STRATEGIES; BIOCHEMICAL SYSTEMS; OPTIMIZATION; ETHANOL},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Corre, Christophe/J-2896-2013},
+ORCID-Numbers = {Corre, Christophe/0000-0002-4292-9315},
+Times-Cited = {2},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000809611300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000911874300031,
+Author = {Liao, Xiaoping and Ma, Hongwu and Tang, Yinjie J.},
+Title = {Artificial intelligence: a solution to involution of
+ design-build-test-learn cycle},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2022},
+Volume = {75},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1016/j.copbio.2022.102712},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {PREDICTION; OPTIMIZATION; NETWORKS; WORKFLOW; ENZYME},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+Times-Cited = {6},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000911874300031},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000816045300001,
+Author = {Xu, Feng and Lu, Ju and Ke, Xiang and Shao, Minghao and Huang, Mingzhi
+ and Chu, Ju},
+Title = {Reconstruction of the Genome-Scale Metabolic Model of
+ Saccharopolyspora erythraea and Its Application in the
+ Overproduction of Erythromycin},
+Journal = {METABOLITES},
+Year = {2022},
+Volume = {12},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3390/metabo12060509},
+Article-Number = {509},
+EISSN = {2218-1989},
+Keywords = {genome-scale metabolic model; Saccharopolyspora erythraea; iJL1426;
+ erythromycin production; n-propanol; process optimization},
+Keywords-Plus = {INDUSTRIAL STRAIN; FEED RATE; ENHANCEMENT; PROPANOL; BIOSYNTHESIS;
+ IMPROVEMENT; FATE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {liu, shanshan/JPA-0852-2023
+ Xu, Feng/AAK-2966-2021
+ Wang, Shan/JPX-1098-2023},
+ORCID-Numbers = {Xu, Feng/0000-0001-5907-5152
+ },
+Times-Cited = {4},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000816045300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000804921800024,
+Author = {Xu, Yameng and Wang, Xinglong and Zhang, Chenyang and Zhou, Xuan and Xu,
+ Xianhao and Han, Luyao and Lv, Xueqin and Liu, Yanfeng and Liu, Song and
+ Li, Jianghua and Du, Guocheng and Chen, Jian and Ledesma-Amaro, Rodrigo
+ and Liu, Long},
+Title = {De novo biosynthesis of rubusoside and rebaudiosides in engineered
+ yeasts},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2022},
+Volume = {13},
+Number = {1},
+Month = {JUN 1},
+Type = {Article},
+DOI = {10.1038/s41467-022-30826-2},
+Article-Number = {3040},
+EISSN = {2041-1723},
+Keywords-Plus = {TRANSCRIPTION FACTOR; GENE-EXPRESSION; ACID; PATHWAY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {li, jianghua/GXG-4735-2022},
+Times-Cited = {27},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000804921800024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000800766400022,
+Author = {Li, Feiran and Chen, Yu and Qi, Qi and Wang, Yanyan and Yuan, Le and
+ Huang, Mingtao and Elsemman, Ibrahim E. and Feizi, Amir and Kerkhoven,
+ Eduard J. and Nielsen, Jens},
+Title = {Improving recombinant protein production by yeast through genome-scale
+ modeling using proteome constraints},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2022},
+Volume = {13},
+Number = {1},
+Month = {MAY 27},
+Type = {Article},
+DOI = {10.1038/s41467-022-30689-7},
+Article-Number = {2969},
+EISSN = {2041-1723},
+Keywords-Plus = {ENDOPLASMIC-RETICULUM STRESS; SACCHAROMYCES-CEREVISIAE; PICHIA-PASTORIS;
+ HEXOSE TRANSPORTER; REGULATORY MECHANISMS; MATHEMATICAL-MODEL; HUMAN
+ HEMOGLOBIN; HXT GENES; SECRETION; GLUCOSE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Li, Feiran/GNP-2168-2022
+ Kerkhoven, Eduard/P-2469-2019
+ zhang, luyu/JJC-4227-2023
+ Nielsen, Jens Bo/C-7632-2015
+ Chen, Yu/AAL-3329-2020
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Li, Feiran/0000-0001-9155-5260
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Chen, Yu/0000-0003-3326-9068
+ Yuan, Le/0000-0003-3317-9011
+ Nielsen, Jens/0000-0002-9955-6003
+ feizi, amir/0000-0002-9627-4190
+ QI, QI/0000-0002-0582-1962
+ Huang, Mingtao/0000-0003-2359-1010
+ Elsemman, Ibrahim/0000-0002-2720-8245},
+Times-Cited = {8},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000800766400022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000848587100001,
+Author = {Dadashi, Andisheh and Martinez, Derek},
+Title = {Flux balance network expansion predicts stage-specific human
+ peri\_implantation embryo metabolism},
+Journal = {JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY},
+Year = {2022},
+Volume = {20},
+Number = {04},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1142/S021972002250010X},
+EarlyAccessDate = {MAY 2022},
+ISSN = {0219-7200},
+EISSN = {1757-6334},
+Keywords = {Network expansion; flux balance analysis; metabolic network; human
+ embryo},
+Keywords-Plus = {INNER CELL MASS; ESCHERICHIA-COLI; BIOCONDUCTOR PACKAGE; STEM-CELLS;
+ TROPHECTODERM; MOUSE; BLASTOCYST; GROWTH; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Computer Science; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Computer Science, Interdisciplinary
+ Applications; Mathematical \& Computational Biology},
+Times-Cited = {1},
+Journal-ISO = {J. Bioinform. Comput. Biol.},
+Unique-ID = {WOS:000848587100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000969749600006,
+Author = {Kocabas, Kadir and Arif, Alina and Uddin, Reaz and Cakir, Tunahan},
+Title = {Dual transcriptome based reconstruction of Salmonella-human integrated
+ metabolic network to screen potential drug targets},
+Journal = {PLOS ONE},
+Year = {2022},
+Volume = {17},
+Number = {5},
+Month = {MAY 24},
+Type = {Article},
+DOI = {10.1371/journal.pone.0268889},
+Article-Number = {e0268889},
+ISSN = {1932-6203},
+Keywords-Plus = {ENTERICA SEROVAR TYPHIMURIUM; WEB SERVER; IDENTIFICATION; BIOSYNTHESIS;
+ INHIBITORS; PATHWAYS; KINASE; GENES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Cakir, Tunahan/F-4523-2011
+ Uddin, Reaz/I-5673-2017
+ },
+ORCID-Numbers = {Cakir, Tunahan/0000-0001-8262-4420
+ Uddin, Reaz/0000-0002-9928-4482
+ KOCABAS, KADIR/0000-0002-7898-8552},
+Times-Cited = {3},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000969749600006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000805370400009,
+Author = {Bourgade, Barbara and Humphreys, Christopher M. and Millard, James and
+ Minton, Nigel P. and Islam, M. Ahsanul},
+Title = {Design, Analysis, and Implementation of a Novel Biochemical Pathway for
+ Ethylene Glycol Production in Clostridium autoethanogenum},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2022},
+Volume = {11},
+Number = {5},
+Pages = {1790-1800},
+Month = {MAY 20},
+Type = {Article},
+DOI = {10.1021/acssynbio.1c00624},
+ISSN = {2161-5063},
+Keywords = {ethylene glycol; synthetic pathway; metabolic engineering; synthetic
+ biology; Clostridium autoethanogenum},
+Keywords-Plus = {THERMODYNAMICS; ETHANOL; CARBON; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ORCID-Numbers = {Millard, James/0000-0001-9026-4453
+ Islam, M. Ahsanul/0000-0001-9585-6263
+ Minton, Nigel/0000-0002-9277-1261
+ Bourgade, Barbara/0009-0000-5792-1052},
+Times-Cited = {3},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000805370400009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000791434200001,
+Author = {Mueller, Tobias and Schick, Simon and Beck, Jonathan and Sprenger, Georg
+ and Takors, Ralf},
+Title = {Synthetic mutualism in engineered E. coli mutant strains as
+ functional basis for microbial production consortia},
+Journal = {ENGINEERING IN LIFE SCIENCES},
+Year = {2023},
+Volume = {23},
+Number = {1, SI},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1002/elsc.202100158},
+EarlyAccessDate = {MAY 2022},
+ISSN = {1618-0240},
+EISSN = {1618-2863},
+Keywords = {metabolic engineering; mutual auxotrophic dependency; spatially linked
+ bioreactors; synthetic co-culture; tryptophan},
+Keywords-Plus = {ESCHERICHIA-COLI; METABOLIC PATHWAY; COCULTURE; DESIGN; OPTIMIZATION;
+ TRYPTOPHAN; INDUCTION; K-12},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {1},
+Journal-ISO = {Eng. Life Sci.},
+Unique-ID = {WOS:000791434200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000790940000026,
+Author = {Kellman, Benjamin P. and Richelle, Anne and Yang, Jeong-Yeh and Chapla,
+ Digantkumar and Chiang, Austin W. T. and Najera, Julia and Bao, Bokan
+ and Koga, Natalia and Mohammad, Mahmoud A. and Bruntse, Anders Bech and
+ Haymond, Morey W. and Moremen, Kelley W. and Bode, Lars and Lewis,
+ Nathan E. and Liang, Chenguang and Furst, Annalee},
+Title = {Elucidating Human Milk Oligosaccharide biosynthetic genes through
+ network-based multi-omics integration},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2022},
+Volume = {13},
+Number = {1},
+Month = {MAY 4},
+Type = {Article},
+DOI = {10.1038/s41467-022-29867-4},
+Article-Number = {2455},
+EISSN = {2041-1723},
+Keywords-Plus = {MOLECULAR-CLONING; EXPRESSION CLONING; CHEMOENZYMATIC SYNTHESIS;
+ N-ACETYLGALACTOSAMINE; MATHEMATICAL-MODEL; SECRETOR GENE; CORE 2; LEWIS;
+ GLYCOSYLATION; MEMBERS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ Mohammad, Mahmoud/GNO-9940-2022
+ Moremen, Kelley/AAD-4661-2019
+ Liang, Chen/HNP-5916-2023
+ liang, chen/HGB-7036-2022},
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Mohammad, Mahmoud/0000-0002-6535-5529
+ },
+Times-Cited = {16},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000790940000026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000815258700018,
+Author = {Chen, Ruibing and Gao, Jiaoqi and Yu, Wei and Chen, Xianghui and Zhai,
+ Xiaoxin and Chen, Yu and Zhang, Lei and Zhou, Yongjin J.},
+Title = {Engineering cofactor supply and recycling to drive phenolic acid
+ biosynthesis in yeast},
+Journal = {NATURE CHEMICAL BIOLOGY},
+Year = {2022},
+Volume = {18},
+Number = {5},
+Pages = {520+},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1038/s41589-022-01014-6},
+ISSN = {1552-4450},
+EISSN = {1552-4469},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; S-ADENOSYLMETHIONINE; BACILLUS-SUBTILIS;
+ ESCHERICHIA-COLI; PHOSPHATIDYLETHANOLAMINE METHYLTRANSFERASE;
+ TRANSCRIPTION ACTIVATION; RIBOFLAVIN BIOSYNTHESIS; MICROBIAL SYNTHESIS;
+ L-HOMOCYSTEINE; CAFFEIC ACID},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Zhou, Yongjin/D-5911-2018
+ Chen, Ruibing/IZD-5195-2023
+ YU, Wei/HTP-9667-2023
+ Chen, Yu/AAL-3329-2020
+ li, jian/IAQ-2794-2023},
+ORCID-Numbers = {Zhou, Yongjin/0000-0002-2369-3079
+ Chen, Ruibing/0000-0002-7933-3670
+ Chen, Yu/0000-0003-3326-9068
+ },
+Times-Cited = {39},
+Journal-ISO = {Nat. Chem. Biol.},
+Unique-ID = {WOS:000815258700018},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000795321000001,
+Author = {Nam, Seungyoon and Lee, Yongmin},
+Title = {Genome-Scale Metabolic Model Analysis of Metabolic Differences between
+ Lauren Diffuse and Intestinal Subtypes in Gastric Cancer},
+Journal = {CANCERS},
+Year = {2022},
+Volume = {14},
+Number = {9},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/cancers14092340},
+Article-Number = {2340},
+EISSN = {2072-6694},
+Keywords = {genome-scale metabolic model; transcriptome; metabolism; gastric cancer},
+Keywords-Plus = {HEPATOCELLULAR-CARCINOMA; VITAMIN-B6 METABOLISM; POOR-PROGNOSIS;
+ PATHWAY; ACTIVATION; EXPRESSION; ADENOCARCINOMA; PROGRESSION; DISCOVERY;
+ SURVIVAL},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ResearcherID-Numbers = {Nam, Seungyoon/ACO-0914-2022},
+ORCID-Numbers = {Nam, Seungyoon/0000-0002-0966-7915},
+Times-Cited = {2},
+Journal-ISO = {Cancers},
+Unique-ID = {WOS:000795321000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000944354300005,
+Author = {Pearcy, Nicole and Garavaglia, Marco and Millat, Thomas and Gilbert,
+ James P. and Song, Yoseb A. and Hartman, Hassan and Woods, Craig R. and
+ Tomi-Andrino, Claudio and Reddy Bommareddy, Rajesh and Cho, Byung-Kwan
+ P. and Fell, David A. A. and Poolman, Mark D. and King, John R. A. and
+ Winzer, Klaus D. and Twycross, Jamie A. and Minton, Nigel P. D.},
+Title = {A genome-scale metabolic model of Cupriavidus necator H16
+ integrated with TraDIS and transcriptomic data reveals metabolic
+ insights for biotechnological applications},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2022},
+Volume = {18},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1010106},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {POLYHYDROXYBUTYRATE PRODUCTION; ESCHERICHIA-COLI; GENE; STRATEGIES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Cho, Byung-Kwan/C-1830-2011
+ King, julie/N-5157-2014
+ Bommareddy, Rajesh Reddy/A-2105-2019},
+ORCID-Numbers = {Millat, Thomas/0000-0002-5023-4142
+ Cho, Byung Kwan/0000-0003-4788-4184
+ Tomi-Andrino, Claudio/0000-0002-3611-2130
+ King, John/0000-0002-6228-8375
+ Hartman, Hassan/0000-0003-0019-1364
+ Garavaglia, Marco/0000-0003-0201-3289
+ Bommareddy, Rajesh Reddy/0000-0002-3071-3453},
+Times-Cited = {5},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000944354300005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000801868000001,
+Author = {Shirai, Tomokazu and Kondo, Akihiko},
+Title = {In Silico Design Strategies for the Production of Target Chemical
+ Compounds Using Iterative Single-Level Linear Programming Problems},
+Journal = {BIOMOLECULES},
+Year = {2022},
+Volume = {12},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/biom12050620},
+Article-Number = {620},
+EISSN = {2218-273X},
+Keywords = {FBA; metabolic model; optimization; AERITH},
+Keywords-Plus = {ESCHERICHIA-COLI; KNOCKOUT STRATEGIES; OPTIMIZATION; SUCCINATE;
+ EVOLUTION; ALANINE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Shirai, Tomokazu/C-7986-2017
+ },
+ORCID-Numbers = {Shirai, Tomokazu/0000-0002-8565-5895},
+Times-Cited = {0},
+Journal-ISO = {Biomolecules},
+Unique-ID = {WOS:000801868000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000788061300031,
+Author = {Ghadermazi, Parsa and Re, Angela and Ricci, Luca and Chan, Siu Hung
+ Joshua},
+Title = {Metabolic Engineering Interventions for Sustainable 2,3-Butanediol
+ Production in Gas-Fermenting Clostridium autoethanogenum},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {2},
+Month = {APR 26},
+Type = {Article},
+DOI = {10.1128/msystems.01111-21},
+Article-Number = {e01111-21},
+ISSN = {2379-5077},
+Keywords = {2, 3-butanediol; Clostridium autoethanogenum; circular economy; gas
+ fermentation; metabolic engineering},
+Keywords-Plus = {ENERGY-CONSERVATION; ETHANOL; PATHWAY; MODEL; FERMENTATION; LJUNGDAHLII;
+ ROBUSTNESS; COMPLEX; SYNGAS; ATP},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Ghadermazi, Parsa/JEO-9454-2023
+ RE, ANGELA/A-4767-2018
+ },
+ORCID-Numbers = {Ghadermazi, Parsa/0009-0005-4112-2105
+ RE, ANGELA/0000-0002-3179-6967
+ Ricci, Luca/0000-0002-0859-3352},
+Times-Cited = {2},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000788061300031},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000788061300011,
+Author = {Lopez-Lopez, Nahikari and San Leon, David and de Castro, Sonia and
+ Diez-Martinez, Roberto and Iglesias-Bexiga, Manuel and Jose Camarasa,
+ Maria and Menendez, Margarita and Nogales, Juan and Garmendia, Junkal},
+Title = {Interrogation of Essentiality in the Reconstructed Haemophilus
+ influenzae Metabolic Network Identifies Lipid Metabolism
+ Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP
+ Synthase Inhibitor},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {2},
+Month = {APR 26},
+Type = {Article},
+DOI = {10.1128/msystems.01459-21},
+Article-Number = {e01459-21},
+ISSN = {2379-5077},
+Keywords = {Haemophilus influenzae; airway infection; genome-scale metabolic model;
+ gene essentiality screening; fatty acid synthesis; FabH inhibition;
+ antimicrobials; preclinical evaluation},
+Keywords-Plus = {HOST-PATHOGEN INTERACTIONS; GENOME; RD; RESISTANCE; MODELS; ACID;
+ COMPETENCE; DISCOVERY; SYSTEMS; LIPOPOLYSACCHARIDE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ Menendez, Margarita/M-1795-2014
+ Garmendia, Juncal/G-4360-2011
+ de castro, sonia/E-7303-2012
+ },
+ORCID-Numbers = {Menendez, Margarita/0000-0002-3267-4443
+ Garmendia, Juncal/0000-0002-7440-2737
+ de castro, sonia/0000-0002-3838-6856
+ Nogales, Juan/0000-0002-4961-0833
+ San Leon Granado, David/0000-0001-8138-500X},
+Times-Cited = {3},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000788061300011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000788061300039,
+Author = {Villada, Juan C. and Duran, Maria F. and Lim, Chee Kent and Stein, Lisa
+ Y. and Lee, Patrick K. H.},
+Title = {Integrative Genome-Scale Metabolic Modeling Reveals Versatile Metabolic
+ Strategies for Methane Utilization in Methylomicrobium album BG8},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {2},
+Month = {APR 26},
+Type = {Article},
+DOI = {10.1128/msystems.00073-22},
+Article-Number = {e00073-22},
+ISSN = {2379-5077},
+Keywords = {methanotroph; methane oxidation; systems biology; integrative modeling;
+ flux balance analysis; fermentation; biotechnology},
+Keywords-Plus = {INITIAL BIOMASS DENSITY; ANAEROBIC OXIDATION; GROWTH; METHANOTROPHS;
+ METHYLOSINUS; FERMENTATION; CHEMICALS; KEGG},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Lee, Patrick K H/L-1844-2016
+ },
+ORCID-Numbers = {Lee, Patrick K H/0000-0003-0911-5317
+ Duran, Maria F./0000-0001-8598-0172
+ Villada Arteaga, Juan Camilo/0000-0003-2216-4279},
+Times-Cited = {1},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000788061300039},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000786571800001,
+Author = {Yeo, Hock Chuan and Park, Seo-Young and Tan, Tessa and Ng, Say K. and
+ Lakshmanan, Meiyappan and Lee, Dong-Yup},
+Title = {Combined multivariate statistical and flux balance analyses uncover
+ media bottlenecks to the growth and productivity of Chinese hamster
+ ovary cell cultures},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2022},
+Volume = {119},
+Number = {7},
+Pages = {1740-1754},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/bit.28104},
+EarlyAccessDate = {APR 2022},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {CHO cells; flux balance analysis; media reformulation; metabolic
+ bottlenecks; multivariate statistical analysis; systems biotechnology},
+Keywords-Plus = {CHO-CELLS; GLUTAMINE; METABOLISM; LACTATE; AMMONIA; GLUCOSE; PROTEIN;
+ IMPROVEMENT; EXPRESSION; APOPTOSIS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lee, Dong-Yup/D-6650-2011
+ Park, Seo-Young/AIC-1913-2022
+ },
+ORCID-Numbers = {Lee, Dong-Yup/0000-0003-0901-708X
+ Park, Seo-Young/0000-0001-6140-412X
+ Yeo, Hock Chuan/0000-0001-5176-8800},
+Times-Cited = {6},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000786571800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000783390300001,
+Author = {Ternes, Dominik and Tsenkova, Mina and Pozdeev, Vitaly Igorevich and
+ Meyers, Marianne and Koncina, Eric and Atatri, Sura and Schmitz, Martine
+ and Karta, Jessica and Schmoetten, Maryse and Heinken, Almut and
+ Rodriguez, Fabien and Delbrouck, Catherine and Gaigneaux, Anthoula and
+ Ginolhac, Aurelien and Tam Thuy Dan Nguyen and Grandmougin, Lea and
+ Frachet-Bour, Audrey and Martin-Gallausiaux, Camille and Pacheco, Maria
+ and Neuberger-Castillo, Lorie and Miranda, Paulo and Zuegel, Nikolaus
+ and Ferrand, Jean-Yves and Gantenbein, Manon and Sauter, Thomas and
+ Slade, Daniel Joseph and Thiele, Ines and Meiser, Johannes and Haan,
+ Serge and Wilmes, Paul and Letellier, Elisabeth},
+Title = {The gut microbial metabolite formate exacerbates colorectal cancer
+ progression},
+Journal = {NATURE METABOLISM},
+Year = {2022},
+Volume = {4},
+Number = {4},
+Pages = {458+},
+Month = {APR},
+Type = {Article},
+DOI = {10.1038/s42255-022-00558-0},
+EarlyAccessDate = {APR 2022},
+EISSN = {2522-5812},
+Keywords-Plus = {EPITHELIAL-MESENCHYMAL TRANSITION; FUSOBACTERIUM-NUCLEATUM; STEM-CELLS;
+ FAP2; METASTASIS; BINDING; TUMORS},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Wilmes, Paul/B-1707-2017
+ Pacheco, Maria Pires/C-4494-2014
+ Meiser, Johannes/S-7571-2018
+ },
+ORCID-Numbers = {Wilmes, Paul/0000-0002-6478-2924
+ Pacheco, Maria Pires/0000-0001-7956-8093
+ Atatri, Sura/0000-0003-3447-5613
+ Tsenkova, Mina/0000-0001-9814-7921
+ Grandmougin, Lea/0009-0009-3820-3958
+ Meiser, Johannes/0000-0002-9093-6210
+ Sauter, Thomas/0000-0001-8225-2954
+ Pozdeev, Vitaly/0000-0002-6526-9890
+ Martin-gallausiaux, Camille/0000-0002-6193-4304
+ GANTENBEIN, Manon/0000-0002-5178-4365},
+Times-Cited = {71},
+Journal-ISO = {Nat. Metab.},
+Unique-ID = {WOS:000783390300001},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000813483300001,
+Author = {Sudhakar, Padhmanand and Andrighetti, Tahila and Verstockt, Sare and
+ Caenepeel, Clara and Ferrante, Marc and Sabino, Joao and Verstockt, Bram
+ and Vermeire, Severine},
+Title = {Integrated analysis of microbe-host interactions in Crohn's disease
+ reveals potential mechanisms of microbial proteins on host gene
+ expression},
+Journal = {ISCIENCE},
+Year = {2022},
+Volume = {25},
+Number = {5},
+Month = {MAY 20},
+Type = {Article},
+DOI = {10.1016/j.isci.2022.103963},
+EarlyAccessDate = {APR 2022},
+Article-Number = {103963},
+EISSN = {2589-0042},
+Keywords-Plus = {INFLAMMATORY-BOWEL-DISEASE; TRANSCRIPTION FACTORS; STAT3 ACTIVATION;
+ EPITHELIAL-CELLS; KAPPA-B; ULCERATIVE-COLITIS; SIGNAL TRANSDUCERS;
+ DENDRITIC CELLS; RNA; PATHWAY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Verstockt, Bram/P-5234-2016
+ },
+ORCID-Numbers = {Verstockt, Bram/0000-0003-3898-7093
+ Caenepeel, Clara/0000-0002-6827-6287
+ Vermeire, Severine/0000-0001-9942-3019
+ Sudhakar, Padhmanand/0000-0003-1907-4491},
+Times-Cited = {7},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000813483300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000791641700014,
+Author = {Jiang, Shouyong and Otero-Muras, Irene and Banga, Julio R. and Wang,
+ Yong and Kaiser, Marcus and Krasnogor, Natalio},
+Title = {OptDesign: Identifying Optimum Design Strategies in Strain Engineering
+ for Biochemical Production},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2022},
+Volume = {11},
+Number = {4},
+Pages = {1531-1541},
+Month = {APR 15},
+Type = {Article},
+DOI = {10.1021/acssynbio.1c00610},
+ISSN = {2161-5063},
+Keywords = {growth-coupled design; flux change; genome-scale metabolic model;
+ systems biology; in silico strain design; biotechnology},
+Keywords-Plus = {ESCHERICHIA-COLI; KNOCKOUT STRATEGIES; CHEMICAL PRODUCTION; METABOLIC
+ NETWORK; ACID PRODUCTION; SUCCINATE; FRAMEWORK; GROWTH; YIELD; FLUX},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Banga, Julio R./A-8388-2008
+ Kaiser, Marcus/AAG-3051-2020
+ Otero-Muras, Irene/K-3832-2014
+ Kaiser, Marcus/A-7166-2008
+ },
+ORCID-Numbers = {Banga, Julio R./0000-0002-4245-0320
+ Otero-Muras, Irene/0000-0003-2895-997X
+ Kaiser, Marcus/0000-0002-4654-3110
+ Jiang, Shouyong/0000-0001-5099-2093},
+Times-Cited = {3},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000791641700014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000867556100001,
+Author = {de Lima, Lorena Azevedo and Ingelman, Henri and Brahmbhatt, Kush and
+ Reinmets, Kristina and Barry, Craig and Harris, Audrey and Marcellin,
+ Esteban and Kopke, Michael and Valgepea, Kaspar},
+Title = {Faster Growth Enhances Low Carbon Fuel and Chemical Production Through
+ Gas Fermentation},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2022},
+Volume = {10},
+Month = {APR 12},
+Type = {Article},
+DOI = {10.3389/fbioe.2022.879578},
+Article-Number = {879578},
+ISSN = {2296-4185},
+Keywords = {gas fermentation; acetogen; Clostridium autoethanogenum; carbon
+ recycling; metabolomics; transcriptomics; genome-scale metabolic
+ modelling; chemostat},
+Keywords-Plus = {CLOSTRIDIUM-AUTOETHANOGENUM; ESCHERICHIA-COLI; ENERGY-CONSERVATION;
+ ETHANOL; SYNGAS; CO2; LJUNGDAHLII; METABOLISM; MONOXIDE; MODEL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Valgepea, Kaspar/ABC-7334-2021
+ },
+ORCID-Numbers = {AZEVEDO DE LIMA, LORENA/0000-0001-5735-035X},
+Times-Cited = {7},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000867556100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000782461400013,
+Author = {Woods, Craig and Humphreys, Christopher M. and Tomi-Andrino, Claudio and
+ Henstra, Anne M. and Kopke, Michael and Simpson, Sean D. and Winzer,
+ Klaus and Minton, Nigel P.},
+Title = {Required Gene Set for Autotrophic Growth of Clostridium
+ autoethanogenum},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2022},
+Volume = {88},
+Number = {7},
+Month = {APR 12},
+Type = {Article},
+DOI = {10.1128/aem.02479-21},
+Article-Number = {e02479-21},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords = {Tn-Seq; TraDIS; acetogen; chemoautotrophy; Clostridium autoethanogenum;
+ gene essentiality; minimal genome; transposon sequencing; transposons;
+ Wood-Ljungdahl},
+Keywords-Plus = {WOOD-LJUNGDAHL PATHWAY; COMMODITY CHEMICALS; METABOLISM; MUTANTS;
+ SYSTEM; CARBON; MODEL; FUELS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ORCID-Numbers = {Minton, Nigel/0000-0002-9277-1261
+ Winzer, Klaus/0000-0002-3956-8096},
+Times-Cited = {6},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000782461400013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000779450200001,
+Author = {Paramasivan, Kalaivani and Abdulla, Aneesha and Gupta, Nabarupa and
+ Mutturi, Sarma},
+Title = {In silico target-based strain engineering of Saccharomyces
+ cerevisiae for terpene precursor improvement},
+Journal = {INTEGRATIVE BIOLOGY},
+Year = {2022},
+Volume = {14},
+Number = {2},
+Pages = {25-36},
+Month = {APR 8},
+Type = {Article},
+DOI = {10.1093/intbio/zyac003},
+ISSN = {1757-9694},
+EISSN = {1757-9708},
+Keywords = {in silico analysis; genome-scale model; knockout; overexpression; S;
+ cerevisiae},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; CONSTRAINT-BASED MODELS; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; YEAST; PLATFORM; TOOLBOX; MUTANTS; ACID},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ORCID-Numbers = {Paramasivan, Kalaivani/0000-0001-6743-0003
+ Mutturi, Sarma/0000-0002-3251-8643},
+Times-Cited = {2},
+Journal-ISO = {Integr. Biol.},
+Unique-ID = {WOS:000779450200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000782153500001,
+Author = {Kutay, Merve and Gozuacik, Devrim and Cakir, Tunahan},
+Title = {Cancer Recurrence and Omics: Metabolic Signatures of Cancer Dormancy
+ Revealed by Transcriptome Mapping of Genome-Scale Networks},
+Journal = {OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY},
+Year = {2022},
+Volume = {26},
+Number = {5},
+Pages = {270-279},
+Month = {MAY 1},
+Type = {Article},
+DOI = {10.1089/omi.2022.0008},
+EarlyAccessDate = {APR 2022},
+ISSN = {1536-2310},
+EISSN = {1557-8100},
+Keywords = {cancer dormancy; metabolic network models; transcriptome; preventive
+ medicine; bioinformatics; cancer drug discovery},
+Keywords-Plus = {MODELS; RECONSTRUCTION; HALLMARKS; CELLS; MECHANISMS; PREDICTION;
+ FLUXES; REDOX},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Cakir, Tunahan/F-4523-2011
+ Gozuacik, Devrim/C-3330-2008},
+ORCID-Numbers = {Cakir, Tunahan/0000-0001-8262-4420
+ KUTAY, MERVE/0000-0001-9985-9621
+ Gozuacik, Devrim/0000-0001-7739-2346},
+Times-Cited = {1},
+Journal-ISO = {OMICS},
+Unique-ID = {WOS:000782153500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000779346100001,
+Author = {Valgepea, Kaspar and Talbo, Gert and Takemori, Nobuaki and Takemori,
+ Ayako and Ludwig, Christina and Mahamkali, Vishnuvardhan and Mueller,
+ Alexander P. and Tappel, Ryan and Kopke, Michael and Simpson, Sean
+ Dennis and Nielsen, Lars Keld and Marcellin, Esteban},
+Title = {Absolute Proteome Quantification in the Gas-Fermenting Acetogen
+ Clostridium autoethanogenum},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {2},
+Month = {APR 26},
+Type = {Article},
+DOI = {10.1128/msystems.00026-22},
+EarlyAccessDate = {APR 2022},
+ISSN = {2379-5077},
+Keywords = {acetogen; gas fermentation; genome-scale metabolic modeling; metabolic
+ modeling; metabolomics; proteomics},
+Keywords-Plus = {WOOD-LJUNGDAHL PATHWAY; ESCHERICHIA-COLI; CARBON-DIOXIDE; FORMATE
+ DEHYDROGENASE; ENERGY-CONSERVATION; CO2; GROWTH; LIFE; GENE; METABOLISM},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Nielsen, Lars K/A-5519-2011
+ Valgepea, Kaspar/ABC-7334-2021
+ Valgepea, Kaspar/H-1473-2018
+ },
+ORCID-Numbers = {Nielsen, Lars K/0000-0001-8191-3511
+ Valgepea, Kaspar/0000-0003-4803-7569
+ Marcellin, Esteban/0000-0003-3173-7956},
+Times-Cited = {7},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000779346100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000789363900014,
+Author = {Goldford, Joshua E. and George, Ashish B. and Flamholz, Avi I. and
+ Segre, Daniel},
+Title = {Protein cost minimization promotes the emergence of coenzyme redundancy},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2022},
+Volume = {119},
+Number = {14},
+Month = {APR 5},
+Type = {Article},
+DOI = {10.1073/pnas.2110787119},
+Article-Number = {e2110787119},
+ISSN = {0027-8424},
+EISSN = {1091-6490},
+Keywords = {metabolism; evolution; coenzymes; constraint-based modeling},
+Keywords-Plus = {METABOLITE CONCENTRATIONS; STEADY-STATE; SPECIFICITY; DEHYDROGENASE;
+ SITE; PREDICTION; EVOLUTION; PHOSPHATE; DATABASE; MODELS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {George, Ashish/GZL-7747-2022
+ Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914
+ Goldford, Joshua/0000-0001-7315-8018
+ Bino George, Ashish/0000-0002-6923-3596
+ Flamholz, Avi/0000-0002-9278-5479},
+Times-Cited = {3},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000789363900014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000778641300001,
+Author = {Regimbeau, Antoine and Budinich, Marko and Larhlimi, Abdelhalim and
+ Karlusich, Juan Jose Pierella and Aumont, Olivier and Memery, Laurent
+ and Bowler, Chris and Eveillard, Damien},
+Title = {Contribution of genome-scale metabolic modelling to niche theory},
+Journal = {ECOLOGY LETTERS},
+Year = {2022},
+Volume = {25},
+Number = {6},
+Pages = {1352-1364},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1111/ele.13954},
+EarlyAccessDate = {APR 2022},
+ISSN = {1461-023X},
+EISSN = {1461-0248},
+Keywords = {marine ecology; metabolic network; metabolic niche; microbial ecology;
+ molecular ecology; niche modelling},
+Keywords-Plus = {SPECIES DISTRIBUTION; ECOLOGY; TAXONOMY},
+Research-Areas = {Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Ecology},
+ResearcherID-Numbers = {Pierella Karlusich, Juan J/AAW-9429-2021
+ aumont, olivier/G-5207-2016
+ Eveillard, Damien/A-1635-2012},
+ORCID-Numbers = {Pierella Karlusich, Juan J/0000-0003-1739-4424
+ aumont, olivier/0000-0003-3954-506X
+ Regimbeau, Antoine/0000-0003-0456-6717
+ Budinich, Marko/0000-0003-3541-0547
+ Eveillard, Damien/0000-0002-8162-7360},
+Times-Cited = {4},
+Journal-ISO = {Ecol. Lett.},
+Unique-ID = {WOS:000778641300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000786731100001,
+Author = {Grausa, Kristina and Mozga, Ivars and Pleiko, Karlis and Pentjuss, Agris},
+Title = {Integrative Gene Expression and Metabolic Analysis Tool IgemRNA},
+Journal = {BIOMOLECULES},
+Year = {2022},
+Volume = {12},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.3390/biom12040586},
+Article-Number = {586},
+EISSN = {2218-273X},
+Keywords = {genome-scale metabolic modeling; transcriptomics; software engineering;
+ Cobra Toolbox 3.0; MATLAB; flux balance analysis; flux variability
+ analysis; omics data analysis},
+Keywords-Plus = {RNA-SEQ; REGULATORY NETWORKS; MODEL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Pleiko, Karlis/HNJ-3059-2023
+ Mozga, Ivars/G-5888-2010
+ },
+ORCID-Numbers = {Pleiko, Karlis/0000-0002-1073-197X
+ Pentjuss, Agris/0000-0001-7880-5130},
+Times-Cited = {1},
+Journal-ISO = {Biomolecules},
+Unique-ID = {WOS:000786731100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000785051900001,
+Author = {He, Bingqing and Cai, Chen and McCubbin, Tim and Muriel, Jorge Carrasco
+ and Sonnenschein, Nikolaus and Hu, Shihu and Yuan, Zhiguo and Marcellin,
+ Esteban},
+Title = {A Genome-Scale Metabolic Model of Methanoperedens nitroreducens:
+ Assessing Bioenergetics and Thermodynamic Feasibility},
+Journal = {METABOLITES},
+Year = {2022},
+Volume = {12},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.3390/metabo12040314},
+Article-Number = {314},
+EISSN = {2218-1989},
+Keywords = {genome-scale metabolic model; ANME archaea; reverse methanogenesis;
+ bioenergetics; electron transfer; thermodynamic feasibility; MEMOTE},
+Keywords-Plus = {ANAEROBIC METHANE OXIDATION; METHANOTROPHIC ARCHAEA; RECONSTRUCTION;
+ METHANOGENESIS; ENRICHMENT; BACTERIA; DATABASE; ENZYME},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Yuan, Zhiguo/C-4980-2013
+ Hu, Shihu/L-6085-2019
+ Sonnenschein, Nikolaus/F-6853-2012
+ },
+ORCID-Numbers = {Yuan, Zhiguo/0000-0002-7566-1482
+ Hu, Shihu/0000-0002-1858-8872
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ McCubbin, Tim/0000-0002-9707-6532
+ Marcellin, Esteban/0000-0003-3173-7956
+ Cai, Chen/0000-0002-0167-1397},
+Times-Cited = {2},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000785051900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000835142100170,
+Author = {Jin, Qusheng and Wu, Qiong and Shapiro, Benjamin M. and McKernan,
+ Shannon E.},
+Title = {Limited Mechanistic Link Between the Monod Equation and Methanogen
+ Growth: a Perspective from Metabolic Modeling},
+Journal = {MICROBIOLOGY SPECTRUM},
+Year = {2022},
+Volume = {10},
+Number = {2},
+Month = {APR},
+Type = {Article},
+DOI = {10.1128/spectrum.02259-21},
+ISSN = {2165-0497},
+Keywords = {Monod equation; half-saturation constant; maximum growth rate; metabolic
+ modeling; methanogenesis; microbial kinetics; specific affinity},
+Keywords-Plus = {METHANOSARCINA-BARKERI; MICROBIAL-GROWTH; HETERODISULFIDE REDUCTASE; M
+ METHYLTRANSFERASE; NUTRIENT-UPTAKE; ATP SYNTHESIS; KINETICS;
+ PURIFICATION; ACETATE; DERIVATION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+Times-Cited = {2},
+Journal-ISO = {Microbiol. Spectr.},
+Unique-ID = {WOS:000835142100170},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000819870000012,
+Author = {Xavier, Joao B. and Monk, Jonathan M. and Poudel, Saugat and Norsigian,
+ Charles J. and Sastry, V, Anand and Liao, Chen and Bento, Jose and
+ Suchard, Marc A. and Arrieta-Ortiz, Mario L. and Peterson, Eliza J. R.
+ and Baliga, Nitin S. and Stoeger, Thomas and Ruffin, Felicia and
+ Richardson, Reese A. K. and Gao, Catherine A. and Horvath, Thomas D. and
+ Haag, Anthony M. and Wu, Qinglong and Savidge, Tor and Yeaman, Michael
+ R.},
+Title = {Mathematical models to study the biology of pathogens and the infectious
+ diseases they cause},
+Journal = {ISCIENCE},
+Year = {2022},
+Volume = {25},
+Number = {4},
+Month = {APR 15},
+Type = {Review},
+DOI = {10.1016/j.isci.2022.104079},
+EarlyAccessDate = {MAR 2022},
+Article-Number = {104079},
+EISSN = {2589-0042},
+Keywords-Plus = {STAPHYLOCOCCUS-AUREUS; REGULATORY NETWORKS; GENE-EXPRESSION; HOST;
+ EVOLUTION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Xavier, Joao/H-5471-2011
+ Richardson, Reese/HLP-9380-2023
+ Horvath, Thomas/AAI-2216-2019},
+ORCID-Numbers = {Xavier, Joao/0000-0003-3592-1689
+ Monk, Jonathan M./0000-0002-3895-8949
+ Poudel, Saugat/0000-0002-3732-2463
+ Gao, Catherine A./0000-0001-5576-3943
+ Richardson, Reese/0000-0002-6058-5886
+ Ruffin, Felicia/0000-0003-2176-6462
+ Stoeger, Thomas/0000-0002-5540-4278
+ Horvath, Thomas/0000-0001-9761-3484},
+Times-Cited = {4},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000819870000012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000773415700001,
+Author = {Li, Gong-Hua and Han, Feifei and Xiao, Fu-Hui and Gu, Kang-Su-Yun and
+ Shen, Qiu and Xu, Weihong and Li, Wen-Xing and Wang, Yan-Li and Liang,
+ Bin and Huang, Jing-Fei and Xiao, Wenzhong and Kong, Qing-Peng},
+Title = {System-level metabolic modeling facilitates unveiling metabolic
+ signature in exceptional longevity},
+Journal = {AGING CELL},
+Year = {2022},
+Volume = {21},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1111/acel.13595},
+EarlyAccessDate = {MAR 2022},
+Article-Number = {e13595},
+ISSN = {1474-9718},
+EISSN = {1474-9726},
+Keywords = {aging; GPMM; longevity; metabolic modeling; omics integration; systems
+ biology},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ HEALTH; CENTENARIANS; INFLAMMATION; DATABASE; DISEASE; TOOLS},
+Research-Areas = {Cell Biology; Geriatrics \& Gerontology},
+Web-of-Science-Categories = {Cell Biology; Geriatrics \& Gerontology},
+ResearcherID-Numbers = {li, wenxin/IYS-5300-2023
+ huang, jing/JDC-2548-2023
+ },
+ORCID-Numbers = {Xiao, Fu-Hui/0000-0001-7478-7801
+ HAN, FEIFEI/0000-0003-4373-8753
+ Li, Wenxing/0000-0001-9984-8439
+ Li, Gong-Hua/0000-0002-9311-6613
+ xiao, wenzhong/0000-0003-4944-6380},
+Times-Cited = {9},
+Journal-ISO = {Aging Cell},
+Unique-ID = {WOS:000773415700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000772481500001,
+Author = {Liu, Defei and Xu, Zixiang and Li, Jingen and Liu, Qian and Yuan,
+ Qianqian and Guo, Yanmei and Ma, Hongwu and Tian, Chaoguang},
+Title = {Reconstruction and analysis of genome-scale metabolic model for
+ thermophilic fungus Myceliophthora thermophila},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2022},
+Volume = {119},
+Number = {7},
+Pages = {1926-1937},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/bit.28080},
+EarlyAccessDate = {MAR 2022},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {genome-scale metabolic model; Myceliophthora thermophila; thermophilic
+ fungi; transcriptomics},
+Keywords-Plus = {FATTY-ACID-COMPOSITION; ASPERGILLUS-NIGER; LIPIDS; BIOLOGY; CARBON},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {3},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000772481500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000807495000001,
+Author = {Rezen, Tadeja and Martins, Alexandre and Mraz, Miha and Zimic, Nikolaj
+ and Rozman, Damjana and Moskon, Miha},
+Title = {Integration of omics data to generate and analyse COVID-19 specific
+ genome-scale metabolic models},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2022},
+Volume = {145},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2022.105428},
+EarlyAccessDate = {MAR 2022},
+Article-Number = {105428},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {COVID-19; Genome-scale metabolic models; Model extraction methods;
+ Context-specific models; Metabolic enrichment analysis},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ORCID-Numbers = {Moskon, Miha/0000-0003-4600-1730
+ Zimic, Nikolaj/0000-0003-4290-0106
+ Rezen, Tadeja/0000-0001-6210-7370},
+Times-Cited = {5},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000807495000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000771557800001,
+Author = {Fan, Xingcun and Zhou, Jingru and Xia, Jianye and Yan, Xuefeng},
+Title = {Genome-Scale Metabolic Model's multi-objective solving algorithm based
+ on the inflexion point of Pareto front including maximum energy
+ utilization and its application in Aspergillus niger DS03043},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2022},
+Volume = {119},
+Number = {6},
+Pages = {1539-1555},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/bit.28078},
+EarlyAccessDate = {MAR 2022},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Aspergillus niger; differential evolution; Genome-Scale Metabolic Model;
+ inflexion point of the Pareto front; maximum resource utilization},
+Keywords-Plus = {ESCHERICHIA-COLI; NETWORK ANALYSIS; OPTIMIZATION; INTEGRATION; STRAINS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Yan, Xuefeng/0000-0001-5622-8686
+ XIA, Jianye/0000-0003-2114-5770},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000771557800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000834238000001,
+Author = {Salehabadi, Ehsan and Motamedian, Ehsan and Shojaosadati, Seyed Abbas},
+Title = {Reconstruction of a generic genome-scale metabolic network for chicken:
+ Investigating network connectivity and finding potential biomarkers},
+Journal = {PLOS ONE},
+Year = {2022},
+Volume = {17},
+Number = {3},
+Month = {MAR 22},
+Type = {Article},
+DOI = {10.1371/journal.pone.0254270},
+Article-Number = {e0254270},
+ISSN = {1932-6203},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GLOBAL RECONSTRUCTION; OBESITY; LIVER;
+ PREDICTION; SEQUENCE; DATABASE; CANCER; ENERGY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {3},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000834238000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000771363200002,
+Author = {Yu, Jason S. L. and Correia-Melo, Clara and Zorrilla, Francisco and
+ Herrera-Dominguez, Lucia and Wu, Mary Y. and Hartl, Johannes and
+ Campbell, Kate and Blasche, Sonja and Kreidl, Marco and Egger,
+ Anna-Sophia and Messner, Christoph B. and Demichev, Vadim and Freiwald,
+ Anja and Mulleder, Michael and Howell, Michael and Berman, Judith and
+ Patil, Kiran R. and Alam, Mohammad Tauqeer and Ralser, Markus},
+Title = {Microbial communities form rich extracellular metabolomes that foster
+ metabolic interactions and promote drug tolerance},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2022},
+Volume = {7},
+Number = {4},
+Pages = {542+},
+Month = {APR},
+Type = {Article},
+DOI = {10.1038/s41564-022-01072-5},
+EarlyAccessDate = {MAR 2022},
+ISSN = {2058-5276},
+Keywords-Plus = {YEAST; EVOLUTION; VITAMIN-B-12; COOPERATION; RESISTANCE; REVEALS;
+ NETWORK; IMPACT; MODEL},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Patil, Kiran R/B-9709-2009
+ alam, mohammed/GXH-3645-2022
+ Messner, Christoph/IUP-2898-2023
+ Berman, Judith/ABA-8528-2021
+ },
+ORCID-Numbers = {Patil, Kiran R/0000-0002-6166-8640
+ Messner, Christoph/0000-0001-7217-0867
+ Berman, Judith/0000-0002-8577-0084
+ Demichev, Vadim/0000-0002-2424-9412
+ Egger, Anna-Sophia/0000-0002-5204-7121
+ Correia-Melo, Clara/0000-0001-6062-1472
+ Hartl, Johannes/0000-0001-8470-5355
+ Wu, Mary Y./0000-0002-2074-6171
+ Mulleder, Michael/0000-0001-9792-3861
+ Ralser, Markus/0000-0001-9535-7413
+ Yu, Jason/0000-0001-5203-3603
+ Zorrilla, Francisco/0000-0002-6206-8655
+ Blasche, Sonja/0000-0001-9422-0474},
+Times-Cited = {28},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000771363200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000772459100002,
+Author = {Odunsi, Kunle and Qian, Feng and Lugade, Amit A. and Yu, Han and Geller,
+ Melissa A. and Fling, Steven P. and Kaiser, Judith C. and Lacroix,
+ Andreanne M. and D'Amico, Leonard and Ramchurren, Nirasha and Morishima,
+ Chihiro and Disis, Mary L. and Dennis, Lucas and Danaher, Patrick and
+ Warren, Sarah and Van Anh Nguyen and Ravi, Sudharshan and Tsuji,
+ Takemasa and Rosario, Spencer and Zha, Wenjuan and Hutson, Alan and Liu,
+ Song and Lele, Shashikant and Zsiros, Emese and McGray, A. J. Robert and
+ Chiello, Jessie and Koya, Richard and Chodon, Thinle and Morrison, Carl
+ D. and Putluri, Vasanta and Putluri, Nagireddy and Mager, Donald E. and
+ Gunawan, Rudiyanto and Cheever, Martin A. and Battaglia, Sebastiano and
+ Matsuzaki, Junko},
+Title = {Metabolic adaptation of ovarian tumors in patients treated with an IDO1
+ inhibitor constrains antitumor immune responses},
+Journal = {SCIENCE TRANSLATIONAL MEDICINE},
+Year = {2022},
+Volume = {14},
+Number = {636},
+Month = {MAR 16},
+Type = {Article},
+DOI = {10.1126/scitranslmed.abg8402},
+Article-Number = {eabg8402},
+ISSN = {1946-6234},
+EISSN = {1946-6242},
+Keywords-Plus = {INDOLEAMINE 2,3-DIOXYGENASE; TRYPTOPHAN CATABOLISM; RESISTANCE
+ MECHANISM; CANCER; EPACADOSTAT; EXPRESSION; NAD; EFFICACY; THERAPY;
+ ARREST},
+Research-Areas = {Cell Biology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Cell Biology; Medicine, Research \& Experimental},
+ORCID-Numbers = {Ramchurren, Nirasha/0000-0002-6613-9342
+ Ravi, Sudharshan/0000-0001-6059-5403
+ Geller, Melissa/0000-0003-4591-620X
+ Matsuzaki, Junko/0000-0002-2555-1234},
+Times-Cited = {23},
+Journal-ISO = {Sci. Transl. Med.},
+Unique-ID = {WOS:000772459100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000784315800001,
+Author = {Amara, Adam and Frainay, Clement and Jourdan, Fabien and Naake, Thomas
+ and Neumann, Steffen and Novoa-del-Toro, Elva Maria and Salek, Reza M.
+ and Salzer, Liesa and Scharfenberg, Sarah and Witting, Michael},
+Title = {Networks and Graphs Discovery in Metabolomics Data Analysis and
+ Interpretation},
+Journal = {FRONTIERS IN MOLECULAR BIOSCIENCES},
+Year = {2022},
+Volume = {9},
+Month = {MAR 8},
+Type = {Review},
+DOI = {10.3389/fmolb.2022.841373},
+Article-Number = {841373},
+EISSN = {2296-889X},
+Keywords = {metabolic network; untargeted metabolomics; graph-based analysis;
+ knowledge network; experimental network; metabolism; systems biology},
+Keywords-Plus = {TANDEM MASS-SPECTRA; BIOCHEMICAL REACTIONS; SPECTROMETRY DATA;
+ METABOLITES; ANNOTATION; SIMILARITY; PREDICTION; ONTOLOGY; PATHWAY;
+ MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Salek, Reza/V-9739-2017
+ Frainay, Clement/B-8636-2019
+ },
+ORCID-Numbers = {Salek, Reza/0000-0001-8604-1732
+ Frainay, Clement/0000-0003-4313-2786
+ Salzer, Liesa/0000-0003-0761-0656
+ Witting, Michael/0000-0002-1462-4426},
+Times-Cited = {18},
+Journal-ISO = {Front. Mol. Biosci.},
+Unique-ID = {WOS:000784315800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000821599000004,
+Author = {Paul, Abhijit and Azhar, Salman and Das, Phonindra Nath and Bairagi,
+ Nandadulal and Chatterjee, Samrat},
+Title = {Elucidating the metabolic characteristics of pancreatic β-cells from
+ patients with type 2 diabetes (T2D) using a genome-scale metabolic
+ modeling},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2022},
+Volume = {144},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2022.105365},
+EarlyAccessDate = {MAR 2022},
+Article-Number = {105365},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Coupling factors; Oxidative phosphorylation; Genetic variation; Insulin
+ secretion; Mitochondrial metabolism; Genome scale models of metabolism},
+Keywords-Plus = {STIMULATED INSULIN-SECRETION; PLASMA SEROTONIN; POSTULATED MECHANISMS;
+ NEUROMEDIN-N; HIGH GLUCOSE; MITOCHONDRIA; DYSFUNCTION; FAILURE; DISEASE;
+ ISLETS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Das, Phonindra Nath/AGZ-4930-2022
+ Bairagi, Nandadulal/S-4557-2016},
+ORCID-Numbers = {Das, Phonindra Nath/0000-0002-6797-8535
+ Bairagi, Nandadulal/0000-0001-8867-7996},
+Times-Cited = {3},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000821599000004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000782759000001,
+Author = {Mohammad, Faiz Khan and Palukuri, Meghana Venkata and Shivakumar, Shruti
+ and Rengaswamy, Raghunathan and Sahoo, Swagatika},
+Title = {A Computational Framework for Studying Gut-Brain Axis in Autism Spectrum
+ Disorder},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2022},
+Volume = {13},
+Month = {MAR 7},
+Type = {Article},
+DOI = {10.3389/fphys.2022.760753},
+Article-Number = {760753},
+EISSN = {1664-042X},
+Keywords = {autism spectrum disorder (ASD); gut-brain axis; gut microbiota;
+ constraint-based metabolic modelling (CBM); physiological-based
+ pharmacokinetic modelling (PBPK)},
+Keywords-Plus = {OXIDATIVE STRESS; PARTITION-COEFFICIENTS; MICROBIOME; METABOLISM;
+ PREDICTION; GLUTAMATE; BARRIER; HEALTH},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+Times-Cited = {5},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000782759000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000773285300001,
+Author = {Koduru, Lokanand and Lakshmanan, Meiyappan and Hoon, Shawn and Lee,
+ Dong-Yup and Lee, Yuan Kun and Ow, Dave Siak-Wei},
+Title = {Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward
+ Anti-inflammatory Probiotics},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2022},
+Volume = {13},
+Month = {MAR 3},
+Type = {Article},
+DOI = {10.3389/fmicb.2022.846555},
+Article-Number = {846555},
+EISSN = {1664-302X},
+Keywords = {systems biology; gut microbiota; inflammatory disorders; probiotics;
+ postbiotics},
+Keywords-Plus = {ARYL-HYDROCARBON RECEPTOR; SCALE METABOLIC MODELS; TRYPTOPHAN;
+ RECONSTRUCTION; COLITIS; HOST},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+Times-Cited = {3},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000773285300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000774139200002,
+Author = {Wendering, Philipp and Nikoloski, Zoran},
+Title = {COMMIT: Consideration of metabolite leakage and community composition
+ improves microbial community reconstructions},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2022},
+Volume = {18},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1009906},
+Article-Number = {e1009906},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {MODELS; BIODIVERSITY; DIVERSITY; FASTER},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Wendering, Philipp/0000-0002-0155-6217
+ Nikoloski, Zoran/0000-0003-2671-6763},
+Times-Cited = {0},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000774139200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000793364700005,
+Author = {Wang, Feng-Sheng and Chen, Ke-Lin and Chu, Sz-Wei},
+Title = {Human/SARS-CoV-2 genome-scale metabolic modeling to discover potential
+ antiviral targets for COVID-19},
+Journal = {JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS},
+Year = {2022},
+Volume = {133},
+Month = {APR},
+Type = {Article},
+DOI = {10.1016/j.jtice.2022.104273},
+EarlyAccessDate = {FEB 2022},
+Article-Number = {104273},
+ISSN = {1876-1070},
+EISSN = {1876-1089},
+Keywords = {Flux balance analysis; Constraint-based modeling; Computer-aided drug
+ discovery; Evolutionary optimization; Bioprocess systems engineering;
+ Fuzzy optimization},
+Keywords-Plus = {DESIGN},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+Times-Cited = {4},
+Journal-ISO = {J. Taiwan Inst. Chem. Eng.},
+Unique-ID = {WOS:000793364700005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000767429100001,
+Author = {Camborda, Stefano and Weder, Jan-Niklas and Toepfer, Nadine},
+Title = {CobraMod: a pathway-centric curation tool for constraint-based metabolic
+ models},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Volume = {38},
+Number = {9},
+Pages = {2654-2656},
+Month = {APR 28},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btac119},
+EarlyAccessDate = {FEB 2022},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {ESCHERICHIA-COLI},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Camborda La Cruz, Stefano Andre/0000-0001-5881-3707
+ Weder, Jan-Niklas/0000-0003-2388-7049},
+Times-Cited = {2},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000767429100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000769523200001,
+Author = {Clark, Teresa J. and Schwender, Jorg},
+Title = {Elucidation of Triacylglycerol Overproduction in the C4
+ Bioenergy Crop Sorghum bicolor by Constraint-Based Analysis},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2022},
+Volume = {13},
+Month = {FEB 17},
+Type = {Article},
+DOI = {10.3389/fpls.2022.787265},
+Article-Number = {787265},
+ISSN = {1664-462X},
+Keywords = {bioenergy grasses; metabolic reconstruction; C-4 photosynthesis; energy
+ balance; plant lipids; triacylglycerol; constraint-based analysis;
+ Sorghum bicolor},
+Keywords-Plus = {CARRIER PROTEIN REDUCTASE; FLUX BALANCE ANALYSIS; LEAF PHOTOSYNTHESIS;
+ METABOLIC NETWORK; AMINO-ACIDS; OIL BODIES; MAIZE; CARBON; BIOMASS;
+ ACCUMULATION},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Schwender, Jorg/P-2282-2014},
+ORCID-Numbers = {Schwender, Jorg/0000-0003-1350-4171},
+Times-Cited = {1},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000769523200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000758837900001,
+Author = {Heinken, Almut and Thiele, Ines},
+Title = {Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of
+ microbiome communities},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Volume = {38},
+Number = {8},
+Pages = {2367-2368},
+Month = {APR 12},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btac082},
+EarlyAccessDate = {FEB 2022},
+Article-Number = {btac082},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {10},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000758837900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000754300200001,
+Author = {Qu, Lisha and Xiu, Xiang and Sun, Guoyun and Zhang, Chenyang and Yang,
+ Haiquan and Liu, Yanfeng and Li, Jianghua and Du, Guocheng and Lv,
+ Xueqin and Liu, Long},
+Title = {Engineered yeast for efficient de novo synthesis of 7-dehydrocholesterol},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2022},
+Volume = {119},
+Number = {5},
+Pages = {1278-1289},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/bit.28055},
+EarlyAccessDate = {FEB 2022},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {7-dehydrocholesterol; CRISPRi system; metabolic engineering; metabolic
+ network model; TY1 transposon},
+Keywords-Plus = {VITAMIN-D; SACCHAROMYCES-CEREVISIAE; MANIPULATION; HORMONE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {li, jianghua/GXG-4735-2022
+ wu, yunhui/JGD-6838-2023
+ Liu, Long/D-6112-2013},
+Times-Cited = {10},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000754300200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000773071700003,
+Author = {Kang, Nam Kyu and Kim, Minsik and Baek, Kwangryul R. and Chang, Yong
+ Keun and Ort, Donald and Jin, Yong-Su},
+Title = {Photoautotrophic organic acid production: Glycolic acid production by
+ microalgal cultivation},
+Journal = {CHEMICAL ENGINEERING JOURNAL},
+Year = {2022},
+Volume = {433},
+Number = {3},
+Month = {APR 1},
+Type = {Article},
+DOI = {10.1016/j.cej.2021.133636},
+EarlyAccessDate = {FEB 2022},
+Article-Number = {133636},
+ISSN = {1385-8947},
+EISSN = {1873-3212},
+Keywords = {Chlamydomonas reinhardtii; Glycolate dehydrogenase; Glycolic acid;
+ Two-stage continuous culture; Flux balance analysis; Techno-economic
+ analysis},
+Keywords-Plus = {CHLAMYDOMONAS-REINHARDTII; TECHNOECONOMIC ANALYSIS; BIOMASS; GENE},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Environmental; Engineering, Chemical},
+ResearcherID-Numbers = {Kang, Nam Kyu/AAW-1788-2021
+ Kim, Minsik/HOH-6250-2023},
+ORCID-Numbers = {Kim, Minsik/0000-0003-1095-840X},
+Times-Cited = {9},
+Journal-ISO = {Chem. Eng. J.},
+Unique-ID = {WOS:000773071700003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000776280200044,
+Author = {Thiele, Sven and von Kamp, Axel and Bekiaris, Pavlos Stephanos and
+ Schneider, Philipp and Klamt, Steffen},
+Title = {CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing
+ metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Volume = {38},
+Number = {5},
+Pages = {1467-1469},
+Month = {FEB 7},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btab828},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Schneider, Philipp/GYU-8053-2022
+ },
+ORCID-Numbers = {Schneider, Philipp/0000-0001-8858-428X
+ Klamt, Steffen/0000-0003-2563-7561
+ Thiele, Sven/0000-0002-5812-6963},
+Times-Cited = {4},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000776280200044},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000753142700002,
+Author = {Barnes, Elle M. and Tringe, Susannah G.},
+Title = {Exploring the roles of microbes in facilitating plant adaptation to
+ climate change},
+Journal = {BIOCHEMICAL JOURNAL},
+Year = {2022},
+Volume = {479},
+Number = {3},
+Pages = {327-335},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1042/BCJ20210793},
+ISSN = {0264-6021},
+EISSN = {1470-8728},
+Keywords-Plus = {ROOT EXUDATION; DECOMPOSITION; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Tringe, Susannah/0000-0001-6479-8427},
+Times-Cited = {6},
+Journal-ISO = {Biochem. J.},
+Unique-ID = {WOS:000753142700002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000765093400001,
+Author = {Berzins, Kristaps and Muiznieks, Reinis and Baumanis, Matiss R. and
+ Strazdina, Inese and Shvirksts, Karlis and Prikule, Santa and
+ Galvanauskas, Vytautas and Pleissner, Daniel and Pentjuss, Agris and
+ Grube, Mara and Kalnenieks, Uldis and Stalidzans, Egils},
+Title = {Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic
+ Acid (DHA) Production Potential by Crypthecodinium cohnii from
+ Glycerol, Glucose and Ethanol},
+Journal = {MARINE DRUGS},
+Year = {2022},
+Volume = {20},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/md20020115},
+Article-Number = {115},
+EISSN = {1660-3397},
+Keywords = {Krebs cycle; central metabolism; kinetic model; constraint-based model;
+ FTIR spectroscopy},
+Keywords-Plus = {POLYUNSATURATED FATTY-ACIDS; OPTIMIZATION; CONSTRAINTS; COMPLEX; COPASI},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Chemistry, Medicinal; Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Stalidzans, Egils/G-5883-2010},
+ORCID-Numbers = {Muiznieks, Reinis/0000-0003-3432-4321
+ Berzins, Kristaps/0000-0002-0244-9253
+ Pentjuss, Agris/0000-0001-7880-5130
+ Stalidzans, Egils/0000-0001-6063-0184},
+Times-Cited = {3},
+Journal-ISO = {Mar. Drugs},
+Unique-ID = {WOS:000765093400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001040822100002,
+Author = {Canto-Encalada, Gabriela and Tec-Campos, Diego and Tibocha-Bonilla, Juan
+ D. and Zengler, Karsten and Zepeda, Alejandro and Zuniga, Cristal},
+Title = {Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas
+ europaea ATCC19718 unravels specific metabolic activities while
+ degrading toxic compounds},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2022},
+Volume = {18},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1009828},
+Article-Number = {e1009828},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {THERMODYNAMICALLY INFEASIBLE LOOPS; METHANE OXIDATION; M-CRESOL; GROWTH;
+ BATCH; BENZENE; REMOVAL; TRANSCRIPTION; CHLOROPLAST; INHIBITION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Zuniga, Cristal/0000-0002-0135-7429
+ Zengler, Karsten/0000-0002-8062-3296
+ Tec-Campos, Diego/0000-0001-8819-4150},
+Times-Cited = {4},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:001040822100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000825154300001,
+Author = {Cipriani, Claudia and Pacheco, Maria Pires and Kishk, Ali and Wachich,
+ Maryem and Abankwa, Daniel and Schaffner-Reckinger, Elisabeth and
+ Sauter, Thomas},
+Title = {Bruceine D Identified as a Drug Candidate against Breast Cancer by a
+ Novel Drug Selection Pipeline and Cell Viability Assay},
+Journal = {PHARMACEUTICALS},
+Year = {2022},
+Volume = {15},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/ph15020179},
+Article-Number = {179},
+EISSN = {1424-8247},
+Keywords = {natural products; bruceine D; emodin; scutellarein; drug prediction
+ workflow; metabolic modelling},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; FERULIC ACID; IN-VITRO; HEPATOCELLULAR-CARCINOMA;
+ OXIDATIVE STRESS; MCF-7 CELLS; APOPTOSIS; GROWTH; EMODIN; PROLIFERATION},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Chemistry, Medicinal; Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Sauter, Thomas/0000-0001-8225-2954
+ Schaffner-Reckinger, Elisabeth/0000-0002-0321-3621
+ Abankwa, Daniel/0000-0003-2769-0745},
+Times-Cited = {2},
+Journal-ISO = {Pharmaceuticals},
+Unique-ID = {WOS:000825154300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000772038800001,
+Author = {Collin, Catherine Bjerre and Gebhardt, Tom and Golebiewski, Martin and
+ Karaderi, Tugce and Hillemanns, Maximilian and Khan, Faiz Muhammad and
+ Salehzadeh-Yazdi, Ali and Kirschner, Marc and Krobitsch, Sylvia and
+ Kuepfer, Lars},
+Title = {Computational Models for Clinical Applications in Personalized
+ Medicine-Guidelines and Recommendations for Data Integration and Model
+ Validation},
+Journal = {JOURNAL OF PERSONALIZED MEDICINE},
+Year = {2022},
+Volume = {12},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/jpm12020166},
+Article-Number = {166},
+EISSN = {2075-4426},
+Keywords = {personalized medicine; computational models; data integration; model
+ validation; guidelines and recommendations; clinical translation;
+ ethical and legal requirements},
+Keywords-Plus = {ARTIFICIAL-INTELLIGENCE; SYSTEMS BIOLOGY; RISK PREDICTION; GENETIC RISK;
+ DISEASE; SIMULATION; NETWORK; PHARMACOKINETICS; RECONSTRUCTION;
+ REPRESENTATION},
+Research-Areas = {Health Care Sciences \& Services; General \& Internal Medicine},
+Web-of-Science-Categories = {Health Care Sciences \& Services; Medicine, General \& Internal},
+ResearcherID-Numbers = {Kockum, Ingrid/O-8781-2018
+ Salehzadeh-Yazdi, Ali/J-9510-2019
+ Kuepfer, Lars/AAD-5884-2022
+ },
+ORCID-Numbers = {Kockum, Ingrid/0000-0002-0867-4726
+ Salehzadeh-Yazdi, Ali/0000-0002-1678-0051
+ Kuepfer, Lars/0000-0002-8741-7786
+ Hillemanns, Maximilian/0000-0002-5698-5924
+ Karaderi, Tugce/0000-0001-9763-8139},
+Times-Cited = {9},
+Journal-ISO = {J. Pers. Med.},
+Unique-ID = {WOS:000772038800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000759631300009,
+Author = {Liu, Zihe and Wang, Junyang and Nielsen, Jens},
+Title = {Yeast synthetic biology advances biofuel production},
+Journal = {CURRENT OPINION IN MICROBIOLOGY},
+Year = {2022},
+Volume = {65},
+Pages = {33-39},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1016/j.mib.2021.10.010},
+ISSN = {1369-5274},
+EISSN = {1879-0364},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; PATHWAY; AUTOMATION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Wang, Junyang/M-3679-2019
+ },
+ORCID-Numbers = {Wang, Junyang/0000-0001-6025-5986
+ Liu, Zihe/0000-0002-4199-1627},
+Times-Cited = {10},
+Journal-ISO = {Curr. Opin. Microbiol.},
+Unique-ID = {WOS:000759631300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000765077100001,
+Author = {Viana, Romeu and Couceiro, Diogo and Carreiro, Tiago and Dias, Oscar and
+ Rocha, Isabel and Teixeira, Miguel Cacho},
+Title = {A Genome-Scale Metabolic Model for the Human Pathogen Candida
+ Parapsilosis and Early Identification of Putative Novel Antifungal
+ Drug Targets},
+Journal = {GENES},
+Year = {2022},
+Volume = {13},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/genes13020303},
+Article-Number = {303},
+EISSN = {2073-4425},
+Keywords = {C; parapsilosis; genome-scale metabolic model; drug target; drug
+ discovery},
+Keywords-Plus = {DATABASE; GENES},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Rocha, Isabel/A-4279-2013
+ Teixeira, Miguel/A-3870-2008
+ Dias, Oscar/A-4359-2010
+ },
+ORCID-Numbers = {Rocha, Isabel/0000-0001-9494-3410
+ Teixeira, Miguel/0000-0002-5676-6174
+ Dias, Oscar/0000-0002-1765-7178
+ Viana, Romeu/0000-0002-9644-5906},
+Times-Cited = {2},
+Journal-ISO = {Genes},
+Unique-ID = {WOS:000765077100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000779379600057,
+Author = {Simensen, Vetle and Schulz, Christian and Karlsen, Emil and Bratelund,
+ Signe and Burgos, Idun and Thorfinnsdottir, Lilja Brekke and
+ Garcia-Calvo, Laura and Bruheim, Per and Almaas, Eivind},
+Title = {Experimental determination of Escherichia coli biomass
+ composition for constraint-based metabolic modeling},
+Journal = {PLOS ONE},
+Year = {2022},
+Volume = {17},
+Number = {1},
+Month = {JAN 27},
+Type = {Article},
+DOI = {10.1371/journal.pone.0262450},
+Article-Number = {e0262450},
+ISSN = {1932-6203},
+Keywords-Plus = {GROWTH; HMDB; KNOWLEDGEBASE; DATABASE; BALANCE; CHITIN; RNA},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Brekke Thorfinnsdott, Lilja/HHM-9912-2022
+ },
+ORCID-Numbers = {Garcia-Calvo, Laura/0000-0002-9885-9854
+ Simensen, Vetle/0000-0002-2511-1052},
+Times-Cited = {5},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000779379600057},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000758331300003,
+Author = {Delangiz, Nasser and Aliyar, Sajad and Pashapoor, Neda and Nobaharan,
+ Khatereh and Lajayer, Behnam Asgari and Rodriguez-Couto, Susana},
+Title = {Can polymer-degrading microorganisms solve the bottleneck of plastics'
+ environmental challenges?},
+Journal = {CHEMOSPHERE},
+Year = {2022},
+Volume = {294},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.chemosphere.2022.133709},
+EarlyAccessDate = {JAN 2022},
+Article-Number = {133709},
+ISSN = {0045-6535},
+EISSN = {1879-1298},
+Keywords = {Biodegradation; Microorganisms; Microplastics; Natural polymers; Omics;
+ Polyethylene terephthalate; Synthetic polymers},
+Keywords-Plus = {POLYETHYLENE TEREPHTHALATE; MICROBIAL-DEGRADATION; IDEONELLA-SAKAIENSIS;
+ POLY(VINYL ALCOHOL); CELLULAR-METABOLISM; THERMOBIFIDA-FUSCA; PROTEOMIC
+ ANALYSIS; SP NOV.; BIODEGRADATION; BACTERIA},
+Research-Areas = {Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Environmental Sciences},
+ResearcherID-Numbers = {Rodriguez-Couto, Susana/U-3919-2019
+ Asgari Lajayer, Behnam/J-5143-2019},
+ORCID-Numbers = {Rodriguez-Couto, Susana/0000-0002-2694-5091
+ Asgari Lajayer, Behnam/0000-0001-7609-5833},
+Times-Cited = {22},
+Journal-ISO = {Chemosphere},
+Unique-ID = {WOS:000758331300003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000746132400023,
+Author = {Tewari, Shivendra G. and Kwan, Bobby and Elahi, Rubayet and Rajaram,
+ Krithika and Reifman, Jaques and Prigge, Sean T. and Vaidya, Akhil B.
+ and Wallqvist, Anders},
+Title = {Metabolic adjustments of blood-stage Plasmodium falciparum in
+ response to sublethal pyrazoleamide exposure},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2022},
+Volume = {12},
+Number = {1},
+Month = {JAN 21},
+Type = {Article},
+DOI = {10.1038/s41598-022-04985-7},
+Article-Number = {1167},
+ISSN = {2045-2322},
+Keywords-Plus = {CATION ATPASE PFATP4; MALARIA; MECHANISM; RESISTANCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Prigge, Sean/GVS-9197-2022
+ },
+ORCID-Numbers = {Prigge, Sean/0000-0001-9684-1733
+ wallqvist, anders/0000-0002-9775-7469
+ Rajaram, Krithika/0000-0003-4830-5471},
+Times-Cited = {6},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000746132400023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000744508100001,
+Author = {Bhalla, Prerna and Rengaswamy, Raghunathan and Karunagaran, Devarajan
+ and Suraishkumar, G. K. and Sahoo, Swagatika},
+Title = {Metabolic modeling of host-microbe interactions for therapeutics in
+ colorectal cancer},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2022},
+Volume = {8},
+Number = {1},
+Month = {JAN 19},
+Type = {Article},
+DOI = {10.1038/s41540-021-00210-9},
+Article-Number = {1},
+EISSN = {2056-7189},
+Keywords-Plus = {XANTHOMONAS-CAMPESTRIS; SILVER NANOPARTICLES; POSSIBLE MECHANISMS; GUT
+ MICROBIOME; FOLIC-ACID; TARGET; GROWTH; PROLIFERATION; CATECHOL;
+ DISEASES},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {Sahoo, Swagatika/0000-0003-3773-8597
+ Suraishkumar, GK/0000-0002-6521-4494},
+Times-Cited = {8},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000744508100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000744372200001,
+Author = {Savizi, Iman Shahidi Pour and Maghsoudi, Nader and Motamedian, Ehsan and
+ Lewis, Nathan E. and Shojaosadati, Seyed Abbas},
+Title = {Valine feeding reduces ammonia production through rearrangement of
+ metabolic fluxes in central carbon metabolism of CHO cells},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2022},
+Volume = {106},
+Number = {3},
+Pages = {1113-1126},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1007/s00253-021-11755-4},
+EarlyAccessDate = {JAN 2022},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {CHO cell; Amino acids; Ammonium; Sialylation; Systems biology},
+Keywords-Plus = {AMINO-ACID SUPPLEMENTATION; ANTIBODY-PRODUCTION; RECOMBINANT
+ ERYTHROPOIETIN; LACTATE CONSUMPTION; FUSION PROTEIN; CULTURE PH;
+ GLUTAMINE; BATCH; GLYCOSYLATION; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Motamedian, Ehsan/GPK-8344-2022
+ Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Shahidi Pour Savizi, Iman/0000-0003-3371-5523},
+Times-Cited = {5},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000744372200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000747033100002,
+Author = {Smith, Kirk and Shen, Fangzhou and Lee, Ho Joon and Chandrasekaran,
+ Sriram},
+Title = {Metabolic signatures of regulation by phosphorylation and acetylation},
+Journal = {ISCIENCE},
+Year = {2022},
+Volume = {25},
+Number = {1},
+Month = {JAN 21},
+Type = {Article},
+DOI = {10.1016/j.isci.2021.103730},
+EarlyAccessDate = {JAN 2022},
+Article-Number = {103730},
+EISSN = {2589-0042},
+Keywords-Plus = {ATP-CITRATE LYASE; ESCHERICHIA-COLI; POSTTRANSLATIONAL REGULATION;
+ CELLULAR-METABOLISM; GENOME; DYNAMICS; FLUX; PHOSPHOPROTEOME; NETWORKS;
+ REVEALS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Chandrasekaran, Sriram/0000-0002-8405-5708},
+Times-Cited = {3},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000747033100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000761024300001,
+Author = {Behravan, Aidin and Hashemi, Atieh and Marashi, Sayed-Amir},
+Title = {A Constraint-based modeling approach to reach an improved chemically
+ defined minimal medium for recombinant antiEpEX-scFv production by
+ Escherichia coli},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2022},
+Volume = {179},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1016/j.bej.2022.108339},
+EarlyAccessDate = {JAN 2022},
+Article-Number = {108339},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {AntiEpEX-scFv; Constrain-based modeling; Dynamic FBA; DoE; Medium
+ formulation},
+Keywords-Plus = {HETEROLOGOUS PROTEIN-PRODUCTION; METABOLIC FLUX ANALYSIS; AMINO-ACID;
+ BALANCE ANALYSIS; CELL; GROWTH; OPTIMIZATION; EXPRESSION; DESIGN},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008},
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449},
+Times-Cited = {1},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000761024300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000742942600002,
+Author = {Kim, Minsuk and Sung, Jaeyun and Chia, Nicholas},
+Title = {Resource-allocation constraint governs structure and function of
+ microbial communities in metabolic modeling},
+Journal = {METABOLIC ENGINEERING},
+Year = {2022},
+Volume = {70},
+Pages = {12-22},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.12.011},
+EarlyAccessDate = {JAN 2022},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic modeling; Microbial communities; Resource allocation; Gut
+ microbiome},
+Keywords-Plus = {ESCHERICHIA-COLI; DEGRADATION; HEALTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Sung, Jaeyun/0000-0002-3005-2798
+ Kim, Minsuk/0000-0001-9958-0380},
+Times-Cited = {3},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000742942600002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000758001700001,
+Author = {Ferreira, Eunice A. and Pacheco, Catarina C. and Rodrigues, Joao S. and
+ Pinto, Filipe and Lamosa, Pedro and Fuente, David and Urchueguia, Javier
+ and Tamagnini, Paula},
+Title = {Heterologous Production of Glycine Betaine Using Synechocystis
+ sp. PCC 6803-Based Chassis Lacking Native Compatible Solutes},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2022},
+Volume = {9},
+Month = {JAN 7},
+Type = {Article},
+DOI = {10.3389/fbioe.2021.821075},
+Article-Number = {821075},
+ISSN = {2296-4185},
+Keywords = {compatible solutes; cyanobacteria; glycine betaine; glucosylglycerol;
+ salt stress; sucrose; Synechocystis; synthetic biology},
+Keywords-Plus = {APHANOTHECE-HALOPHYTICA; NITROGENASE ACTIVITY; SYNTHETIC BIOLOGY;
+ TOLERANCE; GENES; ACCUMULATION; SUCROSE; SYNECHOCOCCUS; METHYLATION;
+ ACCLIMATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Tamagnini, Paula/AGF-3206-2022
+ Pinto, Filipe/J-9448-2013
+ PTNMR, PTNMR/JCE-8050-2023
+ },
+ORCID-Numbers = {Tamagnini, Paula/0000-0003-4396-2122
+ Pinto, Filipe/0000-0002-8554-6648
+ Fuente, David/0000-0003-4141-7948
+ Ferreira, Eunice/0000-0001-6923-5551
+ Lamosa, Pedro/0000-0002-3003-1516},
+Times-Cited = {2},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000758001700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000758003000001,
+Author = {Raajaraam, Lavanya and Raman, Karthik},
+Title = {A Computational Framework to Identify Metabolic Engineering Strategies
+ for the Co-Production of Metabolites},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2022},
+Volume = {9},
+Month = {JAN 7},
+Type = {Article},
+DOI = {10.3389/fbioe.2021.779405},
+Article-Number = {779405},
+ISSN = {2296-4185},
+Keywords = {metabolic modelling; genome-scale models; bioproduction; concomitant
+ production; co-synthesis; constraint-based modelling},
+Keywords-Plus = {OPTIMIZATION FRAMEWORK; FLUX; BUTANOL; ETHANOL; OVERPRODUCTION; GLUCOSE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019},
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093},
+Times-Cited = {2},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000758003000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000745886100028,
+Author = {Casey, John R. and Boiteau, Rene M. and Engqvist, Martin K. M. and
+ Finkel, V, Zoe and Li, Gang and Liefer, Justin and Muller, Christian L.
+ and Munoz, Nathalie and Follows, Michael J.},
+Title = {Basin-scale biogeography of marine phytoplankton reflects cellular-scale
+ optimization of metabolism and physiology},
+Journal = {SCIENCE ADVANCES},
+Year = {2022},
+Volume = {8},
+Number = {3},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1126/sciadv.abl4930},
+Article-Number = {eabl4930},
+ISSN = {2375-2548},
+Keywords-Plus = {PHOTOSYNTHETIC PROKARYOTE; PROCHLOROCOCCUS ECOTYPES;
+ GLUTAMATE-DEHYDROGENASE; ELEMENTAL COMPOSITION; ORGANIC-MATTER;
+ ATLANTIC-OCEAN; NORTH-ATLANTIC; GROWTH-RATE; SYNECHOCOCCUS;
+ CYANOBACTERIA},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Follows, Michael J/G-9824-2011
+ },
+ORCID-Numbers = {Liefer, Justin/0000-0001-5161-940X
+ Munoz, Nathalie/0000-0002-2723-3512
+ Boiteau, Rene/0000-0002-4127-4417
+ Li, Gang/0000-0001-6778-2842
+ Casey, John/0000-0002-8630-0551
+ Engqvist, Martin/0000-0003-2174-2225},
+Times-Cited = {11},
+Journal-ISO = {Sci. Adv.},
+Unique-ID = {WOS:000745886100028},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000747277900001,
+Author = {Forero-Rodriguez, Lady Johanna and Josephs-Spaulding, Jonathan and Flor,
+ Stefano and Pinzon, Andres and Kaleta, Christoph},
+Title = {Parkinson's Disease and the Metal-Microbiome-Gut-Brain Axis: A Systems
+ Toxicology Approach},
+Journal = {ANTIOXIDANTS},
+Year = {2022},
+Volume = {11},
+Number = {1},
+Month = {JAN},
+Type = {Review},
+DOI = {10.3390/antiox11010071},
+Article-Number = {71},
+EISSN = {2076-3921},
+Keywords = {heavy metals; neurotoxicity; Parkinson's disease; ROS; human microbiome;
+ systems toxicology},
+Keywords-Plus = {LACTIC-ACID BACTERIA; ENVIRONMENTAL RISK-FACTORS;
+ CENTRAL-NERVOUS-SYSTEM; LACTOBACILLUS-PLANTARUM CCFM8610;
+ MANGANESE-INDUCED NEUROTOXICITY; ALPHA-SYNUCLEIN OVEREXPRESSION; CADMIUM
+ CHLORIDE TOXICITY; INDUCED OXIDATIVE STRESS; IRRITABLE-BOWEL-SYNDROME;
+ NF-KAPPA-B},
+Research-Areas = {Biochemistry \& Molecular Biology; Pharmacology \& Pharmacy; Food
+ Science \& Technology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Chemistry, Medicinal; Food Science \&
+ Technology},
+ORCID-Numbers = {Josephs-Spaulding, Jonathan/0000-0001-9828-0685
+ Pinzon, Andres/0000-0002-4133-810X
+ Kaleta, Christoph/0000-0001-8004-9514},
+Times-Cited = {4},
+Journal-ISO = {Antioxidants},
+Unique-ID = {WOS:000747277900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001040888600121,
+Author = {Garcia-Tomsig, Natalia I. and Robledo, Marta and diCenzo, George C. and
+ Mengoni, Alessio and Millan, Vicenta and Peregrina, Alexandra and Uceta,
+ Alejandro and Jimenez-Zurdo, Jose I.},
+Title = {Pervasive RNA Regulation of Metabolism Enhances the Root Colonization
+ Ability of Nitrogen-Fixing Symbiotic α-Rhizobia},
+Journal = {MBIO},
+Year = {2022},
+Volume = {13},
+Number = {1},
+Month = {JAN-FEB},
+Type = {Article},
+DOI = {10.1128/mbio.03576-21},
+Article-Number = {e03576-21},
+ISSN = {2150-7511},
+Keywords = {Sinorhizobium meliloti; alphaproteobacteria; noncoding RNA;
+ riboregulation},
+Keywords-Plus = {SMALL NONCODING RNAS; SINORHIZOBIUM-MELILOTI; GENE-EXPRESSION;
+ BRUCELLA-ABORTUS; STRESS-RESPONSE; MESSENGER-RNAS; IDENTIFICATION;
+ PLANT; BACTERIA; LSRB},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Mengoni, Alessio/G-5336-2013
+ Garcia-Tomsig, Natalia/JSE-2591-2023
+ Peregrina, Alexandra/P-7674-2018
+ Jimenez-Zurdo, Jose Ignacio/P-6474-2014},
+ORCID-Numbers = {Mengoni, Alessio/0000-0002-1265-8251
+ Peregrina, Alexandra/0000-0002-3814-462X
+ Garcia-Tomsig, Natalia Isabel/0000-0002-1161-8709
+ Jimenez-Zurdo, Jose Ignacio/0000-0002-6378-2199},
+Times-Cited = {2},
+Journal-ISO = {mBio},
+Unique-ID = {WOS:001040888600121},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000814828000011,
+Author = {Lee, Sang Mi and Lee, GaRyoung and Kim, Hyun Uk},
+Title = {Machine learning-guided evaluation of extraction and simulation methods
+ for cancer patient-specific metabolic models},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2022},
+Volume = {20},
+Pages = {3041-3052},
+Type = {Article},
+DOI = {10.1016/j.csbj.2022.06.027},
+ISSN = {2001-0370},
+Keywords = {Genome-scale metabolic model; Cancer patient-specific metabolic model;
+ Model extraction method; Model simulation method; Evaluation; Machine
+ learning},
+Keywords-Plus = {RECONSTRUCTION; DEPENDS; TARGETS; TISSUE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Kim, Hyun Uk/F-4509-2018
+ },
+ORCID-Numbers = {Kim, Hyun Uk/0000-0001-7224-642X
+ Lee, GaRyoung/0000-0001-7084-1663
+ Lee, Sang Mi/0000-0002-0043-4269},
+Times-Cited = {4},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000814828000011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000746983900001,
+Author = {Loghmani, Seyed Babak and Veith, Nadine and Sahle, Sven and Bergmann,
+ Frank T. and Olivier, Brett G. and Kummer, Ursula},
+Title = {Inspecting the Solution Space of Genome-Scale Metabolic Models},
+Journal = {METABOLITES},
+Year = {2022},
+Volume = {12},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.3390/metabo12010043},
+Article-Number = {43},
+EISSN = {2218-1989},
+Keywords = {solution space; perturbation; sensitivity; robustness; constraints; FBA;
+ FVA},
+Keywords-Plus = {GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Olivier, Brett/0000-0002-5293-5321},
+Times-Cited = {3},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000746983900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000841696100001,
+Author = {Mejia-Gomez, Carlos E. and Rios-Estepa, Rigoberto and Gonzalez-Lopez,
+ Luis A. and Balcazar-Morales, Norman},
+Title = {An experimental and in silico analysis of
+ Lacticaseibacillus paracasei isolated from whey shows an
+ association between lactate production and amino acid catabolism},
+Journal = {ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS},
+Year = {2022},
+Volume = {94},
+Number = {2},
+Type = {Article},
+DOI = {10.1590/0001-3765202220211071},
+Article-Number = {e20211071},
+ISSN = {0001-3765},
+EISSN = {1678-2690},
+Keywords = {flux balance analysis; genome-scale metabolic network model; lactate;
+ lactic acid bacteria; whey},
+Keywords-Plus = {LACTOCOCCUS-LACTIS MG1363; SCALE METABOLIC MODELS; LACTOBACILLUS-CASEI;
+ PYRUVATE METABOLISM; STRESS-RESPONSE; GROWTH; RECONSTRUCTION; PLANTARUM;
+ BACTERIA; FOOD},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {GONZALEZ LOPEZ, LUIS ALBERTO/0000-0002-4935-3320
+ Balcazar, Norman/0000-0002-1860-1176
+ Rios-Estepa, Rigoberto/0000-0002-3287-7056
+ Mejia-Gomez, Carlos Eduardo/0000-0002-1413-9447},
+Times-Cited = {0},
+Journal-ISO = {An. Acad. Bras. Cienc.},
+Unique-ID = {WOS:000841696100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000758405300001,
+Author = {Passi, Anurag and Tibocha-Bonilla, Juan D. and Kumar, Manish and
+ Tec-Campos, Diego and Zengler, Karsten and Zuniga, Cristal},
+Title = {Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big
+ Data},
+Journal = {METABOLITES},
+Year = {2022},
+Volume = {12},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.3390/metabo12010014},
+Article-Number = {14},
+EISSN = {2218-1989},
+Keywords = {genome-scale metabolic models; big data; computational tools;
+ phenotypes; flux balance analysis; machine learning; reconstruction;
+ ME-models},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; PROTEIN SUBCELLULAR-LOCALIZATION;
+ ESCHERICHIA-COLI; SYSTEMS BIOLOGY; ENCODE DATA; RECONSTRUCTION; NETWORK;
+ COLLECTION; PREDICTION; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Kumar, Manish/ABE-8494-2020
+ Passi, Anurag/AAN-5309-2021
+ Zuniga, Cristal/CAA-0015-2022
+ },
+ORCID-Numbers = {Kumar, Manish/0000-0001-8035-3399
+ Passi, Anurag/0000-0002-0448-794X
+ Zuniga, Cristal/0000-0002-0135-7429
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {18},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000758405300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000760997500006,
+Author = {Rangel, Albert E. Tafur and Oviedo, Abel Garcia and Mojica, Freddy
+ Cabrera and Gomez, Jorge M. and Barrios, Andres Fernando Gonzalez},
+Title = {Development of an integrating systems metabolic engineering and
+ bioprocess modeling approach for rational strain improvement},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2022},
+Volume = {178},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.bej.2021.108268},
+Article-Number = {108268},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Systems metabolic engineering; Downstream processing; Metabolic
+ modeling; Cell factories; Succinic acid},
+Keywords-Plus = {SUCCINIC ACID PRODUCTION; ESCHERICHIA-COLI; FERMENTATION BROTH;
+ ORGANIC-ACIDS; GLYCEROL; CONVERSION; RECOVERY; PLATFORM; ETHANOL; DESIGN},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ORCID-Numbers = {Gomez, Jorge Mario/0000-0002-2018-4121
+ Gonzalez Barrios, Andres Fernando/0000-0003-2517-2020
+ Tafur Rangel, Albert/0000-0002-9428-183X},
+Times-Cited = {1},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000760997500006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000748131300001,
+Author = {Sauter, Thomas and Bintener, Tamara and Kishk, Ali and Presta, Luana and
+ Prohaska, Tessy and Guignard, Daniel and Zeng, Ni and Cipriani, Claudia
+ and Arshad, Sundas and Pfau, Thomas and Martins Conde, Patricia and
+ Pires Pacheco, Maria},
+Title = {Project-based learning course on metabolic network modelling in
+ computational systems biology},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2022},
+Volume = {18},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1009711},
+Article-Number = {e1009711},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Martins Conde, Patricia/0000-0003-2246-5469
+ Cipriani, Claudia/0000-0001-8618-4717
+ Presta, Luana/0000-0001-6482-6758
+ Sauter, Thomas/0000-0001-8225-2954},
+Times-Cited = {0},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000748131300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000760774900003,
+Author = {Schulte, Carolin C. M. and Ramachandran, Vinoy K. and Papachristodoulou,
+ Antonis and Poole, Philip S.},
+Title = {Genome-Scale Metabolic Modelling of Lifestyle Changes in Rhizobium
+ leguminosarum},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {1},
+Month = {JAN-FEB},
+Type = {Article},
+Article-Number = {e00975-21},
+ISSN = {2379-5077},
+Keywords = {Rhizobium leguminosarum; metabolic modeling; rhizosphere-inhabiting
+ microbes; symbiosis},
+Keywords-Plus = {SINORHIZOBIUM-MELILOTI; MYOINOSITOL CATABOLISM; SYMBIOTIC PROPERTIES;
+ TRANSPORT MUTANTS; BV VICIAE; PEA; NITROGEN; NODULES; GENES;
+ RECONSTRUCTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Papachristodoulou, Antonis/C-2597-2012
+ },
+ORCID-Numbers = {Papachristodoulou, Antonis/0000-0002-3565-8967
+ Schulte, Carolin/0000-0002-7574-6259},
+Times-Cited = {4},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000760774900003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000749552000001,
+Author = {Taymaz-Nikerel, Hilal and Lara, Alvaro R.},
+Title = {Vitreoscilla Haemoglobin: A Tool to Reduce Overflow Metabolism},
+Journal = {MICROORGANISMS},
+Year = {2022},
+Volume = {10},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.3390/microorganisms10010043},
+Article-Number = {43},
+EISSN = {2076-2607},
+Keywords = {overflow metabolism; P; O ratio; Vitreoscilla haemoglobin; flux balance
+ analysis},
+Keywords-Plus = {ESCHERICHIA-COLI; INTRACELLULAR EXPRESSION; CORYNEBACTERIUM-GLUTAMICUM;
+ BACTERIAL HEMOGLOBIN; AEROBIC EXPRESSION; FLUX ANALYSIS; CELL-CULTURE;
+ GROWTH; ACETATE; GLUCOSE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Lara, Alvaro/A-8397-2012},
+ORCID-Numbers = {Lara, Alvaro/0000-0003-3535-7619},
+Times-Cited = {5},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000749552000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000919216100007,
+Author = {Thiele, Ines and Fleming, Ronan M. T.},
+Title = {Whole-body metabolic modelling predicts isoleucine dependency of
+ SARS-CoV-2 replication},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2022},
+Volume = {20},
+Pages = {4098-4109},
+Type = {Article},
+DOI = {10.1016/j.csbj.2022.07.019},
+ISSN = {2001-0370},
+Keywords = {Covid-19; SARS-CoV-2 infection; Metabolic modelling; Constraint -based
+ modelling; Variants of concerns; Isoleucine},
+Keywords-Plus = {CORONAVIRUS; PROTEIN; COVID-19; RECONSTRUCTION; DATABASE; COMPLEX;
+ KINASE; ROLES; SPIKE; DIET},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812},
+Times-Cited = {7},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000919216100007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000760768900004,
+Author = {Wendering, Philipp and Nikoloski, Zoran},
+Title = {Genome-Scale Modeling Specifies the Metabolic Capabilities of
+ Rhizophagus irregularis},
+Journal = {MSYSTEMS},
+Year = {2022},
+Volume = {7},
+Number = {1},
+Month = {JAN-FEB},
+Type = {Article},
+Article-Number = {e01216-21},
+ISSN = {2379-5077},
+Keywords = {Rhizophagus irregularis; metabolic modeling},
+Keywords-Plus = {ARBUSCULAR MYCORRHIZAL FUNGI; GLOMUS-INTRARADICES;
+ SACCHAROMYCES-CEREVISIAE; EXTRARADICAL MYCELIUM; PHOSPHATE TRANSPORTER;
+ AMMONIUM TRANSPORTER; NITROGEN TRANSFER; LOTUS-JAPONICUS; PLANT; GROWTH},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+Times-Cited = {0},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000760768900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000732814900005,
+Author = {Saa, Pedro and Urrutia, Arles and Silva-Andrade, Claudia and Martin,
+ Alberto J. and Garrido, Daniel},
+Title = {Modeling approaches for probing cross-feeding interactions in the human
+ gut microbiome},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2022},
+Volume = {20},
+Pages = {79-89},
+Type = {Review},
+DOI = {10.1016/j.csbj.2021.12.006},
+EarlyAccessDate = {DEC 2021},
+ISSN = {2001-0370},
+Keywords = {Cross-feeding; Microbial interactions; Ecological modeling; Genome-scale
+ metabolic model},
+Keywords-Plus = {SCALE METABOLIC MODELS; COMMUNITIES; ECOLOGY; COOPERATION; EVOLUTION;
+ BUTYRATE; DIET; COMPETITION; COMPLEXITY; PATHWAYS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Urrutia, Arles/HSC-3767-2023
+ Martin, Alberto Jesus/AAB-4815-2021
+ Saa, Pedro Andrés/X-1987-2018},
+ORCID-Numbers = {Urrutia, Arles/0000-0002-0777-0361
+ Martin, Alberto Jesus/0000-0002-6147-3325
+ Saa, Pedro Andrés/0000-0002-1659-9041},
+Times-Cited = {12},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000732814900005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000728569000002,
+Author = {Schopping, Marie and Gaspar, Paula and Neves, Ana Rute and Franzen, Carl
+ Johan and Zeidan, Ahmad A.},
+Title = {Identifying the essential nutritional requirements of the probiotic
+ bacteria Bifidobacterium animalis and Bifidobacterium
+ longum through genome-scale modeling},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2021},
+Volume = {7},
+Number = {1},
+Month = {DEC 9},
+Type = {Article},
+DOI = {10.1038/s41540-021-00207-4},
+Article-Number = {47},
+EISSN = {2056-7189},
+Keywords-Plus = {S-SULFONIC ACID; GLUCOSE FERMENTATION; TRANSPORT SYSTEMS;
+ GROWTH-RESPONSES; SUBSP LACTIS; COENZYME-A; OLIGOSACCHARIDES;
+ METABOLISM; GALACTOSE; BIFIDUM},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Neves, Ana R/B-9476-2008
+ Franzén, Carl Johan/D-2211-2016
+ Zeidan, Ahmad Adel/A-7845-2012
+ },
+ORCID-Numbers = {Neves, Ana R/0000-0003-4896-9585
+ Franzén, Carl Johan/0000-0001-7540-2002
+ Zeidan, Ahmad Adel/0000-0001-9984-5625
+ Schopping, Marie/0000-0003-0929-7552},
+Times-Cited = {9},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000728569000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000739841800005,
+Author = {Wang, Junmin and Delfarah, Alireza and Gelbach, Patrick E. and Fong,
+ Emma and Macklin, Paul and Mumenthaler, Shannon M. and Graham, Nicholas
+ A. and Finley, Stacey D.},
+Title = {Elucidating tumor-stromal metabolic crosstalk in colorectal cancer
+ through integration of constraint-based models and LC-MS metabolomics},
+Journal = {METABOLIC ENGINEERING},
+Year = {2022},
+Volume = {69},
+Pages = {175-187},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.11.006},
+EarlyAccessDate = {DEC 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Tumor microenvironment; Metabolomics; Mathematical biosciences; Systems
+ biology; Flux balance analysis},
+Keywords-Plus = {ONCOGENIC KRAS; LACTIC-ACID; GROWTH; FIBROBLASTS; INHIBITION; PATHWAYS;
+ MICROENVIRONMENT; RESISTANCE; PROTEOME; CELLS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Mumenthaler, Shannon M/AGY-8535-2022
+ Graham, Nicholas/GYD-5066-2022
+ Graham, Nicholas/X-2738-2019
+ },
+ORCID-Numbers = {Mumenthaler, Shannon M/0000-0003-2687-3769
+ Graham, Nicholas/0000-0002-6811-1941
+ Graham, Nicholas/0000-0002-6811-1941
+ Gelbach, Patrick/0000-0001-9721-5224
+ Finley, Stacey/0000-0001-6901-3692},
+Times-Cited = {2},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000739841800005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000727326900001,
+Author = {Immanuel, Selva Rupa Christinal and Arrieta-Ortiz, Mario L. and Ruiz,
+ Rene A. and Pan, Min and de Lomana, Adrian Lopez Garcia and Peterson,
+ Eliza J. R. and Baliga, Nitin S.},
+Title = {Quantitative prediction of conditional vulnerabilities in regulatory and
+ metabolic networks using PRIME},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2021},
+Volume = {7},
+Number = {1},
+Month = {DEC 6},
+Type = {Article},
+DOI = {10.1038/s41540-021-00205-6},
+Article-Number = {43},
+EISSN = {2056-7189},
+Keywords-Plus = {ESCHERICHIA-COLI; GENE-EXPRESSION; TUBERCULOSIS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ORCID-Numbers = {baliga, nitin/0000-0001-9157-5974
+ Peterson, Eliza/0000-0003-2934-5267
+ Ruiz, Rene/0000-0002-7123-7502
+ Lopez Garcia de Lomana, Adrian/0000-0002-9748-347X
+ Immanuel, Selva Rupa Christinal/0000-0002-3642-9605},
+Times-Cited = {2},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000727326900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000802600300005,
+Author = {Alzahmi, Amnah and Daakour, Sarah and El Assal, Diana Charles and Dohai,
+ Bushra S. and Chaiboonchoe, Amphun and Fu, Weiqi and Nelson, David R.
+ and Mystikou, Alexandra and Salehi-Ashtiani, Kourosh},
+Title = {High-Throughput Metabolic Profiling for Model Refinements of Microalgae},
+Journal = {JOVE-JOURNAL OF VISUALIZED EXPERIMENTS},
+Year = {2021},
+Number = {178},
+Month = {DEC},
+Type = {Article},
+DOI = {10.3791/61913},
+Article-Number = {e61913},
+ISSN = {1940-087X},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; CHLAMYDOMONAS-REINHARDTII; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; MIXOTROPHIC GROWTH; SYSTEMS-ANALYSIS;
+ DATABASE; REVEALS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {FU, WEIQI/E-4167-2019
+ },
+ORCID-Numbers = {FU, WEIQI/0000-0002-7368-383X
+ Dohai, Bushra/0000-0001-8179-8883
+ El Assal, Diana C./0000-0003-1124-5153
+ Mystikou, Alexandra/0000-0002-7961-3015},
+Times-Cited = {0},
+Journal-ISO = {J. Vis. Exp.},
+Unique-ID = {WOS:000802600300005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000735487200001,
+Author = {Xiang, Baoyu and Zhao, Liping and Zhang, Menghui},
+Title = {Metagenome-Scale Metabolic Network Suggests Folate Produced by
+ Bifidobacterium Longum Might Contribute to
+ High-Fiber-Diet-Induced Weight Loss in a Prader-Willi Syndrome Child},
+Journal = {MICROORGANISMS},
+Year = {2021},
+Volume = {9},
+Number = {12},
+Month = {DEC},
+Type = {Article},
+DOI = {10.3390/microorganisms9122493},
+Article-Number = {2493},
+EISSN = {2076-2607},
+Keywords = {folate; high-fiber diet; metagenome-scale metabolic network; gut
+ microbiota; obesity},
+Keywords-Plus = {OBESITY; GUT; INFLAMMATION; MICROBIOME; ADENOSINE; MODELS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {zhang, menghui/Q-3752-2016},
+ORCID-Numbers = {zhang, menghui/0000-0002-9274-487X},
+Times-Cited = {1},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000735487200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000723099000001,
+Author = {Sinha, Neeraj and van Schothorst, Evert M. and Hooiveld, Guido J. E. J.
+ and Keijer, Jaap and dos Santos, Vitor A. P. Martins and Suarez-Diez,
+ Maria},
+Title = {Exploring the associations between transcript levels and fluxes in
+ constraint-based models of metabolism},
+Journal = {BMC BIOINFORMATICS},
+Year = {2021},
+Volume = {22},
+Number = {1},
+Month = {NOV 29},
+Type = {Article},
+DOI = {10.1186/s12859-021-04488-8},
+Article-Number = {574},
+ISSN = {1471-2105},
+Keywords = {E-Flux; Gene expression integration; Transcriptomics; Constraint-based
+ models; Proportionality constant},
+Keywords-Plus = {ESCHERICHIA-COLI; TOOLBOX},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Hooiveld, Guido JEJ/F-4912-2010
+ },
+ORCID-Numbers = {Hooiveld, Guido JEJ/0000-0003-1954-3542
+ Sinha, Neeraj/0000-0002-0173-9849
+ martins dos santos, vitor/0000-0002-2352-9017
+ Suarez-Diez, Maria/0000-0001-5845-146X},
+Times-Cited = {1},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000723099000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000730171000003,
+Author = {Kishk, Ali and Pacheco, Maria Pires and Sauter, Thomas},
+Title = {DCcov: Repositioning of drugs and drug combinations for SARS-CoV-2
+ infected lung through constraint-based modeling},
+Journal = {ISCIENCE},
+Year = {2021},
+Volume = {24},
+Number = {11},
+Month = {NOV 19},
+Type = {Article},
+DOI = {10.1016/j.isci.2021.103331},
+Article-Number = {103331},
+EISSN = {2589-0042},
+Keywords-Plus = {COVID-19; PACKAGE; DISEASE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Sauter, Thomas/0000-0001-8225-2954},
+Times-Cited = {9},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000730171000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000730074200006,
+Author = {Malina, Carl and Di Bartolomeo, Francesca and Kerkhoven, Eduard J. and
+ Nielsen, Jens},
+Title = {Constraint-based modeling of yeast mitochondria reveals the dynamics of
+ protein import and iron-sulfur cluster biogenesis},
+Journal = {ISCIENCE},
+Year = {2021},
+Volume = {24},
+Number = {11},
+Month = {NOV 19},
+Type = {Article},
+DOI = {10.1016/j.isci.2021.103294},
+Article-Number = {103294},
+EISSN = {2589-0042},
+Keywords-Plus = {FERMENTATIVE CAPACITY; GLOBAL ANALYSIS; RECONSTRUCTION; ELECTRON;
+ CULTURES; SYSTEM; YIELDS; PLAYS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Kerkhoven, Eduard/P-2469-2019
+ Nielsen, Jens Bo/C-7632-2015
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Kerkhoven, Eduard/0000-0002-3593-5792
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Nielsen, Jens/0000-0002-9955-6003
+ Malina, Carl/0000-0001-7855-5311},
+Times-Cited = {3},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000730074200006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000730084100010,
+Author = {Niu, Puhua and Soto, Maria J. and Yoon, Byung-Jun and Dougherty, Edward
+ R. and Alexander, Francis J. and Blaby, Ian and Qian, Xiaoning},
+Title = {TRIMER: Transcription Regulation Integrated with Metabolic Regulation},
+Journal = {ISCIENCE},
+Year = {2021},
+Volume = {24},
+Number = {11},
+Month = {NOV 19},
+Type = {Article},
+DOI = {10.1016/j.isci.2021.103218},
+Article-Number = {103218},
+EISSN = {2589-0042},
+Keywords-Plus = {ESCHERICHIA-COLI; SYSTEMS BIOLOGY; MODELS; NETWORKS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Yoon, Byung-Jun/B-1466-2008
+ },
+ORCID-Numbers = {Yoon, Byung-Jun/0000-0001-9328-1101
+ Alexander, Francis/0000-0001-9848-555X
+ Qian, Xiaoning/0000-0002-4347-2476
+ Niu, Puhua/0000-0002-5127-1690
+ Blaby, Ian/0000-0002-1631-3154},
+Times-Cited = {3},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000730084100010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000744220100004,
+Author = {Ibrahim, Maziya and Raman, Karthik},
+Title = {Two-species community design of lactic acid bacteria for optimal
+ production of lactate},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2021},
+Volume = {19},
+Pages = {6039-6049},
+Type = {Article},
+DOI = {10.1016/j.csbj.2021.11.009},
+EarlyAccessDate = {NOV 2021},
+ISSN = {2001-0370},
+Keywords = {Genome-scale metabolic models; Constraint-based modelling; Metabolic
+ engineering; Cross-feeding; Microbial consortia},
+Keywords-Plus = {ESCHERICHIA-COLI; FERMENTATION; GLUCOSE; XYLOSE; RECONSTRUCTION;
+ COCULTURE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019},
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093},
+Times-Cited = {4},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000744220100004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000747962400048,
+Author = {Kratochvil, Miroslav and Heirendt, Laurent and Wilken, St Elmo and Pusa,
+ Taneli and Arreckx, Sylvain and Noronha, Alberto and van Aalst, Marvin
+ and Satagopam, Venkata P. and Ebenhoh, Oliver and Schneider, Reinhard
+ and Trefois, Christophe and Gu, Wei},
+Title = {COBREXA.jl: constraint-based reconstruction and exascale analysis},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Volume = {38},
+Number = {4},
+Pages = {1171-1172},
+Month = {FEB 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btab782},
+EarlyAccessDate = {NOV 2021},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Gu, Wei/G-4003-2010
+ Trefois, Christophe/H-1985-2014
+ Ebenhoeh, Oliver/C-8974-2011
+ Schneider, Reinhard/C-5441-2009
+ Kratochvil, Miroslav/D-2492-2017
+ },
+ORCID-Numbers = {Gu, Wei/0000-0003-3951-6680
+ Trefois, Christophe/0000-0002-8991-6810
+ Ebenhoeh, Oliver/0000-0002-7229-7398
+ Schneider, Reinhard/0000-0002-8278-1618
+ Wilken, St. Elmo/0000-0002-4113-2590
+ Kratochvil, Miroslav/0000-0001-7356-4075
+ Heirendt, Laurent/0000-0003-1861-0037
+ van Aalst, Marvin/0000-0002-7434-0249},
+Times-Cited = {1},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000747962400048},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000726047300001,
+Author = {Karlstaedt, Anja},
+Title = {Stable Isotopes for Tracing Cardiac Metabolism in Diseases},
+Journal = {FRONTIERS IN CARDIOVASCULAR MEDICINE},
+Year = {2021},
+Volume = {8},
+Month = {NOV 11},
+Type = {Review},
+DOI = {10.3389/fcvm.2021.734364},
+Article-Number = {734364},
+ISSN = {2297-055X},
+Keywords = {metabolism; stable-isotope tracer; metabolic flux analysis; systems
+ biology; cardiovascular disease},
+Keywords-Plus = {MASS-SPECTROMETRY; FLUX; HEART; CELLS; MITOCHONDRIA; METABOLOMICS;
+ ACETYLATION; CONSUMPTION; PROTEOMICS; FRAMEWORK},
+Research-Areas = {Cardiovascular System \& Cardiology},
+Web-of-Science-Categories = {Cardiac \& Cardiovascular Systems},
+Times-Cited = {4},
+Journal-ISO = {Front. Cardiovasc. Med.},
+Unique-ID = {WOS:000726047300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000718619900013,
+Author = {Arrieta-Ortiz, Mario L. and Immanuel, Selva Rupa Christinal and
+ Turkarslan, Serdar and Wu, Wei-Ju and Girinathan, Brintha P. and Worley,
+ Jay N. and DiBenedetto, Nicholas and Soutourina, Olga and Peltier,
+ Johann and Dupuy, Bruno and Bry, Lynn and Baliga, Nitin S.},
+Title = {Predictive regulatory and metabolic network models for systems analysis
+ of Clostridioides difficile},
+Journal = {CELL HOST \& MICROBE},
+Year = {2021},
+Volume = {29},
+Number = {11},
+Pages = {1709+},
+Month = {NOV 10},
+Type = {Article},
+DOI = {10.1016/j.chom.2021.09.008},
+EarlyAccessDate = {NOV 2021},
+ISSN = {1931-3128},
+EISSN = {1934-6069},
+Keywords-Plus = {SIGMA-FACTOR; TRANSCRIPTIONAL CONTROL; ADAPTIVE STRATEGIES;
+ GENE-EXPRESSION; VIRULENCE; SPORULATION; ANNOTATION; REPRESSION;
+ DATABASE; CCPA},
+Research-Areas = {Microbiology; Parasitology; Virology},
+Web-of-Science-Categories = {Microbiology; Parasitology; Virology},
+ResearcherID-Numbers = {Peltier, Johann/Q-2001-2017
+ },
+ORCID-Numbers = {Peltier, Johann/0000-0003-3207-9465
+ DiBenedetto, Nicholas/0000-0002-4043-9881
+ Immanuel, Selva Rupa Christinal/0000-0002-3642-9605
+ Bry, Lynn/0000-0002-8792-8527
+ Worley, Jay/0000-0002-5923-1159},
+Times-Cited = {4},
+Journal-ISO = {Cell Host Microbe},
+Unique-ID = {WOS:000718619900013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000717432700001,
+Author = {Gasparyan, Manvel and Van Messem, Arnout and Rao, Shodhan},
+Title = {Parameter estimation for models of chemical reaction networks from
+ experimental data of reaction rates},
+Journal = {INTERNATIONAL JOURNAL OF CONTROL},
+Year = {2023},
+Volume = {96},
+Number = {2},
+Pages = {392-407},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1080/00207179.2021.1998636},
+EarlyAccessDate = {NOV 2021},
+ISSN = {0020-7179},
+EISSN = {1366-5820},
+Keywords = {Systems biology; bottom-up modelling approach; system identification;
+ Bezier curves; least squares method},
+Keywords-Plus = {IDENTIFIABILITY; SYSTEMS; IDENTIFICATION; REDUCTION},
+Research-Areas = {Automation \& Control Systems},
+Web-of-Science-Categories = {Automation \& Control Systems},
+ResearcherID-Numbers = {Rao, Shodhan/AFY-9257-2022
+ Van Messem, Arnout/B-4814-2015
+ Gasparyan, Manvel/AAM-5267-2020},
+ORCID-Numbers = {Rao, Shodhan/0000-0001-8840-6950
+ Van Messem, Arnout/0000-0001-8545-7437
+ Gasparyan, Manvel/0000-0001-7813-9086},
+Times-Cited = {1},
+Journal-ISO = {Int. J. Control},
+Unique-ID = {WOS:000717432700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000715620600001,
+Author = {Nowrouzi, Behnaz and Rios-Solis, Leonardo},
+Title = {Redox metabolism for improving whole-cell P450-catalysed terpenoid
+ biosynthesis},
+Journal = {CRITICAL REVIEWS IN BIOTECHNOLOGY},
+Year = {2022},
+Volume = {42},
+Number = {8},
+Pages = {1213-1237},
+Month = {NOV 17},
+Type = {Review},
+DOI = {10.1080/07388551.2021.1990210},
+EarlyAccessDate = {NOV 2021},
+ISSN = {0738-8551},
+EISSN = {1549-7801},
+Keywords = {Redox; biocatalysis; terpenoids; microbe; P450; reductase; microbial
+ cell factories},
+Keywords-Plus = {ELECTRON-TRANSFER; CYTOCHROME B(5); SACCHAROMYCES-CEREVISIAE;
+ ESCHERICHIA-COLI; OXIDATIVE STRESS; CRYSTAL-STRUCTURE;
+ FERREDOXIN-NADP(+) REDUCTASE; COFACTOR REGENERATION; HYDROPHOBIC
+ RESIDUES; NADPH-P450 REDUCTASE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {11},
+Journal-ISO = {Crit. Rev. Biotechnol.},
+Unique-ID = {WOS:000715620600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000714977900033,
+Author = {Shah, V, Mihir and Nazem-Bokaee, Hadi and Antoney, James and Kang, Suk
+ Woo and Jackson, Colin J. and Scott, Colin},
+Title = {Improved production of the non-native cofactor F420 in
+ Escherichia coli},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2021},
+Volume = {11},
+Number = {1},
+Month = {NOV 5},
+Type = {Article},
+DOI = {10.1038/s41598-021-01224-3},
+Article-Number = {21774},
+ISSN = {2045-2322},
+Keywords-Plus = {COENZYME F-420; DEAZAFLAVIN COFACTOR; ANAEROBIC OXIDATION; BIOSYNTHESIS;
+ METHANE; ENZYME; PHOSPHOENOLPYRUVATE; IDENTIFICATION; METABOLISM;
+ PARAMETERS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Scott, Colin/A-4682-2009
+ Shah, Mihir V/Q-9852-2017
+ Kang, SW/GYJ-4352-2022
+ Jackson, Colin J/C-1500-2008
+ },
+ORCID-Numbers = {Scott, Colin/0000-0001-6110-6982
+ Kang, SW/0000-0002-5678-6394
+ Jackson, Colin J/0000-0001-6150-3822
+ Nazem-Bokaee, Hadi/0000-0002-4246-1804
+ Antoney, James/0000-0003-4033-6898},
+Times-Cited = {6},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000714977900033},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000726914900001,
+Author = {Cheng, Chao-Ting and Wang, Tsun-Yu and Chen, Pei-Rong and Wu, Wu-Hsiung
+ and Lai, Jin-Mei and Chang, Peter Mu-Hsin and Hong, Yi-Ren and Huang,
+ Chi-Ying F. and Wang, Feng-Sheng},
+Title = {Computer-Aided Design for Identifying Anticancer Targets in Genome-Scale
+ Metabolic Models of Colon Cancer},
+Journal = {BIOLOGY-BASEL},
+Year = {2021},
+Volume = {10},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.3390/biology10111115},
+Article-Number = {1115},
+EISSN = {2079-7737},
+Keywords = {metabolite-centric target; reaction-centric target; fuzzy optimization;
+ two-target combination},
+Keywords-Plus = {FUZZY OPTIMIZATION; NETWORK; 5-FLUOROURACIL; TRIPTOLIDE; BIOMARKERS;
+ HALLMARKS; LETHAL; SETS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Hong, Yi-Ren/D-5514-2009
+ Lai, Jin-Mei/AAM-4119-2020
+ Huang, Chi-Ying/AFL-7729-2022
+ Huang, Chi-Ying/AAG-7672-2022
+ },
+ORCID-Numbers = {Huang, Chi-Ying/0000-0003-4898-4937
+ Huang, Chi-Ying/0000-0003-4898-4937
+ Wang, Feng-Sheng/0000-0001-5266-2346
+ Hong, Yi-Ren/0000-0001-5470-6090
+ Wu, Wu-Hsiung/0000-0001-7457-0960},
+Times-Cited = {4},
+Journal-ISO = {Biology-Basel},
+Unique-ID = {WOS:000726914900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000715775700004,
+Author = {Giannari, Dafni and Ho, Cleo Hanchen and Mahadevan, Radhakrishnan},
+Title = {A gap-filling algorithm for prediction of metabolic interactions in
+ microbial communities},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1009060},
+Article-Number = {e1009060},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {FAECALIBACTERIUM-PRAUSNITZII; GUT MICROBIOME; FERMENTATION; CHLOROFORM;
+ MODELS; DICHLOROMETHANE; BIFIDOBACTERIA; DEGRADATION; EVOLUTION; HEALTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Giannari, Dafni/JQW-0887-2023
+ },
+ORCID-Numbers = {Giannari, Dafni/0000-0002-4100-5401
+ Ho, Cleo/0000-0002-2695-9020},
+Times-Cited = {3},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000715775700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000725138700001,
+Author = {Panikov, Nicolai S.},
+Title = {Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes
+ and Challenges},
+Journal = {MICROORGANISMS},
+Year = {2021},
+Volume = {9},
+Number = {11},
+Month = {NOV},
+Type = {Review},
+DOI = {10.3390/microorganisms9112352},
+Article-Number = {2352},
+EISSN = {2076-2607},
+Keywords = {growth kinetics; survival; death; substrate limitation; starvation; gene
+ expression; conditional expression of macromolecules; protein
+ allocation; batch culture; chemostat; cell cycle; metabolic network;
+ pool; metabolic intermediates; cell composition; biomass
+ brutto-formulae; kinetic order},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GLUCOSE-LIMITED GROWTH; ESCHERICHIA-COLI;
+ GENE-EXPRESSION; TRANSCRIPTIONAL REGULATION; METABOLITE CONCENTRATIONS;
+ CELLULAR-METABOLISM; SIGNAL-TRANSDUCTION; BIOMASS COMPOSITION;
+ CONTINUOUS-CULTURE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Panikov, Nikolay/0000-0002-7593-9421},
+Times-Cited = {3},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000725138700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000717696400001,
+Author = {Ravi, Sudharshan A. and Gunawan, Rudiyanto A.},
+Title = {ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic
+ models and differential transcriptomic data},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1009589},
+Article-Number = {e1009589},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {DIABETES-MELLITUS; ACID; EXPRESSION; NETWORK},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Ravi, Sudharshan/0000-0001-6059-5403},
+Times-Cited = {11},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000717696400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000750727700006,
+Author = {Sarathy, Chaitra and Breuer, Marian and Kutmon, Martina and Adriaens,
+ Michiel E. and Evelo, Chris T. and Arts, Ilja C. W.},
+Title = {Comparison of metabolic states using genome-scale metabolic models},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1009522},
+Article-Number = {e1009522},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {LEUCINE; RELEASE; ALANINE; OBESE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Arts, Ilja CW/C-6946-2008
+ Kutmon, Martina/AAT-2718-2021
+ Evelo, Chris TA/D-2914-2009
+ },
+ORCID-Numbers = {Arts, Ilja CW/0000-0001-6462-6692
+ Kutmon, Martina/0000-0002-7699-8191
+ Evelo, Chris TA/0000-0002-5301-3142
+ Breuer, Marian/0000-0002-0529-4031
+ Sarathy, Chaitra/0000-0003-1115-4323},
+Times-Cited = {2},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000750727700006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000726916300001,
+Author = {Whiteside, Theresa L.},
+Title = {The Role of Tumor-Derived Exosomes (TEX) in Shaping Anti-Tumor Immune
+ Competence},
+Journal = {CELLS},
+Year = {2021},
+Volume = {10},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.3390/cells10113054},
+Article-Number = {3054},
+EISSN = {2073-4409},
+Keywords = {tumor-derived exosomes (TEX); extracellular vesicles (EVs);
+ adenosinergic pathway; immune suppression; tumor microenvironment (TME)},
+Keywords-Plus = {T-CELLS; ADENOSINE; IMMUNOTHERAPY; CD73},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ORCID-Numbers = {Whiteside, Theresa L./0000-0001-7316-6181},
+Times-Cited = {10},
+Journal-ISO = {Cells},
+Unique-ID = {WOS:000726916300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000711097200001,
+Author = {Clomburg, James M. and Cintolesi, Angela and Gonzalez, Ramon},
+Title = {In silico and in vivo analyses reveal key metabolic
+ pathways enabling the fermentative utilization of glycerol in
+ Escherichia coli},
+Journal = {MICROBIAL BIOTECHNOLOGY},
+Year = {2022},
+Volume = {15},
+Number = {1},
+Pages = {289-304},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1111/1751-7915.13938},
+EarlyAccessDate = {OCT 2021},
+ISSN = {1751-7915},
+Keywords-Plus = {ANAEROBIC FERMENTATION; PHOSPHOENOLPYRUVATE CARBOXYLASE; MUTATIONAL
+ ANALYSIS; HYDROGEN-PRODUCTION; GENES; PURIFICATION; KINASE; MODEL;
+ SUBSTRATE; BACTERIA},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+Times-Cited = {3},
+Journal-ISO = {Microb. Biotechnol.},
+Unique-ID = {WOS:000711097200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000711099200001,
+Author = {Kruyer, Nicholas S. and Realff, Matthew J. and Sun, Wenting and Genzale,
+ Caroline L. and Peralta-Yahya, Pamela},
+Title = {Designing the bioproduction of Martian rocket propellant via a
+ biotechnology-enabled in situ resource utilization strategy},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2021},
+Volume = {12},
+Number = {1},
+Month = {OCT 25},
+Type = {Article},
+DOI = {10.1038/s41467-021-26393-7},
+Article-Number = {6166},
+EISSN = {2041-1723},
+Keywords-Plus = {ESCHERICHIA-COLI; ATTACHED CULTIVATION; CARBON-DIOXIDE; LIFE-SUPPORT;
+ MARS; SPIRULINA; GROWTH; CO2; 2,3-BUTANEDIOL; CYANOBACTERIA},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Sun, WT/JDN-1302-2023},
+Times-Cited = {13},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000711099200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000713817400001,
+Author = {Moscardo Garcia, Maria and Pacheco, Maria and Bintener, Tamara and
+ Presta, Luana and Sauter, Thomas},
+Title = {Importance of the biomass formulation for cancer metabolic modeling and
+ drug prediction},
+Journal = {ISCIENCE},
+Year = {2021},
+Volume = {24},
+Number = {10},
+Month = {OCT 22},
+Type = {Article},
+DOI = {10.1016/j.isci.2021.103110},
+Article-Number = {103110},
+EISSN = {2589-0042},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; NETWORK; GENERATION; EXPRESSION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Sauter, Thomas/0000-0001-8225-2954
+ Presta, Luana/0000-0001-6482-6758
+ Moscardo Garcia, Maria Isabel/0000-0001-9352-4097},
+Times-Cited = {4},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000713817400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000709795100001,
+Author = {Scott, Jr., William T. and Smid, Eddy J. and Block, David E. and
+ Notebaart, Richard A.},
+Title = {Metabolic flux sampling predicts strain-dependent differences related to
+ aroma production among commercial wine yeasts},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2021},
+Volume = {20},
+Number = {1},
+Month = {OCT 21},
+Type = {Article},
+DOI = {10.1186/s12934-021-01694-0},
+Article-Number = {204},
+EISSN = {1475-2859},
+Keywords = {Flux sampling; Genome-scale metabolic models; Saccharomyces cerevisiae;
+ Volatile organic compounds; Wine},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ASSIMILABLE NITROGEN; EHRLICH PATHWAY;
+ FERMENTATION; MODEL; VOLATILE; GRAPE; 2-PHENYLETHANOL; ISOBUTANOL; JUICE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Notebaart, Richard A./A-1459-2014
+ },
+ORCID-Numbers = {Scott, William/0000-0002-4029-2998},
+Times-Cited = {6},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000709795100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000716636300001,
+Author = {Thomas, John P. and Modos, Dezso and Korcsmaros, Tamas and
+ Brooks-Warburton, Johanne},
+Title = {Network Biology Approaches to Achieve Precision Medicine in Inflammatory
+ Bowel Disease},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2021},
+Volume = {12},
+Month = {OCT 21},
+Type = {Review},
+DOI = {10.3389/fgene.2021.760501},
+Article-Number = {760501},
+EISSN = {1664-8021},
+Keywords = {inflammatory bowel disease; network biology; protein-protein interaction
+ network; gene coexpression network; multilayered network; precision
+ medicine; gene regulatory network; metabolic network},
+Keywords-Plus = {SYSTEMS BIOLOGY; INTERACTION DATABASE; MOLECULAR NETWORKS;
+ GENE-EXPRESSION; IMMUNE CELLS; CANCER; CLASSIFICATION; INTERACTOME;
+ DYSBIOSIS; DISCOVERY},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Módos, Dezső/H-3056-2019
+ Korcsmaros, Tamas/C-3526-2015},
+ORCID-Numbers = {Módos, Dezső/0000-0001-9412-6867
+ Korcsmaros, Tamas/0000-0003-1717-996X},
+Times-Cited = {8},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000716636300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000711623700002,
+Author = {Kim, Kangsan and Choe, Donghui and Song, Yoseb and Kang, Minjeong and
+ Lee, Seung-Goo and Lee, Dae-Hee and Cho, Byung-Kwan},
+Title = {Engineering Bacteroides thetaiotaomicron to produce
+ non-native butyrate based on a genome-scale metabolic model-guided
+ design},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {68},
+Pages = {174-186},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.10.005},
+EarlyAccessDate = {OCT 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Bacteroides thetaiotaomicron; Genome-scale metabolic model; Flux-balance
+ analysis; Butyrate; Commensal microbes},
+Keywords-Plus = {ESCHERICHIA-COLI; GENE-EXPRESSION; KNOCKOUT STRATEGIES; ACETATE
+ METABOLISM; GROWTH; FRAGILIS; BACTERIA; FLUX; RESISTANCE; MICROBIOME},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Cho, Byung-Kwan/C-1830-2011},
+Times-Cited = {9},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000711623700002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000706089200001,
+Author = {Dukovski, Ilija and Bajic, Djordje and Chacon, Jeremy M. and Quintin,
+ Michael and Vila, Jean C. C. and Sulheim, Snorre and Pacheco, Alan R.
+ and Bernstein, David B. and Riehl, William J. and Korolev, Kirill S. and
+ Sanchez, Alvaro and Harcombe, William R. and Segre, Daniel},
+Title = {A metabolic modeling platform for the computation of microbial
+ ecosystems in time and space (COMETS)},
+Journal = {NATURE PROTOCOLS},
+Year = {2021},
+Volume = {16},
+Number = {11},
+Pages = {5030+},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1038/s41596-021-00593-3},
+EarlyAccessDate = {OCT 2021},
+ISSN = {1754-2189},
+EISSN = {1750-2799},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GENE-EXPRESSION; OPTICAL-PROPERTIES; GROWTH;
+ SCALE; EVOLUTION; COMMUNITIES; COOPERATION; DIVERSITY; PROCHLOROCOCCUS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Pacheco, Alan R/IUQ-5711-2023
+ Bajic, Djordje/ABB-4569-2020
+ Bernstein, David B/HLV-8885-2023
+ Segrè, Daniel/A-1993-2009
+ Sulheim, Snorre/ABC-5773-2020
+ },
+ORCID-Numbers = {Pacheco, Alan R/0000-0002-1128-3232
+ Bajic, Djordje/0000-0002-6716-7898
+ Bernstein, David B/0000-0001-6091-4021
+ Segrè, Daniel/0000-0003-4859-1914
+ Sulheim, Snorre/0000-0002-3967-1683
+ Quintin, Michael/0000-0001-6466-4234
+ Vila, Jean/0000-0003-0499-0200
+ Dukovski, Ilija/0000-0002-5160-1944
+ , Alvaro Sanchez/0000-0002-2292-5608},
+Times-Cited = {41},
+Journal-ISO = {Nat. Protoc.},
+Unique-ID = {WOS:000706089200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000705192900003,
+Author = {Vikromvarasiri, Nunthaphan and Shirai, Tomokazu and Kondo, Akihiko},
+Title = {Metabolic engineering design to enhance (R,R)-2,3-butanediol production
+ from glycerol in Bacillus subtilis based on flux balance analysis},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2021},
+Volume = {20},
+Number = {1},
+Month = {OCT 9},
+Type = {Article},
+DOI = {10.1186/s12934-021-01688-y},
+Article-Number = {196},
+EISSN = {1475-2859},
+Keywords = {Glycerol; 2; 3-Butainediol; Bacillus subtilis; Flux balance analysis;
+ Genome-scale metabolic models; Gene knockout},
+Keywords-Plus = {CRUDE GLYCEROL; 2,3-BUTANEDIOL; GENOME; YIELD},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Shirai, Tomokazu/C-7986-2017
+ },
+ORCID-Numbers = {Vikromvarasiri, Nunthaphan/0000-0002-0665-6882},
+Times-Cited = {8},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000705192900003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000710952900001,
+Author = {Joudeh, Nadeem and Saragliadis, Athanasios and Schulz, Christian and
+ Voigt, Andre and Almaas, Eivind and Linke, Dirk},
+Title = {Transcriptomic Response Analysis of Escherichia coli to Palladium
+ Stress},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2021},
+Volume = {12},
+Month = {OCT 8},
+Type = {Article},
+DOI = {10.3389/fmicb.2021.741836},
+Article-Number = {741836},
+EISSN = {1664-302X},
+Keywords = {RNA-seq; heavy metal stress; palladium; precious metals; nanoparticles;
+ oxidative stress; Escherichia coli; transcriptional response},
+Keywords-Plus = {METHIONINE SULFOXIDE REDUCTASES; HEAVY-METAL IONS; OXIDATIVE-STRESS;
+ CADMIUM TOXICITY; REACTIVE OXYGEN; GENE-REGULATION; NANOPARTICLES;
+ HOMEOSTASIS; PROTEINS; RECOVERY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Saragliadis, Athanasios/0000-0001-7950-6781
+ Joudeh, Nadeem/0000-0002-2032-9511},
+Times-Cited = {6},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000710952900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000707426400005,
+Author = {Zhu, Yuan and Li, Ying and Xu, Ya and Zhang, Jian and Ma, Linlin and Qi,
+ Qingsheng and Wang, Qian},
+Title = {Development of bifunctional biosensors for sensing and dynamic control
+ of glycolysis flux in metabolic engineering},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {68},
+Pages = {142-151},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.09.011},
+EarlyAccessDate = {OCT 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Glycolysis flux; Fructose-1; 6-diphosphate; Bifunctional biosensor;
+ Dynamic control; Mevalonate},
+Keywords-Plus = {ESCHERICHIA-COLI; REGULATORY PROTEIN; BINDING; DESIGN; GLUCOSAMINE;
+ PROMOTERS; PATHWAY; MODELS; SYSTEM; SENSOR},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {20},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000707426400005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000703757100001,
+Author = {Khushboo and Kumar, Punit and Dubey, Kashyap K. and Usmani, Zeba and
+ Sharma, Minaxi and Gupta, Vijai Kumar},
+Title = {Biotechnological and industrial applications of Streptomyces
+ metabolites},
+Journal = {BIOFUELS BIOPRODUCTS \& BIOREFINING-BIOFPR},
+Year = {2022},
+Volume = {16},
+Number = {1},
+Pages = {244-264},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1002/bbb.2294},
+EarlyAccessDate = {OCT 2021},
+ISSN = {1932-104X},
+EISSN = {1932-1031},
+Keywords = {antibiotics; Streptomyces; macrolide lactones; lipstatin; cholesterol
+ oxidase},
+Keywords-Plus = {BIOSYNTHETIC GENE CLUSTERS; MICROBIAL TRANSGLUTAMINASE PRODUCTION;
+ CLAVULANIC ACID PRODUCTION; POTATO SOLANUM-TUBEROSUM; ANTIBIOTIC
+ PRODUCTION; HETEROLOGOUS EXPRESSION; FILAMENTOUS MICROORGANISMS;
+ ENDOPHYTIC ACTINOBACTERIA; SECONDARY METABOLITE; CHOLESTEROL OXIDASE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Sharma, Minaxi/L-9405-2019
+ Gupta, Vijai Kumar/O-2445-2014
+ Dubey, Kashyap Kumar/D-6755-2014
+ },
+ORCID-Numbers = {Sharma, Minaxi/0000-0001-6493-5217
+ Gupta, Vijai Kumar/0000-0003-1565-5918
+ Dubey, Kashyap Kumar/0000-0002-4204-009X
+ , KHUSHBOO/0000-0002-0276-7366},
+Times-Cited = {12},
+Journal-ISO = {Biofuels Bioprod. Biorefining},
+Unique-ID = {WOS:000703757100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000710783400001,
+Author = {Antolin, Albert A. and Cascante, Marta},
+Title = {AI delivers Michaelis constants as fuel for genome-scale metabolic
+ models},
+Journal = {PLOS BIOLOGY},
+Year = {2021},
+Volume = {19},
+Number = {10},
+Month = {OCT},
+Type = {Editorial Material},
+DOI = {10.1371/journal.pbio.3001415},
+Article-Number = {e3001415},
+ISSN = {1544-9173},
+EISSN = {1545-7885},
+Research-Areas = {Biochemistry \& Molecular Biology; Life Sciences \& Biomedicine - Other
+ Topics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biology},
+ResearcherID-Numbers = {CASCANTE, MARTA/AAG-4355-2022
+ CASCANTE, MARTA/AFK-5991-2022},
+ORCID-Numbers = {CASCANTE, MARTA/0000-0002-2062-4633
+ CASCANTE, MARTA/0000-0002-2062-4633},
+Times-Cited = {2},
+Journal-ISO = {PLoS. Biol.},
+Unique-ID = {WOS:000710783400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000711353900008,
+Author = {Lu, Hongzhong and Li, Feiran and Yuan, Le and Domenzain, Ivan and Yu,
+ Rosemary and Wang, Hao and Li, Gang and Chen, Yu and Ji, Boyang and
+ Kerkhoven, Eduard J. and Nielsen, Jens},
+Title = {Yeast metabolic innovations emerged via expanded metabolic network and
+ gene positive selection},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.15252/msb.202110427},
+Article-Number = {e10427},
+ISSN = {1744-4292},
+Keywords = {genome analysis; genome-scale metabolic models; metabolic innovation;
+ systems biology},
+Keywords-Plus = {ADAPTIVE EVOLUTION; PROTEIN; DATABASE; RECONSTRUCTION; PATHWAYS;
+ PREDICTION; SEQUENCES; IDENTIFICATION; APPROXIMATION; GENOMICS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Kerkhoven, Eduard/P-2469-2019
+ Ji, Boyang/HMV-6662-2023
+ Chen, Yu/AAL-3329-2020
+ Li, Feiran/GNP-2168-2022
+ Domenzain, Ivan/HCI-9542-2022
+ },
+ORCID-Numbers = {Kerkhoven, Eduard/0000-0002-3593-5792
+ Ji, Boyang/0000-0002-7269-4342
+ Chen, Yu/0000-0003-3326-9068
+ Li, Feiran/0000-0001-9155-5260
+ Domenzain, Ivan/0000-0002-5322-2040
+ Yu, Rosemary/0000-0001-9901-4055
+ Yuan, Le/0000-0003-3317-9011
+ Li, Gang/0000-0001-6778-2842
+ Wang, Hao/0000-0001-7475-0136},
+Times-Cited = {10},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000711353900008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000726836100002,
+Author = {Munro, Lachlan J. and Kell, Douglas B.},
+Title = {Intelligent host engineering for metabolic flux optimisation in
+ biotechnology},
+Journal = {BIOCHEMICAL JOURNAL},
+Year = {2021},
+Volume = {478},
+Number = {20},
+Pages = {3685-3721},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1042/BCJ20210535},
+ISSN = {0264-6021},
+EISSN = {1470-8728},
+Keywords-Plus = {HETEROLOGOUS GENE-EXPRESSION; FEAST/FAMINE REGULATORY PROTEINS; NATURAL
+ TRANSFORMATION MUGENT; CONSTRAINT-BASED MODELS; FACTOR-BASED BIOSENSORS;
+ HIGH MUTATION-RATES; ESCHERICHIA-COLI; DIRECTED EVOLUTION; SYNTHETIC
+ BIOLOGY; SACCHAROMYCES-CEREVISIAE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Kell, Douglas/E-8318-2011},
+ORCID-Numbers = {Kell, Douglas/0000-0001-5838-7963},
+Times-Cited = {5},
+Journal-ISO = {Biochem. J.},
+Unique-ID = {WOS:000726836100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000701311600001,
+Author = {Kuriya, Yuki and Inoue, Mai and Yamamoto, Masaki and Murata, Masahiro
+ and Araki, Michihiro},
+Title = {Knowledge extraction from literature and enzyme sequences complements
+ FBA analysis in metabolic engineering},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2021},
+Volume = {16},
+Number = {12},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1002/biot.202000443},
+EarlyAccessDate = {SEP 2021},
+Article-Number = {e2000443},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {bio-production; flux balance analysis; genome-scale metabolic model;
+ literature mining},
+Keywords-Plus = {FLUX ANALYSIS; CORYNEBACTERIUM-GLUTAMICUM; MODELS; MESH; INTEGRATION;
+ GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Inoue, Mai/0000-0003-3204-1627
+ Araki, Michihiro/0000-0002-6686-4018},
+Times-Cited = {1},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000701311600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000705653800012,
+Author = {Jatain, Indu and Dubey, Kashyap Kumar and Sharma, Manisha and Usmani,
+ Zeba and Sharma, Minaxi and Gupta, Vijai Kumar},
+Title = {Synthetic biology potential for carbon sequestration into biocommodities},
+Journal = {JOURNAL OF CLEANER PRODUCTION},
+Year = {2021},
+Volume = {323},
+Month = {NOV 10},
+Type = {Article},
+DOI = {10.1016/j.jclepro.2021.129176},
+EarlyAccessDate = {SEP 2021},
+Article-Number = {129176},
+ISSN = {0959-6526},
+EISSN = {1879-1786},
+Keywords = {CO2 fixation pathway; CO2 sequestration; Metabolic engineering;
+ Synthetic biology; System biology; Bioproducts},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; FATTY-ACID PRODUCTION; BETA-OXIDATION CYCLE;
+ ESCHERICHIA-COLI; BIOSYNTHETIC-PATHWAY; FIXATION; CO2; SYSTEMS;
+ CYANOBACTERIA; GLYCOLYSIS},
+Research-Areas = {Science \& Technology - Other Topics; Engineering; Environmental
+ Sciences \& Ecology},
+Web-of-Science-Categories = {Green \& Sustainable Science \& Technology; Engineering, Environmental;
+ Environmental Sciences},
+ResearcherID-Numbers = {Gupta, Vijai Kumar/O-2445-2014
+ Dubey, Kashyap Kumar/D-6755-2014
+ Sharma, Minaxi/L-9405-2019
+ },
+ORCID-Numbers = {Gupta, Vijai Kumar/0000-0003-1565-5918
+ Dubey, Kashyap Kumar/0000-0002-4204-009X
+ Sharma, Minaxi/0000-0001-6493-5217
+ Sharma, Manisha/0000-0001-5248-5239},
+Times-Cited = {3},
+Journal-ISO = {J. Clean Prod.},
+Unique-ID = {WOS:000705653800012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000709658300002,
+Author = {Seif, Yara and Palsson, Bernhard Orn},
+Title = {Path to improving the life cycle and quality of genome-scale models of
+ metabolism},
+Journal = {CELL SYSTEMS},
+Year = {2021},
+Volume = {12},
+Number = {9},
+Pages = {842-859},
+Month = {SEP 22},
+Type = {Article},
+DOI = {10.1016/j.cels.2021.06.005},
+EarlyAccessDate = {SEP 2021},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {STAPHYLOCOCCUS-AUREUS; ESCHERICHIA-COLI; METACYC DATABASE; SYSTEMS
+ BIOLOGY; GLOBAL RECONSTRUCTION; BIOCYC COLLECTION; GENE ESSENTIALITY;
+ SWISS-PROT; NETWORK; ENZYMES},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Seif, Yara/T-4012-2017},
+Times-Cited = {10},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000709658300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000703072200001,
+Author = {Medeiros Filho, Fernando and do Nascimento, Ana Paula Barbosa and
+ Cerqueira e Costa, Maiana de Oliveira and Merigueti, Thiago Castanheira
+ and de Menezes, Marcio Argollo and Nicolas, Marisa Fabiana and Santos,
+ Marcelo Trindade dos and Carvalho-Assef, Ana Paula D'Alincourt and da
+ Silva, Fabricio Alves Barbosa},
+Title = {A Systematic Strategy to Find Potential Therapeutic Targets for
+ Pseudomonas aeruginosa Using Integrated Computational Models},
+Journal = {FRONTIERS IN MOLECULAR BIOSCIENCES},
+Year = {2021},
+Volume = {8},
+Month = {SEP 20},
+Type = {Article},
+DOI = {10.3389/fmolb.2021.728129},
+Article-Number = {728129},
+EISSN = {2296-889X},
+Keywords = {Pseudomonas aeruginosa; metabolic network; transcriptome data;
+ integrated model; therapeutic target},
+Keywords-Plus = {TRANSFER-RNA SYNTHETASE; METABOLIC NETWORK ANALYSIS; FATTY-ACID
+ BIOSYNTHESIS; GENOME-SCALE MODELS; ALKALINE-PHOSPHATASE; REGULATORY
+ NETWORKS; ESCHERICHIA-COLI; ISOCITRATE LYASE; MALATE SYNTHASE;
+ INHIBITORS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {de Menezes, Marcio Argollo Ferreira/AAP-9570-2020
+ Carvalho-Assef, Ana Paula/AAS-5071-2021
+ Argollo de Menezes, Marcio/P-6643-2016
+ },
+ORCID-Numbers = {Carvalho-Assef, Ana Paula/0000-0001-7044-4596
+ Argollo de Menezes, Marcio/0000-0002-0450-1668
+ Costa, Maiana/0000-0003-3819-3138
+ Barbosa do Nascimento Oliveira, Ana Paula/0000-0002-4700-1671
+ Silva, Fabricio/0000-0002-8172-5796},
+Times-Cited = {3},
+Journal-ISO = {Front. Mol. Biosci.},
+Unique-ID = {WOS:000703072200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000696834800001,
+Author = {Karvelsson, Sigurdur Trausti and Wang, Qiong and Hilmarsdottir, Bylgja
+ and Sigurdsson, Arnar and Moestue, Siver Andreas and Maelandsmo, Gunhild
+ Mari and Halldorsson, Skarphedinn and Gudmundsson, Steinn and Rolfsson,
+ Ottar},
+Title = {Argininosuccinate lyase is a metabolic vulnerability in breast
+ development and cancer},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2021},
+Volume = {7},
+Number = {1},
+Month = {SEP 17},
+Type = {Article},
+DOI = {10.1038/s41540-021-00195-5},
+Article-Number = {36},
+EISSN = {2056-7189},
+Keywords-Plus = {HEPATOCELLULAR-CARCINOMA; THERAPEUTIC TARGET; METASTASIS; EXPRESSION;
+ GROWTH; PROLIFERATION; TRANSITION; PLASTICITY; HALLMARKS; TUMORS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Hilmarsdottir, Bylgja/AAV-7406-2020
+ Mælandsmo, Gunhild Mari/AFV-4446-2022
+ },
+ORCID-Numbers = {Mælandsmo, Gunhild Mari/0000-0002-4797-1600
+ Rolfsson, Ottar/0000-0003-4258-6057
+ Hilmarsdottir, Bylgja/0000-0001-8693-5541
+ Sigurdsson, Arnar/0000-0001-9617-0829
+ Karvelsson, Sigurdur Trausti/0000-0002-1088-2364
+ Moestue, Siver Andreas/0000-0002-1940-5695},
+Times-Cited = {2},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000696834800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000743380100025,
+Author = {Pio, Gianvito and Mignone, Paolo and Magazzu, Giuseppe and Zampieri,
+ Guido and Ceci, Michelangelo and Angione, Claudio},
+Title = {Integrating genome-scale metabolic modelling and transfer learning for
+ human gene regulatory network reconstruction},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Volume = {38},
+Number = {2},
+Pages = {487-493},
+Month = {JAN 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btab647},
+EarlyAccessDate = {SEP 2021},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {CLASSIFICATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Zampieri, Guido/HJH-7472-2023
+ Mignone, Paolo/Y-5494-2018
+ },
+ORCID-Numbers = {Zampieri, Guido/0000-0002-4518-5913
+ Mignone, Paolo/0000-0002-8641-7880
+ Angione, Claudio/0000-0002-3140-7909
+ Pio, Gianvito/0000-0003-2520-3616},
+Times-Cited = {18},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000743380100025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000692961100001,
+Author = {Lee, Jihoon W. and Su, Yapeng and Baloni, Priyanka and Chen, Daniel and
+ Pavlovitch-Bedzyk, Ana Jimena and Yuan, Dan and Duvvuri, Venkata R. and
+ Ng, Rachel H. and Choi, Jongchan and Xie, Jingyi and Zhang, Rongyu and
+ Murray, Kim and Kornilov, Sergey and Smith, Brett and Magis, Andrew T.
+ and Hoon, Dave S. B. and Hadlock, Jennifer J. and Goldman, Jason D. and
+ Price, Nathan D. and Gottardo, Raphael and Davis, Mark M. and Hood,
+ Leroy and Greenberg, Philip D. and Heath, James R.},
+Title = {Integrated analysis of plasma and single immune cells uncovers metabolic
+ changes in individuals with COVID-19},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2022},
+Volume = {40},
+Number = {1},
+Pages = {110+},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1038/s41587-021-01020-4},
+EarlyAccessDate = {SEP 2021},
+ISSN = {1087-0156},
+EISSN = {1546-1696},
+Keywords-Plus = {RESOLVES; HEALTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Gottardo, Raphael/HCH-3169-2022
+ Yuan, Dan/Q-5563-2017
+ Xie, Jingyi/IUO-6666-2023
+ Goldman, Jason D./AEL-9703-2022
+ Su, Yapeng/JRY-7299-2023
+ Goldman, Jason D./AAD-9419-2020
+ Lee, Jihoon William/AAT-9036-2020
+ Duvvuri, Venkata R/H-2728-2019
+ },
+ORCID-Numbers = {Yuan, Dan/0000-0002-6587-9250
+ Su, Yapeng/0000-0002-6305-8467
+ Goldman, Jason D./0000-0002-3825-6832
+ Lee, Jihoon William/0000-0002-6749-5111
+ Duvvuri, Venkata R/0000-0001-7356-338X
+ Ng, Rachel/0000-0003-3692-8524
+ Yuan, Dan/0000-0001-9651-8020
+ Gottardo, Raphael/0000-0002-3867-0232
+ Chen, Daniel/0000-0001-6660-6257
+ Hadlock, Jennifer/0000-0001-6103-7606
+ Baloni, Priyanka/0000-0002-3382-4941},
+Times-Cited = {63},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000692961100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000692500900001,
+Author = {Yaneske, Elisabeth and Zampieri, Guido and Bertoldi, Loris and
+ Benvenuto, Giuseppe and Angione, Claudio},
+Title = {Genome-scale metabolic modelling of SARS-CoV-2 in cancer cells reveals
+ an increased shift to glycolytic energy production},
+Journal = {FEBS LETTERS},
+Year = {2021},
+Volume = {595},
+Number = {18},
+Pages = {2350-2365},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1002/1873-3468.14180},
+EarlyAccessDate = {SEP 2021},
+ISSN = {0014-5793},
+EISSN = {1873-3468},
+Keywords = {cancer; COVID-19; flux balance analysis; genome-scale metabolic
+ modelling; multi-omics; SARS-CoV-2},
+Keywords-Plus = {SUCCINATE-DEHYDROGENASE; GUANYLATE KINASE; T-CELLS; COVID-19; INFECTION;
+ EXPRESSION; COMPLEX; TARGET; PLASMA; IL-15},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+ResearcherID-Numbers = {Zampieri, Guido/HJH-7472-2023
+ },
+ORCID-Numbers = {Zampieri, Guido/0000-0002-4518-5913
+ Angione, Claudio/0000-0002-3140-7909
+ Yaneske, Elisabeth/0000-0001-6230-4016
+ Bertoldi, Loris/0000-0002-8516-7680
+ Benvenuto, Giuseppe/0000-0001-9147-4946},
+Times-Cited = {8},
+Journal-ISO = {FEBS Lett.},
+Unique-ID = {WOS:000692500900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000695193200001,
+Author = {Dung Hoang Anh Mai and Thu Thi Nguyen and Lee, Eun Yeol},
+Title = {The ethylmalonyl-CoA pathway for methane-based biorefineries: a case
+ study of using Methylosinus trichosporium OB3b, an
+ alpha-proteobacterial methanotroph, for producing 2-hydroxyisobutyric
+ acid and 1,3-butanediol from methane},
+Journal = {GREEN CHEMISTRY},
+Year = {2021},
+Volume = {23},
+Number = {19},
+Pages = {7712-7723},
+Month = {OCT 4},
+Type = {Article},
+DOI = {10.1039/d1gc02866a},
+EarlyAccessDate = {SEP 2021},
+ISSN = {1463-9262},
+EISSN = {1463-9270},
+Keywords-Plus = {METHYLOBACTERIUM-EXTORQUENS; II METHANOTROPH; C-2 COMPOUNDS; GROWTH;
+ CYCLE; (R)-1,3-BUTANEDIOL; HYDROXYVALERATE; TRANSCRIPTOME; BIOSYNTHESIS;
+ ACTIVATION},
+Research-Areas = {Chemistry; Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary; Green \& Sustainable Science \& Technology},
+ORCID-Numbers = {Mai, Dung/0000-0001-5916-3486
+ Lee, Eun Yeol/0000-0002-6974-3262},
+Times-Cited = {6},
+Journal-ISO = {Green Chem.},
+Unique-ID = {WOS:000695193200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000733832700052,
+Author = {Heinken, Almut and Magnusdottir, Stefania and Fleming, Ronan M. T. and
+ Thiele, Ines},
+Title = {DEMETER: efficient simultaneous curation of genome-scale reconstructions
+ guided by experimental data and refined gene annotations},
+Journal = {BIOINFORMATICS},
+Year = {2021},
+Volume = {37},
+Number = {21},
+Pages = {3974-3975},
+Month = {NOV 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btab622},
+EarlyAccessDate = {SEP 2021},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Magnusdottir, Stefania/ABA-2212-2021
+ Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Magnusdottir, Stefania/0000-0001-6506-8696
+ Thiele, Ines/0000-0002-8071-7110
+ Heinken, Almut/0000-0001-6938-8072},
+Times-Cited = {7},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000733832700052},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000703575300001,
+Author = {Khaleghi, Mohammad Karim and Savizi, Iman Shahidi Pour and Lewis, Nathan
+ E. and Shojaosadati, Seyed Abbas},
+Title = {Synergisms of machine learning and constraint-based modeling of
+ metabolism for analysis and optimization of fermentation parameters},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2021},
+Volume = {16},
+Number = {11},
+Month = {NOV},
+Type = {Review},
+DOI = {10.1002/biot.202100212},
+EarlyAccessDate = {SEP 2021},
+Article-Number = {e2100212},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {constraint based modeling; fermentation optimization; genome scale
+ modeling; machine learning},
+Keywords-Plus = {GENOME-SCALE MODELS; NEURAL-NETWORKS; CELL-METABOLISM; KINETIC-MODELS;
+ FLUX ANALYSIS; OMICS DATA; METABOLOMICS; STRATEGY; TRANSCRIPTOMICS;
+ GENERATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Shojaosadati, Seyed Abbas/ABE-1178-2021
+ Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Shojaosadati, Seyed Abbas/0000-0002-8561-2414
+ Lewis, Nathan/0000-0001-7700-3654
+ Shahidi Pour Savizi, Iman/0000-0003-3371-5523},
+Times-Cited = {12},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000703575300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000701850200001,
+Author = {Bogaerts, Philippe and Vande Wouwer, Alain},
+Title = {How to Tackle Underdeterminacy in Metabolic Flux Analysis? A Tutorial
+ and Critical Review},
+Journal = {PROCESSES},
+Year = {2021},
+Volume = {9},
+Number = {9},
+Month = {SEP},
+Type = {Review},
+DOI = {10.3390/pr9091577},
+Article-Number = {1577},
+EISSN = {2227-9717},
+Keywords = {flux variability analysis; flux balance analysis; sampling; metabolic
+ network; elementary flux modes},
+Keywords-Plus = {FED-BATCH CULTURES; MINIMAL CUT SETS; HIT-AND-RUN; BALANCE ANALYSIS;
+ CELL-CULTURES; ELEMENTARY MODES; PHYSIOLOGICAL-STATE;
+ BIOLOGICAL-SYSTEMS; NETWORK; GROWTH},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ORCID-Numbers = {Bogaerts, Philippe/0000-0003-0423-1933
+ Vande Wouwer, Alain/0000-0001-7022-6126},
+Times-Cited = {2},
+Journal-ISO = {Processes},
+Unique-ID = {WOS:000701850200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000699224500001,
+Author = {Frades, Itziar and Foguet, Carles and Cascante, Marta and Arauzo-Bravo,
+ Marcos J.},
+Title = {Genome Scale Modeling to Study the Metabolic Competition between Cells
+ in the Tumor Microenvironment},
+Journal = {CANCERS},
+Year = {2021},
+Volume = {13},
+Number = {18},
+Month = {SEP},
+Type = {Review},
+DOI = {10.3390/cancers13184609},
+Article-Number = {4609},
+EISSN = {2072-6694},
+Keywords = {metabolic reprogramming in cancer; immune system; genome-scale metabolic
+ models; constraint-based modeling; stoichiometric models; kinetic
+ metabolic models; metabolic crosstalk},
+Keywords-Plus = {HIT-AND-RUN; GLOBAL RECONSTRUCTION; IMMUNE-SYSTEM; AMPK-MTOR; CANCER;
+ RESPONSES; HYPOXIA; NETWORK; INFLAMMATION; INTEGRATION},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ResearcherID-Numbers = {CASCANTE, MARTA/AAG-4355-2022
+ Foguet, Carles/W-4864-2018
+ CASCANTE, MARTA/AFK-5991-2022
+ Marcos, Arauzo-Bravo/A-1706-2011},
+ORCID-Numbers = {CASCANTE, MARTA/0000-0002-2062-4633
+ Foguet, Carles/0000-0001-8494-9595
+ CASCANTE, MARTA/0000-0002-2062-4633
+ Marcos, Arauzo-Bravo/0000-0002-3264-464X},
+Times-Cited = {8},
+Journal-ISO = {Cancers},
+Unique-ID = {WOS:000699224500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000711939400011,
+Author = {Jenior, Matthew L. and Leslie, Jhansi L. and Powers, Deborah A. and
+ Garrett, Elizabeth M. and Walker, Kimberly A. and Dickenson, Mary E. and
+ Petri, Jr., William A. and Tamayo, Rita and Papin, Jason A.},
+Title = {Novel Drivers of Virulence in Clostridioides difficile Identified
+ via Context-Specific Metabolic Network Analysis},
+Journal = {MSYSTEMS},
+Year = {2021},
+Volume = {6},
+Number = {5},
+Month = {SEP-OCT},
+Type = {Article},
+DOI = {10.1128/mSystems.00919-21},
+Article-Number = {e00919-21},
+ISSN = {2379-5077},
+Keywords = {Clostridioides difficile; metabolic modeling; transcriptomics; virulence
+ factors},
+Keywords-Plus = {BACTERIAL BIOINFORMATICS DATABASE; ANTIBIOTIC-TREATMENT; READ ALIGNMENT;
+ IN-VIVO; GENOME; GROWTH; SEQUENCE; 630-DELTA-ERM; INFECTION; STRAIN},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Papin, Jason/0000-0002-2769-5805
+ Leslie, Jhansi/0000-0001-5600-210X
+ Jenior, Matthew/0000-0003-1884-3543},
+Times-Cited = {7},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000711939400011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000769986400016,
+Author = {Scott, Jr., William T. and van Mastrigt, Oscar and Block, David E. and
+ Notebaart, Richard A. and Smid, Eddy J.},
+Title = {Nitrogenous Compound Utilization and Production of Volatile Organic
+ Compounds among Commercial Wine Yeasts Highlight Strain-Specific
+ Metabolic Diversity},
+Journal = {MICROBIOLOGY SPECTRUM},
+Year = {2021},
+Volume = {9},
+Number = {1},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1128/Spectrum.00485-21},
+Article-Number = {e00485-21},
+ISSN = {2165-0497},
+Keywords = {volatile organic compounds; HS-SPME/GC-MS; Saccharomyces cerevisiae;
+ fermentation; wine; metabolic modeling},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; AMINO-ACID; CATABOLITE REPRESSION; AROMATIC
+ COMPOSITION; FERMENTATIVE AROMAS; ESTER PRODUCTION; KINETIC-MODEL;
+ MUSTS; EXPRESSION; AMMONIUM},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Notebaart, Richard A./A-1459-2014
+ },
+ORCID-Numbers = {Scott, William/0000-0002-4029-2998
+ Smid, Eddy J./0000-0002-6687-5083},
+Times-Cited = {9},
+Journal-ISO = {Microbiol. Spectr.},
+Unique-ID = {WOS:000769986400016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000702538800001,
+Author = {Stalidzans, Egils and Dace, Elina},
+Title = {Sustainable metabolic engineering for sustainability optimisation of
+ industrial biotechnology},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2021},
+Volume = {19},
+Pages = {4770-4776},
+Type = {Article},
+DOI = {10.1016/j.csbj.2021.08.034},
+EarlyAccessDate = {AUG 2021},
+ISSN = {2001-0370},
+Keywords = {Biotechnology; Genome-scale metabolic models; Mathematical modelling;
+ Ranking; Sustainability optimisation; Sustainable metabolic engineering},
+Keywords-Plus = {GREENHOUSE-GAS EMISSIONS; GENOME-SCALE MODELS; ETHANOL; BIOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Stalidzans, Egils/G-5883-2010},
+ORCID-Numbers = {Stalidzans, Egils/0000-0001-6063-0184},
+Times-Cited = {9},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000702538800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000687347500001,
+Author = {Petrovs, Rudolfs and Stalidzans, Egils and Pentjuss, Agris},
+Title = {IMFLer: A Web Application for Interactive Metabolic Flux Analysis and
+ Visualization},
+Journal = {JOURNAL OF COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {28},
+Number = {10},
+Pages = {1021-1032},
+Month = {OCT 1},
+Type = {Article},
+DOI = {10.1089/cmb.2021.0056},
+EarlyAccessDate = {AUG 2021},
+ISSN = {1066-5277},
+EISSN = {1557-8666},
+Keywords = {cellular metabolism; flux balance analysis; flux variability analysis;
+ genome-scale metabolic models; network visualization},
+Keywords-Plus = {NETWORKS; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Stalidzans, Egils/G-5883-2010
+ },
+ORCID-Numbers = {Stalidzans, Egils/0000-0001-6063-0184
+ Pentjuss, Agris/0000-0001-7880-5130},
+Times-Cited = {5},
+Journal-ISO = {J. Comput. Biol.},
+Unique-ID = {WOS:000687347500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000697354200001,
+Author = {Esvap, Elif and Ulgen, Kutlu O.},
+Title = {Advances in Genome-Scale Metabolic Modeling toward Microbial Community
+ Analysis of the Human Microbiome},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2021},
+Volume = {10},
+Number = {9},
+Pages = {2121-2137},
+Month = {SEP 17},
+Type = {Review},
+DOI = {10.1021/acssynbio.1c00140},
+EarlyAccessDate = {AUG 2021},
+ISSN = {2161-5063},
+Keywords = {genome-scale metabolic models; microbiota; community modeling;
+ personalized medicine},
+Keywords-Plus = {GUT MICROBIOME; BIOCHEMICAL REACTIONS; BIG DATA; CHALLENGES; BALANCE;
+ METANETX/MNXREF; RESOURCE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Esvap, Elif/AAR-4483-2020
+ },
+ORCID-Numbers = {Esvap, Elif/0000-0002-7915-2618
+ Ulgen, Kutlu/0000-0003-3668-3467},
+Times-Cited = {7},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000697354200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000683506000013,
+Author = {Oftadeh, Omid and Salvy, Pierre and Masid, Maria and Curvat, Maxime and
+ Miskovic, Ljubisa and Hatzimanikatis, Vassily},
+Title = {A genome-scale metabolic model of Saccharomyces cerevisiae that
+ integrates expression constraints and reaction thermodynamics},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2021},
+Volume = {12},
+Number = {1},
+Month = {AUG 9},
+Type = {Article},
+DOI = {10.1038/s41467-021-25158-6},
+Article-Number = {4790},
+ISSN = {2041-1723},
+Keywords-Plus = {FERMENTATIVE CAPACITY; RIBOSOMAL-PROTEINS; ESCHERICHIA-COLI; GIBBS
+ ENERGIES; GROWTH; ENCYCLOPEDIA; CULTURES; DATABASE; BALANCE; ENZYMES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Miskovic, Ljubisa/E-8927-2012
+ Hatzimanikatis, Vassily/G-6505-2010
+ Oftadeh, Omid/ABF-1579-2021
+ },
+ORCID-Numbers = {Miskovic, Ljubisa/0000-0001-7333-8211
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Masid, Maria/0000-0001-6470-5083
+ Oftadeh, Omid/0000-0002-8168-738X
+ SALVY, Pierre/0000-0002-3834-0356},
+Times-Cited = {31},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000683506000013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000682521800007,
+Author = {Wagner, Allon and Wang, Chao and Fessler, Johannes and DeTomaso, David
+ and Avila-Pacheco, Julian and Kaminski, James and Zaghouani, Sarah and
+ Christian, Elena and Thakore, Pratiksha and Schellhaass, Brandon and
+ Akama-Garren, Elliot and Pierce, Kerry and Singh, Vasundhara and
+ Ron-Harel, Noga and Douglas, Vivian Paraskevi and Bod, Lloyd and
+ Schnell, Alexandra and Puleston, Daniel and Sobel, Raymond A. and
+ Haigis, Marcia and Pearce, Erika L. and Soleimani, Manoocher and Clish,
+ Clary and Regev, Aviv and Kuchroo, Vijay K. and Yosef, Nir},
+Title = {Metabolic modeling of single Th17 cells reveals regulators of
+ autoimmunity},
+Journal = {CELL},
+Year = {2021},
+Volume = {184},
+Number = {16},
+Pages = {4168+},
+Month = {AUG 5},
+Type = {Article},
+DOI = {10.1016/j.cell.2021.05.045},
+EarlyAccessDate = {AUG 2021},
+ISSN = {0092-8674},
+EISSN = {1097-4172},
+Keywords-Plus = {T(H)17 CELLS; TGF-BETA; T-CELLS; NETWORK; IMMUNOMETABOLISM;
+ DIFFERENTIATION; IMMUNITY; GAMMA; IL-17; MICE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Clish, Clary B/ABB-9374-2021
+ Bod, Lloyd/AAG-2345-2020
+ Thakore, Pratiksha/HDM-5197-2022
+ Akama-Garren, Elliot/JRY-5508-2023
+ Wang, Chao/GYD-5103-2022
+ },
+ORCID-Numbers = {Clish, Clary B/0000-0001-8259-9245
+ Bod, Lloyd/0000-0003-3663-2571
+ Akama-Garren, Elliot/0000-0002-1690-2055
+ Wang, Chao/0000-0003-3084-6093
+ Puleston, Daniel/0000-0002-8437-0732
+ Zaghouani, Sarah/0000-0002-4467-6542
+ Sobel, Raymond/0000-0002-0477-9002
+ Fessler, Johannes/0000-0002-8841-3795
+ Singh, Vasundhara/0000-0001-8391-8527
+ Schnell, Alexandra/0000-0003-3442-7750},
+Times-Cited = {125},
+Journal-ISO = {Cell},
+Unique-ID = {WOS:000682521800007},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000701245000009,
+Author = {Baloni, Priyanka and Funk, Cory C. and Readhead, Ben and Price, Nathan
+ D.},
+Title = {Systems modeling of metabolic dysregulation in neurodegenerative
+ diseases},
+Journal = {CURRENT OPINION IN PHARMACOLOGY},
+Year = {2021},
+Volume = {60},
+Pages = {59-65},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1016/j.coph.2021.06.012},
+EarlyAccessDate = {AUG 2021},
+ISSN = {1471-4892},
+EISSN = {1471-4973},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy},
+ORCID-Numbers = {Readhead, Ben/0000-0003-4353-9965
+ Baloni, Priyanka/0000-0002-3382-4941
+ Funk, Cory/0000-0002-5229-9011},
+Times-Cited = {5},
+Journal-ISO = {Curr. Opin. Pharmacol.},
+Unique-ID = {WOS:000701245000009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000689560700001,
+Author = {Fondi, Marco and Gonzi, Stefano and Dziurzynski, Mikolaj and Turano,
+ Paola and Ghini, Veronica and Calvanese, Marzia and Colarusso, Andrea
+ and Lauro, Concetta and Parrilli, Ermenegilda and Tutino, Maria Luisa},
+Title = {Modelling hCDKL5 Heterologous Expression in Bacteria},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.3390/metabo11080491},
+Article-Number = {491},
+EISSN = {2218-1989},
+Keywords = {CDKL5; genome-scale metabolic modelling; protein production},
+Keywords-Plus = {PROTEIN-PRODUCTION; PICHIA-PASTORIS; PLASMID},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {parrilli, ermenegilda/K-4616-2016
+ Dziurzyński, Mikołaj/IWE-3645-2023
+ TUTINO, MARIA LUISA/L-1834-2013
+ Turano, Paola/F-9089-2011
+ },
+ORCID-Numbers = {parrilli, ermenegilda/0000-0002-9002-5409
+ Dziurzyński, Mikołaj/0000-0002-5593-9432
+ Colarusso, Andrea/0000-0001-6311-4986
+ Tutino, Maria Luisa/0000-0002-4978-6839
+ Lauro, Concetta/0000-0003-0139-5166
+ Fondi, Marco/0000-0001-9291-5467
+ Calvanese, Marzia/0000-0002-7554-0680
+ Turano, Paola/0000-0002-7683-8614
+ GHINI, VERONICA/0000-0003-3759-6701},
+Times-Cited = {4},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000689560700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000688923800001,
+Author = {Ramirez-Malule, Howard and Lopez-Agudelo, Victor A. and Gomez-Rios,
+ David and Ochoa, Silvia and Rios-Estepa, Rigoberto and Junne, Stefan and
+ Neubauer, Peter},
+Title = {TCA Cycle and Its Relationship with Clavulanic Acid Production: A
+ Further Interpretation by Using a Reduced Genome-Scale Metabolic Model
+ of Streptomyces clavuligerus},
+Journal = {BIOENGINEERING-BASEL},
+Year = {2021},
+Volume = {8},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.3390/bioengineering8080103},
+Article-Number = {103},
+EISSN = {2306-5354},
+Keywords = {Streptomyces clavuligerus; clavulanic acid; fed-batch cultivation; TCA
+ cycle intermediate; flux balance analysis; single-use bioreactor; shadow
+ prices},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Biomedical},
+ResearcherID-Numbers = {Neubauer, Peter/N-8146-2013
+ Gómez Ríos, David Andrés/ABA-3229-2021
+ Neubauer, Peter/W-4518-2019
+ },
+ORCID-Numbers = {Neubauer, Peter/0000-0002-1214-9713
+ Lopez-Agudelo, Victor A./0000-0003-1339-972X
+ Rios-Estepa, Rigoberto/0000-0002-3287-7056
+ Gomez Rios, David/0000-0002-9858-9559
+ Ramirez-Malule, Howard/0000-0003-1013-5809
+ Junne, Stefan/0000-0001-6185-2627},
+Times-Cited = {2},
+Journal-ISO = {Bioengineering-Basel},
+Unique-ID = {WOS:000688923800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000691047200014,
+Author = {Wilken, St Elmo and Frazao, Victor Vera and Saadat, Nima P. and
+ Ebenhoeh, Oliver},
+Title = {The view of microbes as energy converters illustrates the trade-off
+ between growth rate and yield},
+Journal = {BIOCHEMICAL SOCIETY TRANSACTIONS},
+Year = {2021},
+Volume = {49},
+Number = {4},
+Pages = {1663-1674},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1042/BST20200977},
+ISSN = {0300-5127},
+EISSN = {1470-8752},
+Keywords-Plus = {THERMODYNAMICALLY INFEASIBLE LOOPS; ENZYME-CATALYZED REACTIONS;
+ METABOLIC PATHWAYS; LINEAR RELATION; BIOMASS YIELDS; OPTIMIZATION;
+ EFFICIENCY; MODEL; ATP; BIOTECHNOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Ebenhoeh, Oliver/C-8974-2011
+ },
+ORCID-Numbers = {Ebenhoeh, Oliver/0000-0002-7229-7398
+ Wilken, St. Elmo/0000-0002-4113-2590},
+Times-Cited = {1},
+Journal-ISO = {Biochem. Soc. Trans.},
+Unique-ID = {WOS:000691047200014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000743380100044,
+Author = {Theorell, Axel and Jadebeck, Johann F. and Noeh, Katharina and Stelling,
+ Joerg},
+Title = {PolyRound: polytope rounding for random sampling in metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2022},
+Volume = {38},
+Number = {2},
+Pages = {566-567},
+Month = {JAN 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btab552},
+EarlyAccessDate = {JUL 2021},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {HIT-AND-RUN},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+Times-Cited = {2},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000743380100044},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000679429100001,
+Author = {Dai, Zongjie and Zhu, Yan and Dong, Hongjun and Zhao, Chunhua and Zhang,
+ Yanping and Li, Yin},
+Title = {Enforcing ATP hydrolysis enhanced anaerobic glycolysis and promoted
+ solvent production in Clostridium acetobutylicum},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2021},
+Volume = {20},
+Number = {1},
+Month = {JUL 29},
+Type = {Article},
+DOI = {10.1186/s12934-021-01639-7},
+Article-Number = {149},
+EISSN = {1475-2859},
+Keywords = {Anaerobic fermentation; Clostridium acetobutylicum; ABE fermentation;
+ ATP hydrolysis; F-1-ATPase; Acidogenesis; Solventogenesis},
+Keywords-Plus = {ESCHERICHIA-COLI; RECOMBINANT STRAINS; CONTINUOUS-CULTURE; FLUX;
+ SOLVENTOGENESIS; METABOLISM; PATHWAYS; ENZYMES; NUCLEOTIDES; EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Zhang, Yanping/C-7114-2009},
+Times-Cited = {9},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000679429100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000680264800007,
+Author = {Echeverri-Pena, Olga Y. and Salazar-Barreto, Diego A. and
+ Rodriguez-Lopez, Alexander and Gonzalez, Janneth and Almeciga-Diaz,
+ Carlos J. and Verano-Guevara, Cristian H. and Barrera, Luis A.},
+Title = {Use of a neuron-glia genome-scale metabolic reconstruction to model the
+ metabolic consequences of the Arylsulphatase a deficiency through a
+ systems biology approach},
+Journal = {HELIYON},
+Year = {2021},
+Volume = {7},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.heliyon.2021.e07671},
+EarlyAccessDate = {JUL 2021},
+Article-Number = {e07671},
+EISSN = {2405-8440},
+Keywords = {Metachromatic leukodystrophy; System biology; Arylsulphatase A; Myelin
+ sheath},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; CARNOSINE; MYELIN; CELL; COMMUNICATION;
+ HOMOCARNOSINE; GLYCOGEN},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Echeverri-Peña, Olga/AAF-8597-2019
+ GONZALEZ, JANNETH/AAB-9948-2020
+ Almeciga-Diaz, Carlos J/A-2494-2017},
+ORCID-Numbers = {Echeverri-Peña, Olga/0000-0001-9704-6387
+ GONZALEZ, JANNETH/0000-0003-4482-256X
+ Almeciga-Diaz, Carlos J/0000-0001-6484-1173},
+Times-Cited = {3},
+Journal-ISO = {Heliyon},
+Unique-ID = {WOS:000680264800007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000677580600004,
+Author = {Alonso-Lavin, Alvar J. and Bajic, Djordje and Poyatos, Juan F.},
+Title = {Tolerance to NADH/NAD+ imbalance anticipates aging and
+ anti-aging interventions},
+Journal = {ISCIENCE},
+Year = {2021},
+Volume = {24},
+Number = {7},
+Month = {JUL 23},
+Type = {Article},
+DOI = {10.1016/j.isci.2021.102697},
+Article-Number = {102697},
+EISSN = {2589-0042},
+Keywords-Plus = {EXTENDS LIFE-SPAN; CAENORHABDITIS-ELEGANS; METABOLISM; AUTOPHAGY;
+ MITOCHONDRIA; RESTRICTION; HOMEOSTASIS; SENESCENCE; INDUCTION; NETWORK},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Bajic, Djordje/ABB-4569-2020},
+ORCID-Numbers = {Bajic, Djordje/0000-0002-6716-7898},
+Times-Cited = {4},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000677580600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000674857300001,
+Author = {Wang, You-Tyun and Lin, Min-Ru and Chen, Wei-Chen and Wu, Wu-Hsiung and
+ Wang, Feng-Sheng},
+Title = {Optimization of a modeling platform to predict oncogenes from
+ genome-scale metabolic networks of non-small-cell lung cancers},
+Journal = {FEBS OPEN BIO},
+Year = {2021},
+Volume = {11},
+Number = {8},
+Pages = {2078-2094},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1002/2211-5463.13231},
+EarlyAccessDate = {JUL 2021},
+ISSN = {2211-5463},
+Keywords = {cancer cell metabolism; constraint-based modeling; flux balance
+ analysis; tissue-specific metabolic models; trilevel optimization},
+Keywords-Plus = {EXPRESSION; TRANSPORTERS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Wu, Wu-Hsiung/0000-0001-7457-0960},
+Times-Cited = {9},
+Journal-ISO = {FEBS Open Bio},
+Unique-ID = {WOS:000674857300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000670203700001,
+Author = {Moyer, Devlin and Pacheco, Alan R. and Bernstein, David B. and Segre,
+ Daniel},
+Title = {Stoichiometric Modeling of Artificial String Chemistries Reveals
+ Constraints on Metabolic Network Structure},
+Journal = {JOURNAL OF MOLECULAR EVOLUTION},
+Year = {2021},
+Volume = {89},
+Number = {7},
+Pages = {472-483},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1007/s00239-021-10018-0},
+EarlyAccessDate = {JUL 2021},
+ISSN = {0022-2844},
+EISSN = {1432-1432},
+Keywords = {Artificial chemistry; Flux balance analysis; Metabolism; Genome-scale
+ metabolic models},
+Keywords-Plus = {RESOURCE-ALLOCATION; EVOLUTION; RECONSTRUCTION; ORGANIZATION; PATHWAYS;
+ OPTIMIZATION; LANGUAGE; BIOMASS},
+Research-Areas = {Biochemistry \& Molecular Biology; Evolutionary Biology; Genetics \&
+ Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Evolutionary Biology; Genetics \&
+ Heredity},
+ResearcherID-Numbers = {Segrè, Daniel/A-1993-2009
+ Pacheco, Alan R/IUQ-5711-2023
+ Bernstein, David B/HLV-8885-2023
+ },
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914
+ Pacheco, Alan R/0000-0002-1128-3232
+ Bernstein, David B/0000-0001-6091-4021
+ Moyer, Devlin/0000-0002-6997-9531
+ pacheco quispe, alan/0000-0002-5112-1430},
+Times-Cited = {1},
+Journal-ISO = {J. Mol. Evol.},
+Unique-ID = {WOS:000670203700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000709920600001,
+Author = {Henriques, David and Minebois, Romain and Mendoza, Sebastian N. and
+ Macias, Laura G. and Perez-Torrado, Roberto and Barrio, Eladio and
+ Teusink, Bas and Querol, Amparo and Balsa-Canto, Eva},
+Title = {A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different
+ Redox Balancing among Yeast Species of the Saccharomyces Genus in
+ Fermentation},
+Journal = {MSYSTEMS},
+Year = {2021},
+Volume = {6},
+Number = {4},
+Month = {JUL-AUG},
+Type = {Article},
+DOI = {10.1128/mSystems.00260-21},
+Article-Number = {e00260-21},
+ISSN = {2379-5077},
+Keywords = {batch fermentation; Saccharomyces species; cryotolerant species; dynamic
+ genome-scale models; redox balance},
+Keywords-Plus = {METABOLIC MODEL; CEREVISIAE; NITROGEN; EXPRESSION; ACID; OPTIMIZATION;
+ SUCCINATE; PATHWAYS; TOOLBOX; ETHANOL},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Henriques, David/AAF-9525-2021
+ Balsa-Canto, Eva/A-9339-2008
+ Barrio, Eladio/G-8969-2015
+ Torrado, Roberto Pérez/E-7613-2012
+ Querol, Amparo/AAW-7469-2020
+ },
+ORCID-Numbers = {Henriques, David/0000-0002-9477-292X
+ Balsa-Canto, Eva/0000-0002-1978-2626
+ Barrio, Eladio/0000-0003-1024-954X
+ Torrado, Roberto Pérez/0000-0002-3118-6755
+ Querol, Amparo/0000-0002-6478-6845
+ Teusink, Bas/0000-0003-3929-0423
+ MINEBOIS, ROMAIN/0000-0001-6959-1572
+ Mendoza, Sebastian/0000-0002-2192-5569},
+Times-Cited = {15},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000709920600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000682137300026,
+Author = {Ozden, Furkan and Siper, Metin Can and Acarsoy, Necmi and Elmas,
+ Tugrulcan and Marty, Bryan and Qi, Xinjian and Cicek, A. Ercument},
+Title = {DORMAN: Database of Reconstructed MetAbolic Networks},
+Journal = {IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS},
+Year = {2021},
+Volume = {18},
+Number = {4},
+Pages = {1474-1480},
+Month = {JUL-AUG},
+Type = {Article},
+DOI = {10.1109/TCBB.2019.2944905},
+ISSN = {1545-5963},
+EISSN = {1557-9964},
+Keywords = {Databases; Biochemistry; Analytical models; Computational modeling;
+ Navigation; Tools; Bars; Genome-scale reconstructed metabolic networks;
+ metabolism; metabolomics; online workbench},
+Keywords-Plus = {LIBRARY; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Computer Science; Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Computer Science, Interdisciplinary
+ Applications; Mathematics, Interdisciplinary Applications; Statistics \&
+ Probability},
+ResearcherID-Numbers = {Elmas, Tugrulcan/HGV-2203-2022
+ Ozden, Furkan/GLR-1427-2022
+ },
+ORCID-Numbers = {Elmas, Tugrulcan/0000-0002-4305-1479
+ Siper, Metin Can/0000-0002-7556-093X
+ Cicek, A. Ercument/0000-0001-8613-6619},
+Times-Cited = {0},
+Journal-ISO = {IEEE-ACM Trans. Comput. Biol. Bioinform.},
+Unique-ID = {WOS:000682137300026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000676138900001,
+Author = {Salahshouri, Pejman and Emadi-Baygi, Modjtaba and Jalili, Mahdi and
+ Khan, Faiz M. and Wolkenhauer, Olaf and Salehzadeh-Yazdi, Ali},
+Title = {A Metabolic Model of Intestinal Secretions: The Link between Human
+ Microbiota and Colorectal Cancer Progression},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.3390/metabo11070456},
+Article-Number = {456},
+EISSN = {2218-1989},
+Keywords = {microbiome; genome-scale metabolic model; community metabolic modeling;
+ colorectal cancer},
+Keywords-Plus = {GUT; DOPAMINE; SEROTONIN; PYRUVATE; BREAST; CELLS; RECEPTORS; APOPTOSIS;
+ PROFILES; GENOME},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Jalili/A-8484-2012
+ Salehzadeh-Yazdi, Ali/J-9510-2019},
+ORCID-Numbers = {Jalili/0000-0002-5491-089X
+ Salehzadeh-Yazdi, Ali/0000-0002-1678-0051},
+Times-Cited = {6},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000676138900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000682353100011,
+Author = {Schulte, Carolin C. M. and Borah, Khushboo and Wheatley, Rachel M. and
+ Terpolilli, Jason J. and Saalbach, Gerhard and Crang, Nick and de Groot,
+ Daan H. and Ratcliffe, R. George and Kruger, Nicholas J. and
+ Papachristodoulou, Antonis and Poole, Philip S.},
+Title = {Metabolic control of nitrogen fixation in rhizobium-legume symbioses},
+Journal = {SCIENCE ADVANCES},
+Year = {2021},
+Volume = {7},
+Number = {31},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1126/sciadv.abh2433},
+Article-Number = {eabh2433},
+ISSN = {2375-2548},
+Keywords-Plus = {LEGUMINOSARUM BV VICIAE; AMINO-ACID PERMEASE; MYOINOSITOL CATABOLISM;
+ ALANINE DEHYDROGENASE; SYSTEMS BIOLOGY; HOST SANCTIONS; BACTEROIDS; PEA;
+ TRANSPORT; NODULES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Borah Slater, Khushboo/AFI-4334-2022
+ Borah, Khushboo/AAF-3763-2022
+ Papachristodoulou, Antonis/C-2597-2012
+ },
+ORCID-Numbers = {Papachristodoulou, Antonis/0000-0002-3565-8967
+ Terpolilli, Jason/0000-0003-4306-3346
+ Ratcliffe, R. George/0000-0001-8394-1575
+ de Groot, Daan/0000-0001-7070-8950
+ Borah Slater, Khushboo/0000-0001-9030-2085
+ Kruger, Nicholas/0000-0003-0492-3542
+ Schulte, Carolin/0000-0002-7574-6259
+ Wheatley, Rachel/0000-0003-1212-2286
+ Crang, Nick/0000-0002-7569-6597},
+Times-Cited = {30},
+Journal-ISO = {Sci. Adv.},
+Unique-ID = {WOS:000682353100011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000671283800002,
+Author = {Zhou, Jingru and Zhuang, Yingping and Xia, Jianye},
+Title = {Integration of enzyme constraints in a genome-scale metabolic model of
+ Aspergillus niger improves phenotype predictions},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2021},
+Volume = {20},
+Number = {1},
+Month = {JUN 30},
+Type = {Article},
+DOI = {10.1186/s12934-021-01614-2},
+Article-Number = {125},
+EISSN = {1475-2859},
+Keywords = {Genome-scale metabolic model; Proteome constraint GSMM; Aspergillus
+ niger; Differential expression of enzymes},
+Keywords-Plus = {RECONSTRUCTION; ORGANISMS; SECRETOME; RESOURCE; REVEALS; NETWORK; YEAST},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Zhou, Jingru/0000-0002-6399-3746
+ XIA, Jianye/0000-0003-2114-5770},
+Times-Cited = {11},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000671283800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000665049200001,
+Author = {Pacheco, Alan R. and Segre, Daniel},
+Title = {An evolutionary algorithm for designing microbial communities via
+ environmental modification},
+Journal = {JOURNAL OF THE ROYAL SOCIETY INTERFACE},
+Year = {2021},
+Volume = {18},
+Number = {179},
+Month = {JUN 23},
+Type = {Article},
+DOI = {10.1098/rsif.2021.0348},
+Article-Number = {20210348},
+ISSN = {1742-5689},
+EISSN = {1742-5662},
+Keywords = {microbial communities; synthetic ecology; genetic algorithm; metabolic
+ modelling},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; SCALE METABOLIC MODEL; FLUX BALANCE ANALYSIS;
+ GENETIC ALGORITHMS; ESCHERICHIA-COLI; GROWTH; COCULTURE; ECOSYSTEM;
+ DYNAMICS; RECONSTRUCTION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Pacheco, Alan R/IUQ-5711-2023
+ Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Pacheco, Alan R/0000-0002-1128-3232
+ Segrè, Daniel/0000-0003-4859-1914
+ pacheco quispe, alan/0000-0002-5112-1430},
+Times-Cited = {4},
+Journal-ISO = {J. R. Soc. Interface},
+Unique-ID = {WOS:000665049200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000662822100002,
+Author = {Qin, Jiufu and Krivoruchko, Anastasia and Ji, Boyang and Chen, Yu and
+ Kristensen, Mette and Ozdemir, Emre and Keasling, Jay D. and Jensen,
+ Michael Krogh and Nielsen, Jens},
+Title = {Engineering yeast metabolism for the discovery and production of
+ polyamines and polyamine analogues},
+Journal = {NATURE CATALYSIS},
+Year = {2021},
+Volume = {4},
+Number = {6},
+Pages = {498+},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1038/s41929-021-00631-z},
+EarlyAccessDate = {JUN 2021},
+ISSN = {2520-1158},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; PATHWAY; BIOSYNTHESIS; SPERMIDINE;
+ IDENTIFICATION; ARABIDOPSIS; NUCLEOTIDE; GENERATION; SYNTHASES;
+ ALIGNMENT},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Physical},
+ResearcherID-Numbers = {Qin, Jiufu/G-5148-2015
+ Nielsen, Jens Bo/C-7632-2015
+ Chen, Yu/AAL-3329-2020
+ Keasling, Jay/HPG-6073-2023
+ Ji, Boyang/HMV-6662-2023
+ Keasling, Jay/J-9162-2012
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Qin, Jiufu/0000-0003-1966-5427
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Chen, Yu/0000-0003-3326-9068
+ Ji, Boyang/0000-0002-7269-4342
+ Jensen, Michael Krogh/0000-0001-7574-4707
+ Keasling, Jay/0000-0003-4170-6088
+ Nielsen, Jens/0000-0002-9955-6003
+ Ozdemir, Emre/0000-0001-5548-6720},
+Times-Cited = {14},
+Journal-ISO = {Nat. Catal.},
+Unique-ID = {WOS:000662822100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000693171600023,
+Author = {Jadebeck, Johann F. and Theorell, Axel and Leweke, Samuel and Noeh,
+ Katharina},
+Title = {HOPS: high-performance library for (non-)uniform sampling of
+ convex-constrained models},
+Journal = {BIOINFORMATICS},
+Year = {2021},
+Volume = {37},
+Number = {12},
+Pages = {1776-1777},
+Month = {JUN 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btaa872},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Jadebeck, Johann Fredrik/AAF-2842-2021
+ },
+ORCID-Numbers = {Jadebeck, Johann Fredrik/0000-0002-5026-1546
+ Leweke, Samuel/0000-0001-9471-4511},
+Times-Cited = {5},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000693171600023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000663785600044,
+Author = {Firoozabadi, Hossein and Mardanpour, Mohammad Mahdi and Motamedian,
+ Ehsan},
+Title = {A system-oriented strategy to enhance electron production of
+ Synechocystis sp. PCC6803 in bio-photovoltaic devices:
+ experimental and modeling insights},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2021},
+Volume = {11},
+Number = {1},
+Month = {JUN 10},
+Type = {Article},
+DOI = {10.1038/s41598-021-91906-9},
+Article-Number = {12294},
+ISSN = {2045-2322},
+Keywords-Plus = {MICROBIAL FUEL-CELLS; CYANOBACTERIUM SYNECHOCYSTIS; PCC 6803;
+ PHOTOSYSTEM-II; FLUX; METABOLISM; GROWTH; GENE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Motamedian, Ehsan/GPK-8344-2022
+ Mardanpour, Mohammad Mahdi/AGR-8308-2022
+ },
+ORCID-Numbers = {Mardanpour, Mohammad Mahdi/0000-0003-3651-2297
+ Firoozabadi, Hossein/0000-0003-4310-1840
+ , Ehsan/0000-0001-8750-2879},
+Times-Cited = {6},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000663785600044},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000659121200001,
+Author = {Henson, Michael A.},
+Title = {Interrogation of the perturbed gut microbiota in gouty arthritis
+ patients through in silico metabolic modeling},
+Journal = {ENGINEERING IN LIFE SCIENCES},
+Year = {2021},
+Volume = {21},
+Number = {7},
+Pages = {489-501},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/elsc.202100003},
+EarlyAccessDate = {JUN 2021},
+ISSN = {1618-0240},
+EISSN = {1618-2863},
+Keywords = {bacterial communities; gout; gut microbiota; machine learning; metabolic
+ modeling},
+Keywords-Plus = {CHAIN FATTY-ACIDS; HYDROGEN-SULFIDE; URIC-ACID; HEALTH; HYPERURICEMIA;
+ IMPACT},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {10},
+Journal-ISO = {Eng. Life Sci.},
+Unique-ID = {WOS:000659121200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000684864900018,
+Author = {Hala, David and Faulkner, Patricia and He, Kai and Kamalanathan, Manoj
+ and Brink, Mikeelee and Simons, Kristina and Apaydin, Meltem and
+ Hernout, Beatrice and Petersen, Lene H. and Ivanov, Ivan and Qian,
+ Xiaoning},
+Title = {An integrated in vivo and in silico analysis of the metabolism
+ disrupting effects of CPI-613 on embryo-larval zebrafish (Danio rerio)},
+Journal = {COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY \& PHARMACOLOGY},
+Year = {2021},
+Volume = {248},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1016/j.cbpc.2021.109084},
+EarlyAccessDate = {JUN 2021},
+Article-Number = {109084},
+ISSN = {1532-0456},
+EISSN = {1878-1659},
+Keywords = {Stoichiometric metabolism model; Metabolism disrupter; Embryo-larval
+ zebrafish; Cellular bioenergetics; Organismal physiology},
+Keywords-Plus = {SWIMMING PERFORMANCE; PATHWAY ANALYSIS; BASIC CONCEPTS; HYPOXIA; MODELS;
+ CAPACITY; FISH; TEMPERATURE; PREDICTION; TOLERANCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Endocrinology \& Metabolism;
+ Toxicology; Zoology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Endocrinology \& Metabolism;
+ Toxicology; Zoology},
+ResearcherID-Numbers = {Apaydin, Meltem/ABG-2598-2021},
+ORCID-Numbers = {Apaydin, Meltem/0000-0001-9225-9455},
+Times-Cited = {0},
+Journal-ISO = {Comp. Biochem. Physiol. C-Toxicol. Pharmacol.},
+Unique-ID = {WOS:000684864900018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000662950400001,
+Author = {Sigmarsdottir, Thora Bjorg and McGarrity, Sarah and Yurkovich, James T.
+ and Rolfsson, Ottar and Sigurjonsson, Olafur Eysteinn},
+Title = {Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation
+ in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model
+ Reconstruction},
+Journal = {FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY},
+Year = {2021},
+Volume = {9},
+Month = {JUN 4},
+Type = {Article},
+DOI = {10.3389/fcell.2021.642681},
+Article-Number = {642681},
+ISSN = {2296-634X},
+Keywords = {GEM; MSCs; osteogenesis; metabolic reconstruction; adipogenesis;
+ metabolic differences},
+Keywords-Plus = {BONE-MARROW; NETWORK MODEL; PROLIFERATION; PREDICTION; MARKERS; BETA;
+ MSCS},
+Research-Areas = {Cell Biology; Developmental Biology},
+Web-of-Science-Categories = {Cell Biology; Developmental Biology},
+ORCID-Numbers = {Sigurjonsson, Olafur/0000-0002-4968-842X},
+Times-Cited = {4},
+Journal-ISO = {Front. Cell. Dev. Biol.},
+Unique-ID = {WOS:000662950400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000665989200001,
+Author = {Hunt, Kristopher A. and Mallette, Natasha D. and Peyton, Brent M. and
+ Carlson, Ross P.},
+Title = {In Silico Analysis of Functionalized Hydrocarbon Production Using
+ Ehrlich Pathway and Fatty Acid Derivatives in an Endophytic Fungus},
+Journal = {JOURNAL OF FUNGI},
+Year = {2021},
+Volume = {7},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3390/jof7060435},
+Article-Number = {435},
+EISSN = {2309-608X},
+Keywords = {endophyte; consolidated bioprocessing; efma; fba; cytosolic pyruvate
+ dehydrogenase},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; NATURAL-PRODUCTS; BIOSYNTHESIS; PREDICTION;
+ ASCOCORYNE; MODELS; YEAST},
+Research-Areas = {Microbiology; Mycology},
+Web-of-Science-Categories = {Microbiology; Mycology},
+ResearcherID-Numbers = {Peyton, Brent/G-5247-2015},
+ORCID-Numbers = {Carlson, Ross/0000-0002-2464-7111
+ Peyton, Brent/0000-0003-0033-0651},
+Times-Cited = {0},
+Journal-ISO = {J. Fungi},
+Unique-ID = {WOS:000665989200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000666318600001,
+Author = {Jalili, Mahdi and Scharm, Martin and Wolkenhauer, Olaf and Damaghi,
+ Mehdi and Salehzadeh-Yazdi, Ali},
+Title = {Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of
+ Context-Specific Models},
+Journal = {JOURNAL OF PERSONALIZED MEDICINE},
+Year = {2021},
+Volume = {11},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3390/jpm11060496},
+Article-Number = {496},
+EISSN = {2075-4426},
+Keywords = {genome-scale metabolic model; data integration; Warburg effect;
+ metabolic pattern; FBA-based feature; cancer metabolism},
+Keywords-Plus = {NEED},
+Research-Areas = {Health Care Sciences \& Services; General \& Internal Medicine},
+Web-of-Science-Categories = {Health Care Sciences \& Services; Medicine, General \& Internal},
+ResearcherID-Numbers = {Jalili/A-8484-2012
+ Salehzadeh-Yazdi, Ali/J-9510-2019
+ },
+ORCID-Numbers = {Jalili/0000-0002-5491-089X
+ Salehzadeh-Yazdi, Ali/0000-0002-1678-0051
+ Damaghi, Mehdi/0000-0002-7744-6161},
+Times-Cited = {9},
+Journal-ISO = {J. Pers. Med.},
+Unique-ID = {WOS:000666318600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000670388300004,
+Author = {Scott, Felipe and Yanez, Luz and Conejeros, Raul and Araya, Blanca and
+ Vergara-Fernandez, Alberto},
+Title = {Two internal bottlenecks cause the overflow metabolism leading to poly
+ (3-hydroxybutyrate) production in Azohydromonas lata DSM1123},
+Journal = {JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING},
+Year = {2021},
+Volume = {9},
+Number = {4},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1016/j.jece.2021.105665},
+EarlyAccessDate = {MAY 2021},
+Article-Number = {105665},
+ISSN = {2213-2929},
+EISSN = {2213-3437},
+Keywords = {Polyhydroxybutyrate; Overflow metabolism; Flux balance analysis;
+ Azohydromonas lata; Biopolymers},
+Keywords-Plus = {FED-BATCH CULTURE; BETA-HYDROXYBUTYRATE; ESCHERICHIA-COLI;
+ ALCALIGENES-EUTROPHUS; ATP SYNTHASE; GROWTH; PHB; POLYHYDROXYALKANOATES;
+ BIOSYNTHESIS; ACCUMULATION},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Environmental; Engineering, Chemical},
+ResearcherID-Numbers = {Conejeros, Raul/ABG-5517-2020
+ Scott, Felipe/K-4193-2016
+ },
+ORCID-Numbers = {Conejeros, Raul/0000-0002-1273-535X
+ Scott, Felipe/0000-0003-2041-4641
+ Araya, Blanca/0000-0003-1268-7906},
+Times-Cited = {3},
+Journal-ISO = {J. Environ. Chem. Eng.},
+Unique-ID = {WOS:000670388300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000650187800001,
+Author = {Ebata, Kyoichi and Yamashiro, Sawa and Iida, Keita and Okada, Mariko},
+Title = {Building patient-specific models for receptor tyrosine kinase signaling
+ networks},
+Journal = {FEBS JOURNAL},
+Year = {2022},
+Volume = {289},
+Number = {1},
+Pages = {90-101},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1111/febs.15831},
+EarlyAccessDate = {MAY 2021},
+ISSN = {1742-464X},
+EISSN = {1742-4658},
+Keywords = {cancer; machine learning; mathematical modeling; omics; patient\&\#8208;
+ specific model; RTK signaling},
+Keywords-Plus = {DRUG-RESISTANCE; CELL VARIABILITY; CANCER MEDICINE; SYSTEMS BIOLOGY;
+ DYNAMIC CONTROL; GENE; GENOME; HETEROGENEITY; FRAMEWORK; AKT},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {3},
+Journal-ISO = {FEBS J.},
+Unique-ID = {WOS:000650187800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000654205900001,
+Author = {Gao, Chenchen and Yang, Jiarui and Hao, Tong and Li, Jingjing and Sun,
+ Jinsheng},
+Title = {Reconstruction of Litopenaeus vannamei Genome-Scale Metabolic
+ Network Model and Nutritional Requirements Analysis of Different Shrimp
+ Commercial Varieties},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2021},
+Volume = {12},
+Month = {MAY 12},
+Type = {Article},
+DOI = {10.3389/fgene.2021.658109},
+Article-Number = {658109},
+EISSN = {1664-8021},
+Keywords = {genome-scale metabolic network; feed; biomass; nutrient requirement;
+ Litopenaeus vannamei},
+Keywords-Plus = {CARBOHYDRATE DIGESTION; PENAEUS-MONODON; GROWTH},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+Times-Cited = {5},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000654205900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000658808600001,
+Author = {Eng, Thomas and Banerjee, Deepanwita and Lau, Andrew K. and Bowden,
+ Emily and Herbert, Robin A. and Trinh, Jessica and Prahl, Jan-Philip and
+ Deutschbauer, Adam and Tanjore, Deepti and Mukhopadhyay, Aindrila},
+Title = {Engineering Pseudomonas putida for efficient aromatic conversion
+ to bioproduct using high throughput screening in a bioreactor},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {66},
+Pages = {229-238},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.04.015},
+EarlyAccessDate = {MAY 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Para-coumarate; Bioreactor; RB-TnSeq; Pseudomonas putida; Metabolic
+ engineering},
+Keywords-Plus = {STRESS-RESPONSE; KT2440; GLUCOSE; GENOME; GROWTH; ACID},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Mukhopadhyay, Aindrila/AAW-7257-2021
+ },
+ORCID-Numbers = {Banerjee, Deepanwita/0000-0002-0083-0608
+ Trinh, Jessica/0000-0002-5044-0720
+ Bowden, Emily/0000-0001-9506-7221
+ Mukhopadhyay, Aindrila/0000-0002-6513-7425},
+Times-Cited = {20},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000658808600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000733829400022,
+Author = {Magazzu, Giuseppe and Zampieri, Guido and Angione, Claudio},
+Title = {Multimodal regularized linear models with flux balance analysis for
+ mechanistic integration of omics data},
+Journal = {BIOINFORMATICS},
+Year = {2021},
+Volume = {37},
+Number = {20},
+Pages = {3546-3552},
+Month = {OCT 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btab324},
+EarlyAccessDate = {MAY 2021},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {YEAST; GENE; PHOSPHATIDYLETHANOLAMINE; METHYLATION; REGRESSION;
+ SELECTION; NETWORKS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Zampieri, Guido/HJH-7472-2023
+ },
+ORCID-Numbers = {Zampieri, Guido/0000-0002-4518-5913
+ Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {10},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000733829400022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000653647200001,
+Author = {Sudhakar, Padhmanand and Machiels, Kathleen and Verstockt, Bram and
+ Korcsmaros, Tamas and Vermeire, Severine},
+Title = {Computational Biology and Machine Learning Approaches to Understand
+ Mechanistic Microbiome-Host Interactions},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2021},
+Volume = {12},
+Month = {MAY 11},
+Type = {Review},
+DOI = {10.3389/fmicb.2021.618856},
+Article-Number = {618856},
+EISSN = {1664-302X},
+Keywords = {health; disease; microbiome-host interactions; molecular mechanisms;
+ computational approaches; machine learning; basic and clinical research},
+Keywords-Plus = {PROTEIN-PROTEIN INTERACTIONS; HEPATITIS-C VIRUS; PATHOGEN INTERACTIONS;
+ SYSTEMS BIOLOGY; GUT MICROBIOTA; SMALL RNAS; INTESTINAL HOMEOSTASIS;
+ MOLECULAR NETWORKS; DATA-BANK; PREDICTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Sudhakar, Padhmanand/P-8205-2019
+ Verstockt, Bram/P-5234-2016
+ Korcsmaros, Tamas/C-3526-2015
+ },
+ORCID-Numbers = {Sudhakar, Padhmanand/0000-0003-1907-4491
+ Verstockt, Bram/0000-0003-3898-7093
+ Korcsmaros, Tamas/0000-0003-1717-996X
+ Vermeire, Severine/0000-0001-9942-3019},
+Times-Cited = {10},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000653647200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000647726800001,
+Author = {Heinken, Almut and Hertel, Johannes and Thiele, Ines},
+Title = {Metabolic modelling reveals broad changes in gut microbial metabolism in
+ inflammatory bowel disease patients with dysbiosis},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2021},
+Volume = {7},
+Number = {1},
+Month = {MAY 6},
+Type = {Article},
+DOI = {10.1038/s41540-021-00178-6},
+Article-Number = {19},
+EISSN = {2056-7189},
+Keywords-Plus = {CHONDROITIN SULFATE; SULFIDE; HEALTH; DIET},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Hertel, Johannes/HZJ-3685-2023},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Hertel, Johannes/0000-0002-7641-0132},
+Times-Cited = {31},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000647726800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000647065800001,
+Author = {Pazhamala, Lekha T. and Kudapa, Himabindu and Weckwerth, Wolfram and
+ Millar, A. Harvey and Varshney, Rajeev K.},
+Title = {Systems biology for crop improvement},
+Journal = {PLANT GENOME},
+Year = {2021},
+Volume = {14},
+Number = {2},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1002/tpg2.20098},
+EarlyAccessDate = {MAY 2021},
+Article-Number = {e20098},
+EISSN = {1940-3372},
+Keywords-Plus = {GENOME-WIDE ASSOCIATION; QUANTITATIVE TRAIT LOCI; PROTEIN-PROTEIN
+ INTERACTIONS; GENE-EXPRESSION ATLAS; SINGLE-CELL OMICS; MULTI-OMICS;
+ NETWORK INFERENCE; PAN-GENOME; REGULATORY NETWORKS; NITROGEN-METABOLISM},
+Research-Areas = {Plant Sciences; Genetics \& Heredity},
+Web-of-Science-Categories = {Plant Sciences; Genetics \& Heredity},
+ResearcherID-Numbers = {Weckwerth, Wolfram/G-5811-2010
+ Pazhamala, Lekha Thankappan/HMD-7161-2023
+ Varshney, Rajeev K/C-5295-2014
+ Millar, A. Harvey/A-5452-2008
+ },
+ORCID-Numbers = {Varshney, Rajeev K/0000-0002-4562-9131
+ Millar, A. Harvey/0000-0001-9679-1473
+ Kudapa, Himabindu/0000-0003-0778-9959
+ Pazhamala, Lekha/0000-0002-0271-7481
+ Weckwerth, Wolfram/0000-0002-9719-6358},
+Times-Cited = {36},
+Journal-ISO = {Plant Genome},
+Unique-ID = {WOS:000647065800001},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000646409100001,
+Author = {Tang, Wen-Tao and Hao, Tian-Wei and Chen, Guang-Hao},
+Title = {Comparative metabolic modeling of multiple sulfate-reducing prokaryotes
+ reveals versatile energy conservation mechanisms},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2021},
+Volume = {118},
+Number = {7},
+Pages = {2676-2693},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1002/bit.27787},
+EarlyAccessDate = {MAY 2021},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {comparative genomics; dissimilatory sulfate reduction; energy
+ metabolism; genome\&\#8208; scale metabolic model; metabolic modeling},
+Keywords-Plus = {DESULFOVIBRIO-VULGARIS HILDENBOROUGH; PROTON TRANSLOCATION; ACETATE
+ OXIDATION; GROWTH YIELDS; HYDROGEN; BACTERIA; REDUCTION; ENERGETICS;
+ MICROORGANISMS; BIOTECHNOLOGY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Tang, Wen-Tao/0000-0002-1839-3485},
+Times-Cited = {4},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000646409100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000648693300002,
+Author = {Ankrah, Nana Y. D. and Barker, Brandon E. and Song, Joan and Wu, Cindy
+ and McMullen, II, John G. and Douglas, Angela E.},
+Title = {Predicted Metabolic Function of the Gut Microbiota of Drosophila
+ melanogaster},
+Journal = {MSYSTEMS},
+Year = {2021},
+Volume = {6},
+Number = {3},
+Month = {MAY-JUN},
+Type = {Article},
+DOI = {10.1128/mSystems.01369-20},
+Article-Number = {e01369-20},
+ISSN = {2379-5077},
+Keywords = {microbiome; constraint-based modeling; mutualism; competition;
+ cross-feeding; Drosophila},
+Keywords-Plus = {SPATIAL-ORGANIZATION; LACTOBACILLUS-PLANTARUM; COMPETITION; MODEL;
+ COOPERATION; ECOLOGY; KNOWLEDGEBASE; DETERMINANTS; POPULATIONS;
+ HOMEOSTASIS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Ankrah, Nana/IUO-8239-2023
+ },
+ORCID-Numbers = {Ankrah, Nana Yaw/0000-0003-0492-545X
+ McMullen, John/0000-0002-6675-3983
+ Barker, Brandon/0000-0001-5732-9550},
+Times-Cited = {7},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000648693300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000648332700019,
+Author = {Kerselidou, Despoina and Dohai, Bushra Saeed and Nelson, David R. and
+ Daakour, Sarah and De Cock, Nicolas and Hassoun, Zahra Al Oula and Kim,
+ Dae-Kyum and Olivet, Julien and El Assal, Diana C. and Jaiswal, Ashish
+ and Alzahmi, Amnah and Saha, Deeya and Pain, Charlotte and Matthijssens,
+ Filip and Lemaitre, Pierre and Herfs, Michael and Chapuis, Julien and
+ Ghesquiere, Bart and Vertommen, Didier and Kriechbaumer, Verena and
+ Knoops, Kevin and Lopez-Iglesias, Carmen and van Zandvoort, Marc and
+ Lambert, Jean-Charles and Hanson, Julien and Desmet, Christophe and
+ Thiry, Marc and Lauersen, Kyle J. and Vidal, Marc and Van Vlierberghe,
+ Pieter and Dequiedt, Franck and Salehi-Ashtiani, Kourosh and Twizere,
+ Jean-Claude},
+Title = {Alternative glycosylation controls endoplasmic reticulum dynamics and
+ tubular extension in mammalian cells},
+Journal = {SCIENCE ADVANCES},
+Year = {2021},
+Volume = {7},
+Number = {19},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1126/sciadv.abe8349},
+Article-Number = {eabe8349},
+ISSN = {2375-2548},
+Keywords-Plus = {TUMOR SUPPRESSORS EXT1; PROTEINS; BIOSYNTHESIS; INACTIVATION;
+ EXPRESSION; REVEALS; NETWORK; FORM},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Lemaitre, Pierre/AGI-3306-2022
+ Jaiswal, Ashish Kumar k/H-8692-2016
+ lambert, jean-charles/F-8787-2013
+ Van Vlierberghe, Pieter/G-8894-2013
+ Ghesquiere, Bart/HGU-8736-2022
+ De Cock, Nicolas/A-9501-2016
+ },
+ORCID-Numbers = {Lemaitre, Pierre/0000-0003-0687-8685
+ Jaiswal, Ashish Kumar k/0000-0002-6193-1824
+ lambert, jean-charles/0000-0003-0829-7817
+ Van Vlierberghe, Pieter/0000-0001-9063-7205
+ Ghesquiere, Bart/0000-0003-1547-1705
+ Hanson, Julien/0000-0001-7063-7590
+ Kriechbaumer, Verena/0000-0003-3782-5834
+ Nelson, David/0000-0001-8868-5734
+ Matthijssens, Filip/0000-0002-6499-4572
+ HASSOUN, Zahrat El Oula/0000-0001-6125-2867
+ De Cock, Nicolas/0000-0002-4009-8845
+ Pain, Charlotte/0000-0003-0350-9921
+ Lauersen, Kyle/0000-0002-5538-7201
+ Chapuis, Julien/0000-0002-5802-2857
+ Knoops, Kevin/0000-0002-7539-1160
+ Dohai, Bushra/0000-0001-8179-8883
+ El Assal, Diana C./0000-0003-1124-5153
+ Kim, Dae-Kyum/0000-0003-4568-8278
+ Dequiedt, Franck/0000-0003-1234-7477
+ TWIZERE, Jean-Claude/0000-0002-8683-705X
+ Olivet, Julien/0000-0003-4115-5546},
+Times-Cited = {6},
+Journal-ISO = {Sci. Adv.},
+Unique-ID = {WOS:000648332700019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000654279700001,
+Author = {Kittikunapong, Cheewin and Ye, Suhui and Magadan-Corpas, Patricia and
+ Perez-Valero, Alvaro and Villar, Claudio J. and Lombo, Felipe and
+ Kerkhoven, Eduard J.},
+Title = {Reconstruction of a Genome-Scale Metabolic Model of Streptomyces
+ albus J1074: Improved Engineering Strategies in Natural Product
+ Synthesis},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/metabo11050304},
+Article-Number = {304},
+EISSN = {2218-1989},
+Keywords = {genome-scale metabolic model; Streptomyces albus J1074; heterologous
+ production; natural products; gene essentiality; minimized genome},
+Keywords-Plus = {SECONDARY METABOLISM; BIOSYNTHESIS; ACTINOMYCETE; IDENTIFICATION;
+ CARBOXYLASE; EXPRESSION; CLUSTERS; INSIGHTS; GENETICS; PATHWAY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Magadán-Corpas, Patricia/ABG-2562-2021
+ Kerkhoven, Eduard/P-2469-2019
+ Lombo, Felipe/H-8183-2015
+ },
+ORCID-Numbers = {Magadán-Corpas, Patricia/0000-0001-9190-8396
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Kittikunapong, Cheewin/0000-0003-1309-9815
+ Perez Valero, Alvaro/0000-0002-4560-3847
+ Lombo, Felipe/0000-0002-6680-6723
+ Ye, Suhui/0000-0002-4466-4242},
+Times-Cited = {8},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000654279700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000709461300094,
+Author = {Porubsky, Veronica and Smith, Lucian and Sauro, Herbert M.},
+Title = {Publishing reproducible dynamic kinetic models},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2021},
+Volume = {22},
+Number = {3},
+Month = {MAY},
+Type = {Review},
+DOI = {10.1093/bib/bbaa152},
+Article-Number = {bbaa152},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {systems biology; kinetic modeling; SBML; standards; reproducibility},
+Keywords-Plus = {SYSTEMS; TOOLS; SBML; ANNOTATION; SIMULATION; REPOSITORY; PLATFORM;
+ NETWORK; LIBRARY; SCIENCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Porubsky, Veronica/0000-0001-7216-3368
+ Smith, Lucian/0000-0001-7002-6386},
+Times-Cited = {2},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000709461300094},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000662268100001,
+Author = {Sanders, David J. and Inniss, Saskia and Sebepos-Rogers, Gregory and
+ Rahman, Farooq Z. and Smith, Andrew M.},
+Title = {The role of the microbiome in gastrointestinal inflammation},
+Journal = {BIOSCIENCE REPORTS},
+Year = {2021},
+Volume = {41},
+Number = {4},
+Month = {MAY},
+Type = {Review},
+DOI = {10.1042/BSR20203850},
+Article-Number = {BSR20203850},
+ISSN = {0144-8463},
+EISSN = {1573-4935},
+Keywords-Plus = {CHAIN FATTY-ACIDS; INNATE LYMPHOID-CELLS; PATTERN-RECOGNITION RECEPTORS;
+ INVASIVE ESCHERICHIA-COLI; SULFATE-REDUCING BACTERIA; ARYL-HYDROCARBON
+ RECEPTOR; EVIDENCE-BASED CONSENSUS; DISTINCT GUT MICROBIOTA; GERM-FREE
+ MICE; FECAL MICROBIOTA},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Smith, Andrew M/C-5705-2009
+ },
+ORCID-Numbers = {Smith, Andrew/0000-0002-4691-5973
+ Sebepos-Rogers, Gregory/0000-0002-5422-323X},
+Times-Cited = {17},
+Journal-ISO = {Biosci. Rep.},
+Unique-ID = {WOS:000662268100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000664311300007,
+Author = {Schulz, Christian and Kumelj, Tjasa and Karlsen, Emil and Almaas, Eivind},
+Title = {Genome-scale metabolic modelling when changes in environmental
+ conditions affect biomass composition},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1008528},
+Article-Number = {e1008528},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI K-12; RECONSTRUCTION; GROWTH; FLUXES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Schulz, Christian/0000-0002-6763-6551
+ Karlsen, Emil/0000-0002-6626-8697
+ Kumelj, Tjasa/0000-0002-1998-0366},
+Times-Cited = {12},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000664311300007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000646183700019,
+Author = {Tamura, Takeyuki},
+Title = {L1 Norm Minimal Mode-Based Methods for Listing Reaction Network Designs
+ for Metabolite Production},
+Journal = {IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS},
+Year = {2021},
+Volume = {E104D},
+Number = {5},
+Pages = {679-687},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1587/transinf.2020EDP7247},
+ISSN = {1745-1361},
+Keywords = {metabolic network; constraint-based model; elementary flux mode; linear
+ programming; polynomial time algorithm},
+Keywords-Plus = {ESCHERICHIA-COLI; KNOCKOUT STRATEGIES; FLUX; FRAMEWORK; GROWTH},
+Research-Areas = {Computer Science},
+Web-of-Science-Categories = {Computer Science, Information Systems; Computer Science, Software
+ Engineering},
+ResearcherID-Numbers = {Tamura, Takeyuki/AGG-2853-2022},
+ORCID-Numbers = {Tamura, Takeyuki/0000-0003-1596-901X},
+Times-Cited = {1},
+Journal-ISO = {IEICE Trans. Inf. Syst.},
+Unique-ID = {WOS:000646183700019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000688301100005,
+Author = {Trigos, A. S. and Goudey, B. W. and Bedo, J. and Conway, T. C. and Faux,
+ N. G. and Wyres, K. L.},
+Title = {Collateral Sensitivity to β-Lactam Drugs in Drug-Resistant Tuberculosis
+ Is Driven by the Transcriptional Wiring of BlaI Operon Genes},
+Journal = {MSPHERE},
+Year = {2021},
+Volume = {6},
+Number = {3},
+Month = {MAY-JUN},
+Type = {Article},
+DOI = {10.1128/mSphere.00245-21},
+Article-Number = {e00245-21},
+EISSN = {2379-5042},
+Keywords = {beta-lactams; antimicrobial resistance; bioinformatics; collateral
+ sensitivity; in silico; network analysis; paradoxical hypersensitivity;
+ tuberculosis},
+Keywords-Plus = {MYCOBACTERIUM-TUBERCULOSIS; BIOCHEMICAL-CHARACTERIZATION;
+ MEROPENEM-CLAVULANATE; PROTEIN; PENICILLIN; INACTIVATION; CARBAPENEMS;
+ OVEREXPRESSION; COMBINATION; METABOLISM},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Goudey, Benjamin/AAA-8492-2022
+ Wyres, Kelly/AAU-7162-2021
+ Faux, Noel/C-4423-2011
+ },
+ORCID-Numbers = {Goudey, Benjamin/0000-0002-2318-985X
+ Wyres, Kelly/0000-0002-4033-6639
+ Faux, Noel/0000-0003-4594-8818
+ Bedo, Justin/0000-0001-5704-0212},
+Times-Cited = {2},
+Journal-ISO = {mSphere},
+Unique-ID = {WOS:000688301100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000654309700001,
+Author = {van Pelt-KleinJan, Eunice and de Groot, Daan H. and Teusink, Bas},
+Title = {Understanding FBA Solutions under Multiple Nutrient Limitations},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/metabo11050257},
+Article-Number = {257},
+EISSN = {2218-1989},
+Keywords = {flux balance analysis; elementary flux modes; elementary conversion
+ modes; genome-scale modeling; stoichiometric modeling; phenotype phase
+ plane analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; COLI BIOCHEMICAL PATHWAYS; ADAPTIVE EVOLUTION;
+ ENERGY-PRODUCTION; ELEMENTARY MODES; GROWTH; BIOMASS; IDENTIFICATION;
+ STRATEGIES; NETWORKS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {van Pelt-KleinJan, Eunice/0000-0002-6590-652X
+ Teusink, Bas/0000-0003-3929-0423
+ de Groot, Daan/0000-0001-7070-8950},
+Times-Cited = {4},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000654309700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000649144200001,
+Author = {Castillo Alfonso, Freddy and Vigueras-Ramirez, Gabriel and
+ Rosales-Colunga, Luis Manuel and del Monte-Martinez, Alberto and
+ Olivares Hernandez, Roberto},
+Title = {Propionate as the preferred carbon source to produce 3-indoleacetic acid
+ in B. subtilis: comparative flux analysis using five carbon
+ sources},
+Journal = {MOLECULAR OMICS},
+Year = {2021},
+Volume = {17},
+Number = {4},
+Pages = {554-564},
+Month = {AUG 1},
+Type = {Article},
+DOI = {10.1039/d1mo00039j},
+EarlyAccessDate = {APR 2021},
+EISSN = {2515-4184},
+Keywords-Plus = {BACILLUS-SUBTILIS; L-TRYPTOPHAN; INDOLE-3-ACETIC-ACID BIOSYNTHESIS;
+ STATIONARY-PHASE; METABOLIC SWITCH; GROWTH; RIBOFLAVIN; DATABASE;
+ ENZYMES; GLUCOSE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Vigueras, Gabriel/0000-0001-9424-5313
+ Rosales-Colunga, Luis Manuel/0000-0002-8901-4964
+ Castillo Alfonso, Freddy/0000-0001-6043-5776},
+Times-Cited = {5},
+Journal-ISO = {Mol. Omics},
+Unique-ID = {WOS:000649144200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000658808700005,
+Author = {Tiso, Till and Narancic, Tanja and Wei, Ren and Pollet, Eric and Beagan,
+ Niall and Schroeder, Katja and Honak, Annett and Jiang, Mengying and
+ Kenny, Shane T. and Wierckx, Nick and Perrin, Remi and Averous, Luc and
+ Zimmermann, Wolfgang and O'Connor, Kevin and Blank, Lars M.},
+Title = {Towards bio-upcycling of polyethylene terephthalate},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {66},
+Pages = {167-178},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.03.011},
+EarlyAccessDate = {APR 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Polyethylene terephthalate (PET) degradation; Metabolic engineering;
+ Biopolymers; Pseudomonas putida; Synthetic biology},
+Keywords-Plus = {ENZYMATIC DEGRADATION; POLYESTER HYDROLASE; PET; METABOLISM;
+ POLY(ETHYLENE-TEREPHTHALATE); POLYURETHANE; HYDROLYSIS; EFFICIENT;
+ CARBOXYLESTERASE; 1,4-BUTANEDIOL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Pollet, Eric/ABE-6727-2020
+ Wierckx, Nick/J-8605-2015
+ Pollet, Eric/F-2581-2010
+ Avérous, Luc/B-3471-2008
+ Tiso, Till/A-5755-2012
+ Wierckx, Nick/ABA-7239-2020
+ Wei, Ren/P-3313-2017
+ Zimmermann, Wolfgang/AAI-4904-2021
+ Blank, Lars M./A-6761-2012},
+ORCID-Numbers = {Wierckx, Nick/0000-0002-1590-1210
+ Pollet, Eric/0000-0002-4920-7024
+ Avérous, Luc/0000-0002-2797-226X
+ Tiso, Till/0000-0003-4420-5609
+ Wierckx, Nick/0000-0002-1590-1210
+ Wei, Ren/0000-0003-3876-1350
+ Zimmermann, Wolfgang/0000-0002-5730-6663
+ Blank, Lars M./0000-0003-0961-4976},
+Times-Cited = {107},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000658808700005},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000642742500104,
+Author = {Kamsen, Ratchaprapa and Kalapanulak, Saowalak and Chiewchankaset,
+ Porntip and Saithong, Treenut},
+Title = {Transcriptome integrated metabolic modeling of carbon assimilation
+ underlying storage root development in cassava},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2021},
+Volume = {11},
+Number = {1},
+Month = {APR 22},
+Type = {Article},
+DOI = {10.1038/s41598-021-88129-3},
+Article-Number = {8758},
+ISSN = {2045-2322},
+Keywords-Plus = {NITROGEN USE EFFICIENCY; PENTOSE-PHOSPHATE PATHWAY; FLUX BALANCE
+ ANALYSIS; GENE-EXPRESSION DATA; RECONSTRUCTION; NETWORK; PREDICTION;
+ REVEALS; GLUCOSE-6-PHOSPHATE-DEHYDROGENASE; ARABIDOPSIS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Kamsen, Ratchaprapa/AAW-6103-2021},
+Times-Cited = {5},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000642742500104},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000670066000001,
+Author = {Hu, Ruiwen and Zhao, Haiming and Xu, Xihui and Wang, Zhigang and Yu, Ke
+ and Shu, Longfei and Yan, Qingyun and Wu, Bo and Mo, Cehui and He, Zhili
+ and Wang, Cheng},
+Title = {Bacteria-driven phthalic acid ester biodegradation: Current status and
+ emerging opportunities},
+Journal = {ENVIRONMENT INTERNATIONAL},
+Year = {2021},
+Volume = {154},
+Month = {SEP},
+Type = {Review},
+DOI = {10.1016/j.envint.2021.106560},
+EarlyAccessDate = {APR 2021},
+Article-Number = {106560},
+ISSN = {0160-4120},
+EISSN = {1873-6750},
+Keywords = {Phthalic acid esters; Degrading bacterial isolates; Molecular
+ mechanisms; In situ biodegradation; Interaction mechanisms; Synthetic
+ microbial ecology},
+Keywords-Plus = {N-BUTYL PHTHALATE; COMPLETE DEGRADATION; OCTYL PHTHALATE; MICROBIAL
+ INTERACTIONS; DIOXYGENASE GENE; BENZYL PHTHALATE; RISK-ASSESSMENT;
+ MICROCOCCUS SP; HUMAN HEALTH; COMMUNITY},
+Research-Areas = {Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Environmental Sciences},
+ResearcherID-Numbers = {He, Zhili/C-2879-2012
+ Shu, Longfei/I-7211-2019
+ Wang, Zhigang/ABC-3873-2020
+ Wu, Bo/GPK-5360-2022
+ },
+ORCID-Numbers = {He, Zhili/0000-0001-8225-7333
+ Shu, Longfei/0000-0001-9683-906X
+ Hu, Ruiwen/0009-0007-1039-6490
+ Yan, Qingyun/0000-0003-0053-892X},
+Times-Cited = {52},
+Journal-ISO = {Environ. Int.},
+Unique-ID = {WOS:000670066000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000648736100007,
+Author = {Norena-Caro, Daniel A. and Zuniga, Cristal and Pete, Amber J. and
+ Saemundsson, Sven A. and Donaldson, Morgan R. and Adams, Alexandria J.
+ and Dooley, Kerry M. and Zengler, Karsten and Benton, Michael G.},
+Title = {Analysis of the cyanobacterial amino acid metabolism with a precise
+ genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2021},
+Volume = {171},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.bej.2021.108008},
+EarlyAccessDate = {APR 2021},
+Article-Number = {108008},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Anabaena; Cyanobacteria; Genome-scale metabolic reconstruction; Nitrogen
+ fixation; Secondary metabolites},
+Keywords-Plus = {C-13 FLUX ANALYSIS; STRAIN PCC 7120; SP PCC-7120; HETEROLOGOUS
+ EXPRESSION; DIAZOTROPHIC GROWTH; NITROGEN LIMITATION; ESCHERICHIA-COLI;
+ OUTER-MEMBRANE; CARBON-DIOXIDE; SP PCC7120},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Zuniga, Cristal/CAA-0015-2022
+ },
+ORCID-Numbers = {Norena-Caro, Daniel/0000-0001-5135-9230
+ Pete, Amber/0000-0002-9379-2179
+ Benton, Michael/0000-0001-5681-9398},
+Times-Cited = {7},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000648736100007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000638267100012,
+Author = {Lugar, Daniel J. and Mack, Sean G. and Sriram, Ganesh},
+Title = {NetRed, an algorithm to reduce genome-scale metabolic networks and
+ facilitate the analysis of flux predictions},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {65},
+Pages = {207-222},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2020.11.003},
+EarlyAccessDate = {APR 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Flux balance analysis; Metabolic flux; Metabolic network reduction;
+ Biomass equation; Matrix transformation},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sriram, Ganesh/A-5154-2010
+ },
+ORCID-Numbers = {Mack, Sean/0000-0002-6253-4839
+ Lugar, Daniel/0000-0002-0943-9066
+ Sriram, Ganesh/0000-0002-6303-1328},
+Times-Cited = {6},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000638267100012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000658808400003,
+Author = {Schinn, Song-Min and Morrison, Carly and Wei, Wei and Zhang, Lin and
+ Lewis, Nathan E.},
+Title = {Systematic evaluation of parameters for genome-scale metabolic models of
+ cultured mammalian cells},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {66},
+Pages = {21-30},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.03.013},
+EarlyAccessDate = {APR 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Chinese Hamster Ovary cells; Flux Balance Analysis; Metabolic Network
+ Modeling; Bioprocess},
+Keywords-Plus = {HAMSTER OVARY CELLS; CONSTRAINT-BASED MODELS; FED-BATCH CULTURES;
+ ESCHERICHIA-COLI; CHO-CELLS; FLUX ANALYSIS; OBJECTIVE FUNCTIONS; BIOMASS
+ COMPOSITION; BALANCE; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Morrison, Carly/0000-0002-3368-4969
+ WEI, WEI/0000-0002-2315-3558},
+Times-Cited = {11},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000658808400003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000643271500001,
+Author = {Altay, Ozlem and Zhang, Cheng and Turkez, Hasan and Nielsen, Jens and
+ Uhlen, Mathias and Mardinoglu, Adil},
+Title = {Revealing the Metabolic Alterations during Biofilm Development of
+ Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.3390/metabo11040221},
+Article-Number = {221},
+EISSN = {2218-1989},
+Keywords = {Burkholderia cenocepacia; biofilm; genome-scale metabolic models;
+ synthetic lethality; transcriptomics; omics integration},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Zhang, Cheng/L-7906-2016
+ Uhlen, Mathias/AAV-8746-2021
+ Uhlen, Mathias/HPB-8445-2023
+ Mardinoglu, Adil/AAS-6360-2021
+ },
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Zhang, Cheng/0000-0002-3721-8586
+ Uhlen, Mathias/0000-0002-4858-8056
+ Mardinoglu, Adil/0000-0002-4254-6090},
+Times-Cited = {4},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000643271500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000668658500016,
+Author = {Alter, Tobias B. and Blank, Lars M. and Ebert, Birgitta E.},
+Title = {Proteome Regulation Patterns Determine Escherichia coli Wild-Type
+ and Mutant Phenotypes},
+Journal = {MSYSTEMS},
+Year = {2021},
+Volume = {6},
+Number = {2},
+Month = {APR},
+Type = {Article},
+DOI = {10.1128/mSystems.00625-20},
+Article-Number = {e00625-20},
+ISSN = {2379-5077},
+Keywords = {constraint-based modeling; enzyme kinetics; metabolic engineering;
+ protein allocation; transcriptional control; Escherichia coli},
+Keywords-Plus = {GENE-EXPRESSION; GROWTH-RATE; TRANSCRIPTIONAL REGULATION; OVERFLOW
+ METABOLISM; GLUCOSE CATABOLISM; K-12 MG1655; KEY; OPTIMIZATION; MODELS;
+ ACTIVATION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Alter, Tobias/HZK-0764-2023
+ Ebert, Birgitta E./B-7845-2014
+ Blank, Lars M./A-6761-2012},
+ORCID-Numbers = {Alter, Tobias/0000-0002-9593-4388
+ Ebert, Birgitta E./0000-0001-9425-7509
+ Blank, Lars M./0000-0003-0961-4976},
+Times-Cited = {5},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000668658500016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000645199600010,
+Author = {Chen, Yu and van Pelt-KleinJan, Eunice and van Olst, Berdien and
+ Douwenga, Sieze and Boeren, Sjef and Bachmann, Herwig and Molenaar,
+ Douwe and Nielsen, Jens and Teusink, Bas},
+Title = {Proteome constraints reveal targets for improving microbial fitness in
+ nutrient-rich environments},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.15252/msb.202010093},
+Article-Number = {e10093},
+ISSN = {1744-4292},
+Keywords = {ccpA; laboratory evolution; Lactococcus lactis; metabolic modeling;
+ proteome constraint},
+Keywords-Plus = {SCALE METABOLIC MODEL; LACTOCOCCUS-LACTIS; ESCHERICHIA-COLI; PYRUVATE
+ METABOLISM; OVERFLOW METABOLISM; SAMPLE PREPARATION; GROWTH; ACID;
+ IDENTIFICATION; STRATEGIES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Chen, Yu/AAL-3329-2020
+ Molenaar, Douwe/D-2017-2010
+ Bachmann, Herwig/ABE-6301-2021
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Chen, Yu/0000-0003-3326-9068
+ Molenaar, Douwe/0000-0001-7108-4545
+ Bachmann, Herwig/0000-0002-8224-0993
+ Teusink, Bas/0000-0003-3929-0423
+ Douwenga, Sieze/0000-0003-3604-7524
+ van Pelt-KleinJan, Eunice/0000-0002-6590-652X
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {19},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000645199600010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000641080300009,
+Author = {Gupta, Ankur and Kumar, Ajay and Anand, Rajat and Bairagi, Nandadulal
+ and Chatterjee, Samrat},
+Title = {Genome scale metabolic model driven strategy to delineate host response
+ to Mycobacterium tuberculosis infection},
+Journal = {MOLECULAR OMICS},
+Year = {2021},
+Volume = {17},
+Number = {2},
+Pages = {296-306},
+Month = {APR 1},
+Type = {Article},
+DOI = {10.1039/d0mo00138d},
+EISSN = {2515-4184},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Bairagi, Nandadulal/S-4557-2016
+ },
+ORCID-Numbers = {Bairagi, Nandadulal/0000-0001-8867-7996
+ Kumar, Ajay/0000-0001-9914-7421},
+Times-Cited = {1},
+Journal-ISO = {Mol. Omics},
+Unique-ID = {WOS:000641080300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000645199600006,
+Author = {Kochanowski, Karl and Okano, Hiroyuki and Patsalo, Vadim and Williamson,
+ James and Sauer, Uwe and Hwa, Terence},
+Title = {Global coordination of metabolic pathways in Escherichia coli by
+ active and passive regulation},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.15252/msb.202010064},
+Article-Number = {e10064},
+ISSN = {1744-4292},
+Keywords = {C-13 flux analysis; Crp; metabolomics; proteomics; regulation analysis},
+Keywords-Plus = {OVERFLOW METABOLISM; GROWTH-RATE; POSTTRANSLATIONAL MODIFICATIONS;
+ TRANSCRIPTIONAL REGULATION; INTRACELLULAR FLUXES; GENE-EXPRESSION;
+ HIGH-THROUGHPUT; KEY REGULATORS; PROTEIN; ENZYME},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Kochanowski, Karl/ABE-7236-2021
+ Hwa, Terence/J-4012-2013
+ },
+ORCID-Numbers = {Hwa, Terence/0000-0003-1837-6842
+ Patsalo, Vadim/0000-0001-6047-5858},
+Times-Cited = {17},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000645199600006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000635692600001,
+Author = {Liu, Peng and Wang, Shuai and Li, Chao and Zhuang, Yingping and Xia,
+ Jianye and Noorman, Henk},
+Title = {Dynamic response of Aspergillus niger to periodical glucose pulse
+ stimuli in chemostat cultures},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2021},
+Volume = {118},
+Number = {6},
+Pages = {2265-2282},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/bit.27739},
+EarlyAccessDate = {APR 2021},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Aspergillus niger; central carbon metabolism; dynamic response;
+ periodically repeating glucose pulse; substrate fluctuation},
+Keywords-Plus = {CENTRAL CARBON METABOLISM; ORYZAE FERMENTATION LEADS; SCALE-DOWN
+ SIMULATORS; IN-VIVO KINETICS; SACCHAROMYCES-CEREVISIAE;
+ PENICILLIUM-CHRYSOGENUM; ESCHERICHIA-COLI; GLUCOAMYLASE PRODUCTION;
+ LIMITING-CARBON; FLUID-DYNAMICS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {XIA, Jianye/0000-0003-2114-5770},
+Times-Cited = {6},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000635692600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000639290400002,
+Author = {Nanda, Piyush and Ghosh, Amit},
+Title = {Genome Scale-Differential Flux Analysis reveals deregulation of lung
+ cell metabolism on SARS-CoV-2 infection},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1008860},
+Article-Number = {e1008860},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Ghosh, Amit/0000-0003-3514-885X
+ Nanda, Piyush/0000-0002-6433-7484},
+Times-Cited = {19},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000639290400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000642282900028,
+Author = {Sangha, Gurneet S. and Goergen, Craig J. and Prior, Steven J. and
+ Ranadive, Sushant M. and Clyne, Alisa M.},
+Title = {Preclinical techniques to investigate exercise training in vascular
+ pathophysiology},
+Journal = {AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY},
+Year = {2021},
+Volume = {320},
+Number = {4},
+Pages = {H1566-H1600},
+Month = {APR},
+Type = {Review},
+DOI = {10.1152/ajpheart.00719.2020},
+ISSN = {0363-6135},
+EISSN = {1522-1539},
+Keywords = {atherosclerosis; bionengineering; cardiovascular; exercise; preclinical},
+Keywords-Plus = {WALL SHEAR-STRESS; APOLIPOPROTEIN-E-DEFICIENT; LOW-DENSITY-LIPOPROTEIN;
+ SMOOTH-MUSCLE-CELLS; MOUSE AORTIC-ARCH; VULNERABLE ATHEROSCLEROTIC
+ PLAQUE; CORONARY-ARTERY CALCIFICATION; OPTICAL COHERENCE TOMOGRAPHY;
+ ADHESION MOLECULE EXPRESSION; CULTURED ENDOTHELIAL-CELLS},
+Research-Areas = {Cardiovascular System \& Cardiology; Physiology},
+Web-of-Science-Categories = {Cardiac \& Cardiovascular Systems; Physiology; Peripheral Vascular
+ Disease},
+ResearcherID-Numbers = {Goergen, Craig J./I-2416-2019
+ Prior, Steven/AAC-8232-2020
+ Ranadive, Sushant/AAN-4098-2021
+ Sangha, Gurneet/AAP-3034-2020
+ },
+ORCID-Numbers = {Goergen, Craig J./0000-0001-8883-7953
+ Ranadive, Sushant/0000-0003-1674-4285
+ Sangha, Gurneet/0000-0003-1421-482X},
+Times-Cited = {6},
+Journal-ISO = {Am. J. Physiol.-Heart Circul. Physiol.},
+Unique-ID = {WOS:000642282900028},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000642801400001,
+Author = {Weglarz-Tomczak, Ewelina and Mondeel, Thierry D. G. A. and Piebes,
+ Diewertje G. E. and Westerhoff, Hans V.},
+Title = {Simultaneous Integration of Gene Expression and Nutrient Availability
+ for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines},
+Journal = {BIOMOLECULES},
+Year = {2021},
+Volume = {11},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.3390/biom11040490},
+Article-Number = {490},
+EISSN = {2218-273X},
+Keywords = {hepatocellular carcinoma; Warburg effect; glutamine addiction; metabolic
+ network modeling; flux balance analysis; genome-scale metabolic map;
+ GENSI},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Westerhoff, Hans V/I-5762-2012
+ },
+ORCID-Numbers = {Westerhoff, Hans V/0000-0002-0443-6114
+ Mondeel, Thierry/0000-0002-8132-8360
+ Weglarz-Tomczak, Ewelina/0000-0001-8080-2801},
+Times-Cited = {8},
+Journal-ISO = {Biomolecules},
+Unique-ID = {WOS:000642801400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000638267100004,
+Author = {Mol, Vivienne and Bennett, Martyn and Sanchez, Benjamin J. and Lisowska,
+ Beata K. and Herrgard, Markus J. and Nielsen, Alex Toftgaard and Leak,
+ David J. and Sonnenschein, Nikolaus},
+Title = {Genome-scale metabolic modeling of P. thermoglucosidasius
+ NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {65},
+Pages = {123-134},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.03.002},
+EarlyAccessDate = {MAR 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Genome-scale metabolic model; Systems metabolic engineering;
+ Thermophile; In silico strain design; Anaerobic metabolism; Flux balance
+ analysis},
+Keywords-Plus = {BACILLUS-SUBTILIS; MICROBIAL-PRODUCTION; MOLECULAR-CLONING; ATP
+ SYNTHESIS; GEOBACILLUS; RECONSTRUCTION; STRAIN; BIOSYNTHESIS; GLYCOLATE;
+ XYLANASES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sonnenschein, Nikolaus/F-6853-2012
+ },
+ORCID-Numbers = {Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Nielsen, Alex Toftgaard/0000-0001-6616-0187},
+Times-Cited = {7},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000638267100004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000638200100001,
+Author = {Tafur Rangel, Albert Enrique and Rios, Wendy and Mejia, Daisy and Ojeda,
+ Carmen and Carlson, Ross and Gomez Ramirez, Jorge Mario and Gonzalez
+ Barrios, Andres Fernando},
+Title = {In silico Design for Systems-Based Metabolic Engineering for the
+ Bioconversion of Valuable Compounds From Industrial By-Products},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2021},
+Volume = {12},
+Month = {MAR 26},
+Type = {Article},
+DOI = {10.3389/fgene.2021.633073},
+Article-Number = {633073},
+EISSN = {1664-8021},
+Keywords = {systems metabolic engineering; transcriptomics; machine learning;
+ adaptive laboratory evolution; metabolic modeling resources; frameworks},
+Keywords-Plus = {COLI K-12 MG1655; ESCHERICHIA-COLI; ADAPTIVE EVOLUTION; FUMARATE
+ REDUCTASE; SUCCINATE-DEHYDROGENASE; OPTIMIZATION FRAMEWORK; NETWORK
+ RECONSTRUCTION; GENE-EXPRESSION; GLYCEROL; MICROORGANISMS},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Ramirez, Jorge M/B-6344-2018
+ },
+ORCID-Numbers = {Ramirez, Jorge M/0000-0002-0402-7484
+ Tafur Rangel, Albert/0000-0002-9428-183X
+ Gonzalez Barrios, Andres Fernando/0000-0003-2517-2020},
+Times-Cited = {2},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000638200100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000637724800001,
+Author = {Azer, Karim and Kaddi, Chanchala D. and Barrett, Jeffrey S. and Bai,
+ Jane P. F. and McQuade, Sean T. and Merrill, Nathaniel J. and Piccoli,
+ Benedetto and Neves-Zaph, Susana and Marchetti, Luca and Lombardo,
+ Rosario and Parolo, Silvia and Immanuel, Selva Rupa Christinal and
+ Baliga, Nitin S.},
+Title = {History and Future Perspectives on the Discipline of Quantitative
+ Systems Pharmacology Modeling and Its Applications},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2021},
+Volume = {12},
+Month = {MAR 25},
+Type = {Review},
+DOI = {10.3389/fphys.2021.637999},
+Article-Number = {637999},
+EISSN = {1664-042X},
+Keywords = {QSP modeling; systems biology; data science; systems pharmacology;
+ bioinformatics; computational biology; drug development},
+Keywords-Plus = {MYCOBACTERIUM-TUBERCULOSIS H37RV; VIRTUAL POPULATIONS; ENTITY
+ RECOGNITION; GENE-REGULATION; QSP MODEL; NETWORK; TEXT; METABOLISM;
+ DATABASE; DYNAMICS},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {Piccoli, Benedetto/HTR-4073-2023
+ },
+ORCID-Numbers = {Immanuel, Selva Rupa Christinal/0000-0002-3642-9605},
+Times-Cited = {33},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000637724800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000670663400008,
+Author = {Vila-Santa, Ana and Islam, M. Ahsanul and Ferreira, Frederico C. and
+ Prather, Kristala L. J. and Mira, Nuno P.},
+Title = {Prospecting Biochemical Pathways to Implement Microbe-Based Production
+ of the New-to-Nature Platform Chemical Levulinic Acid},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2021},
+Volume = {10},
+Number = {4},
+Pages = {724-736},
+Month = {APR 16},
+Type = {Article},
+DOI = {10.1021/acssynbio.0c00518},
+EarlyAccessDate = {MAR 2021},
+ISSN = {2161-5063},
+Keywords = {pathway prospecting; levulinic acid; new-to-nature biosynthetic
+ pathways; metabolic modeling; microbial cell factories},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; S-ADENOSYLMETHIONINE;
+ BIOSYNTHESIS; BIOREFINERY; ORNITHINE; SEARCH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Mira, Nuno Pereira/E-2965-2012
+ Ferreira, Frederico Castelo/K-8642-2012
+ Vila-Santa, Ana/AAN-3194-2021
+ },
+ORCID-Numbers = {Mira, Nuno Pereira/0000-0001-7556-0385
+ Ferreira, Frederico Castelo/0000-0001-5177-6237
+ Vila-Santa, Ana/0000-0002-5880-1498
+ Prather, Kristala/0000-0003-0437-3157
+ Islam, M. Ahsanul/0000-0001-9585-6263},
+Times-Cited = {11},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000670663400008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000631868600039,
+Author = {Chen, Yu and Li, Feiran and Mao, Jiwei and Chen, Yun and Nielsen, Jens},
+Title = {Yeast optimizes metal utilization based on metabolic network and enzyme
+ kinetics},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2021},
+Volume = {118},
+Number = {12},
+Month = {MAR 23},
+Type = {Article},
+DOI = {10.1073/pnas.2020154118},
+Article-Number = {e2020154118},
+ISSN = {0027-8424},
+EISSN = {1091-6490},
+Keywords = {constraint-based model; Saccharomyces cerevisiae; proteome constraint;
+ metabolic engineering; resource allocation},
+Keywords-Plus = {GENOME-SCALE MODELS; SACCHAROMYCES-CEREVISIAE; IRON-DEFICIENCY;
+ EXPRESSION; LIMITATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Li, Feiran/GNP-2168-2022
+ Chen, Yu/AAL-3329-2020
+ Nielsen, Jens Bo/C-7632-2015
+ Chen, Yun/G-6645-2017
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Li, Feiran/0000-0001-9155-5260
+ Chen, Yu/0000-0003-3326-9068
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Chen, Yun/0000-0002-2146-6008
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {15},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000631868600039},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000732709000018,
+Author = {Gollub, Mattia G. and Kaltenbach, Hans-Michael and Stelling, Joerg},
+Title = {Probabilistic thermodynamic analysis of metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2021},
+Volume = {37},
+Number = {18},
+Pages = {2938-2945},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btab194},
+EarlyAccessDate = {MAR 2021},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {HIT-AND-RUN},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Gollub, Mattia/0000-0001-9588-3130
+ Kaltenbach, Hans-Michael/0000-0003-2500-1221},
+Times-Cited = {9},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000732709000018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000630869100001,
+Author = {Hameri, Tuure and Fengos, Georgios and Hatzimanikatis, Vassily},
+Title = {The effects of model complexity and size on metabolic flux distribution
+ and control: case study in Escherichia coli},
+Journal = {BMC BIOINFORMATICS},
+Year = {2021},
+Volume = {22},
+Number = {1},
+Month = {MAR 20},
+Type = {Article},
+DOI = {10.1186/s12859-021-04066-y},
+Article-Number = {134},
+ISSN = {1471-2105},
+Keywords = {Metabolic networks; Kinetic model; Metabolic control analysis; Model
+ complexity; Model reduction},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; KINETIC-MODELS; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; NETWORK MODELS; UNCERTAINTY; IDENTIFICATION;
+ CONSTRUCTION; REDUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Hatzimanikatis, Vassily/G-6505-2010},
+ORCID-Numbers = {Hatzimanikatis, Vassily/0000-0001-6432-4694},
+Times-Cited = {3},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000630869100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000638265500006,
+Author = {Zelle, E. and Pfelzer, N. and Oldiges, M. and Koch-Koerfges, A. and
+ Bott, M. and Noeh, K. and Wiechert, W.},
+Title = {An energetic profile of Corynebacterium glutamicum
+ underpinned by measured biomass yield on ATP},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {65},
+Pages = {66-78},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.03.006},
+EarlyAccessDate = {MAR 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {ATP yield; Metabolic flux analysis; Constraint based methods; Energy
+ metabolism; Branched respiratory chain},
+Keywords-Plus = {METABOLIC FLUX ANALYSIS; CONSTRAINT-BASED MODELS;
+ SACCHAROMYCES-CEREVISIAE; SCALE-DOWN; QUANTITATIVE PREDICTION; SUBSTRATE
+ OSCILLATIONS; OVERFLOW METABOLISM; CELLULAR-METABOLISM; BALANCE
+ ANALYSIS; GLUCOSE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Bott, Michael/E-8004-2011},
+ORCID-Numbers = {Bott, Michael/0000-0002-4701-8254},
+Times-Cited = {6},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000638265500006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000629545700001,
+Author = {Mesquita, Thiago J. B. and Campani, Gilson and Giordano, Roberto C. and
+ Zangirolami, Teresa C. and Horta, Antonio C. L.},
+Title = {Machine learning applied for metabolic flux-based control of
+ micro-aerated fermentations in bioreactors},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2021},
+Volume = {118},
+Number = {5},
+Pages = {2076-2091},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/bit.27721},
+EarlyAccessDate = {MAR 2021},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {alcoholic fermentation; bioreactor advanced control; metabolic flux
+ control; micro\&\#8208; aeration; Saccharomyces cerevisiae},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Horta, Antonio Carlos L/I-2402-2013
+ Mesquita, Thiago/AAN-1437-2021
+ ZANGIROLAMI, TERESA/J-7089-2013
+ },
+ORCID-Numbers = {Horta, Antonio Carlos L/0000-0002-3042-0351
+ Mesquita, Thiago/0000-0002-5100-770X
+ ZANGIROLAMI, TERESA/0000-0002-2882-9588
+ Campani, Gilson/0000-0003-4467-5264},
+Times-Cited = {9},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000629545700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000627492100001,
+Author = {Simensen, Vetle and Voigt, Andre and Almaas, Eivind},
+Title = {High-quality genome-scale metabolic model of Aurantiochytrium sp.
+ T66},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2021},
+Volume = {118},
+Number = {5},
+Pages = {2105-2117},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/bit.27726},
+EarlyAccessDate = {MAR 2021},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Aurantiochytrium sp; T66; genome\&\#8208; scale model; lipid\&\#8208;
+ producing cell factories; thraustochytrids; \&\#969; \&\#8208; 3 PUFAs},
+Keywords-Plus = {POLYUNSATURATED FATTY-ACIDS; DOCOSAHEXAENOIC ACID; LIMACINUM SR21;
+ GENE-EXPRESSION; RECONSTRUCTION; DHA; THRAUSTOCHYTRIDS; BIOSYNTHESIS;
+ OPTIMIZATION; ORGANISMS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Simensen, Vetle/0000-0002-2511-1052},
+Times-Cited = {7},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000627492100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000632294100030,
+Author = {Kamp, H. and Wahrheit, J. and Stinchcombe, S. and Walk, T. and Stauber,
+ F. and von Ravenzwaay, B.},
+Title = {Succinate dehydrogenase inhibitors: in silico flux analysis and
+ in vivo metabolomics investigations show no severe metabolic
+ consequences for rats and humans},
+Journal = {FOOD AND CHEMICAL TOXICOLOGY},
+Year = {2021},
+Volume = {150},
+Month = {APR},
+Type = {Article},
+DOI = {10.1016/j.fct.2021.112085},
+EarlyAccessDate = {MAR 2021},
+Article-Number = {112085},
+ISSN = {0278-6915},
+EISSN = {1873-6351},
+Keywords = {Metabolomics; in silico; Metabolic modeling; SDHI; Mitochondria;
+ Respiratory chain; Lactate; succinate},
+Research-Areas = {Food Science \& Technology; Toxicology},
+Web-of-Science-Categories = {Food Science \& Technology; Toxicology},
+ORCID-Numbers = {Kamp, Hennicke/0000-0002-1316-8756},
+Times-Cited = {5},
+Journal-ISO = {Food Chem. Toxicol.},
+Unique-ID = {WOS:000632294100030},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000632022000001,
+Author = {Abdik, Ecehan and Cakir, Tunahan},
+Title = {Systematic investigation of mouse models of Parkinson's disease by
+ transcriptome mapping on a brain-specific genome-scale metabolic network},
+Journal = {MOLECULAR OMICS},
+Year = {2021},
+Volume = {17},
+Number = {4},
+Pages = {492+},
+Month = {AUG 1},
+Type = {Article},
+DOI = {10.1039/d0mo00135j},
+EarlyAccessDate = {MAR 2021},
+EISSN = {2515-4184},
+Keywords-Plus = {MAGNETIC-RESONANCE-SPECTROSCOPY; ENERGY-METABOLISM; RAT-BRAIN;
+ MITOCHONDRIAL DYSFUNCTION; GENE-EXPRESSION; TCA CYCLE; GLUTAMATE;
+ GLUCOSE; PATHWAYS; NEURONS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Cakir, Tunahan/F-4523-2011
+ Abdik, Ecehan/AHE-4428-2022},
+ORCID-Numbers = {Cakir, Tunahan/0000-0001-8262-4420
+ Abdik, Ecehan/0000-0002-0941-9620},
+Times-Cited = {2},
+Journal-ISO = {Mol. Omics},
+Unique-ID = {WOS:000632022000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000627660900023,
+Author = {Dougherty, V, Bonnie and Rawls, Kristopher D. and Kolling, Glynis L. and
+ Vinnakota, Kalyan C. and Wallqvist, Anders and Papin, Jason A.},
+Title = {Identifying functional metabolic shifts in heart failure with the
+ integration of omics data and a heart-specific, genome-scale model},
+Journal = {CELL REPORTS},
+Year = {2021},
+Volume = {34},
+Number = {10},
+Month = {MAR 9},
+Type = {Article},
+DOI = {10.1016/j.celrep.2021.108836},
+EarlyAccessDate = {MAR 2021},
+Article-Number = {108836},
+ISSN = {2211-1247},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; SELECTIVE REDUCTION; GLUCOSE-OXIDATION; DRUG
+ TARGETS; SIALIC-ACID; HYPERTROPHY; DISEASE; CANCER; BODY},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Vinnakota, Kalyan/G-4706-2010
+ },
+ORCID-Numbers = {Vinnakota, Kalyan/0000-0003-2185-2213
+ Rawls, Kristopher/0000-0001-5873-0127},
+Times-Cited = {6},
+Journal-ISO = {Cell Reports},
+Unique-ID = {WOS:000627660900023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000625166000001,
+Author = {Rangel, Albert Enrique Tafur and Reyes, Luis H. and Ramirez, Jorge Mario
+ Gomez and Barrios, Andres Fernando Gonzalez},
+Title = {Optimization of glycerol consumption in wild-type Escherichia
+ coli using central carbon modeling as an alternative approach},
+Journal = {BIOFUELS BIOPRODUCTS \& BIOREFINING-BIOFPR},
+Year = {2021},
+Volume = {15},
+Number = {3},
+Pages = {825-839},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/bbb.2205},
+EarlyAccessDate = {MAR 2021},
+ISSN = {1932-104X},
+EISSN = {1932-1031},
+Keywords = {optimization; culture medium; glycerol; Escherichia coli;
+ genome\&\#8208; scale models},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Ramirez, Jorge M/B-6344-2018
+ Reyes, Luis H./AFN-2343-2022
+ },
+ORCID-Numbers = {Ramirez, Jorge M/0000-0002-0402-7484
+ Reyes, Luis H./0000-0001-7251-5298
+ Tafur Rangel, Albert/0000-0002-9428-183X
+ Gonzalez Barrios, Andres Fernando/0000-0003-2517-2020
+ Gomez, Jorge Mario/0000-0002-2018-4121},
+Times-Cited = {1},
+Journal-ISO = {Biofuels Bioprod. Biorefining},
+Unique-ID = {WOS:000625166000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000625315900018,
+Author = {Rosario, Dorines and Bidkhori, Gholamreza and Lee, Sunjae and Bedarf,
+ Janis and Hildebrand, Falk and Le Chatelier, Emmanuelle and Uhlen,
+ Mathias and Ehrlich, Stanislav Dusko and Proctor, Gordon and Wuellner,
+ Ullrich and Mardinoglu, Adil and Shoaie, Saeed},
+Title = {Systematic analysis of gut microbiome reveals the role of bacterial
+ folate and homocysteine metabolism in Parkinson's disease},
+Journal = {CELL REPORTS},
+Year = {2021},
+Volume = {34},
+Number = {9},
+Month = {MAR 2},
+Type = {Article},
+DOI = {10.1016/j.celrep.2021.108807},
+EarlyAccessDate = {MAR 2021},
+Article-Number = {108807},
+ISSN = {2211-1247},
+Keywords-Plus = {MODELS; ASSOCIATION; DEFICIENCY; RISK},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Lee, Sunjae/H-9815-2019
+ Wuellner, Ullrich/JLM-9792-2023
+ Uhlen, Mathias/HPB-8445-2023
+ Uhlen, Mathias/AAV-8746-2021
+ EHRLICH, STANISLAV Dusko/Y-2423-2019
+ Hildebrand, Falk/K-1914-2014
+ Bedarf, Janis Rebecca/AAE-3722-2020
+ Mardinoglu, Adil/AAS-6360-2021},
+ORCID-Numbers = {Lee, Sunjae/0000-0002-6428-5936
+ Uhlen, Mathias/0000-0002-4858-8056
+ EHRLICH, STANISLAV Dusko/0000-0002-7563-4046
+ Hildebrand, Falk/0000-0002-0078-8948
+ },
+Times-Cited = {58},
+Journal-ISO = {Cell Reports},
+Unique-ID = {WOS:000625315900018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000645694100001,
+Author = {Bartos, Hunor and Balazs, Marta and Kuzman, Ildiko Hajnalka and Lanyi,
+ Szabolcs and Miklossy, Ildiko},
+Title = {Production of High Added-Value Chemicals in Basfia
+ succiniciproducens: Role of Medium Composition},
+Journal = {SUSTAINABILITY},
+Year = {2021},
+Volume = {13},
+Number = {6},
+Month = {MAR},
+Type = {Article},
+DOI = {10.3390/su13063513},
+Article-Number = {3513},
+EISSN = {2071-1050},
+Keywords = {Basfia succiniciproducens; succinic acid; yeast extract effect;
+ bacterial growth; batch cultivation},
+Research-Areas = {Science \& Technology - Other Topics; Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Green \& Sustainable Science \& Technology; Environmental Sciences;
+ Environmental Studies},
+ORCID-Numbers = {Miklossy, Ildiko/0000-0002-8037-7216
+ , Bartos/0000-0002-4183-5181},
+Times-Cited = {2},
+Journal-ISO = {Sustainability},
+Unique-ID = {WOS:000645694100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000633864200001,
+Author = {Hendry, I, John and Dinh, V, Hoang and Sarkar, Debolina and Wang, Lin
+ and Bandyopadhyay, Anindita and Pakrasi, Himadri B. and Maranas, Costas
+ D.},
+Title = {A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic
+ Modifications to Overproduce Nylon Monomers},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.3390/metabo11030168},
+Article-Number = {168},
+EISSN = {2218-1989},
+Keywords = {cyanobacteria; Anabaena sp; ATCC 33047; genome scale metabolic models;
+ flux balance analysis; OptForce; caprolactam; valerolactam; heterocyst},
+Keywords-Plus = {CORYNEBACTERIUM-GLUTAMICUM; NITROGENASE ACTIVITY; ESCHERICHIA-COLI;
+ ISOLATED HETEROCYSTS; ADIPIC ACID; CYANOBACTERIA; FIXATION;
+ BIOSYNTHESIS; PATHWAY; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Dinh, Hoang/GZB-0309-2022
+ Maranas, Costas D/A-4774-2011
+ Wang, Lin/ABB-2686-2020
+ },
+ORCID-Numbers = {Dinh, Hoang/0000-0002-3861-357X
+ Maranas, Costas D/0000-0002-1508-1398
+ Wang, Lin/0000-0002-9455-5570
+ Pakrasi, Himadri/0000-0001-8240-2123},
+Times-Cited = {1},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000633864200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000625172500012,
+Author = {Kohlmeier, MacLean G. and Bailey-Elkin, Ben A. and Mark, Brian L. and
+ Oresnik, Ivan J.},
+Title = {Characterization of the sorbitol dehydrogenase SmoS from
+ Sinorhizobium meliloti 1021},
+Journal = {ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY},
+Year = {2021},
+Volume = {77},
+Number = {3},
+Pages = {380-390},
+Month = {MAR 1},
+Type = {Article},
+DOI = {10.1107/S2059798321001017},
+ISSN = {2059-7983},
+Keywords = {sorbitol; galactitol; dehydrogenase; oxidation; SmoS; Sinorhizobium
+ meliloti},
+Keywords-Plus = {SHORT-CHAIN DEHYDROGENASE/REDUCTASE; RHODOBACTER-SPHAEROIDES;
+ SUBSTRATE-INHIBITION; METABOLISM; TAGATOSE; CLONING; THERMOSTABILITY;
+ NOMENCLATURE; MECHANISM; TRANSPORT},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Crystallography},
+Web-of-Science-Categories = {Biochemical Research Methods; Biochemistry \& Molecular Biology;
+ Biophysics; Crystallography},
+ORCID-Numbers = {Mark, Brian/0000-0002-7344-1355},
+Times-Cited = {2},
+Journal-ISO = {Acta Crystallogr. Sect. D-Struct. Biol.},
+Unique-ID = {WOS:000625172500012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000626082500005,
+Author = {Toyoshima, Masakazu and Yamamoto, Chiaki and Ueno, Yoshifumi and Toya,
+ Yoshihiro and Akimoto, Seiji and Shimizu, Hiroshi},
+Title = {Role of type I NADH dehydrogenase in Synechocystis sp. PCC 6803 under
+ phycobilisome excited red light},
+Journal = {PLANT SCIENCE},
+Year = {2021},
+Volume = {304},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.plantsci.2020.110798},
+ISSN = {0168-9452},
+EISSN = {1873-2259},
+Keywords = {Cyanobacteria; Flux balance analysis; Genome-scale model; NDH-1; PSI;
+ PSII excitation ratio},
+Keywords-Plus = {CYCLIC ELECTRON-TRANSPORT; NDH-1 COMPLEXES; PHOTOSYSTEM-I; NAD(P)H
+ DEHYDROGENASE; THERMOSYNECHOCOCCUS-ELONGATUS; INTERSYSTEM CHAIN;
+ CYANOBACTERIUM; PROTEIN; FLUX; METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology; Plant Sciences},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Plant Sciences},
+ResearcherID-Numbers = {Toyoshima, Masakazu/ABA-1357-2021
+ Shimizu, Hiroshi/C-3688-2017},
+ORCID-Numbers = {Toyoshima, Masakazu/0000-0002-6322-7806
+ Shimizu, Hiroshi/0000-0002-8986-0861},
+Times-Cited = {5},
+Journal-ISO = {Plant Sci.},
+Unique-ID = {WOS:000626082500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000624979400011,
+Author = {Goyal, Akshit and Wang, Tong and Dubinkina, Veronika and Maslov, Sergei},
+Title = {Ecology-guided prediction of cross-feeding interactions in the human gut
+ microbiome},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2021},
+Volume = {12},
+Number = {1},
+Month = {FEB 26},
+Type = {Article},
+DOI = {10.1038/s41467-021-21586-6},
+Article-Number = {1335},
+ISSN = {2041-1723},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Maslov, Sergei/C-2397-2009
+ Dubinkina, Veronika/O-2628-2015
+ Wang, Tong/ADL-7956-2022},
+ORCID-Numbers = {Maslov, Sergei/0000-0002-3701-492X
+ Dubinkina, Veronika/0000-0002-4844-6795
+ Wang, Tong/0000-0001-9900-0307},
+Times-Cited = {25},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000624979400011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000623221200001,
+Author = {Sulheim, Snorre and Fossheim, Fredrik A. and Wentzel, Alexander and
+ Almaas, Eivind},
+Title = {Automatic reconstruction of metabolic pathways from identified
+ biosynthetic gene clusters},
+Journal = {BMC BIOINFORMATICS},
+Year = {2021},
+Volume = {22},
+Number = {1},
+Month = {FEB 23},
+Type = {Article},
+DOI = {10.1186/s12859-021-03985-0},
+Article-Number = {81},
+ISSN = {1471-2105},
+Keywords = {Biosynthetic gene clusters; Genome-scale metabolic model; AntiSMASH;
+ Polyketide synthases; Natural products; Heterologous expression;
+ Non-ribosomal peptide synthetases},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Sulheim, Snorre/ABC-5773-2020},
+ORCID-Numbers = {Sulheim, Snorre/0000-0002-3967-1683},
+Times-Cited = {3},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000623221200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000619435300001,
+Author = {Schinn, Song-Min and Morrison, Carly and Wei, Wei and Zhang, Lin and
+ Lewis, Nathan E.},
+Title = {A genome-scale metabolic network model and machine learning predict
+ amino acid concentrations in Chinese Hamster Ovary cell cultures},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2021},
+Volume = {118},
+Number = {5},
+Pages = {2118-2123},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/bit.27714},
+EarlyAccessDate = {FEB 2021},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {bioprocess; Chinese Hamster Ovary; metabolic network modeling;
+ metabolism; systems biology},
+Keywords-Plus = {CHO-CELLS; RECONSTRUCTION; RESPONSES; SELECTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Schinn, Song-Min/0000-0002-5727-4016
+ WEI, WEI/0000-0002-2315-3558},
+Times-Cited = {28},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000619435300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000621058000003,
+Author = {Bernstein, David B. and Sulheim, Snorre and Almaas, Eivind and Segre,
+ Daniel},
+Title = {Addressing uncertainty in genome-scale metabolic model reconstruction
+ and analysis},
+Journal = {GENOME BIOLOGY},
+Year = {2021},
+Volume = {22},
+Number = {1},
+Month = {FEB 18},
+Type = {Review},
+DOI = {10.1186/s13059-021-02289-z},
+Article-Number = {64},
+ISSN = {1474-760X},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; BIOMASS COMPOSITION; DE-NOVO;
+ PROBABILISTIC ANNOTATION; SACCHAROMYCES-CEREVISIAE; MAINTENANCE ENERGY;
+ KINETIC-MODELS; BASIC CONCEPTS; GROWTH-RATE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Bernstein, David B/HLV-8885-2023
+ Sulheim, Snorre/ABC-5773-2020
+ Segrè, Daniel/A-1993-2009},
+ORCID-Numbers = {Bernstein, David B/0000-0001-6091-4021
+ Sulheim, Snorre/0000-0002-3967-1683
+ Segrè, Daniel/0000-0003-4859-1914},
+Times-Cited = {41},
+Journal-ISO = {Genome Biol.},
+Unique-ID = {WOS:000621058000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000637053600007,
+Author = {Bourgade, Barbara and Minton, Nigel P. and Islam, M. Ahsanul},
+Title = {Genetic and metabolic engineering challenges of C1-gas fermenting
+ acetogenic chassis organisms},
+Journal = {FEMS MICROBIOLOGY REVIEWS},
+Year = {2021},
+Volume = {45},
+Number = {2},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1093/femsre/fuab008},
+EarlyAccessDate = {FEB 2021},
+Article-Number = {fuab008},
+ISSN = {0168-6445},
+EISSN = {1574-6976},
+Keywords = {acetogen; gas fermentation; genetic engineering; metabolic engineering;
+ biotechnology; fuels and chemicals},
+Keywords-Plus = {WOOD-LJUNGDAHL PATHWAY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Bourgade, Barbara/0009-0000-5792-1052
+ Minton, Nigel/0000-0002-9277-1261
+ Islam, M. Ahsanul/0000-0001-9585-6263},
+Times-Cited = {20},
+Journal-ISO = {Fems Microbiol. Rev.},
+Unique-ID = {WOS:000637053600007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000618057400005,
+Author = {Andersen, Thea Os and Kunath, Benoit J. and Hagen, Live H. and Arntzen,
+ Magnus O. and Pope, Phillip B.},
+Title = {Rumen metaproteomics: Closer to linking rumen microbial function to
+ animal productivity traits},
+Journal = {METHODS},
+Year = {2021},
+Volume = {186},
+Number = {SI},
+Pages = {42-51},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1016/j.ymeth.2020.07.011},
+EarlyAccessDate = {FEB 2021},
+ISSN = {1046-2023},
+EISSN = {1095-9130},
+Keywords = {Rumen; Rumen microbiome; Metaproteomics; Methane; Metagenome-assembled
+ genomes; Microbial diversity},
+Keywords-Plus = {SAMPLE PREPARATION; PROTEIN IDENTIFICATION; METAGENOME; CHALLENGES;
+ PROTEOMICS; LIQUID; EXTRACTION; GENOMES; FRACTIONATION; COMMUNITIES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Pope, Phillip/AAQ-2251-2021
+ },
+ORCID-Numbers = {Pope, Phillip/0000-0002-2067-4059
+ Kunath, Benoit J./0000-0002-3356-8562},
+Times-Cited = {14},
+Journal-ISO = {Methods},
+Unique-ID = {WOS:000618057400005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000620558500001,
+Author = {Ofaim, Shany and Sulheim, Snorre and Almaas, Eivind and Sher, Daniel and
+ Segre, Daniel},
+Title = {Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in
+ a Revised Genome-Scale Model of Prochlorococcus},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2021},
+Volume = {12},
+Month = {FEB 9},
+Type = {Article},
+DOI = {10.3389/fgene.2021.586293},
+Article-Number = {586293},
+EISSN = {1664-8021},
+Keywords = {constraint-based reconstruction and analysis (COBRA); flux balance
+ analysis (FBA); computation of microbial ecosystems in time and space
+ (COMETS); cyanobacteria; exudation; gap-filling algorithm;
+ photosynthesis},
+Keywords-Plus = {DISSOLVED ORGANIC-MATTER; FLUX BALANCE ANALYSIS; SP PCC 6803;
+ PHOTOSYNTHETIC PROKARYOTE; MARINE-PHYTOPLANKTON; RESOURCE-ALLOCATION;
+ HYDROGEN-PEROXIDE; BASIC CONCEPTS; GROWTH; GLYCOGEN},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Segrè, Daniel/A-1993-2009
+ Sulheim, Snorre/ABC-5773-2020},
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914
+ Sulheim, Snorre/0000-0002-3967-1683},
+Times-Cited = {9},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000620558500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000618089100006,
+Author = {Chang, Hui-Yin and Colby, Sean M. and Du, Xiuxia and Gomez, Javier D.
+ and Helf, Maximilian J. and Kechris, Katerina and Kirkpatrick, Christine
+ R. and Li, Shuzhao and Patti, Gary J. and Renslow, Ryan S. and
+ Subramaniam, Shankar and Verma, Mukesh and Xia, Jianguo and Young, Jamey
+ D.},
+Title = {A Practical Guide to Metabolomics Software Development},
+Journal = {ANALYTICAL CHEMISTRY},
+Year = {2021},
+Volume = {93},
+Number = {4},
+Pages = {1912-1923},
+Month = {FEB 2},
+Type = {Article},
+DOI = {10.1021/acs.analchem.0c03581},
+ISSN = {0003-2700},
+EISSN = {1520-6882},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Analytical},
+ResearcherID-Numbers = {Xia, Jianguo/Z-1935-2019
+ },
+ORCID-Numbers = {Xia, Jianguo/0000-0003-2040-2624
+ Kirkpatrick, Christine/0000-0002-4451-8042
+ Helf, Maximilian/0000-0002-1393-3999},
+Times-Cited = {19},
+Journal-ISO = {Anal. Chem.},
+Unique-ID = {WOS:000618089100006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000616652400005,
+Author = {Li, Ying and Xian, He and Xu, Ya and Zhu, Yuan and Sun, Zhijie and Wang,
+ Qian and Qi, Qingsheng},
+Title = {Fine tuning the glycolytic flux ratio of EP-bifido pathway for
+ mevalonate production by enhancing glucose-6-phosphate dehydrogenase
+ (Zwf) and CRISPRi suppressing 6-phosphofructose kinase (PfkA) in
+ Escherichia coli},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2021},
+Volume = {20},
+Number = {1},
+Month = {FEB 2},
+Type = {Article},
+DOI = {10.1186/s12934-021-01526-1},
+Article-Number = {32},
+EISSN = {1475-2859},
+Keywords-Plus = {BIOSYNTHESIS; INTERFERENCE; ACTIVATION; REPRESSION; FIXATION; ETHANOL;
+ DESIGN; MODELS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {8},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000616652400005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000621566000002,
+Author = {Henson, Michael A.},
+Title = {Computational modeling of the gut microbiota reveals putative metabolic
+ mechanisms of recurrent Clostridioides difficile infection},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1008782},
+Article-Number = {e1008782},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {TRANSPLANTATION; ACID},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+Times-Cited = {5},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000621566000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000623776900001,
+Author = {Kim, Dohyeon and Kim, Youngshin and Yoon, Sung Ho},
+Title = {Development of a Genome-Scale Metabolic Model and Phenome Analysis of
+ the Probiotic Escherichia coli Strain Nissle 1917},
+Journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
+Year = {2021},
+Volume = {22},
+Number = {4},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/ijms22042122},
+Article-Number = {2122},
+EISSN = {1422-0067},
+Keywords = {Escherichia coli Nissle 1917; probiotics; metabolic network model;
+ phenome analysis; flux balance analysis},
+Research-Areas = {Biochemistry \& Molecular Biology; Chemistry},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Chemistry, Multidisciplinary},
+Times-Cited = {5},
+Journal-ISO = {Int. J. Mol. Sci.},
+Unique-ID = {WOS:000623776900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000622766800001,
+Author = {Koblitz, Julia and Will, Sabine Eva and Riemer, S. Alexander and Ulas,
+ Thomas and Neumann-Schaal, Meina and Schomburg, Dietmar},
+Title = {The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox
+ Introduced by Two Use Cases},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/metabo11020113},
+Article-Number = {113},
+EISSN = {2218-1989},
+Keywords = {systems biology; metabolic modeling; flux balance analysis; Phaeobacter
+ inhibens; tropodithietic acid},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Neumann-Schaal, Meina/AAM-6389-2021
+ Koblitz, Julia/ABA-1259-2021
+ },
+ORCID-Numbers = {Koblitz, Julia/0000-0002-7260-2129
+ Ulas, Thomas/0000-0002-9785-4197},
+Times-Cited = {1},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000622766800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000618281000008,
+Author = {Rodriguez-Mier, Pablo and Poupin, Nathalie and de Blasio, Carlo and Le
+ Cam, Laurent and Jourdan, Fabien},
+Title = {DEXOM: Diversity-based enumeration of optimal context-specific metabolic
+ networks},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1008730},
+Article-Number = {e1008730},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {MULTIPLE SOLUTIONS; CANCER; TARGETS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Jourdan, Fabien/AAW-5075-2021
+ },
+ORCID-Numbers = {Jourdan, Fabien/0000-0001-9401-2894
+ Poupin, Nathalie/0000-0002-3393-1405
+ Rodriguez-Mier, Pablo/0000-0002-4938-4418},
+Times-Cited = {2},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000618281000008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000667755400014,
+Author = {Shin, Woosub and Hellerstein, Joseph L.},
+Title = {Isolating structural errors in reaction networks in systems biology},
+Journal = {BIOINFORMATICS},
+Year = {2021},
+Volume = {37},
+Number = {3},
+Pages = {388-395},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btaa720},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {MODELS; NOTATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+Times-Cited = {1},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000667755400014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000614153400001,
+Author = {Villate, Aitor and San Nicolas, Markel and Gallastegi, Mara and Aulas,
+ Pierre-Antoine and Olivares, Maitane and Usobiaga, Aresatz and
+ Etxebarria, Nestor and Aizpurua-Olaizola, Oier},
+Title = {Review: Metabolomics as a prediction tool for plants performance under
+ environmental stress},
+Journal = {PLANT SCIENCE},
+Year = {2021},
+Volume = {303},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1016/j.plantsci.2020.110789},
+Article-Number = {110789},
+ISSN = {0168-9452},
+EISSN = {1873-2259},
+Keywords = {Plant metabolomics; Abiotic stress; Metabolic markers; Growth scenarios;
+ High resolution mass spectrometry; Chemometrics},
+Keywords-Plus = {MASS-SPECTROMETRY DATA; DROUGHT TOLERANCE; ANALYSIS REVEALS; SECONDARY
+ METABOLITES; WATER-STRESS; RESPONSES; ARABIDOPSIS; MECHANISMS;
+ ADAPTATION; NITROGEN},
+Research-Areas = {Biochemistry \& Molecular Biology; Plant Sciences},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Plant Sciences},
+ResearcherID-Numbers = {Aizpurua-Olaizola, Oier/G-8007-2016
+ San Nicolas, Markel/AAW-9115-2021
+ Olivares, Maitane/AAY-7123-2021
+ Etxebarria, Nestor/M-6791-2019
+ },
+ORCID-Numbers = {Aizpurua-Olaizola, Oier/0000-0003-2321-2113
+ Gallastegi, Mara/0000-0003-4857-5797
+ Etxebarria, Nestor/0000-0002-2942-9463
+ Villate Uribe, Aitor/0000-0002-3338-4894},
+Times-Cited = {36},
+Journal-ISO = {Plant Sci.},
+Unique-ID = {WOS:000614153400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000615410800001,
+Author = {Weglarz-Tomczak, Ewelina and Rijlaarsdam, Demi J. and Tomczak, Jakub M.
+ and Brul, Stanley},
+Title = {GEM-Based Metabolic Profiling for Human Bone Osteosarcoma under
+ Different Glucose and Glutamine Availability},
+Journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
+Year = {2021},
+Volume = {22},
+Number = {3},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/ijms22031470},
+Article-Number = {1470},
+EISSN = {1422-0067},
+Keywords = {metabolism; transcription; nutrients; genome-scale metabolic models;
+ osteosarcoma},
+Keywords-Plus = {CELLS},
+Research-Areas = {Biochemistry \& Molecular Biology; Chemistry},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Chemistry, Multidisciplinary},
+ResearcherID-Numbers = {Tomczak, Jakub/ABB-7948-2020
+ },
+ORCID-Numbers = {Weglarz-Tomczak, Ewelina/0000-0001-8080-2801
+ Tomczak, Jakub/0000-0001-8634-694X
+ Brul, Stanley/0000-0001-5706-8768},
+Times-Cited = {4},
+Journal-ISO = {Int. J. Mol. Sci.},
+Unique-ID = {WOS:000615410800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000631886700006,
+Author = {van Rosmalen, R. P. and Smith, R. W. and dos Santos, V. A. P. Martins
+ and Fleck, C. and Suarez-Diez, M.},
+Title = {Model reduction of genome-scale metabolic models as a basis for targeted
+ kinetic models},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {64},
+Pages = {74-84},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ymben.2021.01.008},
+EarlyAccessDate = {JAN 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic engineering; DBTL cycle; Model reduction; Model optimisation;
+ Model-driven design; Synthetic biology},
+Keywords-Plus = {PARAMETER-ESTIMATION; SYSTEMS BIOLOGY; OMIC DATA; CONSTRUCTION;
+ THERMODYNAMICS; DECOMPOSITION; ALGORITHM; COLI},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Fleck, Christian/D-1620-2012
+ },
+ORCID-Numbers = {martins dos santos, vitor/0000-0002-2352-9017
+ Suarez-Diez, Maria/0000-0001-5845-146X
+ Fleck, Christian/0000-0002-6371-4495
+ van Rosmalen, Rik/0000-0001-6911-3298},
+Times-Cited = {14},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000631886700006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000615805300001,
+Author = {Dusad, Varshit and Thiel, Denise and Barahona, Mauricio and Keun, Hector
+ C. and Oyarzun, Diego A.},
+Title = {Opportunities at the Interface of Network Science and Metabolic Modeling},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2021},
+Volume = {8},
+Month = {JAN 25},
+Type = {Review},
+DOI = {10.3389/fbioe.2020.591049},
+Article-Number = {591049},
+ISSN = {2296-4185},
+Keywords = {genome scale metabolic modeling; network science; systems biology; flux
+ balance analysis; machine learning; synthetic biology},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Barahona, Mauricio/C-3638-2008
+ Oyarzun, Diego A/A-7945-2008
+ Barahona, Mauricio/M-9747-2019
+ },
+ORCID-Numbers = {Barahona, Mauricio/0000-0002-1089-5675
+ Thiel, Denise/0000-0001-8677-2420},
+Times-Cited = {7},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000615805300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000613016400002,
+Author = {Martins Conde, Patricia and Pfau, Thomas and Pires Pacheco, Maria and
+ Sauter, Thomas},
+Title = {A dynamic multi-tissue model to study human metabolism},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2021},
+Volume = {7},
+Number = {1},
+Month = {JAN 22},
+Type = {Article},
+DOI = {10.1038/s41540-020-00159-1},
+Article-Number = {5},
+EISSN = {2056-7189},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; EXERCISE INTENSITY; INBORN-ERRORS; FAT; FLUXES;
+ CANCER; ACID},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Martins Conde, Patricia/0000-0003-2246-5469
+ Sauter, Thomas/0000-0001-8225-2954},
+Times-Cited = {8},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000613016400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000612991100002,
+Author = {Antoniewicz, Maciek R.},
+Title = {A guide to metabolic flux analysis in metabolic engineering: Methods,
+ tools and applications},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {63},
+Number = {SI},
+Pages = {2-12},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2020.11.002},
+EarlyAccessDate = {JAN 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic flux analysis; Flux balance analysis; Metabolism; Metabolic
+ network model; Stable-isotope tracers; Systems biology},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; MASS ISOTOPOMER DISTRIBUTIONS;
+ BIDIRECTIONAL REACTION STEPS; ESCHERICHIA-COLI; CELLULAR-METABOLISM;
+ NETWORK MODEL; UNITS EMU; CHO-CELLS; GROWTH; PATHWAY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009
+ },
+ORCID-Numbers = {Antoniewicz, Maciek/0000-0002-0087-2875},
+Times-Cited = {49},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000612991100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000612991100005,
+Author = {Otero-Muras, Irene and Carbonell, Pablo},
+Title = {Automated engineering of synthetic metabolic pathways for efficient
+ biomanufacturing},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {63},
+Number = {SI},
+Pages = {61-80},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2020.11.012},
+EarlyAccessDate = {JAN 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic engineering; Retrobiosynthesis; Assembly; Synthetic biology;
+ Automation; Dynamic regulation},
+Keywords-Plus = {MUCONIC ACID PRODUCTION; RIBOSOME BINDING-SITES; COMPUTER-AIDED-DESIGN;
+ ESCHERICHIA-COLI; CHEMICAL PRODUCTION; KINETIC-MODELS; FLUX ANALYSIS;
+ ANALYSIS TOOL; ROUTE SEARCH; TRADE-OFFS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Otero-Muras, Irene/K-3832-2014
+ Carbonell, Pablo/A-3572-2011},
+ORCID-Numbers = {Otero-Muras, Irene/0000-0003-2895-997X
+ Carbonell, Pablo/0000-0002-0993-5625},
+Times-Cited = {22},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000612991100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000612991100003,
+Author = {Suthers, Patrick F. and Foster, Charles J. and Sarkar, Debolina and
+ Wang, Lin and Maranas, Costas D.},
+Title = {Recent advances in constraint and machine learning-based metabolic
+ modeling by leveraging stoichiometric balances, thermodynamic
+ feasibility and kinetic law formalisms},
+Journal = {METABOLIC ENGINEERING},
+Year = {2021},
+Volume = {63},
+Number = {SI},
+Pages = {13-33},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2020.11.013},
+EarlyAccessDate = {JAN 2021},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords-Plus = {CENTRAL CARBON METABOLISM; C-13-METABOLIC FLUX ANALYSIS;
+ ESCHERICHIA-COLI; MOLECULAR THERMODYNAMICS; RESOURCE-ALLOCATION;
+ REGULATORY NETWORKS; CELLULAR-METABOLISM; GIBBS ENERGIES; PREDICTION;
+ ALGORITHM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Wang, Lin/ABB-2686-2020
+ Maranas, Costas D/A-4774-2011
+ },
+ORCID-Numbers = {Wang, Lin/0000-0002-9455-5570
+ Maranas, Costas D/0000-0002-1508-1398
+ Foster, Charles/0000-0003-1494-4566
+ Suthers, Patrick/0000-0002-5560-9986},
+Times-Cited = {19},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000612991100003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000609782400004,
+Author = {Ranganayaki, Sathyanarayanan and Jamshidi, Neema and Aiyaz, Mohamad and
+ Rashmi, Santhosh-Kumar and Gayathri, Narayanappa and Harsha, Pulleri
+ Kandi and Padmanabhan, Balasundaram and Bharath, Muchukunte Mukunda
+ Srinivas},
+Title = {Inhibition of mitochondrial complex II in neuronal cells triggers unique
+ pathways culminating in autophagy with implications for
+ neurodegeneration},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2021},
+Volume = {11},
+Number = {1},
+Month = {JAN 15},
+Type = {Article},
+DOI = {10.1038/s41598-020-79339-2},
+Article-Number = {1483},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; 3-NITROPROPIONIC ACID; QUANTITATIVE PREDICTION;
+ STRIATAL DEGENERATION; CELLULAR-METABOLISM; PARKINSONS-DISEASE;
+ FLAVOPROTEIN GENE; BECLIN 1; DEATH; GLUTATHIONE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {SANTHOSHKUMAR, RASHMI/0000-0002-4964-438X
+ Sathyanarayanan, Ranganayaki/0000-0002-1826-5512},
+Times-Cited = {12},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000609782400004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000621919500079,
+Author = {Liu, Jibin and Cheng, Anchun and Wang, Mingshu and Liu, Mafeng and Zhu,
+ Dekang and Yang, Qiao and Wu, Ying and Jia, Renyong and Chen, Shun and
+ Zhao, Xinxin and Zhang, Shaqiu and Huang, Juan and Ou, Xumin and Mao,
+ Sai and Gao, Qun and Wen, Xingjian and Zhang, Ling and Liu, Yunya and
+ Yu, Yanling and Tian, Bin and Pan, Leichang and Rehman, Mujeeb Ur and
+ Chen, Xiaoyue},
+Title = {Comparative genomics and metabolomics analysis of Riemerella
+ anatipestifer strain CH-1 and CH-2},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2021},
+Volume = {11},
+Number = {1},
+Month = {JAN 12},
+Type = {Article},
+DOI = {10.1038/s41598-020-79733-w},
+Article-Number = {616},
+ISSN = {2045-2322},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {yang, zhou/JKI-3744-2023
+ liu, jiaming/IWE-3196-2023
+ wang, ming/ITV-5378-2023
+ li, jian/IAQ-2794-2023
+ Yu, Yan/GYV-4514-2022
+ wang, ming/HPC-6329-2023
+ Rehman, Mujeeb/L-3379-2019
+ liu, junyang/IXD-1201-2023
+ Wang, Xuemei/GXF-3702-2022
+ XIONG, LIU/JOK-5886-2023},
+ORCID-Numbers = {Rehman, Mujeeb/0000-0002-5078-5657
+ },
+Times-Cited = {3},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000621919500079},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000606878400001,
+Author = {Xu, Nan and Yang, Qiyuan and Yang, Xiaojing and Wang, Mingqi and Guo,
+ Minliang},
+Title = {Reconstruction and analysis of a genome-scale metabolic model for
+ Agrobacterium tumefaciens},
+Journal = {MOLECULAR PLANT PATHOLOGY},
+Year = {2021},
+Volume = {22},
+Number = {3},
+Pages = {348-360},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1111/mpp.13032},
+EarlyAccessDate = {JAN 2021},
+ISSN = {1464-6722},
+EISSN = {1364-3703},
+Keywords = {Agrobacterium tumefaciens; crown gall; genome-scale metabolic model;
+ plant pathogen; systems biology},
+Keywords-Plus = {CHEMICAL-COMPOSITION; GENE-EXPRESSION; RHIZOBIUM; NETWORK; PROTEIN;
+ ACCUMULATION; CATABOLISM; TRANSPORT; SEQUENCE; DATABASE},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ORCID-Numbers = {Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {4},
+Journal-ISO = {Mol. Plant Pathol.},
+Unique-ID = {WOS:000606878400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000637054700003,
+Author = {Domenzain, Ivan and Li, Feiran and Kerkhoven, Eduard J. and Siewers,
+ Verena},
+Title = {Evaluating accessibility, usability and interoperability of genome-scale
+ metabolic models for diverse yeasts species},
+Journal = {FEMS YEAST RESEARCH},
+Year = {2021},
+Volume = {21},
+Number = {1},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1093/femsyr/foab002},
+EarlyAccessDate = {JAN 2021},
+Article-Number = {foab002},
+ISSN = {1567-1356},
+EISSN = {1567-1364},
+Keywords = {genome-scale metabolic models; yeast species; systems biology;
+ accessibility; usability; interoperability},
+Keywords-Plus = {PICHIA-PASTORIS; SYSTEMS BIOLOGY; NETWORK; KLUYVEROMYCES},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+ResearcherID-Numbers = {Domenzain, Ivan/HCI-9542-2022
+ Kerkhoven, Eduard/P-2469-2019
+ Li, Feiran/GNP-2168-2022},
+ORCID-Numbers = {Domenzain, Ivan/0000-0002-5322-2040
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Li, Feiran/0000-0001-9155-5260},
+Times-Cited = {1},
+Journal-ISO = {FEMS Yeast Res.},
+Unique-ID = {WOS:000637054700003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000656825700004,
+Author = {Ciomek, Krzysztof and Kadzinski, Milosz},
+Title = {Polyrun: A Java library for sampling from the bounded convex polytopes},
+Journal = {SOFTWAREX},
+Year = {2021},
+Volume = {13},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.softx.2021.100659},
+EarlyAccessDate = {JAN 2021},
+Article-Number = {100659},
+ISSN = {2352-7110},
+Keywords = {Monte Carlo simulation; Hit-and-Run; Convex polytope; Uniform sampling;
+ Linear constraints; Java},
+Keywords-Plus = {HIT-AND-RUN; MULTICRITERIA ACCEPTABILITY ANALYSIS; WISE ELICITATION
+ QUESTIONS; ROBUST; HEURISTICS; ALGORITHM; VOLUME; WALKS; MODEL},
+Research-Areas = {Computer Science},
+Web-of-Science-Categories = {Computer Science, Software Engineering},
+ResearcherID-Numbers = {Kadziński, Miłosz/L-8304-2014},
+ORCID-Numbers = {Kadziński, Miłosz/0000-0003-1806-3715},
+Times-Cited = {10},
+Journal-ISO = {SoftwareX},
+Unique-ID = {WOS:000656825700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000608437800073,
+Author = {Moretti, Sebastien and Tran, Van Du T. and Mehl, Florence and Ibberson,
+ Mark and Pagni, Marco},
+Title = {MetaNetX/MNXref: unified namespace for metabolites and biochemical
+ reactions in the context of metabolic models},
+Journal = {NUCLEIC ACIDS RESEARCH},
+Year = {2021},
+Volume = {49},
+Number = {D1},
+Pages = {D570-D574},
+Month = {JAN 8},
+Type = {Article},
+DOI = {10.1093/nar/gkaa992},
+ISSN = {0305-1048},
+EISSN = {1362-4962},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {mehl, florence/Q-6651-2019
+ Tran, Van Du/C-7892-2019
+ },
+ORCID-Numbers = {mehl, florence/0000-0002-9619-1707
+ Tran, Van Du/0000-0003-2074-5029
+ Pagni, Marco/0000-0001-9292-9463
+ Moretti, Sebastien/0000-0003-3947-488X
+ Ibberson, Mark/0000-0003-3152-5670},
+Times-Cited = {48},
+Journal-ISO = {Nucleic Acids Res.},
+Unique-ID = {WOS:000608437800073},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000634377100008,
+Author = {Paul, Abhijit and Anand, Rajat and Karmakar, Sonali Porey and Rawat,
+ Surender and Bairagi, Nandadulal and Chatterjee, Samrat},
+Title = {Exploring gene knockout strategies to identify potential drug targets
+ using genome-scale metabolic models},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2021},
+Volume = {11},
+Number = {1},
+Month = {JAN 8},
+Type = {Article},
+DOI = {10.1038/s41598-020-80561-1},
+Article-Number = {213},
+ISSN = {2045-2322},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Bairagi, Nandadulal/S-4557-2016},
+ORCID-Numbers = {Bairagi, Nandadulal/0000-0001-8867-7996},
+Times-Cited = {10},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000634377100008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000614283600001,
+Author = {Rawls, Kristopher D. and Dougherty, V, Bonnie and Vinnakota, Kalyan C.
+ and Pannala, Venkat R. and Wallqvist, Anders and Kolling, Glynis L. and
+ Papin, Jason A.},
+Title = {Predicting changes in renal metabolism after compound exposure with a
+ genome-scale metabolic model},
+Journal = {TOXICOLOGY AND APPLIED PHARMACOLOGY},
+Year = {2021},
+Volume = {412},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1016/j.taap.2020.115390},
+EarlyAccessDate = {JAN 2021},
+Article-Number = {115390},
+ISSN = {0041-008X},
+EISSN = {1096-0333},
+Keywords = {Kidney; Kidney Metabolism; Metabolic Modeling; Nephrotoxicity;
+ Transcriptomics; Metabolomics},
+Research-Areas = {Pharmacology \& Pharmacy; Toxicology},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy; Toxicology},
+ResearcherID-Numbers = {Vinnakota, Kalyan/G-4706-2010},
+ORCID-Numbers = {Rawls, Kristopher/0000-0001-5873-0127
+ Vinnakota, Kalyan/0000-0003-2185-2213},
+Times-Cited = {5},
+Journal-ISO = {Toxicol. Appl. Pharmacol.},
+Unique-ID = {WOS:000614283600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000608270000001,
+Author = {Pham, Nhung and Reijnders, Maarten and Suarez-Diez, Maria and Nijsse,
+ Bart and Springer, Jan and Eggink, Gerrit and Schaap, Peter J.},
+Title = {Genome-scale metabolic modeling underscores the potential of
+ Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for
+ biofuel production},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2021},
+Volume = {14},
+Number = {1},
+Month = {JAN 6},
+Type = {Article},
+DOI = {10.1186/s13068-020-01838-1},
+Article-Number = {2},
+EISSN = {1754-6834},
+Keywords = {Genome-scale metabolic model; Cutaneotrichosporon oleaginosus ATCC
+ 20509; Lipid accumulation; Crude glycerol; Biodiesel production; Flux
+ balance analysis; Oleaginous yeast},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ORCID-Numbers = {Suarez-Diez, Maria/0000-0001-5845-146X
+ Schaap, Peter/0000-0002-4346-6084
+ Pham, Nhung/0000-0003-3091-3962},
+Times-Cited = {13},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000608270000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000608112600003,
+Author = {Woerheide, Maria A. and Krumsiek, Jan and Kastenmueller, Gabi and
+ Arnold, Matthias},
+Title = {Multi-omics integration in biomedical research - A metabolomics-centric
+ review},
+Journal = {ANALYTICA CHIMICA ACTA},
+Year = {2021},
+Volume = {1141},
+Pages = {144-162},
+Month = {JAN 2},
+Type = {Review},
+DOI = {10.1016/j.aca.2020.10.038},
+ISSN = {0003-2670},
+EISSN = {1873-4324},
+Keywords = {Multi-omics; Data integration; Systems biology; Metabolomics; Lipidomics},
+Keywords-Plus = {GENOME-WIDE ASSOCIATION; PRINCIPAL COMPONENT ANALYSIS; CONSTRAINT-BASED
+ MODELS; GLOBAL RECONSTRUCTION; CELLULAR-METABOLISM; ALZHEIMERS-DISEASE;
+ EXPRESSION; ATLAS; KNOWLEDGEBASE; VISUALIZATION},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Analytical},
+ResearcherID-Numbers = {Krumsiek, Jan/B-3961-2013
+ },
+ORCID-Numbers = {Arnold, Matthias/0000-0002-4666-0923
+ Ulmer, Maria/0000-0002-9326-7227},
+Times-Cited = {84},
+Journal-ISO = {Anal. Chim. Acta},
+Unique-ID = {WOS:000608112600003},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000610384500001,
+Author = {Baloni, Priyanka and Dinalankara, Wikum and Earls, John C. and
+ Knijnenburg, Theo A. and Geman, Donald and Marchionni, Luigi and Price,
+ Nathan D.},
+Title = {Identifying Personalized Metabolic Signatures in Breast Cancer},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.3390/metabo11010020},
+Article-Number = {20},
+EISSN = {2218-1989},
+Keywords = {breast cancer; genome-scale metabolic models; constraint-based analysis;
+ divergence analysis; gene expression; metabolism; drug targets;
+ personalized metabolic networks},
+Keywords-Plus = {PROTEASOME INHIBITOR; MG132; CELLS; APOPTOSIS; OSU-03012; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Marchionni, Luigi/S-6774-2017
+ },
+ORCID-Numbers = {Marchionni, Luigi/0000-0002-7336-8071
+ Baloni, Priyanka/0000-0002-3382-4941},
+Times-Cited = {8},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000610384500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000692604500002,
+Author = {Desmet, Sandrien and Brouckaert, Marlies and Boerjan, Wout and Morreel,
+ Kris},
+Title = {Seeing the forest for the trees: Retrieving plant secondary biochemical
+ pathways from metabolome networks},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2021},
+Volume = {19},
+Pages = {72-85},
+Type = {Review},
+DOI = {10.1016/j.csbj.2020.11.050},
+ISSN = {2001-0370},
+Keywords-Plus = {MASS-SPECTRAL DATA; NATURAL-PRODUCTS; STRUCTURAL-CHARACTERIZATION;
+ MOLECULAR NETWORKING; FRAGMENTATION TREES; SPECTROMETRY DATA;
+ IDENTIFICATION; ANNOTATION; ARABIDOPSIS; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Brouckaert, Marlies/0000-0002-5893-3175
+ Desmet, Sandrien Marie Valerie/0000-0002-0957-708X},
+Times-Cited = {8},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000692604500002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000696993100008,
+Author = {Granata, Ilaria and Manzo, Mario and Kusumastuti, Ari and Guarracino,
+ Mario R.},
+Title = {Learning from Metabolic Networks: Current Trends and Future Directions
+ for Precision Medicine},
+Journal = {CURRENT MEDICINAL CHEMISTRY},
+Year = {2021},
+Volume = {28},
+Number = {32},
+Pages = {6619-6653},
+Type = {Review},
+DOI = {10.2174/0929867328666201217103148},
+ISSN = {0929-8673},
+EISSN = {1875-533X},
+Keywords = {Metabolic networks; biochemical databases; precision medicine; omics
+ data; mathematical modeling; machine learning; deep learning},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GENE-EXPRESSION; SYSTEMS BIOLOGY; GUT MICROBIOME;
+ PARKINSONS-DISEASE; GLOBAL RECONSTRUCTION; MINIMUM INFORMATION;
+ DATABASE; MODELS; CANCER},
+Research-Areas = {Biochemistry \& Molecular Biology; Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Chemistry, Medicinal; Pharmacology \&
+ Pharmacy},
+ResearcherID-Numbers = {Granata, Ilaria/Q-2830-2018
+ Guarracino, Mario Rosario/L-3815-2013
+ },
+ORCID-Numbers = {Granata, Ilaria/0000-0002-3450-4667
+ Kusumastuti, Ari/0000-0003-3883-4310
+ Guarracino, Mario Rosario/0000-0003-2870-8134
+ MANZO, Mario/0000-0001-8727-9865},
+Times-Cited = {1},
+Journal-ISO = {Curr. Med. Chem.},
+Unique-ID = {WOS:000696993100008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000613893300007,
+Author = {Haiman, Zachary B. and Zielinski, Daniel C. and Koike, Yuko and
+ Yurkovich, James T. and Palsson, Bernhard O.},
+Title = {MASSpy: Building, simulating, and visualizing dynamic biological models
+ in Python using mass action kinetics},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1008208},
+Article-Number = {e1008208},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; METABOLIC GENOTYPE; NETWORK;
+ SYSTEMS; MECHANISMS; EVOLUTION; SBML},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785
+ Zielinski, Daniel/0000-0001-6452-483X
+ Haiman, Zachary/0000-0001-6175-5050},
+Times-Cited = {11},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000613893300007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000709866600001,
+Author = {Hertel, Johannes and Heinken, Almut and Martinelli, Filippo and Thiele,
+ Ines},
+Title = {Integration of constraint-based modeling with fecal metabolomics reveals
+ large deleterious effects of Fusobacterium spp. on community
+ butyrate production},
+Journal = {GUT MICROBES},
+Year = {2021},
+Volume = {13},
+Number = {1},
+Month = {JAN 1},
+Type = {Article},
+DOI = {10.1080/19490976.2021.1915673},
+ISSN = {1949-0976},
+EISSN = {1949-0984},
+Keywords = {Metabolic modeling; microbiome; fusiobacteria; metagenomic data; flux
+ balance analysis},
+Keywords-Plus = {COLORECTAL-CANCER; GUT MICROBIOTA; INTESTINAL MICROBIOTA; NUCLEATUM;
+ METABOLISM; HEALTH; NUTRITION},
+Research-Areas = {Gastroenterology \& Hepatology; Microbiology},
+Web-of-Science-Categories = {Gastroenterology \& Hepatology; Microbiology},
+ResearcherID-Numbers = {Hertel, Johannes/HZJ-3685-2023},
+ORCID-Numbers = {Hertel, Johannes/0000-0002-7641-0132},
+Times-Cited = {17},
+Journal-ISO = {Gut Microbes},
+Unique-ID = {WOS:000709866600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000618654800001,
+Author = {Hosseinkhani, F. and Heinken, A. and Thiele, I and Lindenburg, P. W. and
+ Harms, A. C. and Hankemeier, T.},
+Title = {The contribution of gut bacterial metabolites in the human immune
+ signaling pathway of non-communicable diseases},
+Journal = {GUT MICROBES},
+Year = {2021},
+Volume = {13},
+Number = {1},
+Pages = {1-22},
+Month = {JAN 1},
+Type = {Review},
+DOI = {10.1080/19490976.2021.1882927},
+ISSN = {1949-0976},
+EISSN = {1949-0984},
+Keywords = {Bacterial metabolites; immune signaling; non-communicable diseases; gut
+ microbiota; metabolomics; system biology},
+Keywords-Plus = {ARYL-HYDROCARBON RECEPTOR; PROTEIN-COUPLED RECEPTORS; CHAIN FATTY-ACIDS;
+ BILE-ACIDS; ENDOCANNABINOID SYSTEM; KYNURENINE PATHWAY; DIETARY FIBER;
+ KAPPA-B; MICROBIOTA; INFLAMMATION},
+Research-Areas = {Gastroenterology \& Hepatology; Microbiology},
+Web-of-Science-Categories = {Gastroenterology \& Hepatology; Microbiology},
+ResearcherID-Numbers = {Hankemeier, Thomas/V-5407-2019
+ Hosseinkhani, Farideh/AAA-1655-2022
+ Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Hankemeier, Thomas/0000-0001-7871-2073
+ Hosseinkhani, Farideh/0000-0002-1880-6964
+ Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {80},
+Journal-ISO = {Gut Microbes},
+Unique-ID = {WOS:000618654800001},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000708843300009,
+Author = {Johnson, Zachary J. and Krutkin, Dennis D. and Bohutskyi, Pavlo and
+ Kalyuzhnaya, Marina G.},
+Editor = {Cotruvo, JA},
+Title = {Metals and methylotrophy: Via global gene expression studies},
+Booktitle = {RARE-EARTH ELEMENT BIOCHEMISTRY: METHANOL DEHYDROGENASES AND LANTHANIDE
+ BIOLOGY},
+Series = {Methods in Enzymology},
+Year = {2021},
+Volume = {650},
+Pages = {185-213},
+Type = {Review; Book Chapter},
+DOI = {10.1016/bs.mie.2021.01.046},
+ISSN = {0076-6879},
+ISBN = {978-0-12-823856-1},
+Keywords-Plus = {RECURRENT NEURAL-NETWORK; GENOME; SEQUENCE; PACKAGE; ANNOTATION;
+ ALIGNMENT; ENZYMES; TOOLS; MODEL},
+Research-Areas = {Biochemistry \& Molecular Biology; Chemistry},
+Web-of-Science-Categories = {Biochemical Research Methods; Biochemistry \& Molecular Biology;
+ Chemistry, Inorganic \& Nuclear; Chemistry, Physical},
+ORCID-Numbers = {Bohutskyi, Pavlo/0000-0002-0462-8132},
+Times-Cited = {0},
+Journal-ISO = {Methods Enzymol.},
+Unique-ID = {WOS:000708843300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000610382900001,
+Author = {Lamichhane, Santosh and Sen, Partho and Alves, Marina Amaral and
+ Ribeiro, Henrique C. and Raunioniemi, Peppi and Hyotylainen, Tuulia and
+ Oresic, Matej},
+Title = {Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations},
+Journal = {METABOLITES},
+Year = {2021},
+Volume = {11},
+Number = {1},
+Month = {JAN},
+Type = {Review},
+DOI = {10.3390/metabo11010055},
+Article-Number = {55},
+EISSN = {2218-1989},
+Keywords = {microbiome; lipidomics; metabolomics; gut; lipids},
+Keywords-Plus = {RNA GENE DATABASE; BILE-ACIDS; FECAL METABOLOME; FATTY-ACIDS; HOST;
+ SPHINGOLIPIDS; BACTERIA; IMPACT; DIET; CHOLESTEROL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Alves, Marina Amaral/N-1945-2015
+ Oresic, Matej/K-7673-2016
+ Sen, Partho/L-8471-2019
+ },
+ORCID-Numbers = {Alves, Marina Amaral/0000-0002-8188-5554
+ Oresic, Matej/0000-0002-2856-9165
+ Sen, Partho/0000-0003-0475-2763
+ Raunioniemi, Peppi/0000-0003-4241-8950
+ Hyotylainen, Tuulia/0000-0002-1389-8302
+ Ribeiro, Henrique/0000-0002-0759-3895},
+Times-Cited = {40},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000610382900001},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000637940300009,
+Author = {Le Feunteun, Steven and Al-Razaz, Ahmed and Dekker, Matthijs and George,
+ Erwin and Laroche, Beatrice and van Aken, George},
+Editor = {Doyle, M and McClements, DJ},
+Title = {Physiologically Based Modeling of Food Digestion and Intestinal
+ Microbiota: State of the Art and Future Challenges. An INFOGEST Review},
+Booktitle = {ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 12, 2021},
+Series = {Annual Review of Food Science and Technology},
+Year = {2021},
+Volume = {12},
+Pages = {149-167},
+Type = {Review; Book Chapter},
+DOI = {10.1146/annurev-food-070620-124140},
+ISSN = {1941-1413},
+EISSN = {1941-1421},
+Keywords = {in silico; gastrointestinal tract; digestion; transit; absorption;
+ microbiota},
+Keywords-Plus = {IN-VITRO; ABSORPTION; ENVIRONMENT; METABOLISM; IMPACT; FLOW},
+Research-Areas = {Food Science \& Technology},
+Web-of-Science-Categories = {Food Science \& Technology},
+ResearcherID-Numbers = {Le Feunteun, Steven/AAA-9521-2021
+ Dekker, Matthijs/O-7135-2014
+ Laroche, Béatrice/J-9404-2014},
+ORCID-Numbers = {Le Feunteun, Steven/0000-0002-4476-2811
+ Dekker, Matthijs/0000-0002-0063-4252
+ Laroche, Béatrice/0000-0001-7821-332X},
+Times-Cited = {18},
+Journal-ISO = {Annu. Rev. Food Sci. Technol.},
+Unique-ID = {WOS:000637940300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000691059500001,
+Author = {Ortiz, Juan P. Molina and McClure, Dale D. and Shanahan, Erin R. and
+ Dehghani, Fariba and Holmes, Andrew J. and Read, Mark N.},
+Title = {Enabling rational gut microbiome manipulations by understanding gut
+ ecology through experimentally-evidenced in silico models},
+Journal = {GUT MICROBES},
+Year = {2021},
+Volume = {13},
+Number = {1},
+Month = {JAN 1},
+Type = {Review},
+DOI = {10.1080/19490976.2021.1965698},
+Article-Number = {1965698},
+ISSN = {1949-0976},
+EISSN = {1949-0984},
+Keywords = {Precision medicine; dietary intervention; gut microbial ecology;
+ host-microbiome interactions; genome-scale modeling; agent-based
+ modeling; microbial culturing; computational microbiology; systems
+ biology},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; DIETARY FIBER; HYDROGEN-SULFIDE; INTESTINAL
+ MICROBIOTA; RESOURCE-ALLOCATION; MOLECULAR ANALYSIS; INNATE IMMUNITY;
+ COLON; CARBOHYDRATE; INFLAMMATION},
+Research-Areas = {Gastroenterology \& Hepatology; Microbiology},
+Web-of-Science-Categories = {Gastroenterology \& Hepatology; Microbiology},
+ResearcherID-Numbers = {Shanahan, Erin R/H-1852-2015
+ },
+ORCID-Numbers = {Shanahan, Erin R/0000-0003-4637-0851
+ McClure, Dale/0000-0001-6790-5179},
+Times-Cited = {2},
+Journal-ISO = {Gut Microbes},
+Unique-ID = {WOS:000691059500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000613082200002,
+Author = {Tomi-Andrino, Claudio and Norman, Rupert and Millat, Thomas and
+ Soucaille, Philippe and Winzer, Klaus and Barrett, David A. and King,
+ John and Kim, Dong-Hyun},
+Title = {Physicochemical and metabolic constraints for thermodynamics-based
+ stoichiometric modelling under mesophilic growth conditions},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2021},
+Volume = {17},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1007694},
+Article-Number = {e1007694},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ELEMENTARY FLUX MODES; ESCHERICHIA-COLI; NETWORK ANALYSIS; SYSTEMS
+ BIOLOGY; BATCH CULTURE; COMPLEX; SYNCHRONIZATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Kim, Dong-Hyun/AAT-3953-2021
+ },
+ORCID-Numbers = {Kim, Dong-Hyun/0000-0002-3689-2130
+ Soucaille, Philippe/0000-0002-1724-7136
+ King, John/0000-0002-6228-8375
+ Tomi-Andrino, Claudio/0000-0002-3611-2130
+ Millat, Thomas/0000-0002-5023-4142},
+Times-Cited = {5},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000613082200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000684868200009,
+Author = {Walakira, Andrew and Rozman, Damjana and Rezen, Tadeja and Mraz, Miha
+ and Moskon, Miha},
+Title = {Guided extraction of genome-scale metabolic models for the integration
+ and analysis of omics data},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2021},
+Volume = {19},
+Pages = {3521-3530},
+Type = {Article},
+DOI = {10.1016/j.csbj.2021.06.0092001-0370/},
+ISSN = {2001-0370},
+Keywords = {Genome-scale metabolic model; Model extraction methods; Context-specific
+ metabolic model; Omics data integration; Subsystem enrichment analysis;
+ Model interpretability},
+Keywords-Plus = {TARGETS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Moškon, Miha/J-3802-2019
+ },
+ORCID-Numbers = {Moškon, Miha/0000-0003-4600-1730
+ Rezen, Tadeja/0000-0001-6210-7370
+ Walakira, Andrew/0000-0002-3651-2679},
+Times-Cited = {10},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000684868200009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000647691000041,
+Author = {Wilken, St. Elmo and Monk, Jonathan M. and Leggieri, Patrick A. and
+ Lawson, Christopher E. and Lankiewicz, Thomas S. and Seppala, Susanna
+ and Daum, Chris G. and Jenkins, Jerry and Lipzen, Anna M. and Mondo,
+ Stephen J. and Barry, Kerrie W. and Grigoriev, Igor V. and Henske, John
+ K. and Theodorou, Michael K. and Palsson, Bernhard O. and Petzold, Linda
+ R. and O'Malley, Michelle A.},
+Title = {Experimentally Validated Reconstruction and Analysis of a Genome-Scale
+ Metabolic Model of an Anaerobic Neocallimastigomycota Fungus},
+Journal = {MSYSTEMS},
+Year = {2021},
+Volume = {6},
+Number = {1},
+Month = {JAN-FEB},
+Type = {Article},
+DOI = {10.1128/mSystems.00002-21},
+Article-Number = {e00002-21},
+ISSN = {2379-5077},
+Keywords = {genome-scale metabolic model; C-13 metabolic flux analysis; nonmodel
+ fungus; Neocallimastigomycota; flux balance analysis; Neocallimastix
+ lanati; anaerobes; anaerobic fungi},
+Keywords-Plus = {DEPENDENT GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE;
+ PYRUVATE-FORMATE-LYASE; GUT FUNGI; FLUX ANALYSIS; LIFE-CYCLE; GROWTH;
+ HYDROGENOSOMES; ENZYMES; RUMEN; OPTIMIZATION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Henske, John/GQP-2638-2022
+ Barry, Kerrie Whitelaw/AAA-5500-2020
+ },
+ORCID-Numbers = {Barry, Kerrie Whitelaw/0000-0002-8999-6785
+ Lipzen, Anna/0000-0003-2293-9329
+ Wilken, St. Elmo/0000-0002-4113-2590},
+Times-Cited = {26},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000647691000041},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000615651600001,
+Author = {Belcour, Arnaud and Frioux, Clemence and Aite, Meziane and Bretaudeau,
+ Anthony and Hildebrand, Falk and Siegel, Anne},
+Title = {Metage2Metabo, microbiota-scale metabolic complementarity for the
+ identification of key species},
+Journal = {ELIFE},
+Year = {2020},
+Volume = {9},
+Month = {DEC 29},
+Type = {Article},
+DOI = {10.7554/eLife.61968},
+Article-Number = {e61968},
+ISSN = {2050-084X},
+Keywords-Plus = {SYSTEMS BIOLOGY; PROBIOTIC PROPERTIES; GENOME; MODELS; RECONSTRUCTION;
+ EFFICIENT; ACCURATE; STRAINS; QUALITY; TOOL},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Frioux, Clémence/A-1517-2019
+ Hildebrand, Falk/K-1914-2014
+ },
+ORCID-Numbers = {Frioux, Clémence/0000-0003-2114-0697
+ Hildebrand, Falk/0000-0002-0078-8948
+ Belcour, Arnaud/0000-0003-1170-0785
+ Siegel, Anne/0000-0001-6542-1568
+ Bretaudeau, Anthony/0000-0003-0914-2470},
+Times-Cited = {24},
+Journal-ISO = {eLife},
+Unique-ID = {WOS:000615651600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000603612300009,
+Author = {Schulz, Christian and Almaas, Eivind},
+Title = {Genome-scale reconstructions to assess metabolic phylogeny and organism
+ clustering},
+Journal = {PLOS ONE},
+Year = {2020},
+Volume = {15},
+Number = {12},
+Month = {DEC 29},
+Type = {Article},
+DOI = {10.1371/journal.pone.0240953},
+Article-Number = {e0240953},
+ISSN = {1932-6203},
+Keywords-Plus = {SEQUENCE; EVOLUTION; ARCHAEA; GENES; TREE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Schulz, Christian/0000-0002-6763-6551},
+Times-Cited = {2},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000603612300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000605963100001,
+Author = {Sun, Renliang and Xu, Yizhou and Zhang, Hang and Yang, Qiangzhen and
+ Wang, Ke and Shi, Yongyong and Wang, Zhuo},
+Title = {Mechanistic Modeling of Gene Regulation and Metabolism Identifies
+ Potential Targets for Hepatocellular Carcinoma},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2020},
+Volume = {11},
+Month = {DEC 23},
+Type = {Article},
+DOI = {10.3389/fgene.2020.595242},
+Article-Number = {595242},
+EISSN = {1664-8021},
+Keywords = {regulatory-metabolic integration; metabolic model; molecular
+ stratification; potential therapeutic target; hepatocellular carcinoma;
+ metabolic reprogramming},
+Keywords-Plus = {MICRORNA EXPRESSION PATTERNS; ETS FACTOR TEL2; COMPREHENSIVE ANALYSIS;
+ TUMOR-SUPPRESSOR; CANCER; KINASE; PROLIFERATION; ASSOCIATION;
+ ACTIVATION; INVASION},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Yang, QiangZhen/HTN-0384-2023
+ Shi, Yongyong/GSO-1627-2022},
+ORCID-Numbers = {Yang, QiangZhen/0000-0001-8648-5560
+ Shi, Yongyong/0000-0003-1710-1505},
+Times-Cited = {4},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000605963100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000600670000064,
+Author = {Vijayakumar, Supreeta and Rahman, Pattanathu K. S. M. and Angione,
+ Claudio},
+Title = {A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates
+ Metabolic Adaptation in Cyanobacteria},
+Journal = {ISCIENCE},
+Year = {2020},
+Volume = {23},
+Number = {12},
+Month = {DEC 18},
+Type = {Article},
+DOI = {10.1016/j.isci.2020.101818},
+Article-Number = {101818},
+EISSN = {2589-0042},
+Keywords-Plus = {SP PCC 7002; GENOME-SCALE MODELS; SYNECHOCOCCUS; LIGHT; ACCLIMATION;
+ MUTANT; PHOTOSYNTHESIS; HOMEOSTASIS; BIOFUEL; PROTEIN},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Rahman, Pattanathu K. S. M./A-4349-2018
+ },
+ORCID-Numbers = {Rahman, Pattanathu K. S. M./0000-0001-7416-4372
+ Vijayakumar, Supreeta/0000-0001-6357-0439
+ Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {24},
+Journal-ISO = {iScience},
+Unique-ID = {WOS:000600670000064},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000599363300017,
+Author = {Bernardes, Joana P. and Mishra, Neha and Tran, Florian and Bahmer,
+ Thomas and Best, Lena and Blase, I, Johanna and Bordoni, Dora and
+ Franzenburg, Jeanette and Geisen, Ulf and Josephs-Spaulding, Jonathan
+ and Koehler, Philipp and Kuenstner, Axel and Rosati, Elisa and
+ Aschenbrenner, Anna C. and Bacher, Petra and Baran, Nathan and Boysen,
+ Teide and Brandt, Burkhard and Bruse, Niklas and Doerr, Jonathan and
+ Draeger, Andreas and Elke, Gunnar and Ellinghaus, David and Fischer,
+ Julia and Forster, Michael and Franke, Andre and Franzenburg, Soeren and
+ Frey, Norbert and Friedrichs, Anette and Fuss, Janina and Glueck,
+ Andreas and Hamm, Jacob and Hinrichsen, Finn and Hoeppner, Marc P. and
+ Imm, Simon and Junker, Ralf and Kaiser, Sina and Kan, Ying H. and Knoll,
+ Rainer and Lange, Christoph and Laue, Georg and Lier, Clemens and
+ Lindner, Matthias and Marinos, Georgios and Markewitz, Robert and
+ Nattermann, Jacob and Noth, Rainer and Pickkers, Peter and Rabe, Klaus
+ F. and Renz, Alina and Roecken, Christoph and Rupp, Jan and Schaffarzyk,
+ Annika and Scheffold, Alexander and Schulte-Schrepping, Jonas and
+ Schunk, Domagoj and Skowasch, Dirk and Ulas, Thomas and Wandinger,
+ Klaus-Peter and Wittig, Michael and Zimmermann, Johannes and Busch,
+ Hauke and Hoyer, Bimba F. and Kaleta, Christoph and Heyckendorf, Jan and
+ Kox, Matthijs and Rybniker, Jan and Schreiber, Stefan and Schultze,
+ Joachim L. and Rosenstiel, Philip and HCA Lung Biol Network and Deutsch
+ COVID-19 Omics Initiative},
+Title = {Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes,
+ Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19},
+Journal = {IMMUNITY},
+Year = {2020},
+Volume = {53},
+Number = {6},
+Pages = {1296+},
+Month = {DEC 15},
+Type = {Article},
+DOI = {10.1016/j.immuni.2020.11.017},
+ISSN = {1074-7613},
+EISSN = {1097-4180},
+Keywords-Plus = {HEMATOPOIETIC STEM; INNATE IMMUNITY; HYPOXIA; DATABASE; DIFFERENTIATION;
+ RECONSTRUCTION; INHIBITION; METABOLISM; EXPRESSION; PLATELETS},
+Research-Areas = {Immunology},
+Web-of-Science-Categories = {Immunology},
+ResearcherID-Numbers = {Bacher, Petra/AAF-1565-2021
+ Ellinghaus, David/G-4467-2012
+ Lindner, Matthias/O-1961-2018
+ B, Niklas/GQH-7080-2022
+ Rabe, Klaus F./AAW-6296-2021
+ Rosati, Elisa/J-6784-2019
+ Hoyer, Bimba Franziska/HPD-4851-2023
+ Elke, Gunnar/S-8579-2016
+ Aschenbrenner, Anna C./JOZ-8769-2023
+ Tran, Florian/AHA-4179-2022
+ Zaragosi, Laure-Emmanuelle/P-9887-2016
+ Rocha, Ulisses/AAE-5158-2021
+ Rupp, Jan/C-8794-2011
+ Bruse, Niklas/Q-3733-2018
+ Scheffold, Alexander/S-2090-2016
+ Geisen, Ulf/AAL-6012-2021
+ Rosenstiel, Philip/A-5137-2009
+ Markewitz, Robert/AAB-2074-2022
+ Fischer, Julia/AAC-6111-2022
+ Koehler, Philipp/J-7985-2019
+ Schulte, Eva C./AAT-2410-2021
+ Busch, Hauke/R-6452-2016
+ Schultze, Joachim L./ABA-8176-2020
+ Vogel, Jörg/D-5574-2011
+ Franke, Andre/B-2151-2010
+ Hamm, Jacob/JNT-0322-2023
+ Zimmermann, Johannes/HTP-7711-2023
+ Keller, Andreas/ABB-6412-2021
+ Dräger, Andreas/F-5620-2015
+ Fischer, Julia/AGD-1069-2022
+ Frey, Norbert/M-7749-2019
+ Diefenbach, Andreas/T-2589-2018
+ Ludwig, Kerstin/H-7828-2019
+ Röcken, Christoph/A-9239-2010
+ Mishra, Neha/HDN-8013-2022
+ Vehreschild, Jorg Janne/G-6764-2013
+ Bartholomaus, Alexander/AAR-1277-2021
+ },
+ORCID-Numbers = {Bacher, Petra/0000-0003-4264-6451
+ Lindner, Matthias/0000-0003-2647-7790
+ B, Niklas/0000-0001-5146-5295
+ Rabe, Klaus F./0000-0002-7020-1401
+ Rosati, Elisa/0000-0002-2635-6422
+ Elke, Gunnar/0000-0002-4948-1605
+ Aschenbrenner, Anna C./0000-0002-9429-5457
+ Tran, Florian/0000-0002-3735-9872
+ Zaragosi, Laure-Emmanuelle/0000-0001-6747-7928
+ Rocha, Ulisses/0000-0001-6972-6692
+ Rupp, Jan/0000-0001-8722-1233
+ Bruse, Niklas/0000-0001-5146-5295
+ Scheffold, Alexander/0000-0002-0626-343X
+ Geisen, Ulf/0000-0002-6583-460X
+ Rosenstiel, Philip/0000-0002-9692-8828
+ Markewitz, Robert/0000-0003-1676-1085
+ Fischer, Julia/0000-0001-6138-7454
+ Koehler, Philipp/0000-0002-7386-7495
+ Busch, Hauke/0000-0003-4763-4521
+ Schultze, Joachim L./0000-0003-2812-9853
+ Vogel, Jörg/0000-0003-2220-1404
+ Franke, Andre/0000-0003-1530-5811
+ Zimmermann, Johannes/0000-0002-5041-1954
+ Keller, Andreas/0000-0002-5361-0895
+ Dräger, Andreas/0000-0002-1240-5553
+ Fischer, Julia/0000-0001-6138-7454
+ Frey, Norbert/0000-0001-7611-378X
+ Diefenbach, Andreas/0000-0002-9176-9530
+ Ludwig, Kerstin/0000-0002-8541-2519
+ Röcken, Christoph/0000-0002-6989-8002
+ Renz, Alina/0000-0003-3851-9978
+ Vehreschild, Jorg Janne/0000-0002-5446-7170
+ MARINOS, GEORGIOS/0000-0002-6443-7696
+ Angelov, Angel/0000-0002-9228-0817
+ Bartholomaus, Alexander/0000-0003-0970-7304
+ Makarewicz, Oliwia/0000-0002-4404-1862
+ Ellinghaus, David/0000-0002-4332-6110
+ Fuss, Janina/0000-0002-7631-9355
+ Tata, Purushothama Rao/0000-0003-4837-0337
+ Marz, Manja/0000-0003-4783-8823
+ Stegle, Oliver/0000-0002-8818-7193
+ Mishra, Neha/0000-0002-7436-1066
+ Ralser, Markus/0000-0001-9535-7413
+ Josephs-Spaulding, Jonathan/0000-0001-9828-0685
+ Forster, Michael/0000-0001-9927-5124
+ Schulte, Eva Christina/0000-0003-3105-5672
+ Bals, Robert/0000-0002-1472-9535
+ Best, Lena/0000-0003-2772-153X
+ Rajewsky, Nikolaus/0000-0002-4785-4332
+ Kan, Ying Hei/0000-0003-1235-2364
+ Hamm, Jacob/0000-0003-4960-6858
+ Frick, Julia-Stefanie/0000-0002-7662-7956
+ Forstner, Konrad U./0000-0002-1481-2996
+ Nawijn, Martijn/0000-0003-3372-6521},
+Times-Cited = {194},
+Journal-ISO = {Immunity},
+Unique-ID = {WOS:000599363300017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000602654200001,
+Author = {Banerjee, Ushashi and Sankar, Santhosh and Singh, Amit and Chandra,
+ Nagasuma},
+Title = {A Multi-Pronged Computational Pipeline for Prioritizing Drug Target
+ Strategies for Latent Tuberculosis},
+Journal = {FRONTIERS IN CHEMISTRY},
+Year = {2020},
+Volume = {8},
+Month = {DEC 14},
+Type = {Article},
+DOI = {10.3389/fchem.2020.593497},
+Article-Number = {593497},
+ISSN = {2296-2646},
+Keywords = {latent tuberculosis; target identification; systems biology;
+ chemoinformatics; lead identification; metabolic modeling; response
+ network},
+Keywords-Plus = {LIGAND-BINDING SITES; MYCOBACTERIUM-TUBERCULOSIS; GENE-EXPRESSION;
+ INTERACTION NETWORK; PROTEIN; METABOLISM; ADAPTATION; DORMANCY;
+ IDENTIFICATION; MACROPHAGES},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary},
+ResearcherID-Numbers = {Banerjee, Ushashi/HOC-6759-2023
+ },
+ORCID-Numbers = {Banerjee, Ushashi/0000-0002-8515-1910},
+Times-Cited = {8},
+Journal-ISO = {Front. Chem.},
+Unique-ID = {WOS:000602654200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000600150800019,
+Author = {Voigt, Christopher A.},
+Title = {Synthetic biology 2020-2030: six commercially-available products that
+ are changing our world},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {DEC 11},
+Type = {Editorial Material},
+DOI = {10.1038/s41467-020-20122-2},
+Article-Number = {6379},
+ISSN = {2041-1723},
+Keywords-Plus = {ESCHERICHIA-COLI; PLANT; DESIGN; ACID; GENE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {80},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000600150800019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000613410600056,
+Author = {Henriksen, Hanne H. and McGarrity, Sarah and Siguroardottir, Rosa S. and
+ Nemkov, Travis and D'Alessandro, Angelo and Palsson, Bernhard O. and
+ Stensballe, Jakob and Wade, Charles E. and Rolfsson, Ottar and
+ Johansson, Par I.},
+Title = {Metabolic Systems Analysis of Shock-Induced Endotheliopathy (SHINE) in
+ Trauma A New Research Paradigm},
+Journal = {ANNALS OF SURGERY},
+Year = {2020},
+Volume = {272},
+Number = {6},
+Pages = {1140-1148},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1097/SLA.0000000000003307},
+ISSN = {0003-4932},
+EISSN = {1528-1140},
+Keywords = {endotheliopathy; genome-scale metabolic model; metabolomics; systems
+ biology; trauma},
+Keywords-Plus = {ORGAN FAILURE; GLYCOCALYX; DAMAGE; PATHOPHYSIOLOGY; DYSFUNCTION;
+ ACTIVATION; MORTALITY; SURGERY},
+Research-Areas = {Surgery},
+Web-of-Science-Categories = {Surgery},
+ResearcherID-Numbers = {D'Alessandro, Angelo/AAA-4695-2019
+ Nemkov, Travis/IST-8202-2023
+ Johansson, Pär/GQB-1032-2022
+ },
+ORCID-Numbers = {D'Alessandro, Angelo/0000-0002-2258-6490
+ Johansson, Pär/0000-0001-9778-5964
+ Hee Henriksen, Hanne/0000-0003-1323-9718},
+Times-Cited = {13},
+Journal-ISO = {Ann. Surg.},
+Unique-ID = {WOS:000613410600056},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000606794900027,
+Author = {Messa, Gian Marco and Napolitano, Francesco and Elsea, Sarah H. and di
+ Bernardo, Diego and Gao, Xin},
+Title = {A Siamese neural network model for the prioritization of metabolic
+ disorders by integrating real and simulated data},
+Journal = {BIOINFORMATICS},
+Year = {2020},
+Volume = {36},
+Number = {2},
+Pages = {I787-I794},
+Month = {DEC},
+Note = {19th European Conference on Computational Biology (ECCB), ELECTR
+ NETWORK, SEP 07-08, 2020},
+Type = {Article; Proceedings Paper},
+DOI = {10.1093/bioinformatics/btaa841},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {INBORN-ERRORS; GLOBAL RECONSTRUCTION; SEMANTIC SIMILARITY; DIAGNOSIS;
+ VIEW},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Gao, Xin/D-5487-2013
+ Messa, Gian Marco/AAT-4482-2021
+ di Bernardo, Diego/AAF-5881-2021
+ Napolitano, Francesco/Q-1669-2016},
+ORCID-Numbers = {Gao, Xin/0000-0002-7108-3574
+ Messa, Gian Marco/0000-0002-4868-9498
+ di Bernardo, Diego/0000-0002-1911-7407
+ Napolitano, Francesco/0000-0002-7782-8506},
+Times-Cited = {2},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000606794900027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000603362700001,
+Author = {Ranjbar, S. and Shahmansouri, M. and Attri, P. and Bogaerts, A.},
+Title = {Effect of plasma-induced oxidative stress on the glycolysis pathway of
+ Escherichia coli},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2020},
+Volume = {127},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2020.104064},
+Article-Number = {104064},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Cold atmospheric plasma; Oxidative stress; Glycolysis pathway; Bacteria
+ killing; COBRA Toolbox},
+Keywords-Plus = {PHOTOTHERMAL AGENTS; ATMOSPHERIC PLASMA; E. COLI; SUCCINATE; BACTERIA;
+ GROWTH; CARBON},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Attri, Pankaj/ABE-7522-2020
+ Bogaerts, Annemie/L-8338-2016
+ Shahmansouri, Mehran/AFL-8364-2022},
+ORCID-Numbers = {Attri, Pankaj/0000-0002-5036-7877
+ Bogaerts, Annemie/0000-0001-9875-6460
+ },
+Times-Cited = {3},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000603362700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000601001000035,
+Author = {Rapp, Kent M. and Jenkins, Jackson P. and Betenbaugh, Michael J.},
+Title = {Partners for life: building microbial consortia for the future},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2020},
+Volume = {66},
+Pages = {292-300},
+Month = {DEC},
+Type = {Review},
+DOI = {10.1016/j.copbio.2020.10.001},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {DESIGN; SYSTEM},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Rapp, Kent/0000-0002-7521-9053},
+Times-Cited = {11},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000601001000035},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000603087500001,
+Author = {Zielinski, Daniel Craig and Patel, Arjun and Palsson, Bernhard O.},
+Title = {The Expanding Computational Toolbox for Engineering Microbial Phenotypes
+ at the Genome Scale},
+Journal = {MICROORGANISMS},
+Year = {2020},
+Volume = {8},
+Number = {12},
+Month = {DEC},
+Type = {Review},
+DOI = {10.3390/microorganisms8122050},
+Article-Number = {2050},
+EISSN = {2076-2607},
+Keywords = {synthetic biology; metabolic modeling; machine learning; metabolic
+ engineering},
+Keywords-Plus = {ESCHERICHIA-COLI; KINETIC-MODELS; THERMODYNAMICS; METABOLISM;
+ EXPRESSION; STRATEGIES; FRAMEWORK; FEATURES; NETWORK; PATHWAY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Zielinski, Daniel/0000-0001-6452-483X
+ Patel, Arjun/0000-0003-1959-0445},
+Times-Cited = {9},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000603087500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000597664500001,
+Author = {Hanna, Eileen Marie and Zhang, Xiaokang and Eide, Marta and Fallahi,
+ Shirin and Furmanek, Tomasz and Yadetie, Fekadu and Zielinski, Daniel
+ Craig and Goksoyr, Anders and Jonassen, Inge},
+Title = {ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic
+ Reconstruction of a Non-model Species},
+Journal = {FRONTIERS IN MOLECULAR BIOSCIENCES},
+Year = {2020},
+Volume = {7},
+Month = {NOV 26},
+Type = {Article},
+DOI = {10.3389/fmolb.2020.591406},
+Article-Number = {591406},
+EISSN = {2296-889X},
+Keywords = {genome-scale metabolic reconstruction; Atlantic cod; less-annotated
+ species; model curation; environmental toxicology},
+Keywords-Plus = {SYSTEMS BIOLOGY; LIVER; ZEBRAFISH; PATHWAYS; REVEALS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Yadetie, Fekadu/HDL-8798-2022
+ zhang, xiaokang/ABD-2054-2021
+ },
+ORCID-Numbers = {zhang, xiaokang/0000-0003-4684-317X
+ Yadetie, Fekadu/0000-0002-2484-9047
+ Eide, Marta/0000-0003-1013-665X
+ Hanna, Eileen Marie/0000-0002-2093-4586
+ Zielinski, Daniel/0000-0001-6452-483X},
+Times-Cited = {7},
+Journal-ISO = {Front. Mol. Biosci.},
+Unique-ID = {WOS:000597664500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000642323000006,
+Author = {Baloni, Priyanka and Funk, Cory C. and Yan, Jingwen and Yurkovich, James
+ T. and Kueider-Paisley, Alexandra and Nho, Kwangsik and Heinken, Almut
+ and Jia, Wei and Mahmoudiandehkordi, Siamak and Louie, Gregory and
+ Saykin, Andrew J. and Arnold, Matthias and Kastenmueller, Gabi and
+ Griffiths, William J. and Thiele, Ines and Kaddurah-Daouk, Rima and
+ Price, Nathan D. and Alzheimers Dis Metabolomics Consor},
+Title = {Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and
+ Metabolism in Alzheimer's Disease},
+Journal = {CELL REPORTS MEDICINE},
+Year = {2020},
+Volume = {1},
+Number = {8},
+Month = {NOV 17},
+Type = {Article},
+DOI = {10.1016/j.xcrm.2020.100138},
+Article-Number = {100138},
+ISSN = {2666-3791},
+Keywords-Plus = {BLOOD-BRAIN-BARRIER; TRANSCRIPTION FACTOR; GUT MICROBIOME; TRANSPORT;
+ CHOLESTEROL; PATHOGENESIS; LINKING; ABCA1; STAT1; AXIS},
+Research-Areas = {Cell Biology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Cell Biology; Medicine, Research \& Experimental},
+ResearcherID-Numbers = {Schork, Andrew/HMV-8149-2023
+ Griffiths, William/N-4641-2016
+ Thiele, Ines/A-7629-2014
+ baillie, rebecca/AAQ-3400-2020
+ },
+ORCID-Numbers = {Schork, Andrew/0000-0003-4164-9335
+ Griffiths, William/0000-0002-4129-6616
+ Thiele, Ines/0000-0002-8071-7110
+ baillie, rebecca/0000-0003-3966-6320
+ Meikle, Peter/0000-0002-2593-4665
+ barupal, dinesh/0000-0002-9954-8628
+ Arnold, Matthias/0000-0002-4666-0923
+ Jia, Wei/0000-0002-3739-8994
+ Toledo, Jon/0000-0003-4366-9268
+ Baloni, Priyanka/0000-0002-3382-4941},
+Times-Cited = {70},
+Journal-ISO = {Cell Rep. Med.},
+Unique-ID = {WOS:000642323000006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000590010700006,
+Author = {Gautam, Jyotshana and Xu, Zhaohui},
+Title = {Construction and Validation of a Genome-Scale Metabolic Network of
+ Thermotoga sp. Strain RQ7},
+Journal = {APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY},
+Year = {2021},
+Volume = {193},
+Number = {3},
+Pages = {896-911},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1007/s12010-020-03470-z},
+EarlyAccessDate = {NOV 2020},
+ISSN = {0273-2289},
+EISSN = {1559-0291},
+Keywords = {Thermotoga; Genome-scale metabolic modeling; Biomass objective function;
+ Constraint-based reconstruction and analysis; Flux balance analysis},
+Keywords-Plus = {ARCHAEON PYROCOCCUS-FURIOSUS; THERMOPHILIC BACTERIUM; ESCHERICHIA-COLI;
+ SP-NOV; MARITIMA; PROTEIN; GROWTH; ACID; TRANSFORMATION; NEAPOLITANA},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Xu, Zhaohui/HNP-4811-2023
+ },
+ORCID-Numbers = {Xu, Zhaohui/0000-0002-1866-3254},
+Times-Cited = {2},
+Journal-ISO = {Appl. Biochem. Biotechnol.},
+Unique-ID = {WOS:000590010700006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000590936400001,
+Author = {Zou, Piao and Zhang, Yunze and Nshimiyimana, Jean Bosco and Cao, Qianwen
+ and Yang, Yang and Geng, Hui and Xiong, Li},
+Title = {Reconstruction of a Context-Specific Model Based on Genome-Scale
+ Metabolic Simulation for Identification of Prochloraz Resistance
+ Mechanisms in Penicillium digitatum},
+Journal = {MICROBIAL DRUG RESISTANCE},
+Year = {2021},
+Volume = {27},
+Number = {6},
+Pages = {776-785},
+Month = {JUN 1},
+Type = {Article},
+DOI = {10.1089/mdr.2020.0018},
+EarlyAccessDate = {NOV 2020},
+ISSN = {1076-6294},
+EISSN = {1931-8448},
+Keywords = {Penicillium digitatum; prochloraz-resistance; genome-scale metabolic
+ model; comparative transcriptomics},
+Keywords-Plus = {GENE; TRANSPORTER},
+Research-Areas = {Infectious Diseases; Microbiology; Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Infectious Diseases; Microbiology; Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Nshimiyimana, Jean Bosco/IAP-7818-2023},
+Times-Cited = {0},
+Journal-ISO = {Microb. Drug Resist.},
+Unique-ID = {WOS:000590936400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000587884200001,
+Author = {Borrero-de Acuna, Jose Manuel and Gutierrez-Urrutia, Izabook and
+ Hidalgo-Dumont, Cristian and Aravena-Carrasco, Carla and Orellana-Saez,
+ Matias and Palominos-Gonzalez, Nestor and van Duuren, Jozef B. J. H. and
+ Wagner, Viktoria and Glaser, Lars and Becker, Judith and Kohlstedt,
+ Michael and Zacconi, Flavia C. and Wittmann, Christoph and
+ Poblete-Castro, Ignacio},
+Title = {Channelling carbon flux through the meta-cleavage route for
+ improved poly(3-hydroxyalkanoate) production from benzoate and
+ lignin-based aromatics in Pseudomonas putida H},
+Journal = {MICROBIAL BIOTECHNOLOGY},
+Year = {2021},
+Volume = {14},
+Number = {6},
+Pages = {2385-2402},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1111/1751-7915.13705},
+EarlyAccessDate = {NOV 2020},
+ISSN = {1751-7915},
+Keywords-Plus = {CHAIN-LENGTH POLYHYDROXYALKANOATES; PHENOL DEGRADATION; ORTHO-PATHWAY;
+ FATTY-ACIDS; GLUCOSE; KT2440; GROWTH; CIS; VALORIZATION; NAPHTHALENE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Poblete-Castro, Ignacio/J-2755-2019
+ Kohlstedt, Michael/AGJ-6334-2022
+ Borrero-de Acuña, José Manuel/AAT-7277-2020
+ Kohlstedt, Michael/AAT-5600-2021
+ },
+ORCID-Numbers = {Borrero-de Acuña, José Manuel/0000-0002-6409-8110
+ Kohlstedt, Michael/0000-0002-0823-5782
+ Wittmann, Christoph/0000-0002-7952-985X
+ Zacconi, Flavia/0000-0002-3676-0453
+ Poblete-Castro, Ignacio/0000-0001-6649-0389},
+Times-Cited = {9},
+Journal-ISO = {Microb. Biotechnol.},
+Unique-ID = {WOS:000587884200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000590718300004,
+Author = {Basile, Arianna and Campanaro, Stefano and Kovalovszki, Adam and
+ Zampieri, Guido and Rossi, Alessandro and Angelidaki, Irini and Valle,
+ Giorgio and Treu, Laura},
+Title = {Revealing metabolic mechanisms of interaction in the anaerobic digestion
+ microbiome by flux balance analysis},
+Journal = {METABOLIC ENGINEERING},
+Year = {2020},
+Volume = {62},
+Pages = {138-149},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2020.08.013},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Anaerobic digestion/flux balance analysis/genone-scale metabolic mode
+ microbial interactions/renewable energy},
+Keywords-Plus = {VOLATILE FATTY-ACIDS; WASTE-WATER; BACTERIA; IDENTIFICATION;
+ COMMUNITIES; GENE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Basile, Arianna/IXW-5482-2023
+ Reyes, Alejandro/AAD-8445-2022
+ Campanaro, Stefano/I-5657-2019
+ Zampieri, Guido/HJH-7472-2023
+ Angelidaki, Irini/AAX-2562-2020
+ Kovalovszki, Adam/GSN-7084-2022
+ },
+ORCID-Numbers = {Basile, Arianna/0000-0003-2461-5221
+ Reyes, Alejandro/0000-0003-2907-3265
+ Zampieri, Guido/0000-0002-4518-5913
+ Angelidaki, Irini/0000-0002-6357-578X
+ Kovalovszki, Adam/0000-0001-7509-4580
+ Treu, Laura/0000-0002-5053-4452
+ Rossi, Alessandro/0000-0001-8841-1047},
+Times-Cited = {32},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000590718300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000593244900001,
+Author = {Zhao, Jinxin and Zhu, Yan and Han, Jiru and Lin, Yu-Wei and Aichem,
+ Michael and Wang, Jiping and Chen, Ke and Velkov, Tony and Schreiber,
+ Falk and Li, Jian},
+Title = {Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of
+ Multidrug-Resistant Acinetobacter baumannii in a Murine
+ Bloodstream Infection Model},
+Journal = {MICROORGANISMS},
+Year = {2020},
+Volume = {8},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.3390/microorganisms8111793},
+Article-Number = {1793},
+EISSN = {2076-2607},
+Keywords = {Acinetobacter baumannii; genome-scale metabolic modeling;
+ transcriptomics; bacteremia; RNA-seq},
+Keywords-Plus = {RECONSTRUCTION; PATHOGENESIS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Zhu, Yan/HLW-8686-2023
+ },
+ORCID-Numbers = {Zhu, Yan/0000-0001-7342-3782
+ velkov, tony/0000-0002-0017-7952
+ Zhao, Jinxin/0000-0002-0604-3541
+ Han, Jiru/0000-0002-4884-1082},
+Times-Cited = {6},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000593244900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000591372100001,
+Author = {Keller, Philipp and Noor, Elad and Meyer, Fabian and Reiter, Michael A.
+ and Anastassov, Stanislav and Kiefer, Patrick and Vorholt, Julia A.},
+Title = {Methanol-dependent Escherichia coli strains with a complete
+ ribulose monophosphate cycle},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {OCT 26},
+Type = {Article},
+DOI = {10.1038/s41467-020-19235-5},
+Article-Number = {5403},
+ISSN = {2041-1723},
+Keywords-Plus = {CARBON; OXIDATION; CO2; ASSIMILATION; CONVERSION; DELETION; BACILLUS;
+ GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Kiefer, Patrick/G-5138-2010
+ Vorholt, Julia A/K-3514-2016
+ },
+ORCID-Numbers = {Vorholt, Julia A/0000-0002-6011-4910
+ Keller, Philipp/0000-0003-3962-5078
+ Noor, Elad/0000-0001-8776-4799},
+Times-Cited = {16},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000591372100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000586509600009,
+Author = {Banerjee, Deepanwita and Eng, Thomas and Lau, Andrew K. and Sasaki,
+ Yusuke and Wang, Brenda and Chen, Yan and Prahl, Jan-Philip and Singan,
+ Vasanth R. and Herbert, Robin A. and Liu, Yuzhong and Tanjore, Deepti
+ and Petzold, Christopher J. and Keasling, Jay D. and Mukhopadhyay,
+ Aindrila},
+Title = {Genome-scale metabolic rewiring improves titers rates and yields of the
+ non-native product indigoidine at scale},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {OCT 23},
+Type = {Article},
+DOI = {10.1038/s41467-020-19171-4},
+Article-Number = {5385},
+ISSN = {2041-1723},
+Keywords-Plus = {ESCHERICHIA-COLI; TOLERANCE; GROWTH; OPTIMIZATION; 1-BUTANOL; GENERATE;
+ PATHWAY; BIOMASS; ACID},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Keasling, Jay/HPG-6073-2023
+ Liu, Yuzhong/P-7198-2017
+ Mukhopadhyay, Aindrila/AAW-7257-2021
+ Sasaki, Yusuke/AAE-9347-2022
+ Chen, Yan/M-9814-2018
+ Sasaki, Yusuke/AFD-8120-2022
+ Banerjee, Deepanwita/AAD-5528-2021
+ },
+ORCID-Numbers = {Liu, Yuzhong/0000-0001-5614-1951
+ Chen, Yan/0000-0002-1125-313X
+ Banerjee, Deepanwita/0000-0002-0083-0608
+ Singan, Vasanth/0000-0002-9983-5707
+ Herbert, Robin/0000-0002-9174-1562
+ Petzold, Christopher/0000-0002-8270-5228
+ Eng, Thomas/0000-0002-4974-3863},
+Times-Cited = {45},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000586509600009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000585204800004,
+Author = {Tsiantis, Nikolaos and Banga, Julio R.},
+Title = {Using optimal control to understand complex metabolic pathways},
+Journal = {BMC BIOINFORMATICS},
+Year = {2020},
+Volume = {21},
+Number = {1},
+Month = {OCT 21},
+Type = {Article},
+DOI = {10.1186/s12859-020-03808-8},
+Article-Number = {472},
+ISSN = {1471-2105},
+Keywords = {Optimal control; Dynamic modeling; Multi-criteria optimization; Pareto
+ optimality},
+Keywords-Plus = {DETERMINISTIC GLOBAL OPTIMIZATION; NONLINEAR OPTIMAL-CONTROL; CELLULAR
+ TRADE-OFFS; DYNAMIC OPTIMIZATION; SYSTEMS BIOLOGY; GENE-EXPRESSION;
+ KINETIC-MODELS; MULTIOBJECTIVE OPTIMIZATION; BIOCHEMICAL SYSTEMS;
+ SYNTHETIC BIOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Banga, Julio R./ABD-8629-2020
+ Banga, Julio R./A-8388-2008
+ },
+ORCID-Numbers = {Banga, Julio R./0000-0002-4245-0320
+ Banga, Julio R./0000-0002-4245-0320
+ Tsiantis, Nikolaos/0000-0003-4199-6126},
+Times-Cited = {14},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000585204800004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000578546100001,
+Author = {Fouladiha, Hamideh and Marashi, Sayed-Amir and Li, Shangzhong and Li,
+ Zerong and Masson, Helen O. and Vaziri, Behrouz and Lewis, Nathan E.},
+Title = {Systematically gap-filling the genome-scale metabolic model of CHO cells},
+Journal = {BIOTECHNOLOGY LETTERS},
+Year = {2021},
+Volume = {43},
+Number = {1},
+Pages = {73-87},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1007/s10529-020-03021-w},
+EarlyAccessDate = {OCT 2020},
+ISSN = {0141-5492},
+EISSN = {1573-6776},
+Keywords = {CHO cells; Constraint-based modeling; Gap-filling; Metabolic network
+ models; Systems biology},
+Keywords-Plus = {SEQUENCE; RECONSTRUCTION; COMPLETION; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Li, Shangzhong/Y-6882-2019
+ Lewis, Nathan/ABE-7290-2020
+ Li, Shangzhong/HHD-1335-2022
+ Marashi, Sayed-Amir/A-5384-2008
+ Li, Shangzhong/HHD-1393-2022
+ },
+ORCID-Numbers = {Li, Shangzhong/0000-0003-0272-3942
+ Lewis, Nathan/0000-0001-7700-3654
+ Marashi, Sayed-Amir/0000-0001-9801-7449
+ Fouladiha, Hamideh/0000-0002-5522-8809},
+Times-Cited = {8},
+Journal-ISO = {Biotechnol. Lett.},
+Unique-ID = {WOS:000578546100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000578446900002,
+Author = {Borujeni, Amin Espah and Zhang, Jing and Doosthosseini, Hamid and
+ Nielsen, Alec A. K. and Voigt, Christopher A.},
+Title = {Genetic circuit characterization by inferring RNA polymerase movement
+ and ribosome usage},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {OCT 5},
+Type = {Article},
+DOI = {10.1038/s41467-020-18630-2},
+Article-Number = {5001},
+EISSN = {2041-1723},
+Keywords-Plus = {IN-VIVO; TRANSLATION INITIATION; COMBINATORIAL DESIGN; BINDING-SITES;
+ TRADE-OFFS; EXPRESSION; SEQ; TRANSCRIPTION; SEQUENCE; REVEALS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Zhang, Jing/0000-0002-3845-8768
+ Doosthosseini, Hamid/0000-0002-1544-1488},
+Times-Cited = {28},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000578446900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000583065000005,
+Author = {Cruz, Fernando and Faria, Jose P. and Rocha, Miguel and Rocha, Isabel
+ and Dias, Oscar},
+Title = {A review of methods for the reconstruction and analysis of integrated
+ genome-scale models of metabolism and regulation},
+Journal = {BIOCHEMICAL SOCIETY TRANSACTIONS},
+Year = {2020},
+Volume = {48},
+Number = {5},
+Pages = {1889-1903},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1042/BST20190840},
+ISSN = {0300-5127},
+EISSN = {1470-8752},
+Keywords-Plus = {GENE-EXPRESSION; ESCHERICHIA-COLI; HIGH-THROUGHPUT; FUNCTIONAL GENOMICS;
+ SYSTEMS BIOLOGY; NETWORKS; TRANSCRIPTION; PHYSIOLOGY; DISCOVERY;
+ PATHWAYS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Dias, Oscar/A-4359-2010
+ Rocha, Isabel/A-4279-2013
+ Rocha, Miguel/B-9404-2011
+ },
+ORCID-Numbers = {Dias, Oscar/0000-0002-1765-7178
+ Rocha, Isabel/0000-0001-9494-3410
+ Rocha, Miguel/0000-0001-8439-8172
+ Lopes Faria, Jose Pedro/0000-0001-9302-7250
+ Cruz, Fernando/0000-0003-2468-7364},
+Times-Cited = {13},
+Journal-ISO = {Biochem. Soc. Trans.},
+Unique-ID = {WOS:000583065000005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000587354800022,
+Author = {Moolamalla, S. T. R. and Vinod, P. K.},
+Title = {Genome-scale metabolic modelling predicts biomarkers and therapeutic
+ targets for neuropsychiatric disorders},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2020},
+Volume = {125},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2020.103994},
+Article-Number = {103994},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Brain metabolism; Reporter metabolites; Drug targets; Transcriptomics;
+ Computational modelling; Network biology},
+Keywords-Plus = {BIPOLAR DISORDER; WIDE ASSOCIATION; GENE-EXPRESSION; SCHIZOPHRENIA;
+ DEPRESSION; BRAIN; HOMOCYSTEINE; DYSFUNCTION; INTEGRATION; FOLATE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ORCID-Numbers = {Vinod, P K/0000-0003-2968-498X},
+Times-Cited = {11},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000587354800022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000586670200005,
+Author = {Yilmaz, Lutfu Safak and Li, Xuhang and Nanda, Shivani and Fox, Bennett
+ and Schroeder, Frank and Walhout, Albertha J. M.},
+Title = {Modeling tissue-relevant Caenorhabditis elegans metabolism at
+ network, pathway, reaction, and metabolite levels},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2020},
+Volume = {16},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.15252/msb.20209649},
+Article-Number = {e9649},
+ISSN = {1744-4292},
+Keywords = {Caenorhabditis elegans; data integration; metabolic network;
+ single\&\#8208; cell RNA\&\#8208; seq; tissue metabolism},
+Keywords-Plus = {BETA-OXIDATION; RECONSTRUCTION; ACID; FEATURES; TAURINE; FAT},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Walhout, Marian/0000-0001-5587-3608
+ Fox, Bennett/0000-0002-9749-3491
+ Nanda, Shivani/0000-0001-6358-2392},
+Times-Cited = {21},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000586670200005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000578770900001,
+Author = {Liu, Ailin and Ku, Yee-Shan and Contador, Carolina A. and Lam, Hon-Ming},
+Title = {The Impacts of Domestication and Agricultural Practices on Legume
+ Nutrient Acquisition Through Symbiosis With Rhizobia and Arbuscular
+ Mycorrhizal Fungi},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2020},
+Volume = {11},
+Month = {SEP 30},
+Type = {Review},
+DOI = {10.3389/fgene.2020.583954},
+Article-Number = {583954},
+EISSN = {1664-8021},
+Keywords = {legume-microbe interaction; arbuscular mycorrhizal fungi; symbiotic
+ nitrogen fixation; rhizobia; domestication; metabolic modeling;
+ metabolic profiling},
+Keywords-Plus = {THAUMATIN-LIKE PROTEIN; NITROGEN-FIXATION; LOTUS-JAPONICUS; GENETIC
+ DIVERSITY; PLANT-GROWTH; ROOT-NODULES; WILD; MEDICAGO; SPECIFICITY;
+ METABOLITES},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Ku, Yee-Shan/ABZ-5538-2022
+ Lam, Hon-Ming/A-9866-2008},
+ORCID-Numbers = {Ku, Yee-Shan/0000-0002-9587-5648
+ Lam, Hon-Ming/0000-0002-6673-8740},
+Times-Cited = {22},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000578770900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000578853500001,
+Author = {Lopez, Javiera and Bustos, Diego and Camilo, Conrado and Arenas, Natalia
+ and Saa, Pedro A. and Agosin, Eduardo},
+Title = {Engineering Saccharomyces cerevisiae for the Overproduction of
+ β-Ionone and Its Precursor β-Carotene},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2020},
+Volume = {8},
+Month = {SEP 30},
+Type = {Article},
+DOI = {10.3389/fbioe.2020.578793},
+Article-Number = {578793},
+ISSN = {2296-4185},
+Keywords = {Saccharomyces cerevisiae; ionone; apocarotenoid biosynthesis; metabolic
+ engineering; synthetic biology},
+Keywords-Plus = {CHROMOSOMAL INTEGRATION; YEAST; EXPRESSION; CLEAVAGE; GENES; PATHWAYS;
+ LYCOPENE; VECTOR},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Saa, Pedro Andrés/X-1987-2018},
+ORCID-Numbers = {Saa, Pedro Andrés/0000-0002-1659-9041},
+Times-Cited = {13},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000578853500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000576985400003,
+Author = {Ben Guebila, Marouen},
+Title = {VFFVA: dynamic load balancing enables large-scale flux variability
+ analysis},
+Journal = {BMC BIOINFORMATICS},
+Year = {2020},
+Volume = {21},
+Number = {1},
+Month = {SEP 29},
+Type = {Article},
+DOI = {10.1186/s12859-020-03711-2},
+Article-Number = {424},
+ISSN = {1471-2105},
+Keywords = {Metabolic models; Flux variability analysis; High performance computing;
+ Systems biology},
+Keywords-Plus = {ALTERNATE OPTIMAL-SOLUTIONS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Ben Guebila, Marouen/0000-0001-5934-966X},
+Times-Cited = {3},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000576985400003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000573192900002,
+Author = {Moreno-Avitia, Fabian and Utrilla, Jose and Bolivar, Francisco and
+ Nogales, Juan and Escalante, Adelfo},
+Title = {Metabolic reconstruction ofPseudomonas chlororaphisATCC 9446 to
+ understand its metabolic potential as a
+ phenazine-1-carboxamide-producing strain},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2020},
+Volume = {104},
+Number = {23},
+Pages = {10119-10132},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1007/s00253-020-10913-4},
+EarlyAccessDate = {SEP 2020},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Pseudomonas chlororaphis; Metabolic reconstruction; Genome-scale model;
+ Phenazine-1-carboxamide; Metabolic engineering},
+Keywords-Plus = {PSEUDOMONAS-CHLORORAPHIS; NITROUS-OXIDE; PHENAZINES; DENITRIFICATION;
+ DEGRADATION; ANNOTATION; BIOCONTROL; RESISTANCE; BACTERIAL; CLUSTERS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Escalante, Adelfo/A-4590-2008
+ Utrilla, Jose/A-3610-2013
+ Nogales, Juan/Y-8829-2019
+ Escalante, Adelfo/ADP-4145-2022
+ },
+ORCID-Numbers = {Escalante, Adelfo/0000-0002-5895-3694
+ Utrilla, Jose/0000-0003-3048-9241
+ Escalante, Adelfo/0000-0002-5895-3694
+ Nogales, Juan/0000-0002-4961-0833},
+Times-Cited = {4},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000573192900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000572989700001,
+Author = {Ozcan, Emrah and Seven, Merve and Sirin, Burcu and Cakir, Tunahan and
+ Nikerel, Emrah and Teusink, Bas and Toksoy Oner, Ebru},
+Title = {Dynamic co-culture metabolic models reveal the fermentation dynamics,
+ metabolic capacities and interplays of cheese starter cultures},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2021},
+Volume = {118},
+Number = {1},
+Pages = {223-237},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1002/bit.27565},
+EarlyAccessDate = {SEP 2020},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {lactic acid bacteria; starter cultures; genome-scale metabolic network;
+ co-culture metabolic modelling},
+Keywords-Plus = {LACTIC-ACID BACTERIA; FLUX BALANCE ANALYSIS; LACTOCOCCUS-LACTIS;
+ STREPTOCOCCUS-THERMOPHILUS; DIACETYL PRODUCTION; FOOD FERMENTATIONS;
+ FLAVOR FORMATION; GROWTH; LEUCONOSTOC; REQUIREMENTS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Cakir, Tunahan/F-4523-2011
+ ÖZCAN, EMRAH/HZH-6141-2023
+ Seven, Merve/AAJ-3791-2021
+ Toksoy Oner, Ebru/E-2637-2014
+ Sirin, Burcu/ADT-1633-2022
+ },
+ORCID-Numbers = {Cakir, Tunahan/0000-0001-8262-4420
+ Toksoy Oner, Ebru/0000-0001-6054-8842
+ Teusink, Bas/0000-0003-3929-0423
+ Nikerel, Emrah/0000-0002-9157-8662
+ Seven, Merve/0000-0002-7734-9978
+ OZCAN, EMRAH/0000-0001-9036-9909},
+Times-Cited = {13},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000572989700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000577829400001,
+Author = {Wang, Bin and Yang, Jiarui and Gao, Chenchen and Hao, Tong and Li,
+ Jingjing and Sun, Jinsheng},
+Title = {Reconstruction ofEriocheir sinensisY-organ Genome-Scale Metabolic
+ Network and Differential Analysis After Eyestalk Ablation},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2020},
+Volume = {11},
+Month = {SEP 25},
+Type = {Article},
+DOI = {10.3389/fgene.2020.532492},
+Article-Number = {532492},
+EISSN = {1664-8021},
+Keywords = {Eriocheir sinensis; genome-scale metabolic network; ecdysterone
+ synthesis; Y-organ; eyestalk ablation},
+Keywords-Plus = {ACID-SPECIFIC LECTIN; CRAB ERIOCHEIR-SINENSIS; CONNECTIVITY STRUCTURE;
+ SWIMMING CRAB; PURIFICATION; GROWTH; ECDYSONE; PROTEIN; BIOSYNTHESIS;
+ GLUTATHIONE},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+Times-Cited = {5},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000577829400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000573738100002,
+Author = {Zhang, Jie and Petersen, Soren D. and Radivojevic, Tijana and Ramirez,
+ Andres and Perez-Manriquez, Andres and Abeliuk, Eduardo and Sanchez,
+ Benjamin J. and Costello, Zak and Chen, Yu and Fero, Michael J. and
+ Martin, Hector Garcia and Nielsen, Jens and Keasling, Jay D. and Jensen,
+ Michael K.},
+Title = {Combining mechanistic and machine learning models for predictive
+ engineering and optimization of tryptophan metabolism},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {SEP 25},
+Type = {Article},
+DOI = {10.1038/s41467-020-17910-1},
+Article-Number = {4880},
+EISSN = {2041-1723},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE
+ SYNTHASE; PYRUVATE-KINASE; PATHWAY; YEAST; GENE; EXPRESSION; EVOLUTION;
+ STRATEGY; PROTEIN},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Keasling, Jay/HPG-6073-2023
+ Chen, Yu/AAL-3329-2020
+ Garcia Martin, Hector/B-5357-2009
+ },
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Chen, Yu/0000-0003-3326-9068
+ Garcia Martin, Hector/0000-0002-4556-9685
+ Radivojevic, Tijana/0000-0002-7165-2909
+ Zhang, Jie/0000-0003-4119-9442
+ Perez-Manriquez, Andres/0000-0003-3803-951X
+ Ramirez Neilson, Juan Andres/0000-0001-6273-5211
+ Petersen, Soren Dalsgard/0000-0003-4104-5144
+ Jensen, Michael Krogh/0000-0001-7574-4707},
+Times-Cited = {98},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000573738100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000571670700001,
+Author = {Fang, Xin and Lloyd, Colton J. and Palsson, Bernhard O.},
+Title = {Reconstructing organisms in silico: genome-scale models and their
+ emerging applications},
+Journal = {NATURE REVIEWS MICROBIOLOGY},
+Year = {2020},
+Volume = {18},
+Number = {12},
+Pages = {731-743},
+Month = {DEC},
+Type = {Review},
+DOI = {10.1038/s41579-020-00440-4},
+EarlyAccessDate = {SEP 2020},
+ISSN = {1740-1526},
+EISSN = {1740-1534},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; METABOLIC MODELS;
+ HIGH-THROUGHPUT; BIOMASS COMPOSITION; STRAIN; GROWTH; CAPABILITIES;
+ GENERATION; ALLOCATION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {105},
+Journal-ISO = {Nat. Rev. Microbiol.},
+Unique-ID = {WOS:000571670700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000552131300054,
+Author = {Stone, Kyle and Hilliard, Matthew and Badr, Kiumars and Bradford,
+ Alisabeth and He, Q. Peter and Wang, Jin},
+Title = {Comparative study of oxygen-limited and methane-limited growth
+ phenotypes of Methylomicrobium buryatense 5GB1},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2020},
+Volume = {161},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2020.107707},
+Article-Number = {107707},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Methanotroph; Methylomicrobium buryatense; Methane metabolism;
+ Methane-limited growth; Oxygen-limited growth; Genome-scale metabolic
+ model; Carbon balance},
+Keywords-Plus = {METHANOTROPH},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ORCID-Numbers = {He, Qinghua/0000-0002-2474-5950
+ Wang, Jin/0000-0002-7638-8537},
+Times-Cited = {1},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000552131300054},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000573754900007,
+Author = {Verma, Anukriti and Sharda, Shivani and Rathi, Bhawna and Somvanshi,
+ Pallavi and Pandey, Bimlesh Dhar},
+Title = {Elucidating potential molecular signatures through host-microbe
+ interactions for reactive arthritis and inflammatory bowel disease using
+ combinatorial approach},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1038/s41598-020-71674-8},
+Article-Number = {15131},
+ISSN = {2045-2322},
+Keywords-Plus = {OUTER-MEMBRANE PROTEIN; CHLAMYDIA-TRACHOMATIS; CROHNS-DISEASE;
+ SALMONELLA; RECONSTRUCTION; CAMPYLOBACTER; EXPRESSION; TARGET;
+ IDENTIFICATION; PROTEOMICS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {SOMVANSHI, PALLAVI/IVV-5681-2023
+ Sharda, Shivani/ABI-5086-2020
+ rathi, bhawna/ABI-5119-2020},
+ORCID-Numbers = {SOMVANSHI, PALLAVI/0000-0003-1214-9374
+ Sharda, Shivani/0000-0002-8838-0823
+ rathi, bhawna/0000-0002-4341-6108},
+Times-Cited = {6},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000573754900007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000555539300008,
+Author = {Ploch, Tobias and von Lieres, Eric and Wiechert, Wolfgang and Mitsos,
+ Alexander and Hannemann-Tamas, Ralf},
+Title = {Simulation of differential-algebraic equation systems with optimization
+ criteria embedded in Modelica},
+Journal = {COMPUTERS \& CHEMICAL ENGINEERING},
+Year = {2020},
+Volume = {140},
+Month = {SEP 2},
+Type = {Article},
+DOI = {10.1016/j.compchemeng.2020.106920},
+Article-Number = {106920},
+ISSN = {0098-1354},
+EISSN = {1873-4375},
+Keywords = {nonsmooth dynamic systems; Karush-Kuhn-Tucker conditions; dynamic flux
+ balance analysis; Modelica},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; FERMENTATION; UNIQUENESS; EXISTENCE; GROWTH},
+Research-Areas = {Computer Science; Engineering},
+Web-of-Science-Categories = {Computer Science, Interdisciplinary Applications; Engineering, Chemical},
+ResearcherID-Numbers = {Mitsos, Alexander/D-5873-2011
+ von Lieres, Eric/A-9562-2012
+ },
+ORCID-Numbers = {Mitsos, Alexander/0000-0003-0335-6566
+ von Lieres, Eric/0000-0002-0309-8408
+ Hannemann-Tamas, Ralf/0000-0001-9765-3013},
+Times-Cited = {5},
+Journal-ISO = {Comput. Chem. Eng.},
+Unique-ID = {WOS:000555539300008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000579368300001,
+Author = {Abdel-Haleem, Alyaa M. and Ravikumar, Vaishnavi and Ji, Boyang and
+ Mineta, Katsuhiko and Gao, Xin and Nielsen, Jens and Gojobori, Takashi
+ and Mijakovic, Ivan},
+Title = {Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain
+ Enhanced Virulence of Vibrio cholerae during Coinfection with
+ Enterotoxigenic Escherichia coli},
+Journal = {MSYSTEMS},
+Year = {2020},
+Volume = {5},
+Number = {5},
+Month = {SEP-OCT},
+Type = {Article},
+DOI = {10.1128/mSystems.00491-20},
+Article-Number = {e00491-20},
+ISSN = {2379-5077},
+Keywords = {infectious diseases; cholera; diarrhea; coinfection; drug target; flux
+ balance analysis; constraint-based model; genome-scale reconstruction;
+ Vibrio cholera; computational modeling; genome-scale modeling},
+Keywords-Plus = {SECRETION SYSTEM; ESSENTIAL GENES; ATP SYNTHASE; IDENTIFICATION;
+ PROTEIN; DATABASE; PATHOGEN; MUTATIONS; RESPONSES; GENOTYPE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Ji, Boyang/HMV-6662-2023
+ Gao, Xin/D-5487-2013
+ Nielsen, Jens Bo/C-7632-2015
+ Mineta, Katsuhiko/A-5455-2012
+ Mijakovic, Ivan/Q-5583-2016
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Ji, Boyang/0000-0002-7269-4342
+ Gao, Xin/0000-0002-7108-3574
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Mineta, Katsuhiko/0000-0002-4727-045X
+ Mijakovic, Ivan/0000-0002-8860-6853
+ Nielsen, Jens/0000-0002-9955-6003
+ Abdel-haleem, Alyaa/0000-0002-3114-1100},
+Times-Cited = {7},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000579368300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000570986300002,
+Author = {Dahal, Sanjeev and Yurkovich, James T. and Xu, Hao and Palsson, Bernhard
+ O. and Yang, Laurence},
+Title = {Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale
+ Models},
+Journal = {PROTEOMICS},
+Year = {2020},
+Volume = {20},
+Number = {17-18, SI},
+Month = {SEP},
+Type = {Review},
+DOI = {10.1002/pmic.201900282},
+Article-Number = {1900282},
+ISSN = {1615-9853},
+EISSN = {1615-9861},
+Keywords = {computational model; genome-scale model; genomics; machine learning;
+ systems biology},
+Keywords-Plus = {MASS-SPECTROMETRY; METABOLOMICS; PROTEOME; RECONSTRUCTION;
+ CHROMATOGRAPHY; ANNOTATION; METABOLISM; SEQUENCE; GROWTH; CELLS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Dahal, Sanjeev/0000-0003-4636-7732
+ Xu, Hao/0000-0003-2546-5528},
+Times-Cited = {18},
+Journal-ISO = {Proteomics},
+Unique-ID = {WOS:000570986300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000572284600004,
+Author = {Herencias, Cristina and Salgado-Briegas, Sergio and Prieto, Maria A. and
+ Nogales, Juan},
+Title = {Providing new insights on the biphasic lifestyle of the predatory
+ bacterium Bdellovibrio bacteriovorus through genome-scale
+ metabolic modeling},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2020},
+Volume = {16},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1007646},
+Article-Number = {e1007646},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; NUCLEOSIDE MONOPHOSPHATES;
+ INTRAPERIPLASMIC GROWTH; IDENTIFICATION; EVOLUTION; ORGANISM; GENES;
+ ACIDS},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ Herencias, Cristina/AAB-3021-2021
+ },
+ORCID-Numbers = {Herencias, Cristina/0000-0002-1384-3109
+ Sergio, Salgado Briegas/0000-0002-5968-465X
+ Nogales, Juan/0000-0002-4961-0833
+ Prieto Jimenez, M. Auxiliadora/0000-0002-8038-1223},
+Times-Cited = {7},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000572284600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000572284600002,
+Author = {Poyatos, Juan F.},
+Title = {Genetic buffering and potentiation in metabolism},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2020},
+Volume = {16},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1008185},
+Article-Number = {e1008185},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {HSP90; EVOLUTION; CAPACITOR; NETWORKS; RESISTANCE; REVEALS; GENOME;
+ ENZYME},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Poyatos, Juan F./0000-0003-4575-8723},
+Times-Cited = {2},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000572284600002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000580268500001,
+Author = {Scott, Jr., William T. and Smid, Eddy J. and Notebaart, Richard A. and
+ Block, David E.},
+Title = {Curation and Analysis of a Saccharomyces cerevisiae Genome-Scale
+ Metabolic Model for Predicting Production of Sensory Impact Molecules
+ under Enological Conditions},
+Journal = {PROCESSES},
+Year = {2020},
+Volume = {8},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.3390/pr8091195},
+Article-Number = {1195},
+EISSN = {2227-9717},
+Keywords = {aroma; flux balance analysis (FBA); genome-scale metabolic models;
+ Saccharomyces cerevisiae; wine fermentation},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; ALCOHOL ACETYLTRANSFERASE;
+ QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; FLUX DISTRIBUTIONS; ESTER
+ PRODUCTION; EHRLICH PATHWAY; AROMA FORMATION; GROWTH},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Notebaart, Richard A./A-1459-2014
+ },
+ORCID-Numbers = {Smid, Eddy J./0000-0002-6687-5083
+ Scott, William/0000-0002-4029-2998},
+Times-Cited = {8},
+Journal-ISO = {Processes},
+Unique-ID = {WOS:000580268500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000580218300001,
+Author = {Viana, Romeu and Dias, Oscar and Lagoa, Davide and Galocha, Monica and
+ Rocha, Isabel and Teixeira, Miguel Cacho},
+Title = {Genome-Scale Metabolic Model of the Human PathogenCandida
+ albicans: A Promising Platform for Drug Target Prediction},
+Journal = {JOURNAL OF FUNGI},
+Year = {2020},
+Volume = {6},
+Number = {3},
+Month = {SEP},
+Type = {Article},
+DOI = {10.3390/jof6030171},
+Article-Number = {171},
+EISSN = {2309-608X},
+Keywords = {Candida albicans; global stoichiometric model; drug targets; metabolic
+ reconstruction; gene essentiality},
+Keywords-Plus = {CANDIDA-ALBICANS; SACCHAROMYCES-CEREVISIAE; SUSCEPTIBILITY PROFILES;
+ CLINICAL BREAKPOINTS; RESISTANCE; YEAST; EPIDEMIOLOGY; ECHINOCANDIN;
+ RECONSTRUCTION; IDENTIFICATION},
+Research-Areas = {Microbiology; Mycology},
+Web-of-Science-Categories = {Microbiology; Mycology},
+ResearcherID-Numbers = {Galocha, Mónica/AAI-2119-2021
+ Dias, Oscar/A-4359-2010
+ Rocha, Isabel/A-4279-2013
+ Teixeira, Miguel/A-3870-2008},
+ORCID-Numbers = {Galocha, Mónica/0000-0002-4090-7016
+ Dias, Oscar/0000-0002-1765-7178
+ Rocha, Isabel/0000-0001-9494-3410
+ Teixeira, Miguel/0000-0002-5676-6174},
+Times-Cited = {10},
+Journal-ISO = {J. Fungi},
+Unique-ID = {WOS:000580218300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000567179200002,
+Author = {Khoshnejat, Maryam and Kavousi, Kaveh and Banaei-Moghaddam, Ali Mohammad
+ and Moosavi-Movahedi, Ali Akbar},
+Title = {Unraveling the molecular heterogeneity in type 2 diabetes: a potential
+ subtype discovery followed by metabolic modeling},
+Journal = {BMC MEDICAL GENOMICS},
+Year = {2020},
+Volume = {13},
+Number = {1},
+Month = {AUG 24},
+Type = {Article},
+DOI = {10.1186/s12920-020-00767-0},
+Article-Number = {119},
+EISSN = {1755-8794},
+Keywords = {Type 2 diabetes; Subtype; Classification; Clustering; Flux variability
+ analysis; Muscle; Insulin resistance; Metabolic modeling},
+Keywords-Plus = {FREE FATTY-ACIDS; SKELETAL-MUSCLE; INSULIN-RESISTANCE; OBESITY;
+ RECONSTRUCTION; INFLAMMATION; OSTEOPONTIN; REGULATOR; NETWORK; PROTEIN},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Banaei-Moghaddam, Ali Mohammad/ABE-5625-2021
+ },
+ORCID-Numbers = {Banaei-Moghaddam, Ali Mohammad/0000-0003-1298-3748
+ Kavousi, Kaveh/0000-0002-1906-3912
+ Moosavi-Movahedi, Ali Akbar/0000-0002-1707-8432},
+Times-Cited = {3},
+Journal-ISO = {BMC Med. Genomics},
+Unique-ID = {WOS:000567179200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000542595600016,
+Author = {Huang, Zhuangrong and Xu, Jianlin and Yongky, Andrew and Morris, Caitlin
+ S. and Polanco, Ashli L. and Reily, Michael and Borys, Michael C. and
+ Li, Zheng Jian and Yoon, Seongkyu},
+Title = {CHO cell productivity improvement by genome-scale modeling and pathway
+ analysis: Application to feed supplements},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2020},
+Volume = {160},
+Month = {AUG 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2020.107638},
+Article-Number = {107638},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {GS CHO-K1 cells; Genome-scale model; Cellular metabolism; Feed
+ improvement; Model simulation; Pathway analysis},
+Keywords-Plus = {METABOLIC FLUX ANALYSIS; PARALLEL LABELING EXPERIMENTS; AMINO-ACID
+ SUPPLEMENTATION; CONSTRAINT-BASED MODELS; PROTEIN-PRODUCTION;
+ QUANTITATIVE PREDICTION; SYSTEMS BIOTECHNOLOGY; MAMMALIAN SYSTEMS;
+ FED-BATCH; CULTURE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Huang, Zhuangrong/AAV-2846-2020
+ },
+ORCID-Numbers = {Li, Zheng Jian/0000-0002-1941-4145
+ yoon, seongkyu/0000-0002-5330-8784
+ Huang, Zhuangrong/0000-0002-9145-5582
+ Xu, Jianlin/0000-0002-6441-0696},
+Times-Cited = {26},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000542595600016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000562671300010,
+Author = {Marinos, Georgios and Kaleta, Christoph and Waschina, Silvio},
+Title = {Defining the nutritional input for genome-scale metabolic models: A
+ roadmap},
+Journal = {PLOS ONE},
+Year = {2020},
+Volume = {15},
+Number = {8},
+Month = {AUG 14},
+Type = {Article},
+DOI = {10.1371/journal.pone.0236890},
+Article-Number = {e0236890},
+ISSN = {1932-6203},
+Keywords-Plus = {BIOCHEMICAL REACTIONS; BASIC CONCEPTS; GROWTH; INCONSISTENCIES;
+ RECONCILIATION; PHYSIOLOGY; SYSTEMS; MEDIA; ACIDS; IRON},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Waschina, Silvio/AAE-2908-2021
+ },
+ORCID-Numbers = {Waschina, Silvio/0000-0002-6290-3593
+ Kaleta, Christoph/0000-0001-8004-9514
+ MARINOS, GEORGIOS/0000-0002-6443-7696},
+Times-Cited = {14},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000562671300010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000562122400001,
+Author = {Curran, David M. and Grote, Alexandra and Nursimulu, Nirvana and Geber,
+ Adam and Voronin, Dennis and Jones, Drew R. and Ghedin, Elodie and
+ Parkinson, John},
+Title = {Modeling the metabolic interplay between a parasitic worm and its
+ bacterial endosymbiont allows the identification of novel drug targets},
+Journal = {ELIFE},
+Year = {2020},
+Volume = {9},
+Month = {AUG 11},
+Type = {Article},
+DOI = {10.7554/eLife.51850},
+Article-Number = {e51850},
+ISSN = {2050-084X},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GENE-EXPRESSION; WUCHERERIA-BANCROFTI;
+ ONCHOCERCA-VOLVULUS; GENOME; SCALE; IVERMECTIN;
+ FRUCTOSE-1,6-BISPHOSPHATASE; RECONSTRUCTION; NETWORK},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Parkinson, John/A-4424-2008
+ },
+ORCID-Numbers = {Parkinson, John/0000-0001-9815-1189
+ Curran, David/0000-0003-2749-869X
+ Ghedin, Elodie/0000-0002-1515-725X
+ Jones, Drew/0000-0001-8732-9818
+ Nursimulu, Nirvana/0000-0001-5962-5863
+ Voronin, Denis/0000-0003-2652-0787},
+Times-Cited = {9},
+Journal-ISO = {eLife},
+Unique-ID = {WOS:000562122400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000575493200008,
+Author = {Culley, Christopher and Vijayakumar, Supreeta and Zampieri, Guido and
+ Angione, Claudio},
+Title = {A mechanism-aware and multiomic machine-learning pipeline characterizes
+ yeast cell growth},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2020},
+Volume = {117},
+Number = {31},
+Pages = {18869-18879},
+Month = {AUG 4},
+Type = {Article},
+DOI = {10.1073/pnas.2002959117},
+ISSN = {0027-8424},
+EISSN = {1091-6490},
+Keywords = {metabolic modeling; machine learning; flux balance analysis; systems
+ biology; multimodal learning},
+Keywords-Plus = {GENE-EXPRESSION; RANDOM FORESTS; TRANSCRIPTION; BIOLOGY; MODELS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Zampieri, Guido/HJH-7472-2023
+ },
+ORCID-Numbers = {Zampieri, Guido/0000-0002-4518-5913
+ Angione, Claudio/0000-0002-3140-7909
+ Vijayakumar, Supreeta/0000-0001-6357-0439},
+Times-Cited = {45},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000575493200008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000556014800001,
+Author = {Zuniga, Cristal and Peacock, Beth and Liang, Bo and McCollum, Greg and
+ Irigoyen, Sonia C. and Tec-Campos, Diego and Marotz, Clarisse and Weng,
+ Nien-Chen and Zepeda, Alejandro and Vidalakis, Georgios and Mandadi,
+ Kranthi K. and Borneman, James and Zengler, Karsten},
+Title = {Linking metabolic phenotypes to pathogenic traits among
+ ``CandidatusLiberibacter asiaticus{''} and its hosts},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2020},
+Volume = {6},
+Number = {1},
+Month = {AUG 4},
+Type = {Article},
+DOI = {10.1038/s41540-020-00142-w},
+Article-Number = {24},
+EISSN = {2056-7189},
+Keywords-Plus = {CANDIDATUS LIBERIBACTER-ASIATICUS; CITRUS-SINENSIS; GENE-EXPRESSION;
+ DISEASE; DATABASE; INFECTION; PREDICTION; BACTERIUM; MODELS; MEMBER},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zuniga, Cristal/CAA-0015-2022
+ },
+ORCID-Numbers = {Zuniga, Cristal/0000-0002-0135-7429},
+Times-Cited = {15},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000556014800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000567939700006,
+Author = {Carey, Maureen A. and Draeger, Andreas and Beber, Moritz E. and Papin,
+ Jason A. and Yurkovich, James T.},
+Title = {Community standards to facilitate development and address challenges in
+ metabolic modeling},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2020},
+Volume = {16},
+Number = {8},
+Month = {AUG},
+Type = {Editorial Material},
+DOI = {10.15252/msb.20199235},
+Article-Number = {e9235},
+ISSN = {1744-4292},
+Keywords-Plus = {INFORMATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Dräger, Andreas/F-5620-2015
+ },
+ORCID-Numbers = {Dräger, Andreas/0000-0002-1240-5553
+ Beber, Moritz Emanuel/0000-0003-2406-1978
+ Carey, Maureen/0000-0003-2890-5445
+ Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {19},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000567939700006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000566467800001,
+Author = {Casey, John R. and Follows, Michael J.},
+Title = {A steady-state model of microbial acclimation to substrate limitation},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2020},
+Volume = {16},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1008140},
+Article-Number = {e1008140},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ESCHERICHIA-COLI; NUTRIENT-UPTAKE; GLUCOSE-TRANSPORT; LIMITED GROWTH;
+ PHYTOPLANKTON; DIFFUSION; KINETICS; PERMEASE; STRAINS; RATES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Follows, Michael J/G-9824-2011
+ },
+ORCID-Numbers = {Casey, John/0000-0002-8630-0551},
+Times-Cited = {8},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000566467800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000576604100015,
+Author = {Chen, Yan and Banerjee, Deepanwita and Mukhopadhyay, Aindrila and
+ Petzold, Christopher J.},
+Title = {Systems and synthetic biology tools for advanced bioproduction hosts},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2020},
+Volume = {64},
+Number = {SI},
+Pages = {101-109},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1016/j.copbio.2019.12.007},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {OPTIMIZATION; WORKFLOW},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Banerjee, Deepanwita/AAD-5528-2021
+ Mukhopadhyay, Aindrila/AAW-7257-2021
+ Chen, Yan/M-9814-2018
+ },
+ORCID-Numbers = {Banerjee, Deepanwita/0000-0002-0083-0608
+ Chen, Yan/0000-0002-1125-313X
+ Petzold, Christopher/0000-0002-8270-5228},
+Times-Cited = {29},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000576604100015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000583062000002,
+Author = {Choi, Yoon-Mi and Lee, Yi Qing and Song, Hyun-Seob and Lee, Dong-Yup},
+Title = {Genome scale metabolic models and analysis for evaluating probiotic
+ potentials},
+Journal = {BIOCHEMICAL SOCIETY TRANSACTIONS},
+Year = {2020},
+Volume = {48},
+Number = {4},
+Pages = {1309-1321},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1042/BST20190668},
+ISSN = {0300-5127},
+EISSN = {1470-8752},
+Keywords-Plus = {BACILLUS-SUBTILIS; RECONSTRUCTION; NETWORK; MECHANISMS; DATABASE;
+ GROWTH; TERM},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Song, Hyun-Seob/IAQ-0503-2023
+ Lee, Dong-Yup/D-6650-2011
+ },
+ORCID-Numbers = {Lee, Dong-Yup/0000-0003-0901-708X
+ Lee, Yi Qing/0000-0002-8970-0729},
+Times-Cited = {3},
+Journal-ISO = {Biochem. Soc. Trans.},
+Unique-ID = {WOS:000583062000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000566200000001,
+Author = {Esch, Bianca M. and Limar, Sergej and Bogdanowski, Andre and Gournas,
+ Christos and More, Tushar and Sundag, Celine and Walter, Stefan and
+ Heinisch, Juergen J. and Ejsing, Christer S. and Andre, Bruno and
+ Froehlich, Florian},
+Title = {Uptake of exogenous serine is important to maintain sphingolipid
+ homeostasis in Saccharomyces cerevisiae},
+Journal = {PLOS GENETICS},
+Year = {2020},
+Volume = {16},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pgen.1008745},
+Article-Number = {e1008745},
+ISSN = {1553-7404},
+Keywords-Plus = {AMINO-ACIDS; PROTEINS; MITOCHONDRIAL; BIOSYNTHESIS; TRANSPORTER;
+ LIPIDOME; PERMEASE; FTY720; GENE; PHOSPHORYLATION},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Ejsing, Christer S/R-5922-2016
+ Gournas, Christos/ADL-6622-2022
+ More, Dr.Aarti Tushar/HKO-6157-2023
+ Heinisch, Juergen J./G-3801-2017
+ Gournas, Christos/ABD-6186-2021
+ },
+ORCID-Numbers = {Gournas, Christos/0000-0003-4755-8602
+ Bogdanowski, Andre/0000-0002-9634-7054
+ Andre, Bruno/0000-0002-4531-4674
+ Esch, Bianca M./0000-0002-3645-3322
+ Frohlich, Florian/0000-0001-8307-2189
+ Ejsing, Christer S./0000-0003-4963-0276},
+Times-Cited = {13},
+Journal-ISO = {PLoS Genet.},
+Unique-ID = {WOS:000566200000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000567939700007,
+Author = {Keating, Sarah M. and Waltemath, Dagmar and Koenig, Matthias and Zhang,
+ Fengkai and Draeger, Andreas and Chaouiya, Claudine and Bergmann, Frank
+ T. and Finney, Andrew and Gillespie, Colin S. and Helikar, Tomas and
+ Hoops, Stefan and Malik-Sheriff, Rahuman S. and Moodie, Stuart L. and
+ Moraru, Ion I. and Myers, Chris J. and Naldi, Aurelien and Olivier,
+ Brett G. and Sahle, Sven and Schaff, James C. and Smith, Lucian P. and
+ Swat, Maciej J. and Thieffry, Denis and Watanabe, Leandro and Wilkinson,
+ Darren J. and Blinov, Michael L. and Begley, Kimberly and Faeder, James
+ R. and Gomez, Harold F. and Hamm, Thomas M. and Inagaki, Yuichiro and
+ Liebermeister, Wolfram and Lister, Allyson L. and Lucio, Daniel and
+ Mjolsness, Eric and Proctor, Carole J. and Raman, Karthik and Rodriguez,
+ Nicolas and Shaffer, Clifford A. and Shapiro, Bruce E. and Stelling,
+ Joerg and Swainston, Neil and Tanimura, Naoki and Wagner, John and
+ Meier-Schellersheim, Martin and Sauro, Herbert M. and Palsson, Bernhard
+ and Bolouri, Hamid and Kitano, Hiroaki and Funahashi, Akira and
+ Hermjakob, Henning and Doyle, John C. and Hucka, Michael and SBML Level
+ 3 Community Members},
+Title = {SBML Level 3: an extensible format for the exchange and reuse of
+ biological models},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2020},
+Volume = {16},
+Number = {8},
+Month = {AUG},
+Type = {Review},
+DOI = {10.15252/msb.20199110},
+Article-Number = {e9110},
+ISSN = {1744-4292},
+Keywords = {computational modeling; file format; interoperability; reproducibility;
+ systems biology},
+Keywords-Plus = {SYSTEMS BIOLOGY; MARKUP LANGUAGE; SIMULATION; STANDARDS; SOFTWARE;
+ INFORMATION; ENVIRONMENT; ANNOTATION; REPOSITORY; ONTOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Lukas, Endler/ABD-2002-2021
+ Naldi, Aurélien/B-5401-2008
+ Saez-Rodriguez, Julio/H-7114-2019
+ Waltemath, Dagmar/K-2499-2019
+ Hucka, Michael/B-1896-2012
+ Gillespie, Colin S/A-8042-2008
+ Rohwer, Johann/A-2027-2008
+ Hermjakob, Henning/AFM-3497-2022
+ Dräger, Andreas/F-5620-2015
+ , Johan/HZL-7312-2023
+ Raman, Karthik/Q-5278-2019
+ Červený, Jan/J-1911-2012
+ Zhukova, Anna/AET-0798-2022
+ Chaouiya, Claudine/F-8560-2012
+ Doyle, John/IAQ-1764-2023
+ Kutmon, Martina/AAT-2718-2021
+ Sheriff, Rahuman/ABB-9034-2020
+ Cox, Chris/A-9451-2013
+ Funahashi, Akira/C-4923-2014
+ Soliman, Sylvain/B-7445-2009
+ },
+ORCID-Numbers = {Lukas, Endler/0000-0002-9115-8756
+ Naldi, Aurélien/0000-0002-6495-2655
+ Saez-Rodriguez, Julio/0000-0002-8552-8976
+ Waltemath, Dagmar/0000-0002-5886-5563
+ Hucka, Michael/0000-0001-9105-5960
+ Rohwer, Johann/0000-0001-6288-8904
+ Hermjakob, Henning/0000-0001-8479-0262
+ Dräger, Andreas/0000-0002-1240-5553
+ Raman, Karthik/0000-0002-9311-7093
+ Červený, Jan/0000-0002-5046-3105
+ Zhukova, Anna/0000-0003-2200-7935
+ Chaouiya, Claudine/0000-0003-2350-0756
+ Kutmon, Martina/0000-0002-7699-8191
+ Sheriff, Rahuman/0000-0003-0705-9809
+ Goncalves, Emanuel/0000-0002-9967-5205
+ Natarajan, Kedar Nath/0000-0002-9264-1280
+ Lister, Allyson/0000-0002-7702-4495
+ Thieffry, Denis/0000-0003-0271-1757
+ Cox, Chris/0000-0001-9818-5477
+ Sullivan, Devin/0000-0001-6176-108X
+ Gillespie, Colin/0000-0003-1787-0275
+ Smith, Lucian/0000-0001-7002-6386
+ Teusink, Bas/0000-0003-3929-0423
+ Machne, Rainer/0000-0002-1274-5099
+ Bergmann, Frank/0000-0001-5553-4702
+ Funahashi, Akira/0000-0003-0605-239X
+ Schubert, Michael/0000-0002-6862-5221
+ Glont, Mihai/0000-0002-8211-7581
+ Dorier, Julien/0000-0002-6717-2451
+ Olivier, Brett/0000-0002-5293-5321
+ Flamm, Christoph/0000-0001-5500-2415
+ Soliman, Sylvain/0000-0001-5525-7418
+ Courtot, Melanie/0000-0002-9551-6370
+ Zhang, Fengkai/0000-0001-7112-9328
+ de Jong, Hidde/0000-0002-2226-650X
+ Pfau, Thomas/0000-0001-5048-2923
+ Konig, Matthias/0000-0003-1725-179X
+ Hu, Bin/0000-0002-0278-8466
+ Antoniotti, Marco/0000-0002-2823-6838
+ Evelo, Chris/0000-0002-5301-3142
+ Keating, Sarah/0000-0002-3356-3542},
+Times-Cited = {115},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000567939700007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000582313500005,
+Author = {Pedram, Narges and Rashedi, Hamid and Motamedian, Ehsan},
+Title = {A systematic strategy using a reconstructed genome-scale metabolic
+ network for pathogen Streptococcus pneumoniae D39 to find novel
+ potential drug targets},
+Journal = {PATHOGENS AND DISEASE},
+Year = {2020},
+Volume = {78},
+Number = {6},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1093/femspd/ftaa051},
+Article-Number = {ftaa051},
+ISSN = {2049-632X},
+Keywords = {Streptococcus pneumoniae; drug target; genome-scale metabolic model;
+ transcriptomics; flux balance analysis},
+Keywords-Plus = {SEROTYPE-2; EXPRESSION; RESOURCE; DATABASE; TOOLBOX; GROWTH; ENZYME;
+ GENES; MODEL; ACID},
+Research-Areas = {Immunology; Infectious Diseases; Microbiology},
+Web-of-Science-Categories = {Immunology; Infectious Diseases; Microbiology},
+ResearcherID-Numbers = {Rashedi, Hamid/O-9619-2017
+ Motamedian, Ehsan/GPK-8344-2022
+ },
+ORCID-Numbers = {, Ehsan/0000-0001-8750-2879},
+Times-Cited = {0},
+Journal-ISO = {Pathog. Dis.},
+Unique-ID = {WOS:000582313500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000592970900012,
+Author = {Sambamoorthy, Gayathri and Raman, Karthik},
+Title = {MINREACT: a systematic approach for identifying minimal metabolic
+ networks},
+Journal = {BIOINFORMATICS},
+Year = {2020},
+Volume = {36},
+Number = {15},
+Pages = {4309-4315},
+Month = {AUG 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btaa497},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {REACTION SETS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019
+ },
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ Sambamoorthy, Gayathri/0000-0003-2444-1700},
+Times-Cited = {1},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000592970900012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000564100700001,
+Author = {Volkova, Svetlana and Matos, Marta R. A. and Mattanovich, Matthias and
+ de Mas, Igor Marin},
+Title = {Metabolic Modelling as a Framework for Metabolomics Data Integration and
+ Analysis},
+Journal = {METABOLITES},
+Year = {2020},
+Volume = {10},
+Number = {8},
+Month = {AUG},
+Type = {Review},
+DOI = {10.3390/metabo10080303},
+Article-Number = {303},
+EISSN = {2218-1989},
+Keywords = {metabolic modelling; data integration; metabolomics},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS; KINETIC-MODELS;
+ ISOTOPOMER DISTRIBUTIONS; CELLULAR-METABOLISM; SYSTEMS BIOLOGY; GROWTH;
+ QUANTIFICATION; CELLS; HOMEOSTASIS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Marin de Mas, Igor/0000-0003-2925-8155
+ Matos, Marta/0000-0003-4288-1005
+ Mattanovich, Matthias/0000-0001-7561-7898
+ Volkova, Svetlana/0000-0002-0361-3246},
+Times-Cited = {34},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000564100700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000560053400012,
+Author = {Zuniga, Cristal and Li, Tingting and Guarnieri, Michael T. and Jenkins,
+ Jackson P. and Li, Chien-Ting and Bingol, Kerem and Kim, Young-Mo and
+ Betenbaugh, Michael J. and Zengler, Karsten},
+Title = {Synthetic microbial communities of heterotrophs and phototrophs
+ facilitate sustainable growth},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {JUL 30},
+Type = {Article},
+DOI = {10.1038/s41467-020-17612-8},
+Article-Number = {3803},
+ISSN = {2041-1723},
+Keywords-Plus = {WATER; BACTERIA; AVAILABILITY; METABOLISM; MICROALGAE; PREDICTION;
+ COCULTURES; NITROGEN; LICHENS; MODELS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Kim, Young-Mo/D-3282-2009
+ Bingol, Kerem/K-7383-2014
+ zhang, ting/IYT-0642-2023
+ Li, Tingting/HKE-0812-2023
+ L, J/JEF-9564-2023
+ Kim, Young-Mo/AAG-2866-2019
+ Zuniga, Cristal/CAA-0015-2022
+ },
+ORCID-Numbers = {Kim, Young-Mo/0000-0002-8972-7593
+ Kim, Young-Mo/0000-0002-8972-7593
+ Zengler, Karsten/0000-0002-8062-3296
+ Guarnieri, Michael/0000-0003-1403-9689},
+Times-Cited = {43},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000560053400012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000551296900001,
+Author = {Chen, Yu and Sun, Yan and Liu, Zhihao and Dong, Fengqing and Li,
+ Yuanyuan and Wang, Yonghong},
+Title = {Genome-scale modeling forBacillus coagulansto understand the
+ metabolic characteristics},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2020},
+Volume = {117},
+Number = {11},
+Pages = {3545-3558},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1002/bit.27488},
+EarlyAccessDate = {JUL 2020},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Bacillus coagulans; chemostat; constraint-based model; lactic acid
+ fermentation; metabolic switch},
+Keywords-Plus = {L-LACTIC ACID; IN-SILICO ANALYSIS; BACILLUS-COAGULANS;
+ LACTOCOCCUS-LACTIS; LACTOBACILLUS-PLANTARUM; FACULTATIVE THERMOPHILE;
+ NUTRIENT-REQUIREMENTS; FERMENTATION BROTH; RESIDUAL SUGAR; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Chen, Yu/AAL-3329-2020},
+ORCID-Numbers = {Chen, Yu/0000-0003-3326-9068},
+Times-Cited = {9},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000551296900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000551297400001,
+Author = {Correa, Sandra M. and Alseekh, Saleh and Atehortua, Lucia and Brotman,
+ Yariv and Rios-Estepa, Rigoberto and Fernie, Alisdair R. and Nikoloski,
+ Zoran},
+Title = {Model-assisted identification of metabolic engineering strategies
+ forJatropha curcaslipid pathways},
+Journal = {PLANT JOURNAL},
+Year = {2020},
+Volume = {104},
+Number = {1},
+Pages = {76-95},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1111/tpj.14906},
+EarlyAccessDate = {JUL 2020},
+ISSN = {0960-7412},
+EISSN = {1365-313X},
+Keywords = {Jatropha curcas; lipid biosynthesis and metabolism; metabolic
+ reconstruction; constrained-based analysis; cell cultures; metabolic
+ engineering},
+Keywords-Plus = {FATTY-ACID SYNTHESIS; FLUX BALANCE ANALYSIS; HETEROTROPHIC ARABIDOPSIS
+ CELLS; GENOME-SCALE RECONSTRUCTION; CAMELINA-SATIVA SEEDS;
+ BRASSICA-NAPUS; OILSEED RAPE; OIL CONTENT; DIACYLGLYCEROL
+ ACYLTRANSFERASE; MICROSOMAL PREPARATIONS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {fernie, alisdair/IWD-9278-2023
+ },
+ORCID-Numbers = {Nikoloski, Zoran/0000-0003-2671-6763
+ Rios-Estepa, Rigoberto/0000-0002-3287-7056
+ Alseekh, Saleh/0000-0003-2067-5235
+ Correa Cordoba, Sandra Marcela/0000-0002-5049-9271},
+Times-Cited = {6},
+Journal-ISO = {Plant J.},
+Unique-ID = {WOS:000551297400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000551555500017,
+Author = {Garcia, Sergio and Trinh, Cong T.},
+Title = {Harnessing Natural Modularity of Metabolism with Goal Attainment
+ Optimization to Design a Modular Chassis Cell for Production of Diverse
+ Chemicals},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2020},
+Volume = {9},
+Number = {7},
+Pages = {1665-1681},
+Month = {JUL 17},
+Type = {Article},
+DOI = {10.1021/acssynbio.9b00518},
+ISSN = {2161-5063},
+Keywords = {biocatalysis; modular design; modular cell; metabolic network modeling;
+ multiobjective optimization; goal programming},
+Keywords-Plus = {ESCHERICHIA-COLI; C-13-LABELING EXPERIMENTS; GENE-KNOCKOUT; FLUX
+ ANALYSIS; FERMENTATIVE PATHWAYS; SUCCINATE PRODUCTION;
+ ENZYME-ACTIVITIES; BIOSYNTHESIS; FRAMEWORK; OPTIMALITY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+Times-Cited = {7},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000551555500017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000537604100024,
+Author = {Huang, Zhuangrong and Yoon, Seongkyu},
+Title = {Identifying metabolic features and engineering targets for productivity
+ improvement in CHO cells by integrated transcriptomics and genome-scale
+ metabolic model},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2020},
+Volume = {159},
+Month = {JUL 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2020.107624},
+Article-Number = {107624},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Metabolic pathway analysis; Genome-scale metabolic model; Chinese
+ hamster ovary; Flux balance analysis; mAb productivity},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; HAMSTER OVARY CELLS; ANTIBODY-PRODUCTION;
+ QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; SYSTEMS BIOLOGY; FLUX
+ ANALYSIS; GROWTH; IDENTIFICATION; ANNOTATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Huang, Zhuangrong/AAV-2846-2020
+ },
+ORCID-Numbers = {Huang, Zhuangrong/0000-0002-9145-5582
+ yoon, seongkyu/0000-0002-5330-8784},
+Times-Cited = {10},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000537604100024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000545606500001,
+Author = {Shene, Carolina and Paredes, Paris and Flores, Liset and Leyton, Allison
+ and Asenjo, Juan A. and Chisti, Yusuf},
+Title = {Dynamic flux balance analysis of biomass and lipid production by
+ Antarctic thraustochytrid Oblongichytrium sp. RT2316-13},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2020},
+Volume = {117},
+Number = {10},
+Pages = {3006-3017},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1002/bit.27463},
+EarlyAccessDate = {JUL 2020},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {docosahexaenoic acid; flux balance analysis; genome-scale metabolic
+ model; lipids; Oblongichytriumsp; thraustochytrids},
+Keywords-Plus = {POLYUNSATURATED FATTY-ACIDS; DOCOSAHEXAENOIC ACID; SCHIZOCHYTRIUM;
+ GROWTH; DHA; IDENTIFICATION; TEMPERATURE; METABOLISM; CONVERSION;
+ CULTURE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Chisti, Mohammad/T-7760-2017
+ Asenjo, Juan JAA/L-8336-2013
+ },
+ORCID-Numbers = {Chisti, Mohammad/0000-0002-2676-9577
+ Asenjo, Juan JAA/0000-0002-3475-7664
+ Leyton, Allison/0000-0002-8665-267X
+ Chisti, Yusuf/0000-0002-0826-7012},
+Times-Cited = {14},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000545606500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000562474100063,
+Author = {Ding, Shaozhen and Tian, Yu and Cai, Pengli and Zhang, Dachuan and
+ Cheng, Xingxiang and Sun, Dandan and Yuan, Le and Chen, Junni and Tu,
+ Weizhong and Wei, Dong-Qing and Hu, Qian-Nan},
+Title = {novoPathFinder: a webserver of designing novel-pathway with integrating
+ GEM-model},
+Journal = {NUCLEIC ACIDS RESEARCH},
+Year = {2020},
+Volume = {48},
+Number = {W1},
+Pages = {W477-W487},
+Month = {JUL 2},
+Type = {Article},
+DOI = {10.1093/nar/gkaa230},
+ISSN = {0305-1048},
+EISSN = {1362-4962},
+Keywords-Plus = {METABOLIC PATHWAYS; SYNTHETIC BIOLOGY; NATURAL-PRODUCTS; PREDICTION;
+ BIOSYNTHESIS; ATLAS; ACID},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Hu, Qian/GWZ-7617-2022
+ sun, dandan/GZG-6540-2022
+ Cai, Pengli/HZL-4422-2023
+ Zhang, Dachuan/AFT-0071-2022
+ },
+ORCID-Numbers = {Zhang, Dachuan/0000-0003-2467-6286
+ Yuan, Le/0000-0003-3317-9011
+ Tian, Yu/0000-0001-8079-6149},
+Times-Cited = {20},
+Journal-ISO = {Nucleic Acids Res.},
+Unique-ID = {WOS:000562474100063},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000572064100018,
+Author = {Blow, Frances and Ankrah, Nana Y. D. and Clark, Noah and Koo, Imhoi and
+ Allman, Erik L. and Liu, Qing and Anitha, Mallappa and Patterson, Andrew
+ D. and Douglas, Angela E.},
+Title = {Impact of Facultative Bacteria on the Metabolic Function of an Obligate
+ Insect-Bacterial Symbiosis},
+Journal = {MBIO},
+Year = {2020},
+Volume = {11},
+Number = {4},
+Month = {JUL-AUG},
+Type = {Article},
+DOI = {10.1128/mBio.00402-20},
+Article-Number = {e00402-20},
+ISSN = {2150-7511},
+Keywords = {Buchnera; Hamiltonella; histidine; metabolism; symbiosis},
+Keywords-Plus = {PEA APHID; ACYRTHOSIPHON-PISUM; HOST GENOTYPE; GUT; DETERMINANTS;
+ MICROBIOTA; IMMUNITY; COSTS; ENDOSYMBIONTS; REQUIREMENTS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Koo, Imhoi/E-5759-2011
+ Patterson, Andrew/ABF-1575-2020
+ Ankrah, Nana/IUO-8239-2023
+ },
+ORCID-Numbers = {Koo, Imhoi/0000-0002-5816-0627
+ Patterson, Andrew/0000-0003-2073-0070
+ Allman, Erik/0000-0002-6560-0889
+ Blow, Frances/0000-0003-3064-5160
+ Ankrah, Nana Yaw/0000-0003-0492-545X},
+Times-Cited = {7},
+Journal-ISO = {mBio},
+Unique-ID = {WOS:000572064100018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000546994200048,
+Author = {Fallahi, Shirin and Skaug, Hans J. and Alendal, Guttorm},
+Title = {A comparison of Monte Carlo sampling methods for metabolic network
+ models},
+Journal = {PLOS ONE},
+Year = {2020},
+Volume = {15},
+Number = {7},
+Month = {JUL 1},
+Type = {Article},
+DOI = {10.1371/journal.pone.0235393},
+Article-Number = {e0235393},
+ISSN = {1932-6203},
+Keywords-Plus = {HIT-AND-RUN; CONVERGENCE; VOLUME},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {17},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000546994200048},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000576139100010,
+Author = {Hoksza, David and Gawron, Piotr and Ostaszewski, Marek and Hasenauer,
+ Jan and Schneider, Reinhard},
+Title = {Closing the gap between formats for storing layout information in
+ systems biology},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2020},
+Volume = {21},
+Number = {4},
+Pages = {1249-1260},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1093/bib/bbz067},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {network layout; molecular network; data format; systems biology;
+ conversion},
+Keywords-Plus = {MODELS; CYTOSCAPE; PATHWAYS; KEGG},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Schneider, Reinhard/C-5441-2009
+ Hoksza, David/Q-6069-2016
+ Hasenauer, Jan/B-8853-2013},
+ORCID-Numbers = {Schneider, Reinhard/0000-0002-8278-1618
+ Hoksza, David/0000-0003-4679-0557
+ Hasenauer, Jan/0000-0002-4935-3312},
+Times-Cited = {12},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000576139100010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000557191000001,
+Author = {Kulyashov, Mikhail and Peltek, Sergey E. and Akberdin, Ilya R.},
+Title = {A Genome-Scale Metabolic Model of 2,3-Butanediol Production by
+ Thermophilic BacteriaGeobacillus icigianus},
+Journal = {MICROORGANISMS},
+Year = {2020},
+Volume = {8},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.3390/microorganisms8071002},
+Article-Number = {1002},
+EISSN = {2076-2607},
+Keywords = {genome-scale; metabolic model; 2; 3-butanediol; flux balance analysis;
+ Geobacillus icigianus},
+Keywords-Plus = {GEOBACILLUS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Akberdin, Ilya/J-3172-2018
+ },
+ORCID-Numbers = {Akberdin, Ilya/0000-0003-0010-8620
+ Kulyashov, Mikhail/0000-0002-4808-0922},
+Times-Cited = {6},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000557191000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000551338300004,
+Author = {Medley, J. Kyle and Hellerstein, Joseph and Sauro, Herbert M.},
+Title = {libsbmljs-Enabling web-based SBML tools},
+Journal = {BIOSYSTEMS},
+Year = {2020},
+Volume = {195},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2020.104150},
+Article-Number = {104150},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {SBML; Systems biology; Web},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ SIMULATION; LIBRARY; SYSTEMS; NETWORK},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+Times-Cited = {2},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000551338300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000545974100031,
+Author = {Rolletschek, Hardy and Schwender, Joerg and Koenig, Christina and
+ Chapman, Kent D. and Romsdahl, Trevor and Lorenz, Christin and Braun,
+ Hans-Peter and Denolf, Peter and Van Audenhove, Katrien and Munz,
+ Eberhard and Heinzel, Nicolas and Ortleb, Stefan and Rutten, Twan and
+ McCorkle, Sean and Borysyuk, Taras and Guendel, Andre and Shi, Hai and
+ Vander Auwermeulen, Michiel and Bourot, Stephane and Borisjuk, Ljudmilla},
+Title = {Cellular Plasticity in Response to Suppression of Storage Proteins in
+ the Brassica napus Embryo},
+Journal = {PLANT CELL},
+Year = {2020},
+Volume = {32},
+Number = {7},
+Pages = {2383-2401},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1105/tpc.19.00879},
+ISSN = {1040-4651},
+EISSN = {1531-298X},
+Keywords-Plus = {ENDOPLASMIC-RETICULUM; OILSEED RAPE; CENTRAL METABOLISM; LIPID DROPLETS;
+ OIL CONTENT; EXPRESSION; OLEOSINS; BODIES; GENE; SEEDS},
+Research-Areas = {Biochemistry \& Molecular Biology; Plant Sciences; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Plant Sciences; Cell Biology},
+ResearcherID-Numbers = {Schwender, Jorg/P-2282-2014
+ Braun, Hans-Peter/E-7149-2011
+ },
+ORCID-Numbers = {Schwender, Jorg/0000-0003-1350-4171
+ McCorkle, Sean/0000-0003-1126-4071
+ Braun, Hans-Peter/0000-0002-4459-9727
+ Munz, Eberhard/0000-0002-4994-3304
+ Chapman, Kent/0000-0003-0489-3072
+ Romsdahl, Trevor/0000-0001-9075-9771
+ Kiel, Christina/0000-0001-5461-4962
+ Gundel, Andre/0000-0003-1055-7577
+ rolletschek, hardy/0000-0002-8619-1391
+ Denolf, Peter/0000-0003-4567-2700},
+Times-Cited = {17},
+Journal-ISO = {Plant Cell},
+Unique-ID = {WOS:000545974100031},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000535710400014,
+Author = {Yeo, Hock Chuan and Hong, Jongkwang and Lakshmanan, Meiyappan and Lee,
+ Dong-Yup},
+Title = {Enzyme capacity-based genome scale modelling of CHO cells},
+Journal = {METABOLIC ENGINEERING},
+Year = {2020},
+Volume = {60},
+Pages = {138-147},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2020.04.005},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {CHO cells; Constraints-based flux analysis; Enzyme capacity; Overflow
+ metabolism; Genome-scale metabolic model; Digital twins; Advanced
+ biomanufacturing},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; LACTATE-DEHYDROGENASE; GLOBAL RECONSTRUCTION;
+ METABOLISM; SEQUENCE; CYCLE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/ABC-7628-2020
+ },
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Yeo, Hock Chuan/0000-0001-5176-8800},
+Times-Cited = {36},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000535710400014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000545968000013,
+Author = {Antonaros, Francesca and Ghini, Veronica and Pulina, Francesca and
+ Ramacieri, Giuseppe and Cicchini, Elena and Mannini, Elisa and Martelli,
+ Anna and Feliciello, Agnese and Lanfranchi, Silvia and Onnivello, Sara
+ and Vianello, Renzo and Locatelli, Chiara and Cocchi, Guido and Pelleri,
+ Maria Chiara and Vitale, Lorenza and Strippoli, Pierluigi and Luchinat,
+ Claudio and Turano, Paola and Piovesan, Allison and Caracausi, Maria},
+Title = {Plasma metabolome and cognitive skills in Down syndrome},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {JUN 26},
+Type = {Article},
+DOI = {10.1038/s41598-020-67195-z},
+Article-Number = {10491},
+ISSN = {2045-2322},
+Keywords-Plus = {BEHAVIORAL-PHENOTYPE; NMR-SPECTROSCOPY; CHILDREN; INDIVIDUALS; BRAIN;
+ ABILITY; SAMPLE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {PIOVESAN, Allison/M-6783-2019
+ Onnivello, Sara/AAF-5972-2021
+ },
+ORCID-Numbers = {PIOVESAN, Allison/0000-0001-7038-5557
+ Onnivello, Sara/0000-0002-6565-7500
+ GHINI, VERONICA/0000-0003-3759-6701
+ CARACAUSI, MARIA/0000-0001-8957-8391
+ LANFRANCHI, SILVIA/0000-0003-2470-6019},
+Times-Cited = {16},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000545968000013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000542107600001,
+Author = {Tas, Huseyin and Amara, Adam and Cueva, Miguel E. and Bongaerts, Nadine
+ and Calvo-Villamanan, Alicia and Hamadache, Samir and Vavitsas,
+ Konstantinos},
+Title = {The synthetic microbiology caucus: are synthetic biology standards
+ applicable in everyday research practice?},
+Journal = {MICROBIAL BIOTECHNOLOGY},
+Year = {2020},
+Volume = {13},
+Number = {5},
+Pages = {1304-1308},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1111/1751-7915.13612},
+EarlyAccessDate = {JUN 2020},
+ISSN = {1751-7915},
+Keywords-Plus = {PLATFORM; DESIGN; MODELS; TOOL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {TAS, HUSEYIN/AHA-5112-2022
+ Vavitsas, Konstantinos/A-5871-2015
+ },
+ORCID-Numbers = {TAS, HUSEYIN/0000-0003-4804-2237
+ Bongaerts, Nadine/0000-0002-6517-4744
+ Cueva, Miguel/0000-0002-4921-7898
+ Amara, Adam/0000-0003-0489-0533
+ Vavitsas, Konstantinos/0000-0002-6828-1000
+ Calvo-Villamanan, Alicia/0000-0001-7033-2834},
+Times-Cited = {8},
+Journal-ISO = {Microb. Biotechnol.},
+Unique-ID = {WOS:000542107600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000540209000001,
+Author = {Hussan, Jagir R. and Hunter, Peter J.},
+Title = {Our natural ``makeup{''} reveals more than it hides: Modeling the skin
+ and its microbiome},
+Journal = {WIRES MECHANISMS OF DISEASE},
+Year = {2021},
+Volume = {13},
+Number = {1},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1002/wsbm.1497},
+EarlyAccessDate = {JUN 2020},
+Article-Number = {e1497},
+ISSN = {2692-9368},
+Keywords = {atopic diseases; skin microbiome; skin resident neuroendocrine system;
+ skin resident immune system; systems biology},
+Keywords-Plus = {VOLATILE ORGANIC-COMPOUNDS; SYSTEMS BIOLOGY APPROACH; T-CELL METABOLISM;
+ STAPHYLOCOCCUS-EPIDERMIDIS; PROPIONIBACTERIUM-ACNES; HOST COMMUNICATION;
+ BIOFILM FORMATION; DIVERSITY; COMMENSAL; GROWTH},
+Research-Areas = {Research \& Experimental Medicine},
+Web-of-Science-Categories = {Medicine, Research \& Experimental},
+ORCID-Numbers = {Razak Jainulabdeen, Jagir Hussan/0000-0002-8333-7869
+ Hunter, Peter/0000-0001-9665-4145},
+Times-Cited = {3},
+Journal-ISO = {WIREs Mech. Dis.},
+Unique-ID = {WOS:000540209000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000543881300001,
+Author = {Popp, Denny and Centler, Florian},
+Title = {μBialSim: Constraint-Based Dynamic Simulation of Complex Microbiomes},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2020},
+Volume = {8},
+Month = {JUN 10},
+Type = {Article},
+DOI = {10.3389/fbioe.2020.00574},
+Article-Number = {574},
+ISSN = {2296-4185},
+Keywords = {microbial communities; metabolic modeling; constraint-based modeling;
+ cross-feeding; microbiome dynamics},
+Keywords-Plus = {ANAEROBIC-DIGESTION; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Centler, Florian/AAU-9111-2020},
+Times-Cited = {24},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000543881300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000541566600002,
+Author = {Baldini, Federico and Hertel, Johannes and Sandt, Estelle and Thinnes,
+ Cyrille C. and Neuberger-Castillo, Lorieza and Pavelka, Lukas and
+ Betsou, Fay and Krueger, Rejko and Thiele, Ines and NCER-PD Consortium},
+Title = {Parkinson's disease-associated alterations of the gut microbiome predict
+ disease-relevant changes in metabolic functions},
+Journal = {BMC BIOLOGY},
+Year = {2020},
+Volume = {18},
+Number = {1},
+Month = {JUN 9},
+Type = {Article},
+DOI = {10.1186/s12915-020-00775-7},
+Article-Number = {62},
+EISSN = {1741-7007},
+Keywords = {Parkinson's disease; Gut microbiome; Computational modelling; Metabolic
+ modelling; Transsulfuration pathway},
+Keywords-Plus = {RIBOSOMAL-RNA GENE; SYSTEMS BIOLOGY; MOUSE; MUTATIONS; BEHAVIOR; MODEL;
+ DIET; RISK},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Gasser, Thomas/JAC-6600-2023
+ Betsou, Fay/ABI-7827-2020
+ May, Patrick/N-1019-2019
+ Thiele, Ines/ABE-5765-2020
+ Glaab, Enrico/A-9136-2012
+ Maetzler, Walter/AAE-5831-2020
+ Gasser, Thomas/GNH-5293-2022
+ Thiele, Ines/A-7629-2014
+ Aguayo, Gloria/W-2580-2019
+ Hertel, Johannes/HZJ-3685-2023
+ },
+ORCID-Numbers = {Gasser, Thomas/0000-0002-1069-1146
+ Betsou, Fay/0000-0002-0558-4653
+ May, Patrick/0000-0001-8698-3770
+ Glaab, Enrico/0000-0003-3977-7469
+ Maetzler, Walter/0000-0002-5945-4694
+ Gasser, Thomas/0000-0002-1069-1146
+ Thiele, Ines/0000-0002-8071-7110
+ Aguayo, Gloria/0000-0002-5625-1664
+ Hertel, Johannes/0000-0002-7641-0132
+ GROUES, Valentin/0000-0001-6501-0806
+ Geffers, Lars/0000-0001-6800-4305
+ Kutzera, Joachim/0000-0003-2527-7893
+ Balling, Rudi/0000-0003-2902-5650
+ Krueger, Rejko/0000-0003-4258-6241
+ Nehrbass, Ulf/0000-0002-7028-8076
+ Diederich, Nico/0000-0001-8537-8595
+ LARUE, Catherine/0000-0002-5803-4671
+ Bobbili, Dheeraj/0000-0002-1368-9623
+ Hanff, Anne-Marie/0000-0002-8955-8697
+ Ostaszewski, Marek/0000-0003-1473-370X
+ GANTENBEIN, Manon/0000-0002-5178-4365
+ Hu, Michele/0000-0001-6382-5841
+ Hiller, Karsten/0000-0001-9322-5820
+ Pavelka, Lukas/0000-0002-7721-3317
+ Meisch, Francoise/0009-0007-7656-8734
+ Perquin, Magali/0000-0002-0386-0212
+ Goncharenko, Nikolai/0000-0002-9873-1885
+ Satagopam, Venkata/0000-0002-6532-5880
+ Mittelbronn, Michel/0000-0002-2998-052X
+ Grunewald, Anne/0000-0002-4179-2994},
+Times-Cited = {101},
+Journal-ISO = {BMC Biol.},
+Unique-ID = {WOS:000541566600002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000545680000019,
+Author = {Bintener, Tamara and Pacheco, Maria Pires and Sauter, Thomas},
+Title = {Towards the routine use of in silico screenings for drug
+ discovery using metabolic modelling},
+Journal = {BIOCHEMICAL SOCIETY TRANSACTIONS},
+Year = {2020},
+Volume = {48},
+Number = {3},
+Pages = {955-969},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1042/BST20190867},
+ISSN = {0300-5127},
+EISSN = {1470-8752},
+Keywords-Plus = {CONSENSUS MOLECULAR SUBTYPES; LARGE-SCALE; HEPATOCELLULAR-CARCINOMA;
+ GLOBAL RECONSTRUCTION; SYNTHETIC LETHALITY; CANCER; GENE; DATABASE;
+ IDENTIFICATION; SENSITIVITY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Pacheco, Maria Pires/C-4494-2014
+ },
+ORCID-Numbers = {Pacheco, Maria Pires/0000-0001-7956-8093
+ Sauter, Thomas/0000-0001-8225-2954},
+Times-Cited = {11},
+Journal-ISO = {Biochem. Soc. Trans.},
+Unique-ID = {WOS:000545680000019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000554612000001,
+Author = {Chanda, Pritam and Costa, Eduardo and Hu, Jie and Sukumar, Shravan and
+ Van Hemert, John and Walia, Rasna},
+Title = {Information Theory in Computational Biology: Where We Stand Today},
+Journal = {ENTROPY},
+Year = {2020},
+Volume = {22},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3390/e22060627},
+Article-Number = {627},
+EISSN = {1099-4300},
+Keywords = {information theory; entropy; computational biology; gene expression;
+ transcriptomics; sequence comparison; error correction; disease-gene
+ association mapping; metabolic networks; metabolomics; protein
+ structure; interaction analysis},
+Keywords-Plus = {PROTEIN-PROTEIN INTERACTIONS; INDEPENDENT COMPONENT ANALYSIS;
+ MAXIMUM-ENTROPY PRODUCTION; CELL FATE DECISIONS; GENE-GENE; GRAPHICAL
+ REPRESENTATION; INTERACTION NETWORKS; MUTUAL INFORMATION; COEVOLUTION;
+ SEQUENCE},
+Research-Areas = {Physics},
+Web-of-Science-Categories = {Physics, Multidisciplinary},
+ResearcherID-Numbers = {Sukumar, Shravan/AFK-3018-2022
+ Costa, Eduardo/K-9876-2013
+ },
+ORCID-Numbers = {Costa, Eduardo/0000-0003-1411-5338
+ Chanda, Pritam/0000-0001-9776-3378
+ Walia, Rasna/0000-0001-7088-5535},
+Times-Cited = {19},
+Journal-ISO = {Entropy},
+Unique-ID = {WOS:000554612000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000545680000015,
+Author = {Frioux, Clemence and Dittami, Simon M. and Siegel, Anne},
+Title = {Using automated reasoning to explore the metabolism of unconventional
+ organisms: a first step to explore host-microbial interactions},
+Journal = {BIOCHEMICAL SOCIETY TRANSACTIONS},
+Year = {2020},
+Volume = {48},
+Number = {3},
+Pages = {901-913},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1042/BST20190667},
+ISSN = {0300-5127},
+EISSN = {1470-8752},
+Keywords-Plus = {HUMAN GUT MICROBIOME; SYSTEMS BIOLOGY; MODEL-ORGANISM; GENOME; NETWORK;
+ BALANCE; RECONSTRUCTION; COMMUNITIES; ANNOTATION; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Frioux, Clémence/A-1517-2019
+ Dittami, Simon M/E-8354-2011
+ },
+ORCID-Numbers = {Frioux, Clémence/0000-0003-2114-0697
+ Dittami, Simon M/0000-0001-7987-7523
+ Siegel, Anne/0000-0001-6542-1568},
+Times-Cited = {3},
+Journal-ISO = {Biochem. Soc. Trans.},
+Unique-ID = {WOS:000545680000015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000550117300026,
+Author = {Jiang, Shouyong and Wang, Yong and Kaiser, Marcus and Krasnogor, Natalio},
+Title = {NIHBA: a network interdiction approach for metabolic engineering design},
+Journal = {BIOINFORMATICS},
+Year = {2020},
+Volume = {36},
+Number = {11},
+Pages = {3482-3492},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btaa163},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {ACCELERATING BENDERS DECOMPOSITION; ESCHERICHIA-COLI; KNOCKOUT
+ STRATEGIES; CHEMICAL PRODUCTION; OPTIMIZATION; FRAMEWORK; OPTIMALITY},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Kaiser, Marcus/AAG-3051-2020
+ Kaiser, Marcus/A-7166-2008
+ },
+ORCID-Numbers = {Kaiser, Marcus/0000-0002-4654-3110
+ Jiang, Shouyong/0000-0001-5099-2093},
+Times-Cited = {6},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000550117300026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000558077600006,
+Author = {Lopez-Agudelo, Victor A. and Mendum, Tom A. and Laing, Emma and Wu,
+ HuiHai and Baena, Andres and Barrera, Luis F. and Beste, Dany J. V. and
+ Rios-Estepa, Rigoberto},
+Title = {A systematic evaluation of Mycobacterium tuberculosis
+ Genome-Scale Metabolic Networks},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2020},
+Volume = {16},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1007533},
+Article-Number = {e1007533},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {ESSENTIAL GENES; ESSENTIALITY; REVEALS; BALANCE; MODELS; ENVIRONMENT;
+ SURVIVAL; PATHWAY; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Baena, Armando/GQA-7105-2022
+ },
+ORCID-Numbers = {Baena, Armando/0000-0001-8717-6911
+ Lopez-Agudelo, Victor A./0000-0003-1339-972X
+ Baena, Andres/0000-0003-1309-1020
+ Beste, Dany/0000-0001-6579-1366
+ Rios-Estepa, Rigoberto/0000-0002-3287-7056
+ Barrera, Luis/0000-0002-6108-6747},
+Times-Cited = {12},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000558077600006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000540594500006,
+Author = {Nochino, Naoya and Toya, Yoshihiro and Shimizu, Hiroshi},
+Title = {Transcription Factor ArcA is a Flux Sensor for the Oxygen Consumption
+ Rate in Escherichia coli},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2020},
+Volume = {15},
+Number = {6, SI},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/biot.201900353},
+Article-Number = {1900353},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {ArcA; continuous culture; Escherichia coli; oxygen consumption rate;
+ transcription factor},
+Keywords-Plus = {METABOLIC-REGULATION; GENE; FNR; AVAILABILITY; AERATION; GLUCOSE;
+ PROTEIN; IMPACT; CRA},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Shimizu, Hiroshi/C-3688-2017},
+ORCID-Numbers = {Shimizu, Hiroshi/0000-0002-8986-0861},
+Times-Cited = {5},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000540594500006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000554600700001,
+Author = {Souto, Eliana B. and Sanchez-Lopez, Elena and Campos, Joana R. and da
+ Ana, Raquel and Espina, Marta and Garcia, Maria L. and Severino,
+ Patricia and Batain, Fernando and F. R. Alves, Thais and Crescencio,
+ Kessi M. M. and Souto, Selma B. and V. Chaud, Marco},
+Title = {Retinal Drug Delivery: Rethinking Outcomes for the Efficient Replication
+ of Retinal Behavior},
+Journal = {APPLIED SCIENCES-BASEL},
+Year = {2020},
+Volume = {10},
+Number = {12},
+Month = {JUN},
+Type = {Review},
+DOI = {10.3390/app10124258},
+Article-Number = {4258},
+EISSN = {2076-3417},
+Keywords = {retina; drug delivery; retinal behavior; neuroscience; computational
+ models; mathematical models},
+Keywords-Plus = {NANOSTRUCTURED LIPID CARRIERS; ENDOTHELIAL GROWTH-FACTOR;
+ ELECTRICAL-STIMULATION; GANGLION-CELLS; PHARMACOKINETIC MODEL; VASCULAR
+ DEVELOPMENT; IN-VITRO; PIGMENT EPITHELIUM; WILD-TYPE; VEGF},
+Research-Areas = {Chemistry; Engineering; Materials Science; Physics},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary; Engineering, Multidisciplinary; Materials
+ Science, Multidisciplinary; Physics, Applied},
+ResearcherID-Numbers = {Crescencio, Kessi M. M./L-4324-2018
+ Souto, Eliana/GQZ-3071-2022
+ Chaud, Marco Vinícius/ABC-4387-2021
+ Batain, Fernando/L-1097-2018
+ Alves, Thais Francine Ribeiro/X-5714-2019
+ López, Elena Sánchez/O-7645-2018
+ Souto, Eliana/T-1645-2019
+ Espina, Marta/M-9964-2014
+ Campos, Joana/HLX-3337-2023
+ Souto, Selma/O-5539-2014
+ Batain, Fernando/AAW-8841-2020
+ },
+ORCID-Numbers = {Crescencio, Kessi M. M./0000-0001-8685-1946
+ Chaud, Marco Vinícius/0000-0003-3618-8415
+ Batain, Fernando/0000-0003-1822-0944
+ Alves, Thais Francine Ribeiro/0000-0002-3586-9457
+ López, Elena Sánchez/0000-0003-2571-108X
+ Souto, Eliana/0000-0002-9737-6017
+ Espina, Marta/0000-0003-1269-3847
+ Souto, Selma/0000-0001-5664-8621
+ Batain, Fernando/0000-0003-1822-0944
+ Campos, Joana/0000-0001-9245-949X
+ Souto, Selma B/0000-0002-6404-8818
+ Severino, Patricia/0000-0001-6527-6612},
+Times-Cited = {3},
+Journal-ISO = {Appl. Sci.-Basel},
+Unique-ID = {WOS:000554600700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000525757000026,
+Author = {Verma, Rashi and Pradhan, Dibyabhaba and Maseet, Mohsin and Singh,
+ Harpreet and Jain, Arun Kumar and Khan, Luqman Ahmad},
+Title = {Genome-wide screening and in silico gene knockout to predict
+ potential candidates for drug designing against Candida albicans},
+Journal = {INFECTION GENETICS AND EVOLUTION},
+Year = {2020},
+Volume = {80},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1016/j.meegid.2020.104196},
+Article-Number = {104196},
+ISSN = {1567-1348},
+EISSN = {1567-7257},
+Keywords = {Protein-protein interaction; FAS2; FOL1; ERG5; Candidiasis; In Silico
+ gene knockout},
+Keywords-Plus = {FLUCONAZOLE RESISTANCE; MOLECULAR EVOLUTION; PROTEIN; IDENTIFICATION;
+ VIRULENCE; TARGET; METABOLISM; INFECTION; KINASE; MODEL},
+Research-Areas = {Infectious Diseases},
+Web-of-Science-Categories = {Infectious Diseases},
+ResearcherID-Numbers = {Verma, Rashi/GQA-9121-2022
+ Pradhan, Dibyabhaba/AFO-4655-2022
+ },
+ORCID-Numbers = {Verma, Rashi/0000-0002-2989-4162
+ Pradhan, Dibyabhaba/0000-0002-2459-5032
+ Kumar, Shashi Nandar/0000-0002-3612-6022
+ Khan, Luqman/0000-0003-0659-4607
+ JAIN, ARUN KUMAR/0000-0001-8325-2892},
+Times-Cited = {6},
+Journal-ISO = {Infect. Genet. Evol.},
+Unique-ID = {WOS:000525757000026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000540471500007,
+Author = {Garcia-Romero, Inmaculada and Nogales, Juan and Diaz, Eduardo and
+ Santero, Eduardo and Floriano, Belen},
+Title = {Understanding the metabolism of the tetralin degrader Sphingopyxis
+ granuli strain TFA through genome-scale metabolic modelling},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {MAY 26},
+Type = {Article},
+DOI = {10.1038/s41598-020-65258-9},
+Article-Number = {8651},
+ISSN = {2045-2322},
+Keywords-Plus = {COENZYME-A COA; ESCHERICHIA-COLI; RECONSTRUCTION; BIODEGRADATION;
+ DEGRADATION; NETWORK; SIMULATION; EXPRESSION; RESOURCE; PLATFORM},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ Diaz, Eduardo/F-8605-2016
+ Floriano, Belen/K-7644-2014
+ Santero, Eduardo/K-6510-2014
+ },
+ORCID-Numbers = {Diaz, Eduardo/0000-0002-9731-6524
+ Floriano, Belen/0000-0002-5326-7601
+ Nogales, Juan/0000-0002-4961-0833
+ Garcia Romero, Inmaculada/0000-0002-8939-3271},
+Times-Cited = {0},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000540471500007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000540472300015,
+Author = {Karimian, Emadoddin and Motamedian, Ehsan},
+Title = {ACBM: An Integrated Agent and Constraint Based Modeling Framework for
+ Simulation of Microbial Communities},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {MAY 26},
+Type = {Article},
+DOI = {10.1038/s41598-020-65659-w},
+Article-Number = {8695},
+ISSN = {2045-2322},
+Keywords-Plus = {OUTER-MEMBRANE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Motamedian, Ehsan/GPK-8344-2022
+ },
+ORCID-Numbers = {, Ehsan/0000-0001-8750-2879},
+Times-Cited = {14},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000540472300015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000537134500021,
+Author = {diCenzo, George C. and Tesi, Michelangelo and Pfau, Thomas and Mengoni,
+ Alessio and Fondi, Marco},
+Title = {Genome-scale metabolic reconstruction of the symbiosis between a
+ leguminous plant and a nitrogen-fixing bacterium},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {MAY 22},
+Type = {Article},
+DOI = {10.1038/s41467-020-16484-2},
+ISSN = {2041-1723},
+Keywords-Plus = {SINORHIZOBIUM-MELILOTI; RHIZOBIUM-MELILOTI; ROOT-NODULES; TRANSPORT
+ MUTANTS; MALIC ENZYME; FIXATION; BACTEROIDS; EVOLUTION; ALFALFA; ALANINE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {diCenzo, George C C/M-1876-2017
+ Mengoni, Alessio/G-5336-2013
+ },
+ORCID-Numbers = {diCenzo, George C C/0000-0003-3889-6570
+ Mengoni, Alessio/0000-0002-1265-8251
+ Pfau, Thomas/0000-0001-5048-2923
+ Fondi, Marco/0000-0001-9291-5467},
+Times-Cited = {37},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000537134500021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000533078600001,
+Author = {Tibocha-Bonilla, Juan D. and Kumar, Manish and Richelle, Anne and
+ Godoy-Silva, Ruben D. and Zengler, Karsten and Zuniga, Cristal},
+Title = {Dynamic resource allocation drives growth under nitrogen starvation in
+ eukaryotes},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2020},
+Volume = {6},
+Number = {1},
+Month = {MAY 15},
+Type = {Article},
+DOI = {10.1038/s41540-020-0135-y},
+Article-Number = {14},
+EISSN = {2056-7189},
+Keywords-Plus = {DIATOM PHAEODACTYLUM-TRICORNUTUM; CHEMICAL-COMPOSITION; METABOLISM;
+ COORDINATION; PROTEOME; MODELS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zuniga, Cristal/CAA-0015-2022
+ Kumar, Manish/ABE-8494-2020
+ },
+ORCID-Numbers = {Kumar, Manish/0000-0001-8035-3399
+ Zuniga, Cristal/0000-0002-0135-7429},
+Times-Cited = {14},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000533078600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000536569900008,
+Author = {Tong, Hao and Kueken, Anika and Nikoloski, Zoran},
+Title = {Integrating molecular markers into metabolic models improves genomic
+ selection for Arabidopsis growth},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {MAY 15},
+Type = {Article},
+DOI = {10.1038/s41467-020-16279-5},
+Article-Number = {2410},
+ISSN = {2041-1723},
+Keywords-Plus = {MAIZE LEAF; PREDICTION; THALIANA; REGRESSION; IMPACT; STARCH; CARBON;
+ RICE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Tong, Hao/ABO-6024-2022
+ Tong, Hao/AAZ-9514-2020
+ },
+ORCID-Numbers = {Tong, Hao/0000-0003-4856-1336
+ Tong, Hao/0000-0003-4856-1336
+ Nikoloski, Zoran/0000-0003-2671-6763
+ Kuken, Anika/0000-0003-1367-0719},
+Times-Cited = {22},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000536569900008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000560353500007,
+Author = {Nouri, Hoda and Fouladiha, Hamideh and Moghimi, Hamid and Marashi,
+ Sayed-Amir},
+Title = {A reconciliation of genome-scale metabolic network model of Zymomonas
+ mobilis ZM4},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {MAY 8},
+Type = {Article},
+DOI = {10.1038/s41598-020-64721-x},
+Article-Number = {7782},
+ISSN = {2045-2322},
+Keywords-Plus = {PATHWAY; GROWTH; GENE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008
+ Moghimi, Hamid/HNS-9811-2023},
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Moghimi, Hamid/0000-0002-9454-7474},
+Times-Cited = {8},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000560353500007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000539315800006,
+Author = {Ahmad, Ahmad and Pathania, Ruchi and Srivastava, Shireesh},
+Title = {Biochemical Characteristics and a Genome-Scale Metabolic Model of an
+ Indian Euryhaline Cyanobacterium with High Polyglucan Content},
+Journal = {METABOLITES},
+Year = {2020},
+Volume = {10},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/metabo10050177},
+Article-Number = {177},
+EISSN = {2218-1989},
+Keywords = {feedstock; biomass; marine; photosynthetic; polyglucans; fast growth},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; PCC 7002; NETWORK; GROWTH; RECONSTRUCTION;
+ PREDICTION; GENES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Srivastava, Shireesh/JDC-9742-2023
+ },
+ORCID-Numbers = {Srivastava, Shireesh/0000-0001-6139-1904
+ pathania, ruchi/0000-0002-4807-2930},
+Times-Cited = {7},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000539315800006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000539340200212,
+Author = {Andrighetti, Tahila and Bohar, Balazs and Lemke, Ney and Sudhakar,
+ Padhmanand and Korcsmaros, Tamas},
+Title = {MicrobioLink: An Integrated Computational Pipeline to Infer Functional
+ Effects of Microbiome-Host Interactions},
+Journal = {CELLS},
+Year = {2020},
+Volume = {9},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/cells9051278},
+EISSN = {2073-4409},
+Keywords = {microbiota-host interactions; protein-protein interactions; systems
+ biology; networks; network diffusion; computational pipeline},
+Keywords-Plus = {AUTOPHAGY; DATABASE; DISEASE; NETWORKS; RESOURCE; BIOINFORMATICS;
+ DYSBIOSIS; BACTERIA; BIOLOGY; CANCER},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Lemke, Ney/L-6761-2019
+ Korcsmaros, Tamas/C-3526-2015
+ },
+ORCID-Numbers = {Lemke, Ney/0000-0001-7463-4303
+ Korcsmaros, Tamas/0000-0003-1717-996X
+ Andrighetti, Tahila/0000-0003-3402-8338
+ Sudhakar, Padhmanand/0000-0003-1907-4491},
+Times-Cited = {21},
+Journal-ISO = {Cells},
+Unique-ID = {WOS:000539340200212},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000539568900021,
+Author = {Bodor, Zsolt and Fazakas, Andrea (Iuhasz) and Bodor, Katalin and Kovacs,
+ Erika and Miklossy, Ildiko and Albert, Beata},
+Title = {Using genome-scale model to predict the metabolic engineering impact on
+ Escherichia coli metabolism during succinic acid production optimization},
+Journal = {ROMANIAN BIOTECHNOLOGICAL LETTERS},
+Year = {2020},
+Volume = {25},
+Number = {3},
+Pages = {1666-1676},
+Month = {MAY-JUN},
+Type = {Article},
+DOI = {10.25083/rbl/25.3/1666.1676},
+ISSN = {1224-5984},
+Keywords = {In silico; Escherichia coli; succinic acid; metabolic engineering;
+ glucose; glycerol},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; IN-SILICO; EASTERN CARPATHIANS; SYSTEMS
+ BIOLOGY; ATMOSPHERIC CIRCULATIONS; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; CHEMICAL PRODUCTION; ADAPTIVE EVOLUTION; CIUC BASIN},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Bodor, Zsolt/ABE-2182-2020
+ },
+ORCID-Numbers = {Bodor, Zsolt/0000-0003-1386-6957},
+Times-Cited = {0},
+Journal-ISO = {Rom. Biotech. Lett.},
+Unique-ID = {WOS:000539568900021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000539315800013,
+Author = {Geryk, Jan and Krsicka, Daniel and Vlckova, Marketa and Havlovicova,
+ Marketa and Macek, Jr., Milan and Pourova, Radka Kremlikova},
+Title = {The Key Role of Purine Metabolism in the Folate-Dependent Phenotype of
+ Autism Spectrum Disorders: An In Silico Analysis},
+Journal = {METABOLITES},
+Year = {2020},
+Volume = {10},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/metabo10050184},
+Article-Number = {184},
+EISSN = {2218-1989},
+Keywords = {autism; ASD; folate; blocked metabolite; purine; ADSL; GART; PFAS; PPAT;
+ PAICS; ATIC; cerebral folate deficiency; Flux Balance Analysis (FBA);
+ metabolic modeling},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; METHIONINE CYCLE; DEFICIENCY; RISK; CHILDREN;
+ MUTATION; ASSOCIATION; METHYLATION; PREVALENCE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Pourova, Radka Kremlikova/AAP-9530-2020
+ },
+ORCID-Numbers = {Krsicka, Daniel/0000-0001-7157-9716
+ Kremlikova Pourova, Radka/0000-0003-4308-1595},
+Times-Cited = {8},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000539315800013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000539315800027,
+Author = {Kuriya, Yuki and Araki, Michihiro},
+Title = {Dynamic Flux Balance Analysis to Evaluate the Strain Production
+ Performance on Shikimic Acid Production in Escherichia coli},
+Journal = {METABOLITES},
+Year = {2020},
+Volume = {10},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/metabo10050198},
+Article-Number = {198},
+EISSN = {2218-1989},
+Keywords = {genome-scale metabolic model; metabolic simulation; dynamic flux balance
+ analysis; data approximation},
+Keywords-Plus = {PARAMETERS; MODELS; BIOSYNTHESIS; FERMENTATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {13},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000539315800027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000538086300002,
+Author = {Thiele, Ines and Sahoo, Swagatika and Heinken, Almut and Hertel,
+ Johannes and Heirendt, Laurent and Aurich, Maike K. and Fleming, Ronan
+ M. T.},
+Title = {Personalized whole-body models integrate metabolism, physiology, and the
+ gut microbiome},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2020},
+Volume = {16},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.15252/msb.20198982},
+Article-Number = {e8982},
+ISSN = {1744-4292},
+Keywords = {flux balance analysis; human metabolism; metabolic modeling; microbiome},
+Keywords-Plus = {ENERGY-EXPENDITURE; ESCHERICHIA-COLI; CARBON NUTRITION; SYSTEMS BIOLOGY;
+ LIVER-DISEASE; ALCOHOL; CELLS; FLUX; CHOLESTEROL; INDIVIDUALS},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ Thiele, Ines/ABE-5765-2020
+ Hertel, Johannes/HZJ-3685-2023
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Hertel, Johannes/0000-0002-7641-0132
+ Heinken, Almut/0000-0001-6938-8072
+ Sahoo, Swagatika/0000-0003-3773-8597},
+Times-Cited = {80},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000538086300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000529580400002,
+Author = {Ankrah, Nana Y. D. and Wilkes, Rebecca A. and Zhang, Freya Q. and Zhu,
+ Dantong and Kaweesi, Tadeo and Aristilde, Ludmilla and Douglas, Angela
+ E.},
+Title = {Syntrophic splitting of central carbon metabolism in host cells bearing
+ functionally different symbiotic bacteria},
+Journal = {ISME JOURNAL},
+Year = {2020},
+Volume = {14},
+Number = {8},
+Pages = {1982-1993},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1038/s41396-020-0661-z},
+EarlyAccessDate = {APR 2020},
+ISSN = {1751-7362},
+EISSN = {1751-7370},
+Keywords-Plus = {INSECTS; PHYSIOLOGY; PATHWAYS; ANCIENT},
+Research-Areas = {Environmental Sciences \& Ecology; Microbiology},
+Web-of-Science-Categories = {Ecology; Microbiology},
+ResearcherID-Numbers = {Aristilde, Ludmilla/V-7611-2019
+ Ankrah, Nana/IUO-8239-2023
+ },
+ORCID-Numbers = {Aristilde, Ludmilla/0000-0002-8566-1486
+ Ankrah, Nana Yaw/0000-0003-0492-545X
+ Kaweesi, Tadeo/0000-0002-0577-6460},
+Times-Cited = {10},
+Journal-ISO = {ISME J.},
+Unique-ID = {WOS:000529580400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000558827500016,
+Author = {Yu, Rosemary and Campbell, Kate and Pereira, Rui and Bjorkeroth, Johan
+ and Qi, Qi and Vorontsov, Egor and Sihlbom, Carina and Nielsen, Jens},
+Title = {Nitrogen limitation reveals large reserves in metabolic and
+ translational capacities of yeast},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {APR 20},
+Type = {Article},
+DOI = {10.1038/s41467-020-15749-0},
+Article-Number = {1881},
+ISSN = {2041-1723},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; RIBOSOMAL-PROTEINS; ESCHERICHIA-COLI;
+ GROWTH-RATE; QUANTIFICATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Yu, Rosemary/0000-0001-9901-4055
+ Pereira, Rui/0000-0002-0572-875X
+ Nielsen, Jens/0000-0002-9955-6003
+ Campbell, Kate/0000-0002-4173-5260
+ QI, QI/0000-0002-0582-1962},
+Times-Cited = {34},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000558827500016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000537473400051,
+Author = {Keaty, Thomas C. and Jensen, Paul A.},
+Title = {GAPSPLIT: efficient random sampling for non-convex constraint-based
+ models},
+Journal = {BIOINFORMATICS},
+Year = {2020},
+Volume = {36},
+Number = {8},
+Pages = {2623-2625},
+Month = {APR 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btz971},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {HIT-AND-RUN; SPACE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+Times-Cited = {8},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000537473400051},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000537473400048,
+Author = {Schultz, Andre and Akbani, Rehan},
+Title = {SAMMI: a semi-automated tool for the visualization of metabolic networks},
+Journal = {BIOINFORMATICS},
+Year = {2020},
+Volume = {36},
+Number = {8},
+Pages = {2616-2617},
+Month = {APR 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btz927},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+Times-Cited = {3},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000537473400048},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000531187700006,
+Author = {Trilla-Fuertes, Lucia and Gamez-Pozo, Angelo and Lopez-Camacho, Elena
+ and Prado-Vazquez, Guillermo and Zapater-Moros, Andrea and Lopez-Vacas,
+ Rocio and Arevalillo, Jorge M. and Diaz-Almiron, Mariana and Navarro,
+ Hilario and Main, Paloma and Espinosa, Enrique and Zamora, Pilar and
+ Fresno Vara, Juan Angel},
+Title = {Computational models applied to metabolomics data hints at the relevance
+ of glutamine metabolism in breast cancer},
+Journal = {BMC CANCER},
+Year = {2020},
+Volume = {20},
+Number = {1},
+Month = {APR 15},
+Type = {Article},
+DOI = {10.1186/s12885-020-06764-x},
+EISSN = {1471-2407},
+Keywords = {Breast cancer; Metabolomics; Glutamine metabolism; Computational
+ analyses},
+Keywords-Plus = {FLUX; SUCCINATE; GROWTH; TISSUE; CELLS; WOMEN},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ResearcherID-Numbers = {Trilla, Lucia/AAG-8392-2019
+ Gamez, Angelo/HSG-7485-2023
+ Vara, Juan Ángel Fresno/Y-9928-2019
+ Zamora, Pilar/AAM-9336-2021
+ Prado-Vazquez, Guillermo/T-1861-2017
+ Gamez-Pozo, Angelo/N-2506-2014
+ },
+ORCID-Numbers = {Trilla, Lucia/0000-0002-4452-3474
+ Vara, Juan Ángel Fresno/0000-0003-1527-1252
+ Zamora, Pilar/0000-0003-2631-9653
+ Prado-Vazquez, Guillermo/0000-0003-2456-6191
+ Gamez-Pozo, Angelo/0000-0002-8931-0624
+ Espinosa Arranz, Enrique/0000-0001-6562-7902
+ Navarro, Hilario/0000-0001-5594-869X
+ Arevalillo, Jorge M/0000-0003-1944-3699},
+Times-Cited = {10},
+Journal-ISO = {BMC Cancer},
+Unique-ID = {WOS:000531187700006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000559946700010,
+Author = {Khodaee, Saeideh and Asgari, Yazdan and Totonchi, Mehdi and
+ Karimi-Jafari, Mohammad Hossein},
+Title = {iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {APR 10},
+Type = {Article},
+DOI = {10.1038/s41598-020-63235-w},
+Article-Number = {6177},
+ISSN = {2045-2322},
+Keywords-Plus = {EXPRESSION; PATHWAYS; KEGG; GS2},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {16},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000559946700010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000524972800020,
+Author = {Rohlenova, Katerina and Goveia, Jermaine and Garcia-Caballero, Melissa
+ and Subramanian, Abhishek and Kalucka, Joanna and Treps, Lucas and
+ Falkenberg, Kim D. and de Rooij, Laura P. M. H. and Zheng, Yingfeng and
+ Lin, Lin and Sokol, Liliana and Teuwen, Laure-Anne and Geldhof, Vincent
+ and Taverna, Federico and Pircher, Andreas and Conradi, Lena-Christin
+ and Khan, Shawez and Stegen, Steve and Panovska, Dena and De Smet,
+ Frederik and Staal, Frank J. T. and Mclaughlin, Rene J. and Vinckier,
+ Stefan and Van Bergen, Tine and Ectors, Nadine and De Haes, Patrik and
+ Wang, Jian and Bolund, Lars and Schoonjans, Luc and Karakach, Tobias K.
+ and Yang, Huanming and Carmeliet, Geert and Liu, Yizhi and Thienpont,
+ Bernard and Dewerchin, Mieke and Eelen, Guy and Li, Xuri and Luo,
+ Yonglun and Carmeliet, Peter},
+Title = {Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in
+ Pathological Angiogenesis},
+Journal = {CELL METABOLISM},
+Year = {2020},
+Volume = {31},
+Number = {4},
+Pages = {862+},
+Month = {APR 7},
+Type = {Article},
+DOI = {10.1016/j.cmet.2020.03.009},
+ISSN = {1550-4131},
+EISSN = {1932-7420},
+Keywords-Plus = {VON-WILLEBRAND-FACTOR; MATRIX GLA-PROTEIN; GENE-EXPRESSION;
+ MATRICELLULAR PROTEIN; MACULAR DEGENERATION; IDENTIFICATION; REVEALS;
+ CYCLE; RECONSTRUCTION; HETEROGENEITY},
+Research-Areas = {Cell Biology; Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Cell Biology; Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Pircher, Andreas/L-2150-2019
+ Thienpont, Bernard/AAG-5423-2019
+ De Smet, Frederik/Q-7808-2016
+ Rohlenova, Katerina/G-9498-2014
+ Li, Nan/IXD-8260-2023
+ Zheng, Yingfeng/CAE-9225-2022
+ de Rooij, Laura/GZH-0307-2022
+ Carmeliet, Peter/AAQ-5140-2020
+ He, Chen/JLM-5059-2023
+ Zheng, Yingfeng/CAH-4522-2022
+ Liu, Shao/JFK-0166-2023
+ Li, Fan/JRY-4017-2023
+ TREPS, Lucas/AAF-2499-2020
+ Zhang, Yiyang/HZI-3668-2023
+ wu, jun/ISB-8607-2023
+ liu, yi/GXE-9662-2022
+ JIN, LIYING/JFB-1980-2023
+ Subramanian, Abhishek/AAN-1302-2020
+ Teuwen, Laure-Anne/GLU-2175-2022
+ Zheng, Yingfeng/AAE-2983-2022
+ Luo, Yonglun/C-4708-2013
+ Garcia-Caballero, Melissa/A-6978-2018
+ Yang, Huanming/C-6513-2013},
+ORCID-Numbers = {Pircher, Andreas/0000-0002-7747-3012
+ De Smet, Frederik/0000-0002-6669-3335
+ Rohlenova, Katerina/0000-0003-3964-8472
+ Zheng, Yingfeng/0000-0002-0914-7864
+ de Rooij, Laura/0000-0002-1810-4620
+ Carmeliet, Peter/0000-0001-7961-1821
+ Zheng, Yingfeng/0000-0002-0914-7864
+ TREPS, Lucas/0000-0003-0735-9000
+ Subramanian, Abhishek/0000-0002-4601-5991
+ Staal, Frank/0000-0003-1588-8519
+ Stegen, Steve/0000-0002-4471-6401
+ Sokol, Liliana/0000-0001-9032-8971
+ Panovska, Dena/0000-0003-0906-3860
+ Thienpont, Bernard/0000-0002-8772-6845
+ Vinckier, Stefan/0009-0000-8301-5395
+ Luo, Yonglun/0000-0002-0007-7759
+ Karakach, Tobias/0000-0003-2460-3781
+ Khan, Shawez/0000-0003-1682-4824
+ Kalucka, Joanna/0000-0003-4887-7672
+ Teuwen, Laure-Anne/0000-0003-1690-8198
+ Garcia-Caballero, Melissa/0000-0002-4263-5536
+ Yang, Huanming/0000-0002-0858-3410},
+Times-Cited = {127},
+Journal-ISO = {Cell Metab.},
+Unique-ID = {WOS:000524972800020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000524577800001,
+Author = {Sundararaghavan, Archanaa and Mukherjee, Amitava and Sahoo, Swagatika
+ and Suraishkumar, G. K.},
+Title = {Mechanism of the oxidative stress-mediated increase in lipid
+ accumulation by the bacterium, R. opacus PD630: Experimental
+ analysis and genome-scale metabolic modeling},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2020},
+Volume = {117},
+Number = {6},
+Pages = {1779-1788},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/bit.27330},
+EarlyAccessDate = {APR 2020},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {acetyl-CoA; genome-scale metabolic modelling; lipid accumulation in
+ Rhodococcus; oxidative stress; TPI},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; CHLORELLA-VULGARIS; TRIACYLGLYCEROL; ENZYME;
+ NANOPARTICLES; CITRATE; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Mukherjee, Amitava/H-5560-2011
+ },
+ORCID-Numbers = {Mukherjee, Amitava/0000-0001-8682-4278
+ Suraishkumar, GK/0000-0002-6521-4494
+ Sundarararaghavan, Archanaa/0000-0002-2930-6965
+ Sahoo, Swagatika/0000-0003-3773-8597},
+Times-Cited = {9},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000524577800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000524180100023,
+Author = {Hu, Bing and Wang, Miaoxiao and Geng, Shuang and Wen, Liqun and Wu,
+ Mengdi and Nie, Yong and Tang, Yue-Qin and Wu, Xiao-Lei},
+Title = {Metabolic Exchange with Non-Alkane-Consuming Pseudomonas stutzeri
+ SLG510A3-8 Improves n-Alkane Biodegradation by the Alkane
+ Degrader Dietzia sp. Strain DQ12-45-1b},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2020},
+Volume = {86},
+Number = {8},
+Month = {APR},
+Type = {Article},
+DOI = {10.1128/AEM.02931-19},
+Article-Number = {e02931-19},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords = {flux balance analysis; interspecies metabolite transfer; metabolomics;
+ proteomics; synergistic biodegradation of n-alkanes},
+Keywords-Plus = {CRUDE-OIL; MICROBIAL COMMUNITIES; EFFICIENT PRODUCTION; BACTERIAL
+ CONSORTIA; DEGRADATION; HYDROCARBONS; BIOREMEDIATION; SOIL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {tang, yu'e/IAO-9657-2023
+ Tang, Yue-Qin/HSG-6400-2023
+ Hu, Bing/AAF-8930-2020
+ Wang, Miaoxiao/AAD-3992-2022},
+ORCID-Numbers = {Tang, Yue-Qin/0000-0001-6872-1099
+ Wang, Miaoxiao/0000-0002-4636-0058},
+Times-Cited = {28},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000524180100023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000533510400047,
+Author = {Lee, Na-Rae and Lee, Choong Hwan and Lee, Dong-Yup and Park, Jin-Byung},
+Title = {Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of
+ Hexanoic acid Producing Megasphaera elsdenii},
+Journal = {MICROORGANISMS},
+Year = {2020},
+Volume = {8},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.3390/microorganisms8040539},
+Article-Number = {539},
+EISSN = {2076-2607},
+Keywords = {Megasphaera elsdenii; hexanoic acid; bifurcated pathway; genome-scale
+ metabolic model; constraint-based modeling},
+Keywords-Plus = {RUMINAL BACTERIUM; FATTY-ACID; FERMENTATION; LACTATE; GROWTH; GLUCOSE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Lee, Dong-Yup/D-6650-2011},
+ORCID-Numbers = {Lee, Dong-Yup/0000-0003-0901-708X},
+Times-Cited = {8},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000533510400047},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000533907300039,
+Author = {Siriwach, Ratklao and Matsuda, Fumio and Yano, Kentaro and Hirai, Masami
+ Yokota},
+Title = {Drought Stress Responses in Context-Specific Genome-Scale Metabolic
+ Models of Arabidopsis thaliana},
+Journal = {METABOLITES},
+Year = {2020},
+Volume = {10},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.3390/metabo10040159},
+Article-Number = {159},
+EISSN = {2218-1989},
+Keywords = {Arabidopsis; drought; flux balance analysis; genome-scale metabolic
+ model; metabolism; metabolome; transcriptome},
+Keywords-Plus = {GENE-EXPRESSION OMNIBUS; PHOTORESPIRATION; PLANTS; GEO},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Hirai, Masami Yokota/D-5319-2009
+ },
+ORCID-Numbers = {Hirai, Masami Yokota/0000-0003-0802-6208
+ Matsuda, Fumio/0000-0003-1091-778X
+ Siriwach, Ratklao/0000-0001-9191-8711},
+Times-Cited = {10},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000533907300039},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000524532100011,
+Author = {Trilla-Fuertes, Lucia and Ghanem, Ismael and Gamez-Pozo, Angelo and
+ Maurel, Joan and G-Pastrian, Laura and Mendiola, Marta and Pena,
+ Cristina and Lopez-Vacas, Rocio and Prado-Vazquez, Guillermo and
+ Lopez-Camacho, Elena and Zapater-Moros, Andrea and Heredia, Victoria and
+ Cuatrecasas, Miriam and Garcia-Alfonso, Pilar and Capdevila, Jaume and
+ Conill, Carles and Garcia-Carbonero, Rocio and Ramos-Ruiz, Ricardo and
+ Fortes, Claudia and Llorens, Carlos and Nanni, Paolo and Fresno Vara,
+ Juan Angel and Feliu, Jaime},
+Title = {Genetic Profile and Functional Proteomics of Anal Squamous Cell
+ Carcinoma: Proposal for a Molecular Classification},
+Journal = {MOLECULAR \& CELLULAR PROTEOMICS},
+Year = {2020},
+Volume = {19},
+Number = {4},
+Pages = {690-700},
+Month = {APR},
+Type = {Article},
+DOI = {10.1074/mcp.RA120.001954},
+EISSN = {1535-9484},
+Keywords-Plus = {CANCER; EXPRESSION; METASTASIS; MUTATIONS; MOTILITY; MODELS; FLUX},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Gamez, Angelo/HSG-7485-2023
+ Vara, Juan Ángel Fresno/Y-9928-2019
+ Prado-Vazquez, Guillermo/T-1861-2017
+ Trilla, Lucia/AAG-8392-2019
+ ramos-ruiz, ricardo/Q-2237-2016
+ Ghanem, Ismael/HTS-9038-2023
+ Gamez-Pozo, Angelo/N-2506-2014},
+ORCID-Numbers = {Vara, Juan Ángel Fresno/0000-0003-1527-1252
+ Prado-Vazquez, Guillermo/0000-0003-2456-6191
+ Trilla, Lucia/0000-0002-4452-3474
+ ramos-ruiz, ricardo/0000-0002-6331-9786
+ Ghanem, Ismael/0000-0002-1859-0737
+ Nanni, Paolo/0000-0001-8429-3557
+ Maurel, Joan/0000-0002-9413-5592
+ Garcia-Carbonero, Rocio/0000-0002-3342-397X
+ Gamez-Pozo, Angelo/0000-0002-8931-0624},
+Times-Cited = {3},
+Journal-ISO = {Mol. Cell. Proteomics},
+Unique-ID = {WOS:000524532100011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000527914500005,
+Author = {Zhu, Yan and Lu, Jing and Zhao, Jinxin and Zhang, Xinru and Yu, Heidi H.
+ and Velkov, Tony and Li, Jian},
+Title = {Complete genome sequence and genome-scale metabolic modelling of
+ Acinetobacter baumannii type strain ATCC 19606},
+Journal = {INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY},
+Year = {2020},
+Volume = {310},
+Number = {3},
+Month = {APR},
+Type = {Article},
+DOI = {10.1016/j.ijmm.2020.151412},
+Article-Number = {151412},
+ISSN = {1438-4221},
+EISSN = {1618-0607},
+Keywords = {Acinetobacter baumannii; Antimicrobial resistance; Virulence factor;
+ Insertion sequence; Genomic island; Genome-scale metabolic modelling},
+Keywords-Plus = {EFFLUX PUMP; COLISTIN RESISTANCE; EPITHELIAL-CELLS; LIPOPOLYSACCHARIDE;
+ PLASMID; GENES; IDENTIFICATION; EXPRESSION; SULBACTAM; ISLANDS},
+Research-Areas = {Microbiology; Virology},
+Web-of-Science-Categories = {Microbiology; Virology},
+ResearcherID-Numbers = {zhang, xinru/GZK-8155-2022
+ Zhu, Yan/HLW-8686-2023
+ Zhang, Xinru/IQX-0944-2023
+ },
+ORCID-Numbers = {Zhu, Yan/0000-0001-7342-3782
+ velkov, tony/0000-0002-0017-7952
+ Zhao, Jinxin/0000-0002-0604-3541},
+Times-Cited = {9},
+Journal-ISO = {Int. J. Med. Microbiol.},
+Unique-ID = {WOS:000527914500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000523188100075,
+Author = {Song, Yoseb and Lee, Jin Soo and Shin, Jongoh and Lee, Gyu Min and Jin,
+ Sangrak and Kang, Seulgi and Lee, Jung-Kul and Kim, Dong Rip and Lee,
+ Eun Yeol and Kim, Sun Chang and Cho, Suhyung and Kim, Donghyuk and Cho,
+ Byung-Kwan},
+Title = {Functional cooperation of the glycine synthase-reductase and
+ Wood-Ljungdahl pathways for autotrophic growth of Clostridium
+ drakei},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2020},
+Volume = {117},
+Number = {13},
+Pages = {7516-7523},
+Month = {MAR 31},
+Type = {Article},
+DOI = {10.1073/pnas.1912289117},
+ISSN = {0027-8424},
+Keywords = {CO2 fixation; acetogen; Wood-Ljungdahl pathway; systems biology; glycine
+ synthase-reductase pathway},
+Keywords-Plus = {EARLY EVOLUTION; METABOLISM; MECHANISM; SEQUENCE; MODELS; FUELS; LIFE;
+ CO2},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Kim, Donghyuk/AAS-9141-2020
+ Lee, JIn/HTL-6278-2023
+ Kim, Dong Rip/AAT-9532-2020
+ Cho, Byung-Kwan/C-1830-2011
+ },
+ORCID-Numbers = {Kim, Dong Rip/0000-0001-6398-9483
+ Lee, Eun Yeol/0000-0002-6974-3262},
+Times-Cited = {56},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000523188100075},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000522515600001,
+Author = {Wegrzyn, Agnieszka B. and Herzog, Katharina and Gerding, Albert and
+ Kwiatkowski, Marcel and Wolters, Justina C. and Dolga, Amalia M. and van
+ Lint, Alida E. M. and Wanders, Ronald J. A. and Waterham, Hans R. and
+ Bakker, Barbara M.},
+Title = {Fibroblast-specific genome-scale modelling predicts an imbalance in
+ amino acid metabolism in Refsum disease},
+Journal = {FEBS JOURNAL},
+Year = {2020},
+Volume = {287},
+Number = {23},
+Pages = {5096-5113},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1111/febs.15292},
+EarlyAccessDate = {MAR 2020},
+ISSN = {1742-464X},
+EISSN = {1742-4658},
+Keywords = {amino acids; fibroblast; genome-scale modelling; metabolism; Refsum
+ disease},
+Keywords-Plus = {PHYTANIC ACID; INBORN-ERRORS; LIVER-METABOLISM; OMEGA-OXIDATION;
+ DISORDERS; DIPEPTIDE; RECONSTRUCTION; IDENTIFICATION; CHROMATOGRAPHY;
+ PEPTIDES},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Wegrzyn, Agnieszka Barbara/T-1519-2017
+ Kwiatkowski, Marcel/M-3384-2016
+ Wolters, Justina Clarinda/IXN-6899-2023
+ },
+ORCID-Numbers = {Wegrzyn, Agnieszka Barbara/0000-0003-4872-8626
+ Kwiatkowski, Marcel/0000-0002-5804-6031
+ Wolters, Justina Clarinda/0000-0003-0066-3720
+ Dolga, Amalia/0000-0001-5400-5614},
+Times-Cited = {5},
+Journal-ISO = {FEBS J.},
+Unique-ID = {WOS:000522515600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000560406800008,
+Author = {Mandakovic, Dinka and Cintolesi, Angela and Maldonado, Jonathan and
+ Mendoza, Sebastian N. and Aite, Meziane and Gaete, Alexis and Saitua,
+ Francisco and Allende, Miguel and Cambiazo, Veronica and Siegel, Anne
+ and Maass, Alejandro and Gonzalez, Mauricio and Latorre, Mauricio},
+Title = {Genome-scale metabolic models of Microbacterium species isolated
+ from a high altitude desert environment},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {MAR 27},
+Type = {Article},
+DOI = {10.1038/s41598-020-62130-8},
+Article-Number = {5560},
+ISSN = {2045-2322},
+Keywords-Plus = {SP NOV.; ORLA-JENSEN; BACTERIAL; PH; SEQUENCE; GROWTH; GENES;
+ RECLASSIFICATION; RECONSTRUCTION; BIOSYNTHESIS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Maldonado, Jonathan E/J-6429-2012
+ Allende, Miguel L/C-5167-2008
+ Cambiazo, Veronica/AAI-1133-2021
+ Gonzalez, Mauricio/I-2772-2013
+ Maass, Alejandro E/D-5848-2012
+ },
+ORCID-Numbers = {Maldonado, Jonathan E/0000-0002-9967-0885
+ Allende, Miguel L/0000-0002-2783-2152
+ Maass, Alejandro E/0000-0002-7038-4527
+ Mendoza, Sebastian/0000-0002-2192-5569
+ Gaete, Alexis/0000-0001-9132-231X
+ Mandakovic, Dinka/0000-0002-1406-8175
+ Gonzalez Canales, Mauricio Alejandro/0000-0002-1592-9758},
+Times-Cited = {13},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000560406800008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000521667200001,
+Author = {Fouladiha, Hamideh and Marashi, Sayed-Amir and Torkashvand, Fatemeh and
+ Mahboudi, Fereidoun and Lewis, Nathan E. and Vaziri, Behrouz},
+Title = {A metabolic network-based approach for developing feeding strategies for
+ CHO cells to increase monoclonal antibody production},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2020},
+Volume = {43},
+Number = {8},
+Pages = {1381-1389},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1007/s00449-020-02332-6},
+EarlyAccessDate = {MAR 2020},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {Metabolic network models; Constrain-based modeling; DoE; Feeding
+ strategies; Plackett-Burman; Central composite design},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ARACHIDONIC-ACID; FATTY-ACIDS; OPTIMIZATION;
+ DESIGN},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008
+ Lewis, Nathan/ABE-7290-2020},
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Lewis, Nathan/0000-0001-7700-3654},
+Times-Cited = {24},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000521667200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000521753000003,
+Author = {Robinson, Jonathan L. and Kocabas, Pinar and Wang, Hao and Cholley,
+ Pierre-Etienne and Cook, Daniel and Nilsson, Avlant and Anton, Mihail
+ and Ferreira, Raphael and Domenzain, Ivan and Billa, Virinchi and
+ Limeta, Angelo and Hedin, Alex and Gustafsson, Johan and Kerkhoven,
+ Eduard J. and Svensson, L. Thomas and Palsson, Bernhard O. and
+ Mardinoglu, Adil and Hansson, Lena and Uhlen, Mathias and Nielsen, Jens},
+Title = {An atlas of human metabolism},
+Journal = {SCIENCE SIGNALING},
+Year = {2020},
+Volume = {13},
+Number = {624},
+Month = {MAR 24},
+Type = {Article},
+DOI = {10.1126/scisignal.aaz1482},
+Article-Number = {eaaz1482},
+ISSN = {1945-0877},
+EISSN = {1937-9145},
+Keywords-Plus = {FATTY-ACID-METABOLISM; GLOBAL RECONSTRUCTION; EXPRESSION; MODELS; TARGET},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Uhlen, Mathias/AAV-8746-2021
+ Kerkhoven, Eduard/P-2469-2019
+ Domenzain, Ivan/HCI-9542-2022
+ Robinson, Jonathan/ABC-2402-2020
+ Ferreira, Raphael/AAA-1917-2021
+ Nilsson, Avlant/AAD-3110-2022
+ Mardinoglu, Adil/AAS-6360-2021
+ Anton, Mihail/GXH-0002-2022
+ },
+ORCID-Numbers = {Kerkhoven, Eduard/0000-0002-3593-5792
+ Domenzain, Ivan/0000-0002-5322-2040
+ Robinson, Jonathan/0000-0001-8567-5960
+ Nilsson, Avlant/0000-0002-9476-4516
+ Anton, Mihail/0000-0002-7753-9042
+ Svensson, Thomas/0000-0002-9190-2979
+ Hedin, Alex/0000-0002-0829-2496
+ Gustafsson, Johan/0000-0001-5072-2659
+ Limeta, Angelo/0000-0002-6093-8426
+ KOCABAS, PINAR/0000-0001-9788-2019
+ Wang, Hao/0000-0001-7475-0136},
+Times-Cited = {140},
+Journal-ISO = {Sci. Signal.},
+Unique-ID = {WOS:000521753000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000526388400012,
+Author = {von Kamp, Axel and Klamt, Steffen},
+Title = {MEMO: A Method for Computing Metabolic Modules for Cell-Free Production
+ Systems},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2020},
+Volume = {9},
+Number = {3},
+Pages = {556-566},
+Month = {MAR 20},
+Type = {Article},
+DOI = {10.1021/acssynbio.9b00434},
+ISSN = {2161-5063},
+Keywords = {synthetic biology; design of cell-free systems; constraint-based
+ modeling; metabolic networks; cofactor regeneration; mixed-integer
+ linear programming},
+Keywords-Plus = {REGENERATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ORCID-Numbers = {Klamt, Steffen/0000-0003-2563-7561},
+Times-Cited = {3},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000526388400012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000520964700006,
+Author = {Zhang, Shan and Reljic, Boris and Liang, Chao and Kerouanton, Baptiste
+ and Francisco, Joel Celio and Peh, Jih Hou and Mary, Camille and
+ Jagannathan, Narendra Suhas and Olexiouk, Volodimir and Tang, Claire and
+ Fidelito, Gio and Nama, Srikanth and Cheng, Ruey-Kuang and Wee, Caroline
+ Lei and Wang, Loo Chien and Roggli, Paula Duek and Sampath, Prabha and
+ Lane, Lydie and Petretto, Enrico and Sobota, Radoslaw M. and Jesuthasan,
+ Suresh and Tucker-Kellogg, Lisa and Reversade, Bruno and Menschaert,
+ Gerben and Sun, Lei and Stroud, David A. and Ho, Lena},
+Title = {Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory
+ complex III assembly},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {MAR 11},
+Type = {Article},
+DOI = {10.1038/s41467-020-14999-2},
+Article-Number = {1312},
+EISSN = {2041-1723},
+Keywords-Plus = {SMALL ORFS; PROTEOMICS DATA; PROTEIN; IDENTIFICATION; DATABASE; UPDATE;
+ SIGNAL; GENE; MICROPEPTIDE; MICROPROTEIN},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Fidelito, Gio/AAM-3342-2021
+ Tucker-Kellogg, Lisa/G-3376-2012
+ Stroud, David Arthur/HGB-4331-2022
+ Jesuthasan, Suresh/B-7870-2016
+ Lane, Lydie/AAQ-4896-2021
+ Tucker-Kellogg, Lisa/AAD-9265-2022
+ },
+ORCID-Numbers = {Fidelito, Gio/0000-0001-7278-2644
+ Tucker-Kellogg, Lisa/0000-0002-1301-7069
+ Stroud, David Arthur/0000-0002-2048-3383
+ Jesuthasan, Suresh/0000-0002-5733-6555
+ Lane, Lydie/0000-0002-9818-3030
+ Sobota, Radoslaw/0000-0002-2455-2526
+ Liang, Chao/0000-0001-6255-8964
+ Jagannathan, N. Suhas/0000-0002-1857-8789
+ Ho, Lena/0000-0002-9358-621X
+ Francisco, Joel/0000-0002-1229-0047
+ Reljic, Boris/0000-0002-4655-8478
+ Petretto, Enrico/0000-0003-2163-5921
+ REVERSADE, Bruno/0000-0002-4070-7997
+ Duek Roggli, Paula/0000-0002-0819-0473
+ Mary, Camille/0000-0002-5734-0298},
+Times-Cited = {59},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000520964700006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000563338200007,
+Author = {Zeng, Hong and Yang, Aidong},
+Title = {Bridging substrate intake kinetics and bacterial growth phenotypes with
+ flux balance analysis incorporating proteome allocation},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {MAR 9},
+Type = {Article},
+DOI = {10.1038/s41598-020-61174-0},
+Article-Number = {4283},
+ISSN = {2045-2322},
+Keywords-Plus = {LIMITED CONTINUOUS-CULTURE; DIFFERENT SLUDGE AGES; ESCHERICHIA-COLI;
+ GENE-EXPRESSION; SUGAR-TRANSPORT; METABOLISM; MODELS; CEREVISIAE;
+ DERIVATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Yang, Aidong/M-2887-2013
+ },
+ORCID-Numbers = {Yang, Aidong/0000-0001-7771-6777
+ Zeng, Hong/0000-0001-6617-4466},
+Times-Cited = {8},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000563338200007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000517739700001,
+Author = {Lieven, Christian and Beber, Moritz E. and Olivier, Brett G. and
+ Bergmann, Frank T. and Ataman, Meric and Babaei, Parizad and Bartell,
+ Jennifer A. and Blank, Lars M. and Chauhan, Siddharth and Correia, Kevin
+ and Diener, Christian and Draeger, Andreas and Ebert, Birgitta E. and
+ Edirisinghe, Janaka N. and Faria, Jose P. and Feist, Adam M. and Fengos,
+ Georgios and Fleming, Ronan M. T. and Garcia-Jimenez, Beatriz and
+ Hatzimanikatis, Vassily and van Helvoirt, Wout and Henry, Christopher S.
+ and Hermjakob, Henning and Herrgard, Markus J. and Kaafarani, Ali and
+ Kim, Hyun Uk and King, Zachary and Klamt, Steffen and Klipp, Edda and
+ Koehorst, Jasper J. and Koenig, Matthias and Lakshmanan, Meiyappan and
+ Lee, Dong-Yup and Lee, Sang Yup and Lee, Sunjae and Lewis, Nathan E. and
+ Liu, Filipe and Ma, Hongwu and Machado, Daniel and Mahadevan,
+ Radhakrishnan and Maia, Paulo and Mardinoglu, Adil and Medlock, Gregory
+ L. and Monk, Jonathan M. and Nielsen, Jens and Nielsen, Lars Keld and
+ Nogales, Juan and Nookaew, Intawat and Palsson, Bernhard O. and Papin,
+ Jason A. and Patil, Kiran R. and Poolman, Mark and Price, Nathan D. and
+ Resendis-Antonio, Osbaldo and Richelle, Anne and Rocha, Isabel and
+ Sanchez, Benjamin J. and Schaap, Peter J. and Malik Sheriff, Rahuman S.
+ and Shoaie, Saeed and Sonnenschein, Nikolaus and Teusink, Bas and
+ Vilaca, Paulo and Vik, Jon Olav and Wodke, Judith A. H. and Xavier,
+ Joana C. and Yuan, Qianqian and Zakhartsev, Maksim and Zhang, Cheng},
+Title = {MEMOTE for standardized genome-scale metabolic model testing},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2020},
+Volume = {38},
+Number = {3},
+Pages = {272-276},
+Month = {MAR},
+Type = {Letter},
+DOI = {10.1038/s41587-020-0446-y},
+EarlyAccessDate = {MAR 2020},
+ISSN = {1087-0156},
+EISSN = {1546-1696},
+Keywords-Plus = {RECONSTRUCTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Mardinoglu, Adil/AAS-6360-2021
+ RESENDIS, OSBALDO/ADE-5280-2022
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Nielsen, Jens Bo/C-7632-2015
+ Sonnenschein, Nikolaus/F-6853-2012
+ Xavier, Joana Rute Calça/Q-2960-2019
+ Ebert, Birgitta E./B-7845-2014
+ Lee, Sang Yup/C-1526-2011
+ Machado, Daniel/O-5493-2015
+ Sheriff, Rahuman/ABB-9034-2020
+ Vik, Jon Olav/B-9350-2008
+ Maia, Paulo/AAM-1025-2021
+ Rocha, Isabel/A-4279-2013
+ Hermjakob, Henning/AFM-3497-2022
+ Liu, Filipe/K-8275-2019
+ Lee, Sunjae/H-9815-2019
+ García-Jiménez, Beatriz/ABH-2355-2020
+ Lewis, Nathan/ABE-7290-2020
+ Feist, Adam Michael/GPS-4989-2022
+ Patil, Kiran R/B-9709-2009
+ Nielsen, Lars K/A-5519-2011
+ Dräger, Andreas/F-5620-2015
+ Diener, Christian/X-9574-2019
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Nogales, Juan/Y-8829-2019
+ Hatzimanikatis, Vassily/G-6505-2010
+ Koehorst, Jasper/G-3595-2013
+ Kim, Hyun Uk/F-4509-2018
+ Blank, Lars M./A-6761-2012
+ Maia, Paulo/F-9148-2010
+ Zhang, Cheng/L-7906-2016
+ },
+ORCID-Numbers = {RESENDIS, OSBALDO/0000-0001-5220-541X
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Xavier, Joana Rute Calça/0000-0001-9242-8968
+ Ebert, Birgitta E./0000-0001-9425-7509
+ Lee, Sang Yup/0000-0003-0599-3091
+ Machado, Daniel/0000-0002-2063-5383
+ Sheriff, Rahuman/0000-0003-0705-9809
+ Vik, Jon Olav/0000-0002-7778-4515
+ Rocha, Isabel/0000-0001-9494-3410
+ Hermjakob, Henning/0000-0001-8479-0262
+ Liu, Filipe/0000-0001-8701-2984
+ Lee, Sunjae/0000-0002-6428-5936
+ García-Jiménez, Beatriz/0000-0002-8129-6506
+ Lewis, Nathan/0000-0001-7700-3654
+ Feist, Adam Michael/0000-0002-8630-4800
+ Patil, Kiran R/0000-0002-6166-8640
+ Nielsen, Lars K/0000-0001-8191-3511
+ Dräger, Andreas/0000-0002-1240-5553
+ Diener, Christian/0000-0002-7476-0868
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Koehorst, Jasper/0000-0001-8172-8981
+ Kim, Hyun Uk/0000-0001-7224-642X
+ Teusink, Bas/0000-0003-3929-0423
+ Babaei, Parizad/0000-0001-9411-0427
+ Chauhan, Siddharth/0000-0001-6674-895X
+ Nogales, Juan/0000-0002-4961-0833
+ Blank, Lars M./0000-0003-0961-4976
+ Beber, Moritz Emanuel/0000-0003-2406-1978
+ Lieven, Christian/0000-0001-5377-4091
+ Schaap, Peter/0000-0002-4346-6084
+ Lopes Faria, Jose Pedro/0000-0001-9302-7250
+ Maia, Paulo/0000-0002-0848-8683
+ Olivier, Brett/0000-0002-5293-5321
+ van Helvoirt, Wout/0000-0002-9143-9726
+ Zhang, Cheng/0000-0002-3721-8586
+ Vilaca, Paulo/0000-0002-1098-5849
+ Kaafarani, Ali/0000-0002-2805-310X
+ Shoaie, Saeed/0000-0001-5834-4533},
+Times-Cited = {198},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000517739700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000512406900027,
+Author = {Das, Manali and Patra, Pradipta and Ghosh, Amit},
+Title = {Metabolic engineering for enhancing microbial biosynthesis of advanced
+ biofuels},
+Journal = {RENEWABLE \& SUSTAINABLE ENERGY REVIEWS},
+Year = {2020},
+Volume = {119},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1016/j.rser.2019.109562},
+Article-Number = {109562},
+ISSN = {1364-0321},
+Keywords = {Butanol; Fatty-acid based biofuel; Isoprenoids; Genome-scale model;
+ CRISPR/Cas9; (13)CMFA},
+Keywords-Plus = {ETHYL-ESTER PRODUCTION; FATTY-ACID PRODUCTION; HIGH-LEVEL PRODUCTION;
+ GENOME-SCALE MODELS; SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI;
+ SYNTHETIC BIOLOGY; YARROWIA-LIPOLYTICA; BETA-OXIDATION; E. COLI},
+Research-Areas = {Science \& Technology - Other Topics; Energy \& Fuels},
+Web-of-Science-Categories = {Green \& Sustainable Science \& Technology; Energy \& Fuels},
+ResearcherID-Numbers = {Ghosh, Amit/AAA-3490-2021},
+ORCID-Numbers = {Ghosh, Amit/0000-0003-3514-885X},
+Times-Cited = {36},
+Journal-ISO = {Renew. Sust. Energ. Rev.},
+Unique-ID = {WOS:000512406900027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000525842000076,
+Author = {Huang, Zhuangrong and Yoon, Seongkyu},
+Title = {Integration of Time-Series Transcriptomic Data with Genome-Scale CHO
+ Metabolic Models for mAb Engineering},
+Journal = {PROCESSES},
+Year = {2020},
+Volume = {8},
+Number = {3},
+Month = {MAR},
+Type = {Article},
+DOI = {10.3390/pr8030331},
+Article-Number = {331},
+EISSN = {2227-9717},
+Keywords = {genome-scale metabolic model; time-series transcriptomics; omics data
+ integration; CHO cell},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ RNA},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Huang, Zhuangrong/AAV-2846-2020
+ },
+ORCID-Numbers = {Huang, Zhuangrong/0000-0002-9145-5582},
+Times-Cited = {9},
+Journal-ISO = {Processes},
+Unique-ID = {WOS:000525842000076},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000522978600001,
+Author = {Tomas-Gamisans, Marius and Paim Andrade, Cristiane Conte and Maresca,
+ Francisco and Monforte, Sergi and Ferrer, Pau and Albiol, Joan},
+Title = {Redox Engineering by Ectopic Overexpression of NADH Kinase in
+ Recombinant Pichia pastoris (Komagataella phaffii): Impact
+ on Cell Physiology and Recombinant Production of Secreted Proteins},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2020},
+Volume = {86},
+Number = {6},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1128/AEM.02038-19},
+Article-Number = {e02038-19},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords = {NADH kinase; Pichia pastoris; Pos5; redox engineering; heterologous
+ protein production},
+Keywords-Plus = {FED-BATCH CULTIVATION; SACCHAROMYCES-CEREVISIAE; METABOLISM; GLYCEROL;
+ GENE; PREDICTION; TOOLBOX; GLUCOSE; MODEL; FLUX},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Tomàs-Gamisans, Màrius/AAG-8539-2020
+ Andrade, Cristiane C P/F-6816-2012
+ Sala, Joan Albiol/A-8280-2008
+ Ferrer, Pau/A-4147-2009
+ },
+ORCID-Numbers = {Tomàs-Gamisans, Màrius/0000-0002-6076-6716
+ Andrade, Cristiane C P/0000-0003-0251-5748
+ Sala, Joan Albiol/0000-0001-5626-429X
+ Ferrer, Pau/0000-0002-5287-4127
+ Monforte, Sergi/0000-0001-9752-5273},
+Times-Cited = {16},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000522978600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000563209800027,
+Author = {Wang, Yuliang and Ma, Shuyi and Ruzzo, Walter L.},
+Title = {Spatial modeling of prostate cancer metabolic gene expression reveals
+ extensive heterogeneity and selective vulnerabilities},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2020},
+Volume = {10},
+Number = {1},
+Month = {FEB 26},
+Type = {Article},
+DOI = {10.1038/s41598-020-60384-w},
+Article-Number = {3490},
+ISSN = {2045-2322},
+Keywords-Plus = {FATTY-ACID; 15-HYDROXYPROSTAGLANDIN DEHYDROGENASE; TUMOR-SUPPRESSOR;
+ GLOBAL RECONSTRUCTION; INHIBITION; ARGINASE; CELLS; ARACHIDONATE;
+ ACTIVATION; PHENOTYPE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Wang, Yuliang/H-9070-2012
+ huang, dezhi/ABC-6566-2021
+ },
+ORCID-Numbers = {Wang, Yuliang/0000-0002-3788-5477
+ Ruzzo, Walter L./0000-0002-6260-2926},
+Times-Cited = {84},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000563209800027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000535229300055,
+Author = {Rokke, Gunvor Bjerkelund and Hohmann-Marriott, Martin Frank and Almaas,
+ Eivind},
+Title = {An adjustable algal chloroplast plug-and-play model for genome-scale
+ metabolic models},
+Journal = {PLOS ONE},
+Year = {2020},
+Volume = {15},
+Number = {2},
+Month = {FEB 24},
+Type = {Article},
+DOI = {10.1371/journal.pone.0229408},
+Article-Number = {e0229408},
+ISSN = {1932-6203},
+Keywords-Plus = {CYCLIC ELECTRON-TRANSPORT; PLASTID TERMINAL OXIDASE; PHOTOSYSTEM-I;
+ AMINO-ACID; PROFILES; PATHWAYS; RECONSTRUCTION; BIOSYNTHESIS;
+ MICROALGAE; FLOW},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Bjerkelund Rokke, Gunvor/0000-0003-0193-2072
+ Hohmann-Marriott, Martin/0000-0002-2957-7052},
+Times-Cited = {3},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000535229300055},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000518036400004,
+Author = {Li, Gong-Hua and Dai, Shaoxing and Han, Feifei and Li, Wenxin and Huang,
+ Jingfei and Xiao, Wenzhong},
+Title = {FastMM: an efficient toolbox for personalized constraint-based metabolic
+ modeling},
+Journal = {BMC BIOINFORMATICS},
+Year = {2020},
+Volume = {21},
+Number = {1},
+Month = {FEB 21},
+Type = {Article},
+DOI = {10.1186/s12859-020-3410-4},
+Article-Number = {67},
+ISSN = {1471-2105},
+Keywords = {FastMM; Constraint-based model; Metabolic modeling; Metabolism},
+Keywords-Plus = {QUANTITATIVE PREDICTION; CELLULAR-METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {li, wenxin/IYS-5300-2023
+ Dai, shaoxing/ABA-8699-2020
+ huang, jing/JDC-2548-2023
+ },
+ORCID-Numbers = {Li, Gong-Hua/0000-0002-9311-6613
+ xiao, wenzhong/0000-0003-4944-6380
+ HAN, FEIFEI/0000-0003-4373-8753
+ Li, Wenxing/0000-0001-9984-8439},
+Times-Cited = {8},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000518036400004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000513995300001,
+Author = {Koduru, Lokanand and Kim, Hyang Yeon and Lakshmanan, Meiyappan and
+ Mohanty, Bijayalaxmi and Lee, Yi Qing and Lee, Choong Hwan and Lee,
+ Dong-Yup},
+Title = {Genome-scale metabolic reconstruction and in silico analysis of the rice
+ leaf blight pathogen, Xanthomonas oryzae},
+Journal = {MOLECULAR PLANT PATHOLOGY},
+Year = {2020},
+Volume = {21},
+Number = {4},
+Pages = {527-540},
+Month = {APR},
+Type = {Article},
+DOI = {10.1111/mpp.12914},
+EarlyAccessDate = {FEB 2020},
+ISSN = {1464-6722},
+EISSN = {1364-3703},
+Keywords = {antibacterial targets; diffusible signal factor; genome-scale metabolic
+ model; nitrogenous fertilizers; rice leaf blight pathogen; systems
+ biology; Xanthomonas oryzae},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; PV.-ORYZAE; BIOFILM FORMATION;
+ BACTERIAL-BLIGHT; ESCHERICHIA-COLI; EXTRACELLULAR POLYSACCHARIDE;
+ NITRIC-OXIDE; VIRULENCE; GENES; CAMPESTRIS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Mohanty, Bijayalaxmi/AAY-7386-2020
+ Koduru, Lokanand/AAY-3079-2020
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Lee, Dong-Yup/D-6650-2011
+ },
+ORCID-Numbers = {Mohanty, Bijayalaxmi/0000-0002-8226-2367
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Lee, Yi Qing/0000-0002-8970-0729
+ Kim, Hyang Yeon/0000-0003-3203-462X},
+Times-Cited = {7},
+Journal-ISO = {Mol. Plant Pathol.},
+Unique-ID = {WOS:000513995300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000514256600031,
+Author = {Dong, Wentao and Moon, Sun Jin and Kelleher, Joanne K. and
+ Stephanopoulos, Gregory},
+Title = {Dissecting Mammalian Cell Metabolism through 13C- and
+ 2H-Isotope Tracing: Interpretations at the Molecular and
+ Systems Levels},
+Journal = {INDUSTRIAL \& ENGINEERING CHEMISTRY RESEARCH},
+Year = {2020},
+Volume = {59},
+Number = {6},
+Pages = {2593-2610},
+Month = {FEB 12},
+Type = {Review},
+DOI = {10.1021/acs.iecr.9b05154},
+ISSN = {0888-5885},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; PARALLEL LABELING EXPERIMENTS; FLUX ANALYSIS;
+ REDUCTIVE CARBOXYLATION; INSULIN-RESISTANCE; MALIC ENZYME; FATTY-ACIDS;
+ MECHANISMS; TRACERS; BRAIN},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Dong, Wentao/ABG-9157-2021
+ },
+ORCID-Numbers = {Dong, Wentao/0000-0001-5490-4265},
+Times-Cited = {7},
+Journal-ISO = {Ind. Eng. Chem. Res.},
+Unique-ID = {WOS:000514256600031},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000514177500018,
+Author = {Krishnan, Aarti and Kloehn, Joachim and Lunghi, Matteo and
+ Chiappino-Pepe, Anush and Waldman, Benjamin S. and Nicolas, Damien and
+ Varesio, Emmanuel and Hehl, Adrian and Lourido, Sebastian and
+ Hatzimanikatis, Vassily and Soldati-Favre, Dominique},
+Title = {Functional and Computational Genomics Reveal Unprecedented Flexibility
+ in Stage-Specific Toxoplasma Metabolism},
+Journal = {CELL HOST \& MICROBE},
+Year = {2020},
+Volume = {27},
+Number = {2},
+Pages = {290+},
+Month = {FEB 12},
+Type = {Article},
+DOI = {10.1016/j.chom.2020.01.002},
+ISSN = {1931-3128},
+EISSN = {1934-6069},
+Keywords-Plus = {HEME-BIOSYNTHESIS PATHWAY; GONDII MYOSIN-A; PLASMODIUM-FALCIPARUM;
+ OXIDATIVE-PHOSPHORYLATION; PROTOPORPHYRIN IX; ESCHERICHIA-COLI;
+ THERMODYNAMIC ANALYSIS; PYRIDOXAL-PHOSPHATE; GLOBAL BURDEN; ACID},
+Research-Areas = {Microbiology; Parasitology; Virology},
+Web-of-Science-Categories = {Microbiology; Parasitology; Virology},
+ResearcherID-Numbers = {Chiappino Pepe, Anush/AAY-8830-2021
+ Soldati-Favre, Dominique/A-2999-2009
+ Hatzimanikatis, Vassily/G-6505-2010
+ Chiappino-Pepe, Anush/E-6560-2017
+ },
+ORCID-Numbers = {Chiappino Pepe, Anush/0000-0002-3993-907X
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Chiappino-Pepe, Anush/0000-0002-3993-907X
+ Soldati-Favre, Dominique/0000-0003-4156-2109
+ Kloehn, Joachim/0000-0002-6366-8599
+ Lunghi, Matteo/0000-0002-9338-9929
+ Krishnan, Aarti/0000-0002-7936-4442
+ Hehl, Adrian/0000-0002-2110-4445
+ Waldman, Benjamin/0000-0002-3488-9966},
+Times-Cited = {58},
+Journal-ISO = {Cell Host Microbe},
+Unique-ID = {WOS:000514177500018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000519108100001,
+Author = {Lavoie, Michel and Saint-Beat, Blanche and Strauss, Jan and Guerin,
+ Sebastien and Allard, Antoine and V. Hardy, Simon and Falciatore, Angela
+ and Lavaud, Johann},
+Title = {Genome-Scale Metabolic Reconstruction and in Silico Perturbation
+ Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts
+ High Metabolic Robustness},
+Journal = {BIOLOGY-BASEL},
+Year = {2020},
+Volume = {9},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.3390/biology9020030},
+Article-Number = {30},
+EISSN = {2079-7737},
+Keywords = {flux balance analysis; metabolic network; arctic; systems biology;
+ reaction deletion; gene deletion},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; MICROALGAE; EVOLUTION; GROWTH; NETWORKS;
+ NITROGEN; TOOLBOX; ACID},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Strauss, Jan/B-5083-2010
+ Lavaud, Johann/N-6185-2014
+ Allard, Antoine/H-3168-2011
+ Hardy, Simon/B-3301-2008
+ Falciatore, Angela/Q-6161-2018
+ },
+ORCID-Numbers = {Strauss, Jan/0000-0002-6208-791X
+ Lavaud, Johann/0000-0002-4704-2502
+ Allard, Antoine/0000-0002-8208-9920
+ Falciatore, Angela/0000-0003-3318-9578
+ Hardy, Simon/0000-0003-4014-2014},
+Times-Cited = {3},
+Journal-ISO = {Biology-Basel},
+Unique-ID = {WOS:000519108100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000518194600004,
+Author = {Pecht, Tal and Aschenbrenner, Anna C. and Ulas, Thomas and Succurro,
+ Antonella},
+Title = {Modeling population heterogeneity from microbial communities to immune
+ response in cells},
+Journal = {CELLULAR AND MOLECULAR LIFE SCIENCES},
+Year = {2020},
+Volume = {77},
+Number = {3},
+Pages = {415-432},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1007/s00018-019-03378-w},
+ISSN = {1420-682X},
+EISSN = {1420-9071},
+Keywords = {Population heterogeneity; Computational modeling; Systems biology;
+ Microbial communities; Immune response},
+Keywords-Plus = {DIFFERENTIAL EXPRESSION; TRANSCRIPTOMIC DATA; GUT MICROBIOME; T-CELLS;
+ REVEALS; GENERATION; DIVERSITY; SYSTEM; AGE; QUANTIFICATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Succurro, Antonella/K-3523-2019
+ Aschenbrenner, Anna C./JOZ-8769-2023
+ },
+ORCID-Numbers = {Succurro, Antonella/0000-0003-0227-2803
+ Aschenbrenner, Anna C./0000-0002-9429-5457
+ Pacht, Tal/0000-0002-6442-0560},
+Times-Cited = {3},
+Journal-ISO = {Cell. Mol. Life Sci.},
+Unique-ID = {WOS:000518194600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000510367200002,
+Author = {Rezazadeh, Mohammad and Babaeipour, Valiollah and Motamedian, Ehsan},
+Title = {Reconstruction, verification and in-silico analysis of a genome-scale
+ metabolic model of bacterial cellulose producing Komagataeibacter
+ xylinus},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2020},
+Volume = {43},
+Number = {6},
+Pages = {1017-1026},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1007/s00449-020-02299-4},
+EarlyAccessDate = {FEB 2020},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {Genome scale metabolic model; Komagataeibacter xylinus; Bacterial
+ cellulose; Flux balance analysis},
+Keywords-Plus = {GLUCONACETOBACTER-XYLINUS; ACETIC-ACID; MICROBIAL CELLULOSE;
+ BIOSYNTHESIS; GENE; FERMENTATION; ENHANCEMENT; SEQUENCE; DATABASE;
+ TOOLBOX},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Motamedian, Ehsan/GPK-8344-2022
+ Babaeipour, Valiollah/J-2770-2018
+ },
+ORCID-Numbers = {, Ehsan/0000-0001-8750-2879
+ Babaeipour, Valiollah/0000-0003-3615-176X
+ Rezazadeh, Mohammad/0000-0001-9818-3201},
+Times-Cited = {5},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000510367200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000519445500008,
+Author = {Xu, Yu and Holic, Roman and Hua, Qiang},
+Title = {Comparison and Analysis of Published Genome-scale Metabolic Models of
+ Yarrowia lipolytica},
+Journal = {BIOTECHNOLOGY AND BIOPROCESS ENGINEERING},
+Year = {2020},
+Volume = {25},
+Number = {1},
+Pages = {53-61},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1007/s12257-019-0208-1},
+ISSN = {1226-8372},
+EISSN = {1976-3816},
+Keywords = {genome-scale metabolic models; Yarrowia lipolytica; intracellular flux
+ distribution; simulation of cell growth and production},
+Keywords-Plus = {RECONSTRUCTION; OVERPRODUCTION; CULTURE; KEGG},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Roman, Holic/X-7500-2018},
+ORCID-Numbers = {Roman, Holic/0000-0003-1347-4785},
+Times-Cited = {6},
+Journal-ISO = {Biotechnol. Bioprocess Eng.},
+Unique-ID = {WOS:000519445500008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000509839500001,
+Author = {Moradali, M. Fata and Rehm, Bernd H. A.},
+Title = {Bacterial biopolymers: from pathogenesis to advanced materials},
+Journal = {NATURE REVIEWS MICROBIOLOGY},
+Year = {2020},
+Volume = {18},
+Number = {4},
+Pages = {195-210},
+Month = {APR},
+Type = {Review},
+DOI = {10.1038/s41579-019-0313-3},
+EarlyAccessDate = {JAN 2020},
+ISSN = {1740-1526},
+EISSN = {1740-1534},
+Keywords-Plus = {PSEUDOMONAS-AERUGINOSA BIOFILM; SYNTHETIC BIOLOGY; CELLULOSE PRODUCTION;
+ HYALURONIC-ACID; POLYHYDROXYALKANOATE BIOSYNTHESIS; ALGINATE PRODUCTION;
+ MOLECULAR-WEIGHT; IN-VITRO; POLYPHOSPHATE; MECHANISM},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Rehm, Bernd HA/B-3675-2011
+ },
+ORCID-Numbers = {Rehm, Bernd/0000-0003-3908-8903},
+Times-Cited = {189},
+Journal-ISO = {Nat. Rev. Microbiol.},
+Unique-ID = {WOS:000509839500001},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000534599100088,
+Author = {Shahkouhi, Ali Malek and Motamedian, Ehsan},
+Title = {Reconstruction of a regulated two-cell metabolic model to study
+ biohydrogen production in a diazotrophic cyanobacterium Anabaena
+ variabilis ATCC 29413},
+Journal = {PLOS ONE},
+Year = {2020},
+Volume = {15},
+Number = {1},
+Month = {JAN 24},
+Type = {Article},
+DOI = {10.1371/journal.pone.0227977},
+Article-Number = {e0227977},
+ISSN = {1932-6203},
+Keywords-Plus = {PHOTOBIOLOGICAL HYDROGEN-PRODUCTION; NITROGEN-FIXING CYANOBACTERIUM;
+ BLUE-GREEN-ALGAE; BIDIRECTIONAL HYDROGENASE; CELLULAR-DIFFERENTIATION;
+ CARBON-DIOXIDE; HETEROCYST; FIXATION; GROWTH; EXPRESSION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Motamedian, Ehsan/GPK-8344-2022
+ },
+ORCID-Numbers = {, Ehsan/0000-0001-8750-2879},
+Times-Cited = {13},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000534599100088},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000508345400001,
+Author = {Ahookhosh, Masoud and Fleming, Ronan M. T. and Vuong, Phan T.},
+Title = {Finding zeros of Holder metrically subregular mappings via globally
+ convergent Levenberg-Marquardt methods},
+Journal = {OPTIMIZATION METHODS \& SOFTWARE},
+Year = {2022},
+Volume = {37},
+Number = {1},
+Pages = {113-149},
+Month = {JAN 2},
+Type = {Article},
+DOI = {10.1080/10556788.2020.1712602},
+EarlyAccessDate = {JAN 2020},
+ISSN = {1055-6788},
+EISSN = {1029-4937},
+Keywords = {Nonlinear equation; Holder metric subregularity; non-isolated solutions;
+ Levenberg-Marquardt methods; global convergence; worst-case global
+ complexity; biochemical reaction network kinetics},
+Keywords-Plus = {TRUST-REGION METHOD; LOCAL CONVERGENCE; OPTIMIZATION; EQUATIONS;
+ NONCONVEX; REGULARIZATION; MINIMIZATION; COMPLEXITY; ALGORITHM},
+Research-Areas = {Computer Science; Operations Research \& Management Science; Mathematics},
+Web-of-Science-Categories = {Computer Science, Software Engineering; Operations Research \&
+ Management Science; Mathematics, Applied},
+ResearcherID-Numbers = {Ahookhosh, Masoud/AAB-9712-2022
+ Fleming, Ronan MT/ABC-4093-2021
+ Phan, Vuong/E-3833-2017},
+ORCID-Numbers = {Ahookhosh, Masoud/0000-0003-4206-9789
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Phan, Vuong/0000-0002-1474-994X},
+Times-Cited = {5},
+Journal-ISO = {Optim. Method Softw.},
+Unique-ID = {WOS:000508345400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000511182000001,
+Author = {Halmschlag, Birthe and Hoffmann, Kyra and Hanke, Rene and Putri, Sastia
+ P. and Fukusaki, Eiichiro and Buechs, Jochen and Blank, Lars M.},
+Title = {Comparison of Isomerase and Weimberg Pathway for γ-PGA Production From
+ Xylose by Engineered Bacillus subtilis},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2020},
+Volume = {7},
+Month = {JAN 21},
+Type = {Article},
+DOI = {10.3389/fbioe.2019.00476},
+Article-Number = {476},
+ISSN = {2296-4185},
+Keywords = {Bacillus subtilis; gamma-PGA; online viscosity measurement; metabolic
+ engineering; weimberg pathway; xylose; metabolome analysis},
+Keywords-Plus = {METABOLIC FLUX ANALYSIS; LICHENIFORMIS; SYSTEM; GROWTH; IDENTIFICATION;
+ BIOSYNTHESIS; FERMENTATION; PROTEIN; GENES; ACID},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Blank, Lars M./A-6761-2012},
+ORCID-Numbers = {Hanke, Rene/0000-0002-5886-6611
+ Putri, Sastia Prama/0000-0002-3045-4252
+ Blank, Lars M./0000-0003-0961-4976},
+Times-Cited = {15},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000511182000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000504828500004,
+Author = {Iranmanesh, Elham and Asadollahi, Mohammad Ali and Biria, Davoud},
+Title = {Improving L-phenylacetylcarbinol production in Saccharomyces
+ cerevisiae by in silico aided metabolic engineering},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2020},
+Volume = {308},
+Pages = {27-34},
+Month = {JAN 20},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2019.11.008},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Metabolic engineering; L-phenylacetylcarbinol; Saccharomyces cerevisiae;
+ Flux balance analysis; OptGene},
+Keywords-Plus = {(R)-PHENYLACETYLCARBINOL PRODUCTION; PYRUVATE DECARBOXYLASE; YEAST;
+ BENZALDEHYDE; BIOTRANSFORMATION; CARBINOL; ENZYMES; RECONSTRUCTION;
+ BIOSYNTHESIS; PREDICTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Biria, Davoud/AAN-4433-2021
+ Asadollahi, Mohammad A./AAF-4999-2020},
+ORCID-Numbers = {Biria, Davoud/0000-0002-3820-811X
+ Asadollahi, Mohammad A./0000-0001-9814-3779},
+Times-Cited = {7},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000504828500004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000510691900001,
+Author = {Bator, Isabel and Wittgens, Andreas and Rosenau, Frank and Tiso, Till
+ and Blank, Lars M.},
+Title = {Comparison of Three Xylose Pathways in Pseudomonas putida KT2440
+ for the Synthesis of Valuable Products},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2020},
+Volume = {7},
+Month = {JAN 17},
+Type = {Article},
+DOI = {10.3389/fbioe.2019.00480},
+Article-Number = {480},
+ISSN = {2296-4185},
+Keywords = {Pseudomonas putida; xylose; metabolic engineering; rhamnolipid;
+ phenazine; pyocyanin; flux balance analysis; heterologous production},
+Keywords-Plus = {GRAM-NEGATIVE BACTERIA; ENGINEERING ESCHERICHIA-COLI; BROAD-HOST-RANGE;
+ CARBON-DIOXIDE; DAHMS PATHWAY; METABOLISM; GENE; EXPRESSION; OXIDATION;
+ CLONING},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Tiso, Till/A-5755-2012
+ Rosenau, Frank/AAM-8062-2020
+ Blank, Lars M./A-6761-2012
+ },
+ORCID-Numbers = {Tiso, Till/0000-0003-4420-5609
+ Blank, Lars M./0000-0003-0961-4976
+ Rosenau, Frank/0000-0002-9297-6419},
+Times-Cited = {59},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000510691900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000526660300023,
+Author = {Pusa, Taneli and Ferrarini, Mariana Galvao and Andrade, Ricardo and
+ Mary, Arnaud and Marchetti-Spaccamela, Alberto and Stougie, Leen and
+ Sagot, Marie-France},
+Title = {MOOMIN - Mathematical explOration of `Omics data on a MetabolIc Network},
+Journal = {BIOINFORMATICS},
+Year = {2020},
+Volume = {36},
+Number = {2},
+Pages = {514-523},
+Month = {JAN 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btz584},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {GENE-EXPRESSION DATA; SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI;
+ OXIDATIVE STRESS; ACID RESISTANCE; INTEGRATION; PATHWAYS; ETHANOL;
+ MODELS; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Pusa, Taneli/0000-0003-2183-8876
+ Galvao Ferrarini, Mariana/0000-0002-9574-9991
+ /0000-0002-5933-9960
+ mary, arnaud/0000-0002-8201-227X},
+Times-Cited = {10},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000526660300023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000513635900002,
+Author = {Bekiaris, Pavlos Stephanos and Klamt, Steffen},
+Title = {Automatic construction of metabolic models with enzyme constraints},
+Journal = {BMC BIOINFORMATICS},
+Year = {2020},
+Volume = {21},
+Number = {1},
+Month = {JAN 14},
+Type = {Article},
+DOI = {10.1186/s12859-019-3329-9},
+Article-Number = {19},
+ISSN = {1471-2105},
+Keywords = {Flux balance analysis; Escherichia coli; Metabolic modeling; Enzyme
+ constraints; Protein allocation; Minimal cut sets; Proteomics},
+Keywords-Plus = {ESCHERICHIA-COLI; BIOLOGY; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Klamt, Steffen/0000-0003-2563-7561
+ Bekiaris, Pavlos Stephanos/0000-0002-3047-4253},
+Times-Cited = {46},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000513635900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000526261400001,
+Author = {Salvy, Pierre and Hatzimanikatis, Vassily},
+Title = {The ETFL formulation allows multi-omics integration in
+ thermodynamics-compliant metabolism and expression models},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {JAN 13},
+Type = {Article},
+DOI = {10.1038/s41467-019-13818-7},
+Article-Number = {30},
+ISSN = {2041-1723},
+Keywords-Plus = {ESCHERICHIA-COLI; DATABASE; GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Hatzimanikatis, Vassily/G-6505-2010
+ },
+ORCID-Numbers = {Hatzimanikatis, Vassily/0000-0001-6432-4694
+ SALVY, Pierre/0000-0002-3834-0356},
+Times-Cited = {47},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000526261400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000502527100002,
+Author = {Troendle, Julia and Schoppel, Kristin and Bleidt, Arne and Trachtmann,
+ Natalia and Sprenger, Georg A. and Weuster-Botz, Dirk},
+Title = {Metabolic control analysis of L-tryptophan production with
+ Escherichia coli based on data from short-term perturbation
+ experiments},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2020},
+Volume = {307},
+Pages = {15-28},
+Month = {JAN 10},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2019.10.009},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Metabolic control analysis; Escherichia coli; Glycerol; L-Tryptophan;
+ Metabolic analysis; Perturbation experiment},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; L-PHENYLALANINE; BIOMASS CONCENTRATION; GENETIC
+ MANIPULATION; COMPOSITE PLASMIDS; PATHWAY ANALYSIS; AMINO-ACIDS;
+ D-GLUCOSE; BIOSYNTHESIS; AROMATICS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sprenger, Georg A./E-2384-2011
+ },
+ORCID-Numbers = {Sprenger, Georg A./0000-0002-7879-8978
+ Weuster-Botz, Dirk/0000-0002-1171-4194},
+Times-Cited = {17},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000502527100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000551399500001,
+Author = {Gutierrez, Jahir M. and Feizi, Amir and Li, Shangzhong and Kallehauge,
+ Thomas B. and Hefzi, Hooman and Grav, Lise M. and Ley, Daniel and Hizal,
+ Deniz Baycin and Betenbaugh, Michael J. and Voldborg, Bjorn and
+ Kildegaard, Helene Faustrup and Lee, Gyun Min and Palsson, Bernhard O.
+ and Nielsen, Jens and Lewis, Nathan E.},
+Title = {Genome-scale reconstructions of the mammalian secretory pathway predict
+ metabolic costs and limitations of protein secretion},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2020},
+Volume = {11},
+Number = {1},
+Month = {JAN 2},
+Type = {Article},
+DOI = {10.1038/s41467-019-13867-y},
+Article-Number = {68},
+EISSN = {2041-1723},
+Keywords-Plus = {CHINESE-HAMSTER OVARY; COAGULATION-FACTOR VIII; RECOMBINANT CHO-CELLS;
+ CRYSTAL-STRUCTURE; SYSTEMS BIOTECHNOLOGY; ANTIBODY-PRODUCTION; GENE
+ AMPLIFICATION; BINDING-PROTEIN; MODEL; GLYCOSYLATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Li, Shangzhong/HHD-1335-2022
+ Li, Shangzhong/HHD-1393-2022
+ Lewis, Nathan/ABE-7290-2020
+ Nielsen, Jens Bo/C-7632-2015
+ Li, Shangzhong/Y-6882-2019
+ Lee, Gyun Min/C-2020-2011
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Li, Shangzhong/0000-0003-0272-3942
+ Grav, Lise Marie/0000-0001-8042-7108
+ Voldborg, Bjorn Gunnar/0000-0002-7005-1642
+ Hefzi, Hooman/0009-0003-4067-6224
+ Kildegaard, Helene Faustrup/0000-0003-3727-5721},
+Times-Cited = {53},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000551399500001},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000659665300002,
+Author = {Anand, Shreya and Mukherjee, Koel and Padmanabhan, Padmini},
+Book-Group-Author = {Taylor \& Francis Ltd},
+Title = {An insight to flux-balance analysis for biochemical networks},
+Booktitle = {BIOTECHNOLOGY AND GENETIC ENGINEERING REVIEWS, VOL 36, NO 1},
+Series = {Biotechnology \& Genetic Engineering Reviews},
+Year = {2020},
+Volume = {36},
+Number = {1},
+Pages = {32-55},
+Type = {Review; Book Chapter},
+DOI = {10.1080/02648725.2020.1847440},
+ISSN = {0264-8725},
+EISSN = {2046-5556},
+Keywords = {Flux-balance analysis (FBA); metabolic pathway; system biology; cellular
+ metabolism},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; METABOLIC FLUX; QUANTITATIVE
+ PREDICTION; INTRACELLULAR FLUXES; MICROBIAL-PRODUCTION;
+ CELLULAR-METABOLISM; ADAPTIVE EVOLUTION; OPTIMAL-GROWTH; OPTIMIZATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Times-Cited = {12},
+Journal-ISO = {Biotechnol. Genet. Eng. Rev.},
+Unique-ID = {WOS:000659665300002},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000614648400011,
+Author = {Clark, Teresa J. and Guo, Longyun and Morgan, John and Schwender, Jorg},
+Editor = {Merchant, SS},
+Title = {Modeling Plant Metabolism: From Network Reconstruction to Mechanistic
+ Models},
+Booktitle = {ANNUAL REVIEW OF PLANT BIOLOGY, VOL 71, 2020},
+Series = {Annual Review of Plant Biology},
+Year = {2020},
+Volume = {71},
+Pages = {303-326},
+Type = {Review; Book Chapter},
+DOI = {10.1146/annurev-arplant-050718-100221},
+ISSN = {1543-5008},
+EISSN = {1545-2123},
+ISBN = {978-0-8243-0671-7},
+Keywords = {plant metabolism; metabolic flux; flux balance analysis; systems biology},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESSENTIAL OIL COMPOSITION; GENOME-SCALE MODELS;
+ KINETIC-MODEL; LABELING EXPERIMENTS; CARBON METABOLISM;
+ ESCHERICHIA-COLI; PATHWAY ANALYSIS; BASIC CONCEPTS; OILSEED RAPE},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Schwender, Jorg/P-2282-2014},
+ORCID-Numbers = {Schwender, Jorg/0000-0003-1350-4171},
+Times-Cited = {17},
+Journal-ISO = {Annu. Rev. Plant Biol.},
+Unique-ID = {WOS:000614648400011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000518855000010,
+Author = {Contador, Carolina A. and Lo, Siu-Kit and Chan, Siu H. J. and Lam,
+ Hon-Ming},
+Title = {Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont
+ Sinorhizobium fredii Using Constraint-Based Modeling},
+Journal = {MSYSTEMS},
+Year = {2020},
+Volume = {5},
+Number = {1},
+Month = {JAN-FEB},
+Type = {Article},
+DOI = {10.1128/mSystems.00516-19},
+Article-Number = {e00516-19},
+ISSN = {2379-5077},
+Keywords = {bacteroid; metabolic model; nitrogen fixation; rhizobia; symbiosis},
+Keywords-Plus = {BRADYRHIZOBIUM-JAPONICUM; PERIBACTEROID MEMBRANE; COMPARATIVE GENOMICS;
+ RHIZOBIUM; MUTANT; BACTEROIDS; GENES; BIOSYNTHESIS; NODULATION;
+ CATABOLISM},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Lam, Hon-Ming/A-9866-2008},
+ORCID-Numbers = {Contador Sariego, Carolina/0000-0003-0761-3101
+ Chan, Siu Hung Joshua/0000-0002-7707-656X
+ Lam, Hon-Ming/0000-0002-6673-8740},
+Times-Cited = {15},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000518855000010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000530581200006,
+Author = {Graudenzi, Alex and Maspero, Davide and Damiani, Chiara},
+Title = {FBCA, A Multiscale Modeling Framework Combining Cellular Automata and
+ Flux Balance Analysis},
+Journal = {JOURNAL OF CELLULAR AUTOMATA},
+Year = {2020},
+Volume = {15},
+Number = {1-2},
+Pages = {75-95},
+Type = {Article},
+ISSN = {1557-5969},
+EISSN = {1557-5977},
+Keywords = {Cellular potts model; metabolic networks; flux balance analysis;
+ population dynamics; multi-cellular systems},
+Keywords-Plus = {CANCER; METABOLISM},
+Research-Areas = {Computer Science; Mathematics},
+Web-of-Science-Categories = {Computer Science, Theory \& Methods; Mathematics, Interdisciplinary
+ Applications},
+ResearcherID-Numbers = {Graudenzi, Alex/AAY-5241-2020
+ Maspero, Davide/AHE-1900-2022},
+ORCID-Numbers = {Graudenzi, Alex/0000-0001-5452-1918
+ Maspero, Davide/0000-0001-8519-4331},
+Times-Cited = {4},
+Journal-ISO = {J. Cell. Autom.},
+Unique-ID = {WOS:000530581200006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000509413400016,
+Author = {Maspero, Davide and Damiani, Chiara and Antoniotti, Marco and Graudenzi,
+ Alex and Di Filippo, Marzia and Vanoni, Marco and Caravagna, Giulio and
+ Colombo, Riccardo and Ramazzotti, Daniele and Pescini, Dario},
+Title = {The Influence of Nutrients Diffusion on a Metabolism-driven Model of a
+ Multi-cellular System},
+Journal = {FUNDAMENTA INFORMATICAE},
+Year = {2020},
+Volume = {171},
+Number = {1-4, SI},
+Pages = {279-295},
+Type = {Article},
+DOI = {10.3233/FI-2020-1883},
+ISSN = {0169-2968},
+EISSN = {1875-8681},
+Keywords = {Multi-scale modeling; Cellular Potts Model; Flux Balance Analysis;
+ Diffusion; Cancer development},
+Keywords-Plus = {INTRATUMOR HETEROGENEITY; CANCER; SIMULATION},
+Research-Areas = {Computer Science; Mathematics},
+Web-of-Science-Categories = {Computer Science, Software Engineering; Mathematics, Applied},
+ResearcherID-Numbers = {Maspero, Davide/AHE-1900-2022
+ Vanoni, Marco/AAA-3699-2021
+ Graudenzi, Alex/AAY-5241-2020
+ Caravagna, Giulio/F-5011-2015
+ Pescini, Dario/H-4866-2017
+ },
+ORCID-Numbers = {Maspero, Davide/0000-0001-8519-4331
+ Vanoni, Marco/0000-0002-8690-2587
+ Graudenzi, Alex/0000-0001-5452-1918
+ Caravagna, Giulio/0000-0003-4240-3265
+ Pescini, Dario/0000-0002-3090-4823
+ RAMAZZOTTI, DANIELE/0000-0002-6087-2666},
+Times-Cited = {0},
+Journal-ISO = {Fundam. Inform.},
+Unique-ID = {WOS:000509413400016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000505731300001,
+Author = {Norsigian, Charles J. and Fang, Xin and Seif, Yara and Monk, Jonathan M.
+ and Palsson, Bernhard O.},
+Title = {A workflow for generating multi-strain genome-scale metabolic models of
+ prokaryotes},
+Journal = {NATURE PROTOCOLS},
+Year = {2020},
+Volume = {15},
+Number = {1},
+Pages = {1-14},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1038/s41596-019-0254-3},
+ISSN = {1754-2189},
+EISSN = {1750-2799},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Seif, Yara/T-4012-2017
+ },
+ORCID-Numbers = {Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {36},
+Journal-ISO = {Nat. Protoc.},
+Unique-ID = {WOS:000505731300001},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000507470800022,
+Author = {Pryor, Rosina and Martinez-Martinez, Daniel and Quintaneiro, Leonor and
+ Cabreiro, Filipe},
+Editor = {Insel, PA},
+Title = {The Role of the Microbiome in Drug Response},
+Booktitle = {ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 60},
+Series = {Annual Review of Pharmacology and Toxicology},
+Year = {2020},
+Volume = {60},
+Pages = {417-435},
+Type = {Review; Book Chapter},
+DOI = {10.1146/annurev-pharmtox-010919-023612},
+ISSN = {0362-1642},
+EISSN = {1545-4304},
+ISBN = {978-0-8243-0460-7},
+Keywords = {microbiome; drugs; metabolism; antipsychotics; metformin; cancer},
+Keywords-Plus = {GLUCAGON-LIKE PEPTIDE-1; CHAIN FATTY-ACIDS; GUT MICROBIOTA;
+ COLORECTAL-CANCER; INTESTINAL MICROBIOTA; METFORMIN ALTERS; C. ELEGANS;
+ GLUCOSE; IMPACT; METABOLISM},
+Research-Areas = {Pharmacology \& Pharmacy; Toxicology},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy; Toxicology},
+ORCID-Numbers = {Martinez-Martinez, Daniel/0000-0001-8468-1357
+ Cabreiro, Filipe/0000-0002-3696-4843},
+Times-Cited = {25},
+Journal-ISO = {Annu. Rev. Pharmacol. Toxicol.},
+Unique-ID = {WOS:000507470800022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000607303700020,
+Author = {Wanichthanarak, Kwanjeera and Boonchai, Chuthamas and Kojonna,
+ Thammaporn and Chadchawan, Supachitra and Sangwongchai, Wichian and
+ Thitisaksakul, Maysaya},
+Title = {Deciphering rice metabolic flux reprograming under salinity stress via
+ in silico metabolic modeling},
+Journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
+Year = {2020},
+Volume = {18},
+Pages = {3555-3566},
+Type = {Article},
+DOI = {10.1016/j.csbj.2020.11.023},
+ISSN = {2001-0370},
+Keywords = {Rice (Oryza sativa L.); Salinity stress; Systems biology; Metabolic flux
+ analysis; Metabolic modeling; Transcriptomics; Metabolomics; Multi-omics
+ analysis},
+Keywords-Plus = {SALT-TOLERANCE; BIOCHEMICAL-CHARACTERIZATION; CARBOHYDRATE-METABOLISM;
+ ANTIOXIDANT RESPONSES; ARABIDOPSIS-THALIANA; BIOSYNTHESIS; AUXIN; SET;
+ PHOTORESPIRATION; EXPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Wanichthanarak, Kwanjeera/AAV-7790-2021
+ },
+ORCID-Numbers = {Thitisaksakul, Maysaya/0000-0003-1485-2610},
+Times-Cited = {10},
+Journal-ISO = {Comp. Struct. Biotechnol. J..},
+Unique-ID = {WOS:000607303700020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000509311700004,
+Author = {Mugahid, D. A. and Sengul, T. G. and You, X. and Wang, Y. and Steil, L.
+ and Bergmann, N. and Radke, M. H. and Ofenbauer, A. and Gesell-Salazar,
+ M. and Balogh, A. and Kempa, S. and Tursun, B. and Robbins, C. T. and
+ Voelker, U. and Chen, W. and Nelson, L. and Gotthardt, M.},
+Title = {Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal
+ Metabolic and Signaling Pathways that Protect against Muscle Atrophy},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2019},
+Volume = {9},
+Month = {DEC 27},
+Type = {Article},
+DOI = {10.1038/s41598-019-56007-8},
+Article-Number = {19976},
+ISSN = {2045-2322},
+Keywords-Plus = {DUPLEX-SPECIFIC NUCLEASE; SKELETAL-MUSCLE; UBIQUITIN LIGASES; DISUSE
+ ATROPHY; WINTER SLEEP; RNA-SEQ; KAPPA-B; GENE; EXPRESSION; ACTIVATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {cao, yutong/JJF-4531-2023
+ Zeng, Yun/JFK-6190-2023
+ Gotthardt, Michael/ABE-8274-2021
+ Li, Zilong/JEZ-8642-2023
+ kempa, stefan/C-5213-2008
+ liu, jiaming/IWE-3196-2023
+ Steil, Leif/F-1246-2010
+ },
+ORCID-Numbers = {Gotthardt, Michael/0000-0003-1788-3172
+ kempa, stefan/0000-0002-0696-9299
+ Steil, Leif/0000-0002-0733-8421
+ Radke, Michael/0000-0003-0112-9917
+ Wang, Yongbo/0000-0003-4383-9423
+ Megahed, Doaa/0000-0002-3455-2992
+ Ofenbauer, Andreas/0000-0003-0379-9105
+ Tursun, Baris/0000-0001-7293-8629},
+Times-Cited = {14},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000509311700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000503858100001,
+Author = {Wang, Guan and Haringa, Cees and Tang, Wenjun and Noorman, Henk and Chu,
+ Ju and Zhuang, Yingping and Zhang, Siliang},
+Title = {Coupled metabolic-hydrodynamic modeling enabling rational scale-up of
+ industrial bioprocesses},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2020},
+Volume = {117},
+Number = {3},
+Pages = {844-867},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1002/bit.27243},
+EarlyAccessDate = {DEC 2019},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {CFD; Euler-Langrange; metabolic model; metabolomics; population
+ heterogeneity; scale down},
+Keywords-Plus = {INTER-COMPARTMENT INTERACTION; DYNAMIC PATHWAY REGULATION; POPULATION
+ BALANCE MODEL; SYSTEMS BIOLOGY; PENICILLIUM-CHRYSOGENUM;
+ ESCHERICHIA-COLI; QUANTITATIVE METABOLOMICS; SACCHAROMYCES-CEREVISIAE;
+ CORYNEBACTERIUM-GLUTAMICUM; SYNTHETIC BIOLOGY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {14},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000503858100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000503211200001,
+Author = {Gokhale, Sucheta and Bhaduri, Anirban},
+Title = {Provitamin D3 modulation through prebiotics supplementation:
+ simulation based assessment},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2019},
+Volume = {9},
+Month = {DEC 17},
+Type = {Article},
+DOI = {10.1038/s41598-019-55699-2},
+Article-Number = {19267},
+ISSN = {2045-2322},
+Keywords-Plus = {VITAMIN-D ABSORPTION; 25-HYDROXYVITAMIN D; D DEFICIENCY; SKIN;
+ METABOLISM; POPULATIONS; PREDICTION; CAPACITY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {11},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000503211200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000500552900001,
+Author = {Johannsson, Freyr and Arnason, Niels A. and Landroe, Ragna and
+ Gudmundsson, Sveinn and Sigurjonsson, Olafur E. and Rolfsson, Ottar},
+Title = {Metabolomics study of platelet concentrates photochemically treated with
+ amotosalen and UVA light for pathogen inactivation},
+Journal = {TRANSFUSION},
+Year = {2020},
+Volume = {60},
+Number = {2},
+Pages = {367-377},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1111/trf.15610},
+EarlyAccessDate = {DEC 2019},
+ISSN = {0041-1132},
+EISSN = {1537-2995},
+Keywords-Plus = {BLOOD-DERIVED PLATELETS; THERAPEUTIC-EFFICACY;
+ FUNCTIONAL-CHARACTERISTICS; BACTERIAL-CONTAMINATION; APHERESIS
+ PLATELETS; CELLULAR-METABOLISM; SPECTROMETRY DATA; ULTRAVIOLET;
+ COMPONENTS; STORAGE},
+Research-Areas = {Hematology},
+Web-of-Science-Categories = {Hematology},
+ORCID-Numbers = {Rolfsson, Ottar/0000-0003-4258-6057
+ Sigurjonsson, Olafur/0000-0002-4968-842X},
+Times-Cited = {4},
+Journal-ISO = {Transfusion},
+Unique-ID = {WOS:000500552900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000501308400001,
+Author = {Devika, N. T. and Raman, Karthik},
+Title = {Deciphering the metabolic capabilities of Bifidobacteria using
+ genome-scale metabolic models},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2019},
+Volume = {9},
+Month = {DEC 3},
+Type = {Article},
+DOI = {10.1038/s41598-019-54696-9},
+Article-Number = {18222},
+ISSN = {2045-2322},
+Keywords-Plus = {GUT MICROBIOTA; PROBIOTIC BACTERIA; CONTROLLED-TRIAL; STRAINS; IMPACT;
+ PREDICTION; LACTIS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019},
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093},
+Times-Cited = {27},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000501308400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000511714800021,
+Author = {Ahookhosh, Masoud and Aragon Artacho, Francisco J. and Fleming, Ronan M.
+ T. and Vuong, Phan T.},
+Title = {Local convergence of the Levenberg-Marquardt method under Holder metric
+ subregularity},
+Journal = {ADVANCES IN COMPUTATIONAL MATHEMATICS},
+Year = {2019},
+Volume = {45},
+Number = {5-6},
+Pages = {2771-2806},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1007/s10444-019-09708-7},
+ISSN = {1019-7168},
+EISSN = {1572-9044},
+Keywords = {Nonlinear equation; Levenberg-Marquardt method; Local convergence rate;
+ Holder metric subregularity; Lojasiewicz inequality},
+Keywords-Plus = {NONLINEAR EQUATIONS; ERROR-BOUNDS; LIPSCHITZIAN DERIVATIVES; ALGORITHM;
+ MAPPINGS; SYSTEMS},
+Research-Areas = {Mathematics},
+Web-of-Science-Categories = {Mathematics, Applied},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Artacho, Francisco Javier Aragón/C-2531-2012
+ Ahookhosh, Masoud/AAB-9712-2022
+ Phan, Vuong/E-3833-2017},
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Artacho, Francisco Javier Aragón/0000-0002-2445-8011
+ Ahookhosh, Masoud/0000-0003-4206-9789
+ Phan, Vuong/0000-0002-1474-994X},
+Times-Cited = {16},
+Journal-ISO = {Adv. Comput. Math.},
+Unique-ID = {WOS:000511714800021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000500728800021,
+Author = {Goldford, Joshua E. and Hartman, Hyman and Marsland, III, Robert and
+ Segre, Daniel},
+Title = {Environmental boundary conditions for the origin of life converge to an
+ organo-sulfur metabolism},
+Journal = {NATURE ECOLOGY \& EVOLUTION},
+Year = {2019},
+Volume = {3},
+Number = {12},
+Pages = {1715+},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1038/s41559-019-1018-8},
+ISSN = {2397-334X},
+Keywords-Plus = {EVOLUTIONARY INNOVATION; ADAPTIVE EVOLUTION; SULFUR-COMPOUNDS; CARBON
+ FIXATION; IRON SULFIDE; BIOCHEMISTRY; REDUCTION; NETWORKS; PATHWAYS;
+ DATABASE},
+Research-Areas = {Environmental Sciences \& Ecology; Evolutionary Biology},
+Web-of-Science-Categories = {Ecology; Evolutionary Biology},
+ResearcherID-Numbers = {Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914
+ Marsland III, Robert/0000-0002-5007-6877
+ Goldford, Joshua/0000-0001-7315-8018},
+Times-Cited = {28},
+Journal-ISO = {Nat. Ecol. Evol.},
+Unique-ID = {WOS:000500728800021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000499071100014,
+Author = {Lopatkin, Allison J. and Stokes, Jonathan M. and Zheng, Erica J. and
+ Yang, Jason H. and Takahashi, Melissa K. and You, Lingchong and Collins,
+ James J.},
+Title = {Bacterial metabolic state more accurately predicts antibiotic lethality
+ than growth rate},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2019},
+Volume = {4},
+Number = {12},
+Pages = {2109-2117},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1038/s41564-019-0536-0},
+ISSN = {2058-5276},
+Keywords-Plus = {ESCHERICHIA-COLI; EFFICIENCY; EFFICACY; BATCH},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {yang, jason/JFA-5026-2023
+ Yang, Jason H./AAB-2608-2019
+ },
+ORCID-Numbers = {Yang, Jason H./0000-0003-0921-4657
+ Takahashi, Melissa/0000-0003-4937-2924
+ Collins, James/0000-0002-5560-8246},
+Times-Cited = {125},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000499071100014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000504805800016,
+Author = {Meyer, Adam and Saaem, Ishtiaq and Silverman, Adam and Varaljay, Vanessa
+ A. and Mickol, Rebecca and Blum, Steven and Tobias, Alexander V. and
+ Schwalm, III, Nathan D. and Mojadedi, Wais and Onderko, Elizabeth and
+ Bristol, Cassandra and Liu, Shangtao and Pratt, Katelin and Casini,
+ Arturo and Eluere, Raissa and Moser, Felix and Drake, Carrie and Gupta,
+ Maneesh and Kelley-Loughnane, Nancy and Lucks, Julius P. and Akingbade,
+ Katherine L. and Lux, Matthew P. and Glaven, Sarah and Crookes-Goodson,
+ Wendy and Jewett, Michael C. and Gordon, D. Benjamin and Voigt,
+ Christopher A.},
+Title = {Organism Engineering for the Bioproduction of the
+ Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG)},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2019},
+Volume = {8},
+Number = {12},
+Pages = {2746-2755},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1021/acssynbio.9b00393},
+ISSN = {2161-5063},
+Keywords = {synthetic biology; military environments; Tri-Service; metabolic
+ engineering; enzyme mining; TX-TL; cell-free sensing},
+Keywords-Plus = {QUORUM-SENSING MOLECULES; DESIGN; SYSTEM; BIOSYNTHESIS; EXPRESSION;
+ REPOSITORY; FRAMEWORK; BIOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Mickol, Rebecca/X-6655-2019
+ Jewett, Michael C/E-3506-2010
+ Lux, Matthew/AFW-4004-2022
+ },
+ORCID-Numbers = {Mickol, Rebecca/0000-0002-4493-7263
+ Jewett, Michael/0000-0003-2948-6211
+ Goodson, Wendy/0000-0001-5147-9291
+ Schwalm, Nathan/0000-0003-1048-8049
+ Onderko, Elizabeth/0009-0003-5329-3468
+ Silverman, Adam/0000-0002-1990-6609
+ Casini, Arturo/0000-0003-2828-5223},
+Times-Cited = {14},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000504805800016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000506646400038,
+Author = {Portela, Rui M. C. and Richelle, Anne and Dumas, Patrick and von Stosch,
+ Moritz},
+Title = {Time Integrated Flux Analysis: Exploiting the Concentration Measurements
+ Directly for Cost-Effective Metabolic Network Flux Analysis},
+Journal = {MICROORGANISMS},
+Year = {2019},
+Volume = {7},
+Number = {12},
+Month = {DEC},
+Type = {Article},
+DOI = {10.3390/microorganisms7120620},
+Article-Number = {620},
+EISSN = {2076-2607},
+Keywords = {Metabolic Flux Analysis; Flux Balance Analysis; Flux Variability
+ Analysis; Metabolic modeling; Specific Flux Estimation; Specific Rate
+ Estimation; Time Integrated Flux Analysis},
+Keywords-Plus = {MODELS; IDENTIFICATION; PHENOTYPE; GROWTH},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Portela, Rui M. C./D-2013-2013
+ },
+ORCID-Numbers = {Portela, Rui M. C./0000-0002-3627-6477},
+Times-Cited = {1},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000506646400038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000501738100005,
+Author = {Rawls, Kristopher D. and Blais, Edik M. and Dougherty, V, Bonnie and
+ Vinnakota, Kalyan C. and Pannala, Venkat R. and Wallqvist, Anders and
+ Kolling, Glynis L. and Papin, Jason A.},
+Title = {Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations
+ in Primary Hepatocytes},
+Journal = {TOXICOLOGICAL SCIENCES},
+Year = {2019},
+Volume = {172},
+Number = {2},
+Pages = {279-291},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1093/toxsci/kfz197},
+ISSN = {1096-6080},
+EISSN = {1096-0929},
+Keywords = {metabolism; constraint-based modeling; toxicology; transcriptomics;
+ metabolomics},
+Keywords-Plus = {ACETAMINOPHEN-INDUCED HEPATOTOXICITY; GENE-EXPRESSION;
+ CARBON-TETRACHLORIDE; KIDNEY INJURY; PREDICTION; MODELS; IDENTIFICATION;
+ METABONOMICS; MECHANISMS; BIOMARKERS},
+Research-Areas = {Toxicology},
+Web-of-Science-Categories = {Toxicology},
+ResearcherID-Numbers = {Vinnakota, Kalyan/G-4706-2010},
+ORCID-Numbers = {Pannala, Venkat/0000-0002-3368-2496
+ Dougherty, Bonnie/0000-0002-1454-4899
+ Rawls, Kristopher/0000-0001-5873-0127
+ Vinnakota, Kalyan/0000-0003-2185-2213},
+Times-Cited = {9},
+Journal-ISO = {Toxicol. Sci.},
+Unique-ID = {WOS:000501738100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000505731200008,
+Author = {Schwalm, III, Nathan D. and Mojadedi, Wais and Gerlach, Elliot S. and
+ Benyamin, Marcus and Perisin, Matthew A. and Akingbade, Katherine L.},
+Title = {Developing a Microbial Consortium for Enhanced Metabolite Production
+ from Simulated Food Waste},
+Journal = {FERMENTATION-BASEL},
+Year = {2019},
+Volume = {5},
+Number = {4},
+Month = {DEC},
+Type = {Article},
+DOI = {10.3390/fermentation5040098},
+Article-Number = {98},
+EISSN = {2311-5637},
+Keywords = {butyrate; Clostridium beijerinckii; cross-feeding; food waste;
+ genome-scale metabolic model; hydrogen; lactate; Yokenella regensburgei},
+Keywords-Plus = {HYDROGEN-PRODUCTION; ESCHERICHIA-COLI; CLOSTRIDIUM-BEIJERINCKII;
+ ANAEROBIC-DIGESTION; SOLVENT PRODUCTION; COCULTURE; IDENTIFICATION;
+ FERMENTATION; BIOREACTORS; BUTYRICUM},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ORCID-Numbers = {Benyamin, Marcus/0000-0002-7081-9914
+ Schwalm, Nathan/0000-0003-1048-8049},
+Times-Cited = {15},
+Journal-ISO = {FERMENTATION},
+Unique-ID = {WOS:000505731200008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000499071100011,
+Author = {Zaramela, Livia S. and Martino, Cameron and Alisson-Silva, Frederico and
+ Rees, Steven D. and Diaz, Sandra L. and Chuzel, Lea and Ganatra, Mehul
+ B. and Taron, Christopher H. and Secrest, Patrick and Zuniga, Cristal
+ and Huang, Jianbo and Siegel, Dionicio and Chang, Geoffrey and Varki,
+ Ajit and Zengler, Karsten},
+Title = {Gut bacteria responding to dietary change encode sialidases that exhibit
+ preference for red meat-associated carbohydrates},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2019},
+Volume = {4},
+Number = {12},
+Pages = {2082-2089},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1038/s41564-019-0564-9},
+ISSN = {2058-5276},
+Keywords-Plus = {VERTEBRATE AMINO-SUGARS; METABOLISM; SPECIFICITY; PREDICTION; SEQUENCE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Rees, Steven/AAM-4932-2020
+ da Silva, Frederico/AAY-4758-2021
+ Zuniga, Cristal/CAA-0015-2022
+ Zaramela, Lívia Soares/AAD-2687-2022
+ },
+ORCID-Numbers = {da Silva, Frederico/0000-0001-6717-2518
+ Zaramela, Lívia Soares/0000-0002-1065-3799
+ Rees, Steven/0000-0002-2258-7469
+ Martino, Cameron/0000-0001-9334-1258
+ Chuzel, Lea/0000-0001-7185-5872
+ Zuniga, Cristal/0000-0002-0135-7429
+ Taron, Christopher/0000-0001-8149-4556},
+Times-Cited = {41},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000499071100011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000499071100022,
+Author = {Zuniga, Cristal and Li, Chien-Ting and Yu, Geng and Al-Bassam, Mahmoud
+ M. and Li, Tingting and Jiang, Liqun and Zaramela, Livia S. and
+ Guarnieri, Michael and Betenbaugh, Michael J. and Zengler, Karsten},
+Title = {Environmental stimuli drive a transition from cooperation to competition
+ in synthetic phototrophic communities},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2019},
+Volume = {4},
+Number = {12},
+Pages = {2184-2191},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1038/s41564-019-0567-6},
+ISSN = {2058-5276},
+Keywords-Plus = {FUNCTIONAL DIVERSITY; LICHENS; EVOLUTION; GROWTH; METABOLISM;
+ PREDICTION; SURVIVAL},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {L, J/JEF-9564-2023
+ Li, Tingting/HKE-0812-2023
+ zhang, ting/IYT-0642-2023
+ Zaramela, Lívia Soares/AAD-2687-2022
+ Zuniga, Cristal/CAA-0015-2022
+ },
+ORCID-Numbers = {Zaramela, Lívia Soares/0000-0002-1065-3799
+ Zuniga, Cristal/0000-0002-0135-7429
+ Guarnieri, Michael/0000-0003-1403-9689
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {46},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000499071100022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000499634100001,
+Author = {Katzir, Rotem and Polat, Ibrahim H. and Harel, Michal and Katz, Shir and
+ Foguet, Carles and Selivanov, Vitaly A. and Sabatier, Philippe and
+ Cascante, Marta and Geiger, Tamar and Ruppin, Eytan},
+Title = {The landscape of tiered regulation of breast cancer cell metabolism},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2019},
+Volume = {9},
+Month = {NOV 28},
+Type = {Article},
+DOI = {10.1038/s41598-019-54221-y},
+Article-Number = {17760},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; TRANSCRIPTIONAL REGULATION; PROTEIN; NETWORK;
+ PHOSPHORYLATION; PREDICTION; DISCOVERY},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {CASCANTE, MARTA/AAG-4355-2022
+ Geiger, Tamar/C-2349-2014
+ CASCANTE, MARTA/AFK-5991-2022
+ Polat, Ibrahim Halil/R-3739-2017
+ Polat, Ibrahim Halil/W-2678-2018
+ Foguet, Carles/W-4864-2018
+ },
+ORCID-Numbers = {CASCANTE, MARTA/0000-0002-2062-4633
+ CASCANTE, MARTA/0000-0002-2062-4633
+ Polat, Ibrahim Halil/0000-0003-2196-6667
+ Polat, Ibrahim Halil/0000-0003-2196-6667
+ Foguet, Carles/0000-0001-8494-9595
+ Geiger, Tamar/0000-0002-9526-197X},
+Times-Cited = {13},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000499634100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000501511700002,
+Author = {Nurcholis, Mochamad and Lertwattanasakul, Noppon and Rodrussamee,
+ Nadchanok and Kosaka, Tomoyuki and Murata, Masayuki and Yamada, Mamoru},
+Title = {Integration of comprehensive data and biotechnological tools for
+ industrial applications of Kluyveromyces marxianus},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2020},
+Volume = {104},
+Number = {2},
+Pages = {475-488},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1007/s00253-019-10224-3},
+EarlyAccessDate = {NOV 2019},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Kluyveromyces marxianus; Useful materials production; Transcriptome;
+ Biotechnological tools; Glucose sensing; Mig1 regulation},
+Keywords-Plus = {BETA-GALACTOSIDASE ACTIVITY; THERMOTOLERANT YEAST; GLUCOSE REPRESSION;
+ ETHANOL-PRODUCTION; XYLITOL PRODUCTION; HIGH-TEMPERATURE;
+ SACCHAROMYCES-CEREVISIAE; TRANSCRIPTOME ANALYSIS; EXTRACELLULAR
+ INULINASE; DEBARYOMYCES-HANSENII},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nurcholis, Mochamad/AAR-9186-2020
+ },
+ORCID-Numbers = {Nurcholis, Mochamad/0000-0002-1517-3698
+ Lertwattanasakul, Noppon/0000-0003-3590-7545
+ Yamada, Mamoru/0000-0003-4354-7324
+ Kosaka, Tomoyuki/0000-0002-8181-9127},
+Times-Cited = {26},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000501511700002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000505248800001,
+Author = {Chauhan, Nutan and Singh, Shailza},
+Title = {Integrative Computational Framework for Understanding Metabolic
+ Modulation in Leishmania},
+Journal = {FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY},
+Year = {2019},
+Volume = {7},
+Month = {NOV 19},
+Type = {Article},
+DOI = {10.3389/fbioe.2019.00336},
+Article-Number = {336},
+ISSN = {2296-4185},
+Keywords = {metabolic network; Forman curvature; Forman-Ricci curvature; network
+ topology; Leishmania; flux balance analysis},
+Keywords-Plus = {ESCHERICHIA-COLI; RICCI CURVATURE; GLYOXALASE SYSTEM; METHYLGLYOXAL;
+ NETWORK; PATHWAY; MODELS; GENERATION; PROTEINS; BIOLOGY},
+Research-Areas = {Biotechnology \& Applied Microbiology; Science \& Technology - Other
+ Topics},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Multidisciplinary Sciences},
+Times-Cited = {4},
+Journal-ISO = {Front. Bioeng. Biotechnol.},
+Unique-ID = {WOS:000505248800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000518140400001,
+Author = {Srinivasan, Aparajitha and Vijayakumar, S. and Raman, Karthik and
+ Srivastava, Smita},
+Title = {Rational metabolic engineering for enhanced alpha-tocopherol production
+ in Helianthus annuus cell culture},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2019},
+Volume = {151},
+Month = {NOV 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2019.107256},
+Article-Number = {107256},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Alpha-tocopherol; Helianthus annuus; Metabolic engineering;
+ Overexpression; Cell suspension},
+Keywords-Plus = {VITAMIN-E CONTENT; HYDROXYPHENYLPYRUVATE-DIOXYGENASE; ARABIDOPSIS;
+ TOBACCO; OVEREXPRESSION; BIOSYNTHESIS; GROWTH; RECONSTRUCTION; ENZYMES;
+ PLANTS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019
+ Srinivasan, Aparajitha/GQQ-4182-2022},
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ },
+Times-Cited = {11},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000518140400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000501261600001,
+Author = {Kalnenieks, Uldis and Balodite, Elina and Straehler, Steffi and
+ Strazdina, Inese and Rex, Julia and Pentjuss, Agris and Fuchino, Katsuya
+ and Bruheim, Per and Rutkis, Reinis and Pappas, Katherine M. and Poole,
+ Robert K. and Sawodny, Oliver and Bettenbrock, Katja},
+Title = {Improvement of Acetaldehyde Production in Zymomonas mobilis by
+ Engineering of Its Aerobic Metabolism},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2019},
+Volume = {10},
+Month = {NOV 14},
+Type = {Article},
+DOI = {10.3389/fmicb.2019.02533},
+Article-Number = {2533},
+ISSN = {1664-302X},
+Keywords = {Zymomonas mobilis; acetaldehyde; metabolic engineering; stoichiometric
+ model; metabolomics},
+Keywords-Plus = {ALCOHOL-DEHYDROGENASE ISOENZYMES; GROWTH; ETHANOL; GENE;
+ PHOSPHOMETABOLOME; RESPIRATION; EXPRESSION; CLONING},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {fuchino, katsuya/AAY-2784-2021
+ Bettenbrock, Katja/AAN-5812-2020
+ },
+ORCID-Numbers = {fuchino, katsuya/0000-0002-1825-2500
+ Pentjuss, Agris/0000-0001-7880-5130
+ Bruheim, Per/0000-0002-7851-8083},
+Times-Cited = {21},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000501261600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000496914200010,
+Author = {Stanway, Rebecca R. and Bushell, Ellen and Chiappino-Pepe, Anush and
+ Roques, Magali and Sanderson, Theo and Franke-Fayard, Blandine and
+ Caldelari, Reto and Golomingi, Murielle and Nyonda, Mary and Pandey,
+ Vikash and Schwach, Frank and Chevalley, Severine and Ramesar, Jai and
+ Metcalf, Tom and Herd, Colin and Burda, Paul-Christian and Rayner,
+ Julian C. and Soldati-Favre, Dominique and Janse, Chris J. and
+ Hatzimanikatis, Vassily and Billker, Oliver and Heussler, Volker T.},
+Title = {Genome-Scale Identification of Essential Metabolic Processes for
+ Targeting the Plasmodium Liver Stage},
+Journal = {CELL},
+Year = {2019},
+Volume = {179},
+Number = {5},
+Pages = {1112+},
+Month = {NOV 14},
+Type = {Article},
+DOI = {10.1016/j.cell.2019.10.030},
+ISSN = {0092-8674},
+EISSN = {1097-4172},
+Keywords-Plus = {ESCHERICHIA-COLI; NUTRITIONAL-REQUIREMENTS; CARBOHYDRATE-METABOLISM;
+ LACTATE PRODUCTION; MALARIA PARASITES; FALCIPARUM; PROTEINS; REVEALS;
+ RESOURCE; DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Chiappino Pepe, Anush/AAY-8830-2021
+ Chiappino-Pepe, Anush/E-6560-2017
+ Hatzimanikatis, Vassily/G-6505-2010
+ Heussler, Volker/H-9322-2019
+ },
+ORCID-Numbers = {Chiappino Pepe, Anush/0000-0002-3993-907X
+ Chiappino-Pepe, Anush/0000-0002-3993-907X
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Heussler, Volker/0000-0001-8028-9825
+ Sanderson, Theo/0000-0003-4177-2851
+ Rayner, Julian/0000-0002-9835-1014
+ Burda, Paul-Christian/0000-0003-0461-4352},
+Times-Cited = {63},
+Journal-ISO = {Cell},
+Unique-ID = {WOS:000496914200010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000496717500004,
+Author = {Hertel, Johannes and Harms, Amy C. and Heinken, Almut and Baldini,
+ Federico and Thinnes, Cyrille C. and Glaab, Enrico and Vasco, Daniel A.
+ and Pietzner, Maik and Stewart, Isobel D. and Wareham, Nicholas J. and
+ Langenberg, Claudia and Trenkwalder, Claudia and Krueger, Rejko and
+ Hankemeier, Thomas and Fleming, Ronan M. T. and Mollenhauer, Brit and
+ Thiele, Ines},
+Title = {Integrated Analyses of Microbiome and Longitudinal Metabolome Data
+ Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's
+ Disease},
+Journal = {CELL REPORTS},
+Year = {2019},
+Volume = {29},
+Number = {7},
+Pages = {1767+},
+Month = {NOV 12},
+Type = {Article},
+DOI = {10.1016/j.celrep.2019.10.035},
+ISSN = {2211-1247},
+Keywords-Plus = {GUT MICROBIOTA; HYDROGEN-SULFIDE; ACID; GLUTATHIONE; INHIBITION;
+ MECHANISM; NONMOTOR; BARRIER; WEIGHT; DESIGN},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Fleming, Ronan MT/ABC-4093-2021
+ Glaab, Enrico/A-9136-2012
+ Hankemeier, Thomas/V-5407-2019
+ Langenberg, Claudia/ABG-9067-2021
+ Hertel, Johannes/HZJ-3685-2023
+ Trenkwalder, Claudia/AHD-1232-2022
+ Trenkwalder, Claudia/ABD-6559-2021
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Glaab, Enrico/0000-0003-3977-7469
+ Hankemeier, Thomas/0000-0001-7871-2073
+ Langenberg, Claudia/0000-0002-5017-7344
+ Hertel, Johannes/0000-0002-7641-0132
+ Trenkwalder, Claudia/0000-0001-6407-1199
+ Wareham, Nicholas/0000-0003-1422-2993
+ Krueger, Rejko/0000-0003-4258-6241
+ Pietzner, Maik/0000-0003-3437-9963},
+Times-Cited = {84},
+Journal-ISO = {Cell Reports},
+Unique-ID = {WOS:000496717500004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000495588100001,
+Author = {Nogales, Juan and Mueller, Joshua and Gudmundsson, Steinn and Canalejo,
+ Francisco J. and Duque, Estrella and Monk, Jonathan and Feist, Adam M.
+ and Ramos, Juan Luis and Niu, Wei and Palsson, Bernhard O.},
+Title = {High-quality genome-scale metabolic modelling of Pseudomonas
+ putida highlights its broad metabolic capabilities},
+Journal = {ENVIRONMENTAL MICROBIOLOGY},
+Year = {2020},
+Volume = {22},
+Number = {1},
+Pages = {255-269},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1111/1462-2920.14843},
+EarlyAccessDate = {NOV 2019},
+ISSN = {1462-2912},
+EISSN = {1462-2920},
+Keywords-Plus = {HIGH-THROUGHPUT; LIGNIN; GROWTH; KT2440; RECONSTRUCTION; STRAINS;
+ NETWORK; OPTIMIZATION; DEGRADATION; OPTIMALITY},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Nogales, Juan/Y-8829-2019
+ },
+ORCID-Numbers = {Ramos, Juan L./0000-0002-8731-7435
+ Niu, Wei/0000-0003-3826-1276
+ Nogales, Juan/0000-0002-4961-0833},
+Times-Cited = {82},
+Journal-ISO = {Environ. Microbiol.},
+Unique-ID = {WOS:000495588100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000484647000005,
+Author = {Biz, Alessandra and Proulx, Scott and Xu, Zhiqing and Siddartha, Kavya
+ and Indrayanti, Alex Mulet and Mahadevan, Radhakrishnan},
+Title = {Systems biology based metabolic engineering for non-natural chemicals},
+Journal = {BIOTECHNOLOGY ADVANCES},
+Year = {2019},
+Volume = {37},
+Number = {6},
+Month = {NOV 1},
+Type = {Review},
+DOI = {10.1016/j.biotechadv.2019.04.001},
+Article-Number = {107379},
+ISSN = {0734-9750},
+EISSN = {1873-1899},
+Keywords = {Stems biology; Non-natural chemicals; In-silico pathway design; Directed
+ evolution; de novo protein engineering; Genome-scale models; Flux
+ balance analysis; Dynamic control; Growth-coupled production;
+ Orthogonality},
+Keywords-Plus = {DYNAMIC PATHWAY REGULATION; MUCONIC ACID PRODUCTION; ESCHERICHIA-COLI;
+ MICROBIAL-PRODUCTION; COMPUTATIONAL DESIGN; BIOCHEMICAL REACTIONS;
+ STRAIN OPTIMIZATION; DIRECTED EVOLUTION; RATIONAL DESIGN;
+ GENE-EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Xu, Zhiqing/AAJ-2198-2020
+ },
+ORCID-Numbers = {Mulet Indrayanti, Alex/0000-0002-7416-883X},
+Times-Cited = {31},
+Journal-ISO = {Biotechnol. Adv.},
+Unique-ID = {WOS:000484647000005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000503185300009,
+Author = {Bodor, Zsolt and Lanyi, Szabolcs and Albert, Beata and Bodor, Katalin
+ and Nechifor, Aurelia Cristina and Miklossy, Ildiko},
+Title = {Model Driven Analysis of the Biosynthesis of 1,4-butanediol from
+ Renewable Feedstocks in Escherichia coli},
+Journal = {REVISTA DE CHIMIE},
+Year = {2019},
+Volume = {70},
+Number = {11},
+Pages = {3808-3817},
+Month = {NOV},
+Type = {Article},
+ISSN = {0034-7752},
+Keywords = {renewable feedstocks; bioconversion; 1,4-butanediol; COBRA; E. coli;
+ strain design},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GENOME-SCALE MODELS; IN-SILICO; CIUC BASIN;
+ QUANTITATIVE PREDICTION; EASTERN CARPATHIANS; CELLULAR-METABOLISM;
+ ADAPTIVE EVOLUTION; SYSTEMS BIOLOGY; PATHWAY},
+Research-Areas = {Chemistry; Engineering},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary; Engineering, Chemical},
+ResearcherID-Numbers = {Aurelia Cristina, Nechifor/AAD-4286-2022
+ Bodor, Zsolt/ABE-2182-2020
+ },
+ORCID-Numbers = {Aurelia Cristina, Nechifor/0000-0001-8891-8948
+ Bodor, Zsolt/0000-0003-1386-6957},
+Times-Cited = {1},
+Journal-ISO = {Rev. Chim.},
+Unique-ID = {WOS:000503185300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000518852300008,
+Author = {Noecker, Cecilia and Chiu, Hsuan-Chao and McNally, Colin P. and
+ Borenstein, Elhanan},
+Title = {Defining and Evaluating Microbial Contributions to Metabolite Variation
+ in Microbiome-Metabolome Association Studies},
+Journal = {MSYSTEMS},
+Year = {2019},
+Volume = {4},
+Number = {6},
+Month = {NOV-DEC},
+Type = {Article},
+DOI = {10.1128/mSystems.00579-19},
+Article-Number = {e00579-19},
+ISSN = {2379-5077},
+Keywords = {correlation; evaluation; metabolic modeling; metabolomics; microbiome},
+Keywords-Plus = {GUT MICROBIOME; DIET; REVEALS; METAGENOMICS; STRATEGIES; PROFILES;
+ GENETICS; DATABASE; MODELS; HEALTH},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Chiu, Hsuan-Chao/F-8963-2011
+ McNally, Colin P/C-4336-2015
+ },
+ORCID-Numbers = {Chiu, Hsuan-Chao/0000-0001-9828-2955
+ McNally, Colin P/0000-0002-2565-6626
+ Noecker, Cecilia/0000-0003-1417-2383},
+Times-Cited = {35},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000518852300008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000490604400010,
+Author = {Pinzon, W. and Vega, H. and Gonzalez, J. and Pinzon, A.},
+Title = {Mathematical Framework Behind the Reconstruction and Analysis of Genome
+ Scale Metabolic Models},
+Journal = {ARCHIVES OF COMPUTATIONAL METHODS IN ENGINEERING},
+Year = {2019},
+Volume = {26},
+Number = {5},
+Pages = {1593-1606},
+Month = {NOV},
+Type = {Review},
+DOI = {10.1007/s11831-018-9290-3},
+ISSN = {1134-3060},
+EISSN = {1886-1784},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ OPTIMIZATION; PATHWAYS},
+Research-Areas = {Computer Science; Engineering; Mathematics},
+Web-of-Science-Categories = {Computer Science, Interdisciplinary Applications; Engineering,
+ Multidisciplinary; Mathematics, Interdisciplinary Applications},
+ResearcherID-Numbers = {GONZALEZ, JANNETH/AAB-9948-2020
+ },
+ORCID-Numbers = {GONZALEZ, JANNETH/0000-0003-4482-256X
+ Gonzalez, Janneth/0000-0003-2009-3374},
+Times-Cited = {2},
+Journal-ISO = {Arch. Comput. Method Eng.},
+Unique-ID = {WOS:000490604400010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000493438700024,
+Author = {Liu, Quanli and Yu, Tao and Li, Xiaowei and Chen, Yu and Campbell, Kate
+ and Nielsen, Jens and Chen, Yun},
+Title = {Rewiring carbon metabolism in yeast for high level production of
+ aromatic chemicals},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2019},
+Volume = {10},
+Month = {OCT 31},
+Type = {Article},
+DOI = {10.1038/s41467-019-12961-5},
+Article-Number = {4976},
+ISSN = {2041-1723},
+Keywords-Plus = {AMINO-ACID BIOSYNTHESIS; DE-NOVO PRODUCTION; P-COUMARIC ACID;
+ SACCHAROMYCES-CEREVISIAE; MICROBIAL-PRODUCTION; DIRECTED EVOLUTION;
+ PATHWAY; STRAIN; ENZYME; PURIFICATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Liu, Quanli/O-8630-2014
+ Chen, Yun/G-6645-2017
+ Chen, Yu/AAL-3329-2020
+ Nielsen, Jens Bo/C-7632-2015
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Chen, Yun/0000-0002-2146-6008
+ Chen, Yu/0000-0003-3326-9068
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Campbell, Kate/0000-0002-4173-5260
+ Nielsen, Jens/0000-0002-9955-6003
+ Yu, Tao/0000-0002-1048-4315},
+Times-Cited = {144},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000493438700024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000490962500001,
+Author = {Molina, Lazaro and La Rosa, Ruggero and Nogales, Juan and Rojo, Fernando},
+Title = {Influence of the Crc global regulator on substrate uptake rates and the
+ distribution of metabolic fluxes in Pseudomonas putida KT2440
+ growing in a complete medium},
+Journal = {ENVIRONMENTAL MICROBIOLOGY},
+Year = {2019},
+Volume = {21},
+Number = {11},
+Pages = {4446-4459},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1111/1462-2920.14812},
+EarlyAccessDate = {OCT 2019},
+ISSN = {1462-2912},
+EISSN = {1462-2920},
+Keywords-Plus = {CARBON CATABOLITE REPRESSION; ESCHERICHIA-COLI; 2-COMPONENT SYSTEM;
+ GLUCOSE; PATHWAYS; GENOME; GROWTH; DEHYDROGENASE; TRANSDUCTION;
+ AERUGINOSA},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {La Rosa, Ruggero/AAR-8197-2021
+ Molina, Lazaro/K-9645-2014
+ Nogales, Juan/Y-8829-2019
+ Rojo, Fernando/A-7038-2008
+ },
+ORCID-Numbers = {La Rosa, Ruggero/0000-0002-6705-3989
+ Molina, Lazaro/0000-0002-8483-9203
+ Rojo, Fernando/0000-0003-1848-7745
+ Nogales, Juan/0000-0002-4961-0833},
+Times-Cited = {29},
+Journal-ISO = {Environ. Microbiol.},
+Unique-ID = {WOS:000490962500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000490842600001,
+Author = {Toyoshima, Masakazu and Toya, Yoshihiro and Shimizu, Hiroshi},
+Title = {Flux balance analysis of cyanobacteria reveals selective use of
+ photosynthetic electron transport components under different spectral
+ light conditions},
+Journal = {PHOTOSYNTHESIS RESEARCH},
+Year = {2020},
+Volume = {143},
+Number = {1},
+Pages = {31-43},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1007/s11120-019-00678-x},
+EarlyAccessDate = {OCT 2019},
+ISSN = {0166-8595},
+EISSN = {1573-5079},
+Keywords = {Cyanobacteria; Flux balance analysis; Genome-scale model; Photosynthetic
+ electron transport},
+Keywords-Plus = {SP PCC 6803; RESPIRATORY TERMINAL OXIDASES; SYNECHOCYSTIS SP PCC-6803;
+ PHOTOSYSTEM-I; ARTHROSPIRA-PLATENSIS; REACTION CENTERS; NDH-1 COMPLEXES;
+ SP PCC6803; Q-CYCLE; STOICHIOMETRY},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Toyoshima, Masakazu/ABA-1357-2021
+ Shimizu, Hiroshi/C-3688-2017
+ },
+ORCID-Numbers = {Toyoshima, Masakazu/0000-0002-6322-7806
+ Shimizu, Hiroshi/0000-0002-8986-0861
+ Toya, Yoshihiro/0000-0001-9670-6961},
+Times-Cited = {15},
+Journal-ISO = {Photosynth. Res.},
+Unique-ID = {WOS:000490842600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000490547200001,
+Author = {Teo, Emelyne and Ravi, Sudharshan and Barardo, Diogo and Kim, Hyung-Seok
+ and Fong, Sheng and Cazenave-Gassiot, Amaury and Tan, Tsze Yin and
+ Ching, Jianhong and Kovalik, Jean-Paul and Wenk, Markus R. and Gunawan,
+ Rudiyanto and Moore, Philip K. and Halliwell, Barry and Tolwinski,
+ Nicholas and Gruber, Jan},
+Title = {Metabolic stress is a primary pathogenic event in transgenic
+ Caenorhabditis elegans expressing pan-neuronal human
+ amyloid beta},
+Journal = {ELIFE},
+Year = {2019},
+Volume = {8},
+Month = {OCT 15},
+Type = {Article},
+DOI = {10.7554/eLife.50069},
+Article-Number = {e50069},
+ISSN = {2050-084X},
+Keywords-Plus = {ALPHA-KETOGLUTARATE DEHYDROGENASE; MILD COGNITIVE IMPAIRMENT;
+ CYTOCHROME-C-OXIDASE; OXIDATIVE STRESS; ALZHEIMER-DISEASE;
+ HYDROGEN-PEROXIDE; GENE-EXPRESSION; MOUSE MODEL; LIFE-SPAN; PROTEIN},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Fong, Sheng/I-3061-2012
+ Tolwinski, Nicholas/Q-5782-2019
+ Barardo, Diogo/GVR-8783-2022
+ Wenk, Markus Rene/D-1441-2014
+ Cazenave-Gassiot, Amaury/E-4536-2014
+ },
+ORCID-Numbers = {Fong, Sheng/0000-0001-5381-8955
+ Tolwinski, Nicholas/0000-0002-8507-2737
+ Kovalik, Jean-Paul/0000-0003-3654-8193
+ Cazenave-Gassiot, Amaury/0000-0002-3050-634X
+ Halliwell, Barry/0000-0002-3560-7123
+ Ravi, Sudharshan/0000-0001-6059-5403
+ Barardo, Diogo/0000-0001-6177-0728
+ Teo, Emelyne/0000-0001-5050-4109},
+Times-Cited = {37},
+Journal-ISO = {eLife},
+Unique-ID = {WOS:000490547200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000488763800001,
+Author = {Kanhaiya, Krishna and Tiwari, Dwitiya},
+Title = {Identification of Drug Targets in Breast Cancer Metabolic Network},
+Journal = {JOURNAL OF COMPUTATIONAL BIOLOGY},
+Year = {2020},
+Volume = {27},
+Number = {6},
+Pages = {975-986},
+Month = {JUN 1},
+Type = {Article},
+DOI = {10.1089/cmb.2019.0258},
+EarlyAccessDate = {OCT 2019},
+ISSN = {1066-5277},
+EISSN = {1557-8666},
+Keywords = {breast cancer; drug-target; HDN; metabolic network; network analysis;
+ statistical model},
+Keywords-Plus = {DISCOVERY; GROWTH; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+Times-Cited = {1},
+Journal-ISO = {J. Comput. Biol.},
+Unique-ID = {WOS:000488763800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000494891200022,
+Author = {Antoniewicz, Maciek R.},
+Title = {Synthetic methylotrophy: Strategies to assimilate methanol for growth
+ and chemicals production},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2019},
+Volume = {59},
+Pages = {165-174},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1016/j.copbio.2019.07.001},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {ESCHERICHIA-COLI; CORYNEBACTERIUM-GLUTAMICUM; BACILLUS-METHANOLICUS;
+ VIBRIO-NATRIEGENS; FLUX ANALYSIS; PATHWAY; METABOLISM; ACTIVATION;
+ CONVERSION; EVOLUTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009},
+Times-Cited = {42},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000494891200022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000500795900001,
+Author = {Bodor, Zsolt and Tompos, Lehel and Nechifor, Aurelia Cristina and Bodor,
+ Katalin},
+Title = {In silico Analysis of 1,4-butanediol Heterologous Pathway Impact
+ on Escherichia coli Metabolism},
+Journal = {REVISTA DE CHIMIE},
+Year = {2019},
+Volume = {70},
+Number = {10},
+Pages = {3448-3455},
+Month = {OCT},
+Type = {Article},
+ISSN = {0034-7752},
+Keywords = {1,4-butanediol; E. coli; flux variability analysis; random sampling; in
+ silico; COBRA},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; EASTERN CARPATHIANS; ATMOSPHERIC CIRCULATIONS;
+ QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; SUCCINIC ACID; CIUC BASIN;
+ CHEMISTRY; GLYCEROL},
+Research-Areas = {Chemistry; Engineering},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary; Engineering, Chemical},
+ResearcherID-Numbers = {Bodor, Zsolt/ABE-2182-2020
+ },
+ORCID-Numbers = {Bodor, Zsolt/0000-0003-1386-6957},
+Times-Cited = {3},
+Journal-ISO = {Rev. Chim.},
+Unique-ID = {WOS:000500795900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000494891200013,
+Author = {Buerger, Josi and Gronenberg, Luisa S. and Genee, Hans Jasper and
+ Sommer, Morten O. A.},
+Title = {Wiring cell growth to product formation},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2019},
+Volume = {59},
+Pages = {85-92},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1016/j.copbio.2019.02.014},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {EXPRESSION; SELECTION; OPTIMIZATION; METABOLISM; CONVERSION; BIOSENSOR;
+ EVOLUTION; SENSORS; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Sommer, Morten Otto Alexander/0000-0003-4005-5674},
+Times-Cited = {9},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000494891200013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000492115800011,
+Author = {Ding, Shaozhen and Cai, Pengli and Yuan, Le and Tian, Yu and Tu,
+ Weizhong and Zhang, Dachuan and Cheng, Xingxiang and Sun, Dandan and
+ Chen, Junni and Hu, Qian-Nan},
+Title = {CF-Targeter: A Rational Biological Cell Factory Targeting Platform for
+ Biosynthetic Target Chemicals},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2019},
+Volume = {8},
+Number = {10},
+Pages = {2280-2286},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1021/acssynbio.9b00070},
+ISSN = {2161-5063},
+Keywords = {chassis hosts selection; genome-scale metabolic model; theoretical
+ yield; heterologous pathway design},
+Keywords-Plus = {SYNTHETIC BIOLOGY; PATHWAYS; ENZYMES; DESIGN; MODELS; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Zhang, Dachuan/AFT-0071-2022
+ sun, dandan/GZG-6540-2022
+ Hu, Qian/GWZ-7617-2022
+ Cai, Pengli/HZL-4422-2023
+ },
+ORCID-Numbers = {Zhang, Dachuan/0000-0003-2467-6286
+ Yuan, Le/0000-0003-3317-9011
+ Tian, Yu/0000-0001-8079-6149},
+Times-Cited = {4},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000492115800011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000487967700004,
+Author = {Long, Christopher P. and Antoniewicz, Maciek R.},
+Title = {High-resolution 13C metabolic flux analysis},
+Journal = {NATURE PROTOCOLS},
+Year = {2019},
+Volume = {14},
+Number = {10},
+Pages = {2856-2877},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1038/s41596-019-0204-0},
+ISSN = {1754-2189},
+EISSN = {1750-2799},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; MASS ISOTOPOMER DISTRIBUTIONS;
+ ESCHERICHIA-COLI; NETWORK MODEL; UNITS EMU; C-13; FRAMEWORK; GLUCOSE;
+ BIOMASS; FERMENTATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009
+ },
+ORCID-Numbers = {Antoniewicz, Maciek/0000-0002-0087-2875
+ Long, Christopher/0000-0003-1007-417X},
+Times-Cited = {106},
+Journal-ISO = {Nat. Protoc.},
+Unique-ID = {WOS:000487967700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000492052000001,
+Author = {Oyelade, Jelili and Isewon, Itunuoluwa and Aromolaran, Olufemi and
+ Uwoghiren, Efosa and Dokunmu, Titilope and Rotimi, Solomon and Aworunse,
+ Oluwadurotimi and Obembe, Olawole and Adebiyi, Ezekiel},
+Title = {Computational Identification of Metabolic Pathways of Plasmodium
+ falciparum using the k-Shortest Path Algorithm},
+Journal = {INTERNATIONAL JOURNAL OF GENOMICS},
+Year = {2019},
+Volume = {2019},
+Month = {OCT 1},
+Type = {Article},
+DOI = {10.1155/2019/1750291},
+Article-Number = {1750291},
+ISSN = {2314-436X},
+EISSN = {2314-4378},
+Keywords-Plus = {PHOSPHATIDYLCHOLINE BIOSYNTHESIS; DRUG TARGETS; INHIBITION; GLYCOLYSIS;
+ NETWORKS; GENES},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Aromolaran, Olufemi/AAA-4710-2022
+ Okuboyejo, Titilope Modupe/J-7932-2013
+ Rotimi, Solomon/H-8683-2012
+ Oyelade, Jelili O./M-8123-2013
+ Uwoghiren, Efosa/T-1918-2017
+ Obembe, Olawole/A-4182-2014
+ },
+ORCID-Numbers = {Aromolaran, Olufemi/0000-0002-2781-1714
+ Okuboyejo, Titilope Modupe/0000-0002-8751-3436
+ Rotimi, Solomon/0000-0002-3678-9977
+ Oyelade, Jelili/0000-0002-5476-4992
+ Uwoghiren, Efosa/0000-0002-6117-0981
+ Obembe, Olawole/0000-0002-0396-0483
+ Isewon, Itunuoluwa/0000-0001-9653-8929},
+Times-Cited = {9},
+Journal-ISO = {Int. J. Genomics},
+Unique-ID = {WOS:000492052000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000498640400007,
+Author = {Trilla-Fuertes, Lucia and Gamez-Pozo, Angelo and Diaz-Almiron, Mariana
+ and Prado-Vazquez, Guillermo and Zapater-Moros, Andrea and Lopez-Vacas,
+ Rocio and Nanni, Paolo and Zamora, Pilar and Espinosa, Enrique and
+ Fresno Vara, Juan Angel},
+Title = {Computational metabolism modeling predicts risk of distant relapse-free
+ survival in breast cancer patients},
+Journal = {FUTURE ONCOLOGY},
+Year = {2019},
+Volume = {15},
+Number = {30},
+Pages = {3483-3490},
+Month = {OCT},
+Type = {Article},
+DOI = {10.2217/fon-2018-0698},
+ISSN = {1479-6694},
+EISSN = {1744-8301},
+Keywords = {breast cancer; flux balance analysis; metabolism; personalized medicine;
+ prognosis},
+Keywords-Plus = {GLUTAMINE-METABOLISM; PROTEOMICS; EXPRESSION; SHOTGUN; PROTEIN; FLUX},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ResearcherID-Numbers = {Trilla, Lucia/AAG-8392-2019
+ Gamez, Angelo/HSG-7485-2023
+ Prado-Vazquez, Guillermo/T-1861-2017
+ Vara, Juan Ángel Fresno/Y-9928-2019
+ Zamora, Pilar/AAM-9336-2021
+ Gamez-Pozo, Angelo/N-2506-2014},
+ORCID-Numbers = {Trilla, Lucia/0000-0002-4452-3474
+ Prado-Vazquez, Guillermo/0000-0003-2456-6191
+ Vara, Juan Ángel Fresno/0000-0003-1527-1252
+ Zamora, Pilar/0000-0003-2631-9653
+ Nanni, Paolo/0000-0001-8429-3557
+ Espinosa Arranz, Enrique/0000-0001-6562-7902
+ Gamez-Pozo, Angelo/0000-0002-8931-0624},
+Times-Cited = {2},
+Journal-ISO = {Future Oncol.},
+Unique-ID = {WOS:000498640400007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000496188400001,
+Author = {Li, Chien-Ting and Yelsky, Jacob and Chen, Yiqun and Zuniga, Cristal and
+ Eng, Richard and Jiang, Liqun and Shapiro, Alison and Huang, Kai-Wen and
+ Zengler, Karsten and Betenbaugh, Michael J.},
+Title = {Utilizing genome-scale models to optimize nutrient supply for sustained
+ algal growth and lipid productivity},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2019},
+Volume = {5},
+Month = {SEP 24},
+Type = {Article},
+DOI = {10.1038/s41540-019-0110-7},
+Article-Number = {33},
+EISSN = {2056-7189},
+Keywords-Plus = {MICROALGA CHLORELLA-PROTOTHECOIDES; PREDICTIVE CONTROL; VULGARIS;
+ RECONSTRUCTION; CULTIVATION; BIOREACTOR; METABOLISM; SYSTEM},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Chen, Yiqun/HSF-6729-2023
+ Chen, Yiqun/IAO-5601-2023
+ Zuniga, Cristal/CAA-0015-2022
+ },
+ORCID-Numbers = {Chen, Yiqun/0000-0003-3074-9605
+ Chen, Yiqun/0000-0003-3074-9605
+ Yelsky, Jacob/0000-0001-9342-6390
+ Shapiro, Alison/0000-0002-4553-7421
+ Zuniga, Cristal/0000-0002-0135-7429},
+Times-Cited = {16},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000496188400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000487327500024,
+Author = {Gilbert, James and Pearcy, Nicole and Norman, Rupert and Millat, Thomas
+ and Winzer, Klaus and King, John and Hodgman, Charlie and Minton, Nigel
+ and Twycross, Jamie},
+Title = {Gsmodutils: a python based framework for test-driven genome scale
+ metabolic model development},
+Journal = {BIOINFORMATICS},
+Year = {2019},
+Volume = {35},
+Number = {18},
+Pages = {3397-3403},
+Month = {SEP 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btz088},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {BIOLOGY MARKUP LANGUAGE; CLOSTRIDIUM-ACETOBUTYLICUM; ESCHERICHIA-COLI;
+ RECONSTRUCTION; GENERATION; PREDICTION; ALGORITHM; DESIGN},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Twycross, Jamie/N-9010-2016},
+ORCID-Numbers = {King, John/0000-0002-6228-8375
+ Hodgman, Charlie/0000-0001-5862-8296
+ Twycross, Jamie/0000-0002-1684-0886},
+Times-Cited = {2},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000487327500024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000496188100002,
+Author = {Herrmann, Helena A. and Dyson, Beth C. and Vass, Lucy and Johnson, Giles
+ N. and Schwartz, Jean-Marc},
+Title = {Flux sampling is a powerful tool to study metabolism under changing
+ environmental conditions},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2019},
+Volume = {5},
+Month = {SEP 2},
+Type = {Article},
+DOI = {10.1038/s41540-019-0109-0},
+Article-Number = {32},
+EISSN = {2056-7189},
+Keywords-Plus = {TRANSGENIC ARABIDOPSIS-THALIANA; GAMMA-AMINOBUTYRIC-ACID; CHAIN
+ MONTE-CARLO; HIT-AND-RUN; COLD-ACCLIMATION; LOW-TEMPERATURES; CARBON;
+ RECONSTRUCTION; CONVERGENCE; MODELS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Schwartz, Jean-Marc/AAS-8274-2020
+ },
+ORCID-Numbers = {Schwartz, Jean-Marc/0000-0002-6472-0184
+ Saunders, Helena Alexandra/0000-0001-9008-0726
+ Johnson, Giles Nicholas/0000-0003-1536-5582
+ Vass, Lucy/0000-0002-2644-7850},
+Times-Cited = {43},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000496188100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000482582100026,
+Author = {Long, Christopher P. and Antoniewicz, Maciek R.},
+Title = {Metabolic flux responses to deletion of 20 core enzymes reveal
+ flexibility and limits of E. coli metabolism},
+Journal = {METABOLIC ENGINEERING},
+Year = {2019},
+Volume = {55},
+Pages = {249-257},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2019.08.003},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Escherichia coli; Gene knockouts; Genotype-to-phenotype; Metabolism;
+ Systems biology},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; MASS ISOTOPOMER DISTRIBUTIONS;
+ ESCHERICHIA-COLI; MUTANTS; GLUCOSE; GENE; KNOCKOUTS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009
+ },
+ORCID-Numbers = {Long, Christopher/0000-0003-1007-417X},
+Times-Cited = {28},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000482582100026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000478674700020,
+Author = {Lularevic, Maximilian and Racher, Andrew J. and Jaques, Colin and
+ Kiparissides, Alexandros},
+Title = {Improving the accuracy of flux balance analysis through the
+ implementation of carbon availability constraints for intracellular
+ reactions},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2019},
+Volume = {116},
+Number = {9},
+Pages = {2339-2352},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1002/bit.27025},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {carbon constraining; CHO; constraint-based modeling; FBA; genome-scale
+ metabolic network},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; ESCHERICHIA-COLI; METABOLIC MODELS;
+ FED-BATCH; REDUNDANCY; GROWTH; GENES; CELLS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Kiparissides, Alexandros/ABH-5729-2020
+ },
+ORCID-Numbers = {Kiparissides, Alexandros/0000-0003-2923-2481
+ Racher, Andy/0000-0003-2546-1228},
+Times-Cited = {18},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000478674700020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000480552400009,
+Author = {Puvendran, Kirubhakaran and Jayaraman, Guhan},
+Title = {Enhancement of acetyl-CoA by acetate co-utilization in recombinant
+ Lactococcus lactis cultures enables the production of high molecular
+ weight hyaluronic acid},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2019},
+Volume = {103},
+Number = {17},
+Pages = {6989-7001},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1007/s00253-019-09987-6},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Acetyl-CoA; Fed-batch process; Hyaluronic acid; Molecular weight;
+ Lactococcus lactis},
+Keywords-Plus = {STREPTOCOCCUS-ZOOEPIDEMICUS; ESCHERICHIA-COLI; BIOSYNTHESIS;
+ OVEREXPRESSION; ACCUMULATION; GENES; HA},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Jayaraman, Guhan/0000-0003-0084-162X},
+Times-Cited = {8},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000480552400009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000483017100006,
+Author = {Poupin, Nathalie and Tremblay-Franco, Marie and Amiel, Aurelien and
+ Canletz, Cecile and Remond, Didier and Debrauwer, Laurent and Dardevet,
+ Dominique and Thiele, Ines and Aurich, Maike K. and Jourdan, Fabien and
+ Savary-Auzeloux, Isabelle and Polakof, Sergio},
+Title = {Arterio-venous metabolomics exploration reveals major changes across
+ liver and intestine in the obese Yucatan minipig},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2019},
+Volume = {9},
+Month = {AUG 29},
+Type = {Article},
+DOI = {10.1038/s41598-019-48997-2},
+Article-Number = {12527},
+ISSN = {2045-2322},
+Keywords-Plus = {CHAIN FATTY-ACIDS; AMINO-ACID; TRYPTOPHAN-KYNURENINE;
+ INSULIN-RESISTANCE; GENOME-SCALE; TIME-COURSE; METABOLISM; DIET; GUT;
+ GLUCOSE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Jourdan, Fabien/AAW-5075-2021
+ Polakof, Sergio/V-1132-2017
+ Dardevet, Dominique/IAM-3666-2023
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Jourdan, Fabien/0000-0001-9401-2894
+ Polakof, Sergio/0000-0002-0976-8732
+ Savary-Auzeloux, Isabelle/0000-0002-3298-9787
+ Poupin, Nathalie/0000-0002-3393-1405
+ Dardevet, Dominique/0000-0001-7320-9970},
+Times-Cited = {14},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000483017100006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000483620600001,
+Author = {Yousefi, Meisam and Marashi, Sayed-Amir and Sharifi-Zarchi, Ali and
+ Taleahmad, Sara},
+Title = {The metabolic network model of primed/naive human embryonic stem cells
+ underlines the importance of oxidation-reduction potential and
+ tryptophan metabolism in primed pluripotency},
+Journal = {CELL AND BIOSCIENCE},
+Year = {2019},
+Volume = {9},
+Number = {1},
+Month = {AUG 29},
+Type = {Article},
+DOI = {10.1186/s13578-019-0334-7},
+Article-Number = {71},
+EISSN = {2045-3701},
+Keywords = {Systems biology; Human embryonic stem cells; Tryptophan metabolism;
+ Kynurenine metabolism; Genome-scale metabolic networks},
+Keywords-Plus = {GROUND-STATE PLURIPOTENCY; NAIVE PLURIPOTENCY; CANCER; RECONSTRUCTION;
+ PROLIFERATION; DIFFERENTIATION; INACTIVATION; MAINTENANCE; DERIVATION;
+ PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008
+ Taleahmad, Sara/ABC-5881-2021
+ Sharifi-Zarchi, Ali/ABB-7910-2020
+ Yousefi, Meisam/AAC-4146-2020
+ },
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Taleahmad, Sara/0000-0003-4666-1907
+ Sharifi-Zarchi, Ali/0000-0002-0087-7596
+ Yousefi, Meisam/0000-0002-7346-803X},
+Times-Cited = {3},
+Journal-ISO = {Cell Biosci.},
+Unique-ID = {WOS:000483620600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000483697600003,
+Author = {Suhail, Yasir and Cain, Margo P. and Vanaja, Kiran and Kurywchak, Paul
+ A. and Levchenko, Andre and Kalluri, Raghu and Kshitiz},
+Title = {Systems Biology of Cancer Metastasis},
+Journal = {CELL SYSTEMS},
+Year = {2019},
+Volume = {9},
+Number = {2},
+Pages = {109-127},
+Month = {AUG 28},
+Type = {Review},
+DOI = {10.1016/j.cels.2019.07.003},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {TO-MESENCHYMAL TRANSITION; TUMOR-CELL INTRAVASATION; BREAST-CANCER;
+ STEM-CELLS; GENE-EXPRESSION; LUNG METASTASIS; CRISPR SCREEN; MODEL;
+ TISSUE; DNA},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Suhail, Yasir/M-7280-2018
+ Kshitiz, ./B-9143-2013
+ Vanaja, Kiran/AAN-4909-2021
+ Kz, Kshitiz/I-3657-2013
+ Kalluri, Raghu/E-2677-2015},
+ORCID-Numbers = {Suhail, Yasir/0000-0002-1296-9738
+ Kshitiz, ./0000-0003-4241-9427
+ Kz, Kshitiz/0000-0003-4241-9427
+ Vanaja, Kiran/0000-0001-5547-4252
+ Cain, Margo/0000-0001-6099-1879
+ Kalluri, Raghu/0000-0002-2190-547X},
+Times-Cited = {189},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000483697600003},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000483396800065,
+Author = {Chen, Yu and Nielsen, Jens},
+Title = {Energy metabolism controls phenotypes by protein efficiency and
+ allocation},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2019},
+Volume = {116},
+Number = {35},
+Pages = {17592-17597},
+Month = {AUG 27},
+Type = {Article},
+DOI = {10.1073/pnas.1906569116},
+ISSN = {0027-8424},
+Keywords = {constraint-based modeling; Escherichia coli; Saccharomyces cerevisiae;
+ metabolic switch; growth rate},
+Keywords-Plus = {COLI K-12 MG1655; ESCHERICHIA-COLI; GROWTH-RATE; TRANSCRIPTIONAL
+ REGULATION; SACCHAROMYCES-CEREVISIAE; OVERFLOW METABOLISM; STRESS;
+ QUANTIFICATION; DEHYDROGENASE; MECHANISM},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Chen, Yu/AAL-3329-2020
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Chen, Yu/0000-0003-3326-9068
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {61},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000483396800065},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000475997500007,
+Author = {Greene, Jennifer and Daniell, James and Kopke, Michael and Broadbelt,
+ Linda and Tyo, Keith E. J.},
+Title = {Kinetic ensemble model of gas fermenting Clostridium
+ autoethanogenum for improved ethanol production},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2019},
+Volume = {148},
+Pages = {46-56},
+Month = {AUG 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2019.04.021},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Ensemble modeling; Kinetic modeling; Metabolic engineering; Clostridium
+ autoethanogenum; Strain design},
+Keywords-Plus = {STIRRED-TANK REACTOR; CARBON-MONOXIDE; COMMODITY CHEMICALS;
+ ENERGY-CONSERVATION; MASS-TRANSFER; LJUNGDAHLII; METABOLISM; STRAIN;
+ GROWTH; ACID},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Tyo, Keith/H-6227-2012
+ Köpke, Michael/I-3963-2019
+ Tyo, Keith/AAM-4543-2020
+ Broadbelt, Linda/B-7640-2009
+ },
+ORCID-Numbers = {Köpke, Michael/0000-0003-0642-1415
+ Tyo, Keith/0000-0002-2342-0687
+ Greene, Jennifer/0000-0002-2994-1088},
+Times-Cited = {24},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000475997500007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000475997500006,
+Author = {Paramasivan, Kalaivani and Kumar, Punil H. N. and Mutturi, Sarma},
+Title = {Systems-based Saccharomyces cerevisiae strain design for improved
+ squalene synthesis},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2019},
+Volume = {148},
+Pages = {37-45},
+Month = {AUG 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2019.04.025},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Squalene; S. cerevisiae; Genome-scale model; LYS1; Fed-batch},
+Keywords-Plus = {HMG-COA REDUCTASE; CONSTRAINT-BASED MODELS; ACETYL-COA; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; YEAST; LEVEL; BIOSYNTHESIS; ACID;
+ OVEREXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Paramasivan, Kalaivani/AFP-5567-2022
+ },
+ORCID-Numbers = {Paramasivan, Kalaivani/0000-0001-6743-0003
+ Mutturi, Sarma/0000-0002-3251-8643},
+Times-Cited = {6},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000475997500006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000479188900019,
+Author = {Lu, Hongzhong and Li, Feiran and Sanchez, Benjamin J. and Zhu, Zhengming
+ and Li, Gang and Domenzain, Ivan and Marcisauskas, Simonas and Anton,
+ Petre Mihail and Lappa, Dimitra and Lieven, Christian and Beber, Moritz
+ Emanuel and Sonnenschein, Nikolaus and Kerkhoven, Eduard J. and Nielsen,
+ Jens},
+Title = {A consensus S. cerevisiae metabolic model Yeast8 and its
+ ecosystem for comprehensively probing cellular metabolism},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2019},
+Volume = {10},
+Month = {AUG 8},
+Type = {Article},
+DOI = {10.1038/s41467-019-11581-3},
+Article-Number = {3586},
+ISSN = {2041-1723},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; PROTEIN; GENE; DATABASE; STRAINS; BIOLOGY;
+ RECONSTRUCTION; COLLECTION; FRAMEWORK; ACID},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Li, Feiran/GNP-2168-2022
+ Anton, Mihail/GXH-0002-2022
+ Domenzain, Ivan/HCI-9542-2022
+ Sonnenschein, Nikolaus/F-6853-2012
+ Kerkhoven, Eduard/P-2469-2019
+ Zhu, Zhengming/AAX-1281-2021
+ },
+ORCID-Numbers = {Li, Feiran/0000-0001-9155-5260
+ Anton, Mihail/0000-0002-7753-9042
+ Domenzain, Ivan/0000-0002-5322-2040
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Li, Gang/0000-0001-6778-2842
+ Sanchez, Benjamin/0000-0001-6093-4110
+ Lieven, Christian/0000-0001-5377-4091
+ Marcisauskas, Simonas/0000-0003-0770-6383
+ Beber, Moritz Emanuel/0000-0003-2406-1978
+ Zhu, Zhengming/0000-0002-4177-2416},
+Times-Cited = {130},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000479188900019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000479172800048,
+Author = {Olin-Sandoval, Viridiana and Yu, Jason Shu Lim and Miller-Fleming,
+ Leonor and Alam, Mohammad Tauqeer and Kamrad, Stephan and Correia-Melo,
+ Clara and Haas, Robert and Segal, Joanna and Navarro, David Alejandro
+ Pena and Herrera-Dominguez, Lucia and Mendez-Lucio, Oscar and Vowinckel,
+ Jakob and Muelleder, Michael and Ralser, Markus},
+Title = {Lysine harvesting is an antioxidant strategy and triggers underground
+ polyamine metabolism},
+Journal = {NATURE},
+Year = {2019},
+Volume = {572},
+Number = {7768},
+Pages = {249+},
+Month = {AUG 8},
+Type = {Article},
+DOI = {10.1038/s41586-019-1442-6},
+ISSN = {0028-0836},
+EISSN = {1476-4687},
+Keywords-Plus = {PENTOSE-PHOSPHATE PATHWAY; OXIDATIVE STRESS; SACCHAROMYCES-CEREVISIAE;
+ ORNITHINE-DECARBOXYLASE; HOMOCITRATE SYNTHASE; FEEDBACK INHIBITION;
+ YEAST; GENE; GROWTH; LOCALIZATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Miller-Fleming, Leonor/J-4309-2015
+ alam, mohammed/GXH-3645-2022
+ },
+ORCID-Numbers = {Miller-Fleming, Leonor/0000-0002-3593-6461
+ Olin Sandoval, Maria Viridiana/0000-0001-8049-807X
+ Ralser, Markus/0000-0001-9535-7413
+ Correia-Melo, Clara/0000-0001-6062-1472
+ Mulleder, Michael/0000-0001-9792-3861
+ Yu, Jason/0000-0001-5203-3603
+ Alam, Mohammad Tauqeer/0000-0002-6872-0691
+ Kamrad, Stephan/0000-0002-5957-4661
+ Herrera-Dominguez, Lucia/0000-0001-8276-2241
+ Haas, Robert/0000-0003-4826-2379},
+Times-Cited = {79},
+Journal-ISO = {Nature},
+Unique-ID = {WOS:000479172800048},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000479188900001,
+Author = {Saifuddin, Mustafa and Bhatnagar, Jennifer M. and Segre, Daniel and
+ Finzi, Adrien C.},
+Title = {Microbial carbon use efficiency predicted from genome-scale metabolic
+ models},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2019},
+Volume = {10},
+Month = {AUG 8},
+Type = {Article},
+DOI = {10.1038/s41467-019-11488-z},
+Article-Number = {3568},
+EISSN = {2041-1723},
+Keywords-Plus = {SOIL-CARBON; STOICHIOMETRY; COMMUNITY; TEMPERATURE; CONSISTENT;
+ RESPONSES; DYNAMICS; BIOLOGY; SEED},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Finzi, Adrien C/A-7017-2016
+ Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Finzi, Adrien C/0000-0003-2220-4533
+ Segrè, Daniel/0000-0003-4859-1914
+ Saifuddin, Mustafa/0009-0005-0803-500X
+ Bhatnagar, Jennifer/0000-0001-6424-4133},
+Times-Cited = {59},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000479188900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000479204200001,
+Author = {Mendoza, Sebastian N. and Olivier, Brett G. and Molenaar, Douwe and
+ Teusink, Bas},
+Title = {A systematic assessment of current genome-scale metabolic reconstruction
+ tools},
+Journal = {GENOME BIOLOGY},
+Year = {2019},
+Volume = {20},
+Number = {1},
+Month = {AUG 7},
+Type = {Article},
+DOI = {10.1186/s13059-019-1769-1},
+Article-Number = {158},
+ISSN = {1474-760X},
+Keywords = {Genome-scale metabolic reconstruction; Systematic evaluation;
+ Genome-scale metabolic models; Bordetella pertussis; Lactobacillus
+ plantarum; Pseudomonas putida},
+Keywords-Plus = {LACTOBACILLUS-PLANTARUM WCFS1; BORDETELLA-PERTUSSIS; MODELS; GROWTH;
+ ANNOTATION; PATHWAYS; PLATFORM; NETWORK},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Molenaar, Douwe/D-2017-2010
+ },
+ORCID-Numbers = {Molenaar, Douwe/0000-0001-7108-4545
+ Mendoza, Sebastian/0000-0002-2192-5569
+ Teusink, Bas/0000-0003-3929-0423
+ Olivier, Brett/0000-0002-5293-5321},
+Times-Cited = {99},
+Journal-ISO = {Genome Biol.},
+Unique-ID = {WOS:000479204200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000476744300006,
+Author = {Kumar, Manish and Ji, Boyang and Zengler, Karsten and Nielsen, Jens},
+Title = {Modelling approaches for studying the microbiome},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2019},
+Volume = {4},
+Number = {8},
+Pages = {1253-1267},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1038/s41564-019-0491-9},
+ISSN = {2058-5276},
+Keywords-Plus = {SCALE METABOLIC MODELS; GUT MICROBIOTA; SYSTEMS BIOLOGY;
+ GROWTH-KINETICS; NETWORKS; GENERATION; PATHWAYS; BALANCE; ASSOCIATION;
+ SELECTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Ji, Boyang/HMV-6662-2023
+ Kumar, Manish/ABE-8494-2020
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Ji, Boyang/0000-0002-7269-4342
+ Kumar, Manish/0000-0001-8035-3399
+ Nielsen, Jens/0000-0002-9955-6003
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {80},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000476744300006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000478852900021,
+Author = {Lasry Testa, Romina and Delpino, Claudio and Estrada, Vanina and Diaz,
+ Soledad M.},
+Title = {In silico strategies to couple production of bioethanol with growth in
+ cyanobacteria},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2019},
+Volume = {116},
+Number = {8},
+Pages = {2061-2073},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1002/bit.26998},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {bilevel programming; bioethanol; coupled mutant; cyanobacteria;
+ genome-scale metabolic model; strain design},
+Keywords-Plus = {TRICARBOXYLIC-ACID CYCLE; METABOLISM; OPTIMALITY; PREDICTION; MODELS;
+ STATE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Delpino, Claudio/0000-0002-3931-9575
+ Diaz, Maria Soledad/0000-0003-3555-9624},
+Times-Cited = {13},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000478852900021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000475695600024,
+Author = {Olavarria, Karel and Fina, Albert and Velasco, Mariana I. and van
+ Loosdrecht, Mark C. M. and Wahl, Sebastian Aljoscha},
+Title = {Metabolism of sucrose in a non-fermentative Escherichia coli under
+ oxygen limitation},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2019},
+Volume = {103},
+Number = {15},
+Pages = {6245-6256},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1007/s00253-019-09909-6},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Sucrose phosphorolysis; Flux balance analysis; Plasmid burden; Data
+ reconciliation; Carbon storage regulator A},
+Keywords-Plus = {EXPRESSION; GROWTH; ACID; TRANSPORT; LACTATE; PATHWAY; ACETATE; GLUCOSE;
+ SYSTEMS; CLONING},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {van Loosdrecht, Mark/AAA-9997-2019
+ van Loosdrecht, Mark C.M./B-2738-2009
+ Gamez, Karel Olavarria/L-7765-2014
+ Olavarria Gamez, Karel/I-8125-2012
+ },
+ORCID-Numbers = {van Loosdrecht, Mark C.M./0000-0003-0658-4775
+ Olavarria Gamez, Karel/0000-0003-0435-7640
+ Fina Romero, Albert/0000-0001-7949-0484},
+Times-Cited = {4},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000475695600024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000489735000052,
+Author = {Paulson, Joel A. and Martin-Casas, Marc and Mesbah, Ali},
+Title = {Fast uncertainty quantification for dynamic flux balance analysis using
+ non-smooth polynomial chaos expansions},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2019},
+Volume = {15},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1007308},
+Article-Number = {e1007308},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {BAYESIAN EXPERIMENTAL-DESIGN; MODELS; SYSTEMS; IDENTIFIABILITY;
+ FERMENTATION; OPTIMIZATION; SIMULATION; PREDICTION; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Mesbah, Ali/0000-0002-1700-0600
+ Paulson, Joel/0000-0002-1518-7985},
+Times-Cited = {11},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000489735000052},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000477027900001,
+Author = {Kim, Minsuk and Park, Beom Gi and Kim, Eun-Jung and Kim, Joonwon and
+ Kim, Byung-Gee},
+Title = {In silico identification of metabolic engineering strategies for
+ improved lipid production in Yarrowia lipolytica by genome-scale
+ metabolic modeling},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2019},
+Volume = {12},
+Month = {JUL 24},
+Type = {Article},
+DOI = {10.1186/s13068-019-1518-4},
+Article-Number = {187},
+ISSN = {1754-6834},
+Keywords = {Genome-scale modeling; Systems biology; Metabolic engineering; Yarrowia
+ lipolytica; eMOMA; Lipid; Non-conventional yeast; TAG},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; OLEAGINOUS MICROORGANISMS; MALIC ENZYME;
+ ACCUMULATION; OPTIMIZATION; RECONSTRUCTION; OVERPRODUCTION; STRAINS;
+ PATHWAY; NADPH},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {kim, byung-gee/AAR-1933-2020
+ },
+ORCID-Numbers = {Kim, Minsuk/0000-0001-9958-0380},
+Times-Cited = {26},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000477027900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000477703600061,
+Author = {Heinonen, Markus and Osmala, Maria and Mannerstrom, Henrik and
+ Wallenius, Janne and Kaski, Samuel and Rousu, Juho and Lahdesmaki, Harri},
+Title = {Bayesian metabolic flux analysis reveals intracellular flux couplings},
+Journal = {BIOINFORMATICS},
+Year = {2019},
+Volume = {35},
+Number = {14},
+Pages = {I548-I557},
+Month = {JUL 15},
+Note = {Biennial Joint Meeting of the 27th Annual Conference on Intelligent
+ Systems for Molecular Biology (ISMB) / 18th European Conference on
+ Computational Biology (ECCB), Basel, SWITZERLAND, JUL 21-25, 2019},
+Type = {Article; Proceedings Paper},
+DOI = {10.1093/bioinformatics/btz315},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; HIT-AND-RUN; MONTE-CARLO; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; BALANCE ANALYSIS; SIMULATION;
+ ALGORITHM; SUBJECT},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Osmala, Maria/O-3627-2019
+ Kaski, Samuel/B-6684-2008
+ Rousu, Juho/E-8195-2012
+ },
+ORCID-Numbers = {Osmala, Maria/0000-0003-0128-4896
+ Kaski, Samuel/0000-0003-1925-9154
+ Rousu, Juho/0000-0002-0705-4314
+ Mannerstrom, Henrik/0000-0001-8492-665X
+ Wallenius, Janne/0000-0003-1786-4027},
+Times-Cited = {13},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000477703600061},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000475528200001,
+Author = {Yu, Han and Blair, Rachael Hageman},
+Title = {Integration of probabilistic regulatory networks into constraint-based
+ models of metabolism with applications to Alzheimer's disease},
+Journal = {BMC BIOINFORMATICS},
+Year = {2019},
+Volume = {20},
+Month = {JUL 10},
+Type = {Article},
+DOI = {10.1186/s12859-019-2872-8},
+Article-Number = {386},
+ISSN = {1471-2105},
+Keywords = {Constraint-based model; Gene network; Bayesian network; Model
+ integration; Probabilistic reasoning; Belief propagation; Metabolism},
+Keywords-Plus = {GENE-EXPRESSION; GRAPHICAL MODELS; INFERENCE; BRAIN; ERYTHROPOIETIN;
+ RECONSTRUCTION; PROPAGATION; PYRUVATE; PACKAGE; GLUCOSE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Blair, Rachael/0000-0001-8538-2447},
+Times-Cited = {7},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000475528200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000474335800004,
+Author = {Baloni, Priyanka and Sangar, Vineet and Yurkovich, James T. and
+ Robinson, Max and Taylor, Scott and Karbowski, Christine M. and Hamadeh,
+ Hisham K. and He, Yudong D. and Price, Nathan D.},
+Title = {Genome-scale metabolic model of the rat liver predicts effects of diet
+ restriction},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2019},
+Volume = {9},
+Month = {JUL 8},
+Type = {Article},
+DOI = {10.1038/s41598-019-46245-1},
+Article-Number = {9807},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GLOBAL RECONSTRUCTION; SPECIES-DIFFERENCES;
+ MOLECULAR-BASIS; ACID; DEFICIENCY; EXPRESSION; NETWORKS; DATABASE;
+ OXIDASE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Baloni, Priyanka/J-9180-2019
+ Robinson, Max/AAS-5856-2021
+ },
+ORCID-Numbers = {Baloni, Priyanka/0000-0002-3382-4941
+ Robinson, Max/0000-0003-0878-114X
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {5},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000474335800004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000477559300001,
+Author = {Sieow, Brendan Fu-Long and Nurminen, Toni Juhani and Ling, Hua and
+ Chang, Matthew Wook},
+Title = {Meta-Omics- and Metabolic Modeling-Assisted Deciphering of Human
+ Microbiota Metabolism},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2019},
+Volume = {14},
+Number = {9, SI},
+Month = {SEP},
+Type = {Review},
+DOI = {10.1002/biot.201800445},
+EarlyAccessDate = {JUL 2019},
+Article-Number = {1800445},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {genome-scale modeling; human microbiota; metabolic networks; meta-omics},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GUT MICROBIOTA; COMMENSAL BACTERIA;
+ NATURAL-PRODUCTS; DISCOVERY; REVEALS; ASSOCIATION; GENERATION;
+ DIVERSITY; SEQUENCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Ling, Hua/0000-0002-0680-6422
+ Sieow, Brendan/0000-0002-0535-1104},
+Times-Cited = {5},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000477559300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000474350600001,
+Author = {Lagziel, Shoval and Lee, Won Dong and Shlomi, Tomer},
+Title = {Studying metabolic flux adaptations in cancer through integrated
+ experimental-computational approaches},
+Journal = {BMC BIOLOGY},
+Year = {2019},
+Volume = {17},
+Month = {JUL 4},
+Type = {Review},
+DOI = {10.1186/s12915-019-0669-x},
+Article-Number = {51},
+ISSN = {1741-7007},
+Keywords = {Cancer metabolism; Metabolic network modeling; Metabolic flux analysis;
+ Constraint-based modeling; COBRA; Isotope tracing; 13C-MFA},
+Keywords-Plus = {REDUCTIVE GLUTAMINE-METABOLISM; CONSTRAINT-BASED MODELS; GLOBAL
+ RECONSTRUCTION; TCA CYCLE; NETWORK; MITOCHONDRIA; TRACERS; REVEAL;
+ QUANTITATION; PREDICTION},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ORCID-Numbers = {Lee, Won Dong/0000-0002-2344-171X},
+Times-Cited = {16},
+Journal-ISO = {BMC Biol.},
+Unique-ID = {WOS:000474350600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000493041400045,
+Author = {Li, Gaoyang and Cao, Huansheng and Xu, Ying},
+Title = {Structural and functional analyses of microbial metabolic networks
+ reveal novel insights into genome-scale metabolic fluxes},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2019},
+Volume = {20},
+Number = {4},
+Pages = {1590-1603},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1093/bib/bby022},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {metabolic network; network organizing principle; scale-free network;
+ clustering coefficient distribution; flux balance analysis; functional
+ modularity},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; SMALL-WORLD; RECONSTRUCTION;
+ ORGANIZATION; TOPOLOGY},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Li, Gaoyang/I-4482-2019
+ Cao, Huansheng/C-2182-2015},
+ORCID-Numbers = {Li, Gaoyang/0000-0001-6837-0719
+ Cao, Huansheng/0000-0002-2538-1589},
+Times-Cited = {4},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000493041400045},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000482629400028,
+Author = {Minato, Yusuke and Gohl, Daryl M. and Thiede, Joshua M. and Chacon,
+ Jeremy M. and Harcombe, William R. and Maruyama, Fumito and Baughn,
+ Anthony D.},
+Title = {Genomewide Assessment of Mycobacterium tuberculosis Conditionally
+ Essential Metabolic Pathways},
+Journal = {MSYSTEMS},
+Year = {2019},
+Volume = {4},
+Number = {4},
+Month = {JUL-AUG},
+Type = {Article},
+DOI = {10.1128/mSystems.00070-19},
+Article-Number = {e00070-19},
+ISSN = {2379-5077},
+Keywords = {comparative genomics; metabolic modeling; metabolism; Tn-seq;
+ tuberculosis},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ ESSENTIAL GENES; DATABASE; IDENTIFICATION; BIOSYNTHESIS; CONSTRUCTION;
+ PERSISTENCE; MUTAGENESIS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Maruyama, Fumito/AAK-5928-2020
+ Baughn, Anthony/ABB-7881-2020
+ Minato, Yusuke/B-9510-2018
+ },
+ORCID-Numbers = {Maruyama, Fumito/0000-0003-2347-616X
+ Minato, Yusuke/0000-0002-0888-8564
+ Baughn, Anthony/0000-0003-1188-4238
+ Gohl, Daryl/0000-0002-4434-2788
+ Thiede, Joshua/0000-0002-6603-281X},
+Times-Cited = {43},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000482629400028},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000474294900013,
+Author = {Molina, Lazaro and La Rosa, Ruggero and Nogales, Juan and Rojo, Fernando},
+Title = {Pseudomonas putida KT2440 metabolism undergoes sequential
+ modifications during exponential growth in a complete medium as
+ compounds are gradually consumed},
+Journal = {ENVIRONMENTAL MICROBIOLOGY},
+Year = {2019},
+Volume = {21},
+Number = {7},
+Pages = {2375-2390},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1111/1462-2920.14622},
+ISSN = {1462-2912},
+EISSN = {1462-2920},
+Keywords-Plus = {CARBON CATABOLITE REPRESSION; CRC GLOBAL REGULATOR; ESCHERICHIA-COLI;
+ GLUCOSE; GENOME; PATHWAYS; PROTEIN; IDENTIFICATION; DEHYDROGENASE;
+ AERUGINOSA},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Rojo, Fernando/A-7038-2008
+ La Rosa, Ruggero/AAR-8197-2021
+ Molina, Lazaro/K-9645-2014
+ Nogales, Juan/Y-8829-2019
+ },
+ORCID-Numbers = {Rojo, Fernando/0000-0003-1848-7745
+ La Rosa, Ruggero/0000-0002-6705-3989
+ Molina, Lazaro/0000-0002-8483-9203
+ Nogales, Juan/0000-0002-4961-0833},
+Times-Cited = {12},
+Journal-ISO = {Environ. Microbiol.},
+Unique-ID = {WOS:000474294900013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000470859400004,
+Author = {Pinhal, Stephane and Ropers, Delphine and Geiselmann, Johannes and de
+ Jong, Hidde},
+Title = {Acetate Metabolism and the Inhibition of Bacterial Growth by Acetate},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2019},
+Volume = {201},
+Number = {13},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1128/JB.00147-19},
+Article-Number = {e00147},
+ISSN = {0021-9193},
+EISSN = {1098-5530},
+Keywords = {Escherichia coli; acetate; acetate metabolism; growth inhibition;
+ metabolic flux analysis; overflow metabolism},
+Keywords-Plus = {ESCHERICHIA-COLI; FERMENTATION ACIDS; ACETYL-PHOSPHATE; FLUX ANALYSIS;
+ ACKA-PTA; PROTEIN; TRANSPORT; PATHWAYS; PH; REDISTRIBUTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Geiselmann, Hans/GVT-8876-2022
+ },
+ORCID-Numbers = {Geiselmann, Hans/0000-0002-1329-7558
+ Ropers, Delphine/0000-0003-2659-3003
+ de Jong, Hidde/0000-0002-2226-650X},
+Times-Cited = {106},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000470859400004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000481577700019,
+Author = {Zampieri, Guido and Vijayakumar, Supreeta and Yaneske, Elisabeth and
+ Angione, Claudio},
+Title = {Machine and deep learning meet genome-scale metabolic modeling},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2019},
+Volume = {15},
+Number = {7},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1371/journal.pcbi.1007084},
+Article-Number = {e1007084},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {OMICS DATA; INTEGRATIVE ANALYSIS; ESSENTIAL GENES; RECONSTRUCTION;
+ EXPRESSION; GENOTYPE; PREDICTION; REDUCTION; NETWORKS; CELL},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zampieri, Guido/HJH-7472-2023
+ },
+ORCID-Numbers = {Zampieri, Guido/0000-0002-4518-5913
+ Vijayakumar, Supreeta/0000-0001-6357-0439
+ Angione, Claudio/0000-0002-3140-7909
+ Yaneske, Elisabeth/0000-0001-6230-4016},
+Times-Cited = {137},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000481577700019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000473134100005,
+Author = {Trilla-Fuertes, Lucia and Gamez-Pozo, Angelo and Prado-Vazquez,
+ Guillermo and Zapater-Moros, Andrea and Diaz-Almiron, Mariana and
+ Arevalillo, Jorge M. and Ferrer-Gomez, Maria and Navarro, Hilario and
+ Main, Paloma and Espinosa, Enrique and Pinto, Alvaro and Fresno Vara,
+ Juan Angel},
+Title = {Biological molecular layer classification of muscle-invasive bladder
+ cancer opens new treatment opportunities},
+Journal = {BMC CANCER},
+Year = {2019},
+Volume = {19},
+Month = {JUN 28},
+Type = {Article},
+DOI = {10.1186/s12885-019-5858-z},
+Article-Number = {636},
+EISSN = {1471-2407},
+Keywords = {Muscle-invasive bladder cancer; Molecular subtypes; Personalized
+ medicine; Androgen receptor; Immune status},
+Keywords-Plus = {MODELS; IDENTIFICATION; PROGRESSION; METABOLISM; SUBTYPES; THERAPY;
+ BASAL},
+Research-Areas = {Oncology},
+Web-of-Science-Categories = {Oncology},
+ResearcherID-Numbers = {Prado-Vazquez, Guillermo/T-1861-2017
+ Gamez, Angelo/HSG-7485-2023
+ Trilla, Lucia/AAG-8392-2019
+ Vara, Juan Ángel Fresno/Y-9928-2019
+ Gamez-Pozo, Angelo/N-2506-2014
+ },
+ORCID-Numbers = {Prado-Vazquez, Guillermo/0000-0003-2456-6191
+ Trilla, Lucia/0000-0002-4452-3474
+ Vara, Juan Ángel Fresno/0000-0003-1527-1252
+ Gamez-Pozo, Angelo/0000-0002-8931-0624
+ Pinto, Alvaro/0000-0002-4719-053X
+ Espinosa Arranz, Enrique/0000-0001-6562-7902
+ Arevalillo, Jorge M/0000-0003-1944-3699
+ Navarro, Hilario/0000-0001-5594-869X},
+Times-Cited = {12},
+Journal-ISO = {BMC Cancer},
+Unique-ID = {WOS:000473134100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000471638300001,
+Author = {Gupta, Ankit and Ahmad, Ahmad and Chothwe, Dipesh and Madhu, Midhun K.
+ and Srivastava, Shireesh and Sharma, Vineet K.},
+Title = {Genome-scale metabolic reconstruction and metabolic versatility of an
+ obligate methanotroph Methylococcus capsulatus str. Bath},
+Journal = {PEERJ},
+Year = {2019},
+Volume = {7},
+Month = {JUN 14},
+Type = {Article},
+DOI = {10.7717/peerj.6685},
+Article-Number = {e6685},
+ISSN = {2167-8359},
+Keywords = {Methanotrophs; Methylococcus capsulatus; Methane mitigation;
+ Constraint-based model; Metabolic model; Metabolic network; Genome-scale},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; METHANE MONOOXYGENASE; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; GROWTH; BIOCONVERSION; ASSIMILATION; OXIDATION;
+ BACTERIA; SEQUENCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Srivastava, Shireesh/JDC-9742-2023
+ },
+ORCID-Numbers = {Srivastava, Shireesh/0000-0001-6139-1904
+ Gupta, Ankit/0009-0002-0406-0716
+ Madhu, Midhun/0000-0002-1787-7920
+ K. Sharma, Vineet/0000-0002-2958-6215},
+Times-Cited = {10},
+Journal-ISO = {PeerJ},
+Unique-ID = {WOS:000471638300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000474216200001,
+Author = {Bernstein, David B. and Dewhirst, Floyd E. and Segre, Daniel},
+Title = {Metabolic network percolation quantifies biosynthetic capabilities
+ across the human oral microbiome},
+Journal = {ELIFE},
+Year = {2019},
+Volume = {8},
+Month = {JUN 13},
+Type = {Article},
+DOI = {10.7554/eLife.39733},
+Article-Number = {e39733},
+ISSN = {2050-084X},
+Keywords-Plus = {GENOME; MODELS; TM7; RECONSTRUCTION; BACTERIA; ECOLOGY; HEALTH; TOOL;
+ CULTIVATION; MEMBRANES},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Bernstein, David B/HLV-8885-2023
+ Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Bernstein, David B/0000-0001-6091-4021
+ Segrè, Daniel/0000-0003-4859-1914
+ Dewhirst, Floyd E./0000-0003-4427-7928},
+Times-Cited = {19},
+Journal-ISO = {eLife},
+Unique-ID = {WOS:000474216200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000471605500005,
+Author = {Kim, Eun-Youn and Ashlock, Daniel and Yoon, Sung Ho},
+Title = {Identification of critical connectors in the directed reaction-centric
+ graphs of microbial metabolic networks},
+Journal = {BMC BIOINFORMATICS},
+Year = {2019},
+Volume = {20},
+Month = {JUN 13},
+Type = {Article},
+DOI = {10.1186/s12859-019-2897-z},
+Article-Number = {328},
+ISSN = {1471-2105},
+Keywords = {Directed network; Metabolic network; Reaction-centric graph; Cascade
+ number; Centrality metric; Information flow},
+Keywords-Plus = {SMALL-WORLD; MODELS; RECONSTRUCTION; PATHWAYS; ORGANIZATION; ROBUSTNESS;
+ MODULARITY; SYSTEM; GENES},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Yoon, Sung Ho/0000-0003-0171-944X},
+Times-Cited = {5},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000471605500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000470985300002,
+Author = {Bernabe, Beatriz Penalver and Thiele, Ines and Galdones, Eugene and
+ Siletz, Anaar and Chandrasekaran, Sriram and Woodruff, Teresa K. and
+ Broadbelt, Linda J. and Shea, Lonnie D.},
+Title = {Dynamic genome-scale cell-specific metabolic models reveal novel
+ inter-cellular and intra-cellular metabolic communications during
+ ovarian follicle development},
+Journal = {BMC BIOINFORMATICS},
+Year = {2019},
+Volume = {20},
+Month = {JUN 10},
+Type = {Article},
+DOI = {10.1186/s12859-019-2825-2},
+Article-Number = {307},
+ISSN = {1471-2105},
+Keywords = {Ovarian follicle development; Metabolism; Metabolic communities;
+ Secreted metabolites; Cell-type specific metabolic models; Genome-scale
+ modeling},
+Keywords-Plus = {MOUSE OOCYTES; MEIOTIC ARREST; GLOBAL RECONSTRUCTION; GRANULOSA-CELLS;
+ EXPRESSION DATA; IN-VITRO; MAINTENANCE; COOPERATIVITY; HYPOXANTHINE;
+ TRANSCRIPT},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Chandrasekaran, Sriram/AAF-4731-2019
+ Thiele, Ines/A-7629-2014
+ Broadbelt, Linda/B-7640-2009
+ Chandrasekaran, Sriram/AAD-9774-2019
+ },
+ORCID-Numbers = {Chandrasekaran, Sriram/0000-0002-8405-5708
+ Thiele, Ines/0000-0002-8071-7110
+ Chandrasekaran, Sriram/0000-0002-8405-5708
+ Shea, Lonnie/0000-0002-9296-9673},
+Times-Cited = {15},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000470985300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000470104900013,
+Author = {Styr, Boaz and Gonen, Nir and Zarhin, Daniel and Ruggiero, Antonella and
+ Atsmon, Refaela and Gazit, Neta and Braun, Gabriella and Frere, Samuel
+ and Vertkin, Irena and Shapira, Ilana and Harel, Michal and Heim, Leore
+ R. and Katsenelson, Maxim and Rechnitz, Ohad and Fadila, Saja and
+ Derdikman, Dori and Rubinstein, Moran and Geiger, Tamar and Ruppin,
+ Eytan and Slutsky, Inna},
+Title = {Mitochondrial Regulation of the Hippocampal Firing Rate Set Point and
+ Seizure Susceptibility},
+Journal = {NEURON},
+Year = {2019},
+Volume = {102},
+Number = {5},
+Pages = {1009+},
+Month = {JUN 5},
+Type = {Article},
+DOI = {10.1016/j.neuron.2019.03.045},
+ISSN = {0896-6273},
+EISSN = {1097-4199},
+Keywords-Plus = {PTZ-INDUCED SEIZURES; DRAVET SYNDROME; MOUSE MODEL; HOMEOSTATIC
+ PLASTICITY; GLOBAL RECONSTRUCTION; RELEASE PROBABILITY; KETOGENIC DIET;
+ VISUAL-CORTEX; NETWORK; DYSFUNCTION},
+Research-Areas = {Neurosciences \& Neurology},
+Web-of-Science-Categories = {Neurosciences},
+ResearcherID-Numbers = {Rubinstein, Moran/JFA-5719-2023
+ Geiger, Tamar/C-2349-2014
+ },
+ORCID-Numbers = {Rubinstein, Moran/0000-0003-2617-2276
+ Geiger, Tamar/0000-0002-9526-197X
+ Katsenelson, Maxim/0000-0001-5561-7065
+ Slutsky, Inna/0000-0002-0700-2266
+ Ruggiero, Antonella/0000-0002-0137-0092},
+Times-Cited = {65},
+Journal-ISO = {Neuron},
+Unique-ID = {WOS:000470104900013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000475306200027,
+Author = {Badri, Abinaya and Raman, Karthik and Jayaraman, Guhan},
+Title = {Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in
+ Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and
+ Experimental Validation},
+Journal = {PROCESSES},
+Year = {2019},
+Volume = {7},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.3390/pr7060343},
+Article-Number = {343},
+ISSN = {2227-9717},
+Keywords = {hyaluronic acid; genome-scale metabolic network model; Lactococcus
+ lactis; metabolic engineering; inosine supplementation},
+Keywords-Plus = {ACID PRODUCTION; STREPTOCOCCUS-ZOOEPIDEMICUS; MOLECULAR-WEIGHT;
+ ESCHERICHIA-COLI; BIOSYNTHESIS; FLUX; FERMENTATION; OPTIMIZATION;
+ FRAMEWORK; OXYGEN},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Raman, Karthik/Q-5278-2019
+ },
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ Jayaraman, Guhan/0000-0003-0084-162X
+ Badri, Abinaya/0000-0003-1565-4595},
+Times-Cited = {11},
+Journal-ISO = {Processes},
+Unique-ID = {WOS:000475306200027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000475294600013,
+Author = {Chu, Su H. and Huang, Mengna and Kelly, Rachel S. and Benedetti, Elisa
+ and Siddiqui, Jalal K. and Zeleznik, Oana A. and Pereira, Alexandre and
+ Herrington, David and Wheelock, Craig E. and Krumsiek, Jan and
+ McGeachie, Michael and Moore, Steven C. and Kraft, Peter and Mathe, Ewy
+ and Lasky-Su, Jessica and Consortium Metab Studies Stat Work},
+Title = {Integration of Metabolomic and Other Omics Data in Population-Based
+ Study Designs: An Epidemiological Perspective},
+Journal = {METABOLITES},
+Year = {2019},
+Volume = {9},
+Number = {6},
+Month = {JUN},
+Type = {Review},
+DOI = {10.3390/metabo9060117},
+Article-Number = {117},
+EISSN = {2218-1989},
+Keywords = {multi-omic integration; systems biology; epidemiology; study design;
+ integrative analysis},
+Keywords-Plus = {GENE REGULATORY NETWORKS; QUANTITATIVE TRAIT LOCI; MENDELIAN
+ RANDOMIZATION; BAYESIAN NETWORKS; WIDE ASSOCIATION; EXPRESSION DATA;
+ PATHWAY; MODELS; LEVEL; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Krumsiek, Jan/B-3961-2013
+ Pereira, Alexandre/HHN-1038-2022
+ Kraft, Peter/GQH-8448-2022
+ Moore, Steven/D-8760-2016
+ kelly, rachel/H-4505-2017
+ },
+ORCID-Numbers = {Moore, Steven/0000-0002-8169-1661
+ kelly, rachel/0000-0003-3023-1822
+ Siddiqui, Jalal/0000-0002-5100-6432
+ Chu, Su/0000-0002-6345-008X
+ Wheelock, Craig/0000-0002-8113-0653
+ Lasky-Su, Jessica/0000-0001-6236-4705},
+Times-Cited = {39},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000475294600013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000472768900068,
+Author = {Guthrie, Leah and Kelly, Libusha},
+Title = {Bringing microbiome-drug interaction research into the clinic},
+Journal = {EBIOMEDICINE},
+Year = {2019},
+Volume = {44},
+Pages = {708-715},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1016/j.ebiom.2019.05.009},
+ISSN = {2352-3964},
+Keywords = {Microbiome; Drug metabolism; Metabolomics; High throughput genomics},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GUT MICROBIOTA; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; XANTHOHUMOL; IMPACT; PHARMACOMICROBIOMICS;
+ PHARMACOGENOMICS; POLYMORPHISMS; INACTIVATION},
+Research-Areas = {General \& Internal Medicine; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Medicine, General \& Internal; Medicine, Research \& Experimental},
+ORCID-Numbers = {Guthrie, Leah/0000-0002-9144-0110},
+Times-Cited = {36},
+Journal-ISO = {EBioMedicine},
+Unique-ID = {WOS:000472768900068},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000473818300105,
+Author = {Mohammadi, Reza and Zahiri, Javad and Niroomand, Mohammad Javad},
+Title = {iMet: A graphical user interface software tool to merge metabolic
+ networks},
+Journal = {HELIYON},
+Year = {2019},
+Volume = {5},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1016/j.heliyon.2019.e01766},
+Article-Number = {e01766},
+EISSN = {2405-8440},
+Keywords = {Bioinformatics; Biotechnology; Microbiology; Systems biology},
+Keywords-Plus = {SP PCC 6803; CYANOBACTERIA; MODELS; DATABASE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Mohammadi, Reza/AAS-6539-2021},
+ORCID-Numbers = {Mohammadi, Reza/0000-0001-5445-2991},
+Times-Cited = {0},
+Journal-ISO = {Heliyon},
+Unique-ID = {WOS:000473818300105},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000500745000008,
+Author = {Park, Junyoung O. and Liu, Nian and Holinski, Kara M. and Emerson, David
+ F. and Qiao, Kangjian and Woolston, Benjamin M. and Xu, Jingyang and
+ Lazar, Zbigniew and Islam, M. Ahsanul and Vidoudez, Charles and Girguis,
+ Peter R. and Stephanopoulos, Gregory},
+Title = {Synergistic substrate cofeeding stimulates reductive metabolism},
+Journal = {NATURE METABOLISM},
+Year = {2019},
+Volume = {1},
+Number = {6},
+Pages = {643-651},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1038/s42255-019-0077-0},
+EISSN = {2522-5812},
+Keywords-Plus = {YARROWIA-LIPOLYTICA; LIPID PRODUCTION; CO2 FIXATION; CONVERSION;
+ PATHWAY; BIOFUEL; CYCLE},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Park, Junyoung/AAL-8090-2020
+ Lazar, Zbigniew/AAA-1972-2020
+ },
+ORCID-Numbers = {Lazar, Zbigniew/0000-0001-7315-1983
+ Islam, M. Ahsanul/0000-0001-9585-6263
+ Park, Jun/0000-0001-9869-8993
+ /0000-0002-6570-2236
+ Emerson, David/0000-0003-4948-9962
+ /0000-0002-1164-8692},
+Times-Cited = {53},
+Journal-ISO = {Nat. Metab.},
+Unique-ID = {WOS:000500745000008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000471746600019,
+Author = {Zeng, Hong and Yang, Aidong},
+Title = {Quantification of proteomic and metabolic burdens predicts growth
+ retardation and overflow metabolism in recombinant Escherichia
+ coli},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2019},
+Volume = {116},
+Number = {6},
+Pages = {1484-1495},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/bit.26943},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {dynamic flux balance analysis; Escherichia coli; genome-scale model;
+ overflow metabolism; proteome allocation constraint; recombinant protein
+ production},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS; PROTEIN-PRODUCTION;
+ PICHIA-PASTORIS; QUANTITATIVE PREDICTION; RESOURCE-ALLOCATION;
+ CELLULAR-METABOLISM; STEADY-STATE; MAINTENANCE; EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Yang, Aidong/M-2887-2013
+ },
+ORCID-Numbers = {Yang, Aidong/0000-0001-7771-6777
+ Zeng, Hong/0000-0001-6617-4466},
+Times-Cited = {11},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000471746600019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000469415100025,
+Author = {Yang, Jason H. and Wright, Sarah N. and Hamblin, Meagan and McCloskey,
+ Douglas and Alcantar, Miguel A. and Schrubbers, Lars and Lopatkin,
+ Allison J. and Satish, Sangeeta and Nili, Amir and Palsson, Bernhard O.
+ and Walker, Graham C. and Collins, James J.},
+Title = {A White-Box Machine Learning Approach for Revealing Antibiotic
+ Mechanisms of Action},
+Journal = {CELL},
+Year = {2019},
+Volume = {177},
+Number = {6},
+Pages = {1649+},
+Month = {MAY 30},
+Type = {Article},
+DOI = {10.1016/j.cell.2019.04.016},
+ISSN = {0092-8674},
+EISSN = {1097-4172},
+Keywords-Plus = {ESCHERICHIA-COLI; BACTERICIDAL ANTIBIOTICS; DRUG DISCOVERY; METABOLISM;
+ EFFICACY; INDUCE; MODEL; PERTURBATIONS; PREDICTION; RESISTANCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Yang, Jason H./AAB-2608-2019
+ yang, jason/JFA-5026-2023
+ },
+ORCID-Numbers = {Yang, Jason H./0000-0003-0921-4657
+ Alcantar, Miguel A./0000-0003-1189-2254
+ Wright, Sarah/0000-0003-3441-5469},
+Times-Cited = {171},
+Journal-ISO = {Cell},
+Unique-ID = {WOS:000469415100025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000468914900001,
+Author = {Orellana-Saez, Matias and Pacheco, Nicolas and Costa, I, Jose and
+ Mendez, Katterinne N. and Miossec, Matthieu J. and Meneses, Claudio and
+ Castro-Nallar, Eduardo and Marcoleta, Andres E. and Poblete-Castro,
+ Ignacio},
+Title = {In-Depth Genomic and Phenotypic Characterization of the Antarctic
+ Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique
+ Metabolic Features, Plasticity, and Biotechnological Potential},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2019},
+Volume = {10},
+Month = {MAY 24},
+Type = {Article},
+DOI = {10.3389/fmicb.2019.01154},
+Article-Number = {1154},
+ISSN = {1664-302X},
+Keywords = {Pseudomonas; genome sequencing; aromatic compounds;
+ poly(3-hydroxyalkanoates); low temperature; heavy metals; extremophile},
+Keywords-Plus = {LOW-TEMPERATURE; RESISTANT PSEUDOMONAS; ARSENIC TOLERANCE;
+ ESCHERICHIA-COLI; CADMIUM TOXICITY; MULTIDRUG EFFLUX; GENE-EXPRESSION;
+ PUTIDA KT2440; SCALE MODELS; HEAVY-METAL},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Miossec, Matthieu/T-3491-2019
+ Poblete-Castro, Ignacio/J-2755-2019
+ Castro-Nallar, Eduardo/I-5925-2019
+ Caldera, Andrés Marcoleta/AFN-3162-2022
+ },
+ORCID-Numbers = {Miossec, Matthieu/0000-0001-8148-7890
+ Castro-Nallar, Eduardo/0000-0003-4384-8661
+ Marcoleta Caldera, Andres Esteban/0000-0003-2950-7510
+ Meneses, Claudio/0000-0002-6452-8950
+ Poblete-Castro, Ignacio/0000-0001-6649-0389},
+Times-Cited = {33},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000468914900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000468194800002,
+Author = {Heinken, Almut and Raycheev, Dmitry A. and Baldini, Federico and
+ Heirendt, Laurent and Fleming, Ronan M. T. and Thiele, Ines},
+Title = {Systematic assessment of secondary bile acid metabolism in gut microbes
+ reveals distinct metabolic capabilities in inflammatory bowel disease},
+Journal = {MICROBIOME},
+Year = {2019},
+Volume = {7},
+Month = {MAY 15},
+Type = {Article},
+DOI = {10.1186/s40168-019-0689-3},
+Article-Number = {75},
+ISSN = {2049-2618},
+Keywords = {Gut microbiome; Bile acids; Host-microbe interactions; Metabolism;
+ Genome-scale reconstruction; Constraint-based modeling; Personalized
+ modeling; Systems biology},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; SALT BIOTRANSFORMATIONS; BIOLOGY; DEHYDROGENASE;
+ PERFORMANCE; CONVERSION; HYDROLASE; TOOLBOX; CLONING},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ Ravcheev, Dmitry A/M-6877-2015},
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Ravcheev, Dmitry A/0000-0002-8435-5516},
+Times-Cited = {155},
+Journal-ISO = {Microbiome},
+Unique-ID = {WOS:000468194800002},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000467543700032,
+Author = {Trilla-Fuertes, Lucia and Gamez-Pozo, Angelo and Prado-Vazquez,
+ Guillermo and Zapater-Moros, Andrea and Diaz-Almiron, Mariana and
+ Fortes, Claudia and Ferrer-Gomez, Maria and Lopez-Vacas, Rocio and
+ Blanco, Veronica Parra and Marquez-Rodas, Ivan and Soria, Ainara and
+ Fresno Vara, Juan Angel and Espinosa, Enrique},
+Title = {Melanoma proteomics suggests functional differences related to
+ mutational status},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2019},
+Volume = {9},
+Month = {MAY 10},
+Type = {Article},
+DOI = {10.1038/s41598-019-43512-z},
+Article-Number = {7217},
+ISSN = {2045-2322},
+Keywords-Plus = {EXPRESSION; METABOLISM; BIOLOGY; CELLS; FLUX},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Gamez, Angelo/HSG-7485-2023
+ Trilla, Lucia/AAG-8392-2019
+ Marquez-Rodas, Ivan/ABD-5532-2021
+ parra-blanco, veronica/ABC-7069-2020
+ Vara, Juan Ángel Fresno/Y-9928-2019
+ Prado-Vazquez, Guillermo/T-1861-2017
+ Gamez-Pozo, Angelo/N-2506-2014},
+ORCID-Numbers = {Trilla, Lucia/0000-0002-4452-3474
+ Marquez-Rodas, Ivan/0000-0002-2476-668X
+ parra-blanco, veronica/0000-0002-7916-5478
+ Vara, Juan Ángel Fresno/0000-0003-1527-1252
+ Prado-Vazquez, Guillermo/0000-0003-2456-6191
+ Espinosa Arranz, Enrique/0000-0001-6562-7902
+ Gamez-Pozo, Angelo/0000-0002-8931-0624},
+Times-Cited = {9},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000467543700032},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000477727500023,
+Author = {Blanco-Miguez, Aitor and Fdez-Riverola, Florentino and Sanchez, Borja
+ and Lourenco, Analia},
+Title = {Resources and tools for the high-throughput, multi-omic study of
+ intestinal microbiota},
+Journal = {BRIEFINGS IN BIOINFORMATICS},
+Year = {2019},
+Volume = {20},
+Number = {3},
+Pages = {1032-1056},
+Month = {MAY},
+Type = {Software Review},
+DOI = {10.1093/bib/bbx156},
+ISSN = {1467-5463},
+EISSN = {1477-4054},
+Keywords = {human gut microbiome; data repositories; large-scale and integrative
+ computational tools; modelling; immunomodulation; drug screening},
+Keywords-Plus = {SCALE METABOLIC MODEL; MASS-SPECTRAL DATA; GUT MICROBIOTA; SYSTEMS
+ BIOLOGY; GASTROINTESTINAL-TRACT; GENOME ANNOTATION; SEQUENCING DATA; BIG
+ DATA; MG-RAST; PROTEIN},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Fdez-Riverola, Florentino/G-1411-2011
+ Blanco-Míguez, Aitor/AAN-2149-2020
+ Lourenço, Anália/G-8879-2013
+ Lourenço, Anália/Y-9447-2019
+ },
+ORCID-Numbers = {Fdez-Riverola, Florentino/0000-0002-3943-8013
+ Blanco-Míguez, Aitor/0000-0001-7386-5572
+ Lourenço, Anália/0000-0001-8401-5362
+ Lourenço, Anália/0000-0001-8401-5362
+ , IIS Galicia Sur/0000-0003-3812-7413},
+Times-Cited = {8},
+Journal-ISO = {Brief. Bioinform.},
+Unique-ID = {WOS:000477727500023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000470965600018,
+Author = {Chiewchankaset, Porntip and Kalapanulak, Saowalak and Saithong, Treenut},
+Title = {Extended Utilization of Constraint-Based Metabolic Model in a
+ Long-Growing Crop},
+Journal = {PROCESSES},
+Year = {2019},
+Volume = {7},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.3390/pr7050259},
+Article-Number = {259},
+EISSN = {2227-9717},
+Keywords = {biomass components; biomass function; carbon flux prediction; cassava
+ storage root model; constraint-based modeling; long-growing crop; model
+ sensitivity; rMeCBM model; specific storage root growth rate; specific
+ sucrose uptake rate},
+Keywords-Plus = {GENOME-SCALE RECONSTRUCTION; FLUX BALANCE ANALYSIS;
+ SACCHAROMYCES-CEREVISIAE; PHOTOSYNTHESIS; GROWTH; PREDICTION; NETWORK;
+ BIOMASS; YIELD},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Saithong, Treenut/L-1395-2019},
+ORCID-Numbers = {Saithong, Treenut/0000-0003-2888-6854},
+Times-Cited = {0},
+Journal-ISO = {Processes},
+Unique-ID = {WOS:000470965600018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000462916400012,
+Author = {Kamata, Kentaro and Toya, Yoshihiro and Shimizu, Hiroshi},
+Title = {Effect of precise control of flux ratio between the glycolytic pathways
+ on mevalonate production in Escherichia coli},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2019},
+Volume = {116},
+Number = {5},
+Pages = {1080-1088},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/bit.26923},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Escherichia coli; metabolic flux control; mevalonate; NADPH; oxidative
+ pentose phosphate pathway},
+Keywords-Plus = {OVERPRODUCTION; METABOLISM; STRAIN},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Shimizu, Hiroshi/C-3688-2017
+ },
+ORCID-Numbers = {Shimizu, Hiroshi/0000-0002-8986-0861
+ Toya, Yoshihiro/0000-0001-9670-6961},
+Times-Cited = {12},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000462916400012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000468697000009,
+Author = {Pereira, Rui and Vilaca, Paulo and Maia, Paulo and Nielsen, Jens and
+ Rocha, Isabel},
+Title = {Turnover Dependent Phenotypic Simulation: A Quantitative
+ Constraint-Based Simulation Method That Accommodates All Main Strain
+ Design Strategies},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2019},
+Volume = {8},
+Number = {5},
+Pages = {976-988},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1021/acssynbio.8b00248},
+ISSN = {2161-5063},
+Keywords = {genome-scale models; Saccharomyces cerevisiae; phenotype simulation;
+ metabolite turnovers; network rigidity; metabolic engineering},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; 3-HYDROXYPROPIONIC ACID; METABOLISM;
+ POLYHYDROXYBUTYRATE; OVERPRODUCTION; PRECURSOR},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Maia, Paulo/AAM-1025-2021
+ Rocha, Isabel/A-4279-2013
+ Maia, Paulo/F-9148-2010
+ },
+ORCID-Numbers = {Rocha, Isabel/0000-0001-9494-3410
+ Maia, Paulo/0000-0002-0848-8683
+ Pereira, Rui/0000-0002-0572-875X
+ Vilaca, Paulo/0000-0002-1098-5849},
+Times-Cited = {0},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000468697000009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000466484100026,
+Author = {Greenhalgh, Kacy and Ramiro-Garcia, Javier and Heinken, Almut and
+ Ullmann, Pit and Bintener, Tamara and Pacheco, Maria Pires and Baginska,
+ Joanna and Shah, Pranjul and Frachet, Audrey and Halder, Rashi and
+ Fritz, Joelle V. and Sauter, Thomas and Thiele, Ines and Haan, Serge and
+ Letellier, Elisabeth and Wilmes, Paul},
+Title = {Integrated In Vitro and In Silico Modeling Delineates the
+ Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived
+ Cells},
+Journal = {CELL REPORTS},
+Year = {2019},
+Volume = {27},
+Number = {5},
+Pages = {1621+},
+Month = {APR 30},
+Type = {Article},
+DOI = {10.1016/j.celrep.2019.04.001},
+ISSN = {2211-1247},
+Keywords-Plus = {CHAIN FATTY-ACIDS; SIGNALING PATHWAY; MULTIDRUG-RESISTANCE; HUMAN
+ MICROBIOME; STEM-CELL; METABOLISM; FIBER; INFLAMMATION; SURVIVAL; RNA},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Ramiro-Garcia, Javier/ABA-6236-2020
+ Wilmes, Paul/B-1707-2017
+ shah, pranjul/D-5658-2012
+ HALDER, RASHI/G-6894-2015
+ Pacheco, Maria Pires/C-4494-2014
+ Letellier, Elisabeth/I-9515-2016
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Ramiro-Garcia, Javier/0000-0003-3896-3833
+ Wilmes, Paul/0000-0002-6478-2924
+ HALDER, RASHI/0000-0002-1402-1254
+ Pacheco, Maria Pires/0000-0001-7956-8093
+ Letellier, Elisabeth/0000-0001-8242-9393
+ Thiele, Ines/0000-0002-8071-7110
+ Shah, Pranjul/0000-0001-9296-690X
+ Sauter, Thomas/0000-0001-8225-2954
+ Baginska, Joanna/0000-0001-5182-7575
+ Fritz, Joelle/0000-0002-4694-3923},
+Times-Cited = {43},
+Journal-ISO = {Cell Reports},
+Unique-ID = {WOS:000466484100026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000465109600002,
+Author = {Sompairac, Nicolas and Modamio, Jennifer and Barillot, Emmanuel and
+ Fleming, Ronan M. T. and Zinovyev, Andrei and Kuperstein, Inna},
+Title = {Metabolic and signalling network maps integration: application to
+ cross-talk studies and omics data analysis in cancer},
+Journal = {BMC BIOINFORMATICS},
+Year = {2019},
+Volume = {20},
+Number = {4},
+Month = {APR 18},
+Note = {17th International Workshop on Network Tools and Applications in Biology
+ (NETTAB) - Methods, Tools and Platforms for Personalized Medicine in the
+ Big Data Era, Palermo, ITALY, OCT 16-18, 2017},
+Type = {Article; Proceedings Paper},
+DOI = {10.1186/s12859-019-2682-z},
+Article-Number = {140},
+ISSN = {1471-2105},
+Keywords = {Signalling; Metabolism; Networks; Comprehensive map; Systems biology;
+ Cancer; Multi-level omics data; Data visualisation},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zinovyev, Andrei/B-4715-2010
+ Fleming, Ronan MT/ABC-4093-2021},
+ORCID-Numbers = {Zinovyev, Andrei/0000-0002-9517-7284
+ Fleming, Ronan MT/0000-0001-5346-9812},
+Times-Cited = {7},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000465109600002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000464755300003,
+Author = {Untaroiu, Ana M. and Carey, Maureen A. and Guler, Jennifer L. and Papin,
+ Jason A.},
+Title = {Leveraging the effects of chloroquine on resistant malaria parasites for
+ combination therapies},
+Journal = {BMC BIOINFORMATICS},
+Year = {2019},
+Volume = {20},
+Month = {APR 15},
+Type = {Article},
+DOI = {10.1186/s12859-019-2756-y},
+Article-Number = {186},
+ISSN = {1471-2105},
+Keywords = {Malaria; Combination therapies; Chloroquine; Metabolic modeling},
+Keywords-Plus = {PLASMODIUM-FALCIPARUM MALARIA; FERRIPROTOPORPHYRIN-IX; HEME DEGRADATION;
+ IN-VITRO; INTRACELLULAR GLUTATHIONE; SULFADOXINE-PYRIMETHAMINE;
+ DRUG-RESISTANCE; INHIBITION; GENE; ERYTHROCYTES},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Guler, Jennifer/0000-0001-6301-4563
+ Papin, Jason/0000-0002-2769-5805
+ Carey, Maureen/0000-0003-2890-5445},
+Times-Cited = {4},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000464755300003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000467530600007,
+Author = {Blazier, Anna S. and Papin, Jason A.},
+Title = {Reconciling high-throughput gene essentiality data with metabolic
+ network reconstructions},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2019},
+Volume = {15},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1006507},
+Article-Number = {e1006507},
+EISSN = {1553-7358},
+Keywords-Plus = {PSEUDOMONAS-AERUGINOSA PAO1; READ ALIGNMENT; IDENTIFICATION; REDUCTASE;
+ LIBRARY; LIFE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Blazier, Anna/0000-0001-5226-0339
+ Papin, Jason/0000-0002-2769-5805},
+Times-Cited = {11},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000467530600007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000467530600051,
+Author = {Jamialahmadi, Oveis and Hashemi-Najafabadi, Sameereh and Motamedian,
+ Ehsan and Romeo, Stefano and Bagheri, Fatemeh},
+Title = {A benchmark-driven approach to reconstruct metabolic networks for
+ studying cancer metabolism},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2019},
+Volume = {15},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1006936},
+Article-Number = {e1006936},
+EISSN = {1553-7358},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; REGULATORY NETWORKS; KEY ROLE; CELL; MODELS;
+ PREDICTION; TOOLBOX},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Atyabi, Fatemeh/O-3356-2019
+ Hashemi-Najafabadi, Sameereh/JSB-1968-2023
+ Motamedian, Ehsan/GPK-8344-2022
+ Romeo, Stefano/L-6861-2015
+ },
+ORCID-Numbers = {Atyabi, Fatemeh/0000-0002-9421-8750
+ Hashemi-Najafabadi, Sameereh/0000-0001-7826-6325
+ Romeo, Stefano/0000-0001-9168-4898
+ Bagheri, Fatemeh/0000-0002-9920-338X
+ , Ehsan/0000-0001-8750-2879},
+Times-Cited = {20},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000467530600051},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000463607300023,
+Author = {Ozcan, Emrah and Selvi, S. Selvin and Nikerel, Emrah and Teusink, Bas
+ and Oner, Ebru Toksoy and Cakir, Tunahan},
+Title = {A genome-scale metabolic network of the aroma bacterium Leuconostoc
+ mesenteroides subsp. cremoris},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2019},
+Volume = {103},
+Number = {7},
+Pages = {3153-3165},
+Month = {APR},
+Type = {Article},
+DOI = {10.1007/s00253-019-09630-4},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Lactic acid bacteria; Leuconostoc mesenteroides subsp; cremoris;
+ Heterolactic fermentation; Flavor metabolism; Genome-scale metabolic
+ model; Flux balance analysis},
+Keywords-Plus = {LACTIC-ACID BACTERIA; LACTOCOCCUS-LACTIS; LACTOBACILLUS-PLANTARUM;
+ STARTER CULTURES; GROWTH; GLUCOSE-6-PHOSPHATE-DEHYDROGENASE; CITRATE;
+ FERMENTATION; PHYSIOLOGY; MECHANISM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Toksoy Oner, Ebru/E-2637-2014
+ ÖZCAN, EMRAH/HZH-6141-2023
+ Cakir, Tunahan/F-4523-2011
+ Nikerel, Emrah/T-8664-2018
+ Oner, Ebru Toksoy/X-2183-2019
+ },
+ORCID-Numbers = {Toksoy Oner, Ebru/0000-0001-6054-8842
+ Cakir, Tunahan/0000-0001-8262-4420
+ Oner, Ebru Toksoy/0000-0001-6054-8842
+ Teusink, Bas/0000-0003-3929-0423
+ OZCAN, EMRAH/0000-0001-9036-9909
+ Nikerel, Emrah/0000-0002-9157-8662},
+Times-Cited = {23},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000463607300023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000467288300009,
+Author = {Zoledowska, Sabina and Presta, Luana and Fondi, Marco and Decorosi,
+ Francesca and Giovannetti, Luciana and Mengoni, Alessio and Lojkowska,
+ Ewa},
+Title = {Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides
+ Insights into Metabolic Pathways of Plant Pathogenic Bacteria},
+Journal = {MICROORGANISMS},
+Year = {2019},
+Volume = {7},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.3390/microorganisms7040101},
+Article-Number = {101},
+ISSN = {2076-2607},
+Keywords = {Flux Balance Analysis; plant pathogenic bacteria; bacterial adaptation;
+ metabolic reactions},
+Keywords-Plus = {ENTEROBACTERIACEAE; RHIZOSPHERE; EVOLUTION; DICKEYA; NETWORK; BALANCE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Lojkowska, Ewa/S-3402-2019
+ Mengoni, Alessio/G-5336-2013
+ Zoledowska, Sabina/D-2401-2017
+ },
+ORCID-Numbers = {Lojkowska, Ewa/0000-0001-8640-2307
+ Mengoni, Alessio/0000-0002-1265-8251
+ Zoledowska, Sabina/0000-0001-6218-8342
+ Presta, Luana/0000-0001-6482-6758},
+Times-Cited = {9},
+Journal-ISO = {Microorganisms},
+Unique-ID = {WOS:000467288300009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000462877200001,
+Author = {Yildiz, Songul Yasar and Nikerel, Emrah and Oner, Ebru Toksoy},
+Title = {Genome-Scale Metabolic Model of a Microbial Cell Factory
+ (Brevibacillus thermoruber 423) with Multi-Industry Potentials
+ for Exopolysaccharide Production},
+Journal = {OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY},
+Year = {2019},
+Volume = {23},
+Number = {4},
+Pages = {237-246},
+Month = {APR 1},
+Type = {Article},
+DOI = {10.1089/omi.2019.0028},
+EarlyAccessDate = {MAR 2019},
+ISSN = {1536-2310},
+EISSN = {1557-8100},
+Keywords = {genome-scale metabolic model; pharmaceutical industry; food industry;
+ exopolysaccharide; thermophilic bacteria; bionanotechnology industry},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS; QUANTITATIVE PREDICTION;
+ SYSTEMS BIOLOGY; RECONSTRUCTION; NETWORKS; OMICS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Oner, Ebru Toksoy/X-2183-2019
+ Nikerel, Emrah/T-8664-2018
+ Toksoy Oner, Ebru/E-2637-2014
+ },
+ORCID-Numbers = {Oner, Ebru Toksoy/0000-0001-6054-8842
+ Toksoy Oner, Ebru/0000-0001-6054-8842
+ Nikerel, Emrah/0000-0002-9157-8662},
+Times-Cited = {3},
+Journal-ISO = {OMICS},
+Unique-ID = {WOS:000462877200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000462705600001,
+Author = {Schwentner, Andreas and Feith, Andre and Muench, Eugenia and
+ Stiefelmaier, Judith and Lauer, Ira and Favilli, Lorenzo and Massner,
+ Christoph and Oehrlein, Johannes and Grund, Bastian and Hueser, Andrea
+ and Takors, Ralf and Blombach, Bastian},
+Title = {Modular systems metabolic engineering enables balancing of relevant
+ pathways for L-histidine production with Corynebacterium
+ glutamicum},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2019},
+Volume = {12},
+Month = {MAR 25},
+Type = {Article},
+DOI = {10.1186/s13068-019-1410-2},
+Article-Number = {65},
+ISSN = {1754-6834},
+Keywords = {Modularized metabolic engineering; LC/MS-QToF-based systems metabolic
+ profiling (SMP); Flux balance analysis (FBA); Energy engineering;
+ L-Histidine production; Corynebacterium glutamicum},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; BIO-BASED PRODUCTION; ESCHERICHIA-COLI;
+ AMINO-ACID; SERINE HYDROXYMETHYLTRANSFERASE; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; BIOSYNTHESIS GENES; L-LYSINE; FERMENTATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ORCID-Numbers = {Takors, Ralf/0000-0001-5837-6906
+ Feith, Andre/0000-0001-5934-3073},
+Times-Cited = {19},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000462705600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000465077600033,
+Author = {Fu, Yanfen and He, Lian and Reeve, Jennifer and Beck, David A. C. and
+ Lidstrom, Mary E.},
+Title = {Core Metabolism Shifts during Growth on Methanol versus Methane in the
+ Methanotroph Methylomicrobium buryatense 5GB1},
+Journal = {MBIO},
+Year = {2019},
+Volume = {10},
+Number = {2},
+Month = {MAR-APR},
+Type = {Article},
+DOI = {10.1128/mBio.00406-19},
+Article-Number = {e00406-19},
+ISSN = {2150-7511},
+Keywords = {13C tracer analysis; flux balance analysis; methanol; methanotrophs},
+Keywords-Plus = {BIOCONVERSION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Reeve, Jennifer/0000-0002-7321-7038},
+Times-Cited = {24},
+Journal-ISO = {mBio},
+Unique-ID = {WOS:000465077600033},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000457633200004,
+Author = {Hameri, Tuure and Fengos, Georgios and Ataman, Meric and Miskovic,
+ Ljubisa and Hatzimanikatis, Vassily},
+Title = {Kinetic models of metabolism that consider alternative steady-state
+ solutions of intracellular fluxes and concentrations},
+Journal = {METABOLIC ENGINEERING},
+Year = {2019},
+Volume = {52},
+Pages = {29-41},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ymben.2018.10.005},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ ESCHERICHIA-COLI; UNCERTAINTY; SYSTEMS; NETWORKS; CAPACITY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Miskovic, Ljubisa/E-8927-2012
+ Hatzimanikatis, Vassily/G-6505-2010
+ },
+ORCID-Numbers = {Miskovic, Ljubisa/0000-0001-7333-8211
+ Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Ataman, Meric/0000-0002-7942-9226},
+Times-Cited = {20},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000457633200004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459890700001,
+Author = {Heirendt, Laurent and Arreckx, Sylvain and Pfau, Thomas and Mendoza,
+ Sebastian N. and Richelle, Anne and Heinken, Almut and Haraldsdottir,
+ Hulda S. and Wachowiak, Jacek and Keating, Sarah M. and Vlasov, Vanja
+ and Magnusdottir, Stefania and Ng, Chiam Yu and Preciat, German and
+ Zagare, Alise and Chan, Siu H. J. and Aurich, Maike K. and Clancy,
+ Catherine M. and Modamio, Jennifer and Sauls, John T. and Noronha,
+ Alberto and Bordbar, Aarash and Cousins, Benjamin and El Assal, Diana C.
+ and Valcarcel, Luis V. and Apaolaza, Inigo and Ghaderi, Susan and
+ Ahookhosh, Masoud and Ben Guebila, Marouen and Kostromins, Andrejs and
+ Sompairac, Nicolas and Le, Hoai M. and Ma, Ding and Sun, Yuekai and
+ Wang, Lin and Yurkovich, James T. and Oliveira, Miguel A. P. and Vuong,
+ Phan T. and El Assal, Lemmer P. and Kuperstein, Inna and Zinovyev,
+ Andrei and Hinton, H. Scott and Bryant, William A. and Aragon Artacho,
+ Francisco J. and Planes, Francisco J. and Stalidzans, Egils and Maass,
+ Alejandro and Vempala, Santosh and Hucka, Michael and Saunders, Michael
+ A. and Maranas, Costas D. and Lewis, Nathan E. and Sauter, Thomas and
+ Palsson, Bernhard O. and Thiele, Ines and Fleming, Ronan M. T.},
+Title = {Creation and analysis of biochemical constraint-based models using the
+ COBRA Toolbox v.3.0},
+Journal = {NATURE PROTOCOLS},
+Year = {2019},
+Volume = {14},
+Number = {3},
+Pages = {639-702},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1038/s41596-018-0098-2},
+ISSN = {1754-2189},
+EISSN = {1750-2799},
+Keywords-Plus = {GENOME-SCALE MODELS; SYSTEMS BIOLOGY; METABOLIC NETWORK; QUANTITATIVE
+ PREDICTION; GLOBAL RECONSTRUCTION; CELLULAR-METABOLISM;
+ PARKINSONS-DISEASE; INBORN-ERRORS; BALANCE; STRAIN},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Zinovyev, Andrei/B-4715-2010
+ Maass, Alejandro E/D-5848-2012
+ Saunders, Michael A/D-1083-2012
+ Hucka, Michael/B-1896-2012
+ Maranas, Costas D/A-4774-2011
+ /AAG-5264-2021
+ Apaolaza, Iñigo/T-6236-2017
+ Planes, Francisco J/H-3341-2013
+ Artacho, Francisco Javier Aragón/C-2531-2012
+ Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ Zinovyev, Andrey/P-8212-2019
+ Oliveira, Miguel/AAB-2753-2022
+ Lewis, Nathan/ABE-7290-2020
+ Ahookhosh, Masoud/AAB-9712-2022
+ Magnusdottir, Stefania/ABA-2212-2021
+ Stalidzans, Egils/G-5883-2010
+ Le, Hoai Minh/P-2579-2014
+ Wang, Lin/ABB-2686-2020
+ Chan, Siu Hung Joshua/N-9777-2016
+ Ghaderi, Susan/AAB-7513-2022
+ Kostromins, Andrejs/G-5855-2012
+ },
+ORCID-Numbers = {Zinovyev, Andrei/0000-0002-9517-7284
+ Maass, Alejandro E/0000-0002-7038-4527
+ Hucka, Michael/0000-0001-9105-5960
+ Maranas, Costas D/0000-0002-1508-1398
+ /0000-0001-6460-6771
+ Apaolaza, Iñigo/0000-0002-8961-4513
+ Planes, Francisco J/0000-0003-1155-3105
+ Artacho, Francisco Javier Aragón/0000-0002-2445-8011
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Oliveira, Miguel/0000-0001-6808-2389
+ Lewis, Nathan/0000-0001-7700-3654
+ Ahookhosh, Masoud/0000-0003-4206-9789
+ Stalidzans, Egils/0000-0001-6063-0184
+ Wang, Lin/0000-0002-9455-5570
+ Ghaderi, Susan/0000-0001-9062-8800
+ Mendoza, Sebastian/0000-0002-2192-5569
+ Ng, Chiam Yu/0000-0002-1567-517X
+ Chan, Siu Hung Joshua/0000-0002-7707-656X
+ MA, Ding/0000-0002-5503-2945
+ Saunders, Michael/0000-0003-3800-4982
+ Valcarcel, Luis Vitores/0000-0003-3769-5419
+ Heinken, Almut/0000-0001-6938-8072
+ Le, Hoai Minh/0000-0001-7337-1505
+ Pfau, Thomas/0000-0001-5048-2923
+ Sauter, Thomas/0000-0001-8225-2954
+ El Assal, Diana C./0000-0003-1124-5153
+ Heirendt, Laurent/0000-0003-1861-0037
+ Magnusdottir, Stefania/0000-0001-6506-8696
+ Noronha, Alberto/0000-0002-0935-4599},
+Times-Cited = {501},
+Journal-ISO = {Nat. Protoc.},
+Unique-ID = {WOS:000459890700001},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000461401800012,
+Author = {Reinhold, Ann Marie and Poole, Geoffrey C. and Izurieta, Clemente and
+ Helton, Ashley M. and Bernhardt, Emily S.},
+Title = {Constraint-based simulation of multiple interactive elemental cycles in
+ biogeochemical systems},
+Journal = {ECOLOGICAL INFORMATICS},
+Year = {2019},
+Volume = {50},
+Pages = {102-121},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1016/j.ecoinf.2018.12.008},
+ISSN = {1574-9541},
+EISSN = {1878-0512},
+Keywords = {Flux network; Microbial metabolism; Optimization; Redox potential;
+ Stoichiometry; Thermodynamics},
+Keywords-Plus = {THERMODYNAMIC CONSTRAINTS; ECOLOGICAL STOICHIOMETRY; NITROGEN; CARBON},
+Research-Areas = {Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Ecology},
+ResearcherID-Numbers = {Bernhardt, Emily S/D-9940-2011
+ Bernhardt, Emily/B-4541-2010
+ },
+ORCID-Numbers = {Bernhardt, Emily S/0000-0003-3031-621X
+ Helton, Ashley/0000-0001-6928-2104
+ Poole, Geoffrey/0000-0002-8458-0203
+ Izurieta, Clemente/0000-0002-1002-3906
+ Reinhold, Ann Marie/0000-0003-0411-3486},
+Times-Cited = {5},
+Journal-ISO = {Ecol. Inform.},
+Unique-ID = {WOS:000461401800012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000467083600007,
+Author = {Thommes, Meghan and Wang, Taiyao and Zhao, Qi and Paschalidis, Ioannis
+ C. and Segre, Daniel},
+Title = {Designing Metabolic Division of Labor in Microbial Communities},
+Journal = {MSYSTEMS},
+Year = {2019},
+Volume = {4},
+Number = {2},
+Month = {MAR-APR},
+Type = {Article},
+DOI = {10.1128/mSystems.00263-18},
+Article-Number = {e00263-18},
+ISSN = {2379-5077},
+Keywords = {division of labor; flux balance analysis; genome-scale stoichiometric
+ models; metabolic networks; microbiome; mixed-integer linear
+ programming; resource allocation; synthetic ecology; microbial
+ communities},
+Keywords-Plus = {TERM EXPERIMENTAL EVOLUTION; TRICARBOXYLIC-ACID CYCLE; NETWORK-BASED
+ TOOL; ESCHERICHIA-COLI; GENE-EXPRESSION; RESOURCE-ALLOCATION; DYNAMICS;
+ MODELS; DIVERSIFICATION; COOPERATION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Segrè, Daniel/A-1993-2009
+ Wang, Taiyao/CAJ-3162-2022},
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914
+ },
+Times-Cited = {65},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000467083600007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459799800113,
+Author = {Chiewchankaset, Porntip and Siriwat, Wanatsanan and Suksangpanomrung,
+ Malinee and Boonseng, Opas and Meechai, Asawin and Tanticharoen, Morakot
+ and Kalapanulak, Saowalak and Saithong, Treenut},
+Title = {Understanding carbon utilization routes between high and low
+ starch-producing cultivars of cassava through Flux Balance Analysis},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2019},
+Volume = {9},
+Month = {FEB 27},
+Type = {Article},
+DOI = {10.1038/s41598-019-39920-w},
+Article-Number = {2964},
+ISSN = {2045-2322},
+Keywords-Plus = {SUBCELLULAR-LOCALIZATION; VARIABILITY ANALYSIS; METABOLIC NETWORK;
+ STORAGE SYNTHESIS; PLANT; GROWTH; PHOTOSYNTHESIS; PROTEIN; YIELD;
+ RECONSTRUCTION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {10},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000459799800113},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459522700016,
+Author = {Kastelic, Miha and Kopac, Drejc and Novak, Uros and Likozar, Blaz},
+Title = {Dynamic metabolic network modeling of mammalian Chinese hamster ovary
+ (CHO) cell cultures with continuous phase kinetics transitions},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2019},
+Volume = {142},
+Pages = {124-134},
+Month = {FEB 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2018.11.015},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Metabolic network modeling; Metabolic pathway; Metabolic engineering;
+ Metabolic flux analysis; Elementary mode analysis; Mammalian Chinese
+ hamster ovary (CHO) cells},
+Keywords-Plus = {ELEMENTARY FLUX MODES; N-LINKED GLYCOSYLATION; RECOMBINANT PROTEIN
+ THERAPEUTICS; PATHWAY ANALYSIS; TIME EVOLUTION; GROWTH; OPTIMIZATION;
+ SECRETION; GLYCOFORM; AUTOPHAGY},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Likozar, Blaž/L-1056-2019
+ },
+ORCID-Numbers = {Novak, Uros/0000-0003-0561-8427
+ Likozar, Blaz/0000-0001-7226-4302},
+Times-Cited = {9},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000459522700016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459315700026,
+Author = {Apaolaza, Inigo and Valcarcel, Luis Vitores and Planes, Francisco J.},
+Title = {gMCS: fast computation of genetic minimal cut sets in large
+ networks},
+Journal = {BIOINFORMATICS},
+Year = {2019},
+Volume = {35},
+Number = {3},
+Pages = {535-537},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/bty656},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {GLOBAL RECONSTRUCTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Planes, Francisco J/H-3341-2013
+ Apaolaza, Iñigo/T-6236-2017
+ },
+ORCID-Numbers = {Planes, Francisco J/0000-0003-1155-3105
+ Apaolaza, Iñigo/0000-0002-8961-4513
+ Valcarcel, Luis Vitores/0000-0003-3769-5419},
+Times-Cited = {11},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000459315700026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000460276500020,
+Author = {Damiani, Chiara and Maspero, Davide and Di Filippo, Marzia and Colombo,
+ Riccardo and Pescini, Dario and Graudenzi, Alex and Westerhoff, Hans
+ Victor and Alberghina, Lilia and Vanoni, Marco and Mauri, Giancarlo},
+Title = {Integration of single-cell RNA-seq data into population models to
+ characterize cancer metabolism},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2019},
+Volume = {15},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1006733},
+Article-Number = {e1006733},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {AEROBIC GLYCOLYSIS; HETEROGENEITY; FIBROBLASTS; DEPENDENCY; PREDICTION;
+ PHENOTYPES; HALLMARKS; PROTEIN},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Vanoni, Marco/AAA-3699-2021
+ Mauri, Giancarlo/M-3258-2013
+ Pescini, Dario/H-4866-2017
+ Graudenzi, Alex/AAY-5241-2020
+ Westerhoff, Hans V/I-5762-2012
+ Maspero, Davide/AAD-9782-2020
+ },
+ORCID-Numbers = {Vanoni, Marco/0000-0002-8690-2587
+ Mauri, Giancarlo/0000-0003-3520-4022
+ Pescini, Dario/0000-0002-3090-4823
+ Graudenzi, Alex/0000-0001-5452-1918
+ Westerhoff, Hans V/0000-0002-0443-6114
+ Damiani, Chiara/0000-0002-5742-8302
+ Di Filippo, Marzia/0000-0002-7428-0522
+ Alberghina, Lilia/0000-0003-1694-931X
+ Maspero, Davide/0000-0001-8519-4331},
+Times-Cited = {47},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000460276500020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000458943300007,
+Author = {Rawls, Kristopher D. and Dougherty, V, Bonnie and Blais, Edik M. and
+ Stancliffe, Ethan and Kolling, Glynis L. and Vinnakota, Kalyan and
+ Pannala, Venkat R. and Wallqvist, Anders and Papin, Jason A.},
+Title = {A simplified metabolic network reconstruction to promote understanding
+ and development of flux balance analysis tools},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2019},
+Volume = {105},
+Pages = {64-71},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2018.12.010},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Systems biology; Metabolic networks; Flux balance analysis;
+ Computational modeling; Metabolic engineering},
+Keywords-Plus = {GLOBAL RECONSTRUCTION},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {wallqvist, anders/W-2584-2019
+ Vinnakota, Kalyan/G-4706-2010
+ },
+ORCID-Numbers = {wallqvist, anders/0000-0002-9775-7469
+ Vinnakota, Kalyan/0000-0003-2185-2213
+ Rawls, Kristopher/0000-0001-5873-0127
+ Dougherty, Bonnie/0000-0002-1454-4899},
+Times-Cited = {18},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000458943300007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000460288400006,
+Author = {Sen, Partho and Oresic, Matej},
+Title = {Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An
+ Overview},
+Journal = {METABOLITES},
+Year = {2019},
+Volume = {9},
+Number = {2},
+Month = {FEB},
+Type = {Review},
+DOI = {10.3390/metabo9020022},
+Article-Number = {22},
+EISSN = {2218-1989},
+Keywords = {gut microbiome; meta-omics; metagenomics; metabolomics; metabolic
+ reconstructions; genome-scale metabolic modeling; constraint-based
+ modeling; flux balance; host-microbiome; metabolism},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; INTESTINAL MICROBIOTA;
+ GLOBAL RECONSTRUCTION; CELLULAR-METABOLISM; DATABASE; GENE; INFORMATION;
+ PATHWAYS; RESOURCE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Oresic, Matej/K-7673-2016
+ Oresic, Matej/AAV-3978-2020
+ Sen, Partho/L-8471-2019},
+ORCID-Numbers = {Oresic, Matej/0000-0002-2856-9165
+ Sen, Partho/0000-0003-0475-2763},
+Times-Cited = {44},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000460288400006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000456752600009,
+Author = {Wegrzyn, Agnieszka B. and Stolle, Sarah and Rienksma, Rienk A. and dos
+ Santos, Vitor A. P. Martins and Bakker, Barbara M. and Suarez-Diez,
+ Maria},
+Title = {Cofactors revisited - Predicting the impact of flavoprotein-related
+ diseases on a genome scale},
+Journal = {BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE},
+Year = {2019},
+Volume = {1865},
+Number = {2},
+Pages = {360-370},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1016/j.bbadis.2018.10.021},
+ISSN = {0925-4439},
+EISSN = {1879-260X},
+Keywords = {FAD; FMN; Flavoprotein; Inborn errors of metabolism; Human genome-scale
+ reconstruction; Constraint-based modelling},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; INBORN-ERRORS; COA DEHYDROGENASE; DEFICIENCY;
+ METABOLISM; MUTATION; VIEW},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+ResearcherID-Numbers = {Wegrzyn, Agnieszka Barbara/T-1519-2017
+ Diez, Maria Suarez/AAI-1354-2020
+ },
+ORCID-Numbers = {Wegrzyn, Agnieszka Barbara/0000-0003-4872-8626
+ Suarez-Diez, Maria/0000-0001-5845-146X},
+Times-Cited = {4},
+Journal-ISO = {Biochim. Biophys. Acta-Mol. Basis Dis.},
+Unique-ID = {WOS:000456752600009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000455747900020,
+Author = {Xu, Xihui and Zarecki, Raphy and Medina, Shlomit and Ofaim, Shany and
+ Liu, Xiaowei and Chen, Chen and Hu, Shunli and Brom, Dan and Gat,
+ Daniella and Porob, Seema and Eizenberg, Hanan and Ronen, Zeev and
+ Jiang, Jiandong and Freilich, Shiri},
+Title = {Modeling microbial communities from atrazine contaminated soils promotes
+ the development of biostimulation solutions},
+Journal = {ISME JOURNAL},
+Year = {2019},
+Volume = {13},
+Number = {2},
+Pages = {494-508},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1038/s41396-018-0288-5},
+ISSN = {1751-7362},
+EISSN = {1751-7370},
+Keywords-Plus = {SP NOV.; METABOLIC INTERACTIONS; AROMATIC-HYDROCARBONS; GENOME;
+ DEGRADATION; FROGS; BIODEGRADATION; SENSITIVITY; CONSORTIUM; DIVERSITY},
+Research-Areas = {Environmental Sciences \& Ecology; Microbiology},
+Web-of-Science-Categories = {Ecology; Microbiology},
+ResearcherID-Numbers = {Gat, Daniella/W-2421-2019
+ Ronen, Zeev/F-1941-2012
+ },
+ORCID-Numbers = {liu, xiaowei/0000-0002-5644-0684
+ Xu, Xihui/0000-0003-2092-9987
+ Gat, Daniella/0000-0002-0595-4626
+ Ronen, Zeev/0000-0002-8399-4295},
+Times-Cited = {95},
+Journal-ISO = {ISME J.},
+Unique-ID = {WOS:000455747900020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459350700022,
+Author = {Janasch, Markus and Asplund-Samuelsson, Johannes and Steuer, Ralf and
+ Hudson, Elton P.},
+Title = {Kinetic modeling of the Calvin cycle identifies flux control and stable
+ metabolomes in Synechocystis carbon fixation},
+Journal = {JOURNAL OF EXPERIMENTAL BOTANY},
+Year = {2019},
+Volume = {70},
+Number = {3},
+Pages = {973-983},
+Month = {JAN 30},
+Type = {Article},
+DOI = {10.1093/jxb/ery382},
+ISSN = {0022-0957},
+EISSN = {1460-2431},
+Keywords = {Calvin cycle; cyanobacteria; flux control; kinetic model; metabolic
+ engineering; metabolic model; metabolome; parameter sampling; system
+ stability},
+Keywords-Plus = {INDUSTRIAL BIOTECHNOLOGY; TRANSGENIC TOBACCO; ANTISENSE RNA;
+ PHOTOSYNTHESIS; ENZYME; GROWTH; CYANOBACTERIA; RUBISCO;
+ PHOSPHORIBULOKINASE; ALLOCATION},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Hudson, Paul/ABH-8177-2020
+ },
+ORCID-Numbers = {Hudson, Elton/0000-0003-1899-7649
+ Steuer, Ralf/0000-0003-2217-1655
+ Asplund-Samuelsson, Johannes/0000-0001-8077-5305},
+Times-Cited = {29},
+Journal-ISO = {J. Exp. Bot.},
+Unique-ID = {WOS:000459350700022},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000456922300002,
+Author = {Martyushenko, Nikolay and Almaas, Eivind},
+Title = {ModelExplorer - software for visual inspection and inconsistency
+ correction of genome-scale metabolic reconstructions},
+Journal = {BMC BIOINFORMATICS},
+Year = {2019},
+Volume = {20},
+Month = {JAN 28},
+Type = {Article},
+DOI = {10.1186/s12859-019-2615-x},
+Article-Number = {56},
+ISSN = {1471-2105},
+Keywords = {Metabolic model; Network visualization; FBA; Constraint based modeling;
+ Consistency checking},
+Keywords-Plus = {BIOLOGY MARKUP LANGUAGE; CONSTRAINT-BASED MODELS; CYTOSCAPE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Almaas, Eivind/0000-0002-9125-326X},
+Times-Cited = {7},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000456922300002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000457659800014,
+Author = {Mekanik, Mahsa and Motamedian, Ehsan and Fotovat, Reza and Jafarian,
+ Vahab},
+Title = {Reconstruction of a genome-scale metabolic model for Auxenochlorella
+ protothecoides to study hydrogen production under anaerobiosis using
+ multiple optimal solutions},
+Journal = {INTERNATIONAL JOURNAL OF HYDROGEN ENERGY},
+Year = {2019},
+Volume = {44},
+Number = {5},
+Pages = {2580-2591},
+Month = {JAN 28},
+Type = {Article},
+DOI = {10.1016/j.ijhydene.2018.12.049},
+ISSN = {0360-3199},
+EISSN = {1879-3487},
+Keywords = {Microalga; Auxenochlorella protothecoides; Genome-scale metabolic model;
+ Hydrogen production; Anaerobiosis; Multiple optimal flux distributions},
+Keywords-Plus = {PHOTOBIOLOGICAL H-2 PRODUCTION; CHLAMYDOMONAS-REINHARDTII;
+ CHLORELLA-PROTOTHECOIDES; NITROGEN LIMITATION; ALTERNATIVE OXIDASE;
+ PHOTOPRODUCTION; CHLOROPLAST; EXPRESSION; PATHWAYS; GROWTH},
+Research-Areas = {Chemistry; Electrochemistry; Energy \& Fuels},
+Web-of-Science-Categories = {Chemistry, Physical; Electrochemistry; Energy \& Fuels},
+ResearcherID-Numbers = {jafarian, vahab/V-2078-2019
+ Fotovat, Reza/I-5930-2018
+ Motamedian, Ehsan/GPK-8344-2022
+ },
+ORCID-Numbers = {jafarian, vahab/0000-0002-8396-3894
+ Fotovat, Reza/0000-0002-0515-7969
+ , Ehsan/0000-0001-8750-2879},
+Times-Cited = {6},
+Journal-ISO = {Int. J. Hydrog. Energy},
+Unique-ID = {WOS:000457659800014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000456545100002,
+Author = {Dunphy, Laura J. and Yen, Phillip and Papin, Jason A.},
+Title = {Integrated Experimental and Computational Analyses Reveal Differential
+ Metabolic Functionality in Antibiotic-Resistant Pseudomonas
+ aeruginosa},
+Journal = {CELL SYSTEMS},
+Year = {2019},
+Volume = {8},
+Number = {1},
+Pages = {3+},
+Month = {JAN 23},
+Type = {Article},
+DOI = {10.1016/j.cels.2018.12.002},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GENETIC-DETERMINANTS; OXIDATIVE STRESS;
+ EVOLUTION; PHENOTYPES; ENVIRONMENT; ADAPTATION; PREDICTION; LEAD},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ORCID-Numbers = {Dunphy, Laura/0000-0003-1797-8403},
+Times-Cited = {29},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000456545100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000456955000002,
+Author = {Contador, Carolina A. and Rodriguez, Vida and Andrews, Barbara A. and
+ Asenjo, Juan A.},
+Title = {Use of genome-scale models to get new insights into the marine
+ actinomycete genus Salinispora},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2019},
+Volume = {13},
+Month = {JAN 21},
+Type = {Article},
+DOI = {10.1186/s12918-019-0683-1},
+Article-Number = {11},
+ISSN = {1752-0509},
+Keywords = {Genome-scale model; Strain-specific adaptation; Metabolic capabilities;
+ Salinispora species},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; PROTEASOME INHIBITOR;
+ CELLULAR-METABOLISM; CHEMICAL PRODUCTION; ESCHERICHIA-COLI;
+ NATURAL-PRODUCTS; SP NOV.; SALINOSPORAMIDE; RECONSTRUCTION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Asenjo, Juan JAA/L-8336-2013},
+ORCID-Numbers = {Asenjo, Juan JAA/0000-0002-3475-7664},
+Times-Cited = {3},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000456955000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000455491400001,
+Author = {Zeng, Hong and Yang, Aidong},
+Title = {Modelling overflow metabolism in Escherichia coli with flux
+ balance analysis incorporating differential proteomic efficiencies of
+ energy pathways},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2019},
+Volume = {13},
+Month = {JAN 10},
+Type = {Article},
+DOI = {10.1186/s12918-018-0677-4},
+ISSN = {1752-0509},
+Keywords = {Flux balance analysis; Proteomic efficiency; Overflow metabolism;
+ Acetate production; Biomass yield; Escherichia coli},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ ACETATE PRODUCTION; GROWTH-RATE; BATCH; CULTURES},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Yang, Aidong/M-2887-2013
+ },
+ORCID-Numbers = {Yang, Aidong/0000-0001-7771-6777
+ Zeng, Hong/0000-0001-6617-4466},
+Times-Cited = {26},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000455491400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000455346200001,
+Author = {Massaiu, Ilaria and Pasotti, Lorenzo and Sonnenschein, Nikolaus and
+ Rama, Erlinda and Cavaletti, Matteo and Magni, Paolo and Calvio, Cinzia
+ and Herrgard, Markus J.},
+Title = {Integration of enzymatic data in Bacillus subtilis genome-scale
+ metabolic model improves phenotype predictions and enables in silico
+ design of poly--glutamic acid production strains},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2019},
+Volume = {18},
+Month = {JAN 9},
+Type = {Article},
+DOI = {10.1186/s12934-018-1052-2},
+Article-Number = {3},
+EISSN = {1475-2859},
+Keywords = {Genome-scale metabolic model; Enzymatic data; Bacillus subtilis;
+ Constraint-based methods; Poly--glutamic acid},
+Keywords-Plus = {ESCHERICHIA-COLI; QUANTITATIVE PREDICTION; TRANSCRIPTOME ANALYSIS;
+ OXALATE DECARBOXYLASE; DEHYDROGENASE; PURIFICATION; NETWORK; ALLOCATION;
+ EXPRESSION; PROTEOMICS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Cinzia, Calvio/E-1353-2011
+ Massaiu, Ilaria/AAZ-3697-2020
+ Sonnenschein, Nikolaus/F-6853-2012
+ Pasotti, Lorenzo/AAA-5215-2022
+ Magni, Paolo/JCE-9169-2023},
+ORCID-Numbers = {Cinzia, Calvio/0000-0003-1631-0452
+ Sonnenschein, Nikolaus/0000-0002-7581-4936
+ Pasotti, Lorenzo/0000-0002-5431-3083
+ Magni, Paolo/0000-0002-8931-4676},
+Times-Cited = {40},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000455346200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000455264400002,
+Author = {Pacheco, Alan R. and Moel, Mauricio and Segre, Daniel},
+Title = {Costless metabolic secretions as drivers of interspecies interactions in
+ microbial ecosystems},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2019},
+Volume = {10},
+Month = {JAN 9},
+Type = {Article},
+DOI = {10.1038/s41467-018-07946-9},
+Article-Number = {103},
+ISSN = {2041-1723},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; RECONSTRUCTION; PROTEIN; GROWTH; COMMUNITIES;
+ COOPERATION; COMPETITION; STABILIZES; GRADIENTS; EVOLUTION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Pacheco, Alan R/IUQ-5711-2023
+ Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Pacheco, Alan R/0000-0002-1128-3232
+ Segrè, Daniel/0000-0003-4859-1914
+ pacheco quispe, alan/0000-0002-5112-1430},
+Times-Cited = {144},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000455264400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000454952800038,
+Author = {Banerjee, Deepanwita and Raghunathan, Anu},
+Title = {Constraints-based analysis identifies NAD+ recycling through
+ metabolic reprogramming in antibiotic resistant Chromobacterium
+ violaceum},
+Journal = {PLOS ONE},
+Year = {2019},
+Volume = {14},
+Number = {1},
+Month = {JAN 4},
+Type = {Article},
+DOI = {10.1371/journal.pone.0210008},
+Article-Number = {e0210008},
+ISSN = {1932-6203},
+Keywords-Plus = {SP NOV.; EVOLUTION; BACTERIAL; MODELS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Banerjee, Deepanwita/AAD-5528-2021
+ },
+ORCID-Numbers = {Banerjee, Deepanwita/0000-0002-0083-0608
+ Raghunathan, Anu/0000-0002-7063-9606},
+Times-Cited = {10},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000454952800038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000472998400001,
+Author = {Angione, Claudio},
+Title = {Human Systems Biology and Metabolic Modelling: A ReviewFrom Disease
+ Metabolism to Precision Medicine},
+Journal = {BIOMED RESEARCH INTERNATIONAL},
+Year = {2019},
+Volume = {2019},
+Type = {Review},
+DOI = {10.1155/2019/8304260},
+Article-Number = {8304260},
+ISSN = {2314-6133},
+EISSN = {2314-6141},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; CELLULAR-METABOLISM; GLOBAL
+ RECONSTRUCTION; OXIDATIVE STRESS; INBORN-ERRORS; FLUX ANALYSIS; NETWORK;
+ BALANCE; CANCER},
+Research-Areas = {Biotechnology \& Applied Microbiology; Research \& Experimental Medicine},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Medicine, Research \&
+ Experimental},
+ORCID-Numbers = {Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {38},
+Journal-ISO = {Biomed Res. Int.},
+Unique-ID = {WOS:000472998400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000456633300016,
+Author = {diCenzo, George C. and Mengoni, Alessio and Fondi, Marco},
+Title = {Tn-Core: A Toolbox for Integrating Tn-seq Gene Essentiality Data and
+ Constraint-Based Metabolic Modeling},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2019},
+Volume = {8},
+Number = {1},
+Pages = {158-169},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1021/acssynbio.8b00432},
+ISSN = {2161-5063},
+Keywords = {transposon sequencing; metabolic network reconstruction; COBRA models;
+ systems biology; bacterial metabolism},
+Keywords-Plus = {GENOME; LIBRARIES; SYMBIONT},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Mengoni, Alessio/G-5336-2013
+ diCenzo, George C C/M-1876-2017
+ },
+ORCID-Numbers = {Mengoni, Alessio/0000-0002-1265-8251
+ diCenzo, George C C/0000-0003-3889-6570
+ Fondi, Marco/0000-0001-9291-5467},
+Times-Cited = {11},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000456633300016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000455058000001,
+Author = {diCenzo, George C. and Zamani, Maryam and Checcucci, Alice and Fondi,
+ Marco and Griffitts, Joel S. and Finan, Turlough M. and Mengoni, Alessio},
+Title = {Multidisciplinary approaches for studying rhizobium-legume symbioses},
+Journal = {CANADIAN JOURNAL OF MICROBIOLOGY},
+Year = {2019},
+Volume = {65},
+Number = {1},
+Pages = {1-33},
+Month = {JAN},
+Type = {Review},
+DOI = {10.1139/cjm-2018-0377},
+ISSN = {0008-4166},
+EISSN = {1480-3275},
+Keywords = {rhizobia; nitrogen fixation; symbiosis; systems biology; multi-omics},
+Keywords-Plus = {LEGUMINOSARUM BV TRIFOLII; MESORHIZOBIUM-LOTI MAFF303099;
+ NITROGEN-FIXING NODULES; BRADYRHIZOBIUM-JAPONICUM BACTEROIDS; GLOBAL
+ TRANSCRIPTIONAL RESPONSE; QUORUM-SENSING SIGNALS;
+ SINORHIZOBIUM-MELILOTI; PROTEOME ANALYSIS; MEDICAGO-TRUNCATULA;
+ GENE-EXPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Immunology; Microbiology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Immunology; Microbiology},
+ResearcherID-Numbers = {Checcucci, Alice/ISR-8746-2023
+ checcucci, alice/AAF-7869-2021
+ diCenzo, George C C/M-1876-2017
+ Mengoni, Alessio/G-5336-2013
+ },
+ORCID-Numbers = {diCenzo, George C C/0000-0003-3889-6570
+ Mengoni, Alessio/0000-0002-1265-8251
+ Zamani, Maryam Manely/0000-0002-3841-6111},
+Times-Cited = {41},
+Journal-ISO = {Can. J. Microbiol.},
+Unique-ID = {WOS:000455058000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000454429700003,
+Author = {Frioux, Clemence and Schaub, Torsten and Schellhorn, Sebastian and
+ Siegel, Anne and Wanko, Philipp},
+Title = {Technical Note Hybrid metabolic network completion},
+Journal = {THEORY AND PRACTICE OF LOGIC PROGRAMMING},
+Year = {2019},
+Volume = {19},
+Number = {1},
+Pages = {83-108},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1017/S1471068418000455},
+ISSN = {1471-0684},
+EISSN = {1475-3081},
+Keywords = {answer set programming; metabolic network; gap-filling; linear
+ programming; hybrid solving; bioinformatics},
+Research-Areas = {Computer Science; Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Computer Science, Software Engineering; Computer Science, Theory \&
+ Methods; Logic},
+ResearcherID-Numbers = {Frioux, Clémence/A-1517-2019
+ Schaub, Torsten/O-5873-2019
+ },
+ORCID-Numbers = {Frioux, Clémence/0000-0003-2114-0697
+ Schaub, Torsten/0000-0002-7456-041X
+ Wanko, Philipp/0000-0003-4986-4881},
+Times-Cited = {5},
+Journal-ISO = {Theory Pract. Log. Program.},
+Unique-ID = {WOS:000454429700003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000456420200012,
+Author = {Garcia, Sergio and Trinh, Cong T.},
+Title = {Multiobjective strain design: A framework for modular cell engineering},
+Journal = {METABOLIC ENGINEERING},
+Year = {2019},
+Volume = {51},
+Pages = {110-120},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.ymben.2018.09.003},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Modular cell engineering; Modular cell; Production modules; Modular
+ design; Modularity; Multiobjective optimization; Multiobjective
+ evolutionary algorithms},
+Keywords-Plus = {ESCHERICHIA-COLI; FERMENTATIVE PATHWAYS; KNOCKOUT STRATEGIES; SYNTHETIC
+ BIOLOGY; BIOSYNTHESIS; ALGORITHM; MODELS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Trinh, Cong T/H-5300-2012
+ },
+ORCID-Numbers = {Garcia, Sergio/0000-0002-3998-986X},
+Times-Cited = {17},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000456420200012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000457372500027,
+Author = {Kueken, Anika and Eloundou-Mbebi, Jeanne M. O. and Basler, Georg and
+ Nikoloski, Zoran},
+Title = {Cellular determinants of metabolite concentration ranges},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2019},
+Volume = {15},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1006687},
+Article-Number = {e1006687},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; FLUXES; PREDICTION;
+ OPTIMALITY},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Nikoloski, Zoran/0000-0003-2671-6763
+ Kuken, Anika/0000-0003-1367-0719},
+Times-Cited = {4},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000457372500027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000455955200003,
+Author = {Sahoo, Swagatika and Ravi Kumar, Ranjith Kumar and Nicolay, Brandon and
+ Mohite, Omkar and Sivaraman, Karthikeyan and Khetan, Vikas and Rishi,
+ Pukhraj and Ganesan, Suganeswari and Subramanyan, Krishnakumar and
+ Raman, Karthik and Miles, Wayne and Elchuri, Sailaja V.},
+Title = {Metabolite systems profiling identifies exploitable weaknesses in
+ retinoblastoma},
+Journal = {FEBS LETTERS},
+Year = {2019},
+Volume = {593},
+Number = {1},
+Pages = {23-41},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1002/1873-3468.13294},
+ISSN = {0014-5793},
+EISSN = {1873-3468},
+Keywords = {cancer metabolism; constraint-based reconstruction and modeling;
+ retinoblastoma; synthetic lethal; systems biology},
+Keywords-Plus = {ACID ACYLTRANSFERASE-BETA; L-GLUTAMATE DECARBOXYLASE; SYNTHETIC
+ LETHALITY; GENE-EXPRESSION; RAT RETINA; GLOBAL RECONSTRUCTION;
+ OVARIAN-CARCINOMA; LIPID-METABOLISM; OCULAR-TISSUES; LPAAT-BETA},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics; Cell Biology},
+ResearcherID-Numbers = {Rishi, Pukhraj/AAZ-5296-2020
+ Raman, Karthik/Q-5278-2019
+ },
+ORCID-Numbers = {Raman, Karthik/0000-0002-9311-7093
+ Miles, Wayne/0000-0002-2054-5206
+ Khetan, Vikas/0000-0003-4396-9877
+ Ravi Kumar, Ranjith Kumar/0000-0003-2809-948X
+ Mohite, Omkar/0000-0002-3240-1656
+ Sahoo, Swagatika/0000-0003-3773-8597},
+Times-Cited = {8},
+Journal-ISO = {FEBS Lett.},
+Unique-ID = {WOS:000455955200003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459313900029,
+Author = {Salvy, Pierre and Fengos, Georgios and Ataman, Meric and Pathier, Thomas
+ and Soh, Keng C. and Hatzimanikatis, Vassily},
+Title = {pyTFA and matTFA: a Python package and a Matlab toolbox for
+ Thermodynamics-based Flux Analysis},
+Journal = {BIOINFORMATICS},
+Year = {2019},
+Volume = {35},
+Number = {1},
+Pages = {167-169},
+Month = {JAN 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/bty499},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {RECONSTRUCTION; METABOLISM; DESIGN; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Hatzimanikatis, Vassily/G-6505-2010
+ },
+ORCID-Numbers = {Hatzimanikatis, Vassily/0000-0001-6432-4694
+ SALVY, Pierre/0000-0002-3834-0356
+ Ataman, Meric/0000-0002-7942-9226},
+Times-Cited = {53},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000459313900029},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000451881700009,
+Author = {Zhang, Yu and Zhang, Yun and Shang, Xiuling and Wang, Bo and Hu, Qitiao
+ and Liu, Shuwen and Wen, Tingyi},
+Title = {Reconstruction of tricarboxylic acid cycle in Corynebacterium
+ glutamicum with a genome-scale metabolic network model for
+ trans-4-hydroxyproline production},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2019},
+Volume = {116},
+Number = {1},
+Pages = {99-109},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1002/bit.26818},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {iCW773; in silico model-based simulation; ribosome binding site
+ optimization; reconstruction of tricarboxylic acid cycle;
+ trans-4-hydroxy-l-proline},
+Keywords-Plus = {RECOMBINANT ESCHERICHIA-COLI; CONSTRAINT-BASED MODELS; PROLINE
+ 4-HYDROXYLASE; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; EXPRESSION;
+ GENE; HYDROXYPROLINE; CONSTRUCTION; SEQUENCE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {WANG, YING/JLM-9219-2023
+ Wang, Bo/V-5152-2019
+ Wen, Tingyi/M-6095-2014
+ },
+ORCID-Numbers = {Wang, Bo/0000-0002-0643-0349
+ Wen, Tingyi/0000-0003-2583-7088
+ Hu, Qitiao/0000-0002-7341-6125
+ Zhang, Yun/0000-0002-2617-8080},
+Times-Cited = {17},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000451881700009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000453632800002,
+Author = {Liu, Ailin and Contador, Carolina A. and Fan, Kejing and Lam, Hon-Ming},
+Title = {Interaction and Regulation of Carbon, Nitrogen, and Phosphorus
+ Metabolisms in Root Nodules of Legumes},
+Journal = {FRONTIERS IN PLANT SCIENCE},
+Year = {2018},
+Volume = {9},
+Month = {DEC 18},
+Type = {Review},
+DOI = {10.3389/fpls.2018.01860},
+Article-Number = {1860},
+ISSN = {1664-462X},
+Keywords = {rhizobia; bacteroids; nitrogen fixation; legumes; root nodule; phosphate
+ homeostasis; metabolism; symbiosis},
+Keywords-Plus = {PERIBACTEROID MEMBRANE ATPASE; MALATE-DEHYDROGENASE MDH;
+ SINORHIZOBIUM-MELILOTI; BRADYRHIZOBIUM-JAPONICUM; MEDICAGO-TRUNCATULA;
+ RHIZOBIUM-MELILOTI; ISOCITRATE DEHYDROGENASE; LOTUS-JAPONICUS;
+ PHOSPHOENOLPYRUVATE CARBOXYLASE; PHOSPHATE DEFICIENCY},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Lam, Hon-Ming/A-9866-2008},
+ORCID-Numbers = {Lam, Hon-Ming/0000-0002-6673-8740},
+Times-Cited = {88},
+Journal-ISO = {Front. Plant Sci.},
+Unique-ID = {WOS:000453632800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000453502900004,
+Author = {Occhipinti, Annalisa and Eyassu, Filmon and Rahman, Thahira J. and
+ Rahman, Pattanathu K. S. M. and Angione, Claudio},
+Title = {In silico engineering of Pseudomonas metabolism reveals new
+ biomarkers for increased biosurfactant production},
+Journal = {PEERJ},
+Year = {2018},
+Volume = {6},
+Month = {DEC 17},
+Type = {Article},
+DOI = {10.7717/peerj.6046},
+Article-Number = {e6046},
+ISSN = {2167-8359},
+Keywords = {Pseudomonas; Rhamnolipids; Biosurfactants; Flux balance analysis;
+ Metabolic engineering; Pseudomonas putida; Multi-omics; Genome-scale
+ metabolic model; Regression; Machine learning},
+Keywords-Plus = {FATTY-ACID SYNTHESIS; RHAMNOLIPID PRODUCTION; ESCHERICHIA-COLI;
+ AERUGINOSA; GENOME; STRAINS; BIOSYNTHESIS; EXPRESSION; PATHWAY; PUTIDA},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Rahman, Pattanathu K. S. M./A-4349-2018
+ Rahman, Pattanathu/ABE-9417-2020
+ },
+ORCID-Numbers = {Rahman, Pattanathu K. S. M./0000-0001-7416-4372
+ Occhipinti, Annalisa/0000-0001-6075-1496
+ Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {12},
+Journal-ISO = {PeerJ},
+Unique-ID = {WOS:000453502900004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000453245000003,
+Author = {Venayak, Naveen and von Kamp, Axel and Klamt, Steffen and Mahadevan,
+ Radhakrishnan},
+Title = {MoVE identifies metabolic valves to switch between phenotypic states},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2018},
+Volume = {9},
+Month = {DEC 14},
+Type = {Article},
+DOI = {10.1038/s41467-018-07719-4},
+Article-Number = {5332},
+ISSN = {2041-1723},
+Keywords-Plus = {DYNAMIC PATHWAY REGULATION; ITACONIC ACID PRODUCTION; CONSTRAINT-BASED
+ MODELS; MINIMAL CUT SETS; ESCHERICHIA-COLI; GENE-EXPRESSION; FLUX;
+ NETWORKS; KNOCKOUT},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Klamt, Steffen/0000-0003-2563-7561},
+Times-Cited = {26},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000453245000003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000452835400002,
+Author = {Botero, Kelly and Restrepo, Silvia and Pinzon, Andres},
+Title = {A genome-scale metabolic model of potato late blight suggests a
+ photosynthesis suppression mechanism},
+Journal = {BMC GENOMICS},
+Year = {2018},
+Volume = {19},
+Number = {8},
+Month = {DEC 11},
+Note = {4th Colombian Congress on Bioinformatics and Computational Biology / 8th
+ SolBio International Conference on Bioinformatics, Santiago de Cali,
+ COLOMBIA, SEP 13-15, 2017},
+Type = {Article; Proceedings Paper},
+DOI = {10.1186/s12864-018-5192-x},
+Article-Number = {863},
+ISSN = {1471-2164},
+Keywords = {Compatible interaction; Phytophthora infestans; Solanum tuberosum;
+ Systems biology; Metabolic reconstruction; Flux balance analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; NETWORK RECONSTRUCTION; PHYTOPHTHORA-INFESTANS;
+ ELECTRON-TRANSPORT; DEFENSE RESPONSES; LIGHT-INTENSITY; DIURNAL CHANGES;
+ SALICYLIC-ACID; NITRIC-OXIDE; ARABIDOPSIS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ORCID-Numbers = {Pinzon, Andres/0000-0002-4133-810X},
+Times-Cited = {21},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000452835400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000453084500001,
+Author = {Ma, Zhongbao and Ye, Chao and Deng, Weiwei and Xu, Mengmeng and Wang,
+ Qiong and Liu, Gaoqiang and Wang, Feng and Liu, Liming and Xu, Zhenghong
+ and Shi, Guiyang and Ding, Zhongyang},
+Title = {Reconstruction and Analysis of a Genome-Scale Metabolic Model of
+ Ganoderma lucidum for Improved Extracellular Polysaccharide
+ Production},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2018},
+Volume = {9},
+Month = {DEC 11},
+Type = {Article},
+DOI = {10.3389/fmicb.2018.03076},
+Article-Number = {3076},
+ISSN = {1664-302X},
+Keywords = {Ganoderma lucidum; extracellular polysaccharide; genome-scale metabolic
+ model; biosynthetic pathway; phenylalanine; simulation},
+Keywords-Plus = {SUBMERGED CULTURE; FERMENTATION; EXPRESSION; COMPONENTS; DATABASE;
+ BALANCE; GENE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Ye, Chao/M-3689-2019
+ Ye, Chao/H-7623-2014
+ Liu, Gao-Qiang/HJH-7103-2023
+ Ye, Chao/HGD-3564-2022
+ Liu, Liming/B-1972-2009
+ },
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Ye, Chao/0000-0002-6671-7819
+ Liu, Gao-Qiang/0000-0001-9620-1752
+ Ye, Chao/0000-0002-6671-7819
+ Liu, Liming/0000-0003-3022-936X
+ Wang, Feng/0000-0001-8790-2696},
+Times-Cited = {22},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000453084500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000452116100001,
+Author = {Karlsen, Emil and Schulz, Christian and Almaas, Eivind},
+Title = {Automated generation of genome-scale metabolic draft reconstructions
+ based on KEGG},
+Journal = {BMC BIOINFORMATICS},
+Year = {2018},
+Volume = {19},
+Month = {DEC 4},
+Type = {Article},
+DOI = {10.1186/s12859-018-2472-z},
+Article-Number = {467},
+ISSN = {1471-2105},
+Keywords = {AutoKEGGRec; Genome-scale metabolic model; Constraint-based analysis;
+ Pipeline; Draft model; Metabolic network reconstruction; Multiple
+ organisms; Community model; Consolidated model; COBRA},
+Keywords-Plus = {MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ORCID-Numbers = {Almaas, Eivind/0000-0002-9125-326X
+ Schulz, Christian/0000-0002-6763-6551},
+Times-Cited = {40},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000452116100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000449879200010,
+Author = {Cankorur-Cetinkaya, Ayca and Narraidoo, Nathalie and Kasavi, Ceyda and
+ Slater, Nigel K. H. and Archer, David B. and Oliver, Stephen G.},
+Title = {Process development for the continuous production of heterologous
+ proteins by the industrial yeast, Komagataella phaffii},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2018},
+Volume = {115},
+Number = {12},
+Pages = {2962-2973},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1002/bit.26846},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {antibody; continuous bioprocessing; human lysozyme (HuLy); Komagataella
+ phaffii (K. phaffi); Pichia pastoris (P. pastoris); process optimization},
+Keywords-Plus = {PICHIA-PASTORIS PROMOTERS; RECOMBINANT PROTEINS; EXPRESSION; SECRETION;
+ GENE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Oliver, Stephen/AAQ-5992-2021
+ Kasavi, Ceyda/GVS-6400-2022
+ },
+ORCID-Numbers = {Oliver, Stephen/0000-0003-3410-6439
+ Kasavi, Ceyda/0000-0003-2970-387X
+ Cankorur Cetinkaya, Ayca/0000-0002-4431-7259},
+Times-Cited = {9},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000449879200010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000454524700031,
+Author = {Klanchui, Amornpan and Dulsawat, Sudarat and Chaloemngam, Kullapat and
+ Cheevadhanarak, Supapon and Prommeenate, Peerada and Meechai, Asawin},
+Title = {An Improved Genome-Scale Metabolic Model of Arthrospira platensis
+ C1 (iAK888) and Its Application in Glycogen Overproduction},
+Journal = {METABOLITES},
+Year = {2018},
+Volume = {8},
+Number = {4},
+Month = {DEC},
+Type = {Article},
+DOI = {10.3390/metabo8040084},
+Article-Number = {84},
+EISSN = {2218-1989},
+Keywords = {Arthrospira platensis C1; bioethanol; cyanobacteria; genome-scale
+ metabolic model; glycogen},
+Keywords-Plus = {SPIRULINA-PLATENSIS; HIGH-TEMPERATURE; COMBINED STRESS; CYANOBACTERIA;
+ BALANCE; BIOSYNTHESIS; ANNOTATION; PATHWAYS; SEQUENCE; DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ORCID-Numbers = {Prommeenate, Peerada/0000-0003-0421-0243},
+Times-Cited = {10},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000454524700031},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000446475700007,
+Author = {Shapiro, Benjamin and Hoehler, Tori M. and Jin, Qusheng},
+Title = {Integrating genome-scale metabolic models into the prediction of
+ microbial kinetics in natural environments},
+Journal = {GEOCHIMICA ET COSMOCHIMICA ACTA},
+Year = {2018},
+Volume = {242},
+Pages = {102-122},
+Month = {DEC 1},
+Type = {Article},
+DOI = {10.1016/j.gca.2018.08.047},
+ISSN = {0016-7037},
+EISSN = {1872-9533},
+Keywords = {Genome-scale metabolic model; Biogeochemical reaction modeling;
+ Microbial kinetics; Flux balance analysis; Nutrient limitation;
+ Methanogenesis},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS;
+ SULFUR-CONTAINING-COMPOUNDS; COASTAL-PLAIN AQUIFER; CARBON-USE
+ EFFICIENCY; METHANOSARCINA-BARKERI; IN-SITU; REACTIVE TRANSPORT;
+ ESCHERICHIA-COLI; URANIUM BIOREMEDIATION},
+Research-Areas = {Geochemistry \& Geophysics},
+Web-of-Science-Categories = {Geochemistry \& Geophysics},
+ResearcherID-Numbers = {Jin, Qusheng/J-8708-2012
+ },
+ORCID-Numbers = {Jin, Qusheng/0000-0002-0808-2122},
+Times-Cited = {8},
+Journal-ISO = {Geochim. Cosmochim. Acta},
+Unique-ID = {WOS:000446475700007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000451173000015,
+Author = {Shene, Carolina and Asenjo, Juan A. and Chisti, Yusuf},
+Title = {Metabolic modelling and simulation of the light and dark metabolism of
+ Chlamydomonas reinhardtii},
+Journal = {PLANT JOURNAL},
+Year = {2018},
+Volume = {96},
+Number = {5},
+Pages = {1076-1088},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1111/tpj.14078},
+ISSN = {0960-7412},
+EISSN = {1365-313X},
+Keywords = {Chlamydomonas; metabolic modelling; starch; triacylglycerols;
+ photoautotrophic growth; heterotrophic growth; technical advance},
+Keywords-Plus = {BETA-OXIDATION; NITRIC-OXIDE; PEROXISOMES; REVEALS; EXPRESSION; CO2},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Asenjo, Juan JAA/L-8336-2013},
+ORCID-Numbers = {Asenjo, Juan JAA/0000-0002-3475-7664},
+Times-Cited = {12},
+Journal-ISO = {Plant J.},
+Unique-ID = {WOS:000451173000015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000449879200004,
+Author = {Troendle, Julia and Trachtmann, Natalia and Sprenger, Georg A. and
+ Weuster-Botz, Dirk},
+Title = {Fed-batch production of l-tryptophan from glycerol using recombinant
+ Escherichia coli},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2018},
+Volume = {115},
+Number = {12},
+Pages = {2881-2892},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1002/bit.26834},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Escherichia coli; fed-batch process; glycerol; l-tryptophan; plasmid},
+Keywords-Plus = {AROMATIC-AMINO-ACIDS; CORYNEBACTERIUM-GLUTAMICUM; GENETIC MANIPULATION;
+ RATIONAL DESIGN; L-PHENYLALANINE; GLUCOSE; PATHWAY; METABOLISM; CELLS;
+ BIOSYNTHESIS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sprenger, Georg A./E-2384-2011
+ },
+ORCID-Numbers = {Sprenger, Georg A./0000-0002-7879-8978
+ Weuster-Botz, Dirk/0000-0002-1171-4194},
+Times-Cited = {26},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000449879200004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000451686100010,
+Author = {Mancini, Alessio and Eyassu, Filmon and Conway, Maxwell and Occhipinti,
+ Annalisa and Lio, Pietro and Angione, Claudio and Pucciarelli, Sandra},
+Title = {CiliateGEM: an open-project and a tool for predictions of ciliate
+ metabolic variations and experimental condition design},
+Journal = {BMC BIOINFORMATICS},
+Year = {2018},
+Volume = {19},
+Number = {15},
+Month = {NOV 30},
+Note = {12th International BBCC Conference, Naples, ITALY, DEC 18-20, 2017},
+Type = {Article; Proceedings Paper},
+DOI = {10.1186/s12859-018-2422-9},
+Article-Number = {442},
+ISSN = {1471-2105},
+Keywords = {Ciliates; Tetrahymena thermophila; Genome scale reconstruction; Flux
+ balance analysis; Metabolic pathways},
+Keywords-Plus = {TETRAHYMENA-THERMOPHILA; QUANTITATIVE-ANALYSIS; GENOME SEQUENCE; MODEL;
+ PARAMECIUMDB; CONSERVATION; INNOVATION; PATHWAYS; RESOURCE; DATABASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {P. Lió, Pietro Lio/AAV-3358-2021
+ },
+ORCID-Numbers = {P. Lió, Pietro Lio/0000-0002-0540-5053
+ Occhipinti, Annalisa/0000-0001-6075-1496
+ Angione, Claudio/0000-0002-3140-7909
+ Mancini, Alessio/0000-0002-4388-3769},
+Times-Cited = {1},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000451686100010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000447645200013,
+Author = {Scott, Felipe and Wilson, Pamela and Conejeros, Raul and Vassiliadis,
+ Vassilios S.},
+Title = {Simulation and optimization of dynamic flux balance analysis models
+ using an interior point method reformulation},
+Journal = {COMPUTERS \& CHEMICAL ENGINEERING},
+Year = {2018},
+Volume = {119},
+Pages = {152-170},
+Month = {NOV 2},
+Type = {Article},
+DOI = {10.1016/j.compchemeng.2018.08.041},
+ISSN = {0098-1354},
+EISSN = {1873-4375},
+Keywords = {Dynamic flux balance analysis; Ordinary differential equations with;
+ embedded optimization; Linear programming; Genome-scale metabolic
+ network},
+Keywords-Plus = {ESCHERICHIA-COLI; PATH CONSTRAINTS; FERMENTATION; METABOLISM;
+ STRATEGIES; GROWTH},
+Research-Areas = {Computer Science; Engineering},
+Web-of-Science-Categories = {Computer Science, Interdisciplinary Applications; Engineering, Chemical},
+ResearcherID-Numbers = {Scott, Felipe/K-4193-2016
+ Conejeros, Raul/ABG-5517-2020
+ Conejeros, Raul/A-2466-2011},
+ORCID-Numbers = {Scott, Felipe/0000-0003-2041-4641
+ Conejeros, Raul/0000-0002-1273-535X
+ },
+Times-Cited = {17},
+Journal-ISO = {Comput. Chem. Eng.},
+Unique-ID = {WOS:000447645200013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000455326000018,
+Author = {Aguilar-Rodriguez, Jose and Wagner, Andreas},
+Title = {Metabolic Determinants of Enzyme Evolution in a Genome-Scale Bacterial
+ Metabolic Network},
+Journal = {GENOME BIOLOGY AND EVOLUTION},
+Year = {2018},
+Volume = {10},
+Number = {11},
+Pages = {3076-3088},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1093/gbe/evy234},
+ISSN = {1759-6653},
+Keywords = {evolutionary rates; molecular evolution; metabolism; flux balance
+ analysis; Escherichia coli},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; SUBSTITUTION RATES; MOLECULAR
+ EVOLUTION; EXPRESSION PATTERN; ADAPTIVE EVOLUTION; ESSENTIAL GENES; FLUX
+ CONTROL; PROTEINS; EVOLVE},
+Research-Areas = {Evolutionary Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Evolutionary Biology; Genetics \& Heredity},
+Times-Cited = {12},
+Journal-ISO = {Genome Biol. Evol.},
+Unique-ID = {WOS:000455326000018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000449892200012,
+Author = {Arif, Muhammad Azharuddin and Mohamad, Mohd Saberi and Abd Latif,
+ Muhammad Shafie and Deris, Safaai and Remli, Muhammad Akmal and Daud,
+ Kauthar Mohd and Ibrahim, Zuwairie and Omatu, Sigeru and Manuel
+ Corchado, Juan},
+Title = {A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to
+ optimize metabolites production in genome-scale models},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2018},
+Volume = {102},
+Pages = {112-119},
+Month = {NOV 1},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2018.09.015},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Artificial intelligence; Bioinformatics; Metabolic engineering; Cuckoo
+ Search; Minimization of Metabolic Adjustment; Gene knockout},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GENE KNOCKOUT STRATEGIES; ANT COLONY
+ OPTIMIZATION; ESCHERICHIA-COLI; SACCHAROMYCES-CEREVISIAE; ALGORITHM;
+ SUCCINATE; LACTATE; IDENTIFICATION; PLATFORM},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Kauthar, Mohd Daud/Z-1275-2019
+ Daud, Kauthar Mohd/AAB-4883-2021
+ Mohamad, Mohd Saberi/J-3201-2014
+ Remli, Muhammad Akmal/K-9914-2017
+ Corchado Rodríguez, Juan/D-3229-2013
+ },
+ORCID-Numbers = {Kauthar, Mohd Daud/0000-0002-4460-9462
+ Daud, Kauthar Mohd/0000-0002-4460-9462
+ Mohamad, Mohd Saberi/0000-0002-1079-4559
+ Remli, Muhammad Akmal/0000-0002-7800-0057
+ Corchado Rodríguez, Juan/0000-0002-2829-1829
+ Ibrahim, Zuwairie/0000-0003-1641-3478},
+Times-Cited = {7},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000449892200012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000452845400004,
+Author = {Costa, Rafael S. and Vinga, Susana},
+Title = {Assessing Escherichia coli metabolism models and simulation
+ approaches in phenotype predictions: Validation against experimental
+ data},
+Journal = {BIOTECHNOLOGY PROGRESS},
+Year = {2018},
+Volume = {34},
+Number = {6},
+Pages = {1344-1354},
+Month = {NOV-DEC},
+Type = {Article},
+DOI = {10.1002/btpr.2700},
+ISSN = {8756-7938},
+EISSN = {1520-6033},
+Keywords = {metabolism models; constraint-based and kinetic modeling; simulation
+ methods; metabolic networks; Escherichia coli; systems metabolic
+ engineering},
+Keywords-Plus = {GENOME-SCALE MODELS; SYSTEMS BIOLOGY; CELLULAR-METABOLISM;
+ KINETIC-MODELS; FLUX; GENES; YEAST; CONSEQUENCES; ENCYCLOPEDIA; OVERFLOW},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Vinga, Susana/B-8450-2008
+ Costa, RS/ABB-5507-2020},
+ORCID-Numbers = {Vinga, Susana/0000-0002-1954-5487
+ Costa, RS/0000-0002-7539-488X},
+Times-Cited = {0},
+Journal-ISO = {Biotechnol. Prog.},
+Unique-ID = {WOS:000452845400004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000460600700004,
+Author = {Graudenzi, Alex and Maspero, Davide and Di Filippo, Marzia and Gnugnoli,
+ Marco and Isella, Claudio and Mauri, Giancarlo and Medico, Enzo and
+ Antoniotti, Marco and Damiani, Chiara},
+Title = {Integration of transcriptomic data and metabolic networks in cancer
+ samples reveals highly significant prognostic power},
+Journal = {JOURNAL OF BIOMEDICAL INFORMATICS},
+Year = {2018},
+Volume = {87},
+Pages = {37-49},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.jbi.2018.09.010},
+ISSN = {1532-0464},
+EISSN = {1532-0480},
+Keywords = {Metabolic networks; RNA-seq data; Genome-wide models; Sample
+ stratification; Cancer metabolism},
+Keywords-Plus = {TRANSPORTERS; EXPRESSION; HALLMARK; ENZYMES; MODELS; TISSUE; GENES},
+Research-Areas = {Computer Science; Medical Informatics},
+Web-of-Science-Categories = {Computer Science, Interdisciplinary Applications; Medical Informatics},
+ResearcherID-Numbers = {Maspero, Davide/AAD-9782-2020
+ Graudenzi, Alex/AAY-5241-2020
+ Mauri, Giancarlo/M-3258-2013
+ Isella, Claudio/F-7327-2012
+ Medico, Enzo/AAC-3185-2021
+ },
+ORCID-Numbers = {Graudenzi, Alex/0000-0001-5452-1918
+ Mauri, Giancarlo/0000-0003-3520-4022
+ Isella, Claudio/0000-0003-0679-4756
+ Medico, Enzo/0000-0002-3917-2438
+ GNUGNOLI, MARCO/0000-0001-6131-0879
+ Maspero, Davide/0000-0001-8519-4331},
+Times-Cited = {19},
+Journal-ISO = {J. Biomed. Inform.},
+Unique-ID = {WOS:000460600700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000446996000008,
+Author = {Kim, Nam-Hoon and Jayakodi, Murukarthick and Lee, Sang-Choon and Choi,
+ Beom-Soon and Jang, Woojong and Lee, Junki and Kim, Hyun Hee and
+ Waminal, Nomar E. and Lakshmanan, Meiyappan and van Nguyen, Binh and
+ Lee, Yun Sun and Park, Hyun-Seung and Koo, Hyun Jo and Park, Jee Young
+ and Perumal, Sampath and Joh, Ho Jun and Lee, Hana and Kim, Jinkyung and
+ Kim, In Seo and Kim, Kyunghee and Koduru, Lokanand and Kang, Kyo Bin and
+ Sung, Sang Hyun and Yu, Yeisoo and Park, Daniel S. and Choi, Doil and
+ Seo, Eunyoung and Kim, Seungill and Kim, Young-Chang and Hyun, Dong Yun
+ and Park, Youn-Il and Kim, Changsoo and Lee, Tae-Ho and Kim, Hyun Uk and
+ Soh, Moon Soo and Lee, Yi and In, Jun Gyo and Kim, Heui-Soo and Kim,
+ Yong-Min and Yang, Deok-Chun and Wing, Rod A. and Lee, Dong-Yup and
+ Paterson, Andrew H. and Yang, Tae-Jin},
+Title = {Genome and evolution of the shade-requiring medicinal herb Panax
+ ginseng},
+Journal = {PLANT BIOTECHNOLOGY JOURNAL},
+Year = {2018},
+Volume = {16},
+Number = {11},
+Pages = {1904-1917},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1111/pbi.12926},
+ISSN = {1467-7644},
+EISSN = {1467-7652},
+Keywords = {Panax ginseng; ginsenosides; evolution; metabolic network; adaptation},
+Keywords-Plus = {COMPLETE CHLOROPLAST; DAMMARENEDIOL-II; GENE-EXPRESSION; KOREAN GINSENG;
+ BIOSYNTHESIS; GINSENOSIDES; ACCUMULATION; SEQUENCE; DYNAMICS;
+ PROTOPANAXADIOL},
+Research-Areas = {Biotechnology \& Applied Microbiology; Plant Sciences},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Plant Sciences},
+ResearcherID-Numbers = {Koduru, Lokanand/AAY-3079-2020
+ Kim, Seungill/AAR-1099-2021
+ Park, Youn-Il/S-2997-2019
+ Yang, Tae-Jin/AAT-5274-2020
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Park, Daniel S/HNT-0851-2023
+ Kim, Changsoo/D-2829-2011
+ KIM, HYUN UK/AAJ-1055-2021
+ Jayakodi, Murukarthick/AAY-7252-2020
+ Choi, Beom-Soon/ABC-5378-2021
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Waminal, Nomar Espinosa/I-7620-2015
+ Kim, Heui-Soo/ABF-3773-2021
+ Bin Kang, Kyo/AAQ-9809-2020
+ Wing, Rod A/Z-2885-2019
+ Lee, Yun Sun/AAF-2932-2021
+ },
+ORCID-Numbers = {Kim, Seungill/0000-0001-6287-8693
+ Park, Youn-Il/0000-0003-2912-2821
+ Park, Daniel S/0000-0003-2783-530X
+ KIM, HYUN UK/0000-0002-4566-3057
+ Jayakodi, Murukarthick/0000-0003-2951-0541
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Waminal, Nomar Espinosa/0000-0001-5119-152X
+ Kim, Heui-Soo/0000-0002-5226-6594
+ Wing, Rod A/0000-0001-6633-6226
+ SOH, MOON-SOO/0000-0002-4430-516X
+ Kim, Changsoo/0000-0002-3596-2934
+ Kang, Kyo Bin/0000-0003-3290-1017},
+Times-Cited = {98},
+Journal-ISO = {Plant Biotechnol. J.},
+Unique-ID = {WOS:000446996000008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000446527200006,
+Author = {Latif, Jr., Majid and May, Elebeoba E.},
+Title = {A Multiscale Agent-Based Model for the Investigation of E-coli
+ K12 Metabolic Response During Biofilm Formation},
+Journal = {BULLETIN OF MATHEMATICAL BIOLOGY},
+Year = {2018},
+Volume = {80},
+Number = {11},
+Pages = {2917-2956},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1007/s11538-018-0494-3},
+ISSN = {0092-8240},
+EISSN = {1522-9602},
+Keywords = {Escherichia coli K12; Biofilm; Agent-based modeling; Quorum sensing;
+ Systems biology},
+Keywords-Plus = {PSEUDOMONAS-AERUGINOSA BIOFILMS; CONSTRAINT-BASED MODELS; TO-CELL
+ COMMUNICATION; COLI K-12; BACTERIAL BIOFILMS; POLYSACCHARIDE ADHESIN;
+ STAPHYLOCOCCUS-AUREUS; EXTRACELLULAR DNA; GENE-EXPRESSION; QUANTITATIVE
+ PREDICTION},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {May, Elebeoba E./HSH-0026-2023},
+ORCID-Numbers = {May, Elebeoba E./0000-0002-5561-1867},
+Times-Cited = {4},
+Journal-ISO = {Bull. Math. Biol.},
+Unique-ID = {WOS:000446527200006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000447187700041,
+Author = {Leon-Saiki, G. Mitsue and Ledo, Narcis Ferrer and Lao-Martil, David and
+ van der Veen, Douwe and Wijffels, Rene H. and Martens, Dirk E.},
+Title = {Metabolic modelling and energy parameter estimation of Tetradesmus
+ obliquus},
+Journal = {ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS},
+Year = {2018},
+Volume = {35},
+Pages = {378-387},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.algal.2018.09.008},
+ISSN = {2211-9264},
+Keywords = {Microalgae; Scenedesmus obliquus; Flux Balance Analysis (FBA);
+ Compartmentalized metabolism; Maintenance requirement},
+Keywords-Plus = {TRIACYLGLYCEROL TAG ACCUMULATION; CONSTRAINT-BASED MODELS; FLUX BALANCE
+ ANALYSIS; PHOTOSYNTHETIC EFFICIENCY; CHLAMYDOMONAS-REINHARDTII;
+ QUANTITATIVE PREDICTION; NITROGEN STARVATION; CELLULAR-METABOLISM;
+ MAINTENANCE ENERGY; LIGHT-INTENSITY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Wijffels, Rene/0000-0001-7630-4295
+ Lao-Martil, David/0000-0002-1615-3875},
+Times-Cited = {6},
+Journal-ISO = {Algal Res.},
+Unique-ID = {WOS:000447187700041},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000451579500004,
+Author = {Moser, Felix and Borujeni, Amin Espah and Ghodasara, Amar N. and
+ Cameron, Ewen and Park, Yongjin and Voigt, Christopher A.},
+Title = {Dynamic control of endogenous metabolism with combinatorial logic
+ circuits},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2018},
+Volume = {14},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.15252/msb.20188605},
+ISSN = {1744-4292},
+Keywords = {control theory; feedback; metabolic engineering; synthetic biology},
+Keywords-Plus = {CELL-CELL COMMUNICATION; ESCHERICHIA-COLI; GENETIC CIRCUIT; PYRUVATE
+ OXIDASE; PATHWAY REGULATION; TCA CYCLE; EXPRESSION; PROTEIN;
+ TRANSCRIPTION; DESIGN},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {73},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000451579500004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000448400400003,
+Author = {Koduru, Lokanand and Lakshmanan, Meiyappan and Lee, Dong-Yup},
+Title = {In silico model-guided identification of transcriptional regulator
+ targets for efficient strain design},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2018},
+Volume = {17},
+Month = {OCT 25},
+Type = {Article},
+DOI = {10.1186/s12934-018-1015-7},
+Article-Number = {167},
+ISSN = {1475-2859},
+Keywords = {Model-guided strain design; Genome-scale metabolic model;
+ Constraint-based flux analysis; Transcriptional regulator; Systems
+ biology},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FATTY-ACID PRODUCTION; ESCHERICHIA-COLI;
+ CORYNEBACTERIUM-GLUTAMICUM; HIERARCHICAL STRUCTURE;
+ MICROBIAL-PRODUCTION; METABOLIC MODELS; OXIDATIVE STRESS; RECEPTOR
+ PROTEIN; GENE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/AAM-1171-2020
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Lee, Dong-Yup/D-6650-2011
+ Koduru, Lokanand/AAY-3079-2020},
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ },
+Times-Cited = {5},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000448400400003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000448040500079,
+Author = {Brunk, Elizabeth and Chang, Roger L. and Xia, Jing and Hefzi, Hooman and
+ Yurkovich, James T. and Kim, Donghyuk and Buckmiller, Evan and Wang,
+ Harris H. and Cho, Byung-Kwan and Yang, Chen and Palsson, Bernhard O.
+ and Church, George M. and Lewis, Nathan E.},
+Title = {Characterizing posttranslational modifications in prokaryotic metabolism
+ using a multiscale workflow},
+Journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
+ AMERICA},
+Year = {2018},
+Volume = {115},
+Number = {43},
+Pages = {11096-11101},
+Month = {OCT 23},
+Type = {Article},
+DOI = {10.1073/pnas.1811971115},
+ISSN = {0027-8424},
+Keywords = {systems biology; posttranslational modifications; metabolism; protein
+ chemistry; omics data},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; LYSINE ACETYLATION;
+ GENE-EXPRESSION; AMBER; PHOSPHOPROTEOME; IDENTIFICATION; TRANSALDOLASE;
+ DYNAMICS; TOOLBOX},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Cho, Byung-Kwan/C-1830-2011
+ Lewis, Nathan/ABE-7290-2020
+ Kim, Donghyuk/AAS-9141-2020
+ },
+ORCID-Numbers = {Lewis, Nathan/0000-0001-7700-3654
+ Chang, Roger/0000-0003-1630-6584
+ church, george/0000-0001-6232-9969
+ Brunk, Elizabeth/0000-0001-8578-8658
+ Hefzi, Hooman/0009-0003-4067-6224
+ Wang, Harris/0000-0003-2164-4318},
+Times-Cited = {31},
+Journal-ISO = {Proc. Natl. Acad. Sci. U. S. A.},
+Unique-ID = {WOS:000448040500079},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000447849100005,
+Author = {Perisin, Matthew A. and Sund, Christian J.},
+Title = {Human gut microbe co-cultures have greater potential than monocultures
+ for food waste remediation to commodity chemicals},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2018},
+Volume = {8},
+Month = {OCT 22},
+Type = {Article},
+DOI = {10.1038/s41598-018-33733-z},
+Article-Number = {15594},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSORTIA; METABOLISM; ALGORITHM; BIOMASS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {sund, christian j/G-3424-2013},
+Times-Cited = {9},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000447849100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000444361100019,
+Author = {Hala, D. and Cullen, J. A. and Hernout, B. and Ivanov, I.},
+Title = {In silico predicted transcriptional regulatory control of
+ steroidogenesis in spawning female fathead minnows (Pimephales
+ promelas)},
+Journal = {JOURNAL OF THEORETICAL BIOLOGY},
+Year = {2018},
+Volume = {455},
+Pages = {179-190},
+Month = {OCT 14},
+Type = {Article},
+DOI = {10.1016/j.jtbi.2018.07.020},
+ISSN = {0022-5193},
+EISSN = {1095-8541},
+Keywords = {Oogenesis; Transcriptional regulation; Steroidogenesis; Extreme pathway
+ analysis; Flux balance analysis},
+Keywords-Plus = {MESSENGER-RNA EXPRESSION; SIDE-CHAIN CLEAVAGE; OVARIAN-FOLLICLES PRIOR;
+ CONSTRAINT-BASED MODELS; GENE-EXPRESSION; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; OOCYTE MATURATION; PATHWAY STRUCTURE; SYSTEMS
+ BIOLOGY},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Ivanov, Ivan/JBJ-0874-2023
+ Hernout, Beatrice/AAG-6196-2020
+ },
+ORCID-Numbers = {Ivanov, Ivan/0000-0003-1773-6009
+ Cullen, Joshua/0000-0002-6935-9340},
+Times-Cited = {1},
+Journal-ISO = {J. Theor. Biol.},
+Unique-ID = {WOS:000444361100019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000450032300001,
+Author = {Kueken, Anika and Sommer, Frederik and Yaneva-Roder, Liliya and
+ Mackinder, Luke C. M. and Hoehne, Melanie and Geimer, Stefan and
+ Jonikas, Martin C. and Schroda, Michael and Stitt, Mark and Nikoloski,
+ Zoran and Mettler-Altmann, Tabea},
+Title = {Effects of microcompartmentation on flux distribution and metabolic
+ pools in Chlamydomonas reinhardtii chloroplasts},
+Journal = {ELIFE},
+Year = {2018},
+Volume = {7},
+Month = {OCT 11},
+Type = {Article},
+DOI = {10.7554/eLife.37960},
+Article-Number = {e37960},
+ISSN = {2050-084X},
+Keywords-Plus = {CARBON-CONCENTRATING MECHANISM; B-12-DEPENDENT 1,2-PROPANEDIOL
+ DEGRADATION; GREEN-ALGAE; CO2-CONCENTRATING MECHANISM;
+ SALMONELLA-TYPHIMURIUM; CO2 CONCENTRATION; ENZYME-ACTIVITIES; ANHYDRASE
+ CAH3; PROTEIN; EXPRESSION},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+ResearcherID-Numbers = {Stitt, Mark/GVT-1242-2022
+ Küken, Anika/AAA-7991-2020
+ Schroda, Michael/A-2651-2015},
+ORCID-Numbers = {Küken, Anika/0000-0003-1367-0719
+ Nikoloski, Zoran/0000-0003-2671-6763
+ Mackinder, Luke/0000-0003-1440-3233
+ Schroda, Michael/0000-0001-6872-0483},
+Times-Cited = {27},
+Journal-ISO = {eLife},
+Unique-ID = {WOS:000450032300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000446383500007,
+Author = {Kumar, Santhust and Mahajan, Saurabh and Jain, Sanjay},
+Title = {Feedbacks from the metabolic network to the genetic network reveal
+ regulatory modules in E. coli and B.
+ subtilis},
+Journal = {PLOS ONE},
+Year = {2018},
+Volume = {13},
+Number = {10},
+Month = {OCT 4},
+Type = {Article},
+DOI = {10.1371/journal.pone.0203311},
+Article-Number = {e0203311},
+ISSN = {1932-6203},
+Keywords-Plus = {TRANSCRIPTIONAL REGULATION; HIERARCHICAL STRUCTURE; ORGANIZATION;
+ EVOLUTION; CONSERVATION; PRINCIPLES; MODELS; MOTIFS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {5},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000446383500007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000448665700016,
+Author = {Boczonadi, Veronika and King, Martin S. and Smith, Anthony C. and
+ Olahova, Monika and Bansagi, Boglarka and Roos, Andreas and Eyassu,
+ Filmon and Borchers, Christoph and Ramesh, Venkateswaran and
+ Lochmueller, Hanns and Polvikoski, Tuomo and Whittaker, Roger G. and
+ Pyle, Angela and Griffin, Helen and Taylor, Robert W. and Chinnery,
+ Patrick F. and Robinson, Alan J. and Kunji, Edmund R. S. and Horvath,
+ Rita},
+Title = {Mitochondrial oxodicarboxylate carrier deficiency is associated with
+ mitochondrial DNA depletion and spinal muscular atrophy-like disease},
+Journal = {GENETICS IN MEDICINE},
+Year = {2018},
+Volume = {20},
+Number = {10},
+Pages = {1224-1235},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1038/gim.2017.251},
+ISSN = {1098-3600},
+EISSN = {1530-0366},
+Keywords = {metabolite transport; metabolomics; mitochondrial respiratory chain
+ deficiency; neural toxicity; spinal motor atrophy},
+Keywords-Plus = {KYNURENINE PATHWAY; MUTATIONS; EXPRESSION; PROTEIN; DHTKD1;
+ IDENTIFICATION; METABOLISM; ASTROCYTES; ZELLWEGER; MYOPATHY},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Smith, Anthony C/B-1891-2009
+ BORCHERS, Christoph/U-5964-2019
+ Kunji, Edmund R.S./AAH-2362-2020
+ Horvath, Rita/AAY-7042-2020
+ King, Martin S/B-6361-2012
+ },
+ORCID-Numbers = {Smith, Anthony C/0000-0003-0141-0434
+ Kunji, Edmund R.S./0000-0002-0610-4500
+ Chinnery, Patrick/0000-0002-7065-6617
+ Griffin, Helen R/0000-0002-5288-3322
+ King, Martin/0000-0001-6030-5154
+ Whittaker, Roger/0000-0002-3403-0182
+ Horvath, Rita/0000-0002-9841-170X},
+Times-Cited = {27},
+Journal-ISO = {Genet. Med.},
+Unique-ID = {WOS:000448665700016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000449465300014,
+Author = {Kabimoldayev, Ilyas and Anh Duc Nguyen and Yang, Laurence and Park,
+ Sunghoon and Lee, Eun Yeol and Kim, Donghyuk},
+Title = {Basics of genome-scale metabolic modeling and applications on
+ C1-utilization},
+Journal = {FEMS MICROBIOLOGY LETTERS},
+Year = {2018},
+Volume = {365},
+Number = {20},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1093/femsle/fny241},
+Article-Number = {fny241},
+ISSN = {0378-1097},
+EISSN = {1574-6968},
+Keywords = {GSM modeling; C1-utilizing bacteria; methylotrophs; acetogens; FBA;
+ metabolic engineering},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; METHYLOBACTERIUM-EXTORQUENS;
+ MICROBIAL-PRODUCTION; SYNTHESIS GAS; CLOSTRIDIUM-LJUNGDAHLII;
+ RECONSTRUCTION; FRAMEWORK; ELIMINATION; PREDICTION; EVOLUTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Kim, Donghyuk/AAS-9141-2020
+ },
+ORCID-Numbers = {Lee, Eun Yeol/0000-0002-6974-3262
+ Yang, Laurence/0000-0001-6663-7643},
+Times-Cited = {10},
+Journal-ISO = {FEMS Microbiol. Lett.},
+Unique-ID = {WOS:000449465300014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000450712400044,
+Author = {Wang, Hao and Marcisauskas, Simonas and Sanchez, Benjamin J. and
+ Domenzain, Ivan and Hermansson, Daniel and Agren, Rasmus and Nielsen,
+ Jens and Kerkhoven, Eduard J.},
+Title = {RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and
+ a case study on Streptomyces coelicolor},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2018},
+Volume = {14},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1006541},
+Article-Number = {e1006541},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; SYSTEMS BIOLOGY; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; GENOME; PATHWAYS; SEQUENCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Agren, Rasmus/I-1434-2012
+ Kerkhoven, Eduard/P-2469-2019
+ Sánchez, Benjamín J./O-6859-2019
+ Domenzain, Ivan/HCI-9542-2022
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Agren, Rasmus/0000-0002-9814-2191
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Sánchez, Benjamín J./0000-0001-6093-4110
+ Domenzain, Ivan/0000-0002-5322-2040
+ Nielsen, Jens/0000-0002-9955-6003
+ Marcisauskas, Simonas/0000-0003-0770-6383
+ Wang, Hao/0000-0001-7475-0136},
+Times-Cited = {153},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000450712400044},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000448100100005,
+Author = {Zou, Wei and Xiong, Xianghua and Zhang, Jing and Zhang, Kaizheng and
+ Zhao, Xingxiu and Zhao, Changqing},
+Title = {Reconstruction and analysis of a genome-scale metabolic model of
+ Methylovorus sp MP688, a high-level pyrroloquinolone quinone
+ producer},
+Journal = {BIOSYSTEMS},
+Year = {2018},
+Volume = {172},
+Pages = {37-42},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2018.07.009},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Methylovorus; Genome-scale metabolic model; Methanol metabolism;
+ Pyrroloquinolone quinone},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; PREDICTION; PATHWAYS; GENES},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Zhang, kaizheng/HKD-9015-2023},
+Times-Cited = {4},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000448100100005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000445930500001,
+Author = {Zhang, Cheng and Bidkhori, Gholamreza and Benfeitas, Rui and Lee, Sunjae
+ and Arif, Muhammad and Uhlen, Mathias and Mardinoglu, Adil},
+Title = {ESS: A Tool for Genome-Scale Quantification of Essentiality Score for
+ Reaction/Genes in Constraint-Based Modeling},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2018},
+Volume = {9},
+Month = {SEP 28},
+Type = {Article},
+DOI = {10.3389/fphys.2018.01355},
+Article-Number = {1355},
+ISSN = {1664-042X},
+Keywords = {constraint-based modeling; gene essentiality; genome-scale metabolic
+ models; reaction essentiality; systems biology},
+Keywords-Plus = {BIOLOGICAL NETWORKS; METABOLIC NETWORKS; CELLS},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {Arif, Muhammad/GSO-0267-2022
+ Mardinoglu, Adil/AAS-6360-2021
+ Zhang, Cheng/L-7906-2016
+ Arif, Muhammad/AFQ-6409-2022
+ Benfeitas, Rui/G-1251-2016
+ Uhlen, Mathias/HPB-8445-2023
+ Uhlen, Mathias/B-3262-2016
+ Lee, Sunjae/H-9815-2019
+ Uhlen, Mathias/AAV-8746-2021},
+ORCID-Numbers = {Arif, Muhammad/0000-0003-2261-0881
+ Zhang, Cheng/0000-0002-3721-8586
+ Arif, Muhammad/0000-0003-2261-0881
+ Benfeitas, Rui/0000-0001-7972-0083
+ Uhlen, Mathias/0000-0002-4858-8056
+ Uhlen, Mathias/0000-0002-4858-8056
+ Lee, Sunjae/0000-0002-6428-5936
+ },
+Times-Cited = {3},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000445930500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000445615100033,
+Author = {Lu, Hongzhong and Cao, Weiqiang and Liu, Xiaoyun and Sui, Yufei and
+ Ouyang, Liming and Xia, Jianye and Huang, Mingzhi and Zhuang, Yingping
+ and Zhang, Siliang and Noorman, Henk and Chu, Ju},
+Title = {Multi-omics integrative analysis with genome-scale metabolic model
+ simulation reveals global cellular adaptation of Aspergillus
+ niger under industrial enzyme production condition},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2018},
+Volume = {8},
+Month = {SEP 26},
+Type = {Article},
+DOI = {10.1038/s41598-018-32341-1},
+Article-Number = {14404},
+ISSN = {2045-2322},
+Keywords-Plus = {RECOMBINANT PROTEIN-PRODUCTION; CONSTRAINT-BASED MODELS;
+ GENE-EXPRESSION; OXYGEN; HYPOXIA; RESPIRATION; SURVIVAL; DATABASE;
+ CARBON},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {liu, shanshan/JPA-0852-2023
+ Wang, Shan/JPX-1098-2023
+ sui, yufei/ISB-7911-2023
+ },
+ORCID-Numbers = {Liu, Xiaoyun/0000-0002-9838-1109},
+Times-Cited = {26},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000445615100033},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000445801500001,
+Author = {Rowe, Elliot and Palsson, Bernhard O. and King, Zachary A.},
+Title = {Escher-FBA: a web application for interactive flux balance analysis},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2018},
+Volume = {12},
+Month = {SEP 26},
+Type = {Article},
+DOI = {10.1186/s12918-018-0607-5},
+Article-Number = {84},
+EISSN = {1752-0509},
+Keywords = {Constraint-based modeling; Flux balance analysis; Escher; Visualization;
+ Metabolism; Web application},
+Keywords-Plus = {CONSTRAINT-BASED MODELS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {King, Zachary/V-3402-2019
+ },
+ORCID-Numbers = {King, Zachary/0000-0003-1238-1499
+ Palsson, Bernhard/0000-0003-2357-6785},
+Times-Cited = {23},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000445801500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000445329700044,
+Author = {Kim, Hanseol and Kim, Sinyeon and Yoon, Sung Ho},
+Title = {Metabolic network reconstruction and phenome analysis of the industrial
+ microbe, Escherichia coli BL21 (DE3)},
+Journal = {PLOS ONE},
+Year = {2018},
+Volume = {13},
+Number = {9},
+Month = {SEP 21},
+Type = {Article},
+DOI = {10.1371/journal.pone.0204375},
+Article-Number = {e0204375},
+ISSN = {1932-6203},
+Keywords-Plus = {B STRAINS REL606; GENOME-SCALE MODELS; GENE; K-12; PATHWAYS;
+ ORGANIZATION; MICROARRAYS; CULTIVATION; EXPRESSION; SEQUENCES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Kim, Hanseol/0000-0002-0201-329X
+ KIM, SINYEON/0000-0002-3987-910X
+ Yoon, Sung Ho/0000-0003-0171-944X},
+Times-Cited = {13},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000445329700044},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000452381400001,
+Author = {Tamura, Takeyuki},
+Title = {Grid-based computational methods for the design of constraint-based
+ parsimonious chemical reaction networks to simulate metabolite
+ production: GridProd},
+Journal = {BMC BIOINFORMATICS},
+Year = {2018},
+Volume = {19},
+Month = {SEP 14},
+Type = {Article},
+DOI = {10.1186/s12859-018-2352-6},
+Article-Number = {325},
+ISSN = {1471-2105},
+Keywords = {Flux balance analysis; Linear programming; Algorithm; Design of
+ metabolic network; Constraint-based model; Growth rate; Production rate;
+ Smaller reaction network},
+Keywords-Plus = {KNOCKOUT STRATEGIES; FRAMEWORK; MODELS; OVERPRODUCTION; ALGORITHM},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Tamura, Takeyuki/ABI-2627-2020
+ Tamura, Takeyuki/AGG-2853-2022},
+ORCID-Numbers = {Tamura, Takeyuki/0000-0003-1596-901X},
+Times-Cited = {5},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000452381400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000444376500005,
+Author = {Taymaz-Nikerel, Hilal and Karabekmez, Muhammed Erkan and Eraslan, Serpil
+ and Kirdar, Betul},
+Title = {Doxorubicin induces an extensive transcriptional and metabolic rewiring
+ in yeast cells},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2018},
+Volume = {8},
+Month = {SEP 12},
+Type = {Article},
+DOI = {10.1038/s41598-018-31939-9},
+Article-Number = {13672},
+ISSN = {2045-2322},
+Keywords-Plus = {TOPOISOMERASE-II; SACCHAROMYCES-CEREVISIAE; FUNCTIONAL-ANALYSIS; SYSTEMS
+ BIOLOGY; CYCLE ARREST; DNA-DAMAGE; CANCER; EXPRESSION; GENE; ANTICANCER},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Karabekmez, Muhammed Erkan/AAI-2436-2019
+ Kirdar, Betul/ABI-7250-2020
+ Taymaz-Nikerel, Hilal/AAQ-9395-2021
+ },
+ORCID-Numbers = {Karabekmez, Muhammed Erkan/0000-0002-0517-5227
+ Taymaz-Nikerel, Hilal/0000-0002-5523-263X
+ Eraslan, Serpil/0000-0002-7674-7384},
+Times-Cited = {86},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000444376500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000449472200058,
+Author = {Ankrah, Nana Y. D. and Chouaia, Bessem and Douglas, Angela E.},
+Title = {The Cost of Metabolic Interactions in Symbioses between Insects and
+ Bacteria with Reduced Genomes},
+Journal = {MBIO},
+Year = {2018},
+Volume = {9},
+Number = {5},
+Month = {SEP-OCT},
+Type = {Article},
+DOI = {10.1128/mBio.01433-18},
+Article-Number = {e01433-18},
+ISSN = {2150-7511},
+Keywords = {constraint-based modeling; flux balance analysis; nitrogen recycling;
+ symbiosis; xylem-feeding insects},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; RNA-SEQ DATA; ANTIMICROBIAL PEPTIDES;
+ EVOLUTION; VIRULENCE; ANCIENT; PLANT; SAP; ENDOSYMBIONTS; CICADELLIDAE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Ankrah, Nana/IUO-8239-2023
+ },
+ORCID-Numbers = {Ankrah, Nana Yaw/0000-0003-0492-545X
+ chouaia, bessem/0000-0003-0726-7237},
+Times-Cited = {37},
+Journal-ISO = {mBio},
+Unique-ID = {WOS:000449472200058},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000447634700016,
+Author = {Englund, Elias and Shabestary, Kiyan and Hudson, Elton P. and Lindberg,
+ Pia},
+Title = {Systematic overexpression study to find target enzymes enhancing
+ production of terpenes in Synechocystis PCC 6803, using isoprene
+ as a model compound},
+Journal = {METABOLIC ENGINEERING},
+Year = {2018},
+Volume = {49},
+Pages = {164-177},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.ymben.2018.07.004},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Metabolic engineering; Cyanobacteria; Isoprene; MEP pathway; Metabolic
+ modeling; Carbon flux},
+Keywords-Plus = {1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE;
+ METHYLERYTHRITOL-PHOSPHATE-PATHWAY; MONOTERPENE HYDROCARBONS PRODUCTION;
+ ESCHERICHIA-COLI; GENE-EXPRESSION; CARBON-DIOXIDE; PHOTOSYNTHETIC
+ PRODUCTION; MEVALONATE PATHWAY; CYANOBACTERIA; BIOSYNTHESIS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Hudson, Paul/ABH-8177-2020
+ Shabestary, Kiyan/JCE-6866-2023
+ },
+ORCID-Numbers = {Shabestary, Kiyan/0000-0002-4207-0547
+ Hudson, Elton/0000-0003-1899-7649},
+Times-Cited = {61},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000447634700016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000444317200043,
+Author = {Garcia-Jimenez, Beatriz and Luis Garcia, Jose and Nogales, Juan},
+Title = {FLYCOP: metabolic modeling-based analysis and engineering microbial
+ communities},
+Journal = {BIOINFORMATICS},
+Year = {2018},
+Volume = {34},
+Number = {17},
+Pages = {954-963},
+Month = {SEP 1},
+Note = {17th European Conference on Computational Biology (ECCB), Athens,
+ GREECE, SEP 08-12, 2018},
+Type = {Article; Proceedings Paper},
+DOI = {10.1093/bioinformatics/bty561},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {LONG-TERM EXPERIMENT; CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI;
+ EXPERIMENTAL EVOLUTION; DYNAMICS; ADAPTATION; DIVERGENCE; ALGORITHM;
+ CONSORTIA; BACTERIA},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {García-Jiménez, Beatriz/ABH-2355-2020
+ Nogales, Juan/Y-8829-2019
+ Garcia Lopez, Jose Luis/G-9139-2015},
+ORCID-Numbers = {García-Jiménez, Beatriz/0000-0002-8129-6506
+ Nogales, Juan/0000-0002-4961-0833
+ Garcia Lopez, Jose Luis/0000-0002-9238-2485},
+Times-Cited = {24},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000444317200043},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000450712200023,
+Author = {Hunt, Kristopher A. and Jennings, Ryan M. and Inskeep, William P. and
+ Carlson, Ross P.},
+Title = {Multiscale analysis of autotroph-heterotroph interactions in a
+ high-temperature microbial community},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2018},
+Volume = {14},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1006431},
+Article-Number = {e1006431},
+EISSN = {1553-7358},
+Keywords-Plus = {YELLOWSTONE-NATIONAL-PARK; ACIDIC GEOTHERMAL SPRINGS; METABOLIC PATHWAY
+ ANALYSIS; METAGENOME SEQUENCE; CELLULAR-METABOLISM; BIOCYC COLLECTION;
+ METACYC DATABASE; IRON; OXIDATION; GENOMES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Carlson, Ross/0000-0002-2464-7111},
+Times-Cited = {9},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000450712200023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000444356800002,
+Author = {Immanuel, Selva Rupa Christinal and Banerjee, Deepanwita and Rajankar,
+ Mayooreshwar P. and Raghunathan, Anu},
+Title = {Integrated constraints based analysis of an engineered violacein pathway
+ in Escherichia coli},
+Journal = {BIOSYSTEMS},
+Year = {2018},
+Volume = {171},
+Pages = {10-19},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2018.06.002},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Violacein; Escherichia coli; Synthetic biology; Metabolism; Flux balance
+ analysis},
+Keywords-Plus = {CONTROL PROTEIN EXPRESSION; CHROMOBACTERIUM-VIOLACEUM; SYNTHETIC
+ BIOLOGY; CELLULAR-METABOLISM; INVIVO MEASUREMENT; OPTIMAL SELECTION;
+ GROWTH; MODELS; BIOSYNTHESIS; NETWORKS},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Banerjee, Deepanwita/AAD-5528-2021
+ },
+ORCID-Numbers = {Banerjee, Deepanwita/0000-0002-0083-0608
+ Immanuel, Selva Rupa Christinal/0000-0002-3642-9605},
+Times-Cited = {8},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000444356800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000443986000029,
+Author = {Maoz, Ben M. and Herland, Anna and FitzGerald, Edward A. and Grevesse,
+ Thomas and Vidoudez, Charles and Pacheco, Alan R. and Sheehy, Sean P.
+ and Park, Tae-Eun and Dauth, Stephanie and Mannix, Robert and Budnik,
+ Nikita and Shores, Kevin and Cho, Alexander and Nawroth, Janna C. and
+ Segre, Daniel and Budnik, Bogdan and Ingber, Donald E. and Parker, Kevin
+ Kit},
+Title = {A linked organ-on-chip model of the human neurovascular unit reveals the
+ metabolic coupling of endothelial and neuronal cells},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2018},
+Volume = {36},
+Number = {9},
+Pages = {865+},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1038/nbt.4226},
+ISSN = {1087-0156},
+EISSN = {1546-1696},
+Keywords-Plus = {BLOOD-BRAIN-BARRIER; ENERGY-METABOLISM; METHAMPHETAMINE; OPPORTUNITIES;
+ PERSPECTIVE; ASTROCYTES; PROTEOMICS; GLUTAMINE; RATS; BBB},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Maoz, Ben M/K-6555-2012
+ Budnik, Bogdan/AAH-9987-2019
+ Budnik, Bogdan/AGG-8824-2022
+ Segrè, Daniel/A-1993-2009
+ Pacheco, Alan R/IUQ-5711-2023
+ Ingber, Donald E/AAC-5894-2019
+ Herland, Anna/J-2923-2012
+ },
+ORCID-Numbers = {Budnik, Bogdan/0000-0003-3622-2003
+ Segrè, Daniel/0000-0003-4859-1914
+ Pacheco, Alan R/0000-0002-1128-3232
+ Maoz, Ben/0000-0002-3823-7682
+ FitzGerald, Edward A./0000-0002-0603-1241
+ Park, Tae-Eun/0000-0003-3979-5405
+ pacheco quispe, alan/0000-0002-5112-1430
+ Vidoudez, Charles/0000-0003-0953-7800
+ Herland, Anna/0000-0002-5002-2537},
+Times-Cited = {247},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000443986000029},
+ESI-Highly-Cited-Paper = {Y},
+ESI-Hot-Paper = {N},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000449353000006,
+Author = {Papapetridis, Ioannis and Verhoeven, Maarten D. and Wiersma, Sanne J.
+ and Goudriaan, Maaike and van Maris, Antonius J. A. and Pronk, Jack T.},
+Title = {Laboratory evolution for forced glucose-xylose co-consumption enables
+ identification of mutations that improve mixed-sugar fermentation by
+ xylose-fermenting Saccharomyces cerevisiae},
+Journal = {FEMS YEAST RESEARCH},
+Year = {2018},
+Volume = {18},
+Number = {6},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1093/femsyr/foy056},
+Article-Number = {foy056},
+ISSN = {1567-1356},
+EISSN = {1567-1364},
+Keywords = {biofuels; yeast; industrial biotechnology; redox engineering;
+ fermentation; pentoses},
+Keywords-Plus = {CARBON CATABOLITE REPRESSION; YEAST HEXOSE TRANSPORTERS;
+ PENTOSE-PHOSPHATE PATHWAY; GLYCOGEN-BINDING DOMAIN; SNF1 KINASE;
+ PHOSPHOGLUCOSE ISOMERASE; ALCOHOLIC FERMENTATION; CHEMOSTAT CULTURES;
+ UBIQUITIN LIGASE; BETA-SUBUNITS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+ORCID-Numbers = {Verhoeven, Maarten/0000-0002-5004-1666
+ Pronk, Jack/0000-0002-5617-4611},
+Times-Cited = {35},
+Journal-ISO = {FEMS Yeast Res.},
+Unique-ID = {WOS:000449353000006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000444994200001,
+Author = {Xu, Zixiang and Guo, Jing and Yue, Yunxia and Meng, Jing and Sun, Xiao},
+Title = {IN SILICO GENOME-SCALE RECONSTRUCTION AND ANALYSIS OF THE
+ SHEWANELLA LOIHICA PV-4 METABOLIC NETWORK},
+Journal = {JOURNAL OF BIOLOGICAL SYSTEMS},
+Year = {2018},
+Volume = {26},
+Number = {3},
+Pages = {373-397},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1142/S0218339018500171},
+ISSN = {0218-3390},
+EISSN = {1793-6470},
+Keywords = {Genome-Scale Metabolic Network; Flux Balance Analysis; Shewanella
+ Loihica; Microbial Fuel Cell},
+Keywords-Plus = {GEOBACTER-SULFURREDUCENS; REDUCTION; BACTERIUM},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+Times-Cited = {1},
+Journal-ISO = {J. Biol. Syst.},
+Unique-ID = {WOS:000444994200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000443071400062,
+Author = {Tack, Ignace L. M. M. and Nimmegeers, Philippe and Akkermans, Simen and
+ Logist, Filip and Van Impe, Jan F. M.},
+Title = {A low-complexity metabolic network model for the respiratory and
+ fermentative metabolism of Escherichia coli},
+Journal = {PLOS ONE},
+Year = {2018},
+Volume = {13},
+Number = {8},
+Month = {AUG 29},
+Type = {Article},
+DOI = {10.1371/journal.pone.0202565},
+Article-Number = {e0202565},
+ISSN = {1932-6203},
+Keywords-Plus = {LACTATE-DEHYDROGENASE; LISTERIA-MONOCYTOGENES; ANAEROBIC FERMENTATION;
+ GENOME SEQUENCE; MICROBIAL LAG; GROWTH-RATE; PH; TEMPERATURE; ACID;
+ MAINTENANCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Akkermans, Simen/F-7549-2018
+ Nimmegeers, Philippe/AAG-1512-2020
+ Nimmegeers, Philippe/ABD-4568-2020
+ Logist, Filip/AAG-4210-2020
+ },
+ORCID-Numbers = {Nimmegeers, Philippe/0000-0002-2086-7694
+ Logist, Filip/0000-0001-8621-7531
+ Akkermans, Simen/0000-0003-2904-0439
+ Van Impe, Jan/0000-0002-5904-1638},
+Times-Cited = {4},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000443071400062},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000443340100002,
+Author = {Kyselova, L. and Kreitmayer, D. and Kremling, A. and Bettenbrock, K.},
+Title = {Type and capacity of glucose transport influences succinate yield in
+ two-stage cultivations},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2018},
+Volume = {17},
+Month = {AUG 28},
+Type = {Article},
+DOI = {10.1186/s12934-018-0980-1},
+Article-Number = {132},
+ISSN = {1475-2859},
+Keywords = {Succinate production; Two stage cultivations; Glucose transport; Flux
+ balance analysis; ATP; Pck},
+Keywords-Plus = {ESCHERICHIA-COLI K-12; PHOSPHOENOLPYRUVATE CARBOXYKINASE; STOICHIOMETRIC
+ MAXIMUM; PYRUVATE-CARBOXYLASE; METABOLIC EVOLUTION; INDUCER EXCLUSION;
+ MALIC ENZYME; ACID; GENE; PROTEIN},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Bettenbrock, Katja/AAN-5812-2020
+ },
+ORCID-Numbers = {Bettenbrock, Katja/0000-0002-2444-7777},
+Times-Cited = {11},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000443340100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000442579900001,
+Author = {Nazem-Bokaee, Hadi and Maranas, Costas D.},
+Title = {A Prospective Study on the Fermentation Landscape of Gaseous Substrates
+ to Biorenewables Using Methanosarcina acetivorans Metabolic Model},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2018},
+Volume = {9},
+Month = {AUG 24},
+Type = {Article},
+DOI = {10.3389/fmicb.2018.01855},
+Article-Number = {1855},
+ISSN = {1664-302X},
+Keywords = {gas fermentation; metabolic modeling; CH4; CO; CO2; M. acetivorans},
+Keywords-Plus = {METHANE OXIDATION; GAS FERMENTATION; CARBON-MONOXIDE; LIQUID FUELS;
+ ETHANOL; CONVERSION; BUTANOL; CHALLENGES; BIOFUEL; SYNGAS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Maranas, Costas D/A-4774-2011
+ },
+ORCID-Numbers = {Maranas, Costas D/0000-0002-1508-1398
+ Nazem-Bokaee, Hadi/0000-0002-4246-1804},
+Times-Cited = {5},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000442579900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000442284800015,
+Author = {Faria, Jose P. and Rocha, Miguel and Rocha, Isabel and Henry,
+ Christopher S.},
+Title = {Methods for automated genome-scale metabolic model reconstruction},
+Journal = {BIOCHEMICAL SOCIETY TRANSACTIONS},
+Year = {2018},
+Volume = {46},
+Number = {4},
+Pages = {931-936},
+Month = {AUG 20},
+Type = {Review},
+DOI = {10.1042/BST20170246},
+ISSN = {0300-5127},
+EISSN = {1470-8752},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; RE-ANNOTATION; PREDICTION; SOFTWARE; DATABASE;
+ METACYC; KEGG; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Rocha, Miguel/B-9404-2011
+ Rocha, Isabel/A-4279-2013
+ Faria, Jose P/K-7628-2019},
+ORCID-Numbers = {Rocha, Miguel/0000-0001-8439-8172
+ Rocha, Isabel/0000-0001-9494-3410
+ Faria, Jose P/0000-0001-9302-7250},
+Times-Cited = {33},
+Journal-ISO = {Biochem. Soc. Trans.},
+Unique-ID = {WOS:000442284800015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000438173900002,
+Author = {Teresita Castaneda, Maria and Nunez, Sebastian and Garelli, Fabricio and
+ Voget, Claudio and De Battista, Hernan},
+Title = {Comprehensive analysis of a metabolic model for lipid production in
+ Rhodosporidium toruloides},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2018},
+Volume = {280},
+Pages = {11-18},
+Month = {AUG 20},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2018.05.010},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Metabolic modeling; Lipid production; Rhodosporidium toruloides; Flux
+ balance analysis},
+Keywords-Plus = {MICROBIAL OIL PRODUCTION; FLUX BALANCE ANALYSIS; YARROWIA-LIPOLYTICA;
+ SACCHAROMYCES-CEREVISIAE; CELL-METABOLISM; CARBON-SOURCES; FATTY-ACIDS;
+ YEAST; BIODIESEL; ACCUMULATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Garelli, Fabricio/0000-0002-8473-1569
+ De Battista, Hernan/0000-0001-5831-3737
+ Nunez, Sebastian/0000-0002-9839-0937
+ Castaneda, Maria Teresita/0000-0001-5346-7817},
+Times-Cited = {27},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000438173900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000440725000002,
+Author = {Rienksma, Rienk A. and Schaap, Peter J. and dos Santos, Vitor A. P.
+ Martins and Suarez-Diez, Maria},
+Title = {Modeling the Metabolic State of Mycobacterium tuberculosis Upon
+ Infection},
+Journal = {FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY},
+Year = {2018},
+Volume = {8},
+Month = {AUG 3},
+Type = {Article},
+DOI = {10.3389/fcimb.2018.00264},
+Article-Number = {264},
+ISSN = {2235-2988},
+Keywords = {metabolic model; Mycobacterium tuberculosis; systems biology;
+ host-pathogen interaction; condition specific; flux balance analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS; TRANSCRIPTIONAL
+ ADAPTATION; EXPRESSION DATA; PREDICTION; NETWORKS; INSIGHTS; PROTEIN},
+Research-Areas = {Immunology; Microbiology},
+Web-of-Science-Categories = {Immunology; Microbiology},
+ResearcherID-Numbers = {Diez, Maria Suarez/AAI-1354-2020
+ },
+ORCID-Numbers = {Schaap, Peter/0000-0002-4346-6084
+ Suarez-Diez, Maria/0000-0001-5845-146X},
+Times-Cited = {11},
+Journal-ISO = {Front. Cell. Infect. Microbiol.},
+Unique-ID = {WOS:000440725000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000443615400009,
+Author = {diCenzo, George C. and Debiec, Klaudia and Krzysztoforski, Jan and
+ Uhrynowski, Witold and Mengoni, Alessio and Fagorzi, Camilla and
+ Gorecki, Adrian and Dziewit, Lukasz and Bajda, Tomasz and Rzepa,
+ Grzegorz and Drewniak, Lukasz},
+Title = {Genomic and Biotechnological Characterization of the Heavy-Metal
+ Resistant, Arsenic-Oxidizing Bacterium Ensifer sp M14},
+Journal = {GENES},
+Year = {2018},
+Volume = {9},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.3390/genes9080379},
+Article-Number = {379},
+EISSN = {2073-4425},
+Keywords = {Ensifer (Sinorhizobium) sp M14; arsenic-oxidizing bacteria; heavy metal
+ resistance; draft genome sequence; comparative genomic analysis;
+ biosafety; biotechnology for arsenic removal; adsorption; water
+ treatment; in situ (bio)remediation},
+Keywords-Plus = {SINORHIZOBIUM SP M14; REFRACTORY GOLD CONCENTRATE; CARBON-DIOXIDE;
+ OXIDATION; SEQUENCE; GENES; BIOAUGMENTATION; BIOOXIDATION; ANNOTATION;
+ METABOLISM},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Mengoni, Alessio/G-5336-2013
+ Drewniak, Lukasz/AAX-8109-2021
+ Debiec, Klaudia/M-4394-2017
+ Bajda, Tomasz/B-2323-2013
+ diCenzo, George C C/M-1876-2017
+ Rzepa, Grzegorz/R-9944-2018
+ Dziewit, Lukasz/L-1131-2016
+ Debiec-Andrzejewska, Klaudia/K-6836-2019
+ },
+ORCID-Numbers = {Mengoni, Alessio/0000-0002-1265-8251
+ Drewniak, Lukasz/0000-0002-3236-0508
+ Debiec, Klaudia/0000-0002-3214-0732
+ Bajda, Tomasz/0000-0003-3849-5558
+ diCenzo, George C C/0000-0003-3889-6570
+ Rzepa, Grzegorz/0000-0001-5791-2308
+ Dziewit, Lukasz/0000-0002-5057-2811
+ Debiec-Andrzejewska, Klaudia/0000-0002-3214-0732
+ Krzysztoforski, Jan/0000-0002-6869-1595
+ Gorecki, Adrian/0000-0003-4028-8136},
+Times-Cited = {18},
+Journal-ISO = {Genes},
+Unique-ID = {WOS:000443615400009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000440939400007,
+Author = {Zou, Wei and Ye, Guangbin and Zhang, Jing and Zhao, Changqing and Zhao,
+ Xingxiu and Zhang, Kaizheng},
+Title = {Genome-scale metabolic reconstruction and analysis for Clostridium
+ kluyveri},
+Journal = {GENOME},
+Year = {2018},
+Volume = {61},
+Number = {8},
+Pages = {605-613},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1139/gen-2017-0177},
+ISSN = {0831-2796},
+EISSN = {1480-3321},
+Keywords = {Clostridium kluyveri; metabolic model; flux balance analysis; hexanoate;
+ baijiu},
+Keywords-Plus = {CAPROIC ACID; FATTY-ACIDS; FERMENTATION; NETWORK; ETHANOL; CO2;
+ QUANTIFICATION; PREDICTION; COCULTURE; PATHWAYS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Zhang, kaizheng/HKD-9015-2023},
+Times-Cited = {14},
+Journal-ISO = {Genome},
+Unique-ID = {WOS:000440939400007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000440299100001,
+Author = {Kim, Osvaldo D. and Rocha, Miguel and Maia, Paulo},
+Title = {A Review of Dynamic Modeling Approaches and Their Application in
+ Computational Strain Optimization for Metabolic Engineering},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2018},
+Volume = {9},
+Month = {JUL 31},
+Type = {Review},
+DOI = {10.3389/fmicb.2018.01690},
+Article-Number = {1690},
+ISSN = {1664-302X},
+Keywords = {dynamic modeling; strain optimization; phenotype prediction; metabolic
+ engineering; hybrid modeling},
+Keywords-Plus = {CENTRAL CARBON METABOLISM; CONSTRAINT-BASED MODELS; FLUX BALANCE
+ ANALYSIS; PARAMETER-ESTIMATION; SYSTEMS BIOLOGY; IDENTIFIABILITY
+ ANALYSIS; BIOCHEMICAL NETWORKS; KINETIC-MODELS; RATE LAWS; GROWTH},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Rocha, Miguel/B-9404-2011
+ Maia, Paulo/AAM-1025-2021
+ Maia, Paulo/F-9148-2010},
+ORCID-Numbers = {Rocha, Miguel/0000-0001-8439-8172
+ Maia, Paulo/0000-0002-0848-8683},
+Times-Cited = {50},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000440299100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000441394800007,
+Author = {Johannsson, Freyr and Gudmundsson, Steinn and Paglia, Giuseppe and
+ Gudmundsson, Sveinn and Palsson, Bernhard and Sigurjonsson, Olafur E.
+ and Rolfsson, Ottar},
+Title = {Systems analysis of metabolism in platelet concentrates during storage
+ in platelet additive solution},
+Journal = {BIOCHEMICAL JOURNAL},
+Year = {2018},
+Volume = {475},
+Number = {13},
+Pages = {2225-2240},
+Month = {JUL 16},
+Type = {Article},
+DOI = {10.1042/BCJ20170921},
+ISSN = {0264-6021},
+EISSN = {1470-8728},
+Keywords-Plus = {EXTENDED STORAGE; POLYOL PATHWAY; GLUCOSE; REVEALS; TRANSFUSION;
+ ACTIVATION; CITRATE; IDENTIFICATION; BIOENERGETICS; PERMEABILITY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Paglia, Giuseppe/H-2012-2018
+ Sigurjonsson, Olafur/T-8190-2019
+ },
+ORCID-Numbers = {Paglia, Giuseppe/0000-0003-4724-6801
+ Sigurjonsson, Olafur/0000-0002-4968-842X
+ Rolfsson, Ottar/0000-0003-4258-6057},
+Times-Cited = {14},
+Journal-ISO = {Biochem. J.},
+Unique-ID = {WOS:000441394800007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000438114200001,
+Author = {Botero, David and Valdes, Ivan and Rodriguez, Maria-Juliana and Henao,
+ Diana and Danies, Giovanna and Gonzalez, Andres F. and Restrepo, Silvia},
+Title = {A Genome-Scale Metabolic Reconstruction of Phytophthora infestans
+ With the Integration of Transcriptional Data Reveals the Key Metabolic
+ Patterns Involved in the Interaction of Its Host},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2018},
+Volume = {9},
+Month = {JUL 10},
+Type = {Article},
+DOI = {10.3389/fgene.2018.00244},
+Article-Number = {244},
+EISSN = {1664-8021},
+Keywords = {context-specific models; flux balance analysis; plant-pathogen
+ interaction; hemibiotrophy; metabolic reconstruction; Phytophthora
+ infestans},
+Keywords-Plus = {EXPRESSION DATA; PLANT; BIOSYNTHESIS; NETWORK; TOOLBOX; MODELS; GROWTH},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ORCID-Numbers = {Valdes, Ivan/0000-0001-6584-5715
+ BOTERO ROZO, DAVID OCTAVIO/0000-0003-4582-4276},
+Times-Cited = {8},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000438114200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000437515000002,
+Author = {Amara, Adam and Takano, Eriko and Breitling, Rainer},
+Title = {Development and validation of an updated computational model of
+ Streptomyces coelicolor primary and secondary metabolism},
+Journal = {BMC GENOMICS},
+Year = {2018},
+Volume = {19},
+Month = {JUL 4},
+Type = {Article},
+DOI = {10.1186/s12864-018-4905-5},
+Article-Number = {519},
+ISSN = {1471-2164},
+Keywords = {Genome-scale metabolic modelling; Streptomyces; Secondary metabolism;
+ Omics; Synthetic biology; Natural products},
+Keywords-Plus = {POLYKETIDE SYNTHASE CPK; CONSTRAINT-BASED MODELS; ANTIBIOTIC PRODUCTION;
+ SYNTHETIC BIOLOGY; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ GENE-CLUSTER; SCALE; RECONSTRUCTION; IDENTIFICATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ORCID-Numbers = {Amara, Adam/0000-0003-0489-0533},
+Times-Cited = {16},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000437515000002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000438374100077,
+Author = {Cottret, Ludovic and Frainay, Clement and Chazalviel, Maxime and
+ Cabanettes, Floreal and Gloaguen, Yoann and Camenen, Etienne and Merlet,
+ Benjamin and Heux, Stephanie and Portais, Jean-Charles and Poupin,
+ Nathalie and Vinson, Florence and Jourdan, Fabien},
+Title = {MetExplore: collaborative edition and exploration of metabolic networks},
+Journal = {NUCLEIC ACIDS RESEARCH},
+Year = {2018},
+Volume = {46},
+Number = {W1},
+Pages = {W495-W502},
+Month = {JUL 2},
+Type = {Article},
+DOI = {10.1093/nar/gky301},
+ISSN = {0305-1048},
+EISSN = {1362-4962},
+Keywords-Plus = {PATHWAYS; MODELS; DATABASE; RECONSTRUCTION; COLLECTION; TOOLBOX; SERVER},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Frainay, Clément/B-8636-2019
+ /AAD-2293-2020
+ Jourdan, Fabien/AAW-5075-2021
+ },
+ORCID-Numbers = {Frainay, Clément/0000-0003-4313-2786
+ /0000-0001-7418-7750
+ Jourdan, Fabien/0000-0001-9401-2894
+ Heux, Stephanie/0000-0003-1312-3002
+ Portais, Jean-Charles/0000-0002-3480-0933
+ Poupin, Nathalie/0000-0002-3393-1405},
+Times-Cited = {68},
+Journal-ISO = {Nucleic Acids Res.},
+Unique-ID = {WOS:000438374100077},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000456271000004,
+Author = {de Souza, Samara Silva and Castro, Julia de Vasconcellos and Porto,
+ Luismar Marques},
+Title = {MODELING THE CORE METABOLISM OF Komagataeibacter hansenii ATCC
+ 23769 TO EVALUATE NANOCELLULOSE BIOSYNTHESIS},
+Journal = {BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING},
+Year = {2018},
+Volume = {35},
+Number = {3},
+Pages = {869-885},
+Month = {JUL-SEP},
+Type = {Article},
+DOI = {10.1590/0104-6632.20180353s20170327},
+ISSN = {0104-6632},
+EISSN = {1678-4383},
+Keywords = {Komagataeibacter hansenii; Bacterial nanocellulose; Core metabolic
+ model; Flux balance analysis},
+Keywords-Plus = {DIFFERENT CARBON-SOURCES; CONSTRAINT-BASED MODELS; FLUX BALANCE
+ ANALYSIS; BACTERIAL CELLULOSE; GLUCONACETOBACTER-XYLINUS;
+ ACETOBACTER-XYLINUM; QUANTITATIVE PREDICTION; CULTURE-CONDITIONS;
+ NETWORKS; BIOLOGY},
+Research-Areas = {Engineering},
+Web-of-Science-Categories = {Engineering, Chemical},
+ResearcherID-Numbers = {Souza, Samara Silva de/O-1395-2018
+ Porto, Luismar Marques/AAN-7806-2020
+ Guelli Souza, Selene/A-4909-2008},
+ORCID-Numbers = {Souza, Samara Silva de/0000-0001-5129-940X
+ Porto, Luismar Marques/0000-0002-5777-5144
+ Guelli Souza, Selene/0000-0001-8981-3056},
+Times-Cited = {6},
+Journal-ISO = {Braz. J. Chem. Eng.},
+Unique-ID = {WOS:000456271000004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000440483300023,
+Author = {Lloyd, Colton J. and Ebrahim, Ali and Yang, Laurence and King, Zachary
+ A. and Catoiu, Edward and O'Brien, Edward J. and Liu, Joanne K. and
+ Polsson, Bernhard O.},
+Title = {COBRAme: A computational framework for genome-scale models of metabolism
+ and gene expression},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2018},
+Volume = {14},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1006302},
+Article-Number = {e1006302},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; PHENOTYPE; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Liu, Joanne/JRY-7564-2023
+ King, Zachary/V-3402-2019
+ },
+ORCID-Numbers = {King, Zachary/0000-0003-1238-1499
+ Palsson, Bernhard/0000-0003-2357-6785
+ Yang, Laurence/0000-0001-6663-7643
+ , Joanne/0000-0001-9973-524X},
+Times-Cited = {78},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000440483300023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000440449600019,
+Author = {Patterson, Kurt and Yu, James and Landberg, Jenny and Chang, Ivan and
+ Shavarebi, Farbod and Bilanchone, Virginia and Sandmeyer, Suzanne},
+Title = {Functional genomics for the oleaginous yeast Yarrowia lipolytica},
+Journal = {METABOLIC ENGINEERING},
+Year = {2018},
+Volume = {48},
+Pages = {184-196},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1016/j.ymben.2018.05.008},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Fitness; Functional genomics; Metabolism; Oleaginous yeast; Hermes;
+ Transposon mutagenesis},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; LIPID-ACCUMULATION; TRANSPOSON; GENES;
+ INTEGRATION; EVOLUTION; SEQUENCE; TRANSFORMATION; MUTAGENESIS;
+ METABOLISM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Bilanchone, Virginia/0000-0001-9169-3698
+ Landberg, Jenny/0000-0002-8094-0478
+ Shavarebi, Farbod/0000-0003-3627-3097},
+Times-Cited = {26},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000440449600019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000438546400001,
+Author = {Sertbas, Mustafa and Ulgen, Kutlu O.},
+Title = {Unlocking Human Brain Metabolism by Genome-Scale and Multiomics
+ Metabolic Models: Relevance for Neurology Research, Health, and Disease},
+Journal = {OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY},
+Year = {2018},
+Volume = {22},
+Number = {7},
+Pages = {455-467},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1089/omi.2018.0088},
+ISSN = {1536-2310},
+EISSN = {1557-8100},
+Keywords = {multiomics; systems biology; genome-scale modeling; human brain
+ metabolism; neurological diseases},
+Keywords-Plus = {AMYOTROPHIC-LATERAL-SCLEROSIS; PARKINSONS-DISEASE; UNITED-STATES;
+ MULTIPLE-SCLEROSIS; GLOBAL RECONSTRUCTION; HUNTINGTONS-DISEASE;
+ ALZHEIMERS-DISEASE; MEDICAL PROGRESS; SYSTEMS BIOLOGY; HEART-DISEASE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Ulgen, Kutlu/AAF-3350-2020
+ Sertbas, Mustafa/ABB-1337-2020
+ },
+ORCID-Numbers = {Sertbas, Mustafa/0000-0002-0278-9397
+ Ulgen, Kutlu/0000-0003-3668-3467},
+Times-Cited = {9},
+Journal-ISO = {OMICS},
+Unique-ID = {WOS:000438546400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000439761800003,
+Author = {Shabestary, Kiyan and Anfelt, Josefine and Ljungqvist, Emil and Jahn,
+ Michael and Yao, Lun and Hudson, Elton P.},
+Title = {Targeted Repression of Essential Genes To Arrest Growth and Increase
+ Carbon Partitioning and Biofuel Titers in Cyanobacteria},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2018},
+Volume = {7},
+Number = {7},
+Pages = {1669-1675},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1021/acssynbio.8b00056},
+ISSN = {2161-5063},
+Keywords = {dynamic metabolic engineering; cyanobacteria; growth-arrest; light
+ availability; CRISPRi},
+Keywords-Plus = {N-BUTANOL PRODUCTION; ESCHERICHIA-COLI; PHOTOSYNTHETIC PRODUCTIVITY;
+ SYNTHETIC BIOLOGY; PCC 6803; SYNECHOCYSTIS; METABOLISM; EXPRESSION;
+ PROTEIN; OPTIMALITY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Jahn, Michael/H-7676-2019
+ Yao, Lun/AAT-4288-2020
+ Shabestary, Kiyan/JCE-6866-2023
+ Hudson, Paul/ABH-8177-2020
+ },
+ORCID-Numbers = {Jahn, Michael/0000-0002-3913-153X
+ Shabestary, Kiyan/0000-0002-4207-0547
+ Hudson, Elton/0000-0003-1899-7649},
+Times-Cited = {53},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000439761800003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000436993200001,
+Author = {Li, Feiran and Xie, Wei and Yuan, Qianqian and Luo, Hao and Li, Peishun
+ and Chen, Tao and Zhao, Xueming and Wang, Zhiwen and Ma, Hongwu},
+Title = {Genome-scale metabolic model analysis indicates low energy production
+ efficiency in marine ammonia-oxidizing archaea},
+Journal = {AMB EXPRESS},
+Year = {2018},
+Volume = {8},
+Month = {JUN 27},
+Type = {Article},
+DOI = {10.1186/s13568-018-0635-y},
+Article-Number = {106},
+ISSN = {2191-0855},
+Keywords = {Genome-scale metabolic model; Ammonia-oxidizing archaea; Nitrosopumilus
+ maritimus SCM1; Ammonia oxidation pathway; Energy production efficiency},
+Keywords-Plus = {RECONSTRUCTION; OCEAN; PATHWAYS; THAUMARCHAEOTA; NITRIFICATION;
+ SULFOLOBUS; AUTOTROPHY; PHYSIOLOGY; COMMUNITY; OXIDATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {CHEN, Tao/N-1817-2015
+ Zhao, Xueming/W-4891-2019
+ Li, Feiran/GNP-2168-2022
+ wang, zhiwen/JDV-9990-2023
+ Ma, Hongwu/I-5263-2013},
+ORCID-Numbers = {CHEN, Tao/0000-0001-9588-1821
+ Li, Feiran/0000-0001-9155-5260
+ Li, Peishun/0000-0003-4200-0474
+ Ma, Hongwu/0000-0001-5325-2314},
+Times-Cited = {3},
+Journal-ISO = {AMB Express},
+Unique-ID = {WOS:000436993200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000436159000001,
+Author = {Rosario, Dorines and Benfeitas, Rui and Bidkhori, Gholamreza and Zhang,
+ Cheng and Uhlen, Mathias and Shoaie, Saeed and Mardinoglu, Adil},
+Title = {Understanding the Representative Gut Microbiota Dysbiosis in
+ Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic
+ Modeling},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2018},
+Volume = {9},
+Month = {JUN 25},
+Type = {Article},
+DOI = {10.3389/fphys.2018.00775},
+Article-Number = {775},
+ISSN = {1664-042X},
+Keywords = {gut microbiota; dysbiosis; host-microbiome interactions; genome-scale
+ metabolic models; systems biology},
+Keywords-Plus = {ESCHERICHIA-COLI; AKKERMANSIA-MUCINIPHILA; SYNTHETIC LETHALITY;
+ AROMATIC-COMPOUNDS; NETWORK; RECONSTRUCTION; GENERATION; METAGENOME;
+ REDUCTION; BACTERIA},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {Uhlen, Mathias/HPB-8445-2023
+ Mardinoglu, Adil/AAS-6360-2021
+ Uhlen, Mathias/AAV-8746-2021
+ Uhlen, Mathias/B-3262-2016
+ Benfeitas, Rui/G-1251-2016
+ Zhang, Cheng/L-7906-2016
+ },
+ORCID-Numbers = {Uhlen, Mathias/0000-0002-4858-8056
+ Uhlen, Mathias/0000-0002-4858-8056
+ Benfeitas, Rui/0000-0001-7972-0083
+ Zhang, Cheng/0000-0002-3721-8586
+ Shoaie, Saeed/0000-0001-5834-4533},
+Times-Cited = {49},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000436159000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000435400600001,
+Author = {Sinha, Neeraj and Suarez-Diez, Maria and Hooiveld, Guido J. E. J. and
+ Keijer, Jaap and dos Santos, Vitor Martin and van Schothorst, Evert M.},
+Title = {A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation
+ to Dietary Interventions of Lipid Type and Lipid Load},
+Journal = {FRONTIERS IN PHYSIOLOGY},
+Year = {2018},
+Volume = {9},
+Month = {JUN 15},
+Type = {Article},
+DOI = {10.3389/fphys.2018.00749},
+Article-Number = {749},
+ISSN = {1664-042X},
+Keywords = {enterocytes; mitochondria; constraint-based metabolic model;
+ mitochondrial dynamics; omega-3 lipids; high fat diet},
+Keywords-Plus = {METABOLISM; BIOENERGETICS; ORIGIN; RECONSTRUCTION; OXIDATION; OBESITY;
+ IMPACT},
+Research-Areas = {Physiology},
+Web-of-Science-Categories = {Physiology},
+ResearcherID-Numbers = {Diez, Maria Suarez/AAI-1354-2020
+ Hooiveld, Guido JEJ/F-4912-2010
+ },
+ORCID-Numbers = {Hooiveld, Guido JEJ/0000-0003-1954-3542
+ Sinha, Neeraj/0000-0001-5105-6475
+ Suarez-Diez, Maria/0000-0001-5845-146X
+ Sinha, Neeraj/0000-0002-0173-9849},
+Times-Cited = {3},
+Journal-ISO = {Front. Physiol.},
+Unique-ID = {WOS:000435400600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000436125900001,
+Author = {Valverde, Jose R. and Gullon, Sonia and Mellado, Rafael P.},
+Title = {Modelling the metabolism of protein secretion through the Tat route in
+ Streptomyces lividans},
+Journal = {BMC MICROBIOLOGY},
+Year = {2018},
+Volume = {18},
+Month = {JUN 14},
+Type = {Article},
+DOI = {10.1186/s12866-018-1199-3},
+Article-Number = {59},
+ISSN = {1471-2180},
+Keywords = {Biotechnology; Metabolic engineering; Genome-scale metabolic network;
+ FBA modelling; Streptomyces lividans; Tat-dependent protein secretion;
+ Sec-dependent protein secretion},
+Keywords-Plus = {COMPLETE GENOME SEQUENCE; ESCHERICHIA-COLI; COELICOLOR A3(2); FLUX
+ ANALYSIS; AMINO-ACID; SCALE; OVERPRODUCTION; AGARASE; HOST; GENE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Gullón, Sonia/P-7460-2018
+ Valverde, Jose R/K-8853-2014
+ Mellado, Rafael P/D-2680-2009},
+ORCID-Numbers = {Valverde, Jose R/0000-0002-6655-7114
+ },
+Times-Cited = {8},
+Journal-ISO = {BMC Microbiol.},
+Unique-ID = {WOS:000436125900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000434384900055,
+Author = {Metz, Zachary P. and Ding, Tong and Baumler, David J.},
+Title = {Using genome-scale metabolic models to compare serovars of the foodborne
+ pathogen Listeria monocytogenes},
+Journal = {PLOS ONE},
+Year = {2018},
+Volume = {13},
+Number = {6},
+Month = {JUN 7},
+Type = {Article},
+DOI = {10.1371/journal.pone.0198584},
+Article-Number = {e0198584},
+ISSN = {1932-6203},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; E.-COLI; RECONSTRUCTION;
+ STRAINS; NETWORK; EVOLUTION; OUTBREAK; SEQUENCE; LIFE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {5},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000434384900055},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000452889400001,
+Author = {Ghasemi-Kahrizsangi, Tahereh and Marashi, Sayed-Amir and Hosseini,
+ Zhaleh},
+Title = {Genome-Scale Metabolic Network Models of Bacillus Species Suggest that
+ Model Improvement is Necessary for Biotechnological Applications},
+Journal = {IRANIAN JOURNAL OF BIOTECHNOLOGY},
+Year = {2018},
+Volume = {16},
+Number = {3},
+Pages = {164-172},
+Month = {SUM},
+Type = {Article},
+DOI = {10.21859/ijb.1684},
+Article-Number = {e1684},
+ISSN = {1728-3043},
+Keywords = {Biochemical capability; Bacillus Species; Computational biotechnology;
+ Model validation; Systems biology},
+Keywords-Plus = {AMINO-ACIDS; RECONSTRUCTION; VALIDATION; CATABOLISM},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008},
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449},
+Times-Cited = {4},
+Journal-ISO = {Iran. J. Biotechnol.},
+Unique-ID = {WOS:000452889400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000435746400012,
+Author = {He, Hai and Edlich-Muth, Christian and Lindner, Steffen N. and Bar-Even,
+ Arren},
+Title = {Ribulose Monophosphate Shunt Provides Nearly All Biomass and Energy
+ Required for Growth of E. coli},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2018},
+Volume = {7},
+Number = {6},
+Pages = {1601-1611},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1021/acssynbio.8b00093},
+ISSN = {2161-5063},
+Keywords = {ribulose monophosphate cycle; formaldehyde assimilation; methylotrophy;
+ metabolic engineering; growth selection; carbon labeling; flux modeling},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; CORYNEBACTERIUM-GLUTAMICUM; ESCHERICHIA-COLI;
+ QUANTITATIVE PREDICTION; SYNTHETIC METHYLOTROPHY; CELLULAR-METABOLISM;
+ METHANOL; FORMALDEHYDE; DEHYDROGENASE; EVOLUTION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Lindner, Steffen/ABF-4407-2020
+ He, Hai/G-6606-2013
+ },
+ORCID-Numbers = {Lindner, Steffen/0000-0003-3226-3043
+ He, Hai/0000-0003-1223-2813
+ Bar-Even, Arren/0000-0002-1039-4328},
+Times-Cited = {34},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000435746400012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000431504800010,
+Author = {Rodenburg, Sander Y. A. and Seidl, Michael F. and De Ridder, Dick and
+ Govers, Francine},
+Title = {Genome-wide characterization of Phytophthora infestans
+ metabolism: a systems biology approach},
+Journal = {MOLECULAR PLANT PATHOLOGY},
+Year = {2018},
+Volume = {19},
+Number = {6},
+Pages = {1403-1413},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1111/mpp.12623},
+ISSN = {1464-6722},
+EISSN = {1364-3703},
+Keywords = {metabolic model; metabolism; oomycete; Phytophthora infestans; systems
+ biology},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FATTY-ACID SYNTHESIS; APPRESSORIUM FORMATION;
+ DRUG TARGETS; NETWORK; IDENTIFICATION; MITOCHONDRIAL; BIOSYNTHESIS;
+ PREDICTION; SEQUENCE},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Govers, Francine/A-5616-2009
+ Seidl, Michael F./ABD-6042-2021
+ de Ridder, Dick/F-3169-2010
+ },
+ORCID-Numbers = {Govers, Francine/0000-0001-5311-929X
+ de Ridder, Dick/0000-0002-4944-4310
+ Seidl, Michael F/0000-0002-5218-2083},
+Times-Cited = {21},
+Journal-ISO = {Mol. Plant Pathol.},
+Unique-ID = {WOS:000431504800010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000430663000015,
+Author = {Tokuyama, Kento and Toya, Yoshihiro and Horinouchi, Takaaki and
+ Furusawa, Chikara and Matsuda, Fumio and Shimizu, Hiroshi},
+Title = {Application of adaptive laboratory evolution to overcome a flux
+ limitation in an Escherichia coli production strain},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2018},
+Volume = {115},
+Number = {6},
+Pages = {1542-1551},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/bit.26568},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {adaptive laboratory evolution; Escherichia coli; flux balance analysis;
+ phosphoenolpyruvate carboxylase; succinate production},
+Keywords-Plus = {PHOSPHOENOLPYRUVATE CARBOXYLASE; KNOCKOUT STRATEGIES; METABOLIC NETWORK;
+ BALANCE MODELS; IDENTIFICATION; BIOSYNTHESIS; INHIBITION; TARGETS;
+ DESIGN; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Horinouchi, Takaaki/ADR-3136-2022
+ Shimizu, Hiroshi/C-3688-2017
+ Horinouchi, Takaaki/AAV-9780-2020
+ Furusawa, Chikara/ABB-6516-2021
+ },
+ORCID-Numbers = {Horinouchi, Takaaki/0000-0001-9141-9103
+ Shimizu, Hiroshi/0000-0002-8986-0861
+ Furusawa, Chikara/0000-0003-3554-4975
+ Tokuyama, Kento/0009-0009-3553-644X
+ Toya, Yoshihiro/0000-0001-9670-6961},
+Times-Cited = {21},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000430663000015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000432531400026,
+Author = {Scheunemann, Michael and Brady, Siobhan M. and Nikoloski, Zoran},
+Title = {Integration of large-scale data for extraction of integrated
+ Arabidopsis root cell-type specific models},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2018},
+Volume = {8},
+Month = {MAY 21},
+Type = {Article},
+DOI = {10.1038/s41598-018-26232-8},
+Article-Number = {7919},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; METABOLIC MODEL; EXPRESSION MAP; PROTEIN;
+ PREDICTION; FRAMEWORK},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Brady, Siobhan/AAY-1729-2021
+ },
+ORCID-Numbers = {Brady, Siobhan/0000-0001-9424-8055},
+Times-Cited = {21},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000432531400026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000432569100001,
+Author = {Elchuri, Sailaja V. and Rajasekaran, Swetha and Miles, Wayne O.},
+Title = {RNA-Sequencing of Primary Retinoblastoma Tumors Provides New Insights
+ and Challenges Into Tumor Development},
+Journal = {FRONTIERS IN GENETICS},
+Year = {2018},
+Volume = {9},
+Month = {MAY 17},
+Type = {Article},
+DOI = {10.3389/fgene.2018.00170},
+Article-Number = {170},
+ISSN = {1664-8021},
+Keywords = {Retinoblastoma; RNA-sequencing; non-coding RNA (LINC-RNA); tumor; RB1;
+ metabolic profiling},
+Keywords-Plus = {HUMAN METABOLIC NETWORK; CONSTRAINT-BASED MODELS; GENE-EXPRESSION; HUMAN
+ RETINA; CELL; CANCER; PROGRESSION; PRB; PHOSPHORYLATION; E2F},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Rajasekaran, Swetha/HPD-6970-2023
+ },
+ORCID-Numbers = {Rajasekaran, Swetha/0000-0002-1271-6204
+ Miles, Wayne/0000-0002-2054-5206},
+Times-Cited = {7},
+Journal-ISO = {Front. Genet.},
+Unique-ID = {WOS:000432569100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000434012100025,
+Author = {Aite, Meaziane and Chevallier, Marie and Frioux, Cleamence and Trottier,
+ Camille and Got, Jeanne and Paz Cortes, Maria and Mendoza, Sebastian N.
+ and Carrier, Gregory and Dameron, Olivier and Guillaudeux, Nicolas and
+ Latorre, Mauricio and Loira, Nicolas and Markov, Gabriel V. and Maass,
+ Alejandro and Siegel, Anne},
+Title = {Traceability, reproducibility and wiki-exploration for ``a-la-carte{''}
+ reconstructions of genome-scale metabolic models},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2018},
+Volume = {14},
+Number = {5},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1006146},
+Article-Number = {e1006146},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; NETWORK; GENERATION; RESOURCE; BIOLOGY; IMPACT},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Frioux, Clémence/A-1517-2019
+ Maass, Alejandro E/D-5848-2012
+ },
+ORCID-Numbers = {Frioux, Clémence/0000-0003-2114-0697
+ Maass, Alejandro E/0000-0002-7038-4527
+ Siegel, Anne/0000-0001-6542-1568
+ Guillaudeux, Nicolas/0000-0002-4381-2960
+ Dameron, Olivier/0000-0001-8959-7189
+ Mendoza, Sebastian/0000-0002-2192-5569
+ Markov, Gabriel V./0000-0002-8566-7482
+ carrier, gregory/0000-0001-6859-5707},
+Times-Cited = {45},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000434012100025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000431509200027,
+Author = {King, Brendan and Farrah, Terry and Richards, Matthew A. and Mundy,
+ Michael and Simeonidis, Evangelos and Price, Nathan D.},
+Title = {ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of
+ metabolic reconstructions},
+Journal = {BIOINFORMATICS},
+Year = {2018},
+Volume = {34},
+Number = {9},
+Pages = {1594-1596},
+Month = {MAY 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btx796},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {GENOMES; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Mundy, Michael/0000-0002-9936-0406
+ Price, Nathan/0000-0002-4157-0267},
+Times-Cited = {4},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000431509200027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000431113100009,
+Author = {McGarrity, Sarah and Anuforo, Osk and Halldorsson, Haraldur and
+ Bergmann, Andreas and Halldorsson, Skarpheoinn and Palsson, Sirus and
+ Henriksen, Hanne H. and Johansson, Par Ingemar and Rolfsson, Ottar},
+Title = {Metabolic systems analysis of LPS induced endothelial dysfunction
+ applied to sepsis patient stratification},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2018},
+Volume = {8},
+Month = {MAY 1},
+Type = {Article},
+DOI = {10.1038/s41598-018-25015-5},
+Article-Number = {6811},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ORGAN FAILURE; GLOBAL RECONSTRUCTION;
+ SPHINGOSINE-1-PHOSPHATE; PLASMA; ACID; DEFINITIONS; CELLS;
+ IDENTIFICATION; INFLAMMATION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Johansson, Pär/GQB-1032-2022
+ },
+ORCID-Numbers = {Johansson, Pär/0000-0001-9778-5964
+ Hee Henriksen, Hanne/0000-0003-1323-9718
+ McGarrity, Sarah/0000-0002-2878-6194
+ Rolfsson, Ottar/0000-0003-4258-6057},
+Times-Cited = {24},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000431113100009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000429800600013,
+Author = {Ramirez-Malule, Howard and Junne, Stefan and Nicolas Cruz-Bournazou,
+ Mariano and Neubauer, Peter and Rios-Estepa, Rigoberto},
+Title = {Streptomyces clavuligerus shows a strong association between TCA
+ cycle intermediate accumulation and clavulanic acid biosynthesis},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2018},
+Volume = {102},
+Number = {9},
+Pages = {4009-4023},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1007/s00253-018-8841-8},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Clavulanic acid; Streptomyces clavuligerus; Continuous cultivation; TCA
+ cycle intermediate accumulation; Flux balance analysis},
+Keywords-Plus = {METABOLIC FLUX ANALYSIS; CLAVAMINATE SYNTHASE 2; NONHEME IRON ENZYME;
+ FED-BATCH; PHOSPHOENOLPYRUVATE CARBOXYLASE; SECONDARY METABOLITES;
+ SCALE-DOWN; CLONING; GENES; MORPHOLOGY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Cruz Bournazou, Mariano Nicolas/N-1068-2018
+ Neubauer, Peter/N-8146-2013
+ Bournazou, Mariano Nicolas Cruz/ABD-7679-2020
+ Ramirez-Malule, Howard/AAB-8214-2020
+ Junne, Stefan/M-7677-2019
+ Neubauer, Peter/W-4518-2019
+ },
+ORCID-Numbers = {Cruz Bournazou, Mariano Nicolas/0000-0001-9461-4414
+ Neubauer, Peter/0000-0002-1214-9713
+ Bournazou, Mariano Nicolas Cruz/0000-0001-9461-4414
+ Ramirez-Malule, Howard/0000-0003-1013-5809
+ Junne, Stefan/0000-0001-6185-2627
+ Rios-Estepa, Rigoberto/0000-0002-3287-7056},
+Times-Cited = {20},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000429800600013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000433423600004,
+Author = {Schwentner, Andreas and Feith, Andre and Muench, Eugenia and Busche,
+ Tobias and Rueckert, Christian and Kalinowski, Joern and Takors, Ralf
+ and Blombach, Bastian},
+Title = {Metabolic engineering to guide evolution - Creating a novel mode for
+ L-valine production with Corynebacterium glutamicum},
+Journal = {METABOLIC ENGINEERING},
+Year = {2018},
+Volume = {47},
+Pages = {31-41},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2018.02.015},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Directed evolution; Metabolic engineering; Isocitrate dehydrogenase;
+ Glyoxylate shunt; L-valine production; Corynebacterium glutamicum},
+Keywords-Plus = {PHOSPHOENOLPYRUVATE CARBOXYKINASE GENE; CONSTRAINT-BASED MODELS;
+ ESCHERICHIA-COLI; DIRECTED EVOLUTION; ACETATE METABOLISM;
+ SEQUENCE-ANALYSIS; BIOCHEMICAL-CHARACTERIZATION; TRANSCRIPTIONAL
+ REGULATOR; QUANTITATIVE PREDICTION; PYRUVATE-CARBOXYLASE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Ruckert-Reed, Christian/0000-0002-9722-4435
+ Takors, Ralf/0000-0001-5837-6906
+ Blombach, Bastian/0000-0002-2996-2049
+ Feith, Andre/0000-0001-5934-3073},
+Times-Cited = {30},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000433423600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000430299200008,
+Author = {Toro, Leon and Pinilla, Laura and Avignone-Rossa, Claudio and
+ Rios-Estepa, Rigoberto},
+Title = {An enhanced genome-scale metabolic reconstruction of Streptomyces
+ clavuligerus identifies novel strain improvement strategies},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2018},
+Volume = {41},
+Number = {5},
+Pages = {657-669},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1007/s00449-018-1900-9},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {Genome-scale metabolic reconstruction; Flux balance analysis;
+ Streptomyces clavuligerus; Strain improvement; Clavulanic acid},
+Keywords-Plus = {CLAVULANIC ACID BIOSYNTHESIS; FLUX BALANCE ANALYSIS; CEPHALOSPORIN
+ PRODUCTION; ESCHERICHIA-COLI; GENES; COELICOLOR; MANIPULATION;
+ CEPHAMYCIN; MODELS; CLAVAM},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Toro, Leon/V-8779-2019
+ },
+ORCID-Numbers = {Pinilla-Mendoza, Laura/0000-0002-8753-0017
+ Rios-Estepa, Rigoberto/0000-0002-3287-7056
+ Toro-Navarro, Leon/0000-0002-3074-396X},
+Times-Cited = {19},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000430299200008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000431621000012,
+Author = {Troendle, Julia and Albermann, Christoph and Weiner, Michael and
+ Sprenger, Georg A. and Weuster-Botz, Dirk},
+Title = {Phosphoenolpyruvate Transporter Enables Targeted Perturbation During
+ Metabolic Analysis of L-Phenylalanine Production With Escherichia
+ coli},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2018},
+Volume = {13},
+Number = {5, SI},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1002/biot.201700611},
+Article-Number = {1700611},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Escherichia coli; L-phenylalanine; metabolic analysis;
+ phosphoenolpyruvate; transporter},
+Keywords-Plus = {FED-BATCH CULTURE; IN-VIVO KINETICS; SUGAR-PHOSPHATE CARRIER; AMINO-ACID
+ PATHWAY; SACCHAROMYCES-CEREVISIAE; STEADY-STATE; GROWTH-RATE; SUBSTRATE
+ SELECTIVITY; BIOMASS CONCENTRATION; LABELING EXPERIMENTS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Sprenger, Georg A./E-2384-2011
+ },
+ORCID-Numbers = {Sprenger, Georg A./0000-0002-7879-8978
+ Weuster-Botz, Dirk/0000-0002-1171-4194},
+Times-Cited = {6},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000431621000012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000432012200003,
+Author = {Zou, Wei and Ye, Guangbin and Zhang, Kaizheng},
+Title = {Diversity, Function, and Application of Clostridium in Chinese
+ Strong Flavor Baijiu Ecosystem: A Review},
+Journal = {JOURNAL OF FOOD SCIENCE},
+Year = {2018},
+Volume = {83},
+Number = {5},
+Pages = {1193-1199},
+Month = {MAY},
+Type = {Review},
+DOI = {10.1111/1750-3841.14134},
+ISSN = {0022-1147},
+EISSN = {1750-3841},
+Keywords = {baijiu; caproic acid; Clostridium; systems biology},
+Keywords-Plus = {INTERPHASE MICROBIAL COMMUNITY; FERMENTATION PIT MUDS; COMBINED
+ PCR-DGGE; LIQUOR FERMENTATION; SP-NOV.; ARCHAEAL COMMUNITY; CAPROIC
+ ACID; PROKARYOTIC COMMUNITIES; BACTERIAL COMMUNITY; GENOME},
+Research-Areas = {Food Science \& Technology},
+Web-of-Science-Categories = {Food Science \& Technology},
+ResearcherID-Numbers = {Zhang, kaizheng/HKD-9015-2023
+ },
+ORCID-Numbers = {Zou, Wei/0000-0002-6335-8785},
+Times-Cited = {65},
+Journal-ISO = {J. Food Sci.},
+Unique-ID = {WOS:000432012200003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000430638900027,
+Author = {Armingol, Erick and Tobar, Eduardo and Cabrera, Ricardo},
+Title = {Understanding the impact of the cofactor swapping of isocitrate
+ dehydrogenase over the growth phenotype of Escherichia coli on
+ acetate by using constraint-based modeling},
+Journal = {PLOS ONE},
+Year = {2018},
+Volume = {13},
+Number = {4},
+Month = {APR 20},
+Type = {Article},
+DOI = {10.1371/journal.pone.0196182},
+Article-Number = {e0196182},
+ISSN = {1932-6203},
+Keywords-Plus = {TRICARBOXYLIC-ACID CYCLE; FLUX ANALYSIS; BRANCH POINT; METABOLIC
+ PATHWAYS; GLYOXYLATE BYPASS; ENZYME; STATE; PHOSPHORYLATION; EVOLUTION;
+ BACTERIA},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Armingol, Erick/AGI-8012-2022
+ Cabrera, Ricardo M/H-8132-2014
+ },
+ORCID-Numbers = {Armingol, Erick/0000-0002-1546-9165
+ Tobar-Calfucoy, Eduardo/0000-0002-4686-8468
+ Cabrera, Ricardo/0000-0002-8896-3172},
+Times-Cited = {8},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000430638900027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000430245100002,
+Author = {Jose, Nicholas A. and Lau, Rebecca and Swenson, Tami L. and Klitgord,
+ Niels and Garcia-Pichel, Ferran and Bowen, Benjamin P. and Baran,
+ Richard and Northen, Trent R.},
+Title = {Flux balance modeling to predict bacterial survival during
+ pulsed-activity events},
+Journal = {BIOGEOSCIENCES},
+Year = {2018},
+Volume = {15},
+Number = {7},
+Pages = {2219-2229},
+Month = {APR 16},
+Type = {Article},
+DOI = {10.5194/bg-15-2219-2018},
+ISSN = {1726-4170},
+EISSN = {1726-4189},
+Keywords-Plus = {BIOLOGICAL SOIL CRUSTS; PRECIPITATION; TEMPERATURE; GLYCOGEN; CARBON},
+Research-Areas = {Environmental Sciences \& Ecology; Geology},
+Web-of-Science-Categories = {Ecology; Geosciences, Multidisciplinary},
+ResearcherID-Numbers = {Northen, Trent R/K-3139-2012
+ },
+ORCID-Numbers = {Lau, Rebecca K./0000-0002-4182-4394},
+Times-Cited = {6},
+Journal-ISO = {Biogeosciences},
+Unique-ID = {WOS:000430245100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000429009500020,
+Author = {Kim, Donghyuk and Seo, Sang Woo and Gao, Ye and Nam, Hojung and Guzman,
+ Gabriela I. and Cho, Byung-Kwan and Palsson, Bernhard O.},
+Title = {Systems assessment of transcriptional regulation on central carbon
+ metabolism by Cra and CRP},
+Journal = {NUCLEIC ACIDS RESEARCH},
+Year = {2018},
+Volume = {46},
+Number = {6},
+Pages = {2901-2917},
+Month = {APR 6},
+Type = {Article},
+DOI = {10.1093/nar/gky069},
+ISSN = {0305-1048},
+EISSN = {1362-4962},
+Keywords-Plus = {ESCHERICHIA-COLI; IN-VITRO; RECEPTOR PROTEIN; BINDING; OPERON; CAMP;
+ FRUR; ACTIVATION; MECHANISMS; REPRESSION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Kim, Donghyuk/AAS-9141-2020
+ Cho, Byung-Kwan/C-1830-2011
+ Gao, Ye/AAV-8396-2020
+ Nam, Hojung/AAR-4065-2020
+ },
+ORCID-Numbers = {Gao, Ye/0000-0001-8519-1392
+ Nam, Hojung/0000-0002-5109-9114
+ Seo, Sang Woo/0000-0002-7434-7053},
+Times-Cited = {45},
+Journal-ISO = {Nucleic Acids Res.},
+Unique-ID = {WOS:000429009500020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000429433500001,
+Author = {Feng, Jun and Yang, Jing and Yang, Wenwen and Chen, Jie and Jiang, Min
+ and Zou, Xiang},
+Title = {Metabolome- and genome-scale model analyses for engineering of
+ Aureobasidium pullulans to enhance polymalic acid and malic acid
+ production from sugarcane molasses},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2018},
+Volume = {11},
+Month = {APR 4},
+Type = {Article},
+DOI = {10.1186/s13068-018-1099-7},
+Article-Number = {94},
+EISSN = {1754-6834},
+Keywords = {Aureobasidium pullulans; Metabolic engineering; Polymalic acid; Pyruvate
+ carboxylase; Sugarcane molasses},
+Keywords-Plus = {PYRUVATE-CARBOXYLASE; ORGANIC-ACIDS; SUCCINIC ACID; BIOSYNTHESIS;
+ FERMENTATION; HYDROLYSATE; PREDICTION; GLYOXYLATE; TREHALOSE; KINETICS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Yang, Jing/HZJ-3722-2023
+ },
+ORCID-Numbers = {, xiang/0000-0002-5875-1224},
+Times-Cited = {29},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000429433500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000431115700056,
+Author = {Dicenzo, George C. and Benedict, Alex B. and Fondi, Marco and Walker,
+ Graham C. and Finan, Turlough M. and Mengoni, Alessio and Griffitts,
+ Joel S.},
+Title = {Robustness encoded across essential and accessory replicons of the
+ ecologically versatile bacterium Sinorhizobium meliloti},
+Journal = {PLOS GENETICS},
+Year = {2018},
+Volume = {14},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1371/journal.pgen.1007357},
+ISSN = {1553-7404},
+Keywords-Plus = {GENOME-SCALE MODELS; RHIZOBIUM-MELILOTI; METABOLIC NETWORK; ESSENTIAL
+ GENES; MINIMAL CELL; REVEALS; MEGAPLASMID; EVOLUTION; RECONSTRUCTION;
+ IDENTIFICATION},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {diCenzo, George C C/M-1876-2017
+ Mengoni, Alessio/G-5336-2013
+ },
+ORCID-Numbers = {diCenzo, George C C/0000-0003-3889-6570
+ Mengoni, Alessio/0000-0002-1265-8251
+ Fondi, Marco/0000-0001-9291-5467
+ Benedict, Alex/0000-0002-4801-2989},
+Times-Cited = {38},
+Journal-ISO = {PLoS Genet.},
+Unique-ID = {WOS:000431115700056},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000428391900009,
+Author = {Flowers, Jason J. and Richards, Matthew A. and Baliga, Nitin and Meyer,
+ Birte and Stahl, David A.},
+Title = {Constraint-based modelling captures the metabolic versatility of
+ Desulfovibrio vulgaris},
+Journal = {ENVIRONMENTAL MICROBIOLOGY REPORTS},
+Year = {2018},
+Volume = {10},
+Number = {2},
+Pages = {190-201},
+Month = {APR},
+Type = {Article},
+DOI = {10.1111/1758-2229.12619},
+ISSN = {1758-2229},
+Keywords-Plus = {ELECTRON-TRANSFER SYSTEM; SULFATE REDUCTION; ENERGY; HILDENBOROUGH;
+ PROTEINS; BACTERIA; GROWTH},
+Research-Areas = {Environmental Sciences \& Ecology; Microbiology},
+Web-of-Science-Categories = {Environmental Sciences; Microbiology},
+ORCID-Numbers = {baliga, nitin/0000-0001-9157-5974
+ , ENIGMA/0000-0002-0894-2831},
+Times-Cited = {7},
+Journal-ISO = {Environ. Microbiol. Rep.},
+Unique-ID = {WOS:000428391900009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000428316700001,
+Author = {Xu, Nan and Ye, Chao and Liu, Liming},
+Title = {Genome-scale biological models for industrial microbial systems},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2018},
+Volume = {102},
+Number = {8},
+Pages = {3439-3451},
+Month = {APR},
+Type = {Review},
+DOI = {10.1007/s00253-018-8803-1},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Genome-scale modeling; Systematic metabolic engineering; Cell growth;
+ Microbial biosynthesis},
+Keywords-Plus = {TRANSCRIPTIONAL REGULATORY NETWORKS; PROTEIN-PROTEIN INTERACTIONS;
+ ESCHERICHIA-COLI; METABOLIC NETWORK; GENE-REGULATION; RECONSTRUCTION;
+ GENERATION; EVOLUTION; DESIGN; CELL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Ye, Chao/M-3689-2019
+ Liu, Liming/B-1972-2009
+ Ye, Chao/HGD-3564-2022
+ Ye, Chao/H-7623-2014
+ },
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Liu, Liming/0000-0003-3022-936X
+ Ye, Chao/0000-0002-6671-7819
+ Ye, Chao/0000-0002-6671-7819
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {12},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000428316700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000428972200019,
+Author = {Casini, Arturo and Chang, Fang-Yuan and Eluere, Raissa and King, Andrew
+ M. and Young, Eric M. and Dudley, Quentin M. and Karim, Ashty and Pratt,
+ Katelin and Bristol, Cassandra and Forget, Anthony and Ghodasara, Amar
+ and Warden-Rothman, Robert and Gan, Rui and Cristofaro, Alexander and
+ Borujeni, Amin Espah and Ryu, Min-Hyung and Li, Jian and Kwon, Yong-Chan
+ and Wang, He and Tatsis, Evangelos and Rodriguez-Lopez, Carlos and
+ O'Connor, Sarah and Medema, Marnix H. and Fischbach, Michael A. and
+ Jewett, Michael C. and Voigt, Christopher and Gordon, D. Benjamin},
+Title = {A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of
+ Methods to Engineer Biology},
+Journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY},
+Year = {2018},
+Volume = {140},
+Number = {12},
+Pages = {4302-4316},
+Month = {MAR 28},
+Type = {Article},
+DOI = {10.1021/jacs.7b13292},
+ISSN = {0002-7863},
+Keywords-Plus = {BIOSYNTHETIC GENE-CLUSTER; ESCHERICHIA-COLI; HETEROLOGOUS EXPRESSION;
+ NATURAL-PRODUCTS; SACCHAROMYCES-CEREVISIAE; PHENAZINE PRODUCTION;
+ SYNTHETIC BIOLOGY; DESIGN; DISCOVERY; OPTIMIZATION},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary},
+ResearcherID-Numbers = {O'Connor, Sarah Ellen/X-2893-2019
+ Rodriguez-Lopez, Carlos E/HGC-0178-2022
+ Li, Jian/J-3997-2016
+ Kwon, Yongchan/IUQ-7799-2023
+ Medema, Marnix H./AAR-3138-2021
+ Tatsis, Evangelos/AAI-4026-2020
+ Jewett, Michael C/E-3506-2010
+ Young, Eric M./AAF-6846-2020
+ },
+ORCID-Numbers = {O'Connor, Sarah Ellen/0000-0003-0356-6213
+ Rodriguez-Lopez, Carlos E/0000-0001-9224-0455
+ Li, Jian/0000-0003-2359-238X
+ Medema, Marnix H./0000-0002-2191-2821
+ Tatsis, Evangelos/0000-0002-4013-1537
+ Young, Eric M./0000-0001-5276-2873
+ Karim, Ashty/0000-0002-5789-7715
+ Jewett, Michael/0000-0003-2948-6211
+ Casini, Arturo/0000-0003-2828-5223
+ Cristofaro, Alexander/0000-0001-7905-9264
+ Fischbach, Michael/0000-0003-3079-8247
+ Chang, Fang-Yuan/0000-0001-5819-6454},
+Times-Cited = {92},
+Journal-ISO = {J. Am. Chem. Soc.},
+Unique-ID = {WOS:000428972200019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000427946100002,
+Author = {Mishra, Pranjul and Lee, Na-Rae and Lakshmanan, Meiyappan and Kim,
+ Minsuk and Kim, Byung-Gee and Lee, Dong-Yup},
+Title = {Genome-scale model-driven strain design for dicarboxylic acid production
+ in Yarrowia lipolytica},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2018},
+Volume = {12},
+Number = {2},
+Month = {MAR 19},
+Note = {28th International Conference on Genome Informatics - Systems Biology,
+ Seoul, SOUTH KOREA, OCT 31-NOV 03, 2017},
+Type = {Article; Proceedings Paper},
+DOI = {10.1186/s12918-018-0542-5},
+Article-Number = {12},
+ISSN = {1752-0509},
+Keywords = {Yarrowia lipolytica; Dicarboxylic acid; Genome-scale metabolic models;
+ Strain design; Metabolic engineering},
+Keywords-Plus = {FATTY-ACIDS; LIPID-ACCUMULATION; ESCHERICHIA-COLI;
+ SACCHAROMYCES-CEREVISIAE; OLEAGINOUS YEAST; MALIC ENZYME; NADPH; GENE;
+ METABOLISM; MUTANTS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/AAM-1171-2020
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ },
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Kim, Minsuk/0000-0001-9958-0380},
+Times-Cited = {40},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000427946100002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000433062600001,
+Author = {Zhu, Yan and Czauderna, Tobias and Zhao, Jinxin and Klapperstueck,
+ Matthias and Maifiah, Mohd Hafidz Mahamad and Han, Mei-Ling and Lu, Jing
+ and Sommer, Bjoern and Velkov, Tony and Lithgow, Trevor and Song,
+ Jiangning and Schreiber, Falk and Li, Jian},
+Title = {Genome-scale metabolic modeling of responses to polymyxins in
+ Pseudomonas aeruginosa},
+Journal = {GIGASCIENCE},
+Year = {2018},
+Volume = {7},
+Number = {4},
+Month = {MAR 13},
+Type = {Article},
+DOI = {10.1093/gigascience/giy021},
+ISSN = {2047-217X},
+Keywords = {genome-scale metabolic model; Pseudomonas aeruginosa; polymyxin; lipid A
+ modification; outer membrane},
+Keywords-Plus = {2-COMPONENT REGULATORY SYSTEMS; TRANSPOSON MUTANT LIBRARY;
+ CONSTRAINT-BASED MODELS; ADAPTIVE RESISTANCE; NETWORK ANALYSIS;
+ OUTER-MEMBRANE; AMINO-ACIDS; DATABASE; COLISTIN; BACTERIAL},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Science \& Technology -
+ Other Topics},
+Web-of-Science-Categories = {Biology; Multidisciplinary Sciences},
+ResearcherID-Numbers = {Lithgow, Trevor J/H-5925-2017
+ Zhu, Yan/HLW-8686-2023
+ Song, Jiangning/F-9787-2010
+ Bin Mahamad Maifiah, Mohd Hafidz/AAS-5609-2020
+ Zhao, Jinxin/N-7963-2019
+ Lu, Jing/AAB-8426-2020
+ Li, Jian/I-5538-2016
+ },
+ORCID-Numbers = {Lithgow, Trevor J/0000-0002-0102-7884
+ Zhu, Yan/0000-0001-7342-3782
+ Song, Jiangning/0000-0001-8031-9086
+ Bin Mahamad Maifiah, Mohd Hafidz/0000-0002-3165-0343
+ Lu, Jing/0000-0002-5834-7942
+ Zhao, Jinxin/0000-0002-0604-3541
+ Li, Jian/0000-0001-7953-8230
+ Sommer, Bjorn/0000-0003-1514-9898
+ velkov, tony/0000-0002-0017-7952
+ Czauderna, Tobias/0000-0002-1788-9593},
+Times-Cited = {36},
+Journal-ISO = {GigaScience},
+Unique-ID = {WOS:000433062600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000442625700004,
+Author = {Cuperlovic-Culf, Miroslava},
+Title = {Machine Learning Methods for Analysis of Metabolic Data and Metabolic
+ Pathway Modeling},
+Journal = {METABOLITES},
+Year = {2018},
+Volume = {8},
+Number = {1},
+Month = {MAR},
+Type = {Review},
+DOI = {10.3390/metabo8010004},
+Article-Number = {4},
+EISSN = {2218-1989},
+Keywords = {system biology; metabolomics; metabolism modeling; machine learning;
+ genomics},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; SYSTEMS BIOLOGY; MULTIVARIATE-ANALYSIS;
+ KINETIC-MODELS; PREDICTION; SELECTION; TOOLBOX; IDENTIFICATION;
+ INHIBITION; DISCOVERY},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Cuperlovic-Culf, Miroslava/C-7876-2016},
+ORCID-Numbers = {Cuperlovic-Culf, Miroslava/0000-0002-9483-8159},
+Times-Cited = {88},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000442625700004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000430490800013,
+Author = {Kelly, William and Veigne, Sorelle and Li, Xianhua and Subramanian,
+ Shyam Sundar and Huang, Zuyi and Schaefer, Eugene},
+Title = {Optimizing Performance of Semi-Continuous Cell Culture in an ambr15™
+ Microbioreactor Using Dynamic Flux Balance Modeling},
+Journal = {BIOTECHNOLOGY PROGRESS},
+Year = {2018},
+Volume = {34},
+Number = {2},
+Pages = {420-431},
+Month = {MAR-APR},
+Type = {Article},
+DOI = {10.1002/btpr.2585},
+ISSN = {8756-7938},
+EISSN = {1520-6033},
+Keywords = {microbioreactor; dynamic flux balance model; semi-continuous cell
+ culture; dissolved CO2; lactate metabolism},
+Keywords-Plus = {ESCHERICHIA-COLI; METABOLISM; PLATFORM; SCALE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ORCID-Numbers = {Schaefer, Gene/0000-0002-2937-8870},
+Times-Cited = {9},
+Journal-ISO = {Biotechnol. Prog.},
+Unique-ID = {WOS:000430490800013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000432198800008,
+Author = {Mienda, Bashir Sajo and Salihu, Rabiu and Adamu, Aliyu and Idris, Shehu},
+Title = {Genome-scale metabolic models as platforms for identification of novel
+ genes as antimicrobial drug targets},
+Journal = {FUTURE MICROBIOLOGY},
+Year = {2018},
+Volume = {13},
+Number = {4},
+Pages = {455-467},
+Month = {MAR},
+Type = {Review},
+DOI = {10.2217/fmb-2017-0195},
+ISSN = {1746-0913},
+EISSN = {1746-0921},
+Keywords = {antimicrobial drug targets; essential genes; genome-scale metabolic
+ models (GEMs); identification of novel genes},
+Keywords-Plus = {BRANCHED-CHAIN AMINOTRANSFERASE; CONSTRAINT-BASED MODELS; FLUX BALANCE
+ ANALYSIS; MYCOBACTERIUM-TUBERCULOSIS; STAPHYLOCOCCUS-AUREUS;
+ ESCHERICHIA-COLI; PSEUDOMONAS-AERUGINOSA; DRIVEN DISCOVERY; RESISTANCE;
+ RECONSTRUCTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Adamu, Aliyu/H-2381-2018
+ Salihu, Rabiu/M-5186-2019
+ Mienda, Bashir Sajo/N-8908-2017
+ Adamu, Aliyu/K-3941-2019
+ Idris, Shehu/ACQ-5580-2022},
+ORCID-Numbers = {Adamu, Aliyu/0000-0003-1206-9067
+ Salihu, Rabiu/0000-0003-1583-9346
+ Mienda, Bashir Sajo/0000-0002-7205-2753
+ Adamu, Aliyu/0000-0003-1206-9067
+ Idris, Shehu/0000-0003-3912-7837},
+Times-Cited = {16},
+Journal-ISO = {Future Microbiol.},
+Unique-ID = {WOS:000432198800008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000426693800007,
+Author = {Pearl, John E. and Das, Mrinal and Cooper, Andrea M.},
+Title = {Immunological roulette: Luck or something more? Considering the
+ connections between host and environment in TB},
+Journal = {CELLULAR \& MOLECULAR IMMUNOLOGY},
+Year = {2018},
+Volume = {15},
+Number = {3, SI},
+Pages = {226-232},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1038/cmi.2017.145},
+ISSN = {1672-7681},
+EISSN = {2042-0226},
+Keywords = {gut-liver-lung axis; microbiome; tuberculosis},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; MYCOBACTERIUM-TUBERCULOSIS; GUT MICROBIOTA;
+ PULMONARY TUBERCULOSIS; PPAR-GAMMA; BETA(2)-ADRENERGIC RECEPTOR;
+ QUANTITATIVE PREDICTION; CONVERGING EPIDEMICS; CELLULAR-METABOLISM;
+ DIRECTED THERAPIES},
+Research-Areas = {Immunology},
+Web-of-Science-Categories = {Immunology},
+ORCID-Numbers = {Pearl, John/0000-0001-7496-6367
+ Cooper, Andrea/0000-0001-6050-3863},
+Times-Cited = {3},
+Journal-ISO = {Cell. Mol. Immunol.},
+Unique-ID = {WOS:000426693800007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000426363200006,
+Author = {Tajparast, Mohammad and Frigon, Dominic},
+Title = {Predicting the accumulation of storage compounds by Rhodococcus
+ jostii RHA1 in the feast-famine growth cycles using genome-scale
+ flux balance analysis},
+Journal = {PLOS ONE},
+Year = {2018},
+Volume = {13},
+Number = {3},
+Month = {MAR 1},
+Type = {Article},
+DOI = {10.1371/journal.pone.0191835},
+Article-Number = {e0191835},
+ISSN = {1932-6203},
+Keywords-Plus = {ESCHERICHIA-COLI; METABOLIC NETWORKS; SYSTEMS; MODELS; LIPIDS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Frigon, Dominic/P-7898-2018},
+ORCID-Numbers = {Frigon, Dominic/0000-0003-1587-8943},
+Times-Cited = {9},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000426363200006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000429399300010,
+Author = {Zhang, Yunze and Chen, Huxing and Liu, Jiamei and Geng, Ge and Liu, Deli
+ and Geng, Hui and Xiong, Li},
+Title = {Genome sequencing and biodegradation characteristics of the
+ n-butyl benzyl phthalate degrading bacterium-Rhodococcus
+ sp HS-D2},
+Journal = {INTERNATIONAL BIODETERIORATION \& BIODEGRADATION},
+Year = {2018},
+Volume = {128},
+Number = {SI},
+Pages = {56-62},
+Month = {MAR},
+Note = {1st International Symposium and the 4th Sino-Hungarian Workshop on
+ Remediation and Restoration of Polluted Mining Areas, Wuhan, PEOPLES R
+ CHINA, MAY 22-24, 2015},
+Type = {Article; Proceedings Paper},
+DOI = {10.1016/j.ibiod.2016.08.024},
+ISSN = {0964-8305},
+EISSN = {1879-0208},
+Keywords = {n-butyl benzyl phthalate; Biodegradation; Biochemical pathway;
+ Rhodococcus sp.; Genome sequencing; Genome-scale metabolic model},
+Keywords-Plus = {DIMETHYL PHTHALATE; TWEEN 80; DEGRADATION; STRAIN; ESTERS; METABOLISM;
+ REMOVAL; KINETICS; PATHWAY; MODELS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Environmental Sciences},
+Times-Cited = {19},
+Journal-ISO = {Int. Biodeterior. Biodegrad.},
+Unique-ID = {WOS:000429399300010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000459653300001,
+Author = {Cordes, Henrik and Thiel, Christoph and Baier, Vanessa and Blank, Lars
+ M. and Kuepfer, Lars},
+Title = {Integration of genome-scale metabolic networks into whole-body PBPK
+ models shows phenotype-specific cases of drug-induced metabolic
+ perturbation},
+Journal = {NPJ SYSTEMS BIOLOGY AND APPLICATIONS},
+Year = {2018},
+Volume = {4},
+Month = {FEB 26},
+Type = {Article},
+DOI = {10.1038/s41540-018-0048-1},
+Article-Number = {10},
+EISSN = {2056-7189},
+Keywords-Plus = {INDUCED LIVER-INJURY; EXPRESSION DATA; RISK-FACTOR; MECHANISMS; GENE;
+ MINIMIZATION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Kuepfer, Lars/F-5795-2012
+ Kuepfer, Lars/AAD-5884-2022
+ Blank, Lars M./A-6761-2012},
+ORCID-Numbers = {Kuepfer, Lars/0000-0002-8741-7786
+ Baier, Vanessa/0000-0002-7001-6804
+ Cordes, Henrik/0000-0002-0654-3386
+ Blank, Lars M./0000-0003-0961-4976},
+Times-Cited = {23},
+Journal-ISO = {npj Syst. Biol. Appl.},
+Unique-ID = {WOS:000459653300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000425633200001,
+Author = {Moskon, Miha and Zimic, Nikolaj and Mraz, Miha},
+Title = {Grohar: Automated Visualization of Genome-Scale Metabolic Models and
+ Their Pathways},
+Journal = {JOURNAL OF COMPUTATIONAL BIOLOGY},
+Year = {2018},
+Volume = {25},
+Number = {5},
+Pages = {505-508},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1089/cmb.2017.0209},
+EarlyAccessDate = {FEB 2018},
+ISSN = {1066-5277},
+EISSN = {1557-8666},
+Keywords = {flux balance analysis; genome-scale metabolic models; pathway alignment;
+ systems biology; visualization of metabolic networks},
+Keywords-Plus = {COBRA TOOLBOX EXTENSION; BIGG},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Moškon, Miha/J-3802-2019},
+ORCID-Numbers = {Moškon, Miha/0000-0003-4600-1730},
+Times-Cited = {2},
+Journal-ISO = {J. Comput. Biol.},
+Unique-ID = {WOS:000425633200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000414922600160,
+Author = {Yu, Ran and Perez-Garcia, Octavio and Lu, Huijie and Chandran, Kartik},
+Title = {Nitrosomonas europaea adaptation to anoxic-oxic cycling: Insights
+ from transcription analysis, proteomics and metabolic network modeling},
+Journal = {SCIENCE OF THE TOTAL ENVIRONMENT},
+Year = {2018},
+Volume = {615},
+Pages = {1566-1573},
+Month = {FEB 15},
+Type = {Article},
+DOI = {10.1016/j.scitotenv.2017.09.142},
+ISSN = {0048-9697},
+EISSN = {1879-1026},
+Keywords = {Nitrification; Nitrous oxide; Proteomics; Ammonia oxidizing bacteria},
+Keywords-Plus = {ANAEROBIC AMMONIA OXIDATION; FLUX BALANCE ANALYSIS; NITROUS-OXIDE;
+ NITRIC-OXIDE; N2O-PRODUCING PATHWAYS; OXIDIZING BACTERIUM;
+ NITRIFICATION; HYDROXYLAMINE; EMISSION; EUTROPHA},
+Research-Areas = {Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Environmental Sciences},
+ResearcherID-Numbers = {Lu, Huijie/AAQ-6296-2021},
+ORCID-Numbers = {Lu, Huijie/0000-0002-0076-4508},
+Times-Cited = {34},
+Journal-ISO = {Sci. Total Environ.},
+Unique-ID = {WOS:000414922600160},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000424985800015,
+Author = {Caracausi, Maria and Ghini, Veronica and Locatelli, Chiara and Mericio,
+ Martina and Piovesan, Allison and Antonaros, Francesca and Pelleri,
+ Maria Chiara and Vitale, Lorenza and Vacca, Rosa Anna and Bedetti,
+ Federica and Mimmi, Maria Chiara and Luchinat, Claudio and Turano, Paola
+ and Strippoli, Pierluigi and Cocchi, Guido},
+Title = {Plasma and urinary metabolomic profiles of Down syndrome correlate with
+ alteration of mitochondrial metabolism},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2018},
+Volume = {8},
+Month = {FEB 14},
+Type = {Article},
+DOI = {10.1038/s41598-018-20834-y},
+Article-Number = {2977},
+ISSN = {2045-2322},
+Keywords-Plus = {TRIMETHYLAMINE N-OXIDE; GUT MICROBIOTA; AMINO-ACIDS; NMR-SPECTROSCOPY;
+ AMNIOTIC-FLUID; CHILDREN; DYSFUNCTION; TMAO; IMPAIRMENT; EXPRESSION},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Vacca, Rosa Anna/AAX-1388-2020
+ Mimmi, Maria Chiara/AAA-4925-2020
+ PIOVESAN, Allison/M-6783-2019
+ Mimmi, Maria Chiara/GYD-9155-2022
+ Turano, Paola/F-9089-2011
+ },
+ORCID-Numbers = {Vacca, Rosa Anna/0000-0003-2438-6449
+ Mimmi, Maria Chiara/0000-0002-5165-9230
+ PIOVESAN, Allison/0000-0001-7038-5557
+ Mimmi, Maria Chiara/0000-0002-5165-9230
+ CARACAUSI, MARIA/0000-0001-8957-8391
+ GHINI, VERONICA/0000-0003-3759-6701
+ Turano, Paola/0000-0002-7683-8614
+ STRIPPOLI, PIERLUIGI/0000-0001-8769-8832},
+Times-Cited = {49},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000424985800015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000424189400028,
+Author = {Akberdin, Ilya R. and Thompson, Merlin and Hamilton, Richard and Desai,
+ Nalini and Alexander, Danny and Henard, Calvin A. and Guarnieri, Michael
+ T. and Kalyuzhnaya, Marina G.},
+Title = {Methane utilization in Methylomicrobium alcaliphilum
+ 20ZR: a systems approach},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2018},
+Volume = {8},
+Month = {FEB 6},
+Type = {Article},
+DOI = {10.1038/s41598-018-20574-z},
+Article-Number = {2512},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; METHANOTROPHIC BACTERIUM; PHOSPHOKETOLASE
+ PATHWAY; GENUS METHYLOMICROBIUM; BIOCHEMICAL-PROPERTIES;
+ ESCHERICHIA-COLI; LIQUID FUELS; METABOLISM; PYROPHOSPHATE; GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Akberdin, Ilya/J-3172-2018
+ },
+ORCID-Numbers = {Akberdin, Ilya/0000-0003-0010-8620
+ Guarnieri, Michael/0000-0003-1403-9689},
+Times-Cited = {66},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000424189400028},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000423978700017,
+Author = {Angione, Claudio},
+Title = {Integrating splice-isoform expression into genome-scale models
+ characterizes breast cancer metabolism},
+Journal = {BIOINFORMATICS},
+Year = {2018},
+Volume = {34},
+Number = {3},
+Pages = {494-501},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btx562},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {CELLS; RECONSTRUCTION; PROLIFERATION; TRANSCRIPTOME; LEVEL; GENE; FLUX},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ORCID-Numbers = {Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {17},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000423978700017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000425443400004,
+Author = {Asgari, Yazdan and Khosravi, Pegah and Zabihinpour, Zahra and Habibi,
+ Mahnaz},
+Title = {Exploring candidate biomarkers for lung and prostate cancers using gene
+ expression and flux variability analysis},
+Journal = {INTEGRATIVE BIOLOGY},
+Year = {2018},
+Volume = {10},
+Number = {2},
+Pages = {113-120},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1039/c7ib00135e},
+ISSN = {1757-9694},
+EISSN = {1757-9708},
+Keywords-Plus = {METABOLISM; IDENTIFICATION; PROGRESSION; PREDICTION; CARCINOMA;
+ NETWORKS; TARGETS; MODELS; CELLS; WOMEN},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Habibi, Mahnaz/ACD-2662-2022
+ asgari, yazdan/AAL-9037-2020
+ Khosravi, Pegah/IWD-4672-2023},
+ORCID-Numbers = {Habibi, Mahnaz/0000-0002-8969-2706
+ asgari, yazdan/0000-0001-6993-6956
+ Khosravi, Pegah/0000-0003-3497-2820},
+Times-Cited = {8},
+Journal-ISO = {Integr. Biol.},
+Unique-ID = {WOS:000425443400004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000424885900030,
+Author = {Fouladiha, Hamideh and Marashi, Sayed-Amir and Shokrgozar, Mohammad Ali
+ and Farokhi, Mehdi and Atashi, Amir},
+Title = {Applications of a metabolic network model of mesenchymal stem cells for
+ controlling cell proliferation and differentiation},
+Journal = {CYTOTECHNOLOGY},
+Year = {2018},
+Volume = {70},
+Number = {1},
+Pages = {331-338},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1007/s10616-017-0148-6},
+ISSN = {0920-9069},
+EISSN = {1573-0778},
+Keywords = {Metabolic networks; Mesenchymal stem cell (MSC); Proliferation;
+ Differentiation; Modeling},
+Keywords-Plus = {AMINO-ACID SUPPLEMENTATION; HAMSTER OVARY CELLS; GENOME-SCALE MODELS;
+ RATIONAL DESIGN; CULTURE-MEDIUM; FLUX ANALYSIS; RECONSTRUCTION;
+ MITOCHONDRIA; PHOSPHATIDYLETHANOLAMINE; CAPABILITIES},
+Research-Areas = {Biotechnology \& Applied Microbiology; Cell Biology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Cell Biology},
+ResearcherID-Numbers = {Shokrgozar, Mohammad Ali/HDM-1639-2022
+ Farokhi, Mehdi/V-3661-2019
+ Marashi, Sayed-Amir/A-5384-2008
+ Atashi, Amir/B-1715-2017
+ },
+ORCID-Numbers = {Farokhi, Mehdi/0000-0001-7023-2905
+ Marashi, Sayed-Amir/0000-0001-9801-7449
+ atashi, Amir/0000-0002-3889-5642},
+Times-Cited = {10},
+Journal-ISO = {Cytotechnology},
+Unique-ID = {WOS:000424885900030},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000426012600034,
+Author = {Zhang, Yun and Shang, Xiuling and Lai, Shujuan and Zhang, Yu and Hu,
+ Qitiao and Chai, Xin and Wang, Bo and Liu, Shuwen and We, Tingyi},
+Title = {Reprogramming One-Carbon Metabolic Pathways To Decouple L-Serine
+ Catabolism from Cell Growth in Corynebacterium glutamicum},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2018},
+Volume = {7},
+Number = {2},
+Pages = {635-646},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1021/acssynbio.7b00373},
+ISSN = {2161-5063},
+Keywords = {Corynebacterium glutamicum; L-serine; serine hydroxymethyltransferase;
+ glycine cleavage system; one-carbon units; in silico model-based
+ simulation},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI K-12; AMINO-ACIDS;
+ HYDROXYMETHYLTRANSFERASE GENE; QUANTITATIVE PREDICTION; RNA-POLYMERASE;
+ COBRA TOOLBOX; GLYCINE; BIOSYNTHESIS; SYSTEM},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Wen, Tingyi/M-6095-2014
+ WANG, YING/JLM-9219-2023
+ Wang, Bo/V-5152-2019
+ },
+ORCID-Numbers = {Wen, Tingyi/0000-0003-2583-7088
+ Wang, Bo/0000-0002-0643-0349
+ Zhang, Yu/0000-0002-3681-4298
+ Lai, Shujuan/0000-0003-1249-4258
+ Hu, Qitiao/0000-0002-7341-6125
+ Zhang, Yun/0000-0002-2617-8080},
+Times-Cited = {14},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000426012600034},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000423617800002,
+Author = {Nag, Ambarish and John, Peter C. St. and Crowley, Michael F. and Bomble,
+ Yannick J.},
+Title = {Prediction of reaction knockouts to maximize succinate production by
+ Actinobacillus succinogenes},
+Journal = {PLOS ONE},
+Year = {2018},
+Volume = {13},
+Number = {1},
+Month = {JAN 30},
+Type = {Article},
+DOI = {10.1371/journal.pone.0189144},
+Article-Number = {e0189144},
+ISSN = {1932-6203},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS; METABOLIC NETWORK;
+ FERMENTATIVE METABOLISM; GENOME; ACID; GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {crowley, michael F/A-4852-2013
+ St. John, Peter/AAQ-1508-2021
+ Bomble, Yannick J/A-5146-2009
+ },
+ORCID-Numbers = {crowley, michael F/0000-0001-5163-9398
+ St. John, Peter/0000-0002-7928-3722
+ Bomble, Yannick/0000-0001-7624-8000
+ Nag, Ambarish/0000-0001-5174-4673},
+Times-Cited = {11},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000423617800002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000423155700008,
+Author = {Ho, Wei-Chin and Zhang, Jianzhi},
+Title = {Evolutionary adaptations to new environments generally reverse plastic
+ phenotypic changes},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2018},
+Volume = {9},
+Month = {JAN 24},
+Type = {Article},
+DOI = {10.1038/s41467-017-02724-5},
+Article-Number = {350},
+ISSN = {2041-1723},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; GENE-EXPRESSION; ADAPTIVE
+ EVOLUTION; GROWTH; EPISTASIS; STRAINS; CELLS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Zhang, Jianzhi/0000-0001-6141-1290},
+Times-Cited = {77},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000423155700008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000419999700002,
+Author = {Chen, Xiulai and Gao, Cong and Guo, Liang and Hu, Guipeng and Luo,
+ Qiuling and Liu, Jia and Nielsen, Jens and Chen, Jian and Liu, Liming},
+Title = {DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize
+ the Metabolic Pathway for Biosynthesis of Chemicals},
+Journal = {CHEMICAL REVIEWS},
+Year = {2018},
+Volume = {118},
+Number = {1},
+Pages = {4-72},
+Month = {JAN 10},
+Type = {Review},
+DOI = {10.1021/acs.chemrev.6b00804},
+ISSN = {0009-2665},
+EISSN = {1520-6890},
+Keywords-Plus = {RECOMBINANT ESCHERICHIA-COLI; L-TYROSINE PRODUCTION; IN-VITRO
+ RECONSTITUTION; FUMARIC-ACID PRODUCTION; MYO-INOSITOL-PHOSPHATE;
+ LARGE-SCALE PRODUCTION; ZINC-FINGER NUCLEASES; TRANSCRIPTIONAL
+ REGULATORY NETWORKS; HETEROLOGOUS MEVALONATE PATHWAY; PROTEIN-PROTEIN
+ INTERACTIONS},
+Research-Areas = {Chemistry},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary},
+ResearcherID-Numbers = {Chen, Xiulai/AAB-8395-2020
+ Liu, Liming/B-1972-2009
+ Nielsen, Jens Bo/C-7632-2015
+ Gao, Cong/AAB-4849-2022
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Chen, Xiulai/0000-0002-5154-3860
+ Liu, Liming/0000-0003-3022-936X
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Gao, Cong/0000-0001-8505-2026
+ Nielsen, Jens/0000-0002-9955-6003
+ Guo, Liang/0000-0001-5671-3438},
+Times-Cited = {124},
+Journal-ISO = {Chem. Rev.},
+Unique-ID = {WOS:000419999700002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000419616200001,
+Author = {Piubeli, Francine and Salvador, Manuel and Argandona, Montserrat and
+ Nieto, Joaquin J. and Bernal, Vicente and Pastor, Jose M. and Canovas,
+ Manuel and Vargas, Carmen},
+Title = {Insights into metabolic osmoadaptation of the ectoines-producer
+ bacterium Chromohalobacter salexigens through a high-quality
+ genome scale metabolic model},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2018},
+Volume = {17},
+Month = {JAN 9},
+Type = {Article},
+DOI = {10.1186/s12934-017-0852-0},
+Article-Number = {2},
+EISSN = {1475-2859},
+Keywords = {Genome-scale metabolic model; Flux balance analysis; Chromohalobacter
+ salexigens; Metabolic osmoadaptation},
+Keywords-Plus = {OSMOTIC-STRESS; NETWORK; RECONSTRUCTION; HYDROXYECTOINE; OVERPRODUCTION;
+ OPTIMIZATION; EVOLUTION; ALIGNMENT; SEQUENCE; TOOL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Bernal, Vicente/M-4119-2014
+ Argandoña, Montserrat/H-5531-2015
+ Canovas, Manuel/K-3860-2014
+ Gutiérrez, Joaquín José Nieto/K-9974-2014
+ Vargas, Carmen/A-6283-2018
+ Salvador, Manuel/H-2960-2015
+ Piubeli, Francine/H-1991-2015
+ },
+ORCID-Numbers = {Bernal, Vicente/0000-0003-2482-3477
+ Canovas, Manuel/0000-0003-3254-1736
+ Gutiérrez, Joaquín José Nieto/0000-0001-8879-819X
+ Vargas, Carmen/0000-0002-4094-4319
+ Salvador, Manuel/0000-0002-1966-2480
+ Piubeli, Francine/0000-0002-5065-5297
+ Argandona, Montserrat/0000-0002-2635-1023},
+Times-Cited = {15},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000419616200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:001029031700001,
+Author = {Sen, Partho and Kemppainen, Esko and Oresic, Matej},
+Title = {Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear
+ Cells},
+Journal = {FRONTIERS IN MOLECULAR BIOSCIENCES},
+Year = {2018},
+Volume = {4},
+Month = {JAN 9},
+Type = {Review},
+DOI = {10.3389/fmolb.2017.00096},
+Article-Number = {96},
+EISSN = {2296-889X},
+Keywords = {systems biology; multi-omics; peripheral blood mononuclear cells; PBMCs;
+ immune system; metabolomics; genome-scale metabolic models; pathways},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Sen, Partho/L-8471-2019
+ Kemppainen, Esko/AAF-7618-2019
+ Oresic, Matej/K-7673-2016},
+ORCID-Numbers = {Sen, Partho/0000-0003-0475-2763
+ Oresic, Matej/0000-0002-2856-9165},
+Times-Cited = {45},
+Journal-ISO = {Front. Mol. Biosci.},
+Unique-ID = {WOS:001029031700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000423845000009,
+Author = {Abdel-Haleem, Alyaa M. and Hefzi, Hooman and Mineta, Katsuhiko and Gao,
+ Xin and Gojobori, Takashi and Palsson, Bernhard O. and Lewis, Nathan E.
+ and Jamshidi, Neema},
+Title = {Functional interrogation of Plasmodium genus metabolism
+ identifies species- and stage-specific differences in nutrient
+ essentiality and drug targeting},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2018},
+Volume = {14},
+Number = {1},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1005895},
+Article-Number = {e1005895},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; MYCOBACTERIUM-TUBERCULOSIS; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; ESCHERICHIA-COLI; FALCIPARUM;
+ DISCOVERY; TRANSMISSION; PATHWAYS; CULTURE},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Gao, Xin/D-5487-2013
+ Mineta, Katsuhiko/A-5455-2012
+ Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Gao, Xin/0000-0002-7108-3574
+ Mineta, Katsuhiko/0000-0002-4727-045X
+ Lewis, Nathan/0000-0001-7700-3654
+ Abdel-haleem, Alyaa/0000-0002-3114-1100
+ Palsson, Bernhard/0000-0003-2357-6785
+ Jamshidi, Neema/0000-0003-3857-9735
+ Hefzi, Hooman/0009-0003-4067-6224},
+Times-Cited = {20},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000423845000009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000458105800008,
+Author = {Ang, Kok Siong and Lakshmanan, Meiyappan and Lee, Na-Rae and Lee,
+ Dong-Yup},
+Title = {Metabolic Modeling of Microbial Community Interactions for Health,
+ Environmental and Biotechnological Applications},
+Journal = {CURRENT GENOMICS},
+Year = {2018},
+Volume = {19},
+Number = {8},
+Pages = {712-722},
+Type = {Review},
+DOI = {10.2174/1389202919666180911144055},
+ISSN = {1389-2029},
+EISSN = {1875-5488},
+Keywords = {Microbial communities; Metabolism; Community modeling; Genome-scale
+ metabolic models; Flux balance analysis; Kinetic models},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; GUT MICROBIOTA; DYNAMICS; CULTURE;
+ RECONSTRUCTION; BIOREMEDIATION; MICROORGANISMS; SIMULATION; PREDICTION;
+ DIVERSITY},
+Research-Areas = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/AAM-1171-2020
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ Ang, Kok Siong/M-2674-2019},
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ },
+Times-Cited = {18},
+Journal-ISO = {Curr. Genomics},
+Unique-ID = {WOS:000458105800008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000425531200013,
+Author = {Asgari, Yazdan and Zabihinpour, Zahra and Masoudi-Nejad, Ali},
+Title = {SCAN-Toolbox: Structural COBRA Add-oN (SCAN) for Analysing Large
+ Metabolic Networks},
+Journal = {CURRENT BIOINFORMATICS},
+Year = {2018},
+Volume = {13},
+Number = {1},
+Pages = {100-107},
+Type = {Article},
+DOI = {10.2174/1574893611666161123123729},
+ISSN = {1574-8936},
+EISSN = {2212-392X},
+Keywords = {Metabolic networks; metabolic modelling; structural analysis; COBRA
+ toolbox; Cytoscape; MATLAB},
+Keywords-Plus = {MODEL; RECONSTRUCTION; BIOLOGY; MATLAB; SBML},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {asgari, yazdan/AAL-9037-2020
+ Masoudi-Nejad, Ali/ABH-2078-2021
+ },
+ORCID-Numbers = {asgari, yazdan/0000-0001-6993-6956
+ Masoudi-Nejad, Ali/0000-0003-0659-5183},
+Times-Cited = {1},
+Journal-ISO = {Curr. Bioinform.},
+Unique-ID = {WOS:000425531200013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000444088900005,
+Author = {Bhatia, Shashi Kant and Bhatia, Ravi Kant and Choi, Yong-Keun and Kan,
+ Eunsung and Kim, Yun-Gon and Yang, Yung-Hun},
+Title = {Biotechnological potential of microbial consortia and future
+ perspectives},
+Journal = {CRITICAL REVIEWS IN BIOTECHNOLOGY},
+Year = {2018},
+Volume = {38},
+Number = {8},
+Pages = {1209-1229},
+Type = {Review},
+DOI = {10.1080/07388551.2018.1471445},
+ISSN = {0738-8551},
+EISSN = {1549-7801},
+Keywords = {Bioenergy; biochemical; bioremediation; biopolymer; microbial consortia},
+Keywords-Plus = {POLYCYCLIC AROMATIC-HYDROCARBONS; PALM BIOMASS HYDROLYSATE; CELL
+ PROTEIN-PRODUCTION; MIXED CULTURE; STREPTOMYCES-COELICOLOR; BIOHYDROGEN
+ PRODUCTION; BACTERIAL COMMUNITY; POLYHYDROXYBUTYRATE PRODUCTION;
+ BIOFLOCCULANT PRODUCTION; KLUYVEROMYCES-MARXIANUS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Bhatia, Shashi/N-4550-2018
+ Choi, Yong-Keun/Q-6236-2017
+ Kim, Yun-Gon/HLP-9951-2023
+ },
+ORCID-Numbers = {Bhatia, Shashi/0000-0002-7688-6069
+ Kim, Yun-Gon/0000-0001-7388-2989
+ Kan, Eunsung/0000-0001-6298-6096},
+Times-Cited = {57},
+Journal-ISO = {Crit. Rev. Biotechnol.},
+Unique-ID = {WOS:000444088900005},
+DA = {2023-12-20},
+}
+
+@incollection{ WOS:000452369600015,
+Author = {Collins, David A. and Kalyuzhnaya, Marina G.},
+Editor = {Armstrong, F},
+Title = {Navigating methane metabolism: Enzymes, compartments, and networks},
+Booktitle = {ENZYMES OF ENERGY TECHNOLOGY},
+Series = {Methods in Enzymology},
+Year = {2018},
+Volume = {613},
+Pages = {349-383},
+Type = {Review; Book Chapter},
+DOI = {10.1016/bs.mie.2018.10.010},
+ISSN = {0076-6879},
+ISBN = {978-0-12-816361-0},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GENETIC MANIPULATION; DEHYDROGENASE; SYSTEM;
+ MUTAGENESIS; GROWTH},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
+Times-Cited = {4},
+Journal-ISO = {Methods Enzymol.},
+Unique-ID = {WOS:000452369600015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000454855400001,
+Author = {Hao, Tong and Wang, Bin and Zhao, Lingxuan and Feng, Xin and Sun,
+ Jinsheng},
+Title = {Reconstruction and Analysis of a Genome-Scale Metabolic Network for
+ Eriocheir Sinensis Hepatopancreas},
+Journal = {IEEE ACCESS},
+Year = {2018},
+Volume = {6},
+Pages = {79235-79244},
+Type = {Article},
+DOI = {10.1109/ACCESS.2018.2885005},
+ISSN = {2169-3536},
+Keywords = {Eriocheir sinensis; hepatopancreas; metabolic network; transcriptome
+ sequencing},
+Research-Areas = {Computer Science; Engineering; Telecommunications},
+Web-of-Science-Categories = {Computer Science, Information Systems; Engineering, Electrical \&
+ Electronic; Telecommunications},
+Times-Cited = {3},
+Journal-ISO = {IEEE Access},
+Unique-ID = {WOS:000454855400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000418314600001,
+Author = {Majd, Homa and King, Martin S. and Smith, Anthony C. and Kunji, Edmund
+ R. S.},
+Title = {Pathogenic mutations of the human mitochondrial citrate carrier SLC25A1
+ lead to impaired citrate export required for lipid, dolichol, ubiquinone
+ and sterol synthesis},
+Journal = {BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS},
+Year = {2018},
+Volume = {1859},
+Number = {1},
+Pages = {1-7},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1016/j.bbabio.2017.10.002},
+ISSN = {0005-2728},
+EISSN = {0006-3002},
+Keywords = {Mitochondrial disease; Mitochondrial carriers; Structure-function
+ relationships; Citrate metabolism; Mitochondrial tricarboxylate carrier;
+ Transport},
+Keywords-Plus = {L-2-HYDROXYGLUTARIC ACIDURIA; LACTOCOCCUS-LACTIS; TRANSPORT PROTEIN;
+ DEFICIENCY; EXPRESSION; D-2-HYDROXYGLUTARATE; DEHYDROGENASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Biophysics},
+ResearcherID-Numbers = {King, Martin S/B-6361-2012
+ Kunji, Edmund R.S./AAH-2362-2020
+ Smith, Anthony C/B-1891-2009
+ },
+ORCID-Numbers = {Kunji, Edmund R.S./0000-0002-0610-4500
+ Smith, Anthony C/0000-0003-0141-0434
+ Majd, Homa/0000-0002-2048-1839
+ King, Martin/0000-0001-6030-5154},
+Times-Cited = {24},
+Journal-ISO = {Biochim. Biophys. Acta-Bioenerg.},
+Unique-ID = {WOS:000418314600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000418789600023,
+Author = {Tomas-Gamisans, Marius and Ferrer, Pau and Albiol, Joan},
+Title = {Fine-tuning the P-pastoris iMT1026 genome-scale metabolic model
+ for improved prediction of growth on methanol or glycerol as sole carbon
+ sources},
+Journal = {MICROBIAL BIOTECHNOLOGY},
+Year = {2018},
+Volume = {11},
+Number = {1, SI},
+Pages = {224-237},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1111/1751-7915.12871},
+ISSN = {1751-7915},
+Keywords-Plus = {YEAST PICHIA-PASTORIS; CRUDE GLYCEROL; SACCHAROMYCES-CEREVISIAE;
+ PROTEIN-PRODUCTION; CELL FACTORIES; GLYCEROL/METHANOL MIXTURES;
+ CHEMOSTAT CULTURES; MAINTENANCE ENERGY; BY-PRODUCT; GLUCOSE},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Tomàs-Gamisans, Màrius/AAG-8539-2020
+ Sala, Joan Albiol/A-8280-2008
+ Albiol, Joan/Z-5173-2019
+ Tomàs-Gamisans, Màrius/B-4136-2016
+ Ferrer, Pau/A-4147-2009},
+ORCID-Numbers = {Tomàs-Gamisans, Màrius/0000-0002-6076-6716
+ Sala, Joan Albiol/0000-0001-5626-429X
+ Albiol, Joan/0000-0001-5626-429X
+ Tomàs-Gamisans, Màrius/0000-0002-6076-6716
+ Ferrer, Pau/0000-0002-5287-4127},
+Times-Cited = {38},
+Journal-ISO = {Microb. Biotechnol.},
+Unique-ID = {WOS:000418789600023},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000443860500009,
+Author = {Wang, Junhua and Wang, Cheng and Liu, Huanhuan and Qi, Haishan and Chen,
+ Hong and Wen, Jianping},
+Title = {Metabolomics assisted metabolic network modeling and network wide
+ analysis of metabolites in microbiology},
+Journal = {CRITICAL REVIEWS IN BIOTECHNOLOGY},
+Year = {2018},
+Volume = {38},
+Number = {7},
+Pages = {1106-1120},
+Type = {Review},
+DOI = {10.1080/07388551.2018.1462141},
+ISSN = {0738-8551},
+EISSN = {1549-7801},
+Keywords = {Metabolomics; microbiology; metabolic network model; network modeling;
+ network analysis; metabolic flux},
+Keywords-Plus = {SET ENRICHMENT ANALYSIS; CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS;
+ WEB-BASED TOOL; STREPTOMYCES-TSUKUBAENSIS; PATHWAY ANALYSIS;
+ CELLULAR-METABOLISM; SCALE; IDENTIFICATION; VISUALIZATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {liu, huan/JEO-4705-2023
+ },
+ORCID-Numbers = {Wang, Cheng/0000-0003-3665-4965},
+Times-Cited = {10},
+Journal-ISO = {Crit. Rev. Biotechnol.},
+Unique-ID = {WOS:000443860500009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000461106800026,
+Author = {Zhuang, Zhendong and Huang, Mingzhi and Chu, Ju},
+Title = {In silico reconstruction and experimental validation of
+ Saccharopolyspora erythraea genome-scale metabolic model iZZ1342
+ that accounts for 1685 ORFs},
+Journal = {BIORESOURCES AND BIOPROCESSING},
+Year = {2018},
+Volume = {5},
+Type = {Article},
+DOI = {10.1186/s40643-018-0212-x},
+Article-Number = {26},
+EISSN = {2197-4365},
+Keywords = {Saccharopolyspora erythraea; Genome-scale metabolic model; Multi-omics;
+ Erythromycin},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ERYTHROMYCIN PRODUCTION; ENHANCEMENT;
+ IMPROVEMENT; SEQUENCE; STRAIN; GROWTH; BATCH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Wang, Shan/JPX-1098-2023
+ liu, shanshan/JPA-0852-2023},
+Times-Cited = {6},
+Journal-ISO = {Bioresour. Bioprocess.},
+Unique-ID = {WOS:000461106800026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000419675300035,
+Author = {Zuniga, Cristal and Levering, Jennifer and Antoniewicz, Maciek R. and
+ Guarnieri, Michael T. and Betenbaugh, Michael J. and Zengler, Karsten},
+Title = {Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote
+ Chlorella vulgaris},
+Journal = {PLANT PHYSIOLOGY},
+Year = {2018},
+Volume = {176},
+Number = {1},
+Pages = {450-462},
+Month = {JAN},
+Type = {Article},
+DOI = {10.1104/pp.17.00605},
+ISSN = {0032-0889},
+EISSN = {1532-2548},
+Keywords-Plus = {ESCHERICHIA-COLI; ALLOSTERIC REGULATION; GENE-EXPRESSION;
+ KINETIC-MODELS; FLUX ANALYSIS; GREEN-ALGA; RECONSTRUCTION; GROWTH;
+ MICROALGAE; BIOMASS},
+Research-Areas = {Plant Sciences},
+Web-of-Science-Categories = {Plant Sciences},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009
+ Zuniga, Cristal/CAA-0015-2022
+ },
+ORCID-Numbers = {Zuniga, Cristal/0000-0002-0135-7429
+ Guarnieri, Michael/0000-0003-1403-9689
+ Zengler, Karsten/0000-0002-8062-3296},
+Times-Cited = {43},
+Journal-ISO = {Plant Physiol.},
+Unique-ID = {WOS:000419675300035},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000418595300001,
+Author = {Pandit, Santosh and Ravikumar, Vaishnavi and Abdel-Haleem, Alyaa M. and
+ Derouiche, Abderahmane and Mokkapati, V. R. S. S. and Sihlbom, Carina
+ and Mineta, Katsuhiko and Gojobori, Takashi and Gao, Xin and Westerlund,
+ Fredrik and Mijakovic, Ivan},
+Title = {Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular
+ Polymers and Destabilize Bacterial Biofilms},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2017},
+Volume = {8},
+Month = {DEC 22},
+Type = {Article},
+DOI = {10.3389/fmicb.2017.02599},
+Article-Number = {2599},
+ISSN = {1664-302X},
+Keywords = {biofilms; exopolymeric matrix; quantitative proteomics; Bacillus
+ subtilis; vitamin C},
+Keywords-Plus = {BACILLUS-SUBTILIS; MYCOBACTERIUM-TUBERCULOSIS; PSEUDOMONAS-AERUGINOSA;
+ COMPUTATIONAL PLATFORM; STAPHYLOCOCCUS-AUREUS; SUBSTANCES EPS; MATRIX;
+ PROTEOMICS; IDENTIFICATION; BIOSYNTHESIS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Westerlund, Fredrik/A-2340-2011
+ Mineta, Katsuhiko/A-5455-2012
+ Pandit, Santosh/H-6817-2014
+ Gao, Xin/D-5487-2013
+ Derouiche, Abderahmane/N-1075-2015
+ Mijakovic, Ivan/Q-5583-2016},
+ORCID-Numbers = {Westerlund, Fredrik/0000-0002-4767-4868
+ Mineta, Katsuhiko/0000-0002-4727-045X
+ Pandit, Santosh/0000-0002-8357-758X
+ Gao, Xin/0000-0002-7108-3574
+ Abdel-haleem, Alyaa/0000-0002-3114-1100
+ Derouiche, Abderahmane/0000-0002-3241-1424
+ Mijakovic, Ivan/0000-0002-8860-6853},
+Times-Cited = {54},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000418595300001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000418829200001,
+Author = {Hartmann, Andras and Vila-Santa, Ana and Kallscheuer, Nicolai and Vogt,
+ Michael and Julien-Laferriere, Alice and Sagot, Marie-France and
+ Marienhagen, Jan and Vinga, Susana},
+Title = {OptPipe - a pipeline for optimizing metabolic engineering targets},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {DEC 21},
+Type = {Article},
+DOI = {10.1186/s12918-017-0515-0},
+Article-Number = {143},
+ISSN = {1752-0509},
+Keywords = {Metabolic engineering; Metabolic networks; Optimization; Software; Rank
+ product},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ FRAMEWORK; PLATFORM; STRAIN; FLAVANONE; NARINGIN},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Hartmann, Andras/D-5867-2015
+ Kallscheuer, Nicolai/AAF-5247-2020
+ Vinga, Susana/B-8450-2008
+ Vila-Santa, Ana/AAN-3194-2021
+ Kallscheuer, Nicolai/AAJ-9200-2021
+ Marienhagen, Jan/E-9593-2011
+ Kallscheuer, Nicolai/AAZ-6904-2021
+ },
+ORCID-Numbers = {Hartmann, Andras/0000-0001-6628-8711
+ Vinga, Susana/0000-0002-1954-5487
+ Vila-Santa, Ana/0000-0002-5880-1498
+ Kallscheuer, Nicolai/0000-0003-4925-6923
+ Marienhagen, Jan/0000-0001-5513-3730
+ /0000-0002-5933-9960
+ Julien-Laferriere, Alice/0000-0003-1039-8529},
+Times-Cited = {10},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000418829200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000417549500016,
+Author = {Perez-Garcia, Octavio and Mankelow, Cody and Chandran, Kartik and
+ Villas-Boas, Silas G. and Singhal, Naresh},
+Title = {Modulation of Nitrous Oxide (N2O) Accumulation by Primary
+ Metabolites in Denitrifying Cultures Adapting to Changes in
+ Environmental C and N},
+Journal = {ENVIRONMENTAL SCIENCE \& TECHNOLOGY},
+Year = {2017},
+Volume = {51},
+Number = {23},
+Pages = {13678-13688},
+Month = {DEC 5},
+Type = {Article},
+DOI = {10.1021/acs.est.7b03345},
+ISSN = {0013-936X},
+EISSN = {1520-5851},
+Keywords-Plus = {WASTE-WATER TREATMENT; FLUX BALANCE ANALYSIS; ELECTRON COMPETITION;
+ ACTIVATED-SLUDGE; CARBON SOURCE; DENITRIFICATION; REDUCTION; EMISSIONS;
+ BACTERIA; METHANOL},
+Research-Areas = {Engineering; Environmental Sciences \& Ecology},
+Web-of-Science-Categories = {Engineering, Environmental; Environmental Sciences},
+ResearcherID-Numbers = {Villas-Boas, Silas/AAS-5888-2020
+ Villas-Boas, Silas/AAR-6748-2020
+ Singhal, Naresh/C-2769-2008
+ Villas-Boas, Silas Granato/HLQ-1860-2023
+ Chandran, Kartik/O-1202-2013},
+ORCID-Numbers = {Villas-Boas, Silas/0000-0003-0148-5882
+ Singhal, Naresh/0000-0002-9461-688X
+ Mankelow, Cody/0000-0003-2949-6794
+ Chandran, Kartik/0000-0002-7526-3724},
+Times-Cited = {21},
+Journal-ISO = {Environ. Sci. Technol.},
+Unique-ID = {WOS:000417549500016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000413446100003,
+Author = {Wagner, Andreas},
+Title = {Information theory, evolutionary innovations and evolvability},
+Journal = {PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
+Year = {2017},
+Volume = {372},
+Number = {1735},
+Month = {DEC 5},
+Type = {Article},
+DOI = {10.1098/rstb.2016.0416},
+Article-Number = {20160416},
+ISSN = {0962-8436},
+EISSN = {1471-2970},
+Keywords = {evolvability; gene duplication; progress},
+Keywords-Plus = {IN-VITRO SELECTION; FITNESS LANDSCAPE; ESCHERICHIA-COLI; ROBUSTNESS;
+ COMPLEXITY; RECONSTRUCTION; ADAPTATION; DIVERSITY; SEQUENCES},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics},
+Web-of-Science-Categories = {Biology},
+Times-Cited = {10},
+Journal-ISO = {Philos. Trans. R. Soc. B-Biol. Sci.},
+Unique-ID = {WOS:000413446100003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000418984100012,
+Author = {Chapman, Stephen P. and dos Santos, Marcelo Trindade and Johnson, Giles
+ N. and Kritz, Mauricio Vieira and Schwartz, Jean-Marc},
+Title = {Cyclic decomposition explains a photosynthetic down regulation for
+ Chlamydomonas reinhardtii},
+Journal = {BIOSYSTEMS},
+Year = {2017},
+Volume = {162},
+Pages = {119-127},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1016/j.biosystems.2017.09.014},
+ISSN = {0303-2647},
+EISSN = {1872-8324},
+Keywords = {Glycolysis; Mixotrophic growth; Metabolic model; Photosynthesis; Green
+ algae; Flux balance analysis; Acetate metabolism; Cyclic electron flow},
+Keywords-Plus = {ELECTRON-TRANSPORT; METABOLIC NETWORKS; SUBSTRATE CYCLES; GREEN-ALGA;
+ ORGANIZATION; PATHWAYS; ORGANISM; SYSTEMS; FLOW},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Vieira Kritz, Maurício/N-7058-2013
+ Schwartz, Jean-Marc/AAS-8274-2020
+ },
+ORCID-Numbers = {Vieira Kritz, Maurício/0000-0002-2205-9981
+ Schwartz, Jean-Marc/0000-0002-6472-0184
+ Chapman, Stephen/0000-0001-6982-4591
+ Johnson, Giles Nicholas/0000-0003-1536-5582},
+Times-Cited = {3},
+Journal-ISO = {Biosystems},
+Unique-ID = {WOS:000418984100012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416769400012,
+Author = {Haesler, Robert and Sheibani-Tezerji, Raheleh and Sinha, Anupam and
+ Barann, Matthias and Rehman, Ateequr and Esser, Daniela and Aden, Konrad
+ and Knecht, Carolin and Brandt, Berenice and Nikolaus, Susanna and
+ Schaeuble, Sascha and Kaleta, Christoph and Franke, Andre and Fretter,
+ Christoph and Mueller, Werner and Huett, Marc-Thorsten and Krawczak,
+ Michael and Schreiber, Stefan and Rosenstiel, Philip},
+Title = {Uncoupling of mucosal gene regulation, mRNA splicing and adherent
+ microbiota signatures in inflammatory bowel disease},
+Journal = {GUT},
+Year = {2017},
+Volume = {66},
+Number = {12},
+Pages = {2087-2097},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1136/gutjnl-2016-311651},
+ISSN = {0017-5749},
+EISSN = {1468-3288},
+Keywords-Plus = {ULCERATIVE-COLITIS; CROHNS-DISEASE; GUT MICROBIOTA; EXPRESSION;
+ SUSCEPTIBILITY; TRANSCRIPTOME; IBD; OLIGONUCLEOTIDE; MICROARRAYS;
+ METABOLISM},
+Research-Areas = {Gastroenterology \& Hepatology},
+Web-of-Science-Categories = {Gastroenterology \& Hepatology},
+ResearcherID-Numbers = {Schäuble, Sascha/AAF-7809-2021
+ Fretter, Christoph/A-1318-2011
+ Rehman, Ateequr/O-3727-2016
+ Aden, Konrad/H-1477-2014
+ Rosenstiel, Philip/A-5137-2009
+ Franke, Andre/B-2151-2010
+ Krawczak, Michael/A-8964-2010
+ Esser, Daniela/ABB-9383-2020
+ Muller, Werner/B-9044-2008
+ Aden, Konrad/AAG-3290-2020
+ Häsler, Robert/A-4908-2009
+ },
+ORCID-Numbers = {Rehman, Ateequr/0000-0002-5664-4628
+ Aden, Konrad/0000-0003-3482-7316
+ Rosenstiel, Philip/0000-0002-9692-8828
+ Franke, Andre/0000-0003-1530-5811
+ Krawczak, Michael/0000-0003-2603-1502
+ Muller, Werner/0000-0002-1297-9725
+ Häsler, Robert/0000-0003-4174-8229
+ Kaleta, Christoph/0000-0001-8004-9514
+ Sheibani Tezerji, Raheleh/0000-0002-1025-646X},
+Times-Cited = {55},
+Journal-ISO = {Gut},
+Unique-ID = {WOS:000416769400012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000418395600010,
+Author = {Morell, William C. and Birkel, Garrett W. and Forrer, Mark and Lopez,
+ Teresa and Backman, Tyler W. H. and Dussault, Michael and Petzold,
+ Christpoher J. and Baidoo, Edward E. K. and Costello, Zak and Ando,
+ David and Alonso-Gutierrez, Jorge and George, Kevin W. and Mukhopadhyay,
+ Aindrila and Vaino, Ian and Keasling, Jay D. and Adams, Paul D. and
+ Hillson, Nathan J. and Garcia Martin, Hector},
+Title = {The Experiment Data Depot: A Web-Based Software Tool for Biological
+ Experimental Data Storage, Sharing, and Visualization},
+Journal = {ACS SYNTHETIC BIOLOGY},
+Year = {2017},
+Volume = {6},
+Number = {12},
+Pages = {2248-2259},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1021/acssynbio.7b00204},
+ISSN = {2161-5063},
+Keywords = {database; -omics data; data standards; data mining; flux analysis;
+ synthetic biology},
+Keywords-Plus = {ESCHERICHIA-COLI; PUBLIC REPOSITORY; GENE-EXPRESSION; SYSTEMS BIOLOGY;
+ PROTEOMICS; PROTEIN; STANDARDS; MODELS; PRIDE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemical Research Methods},
+ResearcherID-Numbers = {Adams, Paul David/A-1977-2013
+ Keasling, Jay/HPG-6073-2023
+ Keasling, Jay D/J-9162-2012
+ Mukhopadhyay, Aindrila/AAW-7257-2021
+ Garcia Martin, Hector/B-5357-2009
+ },
+ORCID-Numbers = {Adams, Paul David/0000-0001-9333-8219
+ Keasling, Jay D/0000-0003-4170-6088
+ Garcia Martin, Hector/0000-0002-4556-9685
+ Petzold, Christopher/0000-0002-8270-5228},
+Times-Cited = {30},
+Journal-ISO = {ACS Synth. Biol.},
+Unique-ID = {WOS:000418395600010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000414647400002,
+Author = {Motamedian, E. and Taheri, E. and Bagheri, F.},
+Title = {Proliferation inhibition of cisplatin-resistant ovarian cancer cells
+ using drugs screened by integrating a metabolic model and transcriptomic
+ data},
+Journal = {CELL PROLIFERATION},
+Year = {2017},
+Volume = {50},
+Number = {6},
+Month = {DEC},
+Type = {Article},
+DOI = {10.1111/cpr.12370},
+Article-Number = {e12370},
+ISSN = {0960-7722},
+EISSN = {1365-2184},
+Keywords-Plus = {IN-VIVO; COMBINATION THERAPY; SODIUM VALPROATE; NETWORK; GROWTH;
+ RECONSTRUCTION; DEXAMETHASONE; TERBINAFINE; STRATEGY; VITRO},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Motamedian, Ehsan/GPK-8344-2022
+ },
+ORCID-Numbers = {, Ehsan/0000-0001-8750-2879
+ Bagheri, Fatemeh/0000-0002-9920-338X},
+Times-Cited = {8},
+Journal-ISO = {Cell Prolif.},
+Unique-ID = {WOS:000414647400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416454100001,
+Author = {Hirokawa, Yasutaka and Matsuo, Shingo and Hamada, Hiroyuki and Matsuda,
+ Fumio and Hanai, Taizo},
+Title = {Metabolic engineering of Synechococcus elongatus PCC 7942 for
+ improvement of 1,3-propanediol and glycerol production based on in
+ silico simulation of metabolic flux distribution},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2017},
+Volume = {16},
+Month = {NOV 25},
+Type = {Article},
+DOI = {10.1186/s12934-017-0824-4},
+Article-Number = {212},
+EISSN = {1475-2859},
+Keywords = {Cyanobacteria; Flux balance analysis; Synthetic metabolic pathway;
+ 1,3-Propanediol},
+Keywords-Plus = {PHOTOSYNTHETIC PRODUCTION; CARBON-DIOXIDE; ESCHERICHIA-COLI;
+ SYNECHOCYSTIS; CYANOBACTERIUM; GENE; CO2; PATHWAY; OPTIMIZATION; BIOFUEL},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {26},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000416454100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416127700002,
+Author = {Smith, Anthony C. and Eyassu, Filmon and Mazat, Jean-Pierre and
+ Robinson, Alan J.},
+Title = {MitoCore: a curated constraint-based model for simulating human central
+ metabolism},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {NOV 25},
+Type = {Article},
+DOI = {10.1186/s12918-017-0500-7},
+Article-Number = {114},
+EISSN = {1752-0509},
+Keywords = {Constraint-based model; Metabolic network; Flux balance analysis;
+ Central metabolism; Mitochondria; Mitochondrial metabolism},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; FUMARIC ACIDURIA; MITOCHONDRIAL; PREDICTION;
+ MEMBRANE; GENOME; GENE},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Smith, Anthony C/B-1891-2009},
+ORCID-Numbers = {Smith, Anthony C/0000-0003-0141-0434},
+Times-Cited = {21},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000416127700002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416533900002,
+Author = {Yurkovich, James T. and Yurkovich, Benjamin J. and Draeger, Andreas and
+ Palsson, Bernhard O. and King, Zachary A.},
+Title = {A Padawan Programmer's Guide to Developing Software Libraries},
+Journal = {CELL SYSTEMS},
+Year = {2017},
+Volume = {5},
+Number = {5},
+Pages = {431-437},
+Month = {NOV 22},
+Type = {Editorial Material},
+DOI = {10.1016/j.cels.2017.08.003},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {INTEGRATION; CYTOSCAPE; MODELS; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {King, Zachary/V-3402-2019
+ Dräger, Andreas/F-5620-2015},
+ORCID-Numbers = {King, Zachary/0000-0003-1238-1499
+ Dräger, Andreas/0000-0002-1240-5553},
+Times-Cited = {5},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000416533900002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000415282900036,
+Author = {Koduru, Lokanand and Kim, Yujin and Bang, Jeongsu and Lakshmanan,
+ Meiyappan and Han, Nam Soo and Lee, Dong-Yup},
+Title = {Genome-scale modeling and transcriptome analysis of Leuconostoc
+ mesenteroides unravel the redox governed metabolic states in
+ obligate heterofermentative lactic acid bacteria},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {NOV 16},
+Type = {Article},
+DOI = {10.1038/s41598-017-16026-9},
+Article-Number = {15721},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; MALOLACTIC ENZYME; LACTOBACILLUS-PLANTARUM;
+ OENOCOCCUS-OENI; PROTEIN; GROWTH; DATABASE; STRAIN; PURIFICATION;
+ ENERGETICS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/ABC-7628-2020
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Koduru, Lokanand/AAY-3079-2020
+ Lee, Dong-Yup/D-6650-2011
+ },
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Lee, Darrall/0000-0002-6990-4441
+ Koduru, Lokanand/0000-0001-9223-8742},
+Times-Cited = {25},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000415282900036},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000415323700010,
+Author = {Zomorrodi, Ali R. and Segre, Daniel},
+Title = {Genome-driven evolutionary game theory helps understand the rise of
+ metabolic interdependencies in microbial communities},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2017},
+Volume = {8},
+Month = {NOV 16},
+Type = {Article},
+DOI = {10.1038/s41467-017-01407-5},
+Article-Number = {1563},
+ISSN = {2041-1723},
+Keywords-Plus = {CELLULAR-METABOLISM; COOPERATION; DYNAMICS; NETWORKS; FITNESS; YEAST},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Segrè, Daniel/A-1993-2009
+ },
+ORCID-Numbers = {Segrè, Daniel/0000-0003-4859-1914
+ Zomorrodi, Ali/0000-0002-9134-8082},
+Times-Cited = {72},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000415323700010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000415074800012,
+Author = {Chan, Siu H. J. and Cai, Jingyi and Wang, Lin and Simons-Senftle,
+ Margaret N. and Maranas, Costas D.},
+Title = {Standardizing biomass reactions and ensuring complete mass balance in
+ genome-scale metabolic models},
+Journal = {BIOINFORMATICS},
+Year = {2017},
+Volume = {33},
+Number = {22},
+Pages = {3603-3609},
+Month = {NOV 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btx453},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {ELEMENTARY FLUX MODES; HUMAN GUT; RECONSTRUCTION; PREDICTION; PHENOTYPE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Wang, Lin/ABB-2686-2020
+ Maranas, Costas D/A-4774-2011
+ Chan, Siu Hung Joshua/N-9777-2016
+ },
+ORCID-Numbers = {Wang, Lin/0000-0002-9455-5570
+ Maranas, Costas D/0000-0002-1508-1398
+ Chan, Siu Hung Joshua/0000-0002-7707-656X
+ Cai, Jingyi/0000-0002-2018-1174},
+Times-Cited = {55},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000415074800012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000412254600001,
+Author = {Dvorak, Pavel and Nikel, Pablo I. and Damborsky, Jiri and de Lorenzo,
+ Victor},
+Title = {Bioremediation 3.0: Engineering pollutant-removing bacteria in
+ the times of systemic biology},
+Journal = {BIOTECHNOLOGY ADVANCES},
+Year = {2017},
+Volume = {35},
+Number = {7},
+Pages = {845-866},
+Month = {NOV 15},
+Type = {Review},
+DOI = {10.1016/j.biotechadv.2017.08.001},
+ISSN = {0734-9750},
+EISSN = {1873-1899},
+Keywords = {Bioremediation; Biodegradation pathway engineering; Emerging pollutants;
+ Environmental biotechnology; Systemic biology; Metabolic engineering;
+ Systems biology; Synthetic biology},
+Keywords-Plus = {PSEUDOMONAS-PUTIDA KT2440; HYDROCARBON-DEGRADING BACTERIA; COMPLETE
+ GENOME SEQUENCE; FREE SYNTHETIC BIOLOGY; HALOALKANE DEHALOGENASE;
+ METABOLIC PATHWAYS; POLYETHYLENE TEREPHTHALATE; BIODEGRADATION PATHWAYS;
+ ANOXIC BIODEGRADATION; MICROBIAL BIOSENSORS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Dvorak, Pavel/AAO-7902-2020
+ Damborsky, Jiri/H-3799-2012
+ Nikel, Pablo Ivan/L-4146-2014
+ },
+ORCID-Numbers = {Dvorak, Pavel/0000-0002-3215-4763
+ Damborsky, Jiri/0000-0002-7848-8216
+ Nikel, Pablo Ivan/0000-0002-9313-7481
+ de Lorenzo, Victor/0000-0002-6041-2731},
+Times-Cited = {170},
+Journal-ISO = {Biotechnol. Adv.},
+Unique-ID = {WOS:000412254600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000413586900027,
+Author = {von Kamp, Axel and Thiele, Sven and Haedicke, Oliver and Klamt, Steffen},
+Title = {Use of CellNetAnalyzer in biotechnology and metabolic engineering},
+Journal = {JOURNAL OF BIOTECHNOLOGY},
+Year = {2017},
+Volume = {261},
+Number = {SI},
+Pages = {221-228},
+Month = {NOV 10},
+Type = {Article},
+DOI = {10.1016/j.jbiotec.2017.05.001},
+ISSN = {0168-1656},
+EISSN = {1873-4863},
+Keywords = {Metabolic networks; Metabolic flux analysis; Flux balance analysis;
+ Elementary modes; Strain optimization; Minimal cut sets},
+Keywords-Plus = {MINIMAL CUT SETS; ELEMENTARY FLUX MODES; GENOME-SCALE MODELS;
+ CELLULAR-METABOLISM; MICROBIAL STRAINS; SYSTEMS BIOLOGY; NETWORKS;
+ STRATEGIES; BIOFUELS; CALCULABILITY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Klamt, Steffen/0000-0003-2563-7561},
+Times-Cited = {61},
+Journal-ISO = {J. Biotechnol.},
+Unique-ID = {WOS:000413586900027},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000411699200018,
+Author = {Cankorur-Cetinkaya, Ayca and Dikicioglu, Duygu and Oliver, Stephen G.},
+Title = {Metabolic modeling to identify engineering targets for Komagataella
+ phaffii: The effect of biomass composition on gene target
+ identification},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2017},
+Volume = {114},
+Number = {11},
+Pages = {2605-2615},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1002/bit.26380},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {biomass composition; genome-scale metabolic model; Komagataella phaffii;
+ metabolic target identification; Pichia pastoris; recombinant protein
+ production},
+Keywords-Plus = {BIOLOGY MARKUP LANGUAGE; PICHIA-PASTORIS; ONTOLOGY; RECONSTRUCTION;
+ INFORMATION; RESOURCE; DATABASE; KEGG},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Oliver, Stephen/AAQ-5992-2021
+ Dikicioglu, Duygu/W-4354-2019
+ },
+ORCID-Numbers = {Oliver, Stephen/0000-0003-3410-6439
+ Dikicioglu, Duygu/0000-0002-3018-4790
+ Cankorur Cetinkaya, Ayca/0000-0002-4431-7259},
+Times-Cited = {11},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000411699200018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416513600020,
+Author = {Cordova, Lauren T. and Cipolla, Robert M. and Swarup, Adti and Long,
+ Christopher P. and Antoniewicz, Maciek R.},
+Title = {13C metabolic flux analysis of three divergent extremely
+ thermophilic bacteria: Geobacillus sp LC300, Thermus
+ thermophilus HB8, and Rhodothermus marinus DSM 4252},
+Journal = {METABOLIC ENGINEERING},
+Year = {2017},
+Volume = {44},
+Pages = {182-190},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2017.10.007},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Parallel labeling experiments; Metabolic model validation; Thermophiles;
+ Metabolic flux analysis},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; MASS ISOTOPOMER DISTRIBUTIONS;
+ ESCHERICHIA-COLI; NETWORK MODEL; STRAIN; GENE; BIOMASS; GENOME; GLUCOSE;
+ XYLOSE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009
+ Swarup, Aditi/AAD-4101-2019
+ },
+ORCID-Numbers = {Long, Christopher/0000-0003-1007-417X},
+Times-Cited = {22},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000416513600020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416838500020,
+Author = {Fernandez-de-Cossio-Diaz, Jorge and Leon, Kalet and Mulet, Roberto},
+Title = {Characterizing steady states of genome-scale metabolic networks in
+ continuous cell cultures},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2017},
+Volume = {13},
+Number = {11},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1005835},
+Article-Number = {e1005835},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI;
+ CHO-CELLS; QUANTITATIVE PREDICTION; OVERFLOW METABOLISM; HYBRIDOMA
+ GROWTH; ANIMAL-CELLS; LACTATE; BATCH},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ORCID-Numbers = {Fernandez de Cossio Diaz, Jorge/0000-0002-4476-805X
+ Mulet, Roberto/0000-0001-5168-5116
+ Leon, Kalet/0000-0002-3709-7091},
+Times-Cited = {17},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000416838500020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416721200004,
+Author = {Hara, Kiyotaka Y. and Kobayashi, Jyumpei and Yamada, Ryosuke and Sasaki,
+ Daisuke and Kuriya, Yuki and Hirono-Hara, Yoko and Ishii, Jun and Araki,
+ Michihiro and Kondo, Akihiko},
+Title = {Transporter engineering in biomass utilization by yeast},
+Journal = {FEMS YEAST RESEARCH},
+Year = {2017},
+Volume = {17},
+Number = {7},
+Month = {NOV},
+Type = {Review},
+DOI = {10.1093/femsyr/fox061},
+Article-Number = {fox061},
+ISSN = {1567-1356},
+EISSN = {1567-1364},
+Keywords = {transporter; sugar uptake; exporter; synthetic bioengineering; yeast;
+ biomass-utilizing bioprocess},
+Keywords-Plus = {ALPHA-GLUCOSIDE TRANSPORT; DIRECT ETHANOL-PRODUCTION;
+ SACCHAROMYCES-CEREVISIAE; XYLOSE FERMENTATION; HEXOSE TRANSPORTERS;
+ DIRECTED EVOLUTION; ACID PRODUCTION; CELLOBIOSE FERMENTATION;
+ SIMULTANEOUS SACCHARIFICATION; CELLODEXTRIN TRANSPORTER},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+ResearcherID-Numbers = {Ishii, Jun/D-7670-2016
+ SASAKI, Daisuke/F-9597-2015
+ Kondo, Akihiko/A-2130-2015
+ Yamada, Ryosuke/N-2029-2015},
+ORCID-Numbers = {Ishii, Jun/0000-0003-2568-515X
+ Yamada, Ryosuke/0000-0003-3820-7501},
+Times-Cited = {28},
+Journal-ISO = {FEMS Yeast Res.},
+Unique-ID = {WOS:000416721200004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000413256800032,
+Author = {Joshi, Chintan J. and Peebles, Christie A. M. and Prasad, Ashok},
+Title = {Modeling and analysis of flux distribution and bioproduct formation in
+ Synechocystis sp PCC 6803 using a new genome-scale metabolic
+ reconstruction},
+Journal = {ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS},
+Year = {2017},
+Volume = {27},
+Pages = {295-310},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.algal.2017.09.013},
+ISSN = {2211-9264},
+Keywords = {Metabolic engineering; Dynamic flux balance analysis; Cyanobacteria;
+ Biofuels; Genome-scale models},
+Keywords-Plus = {BALANCE ANALYSIS; ESCHERICHIA-COLI; CYANOBACTERIA; DATABASE; NETWORK;
+ PATHWAY; PHOTORESPIRATION; GROWTH; IDENTIFICATION; DEHYDROGENASE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Prasad, Ashok/HDN-5956-2022
+ },
+ORCID-Numbers = {Joshi, Chintan/0000-0002-9339-2511
+ Prasad, Ashok/0000-0002-0832-8153},
+Times-Cited = {15},
+Journal-ISO = {Algal Res.},
+Unique-ID = {WOS:000413256800032},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416513600011,
+Author = {Long, Christopher P. and Gonzalez, Jacqueline E. and Feist, Adam M. and
+ Palsson, Bernhard O. and Antoniewicz, Maciek R.},
+Title = {Fast growth phenotype of E. coli K-12 from adaptive
+ laboratory evolution does not require intracellular flux rewiring},
+Journal = {METABOLIC ENGINEERING},
+Year = {2017},
+Volume = {44},
+Pages = {100-107},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2017.09.012},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Adaptive evolution; Escherichia coli; Metabolic flux analysis; Flux
+ balance analysis; Fast growth},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; MASS ISOTOPOMER DISTRIBUTIONS;
+ ESCHERICHIA-COLI; MG1655; METABOLISM; GLUCOSE; XYLOSE; MODEL;
+ FERMENTATION; KNOCKOUTS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009
+ },
+ORCID-Numbers = {Long, Christopher/0000-0003-1007-417X},
+Times-Cited = {44},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000416513600011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416513600021,
+Author = {Long, Christopher P. and Gonzalez, Jacqueline E. and Cipolla, Robert M.
+ and Antoniewicz, Maciek R.},
+Title = {Metabolism of the fast-growing bacterium Vibrio natriegens
+ elucidated by 13C metabolic flux analysis},
+Journal = {METABOLIC ENGINEERING},
+Year = {2017},
+Volume = {44},
+Pages = {191-197},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.ymben.2017.10.008},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Fast growth; Glucose uptake; Vibrio natriegens; Metabolism; Metabolic
+ network model},
+Keywords-Plus = {PARALLEL LABELING EXPERIMENTS; MASS ISOTOPOMER DISTRIBUTIONS; ADAPTIVE
+ LABORATORY EVOLUTION; CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI;
+ QUANTITATIVE PREDICTION; PSEUDOMONAS-NATRIEGENS; CELLULAR-METABOLISM;
+ BIOMASS COMPOSITION; GLUCOSE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Antoniewicz, Maciek R/D-4015-2009
+ },
+ORCID-Numbers = {Long, Christopher/0000-0003-1007-417X},
+Times-Cited = {49},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000416513600021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000413685300004,
+Author = {Pan, Xiao and Dalm, Ciska and Wijffels, Rene H. and Martens, Dirk E.},
+Title = {Metabolic characterization of a CHO cell size increase phase in
+ fed-batch cultures},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2017},
+Volume = {101},
+Number = {22},
+Pages = {8101-8113},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1007/s00253-017-8531-y},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Chinese hamster ovary (CHO) cell; Fed-batch; Antibody production; Phase
+ transition; Metabolic flux analysis; Cell size increase},
+Keywords-Plus = {FLUX ANALYSIS; HYBRIDOMA CELLS; ANIMAL-CELLS; GROWTH; PRODUCTIVITY;
+ MEDIA},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Pan, Xiao/0000-0003-0561-846X
+ Wijffels, Rene/0000-0001-7630-4295},
+Times-Cited = {70},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000413685300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000410011800004,
+Author = {Schwarzhans, Jan-Philipp and Luttermann, Tobias and Geier, Martina and
+ Kalinowski, Joern and Friehs, Karl},
+Title = {Towards systems metabolic engineering in Pichia pastoris},
+Journal = {BIOTECHNOLOGY ADVANCES},
+Year = {2017},
+Volume = {35},
+Number = {6},
+Pages = {681-710},
+Month = {NOV 1},
+Type = {Review},
+DOI = {10.1016/j.biotechadv.2017.07.009},
+ISSN = {0734-9750},
+EISSN = {1873-1899},
+Keywords = {Pichia pastoris; Komagataella phaffii; Non-conventional yeasts; Genetic
+ engineering; Metabolic engineering; Recombinant protein production;
+ Promoters; Systems biology; Physiology},
+Keywords-Plus = {RECOMBINANT PROTEIN-PRODUCTION; GENOME-SCALE MODELS; IN-SILICO ANALYSIS;
+ AUTONOMOUSLY REPLICATING SEQUENCE; SYNTHETIC CORE PROMOTERS; HIGH-LEVEL
+ PRODUCTION; CELL-WALL INTEGRITY; SACCHAROMYCES-CEREVISIAE;
+ OVER-EXPRESSION; GENE-EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {93},
+Journal-ISO = {Biotechnol. Adv.},
+Unique-ID = {WOS:000410011800004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000411699200017,
+Author = {Thompson, R. Adam and Trinh, Cong T.},
+Title = {Overflow metabolism and growth cessation in Clostridium
+ thermocellum DSM1313 during high cellulose loading fermentations},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2017},
+Volume = {114},
+Number = {11},
+Pages = {2592-2604},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1002/bit.26374},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {clostridium thermocellum; metabolic network analysis; consolidated
+ bioprocessing; overflow metabolism; biofuels and biochemicals; redox
+ valve},
+Keywords-Plus = {ETHANOL-PRODUCTION; PYRUVATE CATABOLISM; HYDROGEN-PRODUCTION;
+ ZYMOMONAS-MOBILIS; ENZYME-ACTIVITIES; ELECTRON FLUX; STRAINS; CULTURE;
+ CELL; QUANTIFICATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Trinh, Cong T/H-5300-2012
+ },
+ORCID-Numbers = {Thompson, R. Adam/0000-0002-9862-4801},
+Times-Cited = {18},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000411699200017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000411538900008,
+Author = {Zheng, Yangyang and Yuan, Qianqian and Yang, Xiaoyan and Ma, Hongwu},
+Title = {Engineering Escherichia coli for poly-(3-hydroxybutyrate)
+ production guided by genome-scale metabolic network analysis},
+Journal = {ENZYME AND MICROBIAL TECHNOLOGY},
+Year = {2017},
+Volume = {106},
+Pages = {60-66},
+Month = {NOV},
+Type = {Article},
+DOI = {10.1016/j.enzmictec.2017.07.003},
+ISSN = {0141-0229},
+EISSN = {1879-0909},
+Keywords = {Poly-(3-hydroxybutyrate); Escherichia colt; Genome-scale metabolic
+ network analysis; Non-oxidative glycolysis pathway},
+Keywords-Plus = {TRANSHYDROGENASE UDHA; HALOMONAS TD01; POLYHYDROXYALKANOATES; ACETATE;
+ POLY(3-HYDROXYBUTYRATE); OVEREXPRESSION; ACCUMULATION; PATHWAYS; FLUX;
+ COA},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+Times-Cited = {21},
+Journal-ISO = {Enzyme Microb. Technol.},
+Unique-ID = {WOS:000411538900008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000413904000028,
+Author = {Zuniga, Cristal and Zaramela, Livia and Zengler, Karsten},
+Title = {Elucidation of complexity and prediction of interactions in microbial
+ communities},
+Journal = {MICROBIAL BIOTECHNOLOGY},
+Year = {2017},
+Volume = {10},
+Number = {6, SI},
+Pages = {1500-1522},
+Month = {NOV},
+Type = {Review},
+DOI = {10.1111/1751-7915.12855},
+ISSN = {1751-7915},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; HUMAN GUT MICROBIOME; ESCHERICHIA-COLI;
+ METAPROTEOMICS REVEALS; RHIZOSPHERE MICROBIOME; METABOLIC INTERACTIONS;
+ SYSTEMS BIOLOGY; AMINO-ACID; GENOME; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Zuniga, Cristal/CAA-0015-2022
+ Zaramela, Lívia Soares/AAD-2687-2022},
+ORCID-Numbers = {Zaramela, Lívia Soares/0000-0002-1065-3799},
+Times-Cited = {82},
+Journal-ISO = {Microb. Biotechnol.},
+Unique-ID = {WOS:000413904000028},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000413436200002,
+Author = {Abdel-Haleem, Alyaa M. and Lewis, Nathan E. and Jamshidi, Neema and
+ Mineta, Katsuhiko and Gao, Xin and Gojobori, Takashi},
+Title = {The Emerging Facets of Non-Cancerous Warburg Effect},
+Journal = {FRONTIERS IN ENDOCRINOLOGY},
+Year = {2017},
+Volume = {8},
+Month = {OCT 23},
+Type = {Article},
+DOI = {10.3389/fendo.2017.00279},
+Article-Number = {279},
+ISSN = {1664-2392},
+Keywords = {Warburg effect; cancer; immune cells; malaria; angiogenesis;
+ pluripotency; rapid proliferation; constraint-based metabolic modeling},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; T-CELL-ACTIVATION; METABOLIC REQUIREMENTS;
+ MITOCHONDRIAL BIOGENESIS; GLUCOSE-UPTAKE; CANCER; GLYCOLYSIS;
+ DIFFERENTIATION; AMPK; INFLAMMATION},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Mineta, Katsuhiko/A-5455-2012
+ Lewis, Nathan/ABE-7290-2020
+ Gao, Xin/D-5487-2013
+ },
+ORCID-Numbers = {Mineta, Katsuhiko/0000-0002-4727-045X
+ Lewis, Nathan/0000-0001-7700-3654
+ Gao, Xin/0000-0002-7108-3574
+ Abdel-haleem, Alyaa/0000-0002-3114-1100},
+Times-Cited = {45},
+Journal-ISO = {Front. Endocrinol.},
+Unique-ID = {WOS:000413436200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000411307200011,
+Author = {Weiner, Michael and Troendle, Julia and Albermann, Christoph and
+ Sprenger, Georg A. and Weuster-Botz, Dirk},
+Title = {Metabolic control analysis of L-phenylalanine production from glycerol
+ with engineered E. coli using data from short-term
+ steady-state perturbation experiments},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2017},
+Volume = {126},
+Pages = {86-100},
+Month = {OCT 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2017.06.016},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {Metabolic control analysis; Perturbation experiments; L-Phenylalanine;
+ Constraint-based flux estimation; Metabolomics; Thermodynamics},
+Keywords-Plus = {RECOMBINANT ESCHERICHIA-COLI; FLUX ANALYSIS; IN-VIVO; SYNTHASE; KINASE;
+ MECHANISM; PATHWAYS; GLUCOSE; BIOSYNTHESIS; FACILITATOR},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Sprenger, Georg A./E-2384-2011
+ },
+ORCID-Numbers = {Sprenger, Georg A./0000-0002-7879-8978
+ Weuster-Botz, Dirk/0000-0002-1171-4194},
+Times-Cited = {9},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000411307200011},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000412192200002,
+Author = {Wang, Junhua and Wang, Cheng and Song, Kejing and Wen, Jianping},
+Title = {Metabolic network model guided engineering ethylmalonyl-CoA pathway to
+ improve ascomycin production in Streptomyces hygroscopicus
+ var. ascomyceticus},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2017},
+Volume = {16},
+Month = {OCT 3},
+Type = {Article},
+DOI = {10.1186/s12934-017-0787-5},
+Article-Number = {169},
+ISSN = {1475-2859},
+Keywords = {Ascomycin; FK520; Metabolic network model; Ethylmalonyl-CoA pathway;
+ Streptomyces hygroscopicus var. ascomyceticus},
+Keywords-Plus = {POLYKETIDE EXTENDER UNITS; COELICOLOR A3(2); FK506 PRODUCTION; CLONING
+ VECTORS; BIOSYNTHESIS; GENE; ENHANCEMENT; FK520; RECONSTRUCTION;
+ IDENTIFICATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Wang, Cheng/0000-0003-3665-4965},
+Times-Cited = {19},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000412192200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000411735900029,
+Author = {Cvitanovic, Tanja and Reichert, Matthias C. and Moskon, Miha and Mraz,
+ Miha and Lammert, Frank and Rozman, Damjana},
+Title = {Large-Scale Computational Models of Liver Metabolism: How Far From the
+ Clinics?},
+Journal = {HEPATOLOGY},
+Year = {2017},
+Volume = {66},
+Number = {4},
+Pages = {1323-1334},
+Month = {OCT},
+Type = {Review},
+DOI = {10.1002/hep.29268},
+ISSN = {0270-9139},
+EISSN = {1527-3350},
+Keywords-Plus = {HEPATITIS-C VIRUS; HEPATOCELLULAR-CARCINOMA; GENETIC-VARIATION; SYSTEMS
+ BIOLOGY; EXPRESSION DATA; NETWORK MODEL; CANCER; RECONSTRUCTION;
+ THERAPY; INTEGRATION},
+Research-Areas = {Gastroenterology \& Hepatology},
+Web-of-Science-Categories = {Gastroenterology \& Hepatology},
+ResearcherID-Numbers = {Moškon, Miha/J-3802-2019},
+ORCID-Numbers = {Moškon, Miha/0000-0003-4600-1730},
+Times-Cited = {16},
+Journal-ISO = {Hepatology},
+Unique-ID = {WOS:000411735900029},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000413965600005,
+Author = {Eyassu, Filmon and Angione, Claudio},
+Title = {Modelling pyruvate dehydrogenase under hypoxia and its role in cancer
+ metabolism},
+Journal = {ROYAL SOCIETY OPEN SCIENCE},
+Year = {2017},
+Volume = {4},
+Number = {10},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1098/rsos.170360},
+Article-Number = {170360},
+ISSN = {2054-5703},
+Keywords = {constraint-based models; flux balance analysis; cancer metabolism;
+ pyruvate dehydrogenase; hypoxia},
+Keywords-Plus = {GLUTAMINE-METABOLISM; SUCCINATE; FUMARATE; ADAPTATION; PREDICTION;
+ RECONSTRUCTION; REPERFUSION; ISCHEMIA; LACTATE; ENZYMES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Angione, Claudio/0000-0002-3140-7909},
+Times-Cited = {13},
+Journal-ISO = {R. Soc. Open Sci.},
+Unique-ID = {WOS:000413965600005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000413070300004,
+Author = {Jian, Xingxing and Li, Ningchuan and Chen, Qian and Hua, Qiang},
+Title = {Model-guided identification of novel gene amplification targets for
+ improving succinate production in Escherichia coli NZN111},
+Journal = {INTEGRATIVE BIOLOGY},
+Year = {2017},
+Volume = {9},
+Number = {10},
+Pages = {830-835},
+Month = {OCT 1},
+Type = {Article},
+DOI = {10.1039/c7ib00077d},
+ISSN = {1757-9694},
+EISSN = {1757-9708},
+Keywords-Plus = {FERMENTATIVE LACTATE-DEHYDROGENASE; SCALE METABOLIC MODELS; ACID
+ PRODUCTION; KNOCKOUT STRATEGIES; BURDEN; OVEREXPRESSION; CARBOXYLASE;
+ FRAMEWORK; GLYCEROL; STRAINS},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ORCID-Numbers = {Jian, Xingxing/0000-0003-3587-662X},
+Times-Cited = {5},
+Journal-ISO = {Integr. Biol.},
+Unique-ID = {WOS:000413070300004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000408777100018,
+Author = {Kamminga, Tjerko and Slagman, Simen-Jan and Bijlsma, Jetta J. E. and dos
+ Santos, Vitor A. P. Martins and Suarez-Diez, Maria and Schaap, Peter J.},
+Title = {Metabolic modeling of energy balances in Mycoplasma hyopneumoniae
+ shows that pyruvate addition increases growth rate},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2017},
+Volume = {114},
+Number = {10},
+Pages = {2339-2347},
+Month = {OCT},
+Type = {Article},
+DOI = {10.1002/bit.26347},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Mycoplasma hyopneumoniae; metabolic networks; constraint-based metabolic
+ modeling; energy balances; process optimization},
+Keywords-Plus = {DEFINED MEDIUM; GENOME; PREDICTION; CELLS},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Diez, Maria Suarez/AAI-1354-2020
+ },
+ORCID-Numbers = {Schaap, Peter/0000-0002-4346-6084
+ Suarez-Diez, Maria/0000-0001-5845-146X},
+Times-Cited = {9},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000408777100018},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000412764600009,
+Author = {Monk, Jonathan M. and Lloyd, Colton J. and Brunk, Elizabeth and Mih,
+ Nathan and Sastry, Anand and King, Zachary and Takeuchi, Rikiya and
+ Nomura, Wataru and Zhang, Zhen and Mori, Hirotada and Feist, Adam M. and
+ Palsson, Bernhard O.},
+Title = {iML1515, a knowledgebase that computes Escherichia coli
+ traits},
+Journal = {NATURE BIOTECHNOLOGY},
+Year = {2017},
+Volume = {35},
+Number = {10},
+Pages = {904-908},
+Month = {OCT},
+Type = {Letter},
+DOI = {10.1038/nbt.3956},
+ISSN = {1087-0156},
+EISSN = {1546-1696},
+Keywords-Plus = {K-12; MODEL; DISCOVERY},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {King, Zachary/V-3402-2019
+ Takeuchi, Rikiya/ABE-8480-2020
+ },
+ORCID-Numbers = {King, Zachary/0000-0003-1238-1499
+ Sastry, Anand/0000-0002-8293-3909
+ Brunk, Elizabeth/0000-0001-8578-8658
+ Takeuchi, Rikiya/0000-0003-2621-4077
+ Monk, Jonathan M./0000-0002-3895-8949},
+Times-Cited = {257},
+Journal-ISO = {Nat. Biotechnol.},
+Unique-ID = {WOS:000412764600009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000410462300017,
+Author = {Greene, Jennifer L. and Waechter, Andreas and Tyo, Keith E. J. and
+ Broadbelt, Linda J.},
+Title = {Acceleration Strategies to Enhance Metabolic Ensemble Modeling
+ Performance},
+Journal = {BIOPHYSICAL JOURNAL},
+Year = {2017},
+Volume = {113},
+Number = {5},
+Pages = {1150-1162},
+Month = {SEP 5},
+Type = {Article},
+DOI = {10.1016/j.bpj.2017.07.018},
+ISSN = {0006-3495},
+EISSN = {1542-0086},
+Keywords-Plus = {ESCHERICHIA-COLI; KINETIC-MODELS; CONSERVATION ANALYSIS; BIOCHEMICAL
+ NETWORKS; CELLULAR-METABOLISM; FLUX DATA; IDENTIFICATION; PERTURBATIONS;
+ ROBUSTNESS; PREDICTION},
+Research-Areas = {Biophysics},
+Web-of-Science-Categories = {Biophysics},
+ResearcherID-Numbers = {Waechter, Andreas/G-2499-2011
+ Tyo, Keith/AAM-4543-2020
+ Broadbelt, Linda/B-7640-2009
+ Tyo, Keith/H-6227-2012
+ },
+ORCID-Numbers = {Greene, Jennifer/0000-0002-2994-1088
+ Tyo, Keith/0000-0002-2342-0687},
+Times-Cited = {18},
+Journal-ISO = {Biophys. J.},
+Unique-ID = {WOS:000410462300017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000411981000040,
+Author = {Damiani, Chiara and Colombo, Riccardo and Gaglio, Daniela and
+ Mastroianni, Fabrizia and Pescini, Dario and Westerhoff, Hans Victor and
+ Mauri, Giancarlo and Vanoni, Marco and Alberghina, Lilia},
+Title = {A metabolic core model elucidates how enhanced utilization of glucose
+ and glutamine, with enhanced glutamine-dependent lactate production,
+ promotes cancer cell growth: The WarburQ effect},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2017},
+Volume = {13},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1005758},
+Article-Number = {e1005758},
+ISSN = {1553-734X},
+EISSN = {1553-7358},
+Keywords-Plus = {REDUCTIVE CARBOXYLATION; TCA CYCLE; OXIDATION; NETWORK; FLUX;
+ HETEROGENEITY; REQUIREMENTS; DYSFUNCTION; EXPRESSION; STRATEGIES},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Mauri, Giancarlo/M-3258-2013
+ Westerhoff, Hans V/I-5762-2012
+ Gaglio, Daniela/AEZ-3835-2022
+ Vanoni, Marco/AAA-3699-2021
+ Pescini, Dario/H-4866-2017
+ },
+ORCID-Numbers = {Mauri, Giancarlo/0000-0003-3520-4022
+ Westerhoff, Hans V/0000-0002-0443-6114
+ Vanoni, Marco/0000-0002-8690-2587
+ Pescini, Dario/0000-0002-3090-4823
+ Alberghina, Lilia/0000-0003-1694-931X},
+Times-Cited = {55},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000411981000040},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000408214300021,
+Author = {Ghadiri, Mehrdad and Heidari, Mahshid and Marashi, Sayed-Amir and
+ Mousavi, Seyed Hasan},
+Title = {A multiscale agent-based framework integrated with a constraint-based
+ metabolic network model of cancer for simulating avascular tumor growth},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2017},
+Volume = {13},
+Number = {9},
+Pages = {1888-1897},
+Month = {SEP 1},
+Type = {Article},
+DOI = {10.1039/c7mb00050b},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {CELLULAR-AUTOMATON MODEL; MULTICELLULAR SPHEROIDS; OXYGEN; EXPRESSION;
+ TARGET},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Ghadiri, Mehrdad/Y-4598-2019
+ Marashi, Sayed-Amir/A-5384-2008
+ },
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449
+ Heidari, Mahshid/0000-0001-8306-6774},
+Times-Cited = {11},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000408214300021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000411981000024,
+Author = {Labhsetwar, Piyush and Melo, Marcelo C. R. and Cole, John A. and
+ Luthey-Schulten, Zaida},
+Title = {Population FBA predicts metabolic phenotypes in yeast},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2017},
+Volume = {13},
+Number = {9},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1005728},
+Article-Number = {e1005728},
+EISSN = {1553-7358},
+Keywords-Plus = {GENOME-SCALE MODELS; GENE-EXPRESSION; SERINE; NOISE; RECONSTRUCTION;
+ STOCHASTICITY; MITOCHONDRIAL; NETWORKS; KINETICS; PROTEOME},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Melo, Marcelo Cardoso dos Reis/V-4019-2019
+ Labhsetwar, Piyush/P-3227-2019
+ },
+ORCID-Numbers = {Melo, Marcelo Cardoso dos Reis/0000-0001-6901-1646
+ Labhsetwar, Piyush/0000-0001-5933-3609
+ Luthey-Schulten, Zaida/0000-0001-9749-8367},
+Times-Cited = {16},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000411981000024},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000416271100090,
+Author = {Morin, Manon and Ropers, Delphine and Cinquemani, Eugenio and Portais,
+ Jean-Charles and Enjalbert, Brice and Cocaign-Bousquet, Muriel},
+Title = {The Csr System Regulates Escherichia coli Fitness by Controlling
+ Glycogen Accumulation and Energy Levels},
+Journal = {MBIO},
+Year = {2017},
+Volume = {8},
+Number = {5},
+Month = {SEP-OCT},
+Type = {Article},
+DOI = {10.1128/mBio.01628-17},
+Article-Number = {e01628-17},
+ISSN = {2150-7511},
+Keywords = {Csr system; carbon metabolism; Escherichia coli; glycogen},
+Keywords-Plus = {BINDING PROTEIN CSRA; MOUSE INTESTINE; ACETATE TRANSITION; CIRCUITRY
+ LINKING; CARBON NUTRITION; FLHDC EXPRESSION; GENE-EXPRESSION; GUT
+ MICROBIOTA; MESSENGER-RNA; GROWTH-RATES},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Cocaign-Bousquet, Muriel/ISV-5020-2023
+ Morin, Manon/AAB-4837-2021
+ Enjalbert, Brice/JFJ-8505-2023
+ },
+ORCID-Numbers = {Cocaign-Bousquet, Muriel/0000-0003-2033-9901
+ Enjalbert, Brice/0000-0003-1291-1373
+ Portais, Jean-Charles/0000-0002-3480-0933
+ Morin, Manon/0000-0003-2158-0473
+ Ropers, Delphine/0000-0003-2659-3003},
+Times-Cited = {16},
+Journal-ISO = {mBio},
+Unique-ID = {WOS:000416271100090},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000408730900010,
+Author = {Ottman, Noora and Davids, Mark and Suarez-Diez, Maria and Boeren, Sjef
+ and Schaap, Peter J. and dos Santos, Vitor A. P. Martins and Smidt,
+ Hauke and Belzer, Clara and de Vos, Willem M.},
+Title = {Genome-Scale Model and Omics Analysis of Metabolic Capacities of
+ Akkermansia muciniphila Reveal a Preferential Mucin-Degrading
+ Lifestyle},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2017},
+Volume = {83},
+Number = {18},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1128/AEM.01014-17},
+Article-Number = {e01014},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords = {Akkermansia; acetate; gut microbiota; metabolic modeling; mucin;
+ propionate; proteomics; transcriptomics},
+Keywords-Plus = {INTESTINAL MICROBIOTA; GUT; COLON; PROTEINS; PROTEOME; PATHWAYS;
+ BACTERIA; SHAPES; GENE; RNA},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ResearcherID-Numbers = {Ottman, Noora/C-2225-2018
+ Diez, Maria Suarez/AAI-1354-2020
+ Belzer, Clara/P-6500-2018
+ Smidt, Hauke/D-7054-2014
+ },
+ORCID-Numbers = {Belzer, Clara/0000-0001-6922-836X
+ Smidt, Hauke/0000-0002-6138-5026
+ Davids, Mark/0000-0003-3081-9124
+ Schaap, Peter/0000-0002-4346-6084
+ Suarez-Diez, Maria/0000-0001-5845-146X
+ Ottman, Noora/0000-0001-5011-9294},
+Times-Cited = {133},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000408730900010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000415852700013,
+Author = {Pinu, Farhana R. and Villas-Boas, Silas G.},
+Title = {Extracellular Microbial Metabolomics: The State of the Art},
+Journal = {METABOLITES},
+Year = {2017},
+Volume = {7},
+Number = {3},
+Month = {SEP},
+Type = {Review},
+DOI = {10.3390/metabo7030043},
+Article-Number = {43},
+ISSN = {2218-1989},
+Keywords = {metabolite footprinting; exometabolome; culture medium; metabolic
+ modelling; sample preparation; analytical instruments; data integration;
+ extracellular metabolites; intracellular metabolites},
+Keywords-Plus = {SOLID-PHASE MICROEXTRACTION; FUNCTIONAL GENOMICS;
+ SACCHAROMYCES-CEREVISIAE; SAMPLE PREPARATION; ESCHERICHIA-COLI; YEAST;
+ WATER; METABOLISM; EXTRACTION; PROTOCOL},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Villas-Boas, Silas/AAR-6748-2020
+ Villas-Boas, Silas/AAS-5888-2020
+ Villas-Boas, Silas Granato/HLQ-1860-2023
+ Pinu, Farhana/Q-8308-2017},
+ORCID-Numbers = {Villas-Boas, Silas/0000-0003-0148-5882
+ Pinu, Farhana/0000-0002-0180-9341},
+Times-Cited = {67},
+Journal-ISO = {Metabolites},
+Unique-ID = {WOS:000415852700013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000410016300016,
+Author = {Rejc, Ziva and Magdevska, Lidija and Trselic, Tilen and Osolin, Timotej
+ and Vodopivec, Rok and Mraz, Jakob and Pavliha, Eva and Zimic, Nikolaj
+ and Cvitanovic, Tanja and Rozman, Damjana and Moskon, Miha and Mraz,
+ Miha},
+Title = {Computational modelling of genome-scale metabolic networks and its
+ application to CHO cell cultures},
+Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
+Year = {2017},
+Volume = {88},
+Pages = {150-160},
+Month = {SEP 1},
+Type = {Article},
+DOI = {10.1016/j.compbiomed.2017.07.005},
+ISSN = {0010-4825},
+EISSN = {1879-0534},
+Keywords = {Metabolic networks; Genome-scale metabolic models; Chinese hamster ovary
+ cells; Flux balance analysis; Modelling and analysis},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS; SYSTEMS BIOLOGY;
+ QUANTITATIVE PREDICTION; RECONSTRUCTION; SOFTWARE; SEQUENCE; GROWTH;
+ VISUALIZATION; CYTOSCAPE},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
+ Engineering; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
+ Biomedical; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Moškon, Miha/J-3802-2019},
+ORCID-Numbers = {Moškon, Miha/0000-0003-4600-1730},
+Times-Cited = {20},
+Journal-ISO = {Comput. Biol. Med.},
+Unique-ID = {WOS:000410016300016},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000411731800039,
+Author = {Shah, Ab Rauf and Ahmad, Ahmad and Srivastava, Shireesh and Ali, B. M.
+ Jaffar},
+Title = {Reconstruction and analysis of a genome-scale metabolic model of
+ Nannochloropsis gaditana},
+Journal = {ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS},
+Year = {2017},
+Volume = {26},
+Pages = {354-364},
+Month = {SEP},
+Type = {Article},
+DOI = {10.1016/j.algal.2017.08.014},
+ISSN = {2211-9264},
+Keywords = {Nannochloropsis gaditana; Flux balance analysis; Biomass; Lipid;
+ Nitrogen limitation; Genome-scale reconstruction},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION;
+ CELLULAR-METABOLISM; GROWTH; PATHWAYS; CARBON; EUSTIGMATOPHYCEAE;
+ CULTIVATION; DATABASE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Shah, Ab Rauf/AAI-2726-2021
+ Mohammed, Jaffar Ali Baquir/AAU-5358-2020
+ Srivastava, Shireesh/JDC-9742-2023},
+ORCID-Numbers = {Shah, Ab Rauf/0000-0002-5779-154X
+ Srivastava, Shireesh/0000-0001-6139-1904},
+Times-Cited = {27},
+Journal-ISO = {Algal Res.},
+Unique-ID = {WOS:000411731800039},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000408622400194,
+Author = {Gamez-Pozo, Angelo and Trilla-Fuertes, Lucia and Berges-Soria, Julia and
+ Selevsek, Nathalie and Lopez-Vacas, Rocio and Diaz-Almiron, Mariana and
+ Nanni, Paolo and Arevalillo, Jorge M. and Navarro, Hilario and
+ Grossmann, Jonas and Gaya Moreno, Francisco and Gomez Rioja, Ruben and
+ Prado-Vazquez, Guillermo and Zapater-Moros, Andrea and Main, Paloma and
+ Feliu, Jaime and Martinez del Prado, Purificacion and Zamora, Pilar and
+ Ciruelos, Eva and Espinosa, Enrique and Fresno Vara, Juan Angel},
+Title = {Functional proteomics outlines the complexity of breast cancer molecular
+ subtypes},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {AUG 30},
+Type = {Article},
+DOI = {10.1038/s41598-017-10493-w},
+Article-Number = {10100},
+ISSN = {2045-2322},
+Keywords-Plus = {STROMAL MAST-CELLS; GENE-EXPRESSION; TAMOXIFEN RESISTANCE; MICROARRAY
+ DATA; PROTEIN; MARKER; METABOLISM; PREDICTION; SIGNATURE; SURVIVAL},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Vara, Juan Ángel Fresno/Y-9928-2019
+ Prado-Vazquez, Guillermo/T-1861-2017
+ Zamora, Pilar/AAM-9336-2021
+ Gamez, Angelo/HSG-7485-2023
+ Trilla, Lucia/AAG-8392-2019
+ Großmann, Jonas/IWD-9393-2023
+ Gayá Moreno, Francisco/ABE-9251-2021
+ Gamez-Pozo, Angelo/N-2506-2014
+ },
+ORCID-Numbers = {Vara, Juan Ángel Fresno/0000-0003-1527-1252
+ Prado-Vazquez, Guillermo/0000-0003-2456-6191
+ Zamora, Pilar/0000-0003-2631-9653
+ Trilla, Lucia/0000-0002-4452-3474
+ Gayá Moreno, Francisco/0000-0002-9779-4876
+ Nanni, Paolo/0000-0001-8429-3557
+ Arevalillo, Jorge M/0000-0003-1944-3699
+ Gamez-Pozo, Angelo/0000-0002-8931-0624
+ Navarro, Hilario/0000-0001-5594-869X
+ Espinosa Arranz, Enrique/0000-0001-6562-7902},
+Times-Cited = {26},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000408622400194},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000407980000038,
+Author = {Sinha, Neeraj and Suarez-Diez, Maria and van Schothorst, Evert M. and
+ Keijer, Jaap and dos Santos, Vitor A. P. Martins and Hooiveld, Guido J.
+ E. J.},
+Title = {Predicting the murine enterocyte metabolic response to diets that differ
+ in lipid and carbohydrate composition},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {AUG 18},
+Type = {Article},
+DOI = {10.1038/s41598-017-07350-1},
+Article-Number = {8784},
+ISSN = {2045-2322},
+Keywords-Plus = {INTESTINE; ABSORPTION; DISEASE; MODELS; ADULTS; LIVER},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Diez, Maria Suarez/AAI-1354-2020
+ Hooiveld, Guido JEJ/F-4912-2010
+ },
+ORCID-Numbers = {Hooiveld, Guido JEJ/0000-0003-1954-3542
+ Suarez-Diez, Maria/0000-0001-5845-146X
+ Sinha, Neeraj/0000-0002-0173-9849
+ van Schothorst, Evert/0000-0002-3036-5903
+ Sinha, Neeraj/0000-0001-5105-6475},
+Times-Cited = {7},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000407980000038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000407910200001,
+Author = {Vavitsas, Konstantinos and Rue, Emil Ostergaard and Stefansdottir, Lara
+ Kristin and Gnanasekaran, Thiyagarajan and Blennow, Andreas and Crocoll,
+ Christoph and Gudmundsson, Steinn and Jensen, Poul Erik},
+Title = {Responses of Synechocystis sp PCC 6803 to heterologous
+ biosynthetic pathways},
+Journal = {MICROBIAL CELL FACTORIES},
+Year = {2017},
+Volume = {16},
+Month = {AUG 15},
+Type = {Article},
+DOI = {10.1186/s12934-017-0757-y},
+Article-Number = {140},
+EISSN = {1475-2859},
+Keywords = {Cyanobacteria; Metabolism; Terpenoids; Amino acids; Metabolic modelling},
+Keywords-Plus = {SYNTHETIC BIOLOGY; CYANOBACTERIA; PHOTOSYNTHESIS; EXPRESSION; REGULATOR},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Jensen, Poul Erik/A-4862-2014
+ Crocoll, Christoph/C-2093-2015
+ Vavitsas, Konstantinos/A-5871-2015
+ },
+ORCID-Numbers = {Jensen, Poul Erik/0000-0001-6524-7723
+ Crocoll, Christoph/0000-0003-2754-3518
+ Vavitsas, Konstantinos/0000-0002-6828-1000
+ Gnanasekaran, Thiyagarajan/0000-0001-8645-7703},
+Times-Cited = {17},
+Journal-ISO = {Microb. Cell. Fact.},
+Unique-ID = {WOS:000407910200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000407632200002,
+Author = {Blass, Lisa Katharina and Weyler, Christian and Heinzle, Elmar},
+Title = {Network design and analysis for multi-enzyme biocatalysis},
+Journal = {BMC BIOINFORMATICS},
+Year = {2017},
+Volume = {18},
+Month = {AUG 10},
+Type = {Article},
+DOI = {10.1186/s12859-017-1773-y},
+Article-Number = {366},
+ISSN = {1471-2105},
+Keywords = {Network design; Network analysis; Pathway; Biocatalysis; Multi-enzyme
+ catalysis; Mixed-integer linear program; Path-finding; Side reactions;
+ Thermodynamics; Synthetic biology},
+Keywords-Plus = {LARGE-SCALE PRODUCTION; CYTOSCAPE; FRAMEWORK; MODELS; ROUTES; ENZYME;
+ CARBON; KEGG; TOOL},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+Times-Cited = {4},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000407632200002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000407401000001,
+Author = {Sexton, D. Joseph and Schuster, Martin},
+Title = {Nutrient limitation determines the fitness of cheaters in bacterial
+ siderophore cooperation},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2017},
+Volume = {8},
+Month = {AUG 10},
+Type = {Article},
+DOI = {10.1038/s41467-017-00222-2},
+Article-Number = {230},
+EISSN = {2041-1723},
+Keywords-Plus = {PSEUDOMONAS-AERUGINOSA; PYOVERDINE BIOSYNTHESIS; ESCHERICHIA-COLI;
+ PUBLIC-GOODS; EVOLUTION; COMPETITION; METABOLISM; ENERGETICS; DYNAMICS;
+ GROWTH},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+Times-Cited = {44},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000407401000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000406850500001,
+Author = {Menendez-Bravo, Simon and Paganini, Julian and Avignone-Rossa, Claudio
+ and Gramajo, Hugo and Arabolaza, Ana},
+Title = {Identification of FadAB Complexes Involved in Fatty Acid β-Oxidation in
+ Streptomyces coelicolor and Construction of a Triacylglycerol
+ Overproducing strain},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2017},
+Volume = {8},
+Month = {AUG 2},
+Type = {Article},
+DOI = {10.3389/fmicb.2017.01428},
+Article-Number = {1428},
+ISSN = {1664-302X},
+Keywords = {Streptomyces coelicolor; triacylglycerol accumulation; beta-oxidation of
+ fatty acids; neutral lipid; chemostat system},
+Keywords-Plus = {ESCHERICHIA-COLI; MYCOBACTERIUM-TUBERCULOSIS; RESISTANCE DETERMINANT;
+ ANTIBIOTIC PRODUCTION; TRANSCRIPTION FACTOR; YARROWIA-LIPOLYTICA;
+ MULTIENZYME COMPLEX; STORAGE LIPIDS; COA HYDRATASE; A3(2)},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Menendez-Bravo, Simon/0000-0003-2288-3759},
+Times-Cited = {12},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000406850500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000405176200014,
+Author = {Ankrah, Nana Y. D. and Luan, Junbo and Douglas, Angela E.},
+Title = {Cooperative Metabolism in a Three-Partner Insect-Bacterial Symbiosis
+ Revealed by Metabolic Modeling},
+Journal = {JOURNAL OF BACTERIOLOGY},
+Year = {2017},
+Volume = {199},
+Number = {15},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1128/JB.00872-16},
+Article-Number = {e00872},
+ISSN = {0021-9193},
+EISSN = {1098-5530},
+Keywords = {flux balance analysis; genome reduction; metabolic model; ``Candidatus
+ Hamiltonella defensa{''}; nutrient exchange; ``Candidatus Portiera
+ aleyrodidarum{''}; metabolic modeling},
+Keywords-Plus = {CANDIDATUS PORTIERA ALEYRODIDARUM; BEMISIA-TABACI B; GENOME SEQUENCE;
+ ENDOSYMBIOTIC BACTERIA; CAROTENOIDS; WHITEFLIES; EVOLUTION; DATABASE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Ankrah, Nana/IUO-8239-2023
+ },
+ORCID-Numbers = {Ankrah, Nana Yaw/0000-0003-0492-545X},
+Times-Cited = {49},
+Journal-ISO = {J. Bacteriol.},
+Unique-ID = {WOS:000405176200014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000408759400025,
+Author = {Aurich, Maike K. and Fleming, Ronan M. T. and Thiele, Ines},
+Title = {A systems approach reveals distinct metabolic strategies among the
+ NCI-60 cancer cell lines},
+Journal = {PLOS COMPUTATIONAL BIOLOGY},
+Year = {2017},
+Volume = {13},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1371/journal.pcbi.1005698},
+Article-Number = {e1005698},
+EISSN = {1553-7358},
+Keywords-Plus = {HYPOXIA-INDUCIBLE FACTORS; GLUTAMINE-METABOLISM; ITACONIC ACID; GLOBAL
+ RECONSTRUCTION; MELANOMA-CELLS; GLUCOSE; GROWTH; OXYGEN; SKIN; FLUX},
+Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014},
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110},
+Times-Cited = {16},
+Journal-ISO = {PLoS Comput. Biol.},
+Unique-ID = {WOS:000408759400025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000408602900007,
+Author = {Iman, Maryam and Sobati, Tabassom and Panahi, Yunes and Mobasheri,
+ Meysam},
+Title = {Systems Biology Approach to Bioremediation of Nitroaromatics:
+ Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by
+ Escherichia coli},
+Journal = {MOLECULES},
+Year = {2017},
+Volume = {22},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.3390/molecules22081242},
+Article-Number = {1242},
+ISSN = {1420-3049},
+Keywords = {nitroaromatics; 2,4,6-trinitrotoluene; environment; bioremediation;
+ biotransformation; bio-degradation; constraint-based analysis; systems
+ biology; metabolic engineering},
+Keywords-Plus = {PSEUDOMONAS-PUTIDA KT2440; FLUX BALANCE ANALYSIS; REDUCTIVE
+ TRANSFORMATION; QUANTITATIVE PREDICTION; TNT BIOTRANSFORMATION;
+ MICROBIAL REMEDIATION; KNOCKOUT STRATEGIES; CELLULAR-METABOLISM;
+ BIODEGRADATION; DEGRADATION},
+Research-Areas = {Biochemistry \& Molecular Biology; Chemistry},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Chemistry, Multidisciplinary},
+ResearcherID-Numbers = {Iman, Maryam/V-6443-2019
+ Iman, Maryam/T-6168-2018
+ },
+ORCID-Numbers = {Iman, Maryam/0000-0002-2753-6089
+ Iman, Maryam/0000-0002-2753-6089
+ Panahi, Yunes/0000-0002-2504-8356},
+Times-Cited = {8},
+Journal-ISO = {Molecules},
+Unique-ID = {WOS:000408602900007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000407216400002,
+Author = {Mueller, Alan J. and Peffers, Mandy J. and Proctor, Carole J. and Clegg,
+ Peter D.},
+Title = {Systems Approaches in Osteoarthritis: Identifying Routes to Novel
+ Diagnostic and Therapeutic Strategies},
+Journal = {JOURNAL OF ORTHOPAEDIC RESEARCH},
+Year = {2017},
+Volume = {35},
+Number = {8},
+Pages = {1573-1588},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1002/jor.23563},
+ISSN = {0736-0266},
+EISSN = {1554-527X},
+Keywords = {osteoarthritis; systems biology; cartilage; modelling},
+Keywords-Plus = {CHONDROCYTE PERICELLULAR MATRIX; FINITE-ELEMENT MODEL;
+ ARTICULAR-CARTILAGE; GENE-EXPRESSION; KNEE OSTEOARTHRITIS; SUBCHONDRAL
+ BONE; BIOLOGY APPROACH; MECHANICAL-PROPERTIES; RHEUMATOID-ARTHRITIS;
+ METABOLIC MODELS},
+Research-Areas = {Orthopedics},
+Web-of-Science-Categories = {Orthopedics},
+ResearcherID-Numbers = {Peffers, Mandy Jayne/AAV-9411-2020
+ },
+ORCID-Numbers = {Peffers, Mandy Jayne/0000-0001-6979-0440
+ Mueller-Breckenridge, Alan/0000-0001-5277-0793
+ Clegg, Peter/0000-0003-0632-0032
+ Proctor, Carole/0000-0002-1366-1399},
+Times-Cited = {8},
+Journal-ISO = {J. Orthop. Res.},
+Unique-ID = {WOS:000407216400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000405498900006,
+Author = {Pentjuss, A. and Stalidzans, E. and Liepins, J. and Kokina, A. and
+ Martynova, J. and Zikmanis, P. and Mozga, I. and Scherbaka, R. and
+ Hartman, H. and Poolman, M. G. and Fell, D. A. and Vigants, A.},
+Title = {Model-based biotechnological potential analysis of Kluyveromyces
+ marxianus central metabolism},
+Journal = {JOURNAL OF INDUSTRIAL MICROBIOLOGY \& BIOTECHNOLOGY},
+Year = {2017},
+Volume = {44},
+Number = {8},
+Pages = {1177-1190},
+Month = {AUG},
+Type = {Article},
+DOI = {10.1007/s10295-017-1946-8},
+ISSN = {1367-5435},
+EISSN = {1476-5535},
+Keywords = {Kluyveromyces marxianus; Modelling; Central metabolism; Metabolic
+ engineering; Essentiality analysis},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ETHANOL-PRODUCTION; ALCOHOLIC FERMENTATION;
+ XYLITOL PRODUCTION; ACID PRODUCTION; FUNCTIONAL-CHARACTERIZATION;
+ ELEVATED-TEMPERATURES; ACETYL-COENZYME; L-PHENYLALANINE; ETHYL-ACETATE},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Vigants, Armands/IAR-5597-2023
+ Mozga, Ivars/G-5888-2010
+ Stalidzans, Egils/G-5883-2010
+ Zikmanis, Peteris/W-2571-2019
+ Liepins, Janis/AGF-7603-2022
+ Martynova, Jekaterina/IAR-5779-2023
+ Fell, David A/B-2109-2009
+ },
+ORCID-Numbers = {Vigants, Armands/0000-0002-3742-4531
+ Stalidzans, Egils/0000-0001-6063-0184
+ Liepins, Janis/0000-0001-7778-5561
+ Martynova, Jekaterina/0000-0002-6768-4596
+ Fell, David A/0000-0001-6669-2247
+ Pentjuss, Agris/0000-0001-7880-5130
+ Kokina, Agnese/0000-0001-6043-1986
+ Mozga, Ivars/0000-0002-3357-0590},
+Times-Cited = {25},
+Journal-ISO = {J. Ind. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000405498900006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000406943100001,
+Author = {Sanchez, Benjamin J. and Zhang, Cheng and Nilsson, Avlant and Lahtvee,
+ Petri-Jaan and Kerkhoven, Eduard J. and Nielsen, Jens},
+Title = {Improving the phenotype predictions of a yeast genome-scale metabolic
+ model by incorporating enzymatic constraints},
+Journal = {MOLECULAR SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {13},
+Number = {8},
+Month = {AUG},
+Type = {Article},
+DOI = {10.15252/msb.20167411},
+Article-Number = {935},
+ISSN = {1744-4292},
+Keywords = {enzyme kinetics; flux balance analysis; molecular crowding; proteomics;
+ Saccharomyces cerevisiae},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; QUANTITATIVE PREDICTION;
+ FERMENTATIVE CAPACITY; GROWTH; PROTEIN; EXPRESSION; EVOLUTIONARY;
+ QUANTIFICATION; CONSISTENT},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {Kerkhoven, Eduard/H-2072-2014
+ Kerkhoven, Eduard/P-2469-2019
+ Lahtvee, Petri-Jaan/G-5257-2016
+ Sánchez, Benjamín J./O-6859-2019
+ Nielsen, Jens Bo/C-7632-2015
+ Zhang, Cheng/L-7906-2016
+ Nilsson, Avlant/AAD-3110-2022
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Kerkhoven, Eduard/0000-0002-3593-5792
+ Kerkhoven, Eduard/0000-0002-3593-5792
+ Lahtvee, Petri-Jaan/0000-0002-3327-3190
+ Sánchez, Benjamín J./0000-0001-6093-4110
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Zhang, Cheng/0000-0002-3721-8586
+ Nilsson, Avlant/0000-0002-9476-4516
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {242},
+Journal-ISO = {Mol. Syst. Biol.},
+Unique-ID = {WOS:000406943100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000409533800001,
+Author = {Schatschneider, Sarah and Schneider, Jessica and Blom, Jochen and
+ Letisse, Fabien and Niehaus, Karsten and Goesmann, Alexander and
+ Vorhoelter, Frank-Joerg},
+Title = {Systems and synthetic biology perspective of the versatile
+ plant-pathogenic and polysaccharide-producing bacterium Xanthomonas
+ campestris},
+Journal = {MICROBIOLOGY-SGM},
+Year = {2017},
+Volume = {163},
+Number = {8},
+Pages = {1117-1144},
+Month = {AUG},
+Type = {Review},
+DOI = {10.1099/mic.0.000473},
+ISSN = {1350-0872},
+EISSN = {1465-2080},
+Keywords = {plant pathogenesis; infection; bioinformatics tools; OMICS; metabolic
+ modelling; biotechnology},
+Keywords-Plus = {ORYZAE PV. ORYZAE; METABOLIC FLUX ANALYSIS; COMPARATIVE PROTEOMIC
+ ANALYSIS; XANTHAN GUM BIOSYNTHESIS; DIFFUSIBLE SIGNAL FACTOR; CELL-CELL
+ COMMUNICATION; TRANSCRIPTOME ANALYSIS; ESCHERICHIA-COLI; QUANTITATIVE
+ PROTEOMICS; SECRETOME ANALYSIS},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ORCID-Numbers = {Goesmann, Alexander/0000-0002-7086-2568
+ Fabien, Letisse/0000-0002-1490-0152},
+Times-Cited = {7},
+Journal-ISO = {Microbiology-(UK)},
+Unique-ID = {WOS:000409533800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000405889600004,
+Author = {Carey, Maureen A. and Papin, Jason A. and Guler, Jennifer L.},
+Title = {Novel Plasmodium falciparum metabolic network reconstruction
+ identifies shifts associated with clinical antimalarial resistance},
+Journal = {BMC GENOMICS},
+Year = {2017},
+Volume = {18},
+Month = {JUL 19},
+Type = {Article},
+DOI = {10.1186/s12864-017-3905-1},
+Article-Number = {543},
+ISSN = {1471-2164},
+Keywords = {Plasmodium falciparum; Malaria; Metabolism; Network reconstruction;
+ Artemisinin resistance; Flux balance analysis},
+Keywords-Plus = {MALARIA PARASITES; OXIDATIVE STRESS; SERINE HYDROXYMETHYLTRANSFERASE;
+ NUTRITIONAL-REQUIREMENTS; PERMEABILITY PATHWAYS; ASEXUAL BLOOD;
+ FUNCTIONAL GENOMICS; TOXOPLASMA-GONDII; MULTIPLE-TARGETS;
+ ACID-METABOLISM},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ORCID-Numbers = {Carey, Maureen/0000-0003-2890-5445
+ Guler, Jennifer/0000-0001-6301-4563},
+Times-Cited = {27},
+Journal-ISO = {BMC Genomics},
+Unique-ID = {WOS:000405889600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000405289100038,
+Author = {Damiani, Chiara and Di Filippo, Marzia and Pescini, Dario and Maspero,
+ Davide and Colombo, Riccardo and Mauri, Giancarlo},
+Title = {popFBA: tackling intratumour heterogeneity with Flux Balance Analysis},
+Journal = {BIOINFORMATICS},
+Year = {2017},
+Volume = {33},
+Number = {14},
+Pages = {I311-I318},
+Month = {JUL 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btx251},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; LACTATE SHUTTLE; TUMOR HETEROGENEITY;
+ CANCER-CELLS; METABOLISM; HALLMARK},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Mauri, Giancarlo/M-3258-2013
+ Maspero, Davide/AAD-9782-2020
+ Pescini, Dario/H-4866-2017
+ },
+ORCID-Numbers = {Mauri, Giancarlo/0000-0003-3520-4022
+ Pescini, Dario/0000-0002-3090-4823
+ Maspero, Davide/0000-0001-8519-4331
+ Damiani, Chiara/0000-0002-5742-8302},
+Times-Cited = {24},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000405289100038},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000402947900006,
+Author = {Wang, Cheng and Liu, Jiao and Liu, Huanhuan and Wang, Junhua and Wen,
+ Jianping},
+Title = {A genome-scale dynamic flux balance analysis model of Streptomyces
+ tsukubaensis NRRL18488 to predict the targets for increasing FK506
+ production},
+Journal = {BIOCHEMICAL ENGINEERING JOURNAL},
+Year = {2017},
+Volume = {123},
+Pages = {45-56},
+Month = {JUL 15},
+Type = {Article},
+DOI = {10.1016/j.bej.2017.03.017},
+ISSN = {1369-703X},
+EISSN = {1873-295X},
+Keywords = {FK506; Tacrolimus; GS-DFBA; S. tsukubaensis NRRL18488},
+Keywords-Plus = {ESCHERICHIA-COLI; SEMIALDEHYDE DEHYDROGENASE; SACCHAROMYCES-CEREVISIAE;
+ FEEDING STRATEGIES; BIOSYNTHESIS; METABOLISM; ASPARTOKINASE;
+ FERMENTATION; GROWTH; IMPROVEMENT},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {liu, huan/JEO-4705-2023
+ },
+ORCID-Numbers = {Wang, Cheng/0000-0003-3665-4965},
+Times-Cited = {22},
+Journal-ISO = {Biochem. Eng. J.},
+Unique-ID = {WOS:000402947900006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000404918700001,
+Author = {Loira, Nicolas and Mendoza, Sebastian and Paz Cortes, Maria and Rojas,
+ Natalia and Travisany, Dante and Di Genova, Alex and Gajardo, Natalia
+ and Ehrenfeld, Nicole and Maass, Alejandro},
+Title = {Reconstruction of the microalga Nannochloropsis salina genome-scale
+ metabolic model with applications to lipid production},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {JUL 4},
+Type = {Article},
+DOI = {10.1186/s12918-017-0441-1},
+Article-Number = {66},
+EISSN = {1752-0509},
+Keywords = {Genome-scale Metabolic model; Nannochloropsis salina; TAG; Microalg ae},
+Keywords-Plus = {FLUX BALANCE ANALYSIS; ESCHERICHIA-COLI; PHAEODACTYLUM-TRICORNUTUM;
+ SACCHAROMYCES-CEREVISIAE; CHLORELLA-VULGARIS; GROWTH; BIOSYNTHESIS;
+ PATHWAYS; NETWORK; GENES},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Maass, Alejandro E/D-5848-2012
+ },
+ORCID-Numbers = {Maass, Alejandro E/0000-0002-7038-4527
+ Travisany, Dante/0000-0002-2545-176X
+ Mendoza, Sebastian/0000-0002-2192-5569
+ Di Genova, Alex/0000-0002-3120-9283
+ Loira, Nicolas/0000-0002-3653-2901},
+Times-Cited = {32},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000404918700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000405854400012,
+Author = {Chao, Ran and Mishra, Shekhar and Si, Tong and Zhao, Huimin},
+Title = {Engineering biological systems using automated biofoundries},
+Journal = {METABOLIC ENGINEERING},
+Year = {2017},
+Volume = {42},
+Pages = {98-108},
+Month = {JUL},
+Type = {Review},
+DOI = {10.1016/j.ymben.2017.06.003},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords-Plus = {METABOLIC-CONTROL ANALYSIS; SYNTHETIC BIOLOGY; HIGH-THROUGHPUT;
+ HOMOLOGOUS RECOMBINATION; COMBINATORIAL DESIGN; ESCHERICHIA-COLI;
+ SACCHAROMYCES-CEREVISIAE; DYNAMIC-MODEL; DNA-SYNTHESIS; IN-VITRO},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Si, Tong/K-4513-2012
+ },
+ORCID-Numbers = {Si, Tong/0000-0003-2985-9014
+ Mishra, Shekhar/0000-0003-4737-685X},
+Times-Cited = {113},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000405854400012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000404054700012,
+Author = {Chen, Yu and Wang, Yonghong and Nielsen, Jens},
+Title = {Systematic inference of functional phosphorylation events in yeast
+ metabolism},
+Journal = {BIOINFORMATICS},
+Year = {2017},
+Volume = {33},
+Number = {13},
+Pages = {1995-2001},
+Month = {JUL 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btx110},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {CARBON},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Nielsen, Jens Bo/C-7632-2015
+ Chen, Yu/AAL-3329-2020
+ Nielsen, Jens/Q-1347-2017},
+ORCID-Numbers = {Nielsen, Jens Bo/0000-0001-5568-2916
+ Chen, Yu/0000-0003-3326-9068
+ Nielsen, Jens/0000-0002-9955-6003},
+Times-Cited = {8},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000404054700012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000404133800010,
+Author = {Cheng, Yougan and Thalhauser, Craig J. and Smithline, Shepard and
+ Pagidala, Jyotsna and Miladinov, Marko and Vezina, Heather E. and Gupta,
+ Manish and Leil, Tarek A. and Schmidt, Brian J.},
+Title = {QSP Toolbox: Computational Implementation of Integrated Workflow
+ Components for Deploying Multi-Scale Mechanistic Models},
+Journal = {AAPS JOURNAL},
+Year = {2017},
+Volume = {19},
+Number = {4},
+Pages = {1002-1016},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1208/s12248-017-0100-x},
+ISSN = {1550-7416},
+Keywords = {quantitative systems pharmacology; ordinary differential equations;
+ optimization; virtual patient; virtual population},
+Keywords-Plus = {QUANTITATIVE SYSTEMS PHARMACOLOGY; DRUG DISCOVERY; AFFINITY; SUPPORT;
+ TRANSLATION; METABOLISM; SIMULATION; PREDICTION; EFFICIENCY; SOFTWARE},
+Research-Areas = {Pharmacology \& Pharmacy},
+Web-of-Science-Categories = {Pharmacology \& Pharmacy},
+ResearcherID-Numbers = {Schmidt, Brian J/A-3805-2009
+ Cheng, Yougan/AAM-6024-2020
+ },
+ORCID-Numbers = {Schmidt, Brian/0000-0001-6015-9636
+ Leil, Tarek/0000-0002-6124-8638},
+Times-Cited = {38},
+Journal-ISO = {AAPS J.},
+Unique-ID = {WOS:000404133800010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403779800005,
+Author = {Jung, Eun Sung and Park, Hye Min and Hyun, Seung Min and Shon, Jong
+ Cheol and Lakshmanan, Meiyappan and Noh, Minsoo and Yeo, Hock Chuan and
+ Liu, Kwang-Hyeon and Lee, Dong-Yup and Hwang, Jae Sung and Lee, Choong
+ Hwan},
+Title = {Integrative metabolomic analysis reveals diet supplementation with green
+ tea alleviates UVB-damaged mouse skin correlated with ascorbate
+ metabolism and urea cycle},
+Journal = {METABOLOMICS},
+Year = {2017},
+Volume = {13},
+Number = {7},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1007/s11306-017-1218-7},
+Article-Number = {82},
+ISSN = {1573-3882},
+EISSN = {1573-3890},
+Keywords = {Anti-photoaging; Green tea; Metabolomics; Transcriptomics; Ascorbate
+ metabolism; Urea cycle},
+Keywords-Plus = {STRATUM-CORNEUM; LYSOPHOSPHATIDYLCHOLINE; IDENTIFICATION; PREVENTION;
+ CERAMIDES; ORNITHINE; EPIDERMIS; NETWORK; DEFENSE; STRESS},
+Research-Areas = {Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Endocrinology \& Metabolism},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/ABC-7628-2020
+ Lakshmanan, Meiyappan/AAM-1171-2020
+ Lee, Dong-Yup/D-6650-2011
+ },
+ORCID-Numbers = {Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Lee, Dong-Yup/0000-0003-0901-708X
+ Shon, Jong Cheol/0000-0002-1994-9465
+ Yeo, Hock Chuan/0000-0001-5176-8800},
+Times-Cited = {3},
+Journal-ISO = {Metabolomics},
+Unique-ID = {WOS:000403779800005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403495700007,
+Author = {Sandberg, Troy E. and Lloyd, Colton J. and Palsson, Bernhard O. and
+ Feist, Adam M.},
+Title = {Laboratory Evolution to Alternating Substrate Environments Yields
+ Distinct Phenotypic and Genetic Adaptive Strategies},
+Journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
+Year = {2017},
+Volume = {83},
+Number = {13},
+Month = {JUL},
+Type = {Article},
+DOI = {10.1128/AEM.00410-17},
+Article-Number = {e00410-17},
+ISSN = {0099-2240},
+EISSN = {1098-5336},
+Keywords = {adaptive laboratory evolution; Escherichia coli; adaptive mutations;
+ phenotypic variation},
+Keywords-Plus = {GENOME-SCALE MODELS; ESCHERICHIA-COLI; METABOLISM; GROWTH; MUTATIONS;
+ ADAPTATION; GLUCOSE; RECONSTRUCTION; MAINTENANCE; EXPRESSION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology},
+ORCID-Numbers = {Sandberg, Troy/0000-0003-3240-3659},
+Times-Cited = {52},
+Journal-ISO = {Appl. Environ. Microbiol.},
+Unique-ID = {WOS:000403495700007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000404535500001,
+Author = {Zhang, Yu and Cai, Jingyi and Shang, Xiuling and Wang, Bo and Liu,
+ Shuwen and Chai, Xin and Tan, Tianwei and Zhang, Yun and Wen, Tingyi},
+Title = {A new genome-scale metabolic model of Corynebacterium glutamicum
+ and its application},
+Journal = {BIOTECHNOLOGY FOR BIOFUELS},
+Year = {2017},
+Volume = {10},
+Month = {JUN 30},
+Type = {Article},
+DOI = {10.1186/s13068-017-0856-3},
+Article-Number = {169},
+ISSN = {1754-6834},
+Keywords = {Corynebacterium glutamicum; Genome-scale metabolic model; L-proline
+ production; Model-driven experimentation; Metabolic engineering},
+Keywords-Plus = {L-LYSINE PRODUCTION; DEHYDROGENASE COMPLEX-DEFICIENT; CONSTRAINT-BASED
+ MODELS; AMINO-ACID PRODUCTION; ESCHERICHIA-COLI; QUANTITATIVE
+ PREDICTION; CELLULAR-METABOLISM; PROLINE PRODUCTION; FLUX ANALYSIS;
+ CARBON-FLUX},
+Research-Areas = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Energy \& Fuels},
+ResearcherID-Numbers = {Wang, Bo/V-5152-2019
+ Wen, Tingyi/M-6095-2014
+ },
+ORCID-Numbers = {Wang, Bo/0000-0002-0643-0349
+ Wen, Tingyi/0000-0003-2583-7088
+ Cai, Jingyi/0000-0002-2018-1174},
+Times-Cited = {56},
+Journal-ISO = {Biotechnol. Biofuels},
+Unique-ID = {WOS:000404535500001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000404607900056,
+Author = {Acevedo, Alejandro and Conejeros, Raul and Aroca, German},
+Title = {Ethanol production improvement driven by genome-scale metabolic modeling
+ and sensitivity analysis in Scheffersomyces stipitis},
+Journal = {PLOS ONE},
+Year = {2017},
+Volume = {12},
+Number = {6},
+Month = {JUN 28},
+Type = {Article},
+DOI = {10.1371/journal.pone.0180074},
+Article-Number = {e0180074},
+ISSN = {1932-6203},
+Keywords-Plus = {YEAST PICHIA-STIPITIS; CONSTRAINT-BASED MODELS;
+ SACCHAROMYCES-CEREVISIAE; XYLOSE FERMENTATION; NADH AVAILABILITY;
+ ESCHERICHIA-COLI; CARBON SOURCE; GROWTH; OPTIMIZATION; GENE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Conejeros, Raul/A-2466-2011
+ Aroca, German/ABG-6714-2020
+ Conejeros, Raul/ABG-5517-2020},
+ORCID-Numbers = {Aroca, German/0000-0003-1376-7940
+ Conejeros, Raul/0000-0002-1273-535X},
+Times-Cited = {11},
+Journal-ISO = {PLoS One},
+Unique-ID = {WOS:000404607900056},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000405776200001,
+Author = {Schauble, Sascha and Stavrum, Anne-Kristin and Bockwoldt, Mathias and
+ Puntervoll, Pal and Heiland, Ines},
+Title = {SBMLmod: a Python-based web application and web service for efficient
+ data integration and model simulation},
+Journal = {BMC BIOINFORMATICS},
+Year = {2017},
+Volume = {18},
+Month = {JUN 24},
+Type = {Article},
+DOI = {10.1186/s12859-017-1722-9},
+Article-Number = {314},
+ISSN = {1471-2105},
+Keywords = {Web application; Web service; Data integration; Model simulation},
+Keywords-Plus = {IRRITABLE-BOWEL-SYNDROME; ANTICANCER DRUG SCREEN; SYSTEMS BIOLOGY;
+ INDOLEAMINE 2,3-DIOXYGENASE; METABOLIC NETWORK; KYNURENINE PATHWAY;
+ GENE-EXPRESSION; TRYPTOPHAN; SEROTONIN; DISEASE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Heiland, Ines/B-9212-2014
+ Schäuble, Sascha/AAF-7809-2021
+ },
+ORCID-Numbers = {Heiland, Ines/0000-0002-9124-5112
+ Bockwoldt, Mathias/0000-0002-4646-9969},
+Times-Cited = {5},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000405776200001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403403600001,
+Author = {Ben Said, Sami and Or, Dani},
+Title = {Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2017},
+Volume = {8},
+Month = {JUN 16},
+Type = {Article},
+DOI = {10.3389/fmicb.2017.01125},
+Article-Number = {1125},
+ISSN = {1664-302X},
+Keywords = {synthetic ecology; microbial ecology; microbial consortia; consortia
+ assembly; modular consortia; engineering consortia; engineering habitats},
+Keywords-Plus = {ANAEROBIC AMMONIUM OXIDATION; POLYCYCLIC AROMATIC-HYDROCARBONS;
+ NITROBACTER-AGILIS CELLS; MICROFLUIDIC SYSTEMS; NITROGEN-CYCLE;
+ GEOBACTER-METALLIREDUCENS; SYMBIOTIC BACTERIUM; KINETIC-PARAMETERS;
+ ETHANOL-PRODUCTION; NITRITE OXIDATION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Or, Dani/D-8768-2012},
+ORCID-Numbers = {Or, Dani/0000-0002-3236-2933},
+Times-Cited = {68},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000403403600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403413700068,
+Author = {Presta, Luana and Bosi, Emanuele and Mansouri, Leila and Dijkshoorn,
+ Lenie and Fani, Renato and Fondi, Marco},
+Title = {Constraint-based modeling identifies new putative targets to fight
+ colistin-resistant A. baumannii infections},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {JUN 16},
+Type = {Article},
+DOI = {10.1038/s41598-017-03416-2},
+Article-Number = {3706},
+ISSN = {2045-2322},
+Keywords-Plus = {SCALE METABOLIC RECONSTRUCTION; FLUX BALANCE ANALYSIS;
+ ACINETOBACTER-BAUMANNII; DELETION MUTANTS; NETWORKS; INFORMATION;
+ DATABASE; GSM/GPR; GENOMES; DRUGS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Mansouri, Leila/AAY-3337-2020
+ },
+ORCID-Numbers = {Mansouri, Leila/0000-0001-8442-9709
+ Presta, Luana/0000-0001-6482-6758
+ Bosi, Emanuele/0000-0002-4769-8667},
+Times-Cited = {25},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000403413700068},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403332400015,
+Author = {Weis, Sebastian and Carlos, Ana Rita and Moita, Maria Raquel and Singh,
+ Sumnima and Blankenhaus, Birte and Cardoso, Silvia and Larsen, Rasmus
+ and Rebelo, Sofia and Schaeuble, Sascha and Del Barrio, Laura and
+ Mithieux, Gilles and Rajas, Fabienne and Lindig, Sandro and Bauer,
+ Michael and Soares, Miguel P.},
+Title = {Metabolic Adaptation Establishes Disease Tolerance to Sepsis},
+Journal = {CELL},
+Year = {2017},
+Volume = {169},
+Number = {7},
+Pages = {1263+},
+Month = {JUN 15},
+Type = {Article},
+DOI = {10.1016/j.cell.2017.05.031},
+ISSN = {0092-8674},
+EISSN = {1097-4172},
+Keywords-Plus = {GLUCOSE-6-PHOSPHATASE GENE-EXPRESSION; IRON STORAGE; FERRITIN H; HEME;
+ LIVER; INFLAMMATION; BINDING; MICE; HOMEOSTASIS; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Soares, Miguel P/G-4188-2011
+ Soares, Maria/JGM-5854-2023
+ Carlos, Ana Rita/K-6014-2019
+ Carlos, Ana Rita/N-1137-2016
+ Weis, Sebastian/P-9016-2014
+ Schäuble, Sascha/AAF-7809-2021
+ Barrio, Laura/B-3767-2017
+ },
+ORCID-Numbers = {Carlos, Ana Rita/0000-0002-6953-1163
+ Carlos, Ana Rita/0000-0002-6953-1163
+ Weis, Sebastian/0000-0003-3201-2375
+ Barrio, Laura/0000-0001-9203-3296
+ Bauer, Michael/0000-0002-1521-3514
+ Gilles, Mithieux/0000-0003-3579-8529
+ Cardoso, Silvia/0000-0003-4639-698X
+ Rebelo, Sofia/0000-0001-8399-0262
+ Blankenhaus, Birte/0000-0003-0987-5228
+ Soares, Miguel/0000-0002-9314-4833
+ Singh, Sumnima/0000-0002-1826-0180
+ Moita, Maria Raquel/0000-0002-4624-8154},
+Times-Cited = {171},
+Journal-ISO = {Cell},
+Unique-ID = {WOS:000403332400015},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403958400001,
+Author = {Gonzalez, German A. Preciat and El Assal, Lemmer R. P. and Noronha,
+ Alberto and Thiele, Ines and Haraldsdottir, Hulda S. and Fleming, Ronan
+ M. T.},
+Title = {Comparative evaluation of atom mapping algorithms for balanced metabolic
+ reactions: application to Recon 3D},
+Journal = {JOURNAL OF CHEMINFORMATICS},
+Year = {2017},
+Volume = {9},
+Month = {JUN 14},
+Type = {Article},
+DOI = {10.1186/s13321-017-0223-1},
+Article-Number = {39},
+ISSN = {1758-2946},
+Keywords = {Atom mapping; Metabolic network reconstruction; Automation; RDT; DREAM;
+ AutoMapper; CLCA; MWED; ICMAP; Recon 3D},
+Keywords-Plus = {METRXN; MODELS; TOOL},
+Research-Areas = {Chemistry; Computer Science},
+Web-of-Science-Categories = {Chemistry, Multidisciplinary; Computer Science, Information Systems;
+ Computer Science, Interdisciplinary Applications},
+ResearcherID-Numbers = {Fleming, Ronan MT/ABC-4093-2021
+ Thiele, Ines/A-7629-2014
+ },
+ORCID-Numbers = {Fleming, Ronan MT/0000-0001-5346-9812
+ Thiele, Ines/0000-0002-8071-7110
+ Noronha, Alberto/0000-0002-0935-4599},
+Times-Cited = {17},
+Journal-ISO = {J. Cheminformatics},
+Unique-ID = {WOS:000403958400001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403884000001,
+Author = {Chenard, Thierry and Guenard, Frederic and Vohl, Marie-Claude and
+ Carpentier, Andre and Tchernof, Andre and Najmanovich, Rafael J.},
+Title = {Remodeling adipose tissue through in silico modulation of fat storage
+ for the prevention of type 2 diabetes},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Pages = {1-15},
+Month = {JUN 12},
+Type = {Article},
+DOI = {10.1186/s12918-017-0438-9},
+Article-Number = {60},
+ISSN = {1752-0509},
+Keywords = {Metabolic network; Diabetes; Adipocytes; Lipid metabolism; Flux balance
+ analysis; in-silico single gene deletion; Biomass production; Lipid
+ droplet production},
+Keywords-Plus = {MITOCHONDRIAL TRIFUNCTIONAL PROTEIN; PYRUVATE-DEHYDROGENASE DEFICIENCY;
+ METABOLIC NETWORK MODEL; GENOME-SCALE; GLOBAL RECONSTRUCTION; TARGETED
+ DISRUPTION; ACYLGLYCEROL KINASE; GENE-EXPRESSION; ACID; OBESITY},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Vohl, Marie-Claude/AAQ-1378-2021
+ },
+ORCID-Numbers = {Tchernof, Andre/0000-0002-2587-1000
+ Vohl, Marie-Claude/0000-0002-7017-5848},
+Times-Cited = {5},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000403884000001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000402131500025,
+Author = {Haraldsdottir, Hulda S. and Cousins, Ben and Thiele, Ines and Fleming,
+ Ronan M. T. and Vempala, Santosh},
+Title = {CHRR: coordinate hit-and-run with rounding for uniform sampling of
+ constraint-based models},
+Journal = {BIOINFORMATICS},
+Year = {2017},
+Volume = {33},
+Number = {11},
+Pages = {1741-1743},
+Month = {JUN 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btx052},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {VOLUME ALGORITHM; METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Fleming, Ronan MT/ABC-4093-2021},
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Fleming, Ronan MT/0000-0001-5346-9812},
+Times-Cited = {48},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000402131500025},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000402819000006,
+Author = {Hintermayer, Sarah B. and Weuster-Botz, Dirk},
+Title = {Experimental validation of in silico estimated biomass yields of
+ Pseudomonas putida KT2440},
+Journal = {BIOTECHNOLOGY JOURNAL},
+Year = {2017},
+Volume = {12},
+Number = {6},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1002/biot.201600720},
+Article-Number = {1600720},
+ISSN = {1860-6768},
+EISSN = {1860-7314},
+Keywords = {Batch cultivation process; Biomass yield; Flux balance analysis; Genome
+ scale model; Stirred-tank bioreactor},
+Keywords-Plus = {METABOLIC-RESPONSE; ESCHERICHIA-COLI; GENOME; GROWTH; GLUCOSE;
+ POLYHYDROXYALKANOATE; PATHWAYS; TOLUENE},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+ORCID-Numbers = {Weuster-Botz, Dirk/0000-0002-1171-4194},
+Times-Cited = {14},
+Journal-ISO = {Biotechnol. J.},
+Unique-ID = {WOS:000402819000006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000402142600003,
+Author = {Kim, Do Gyun and Lee, Wang-Hee and Seo, Sung-Won and Park, Hye-Sun},
+Title = {METABOLIC RECONSTRUCTION FOR DEVELOPING A TISSUE-SPECIFIC MODEL FOR
+ CATTLE GLYCOLYSIS USING COBRA},
+Journal = {JOURNAL OF BIOLOGICAL SYSTEMS},
+Year = {2017},
+Volume = {25},
+Number = {2},
+Pages = {231-246},
+Month = {JUN},
+Type = {Article},
+DOI = {10.1142/S0218339017500127},
+ISSN = {0218-3390},
+EISSN = {1793-6470},
+Keywords = {Metabolic Reconstruction; Cattle Glycolysis; Tissue-Specific Model;
+ COBRA},
+Keywords-Plus = {ESCHERICHIA-COLI; SCALE; COW; PREDICTION},
+Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Mathematical \&
+ Computational Biology},
+Web-of-Science-Categories = {Biology; Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Seo, Seongwon/E-9687-2013
+ },
+ORCID-Numbers = {Kim, Do-Gyun/0000-0002-0962-6515
+ Lee, Wang-Hee/0000-0002-8834-1779},
+Times-Cited = {0},
+Journal-ISO = {J. Biol. Syst.},
+Unique-ID = {WOS:000402142600003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000403138500019,
+Author = {Kruyer, Nicholas S. and Peralta-Yahya, Pamela},
+Title = {Metabolic engineering strategies to bio-adipic acid production},
+Journal = {CURRENT OPINION IN BIOTECHNOLOGY},
+Year = {2017},
+Volume = {45},
+Pages = {136-143},
+Month = {JUN},
+Type = {Review},
+DOI = {10.1016/j.copbio.2017.03.006},
+ISSN = {0958-1669},
+EISSN = {1879-0429},
+Keywords-Plus = {ESCHERICHIA-COLI; MUCONIC ACID; SACCHAROMYCES-CEREVISIAE;
+ BIOTECHNOLOGICAL PRODUCTION; BIOLOGICAL PRODUCTION; CIS,CIS-MUCONIC
+ ACID; CELLULAR-METABOLISM; FINE CHEMICALS; PATHWAY; BIOSYNTHESIS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology},
+Times-Cited = {76},
+Journal-ISO = {Curr. Opin. Biotechnol.},
+Unique-ID = {WOS:000403138500019},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000404756200008,
+Author = {Osorio, Daniel and Gonzalez, Janneth and Pinzon, Andres},
+Title = {minval: An R package for MINimal VALidation of Stoichiometric Reactions},
+Journal = {R JOURNAL},
+Year = {2017},
+Volume = {9},
+Number = {1},
+Pages = {114-123},
+Month = {JUN},
+Type = {Article},
+ISSN = {2073-4859},
+Research-Areas = {Computer Science; Mathematics},
+Web-of-Science-Categories = {Computer Science, Interdisciplinary Applications; Statistics \&
+ Probability},
+ResearcherID-Numbers = {GONZALEZ, JANNETH/AAB-9948-2020
+ Osorio Hurtado, Daniel C/U-6368-2017
+ Hurtado, Daniel Camilo Osorio/AAF-3138-2019
+ },
+ORCID-Numbers = {GONZALEZ, JANNETH/0000-0003-4482-256X
+ Osorio Hurtado, Daniel C/0000-0003-4424-8422
+ Hurtado, Daniel Camilo Osorio/0000-0003-4424-8422
+ Pinzon, Andres/0000-0002-4133-810X},
+Times-Cited = {2},
+Journal-ISO = {R Journal},
+Unique-ID = {WOS:000404756200008},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000402755600006,
+Author = {Lahtvee, Petri-Jaan and Sanchez, Benjamin J. and Smialowska, Agata and
+ Kasvandik, Sergo and Elsemman, Ibrahim E. and Gatto, Francesco and
+ Nielsen, Jens},
+Title = {Absolute Quantification of Protein and mRNA Abundances Demonstrate
+ Variability in Gene-Specific Translation Efficiency in Yeast},
+Journal = {CELL SYSTEMS},
+Year = {2017},
+Volume = {4},
+Number = {5},
+Pages = {495+},
+Month = {MAY 24},
+Type = {Article},
+DOI = {10.1016/j.cels.2017.03.003},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; TRANSCRIPTIONAL CONTROL;
+ CELL-WALL; IN-VIVO; TURNOVER; GROWTH; DYNAMICS; MASS; METABOLISM},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Gatto, Francesco/AAA-6682-2020
+ Nielsen, Jens Bo/C-7632-2015
+ Lahtvee, Petri-Jaan/G-5257-2016
+ Sánchez, Benjamín J./O-6859-2019
+ Nielsen, Jens/Q-1347-2017
+ },
+ORCID-Numbers = {Gatto, Francesco/0000-0002-9031-9562
+ Nielsen, Jens Bo/0000-0001-5568-2916
+ Lahtvee, Petri-Jaan/0000-0002-3327-3190
+ Sánchez, Benjamín J./0000-0001-6093-4110
+ Kasvandik, Sergo/0000-0003-0218-2410
+ Nielsen, Jens/0000-0002-9955-6003
+ Elsemman, Ibrahim/0000-0002-2720-8245},
+Times-Cited = {110},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000402755600006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000402755600007,
+Author = {Valgepea, Kaspar and Lemgruber, Renato de Souza Pinto and Meaghan,
+ Kieran and Palfreyman, Robin William and Abdalla, Tanus and Heijstra,
+ Bjom Daniel and Behrendorff, James Bruce and Tappel, Ryan and Kopke,
+ Michael and Simpson, Sean Dennis and Nielsen, Lars Keld and Marcellin,
+ Esteban},
+Title = {Maintenance of ATP Homeostasis Triggers Metabolic Shifts in
+ Gas-Fermenting Acetogens},
+Journal = {CELL SYSTEMS},
+Year = {2017},
+Volume = {4},
+Number = {5},
+Pages = {505+},
+Month = {MAY 24},
+Type = {Article},
+DOI = {10.1016/j.cels.2017.04.008},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {CARBON-MONOXIDE FERMENTATION; CONSTRAINT-BASED MODELS; WOOD-LJUNGDAHL
+ PATHWAY; CLOSTRIDIUM-AUTOETHANOGENUM; ENERGY-CONSERVATION;
+ ESCHERICHIA-COLI; ETHANOL; GENOME; SYNGAS; SYSTEMS},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Behrendorff, James/M-5452-2019
+ Valgepea, Kaspar/H-1473-2018
+ Nielsen, Lars K/A-5519-2011
+ Köpke, Michael/I-3963-2019
+ Behrendorff, James B Y H/G-1601-2010
+ Palfreyman, Robin W/V-8516-2017
+ Valgepea, Kaspar/ABC-7334-2021
+ },
+ORCID-Numbers = {Behrendorff, James/0000-0003-4130-6252
+ Valgepea, Kaspar/0000-0003-4803-7569
+ Nielsen, Lars K/0000-0001-8191-3511
+ Köpke, Michael/0000-0003-0642-1415
+ Behrendorff, James B Y H/0000-0003-4130-6252
+ Palfreyman, Robin W/0000-0002-1088-7069
+ Heijstra, Bjorn/0000-0002-7632-0823
+ Marcellin, Esteban/0000-0003-3173-7956},
+Times-Cited = {95},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000402755600007},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000402755600009,
+Author = {Yusufi, Faraaz Noor Khan and Lakshmanan, Meiyappan and Ho, Ying Swan and
+ Loo, Bernard Liat Wen and Ariyaratne, Pramila and Yang, Yuansheng and
+ Ng, Say Kong and Tan, Tessa Rui Min and Yeo, Hock Chuan and Lim, Hsueh
+ Lee and Ng, Sze Wai and Hiu, Ai Ping and Chow, Chung Ping and Wan,
+ Corrine and Chen, Shuwen and Teo, Gavin and Song, Gao and Chin, Ju Xin
+ and Ruan, Xiaoan and Sung, Ken Wing Kin and Hu, Wei-Shou and Yap,
+ Miranda Gek Sim and Bardor, Muriel and Nagarajan, Niranjan and Lee,
+ Dong-Yup},
+Title = {Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a
+ Recombinant CHO Cell Line},
+Journal = {CELL SYSTEMS},
+Year = {2017},
+Volume = {4},
+Number = {5},
+Pages = {530+},
+Month = {MAY 24},
+Type = {Article},
+DOI = {10.1016/j.cels.2017.04.009},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {HAMSTER OVARY CELLS; THERAPEUTIC MONOCLONAL-ANTIBODIES; CHINESE-HAMSTER;
+ MASS-SPECTROMETRY; TRANSCRIPTOME ANALYSIS; PROTEIN THERAPEUTICS; GENOME;
+ METABOLOMICS; EXPRESSION; SEQUENCE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Lakshmanan, Meiyappan/AAM-1171-2020
+ wan, corrine/JSK-1662-2023
+ Lee, Dong-Yup/D-6650-2011
+ Chen, Shuwen/JRY-0282-2023
+ Lakshmanan, Meiyappan/ABC-7628-2020
+ },
+ORCID-Numbers = {Lee, Dong-Yup/0000-0003-0901-708X
+ Chen, Shuwen/0000-0003-1245-1469
+ Lakshmanan, Meiyappan/0000-0003-2356-3458
+ Sung, Wing-Kin/0000-0001-7806-7086
+ Nagarajan, Niranjan/0000-0003-0850-5604
+ Ho, Ying Swan/0000-0002-9292-3106
+ Yeo, Hock Chuan/0000-0001-5176-8800},
+Times-Cited = {73},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000402755600009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000401613500002,
+Author = {van Hoek, Milan J. A. and Merks, Roeland M. H.},
+Title = {Emergence of microbial diversity due to cross-feeding interactions in a
+ spatial model of gut microbial metabolism},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {MAY 16},
+Type = {Article},
+DOI = {10.1186/s12918-017-0430-4},
+Article-Number = {56},
+ISSN = {1752-0509},
+Keywords = {Flux-balance analysis with molecular crowding; Dynamic multi-species
+ metabolic modeling; Intestinal microbiota; Multiscale modeling;
+ Compensated trait loss; Microbial communities},
+Keywords-Plus = {ESCHERICHIA-COLI; ISOLOGOUS DIVERSIFICATION; FECAL MICROBIOTA; SYSTEMS
+ BIOLOGY; LARGE-INTESTINE; GROWTH; EVOLUTION; BALANCE; DIET; BACTERIA},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Merks, Roeland MH/A-2249-2008},
+ORCID-Numbers = {Merks, Roeland MH/0000-0002-6152-687X},
+Times-Cited = {58},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000401613500002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000401568800001,
+Author = {Fondi, Marco and Pinatel, Eva and Tala, Adelfia and Damiano, Fabrizio
+ and Consolandi, Clarissa and Mattorre, Benedetta and Fico, Daniela and
+ Testini, Mariangela and De Benedetto, Giuseppe E. and Siculella, Luisa
+ and De Bellis, Gianluca and Alifano, Pietro and Peano, Clelia},
+Title = {Time-Resolved Transcriptomics and Constraint-Based Modeling Identify
+ System-Level Metabolic Features and Overexpression Targets to Increase
+ Spiramycin Production in Streptomyces ambofaciens},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2017},
+Volume = {8},
+Month = {MAY 12},
+Type = {Article},
+DOI = {10.3389/fmicb.2017.00835},
+Article-Number = {835},
+ISSN = {1664-302X},
+Keywords = {Streptomyces ambofaciens; antibiotic production; strain improvement;
+ metabolic modeling; transcriptomics; systems biology},
+Keywords-Plus = {OPTIMIZATION; RECONSTRUCTION; IDENTIFICATION; METRONIDAZOLE; POLYKETIDE;
+ GENERATION; PREDICTION; ALIGNMENT; MASIGPRO; SEQUENCE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Pinatel, Eva Maria/AAC-1365-2019
+ Peano, Clelia/C-4015-2018
+ Mattorre, Benedetta/AAC-2448-2022
+ De Bellis, Gianluca/H-9725-2013
+ Damiano, Fabrizio/AAF-9594-2020
+ De Benedetto, Giuseppe Egidio/G-9470-2012
+ },
+ORCID-Numbers = {Pinatel, Eva Maria/0000-0002-2544-4594
+ Peano, Clelia/0000-0001-7055-3629
+ De Bellis, Gianluca/0000-0002-1622-4477
+ Damiano, Fabrizio/0000-0001-7828-9519
+ De Benedetto, Giuseppe Egidio/0000-0002-0832-5470
+ Fico, Daniela/0000-0003-2728-3306
+ Alifano, Pietro/0000-0003-3768-7275},
+Times-Cited = {10},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000401568800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000407254700002,
+Author = {Bhutada, Govindprasad and Kavscek, Martin and Ledesma-Amaro, Rodrigo and
+ Thomas, Stephane and Rechberger, Gerald N. and Nicaud, Jean-Marc and
+ Natter, Klaus},
+Title = {Sugar versus fat: elimination of glycogen storage improves lipid
+ accumulation in Yarrowia lipolytica},
+Journal = {FEMS YEAST RESEARCH},
+Year = {2017},
+Volume = {17},
+Number = {3},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1093/femsyr/fox020},
+Article-Number = {fox020},
+ISSN = {1567-1356},
+EISSN = {1567-1364},
+Keywords = {oleaginous yeast; triacylglycerol; glycogen synthase; storage metabolism},
+Keywords-Plus = {YEAST SACCHAROMYCES-CEREVISIAE; ACTIVATED PROTEIN-KINASE; GENE
+ DISRUPTION; OLEAGINOUS YEASTS; MALIC ENZYME; METABOLISM; CARBON;
+ IDENTIFICATION; GLUCOSE; MUTANTS},
+Research-Areas = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Microbiology; Mycology},
+ResearcherID-Numbers = {Rechberger, Gerald Nikolaus/AGB-1206-2022
+ NICAUD, Jean-marc/ABA-9076-2021
+ Ledesma-Amaro, Rodrigo/A-7545-2017},
+ORCID-Numbers = {Rechberger, Gerald Nikolaus/0000-0002-0071-317X
+ Bhutada, Govindprasad/0000-0002-3945-9527
+ Kavscek, Martin/0000-0002-0109-565X
+ Ledesma-Amaro, Rodrigo/0000-0003-2631-5898},
+Times-Cited = {51},
+Journal-ISO = {FEMS Yeast Res.},
+Unique-ID = {WOS:000407254700002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000402130100029,
+Author = {Heirendt, Laurent and Thiele, Ines and Fleming, Ronan M. T.},
+Title = {DistributedFBA.jl: high-level, high-performance flux balance analysis in
+ Julia},
+Journal = {BIOINFORMATICS},
+Year = {2017},
+Volume = {33},
+Number = {9},
+Pages = {1421-1423},
+Month = {MAY 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btw838},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Keywords-Plus = {GLOBAL RECONSTRUCTION; METABOLISM; PREDICTION},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Fleming, Ronan MT/ABC-4093-2021
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Heirendt, Laurent/0000-0003-1861-0037},
+Times-Cited = {18},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000402130100029},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000401696800017,
+Author = {Islam, M. Ahsanul and Hadadi, Noushin and Ataman, Meric and
+ Hatzimanikatis, Vassily and Stephanopoulos, Gregory},
+Title = {Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis
+ from synthesis gas},
+Journal = {METABOLIC ENGINEERING},
+Year = {2017},
+Volume = {41},
+Pages = {173-181},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2017.04.005},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords-Plus = {COMPLEX METABOLIC NETWORKS; MOORELLA-THERMOACETICA; ESCHERICHIA-COLI;
+ CLOSTRIDIUM-LJUNGDAHLII; DESIGN; CHEMICALS; PREDICTION; DATABASES;
+ BIOFUELS; ENZYMES},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Hatzimanikatis, Vassily/G-6505-2010
+ Hadadi, Noushin/HLQ-3023-2023
+ Hadadi, Noushin/S-3193-2017
+ },
+ORCID-Numbers = {Hatzimanikatis, Vassily/0000-0001-6432-4694
+ Hadadi, Noushin/0000-0001-6614-4910
+ Ataman, Meric/0000-0002-7942-9226
+ Islam, M. Ahsanul/0000-0001-9585-6263},
+Times-Cited = {22},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000401696800017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000401696800014,
+Author = {Rivera, Jimmy G. Lafontaine and Theisen, Matthew K. and Chen, Po-Wei and
+ Liao, James C.},
+Title = {Kinetically accessible yield (KAY) for redirection of metabolism to
+ produce exo-metabolites},
+Journal = {METABOLIC ENGINEERING},
+Year = {2017},
+Volume = {41},
+Pages = {144-151},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2017.03.011},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Systems biology; Kinetic modeling; Yield calculation; Bioprocessing},
+Keywords-Plus = {C-13 FLUX ANALYSIS; ESCHERICHIA-COLI; MODELS; BIOFUELS; PATHWAY;
+ OVERPRODUCTION; CONSTRAINTS; INFORMATION; NETWORKS; GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Rivera, Jimmy G Lafontaine/E-5652-2015
+ },
+ORCID-Numbers = {Rivera, Jimmy G Lafontaine/0000-0002-3858-0835
+ Liao, James/0000-0002-4580-7276},
+Times-Cited = {3},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000401696800014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000400659600013,
+Author = {Sharma, Mahesh and Shaikh, Naeem and Yadav, Shailendra and Singh, Sushma
+ and Garg, Prabha},
+Title = {A systematic reconstruction and constraint-based analysis of
+ Leishmania donovani metabolic network: identification of
+ potential antileishmanial drug targets},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2017},
+Volume = {13},
+Number = {5},
+Pages = {955-969},
+Month = {MAY 1},
+Type = {Article},
+DOI = {10.1039/c6mb00823b},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {REDOX CONTROL; MODELS; DATABASE; PATHWAYS; BALANCE; SUSCEPTIBILITY;
+ CULTIVATION; EXPRESSION; PREDICTION; REDUCTASE},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+ResearcherID-Numbers = {yadav, Shailendra/G-1295-2017
+ },
+ORCID-Numbers = {yadav, Shailendra/0000-0002-0520-266X
+ Singh, Sushma/0000-0002-7089-6442
+ Garg, Prabha/0000-0002-6922-4809},
+Times-Cited = {28},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000400659600013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000401696800020,
+Author = {Valgepea, Kaspar and Loi, Kim Q. and Behrendorff, James B. and
+ Lemgruber, Renato de S. P. and Plan, Manuel and Hodson, Mark P. and
+ Koepke, Michael and Nielsen, Lars K. and Marcellin, Esteban},
+Title = {Arginine deiminase pathway provides ATP and boosts growth of the
+ gas-fermenting acetogen Clostridium autoethanogenum},
+Journal = {METABOLIC ENGINEERING},
+Year = {2017},
+Volume = {41},
+Pages = {202-211},
+Month = {MAY},
+Type = {Article},
+DOI = {10.1016/j.ymben.2017.04.007},
+ISSN = {1096-7176},
+EISSN = {1096-7184},
+Keywords = {Acetogen; Clostridium autoethanogenum; Syngas; Genome-scale modelling;
+ Arginine catabolism; RNA-sequencing},
+Keywords-Plus = {SCALE METABOLIC RECONSTRUCTION; CONSTRAINT-BASED MODELS;
+ LOW-CARBON-FUELS; COMMODITY CHEMICALS; ENERGY-CONSERVATION;
+ LACTOCOCCUS-LACTIS; GENOME; ETHANOL; ACETOBUTYLICUM; FERMENTATION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Nielsen, Lars K/A-5519-2011
+ Köpke, Michael/I-3963-2019
+ Valgepea, Kaspar/H-1473-2018
+ Loi, Quang Kim/A-6574-2018
+ Valgepea, Kaspar/ABC-7334-2021
+ Behrendorff, James B Y H/G-1601-2010
+ Behrendorff, James/M-5452-2019
+ Hodson, Mark/J-7609-2013},
+ORCID-Numbers = {Nielsen, Lars K/0000-0001-8191-3511
+ Köpke, Michael/0000-0003-0642-1415
+ Valgepea, Kaspar/0000-0003-4803-7569
+ Loi, Quang Kim/0000-0003-1913-5215
+ Behrendorff, James B Y H/0000-0003-4130-6252
+ Behrendorff, James/0000-0003-4130-6252
+ Marcellin, Esteban/0000-0003-3173-7956
+ Hodson, Mark/0000-0002-5436-1886},
+Times-Cited = {67},
+Journal-ISO = {Metab. Eng.},
+Unique-ID = {WOS:000401696800020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000401613100001,
+Author = {Banerjee, Deepanwita and Parmar, Dharmeshkumar and Bhattacharya,
+ Nivedita and Ghanate, Avinash D. and Panchagnula, Venkateswarlu and
+ Raghunathan, Anu},
+Title = {A scalable metabolite supplementation strategy against antibiotic
+ resistant pathogen Chromobacterium violaceum induced by
+ NAD+/NADH+ imbalance},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {APR 26},
+Type = {Article},
+DOI = {10.1186/s12918-017-0427-z},
+Article-Number = {51},
+ISSN = {1752-0509},
+Keywords = {Antibiotic resistance; Metabolomic; Flux balance analysis; Flux
+ variability analysis; Redox homeostasis; NAD; NADH; Metabolism},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; AMINODEOXYCHORISMATE LYASE;
+ QUANTITATIVE PREDICTION; STAPHYLOCOCCUS-AUREUS; CELLULAR-METABOLISM;
+ COBRA TOOLBOX; L-TRYPTOPHAN; EFFLUX PUMP; PROTEIN S12},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Banerjee, Deepanwita/AAD-5528-2021
+ Panchagnula, Venkateswarlu/X-4063-2019
+ },
+ORCID-Numbers = {Banerjee, Deepanwita/0000-0002-0083-0608
+ Panchagnula, Venkateswarlu/0000-0001-6441-2598
+ Ghanate, Avinash/0000-0002-6284-7667
+ Parmar, Dharmeshkumar/0000-0001-7956-7429},
+Times-Cited = {12},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000401613100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000400505800003,
+Author = {Rowland, Michael A. and Abdelzaher, Ahmed and Ghosh, Preetam and Mayo,
+ Michael L.},
+Title = {Crosstalk and the Dynamical Modularity of Feed-Forward Loops in
+ Transcriptional Regulatory Networks},
+Journal = {BIOPHYSICAL JOURNAL},
+Year = {2017},
+Volume = {112},
+Number = {8},
+Pages = {1539-1550},
+Month = {APR 25},
+Type = {Article},
+DOI = {10.1016/j.bpj.2017.02.044},
+ISSN = {0006-3495},
+EISSN = {1542-0086},
+Keywords-Plus = {GENE-REGULATION; EVOLUTION; MOTIFS; SPECIFICITY; INSULATION; MODELS},
+Research-Areas = {Biophysics},
+Web-of-Science-Categories = {Biophysics},
+ORCID-Numbers = {Ghosh, Preetam/0000-0003-3880-5886},
+Times-Cited = {9},
+Journal-ISO = {Biophys. J.},
+Unique-ID = {WOS:000400505800003},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000399708800001,
+Author = {Labena, Abraham A. and Ye, Yuan-Nong and Dong, Chuan and Zhang, Fa-Z and
+ Guo, Feng-Biao},
+Title = {SSER: Species specific essential reactions database},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {APR 19},
+Type = {Article},
+DOI = {10.1186/s12918-017-0426-0},
+Article-Number = {50},
+ISSN = {1752-0509},
+Keywords = {SSER; Database; Essential Reactions; Flux Balance Analysis (FBA);
+ Metabolic Networks},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; FLUX BALANCE ANALYSIS; EVOLUTIONARY
+ CONSERVATION; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM; ESSENTIAL
+ GENES; COBRA TOOLBOX; GENOME; NETWORKS; SYSTEMS},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Guo, Feng-Biao/JAZ-0458-2023
+ Guo, Feng-Biao/C-2761-2015
+ Labena, Abraham A/E-2549-2017
+ Ye, Yuan-Nong/C-2321-2015},
+ORCID-Numbers = {Guo, Feng-Biao/0000-0002-1129-5233
+ Labena, Abraham A/0000-0002-1418-3800
+ Ye, Yuan-Nong/0000-0002-2029-4558},
+Times-Cited = {3},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000399708800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000399374100001,
+Author = {Kalantari, Aida and Chen, Tao and Ji, Boyang and Stancik, Ivan A. and
+ Ravikumar, Vaishnavi and Franjevic, Damjan and Saulou-Berion, Claire and
+ Goelzer, Anne and Mijakovic, Ivan},
+Title = {Conversion of Glycerol to 3-Hydroxypropanoic Acid by Genetically
+ Engineered Bacillus subtilis},
+Journal = {FRONTIERS IN MICROBIOLOGY},
+Year = {2017},
+Volume = {8},
+Month = {APR 18},
+Type = {Article},
+DOI = {10.3389/fmicb.2017.00638},
+Article-Number = {638},
+ISSN = {1664-302X},
+Keywords = {3-hydroxypropanoic acid; glycerol; Bacillus subtilis; metabolic
+ engineering; glycerol kinase knock-out},
+Keywords-Plus = {ESCHERICHIA-COLI; SYNTHETIC PATHWAY; CARBON SOURCE; 1,3-PROPANEDIOL;
+ METABOLISM; BIOSYNTHESIS; GLUCOSE; COPRODUCTION; MODULATION; EVOLUTION},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Franjevic, Damjan/AAJ-2427-2020
+ CHEN, Tao/N-1817-2015
+ Ji, Boyang/HMV-6662-2023
+ Mijakovic, Ivan/Q-5583-2016
+ },
+ORCID-Numbers = {Franjevic, Damjan/0000-0001-6989-4426
+ CHEN, Tao/0000-0001-9588-1821
+ Ji, Boyang/0000-0002-7269-4342
+ SAULOU, Claire/0000-0003-4843-6076
+ Mijakovic, Ivan/0000-0002-8860-6853
+ Goelzer, Anne/0000-0003-2222-6142},
+Times-Cited = {17},
+Journal-ISO = {Front. Microbiol.},
+Unique-ID = {WOS:000399374100001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000399180800001,
+Author = {Valadez-Cano, Cecilio and Olivares-Hernandez, Roberto and
+ Resendis-Antonio, Osbaldo and DeLuna, Alexander and Delaye, Luis},
+Title = {Natural selection drove metabolic specialization of the chromatophore in
+ Paulinella chromatophora},
+Journal = {BMC EVOLUTIONARY BIOLOGY},
+Year = {2017},
+Volume = {17},
+Month = {APR 14},
+Type = {Article},
+DOI = {10.1186/s12862-017-0947-6},
+Article-Number = {99},
+ISSN = {1471-2148},
+Keywords = {Endosymbiont; Metabolic evolution; Adaptation; Metabolic integration},
+Keywords-Plus = {BACTERIUM BUCHNERA-APHIDICOLA; HORIZONTAL GENE-TRANSFER; FLUX BALANCE
+ ANALYSIS; PHOTOSYNTHETIC ORGANELLE; ENDOSYMBIOTIC BACTERIA; GENOME
+ SEQUENCE; EVOLUTION; CHLOROPLASTS; SYMBIOSIS; NETWORKS},
+Research-Areas = {Evolutionary Biology; Genetics \& Heredity},
+Web-of-Science-Categories = {Evolutionary Biology; Genetics \& Heredity},
+ResearcherID-Numbers = {RESENDIS, OSBALDO/ADE-5280-2022
+ DeLuna, Alexander/H-9986-2016
+ Arredondo, Luis José Delaye/A-9574-2015
+ },
+ORCID-Numbers = {RESENDIS, OSBALDO/0000-0001-5220-541X
+ DeLuna, Alexander/0000-0002-9236-2804
+ Arredondo, Luis José Delaye/0000-0003-4193-2720
+ Valadez-Cano, Cecilio/0000-0003-2022-1612
+ Olivares-Hernandez, Roberto/0000-0002-8431-4052},
+Times-Cited = {3},
+Journal-ISO = {BMC Evol. Biol.},
+Unique-ID = {WOS:000399180800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000398551900001,
+Author = {Bordbar, Aarash and Yurkovich, James T. and Paglia, Giuseppe and
+ Rolfsson, Ottar and Sigurjonsson, Olafur E. and Palsson, Bernhard O.},
+Title = {Elucidating dynamic metabolic physiology through network integration of
+ quantitative time-course metabolomics},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {APR 7},
+Type = {Article},
+DOI = {10.1038/srep46249},
+Article-Number = {46249},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; FLUX ANALYSIS;
+ SACCHAROMYCES-CEREVISIAE; PLATELET METABOLISM; CELLULAR-METABOLISM;
+ STORAGE; XYLOSE; RECONSTRUCTION; TECHNOLOGIES},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Sigurjonsson, Olafur/T-8190-2019
+ Paglia, Giuseppe/H-2012-2018
+ /AAG-5264-2021
+ },
+ORCID-Numbers = {Sigurjonsson, Olafur/0000-0002-4968-842X
+ Paglia, Giuseppe/0000-0003-4724-6801
+ /0000-0001-6460-6771
+ Rolfsson, Ottar/0000-0003-4258-6057},
+Times-Cited = {88},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000398551900001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000398548100009,
+Author = {Ye, Chao and Xu, Nan and Dong, Chuan and Ye, Yuannong and Zou, Xuan and
+ Chen, Xiulai and Guo, Fengbiao and Liu, Liming},
+Title = {IMGMD: A platform for the integration and standardisation of In
+ silico Microbial Genome-scale Metabolic Models},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {APR 7},
+Type = {Article},
+DOI = {10.1038/s41598-017-00820-6},
+Article-Number = {727},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; KNOCKOUT STRATEGIES; ESCHERICHIA-COLI;
+ RECONSTRUCTION; NETWORK; GENE; RESOURCE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Ye, Chao/M-3689-2019
+ Ye, Chao/H-7623-2014
+ Ye, Chao/HGD-3564-2022
+ Ye, Yuan-Nong/C-2321-2015
+ Liu, Liming/B-1972-2009
+ Guo, Feng-Biao/JAZ-0458-2023
+ Guo, Feng-Biao/C-2761-2015
+ Chen, Xiulai/AAB-8395-2020
+ },
+ORCID-Numbers = {Ye, Chao/0000-0002-6671-7819
+ Ye, Chao/0000-0002-6671-7819
+ Ye, Chao/0000-0002-6671-7819
+ Ye, Yuan-Nong/0000-0002-2029-4558
+ Liu, Liming/0000-0003-3022-936X
+ Guo, Feng-Biao/0000-0002-1129-5233
+ Chen, Xiulai/0000-0002-5154-3860
+ Xu, Nan/0000-0002-2510-3394},
+Times-Cited = {5},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000398548100009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000398414600001,
+Author = {Braunstein, Alfredo and Muntoni, Anna Paola and Pagnani, Andrea},
+Title = {An analytic approximation of the feasible space of metabolic networks},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2017},
+Volume = {8},
+Month = {APR 6},
+Type = {Article},
+DOI = {10.1038/ncomms14915},
+Article-Number = {14915},
+ISSN = {2041-1723},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; SCALE MODELS; SIZE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Braunstein, Alfredo/E-6924-2012
+ Pagnani, Andrea/J-2363-2015
+ Muntoni, Anna Paola/CAH-9476-2022},
+ORCID-Numbers = {Braunstein, Alfredo/0000-0002-4562-3610
+ Pagnani, Andrea/0000-0002-6509-0807
+ Muntoni, Anna Paola/0000-0003-3937-3763},
+Times-Cited = {19},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000398414600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000398614600002,
+Author = {Birkel, Garrett W. and Ghosh, Amit and Kumar, Vinay S. and Weaver,
+ Daniel and Ando, David and Backman, Tyler W. H. and Arkin, Adam P. and
+ Keasling, Jay D. and Martin, Hector Garcia},
+Title = {The JBEI quantitative metabolic modeling library (jQMM): a python
+ library for modeling microbial metabolism},
+Journal = {BMC BIOINFORMATICS},
+Year = {2017},
+Volume = {18},
+Month = {APR 5},
+Type = {Article},
+DOI = {10.1186/s12859-017-1615-y},
+Article-Number = {205},
+ISSN = {1471-2105},
+Keywords = {Flux analysis; C-13 Metabolic Flux Analysis; -omics data; Predictive
+ biology},
+Keywords-Plus = {C-13-METABOLIC FLUX ANALYSIS; ESCHERICHIA-COLI; CELLULAR-METABOLISM;
+ FATTY-ACIDS; SOFTWARE; BIOTECHNOLOGY; PROTEINS; GROWTH; FUELS; SOIL},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Keasling, Jay D/J-9162-2012
+ Martin, Hector Garcia/B-5357-2009
+ Keasling, Jay/HPG-6073-2023
+ Arkin, Adam/M-9941-2019
+ Ghosh, Amit/AAA-3490-2021
+ Ghosh, Amit/AAB-3140-2019
+ Arkin, Adam P/A-6751-2008
+ },
+ORCID-Numbers = {Keasling, Jay D/0000-0003-4170-6088
+ Martin, Hector Garcia/0000-0002-4556-9685
+ Arkin, Adam/0000-0002-4999-2931
+ Ghosh, Amit/0000-0003-3514-885X
+ Arkin, Adam P/0000-0002-4999-2931
+ Backman, Tyler/0000-0002-6056-353X},
+Times-Cited = {13},
+Journal-ISO = {BMC Bioinformatics},
+Unique-ID = {WOS:000398614600002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394921600001,
+Author = {Feng, Jun and Yang, Jing and Li, Xiaorong and Guo, Meijin and Wang,
+ Bochu and Yang, Shang-tian and Zou, Xiang},
+Title = {Reconstruction of a genome-scale metabolic model and in silico
+ analysis of the polymalic acid producer Aureobasidium pullulans
+ CCTCC M2012223},
+Journal = {GENE},
+Year = {2017},
+Volume = {607},
+Pages = {1-8},
+Month = {APR 5},
+Type = {Article},
+DOI = {10.1016/j.gene.2016.12.034},
+ISSN = {0378-1119},
+EISSN = {1879-0038},
+Keywords = {Biopolymers; Metabolic engineering; Pyruvate carboxylase; Reducing
+ equivalents},
+Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; MALIC-ACID; CARBON; XYLOSE},
+Research-Areas = {Genetics \& Heredity},
+Web-of-Science-Categories = {Genetics \& Heredity},
+ResearcherID-Numbers = {Zhang, Yiyang/HZI-3668-2023
+ Yang, Shang-Tian/A-7892-2009
+ },
+ORCID-Numbers = {, xiang/0000-0002-5875-1224},
+Times-Cited = {16},
+Journal-ISO = {Gene},
+Unique-ID = {WOS:000394921600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000398037400005,
+Author = {Appleton, Evan and Madsen, Curtis and Roehner, Nicholas and Densmore,
+ Douglas},
+Title = {Design Automation in Synthetic Biology},
+Journal = {COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY},
+Year = {2017},
+Volume = {9},
+Number = {4},
+Month = {APR},
+Type = {Article},
+DOI = {10.1101/cshperspect.a023978},
+Article-Number = {a023978},
+ISSN = {1943-0264},
+Keywords-Plus = {COMBINATORIAL DESIGN; MARKUP LANGUAGE; SYSTEMS; TOOL; DNA; OPTIMIZATION;
+ SIMULATION; SELECTION; STANDARD; PLATFORM},
+Research-Areas = {Cell Biology},
+Web-of-Science-Categories = {Cell Biology},
+ResearcherID-Numbers = {Densmore, Douglas/AAC-7059-2020},
+Times-Cited = {43},
+Journal-ISO = {Cold Spring Harbor Perspect. Biol.},
+Unique-ID = {WOS:000398037400005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000400631800012,
+Author = {Mendes-Soares, Helena and Chia, Nicholas},
+Title = {Community metabolic modeling approaches to understanding the gut
+ microbiome: Bridging biochemistry and ecology},
+Journal = {FREE RADICAL BIOLOGY AND MEDICINE},
+Year = {2017},
+Volume = {105},
+Number = {SI},
+Pages = {102-109},
+Month = {APR},
+Type = {Review},
+DOI = {10.1016/j.freeradbiomed.2016.12.017},
+ISSN = {0891-5849},
+EISSN = {1873-4596},
+Keywords = {Microbiome; Ecological models; Metabolic models; Community metabolic
+ models},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; CELLULAR-METABOLISM;
+ BIOCYC COLLECTION; METACYC DATABASE; IN-VITRO; GENOME; NETWORKS;
+ PATHWAYS; OXYGEN},
+Research-Areas = {Biochemistry \& Molecular Biology; Endocrinology \& Metabolism},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Endocrinology \& Metabolism},
+Times-Cited = {10},
+Journal-ISO = {Free Radic. Biol. Med.},
+Unique-ID = {WOS:000400631800012},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000399379900009,
+Author = {Opdam, Sjoerd and Richelle, Anne and Kellman, Benjamin and Li, Shanzhong
+ and Zielinski, Daniel C. and Lewis, Nathan E.},
+Title = {A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic
+ Models},
+Journal = {CELL SYSTEMS},
+Year = {2017},
+Volume = {4},
+Number = {3},
+Pages = {318-329},
+Month = {MAR 22},
+Type = {Article},
+DOI = {10.1016/j.cels.2017.01.010},
+ISSN = {2405-4712},
+EISSN = {2405-4720},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GLOBAL RECONSTRUCTION; ESSENTIAL GENES; FLUX
+ ANALYSIS; CELLS; CANCER; PREDICTION; GENOTYPE},
+Research-Areas = {Biochemistry \& Molecular Biology; Cell Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology; Cell Biology},
+ResearcherID-Numbers = {Li, Shangzhong/HHD-1393-2022
+ Li, Shangzhong/Y-6882-2019
+ Lewis, Nathan/ABE-7290-2020
+ },
+ORCID-Numbers = {Li, Shangzhong/0000-0003-0272-3942
+ Lewis, Nathan/0000-0001-7700-3654
+ Kellman, Ben/0000-0002-0780-6096
+ Zielinski, Daniel/0000-0001-6452-483X},
+Times-Cited = {125},
+Journal-ISO = {Cell Syst.},
+Unique-ID = {WOS:000399379900009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000396847900029,
+Author = {MacGillivray, Michael and Ko, Amy and Gruber, Emily and Sawyer, Miranda
+ and Almaas, Eivind and Holder, Allen},
+Title = {Robust Analysis of Fluxes in Genome-Scale Metabolic Pathways},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {MAR 21},
+Type = {Article},
+DOI = {10.1038/s41598-017-00170-3},
+Article-Number = {268},
+ISSN = {2045-2322},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; ESCHERICHIA-COLI; INTRACELLULAR FLUXES;
+ RECONSTRUCTION; OPTIMALITY; EXPRESSION; LEVEL},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ORCID-Numbers = {Almaas, Eivind/0000-0002-9125-326X},
+Times-Cited = {12},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000396847900029},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000395909600001,
+Author = {Bartell, Jennifer A. and Blazier, Anna S. and Yen, Phillip and
+ Thogersen, Juliane C. and Jelsbak, Lars and Goldberg, Joanna B. and
+ Papin, Jason A.},
+Title = {Reconstruction of the metabolic network of Pseudomonas aeruginosa
+ to interrogate virulence factor synthesis},
+Journal = {NATURE COMMUNICATIONS},
+Year = {2017},
+Volume = {8},
+Month = {MAR 7},
+Type = {Article},
+DOI = {10.1038/ncomms14631},
+Article-Number = {14631},
+ISSN = {2041-1723},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; QUANTITATIVE PREDICTION; TARGETING VIRULENCE;
+ CELLULAR-METABOLISM; COBRA TOOLBOX; STRAIN PA14; RESISTANCE; GENOME;
+ LUNG; INHIBITORS},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Jelsbak, Lars/B-6195-2013
+ },
+ORCID-Numbers = {Jelsbak, Lars/0000-0002-5759-9769
+ Bartell, Jennifer/0000-0003-2750-9678
+ Blazier, Anna/0000-0001-5226-0339
+ Yen, Phillip/0000-0002-0234-7791},
+Times-Cited = {79},
+Journal-ISO = {Nat. Commun.},
+Unique-ID = {WOS:000395909600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394372600004,
+Author = {Balagurunathan, Balaji and Jain, Vishist Kumar and Tear, Crystal Jing
+ Ying and Lim, Chan Yuen and Zhao, Hua},
+Title = {In silico design of anaerobic growth-coupled product formation in
+ Escherichia coli: experimental validation using a simple polyol,
+ glycerol},
+Journal = {BIOPROCESS AND BIOSYSTEMS ENGINEERING},
+Year = {2017},
+Volume = {40},
+Number = {3},
+Pages = {361-372},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1007/s00449-016-1703-9},
+ISSN = {1615-7591},
+EISSN = {1615-7605},
+Keywords = {In silico design; Reaction knockout; Genome-scale metabolic models;
+ Metabolic flux analysis; Glycerol},
+Keywords-Plus = {METABOLIC PATHWAY ANALYSIS; CONSTRAINT-BASED MODELS; KNOCKOUT
+ STRATEGIES; CHEMICAL PRODUCTION; GENOME; RECONSTRUCTION; FERMENTATION;
+ STRAINS; YEAST; GENERATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Engineering},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Engineering, Chemical},
+ResearcherID-Numbers = {Balagurunathan, Balaji/GXZ-8736-2022
+ Balagurunathan, Balaji/Q-4282-2016},
+ORCID-Numbers = {Balagurunathan, Balaji/0000-0003-0003-3040
+ Balagurunathan, Balaji/0000-0003-0003-3040},
+Times-Cited = {3},
+Journal-ISO = {Bioprocess. Biosyst. Eng.},
+Unique-ID = {WOS:000394372600004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000408195200004,
+Author = {Dufault-Thompson, Keith and Jian, Huahua and Cheng, Ruixue and Li, Jiefu
+ and Wang, Fengping and Zhang, Ying},
+Title = {A Genome-Scale Model of Shewanella piezotolerans Simulates
+ Mechanisms of Metabolic Diversity and Energy Conservation},
+Journal = {MSYSTEMS},
+Year = {2017},
+Volume = {2},
+Number = {2},
+Month = {MAR-APR},
+Type = {Article},
+DOI = {10.1128/mSystems.00165-16},
+Article-Number = {e00165-16},
+ISSN = {2379-5077},
+Keywords = {Shewanella; metabolic modeling},
+Keywords-Plus = {GLOBAL TRANSCRIPTOME ANALYSIS; CONSTRAINT-BASED MODELS; FILAMENTOUS
+ PHAGE SW1; ONEIDENSIS MR-1; OUTER-MEMBRANE; SYSTEMS BIOLOGY;
+ SUBCELLULAR-LOCALIZATION; ANAEROBIC RESPIRATION; ESCHERICHIA-COLI;
+ LOW-TEMPERATURE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Jian, Huahua/E-6732-2016
+ Zhang, Ying/HKF-2437-2023
+ Zhang, Ying/ABA-6518-2021
+ /M-8065-2017},
+ORCID-Numbers = {Zhang, Ying/0000-0001-8759-0194
+ Zhang, Ying/0000-0001-8759-0194
+ Jian, Huahua/0000-0001-5507-497X
+ Dufault-Thompson, Keith/0000-0002-0991-2255
+ /0000-0002-0062-4652},
+Times-Cited = {11},
+Journal-ISO = {mSystems},
+Unique-ID = {WOS:000408195200004},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000404133500005,
+Author = {Korla, Kalyani and Chandra, Nagasuma},
+Title = {A Systems Perspective of Signalling Networks in Host-Pathogen
+ Interactions},
+Journal = {JOURNAL OF THE INDIAN INSTITUTE OF SCIENCE},
+Year = {2017},
+Volume = {97},
+Number = {1},
+Pages = {41-57},
+Month = {MAR},
+Type = {Review},
+DOI = {10.1007/s41745-016-0017-x},
+ISSN = {0970-4140},
+EISSN = {0019-4964},
+Keywords = {Transcriptomics; Phylogenetic profiling; Quantitative modelling;
+ Genome-wide interaction network; Stochastic simulations},
+Keywords-Plus = {NF-KAPPA-B; YELLOW-FEVER VACCINE; MYCOBACTERIUM-TUBERCULOSIS;
+ IMMUNE-RESPONSE; PROTEIN; PATHWAYS; DYNAMICS; BIOLOGY; MODELS; IRON},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Korla, Kalyani/W-2179-2019
+ },
+ORCID-Numbers = {Chandra, Nagasuma/0000-0002-9939-8439},
+Times-Cited = {0},
+Journal-ISO = {J. Indian Inst. Sci.},
+Unique-ID = {WOS:000404133500005},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394606000020,
+Author = {Lu, Hongzhong and Cao, Weiqiang and Ouyang, Liming and Xia, Jianye and
+ Huang, Mingzhi and Chu, Ju and Zhuang, Yingping and Zhang, Siliang and
+ Noorman, Henk},
+Title = {Comprehensive reconstruction and in silico analysis of Aspergillus
+ niger genome-scale metabolic network model that accounts for 1210
+ ORFs},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2017},
+Volume = {114},
+Number = {3},
+Pages = {685-695},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1002/bit.26195},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {Aspergillus niger; genome-scale metabolic model; multi-omics;
+ glucoamylase},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; RNA-SEQ},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {liu, shanshan/JPA-0852-2023},
+Times-Cited = {23},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000394606000020},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000397205400002,
+Author = {Mobegi, Fredrick M. and Zomer, Aldert and de Jonge, Marien I. and van
+ Hijum, Sacha A. F. T.},
+Title = {Advances and perspectives in computational prediction of microbial gene
+ essentiality},
+Journal = {BRIEFINGS IN FUNCTIONAL GENOMICS},
+Year = {2017},
+Volume = {16},
+Number = {2},
+Pages = {70-79},
+Month = {MAR},
+Type = {Article},
+DOI = {10.1093/bfgp/elv063},
+ISSN = {2041-2649},
+EISSN = {2041-2657},
+Keywords = {gene essentiality prediction; computational methods; homology;
+ transposons; next-generation sequencing},
+Keywords-Plus = {MULTIPLE SEQUENCE ALIGNMENT; GLOBAL TRANSPOSON MUTAGENESIS; CLUSTAL-W;
+ GENOME; IDENTIFICATION; PHENOTYPE; NETWORK; RECONSTRUCTION;
+ LOCALIZATION; OPTIMIZATION},
+Research-Areas = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Genetics \& Heredity},
+ResearcherID-Numbers = {Zomer, Aldert L/B-3172-2010
+ de Jonge, Marien I./P-5869-2015
+ Mobegi, Fredrick/D-1058-2015
+ van Hijum, Sacha A.F.T./F-6445-2014
+ },
+ORCID-Numbers = {de Jonge, Marien I./0000-0003-2812-5895
+ Mobegi, Fredrick/0000-0003-0554-9919
+ Zomer, Aldert/0000-0002-0758-5190
+ van Hijum, Sacha/0000-0003-0741-2991},
+Times-Cited = {19},
+Journal-ISO = {Brief. Funct. Genomics},
+Unique-ID = {WOS:000397205400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000395894400017,
+Author = {Yang, Yi and Hu, Xiao-Pan and Ma, Bin-Guang},
+Title = {Construction and simulation of the Bradyrhizobium diazoefficiens
+ USDA110 metabolic network: a comparison between free-living and
+ symbiotic states},
+Journal = {MOLECULAR BIOSYSTEMS},
+Year = {2017},
+Volume = {13},
+Number = {3},
+Pages = {607-620},
+Month = {MAR 1},
+Type = {Article},
+DOI = {10.1039/c6mb00553e},
+ISSN = {1742-206X},
+EISSN = {1742-2051},
+Keywords-Plus = {SOYBEAN ROOT-NODULES; NITROGEN-FIXATION; SP-NOV; JAPONICUM BACTEROIDS;
+ MUTUALISM STABILITY; MESORHIZOBIUM-LOTI; RHIZOBIA; SANCTIONS; ALANINE;
+ NODULATION},
+Research-Areas = {Biochemistry \& Molecular Biology},
+Web-of-Science-Categories = {Biochemistry \& Molecular Biology},
+Times-Cited = {15},
+Journal-ISO = {Mol. Biosyst.},
+Unique-ID = {WOS:000395894400017},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394824600001,
+Author = {Saitua, Francisco and Torres, Paulina and Ricardo Perez-Correa, Jose and
+ Agosin, Eduardo},
+Title = {Dynamic genome-scale metabolic modeling of the yeast Pichia
+ pastoris},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {FEB 21},
+Type = {Article},
+DOI = {10.1186/s12918-017-0408-2},
+Article-Number = {27},
+ISSN = {1752-0509},
+Keywords = {dFBA; Pichia pastoris; Pre/post regression diagnostics; Sensitivity;
+ Identifiability; Significance; Genome-scale metabolic modeling;
+ Fed-batch; MOMA; Bioprocess optimization; Reparametrization},
+Keywords-Plus = {RECOMBINANT PROTEIN-PRODUCTION; FED-BATCH CULTIVATION; FLUX BALANCE
+ ANALYSIS; SACCHAROMYCES-CEREVISIAE; ESCHERICHIA-COLI; HETEROLOGOUS
+ PROTEINS; CHEMOSTAT CULTURES; GLUCOSE-TRANSPORT; PRODUCTION HOST;
+ EXPRESSION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Perez-Correa, Jose Ricardo/I-5565-2012
+ Torres, Paulina/AAA-6852-2020
+ Agosin, Eduardo/D-1411-2014},
+ORCID-Numbers = {Perez-Correa, Jose Ricardo/0000-0002-1278-7782
+ Torres, Paulina/0000-0001-5569-9830
+ Agosin, Eduardo/0000-0003-1656-150X},
+Times-Cited = {32},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000394824600001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394290400002,
+Author = {Kashaf, Sara Saheb and Angione, Claudio and Lio, Pietro},
+Title = {Making life difficult for Clostridium difficile: augmenting the
+ pathogen's metabolic model with transcriptomic and codon usage data for
+ better therapeutic target characterization},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {FEB 16},
+Type = {Article},
+DOI = {10.1186/s12918-017-0395-3},
+Article-Number = {25},
+EISSN = {1752-0509},
+Keywords = {Clostridium difficile; Metabolic networks; Metabolic pathways; Metabolic
+ modeling; Genome scale modeling; Flux balance analysis; Sensitivity
+ analysis; Antibiotic resistance},
+Keywords-Plus = {CONSTRAINT-BASED MODELS; GROWTH; STRATEGIES; PREDICTION},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {P. Lió, Pietro Lio/AAV-3358-2021
+ },
+ORCID-Numbers = {P. Lió, Pietro Lio/0000-0002-0540-5053
+ Angione, Claudio/0000-0002-3140-7909
+ Saheb Kashaf, Sara/0000-0003-1079-6009},
+Times-Cited = {15},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000394290400002},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000397264100033,
+Author = {Noronha, Alberto and Danielsdottir, Anna Drofn and Gawron, Piotr and
+ Johannsson, Freyr and Jonsdottir, Soffia and Jarlsson, Sindri and
+ Gunnarsson, Jon Petur and Brynjolfsson, Sigurdur and Schneider, Reinhard
+ and Thiele, Ines and Fleming, Ronan M. T.},
+Title = {ReconMap: an interactive visualization of human metabolism},
+Journal = {BIOINFORMATICS},
+Year = {2017},
+Volume = {33},
+Number = {4},
+Pages = {605-607},
+Month = {FEB 15},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btw667},
+ISSN = {1367-4803},
+EISSN = {1460-2059},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Brynjolfsson, Sigurdur/H-4588-2012
+ Fleming, Ronan MT/ABC-4093-2021
+ Schneider, Reinhard/C-5441-2009
+ Brynjolfsson, Sigurdur/AAT-4654-2020
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Brynjolfsson, Sigurdur/0000-0001-9435-2258
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Schneider, Reinhard/0000-0002-8278-1618
+ Noronha, Alberto/0000-0002-0935-4599},
+Times-Cited = {40},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000397264100033},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000393652800001,
+Author = {Hosseini, Zhaleh and Marashi, Sayed-Amir},
+Title = {Discovering missing reactions of metabolic networks by using gene
+ co-expression data},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {FEB 2},
+Type = {Article},
+DOI = {10.1038/srep41774},
+Article-Number = {41774},
+ISSN = {2045-2322},
+Keywords-Plus = {FLUX COUPLING ANALYSIS; ESCHERICHIA-COLI K-12; CELLULAR-METABOLISM;
+ MODELS; METHYLGLYOXAL},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Marashi, Sayed-Amir/A-5384-2008},
+ORCID-Numbers = {Marashi, Sayed-Amir/0000-0001-9801-7449},
+Times-Cited = {10},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000393652800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000397104900014,
+Author = {Cotton, James A. and Bennuru, Sasisekhar and Grote, Alexandra and
+ Harsha, Bhavana and Tracey, Alan and Beech, Robin and Doyle, Stephen R.
+ and Dunn, Matthew and Hotopp, Julie C. Dunning and Holroyd, Nancy and
+ Kikuchi, Taisei and Lambert, Olivia and Mhashilkar, Amruta and Mutowo,
+ Prudence and Nursimulu, Nirvana and Ribeiro, Jose M. C. and Rogers,
+ Matthew B. and Stanley, Eleanor and Swapna, Lakshmipuram S. and Tsai,
+ Isheng J. and Unnasch, Thomas R. and Voronin, Denis and Parkinson, John
+ and Nutman, Thomas B. and Ghedin, Elodie and Berriman, Matthew and
+ Lustigman, Sara},
+Title = {The genome of Onchocerca volvulus, agent of river blindness},
+Journal = {NATURE MICROBIOLOGY},
+Year = {2017},
+Volume = {2},
+Number = {2},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1038/nmicrobiol.2016.216},
+Article-Number = {16216},
+ISSN = {2058-5276},
+Keywords-Plus = {BRUGIA-MALAYI; IVERMECTIN TREATMENT; LOA-LOA; FILARIAL PARASITE; GLOBAL
+ BURDEN; DRAFT GENOME; CHANNEL GENE; ENZYME; ANNOTATION; DATABASE},
+Research-Areas = {Microbiology},
+Web-of-Science-Categories = {Microbiology},
+ResearcherID-Numbers = {Doyle, Stephen/GRJ-3949-2022
+ Parkinson, John/A-4424-2008
+ Cotton, James A/B-8806-2008
+ Beech, Robin/U-7759-2019
+ Berriman, Matthew/A-7618-2011
+ Tsai, Isheng J/H-6606-2014
+ Ghedin, Elodie/Y-5654-2019
+ Doyle, Stephen/AAS-8224-2021
+ Ribeiro, Jose MC/J-7011-2015
+ Tsai, Isheng Jason/ABB-8273-2021
+ },
+ORCID-Numbers = {Doyle, Stephen/0000-0001-9167-7532
+ Parkinson, John/0000-0001-9815-1189
+ Cotton, James A/0000-0001-5475-3583
+ Berriman, Matthew/0000-0002-9581-0377
+ Ghedin, Elodie/0000-0002-1515-725X
+ Doyle, Stephen/0000-0001-9167-7532
+ Tsai, Isheng Jason/0000-0002-2123-5058
+ Harsha, Bhavana/0000-0001-8234-9174
+ Mutowo, Prudence/0000-0002-4646-4172
+ Voronin, Denis/0000-0003-2652-0787
+ Nursimulu, Nirvana/0000-0001-5962-5863
+ Seshadri, Swapna/0000-0001-5906-7574
+ Ribeiro, Jose/0000-0002-9107-0818
+ Mhashilkar, Amruta/0000-0001-8912-8278
+ Kikuchi, Taisei/0000-0003-2759-9167},
+Times-Cited = {67},
+Journal-ISO = {NAT. MICROBIOL},
+Unique-ID = {WOS:000397104900014},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394314500010,
+Author = {Dang, Lanqing and Liu, Jiao and Wang, Cheng and Liu, Huanhuan and Wen,
+ Jianping},
+Title = {Enhancement of rapamycin production by metabolic engineering in
+ Streptomyces hygroscopicus based on genome-scale metabolic model},
+Journal = {JOURNAL OF INDUSTRIAL MICROBIOLOGY \& BIOTECHNOLOGY},
+Year = {2017},
+Volume = {44},
+Number = {2},
+Pages = {259-270},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1007/s10295-016-1880-1},
+ISSN = {1367-5435},
+EISSN = {1476-5535},
+Keywords = {Streptomyces hygroscopicus ATCC 29253; Rapamycin; Genome-scale metabolic
+ model; Target prediction; Metabolic engineering},
+Keywords-Plus = {GENE KNOCKOUT SIMULATION; ESCHERICHIA-COLI; LYCOPENE BIOSYNTHESIS; ATCC
+ 29253; ACID; TARGETS; FK506; SUBSTANCES; EXPRESSION; NETWORK},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {liu, huan/JEO-4705-2023},
+Times-Cited = {17},
+Journal-ISO = {J. Ind. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000394314500010},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392539800021,
+Author = {Liu, Di and Wan, Ni and Zhang, Fuzhong and Tang, Yinjie J. and Wu,
+ Stephen G.},
+Title = {Enhancing fatty acid production in Escherichia coli by
+ Vitreoscilla hemoglobin overexpression},
+Journal = {BIOTECHNOLOGY AND BIOENGINEERING},
+Year = {2017},
+Volume = {114},
+Number = {2},
+Pages = {463-467},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1002/bit.26067},
+ISSN = {0006-3592},
+EISSN = {1097-0290},
+Keywords = {oxygen uptake; metabolic burden; synthetic biology; flux balance
+ analysis; energy metabolism},
+Keywords-Plus = {E. COLI; EXPRESSION; CHEMICALS; FUELS; GENE; OVERPRODUCTION; CLONING;
+ GROWTH},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Tang, Yinjie/AAI-5584-2020
+ },
+ORCID-Numbers = {Zhang, Fuzhong/0000-0001-6979-7909},
+Times-Cited = {26},
+Journal-ISO = {Biotechnol. Bioeng.},
+Unique-ID = {WOS:000392539800021},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000397260800013,
+Author = {Liu, Lili and Zhang, Zijun and Sheng, Taotao and Chen, Ming},
+Title = {DEF: an automated dead-end filling approach based on quasi-endosymbiosis},
+Journal = {BIOINFORMATICS},
+Year = {2017},
+Volume = {33},
+Number = {3},
+Pages = {405-413},
+Month = {FEB 1},
+Type = {Article},
+DOI = {10.1093/bioinformatics/btw604},
+ISSN = {1367-4803},
+EISSN = {1367-4811},
+Keywords-Plus = {CARDIOLIPIN; RECONSTRUCTION; METABOLISM; MODELS},
+Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
+ Microbiology; Computer Science; Mathematical \& Computational Biology;
+ Mathematics},
+Web-of-Science-Categories = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
+ Computer Science, Interdisciplinary Applications; Mathematical \&
+ Computational Biology; Statistics \& Probability},
+ResearcherID-Numbers = {Zhang, Zijun/JDC-9191-2023
+ Chen, Ming/AAV-3682-2020
+ Liu, Lili/I-7619-2019},
+ORCID-Numbers = {Zhang, Zijun/0000-0003-2016-8014
+ Chen, Ming/0000-0002-9677-1699
+ Liu, Lili/0000-0002-2622-9669},
+Times-Cited = {3},
+Journal-ISO = {Bioinformatics},
+Unique-ID = {WOS:000397260800013},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000395224000006,
+Author = {Wada, Keisuke and Toya, Yoshihiro and Banno, Satomi and Yoshikawa,
+ Katsunori and Matsuda, Fumio and Shimizu, Hiroshi},
+Title = {13C-metabolic flux analysis for mevalonate-producing strain
+ of Escherichia coli},
+Journal = {JOURNAL OF BIOSCIENCE AND BIOENGINEERING},
+Year = {2017},
+Volume = {123},
+Number = {2},
+Pages = {177-182},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1016/j.jbiosc.2016.08.001},
+ISSN = {1389-1723},
+EISSN = {1347-4421},
+Keywords = {C-13-metabolic flux analysis; Mevalonate; Escherichia coli; {[}1-C-13]
+ glucose; Flux distribution; Redox balance; Flux balance analysis},
+Keywords-Plus = {ACID PRODUCTION; METABOLISM; PATHWAY},
+Research-Areas = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology; Food Science \& Technology},
+ResearcherID-Numbers = {Shimizu, Hiroshi/C-3688-2017
+ Wada, Keisuke/AAW-7752-2021
+ Wada, Keisuke/J-1522-2018
+ },
+ORCID-Numbers = {Shimizu, Hiroshi/0000-0002-8986-0861
+ Wada, Keisuke/0000-0002-1454-6093
+ Wada, Keisuke/0000-0002-1454-6093
+ Toya, Yoshihiro/0000-0001-9670-6961
+ Banno, Satomi/0000-0002-5853-5003},
+Times-Cited = {40},
+Journal-ISO = {J. Biosci. Bioeng.},
+Unique-ID = {WOS:000395224000006},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000393246000009,
+Author = {Wagner, Andreas},
+Title = {The White-Knight Hypothesis, or Does the Environment Limit Innovations?},
+Journal = {TRENDS IN ECOLOGY \& EVOLUTION},
+Year = {2017},
+Volume = {32},
+Number = {2},
+Pages = {131-140},
+Month = {FEB},
+Type = {Review},
+DOI = {10.1016/j.tree.2016.10.017},
+ISSN = {0169-5347},
+EISSN = {1872-8383},
+Keywords-Plus = {PROMISCUOUS PROTEIN FUNCTIONS; CATALYTIC PROMISCUITY; MICROBIAL
+ COMMUNITIES; FUNCTIONAL EVOLUTION; EXPRESSION PROFILES;
+ ESCHERICHIA-COLI; KEY INNOVATION; CONTINGENCY; METABOLISM; EXAPTATION},
+Research-Areas = {Environmental Sciences \& Ecology; Evolutionary Biology; Genetics \&
+ Heredity},
+Web-of-Science-Categories = {Ecology; Evolutionary Biology; Genetics \& Heredity},
+Times-Cited = {11},
+Journal-ISO = {Trends Ecol. Evol.},
+Unique-ID = {WOS:000393246000009},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000393687400026,
+Author = {Whitham, Jason M. and Schulte, Mark J. and Bobay, Benjamin G. and
+ Bruno-Barcena, Jose M. and Chinn, Mari S. and Flickinger, Michael C. and
+ Pawlak, Joel J. and Grunden, Amy M.},
+Title = {Characterization of Clostridium ljungdahlii OTA1: a
+ non-autotrophic hyper ethanol-producing strain},
+Journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
+Year = {2017},
+Volume = {101},
+Number = {4},
+Pages = {1615-1630},
+Month = {FEB},
+Type = {Article},
+DOI = {10.1007/s00253-016-7978-6},
+ISSN = {0175-7598},
+EISSN = {1432-0614},
+Keywords = {Acetyl-coA; Carbon monoxide dehydrogenase; Clostridium ljungdahlii;
+ Ethanol; Wood-Ljungdahl pathway},
+Keywords-Plus = {UPGRADING DILUTE ETHANOL; ENERGY-CONSERVATION; CRYSTAL-STRUCTURE;
+ AUTOETHANOGENUM; FUELS; AMINOTRANSFERASE; FERMENTATION; METABOLISM;
+ PREDICTION; REDUCTION},
+Research-Areas = {Biotechnology \& Applied Microbiology},
+Web-of-Science-Categories = {Biotechnology \& Applied Microbiology},
+ResearcherID-Numbers = {Core, UNC Microbiome/AAB-3304-2022
+ Bobay, Benjamin G/ABF-8860-2021
+ Bruno-Bárcena, Jose M/AAM-6942-2020
+ Whitham, Jason/I-1173-2018
+ },
+ORCID-Numbers = {Bruno-Bárcena, Jose M/0000-0003-2876-1496
+ Chinn, Mari/0000-0002-2177-1774
+ Whitham, Jason/0000-0003-2623-6292
+ Bobay, Benjamin/0000-0003-4775-3686
+ Grunden, Amy/0000-0002-8025-753X
+ Flickinger, Michael/0000-0002-6814-0427
+ Pawlak, Joel/0000-0002-9803-9004},
+Times-Cited = {6},
+Journal-ISO = {Appl. Microbiol. Biotechnol.},
+Unique-ID = {WOS:000393687400026},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392959700001,
+Author = {Mueller, Thomas J. and Ungerer, Justin L. and Pakrasi, Himadri B. and
+ Maranas, Costas D.},
+Title = {Identifying the Metabolic Differences of a Fast-Growth Phenotype in
+ Synechococcus UTEX 2973},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {JAN 31},
+Type = {Article},
+DOI = {10.1038/srep41569},
+Article-Number = {41569},
+ISSN = {2045-2322},
+Keywords-Plus = {MARINE CYANOBACTERIA; CARBON-DIOXIDE; MICROALGAE; PCC-6803; GENE},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Maranas, Costas D/A-4774-2011},
+ORCID-Numbers = {Maranas, Costas D/0000-0002-1508-1398},
+Times-Cited = {40},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000392959700001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000394288800001,
+Author = {Gardner, Joseph J. and Boyle, Nanette R.},
+Title = {The use of genome-scale metabolic network reconstruction to predict
+ fluxes and equilibrium composition of N-fixing versus C-fixing cells in
+ a diazotrophic cyanobacterium, Trichodesmium erythraeum},
+Journal = {BMC SYSTEMS BIOLOGY},
+Year = {2017},
+Volume = {11},
+Month = {JAN 19},
+Type = {Article},
+DOI = {10.1186/s12918-016-0383-z},
+Article-Number = {4},
+ISSN = {1752-0509},
+Keywords = {Flux balance analysis; Constraints based modeling; Flux variability
+ analysis; Nitrogen cycle; Diazotrophy; Marine cyanobacteria},
+Keywords-Plus = {BLUE-GREEN-ALGA; NITROGEN-FIXATION; NONHETEROCYSTOUS CYANOBACTERIUM;
+ MARINE CYANOBACTERIUM; N-2 FIXATION; LIPID-ACCUMULATION; GLYOXYLATE
+ CYCLE; BALANCE ANALYSIS; NORTH PACIFIC; GROWTH},
+Research-Areas = {Mathematical \& Computational Biology},
+Web-of-Science-Categories = {Mathematical \& Computational Biology},
+ResearcherID-Numbers = {Boyle, Nanette/AFM-1806-2022},
+ORCID-Numbers = {Boyle, Nanette/0000-0002-9103-0007},
+Times-Cited = {12},
+Journal-ISO = {BMC Syst. Biol.},
+Unique-ID = {WOS:000394288800001},
+DA = {2023-12-20},
+}
+
+@article{ WOS:000392188100001,
+Author = {Ma, Ding and Yang, Laurence and Fleming, Ronan M. T. and Thiele, Ines
+ and Palsson, Bernhard O. and Saunders, Michael A.},
+Title = {Reliable and efficient solution of genome-scale models of Metabolism and
+ macromolecular Expression},
+Journal = {SCIENTIFIC REPORTS},
+Year = {2017},
+Volume = {7},
+Month = {JAN 18},
+Type = {Article},
+DOI = {10.1038/srep40863},
+Article-Number = {40863},
+ISSN = {2045-2322},
+Keywords-Plus = {ALGORITHM},
+Research-Areas = {Science \& Technology - Other Topics},
+Web-of-Science-Categories = {Multidisciplinary Sciences},
+ResearcherID-Numbers = {Thiele, Ines/A-7629-2014
+ Fleming, Ronan MT/ABC-4093-2021
+ Saunders, Michael A/D-1083-2012
+ },
+ORCID-Numbers = {Thiele, Ines/0000-0002-8071-7110
+ Fleming, Ronan MT/0000-0001-5346-9812
+ Yang, Laurence/0000-0001-6663-7643
+ Saunders, Michael/0000-0003-3800-4982
+ MA, Ding/0000-0002-5503-2945},
+Times-Cited = {20},
+Journal-ISO = {Sci Rep},
+Unique-ID = {WOS:000392188100001},
+DA = {2023-12-20},
+}
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 7d999542f6..a23a3a1c0d 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,9 +1,13 @@
#git+https://github.com/LCSB-BioCore/sphinx.git@develop#egg=sphinx
sphinxcontrib-matlabdomain==0.18.0
-recommonmark==0.7.1
+recommonmark
sphinxcontrib-fulltoc==1.2.0
+sphinx-tabs
sphinx_rtd_theme==1.2.2
git+https://github.com/opencobra/sphinx_cobra_theme.git@develop#egg=sphinx_cobra_theme
#git+https://github.com/syarra/Documenter.py@master#egg=documenter
-sphinxcontrib-napoleon==0.7
-pyGithub==1.59.0
+sphinxcontrib-napoleon
+pyGithub
+sphinxcontrib-bibtex
+
+
diff --git a/docs/requirements2.txt b/docs/requirements2.txt
new file mode 100644
index 0000000000..7d999542f6
--- /dev/null
+++ b/docs/requirements2.txt
@@ -0,0 +1,9 @@
+#git+https://github.com/LCSB-BioCore/sphinx.git@develop#egg=sphinx
+sphinxcontrib-matlabdomain==0.18.0
+recommonmark==0.7.1
+sphinxcontrib-fulltoc==1.2.0
+sphinx_rtd_theme==1.2.2
+git+https://github.com/opencobra/sphinx_cobra_theme.git@develop#egg=sphinx_cobra_theme
+#git+https://github.com/syarra/Documenter.py@master#egg=documenter
+sphinxcontrib-napoleon==0.7
+pyGithub==1.59.0
From dcfc1616d062204ba167edbcb94a7bdeba977c37 Mon Sep 17 00:00:00 2001
From: pavan-kumar-s <138394293+pavan-kumar-s@users.noreply.github.com>
Date: Wed, 20 Dec 2023 17:10:25 +0530
Subject: [PATCH 3/4] Add files via upload
---
docs/source/CitationStyle.py | 465 +++++++++++++++++++++++++++++++++++
docs/source/conf.py | 26 +-
docs/source/contents.rst | 1 +
docs/source/publications.rst | 116 +++++++++
4 files changed, 597 insertions(+), 11 deletions(-)
create mode 100644 docs/source/CitationStyle.py
create mode 100644 docs/source/publications.rst
diff --git a/docs/source/CitationStyle.py b/docs/source/CitationStyle.py
new file mode 100644
index 0000000000..d198b932c2
--- /dev/null
+++ b/docs/source/CitationStyle.py
@@ -0,0 +1,465 @@
+# Copyright (c) 2006-2021 Andrey Golovizin
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+from __future__ import unicode_literals
+
+import re
+
+from pybtex.richtext import Symbol, Text
+from pybtex.style.formatting import BaseStyle, toplevel
+from pybtex.style.template import (
+ field, first_of, href, join, names, optional, optional_field, sentence,
+ tag, together, words
+)
+
+
+def dashify(text):
+ dash_re = re.compile(r'-+')
+ return Text(Symbol('ndash')).join(text.split(dash_re))
+
+
+pages = field('pages', apply_func=dashify)
+
+date = words [optional_field('month'), field('year')]
+
+
+class ModStyle(BaseStyle):
+
+ def format_names(self, role, as_sentence=True):
+ formatted_names = names(role, sep=', ', sep2 = ' and ', last_sep=', and ')
+ if as_sentence:
+ return sentence [formatted_names]
+ else:
+ return formatted_names
+
+ def get_article_template(self, e):
+ volume_and_pages = first_of [
+ # volume and pages, with optional issue number
+ optional [
+ join [
+ field('volume'),
+ optional['(', field('number'),')'],
+ ':', pages
+ ],
+ ],
+ # pages only
+ words ['pages', pages],
+ ]
+ template = toplevel [
+ self.format_names('author'),
+ self.format_title(e, 'title'),
+ sentence [
+ tag('em') [field('journal')],
+ optional[ volume_and_pages ],
+ date],
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def format_author_or_editor(self, e):
+ return first_of [
+ optional[ self.format_names('author') ],
+ self.format_editor(e),
+ ]
+
+ def format_editor(self, e, as_sentence=True):
+ editors = self.format_names('editor', as_sentence=False)
+ if 'editor' not in e.persons:
+ # when parsing the template, a FieldIsMissing exception
+ # will be thrown anyway; no need to do anything now,
+ # just return the template that will throw the exception
+ return editors
+ if len(e.persons['editor']) > 1:
+ word = 'editors'
+ else:
+ word = 'editor'
+ result = join(sep=', ') [editors, word]
+ if as_sentence:
+ return sentence [result]
+ else:
+ return result
+
+ def format_volume_and_series(self, e, as_sentence=True):
+ volume_and_series = optional [
+ words [
+ together ['Volume' if as_sentence else 'volume', field('volume')], optional [
+ words ['of', field('series')]
+ ]
+ ]
+ ]
+ number_and_series = optional [
+ words [
+ join(sep=Symbol('nbsp')) ['Number' if as_sentence else 'number', field('number')],
+ optional [
+ words ['in', field('series')]
+ ]
+ ]
+ ]
+ series = optional_field('series')
+ result = first_of [
+ volume_and_series,
+ number_and_series,
+ series,
+ ]
+ if as_sentence:
+ return sentence(capfirst=True) [result]
+ else:
+ return result
+
+ def format_chapter_and_pages(self, e):
+ return join(sep=', ') [
+ optional [together ['chapter', field('chapter')]],
+ optional [together ['pages', pages]],
+ ]
+
+ def format_edition(self, e):
+ return optional [
+ words [
+ field('edition', apply_func=lambda x: x.lower()),
+ 'edition',
+ ]
+ ]
+
+ def format_title(self, e, which_field, as_sentence=True):
+ formatted_title = field(
+ which_field, apply_func=lambda text: text.capitalize()
+ )
+ if as_sentence:
+ return sentence [ formatted_title ]
+ else:
+ return formatted_title
+
+ def format_btitle(self, e, which_field, as_sentence=True):
+ formatted_title = tag('em') [ field(which_field) ]
+ if as_sentence:
+ return sentence[ formatted_title ]
+ else:
+ return formatted_title
+
+ def format_address_organization_publisher_date(
+ self, e, include_organization=True):
+ """Format address, organization, publisher, and date.
+ Everything is optional, except the date.
+ """
+ # small difference from unsrt.bst here: unsrt.bst
+ # starts a new sentence only if the address is missing;
+ # for simplicity here we always start a new sentence
+ if include_organization:
+ organization = optional_field('organization')
+ else:
+ organization = None
+ return first_of[
+ # this will be rendered if there is an address
+ optional [
+ join(sep=' ') [
+ sentence[
+ field('address'),
+ date,
+ ],
+ sentence[
+ organization,
+ optional_field('publisher'),
+ ],
+ ],
+ ],
+ # if there is no address then we have this
+ sentence[
+ organization,
+ optional_field('publisher'),
+ date,
+ ],
+ ]
+
+ def get_book_template(self, e):
+ template = toplevel [
+ self.format_author_or_editor(e),
+ self.format_btitle(e, 'title'),
+ self.format_volume_and_series(e),
+ sentence [
+ field('publisher'),
+ optional_field('address'),
+ self.format_edition(e),
+ date
+ ],
+ optional[ sentence [ self.format_isbn(e) ] ],
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_booklet_template(self, e):
+ template = toplevel [
+ self.format_names('author'),
+ self.format_title(e, 'title'),
+ sentence [
+ optional_field('howpublished'),
+ optional_field('address'),
+ date,
+ optional_field('note'),
+ ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_inbook_template(self, e):
+ template = toplevel [
+ self.format_author_or_editor(e),
+ sentence [
+ self.format_btitle(e, 'title', as_sentence=False),
+ self.format_chapter_and_pages(e),
+ ],
+ self.format_volume_and_series(e),
+ sentence [
+ field('publisher'),
+ optional_field('address'),
+ optional [
+ words [field('edition'), 'edition']
+ ],
+ date,
+ optional_field('note'),
+ ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_incollection_template(self, e):
+ template = toplevel [
+ sentence [self.format_names('author')],
+ self.format_title(e, 'title'),
+ words [
+ 'In',
+ sentence [
+ optional[ self.format_editor(e, as_sentence=False) ],
+ self.format_btitle(e, 'booktitle', as_sentence=False),
+ self.format_volume_and_series(e, as_sentence=False),
+ self.format_chapter_and_pages(e),
+ ],
+ ],
+ sentence [
+ optional_field('publisher'),
+ optional_field('address'),
+ self.format_edition(e),
+ date,
+ ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_inproceedings_template(self, e):
+ template = toplevel [
+ sentence [self.format_names('author')],
+ self.format_title(e, 'title'),
+ words [
+ 'In',
+ sentence [
+ optional[ self.format_editor(e, as_sentence=False) ],
+ self.format_btitle(e, 'booktitle', as_sentence=False),
+ self.format_volume_and_series(e, as_sentence=False),
+ optional[ pages ],
+ ],
+ self.format_address_organization_publisher_date(e),
+ ],
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_manual_template(self, e):
+ # TODO this only corresponds to the bst style if author is non-empty
+ # for empty author we should put the organization first
+ template = toplevel [
+ optional [ sentence [ self.format_names('author') ] ],
+ self.format_btitle(e, 'title'),
+ sentence [
+ optional_field('organization'),
+ optional_field('address'),
+ self.format_edition(e),
+ optional[ date ],
+ ],
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_mastersthesis_template(self, e):
+ template = toplevel [
+ sentence [self.format_names('author')],
+ self.format_title(e, 'title'),
+ sentence[
+ "Master's thesis",
+ field('school'),
+ optional_field('address'),
+ date,
+ ],
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_misc_template(self, e):
+ template = toplevel [
+ optional[ sentence [self.format_names('author')] ],
+ optional[ self.format_title(e, 'title') ],
+ sentence[
+ optional[ field('howpublished') ],
+ optional[ date ],
+ ],
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_online_template(self, e):
+ return self.get_misc_template(e)
+
+ def get_phdthesis_template(self, e):
+ template = toplevel [
+ sentence [self.format_names('author')],
+ self.format_btitle(e, 'title'),
+ sentence[
+ first_of [
+ optional_field('type'),
+ 'PhD thesis',
+ ],
+ field('school'),
+ optional_field('address'),
+ date,
+ ],
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_proceedings_template(self, e):
+ if 'editor' in e.persons:
+ main_part = [
+ self.format_editor(e),
+ sentence [
+ self.format_btitle(e, 'title', as_sentence=False),
+ self.format_volume_and_series(e, as_sentence=False),
+ self.format_address_organization_publisher_date(e),
+ ],
+ ]
+ else:
+ main_part = [
+ optional [ sentence [ field('organization') ] ],
+ sentence [
+ self.format_btitle(e, 'title', as_sentence=False),
+ self.format_volume_and_series(e, as_sentence=False),
+ self.format_address_organization_publisher_date(
+ e, include_organization=False),
+ ],
+ ]
+ template = toplevel [
+ main_part + [
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ ]
+ return template
+
+ def get_techreport_template(self, e):
+ template = toplevel [
+ sentence [self.format_names('author')],
+ self.format_title(e, 'title'),
+ sentence [
+ words[
+ first_of [
+ optional_field('type'),
+ 'Technical Report',
+ ],
+ optional_field('number'),
+ ],
+ field('institution'),
+ optional_field('address'),
+ date,
+ ],
+ sentence [ optional_field('note') ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def get_unpublished_template(self, e):
+ template = toplevel [
+ sentence [self.format_names('author')],
+ self.format_title(e, 'title'),
+ sentence [
+ field('note'),
+ optional[ date ]
+ ],
+ self.format_web_refs(e),
+ ]
+ return template
+
+ def format_web_refs(self, e):
+ # based on urlbst output.web.refs
+ return sentence [
+ optional [ self.format_url(e) ],
+ optional [ self.format_pubmed(e) ],
+ optional [ self.format_doi(e) ]
+ ]
+
+ def format_url(self, e):
+ # based on urlbst format.url
+ return words [
+ '',
+ href [
+ field('url', raw=True),
+ '[URL]'
+ ]
+ ]
+
+ def format_pubmed(self, e):
+ # based on urlbst format.pubmed
+ return href [
+ join [
+ 'https://www.ncbi.nlm.nih.gov/pubmed/',
+ field('pubmed', raw=True)
+ ],
+ '[PubMed]'
+ ]
+
+ def format_doi(self, e):
+ # based on urlbst format.doi
+ return href [
+ join [
+ 'https://doi.org/',
+ field('doi', raw=True)
+ ],
+ '[DOI]'
+ ]
+
+ def format_eprint(self, e):
+ # based on urlbst format.eprint
+ return href [
+ join [
+ 'https://arxiv.org/abs/',
+ field('eprint', raw=True)
+ ],
+ join [
+ 'arXiv:',
+ field('eprint', raw=True)
+ ]
+ ]
+
+ def format_isbn(self, e):
+ return join(sep=' ') [ 'ISBN', field('isbn') ]
diff --git a/docs/source/conf.py b/docs/source/conf.py
index baf66521fe..ed04c31164 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -19,10 +19,16 @@
import os # imports os
import sys
+import pybtex
+
+
sys.path.append('sphinxext')
from github_linkcode import github_linkcode_resolve
+sys.path.append('./')
+from CitationStyle import ModStyle
+
sys.path.insert(0, os.path.abspath(os.path.join('..', '..', '..')))
# sys.path.insert(0, os.path.abspath('.'))
@@ -45,19 +51,15 @@
'github',
'sphinx.ext.mathjax',
'sphinx.ext.linkcode',
- 'sphinxcontrib.fulltoc']
+ 'sphinxcontrib.fulltoc','sphinxcontrib.bibtex','sphinx_tabs.tabs']
mathjax_path = 'https://cdn.jsdelivr.net/gh/mathjax/MathJax@2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
-
-def linkcode_resolve(domain, info):
- return github_linkcode_resolve(
- domain=domain,
- info=info,
- allowed_module_names=['src'],
- github_org_id='opencobra',
- github_repo_id='cobratoolbox',
- branch='master',
- source_prefix='')
+matlab_auto_link="all"
+
+def linkcode_resolve():
+ return 'https://github.com/'
+bibtex_bibfiles = ['../COBRA.bib']
+bibtex_default_style = 'unsrt'
# autodoc_member_order='groupwise'
@@ -393,3 +395,5 @@ def linkcode_resolve(domain, info):
# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False
+
+pybtex.plugin.register_plugin('pybtex.style.formatting', 'modstyle', ModStyle)
diff --git a/docs/source/contents.rst b/docs/source/contents.rst
index 01a5f9aa57..6effbc5d1d 100644
--- a/docs/source/contents.rst
+++ b/docs/source/contents.rst
@@ -16,3 +16,4 @@ The COBRA Toolbox
funding
plan
contact
+ publications
diff --git a/docs/source/publications.rst b/docs/source/publications.rst
new file mode 100644
index 0000000000..5b8ccd0c13
--- /dev/null
+++ b/docs/source/publications.rst
@@ -0,0 +1,116 @@
+Publications
+============
+
+|br|
+
+Publications that used COBRA Toolbox
+------------------------------------
+.. tabs::
+ .. tab:: 2007
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2007"
+ :style: modstyle
+
+ .. tab:: 2008
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2008"
+ :style: modstyle
+
+ .. tab:: 2009
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2009"
+ :style: modstyle
+
+ .. tab:: 2010
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2010"
+ :style: modstyle
+
+ .. tab:: 2011
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2011"
+ :style: modstyle
+
+ .. tab:: 2012
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2012"
+ :style: modstyle
+
+
+ .. tab:: 2013
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2013"
+ :style: modstyle
+
+ .. tab:: 2014
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2014"
+ :style: modstyle
+
+ .. tab:: 2015
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2015"
+ :style: modstyle
+
+ .. tab:: 2016
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2016"
+ :style: modstyle
+
+ .. tab:: 2017
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2017"
+ :style: modstyle
+
+ .. tab:: 2018
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2018"
+ :style: modstyle
+
+
+ .. tab:: 2019
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2019"
+ :style: modstyle
+
+ .. tab:: 2020
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2020"
+ :style: modstyle
+
+ .. tab:: 2021
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2021"
+ :style: modstyle
+
+ .. tab:: 2022
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2022"
+ :style: modstyle
+
+ .. tab:: 2023
+ .. bibliography::
+ :list: enumerated
+ :filter: year == "2023"
+ :style: modstyle
+
+
+.. |br| raw:: html
+
+
From 3b73177dda87720ba73c8804cbdcb7c855a28b22 Mon Sep 17 00:00:00 2001
From: pavan-kumar-s <138394293+pavan-kumar-s@users.noreply.github.com>
Date: Wed, 20 Dec 2023 17:12:09 +0530
Subject: [PATCH 4/4] Update UpdateFunctionDocs.yml
---
.github/workflows/UpdateFunctionDocs.yml | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/.github/workflows/UpdateFunctionDocs.yml b/.github/workflows/UpdateFunctionDocs.yml
index 245b28d149..c7b35c7e29 100644
--- a/.github/workflows/UpdateFunctionDocs.yml
+++ b/.github/workflows/UpdateFunctionDocs.yml
@@ -1,13 +1,9 @@
name: Update function docs
on:
- pull_request_target:
- types:
- - closed
- branches: [ master ]
+ workflow_dispatch:
jobs:
build:
- if: github.event.pull_request.merged == true
runs-on: ubuntu-latest
steps: