Okada Lab

All

30 repositories

cREscENDO
Public
Python
•
MIT License
•1•0•0•0•Updated Oct 23, 2024Oct 23, 2024
DynProfiler
Public
Jupyter Notebook
•1•0•0•0•Updated Oct 9, 2024Oct 9, 2024
text2model-from-knowledge
Public
Extending BioMASS to construct mathematical models from external knowledge (Arakane et al., 2024)
Python
•
Apache License 2.0
•1•0•0•0•Updated Jun 9, 2024Jun 9, 2024
HER2_Cellcycle
Public
R
•0•0•0•0•Updated May 30, 2024May 30, 2024
Haga2023
Public
R
•
MIT License
•0•0•0•0•Updated Jan 24, 2024Jan 24, 2024
periodontitis
Public
Python
•0•0•0•0•Updated Jun 8, 2023Jun 8, 2023
inflammatory-aging
Public
Tabata, S. et al.
R
•
MIT License
•0•0•0•0•Updated Mar 9, 2023Mar 9, 2023
BioMASS.jl
Public
Julia interface to BioMASS, tailored to parameter estimation in systems biology models
Julia
•
MIT License
•2•0•0•0•Updated Feb 28, 2023Feb 28, 2023
biomass
Public
A Python Framework for Modeling and Analysis of Signaling Systems
Python
•
Apache License 2.0
•13•1•0•0•Updated Feb 17, 2023Feb 17, 2023
pasmopy
Public
Patient-Specific Modeling in Python
Python
•
Apache License 2.0
•7•0•0•0•Updated Feb 16, 2023Feb 16, 2023
ASURAT
Public
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes
single-cell-transcriptomics
R
•
GNU General Public License v3.0
•3•0•0•0•Updated Jan 19, 2023Jan 19, 2023
Wibisana2021
Public
Imaging and single cell sequencing analyses of super-enhancer activation mediated by NF-κB in B cells (Wibisana, JN et al., 2021)
R
•
MIT License
•0•4•0•0•Updated Jun 2, 2022Jun 2, 2022
findfoci
Public
ImageJ2 and R package for quantitative analysis of NF-κB foci
ImageJ Macro
•
Other
•1•0•0•0•Updated Mar 3, 2022Mar 3, 2022
Ando2021
Public
Ando, M. et al. IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells. npj Syst Biol Appl 7, 42 (2021).
R
•
MIT License
•0•0•0•0•Updated Jan 14, 2022Jan 14, 2022
ccle_extractor
Public
Python script for extracting dataset from CCLE (Cancer Cell Line Encyclopedia)
python cancer pandas gene-expression metabolomics ccle
Python
•
MIT License
•3•7•0•0•Updated Jul 15, 2021Jul 15, 2021
Kanazawa2021
Public
Cell shape‐based chemical screening reveals an epigenetic network mediated by focal adhesions
rna-seq chip-seq atac-seq super-enhancer go-analysis
R
•
MIT License
•0•0•0•0•Updated Mar 11, 2021Mar 11, 2021
Imoto_Cancers_2020
Public
Imoto, H., Zhang, S. & Okada, M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. Cancers (Basel). 12, 2878 (2020).
parameter-estimation predictive-modeling breast-cancer erbb-signaling-network
Python
•
MIT License
•0•0•0•0•Updated Oct 10, 2020Oct 10, 2020
Inoue2016
Public
Inoue, K. et al. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. npj Syst. Biol. Appl. 2, 16024 (2016).
julia systems-biology dde delay-differential-equations nfkb-dynamics
Julia
•
MIT License
•1•0•0•0•Updated Aug 25, 2020Aug 25, 2020
Imoto2019
Public
Imoto, H. & Okada, M. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view. Curr. Opin. Syst. Biol. 15, 100–108 (2019).
julia systems-biology bifurcation cell-cycle
Julia
•
MIT License
•0•0•0•0•Updated Aug 25, 2020Aug 25, 2020
Nakakuki2010
Public
Nakakuki, T. et al. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell 141, 884–896 (2010).
systems-biology ode erbb-signaling-network python
Python
•
MIT License
•1•0•0•0•Updated Aug 22, 2020Aug 22, 2020
Birtwistle2007
Public
Birtwistle, M. R. et al. Ligand-dependent responses of the ErbB signaling network: Experimental and modeling analyses. Mol. Syst. Biol. 3, (2007).
python systems-biology ode julia erbb-signaling-network
Python
•
MIT License
•1•1•0•0•Updated Aug 16, 2020Aug 16, 2020
Hatakeyama2003
Public
Hatakeyama, M. et al. A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. Biochem. J. 373, 451–463 (2003).
python modeling systems-biology ode erbb-signaling-network matlab
Python
•
MIT License
•0•0•0•0•Updated Aug 5, 2020Aug 5, 2020
cancer_modeling
Public
Modeling signaling networks in cancer
modeling systems-biology computational-biology ode dde reaction-network differential-equations cancer signaling-pathways
Python
•
MIT License
•3•2•0•0•Updated Jul 20, 2020Jul 20, 2020
Michida2020
Public
Michida, H. et al. The number of transcription factors at an enhancer determines switch-like gene expression.
scrna-seq chip-seq atac-seq enhancer
R
•
MIT License
•0•1•0•0•Updated Jun 30, 2020Jun 30, 2020
sensitivity_analysis
Public archive
Calculation of sensitivity coefficients and visualization
python systems-biology robustness sensitivity sensitivity-analysis
Python
•
MIT License
•0•0•0•0•Updated Jun 29, 2020Jun 29, 2020
Shinohara2014
Public
Shinohara, H. et al. Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activation. Science (80-. ). 344, 760–764 (2014).
python systems-biology ode nfkb-dynamics
Python
•
MIT License
•1•0•0•0•Updated Jun 21, 2020Jun 21, 2020
intro_to_param_estim
Public archive
Parameter estimation of ODE models describing biological processes
python optimization modeling systems-biology computational-biology parameter-estimation genetic-algorithm
Python
•
MIT License
•1•10•0•0•Updated Jun 19, 2020Jun 19, 2020
Chiang2020
Public
Chiang, S., Shinohara, H., Huang, J. H., Tsai, H. K. & Okada, M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Lett. (2020).
c transcription-factors systems-biology computational-biology mrna gene-regulatory-network
C
•
BSD 2-Clause "Simplified" License
•0•0•0•0•Updated Apr 23, 2020Apr 23, 2020
py2jl
Public archive
Converting Python code to Julia for ODE model construction
python converter julia ode ordinary-differential-equations biomass
Python
•
MIT License
•1•1•0•0•Updated Apr 1, 2020Apr 1, 2020
egf_signaling
Public
Computational modeling of the short term pattern of cellular responses to epidermal growth factor
matlab modeling systems-biology computational-biology ode-model
MATLAB
•
MIT License
•0•0•0•0•Updated Jan 12, 2020Jan 12, 2020