Publications

Published peer-reviewed publications

1. Chen Y, Knight R, Gallo RL. Evolving approaches to profiling the microbiome in skin disease. Frontiers in Immunology. 2023 Apr 4;14:1151527. doi: 10.3389/fimmu.2023.1151527. PMID: 37081873; PMCID: PMC10110978. PDF

2. Dokoshi T, Chen Y, Cavagnero KJ, Rahman G, Brinton S, Schwarz H, Nakamura Y, Li F, Salzman N, Knight R, Gallo RL, Dermal injury disrupts the intestinal microbiome and immune homeostasis. doi: 10.1038/s41467-024-47072-3. PMID: 38589392 PMCID: PMC11001995 PDF

3. O’Neill AM, Cavagnero KJ, Seidman JS, Zaramela L, Chen Y, Li F, Nakatsuji T, Cheng JY, Tong YL, Do TH, Brinton SL, Cau L, Hata TR, Modlin RL, Gallo RL* . Genetic and functional analyses of Cutibacterium acnes isolates reveal association of a linear plasmid with skin inflammation. Journal of Investigative Dermatology. 2023 Jul 19:S0022-202X(23)02415-6. doi: 10.1016/j.jid.2023.05.029. PMID: 37478901. PDF

4. Nakatsuji T, Brinton SL, Cavagnero KJ, O’Neil AM, Chen Y, Dokoshi T, Butcher AM, Osuoji O, Shafiq F, Espinoza JL, Dupont CL, Hata TR, Gallo RL. Competition between host antimicrobial peptides and commensal bacteria enables survival of Staphylococcus aureus on skin with type 2 inflammation. Cell Reports. 2023 May 30;42(5):112494. doi: 10.1016/j.celrep.2023.112494. PMID: 37167061; PMCID: PMC10303920. PDF

5. Chen Y¹, St. Leger J¹, Sakamaki K, Mena L, Rotstein D, Grigg ME. Fatal hepatic Sarcocystosis in three captive and one free-ranging pinniped. Veterinary Parasitology. doi: 10.1016/j.ijppaw.2023.10.010. PDF

6. De Pessemier B, Lopez CD, Taelman S, Verdonck M, Chen Y, Stockman A, Lambert J, Van de Wiele T, Callewaert C. Comparative whole metagenome analysis in lesional and nonlesional scalp areas of patients with Psoriasis capitis and healthy individuals. doi: 10.1016/j.jid.2024.07.020. PMID: 39128495. PDF

Works in review

7. Rahman G, Morton JT, Martino C, Sepich-Poore GD, Allaband C, Guccione C, Chen Y, Hakim D, Estaki M, Knight R. BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. BioRxiv. 2023 Feb 2. doi: 10.1101/2023.01.30.526328. PDF

8. Guiccione C¹, Patel L¹, Tomofuji Yoshihiko, Martino Cameron, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Chen Y, Dilmore AH, Damle N, Nakatsuji T, Gallo RL, Okada Y, Curtius K, Knight R. Incomplete human reference genomes can drive false sex biases and expose patient-identifying human sequences in metagenomic data. In review at Nature Communications. 2024.

9. Chan H, Li Fengwu, Dokoshi T, Cavagnero KJ, Qing L, Chen Y, Aguilera C, Nakatsuji T, Liu E, Indra A, Yang D, Ottaviani V, Numata T, Williams KJ, Chiu IM, Bensinger SJ, Chen W, Gallo RL. Psychological stress increases susceptibility to Staphylococcus aureus infection by the action of TGFβ to suppress immune-acting fibroblasts. In review at Cell. 2024