Eric A. Franzosa

High-sensitivity pattern discovery in large, paired multiomic datasets.

Ghazi AR, Sucipto K, Rahnavard A, Franzosa EA, McIver LJ, Lloyd-Price J, Schwager E, Weingart G, Moon YS, Morgan XC, Waldron L, Huttenhower C.

Bioinformatics. 2022 06 24. 38(Suppl 1):i378-i385. PMID: 35758795

Discovery of bioactive microbial gene products in inflammatory bowel disease.

Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA.

Nature. 2022 06. 606(7915):754-760. PMID: 35614211

Human gut bacteria produce ??17-modulating bile acid metabolites.

Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS.

Nature. 2022 03. 603(7903):907-912. PMID: 35296854

Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite.

Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S.

Cell. 2022 02 03. 185(3):513-529.e21. PMID: 35120663

Multivariable association discovery in population-scale meta-omics studies.

Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C.

PLoS Comput Biol. 2021 11. 17(11):e1009442. PMID: 34784344

A statistical model for describing and simulating microbial community profiles.

Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, Tickle TL, Lu Y, Carmody RN, Franzosa EA, Janson L, Huttenhower C.

PLoS Comput Biol. 2021 09. 17(9):e1008913. PMID: 34516542

A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1.

Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M, Wang G, McCurry MD, Bae M, Paik D, Franzosa EA, Rastinejad F, Huttenhower C, Yao L, Devlin AS, Huh JR.

Cell Host Microbe. 2021 09 08. 29(9):1366-1377.e9. PMID: 34416161

Statistical approaches for differential expression analysis in metatranscriptomics.

Zhang Y, Thompson KN, Huttenhower C, Franzosa EA.

Bioinformatics. 2021 07 12. 37(Suppl_1):i34-i41. PMID: 34252963

Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men.

Ma W, Nguyen LH, Song M, Wang DD, Franzosa EA, Cao Y, Joshi A, Drew DA, Mehta R, Ivey KL, Strate LL, Giovannucci EL, Izard J, Garrett W, Rimm EB, Huttenhower C, Chan AT.

Genome Med. 2021 06 17. 13(1):102. PMID: 34140026

Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling.

Zhang Y, Thompson KN, Branck T, Nguyen LH, Franzosa EA, Huttenhower C.

Annu Rev Biomed Data Sci. 2021 07 20. 4:279-311. PMID: 34465175