Eric A. Franzosa

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease.

Mehta RS, Mayers JR, Zhang Y, Bhosle A, Glasser NR, Nguyen LH, Ma W, Bae S, Branck T, Song K, Sebastian L, Pacheco JA, Seo HS, Clish C, Dhe-Paganon S, Ananthakrishnan AN, Franzosa EA, Balskus EP, Chan AT, Huttenhower C.

Nat Med. 2023 Mar. 29(3):700-709. PMID: 36823301

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.

Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Puncochár M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N.

Nat Biotechnol. 2023 Feb 23. PMID: 36823356

Microbiome epidemiology and association studies in human health.

VanEvery H, Franzosa EA, Nguyen LH, Huttenhower C.

Nat Rev Genet. 2023 02. 24(2):109-124. PMID: 36198908

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin.

Ma S, Shungin D, Mallick H, Schirmer M, Nguyen LH, Kolde R, Franzosa E, Vlamakis H, Xavier R, Huttenhower C.

Genome Biol. 2022 10 03. 23(1):208. PMID: 36192803

Progress and opportunities in microbial community metabolomics.

Bhosle A, Wang Y, Franzosa EA, Huttenhower C.

Curr Opin Microbiol. 2022 12. 70:102195. PMID: 36063685

A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria.

Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS.

Nat Microbiol. 2022 09. 7(9):1404-1418. PMID: 35982310

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