Eric A. Franzosa

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 Jun 17. 13(1):102. PMID: 34140026

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.

Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N.

Elife. 2021 May 04. 10. PMID: 33944776

A framework for microbiome science in public health.

Wilkinson JE, Franzosa EA, Everett C, Li C, Hu FB, Wirth DF, Song M, Chan AT, Rimm E, Garrett WS, Huttenhower C.

Nat Med. 2021 05. 27(5):766-774. PMID: 33820996

Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome.

Accorsi EK, Franzosa EA, Hsu T, Joice Cordy R, Maayan-Metzger A, Jaber H, Reiss-Mandel A, Kline M, DuLong C, Lipsitch M, Regev-Yochay G, Huttenhower C.

Genome Biol. 2020 12 11. 21(1):301. PMID: 33308267

Identification of Natural CRISPR Systems and Targets in the Human Microbiome.

Münch PC, Franzosa EA, Stecher B, McHardy AC, Huttenhower C.

Cell Host Microbe. 2021 01 13. 29(1):94-106.e4. PMID: 33217332

Strain-level epidemiology of microbial communities and the human microbiome.

Yan Y, Nguyen LH, Franzosa EA, Huttenhower C.

Genome Med. 2020 08 13. 12(1):71. PMID: 32791981

Global chemical effects of the microbiome include new bile-acid conjugations.

Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC.

Nature. 2020 03. 579(7797):123-129. PMID: 32103176

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.

Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, Vlamakis H, Xavier RJ.

Nat Microbiol. 2020 03. 5(3):486-497. PMID: 31959971

Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.

Thingholm LB, Rühlemann MC, Koch M, Fuqua B, Laucke G, Boehm R, Bang C, Franzosa EA, Hübenthal M, Rahnavard A, Frost F, Lloyd-Price J, Schirmer M, Lusis AJ, Vulpe CD, Lerch MM, Homuth G, Kacprowski T, Schmidt CO, Nöthlings U, Karlsen TH, Lieb W, Laudes M, Franke A, Huttenhower C.

Cell Host Microbe. 2019 08 14. 26(2):252-264.e10. PMID: 31399369