Eric A. Franzosa

BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures.

Geistlinger L, Mirzayi C, Zohra F, Azhar R, Elsafoury S, Grieve C, Wokaty J, Gamboa-Tuz SD, Sengupta P, Hecht I, Ravikrishnan A, Gonçalves RS, Franzosa E, Raman K, Carey V, Dowd JB, Jones HE, Davis S, Segata N, Huttenhower C, Waldron L.

Nat Biotechnol. 2023 Sep 11. PMID: 37697152

Profiling novel lateral gene transfer events in the human microbiome.

Hsu TY, Nzabarushimana E, Wong D, Luo C, Beiko RG, Langille M, Huttenhower C, Nguyen LH, Franzosa EA.

bioRxiv. 2023 Aug 14. PMID: 37609252

RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities.

Wang Y, Thompson KN, Yan Y, Short MI, Zhang Y, Franzosa EA, Shen J, Hartmann EM, Huttenhower C.

Microbiome. 2023 06 13. 11(1):131. PMID: 37312147

Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects.

Münch PC, Eberl C, Woelfel S, Ring D, Fritz A, Herp S, Lade I, Geffers R, Franzosa EA, Huttenhower C, McHardy AC, Stecher B.

Cell Host Microbe. 2023 Jun 14. 31(6):1007-1020.e4. PMID: 37279755

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 03. 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 Nov. 41(11):1633-1644. 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 Dec. 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