Eric A. Franzosa

Author Correction: Optimized model architectures for deep learning on genomic data.

Gündüz HA, Mreches R, Moosbauer J, Robertson G, To XY, Franzosa EA, Huttenhower C, Rezaei M, McHardy AC, Bischl B, Münch PC, Binder M.

Commun Biol. 2024 May 23. 7(1):625. PMID: 38783006

Optimized model architectures for deep learning on genomic data.

Gündüz HA, Mreches R, Moosbauer J, Robertson G, To XY, Franzosa EA, Huttenhower C, Rezaei M, McHardy AC, Bischl B, Münch PC, Binder M.

Commun Biol. 2024 Apr 30. 7(1):516. PMID: 38693292

A host-microbiota interactome reveals extensive transkingdom connectivity.

Sonnert ND, Rosen CE, Ghazi AR, Franzosa EA, Duncan-Lowey B, González-Hernández JA, Huck JD, Yang Y, Dai Y, Rice TA, Nguyen MT, Song D, Cao Y, Martin AL, Bielecka AA, Fischer S, Guan C, Oh J, Huttenhower C, Ring AM, Palm NW.

Nature. 2024 Apr. 628(8006):171-179. PMID: 38509360

Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease.

Bhosle A, Bae S, Zhang Y, Chun E, Avila-Pacheco J, Geistlinger L, Pishchany G, Glickman JN, Michaud M, Waldron L, Clish CB, Xavier RJ, Vlamakis H, Franzosa EA, Garrett WS, Huttenhower C.

Mol Syst Biol. 2024 Apr. 20(4):338-361. PMID: 38467837

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples.

Zolfo M, Silverj A, Blanco-Míguez A, Manghi P, Rota-Stabelli O, Heidrich V, Jensen J, Maharjan S, Franzosa E, Menni C, Visconti A, Pinto F, Ciciani M, Huttenhower C, Cereseto A, Asnicar F, Kitano H, Yamada T, Segata N.

bioRxiv. 2024 Feb 19. PMID: 38464031

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. 2024 May. 42(5):790-802. 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 06 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