Publications

Lloyd-Price J; Arze C; Ananthakrishnan AN; Schirmer M; Avila-Pacheco J; Poon TW; Andrews E; Ajami NJ; Bonham KS; Brislawn CJ; Casero D; Courtney H; Gonzalez A; Graeber TG; Hall AB; Lake K; Landers CJ; Mallick H; Plichta DR; Prasad M; Rahnavard G; Sauk J; Shungin D; Vázquez-Baeza Y; White RA 3rd; Braun J; Denson LA; Jansson JK; Knight R; Kugathasan S; McGovern DPB; Petrosino JF; Stappenbeck TS; Winter HS; Clish CB; Franzosa EA; Vlamakis H; Xavier RJ; Huttenhower C, 2019. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.  Nature 569(7758):655-662

2019. The Integrative Human Microbiome Project.  Nature 569(7758):641-648

Brown EM; Ke X; Hitchcock D; Jeanfavre S; Avila-Pacheco J; Nakata T; Arthur TD; Fornelos N; Heim C; Franzosa EA; Watson N; Huttenhower C; Haiser HJ; Dillow G; Graham DB; Finlay BB; Kostic AD; Porter JA; Vlamakis H; Clish CB; Xavier RJ, 2019. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.  Cell Host Microbe 25(5):668-680.e7

Schiffer L; Azhar R; Shepherd L; Ramos M; Geistlinger L; Huttenhower C; Dowd JB; Segata N; Waldron L, 2019. HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.  Am J Epidemiol 188(6):1023-1026

Haberman Y; Karns R; Dexheimer PJ; Schirmer M; Somekh J; Jurickova I; Braun T; Novak E; Bauman L; Collins MH; Mo A; Rosen MJ; Bonkowski E; Gotman N; Marquis A; Nistel M; Rufo PA; Baker SS; Sauer CG; Markowitz J; Pfefferkorn MD; Rosh JR; Boyle BM; Mack DR; Baldassano RN; Shah S; Leleiko NS; Heyman MB; Grifiths AM; Patel AS; Noe JD; Aronow BJ; Kugathasan S; Walters TD; Gibson G; Thomas SD; Mollen K; Shen-Orr S; Huttenhower C; Xavier RJ; Hyams JS; Denson LA, 2019. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.  Nat Commun 10(1):38

Franzosa EA; Sirota-Madi A; Avila-Pacheco J; Fornelos N; Haiser HJ; Reinker S; Vatanen T; Hall AB; Mallick H; McIver LJ; Sauk JS; Wilson RG; Stevens BW; Scott JM; Pierce K; Deik AA; Bullock K; Imhann F; Porter JA; Zhernakova A; Fu J; Weersma RK; Wijmenga C; Clish CB; Vlamakis H; Huttenhower C; Xavier RJ, 2019. Gut microbiome structure and metabolic activity in inflammatory bowel disease.  Nat Microbiol 4(2):293-305

Chang YL; Rossetti M; Vlamakis H; Casero D; Sunga G; Harre N; Miller S; Humphries R; Stappenbeck T; Simpson KW; Sartor RB; Wu G; Lewis J; Bushman F; McGovern DPB; Salzman N; Borneman J; Xavier R; Huttenhower C; Braun J, 2019. A screen of Crohn's disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells.  Mucosal Immunol 12(2):457-467

Franzosa EA; McIver LJ; Rahnavard G; Thompson LR; Schirmer M; Weingart G; Lipson KS; Knight R; Caporaso JG; Segata N; Huttenhower C, 2018. Species-level functional profiling of metagenomes and metatranscriptomes.  Nat Methods 15(11):962-968

Schirmer M; Denson L; Vlamakis H; Franzosa EA; Thomas S; Gotman NM; Rufo P; Baker SS; Sauer C; Markowitz J; Pfefferkorn M; Oliva-Hemker M; Rosh J; Otley A; Boyle B; Mack D; Baldassano R; Keljo D; LeLeiko N; Heyman M; Griffiths A; Patel AS; Noe J; Kugathasan S; Walters T; Huttenhower C; Hyams J; Xavier RJ, 2018. Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.  Cell Host Microbe 24(4):600-610.e4

Kolde R; Franzosa EA; Rahnavard G; Hall AB; Vlamakis H; Stevens C; Daly MJ; Xavier RJ; Huttenhower C, 2018. Host genetic variation and its microbiome interactions within the Human Microbiome Project.  Genome Med 10(1):6

Schirmer M; Franzosa EA; Lloyd-Price J; McIver LJ; Schwager R; Poon TW; Ananthakrishnan AN; Andrews E; Barron G; Lake K; Prasad M; Sauk J; Stevens B; Wilson RG; Braun J; Denson LA; Kugathasan S; McGovern DPB; Vlamakis H; Xavier RJ; Huttenhower C, 2018. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.  Nat Microbiol 3(3):337-346

Hall AB; Yassour M; Sauk J; Garner A; Jiang X; Arthur T; Lagoudas GK; Vatanen T; Fornelos N; Wilson R; Bertha M; Cohen M; Garber J; Khalili H; Gevers D; Ananthakrishnan AN; Kugathasan S; Lander ES; Blainey P; Vlamakis H; Xavier RJ; Huttenhower C, 2017. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.  Genome Med 9(1):103

Publication list retrieved from NCBI using ImpactPubs

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