Publications

Henke MT; Brown EM; Cassilly CD; Vlamakis H; Xavier RJ; Clardy J, 2021. Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus.  Proc Natl Acad Sci U S A 118.

Borren NZ; Plichta D; Joshi AD; Bonilla G; Peng V; Colizzo FP; Luther J; Khalili H; Garber JJ; Janneke van der Woude C; Sadreyev R; Vlamakis H; Xavier RJ; Ananthakrishnan AN, 2021. Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases.  Clin Gastroenterol Hepatol 19(3):519-527.e5

Everett C; Li C; Wilkinson JE; Nguyen LH; McIver LJ; Ivey K; Izard J; Palacios N; Eliassen AH; Willett WC; Ascherio A; Sun Q; Tworoger SS; Chan AT; Garrett WS; Huttenhower C; Rimm EB; Song M, 2021. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies.  Nat Protoc 16(6):2724-2731

Wilkinson JE; Franzosa EA; Everett C; Li C; Hu FB; Wirth DF; Song M; Chan AT; Rimm E; Garrett WS; Huttenhower C, 2021. A framework for microbiome science in public health.  Nat Med 27(5):766-774

Creasy HH; Felix V; Aluvathingal J; Crabtree J; Ifeonu O; Matsumura J; McCracken C; Nickel L; Orvis J; Schor M; Giglio M; Mahurkar A; White O, 2021. HMPDACC: a Human Microbiome Project Multi-omic data resource.  Nucleic Acids Res 49(D1):D734-D742

Münch PC; Franzosa EA; Stecher B; McHardy AC; Huttenhower C, 2021. Identification of Natural CRISPR Systems and Targets in the Human Microbiome.  Cell Host Microbe 29(1):94-106.e4

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, 2021. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.  Elife 10.

Lavoie S; Chun E; Bae S; Brennan CA; Gallini Comeau CA; Lang JK; Michaud M; Hoveyda HR; Fraser GL; Fuller MH; Layden BT; Glickman JN; Garrett WS, 2020. Expression of Free Fatty Acid Receptor 2 by Dendritic Cells Prevents Their Expression of Interleukin 27 and Is Required for Maintenance of Mucosal Barrier and Immune Response Against Colorectal Tumors in Mice.  Gastroenterology 158(5):1359-1372.e9

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, 2020. Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.  Nat Microbiol 5(3):486-497

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, 2020. Global chemical effects of the microbiome include new bile-acid conjugations.  Nature 579(7797):123-129

Borren NZ; Plichta D; Joshi AD; Bonilla G; Sadreyev R; Vlamakis H; Xavier RJ; Ananthakrishnan AN, 2020. Multi-"-Omics" Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse.  Inflamm Bowel Dis 26(10):1524-1532

Yan Y; Nguyen LH; Franzosa EA; Huttenhower C, 2020. Strain-level epidemiology of microbial communities and the human microbiome.  Genome Med 12(1):71

Kong L; Lloyd-Price J; Vatanen T; Seksik P; Beaugerie L; Simon T; Vlamakis H; Sokol H; Xavier RJ, 2020. Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn's Disease.  Gastroenterology 159(6):2193-2202.e5

Lobel L; Cao YG; Fenn K; Glickman JN; Garrett WS, 2020. Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function.  Science 369(6510):1518-1524

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

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; 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

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

Chun E; Lavoie S; Fonseca-Pereira D; Bae S; Michaud M; Hoveyda HR; Fraser GL; Gallini Comeau CA; Glickman JN; Fuller MH; Layden BT; Garrett WS, 2019. Metabolite-Sensing Receptor Ffar2 Regulates Colonic Group 3 Innate Lymphoid Cells and Gut Immunity.  Immunity 51(5):871-884.e6

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

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

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

Mallick H; Franzosa EA; Mclver LJ; Banerjee S; Sirota-Madi A; Kostic AD; Clish CB; Vlamakis H; Xavier RJ; Huttenhower C, 2019. Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.  Nat Commun 10(1):3136

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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