CH132CurtisHuttenhowerCurtis Huttenhower, Ph.D.42.33546850000000-71.1015102000000016016Huttenhower, CurtisResearch
Dr. Huttenhower’s research focuses on computational biology at the intersection of microbial community function and human health. The human body carries some four pounds of microbes, primarily in the gut, and understanding their biomolecular functions, their influences on human hosts, and the metabolic and functional roles of microbial communities generally is one of the key areas of study enabled by high-throughput sequencing. First, computational methods are needed to advance functional metagenomics. How can we understand what a microbial community is doing, what small molecule metabolites or signaling mechanisms it’s employing, and how its function relates to its organismal composition? Second, our understanding of the human microbiome and its relationship with public health remains limited. Pathogens have been examined by centuries of microbiology and epidemiology, but we know relatively little about the transmission or heritability of the normal commensal microbiota, its carriage of pathogenic functionality, or its interaction with host immunity, environment, and genetics. Finally, more broadly, novel machine learning methodology is needed to leverage structured biological knowledge in high-dimensional genomic data analysis. The Huttenhower group works on a variety of computational methods for data mining in microbial communities, model organisms, pathogens, and the human genome.
In practice, this entails a combination of computational methods development for mining and integrating large multi’omic data collections, as well as biological analyses and laboratory experiments to link the microbiome in human populations to specific microbiological mechanisms. The lab has worked extensively with the NIH Human Microbiome Project to help develop the first comprehensive map of the healthy Western adult microbiome, and it currently co-leads one of the “HMP2” Centers for Characterizing the Gut Microbial Ecosystem in Inflammatory Bowel Disease. This is one of many open problems in understanding how human-associated microbial communities can be used as a means of diagnosis or therapeutic intervention on the continuum between health and disease.617/432-4912Professor of Computational Biology and Bioinformaticscatalyst:eCommonsLogineCommons Loginplugins:TwitterTwitterprns:coAuthorOfcoauthor ofprns:endDateend dateFaculty Rankprns:fullNamefull nameprns:hasAuthorListauthor listprns:hasFacultyRankhas faculty rankprns:hasNetworkhas networkprns:hasPublicationVenuepublished inprns:informationResourceReferenceinformation resource referenceprns:isPrimaryPositionis primary positionprns:latitudelatitudeprns:longitudelongitudeprns:mainImagephotoprns:maxWeightmaximum weightprns:medlineTAjournal title abbreviationprns:meshDescriptorUIMeSH DescriptorUIprns:meshSemanticGroupNameMeSH semantic group nameprns:minWeightminimum weightprns:numberOfAuthorsnumber of authorsprns:numberOfConnectionsnumber of connectionsprns:numberOfPublicationsnumber of publicationsprns:personIdPerson IDprns:personInPrimaryPositionperson in primary positionprns:physicalNeighborOfphysical neighborProfilesRNS Plugin Instanceprns:pluginSearchableDataProfilesRNS Plugin Searchable Dataprns:positionInDepartmentposition in departmentprns:positionInDivisionposition in divisionprns:predicateNodepredicate nodeprns:principalInvestigatorNameprincipal investigator nameprns:publicationDatepublication dateprns:similarTosimilar toprns:sortOrdersort orderprns:startDatestart dateprns:trainingAtOrganizationeducational organizationprns:uniquenessWeightuniqueness weightprns:yearyearAcademic ArticleArticleDocumentbibo:pmidPubMed IdentifierAddressvivo:address1address line 1vivo:address2address line 2vivo:address3address line 3vivo:addressCitycityvivo:addressPostalCodepostal codevivo:addressStatestate or provincevivo:authorInAuthorshipselected publicationsvivo:authorRankauthor rank in publicationAuthorshipvivo:degreeEarneddegree earnedDepartmentDivisionvivo:educationalTrainingeducation and trainingEducational TrainingGrantvivo:hasResearchArearesearch areasvivo:hasResearcherRoleresearch activitiesvivo:hrJobTitleHR job titleInformation Resourcevivo:linkAnchorTextlink anchor textvivo:linkedAuthorlinked authorvivo:linkedInformationResourcelinked information resourcevivo:mailingAddressmailing addressvivo:majorFieldmajor field of degreevivo:overviewoverviewvivo:personInPositionpositionsvivo:phoneNumberphonePositionvivo:positionInOrganizationposition in organizationvivo:preferredTitlepreferred titleResearcher Rolevivo:researcherRoleOfresearcher role ofvivo:roleContributesTocontributes tovivo:sponsorAwardIdsponsor award idURLLinkvivo:webpagewebpagerdf:predicatepredicaterdf:typetyperdfs:labellabelConceptAgentfoaf:firstNamefirst namefoaf:lastNamelast nameOrganizationPersonAuthorship 10499651129440750Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork PNature microbiologyPublisher Correction: Enterotypes in the landscape of gut microbial community composition. Nat Microbiol. 2018 Mar; 3(3):388.Nat Microbiol2018-03-01T00:00:002018Publisher Correction: Enterotypes in the landscape of gut microbial community composition.Authorship 1052800829529379Cho Y, Abu-Ali G, Tashiro H, Kasahara DI, Brown TA, Brand JD, Mathews JA, Huttenhower C, Shore SAAmerican journal of respiratory cell and molecular biologyThe Microbiome Regulates Pulmonary Responses to Ozone in Mice. Am J Respir Cell Mol Biol. 2018 09; 59(3):346-354.Am J Respir Cell Mol Biol2018-09-01T00:00:002018The Microbiome Regulates Pulmonary Responses to Ozone in Mice.23013615Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower CGenome biologyDysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012 Apr 16; 13(9):R79.Genome Biol2012-04-16T00:00:002012Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.18499696Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OGBioinformatics (Oxford, England)The Sleipnir library for computational functional genomics. Bioinformatics. 2008 Jul 01; 24(13):1559-61.Bioinformatics2008-05-21T00:00:002008The Sleipnir library for computational functional genomics.19300515Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OGPLoS computational biologyDirecting experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol. 2009 Mar; 5(3):e1000322.PLoS Comput Biol2009-03-20T00:00:002009Directing experimental biology: a case study in mitochondrial biogenesis.Authorship 10610291929695840Chang 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 JMucosal immunologyA screen of Crohn's disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells. Mucosal Immunol. 2019 03; 12(2):457-467.Mucosal Immunol2018-04-25T00:00:002018A screen of Crohn's disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells.22719234Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower CPLoS computational biologyMetabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012; 8(6):e1002358.PLoS Comput Biol2012-06-13T00:00:002012Metabolic reconstruction for metagenomic data and its application to the human microbiome.Authorship 10662681229739900Obaldia N, Meibalan E, Sa JM, Ma S, Clark MA, Mejia P, Moraes Barros RR, Otero W, Ferreira MU, Mitchell JR, Milner DA, Huttenhower C, Wirth DF, Duraisingh MT, Wellems TE, Marti MmBioBone Marrow Is a Major Parasite Reservoir in Plasmodium vivax Infection. mBio. 2018 05 08; 9(3).mBio2018-05-08T00:00:002018Bone Marrow Is a Major Parasite Reservoir in Plasmodium vivax Infection.17724061Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OGBioinformatics (Oxford, England)Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics. 2007 Oct 15; 23(20):2692-9.Bioinformatics2007-08-27T00:00:002007Exploring the functional landscape of gene expression: directed search of large microarray compendia.17959824Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein DMolecular biology of the cellCoordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell. 2008 Jan; 19(1):352-67.Mol Biol Cell2007-10-24T00:00:002007Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.19246570Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OGGenome researchExploring the human genome with functional maps. Genome Res. 2009 Jun; 19(6):1093-106.Genome Res2009-02-26T00:00:002009Exploring the human genome with functional maps.Authorship 10677732129795809McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight RmSystemsAmerican Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3).mSystems2018-05-15T00:00:002018American Gut: an Open Platform for Citizen Science Microbiome Research.20523745Huttenhower C, Hofmann OPLoS computational biologyA quick guide to large-scale genomic data mining. PLoS Comput Biol. 2010 May 27; 6(5):e1000779.PLoS Comput Biol2010-05-27T00:00:002010A quick guide to large-scale genomic data mining.21314883Ballal SA, Gallini CA, Segata N, Huttenhower C, Garrett WSCellular microbiologyHost and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts. Cell Microbiol. 2011 Apr; 13(4):508-17.Cell Microbiol2011-02-14T00:00:002011Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts.Authorship 10696551129806032De Niz M, Meibalan E, Mejia P, Ma S, Brancucci NMB, Agop-Nersesian C, Mandt R, Ngotho P, Hughes KR, Waters AP, Huttenhower C, Mitchell JR, Martinelli R, Frischknecht F, Seydel KB, Taylor T, Milner D, Heussler VT, Marti MScience advancesPlasmodium gametocytes display homing and vascular transmigration in the host bone marrow. Sci Adv. 2018 05; 4(5):eaat3775.Sci Adv2018-05-23T00:00:002018Plasmodium gametocytes display homing and vascular transmigration in the host bone marrow.22204305Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJGenome biologyGenomics in 2011: challenges and opportunities. Genome Biol. 2011 Dec 28; 12(12):137.Genome Biol2011-12-28T00:00:002011Genomics in 2011: challenges and opportunities.22698087Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard JGenome biologyComposition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 2012 Jun 14; 13(6):R42.Genome Biol2012-06-14T00:00:002012Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples.17005538Huttenhower C, Hibbs M, Myers C, Troyanskaya OGBioinformatics (Oxford, England)A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics. 2006 Dec 01; 22(23):2890-7.Bioinformatics2006-09-27T00:00:002006A scalable method for integration and functional analysis of multiple microarray datasets.22688413Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower CNature methodsMetagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012 Jun 10; 9(8):811-4.Nat Methods2012-06-10T00:00:002012Metagenomic microbial community profiling using unique clade-specific marker genes.23550061Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron LDatabase : the journal of biological databases and curationcuratedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database (Oxford). 2013; 2013:bat013.Database (Oxford)2013-04-02T00:00:002013curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome.23563424Brown J, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh PNature biotechnologyTranslating the human microbiome. Nat Biotechnol. 2013 Apr; 31(4):304-8.Nat Biotechnol2013-04-01T00:00:002013Translating the human microbiome.21062826Sathirapongsasuti JF, Sathira N, Suzuki Y, Huttenhower C, Sugano SNucleic acids researchUltraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing. Nucleic Acids Res. 2011 Mar; 39(6):1967-79.Nucleic Acids Res2010-11-09T00:00:002010Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing.Authorship 107988419Authorship 10826634330001516Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata NCell host & microbeMother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host Microbe. 2018 07 11; 24(1):133-145.e5.Cell Host Microbe2018-07-11T00:00:002018Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.30001517Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyöty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJCell host & microbeStrain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. Cell Host Microbe. 2018 07 11; 24(1):146-154.e4.Cell Host Microbe2018-07-11T00:00:002018Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.22156367Waldron L, Pintilie M, Tsao MS, Shepherd FA, Huttenhower C, Jurisica IBioinformatics (Oxford, England)Optimized application of penalized regression methods to diverse genomic data. Bioinformatics. 2011 Dec 15; 27(24):3399-406.Bioinformatics2011-12-15T00:00:002011Optimized application of penalized regression methods to diverse genomic data.22427238Yamauchi M, Morikawa T, Kuchiba A, Imamura Y, Qian ZR, Nishihara R, Liao X, Waldron L, Hoshida Y, Huttenhower C, Chan AT, Giovannucci E, Fuchs C, Ogino SGutAssessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum. Gut. 2012 Jun; 61(6):847-54.Gut2012-03-17T00:00:002012Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum.22458912Waldron L, Simpson P, Parmigiani G, Huttenhower CBMC cancerReport on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. BMC Cancer. 2012 Mar 29; 12:124.BMC Cancer2012-03-29T00:00:002012Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues.Authorship 122820120003429Huttenhower C, Mehmood SO, Troyanskaya OGBMC bioinformaticsGraphle: Interactive exploration of large, dense graphs. BMC Bioinformatics. 2009 Dec 14; 10:417.BMC Bioinformatics2009-12-14T00:00:002009Graphle: Interactive exploration of large, dense graphs.21124865Park CY, Hess DC, Huttenhower C, Troyanskaya OGPLoS computational biologySimultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PLoS Comput Biol. 2010 Nov 24; 6(11):e1001009.PLoS Comput Biol2010-11-24T00:00:002010Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.22130880Waldron L, Coller HA, Huttenhower CMethods in molecular biology (Clifton, N.J.)Integrative approaches for microarray data analysis. Methods Mol Biol. 2012; 802:157-82.Methods Mol Biol2012-01-01T00:00:002012Integrative approaches for microarray data analysis.22719821Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BAPloS oneA case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PLoS One. 2012; 7(6):e29044.PLoS One2012-06-13T00:00:002012A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).22719832Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic JPloS oneA metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One. 2012; 7(6):e36466.PLoS One2012-06-13T00:00:002012A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.20682317Baba Y, Nosho K, Shima K, Huttenhower C, Tanaka N, Hazra A, Giovannucci EL, Fuchs CS, Ogino SGastroenterologyHypomethylation of the IGF2 DMR in colorectal tumors, detected by bisulfite pyrosequencing, is associated with poor prognosis. Gastroenterology. 2010 Dec; 139(6):1855-64.Gastroenterology2010-08-02T00:00:002010Hypomethylation of the IGF2 DMR in colorectal tumors, detected by bisulfite pyrosequencing, is associated with poor prognosis.Authorship 109348924Authorship 1093798730228205Hamada T, Zhang X, Mima K, Bullman S, Sukawa Y, Nowak JA, Kosumi K, Masugi Y, Twombly TS, Cao Y, Song M, Liu L, da Silva A, Shi Y, Gu M, Li W, Koh H, Nosho K, Inamura K, Keum N, Wu K, Meyerhardt JA, Kostic AD, Huttenhower C, Garrett WS, Meyerson M, Giovannucci EL, Chan AT, Fuchs CS, Nishihara R, Giannakis M, Ogino SCancer immunology researchFusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status. Cancer Immunol Res. 2018 11; 6(11):1327-1336.Cancer Immunol Res2018-09-18T00:00:002018Fusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status.30240285Cho Y, Abu-Ali G, Tashiro H, Brown TA, Osgood RS, Kasahara DI, Huttenhower C, Shore SAAmerican journal of respiratory cell and molecular biologySex Differences in Pulmonary Responses to Ozone in Mice. Role of the Microbiome. Am J Respir Cell Mol Biol. 2019 02; 60(2):198-208.Am J Respir Cell Mol Biol2019-02-01T00:00:002019Sex Differences in Pulmonary Responses to Ozone in Mice. Role of the Microbiome.21194434Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OGBMC systems biologyIntegrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst Biol. 2010 Dec 31; 4:180.BMC Syst Biol2010-12-31T00:00:002010Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.22009990Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, Huttenhower C, Garrett WS, Meyerson MGenome researchGenomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2012 Feb; 22(2):292-8.Genome Res2011-10-18T00:00:002011Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.23140990Morgan XC, Segata N, Huttenhower CTrends in genetics : TIGBiodiversity and functional genomics in the human microbiome. Trends Genet. 2013 Jan; 29(1):51-8.Trends Genet2012-11-07T00:00:002012Biodiversity and functional genomics in the human microbiome.23409037Ballarini A, Segata N, Huttenhower C, Jousson OPloS oneSimultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. PLoS One. 2013; 8(2):e55764.PLoS One2013-02-11T00:00:002013Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes.Authorship 109646718Authorship 10962332730243655Kosumi K, Hamada T, Koh H, Borowsky J, Bullman S, Twombly TS, Nevo D, Masugi Y, Liu L, da Silva A, Chen Y, Du C, Gu M, Li C, Li W, Liu H, Shi Y, Mima K, Song M, Nosho K, Nowak JA, Nishihara R, Baba H, Zhang X, Wu K, Wang M, Huttenhower C, Garrett WS, Meyerson ML, Lennerz JK, Giannakis M, Chan AT, Meyerhardt JA, Fuchs CS, Ogino SThe American journal of pathologyThe Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome. Am J Pathol. 2018 12; 188(12):2839-2852.Am J Pathol2018-09-20T00:00:002018The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome.30253799Ma S, Ogino S, Parsana P, Nishihara R, Qian Z, Shen J, Mima K, Masugi Y, Cao Y, Nowak JA, Shima K, Hoshida Y, Giovannucci EL, Gala MK, Chan AT, Fuchs CS, Parmigiani G, Huttenhower C, Waldron LGenome biologyContinuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biol. 2018 09 25; 19(1):142.Genome Biol2018-09-25T00:00:002018Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis.17369653Huttenhower C, Troyanskaya OGComputational systems bioinformatics. Computational Systems Bioinformatics ConferenceBayesian data integration: a functional perspective. Comput Syst Bioinformatics Conf. 2006; 341-51.Comput Syst Bioinformatics Conf2006-01-01T00:00:002006Bayesian data integration: a functional perspective.Authorship 109847412Authorship 11074442630333051Fahimipour AK, Hartmann EM, Siemens A, Kline J, Levin DA, Wilson H, Betancourt-Román CM, Brown GZ, Fretz M, Northcutt D, Siemens KN, Huttenhower C, Green JL, Van Den Wymelenberg KMicrobiomeDaylight exposure modulates bacterial communities associated with household dust. Microbiome. 2018 10 18; 6(1):175.Microbiome2018-10-18T00:00:002018Daylight exposure modulates bacterial communities associated with household dust.30308161Schirmer 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 RJCell host & microbeCompositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. Cell Host Microbe. 2018 10 10; 24(4):600-610.e4.Cell Host Microbe2018-10-10T00:00:002018Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.19300474Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AAPLoS geneticsComputationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. 2009 Mar; 5(3):e1000407.PLoS Genet2009-03-20T00:00:002009Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.Authorship 110834721Authorship 11083941430356187Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JFNatureTemporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018 10; 562(7728):583-588.Nature2018-10-24T00:00:002018Temporal development of the gut microbiome in early childhood from the TEDDY study.30356183Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJNatureThe human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 2018 10; 562(7728):589-594.Nature2018-10-24T00:00:002018The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.22508672Morikawa T, Tanaka N, Kuchiba A, Nosho K, Yamauchi M, Hornick JL, Swanson RS, Chan AT, Meyerhardt JA, Huttenhower C, Schrag D, Fuchs CS, Ogino SArchives of surgery (Chicago, Ill. : 1960)Predictors of lymph node count in colorectal cancer resections: data from US nationwide prospective cohort studies. Arch Surg. 2012 Aug; 147(8):715-23.Arch Surg2012-08-01T00:00:002012Predictors of lymph node count in colorectal cancer resections: data from US nationwide prospective cohort studies.23209389Gevers D, Pop M, Schloss PD, Huttenhower CPLoS computational biologyBioinformatics for the Human Microbiome Project. PLoS Comput Biol. 2012; 8(11):e1002779.PLoS Comput Biol2012-11-29T00:00:002012Bioinformatics for the Human Microbiome Project.Authorship 11095101130377376Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower CNature methodsSpecies-level functional profiling of metagenomes and metatranscriptomes. Nat Methods. 2018 11; 15(11):962-968.Nat Methods2018-10-30T00:00:002018Species-level functional profiling of metagenomes and metatranscriptomes.Authorship 1110847930412201Taroncher-Oldenburg G, Jones S, Blaser M, Bonneau R, Christey P, Clemente JC, Elinav E, Ghedin E, Huttenhower C, Kelly D, Kyle D, Littman D, Maiti A, Maue A, Olle B, Segal L, van Hylckama Vlieg JET, Wang JNature biotechnologyTranslating microbiome futures. Nat Biotechnol. 2018 11 09; 36(11):1037-1042.Nat Biotechnol2018-11-09T00:00:002018Translating microbiome futures.Authorship 11121851230420441Gerke T, Beltran H, Wang X, Lee GM, Sboner A, Karnes RJ, Klein EA, Davicioni E, Yousefi K, Ross AE, Börnigen D, Huttenhower C, Mucci LA, Trock BJ, Sweeney CJCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive OncologyLow Tristetraprolin Expression Is Associated with Lethal Prostate Cancer. Cancer Epidemiol Biomarkers Prev. 2019 03; 28(3):584-590.Cancer Epidemiol Biomarkers Prev2018-11-12T00:00:002018Low Tristetraprolin Expression Is Associated with Lethal Prostate Cancer.Authorship 11158641130477563Sinha R, Ahsan H, Blaser M, Caporaso JG, Carmical JR, Chan AT, Fodor A, Gail MH, Harris CC, Helzlsouer K, Huttenhower C, Knight R, Kong HH, Lai GY, Hutchinson DLS, Le Marchand L, Li H, Orlich MJ, Shi J, Truelove A, Verma M, Vogtmann E, White O, Willett W, Zheng W, Mahabir S, Abnet CMicrobiomeNext steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017. 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Curr Infect Dis Rep. 2011 Feb; 13(1):28-34.Curr Infect Dis Rep2011-02-01T00:00:002011Current concepts of the intestinal microbiota and the pathogenesis of infection.Authorship 111953626Authorship 112001426Authorship 112057836Authorship 11212681130531976Franzosa 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 RJNature microbiologyGut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 02; 4(2):293-305.Nat Microbiol2018-12-10T00:00:002018Gut microbiome structure and metabolic activity in inflammatory bowel disease.30574558Fahimipour AK, Ben Mamaar S, McFarland AG, Blaustein RA, Chen J, Glawe AJ, Kline J, Green JL, Halden RU, Van Den Wymelenberg K, Huttenhower C, Hartmann EMmSystemsAntimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors. mSystems. 2018 Nov-Dec; 3(6).mSystems2018-12-11T00:00:002018Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors.30542108Haberman Y, Schirmer M, Dexheimer PJ, Karns R, Braun T, Kim MO, Walters TD, Baldassano RN, Noe JD, Rosh J, Markowitz J, Crandall WV, Mack DR, Griffiths AM, Heyman MB, Baker SS, Kellermayer R, Moulton D, Patel AS, Gulati AS, Steiner SJ, LeLeiko N, Otley A, Oliva-Hemker M, Ziring D, Kirschner BS, Keljo DJ, Guthery SL, Cohen SA, Snapper S, Evans J, Dubinsky M, Aronow B, Hyams JS, Kugathasan S, Huttenhower C, Xavier RJ, Denson LAMucosal immunologyAge-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis. Mucosal Immunol. 2019 03; 12(2):491-502.Mucosal Immunol2018-12-12T00:00:002018Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis.30559407Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJNature microbiologyGenomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol. 2019 03; 4(3):470-479.Nat Microbiol2018-12-17T00:00:002018Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.Authorship 11231893930604764Haberman 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 LANature communicationsUlcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nat Commun. 2019 01 03; 10(1):38.Nat Commun2019-01-03T00:00:002019Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.Authorship 1121952Authorship 1126408630649166Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron LAmerican journal of epidemiologyHMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Am J Epidemiol. 2019 06 01; 188(6):1023-1026.Am J Epidemiol2019-06-01T00:00:002019HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.19119411Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OGPLoS computational biologyPredicting cellular growth from gene expression signatures. PLoS Comput Biol. 2009 Jan; 5(1):e1000257.PLoS Comput Biol2009-01-02T00:00:002009Predicting cellular growth from gene expression signatures.Authorship 11275871730661755Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata NCellExtensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell. 2019 01 24; 176(3):649-662.e20.Cell2019-01-17T00:00:002019Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.21931822Segata N, Huttenhower CPloS oneToward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. PLoS One. 2011; 6(9):e24704.PLoS One2011-09-12T00:00:002011Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies.Authorship 11300212630723264Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJNature microbiologyPublisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol. 2019 Mar; 4(3):545.Nat Microbiol2019-03-01T00:00:002019Publisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.D010802Concepts & Ideas101927890.57031PhylogenyD056186Occupations2104280.750198MetagenomicsAuthorship 11416542630971771Franzosa 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 RJNature microbiologyAuthor Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 May; 4(5):898.Nat Microbiol2019-05-01T00:00:002019Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease.D019295Occupations148035060.404415Computational BiologyD001419Living Beings93121060.445089BacteriaD054892Genes & Molecular SequencesLiving Beings1964170.756821MetagenomeAuthorship 11513981231071294Brown 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 RJCell host & microbeBacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis. Cell Host Microbe. 2019 05 08; 25(5):668-680.e7.Cell Host Microbe2019-05-08T00:00:002019Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.BiostatisticsImmunology and Infectious DiseasesMedicinePathologyGastroenterologyBrigham and Women's HospitalHarvard T.H. Chan School of Public HealthMassachusetts General HospitalRX1RamnikXavierRamnik Xavier, M.B.,B.Ch.42.36125700000000-71.0655270000000064506Xavier, RamnikKurt J. Isselbacher Professor of Medicine in the Field of GastroenterologyJQ6JohnQuackenbushJohn Quackenbush, Ph.D.42.33546850000000-71.1015102000000043077Quackenbush, JohnHenry Pickering Walcott Professor of Computational Biology and BioinformaticsTM33ThomasMangioneThomas William Mangione, Ph.D.42.33546850000000-71.1015102000000064751Mangione, ThomasInstructorVGD1VictorDe GruttolaVictor De Gruttola, D.Sc.42.33546850000000-71.1015102000000048505De Gruttola, VictorProfessor of Biostatistics, Emeritus31142855Lloyd-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, 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 CNatureMulti-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019 05; 569(7758):655-662.Nature2019-05-29T00:00:002019Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.ANA8AshwinAnanthakrishnanAshwin N Ananthakrishnan, M.B.,B.S.42.36127360000000-71.0647979000000091281Ananthakrishnan, AshwinAssociate Professor of MedicineAuthorship 115791440Authorship 1156833831144984Tashiro H, Cho Y, Kasahara DI, Brand JD, Bry L, Yeliseyev V, Abu-Ali G, Huttenhower C, Shore SAAmerican journal of respiratory cell and molecular biologyMicrobiota Contribute to Obesity-related Increases in the Pulmonary Response to Ozone. Am J Respir Cell Mol Biol. 2019 12; 61(6):702-712.Am J Respir Cell Mol Biol2019-12-01T00:00:002019Microbiota Contribute to Obesity-related Increases in the Pulmonary Response to Ozone.Authorship 115964227Authorship 11593841231167926Dantzler KW, Ma S, Ngotho P, Stone WJR, Tao D, Rijpma S, De Niz M, Nilsson Bark SK, Jore MM, Raaijmakers TK, Early AM, Ubaida-Mohien C, Lemgruber L, Campo JJ, Teng AA, Le TQ, Walker CL, Hermand P, Deterre P, Davies DH, Felgner P, Morlais I, Wirth DF, Neafsey DE, Dinglasan RR, Laufer M, Huttenhower C, Seydel K, Taylor T, Bousema T, Marti MScience translational medicineNaturally acquired immunity against immature Plasmodium falciparum gametocytes. Sci Transl Med. 2019 06 05; 11(495).Sci Transl Med2019-06-05T00:00:002019Naturally acquired immunity against immature Plasmodium falciparum gametocytes.31169073Hsu T, Gemmell MR, Franzosa EA, Berry S, Mukhopadhya I, Hansen R, Michaud M, Nielsen H, Miller WG, Nielsen H, Bajaj-Elliott M, Huttenhower C, Garrett WS, Hold GLEmerging microbes & infectionsComparative genomics and genome biology of Campylobacter showae. Emerg Microbes Infect. 2019; 8(1):827-840.Emerg Microbes Infect2019-01-01T00:00:002019Comparative genomics and genome biology of Campylobacter showae.WSG2WendyGarrettWendy S. Garrett, M.D., Ph.D.42.33547570000000-71.1014834000000045556Garrett, WendyIrene Heinz Given Professor of Immunology and Infectious Diseases11287selected publications8.964920.00563758766research areas9.584480.0239611179coauthor of309.05237.426360similar toSO8ShujiOginoShuji Ogino, M.D., Ph.D.42.33789600000000-71.107249300000003507Ogino, ShujiProfessor of PathologyTC24TianxiCaiTianxi Cai, Sc.D.42.33546850000000-71.1015102000000055356Cai, TianxiJohn Rock Professor of Population and Translational Data SciencesATC1AndrewChanAndrew Chan, M.D.42.36241700000000-71.0689370000000044598Chan, AndrewDaniel K. Podolsky Professor of MedicineAGR5AndreaRotnitzkyAndrea Gloria Rotnitzky, Ph.D.42.33546850000000-71.1015102000000042041Rotnitzky, AndreaAdjunct Professor of BiostatisticsAuthorship 11734251031316056Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower CNature communicationsPredictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Nat Commun. 2019 07 17; 10(1):3136.Nat Commun2019-07-17T00:00:002019Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.Authorship 11757344031341288Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JGNature biotechnologyReproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857.Nat Biotechnol2019-08-01T00:00:002019Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.Authorship 14376010Authorship 1178146531373365McBurney MI, Davis C, Fraser CM, Schneeman BO, Huttenhower C, Verbeke K, Walter J, Latulippe METhe Journal of nutritionEstablishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions. J Nutr. 2019 11 01; 149(11):1882-1895.J Nutr2019-11-01T00:00:002019Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions.Authorship 117937125Authorship 11800174031399723Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JGNature biotechnologyAuthor Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Sep; 37(9):1091.Nat Biotechnol2019-09-01T00:00:002019Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.31399369Thingholm 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 CCell host & microbeObese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition. Cell Host Microbe. 2019 08 14; 26(2):252-264.e10.Cell Host Microbe2019-08-06T00:00:002019Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.Authorship 1183285531455422Kasahara DI, Wilkinson JE, Cho Y, Cardoso AP, Huttenhower C, Shore SARespiratory researchThe interleukin-33 receptor contributes to pulmonary responses to ozone in male mice: role of the microbiome. Respir Res. 2019 Aug 27; 20(1):197.Respir Res2019-08-27T00:00:002019The interleukin-33 receptor contributes to pulmonary responses to ozone in male mice: role of the microbiome.Authorship 11967492631607556Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata NCell host & microbeThe Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host Microbe. 2019 11 13; 26(5):666-679.e7.Cell Host Microbe2019-10-10T00:00:002019The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.Authorship 1601224true1Kurt J. Isselbacher Professor of Medicine in the Field of GastroenterologyKurt J. Isselbacher Professor of Medicine in the Field of Gastroenterologytrue1Associate Professor of MedicineAssociate Professor of MedicineAuthorship 12067562631792218Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight RNature communicationsPhylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun. 2019 12 02; 10(1):5477.Nat Commun2019-12-02T00:00:002019Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.Authorship 12132662731880318Haruki K, Kosumi K, Hamada T, Twombly TS, Väyrynen JP, Kim SA, Masugi Y, Qian ZR, Mima K, Baba Y, da Silva A, Borowsky J, Arima K, Fujiyoshi K, Lau MC, Li P, Guo C, Chen Y, Song M, Nowak JA, Nishihara R, Yanaga K, Zhang X, Wu K, Bullman S, Garrett WS, Huttenhower C, Meyerhardt JA, Giannakis M, Chan AT, Fuchs CS, Ogino SThe Journal of pathologyAssociation of autophagy status with amount of Fusobacterium nucleatum in colorectal cancer. 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PLoS Pathog. 2020 01; 16(1):e1008211.PLoS Pathog2020-01-23T00:00:002020Mobilizable antibiotic resistance genes are present in dust microbial communities.31959971Fornelos 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 RJNature microbiologyGrowth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Nat Microbiol. 2020 03; 5(3):486-497.Nat Microbiol2020-01-20T00:00:002020Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.Authorship 12299465332103176Quinn 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 PCNatureGlobal chemical effects of the microbiome include new bile-acid conjugations. Nature. 2020 03; 579(7797):123-129.Nature2020-02-26T00:00:002020Global chemical effects of the microbiome include new bile-acid conjugations.Authorship 12366351932240601Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower CCell host & microbeStructure of the Mucosal and Stool Microbiome in Lynch Syndrome. Cell Host Microbe. 2020 04 08; 27(4):585-600.e4.Cell Host Microbe2020-04-01T00:00:002020Structure of the Mucosal and Stool Microbiome in Lynch Syndrome.Authorship 12480071732427907Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata NNature communicationsPrecise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun. 2020 05 19; 11(1):2500.Nat Commun2020-05-19T00:00:002020Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.Authorship 1251974732483366Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGINature biotechnologyPICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020 06; 38(6):685-688.Nat Biotechnol2020-06-01T00:00:002020PICRUSt2 for prediction of metagenome functions.Authorship 12566002132513234Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata NGenome biologyAnalysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biol. 2020 06 08; 21(1):138.Genome Biol2020-06-08T00:00:002020Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations.Authorship 13879032025-06-30HUTTENHOWER, CURTIS ;LIN, XIHONG2020-07-01Interdisciplinary training: Statistical Genetics/Genomics and Computational BiologyT32GM135117Co-Principal InvestigatorAuthorship 1653164Authorship 1660383Authorship 1686911Authorship 1273302632763240Henn MR, O'Brien EJ, Diao L, Feagan BG, Sandborn WJ, Huttenhower C, Wortman JR, McGovern BH, Wang-Weigand S, Lichter DI, Chafee M, Ford CB, Bernardo P, Zhao P, Simmons S, Tomlinson AD, Cook DN, Pomerantz RJ, Misra BK, Auninš JG, Trucksis MGastroenterologyA Phase 1b Safety Study of SER-287, a Spore-Based Microbiome Therapeutic, for Active Mild to Moderate Ulcerative Colitis. Gastroenterology. 2021 01; 160(1):115-127.e30.Gastroenterology2020-08-04T00:00:002020A Phase 1b Safety Study of SER-287, a Spore-Based Microbiome Therapeutic, for Active Mild to Moderate Ulcerative Colitis.Authorship 1278073432791981Yan Y, Nguyen LH, Franzosa EA, Huttenhower CGenome medicineStrain-level epidemiology of microbial communities and the human microbiome. Genome Med. 2020 08 13; 12(1):71.Genome Med2020-08-13T00:00:002020Strain-level epidemiology of microbial communities and the human microbiome. 2000Rose-Hulman Inst. of Tech.Rose-Hulman Inst. of Tech., Computer Science/Math/ChemistryB.S.Computer Science/Math/Chemistry2003Carnegie Mellon UniversityCarnegie Mellon University, Computer ScienceM.S.Computer Science2008Princeton UniversityPrinceton University, Computer SciencePh.D. Computer Sciencehttps://huttenhower.sph.harvard.edu/The Huttenhower Labhttps://hcmph.sph.harvard.edu/Harvard Chan Microbiome in Public Health CenterAuthorship 13028875Authorship 1304720933135936Nicholson K, Bjornevik K, Abu-Ali G, Chan J, Cortese M, Dedi B, Jeon M, Xavier R, Huttenhower C, Ascherio A, Berry JDAmyotrophic lateral sclerosis & frontotemporal degenerationThe human gut microbiota in people with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener. 2021 05; 22(3-4):186-194.Amyotroph Lateral Scler Frontotemporal Degener2020-11-02T00:00:002020The human gut microbiota in people with amyotrophic lateral sclerosis.33217332Münch PC, Franzosa EA, Stecher B, McHardy AC, Huttenhower CCell host & microbeIdentification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe. 2021 01 13; 29(1):94-106.e4.Cell Host Microbe2020-11-19T00:00:002020Identification of Natural CRISPR Systems and Targets in the Human Microbiome.33283299Simon TG, Chan AT, Huttenhower CHepatology (Baltimore, Md.)Microbiome Biomarkers: One Step Closer in NAFLD Cirrhosis. 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Cell Rep Med. 2020 12 22; 1(9):100156.Cell Rep Med2020-12-22T00:00:002020Delivery Mode Affects Stability of Early Infant Gut Microbiota.https://www.hsph.harvard.edu/profile/curtis-huttenhower/Academic ProfileAuthorship 131962910Authorship 132184037Authorship 1320020533432175Asnicar F, Berry SE, Valdes AM, Nguyen LH, Piccinno G, Drew DA, Leeming E, Gibson R, Le Roy C, Khatib HA, Francis L, Mazidi M, Mompeo O, Valles-Colomer M, Tett A, Beghini F, Dubois L, Bazzani D, Thomas AM, Mirzayi C, Khleborodova A, Oh S, Hine R, Bonnett C, Capdevila J, Danzanvilliers S, Giordano F, Geistlinger L, Waldron L, Davies R, Hadjigeorgiou G, Wolf J, Ordovás JM, Gardner C, Franks PW, Chan AT, Huttenhower C, Spector TD, Segata NNature medicineMicrobiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat Med. 2021 02; 27(2):321-332.Nat Med2021-01-11T00:00:002021Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.33483311McFarland AG, Bertucci HK, Littman E, Shen J, Huttenhower C, Hartmann EMApplied and environmental microbiologyTriclosan Tolerance Is Driven by a Conserved Mechanism in Diverse Pseudomonas Species. Appl Environ Microbiol. 2021 03 11; 87(7).Appl Environ Microbiol2021-03-11T00:00:002021Triclosan Tolerance Is Driven by a Conserved Mechanism in Diverse Pseudomonas Species.33478576Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower CMicrobiomeWhole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome. 2021 01 21; 9(1):17.Microbiome2021-01-21T00:00:002021Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach.33574608Wang DD, Nguyen LH, Li Y, Yan Y, Ma W, Rinott E, Ivey KL, Shai I, Willett WC, Hu FB, Rimm EB, Stampfer MJ, Chan AT, Huttenhower CNature medicineThe gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. Nat Med. 2021 02; 27(2):333-343.Nat Med2021-02-11T00:00:002021The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk.Authorship 132894014Authorship 13314541533593386Young C, Wood HM, Seshadri RA, Van Nang P, Vaccaro C, Melendez LC, Bose M, Van Doi M, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke PGenome medicineThe colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries. Genome Med. 2021 02 16; 13(1):27.Genome Med2021-02-16T00:00:002021The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries.Authorship 13330202833632927Borowsky J, Haruki K, Lau MC, Dias Costa A, Väyrynen JP, Ugai T, Arima K, da Silva A, Felt KD, Zhao M, Gurjao C, Twombly TS, Fujiyoshi K, Väyrynen SA, Hamada T, Mima K, Bullman S, Harrison TA, Phipps AI, Peters U, Ng K, Meyerhardt JA, Song M, Giovannucci EL, Wu K, Zhang X, Freeman GJ, Huttenhower C, Garrett WS, Chan AT, Leggett BA, Whitehall VLJ, Walker N, Brown I, Bettington M, Nishihara R, Fuchs CS, Lennerz JK, Giannakis M, Nowak JA, Ogino SClinical cancer research : an official journal of the American Association for Cancer ResearchAssociation of Fusobacterium nucleatum with Specific T-cell Subsets in the Colorectal Carcinoma Microenvironment. 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Clin Cancer Res. 2021 04 15; 27(8):2246-2254.Clin Cancer Res2021-03-03T00:00:002021Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy.Authorship 13441641333820996Wilkinson JE, Franzosa EA, Everett C, Li C, Hu FB, Wirth DF, Song M, Chan AT, Rimm E, Garrett WS, Huttenhower CNature medicineA framework for microbiome science in public health. Nat Med. 2021 05; 27(5):766-774.Nat Med2021-04-05T00:00:002021A framework for microbiome science in public health.33926968Li J, Li Y, Ivey KL, Wang DD, Wilkinson JE, Franke A, Lee KH, Chan A, Huttenhower C, Hu FB, Rimm EB, Sun QGutInterplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men. 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Sci Transl Med. 2023 07 26; 15(706):eabn4722.Sci Transl Med2023-07-26T00:00:002023Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes.37299414Hughes RL, Frankenfeld CL, Gohl DM, Huttenhower C, Jackson SA, Vandeputte D, Vogtmann E, Comstock SS, Kable MENutrientsMethods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]. Nutrients. 2023 May 24; 15(11).Nutrients2023-05-24T00:00:002023Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022].37312147Wang Y, Thompson KN, Yan Y, Short MI, Zhang Y, Franzosa EA, Shen J, Hartmann EM, Huttenhower CMicrobiomeRNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities. 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Neurology. 2023 11 14; 101(20):e2014-e2025.Neurology2023-09-29T00:00:002023Association Between Bowel Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome.37739776Hu Y, Li J, Wang B, Zhu L, Li Y, Ivey KL, Lee KH, Eliassen AH, Chan A, Huttenhower C, Hu FB, Qi Q, Rimm EB, Sun QGutInterplay between diet, circulating indolepropionate concentrations and cardiometabolic health in US populations. Gut. 2023 Nov 24; 72(12):2260-2271.Gut2023-11-24T00:00:002023Interplay between diet, circulating indolepropionate concentrations and cardiometabolic health in US populations.Authorship 158755220Authorship 158249610Authorship 158638610Authorship 1585164737697152Geistlinger 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 LNature biotechnologyBugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nat Biotechnol. 2023 Sep 11.Nat Biotechnol2023-09-11T00:00:002023BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures.37609252Hsu TY, Nzabarushimana E, Wong D, Luo C, Beiko RG, Langille M, Huttenhower C, Nguyen LH, Franzosa EAbioRxiv : the preprint server for biologyProfiling novel lateral gene transfer events in the human microbiome. bioRxiv. 2023 Aug 14.bioRxiv2023-08-14T00:00:002023Profiling novel lateral gene transfer events in the human microbiome.Authorship 159512711Authorship 15949581Authorship 1594987837783751Huttenhower C, Finn RD, McHardy ACNature microbiologyChallenges and opportunities in sharing microbiome data and analyses. Nat Microbiol. 2023 Nov; 8(11):1960-1970.Nat Microbiol2023-10-02T00:00:002023Challenges and opportunities in sharing microbiome data and analyses.37786251Wang Y, Ma W, Mehta R, Nguyen LH, Song M, Drew DA, Asnicar F, Huttenhower C, Segata N, Wolf J, Spector T, Berry S, Staller K, Chan ATGut microbesDiet and gut microbial associations in irritable bowel syndrome according to disease subtype. Gut Microbes. 2023 12; 15(2):2262130.Gut Microbes2023-10-02T00:00:002023Diet and gut microbial associations in irritable bowel syndrome according to disease subtype.37790300Mayers JR, Varon J, Zhou RR, Daniel-Ivad M, Beaulieu C, Bholse A, Glasser NR, Lichtenauer FM, Ng J, Vera MP, Huttenhower C, Perrella MA, Clish CB, Zhao SD, Baron RM, Balskus EPbioRxiv : the preprint server for biologyIdentification and targeting of microbial putrescine acetylation in bloodstream infections. bioRxiv. 2023 Sep 21.bioRxiv2023-09-21T00:00:002023Identification and targeting of microbial putrescine acetylation in bloodstream infections.Authorship 1596752337810879Okoro PC, Orwoll ES, Huttenhower C, Morgan X, Kuntz TM, McIver LJ, Dufour AB, Bouxsein ML, Langsetmo L, Farsijani S, Kado DM, Pacifici R, Sahni S, Kiel DPFrontiers in endocrinologyA two-cohort study on the association between the gut microbiota and bone density, microarchitecture, and strength. Front Endocrinol (Lausanne). 2023; 14:1237727.Front Endocrinol (Lausanne)2023-09-21T00:00:002023A two-cohort study on the association between the gut microbiota and bone density, microarchitecture, and strength.Authorship 1613618938134274Bonham KS, Fahur Bottino G, McCann SH, Beauchemin J, Weisse E, Barry F, Cano Lorente R, Huttenhower C, Bruchhage M, D'Sa V, Deoni S, Klepac-Ceraj VScience advancesGut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children. Sci Adv. 2023 Dec 22; 9(51):eadi0497.Sci Adv2023-12-22T00:00:002023Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children.Authorship 1626327438295024Zebrowska M, Strohmaier S, Westgarth C, Huttenhower C, Eliassen HA, Haghayegh S, Huang T, Laden F, Hart J, Rosner B, Kawachi I, Chavarro JE, Okereke OI, Schernhammer ESPloS oneTiming and duration of dog walking and dog owner's chronotype in relation to incident depression risk among middle to older-aged female nurses. PLoS One. 2024; 19(1):e0296922.PLoS One2024-01-31T00:00:002024Timing and duration of dog walking and dog owner's chronotype in relation to incident depression risk among middle to older-aged female nurses.true1Professor of Biostatistics, EmeritusProfessor of Biostatistics, Emeritustrue1Daniel K. Podolsky Professor of MedicineDaniel K. Podolsky Professor of Medicinetrue1Irene Heinz Given Professor of Immunology and Infectious DiseasesIrene Heinz Given Professor of Immunology and Infectious Diseasestrue1Henry Pickering Walcott Professor of Computational Biology and BioinformaticsHenry Pickering Walcott Professor of Computational Biology and Bioinformaticstrue1InstructorInstructortrue1Senior Research ScientistSenior Research Scientist2Faculty Affiliate in the Department of Immunology and Infectious DiseasesFaculty Affiliate in the Department of Immunology and Infectious Diseasestrue1John Rock Professor of Population and Translational Data SciencesJohn Rock Professor of Population and Translational Data Sciencestrue1Professor of Computational Biology and BioinformaticsProfessor of Computational Biology and Bioinformaticstrue1Adjunct Professor of BiostatisticsAdjunct Professor of Biostatisticstrue1Professor of PathologyProfessor of PathologyAuthorship 615722Authorship 36738811Authorship 6648142Authorship 6477886Authorship 6674952Authorship 647971423741402Glass K, Huttenhower C, Quackenbush J, Yuan GCPloS onePassing messages between biological networks to refine predicted interactions. PLoS One. 2013; 8(5):e64832.PLoS One2013-05-31T00:00:002013Passing messages between biological networks to refine predicted interactions.23942190Segata N, Börnigen D, Morgan XC, Huttenhower CNature communicationsPhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013; 4:2304.Nat Commun2013-01-01T00:00:002013PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.23570996Larson JL, Huttenhower C, Quackenbush J, Yuan GCGenomicsA tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 Jul; 102(1):1-7.Genomics2013-04-06T00:00:002013A tiered hidden Markov model characterizes multi-scale chromatin states.23670539Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower CMolecular systems biologyComputational meta'omics for microbial community studies. Mol Syst Biol. 2013 May 14; 9:666.Mol Syst Biol2013-05-14T00:00:002013Computational meta'omics for microbial community studies.Authorship 6765141223975157Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower CNature biotechnologyPredictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013 Sep; 31(9):814-21.Nat Biotechnol2013-08-25T00:00:002013Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.Authorship 679810423921638Börnigen D, Pers TH, Thorrez L, Huttenhower C, Moreau Y, Brunak SNucleic acids researchConcordance of gene expression in human protein complexes reveals tissue specificity and pathology. 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ISME J. 2013 Dec; 7(12):2330-9.ISME J2013-08-15T00:00:002013Two-stage microbial community experimental design.Authorship 3766961Authorship 6975841024315099Zhang YJ, Reddy MC, Ioerger TR, Rothchild AC, Dartois V, Schuster BM, Trauner A, Wallis D, Galaviz S, Huttenhower C, Sacchettini JC, Behar SM, Rubin EJCellTryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing. Cell. 2013 Dec 05; 155(6):1296-308.Cell2013-12-05T00:00:002013Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing.Authorship 6986291624348235Joice R, Narasimhan V, Montgomery J, Sidhu AB, Oh K, Meyer E, Pierre-Louis W, Seydel K, Milner D, Williamson K, Wiegand R, Ndiaye D, Daily J, Wirth D, Taylor T, Huttenhower C, Marti MPLoS computational biologyInferring developmental stage composition from gene expression in human malaria. PLoS Comput Biol. 2013; 9(12):e1003392.PLoS Comput Biol2013-12-12T00:00:002013Inferring developmental stage composition from gene expression in human malaria.Authorship 700323624203705Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, Segata NNucleic acids researchMetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res. 2014 Jan; 42(Database issue):D617-24.Nucleic Acids Res2013-11-06T00:00:002013MetaRef: a pan-genomic database for comparative and community microbial genomics.Authorship 70424712Authorship 7042481024450576Morrow AL, Lagomarcino AJ, Schibler KR, Taft DH, Yu Z, Wang B, Altaye M, Wagner M, Gevers D, Ward DV, Kennedy MA, Huttenhower C, Newburg DSMicrobiomeEarly microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome. 2013 Apr 16; 1(1):13.Microbiome2013-04-16T00:00:002013Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants.24450808McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR, Graeber TG, Sonnenburg JL, Horvath S, Huttenhower C, McGovern DP, Fornace AJ, Borneman J, Braun JMicrobiomeIntegrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome. 2013 Jun 05; 1(1):17.Microbiome2013-06-05T00:00:002013Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships.24500617Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, Gallini CA, Beal C, van Hylckama-Vlieg JE, Ballal SA, Morgan XC, Glickman JN, Gevers D, Huttenhower C, Garrett WSThe ISME journalGut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. ISME J. 2014 Jul; 8(7):1403-17.ISME J2014-02-06T00:00:002014Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission.Authorship 2898202Authorship 2803524Authorship 3077724Authorship 7181826Authorship 71937030Authorship 710984223796786Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers DJournal of innate immunitySkin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. J Innate Immun. 2014; 6(3):253-62.J Innate Immun2013-06-22T00:00:002013Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses.24108330Lee S, Cantarel B, Henrissat B, Gevers D, Birren BW, Huttenhower C, Ko GThe ISME journalGene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. ISME J. 2014 Mar; 8(3):493-503.ISME J2013-10-10T00:00:002013Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota.24629344Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJCell host & microbeThe treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014 Mar 12; 15(3):382-392.Cell Host Microbe2014-03-12T00:00:002014The treatment-naive microbiome in new-onset Crohn's disease.Authorship 2968031Authorship 920513Authorship 726515224486053Morgan XC, Huttenhower CGastroenterologyMeta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology. 2014 May; 146(6):1437-1448.e1.Gastroenterology2014-01-28T00:00:002014Meta'omic analytic techniques for studying the intestinal microbiome.Authorship 72951812Authorship 730350924700803Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJJournal of the National Cancer InstituteRisk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. J Natl Cancer Inst. 2014 Apr 03; 106(5).J Natl Cancer Inst2014-04-03T00:00:002014Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.24700801Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani GJournal of the National Cancer InstituteComparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. J Natl Cancer Inst. 2014 Apr 03; 106(5).J Natl Cancer Inst2014-04-03T00:00:002014Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.Authorship 732635424618403Shafquat A, Joice R, Simmons SL, Huttenhower CTrends in microbiologyFunctional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol. 2014 May; 22(5):261-6.Trends Microbiol2014-03-05T00:00:002014Functional and phylogenetic assembly of microbial communities in the human microbiome.Authorship 7362115Authorship 7363591424931973Bernau C, Riester M, Boulesteix AL, Parmigiani G, Huttenhower C, Waldron L, Trippa LBioinformatics (Oxford, England)Cross-study validation for the assessment of prediction algorithms. Bioinformatics. 2014 Jun 15; 30(12):i105-12.Bioinformatics2014-06-15T00:00:002014Cross-study validation for the assessment of prediction algorithms.24843156Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower CProceedings of the National Academy of Sciences of the United States of AmericaRelating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A. 2014 Jun 03; 111(22):E2329-38.Proc Natl Acad Sci U S A2014-05-19T00:00:002014Relating the metatranscriptome and metagenome of the human gut.Authorship 7372867Authorship 7375831423906180Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower CGenome medicineFunctional profiling of the gut microbiome in disease-associated inflammation. Genome Med. 2013; 5(7):65.Genome Med2013-07-31T00:00:002013Functional profiling of the gut microbiome in disease-associated inflammation.Authorship 4045215Authorship 74789016Authorship 7529966Authorship 751539125003194Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LAThe Journal of clinical investigationPediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest. 2014 Aug; 124(8):3617-33.J Clin Invest2014-07-08T00:00:002014Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.23651518Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GMGenome biologySixty years of genome biology. Genome Biol. 2013 Apr 25; 14(4):113.Genome Biol2013-04-25T00:00:002013Sixty years of genome biology.24950204Huttenhower C, Kostic AD, Xavier RJImmunityInflammatory bowel disease as a model for translating the microbiome. Immunity. 2014 Jun 19; 40(6):843-54.Immunity2014-06-19T00:00:002014Inflammatory bowel disease as a model for translating the microbiome.Authorship 763949125303518Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, White OCellAdvancing the microbiome research community. Cell. 2014 Oct 09; 159(2):227-30.Cell2014-10-09T00:00:002014Advancing the microbiome research community.25061068Zhao SD, Parmigiani G, Huttenhower C, Waldron LBioinformatics (Oxford, England)Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics. 2014 Nov 01; 30(21):3062-9.Bioinformatics2014-07-23T00:00:002014Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis.Authorship 4947821Authorship 5040735Authorship 548204225722744Pelle KG, Oh K, Buchholz K, Narasimhan V, Joice R, Milner DA, Brancucci NM, Ma S, Voss TS, Ketman K, Seydel KB, Taylor TE, Barteneva NS, Huttenhower C, Marti MGenome medicineTranscriptional profiling defines dynamics of parasite tissue sequestration during malaria infection. Genome Med. 2015; 7(1):19.Genome Med2015-02-27T00:00:002015Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection.EAF23EricFranzosaEric A. Franzosa, Ph.D.113040Franzosa, EricSenior Research Scientist25440055Joice R, Yasuda K, Shafquat A, Morgan XC, Huttenhower CCell metabolismDetermining microbial products and identifying molecular targets in the human microbiome. Cell Metab. 2014 Nov 04; 20(5):731-741.Cell Metab2014-11-04T00:00:002014Determining microbial products and identifying molecular targets in the human microbiome.25732063Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, Miller AD, Westmoreland SV, Mansfield KG, Vallender EJ, Miller GM, Rowlett JK, Gevers D, Huttenhower C, Morgan XCCell host & microbeBiogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe. 2015 Mar 11; 17(3):385-391.Cell Host Microbe2015-02-26T00:00:002015Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque.Authorship 4189462Authorship 4292816Authorship 4835096Authorship 37764910Authorship 54060112Authorship 3936083Authorship 4955477Authorship 677482Authorship 5302674Authorship 5185294Authorship 332352Authorship 2795371Authorship 32543Authorship 39464910Authorship 3824991Authorship 233705425915636Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower CNature reviews. MicrobiologySequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol. 2015 Jun; 13(6):360-72.Nat Rev Microbiol2015-04-27T00:00:002015Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.25992865Anahtar MN, Byrne EH, Doherty KE, Bowman BA, Yamamoto HS, Soumillon M, Padavattan N, Ismail N, Moodley A, Sabatini ME, Ghebremichael MS, Nusbaum C, Huttenhower C, Virgin HW, Ndung'u T, Dong KL, Walker BD, Fichorova RN, Kwon DSImmunityCervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract. Immunity. 2015 May 19; 42(5):965-76.Immunity2015-05-19T00:00:002015Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract.Authorship 2697241Authorship 2751706Authorship 4335171Authorship 4684915Authorship 1602414Authorship 3254641525729854Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LAThe Journal of clinical investigationCorrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest. 2015 Mar 02; 125(3):1363.J Clin Invest2015-03-02T00:00:002015Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.25964341Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower CProceedings of the National Academy of Sciences of the United States of AmericaIdentifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):E2930-8.Proc Natl Acad Sci U S A2015-05-11T00:00:002015Identifying personal microbiomes using metagenomic codes.25887922Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower CGenome biologyAssociations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol. 2015 Apr 08; 16:67.Genome Biol2015-04-08T00:00:002015Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.25587358Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJGenome medicineComplex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 2014; 6(12):107.Genome Med2014-12-02T00:00:002014Complex host genetics influence the microbiome in inflammatory bowel disease.25662751Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešic M, Huttenhower C, Knip M, Xavier RJCell host & microbeThe dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015 Feb 11; 17(2):260-73.Cell Host Microbe2015-02-05T00:00:002015The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.LDN9LongNguyenLong Nguyen, M.D.139525Nguyen, LongAssistant Professor of Medicine26157642Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower CPeerJA reproducible approach to high-throughput biological data acquisition and integration. PeerJ. 2015; 3:e791.PeerJ2015-03-31T00:00:002015A reproducible approach to high-throughput biological data acquisition and integration.Authorship 81663718Authorship 81734210Authorship 81736420Authorship 8174817Authorship 81776813Authorship 81798514Authorship 8176007Authorship 8176205Authorship 81757911Authorship 81673514Authorship 8170954Authorship 81698512Authorship 81662616Authorship 817202324781901Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, Li X, Graeber TG, Schwager E, Huttenhower C, Fornace AJ, Sonnenburg JL, McGovern DP, Borneman J, Braun JThe ISME journalReprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. ISME J. 2014 Nov; 8(11):2193-206.ISME J2014-04-29T00:00:002014Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism.26157614Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata NPeerJCompact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ. 2015; 3:e1029.PeerJ2015-06-18T00:00:002015Compact graphical representation of phylogenetic data and metadata with GraPhlAn.26181352Mima K, Sukawa Y, Nishihara R, Qian ZR, Yamauchi M, Inamura K, Kim SA, Masuda A, Nowak JA, Nosho K, Kostic AD, Giannakis M, Watanabe H, Bullman S, Milner DA, Harris CC, Giovannucci E, Garraway LA, Freeman GJ, Dranoff G, Chan AT, Garrett WS, Huttenhower C, Fuchs CS, Ogino SJAMA oncologyFusobacterium nucleatum and T Cells in Colorectal Carcinoma. JAMA Oncol. 2015 Aug; 1(5):653-61.JAMA Oncol2015-08-01T00:00:002015Fusobacterium nucleatum and T Cells in Colorectal Carcinoma.Authorship 82434123Authorship 43945226311717Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA, Yang J, Dou R, Masugi Y, Song M, Kostic AD, Giannakis M, Bullman S, Milner DA, Baba H, Giovannucci EL, Garraway LA, Freeman GJ, Dranoff G, Garrett WS, Huttenhower C, Meyerson M, Meyerhardt JA, Chan AT, Fuchs CS, Ogino SGutFusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut. 2016 12; 65(12):1973-1980.Gut2015-08-26T00:00:002015Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis.Authorship 838641826418763Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata NNature methodsMetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015 Oct; 12(10):902-3.Nat Methods2015-10-01T00:00:002015MetaPhlAn2 for enhanced metagenomic taxonomic profiling.Authorship 46582319Authorship 8476445Authorship 848898526568784Lee KC, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MBStandards in genomic sciencesComplete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T). Stand Genomic Sci. 2015; 10:101.Stand Genomic Sci2015-11-14T00:00:002015Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).26420863Semenkovich CF, Danska J, Darsow T, Dunne JL, Huttenhower C, Insel RA, McElvaine AT, Ratner RE, Shuldiner AR, Blaser MJDiabetesAmerican Diabetes Association and JDRF Research Symposium: Diabetes and the Microbiome. Diabetes. 2015 Dec; 64(12):3967-77.Diabetes2015-09-29T00:00:002015American Diabetes Association and JDRF Research Symposium: Diabetes and the Microbiome.Authorship 8529856Authorship 8525445Authorship 851954626579106Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T, Raes JFrontiers in microbiologyCross-biome comparison of microbial association networks. Front Microbiol. 2015; 6:1200.Front Microbiol2015-10-27T00:00:002015Cross-biome comparison of microbial association networks.26682918Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower CPLoS computational biologyHigh-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PLoS Comput Biol. 2015 Dec; 11(12):e1004557.PLoS Comput Biol2015-12-18T00:00:002015High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.26653756Sinha R, Abnet CC, White O, Knight R, Huttenhower CGenome biologyThe microbiome quality control project: baseline study design and future directions. Genome Biol. 2015 Dec 09; 16:276.Genome Biol2015-12-09T00:00:002015The microbiome quality control project: baseline study design and future directions.Authorship 607928Authorship 87029215Authorship 86630016Authorship 8694981026849729Liu TC, Gurram B, Baldridge M, Head R, Lam V, Luo C, Cao Y, Simpson P, Hayward M, Holtz M, Noe J, Lerner D, Cabrera J, Biank V, Stephens M, Huttenhower C, McGovern D, Xavier R, Stappenbeck T, Salzman NInflammatory bowel diseasesO-011 Paneth Cell Phenotypes Define a Subtype of Pediatric Crohn's Disease Through Alterations in Host-Microbial Interactions. Inflamm Bowel Dis. 2016 Mar; 22 Suppl 1:S4.Inflamm Bowel Dis2016-03-01T00:00:002016O-011 Paneth Cell Phenotypes Define a Subtype of Pediatric Crohn's Disease Through Alterations in Host-Microbial Interactions.26837003Dubin K, Callahan MK, Ren B, Khanin R, Viale A, Ling L, No D, Gobourne A, Littmann E, Huttenhower C, Pamer EG, Wolchok JDNature communicationsIntestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat Commun. 2016 Feb 02; 7:10391.Nat Commun2016-02-02T00:00:002016Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis.26884067Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower CGenome medicineSub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Genome Med. 2016 Feb 17; 8(1):17.Genome Med2016-02-17T00:00:002016Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.Authorship 3067901Authorship 338506326961995Drew DA, Lochhead P, Abu-Ali G, Chan AT, Huttenhower C, Izard JCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive OncologyFecal Microbiome in Epidemiologic Studies-Letter. Cancer Epidemiol Biomarkers Prev. 2016 05; 25(5):869.Cancer Epidemiol Biomarkers Prev2016-03-09T00:00:002016Fecal Microbiome in Epidemiologic Studies-Letter.Authorship 876547827078000Börnigen D, Tyekucheva S, Wang X, Rider JR, Lee GS, Mucci LA, Sweeney C, Huttenhower CPLoS computational biologyComputational Reconstruction of NF?B Pathway Interaction Mechanisms during Prostate Cancer. PLoS Comput Biol. 2016 Apr; 12(4):e1004820.PLoS Comput Biol2016-04-14T00:00:002016Computational Reconstruction of NF?B Pathway Interaction Mechanisms during Prostate Cancer.Authorship 8792343Authorship 8792362727126040Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu JScience (New York, N.Y.)Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. 2016 Apr 29; 352(6285):565-9.Science2016-04-28T00:00:002016Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.27122046Lloyd-Price J, Abu-Ali G, Huttenhower CGenome medicineThe healthy human microbiome. Genome Med. 2016 04 27; 8(1):51.Genome Med2016-04-27T00:00:002016The healthy human microbiome.Authorship 4800147Authorship 88095521Authorship 881255527133167Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, Xavier RJCellVariation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016 May 05; 165(4):842-53.Cell2016-04-28T00:00:002016Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.Authorship 885197427060125Lee KC, Stott MB, Dunfield PF, Huttenhower C, McDonald IR, Morgan XCApplied and environmental microbiologyThe Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupo Volcanic Zone. Appl Environ Microbiol. 2016 06 15; 82(12):3572-81.Appl Environ Microbiol2016-05-31T00:00:002016The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupo Volcanic Zone.Authorship 886619927306663Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, Xavier RJScience translational medicineNatural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med. 2016 06 15; 8(343):343ra81.Sci Transl Med2016-06-15T00:00:002016Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.2Assistant Professor1Associate Professor0Full Professor4Instructor5Other FacultyAuthorship 73093Authorship 9096931027572971Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata NNature microbiologyUncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat Microbiol. 2016 05 27; 1(7):16070.Nat Microbiol2016-05-27T00:00:002016Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.2021-02-28CHAN, ANDREW T2016-03-01Dietary sulfur, the gut microbiome, and colorectal cancerR01CA2027042016-08-31XAVIER, RAMNIK J2013-09-06Characterizing the gut microbial ecosystem for diagnosis and therapy in IBDU54DE0237982017-08-31XAVIER, RAMNIK J2013-09-06Characterizing the gut microbial ecosystem for diagnosis and therapy in IBDU54DK1025572018-07-31HUTTENHOWER, CURTIS2015-08-10Staphylococcus Aureus Carriage and the Nasal MicrobiomeR21AI1129912020-06-30LIN, XIHONG2005-07-01Interdisciplinary training: Statistical Genetics/Genomics & Computational BiologyT32GM0748972015-06-30HUTTENHOWER, CURTIS2010-09-27Functional activity and inter-organismal interactions in the human microbiomeR01HG005969Principal InvestigatorCo-Principal InvestigatorPrincipal InvestigatorPrincipal InvestigatorPrincipal InvestigatorPrincipal InvestigatorAuthorship 9169581027599587Hartmann EM, Hickey R, Hsu T, Betancourt Román CM, Chen J, Schwager R, Kline J, Brown GZ, Halden RU, Huttenhower C, Green JLEnvironmental science & technologyAntimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome. Environ Sci Technol. 2016 09 20; 50(18):9807-15.Environ Sci Technol2016-09-07T00:00:002016Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome.Authorship 92873913Authorship 92271921Authorship 9206261427687735Nelms BD, Waldron L, Barrera LA, Weflen AW, Goettel JA, Guo G, Montgomery RK, Neutra MR, Breault DT, Snapper SB, Orkin SH, Bulyk ML, Huttenhower C, Lencer WIGenome biologyCellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biol. 2016 09 29; 17(1):201.Genome Biol2016-09-29T00:00:002016CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types.27259157Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, Xavier RJCellVariation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016 Jun 02; 165(6):1551.Cell2016-06-02T00:00:002016Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.27721445Mantel PY, Hjelmqvist D, Walch M, Kharoubi-Hess S, Nilsson S, Ravel D, Ribeiro M, Grüring C, Ma S, Padmanabhan P, Trachtenberg A, Ankarklev J, Brancucci NM, Huttenhower C, Duraisingh MT, Ghiran I, Kuo WP, Filgueira L, Martinelli R, Marti MNature communicationsInfected erythrocyte-derived extracellular vesicles alter vascular function via regulatory Ago2-miRNA complexes in malaria. Nat Commun. 2016 10 10; 7:12727.Nat Commun2016-10-10T00:00:002016Infected erythrocyte-derived extracellular vesicles alter vascular function via regulatory Ago2-miRNA complexes in malaria.27811909Mima K, Cao Y, Chan AT, Qian ZR, Nowak JA, Masugi Y, Shi Y, Song M, da Silva A, Gu M, Li W, Hamada T, Kosumi K, Hanyuda A, Liu L, Kostic AD, Giannakis M, Bullman S, Brennan CA, Milner DA, Baba H, Garraway LA, Meyerhardt JA, Garrett WS, Huttenhower C, Meyerson M, Giovannucci EL, Fuchs CS, Nishihara R, Ogino SClinical and translational gastroenterologyFusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location. Clin Transl Gastroenterol. 2016 Nov 03; 7(11):e200.Clin Transl Gastroenterol2016-11-03T00:00:002016Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location.Authorship 5363097655 Huntington AveHarvard School of Public HealthBldg 2-451655 Huntington AveBoston02115MAAuthorship 190524Authorship 93508713Authorship 9310311727822528Hsu T, Joice R, Vallarino J, Abu-Ali G, Hartmann EM, Shafquat A, DuLong C, Baranowski C, Gevers D, Green JL, Morgan XC, Spengler JD, Huttenhower CmSystemsUrban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. mSystems. 2016 May-Jun; 1(3).mSystems2016-06-28T00:00:002016Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment.27699268Liu TC, Gurram B, Baldridge MT, Head R, Lam V, Luo C, Cao Y, Simpson P, Hayward M, Holtz ML, Bousounis P, Noe J, Lerner D, Cabrera J, Biank V, Stephens M, Huttenhower C, McGovern DP, Xavier RJ, Stappenbeck TS, Salzman NHJCI insightPaneth cell defects in Crohn's disease patients promote dysbiosis. 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Genome Biol. 2011 Aug 23; 12(8):307.Genome Biol2011-08-23T00:00:002011Computational biology: plus c'est la même chose, plus ça change.Authorship 10240491129088129Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, Huttenhower C, Morgan M, Segata N, Waldron LNature methodsAccessible, curated metagenomic data through ExperimentHub. Nat Methods. 2017 10 31; 14(11):1023-1024.Nat Methods2017-10-31T00:00:002017Accessible, curated metagenomic data through ExperimentHub.Authorship 1027514429140991Schwager E, Mallick H, Ventz S, Huttenhower CPLoS computational biologyA Bayesian method for detecting pairwise associations in compositional data. 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