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Curtis Huttenhower, Ph.D.

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Overview
Dr. Huttenhower's research is concerned with the discovery of useful biological knowledge in large collections of genomic data. Modern biological experiments each represent a detailed snapshot of a cell or organism's internal state, and public repositories already contain many thousands of experimental results and are constantly growing in size and diversity. Taken together, these data can be used to reconstruct detailed models of cellular behavior in response to changing environmental conditions, regulatory and metabolic regimes, and disease states. The goal of this research is to allow any new biomedical question to be answered by extracting information from the entire body of existing and novel experimental data, using data integration to allow results from basic research to be applied to genomic and personalized medicine (and vice versa).

In practice, this requires the development of computational methodology that is efficient enough to deal with billions of data points while remaining biologically rich enough to capture the complexities of metazoan molecular biology. This can include techniques from statistical machine learning, graphical models, and information retrieval, applied to biological systems as diverse as growth control in yeast or survival mechanisms in human fibroblasts. Many results also rely on the construction and analysis of biological networks, including physical protein-protein interactions, regulatory networks, or functional associations among genes and gene products. The challenge is not only to develop useful computational models, but also to apply them collaboratively to drive novel experimental biology and to better understand biomedical results.

Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R24DK110499 (HUTTENHOWER, CURTIS) Sep 20, 2017 - Jun 30, 2022
    NIH/NIDDK
    A comprehensive platform for novel therapy development from the microbiome
    Role: Principal Investigator
  2. R01CA202704 (CHAN, ANDREW T) Mar 1, 2016 - Feb 28, 2021
    NIH/NCI
    Dietary sulfur, the gut microbiome, and colorectal cancer
    Role: Co-Principal Investigator
  3. R21AI112991 (HUTTENHOWER, CURTIS) Aug 10, 2015 - Jul 31, 2017
    NIH/NIAID
    Staphylococcus Aureus Carriage and the Nasal Microbiome
    Role: Principal Investigator
  4. U54DE023798 (XAVIER, RAMNIK J) Sep 6, 2013 - Aug 31, 2016
    NIH/NIDCR
    Characterizing the gut microbial ecosystem for diagnosis and therapy in IBD
    Role: Principal Investigator
  5. U54DK102557 (XAVIER, RAMNIK J) Sep 6, 2013 - Aug 31, 2016
    NIH/NIDDK
    Characterizing the gut microbial ecosystem for diagnosis and therapy in IBD
    Role: Principal Investigator
This researcher has shared information about their research resources in the eagle-i Network. To update or add resource records, contact eagle-i@hms.harvard.edu.
HSPH Microbiome Analysis Core - Core services (6), Instruments (3) and Software (1)

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Dantzler 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 M. Naturally acquired immunity against immature Plasmodium falciparum gametocytes. Sci Transl Med. 2019 Jun 05; 11(495). PMID: 31167926.
    Citations:    
  2. Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L. HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Am J Epidemiol. 2019 Jun 01; 188(6):1023-1026. PMID: 30649166.
    Citations:    Fields:    
  3. Tashiro H, Cho Y, Kasahara DI, Brand JD, Bry L, Yeliseyev V, Abu-Ali G, Huttenhower C, Shore SA. Microbiota contribute to obesity-related increases in the pulmonary response to ozone. Am J Respir Cell Mol Biol. 2019 May 30. PMID: 31144984.
    Citations:    
  4. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019 May; 569(7758):655-662. PMID: 31142855.
    Citations:    
  5. Brown EM, Ke X, Hitchcock D, Jeanfavre S, Avila-Pacheco J, Nakata T, Arthur TD, Fornelos N, Heim C, Franzosa EA, Watson N, Huttenhower C, Haiser HJ, Dillow G, Graham DB, Finlay BB, Kostic AD, Porter JA, Vlamakis H, Clish CB, Xavier RJ. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis. Cell Host Microbe. 2019 May 08; 25(5):668-680.e7. PMID: 31071294.
    Citations:    
  6. Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 May; 4(5):898. PMID: 30971771.
    Citations:    
  7. Vatanen 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 RJ. Publisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol. 2019 Mar; 4(3):545. PMID: 30723264.
    Citations:    
  8. Cho Y, Abu-Ali G, Tashiro H, Brown TA, Osgood RS, Kasahara DI, Huttenhower C, Shore SA. Sex Differences in Pulmonary Responses to Ozone in Mice. Role of the Microbiome. Am J Respir Cell Mol Biol. 2019 Feb; 60(2):198-208. PMID: 30240285.
    Citations:    Fields:    
  9. Pasolli 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 N. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell. 2019 Jan 24; 176(3):649-662.e20. PMID: 30661755.
    Citations:    Fields:    
  10. Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, Nistel M, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, Leleiko NS, Heyman MB, Grifiths AM, Patel AS, Noe JD, Aronow BJ, Kugathasan S, Walters TD, Gibson G, Thomas SD, Mollen K, Shen-Orr S, Huttenhower C, Xavier RJ, Hyams JS, Denson LA. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nat Commun. 2019 01 03; 10(1):38. PMID: 30604764.
    Citations:    Fields:    
  11. Hsu 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 GL. Comparative genomics and genome biology of Campylobacter showae. Emerg Microbes Infect. 2019; 8(1):827-840. PMID: 31169073.
    Citations:    
  12. Vatanen 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 RJ. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol. 2019 03; 4(3):470-479. PMID: 30559407.
    Citations:    Fields:    
  13. Haberman 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 LA. Age-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. PMID: 30542108.
    Citations:    Fields:    
  14. Fahimipour 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 EM. Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors. mSystems. 2018 Nov-Dec; 3(6). PMID: 30574558.
    Citations:    
  15. Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 02; 4(2):293-305. PMID: 30531976.
    Citations:    Fields:    
  16. Sinha 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 C. Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017. Microbiome. 2018 11 26; 6(1):210. PMID: 30477563.
    Citations:    Fields:    
  17. Gerke 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 CJ. Low Tristetraprolin Expression Is Associated with Lethal Prostate Cancer. Cancer Epidemiol Biomarkers Prev. 2019 Mar; 28(3):584-590. PMID: 30420441.
    Citations:    Fields:    
  18. Taroncher-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 J. Translating microbiome futures. Nat Biotechnol. 2018 11 09; 36(11):1037-1042. PMID: 30412201.
    Citations:    Fields:    
  19. Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods. 2018 11; 15(11):962-968. PMID: 30377376.
    Citations:    Fields:    
  20. Vatanen 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 RJ. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 2018 10; 562(7728):589-594. PMID: 30356183.
    Citations:    Fields:    
  21. Stewart 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 JF. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018 10; 562(7728):583-588. PMID: 30356187.
    Citations:    Fields:    
  22. Fahimipour 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 K. Daylight exposure modulates bacterial communities associated with household dust. Microbiome. 2018 10 18; 6(1):175. PMID: 30333051.
    Citations:    Fields:    
  23. Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ. Compositional 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. PMID: 30308161.
    Citations:    Fields:    Translation:HumansCells
  24. Ma 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 L. Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biol. 2018 09 25; 19(1):142. PMID: 30253799.
    Citations:    Fields:    Translation:HumansCells
  25. Kosumi 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 S. The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome. Am J Pathol. 2018 Dec; 188(12):2839-2852. PMID: 30243655.
    Citations: 1     Fields:    
  26. Hamada 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 S. Fusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status. Cancer Immunol Res. 2018 11; 6(11):1327-1336. PMID: 30228205.
    Citations:    Fields:    
  27. Cho Y, Abu-Ali G, Tashiro H, Kasahara DI, Brown TA, Brand JD, Mathews JA, Huttenhower C, Shore SA. The Microbiome Regulates Pulmonary Responses to Ozone in Mice. Am J Respir Cell Mol Biol. 2018 09; 59(3):346-354. PMID: 29529379.
    Citations: 2     Fields:    
  28. Yassour 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 RJ. Strain-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. PMID: 30001517.
    Citations:    Fields:    
  29. Ferretti 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 N. Mother-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. PMID: 30001516.
    Citations:    Fields:    
  30. De 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 M. Plasmodium gametocytes display homing and vascular transmigration in the host bone marrow. Sci Adv. 2018 05; 4(5):eaat3775. PMID: 29806032.
    Citations:    Fields:    
  31. McDonald 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 R. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3). PMID: 29795809.
    Citations: 8     
  32. Obaldia 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 M. Bone Marrow Is a Major Parasite Reservoir in Plasmodium vivax Infection. MBio. 2018 05 08; 9(3). PMID: 29739900.
    Citations:    Fields:    Translation:HumansAnimals
  33. Chang YL, Rossetti M, Vlamakis H, Casero D, Sunga G, Harre N, Miller S, Humphries R, Stappenbeck T, Simpson KW, Sartor RB, Wu G, Lewis J, Bushman F, McGovern DPB, Salzman N, Borneman J, Xavier R, Huttenhower C, Braun J. A 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. PMID: 29695840.
    Citations:    Fields:    
  34. McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C. bioBakery: a meta'omic analysis environment. Bioinformatics. 2018 04 01; 34(7):1235-1237. PMID: 29194469.
    Citations: 2     Fields:    
  35. Costea 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 P. Publisher Correction: Enterotypes in the landscape of gut microbial community composition. Nat Microbiol. 2018 Mar; 3(3):388. PMID: 29440750.
    Citations:    Fields:    
  36. Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C. Host genetic variation and its microbiome interactions within the Human Microbiome Project. Genome Med. 2018 01 29; 10(1):6. PMID: 29378630.
    Citations: 1     Fields:    Translation:Humans
  37. Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A, Lochhead P, Joshi AD, Ivey KL, Khalili H, Brown GT, DuLong C, Song M, Nguyen LH, Mallick H, Rimm EB, Izard J, Huttenhower C, Chan AT. Stability of the human faecal microbiome in a cohort of adult men. Nat Microbiol. 2018 03; 3(3):347-355. PMID: 29335554.
    Citations: 1     Fields:    
  38. Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branck T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, Chan AT, Huttenhower C. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nat Microbiol. 2018 03; 3(3):356-366. PMID: 29335555.
    Citations: 4     Fields:    
  39. Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018 03; 3(3):337-346. PMID: 29311644.
    Citations: 4     Fields:    
  40. Costea 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 P. Enterotypes in the landscape of gut microbial community composition. Nat Microbiol. 2018 Jan; 3(1):8-16. PMID: 29255284.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  41. Börnigen D, Ren B, Pickard R, Li J, Ozer E, Hartmann EM, Xiao W, Tickle T, Rider J, Gevers D, Franzosa EA, Davey ME, Gillison ML, Huttenhower C. Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer. Sci Rep. 2017 Dec 15; 7(1):17686. PMID: 29247187.
    Citations:    Fields:    
  42. Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol. 2017 11 30; 18(1):228. PMID: 29187204.
    Citations: 2     Fields:    Translation:HumansAnimals
  43. Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med. 2017 Nov 28; 9(1):103. PMID: 29183332.
    Citations: 3     Fields:    Translation:HumansCells
  44. Schwager E, Mallick H, Ventz S, Huttenhower C. A Bayesian method for detecting pairwise associations in compositional data. PLoS Comput Biol. 2017 Nov; 13(11):e1005852. PMID: 29140991.
    Citations: 1     Fields:    Translation:HumansCells
  45. Pasolli 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 L. Accessible, curated metagenomic data through ExperimentHub. Nat Methods. 2017 10 31; 14(11):1023-1024. PMID: 29088129.
    Citations: 9     Fields:    
  46. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017 11 09; 551(7679):256. PMID: 29022944.
    Citations:    Fields:    
  47. Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S, Abnet CC, Knight R, White O, Huttenhower C. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat Biotechnol. 2017 Nov; 35(11):1077-1086. PMID: 28967885.
    Citations: 18     Fields:    Translation:HumansCells
  48. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017 10 05; 550(7674):61-66. PMID: 28953883.
    Citations: 27     Fields:    Translation:Humans
  49. Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, Gavert N, Zwang Y, Cooper ZA, Shee K, Thaiss CA, Reuben A, Livny J, Avraham R, Frederick DT, Ligorio M, Chatman K, Johnston SE, Mosher CM, Brandis A, Fuks G, Gurbatri C, Gopalakrishnan V, Kim M, Hurd MW, Katz M, Fleming J, Maitra A, Smith DA, Skalak M, Bu J, Michaud M, Trauger SA, Barshack I, Golan T, Sandbank J, Flaherty KT, Mandinova A, Garrett WS, Thayer SP, Ferrone CR, Huttenhower C, Bhatia SN, Gevers D, Wargo JA, Golub TR, Straussman R. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science. 2017 09 15; 357(6356):1156-1160. PMID: 28912244.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  50. Golombos DM, Ayangbesan A, O'Malley P, Lewicki P, Barlow L, Barbieri CE, Chan C, DuLong C, Abu-Ali G, Huttenhower C, Scherr DS. The Role of Gut Microbiome in the Pathogenesis of Prostate Cancer: A Prospective, Pilot Study. Urology. 2018 Jan; 111:122-128. PMID: 28888753.
    Citations:    Fields:    Translation:Humans
  51. Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome. 2017 08 16; 5(1):86. PMID: 28810907.
    Citations: 6     Fields:    Translation:HumansCells
  52. Yasuda K, Hsu T, Gallini CA, Mclver LJ, Schwager E, Shi A, DuLong CR, Schwager RN, Abu-Ali GS, Franzosa EA, Garrett WS, Huttenhower C, Morgan XC. Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. mSystems. 2017 Jul-Aug; 2(4). PMID: 28808691.
    Citations:    
  53. Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ. Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. Cell Host Microbe. 2017 Jul 12; 22(1):25-37.e6. PMID: 28704649.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  54. Mehta RS, Nishihara R, Cao Y, Song M, Mima K, Qian ZR, Nowak JA, Kosumi K, Hamada T, Masugi Y, Bullman S, Drew DA, Kostic AD, Fung TT, Garrett WS, Huttenhower C, Wu K, Meyerhardt JA, Zhang X, Willett WC, Giovannucci EL, Fuchs CS, Chan AT, Ogino S. Association of Dietary Patterns With Risk of Colorectal Cancer Subtypes Classified by Fusobacterium nucleatum in Tumor Tissue. JAMA Oncol. 2017 Jul 01; 3(7):921-927. PMID: 28125762.
    Citations: 20     Fields:    Translation:HumansCells
  55. Cao Y, Wu K, Mehta R, Drew DA, Song M, Lochhead P, Nguyen LH, Izard J, Fuchs CS, Garrett WS, Huttenhower C, Ogino S, Giovannucci EL, Chan AT. Long-term use of antibiotics and risk of colorectal adenoma. Gut. 2018 04; 67(4):672-678. PMID: 28377387.
    Citations: 7     Fields:    Translation:Humans
  56. Kugathasan S, Denson LA, Walters TD, Kim MO, Marigorta UM, Schirmer M, Mondal K, Liu C, Griffiths A, Noe JD, Crandall WV, Snapper S, Rabizadeh S, Rosh JR, Shapiro JM, Guthery S, Mack DR, Kellermayer R, Kappelman MD, Steiner S, Moulton DE, Keljo D, Cohen S, Oliva-Hemker M, Heyman MB, Otley AR, Baker SS, Evans JS, Kirschner BS, Patel AS, Ziring D, Trapnell BC, Sylvester FA, Stephens MC, Baldassano RN, Markowitz JF, Cho J, Xavier RJ, Huttenhower C, Aronow BJ, Gibson G, Hyams JS, Dubinsky MC. Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study. Lancet. 2017 04 29; 389(10080):1710-1718. PMID: 28259484.
    Citations: 15     Fields:    Translation:HumansCTClinical Trials
  57. Levin BJ, Huang YY, Peck SC, Wei Y, Martínez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science. 2017 02 10; 355(6325). PMID: 28183913.
    Citations: 9     Fields:    Translation:HumansCells
  58. Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 2017 04; 27(4):626-638. PMID: 28167665.
    Citations: 23     Fields:    Translation:HumansCells
  59. Drew DA, Chin SM, Gilpin KK, Parziale M, Pond E, Schuck MM, Stewart K, Flagg M, Rawlings CA, Backman V, Carolan PJ, Chung DC, Colizzo FP, Freedman M, Gala M, Garber JJ, Huttenhower C, Kedrin D, Khalili H, Kwon DS, Markowitz SD, Milne GL, Nishioka NS, Richter JM, Roy HK, Staller K, Wang M, Chan AT. ASPirin Intervention for the REDuction of colorectal cancer risk (ASPIRED): a study protocol for a randomized controlled trial. Trials. 2017 02 01; 18(1):50. PMID: 28143522.
    Citations: 7     Fields:    Translation:Humans
  60. Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2017 02; 28(2):167-176. PMID: 28097472.
    Citations: 4     Fields:    Translation:Humans
  61. Gosmann C, Anahtar MN, Handley SA, Farcasanu M, Abu-Ali G, Bowman BA, Padavattan N, Desai C, Droit L, Moodley A, Dong M, Chen Y, Ismail N, Ndung'u T, Ghebremichael MS, Wesemann DR, Mitchell C, Dong KL, Huttenhower C, Walker BD, Virgin HW, Kwon DS. Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women. Immunity. 2017 01 17; 46(1):29-37. PMID: 28087240.
    Citations: 29     Fields:    Translation:HumansAnimalsCells
  62. Rooks MG, Veiga P, Reeves AZ, Lavoie S, Yasuda K, Asano Y, Yoshihara K, Michaud M, Wardwell-Scott L, Gallini CA, Glickman JN, Sudo N, Huttenhower C, Lesser CF, Garrett WS. QseC inhibition as an antivirulence approach for colitis-associated bacteria. Proc Natl Acad Sci U S A. 2017 01 03; 114(1):142-147. PMID: 27980034.
    Citations: 4     Fields:    Translation:AnimalsCells
  63. Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell. 2016 12 15; 167(7):1897. PMID: 27984736.
    Citations: 7     Fields:    
  64. Hill JH, Franzosa EA, Huttenhower C, Guillemin K. A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. Elife. 2016 12 13; 5. PMID: 27960075.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  65. Mima 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 S. Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location. Clin Transl Gastroenterol. 2016 Nov 03; 7(11):e200. PMID: 27811909.
    Citations: 20     
  66. Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell. 2016 11 03; 167(4):1125-1136.e8. PMID: 27814509.
    Citations: 37     Fields:    Translation:HumansAnimalsCells
  67. Mantel 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 M. Infected erythrocyte-derived extracellular vesicles alter vascular function via regulatory Ago2-miRNA complexes in malaria. Nat Commun. 2016 10 10; 7:12727. PMID: 27721445.
    Citations: 23     Fields:    Translation:HumansCells
  68. Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RWF, Huttenhower C, Dijkstra G, Xavier RJ, Festen EAM, Wijmenga C, Zhernakova A, Weersma RK. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut. 2018 01; 67(1):108-119. PMID: 27802154.
    Citations: 22     Fields:    Translation:Humans
  69. Nelms 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 WI. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biol. 2016 09 29; 17(1):201. PMID: 27687735.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  70. Hartmann EM, Hickey R, Hsu T, Betancourt Román CM, Chen J, Schwager R, Kline J, Brown GZ, Halden RU, Huttenhower C, Green JL. Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome. Environ Sci Technol. 2016 09 20; 50(18):9807-15. PMID: 27599587.
    Citations: 5     Fields:    Translation:Humans
  71. Hsu 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 C. Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. mSystems. 2016 May-Jun; 1(3). PMID: 27822528.
    Citations: 10     
  72. Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, Xavier RJ. Natural 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. PMID: 27306663.
    Citations: 76     Fields:    Translation:HumansCells
  73. Vatanen 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 RJ. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016 Jun 02; 165(6):1551. PMID: 27259157.
    Citations: 20     Fields:    
  74. Liu 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 NH. Paneth cell defects in Crohn's disease patients promote dysbiosis. JCI Insight. 2016 06 02; 1(8):e86907. PMID: 27699268.
    Citations: 3     Fields:    Translation:HumansCells
  75. Lee KC, Stott MB, Dunfield PF, Huttenhower C, McDonald IR, Morgan XC. The 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. PMID: 27060125.
    Citations: 1     Fields:    Translation:CellsPHPublic Health
  76. Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat Microbiol. 2016 05 27; 1(7):16070. PMID: 27572971.
    Citations: 8     Fields:    Translation:HumansCells
  77. Zhernakova 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 J. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. 2016 Apr 29; 352(6285):565-9. PMID: 27126040.
    Citations: 116     Fields:    Translation:HumansCells
  78. Vatanen 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 RJ. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016 May 05; 165(4):842-53. PMID: 27133167.
    Citations: 83     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  79. Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016 04 27; 8(1):51. PMID: 27122046.
    Citations: 66     Fields:    Translation:HumansCells
  80. Börnigen D, Tyekucheva S, Wang X, Rider JR, Lee GS, Mucci LA, Sweeney C, Huttenhower C. Computational Reconstruction of NF?B Pathway Interaction Mechanisms during Prostate Cancer. PLoS Comput Biol. 2016 Apr; 12(4):e1004820. PMID: 27078000.
    Citations: 3     Fields:    Translation:HumansCells
  81. Drew DA, Lochhead P, Abu-Ali G, Chan AT, Huttenhower C, Izard J. Fecal Microbiome in Epidemiologic Studies-Letter. Cancer Epidemiol Biomarkers Prev. 2016 05; 25(5):869. PMID: 26961995.
    Citations:    Fields:    Translation:Humans
  82. Liu 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 N. O-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. PMID: 26849729.
    Citations:    
  83. Yassour 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 C. Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Genome Med. 2016 Feb 17; 8(1):17. PMID: 26884067.
    Citations: 18     Fields:    Translation:HumansCells
  84. Dubin K, Callahan MK, Ren B, Khanin R, Viale A, Ling L, No D, Gobourne A, Littmann E, Huttenhower C, Pamer EG, Wolchok JD. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat Commun. 2016 Feb 02; 7:10391. PMID: 26837003.
    Citations: 54     Fields:    Translation:HumansCells
  85. Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C. High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PLoS Comput Biol. 2015 Dec; 11(12):e1004557. PMID: 26682918.
    Citations: 12     Fields:    Translation:Humans
  86. Sinha R, Abnet CC, White O, Knight R, Huttenhower C. The microbiome quality control project: baseline study design and future directions. Genome Biol. 2015 Dec 09; 16:276. PMID: 26653756.
    Citations: 28     Fields:    Translation:Humans
  87. Lee KC, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MB. Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T). Stand Genomic Sci. 2015; 10:101. PMID: 26568784.
    Citations: 3     
  88. Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T, Raes J. Cross-biome comparison of microbial association networks. Front Microbiol. 2015; 6:1200. PMID: 26579106.
    Citations: 9     
  89. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015 Oct; 12(10):902-3. PMID: 26418763.
    Citations: 104     Fields:    Translation:HumansCells
  90. Semenkovich CF, Danska J, Darsow T, Dunne JL, Huttenhower C, Insel RA, McElvaine AT, Ratner RE, Shuldiner AR, Blaser MJ. American Diabetes Association and JDRF Research Symposium: Diabetes and the Microbiome. Diabetes. 2015 Dec; 64(12):3967-77. PMID: 26420863.
    Citations: 8     Fields:    Translation:HumansAnimals
  91. Mima 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 S. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut. 2016 12; 65(12):1973-1980. PMID: 26311717.
    Citations: 71     Fields:    Translation:HumansCells
  92. Mima 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 S. Fusobacterium nucleatum and T Cells in Colorectal Carcinoma. JAMA Oncol. 2015 Aug; 1(5):653-61. PMID: 26181352.
    Citations: 68     Fields:    Translation:HumansCells
  93. Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ. 2015; 3:e1029. PMID: 26157614.
    Citations: 67     
  94. Anahtar 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 DS. Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract. Immunity. 2015 May 19; 42(5):965-76. PMID: 25992865.
    Citations: 65     Fields:    Translation:HumansCells
  95. Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C. Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):E2930-8. PMID: 25964341.
    Citations: 50     Fields:    Translation:Humans
  96. Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol. 2015 Jun; 13(6):360-72. PMID: 25915636.
    Citations: 58     Fields:    Translation:Humans
  97. Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C. Associations 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. PMID: 25887922.
    Citations: 30     Fields:    Translation:Humans
  98. Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C. A reproducible approach to high-throughput biological data acquisition and integration. PeerJ. 2015; 3:e791. PMID: 26157642.
    Citations: 5     
  99. Haberman 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 LA. Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest. 2015 Mar 02; 125(3):1363. PMID: 25729854.
    Citations: 1     Fields:    
  100. Pelle 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 M. Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection. Genome Med. 2015; 7(1):19. PMID: 25722744.
    Citations: 18     Fields:    
  101. Yasuda 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 XC. Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe. 2015 Mar 11; 17(3):385-391. PMID: 25732063.
    Citations: 30     Fields:    Translation:Animals
  102. Kostic 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 RJ. The 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. PMID: 25662751.
    Citations: 149     Fields:    Translation:Humans
  103. Knights 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 RJ. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 2014; 6(12):107. PMID: 25587358.
    Citations: 68     Fields:    
  104. Joice R, Yasuda K, Shafquat A, Morgan XC, Huttenhower C. Determining microbial products and identifying molecular targets in the human microbiome. Cell Metab. 2014 Nov 04; 20(5):731-741. PMID: 25440055.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  105. Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, White O. Advancing the microbiome research community. Cell. 2014 Oct 09; 159(2):227-30. PMID: 25303518.
    Citations: 17     Fields:    Translation:HumansAnimals
  106. Zhao SD, Parmigiani G, Huttenhower C, Waldron L. Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics. 2014 Nov 01; 30(21):3062-9. PMID: 25061068.
    Citations: 9     Fields:    Translation:Humans
  107. Haberman 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 LA. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest. 2014 Aug; 124(8):3617-33. PMID: 25003194.
    Citations: 87     Fields:    Translation:HumansCells
  108. Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity. 2014 Jun 19; 40(6):843-54. PMID: 24950204.
    Citations: 72     Fields:    Translation:HumansAnimals
  109. Bernau C, Riester M, Boulesteix AL, Parmigiani G, Huttenhower C, Waldron L, Trippa L. Cross-study validation for the assessment of prediction algorithms. Bioinformatics. 2014 Jun 15; 30(12):i105-12. PMID: 24931973.
    Citations: 6     Fields:    Translation:Humans
  110. Franzosa 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 C. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A. 2014 Jun 03; 111(22):E2329-38. PMID: 24843156.
    Citations: 111     Fields:    Translation:HumansCells
  111. Tong 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 J. Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. ISME J. 2014 Nov; 8(11):2193-206. PMID: 24781901.
    Citations: 47     Fields:    Translation:HumansAnimalsCells
  112. Waldron 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 G. Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. J Natl Cancer Inst. 2014 Apr 03; 106(5). PMID: 24700801.
    Citations: 28     Fields:    Translation:HumansCells
  113. Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. J Natl Cancer Inst. 2014 Apr 03; 106(5). PMID: 24700803.
    Citations: 38     Fields:    Translation:HumansCells
  114. Gevers 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 RJ. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014 Mar 12; 15(3):382-392. PMID: 24629344.
    Citations: 418     Fields:    Translation:HumansCells
  115. Shafquat A, Joice R, Simmons SL, Huttenhower C. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol. 2014 May; 22(5):261-6. PMID: 24618403.
    Citations: 25     Fields:    Translation:Humans
  116. Rooks 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 WS. Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. ISME J. 2014 Jul; 8(7):1403-17. PMID: 24500617.
    Citations: 71     Fields:    Translation:HumansAnimalsCells
  117. Morgan XC, Huttenhower C. Meta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology. 2014 May; 146(6):1437-1448.e1. PMID: 24486053.
    Citations: 35     Fields:    Translation:HumansAnimalsCells
  118. Joice 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 M. Inferring developmental stage composition from gene expression in human malaria. PLoS Comput Biol. 2013; 9(12):e1003392. PMID: 24348235.
    Citations: 20     Fields:    Translation:HumansAnimals
  119. Zhang YJ, Reddy MC, Ioerger TR, Rothchild AC, Dartois V, Schuster BM, Trauner A, Wallis D, Galaviz S, Huttenhower C, Sacchettini JC, Behar SM, Rubin EJ. Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing. Cell. 2013 Dec 05; 155(6):1296-308. PMID: 24315099.
    Citations: 60     Fields:    Translation:HumansAnimalsCells
  120. Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, Segata N. MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res. 2014 Jan; 42(Database issue):D617-24. PMID: 24203705.
    Citations: 19     Fields:    Translation:Cells
  121. Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB, Huttenhower C, Littman DR. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife. 2013 Nov 05; 2:e01202. PMID: 24192039.
    Citations: 256     Fields:    Translation:HumansAnimalsCells
  122. Lee S, Cantarel B, Henrissat B, Gevers D, Birren BW, Huttenhower C, Ko G. Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. ISME J. 2014 Mar; 8(3):493-503. PMID: 24108330.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  123. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013 Sep; 31(9):814-21. PMID: 23975157.
    Citations: 916     Fields:    Translation:HumansCells
  124. Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C. Two-stage microbial community experimental design. ISME J. 2013 Dec; 7(12):2330-9. PMID: 23949665.
    Citations: 4     Fields:    Translation:Humans
  125. Börnigen D, Pers TH, Thorrez L, Huttenhower C, Moreau Y, Brunak S. Concordance of gene expression in human protein complexes reveals tissue specificity and pathology. Nucleic Acids Res. 2013 Oct; 41(18):e171. PMID: 23921638.
    Citations: 9     Fields:    Translation:Humans
  126. Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C. Functional profiling of the gut microbiome in disease-associated inflammation. Genome Med. 2013; 5(7):65. PMID: 23906180.
    Citations: 11     Fields:    
  127. Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers D. Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. J Innate Immun. 2014; 6(3):253-62. PMID: 23796786.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  128. McHardy 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 J. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome. 2013 Jun 05; 1(1):17. PMID: 24450808.
    Citations: 46     Fields:    
  129. Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS One. 2013; 8(5):e64832. PMID: 23741402.
    Citations: 23     Fields:    Translation:AnimalsCells
  130. Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C. Computational meta'omics for microbial community studies. Mol Syst Biol. 2013 May 14; 9:666. PMID: 23670539.
    Citations: 63     Fields:    Translation:HumansCells
  131. Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM. Sixty years of genome biology. Genome Biol. 2013 Apr 25; 14(4):113. PMID: 23651518.
    Citations: 3     Fields:    Translation:Humans
  132. Morrow AL, Lagomarcino AJ, Schibler KR, Taft DH, Yu Z, Wang B, Altaye M, Wagner M, Gevers D, Ward DV, Kennedy MA, Huttenhower C, Newburg DS. Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome. 2013 Apr 16; 1(1):13. PMID: 24450576.
    Citations: 73     Fields:    
  133. Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 Jul; 102(1):1-7. PMID: 23570996.
    Citations: 3     Fields:    Translation:HumansCells
  134. Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L. curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database (Oxford). 2013; 2013:bat013. PMID: 23550061.
    Citations: 43     Fields:    Translation:HumansCells
  135. Brown J, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh P. Translating the human microbiome. Nat Biotechnol. 2013 Apr; 31(4):304-8. PMID: 23563424.
    Citations: 7     Fields:    Translation:HumansAnimals
  136. Ballarini A, Segata N, Huttenhower C, Jousson O. Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. PLoS One. 2013; 8(2):e55764. PMID: 23409037.
    Citations: 4     Fields:    Translation:HumansCells
  137. Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol. 2013; 9(1):e1002863. PMID: 23326225.
    Citations: 136     Fields:    Translation:HumansCells
  138. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013; 4:2304. PMID: 23942190.
    Citations: 124     Fields:    Translation:Cells
  139. Morgan XC, Huttenhower C. Chapter 12: Human microbiome analysis. PLoS Comput Biol. 2012; 8(12):e1002808. PMID: 23300406.
    Citations: 69     Fields:    Translation:HumansCells
  140. Gevers D, Pop M, Schloss PD, Huttenhower C. Bioinformatics for the Human Microbiome Project. PLoS Comput Biol. 2012; 8(11):e1002779. PMID: 23209389.
    Citations: 22     Fields:    Translation:Humans
  141. Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, Golub TR, Fuchs CS, Parmigiani G, Huttenhower C. Expression profiling of archival tumors for long-term health studies. Clin Cancer Res. 2012 Nov 15; 18(22):6136-46. PMID: 23136189.
    Citations: 12     Fields:    Translation:HumansCells
  142. Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends Genet. 2013 Jan; 29(1):51-8. PMID: 23140990.
    Citations: 52     Fields:    Translation:Humans
  143. Zhang YJ, Ioerger TR, Huttenhower C, Long JE, Sassetti CM, Sacchettini JC, Rubin EJ. Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. PLoS Pathog. 2012 Sep; 8(9):e1002946. PMID: 23028335.
    Citations: 80     Fields:    Translation:Cells
  144. Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methé BA, Huttenhower C. The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol. 2012; 10(8):e1001377. PMID: 22904687.
    Citations: 71     Fields:    Translation:Humans
  145. Morikawa T, Tanaka N, Kuchiba A, Nosho K, Yamauchi M, Hornick JL, Swanson RS, Chan AT, Meyerhardt JA, Huttenhower C, Schrag D, Fuchs CS, Ogino S. Predictors of lymph node count in colorectal cancer resections: data from US nationwide prospective cohort studies. Arch Surg. 2012 Aug; 147(8):715-23. PMID: 22508672.
    Citations: 13     Fields:    Translation:HumansCells
  146. Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol. 2012; 8(7):e1002606. PMID: 22807668.
    Citations: 254     Fields:    Translation:HumansCells
  147. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J. Composition 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. PMID: 22698087.
    Citations: 175     Fields:    Translation:HumansCells
  148. Abubucker 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 C. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012; 8(6):e1002358. PMID: 22719234.
    Citations: 267     Fields:    Translation:Humans
  149. Aagaard 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 J. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One. 2012; 7(6):e36466. PMID: 22719832.
    Citations: 100     Fields:    Translation:HumansCells
  150. Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BA. A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PLoS One. 2012; 7(6):e29044. PMID: 22719821.
    Citations: 5     Fields:    Translation:HumansCells
  151. Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012 Jun 10; 9(8):811-4. PMID: 22688413.
    Citations: 328     Fields:    Translation:HumansCells
  152. Morgan 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 C. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012 Apr 16; 13(9):R79. PMID: 23013615.
    Citations: 416     Fields:    Translation:HumansCells
  153. Yamauchi M, Lochhead P, Morikawa T, Huttenhower C, Chan AT, Giovannucci E, Fuchs C, Ogino S. Colorectal cancer: a tale of two sides or a continuum? Gut. 2012 Jun; 61(6):794-7. PMID: 22490520.
    Citations: 88     Fields:    Translation:Humans
  154. Waldron L, Simpson P, Parmigiani G, Huttenhower C. Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. BMC Cancer. 2012 Mar 29; 12:124. PMID: 22458912.
    Citations: 9     Fields:    Translation:Humans
  155. Merrick CJ, Huttenhower C, Buckee C, Amambua-Ngwa A, Gomez-Escobar N, Walther M, Conway DJ, Duraisingh MT. Epigenetic dysregulation of virulence gene expression in severe Plasmodium falciparum malaria. J Infect Dis. 2012 May 15; 205(10):1593-600. PMID: 22448008.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  156. Yamauchi 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 S. Assessment 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. PMID: 22427238.
    Citations: 177     Fields:    Translation:HumansCells
  157. Waldron L, Coller HA, Huttenhower C. Integrative approaches for microarray data analysis. Methods Mol Biol. 2012; 802:157-82. PMID: 22130880.
    Citations: 3     Fields:    Translation:Humans
  158. Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ. Genomics in 2011: challenges and opportunities. Genome Biol. 2011 Dec 28; 12(12):137. PMID: 22204305.
    Citations:    Fields:    Translation:HumansAnimals
  159. Waldron L, Pintilie M, Tsao MS, Shepherd FA, Huttenhower C, Jurisica I. Optimized application of penalized regression methods to diverse genomic data. Bioinformatics. 2011 Dec 15; 27(24):3399-406. PMID: 22156367.
    Citations: 21     Fields:    Translation:HumansCells
  160. Kostic 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 M. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2012 Feb; 22(2):292-8. PMID: 22009990.
    Citations: 389     Fields:    Translation:HumansCells
  161. Sczesnak A, Segata N, Qin X, Gevers D, Petrosino JF, Huttenhower C, Littman DR, Ivanov II. The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host Microbe. 2011 Sep 15; 10(3):260-72. PMID: 21925113.
    Citations: 67     Fields:    Translation:HumansAnimalsCells
  162. Segata N, Huttenhower C. Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. PLoS One. 2011; 6(9):e24704. PMID: 21931822.
    Citations: 14     Fields:    Translation:Cells
  163. Huttenhower C. Computational biology: plus c'est la même chose, plus ça change. Genome Biol. 2011 Aug 23; 12(8):307. PMID: 21861851.
    Citations:    Fields:    
  164. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011 Jun 24; 12(6):R60. PMID: 21702898.
    Citations: 965     Fields:    Translation:HumansAnimalsCells
  165. Livstone MS, Oughtred R, Heinicke S, Vernot B, Huttenhower C, Durand D, Dolinski K. Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD). Curr Protoc Bioinformatics. 2011 Mar; Chapter 6:Unit 6.11. PMID: 21400696.
    Citations: 3     Fields:    
  166. Ballal SA, Gallini CA, Segata N, Huttenhower C, Garrett WS. Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts. Cell Microbiol. 2011 Apr; 13(4):508-17. PMID: 21314883.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  167. Morikawa T, Baba Y, Yamauchi M, Kuchiba A, Nosho K, Shima K, Tanaka N, Huttenhower C, Frank DA, Fuchs CS, Ogino S. STAT3 expression, molecular features, inflammation patterns, and prognosis in a database of 724 colorectal cancers. Clin Cancer Res. 2011 Mar 15; 17(6):1452-62. PMID: 21310826.
    Citations: 49     Fields:    Translation:HumansCells
  168. Wardwell LH, Huttenhower C, Garrett WS. Current concepts of the intestinal microbiota and the pathogenesis of infection. Curr Infect Dis Rep. 2011 Feb; 13(1):28-34. PMID: 21308452.
    Citations: 24     
  169. Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG. Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst Biol. 2010 Dec 31; 4:180. PMID: 21194434.
    Citations: 11     Fields:    Translation:Animals
  170. Park CY, Hess DC, Huttenhower C, Troyanskaya OG. Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PLoS Comput Biol. 2010 Nov 24; 6(11):e1001009. PMID: 21124865.
    Citations: 13     Fields:    Translation:AnimalsCells
  171. Sathirapongsasuti JF, Sathira N, Suzuki Y, Huttenhower C, Sugano S. Ultraconserved 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. PMID: 21062826.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  172. Tanaka N, Huttenhower C, Nosho K, Baba Y, Shima K, Quackenbush J, Haigis KM, Giovannucci E, Fuchs CS, Ogino S. Novel application of structural equation modeling to correlation structure analysis of CpG island methylation in colorectal cancer. Am J Pathol. 2010 Dec; 177(6):2731-40. PMID: 21037082.
    Citations: 19     Fields:    Translation:HumansCells
  173. Baba Y, Nosho K, Shima K, Huttenhower C, Tanaka N, Hazra A, Giovannucci EL, Fuchs CS, Ogino S. Hypomethylation of the IGF2 DMR in colorectal tumors, detected by bisulfite pyrosequencing, is associated with poor prognosis. Gastroenterology. 2010 Dec; 139(6):1855-64. PMID: 20682317.
    Citations: 27     Fields:    Translation:HumansCells
  174. Huttenhower C, Hofmann O. A quick guide to large-scale genomic data mining. PLoS Comput Biol. 2010 May 27; 6(5):e1000779. PMID: 20523745.
    Citations: 9     Fields:    Translation:Humans
  175. Baba Y, Huttenhower C, Nosho K, Tanaka N, Shima K, Hazra A, Schernhammer ES, Hunter DJ, Giovannucci EL, Fuchs CS, Ogino S. Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors. Mol Cancer. 2010 May 27; 9:125. PMID: 20507599.
    Citations: 59     Fields:    Translation:HumansCells
  176. Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: Interactive exploration of large, dense graphs. BMC Bioinformatics. 2009 Dec 14; 10:417. PMID: 20003429.
    Citations: 10     Fields:    
  177. Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA. Detailing regulatory networks through large scale data integration. Bioinformatics. 2009 Dec 15; 25(24):3267-74. PMID: 19825796.
    Citations: 28     Fields:    
  178. Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG. The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics. 2009 Sep 15; 25(18):2404-10. PMID: 19561015.
    Citations: 17     Fields:    Translation:AnimalsCells
  179. Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comput Biol. 2009 Jun; 5(6):e1000417. PMID: 19543383.
    Citations: 49     Fields:    Translation:AnimalsCells
  180. Hess 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 AA. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. 2009 Mar; 5(3):e1000407. PMID: 19300474.
    Citations: 64     Fields:    Translation:AnimalsCells
  181. Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG. Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol. 2009 Mar; 5(3):e1000322. PMID: 19300515.
    Citations: 21     Fields:    Translation:AnimalsCells
  182. Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. Exploring the human genome with functional maps. Genome Res. 2009 Jun; 19(6):1093-106. PMID: 19246570.
    Citations: 104     Fields:    Translation:HumansCells
  183. Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. PLoS Comput Biol. 2009 Jan; 5(1):e1000257. PMID: 19119411.
    Citations: 43     Fields:    Translation:Animals
  184. Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG. Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data. Methods Mol Biol. 2009; 548:273-93. PMID: 19521830.
    Citations: 1     Fields:    Translation:Animals
  185. Huttenhower C, Troyanskaya OG. Assessing the functional structure of genomic data. Bioinformatics. 2008 Jul 01; 24(13):i330-8. PMID: 18586732.
    Citations: 8     Fields:    Translation:AnimalsCells
  186. Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG. The Sleipnir library for computational functional genomics. Bioinformatics. 2008 Jul 01; 24(13):1559-61. PMID: 18499696.
    Citations: 37     Fields:    
  187. Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell. 2008 Jan; 19(1):352-67. PMID: 17959824.
    Citations: 198     Fields:    Translation:AnimalsCells
  188. Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics. 2007 Oct 15; 23(20):2692-9. PMID: 17724061.
    Citations: 109     Fields:    Translation:Animals
  189. Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA. Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC Bioinformatics. 2007 Jul 12; 8:250. PMID: 17626636.
    Citations: 17     Fields:    Translation:Animals
  190. Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A. 2007 Feb 13; 104(7):2193-8. PMID: 17287358.
    Citations: 205     Fields:    Translation:Cells
  191. Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics. 2006 Oct 10; 7:443. PMID: 17032457.
    Citations: 27     Fields:    
  192. Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics. 2006 Dec 01; 22(23):2890-7. PMID: 17005538.
    Citations: 56     Fields:    Translation:Animals
  193. Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG. Finding function: evaluation methods for functional genomic data. BMC Genomics. 2006 Jul 25; 7:187. PMID: 16869964.
    Citations: 80     Fields:    
  194. Huttenhower C, Troyanskaya OG. Bayesian data integration: a functional perspective. Comput Syst Bioinformatics Conf. 2006; 341-51. PMID: 17369653.
    Citations: 5     Fields:    Translation:Animals
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