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profileCurtis Huttenhower, Ph.D.

TitleAssociate Professor of Computational Biology and Bioinformatics
InstitutionHarvard T.H. Chan School of Public Health
DepartmentBiostatistics
AddressHarvard School of Public Health
Bldg 2-451
655 Huntington Ave
Boston MA 02115
Phone617/432-4912
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Collapse Overview 
Collapse 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.


Collapse Research 
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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.
R01CA202704     (CHAN, ANDREW T.)Mar 1, 2016 - Feb 28, 2021
NIH/NCI
Dietary sulfur, the gut microbiome, and colorectal cancer
Role: Co-Principal Investigator

R21AI112991     (HUTTENHOWER, CURTIS)Aug 10, 2015 - Jul 31, 2017
NIH/NIAID
Staphylococcus Aureus Carriage and the Nasal Microbiome
Role: Principal Investigator

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

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

R01HG005969     (HUTTENHOWER, CURTIS)Sep 27, 2010 - Jun 30, 2013
NIH/NHGRI
Functional activity and inter-organismal interactions in the human microbiome
Role: Principal Investigator
Collapse research resources
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 (2) and Software (1)

Collapse Bibliographic 
Collapse selected publications
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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  1. 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 Aug 16; 5(1):86. PMID: 28810907.
    View in: PubMed
  2. 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.
    View in: PubMed
  3. 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.
    View in: PubMed
  4. 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.
    View in: PubMed
  5. 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. 2017 Apr 04. PMID: 28377387.
    View in: PubMed
  6. 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 Apr 29; 389(10080):1710-1718. PMID: 28259484.
    View in: PubMed
  7. 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.
    View in: PubMed
  8. Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 2017 Apr; 27(4):626-638. PMID: 28167665.
    View in: PubMed
  9. 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 Feb 01; 18(1):50. PMID: 28143522.
    View in: PubMed
  10. 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 Feb; 28(2):167-176. PMID: 28097472.
    View in: PubMed
  11. 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 Jan 17; 46(1):29-37. PMID: 28087240.
    View in: PubMed
  12. 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 Jan 03; 114(1):142-147. PMID: 27980034.
    View in: PubMed
  13. 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 LA, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell. 2016 Dec 15; 167(7):1897. PMID: 27984736.
    View in: PubMed
  14. Hill JH, Franzosa EA, Huttenhower C, Guillemin K. A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. Elife. 2016 Dec 13; 5. PMID: 27960075.
    View in: PubMed
  15. 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.
    View in: PubMed
  16. Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, 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.
    View in: PubMed
  17. 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 Oct 10; 7:12727. PMID: 27721445.
    View in: PubMed
  18. Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, Wijmenga C, Zhernakova A, Weersma RK. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut. 2016 Oct 08. PMID: 27802154.
    View in: PubMed
  19. 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 Sep 29; 17(1):201. PMID: 27687735.
    View in: PubMed
  20. 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 Sep 20; 50(18):9807-15. PMID: 27599587; PMCID: PMC5032049.
  21. 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.
    View in: PubMed
  22. 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 Jun 15; 8(343):343ra81. PMID: 27306663; PMCID: PMC5032909 [Available on 06/15/17].
  23. 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.
    View in: PubMed
  24. 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 Jun 02; 1(8):e86907. PMID: 27699268.
    View in: PubMed
  25. 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 Jun 15; 82(12):3572-81. PMID: 27060125; PMCID: PMC4959169.
  26. 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 May 27; 1(7):16070. PMID: 27572971.
    View in: PubMed
  27. 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.
    View in: PubMed
  28. 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; PMCID: PMC4950857 [Available on 05/05/17].
  29. Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016 04 27; 8(1):51. PMID: 27122046; PMCID: PMC4848870.
  30. 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; PMCID: PMC4831844.
  31. 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; PMCID: PMC4898650 [Available on 05/01/17].
  32. 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.
    View in: PubMed
  33. 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; PMCID: PMC4756455.
  34. 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; PMCID: PMC4740747.
  35. 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; PMCID: PMC4684307.
  36. 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.
    View in: PubMed
  37. 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; PMCID: PMC4644332.
  38. 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; PMCID: PMC4621437.
  39. 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.
    View in: PubMed
  40. 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; PMCID: PMC4876761 [Available on 12/01/16].
  41. 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 Dec; 65(12):1973-1980. PMID: 26311717.
    View in: PubMed
  42. 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; PMCID: PMC4537376.
  43. 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; PMCID: PMC4476132.
  44. 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; PMCID: PMC4461369.
  45. 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; PMCID: PMC4460507 [Available on 12/02/15].
  46. 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; PMCID: PMC4800835.
  47. 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; PMCID: PMC4414286.
  48. 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; PMCID: PMC4493686.
  49. 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; PMCID: PMC4362234.
  50. 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; PMCID: PMC4342211.
  51. 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):385-91. PMID: 25732063; PMCID: PMC4369771.
  52. 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; PMCID: PMC4689191.
  53. 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; PMCID: PMC4292994.
  54. 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):731-41. PMID: 25440055; PMCID: PMC4254638.
  55. 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; PMCID: PMC4221798.
  56. 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; PMCID: PMC4201155.
  57. 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; PMCID: PMC4109533.
  58. 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; PMCID: PMC4135443.
  59. 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; PMCID: PMC4058929.
  60. 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; PMCID: PMC4050606.
  61. 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; PMCID: PMC4992076.
  62. 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; PMCID: PMC4580554.
  63. 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; PMCID: PMC4580556.
  64. 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; PMCID: PMC4059512.
  65. 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; PMCID: PMC4008634.
  66. 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; PMCID: PMC4069400.
  67. Morgan XC, Huttenhower C. Meta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology. 2014 May; 146(6):1437-1448.e1. PMID: 24486053.
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  68. 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; PMCID: PMC3861035.
  69. 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; PMCID: PMC3902092.
  70. 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; PMCID: PMC3964974.
  71. 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; PMCID: PMC3816614.
  72. 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; PMCID: PMC3930310.
  73. 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; PMCID: PMC3819121.
  74. 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; PMCID: PMC3834858.
  75. 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; PMCID: PMC3794609.
  76. 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; PMCID: PMC3978847.
  77. 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; PMCID: PMC4045018.
  78. 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; PMCID: PMC3971612.
  79. 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; PMCID: PMC3669401.
  80. 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; PMCID: PMC4039370.
  81. 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; PMCID: PMC3663092.
  82. 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; PMCID: PMC3971624.
  83. 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; PMCID: PMC3676702.
  84. 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; PMCID: PMC3625954.
  85. 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.
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  86. 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; PMCID: PMC3569451.
  87. 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; PMCID: PMC3542080.
  88. 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; PMCID: PMC3760377.
  89. Morgan XC, Huttenhower C. Chapter 12: Human microbiome analysis. PLoS Comput Biol. 2012; 8(12):e1002808. PMID: 23300406; PMCID: PMC3531975.
  90. Gevers D, Pop M, Schloss PD, Huttenhower C. Bioinformatics for the Human Microbiome Project. PLoS Comput Biol. 2012; 8(11):e1002779. PMID: 23209389; PMCID: PMC3510052.
  91. 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; PMCID: PMC3500412.
  92. Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends Genet. 2013 Jan; 29(1):51-8. PMID: 23140990; PMCID: PMC3534939.
  93. 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; PMCID: PMC3460630.
  94. 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; PMCID: PMC3419203.
  95. 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; PMCID: PMC3404227.
  96. 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; PMCID: PMC3395616.
  97. 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; PMCID: PMC3446314.
  98. 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; PMCID: PMC3374609.
  99. 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; PMCID: PMC3374618.
  100. 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; PMCID: PMC3374610.
  101. 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; PMCID: PMC3443552.
  102. 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; PMCID: PMC3506950.
  103. 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; PMCID: PMC3345045.
  104. 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; PMCID: PMC3342119.
  105. 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; PMCID: PMC3415821.
  106. 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; PMCID: PMC3345105.
  107. Waldron L, Coller HA, Huttenhower C. Integrative approaches for microarray data analysis. Methods Mol Biol. 2012; 802:157-82. PMID: 22130880.
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  108. 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; PMCID: PMC3334607.
  109. 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; PMCID: PMC3232376.
  110. 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; PMCID: PMC3266036.
  111. 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; PMCID: PMC3209701.
  112. 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; PMCID: PMC3171473.
  113. Huttenhower C. Computational biology: plus c'est la même chose, plus ça change. Genome Biol. 2011 Aug 23; 12(8):307. PMID: 21861851; PMCID: PMC3245610.
  114. 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; PMCID: PMC3218848.
  115. 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; PMCID: PMC3763948.
  116. 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.
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  117. 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; PMCID: PMC3077111.
  118. 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; PMCID: PMC3077078.
  119. 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; PMCID: PMC3023688.
  120. 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; PMCID: PMC2991250.
  121. 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; PMCID: PMC3064809.
  122. 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; PMCID: PMC2993288.
  123. 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; PMCID: PMC2995815.
  124. Huttenhower C, Hofmann O. A quick guide to large-scale genomic data mining. PLoS Comput Biol. 2010 May 27; 6(5):e1000779. PMID: 20523745; PMCID: PMC2877728.
  125. 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; PMCID: PMC2892454.
  126. Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: Interactive exploration of large, dense graphs. BMC Bioinformatics. 2009 Dec 14; 10:417. PMID: 20003429; PMCID: PMC2803856.
  127. 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; PMCID: PMC2788929.
  128. 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; PMCID: PMC2735660.
  129. 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; PMCID: PMC2692103.
  130. 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; PMCID: PMC2648979.
  131. 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; PMCID: PMC2654405.
  132. 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; PMCID: PMC2694471.
  133. 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; PMCID: PMC2599889.
  134. 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.
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  135. Huttenhower C, Troyanskaya OG. Assessing the functional structure of genomic data. Bioinformatics. 2008 Jul 01; 24(13):i330-8. PMID: 18586732; PMCID: PMC2718638.
  136. 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; PMCID: PMC2718674.
  137. 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; PMCID: PMC2174172.
  138. 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.
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  139. 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; PMCID: PMC1941745.
  140. 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; PMCID: PMC1892997.
  141. 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; PMCID: PMC1618863.
  142. 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.
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  143. 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; PMCID: PMC1560386.
  144. Huttenhower C, Troyanskaya OG. Bayesian data integration: a functional perspective. Comput Syst Bioinformatics Conf. 2006; 341-51. PMID: 17369653.
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