Photo of Curtis Huttenhower,  PhD

Curtis Huttenhower, PhD

Harvard T.H. Chan School Of Public Health

Harvard T.H. Chan School Of Public Health
Phone: (617) 432-4912


chuttenh@hsph.harvard.edu

Curtis Huttenhower, PhD

Harvard T.H. Chan School Of Public Health

EDUCATIONAL TITLES

  • Associate Professor, Biostatistics, Harvard T.H. Chan School Of Public Health

DF/HCC PROGRAM AFFILIATION

Research Abstract

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 molecular biology. This can include techniques from statistical machine learning, graphical models, and information retrieval. The lab is currently applying these methods to biological systems including both human populations (e.g. genomic data from large prospective cohort studies) and microbial populations (e.g. pathogen populations and metagenomic communities such as the gut microflora). 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.

Publications

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  • Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma W, Wang DD, Thompson KN, Yan Y, Branck T, Wilkinson JE, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song M, Huttenhower C, Ogino S, Chan AT. The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. Clin Transl Gastroenterol 2021; 12:e00338. PubMed
  • Nguyen LH, Cao Y, Hur J, Mehta RS, Sikavi DR, Wang Y, Ma W, Wu K, Song M, Giovannucci EL, Rimm EB, Willett WC, Garrett WS, Izard J, Huttenhower C, Chan AT. The Sulfur Microbial Diet Is Associated With Increased Risk of Early-Onset Colorectal Cancer Precursors. Gastroenterology 2021. PubMed
  • Wang V, Geybels MS, Jordahl KM, Gerke T, Hamid A, Penney KL, Markt SC, Freedman M, Pomerantz M, Lee GM, Rana H, Börnigen D, Rebbeck TR, Huttenhower C, Eeles RA, Stanford JL, Consortium P, Berndt SI, Claessens F, Sørensen KD, Park JY, Vega A, Usmani N, Mucci L, Sweeney CJ. A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer. Prostate 2021; 81:683-693. PubMed
  • Li Y, Wang DD, Satija A, Ivey KL, Li J, Wilkinson JE, Li R, Baden M, Chan AT, Huttenhower C, Rimm EB, Hu FB, Sun Q. Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome. J Nutr 2021. PubMed
  • Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife 2021. PubMed
  • Wilkinson JE, Franzosa EA, Everett C, Li C, , , Hu FB, Wirth DF, Song M, Chan AT, Rimm E, Garrett WS, Huttenhower C. A framework for microbiome science in public health. Nat Med 2021; 27:766-774. PubMed
  • Everett C, Li C, Wilkinson JE, Nguyen LH, McIver LJ, Ivey K, Izard J, Palacios N, Eliassen AH, Willett WC, Ascherio A, Sun Q, Tworoger SS, Chan AT, Garrett WS, Huttenhower C, Rimm EB, Song M. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies. Nat Protoc 2021. PubMed
  • Young C, Wood HM, Fuentes Balaguer A, Bottomley D, Gallop N, Wilkinson L, Benton SC, Brealey M, John C, Burtonwood C, Thompson KN, Yan Y, Barrett JH, Morris EJA, Huttenhower C, Quirke P. Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy. Clin Cancer Res 2021; 27:2246-2254. PubMed
  • Borowsky J, Haruki K, Lau MC, Dias Costa A, Väyrynen JP, Ugai T, Arima K, da Silva A, Felt K, Zhao M, Gurjao C, Twombly TS, Fujiyoshi K, Väyrynen SA, Hamada T, Mima K, Bullman S, Harrison TA, Phipps AI, Peters U, Ng K, Meyerhardt JA, Song M, Giovannucci EL, Wu K, Zhang X, Freeman GJ, Huttenhower C, Garrett WS, Chan AT, Leggett BA, Whitehall VL, Walker N, Brown I, Bettington M, Nishihara R, Fuchs CS, Lennerz JK, Giannakis M, Nowak JA, Ogino S. Association of with Specific T Cell Subsets in the Colorectal Carcinoma Microenvironment. Clin Cancer Res 2021. PubMed
  • Young C, Wood HM, Seshadri RA, Van Nang P, Vaccaro C, Melendez LC, Bose M, Van Doi M, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P. The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries. Genome Med 2021; 13:27. PubMed
  • Asnicar F, Berry SE, Valdes AM, Nguyen LH, Piccinno G, Drew DA, Leeming E, Gibson R, Le Roy C, Khatib HA, Francis L, Mazidi M, Mompeo O, Valles-Colomer M, Tett A, Beghini F, Dubois L, Bazzani D, Thomas AM, Mirzayi C, Khleborodova A, Oh S, Hine R, Bonnett C, Capdevila J, Danzanvilliers S, Giordano F, Geistlinger L, Waldron L, Davies R, Hadjigeorgiou G, Wolf J, Ordovás JM, Gardner C, Franks PW, Chan AT, Huttenhower C, Spector TD, Segata N. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat Med 2021; 27:321-332. PubMed
  • Zhang Y, Thompson KN, Huttenhower C, Franzosa EA. Statistical approaches for differential expression analysis in metatranscriptomics. Bioinformatics 2021; 37:i34-i41. PubMed
  • Simon TG, Chan AT, Huttenhower C. Microbiome Biomarkers: One Step Closer in NAFLD-Cirrhosis. Hepatology 2020. PubMed
  • Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020; 12:71. PubMed
  • Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata N. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biol 2020; 21:138. PubMed
  • Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, Branck T, DuLong C, Ivey KL, Ogino S, Rimm EB, Song M, Garrett WS, Izard J, Huttenhower C, Chan AT. Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Gastroenterology 2020; 158:1313-1325. PubMed
  • Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C. Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. Cell Host Microbe 2020. PubMed
  • Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. Global chemical effects of the microbiome include new bile-acid conjugations. Nature 2020; 579:123-129. PubMed
  • Haruki K, Kosumi K, Hamada T, Twombly TS, Väyrynen JP, Kim SA, Masugi Y, Qian ZR, Mima K, Baba Y, da Silva A, Borowsky J, Arima K, Fujiyoshi K, Lau MC, Li P, Guo C, Chen Y, Song M, Nowak JA, Nishihara R, Yanaga K, Zhang X, Wu K, Bullman S, Garrett WS, Huttenhower C, Meyerhardt JA, Giannakis M, Chan AT, Fuchs CS, Ogino S. Association of autophagy status with amount of Fusobacterium nucleatum in colorectal cancer. J Pathol 2019. PubMed
  • McBurney MI, Davis C, Fraser CM, Schneeman BO, Huttenhower C, Verbeke K, Walter J, Latulippe ME. Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions. J Nutr 2019. PubMed
  • Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019; 37:852-857. PubMed
  • 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. PubMed
  • 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 . Emerg Microbes Infect 2019; 8:827-840. PubMed
  • 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 2018. PubMed
  • 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; 19:142. PubMed
  • 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; 3:356-366. PubMed
  • 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; 3:347-355. PubMed
  • 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; 10:6. PubMed
  • 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; 7:17686. PubMed
  • Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol 2017; 18:228. PubMed
  • Schwager E, Mallick H, Ventz S, Huttenhower C. A Bayesian method for detecting pairwise associations in compositional data. PLoS Comput. Biol. 2017; 13:e1005852. PubMed
  • 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; 14:1023-1024. PubMed
  • 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; 550:61-66. PubMed
  • 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. PubMed
  • 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; 357:1156-1160. PubMed
  • 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 2017. PubMed
  • 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. PubMed
  • 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; 18:50. PubMed
  • 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 2016; 114:142-147. PubMed
  • Börnigen D, Tyekucheva S, Wang X, Rider JR, Lee GS, Mucci LA, Sweeney C, Huttenhower C. Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PLoS Comput. Biol. 2016; 12:e1004820. PubMed
  • 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 2015. PubMed
  • 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. PubMed
  • 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; 30:i105-12. PubMed
  • 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. Journal of the National Cancer Institute 2014. PubMed
  • 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. Journal of the National Cancer Institute 2014. PubMed
  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics 2013. PubMed
  • 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; 31:304-8. PubMed
  • 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. PubMed
  • Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE 2013; 8:e64832. PubMed
  • 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; 18:6136-46. PubMed
  • 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; 147:715-23. PubMed
  • 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; 17:1452-62. PubMed
  • 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; 39:1967-79. PubMed
  • 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; Chapter 6:Unit 6.11. PubMed
  • 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; 139:1855-64. PubMed
  • 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; 177:2731-40. PubMed
  • 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; 9:125. PubMed
  • Huttenhower C, Hofmann O. A quick guide to large-scale genomic data mining. PLoS Comput. Biol. 2010; 6:e1000779. PubMed
  • Park CY, Hess DC, Huttenhower C, Troyanskaya OG. Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PLoS Comput. Biol. 2010; 6:e1001009. PubMed
  • 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 2011; 4:180. PubMed
  • 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; 25:3267-74. PubMed
  • 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; 25:2404-10. PubMed
  • Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. Exploring the human genome with functional maps. Genome Res 2009; 19:1093-106. PubMed
  • 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; 5:e1000417. PubMed
  • Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: Interactive exploration of large, dense graphs. BMC Bioinformatics 2010; 10:417. PubMed
  • Huttenhower C, Troyanskaya OG.. Assessing the functional structure of genomic data. Bioinformatics 2008.
  • 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 Comp Bio 2009.
  • 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.
  • Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG.. Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comp Bio 2009.
  • Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG.. The Sleipnir library for computational functional genomics. Bioinformatics 2008.
  • 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.
  • Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG.. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comp Bio 2009.
  • 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. PubMed
  • Huttenhower C, Hibbs M, Myers C, Troyanskaya OG.. A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics 2006.
  • 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; 17:201. PubMed
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