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Curtis Huttenhower, Ph.D.

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

 Overview 
 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.


 Bibliographic 
 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. 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 Dec; 9(12):e1003392.
    View in: PubMed
  2. 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 5; 155(6):1296-308.
    View in: PubMed
  3. 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 1; 42(1):D617-24.
    View in: PubMed
  4. 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; 2(0).
    View in: PubMed
  5. 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.
    View in: PubMed
  6. Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C. Two-stage microbial community experimental design. ISME J. 2013 Dec; 7(12):2330-9.
    View in: PubMed
  7. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013 Aug 14; 4:2304.
    View in: PubMed
  8. 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 1; 41(18):e171.
    View in: PubMed
  9. 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; 1(1):17.
    View in: PubMed
  10. Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing Messages between Biological Networks to Refine Predicted Interactions. PLoS One. 2013; 8(5):e64832.
    View in: PubMed
  11. Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C. Computational meta'omics for microbial community studies. Mol Syst Biol. 2013; 9:666.
    View in: PubMed
  12. 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; 1(1):13.
    View in: PubMed
  13. 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.
    View in: PubMed
  14. 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.
    View in: PubMed
  15. 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.
    View in: PubMed
  16. 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.
    View in: PubMed
  17. 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 Jan; 9(1):e1002863.
    View in: PubMed
  18. Morgan XC, Huttenhower C. Chapter 12: human microbiome analysis. PLoS Comput Biol. 2012 Dec; 8(12):e1002808.
    View in: PubMed
  19. Gevers D, Pop M, Schloss PD, Huttenhower C. Bioinformatics for the human microbiome project. PLoS Comput Biol. 2012 Nov; 8(11):e1002779.
    View in: PubMed
  20. 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.
    View in: PubMed
  21. Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends Genet. 2013 Jan; 29(1):51-8.
    View in: PubMed
  22. 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.
    View in: PubMed
  23. 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.
    View in: PubMed
  24. 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.
    View in: PubMed
  25. 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.
    View in: PubMed
  26. 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; 13(6):R42.
    View in: PubMed
  27. 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.
    View in: PubMed
  28. 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.
    View in: PubMed
  29. 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.
    View in: PubMed
  30. 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 Aug; 9(8):811-4.
    View in: PubMed
  31. 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; 13(9):R79.
    View in: PubMed
  32. 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.
    View in: PubMed
  33. 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; 12:124.
    View in: PubMed
  34. 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.
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  35. 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.
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  36. Waldron L, Coller HA, Huttenhower C. Integrative approaches for microarray data analysis. Methods Mol Biol. 2012; 802:157-82.
    View in: PubMed
  37. 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; 12(12):137.
    View in: PubMed
  38. 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.
    View in: PubMed
  39. 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.
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  40. 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.
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  41. Segata N, Huttenhower C. Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. PLoS One. 2011; 6(9):e24704.
    View in: PubMed
  42. Huttenhower C. Computational biology: plus c'est la même chose, plus ça change. Genome Biol. 2011; 12(8):307.
    View in: PubMed
  43. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011; 12(6):R60.
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  44. 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.
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  45. 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.
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  46. 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.
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  47. 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.
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  48. 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; 4:180.
    View in: PubMed
  49. 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(11):e1001009.
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  50. 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.
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  51. 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.
    View in: PubMed
  52. 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.
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  53. Huttenhower C, Hofmann O. A quick guide to large-scale genomic data mining. PLoS Comput Biol. 2010 May; 6(5):e1000779.
    View in: PubMed
  54. 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.
    View in: PubMed
  55. Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: Interactive exploration of large, dense graphs. BMC Bioinformatics. 2009; 10:417.
    View in: PubMed
  56. 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.
    View in: PubMed
  57. 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.
    View in: PubMed
  58. 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.
    View in: PubMed
  59. 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.
    View in: PubMed
  60. 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.
    View in: PubMed
  61. 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.
    View in: PubMed
  62. 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.
    View in: PubMed
  63. 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.
    View in: PubMed
  64. Huttenhower C, Troyanskaya OG. Assessing the functional structure of genomic data. Bioinformatics. 2008 Jul 1; 24(13):i330-8.
    View in: PubMed
  65. Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG. The Sleipnir library for computational functional genomics. Bioinformatics. 2008 Jul 1; 24(13):1559-61.
    View in: PubMed
  66. 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.
    View in: PubMed
  67. 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.
    View in: PubMed
  68. 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; 8:250.
    View in: PubMed
  69. 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.
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  70. Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics. 2006; 7:443.
    View in: PubMed
  71. Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics. 2006 Dec 1; 22(23):2890-7.
    View in: PubMed
  72. Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG. Finding function: evaluation methods for functional genomic data. BMC Genomics. 2006; 7:187.
    View in: PubMed
  73. Huttenhower C, Troyanskaya OG. Bayesian data integration: a functional perspective. Comput Syst Bioinformatics Conf. 2006; 341-51.
    View in: PubMed
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