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

Curtis Huttenhower, PhD

Harvard T.H. Chan School Of Public Health


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


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.


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  • 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, DorĂ© 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; 18:6136-6146. 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
  • 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:Unit6.11. 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
  • 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, 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
  • 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
  • Huttenhower C, Hofmann O. A quick guide to large-scale genomic data mining. PLoS Comput. Biol. 2010; 6:e1000779. 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
  • 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
  • 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, 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
  • Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: Interactive exploration of large, dense graphs. BMC Bioinformatics 2010; 10:417. PubMed
  • 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, Troyanskaya OG.. Assessing the functional structure of genomic data. Bioinformatics 2008.
  • Huttenhower C, Hibbs M, Myers C, Troyanskaya OG.. A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics 2006.
  • 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.
  • 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.
  • Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG.. The Sleipnir library for computational functional genomics. Bioinformatics 2008.