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Curtis Huttenhower, PhD


  • 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.
  • 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 May(5).
  • 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 May(5).
  • Glass K, Huttenhower C, Quackenbush J, Yuan GC.Passing messages between biological networks to refine predicted interactions.PLoS ONE. 2013;8(5):e64832.
  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC.A tiered hidden Markov model characterizes multi-scale chromatin states.Genomics. 2013 Apr 6.
  • 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 Apr;31(4):304-8.
  • 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.
  • 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):6136-6146.
  • 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.
  • 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 1;39(6):1967-79.
  • 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.
  • 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:Unit6.11.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Huttenhower C, Hofmann O.A quick guide to large-scale genomic data mining.PLoS Comput. Biol. 2010;6(5):e1000779.
  • Huttenhower C, Mehmood SO, Troyanskaya OG.Graphle: Interactive exploration of large, dense graphs.BMC Bioinformatics. 2009;10:417.
  • 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.
  • 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.
  • 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.
  • 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..
  • 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.
  • 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..
  • 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..
  • 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..
  • Huttenhower C, Troyanskaya OG.Assessing the functional structure of genomic data.Bioinformatics..
  • Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG.The Sleipnir library for computational functional genomics.Bioinformatics..
  • 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..
  • Huttenhower C, Hibbs M, Myers C, Troyanskaya OG.A scalable method for integration and functional analysis of multiple microarray datasets.Bioinformatics..