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2012
Waldron, L, Coller HA, Huttenhower C.  2012.  Integrative approaches for microarray data analysis.. Methods in molecular biology (Clifton, N.J.). 802:157-82. Abstract
2011
Sczesnak, A, Segata N, Qin X, Gevers D, Petrosino JF, Huttenhower C, Littman DR, Ivanov II.  2011.  The genome of Th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.. Cell host & microbe. 10(3):260-72. Abstract
Kostic, AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J et al..  2011.  Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.. Genome research. Abstract
Livstone, MS, Oughtred R, Heinicke S, Vernot B, Huttenhower C, Durand D, Dolinski K.  2011.  Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD).. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 6:Unit6.11. Abstract
Ballal, SA, Gallini CA, Segata N, Huttenhower C, Garrett WS.  2011.  Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts.. Cellular microbiology. Abstract
Morikawa, T, Baba Y, Yamauchi M, Kuchiba A, Nosho K, Shima K, Tanaka N, Huttenhower C, Frank DA, Fuchs CS et al..  2011.  STAT3 Expression, Molecular Features, Inflammation Patterns and Prognosis in a Database of 724 Colorectal Cancers.. Clinical cancer research : an official journal of the American Association for Cancer Research. Abstract
Wardwell, LH, Huttenhower C, Garrett WS.  2011.  Current concepts of the intestinal microbiota and the pathogenesis of infection.. Current infectious disease reports. 13(1):28-34. Abstract
Adams, D, Berger B, Harismendy O, Huttenhower C, Liu SX, Myers C, Oshlack A, Rinn J, Walhout M.  2011.  Genomics in 2011: challenges and opportunities.. Genome biology. 12(12):137. Abstract
Waldron, L, Pintilie M, Tsao M-S, Shepherd FA, Huttenhower C, Jurisica I.  2011.  Optimized application of penalized regression methods to diverse genomic data.. Bioinformatics (Oxford, England). 27(24):3399-406. Abstract
Huttenhower, C.  2011.  Computational biology: plus c'est la même chose, plus ça change.. Genome biology. 12(8):307. Abstract
Segata, N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C.  2011.  Metagenomic biomarker discovery and explanation.. Genome biology. 12(6):R60. Abstract
Segata, N, Huttenhower C.  2011.  Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies.. PloS one. 6(9):e24704. Abstract
2010
Sathirapongsasuti, FJ, Sathira N, Suzuki Y, Huttenhower C, Sugano S.  2010.  Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing.. Nucleic acids research. Abstract
Park, CY, Hess DC, Huttenhower C, Troyanskaya OG.  2010.  Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.. PLoS computational biology. 6(11):e1001009. Abstract
Baba, Y, Nosho K, Shima K, Huttenhower C, Tanaka N, Hazra A, Giovannucci EL, Fuchs CS, Ogino S.  2010.  Hypomethylation of the IGF2 DMR in Colorectal Tumors, Detected by Bisulfite Pyrosequencing, is Associated with Poor Prognosis.. Gastroenterology. Abstract
Tanaka, N, Huttenhower C, Nosho K, Baba Y, Shima K, Quackenbush J, Haigis KM, Giovannucci E, Fuchs CS, Ogino S.  2010.  Novel application of structural equation modeling to correlation structure analysis of CpG island methylation in colorectal cancer.. The American journal of pathology. 177(6):2731-40. Abstract
Baba, Y, Huttenhower C, Nosho K, Tanaka N, Shima K, Hazra A, Schernhammer ES, Hunter DJ, Giovannucci EL, Fuchs CS et al..  2010.  Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors.. Molecular cancer. 9:125. Abstract
Pop, A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG.  2010.  Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.. BMC systems biology. 4:180. Abstract
Huttenhower, C, Hofmann O.  2010.  A quick guide to large-scale genomic data mining.. PLoS computational biology. 6(5):e1000779.
2009
Huttenhower, C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG.  2009.  The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.. Bioinformatics (Oxford, England). 25(18):2404-10. Abstract
Hess, DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C et al..  2009.  Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.. PLoS genetics. 5(3):e1000407. Abstract
Hibbs, MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG.  2009.  Directing experimental biology: a case study in mitochondrial biogenesis.. PLoS computational biology. 5(3):e1000322. Abstract
Huttenhower, C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG.  2009.  Exploring the human genome with functional maps.. Genome research. 19(6):1093-106. Abstract
Chikina, MD, Huttenhower C, Murphy CT, Troyanskaya OG.  2009.  Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.. PLoS computational biology. 5(6):e1000417. Abstract
Airoldi, EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG.  2009.  Predicting cellular growth from gene expression signatures.. PLoS computational biology. 5(1):e1000257. Abstract