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2006

Huttenhower, C, Troyanskaya OG. 2006. Bayesian data integration: a functional perspective.. Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. :341-51. Abstract

Myers, CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG. 2006. Finding function: evaluation methods for functional genomic data.. BMC genomics. 7:187. Abstract

Sealfon, RSG, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. 2006. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.. BMC bioinformatics. 7:443. Abstract

Huttenhower, C, Hibbs M, Myers C, Troyanskaya OG. 2006. A scalable method for integration and functional analysis of multiple microarray datasets.. Bioinformatics (Oxford, England). 22(23):2890-7. Abstract

2007

Huttenhower, C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA. 2007. Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.. BMC bioinformatics. 8:250. Abstract

Chi, A, Huttenhower C, Geer LY, Coon JJ, Syka JEP, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. 2007. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.. Proceedings of the National Academy of Sciences of the United States of America. 104(7):2193-8. Abstract

Hibbs, MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. 2007. Exploring the functional landscape of gene expression: directed search of large microarray compendia.. Bioinformatics (Oxford, England). 23(20):2692-9. Abstract

2008

Brauer, MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. 2008. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.. Molecular biology of the cell. 19(1):352-67. Abstract

Huttenhower, C, Schroeder M, Chikina MD, Troyanskaya OG. 2008. The Sleipnir library for computational functional genomics.. Bioinformatics (Oxford, England). 24(13):1559-61. Abstract

2009

Huttenhower, C, Myers CL, Hibbs MA, Troyanskaya OG. 2009. Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.. Methods in molecular biology (Clifton, N.J.). 548:273-93. Abstract

Huttenhower, C, Mehmood SO, Troyanskaya OG. 2009. Graphle: Interactive exploration of large, dense graphs.. BMC bioinformatics. 10:417. Abstract

Huttenhower, C, Mutungu TK, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA. 2009. Detailing regulatory networks through large scale data integration.. Bioinformatics (Oxford, England). 25(24):3267-74. 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

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

Hess, DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis B S, 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, 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