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A
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
B
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
C
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
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
H
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, 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
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
Huttenhower, C, Troyanskaya OG.  2008.  Assessing the functional structure of genomic data.. Bioinformatics (Oxford, England). 24(13):i330-8. 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
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
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
Huttenhower, C, Schroeder M, Chikina MD, Troyanskaya OG.  2008.  The Sleipnir library for computational functional genomics.. Bioinformatics (Oxford, England). 24(13):1559-61. Abstract
Huttenhower, C, Mehmood SO, Troyanskaya OG.  2009.  Graphle: Interactive exploration of large, dense graphs.. BMC bioinformatics. 10:417. 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
Huttenhower, C, Troyanskaya OG.  2006.  Bayesian data integration: a functional perspective.. Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. :341-51. Abstract
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
M
Myers, CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG.  2006.  Finding function: evaluation methods for functional genomic data.. BMC genomics. 7:187. Abstract
S
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