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Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis B, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA.  2009.  Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genetics. 5: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: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. 19:1093–106. 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. 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. 23:2692–9. 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, Hibbs MA, Myers CL, Troyanskaya OG.  2006.  A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics. 22:2890–7. 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