Hibbs, Matthew A, David C Hess, Chad L Myers, Curtis Huttenhower, Kai Li, and Olga G Troyanskaya. (2007) 2007. “Exploring the Functional Landscape of Gene Expression: Directed Search of Large Microarray Compendia.”. Bioinformatics 23 (20): 2692-9.

Hibbs, Matthew A, Nathaniel C Dirksen, Kai Li, and Olga G Troyanskaya. 2005. “Visualization Methods for Statistical Analysis of Microarray Clusters.”. BMC Bioinformatics 6: 115.

Myers, Chad L, and Olga G Troyanskaya. (2007) 2007. “Context-Sensitive Data Integration and Prediction of Biological Networks.”. Bioinformatics 23 (17): 2322-30.

Gollub, Jeremy, Catherine A Ball, Gail Binkley, Janos Demeter, David B Finkelstein, Joan M Hebert, Tina Hernandez-Boussard, et al. (2003) 2003. “The Stanford Microarray Database: Data Access and Quality Assessment Tools.”. Nucleic Acids Res 31 (1): 94-6.

DiMaggio, Peter A, Scott R McAllister, Christodoulos A Floudas, Xiao-Jiang Feng, Joshua D Rabinowitz, and Herschel A Rabitz. 2008. “Biclustering via Optimal Re-Ordering of Data Matrices in Systems Biology: Rigorous Methods and Comparative Studies.”. BMC Bioinformatics 9: 458.

Diehn, Maximilian, Gavin Sherlock, Gail Binkley, Heng Jin, John C Matese, Tina Hernandez-Boussard, Christian A Rees, et al. (2003) 2003. “SOURCE: A Unified Genomic Resource of Functional Annotations, Ontologies, and Gene Expression Data.”. Nucleic Acids Res 31 (1): 219-23.

Huttenhower, Curtis, Mark Schroeder, Maria D Chikina, and Olga G Troyanskaya. (2008) 2008. “The Sleipnir Library for Computational Functional Genomics.”. Bioinformatics 24 (13): 1559-61.

Huttenhower, Curtis, Matt Hibbs, Chad Myers, and Olga G Troyanskaya. (2006) 2006. “A Scalable Method for Integration and Functional Analysis of Multiple Microarray Datasets.”. Bioinformatics 22 (23): 2890-7.

Dwight, Selina S, Rama Balakrishnan, Karen R Christie, Maria C Costanzo, Kara Dolinski, Stacia R Engel, Becket Feierbach, et al. (2004) 2004. “Saccharomyces Genome Database: Underlying Principles and Organisation.”. Brief Bioinform 5 (1): 9-22.

Christie, Karen R, Shuai Weng, Rama Balakrishnan, Maria C Costanzo, Kara Dolinski, Selina S Dwight, Stacia R Engel, et al. (2004) 2004. “Saccharomyces Genome Database (SGD) Provides Tools to Identify and Analyze Sequences from Saccharomyces Cerevisiae and Related Sequences from Other Organisms.”. Nucleic Acids Res 32 (Database issue).

Dwight, Selina S, Midori A Harris, Kara Dolinski, Catherine A Ball, Gail Binkley, Karen R Christie, Dianna G Fisk, et al. (2002) 2002. “Saccharomyces Genome Database (SGD) Provides Secondary Gene Annotation Using the Gene Ontology (GO).”. Nucleic Acids Res 30 (1): 69-72.

Engel, Stacia R, Rama Balakrishnan, Gail Binkley, Karen R Christie, Maria C Costanzo, Selina S Dwight, Dianna G Fisk, et al. (2010) 2010. “Saccharomyces Genome Database Provides Mutant Phenotype Data.”. Nucleic Acids Res 38 (Database issue).

Troyanskaya, Olga G. (2005) 2005. “Putting Microarrays in a Context: Integrated Analysis of Diverse Biological Data.”. Brief Bioinform 6 (1): 34-43.

Tkačik, Gašper, Aleksandra M Walczak, and William Bialek. (2012) 2012. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.”. Phys Rev E Stat Nonlin Soft Matter Phys 85 (4 Pt 1): 041903.

Troyanskaya, Olga G. 2007. “Integrated Analysis of Microarray Results.”. Methods Mol Biol 382: 429-37.

Boyle, Elizabeth I, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, Michael Cherry, and Gavin Sherlock. (2004) 2004. “GO::TermFinder--Open Source Software for Accessing Gene Ontology Information and Finding Significantly Enriched Gene Ontology Terms Associated With a List of Genes.”. Bioinformatics 20 (18): 3710-5.

Sealfon, Rachel S G, Matthew A Hibbs, Curtis Huttenhower, Chad L Myers, and Olga G Troyanskaya. 2006. “GOLEM: An Interactive Graph-Based Gene-Ontology Navigation and Analysis Tool.”. BMC Bioinformatics 7: 443.

Consortium, Gene Ontology. (2010) 2010. “The Gene Ontology in 2010: Extensions and Refinements.”. Nucleic Acids Res 38 (Database issue).