Shakoury-Elizeh, Minoo, John Tiedeman, Jared Rashford, Tracey Ferea, Janos Demeter, Emily Garcia, Ronda Rolfes, Patrick O Brown, David Botstein, and Caroline C Philpott. (2004) 2004. “Transcriptional Remodeling in Response to Iron Deprivation in Saccharomyces Cerevisiae.”. Mol Biol Cell 15 (3): 1233-43.

Leung, Suet Y, Xin Chen, Kent M Chu, Siu T Yuen, Jonathan Mathy, Jiafu Ji, Annie S Y Chan, et al. (2002) 2002. “Phospholipase A2 Group IIA Expression in Gastric Adenocarcinoma Is Associated With Prolonged Survival and Less Frequent Metastasis.”. Proc Natl Acad Sci U S A 99 (25): 16203-8.

Brauer, Matthew J, Alok J Saldanha, Kara Dolinski, and David Botstein. (2005) 2005. “Homeostatic Adjustment and Metabolic Remodeling in Glucose-Limited Yeast Cultures.”. Mol Biol Cell 16 (5): 2503-17.

Chen, Xin, Siu Tim Cheung, Samuel So, Sheung Tat Fan, Christopher Barry, John Higgins, Kin-Man Lai, et al. (2002) 2002. “Gene Expression Patterns in Human Liver Cancers.”. Mol Biol Cell 13 (6): 1929-39.

Cande, Jessica Doran, Yury Goltsev, and Michael S Levine. (2009) 2009. “Conservation of Enhancer Location in Divergent Insects.”. Proc Natl Acad Sci U S A 106 (34): 14414-9.

Myers, Chad L, Maitreya Dunham, S Y Kung, and Olga G Troyanskaya. (2004) 2004. “Accurate Detection of Aneuploidies in Array CGH and Gene Expression Microarray Data.”. Bioinformatics 20 (18): 3533-43.

Nielsen, Torsten O, Forrest D Hsu, John X O’Connell, Blake Gilks, Poul H B Sorensen, Sabine Linn, Robert B West, et al. (2003) 2003. “Tissue Microarray Validation of Epidermal Growth Factor Receptor and SALL2 in Synovial Sarcoma With Comparison to Tumors of Similar Histology.”. Am J Pathol 163 (4): 1449-56.

Gresham, David, Bo Curry, Alexandra Ward, Benjamin Gordon, Leonardo Brizuela, Leonid Kruglyak, and David Botstein. (2010) 2010. “Optimized Detection of Sequence Variation in Heterozygous Genomes Using DNA Microarrays With Isothermal-Melting Probes.”. Proc Natl Acad Sci U S A 107 (4): 1482-7.

Barutcuoglu, Zafer, Robert E Schapire, and Olga G Troyanskaya. (2006) 2006. “Hierarchical Multi-Label Prediction of Gene Function.”. Bioinformatics 22 (7): 830-6.

Linn, Sabine C, Rob B West, Jonathan R Pollack, Shirley Zhu, Tina Hernandez-Boussard, Torsten O Nielsen, Brian P Rubin, et al. (2003) 2003. “Gene Expression Patterns and Gene Copy Number Changes in Dermatofibrosarcoma Protuberans.”. Am J Pathol 163 (6): 2383-95.

Oliveira, Riva P, Jess Porter Abate, Kieran Dilks, Jessica Landis, Jasmine M Ashraf, Coleen T Murphy, and Keith Blackwell. (2009) 2009. “Condition-Adapted Stress and Longevity Gene Regulation by Caenorhabditis Elegans SKN-1 Nrf.”. Aging Cell 8 (5): 524-41.

Roose, Jeroen P, Maximilian Diehn, Michael G Tomlinson, Joseph Lin, Ash A Alizadeh, David Botstein, Patrick O Brown, and Arthur Weiss. (2003) 2003. “T Cell Receptor-Independent Basal Signaling via Erk and Abl Kinases Suppresses RAG Gene Expression.”. PLoS Biol 1 (2): E53.

Lee, Young-suk, Arjun Krishnan, Qian Zhu, and Olga G Troyanskaya. (2013) 2013. “Ontology-Aware Classification of Tissue and Cell-Type Signals in Gene Expression Profiles across Platforms and Technologies.”. Bioinformatics 29 (23): 3036-44.

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.

Ayroles, Julien, Brooke A Laflamme, Eric A Stone, Mariana F Wolfner, and Trudy F C Mackay. (2011) 2011. “Functional Genome Annotation of Drosophila Seminal Fluid Proteins Using Transcriptional Genetic Networks.”. Genet Res (Camb) 93 (6): 387-95.

Markowetz, Florian, and Olga G Troyanskaya. (2007) 2007. “Computational Identification of Cellular Networks and Pathways.”. Mol Biosyst 3 (7): 478-82.

Guan, Yuanfang, Maitreya Dunham, Amy A Caudy, and Olga Troyanskaya. (2010) 2010. “Systematic Planning of Genome-Scale Experiments in Poorly Studied Species.”. PLoS Comput Biol 6 (3): e1000698.

Saldanha, Alok J, Matthew J Brauer, and David Botstein. (2004) 2004. “Nutritional Homeostasis in Batch and Steady-State Culture of Yeast.”. Mol Biol Cell 15 (9): 4089-104.

Chikina, Maria D, Curtis Huttenhower, Coleen T Murphy, and Olga G Troyanskaya. (2009) 2009. “Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis Elegans.”. PLoS Comput Biol 5 (6): e1000417.

van de Rijn, Matt, Charles M Perou, Rob Tibshirani, Phillippe Haas, Olli Kallioniemi, Juha Kononen, Joachim Torhorst, et al. (2002) 2002. “Expression of Cytokeratins 17 and 5 Identifies a Group of Breast Carcinomas With Poor Clinical Outcome.”. Am J Pathol 161 (6): 1991-6.

Biemar, Frédéric, David A Nix, Jessica Piel, Brant Peterson, Matthew Ronshaugen, Victor Sementchenko, Ian Bell, Robert Manak, and Michael S Levine. (2006) 2006. “Comprehensive Identification of Drosophila Dorsal-Ventral Patterning Genes Using a Whole-Genome Tiling Array.”. Proc Natl Acad Sci U S A 103 (34): 12763-8.

Boldrick, Jennifer C, Ash A Alizadeh, Maximilian Diehn, Sandrine Dudoit, Chih Long Liu, Christopher E Belcher, David Botstein, Louis M Staudt, Patrick O Brown, and David A Relman. (2002) 2002. “Stereotyped and Specific Gene Expression Programs in Human Innate Immune Responses to Bacteria.”. Proc Natl Acad Sci U S A 99 (2): 972-7.

Troyanskaya, Olga G, Mitchell E Garber, Patrick O Brown, David Botstein, and Russ B Altman. (2002) 2002. “Nonparametric Methods for Identifying Differentially Expressed Genes in Microarray Data.”. Bioinformatics 18 (11): 1454-61.

Troyanskaya, Olga. (2007) 2007. “‘Getting Started in. ’: A Series Not to Miss.”. PLoS Comput Biol 3 (10): 1841.

Jeffrey, Stefanie S, Michael J Fero, Anne-Lise Børresen-Dale, and David Botstein. (2002) 2002. “Expression Array Technology in the Diagnosis and Treatment of Breast Cancer.”. Mol Interv 2 (2): 101-9.

Gresham, David, Maitreya Dunham, and David Botstein. (2008) 2008. “Comparing Whole Genomes Using DNA Microarrays.”. Nat Rev Genet 9 (4): 291-302.

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.

Nielsen, Torsten O, Rob B West, Sabine C Linn, Orly Alter, Margaret A Knowling, John X O’Connell, Shirley Zhu, et al. (2002) 2002. “Molecular Characterisation of Soft Tissue Tumours: A Gene Expression Study.”. Lancet 359 (9314): 1301-7.

Gresham, David, Douglas M Ruderfer, Stephen C Pratt, Joseph Schacherer, Maitreya Dunham, David Botstein, and Leonid Kruglyak. (2006) 2006. “Genome-Wide Detection of Polymorphisms at Nucleotide Resolution With a Single DNA Microarray.”. Science 311 (5769): 1932-6.

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.

McCarroll, Steven A, Coleen T Murphy, Sige Zou, Scott D Pletcher, Chen-Shan Chin, Yuh Nung Jan, Cynthia Kenyon, Cornelia I Bargmann, and Hao Li. (2004) 2004. “Comparing Genomic Expression Patterns across Species Identifies Shared Transcriptional Profile in Aging.”. Nat Genet 36 (2): 197-204.

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.

Segal, Eran, Michael Shapira, Aviv Regev, Dana Pe’er, David Botstein, Daphne Koller, and Nir Friedman. (2003) 2003. “Module Networks: Identifying Regulatory Modules and Their Condition-Specific Regulators from Gene Expression Data.”. Nat Genet 34 (2): 166-76.

Schacherer, Joseph, Douglas M Ruderfer, David Gresham, Kara Dolinski, David Botstein, and Leonid Kruglyak. 2007. “Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces Cerevisiae Strains.”. PLoS One 2 (3): e322.

Shyamsundar, Radha, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, and Jonathan R Pollack. 2005. “A DNA Microarray Survey of Gene Expression in Normal Human Tissues.”. Genome Biol 6 (3): R22.

Dunham, Maitreya, Hassan Badrane, Tracy Ferea, Julian Adams, Patrick O Brown, Frank Rosenzweig, and David Botstein. (2002) 2002. “Characteristic Genome Rearrangements in Experimental Evolution of Saccharomyces Cerevisiae.”. Proc Natl Acad Sci U S A 99 (25): 16144-9.

Hong, Joung-Woo, David A Hendrix, and Michael S Levine. (2008) 2008. “Shadow Enhancers As a Source of Evolutionary Novelty.”. Science 321 (5894): 1314.

Troyanskaya, O, M Cantor, G Sherlock, P Brown, T Hastie, R Tibshirani, D Botstein, and Russ B Altman. (2001) 2001. “Missing Value Estimation Methods for DNA Microarrays.”. Bioinformatics 17 (6): 520-5.

Yoshimoto, Hiroyuki, Kirstie Saltsman, Audrey P Gasch, Hong Xia Li, Nobuo Ogawa, David Botstein, Patrick O Brown, and Martha S Cyert. (2002) 2002. “Genome-Wide Analysis of Gene Expression Regulated by the Calcineurin Crz1p Signaling Pathway in Saccharomyces Cerevisiae.”. J Biol Chem 277 (34): 31079-88.

Chang, Howard Y, Jen-Tsan Chi, Sandrine Dudoit, Chanda Bondre, Matt van de Rijn, David Botstein, and Patrick O Brown. (2002) 2002. “Diversity, Topographic Differentiation, and Positional Memory in Human Fibroblasts.”. Proc Natl Acad Sci U S A 99 (20): 12877-82.

Pollack, Jonathan R, Matt van de Rijn, and David Botstein. (2002) 2002. “Challenges in Developing a Molecular Characterization of Cancer.”. Semin Oncol 29 (3): 280-5.

Hughes, Kimberly A, Julien Ayroles, Melissa M Reedy, Jenny M Drnevich, Kevin C Rowe, Elizabeth A Ruedi, Carla E Cáceres, and Ken N Paige. (2006) 2006. “Segregating Variation in the Transcriptome: Cis Regulation and Additivity of Effects.”. Genetics 173 (3): 1347-55.

Trotter, Eleanor W, Camilla M-F Kao, Ludmilla Berenfeld, David Botstein, Gregory A Petsko, and Joseph Gray V. (2002) 2002. “Misfolded Proteins Are Competent to Mediate a Subset of the Responses to Heat Shock in Saccharomyces Cerevisiae.”. J Biol Chem 277 (47): 44817-25.

Diehn, Maximilian, Ramona Bhattacharya, David Botstein, and Patrick O Brown. (2006) 2006. “Genome-Scale Identification of Membrane-Associated Human MRNAs.”. PLoS Genet 2 (1): e11.

Zhao, Hongjuan, Michael L Whitfield, Tong Xu, David Botstein, and James D Brooks. (2004) 2004. “Diverse Effects of Methylseleninic Acid on the Transcriptional Program of Human Prostate Cancer Cells.”. Mol Biol Cell 15 (2): 506-19.

Smith, Kevin S, Sumit K Chanda, Merel Lingbeek, Douglas T Ross, David Botstein, Maarten van Lohuizen, and Michael L Cleary. (2003) 2003. “Bmi-1 Regulation of INK4A-ARF Is a Downstream Requirement for Transformation of Hematopoietic Progenitors by E2a-Pbx1.”. Mol Cell 12 (2): 393-400.

Stathopoulos, Angelike, Madeleine Van Drenth, Albert Erives, Michele Markstein, and Michael Levine. (2002) 2002. “Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo.”. Cell 111 (5): 687-701.

Gresham, David, Michael M Desai, Cheryl M Tucker, Harry T Jenq, Dave A Pai, Alexandra Ward, Christopher G DeSevo, David Botstein, and Maitreya Dunham. (2008) 2008. “The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast.”. PLoS Genet 4 (12): e1000303.

Pollack, Jonathan R, Therese Sørlie, Charles M Perou, Christian A Rees, Stefanie S Jeffrey, Per E Lonning, Robert Tibshirani, David Botstein, Anne-Lise Børresen-Dale, and Patrick O Brown. (2002) 2002. “Microarray Analysis Reveals a Major Direct Role of DNA Copy Number Alteration in the Transcriptional Program of Human Breast Tumors.”. Proc Natl Acad Sci U S A 99 (20): 12963-8.

Rees, Christian A, Janos Demeter, John C Matese, David Botstein, and Gavin Sherlock. (2004) 2004. “GeneXplorer: An Interactive Web Application for Microarray Data Visualization and Analysis.”. BMC Bioinformatics 5: 141.