Ronen, Michal, and David Botstein. (2006) 2006. “Transcriptional Response of Steady-State Yeast Cultures to Transient Perturbations in Carbon Source.”. Proc Natl Acad Sci U S A 103 (2): 389-94. Reference Link
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. Reference Link
Lossos, Izidore S, Debra K Czerwinski, Ash A Alizadeh, Mark A Wechser, Rob Tibshirani, David Botstein, and Ronald Levy. (2004) 2004. “Prediction of Survival in Diffuse Large-B-Cell Lymphoma Based on the Expression of Six Genes.”. N Engl J Med 350 (18): 1828-37. Reference Link
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. Reference Link
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. Reference Link
Chang, Howard Y, Julie B Sneddon, Ash A Alizadeh, Ruchira Sood, Rob B West, Kelli Montgomery, Jen-Tsan Chi, Matt van de Rijn, David Botstein, and Patrick O Brown. (2004) 2004. “Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities Between Tumors and Wounds.”. PLoS Biol 2 (2): E7. Reference Link
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. Reference Link
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. Reference Link
Sayama, Koichi, Maximilian Diehn, Kentaro Matsuda, Carolina Lunderius, Mindy Tsai, See-Ying Tam, David Botstein, Patrick O Brown, and Stephen J Galli. (2002) 2002. “Transcriptional Response of Human Mast Cells Stimulated via the Fc(epsilon)RI and Identification of Mast Cells As a Source of IL-11.”. BMC Immunol 3: 5. Reference Link
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. Reference Link
Airoldi, Edoardo M, Curtis Huttenhower, David Gresham, Charles Lu, Amy A Caudy, Maitreya Dunham, James R Broach, David Botstein, and Olga G Troyanskaya. (2009) 2009. “Predicting Cellular Growth from Gene Expression Signatures.”. PLoS Comput Biol 5 (1): e1000257. Reference Link
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. Reference Link
Boer, Viktor M, Christopher A Crutchfield, Patrick H Bradley, David Botstein, and Joshua D Rabinowitz. (2010) 2010. “Growth-Limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations.”. Mol Biol Cell 21 (1): 198-211. Reference Link
Liang, Yu, Maximilian Diehn, Nathan Watson, Andrew W Bollen, Ken D Aldape, Kelly Nicholas, Kathleen R Lamborn, et al. (2005) 2005. “Gene Expression Profiling Reveals Molecularly and Clinically Distinct Subtypes of Glioblastoma Multiforme.”. Proc Natl Acad Sci U S A 102 (16): 5814-9. Reference Link
Murray, John Isaac, Michael L Whitfield, Nathan D Trinklein, Richard M Myers, Patrick O Brown, and David Botstein. (2004) 2004. “Diverse and Specific Gene Expression Responses to Stresses in Cultured Human Cells.”. Mol Biol Cell 15 (5): 2361-74. Reference Link
Dolinski, Kara, and David Botstein. (2005) 2005. “Changing Perspectives in Yeast Research Nearly a Decade After the Genome Sequence.”. Genome Res 15 (12): 1611-9. Reference Link
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. Reference Link
Lu, Charles, Matthew J Brauer, and David Botstein. (2009) 2009. “Slow Growth Induces Heat-Shock Resistance in Normal and Respiratory-Deficient Yeast.”. Mol Biol Cell 20 (3): 891-903. Reference Link
Ranade, Koustubh, Eric Jorgenson, Wayne H-H Sheu, Dee Pei, Chao Agnes Hsiung, Fu-tien Chiang, Yii-Der I Chen, et al. (2002) 2002. “A Polymorphism in the Beta1 Adrenergic Receptor Is Associated With Resting Heart Rate.”. Am J Hum Genet 70 (4): 935-42. Reference Link
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. Reference Link
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. Reference Link
Lapointe, Jacques, Chunde Li, John P Higgins, Matt van de Rijn, Eric Bair, Kelli Montgomery, Michelle Ferrari, et al. (2004) 2004. “Gene Expression Profiling Identifies Clinically Relevant Subtypes of Prostate Cancer.”. Proc Natl Acad Sci U S A 101 (3): 811-6. Reference Link
Shapira, Michael, Eran Segal, and David Botstein. (2004) 2004. “Disruption of Yeast Forkhead-Associated Cell Cycle Transcription by Oxidative Stress.”. Mol Biol Cell 15 (12): 5659-69. Reference Link
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. Reference Link
Welch, Aaron Z, Patrick A Gibney, David Botstein, and Douglas E Koshland. (2013) 2013. “TOR and RAS Pathways Regulate Desiccation Tolerance in Saccharomyces Cerevisiae.”. Mol Biol Cell 24 (2): 115-28. Reference Link
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. Reference Link
Uhlmann, Wendy R, Robin Bennett, Jeffrey R Botkin, David Botstein, Joann A Boughman, Aravinda Chakravarti, Ellen Wright Clayton, et al. (2003) 2003. “Planning the Genome institute’s Future.”. Science 299 (5612): 1515; author reply 1515. Reference Link
Tu, I-Ping, Marci Schaner, Maximilian Diehn, Branimir I Sikic, Patrick O Brown, David Botstein, and Michael J Fero. (2004) 2004. “A Method for Detecting and Correcting Feature Misidentification on Expression Microarrays.”. BMC Genomics 5: 64. Reference Link
Diehn, Maximilian, Ash A Alizadeh, Oliver J Rando, Chih Long Liu, Kryn Stankunas, David Botstein, Gerald R Crabtree, and Patrick O Brown. (2002) 2002. “Genomic Expression Programs and the Integration of the CD28 Costimulatory Signal in T Cell Activation.”. Proc Natl Acad Sci U S A 99 (18): 11796-801. Reference Link
Sørlie, Therese, Charles M Perou, Cheng Fan, Stephanie Geisler, Turid Aas, Andrew Nobel, Gun Anker, et al. (2006) 2006. “Gene Expression Profiles Do Not Consistently Predict the Clinical Treatment Response in Locally Advanced Breast Cancer.”. Mol Cancer Ther 5 (11): 2914-8. Reference Link
Botstein, David, and Neil Risch. (2003) 2003. “Discovering Genotypes Underlying Human Phenotypes: Past Successes for Mendelian Disease, Future Approaches for Complex Disease.”. Nat Genet 33 Suppl: 228-37. Reference Link
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. Reference Link
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. Reference Link
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). Reference Link
Gibney, Patrick A, Mark J Hickman, Patrick H Bradley, John C Matese, and David Botstein. (2013) 2013. “Phylogenetic Portrait of the Saccharomyces Cerevisiae Functional Genome.”. G3 (Bethesda) 3 (8): 1335-40. Reference Link
Slavov, Nikolai, Joanna Macinskas, Amy A Caudy, and David Botstein. (2011) 2011. “Metabolic Cycling Without Cell Division Cycling in Respiring Yeast.”. Proc Natl Acad Sci U S A 108 (47): 19090-5. Reference Link
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. Reference Link
Schaner, Marci E, Douglas T Ross, Giuseppe Ciaravino, Therese Sorlie, Olga Troyanskaya, Maximilian Diehn, Yan C Wang, et al. (2003) 2003. “Gene Expression Patterns in Ovarian Carcinomas.”. Mol Biol Cell 14 (11): 4376-86. Reference Link
Zhao, Hongjuan, Anita Langerød, Youngran Ji, Kent W Nowels, Jahn M Nesland, Rob Tibshirani, Ida K Bukholm, et al. (2004) 2004. “Different Gene Expression Patterns in Invasive Lobular and Ductal Carcinomas of the Breast.”. Mol Biol Cell 15 (6): 2523-36. Reference Link
Troyanskaya, Olga G, Kara Dolinski, Art B Owen, Russ B Altman, and David Botstein. (2003) 2003. “A Bayesian Framework for Combining Heterogeneous Data Sources for Gene Function Prediction (in Saccharomyces cerevisiae).”. Proc Natl Acad Sci U S A 100 (14): 8348-53. Reference Link
Lang, Gregory I, and David Botstein. 2011. “A Test of the Coordinated Expression Hypothesis for the Origin and Maintenance of the GAL Cluster in Yeast.”. PLoS One 6 (9): e25290. Reference Link
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. Reference Link
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. Reference Link
Silverman, Sanford J, Allegra A Petti, Nikolai Slavov, Lance Parsons, Ryan Briehof, Stephan Y Thiberge, Daniel Zenklusen, et al. (2010) 2010. “Metabolic Cycling in Single Yeast Cells from Unsynchronized Steady-State Populations Limited on Glucose or Phosphate.”. Proc Natl Acad Sci U S A 107 (15): 6946-51. Reference Link
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. Reference Link
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. Reference Link
Slavov, Nikolai, and David Botstein. (2013) 2013. “Decoupling Nutrient Signaling from Growth Rate Causes Aerobic Glycolysis and Deregulation of Cell Size and Gene Expression.”. Mol Biol Cell 24 (2): 157-68. Reference Link
Wingreen, Ned, and David Botstein. (2006) 2006. “Back to the Future: Education for Systems-Level Biologists.”. Nat Rev Mol Cell Biol 7 (11): 829-32. Reference Link
Botstein, David. (2010) 2010. “Technological Innovation Leads to Fundamental Understanding in Cell Biology.”. Mol Biol Cell 21 (22): 3791-2. Reference Link
Weng, Shuai, Qing Dong, Rama Balakrishnan, Karen R Christie, Maria Costanzo, Kara Dolinski, Selina S Dwight, et al. (2003) 2003. “Saccharomyces Genome Database (SGD) Provides Biochemical and Structural Information for Budding Yeast Proteins.”. Nucleic Acids Res 31 (1): 216-8. Reference Link