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.

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.

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.

Myers, Chad L, Xing Chen, and Olga G Troyanskaya. 2005. “Visualization-Based Discovery and Analysis of Genomic Aberrations in Microarray Data.”. BMC Bioinformatics 6: 146.

Sorlie, Therese, Robert Tibshirani, Joel Parker, Trevor Hastie, J S Marron, Andrew Nobel, Shibing Deng, et al. (2003) 2003. “Repeated Observation of Breast Tumor Subtypes in Independent Gene Expression Data Sets.”. Proc Natl Acad Sci U S A 100 (14): 8418-23.

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.

Murphy, Coleen T, Steven A McCarroll, Cornelia I Bargmann, Andrew Fraser, Ravi S Kamath, Julie Ahringer, Hao Li, and Cynthia Kenyon. (2003) 2003. “Genes That Act Downstream of DAF-16 to Influence the Lifespan of Caenorhabditis Elegans.”. Nature 424 (6946): 277-83.

Desai, Keyur H, Chuen Seng Tan, Jeffrey T Leek, Ronald Maier V, Ronald G Tompkins, John D Storey, and Inflammation and the Host Response to Injury Large-Scale Collaborative Research Program. (2011) 2011. “Dissecting Inflammatory Complications in Critically Injured Patients by Within-Patient Gene Expression Changes: A Longitudinal Clinical Genomics Study.”. PLoS Med 8 (9): e1001093.

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.

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.

Baryshnikova, Anastasia, Michael Costanzo, Yungil Kim, Huiming Ding, Judice Koh, Kiana Toufighi, Ji-Young Youn, et al. (2010) 2010. “Quantitative Analysis of Fitness and Genetic Interactions in Yeast on a Genome Scale.”. Nat Methods 7 (12): 1017-24.

Bloom, Joshua S, Zia Khan, Leonid Kruglyak, Mona Singh, and Amy A Caudy. 2009. “Measuring Differential Gene Expression by Short Read Sequencing: Quantitative Comparison to 2-Channel Gene Expression Microarrays.”. BMC Genomics 10: 221.

Alter, Orly, Patrick O Brown, and David Botstein. (2003) 2003. “Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Data Sets of Two Different Organisms.”. Proc Natl Acad Sci U S A 100 (6): 3351-6.

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.

Barutcuoglu, Zafer, Edoardo M Airoldi, Vanessa Dumeaux, Robert E Schapire, and Olga G Troyanskaya. (2009) 2009. “Aneuploidy Prediction and Tumor Classification With Heterogeneous Hidden Conditional Random Fields.”. Bioinformatics 25 (10): 1307-13.

Chen, Xin, Suet Y Leung, Siu T Yuen, Kent-Man Chu, Jiafu Ji, Rui Li, Annie S Y Chan, et al. (2003) 2003. “Variation in Gene Expression Patterns in Human Gastric Cancers.”. Mol Biol Cell 14 (8): 3208-15.

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

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

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.

Goltsev, Yury, Gustavo L Rezende, Karen Vranizan, Greg Lanzaro, Denise Valle, and Michael Levine. (2009) 2009. “Developmental and Evolutionary Basis for Drought Tolerance of the Anopheles Gambiae Embryo.”. Dev Biol 330 (2): 462-70.

Ayroles, Julien, and Greg Gibson. 2006. “Analysis of Variance of Microarray Data.”. Methods Enzymol 411: 214-33.

Novoradovskaya, Natalia, Michael L Whitfield, Lee S Basehore, Alexey Novoradovsky, Robert Pesich, Jerry Usary, Mehmet Karaca, et al. (2004) 2004. “Universal Reference RNA As a Standard for Microarray Experiments.”. BMC Genomics 5 (1): 20.

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.

Wang, Wei, Michael Cherry, Yigal Nochomovitz, Emmitt Jolly, David Botstein, and Hao Li. (2005) 2005. “Inference of Combinatorial Regulation in Yeast Transcriptional Networks: A Case Study of Sporulation.”. Proc Natl Acad Sci U S A 102 (6): 1998-2003.

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.

Huttenhower, Curtis, Tsheko Mutungu, Natasha Indik, Woongcheol Yang, Mark Schroeder, Joshua J Forman, Olga G Troyanskaya, and Hilary A Coller. (2009) 2009. “Detailing Regulatory Networks through Large Scale Data Integration.”. Bioinformatics 25 (24): 3267-74.

Hess, David C, Wenyun Lu, Joshua D Rabinowitz, and David Botstein. (2006) 2006. “Ammonium Toxicity and Potassium Limitation in Yeast.”. PLoS Biol 4 (11): e351.

Christiaen, Lionel, Brad Davidson, Takeshi Kawashima, Weston Powell, Hector Nolla, Karen Vranizan, and Michael Levine. (2008) 2008. “The Transcription Migration Interface in Heart Precursors of Ciona Intestinalis.”. Science 320 (5881): 1349-52.

Persikov, Anton, V, Robert Osada, and Mona Singh. (2009) 2009. “Predicting DNA Recognition by Cys2His2 Zinc Finger Proteins.”. Bioinformatics 25 (1): 22-9.

Kocher, Sarah D, Julien Ayroles, Eric A Stone, and Christina M Grozinger. 2010. “Individual Variation in Pheromone Response Correlates With Reproductive Traits and Brain Gene Expression in Worker Honey Bees.”. PLoS One 5 (2): e9116.

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.

Goodliffe, Julie M, Michael D Cole, and Eric Wieschaus. 2007. “Coordinated Regulation of Myc Trans-Activation Targets by Polycomb and the Trithorax Group Protein Ash1.”. BMC Mol Biol 8: 40.

Gresham, David, Renata Usaite, Susanne Manuela Germann, Michael Lisby, David Botstein, and Birgitte Regenberg. (2010) 2010. “Adaptation to Diverse Nitrogen-Limited Environments by Deletion or Extrachromosomal Element Formation of the GAP1 Locus.”. Proc Natl Acad Sci U S A 107 (43): 18551-6.

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.

Goodliffe, Julie M, Eric Wieschaus, and Michael D Cole. (2005) 2005. “Polycomb Mediates Myc Autorepression and Its Transcriptional Control of Many Loci in Drosophila.”. Genes Dev 19 (24): 2941-6.

Whitfield, Michael L, Gavin Sherlock, Alok J Saldanha, John I Murray, Catherine A Ball, Karen E Alexander, John C Matese, et al. (2002) 2002. “Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors.”. Mol Biol Cell 13 (6): 1977-2000.

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.

Slavov, Nikolai, Edoardo M Airoldi, Alexander van Oudenaarden, and David Botstein. (2012) 2012. “A Conserved Cell Growth Cycle Can Account for the Environmental Stress Responses of Divergent Eukaryotes.”. Mol Biol Cell 23 (10): 1986-97.

Chikina, Maria D, and Olga G Troyanskaya. 2011. “Accurate Quantification of Functional Analogy Among Close Homologs.”. PLoS Comput Biol 7 (2): e1001074.

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.