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Trinklein, Nathan D, John I Murray, Sara J Hartman, David Botstein, and Richard M Myers. (2004) 2004. “The Role of Heat Shock Transcription Factor 1 in the Genome-Wide Regulation of the Mammalian Heat Shock Response.”. Mol Biol Cell 15 (3): 1254-61.

Huttenhower, Curtis, Avi I Flamholz, Jessica N Landis, Sauhard Sahi, Chad L Myers, Kellen L Olszewski, Matthew A Hibbs, Nathan O Siemers, Olga G Troyanskaya, and Hilary A Coller. 2007. “Nearest Neighbor Networks: Clustering Expression Data Based on Gene Neighborhoods.”. BMC Bioinformatics 8: 250.

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.

Wyart, Matthieu, David Botstein, and Ned S Wingreen. 2010. “Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data.”. PLoS Comput Biol 6 (11): e1000979.

Guan, Yuanfang, Maitreya Dunham, Olga G Troyanskaya, and Amy A Caudy. 2013. “Comparative Gene Expression Between Two Yeast Species.”. BMC Genomics 14: 33.

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.

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.

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.

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.

Chi, Jen-Tsan, Howard Y Chang, Guttorm Haraldsen, Frode L Jahnsen, Olga G Troyanskaya, Dustin S Chang, Zhen Wang, et al. (2003) 2003. “Endothelial Cell Diversity Revealed by Global Expression Profiling.”. Proc Natl Acad Sci U S A 100 (19): 10623-8.

Petti, Allegra A, Scott McIsaac, Olivia Ho-Shing, Harmen J Bussemaker, and David Botstein. (2012) 2012. “Combinatorial Control of Diverse Metabolic and Physiological Functions by Transcriptional Regulators of the Yeast Sulfur Assimilation Pathway.”. Mol Biol Cell 23 (15): 3008-24.

Bohen, Sean P, Olga G Troyanskaya, Orly Alter, Roger Warnke, David Botstein, Patrick O Brown, and Ronald Levy. (2003) 2003. “Variation in Gene Expression Patterns in Follicular Lymphoma and the Response to Rituximab.”. Proc Natl Acad Sci U S A 100 (4): 1926-30.

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.

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.

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.

Christiaen, Lionel, Eileen Wagner, Weiyang Shi, and Michael Levine. (2009) 2009. “Electroporation of Transgenic DNAs in the Sea Squirt Ciona.”. Cold Spring Harb Protoc 2009 (12): pdb.prot5345.

Papatsenko, Dmitri, Michael Levine, and Yury Goltsev. 2011. “Clusters of Temporal Discordances Reveal Distinct Embryonic Patterning Mechanisms in Drosophila and Anopheles.”. PLoS Biol 9 (1): e1000584.

De Renzis, Stefano, Olivier Elemento, Saeed Tavazoie, and Eric F Wieschaus. (2007) 2007. “Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo.”. PLoS Biol 5 (5): e117.

Khan, Zia, Joshua S Bloom, Sasan Amini, Mona Singh, David H Perlman, Amy A Caudy, and Leonid Kruglyak. 2012. “Quantitative Measurement of Allele-Specific Protein Expression in a Diploid Yeast Hybrid by LC-MS.”. Mol Syst Biol 8: 602.

Stone, Eric A, and Julien Ayroles. (2009) 2009. “Modulated Modularity Clustering As an Exploratory Tool for Functional Genomic Inference.”. PLoS Genet 5 (5): e1000479.

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.

Chen, Lin S, and John D Storey. (2008) 2008. “Eigen-R2 for Dissecting Variation in High-Dimensional Studies.”. Bioinformatics 24 (19): 2260-2.

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.

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.

Morrison, Alexander H, Martin Scheeler, Julien Dubuis, and Thomas Gregor. (2012) 2012. “Quantifying the Bicoid Morphogen Gradient in Living Fly Embryos.”. Cold Spring Harb Protoc 2012 (4): 398-406.

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.

Lakhina, Vanisha, Rachel Arey, Rachel Kaletsky, Amanda Kauffman, Geneva Stein, William Keyes, Daniel Xu, and Coleen T Murphy. (2015) 2015. “Genome-Wide Functional Analysis of CREB Long-Term Memory-Dependent Transcription Reveals Distinct Basal and Memory Gene Expression Programs.”. Neuron 85 (2): 330-45.

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.

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.

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.

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

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.

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.

Garber, M E, O G Troyanskaya, K Schluens, S Petersen, Z Thaesler, M Pacyna-Gengelbach, M van de Rijn, et al. (2001) 2001. “Diversity of Gene Expression in Adenocarcinoma of the Lung.”. Proc Natl Acad Sci U S A 98 (24): 13784-9.

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

Edwards, Alexis C, Julien Ayroles, Eric A Stone, Mary Anna Carbone, Richard F Lyman, and Trudy F C Mackay. 2009. “A Transcriptional Network Associated With Natural Variation in Drosophila Aggressive Behavior.”. Genome Biol 10 (7): R76.

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.

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.

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.

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.

Dubuis, Julien, Reba Samanta, and Thomas Gregor. 2013. “Accurate Measurements of Dynamics and Reproducibility in Small Genetic Networks.”. Mol Syst Biol 9: 639.

Lu, Rong, Florian Markowetz, Richard D Unwin, Jeffrey T Leek, Edoardo M Airoldi, Ben D MacArthur, Alexander Lachmann, et al. (2009) 2009. “Systems-Level Dynamic Analyses of Fate Change in Murine Embryonic Stem Cells.”. Nature 462 (7271): 358-62.

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.

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.

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.

Gregor, Thomas, William Bialek, Rob R de Ruyter van Steveninck, David W Tank, and Eric F Wieschaus. (2005) 2005. “Diffusion and Scaling During Early Embryonic Pattern Formation.”. Proc Natl Acad Sci U S A 102 (51): 18403-7.

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.

Whitfield, Michael L, Deborah R Finlay, John Isaac Murray, Olga G Troyanskaya, Jen-Tsan Chi, Alexander Pergamenschikov, Timothy H McCalmont, Patrick O Brown, David Botstein, and Kari Connolly. (2003) 2003. “Systemic and Cell Type-Specific Gene Expression Patterns in Scleroderma Skin.”. Proc Natl Acad Sci U S A 100 (21): 12319-24.

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.