Botstein, David. (2006) 2006. “Willing to Do the Math: An Interview With David Botstein. Interview by Jane Gitschier.”. PLoS Genet 2 (5): e79.

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.

Fisk, Dianna G, Catherine A Ball, Kara Dolinski, Stacia R Engel, Eurie L Hong, Laurie Issel-Tarver, Katja Schwartz, et al. (2006) 2006. “Saccharomyces Cerevisiae S288C Genome Annotation: A Working Hypothesis.”. Yeast 23 (12): 857-65.

Dolinski, Kara, and David Botstein. 2007. “Orthology and Functional Conservation in Eukaryotes.”. Annu Rev Genet 41: 465-507.

Botstein, David. (2004) 2004. “Ira Herskowitz: 1946-2003.”. Genetics 166 (2): 653-60.

Hirschman, Jodi E, Rama Balakrishnan, Karen R Christie, Maria C Costanzo, Selina S Dwight, Stacia R Engel, Dianna G Fisk, et al. (2006) 2006. “Genome Snapshot: A New Resource at the Saccharomyces Genome Database (SGD) Presenting an Overview of the Saccharomyces Cerevisiae Genome.”. Nucleic Acids Res 34 (Database issue).

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.

Hickman, Mark J, Allegra A Petti, Olivia Ho-Shing, Sanford J Silverman, Scott McIsaac, Traci A Lee, and David Botstein. (2011) 2011. “Coordinated Regulation of Sulfur and Phospholipid Metabolism Reflects the Importance of Methylation in the Growth of Yeast.”. Mol Biol Cell 22 (21): 4192-204.

Heck, Julie Akiko, David Gresham, David Botstein, and Eric Alani. (2006) 2006. “Accumulation of Recessive Lethal Mutations in Saccharomyces Cerevisiae Mlh1 Mismatch Repair Mutants Is Not Associated With Gross Chromosomal Rearrangements.”. Genetics 174 (1): 519-23.

Botstein, David. (2012) 2012. “Why We Need More Basic Biology Research, Not Less.”. Mol Biol Cell 23 (21): 4160-1.

Click, Eleanor S, Tim Stearns, and David Botstein. (2002) 2002. “Systematic Structure-Function Analysis of the Small GTPase Arf1 in Yeast.”. Mol Biol Cell 13 (5): 1652-64.

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.

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.

Bialek, William, and David Botstein. (2004) 2004. “Introductory Science and Mathematics Education for 21st-Century Biologists.”. Science 303 (5659): 788-90.

Ranade, Koustubh, David Hinds, Chao Agnes Hsiung, Lee-Ming Chuang, Mau-Song Chang, Ying-Tsung Chen, Robert Pesich, et al. (2003) 2003. “A Genome Scan for Hypertension Susceptibility Loci in Populations of Chinese and Japanese Origins.”. Am J Hypertens 16 (2): 158-62.

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.

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.

Hackett, Sean R, Vito R T Zanotelli, Wenxin Xu, Jonathan Goya, Junyoung O Park, David H Perlman, Patrick A Gibney, David Botstein, John D Storey, and Joshua D Rabinowitz. (2016) 2016. “Systems-Level Analysis of Mechanisms Regulating Yeast Metabolic Flux.”. Science 354 (6311). doi:10.1126/science.aaf2786.

McIsaac, Scott, Sanford J Silverman, Lance Parsons, Ping Xu, Ryan Briehof, Megan N McClean, and David Botstein. 2013. “Visualization and Analysis of MRNA Molecules Using Fluorescence in Situ Hybridization in Saccharomyces Cerevisiae.”. J Vis Exp, no. 76: e50382.

Wang, Wei, Michael Cherry, David Botstein, and Hao Li. (2002) 2002. “A Systematic Approach to Reconstructing Transcription Networks in Saccharomycescerevisiae.”. Proc Natl Acad Sci U S A 99 (26): 16893-8.

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.

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.

Boer, Viktor M, Sasan Amini, and David Botstein. (2008) 2008. “Influence of Genotype and Nutrition on Survival and Metabolism of Starving Yeast.”. Proc Natl Acad Sci U S A 105 (19): 6930-5.

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.

Nash, Robert, Shuai Weng, Ben Hitz, Rama Balakrishnan, Karen R Christie, Maria C Costanzo, Selina S Dwight, et al. (2007) 2007. “Expanded Protein Information at SGD: New Pages and Proteome Browser.”. Nucleic Acids Res 35 (Database issue).

Brauer, Matthew J, Jie Yuan, Bryson D Bennett, Wenyun Lu, Elizabeth Kimball, David Botstein, and Joshua D Rabinowitz. (2006) 2006. “Conservation of the Metabolomic Response to Starvation across Two Divergent Microbes.”. Proc Natl Acad Sci U S A 103 (51): 19302-7.

Møller, Henrik D, Rasmus K Bojsen, Chris Tachibana, Lance Parsons, David Botstein, and Birgitte Regenberg. (2016) 2016. “Genome-Wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.”. J Vis Exp, no. 110: e54239 |. doi:10.3791/54239.

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.

McIsaac, Scott, Benjamin L Oakes, Xin Wang, Krysta A Dummit, David Botstein, and Marcus B Noyes. (2013) 2013. “Synthetic Gene Expression Perturbation Systems With Rapid, Tunable, Single-Gene Specificity in Yeast.”. Nucleic Acids Res 41 (4): e57.

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.

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.

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.

Lang, Gregory I, David Botstein, and Michael M Desai. (2011) 2011. “Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations.”. Genetics 188 (3): 647-61.

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

Reguly, Teresa, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, et al. 2006. “Comprehensive Curation and Analysis of Global Interaction Networks in Saccharomyces Cerevisiae.”. J Biol 5 (4): 11.

Gibney, Patrick A, Ariel Schieler, Jonathan C Chen, Jessie M Bacha-Hummel, Maxim Botstein, Matthew Volpe, Sanford J Silverman, et al. (2018) 2018. “Common and Divergent Features of Galactose-1-Phosphate and Fructose-1-Phosphate Toxicity in Yeast.”. Mol Biol Cell 29 (8): 897-910. doi:10.1091/mbc.E17-11-0666.

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.

McIsaac, Scott, Patrick A Gibney, Sunil S Chandran, Kirsten R Benjamin, and David Botstein. (2014) 2014. “Synthetic Biology Tools for Programming Gene Expression Without Nutritional Perturbations in Saccharomyces Cerevisiae.”. Nucleic Acids Res 42 (6): e48.

Salwinski, Lukasz, Luana Licata, Andrew Winter, David Thorneycroft, Jyoti Khadake, Arnaud Ceol, Andrew Chatr Aryamontri, et al. (2009) 2009. “Recurated Protein Interaction Datasets.”. Nat Methods 6 (12): 860-1.

Caudy, Amy A, Yuanfang Guan, Yue Jia, Christina Hansen, Chris DeSevo, Alicia P Hayes, Joy Agee, et al. (2013) 2013. “A New System for Comparative Functional Genomics of Saccharomyces Yeasts.”. Genetics 195 (1): 275-87.

Mulholland, Jon, and David Botstein. 2002. “Immunoelectron Microscopy of Aldehyde-Fixed Yeast Cells.”. Methods Enzymol 351: 50-81.

Reisser, Cyrielle, Cindy Dick, Leonid Kruglyak, David Botstein, Joseph Schacherer, and David Hess. (2013) 2013. “Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case.”. G3 (Bethesda).

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.

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

Xu, Yi-Fan, Wenyun Lu, Jonathan C Chen, Sarah A Johnson, Patrick A Gibney, David G Thomas, Greg Brown, et al. (2018) 2018. “Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.”. ACS Chem Biol 13 (10): 3011-20. doi:10.1021/acschembio.8b00804.

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.

Petti, Allegra A, Christopher A Crutchfield, Joshua D Rabinowitz, and David Botstein. (2011) 2011. “Survival of Starving Yeast Is Correlated With Oxidative Stress Response and Nonrespiratory Mitochondrial Function.”. Proc Natl Acad Sci U S A 108 (45).

McIsaac, Scott, Benjamin L Oakes, David Botstein, and Marcus B Noyes. 2013. “Rapid Synthesis and Screening of Chemically Activated Transcription Factors With GFP-Based Reporters.”. J Vis Exp, no. 81: e51153.

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.

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.