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.

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.

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.

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

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.

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.

Gibney, Patrick A, Charles Lu, Amy A Caudy, David C Hess, and David Botstein. (2013) 2013. “Yeast Metabolic and Signaling Genes Are Required for Heat-Shock Survival and Have Little Overlap With the Heat-Induced Genes.”. Proc Natl Acad Sci U S A 110 (46).

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

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.

Klosinska, Maja M, Christopher A Crutchfield, Patrick H Bradley, Joshua D Rabinowitz, and James R Broach. (2011) 2011. “Yeast Cells Can Access Distinct Quiescent States.”. Genes Dev 25 (4): 336-49.

Slonim, Noam, Gurinder Singh Atwal, Gašper Tkačik, and William Bialek. (2005) 2005. “Information-Based Clustering.”. Proc Natl Acad Sci U S A 102 (51): 18297-302.

Choi, Joonhyuk, Abbhirami Rajagopal, Yi-Fan Xu, Joshua D Rabinowitz, and Erin K O’Shea. 2017. “A Systematic Genetic Screen for Genes Involved in Sensing Inorganic Phosphate Availability in Saccharomyces Cerevisiae.”. PLoS One 12 (5): e0176085. doi:10.1371/journal.pone.0176085.

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.

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.

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.

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.

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.

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.

Costanzo, Michael, Anastasia Baryshnikova, Jeremy Bellay, Yungil Kim, Eric D Spear, Carolyn S Sevier, Huiming Ding, et al. (2010) 2010. “The Genetic Landscape of a Cell.”. Science 327 (5964): 425-31.

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).

Guan, Yuanfang, Maitreya Dunham, and Olga G Troyanskaya. (2007) 2007. “Functional Analysis of Gene Duplications in Saccharomyces Cerevisiae.”. Genetics 175 (2): 933-43.

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.

McIsaac, Scott, Sanford J Silverman, Megan N McClean, Patrick A Gibney, Joanna Macinskas, Mark J Hickman, Allegra A Petti, and David Botstein. (2011) 2011. “Fast-Acting and Nearly Gratuitous Induction of Gene Expression and Protein Depletion in Saccharomyces Cerevisiae.”. Mol Biol Cell 22 (22): 4447-59.

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.

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

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.

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.

McIsaac, Scott, Allegra A Petti, Harmen J Bussemaker, and David Botstein. (2012) 2012. “Perturbation-Based Analysis and Modeling of Combinatorial Regulation in the Yeast Sulfur Assimilation Pathway.”. Mol Biol Cell 23 (15): 2993-3007.

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.

Xu, Yi-Fan, Fabien Létisse, Farnaz Absalan, Wenyun Lu, Ekaterina Kuznetsova, Greg Brown, Amy A Caudy, Alexander F Yakunin, James R Broach, and Joshua D Rabinowitz. 2013. “Nucleotide Degradation and Ribose Salvage in Yeast.”. Mol Syst Biol 9: 665.

Slavov, Nikolai, and David Botstein. (2011) 2011. “Coupling Among Growth Rate Response, Metabolic Cycle, and Cell Division Cycle in Yeast.”. Mol Biol Cell 22 (12): 1997-2009.

Guan, Yuanfang, Victoria Yao, Kyle Tsui, Marinella Gebbia, Maitreya Dunham, Corey Nislow, and Olga G Troyanskaya. 2011. “Nucleosome-Coupled Expression Differences in Closely-Related Species.”. BMC Genomics 12: 466.

Lang, Gregory I, Andrew W Murray, and David Botstein. (2009) 2009. “The Cost of Gene Expression Underlies a Fitness Trade-off in Yeast.”. Proc Natl Acad Sci U S A 106 (14): 5755-60.

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, Curtis Huttenhower, Edoardo M Airoldi, Rachel Rosenstein, John C Matese, David Gresham, Viktor M Boer, Olga G Troyanskaya, and David Botstein. (2008) 2008. “Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast.”. Mol Biol Cell 19 (1): 352-67.