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. Reference Link
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. Reference Link
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. Reference Link
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
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
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. 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
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. Reference Link
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. Reference Link
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. Reference Link
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). Reference Link
Guan, Yuanfang, Maitreya Dunham, and Olga G Troyanskaya. (2007) 2007. “Functional Analysis of Gene Duplications in Saccharomyces Cerevisiae.”. Genetics 175 (2): 933-43. 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
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. Reference Link
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. Reference Link
Wyart, Matthieu, David Botstein, and Ned S Wingreen. 2010. “Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data.”. PLoS Comput Biol 6 (11): e1000979. Reference Link
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. 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
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. 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
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. Reference Link
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. 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
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. 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
Guan, Yuanfang, Maitreya Dunham, Olga G Troyanskaya, and Amy A Caudy. 2013. “Comparative Gene Expression Between Two Yeast Species.”. BMC Genomics 14: 33. 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
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. Reference Link
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). Reference Link
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. Reference Link