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.

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.

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.

Brown, James A, Gavin Sherlock, Chad L Myers, Nicola M Burrows, Changchun Deng, Irene Wu, Kelly E McCann, Olga G Troyanskaya, and Martin Brown. 2006. “Global Analysis of Gene Function in Yeast by Quantitative Phenotypic Profiling.”. Mol Syst Biol 2: 2006.0001.

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).

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.

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, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy, and Olga G Troyanskaya. 2008. “Predicting Gene Function in a Hierarchical Context With an Ensemble of Classifiers.”. Genome Biol 9 Suppl 1: S3.

Lu, Wenyun, Michelle F Clasquin, Eugene Melamud, Daniel Amador-Noguez, Amy A Caudy, and Joshua D Rabinowitz. (2010) 2010. “Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer.”. Anal Chem 82 (8): 3212-21.

Rossi, J M, D T Burke, J C Leung, D S Koos, H Chen, and S M Tilghman. (1992) 1992. “Genomic Analysis Using a Yeast Artificial Chromosome Library With Mouse DNA Inserts.”. Proc Natl Acad Sci U S A 89 (6): 2456-60.

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

McCarroll, Steven A, Coleen T Murphy, Sige Zou, Scott D Pletcher, Chen-Shan Chin, Yuh Nung Jan, Cynthia Kenyon, Cornelia I Bargmann, and Hao Li. (2004) 2004. “Comparing Genomic Expression Patterns across Species Identifies Shared Transcriptional Profile in Aging.”. Nat Genet 36 (2): 197-204.

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.

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.

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.

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.

Guan, Yuanfang, Chad L Myers, Rong Lu, Ihor R Lemischka, Carol J Bult, and Olga G Troyanskaya. 2008. “A Genomewide Functional Network for the Laboratory Mouse.”. PLoS Comput Biol 4 (9): e1000165.

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.

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

Park, Christopher Y, David C Hess, Curtis Huttenhower, and Olga G Troyanskaya. 2010. “Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components.”. PLoS Comput Biol 6 (11): e1001009.

Gibney, Patrick A, Mark J Hickman, Patrick H Bradley, John C Matese, and David Botstein. (2013) 2013. “Phylogenetic Portrait of the Saccharomyces Cerevisiae Functional Genome.”. G3 (Bethesda) 3 (8): 1335-40.

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.

Gresham, David, Douglas M Ruderfer, Stephen C Pratt, Joseph Schacherer, Maitreya Dunham, David Botstein, and Leonid Kruglyak. (2006) 2006. “Genome-Wide Detection of Polymorphisms at Nucleotide Resolution With a Single DNA Microarray.”. Science 311 (5769): 1932-6.

Myers, Chad L, Drew Robson, Adam Wible, Matthew A Hibbs, Camelia Chiriac, Chandra L Theesfeld, Kara Dolinski, and Olga G Troyanskaya. 2005. “Discovery of Biological Networks from Diverse Functional Genomic Data.”. Genome Biol 6 (13): R114.

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).

Pritykin, Yuri, and Mona Singh. 2013. “Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks.”. PLoS Comput Biol 9 (10): e1003243.

Lang, Gregory I, Daniel P Rice, Mark J Hickman, Erica Sodergren, George M Weinstock, David Botstein, and Michael M Desai. (2013) 2013. “Pervasive Genetic Hitchhiking and Clonal Interference in Forty Evolving Yeast Populations.”. Nature 500 (7464): 571-4.

Doherty, Kevin M, Leah D Pride, James Lukose, Brian E Snydsman, Ronald Charles, Ajay Pramanik, Eric G Muller, David Botstein, and Carol Wood Moore. (2012) 2012. “Loss of a 20S Proteasome Activator in Saccharomyces Cerevisiae Downregulates Genes Important for Genomic Integrity, Increases DNA Damage, and Selectively Sensitizes Cells to Agents With Diverse Mechanisms of Action.”. G3 (Bethesda) 2 (8): 943-59.

Schacherer, Joseph, Douglas M Ruderfer, David Gresham, Kara Dolinski, David Botstein, and Leonid Kruglyak. 2007. “Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces Cerevisiae Strains.”. PLoS One 2 (3): e322.

Hibbs, Matthew A, Chad L Myers, Curtis Huttenhower, David C Hess, Kai Li, Amy A Caudy, and Olga G Troyanskaya. (2009) 2009. “Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis.”. PLoS Comput Biol 5 (3): e1000322.

Kliegman, Joseph I, Dorothea Fiedler, Colm J Ryan, Yi-Fan Xu, Xiao-Yang Su, David Thomas, Max C Caccese, et al. (2013) 2013. “Chemical Genetics of Rapamycin-Insensitive TORC2 in S. Cerevisiae.”. Cell Rep 5 (6): 1725-36.

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.

Huttenhower, Curtis, Matt Hibbs, Chad Myers, and Olga G Troyanskaya. (2006) 2006. “A Scalable Method for Integration and Functional Analysis of Multiple Microarray Datasets.”. Bioinformatics 22 (23): 2890-7.

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.

Botstein, David. (2010) 2010. “It’s the Data!”. Mol Biol Cell 21 (1): 4-6.

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.

Robinson, David G, Wei Chen, John D Storey, and David Gresham. (2014) 2014. “Design and Analysis of Bar-Seq Experiments.”. G3 (Bethesda) 4 (1): 11-8.

Dunham, Maitreya, Hassan Badrane, Tracy Ferea, Julian Adams, Patrick O Brown, Frank Rosenzweig, and David Botstein. (2002) 2002. “Characteristic Genome Rearrangements in Experimental Evolution of Saccharomyces Cerevisiae.”. Proc Natl Acad Sci U S A 99 (25): 16144-9.

Botstein, David, and Gerald R Fink. (2011) 2011. “Yeast: An Experimental Organism for 21st Century Biology.”. Genetics 189 (3): 695-704.

Dwight, Selina S, Rama Balakrishnan, Karen R Christie, Maria C Costanzo, Kara Dolinski, Stacia R Engel, Becket Feierbach, et al. (2004) 2004. “Saccharomyces Genome Database: Underlying Principles and Organisation.”. Brief Bioinform 5 (1): 9-22.

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

Lu, Wenyun, Yun Kyung Kwon, and Joshua D Rabinowitz. (2007) 2007. “Isotope Ratio-Based Profiling of Microbial Folates.”. J Am Soc Mass Spectrom 18 (5): 898-909.

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).

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.

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.

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.

Christie, Karen R, Shuai Weng, Rama Balakrishnan, Maria C Costanzo, Kara Dolinski, Selina S Dwight, Stacia R Engel, et al. (2004) 2004. “Saccharomyces Genome Database (SGD) Provides Tools to Identify and Analyze Sequences from Saccharomyces Cerevisiae and Related Sequences from Other Organisms.”. Nucleic Acids Res 32 (Database issue).

Banks, Eric, Elena Nabieva, Bernard Chazelle, and Mona Singh. (2008) 2008. “Organization of Physical Interactomes As Uncovered by Network Schemas.”. PLoS Comput Biol 4 (10): e1000203.