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.

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.

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.

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.

DiMaggio, Peter A, Scott R McAllister, Christodoulos A Floudas, Xiao-Jiang Feng, Joshua D Rabinowitz, and Herschel A Rabitz. 2008. “Biclustering via Optimal Re-Ordering of Data Matrices in Systems Biology: Rigorous Methods and Comparative Studies.”. BMC Bioinformatics 9: 458.

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.

Dwight, Selina S, Midori A Harris, Kara Dolinski, Catherine A Ball, Gail Binkley, Karen R Christie, Dianna G Fisk, et al. (2002) 2002. “Saccharomyces Genome Database (SGD) Provides Secondary Gene Annotation Using the Gene Ontology (GO).”. Nucleic Acids Res 30 (1): 69-72.

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.

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.

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.

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.

Troyanskaya, Olga G, Kara Dolinski, Art B Owen, Russ B Altman, and David Botstein. (2003) 2003. “A Bayesian Framework for Combining Heterogeneous Data Sources for Gene Function Prediction (in Saccharomyces cerevisiae).”. Proc Natl Acad Sci U S A 100 (14): 8348-53.

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.

Weng, Shuai, Qing Dong, Rama Balakrishnan, Karen R Christie, Maria Costanzo, Kara Dolinski, Selina S Dwight, et al. (2003) 2003. “Saccharomyces Genome Database (SGD) Provides Biochemical and Structural Information for Budding Yeast Proteins.”. Nucleic Acids Res 31 (1): 216-8.

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.

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.

Breunig, Jeffrey S, Sean R Hackett, Joshua D Rabinowitz, and Leonid Kruglyak. (2014) 2014. “Genetic Basis of Metabolome Variation in Yeast.”. PLoS Genet 10 (3): e1004142.

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.

Huttenhower, Curtis, and Olga G Troyanskaya. 2006. “Bayesian Data Integration: A Functional Perspective.”. Comput Syst Bioinformatics Conf, 341-51.

Welch, Aaron Z, Patrick A Gibney, David Botstein, and Douglas E Koshland. (2013) 2013. “TOR and RAS Pathways Regulate Desiccation Tolerance in Saccharomyces Cerevisiae.”. Mol Biol Cell 24 (2): 115-28.

Engel, Stacia R, Rama Balakrishnan, Gail Binkley, Karen R Christie, Maria C Costanzo, Selina S Dwight, Dianna G Fisk, et al. (2010) 2010. “Saccharomyces Genome Database Provides Mutant Phenotype Data.”. Nucleic Acids Res 38 (Database issue).

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.

Huttenhower, Curtis, Matthew A Hibbs, Chad L Myers, Amy A Caudy, David C Hess, and Olga G Troyanskaya. (2009) 2009. “The Impact of Incomplete Knowledge on Evaluation: An Experimental Benchmark for Protein Function Prediction.”. Bioinformatics 25 (18): 2404-10.

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.

Bradley, Patrick H, Matthew J Brauer, Joshua D Rabinowitz, and Olga G Troyanskaya. (2009) 2009. “Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces Cerevisiae.”. PLoS Comput Biol 5 (1): e1000270.

Huttenhower, C, and O G Troyanskaya. (2008) 2008. “Assessing the Functional Structure of Genomic Data.”. Bioinformatics 24 (13).

Lang, Gregory I, and David Botstein. 2011. “A Test of the Coordinated Expression Hypothesis for the Origin and Maintenance of the GAL Cluster in Yeast.”. PLoS One 6 (9): e25290.

Issel-Tarver, Laurie, Karen R Christie, Kara Dolinski, Rey Andrada, Rama Balakrishnan, Catherine A Ball, Gail Binkley, et al. 2002. “Saccharomyces Genome Database.”. Methods Enzymol 350: 329-46.

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.

Song, Jimin, and Mona Singh. (2009) 2009. “How and When Should Interactome-Derived Clusters Be Used to Predict Functional Modules and Protein Function?”. Bioinformatics 25 (23): 3143-50.

Hong, Eurie L, Rama Balakrishnan, Qing Dong, Karen R Christie, Julie Park, Gail Binkley, Maria C Costanzo, et al. (2008) 2008. “Gene Ontology Annotations at SGD: New Data Sources and Annotation Methods.”. Nucleic Acids Res 36 (Database issue).

Wingreen, Ned S, and Simon A Levin. (2006) 2006. “Cooperation Among Microorganisms.”. PLoS Biol 4 (9): e299.

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.

Gresham, David, Viktor M Boer, Amy A Caudy, Naomi Ziv, Nathan J Brandt, John D Storey, and David Botstein. (2011) 2011. “System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces Cerevisiae.”. Genetics 187 (1): 299-317.