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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.

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).

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.

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.

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.

Balakrishnan, Rama, Karen R Christie, Maria C Costanzo, Kara Dolinski, Selina S Dwight, Stacia R Engel, Dianna G Fisk, et al. (2005) 2005. “Fungal BLAST and Model Organism BLASTP Best Hits: New Comparison Resources at the Saccharomyces Genome Database (SGD).”. Nucleic Acids Res 33 (Database issue).

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.

Guan, Yuanfang, Maitreya Dunham, Amy A Caudy, and Olga Troyanskaya. (2010) 2010. “Systematic Planning of Genome-Scale Experiments in Poorly Studied Species.”. PLoS Comput Biol 6 (3): e1000698.

Caspary, T, M A Cleary, E J Perlman, P Zhang, S J Elledge, and S M Tilghman. (1999) 1999. “Oppositely Imprinted Genes p57(Kip2) and Igf2 Interact in a Mouse Model for Beckwith-Wiedemann Syndrome.”. Genes Dev 13 (23): 3115-24.

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.

Chi, An, Curtis Huttenhower, Lewis Y Geer, Joshua J Coon, John E P Syka, Dina L Bai, Jeffrey Shabanowitz, Daniel J Burke, Olga G Troyanskaya, and Donald F Hunt. (2007) 2007. “Analysis of Phosphorylation Sites on Proteins from Saccharomyces Cerevisiae by Electron Transfer Dissociation (ETD) Mass Spectrometry.”. Proc Natl Acad Sci U S A 104 (7): 2193-8.

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.

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.

Hibbs, Matthew A, David C Hess, Chad L Myers, Curtis Huttenhower, Kai Li, and Olga G Troyanskaya. (2007) 2007. “Exploring the Functional Landscape of Gene Expression: Directed Search of Large Microarray Compendia.”. Bioinformatics 23 (20): 2692-9.

Gresham, David, Renata Usaite, Susanne Manuela Germann, Michael Lisby, David Botstein, and Birgitte Regenberg. (2010) 2010. “Adaptation to Diverse Nitrogen-Limited Environments by Deletion or Extrachromosomal Element Formation of the GAP1 Locus.”. Proc Natl Acad Sci U S A 107 (43): 18551-6.

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.

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.

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).

Chikina, Maria D, and Olga G Troyanskaya. 2011. “Accurate Quantification of Functional Analogy Among Close Homologs.”. PLoS Comput Biol 7 (2): e1001074.

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.

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.

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

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.

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).

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.

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.

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.

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.

Haarer, Brian, Susan Viggiano, Mathew A Hibbs, Olga G Troyanskaya, and David C Amberg. (2007) 2007. “Modeling Complex Genetic Interactions in a Simple Eukaryotic Genome: Actin Displays a Rich Spectrum of Complex Haploinsufficiencies.”. Genes Dev 21 (2): 148-59.

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.

Costanzo, Michael, Benjamin VanderSluis, Elizabeth N Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, et al. (2016) 2016. “A Global Genetic Interaction Network Maps a Wiring Diagram of Cellular Function.”. Science 353 (6306). doi:10.1126/science.aaf1420.

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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.

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.

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.

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.

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.

Pane, Attilio, Peng Jiang, Dorothy Yanling Zhao, Mona Singh, and Trudi Schüpbach. (2011) 2011. “The Cutoff Protein Regulates PiRNA Cluster Expression and PiRNA Production in the Drosophila Germline.”. EMBO J 30 (22): 4601-15.

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.

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.

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.

Goentoro, Lea A, Nir Yakoby, Joseph Goodhouse, Trudi Schüpbach, and Stanislav Y Shvartsman. (2006) 2006. “Quantitative Analysis of the GAL4 UAS System in Drosophila Oogenesis.”. Genesis 44 (2): 66-74.

Brauer, Matthew J, Alok J Saldanha, Kara Dolinski, and David Botstein. (2005) 2005. “Homeostatic Adjustment and Metabolic Remodeling in Glucose-Limited Yeast Cultures.”. Mol Biol Cell 16 (5): 2503-17.

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.

Schupbach, T, and E Wieschaus. 1998. “Probing for Gene Specificity in Epithelial Development.”. Int J Dev Biol 42 (3): 249-55.

Barutcuoglu, Zafer, Robert E Schapire, and Olga G Troyanskaya. (2006) 2006. “Hierarchical Multi-Label Prediction of Gene Function.”. Bioinformatics 22 (7): 830-6.

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.

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.

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.