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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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.

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.

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.

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).