List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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Saccharomyces cerevisiae Proteins
M. Shakoury-Elizeh, Tiedeman, J., Rashford, J., Ferea, T., Demeter, J., Garcia, E., Rolfes, R., Brown, P. O., Botstein, D., and Philpott, C. C., “Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
G. I. Lang and Botstein, D., “A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast.”, PLoS One, vol. 6, no. 9, p. e25290, 2011.
S. R McIsaac, Petti, A. A., Bussemaker, H. J., and Botstein, D., “Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 2993-3007, 2012.
H. Yoshimoto, Saltsman, K., Gasch, A. P., Li, H. Xia, Ogawa, N., Botstein, D., Brown, P. O., and Cyert, M. S., “Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 34, pp. 31079-88, 2002.
J. E. Hirschman, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., Park, J., Oughtred, R., Skrzypek, M., Starr, B., Theesfeld, C. L., Williams, J., Andrada, R., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Thanawala, M. K., Weng, S., Dolinski, K., Botstein, D., and J Cherry, M., “Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.”, Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
S. S. Dwight, Harris, M. A., Dolinski, K., Ball, C. A., Binkley, G., Christie, K. R., Fisk, D. G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).”, Nucleic Acids Res, vol. 30, no. 1, pp. 69-72, 2002.
M. Wyart, Botstein, D., and Wingreen, N. S., “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
J. Akiko Heck, Gresham, D., Botstein, D., and Alani, E., “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.”, Genetics, vol. 174, no. 1, pp. 519-23, 2006.
T. Reguly, Breitkreutz, A., Boucher, L., Breitkreutz, B. - J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., and Tyers, M., “Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.”, J Biol, vol. 5, no. 4, p. 11, 2006.
E. W. Trotter, Kao, C. M. - F., Berenfeld, L., Botstein, D., Petsko, G. A., and Gray, J. V., “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
M. Shapira, Segal, E., and Botstein, D., “Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.”, Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
A. Z. Welch, Gibney, P. A., Botstein, D., and Koshland, D. E., “TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
A. J. Saldanha, Brauer, M. J., and Botstein, D., “Nutritional homeostasis in batch and steady-state culture of yeast.”, Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
M. Ronen and Botstein, D., “Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.”, Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
S. Weng, Dong, Q., Balakrishnan, R., Christie, K., Costanzo, M., Dolinski, K., Dwight, S. S., Engel, S., Fisk, D. G., Hong, E., Issel-Tarver, L., Sethuraman, A., Theesfeld, C., Andrada, R., Binkley, G., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
M. J. Brauer, Saldanha, A. J., Dolinski, K., and Botstein, D., “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
R. Balakrishnan, Christie, K. R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Nash, R., Oughtred, R., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Sethuraman, A., Weng, S., Botstein, D., and J Cherry, M., “Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).”, Nucleic Acids Res, vol. 33, no. Database issue, pp. D374-7, 2005.
K. Dolinski and Botstein, D., “Changing perspectives in yeast research nearly a decade after the genome sequence.”, Genome Res, vol. 15, no. 12, pp. 1611-9, 2005.
D. Gresham, Desai, M. M., Tucker, C. M., Jenq, H. T., Pai, D. A., Ward, A., DeSevo, C. G., Botstein, D., and Dunham, M. J., “The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.”, PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
D. Gresham, Usaite, R., Germann, S. Manuela, Lisby, M., Botstein, D., and Regenberg, B., “Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.”, Proc Natl Acad Sci U S A, vol. 107, no. 43, pp. 18551-6, 2010.
Saccharomyces cerevisiae
E. M. Airoldi, Huttenhower, C., Gresham, D., Lu, C., Caudy, A. A., Dunham, M. J., Broach, J. R., Botstein, D., and Troyanskaya, O. G., “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
E. L. Hong, Balakrishnan, R., Dong, Q., Christie, K. R., Park, J., Binkley, G., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R. S., Oughtred, R., Skrzypek, M. S., Weng, S., Wong, E. D., Zhu, K. K., Dolinski, K., Botstein, D., and J Cherry, M., “Gene Ontology annotations at SGD: new data sources and annotation methods.”, Nucleic Acids Res, vol. 36, no. Database issue, pp. D577-81, 2008.
Y. - F. Xu, Lu, W., Chen, J. C., Johnson, S. A., Gibney, P. A., Thomas, D. G., Brown, G., May, A. L., Campagna, S. R., Yakunin, A. F., Botstein, D., and Rabinowitz, J. D., “Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.”, ACS Chem Biol, vol. 13, no. 10, pp. 3011-3020, 2018.
N. Slavov and Botstein, D., “Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.”, Mol Biol Cell, vol. 22, no. 12, pp. 1997-2009, 2011.
P. A. Gibney, Hickman, M. J., Bradley, P. H., Matese, J. C., and Botstein, D., “Phylogenetic portrait of the Saccharomyces cerevisiae functional genome.”, G3 (Bethesda), vol. 3, no. 8, pp. 1335-40, 2013.
P. A. Gibney, Lu, C., Caudy, A. A., Hess, D. C., and Botstein, D., “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, vol. 110, no. 46, pp. E4393-402, 2013.
E. Segal, Shapira, M., Regev, iv, A., Pe'er, D., Botstein, D., Koller, D., and Friedman, N., “Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.”, Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
M. J. Hickman, Petti, A. A., Ho-Shing, O., Silverman, S. J., R McIsaac, S., Lee, T. A., and Botstein, D., “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
K. M. Doherty, Pride, L. D., Lukose, J., Snydsman, B. E., Charles, R., Pramanik, A., Muller, E. G., Botstein, D., and Moore, C. Wood, “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), vol. 2, no. 8, pp. 943-59, 2012.
M. J. Brauer, Yuan, J., Bennett, B. D., Lu, W., Kimball, E., Botstein, D., and Rabinowitz, J. D., “Conservation of the metabolomic response to starvation across two divergent microbes.”, Proc Natl Acad Sci U S A, vol. 103, no. 51, pp. 19302-7, 2006.
K. Dolinski and Botstein, D., “Orthology and functional conservation in eukaryotes.”, Annu Rev Genet, vol. 41, pp. 465-507, 2007.
H. Yoshimoto, Saltsman, K., Gasch, A. P., Li, H. Xia, Ogawa, N., Botstein, D., Brown, P. O., and Cyert, M. S., “Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 34, pp. 31079-88, 2002.
G. I. Lang, Botstein, D., and Desai, M. M., “Genetic variation and the fate of beneficial mutations in asexual populations.”, Genetics, vol. 188, no. 3, pp. 647-61, 2011.
S. R McIsaac, Petti, A. A., Bussemaker, H. J., and Botstein, D., “Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 2993-3007, 2012.
D. Botstein and Fink, G. R., “Yeast: an experimental organism for 21st Century biology.”, Genetics, vol. 189, no. 3, pp. 695-704, 2011.
J. E. Hirschman, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., Park, J., Oughtred, R., Skrzypek, M., Starr, B., Theesfeld, C. L., Williams, J., Andrada, R., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Thanawala, M. K., Weng, S., Dolinski, K., Botstein, D., and J Cherry, M., “Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.”, Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
M. Wyart, Botstein, D., and Wingreen, N. S., “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
M. J. Dunham, Badrane, H., Ferea, T., Adams, J., Brown, P. O., Rosenzweig, F., and Botstein, D., “Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16144-9, 2002.
M. Shakoury-Elizeh, Tiedeman, J., Rashford, J., Ferea, T., Demeter, J., Garcia, E., Rolfes, R., Brown, P. O., Botstein, D., and Philpott, C. C., “Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
D. Gresham, Curry, B., Ward, A., D Gordon, B., Brizuela, L., Kruglyak, L., and Botstein, D., “Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.”, Proc Natl Acad Sci U S A, vol. 107, no. 4, pp. 1482-7, 2010.
G. I. Lang and Botstein, D., “A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast.”, PLoS One, vol. 6, no. 9, p. e25290, 2011.
V. M. Boer, Crutchfield, C. A., Bradley, P. H., Botstein, D., and Rabinowitz, J. D., “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
D. Gresham, Desai, M. M., Tucker, C. M., Jenq, H. T., Pai, D. A., Ward, A., DeSevo, C. G., Botstein, D., and Dunham, M. J., “The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.”, PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
J. Akiko Heck, Gresham, D., Botstein, D., and Alani, E., “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.”, Genetics, vol. 174, no. 1, pp. 519-23, 2006.
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
D. C. Hess, Lu, W., Rabinowitz, J. D., and Botstein, D., “Ammonium toxicity and potassium limitation in yeast.”, PLoS Biol, vol. 4, no. 11, p. e351, 2006.
S. S. Dwight, Harris, M. A., Dolinski, K., Ball, C. A., Binkley, G., Christie, K. R., Fisk, D. G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).”, Nucleic Acids Res, vol. 30, no. 1, pp. 69-72, 2002.
L. Issel-Tarver, Christie, K. R., Dolinski, K., Andrada, R., Balakrishnan, R., Ball, C. A., Binkley, G., Dong, S., Dwight, S. S., Fisk, D. G., Harris, M., Schroeder, M., Sethuraman, A., Tse, K., Weng, S., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database.”, Methods Enzymol, vol. 350, pp. 329-46, 2002.
E. W. Trotter, Kao, C. M. - F., Berenfeld, L., Botstein, D., Petsko, G. A., and Gray, J. V., “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
D. Gresham, Ruderfer, D. M., Pratt, S. C., Schacherer, J., Dunham, M. J., Botstein, D., and Kruglyak, L., “Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray.”, Science, vol. 311, no. 5769, pp. 1932-6, 2006.
C. Lu, Brauer, M. J., and Botstein, D., “Slow growth induces heat-shock resistance in normal and respiratory-deficient yeast.”, Mol Biol Cell, vol. 20, no. 3, pp. 891-903, 2009.
T. Reguly, Breitkreutz, A., Boucher, L., Breitkreutz, B. - J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., and Tyers, M., “Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.”, J Biol, vol. 5, no. 4, p. 11, 2006.
M. Ronen and Botstein, D., “Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.”, Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
M. Shapira, Segal, E., and Botstein, D., “Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.”, Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
G. I. Lang, Murray, A. W., and Botstein, D., “The cost of gene expression underlies a fitness trade-off in yeast.”, Proc Natl Acad Sci U S A, vol. 106, no. 14, pp. 5755-60, 2009.
A. J. Saldanha, Brauer, M. J., and Botstein, D., “Nutritional homeostasis in batch and steady-state culture of yeast.”, Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
D. G. Fisk, Ball, C. A., Dolinski, K., Engel, S. R., Hong, E. L., Issel-Tarver, L., Schwartz, K., Sethuraman, A., Botstein, D., and J Cherry, M., “Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.”, Yeast, vol. 23, no. 12, pp. 857-65, 2006.
A. Z. Welch, Gibney, P. A., Botstein, D., and Koshland, D. E., “TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
M. J. Brauer, Saldanha, A. J., Dolinski, K., and Botstein, D., “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
R. Balakrishnan, Christie, K. R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Nash, R., Oughtred, R., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Sethuraman, A., Weng, S., Botstein, D., and J Cherry, M., “Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).”, Nucleic Acids Res, vol. 33, no. Database issue, pp. D374-7, 2005.
S. Weng, Dong, Q., Balakrishnan, R., Christie, K., Costanzo, M., Dolinski, K., Dwight, S. S., Engel, S., Fisk, D. G., Hong, E., Issel-Tarver, L., Sethuraman, A., Theesfeld, C., Andrada, R., Binkley, G., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
S. S. Dwight, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dolinski, K., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J., Hong, E. L., Issel-Tarver, L., Nash, R. S., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Weng, S., Botstein, D., and J Cherry, M., “Saccharomyces genome database: underlying principles and organisation.”, Brief Bioinform, vol. 5, no. 1, pp. 9-22, 2004.
O. Alter, Brown, P. O., and Botstein, D., “Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.”, Proc Natl Acad Sci U S A, vol. 100, no. 6, pp. 3351-6, 2003.
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
K. Dolinski and Botstein, D., “Changing perspectives in yeast research nearly a decade after the genome sequence.”, Genome Res, vol. 15, no. 12, pp. 1611-9, 2005.
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
M. J. Brauer, Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., and Botstein, D., “Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.”, Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
V. M. Boer, Amini, S., and Botstein, D., “Influence of genotype and nutrition on survival and metabolism of starving yeast.”, Proc Natl Acad Sci U S A, vol. 105, no. 19, pp. 6930-5, 2008.
O. G. Troyanskaya, Dolinski, K., Owen, A. B., Altman, R. B., and Botstein, D., “A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8348-53, 2003.
J. Schacherer, Ruderfer, D. M., Gresham, D., Dolinski, K., Botstein, D., and Kruglyak, L., “Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains.”, PLoS One, vol. 2, no. 3, p. e322, 2007.
D. Gresham, Usaite, R., Germann, S. Manuela, Lisby, M., Botstein, D., and Regenberg, B., “Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.”, Proc Natl Acad Sci U S A, vol. 107, no. 43, pp. 18551-6, 2010.
S. J. Silverman, Petti, A. A., Slavov, N., Parsons, L., Briehof, R., Thiberge, S. Y., Zenklusen, D., Gandhi, S. J., Larson, D. R., Singer, R. H., and Botstein, D., “Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.”, Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
R. Nash, Weng, S., Hitz, B., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Livstone, M. S., Oughtred, R., Park, J., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Dolinski, K., Botstein, D., and J Cherry, M., “Expanded protein information at SGD: new pages and proteome browser.”, Nucleic Acids Res, vol. 35, no. Database issue, pp. D468-71, 2007.
D. Botstein, “It's the data!”, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
G. I. Lang, Rice, D. P., Hickman, M. J., Sodergren, E., Weinstock, G. M., Botstein, D., and Desai, M. M., “Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.”, Nature, vol. 500, no. 7464, pp. 571-4, 2013.
S. R McIsaac, Silverman, S. J., Parsons, L., Xu, P., Briehof, R., McClean, M. N., and Botstein, D., “Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae.”, J Vis Exp, no. 76, p. e50382, 2013.
A. A. Petti, R McIsaac, S., Ho-Shing, O., Bussemaker, H. J., and Botstein, D., “Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 3008-24, 2012.
A. A. Petti, Crutchfield, C. A., Rabinowitz, J. D., and Botstein, D., “Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function.”, Proc Natl Acad Sci U S A, vol. 108, no. 45, pp. E1089-98, 2011.
S. R McIsaac, Silverman, S. J., McClean, M. N., Gibney, P. A., Macinskas, J., Hickman, M. J., Petti, A. A., and Botstein, D., “Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 22, no. 22, pp. 4447-59, 2011.
S. R. Engel, Balakrishnan, R., Binkley, G., Christie, K. R., Costanzo, M. C., Dwight, S. S., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Hong, E. L., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R., Oughtred, R., Park, J., Skrzypek, M. S., Weng, S., Wong, E. D., Dolinski, K., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database provides mutant phenotype data.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
K. R. Christie, Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J. E., Hong, E. L., Issel-Tarver, L., Nash, R., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.”, Nucleic Acids Res, vol. 32, no. Database issue, pp. D311-4, 2004.
S. R McIsaac, Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., and Noyes, M. B., “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
Saccharomyces
A. A. Caudy, Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., J Breunig, S., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., Combs, P. A., Doucette, C., Demuren, O., Fellowes, P., Freeman, S., Frenkel, E., Gadala-Maria, D., Gawande, R., Glass, D., Grossberg, S., Gupta, A., Hammonds-Odie, L., Hoisos, A., Hsi, J., Hsu, Y. - H. Huang, Inukai, S., Karczewski, K. J., Ke, X., Kojima, M., Leachman, S., Lieber, D., Liebowitz, A., Liu, J., Liu, Y., Martin, T., Mena, J., Mendoza, R., Myhrvold, C., Millian, C., Pfau, S., Raj, S., Rich, M., Rokicki, J., Rounds, W., Salazar, M., Salesi, M., Sharma, R., Silverman, S., Singer, C., Sinha, S., Staller, M., Stern, P., Tang, H., Weeks, S., Weidmann, M., Wolf, A., Young, C., Yuan, J., Crutchfield, C., McClean, M., Murphy, C. T., Llinás, M., Botstein, D., Troyanskaya, O. G., and Dunham, M. J., “A new system for comparative functional genomics of Saccharomyces yeasts.”, Genetics, vol. 195, no. 1, pp. 275-87, 2013.
S-Adenosylmethionine
M. J. Hickman, Petti, A. A., Ho-Shing, O., Silverman, S. J., R McIsaac, S., Lee, T. A., and Botstein, D., “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
RNA, Neoplasm
X. Chen, Cheung, S. Tim, So, S., Fan, S. Tat, Barry, C., Higgins, J., Lai, K. - M., Ji, J., Dudoit, S., Ng, I. O. L., van de Rijn, M., Botstein, D., and Brown, P. O., “Gene expression patterns in human liver cancers.”, Mol Biol Cell, vol. 13, no. 6, pp. 1929-39, 2002.
RNA, Messenger
S. R McIsaac, Silverman, S. J., Parsons, L., Xu, P., Briehof, R., McClean, M. N., and Botstein, D., “Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae.”, J Vis Exp, no. 76, p. e50382, 2013.
H. Y. Chang, Chi, J. - T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., and Brown, P. O., “Diversity, topographic differentiation, and positional memory in human fibroblasts.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
N. Slavov and Botstein, D., “Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.”, Mol Biol Cell, vol. 22, no. 12, pp. 1997-2009, 2011.
M. Wyart, Botstein, D., and Wingreen, N. S., “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
V. M. Boer, Crutchfield, C. A., Bradley, P. H., Botstein, D., and Rabinowitz, J. D., “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
N. Slavov, Macinskas, J., Caudy, A., and Botstein, D., “Metabolic cycling without cell division cycling in respiring yeast.”, Proc Natl Acad Sci U S A, vol. 108, no. 47, pp. 19090-5, 2011.
O. Alter, Brown, P. O., and Botstein, D., “Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.”, Proc Natl Acad Sci U S A, vol. 100, no. 6, pp. 3351-6, 2003.
R. Shyamsundar, Kim, Y. H., Higgins, J. P., Montgomery, K., Jorden, M., Sethuraman, A., van de Rijn, M., Botstein, D., Brown, P. O., and Pollack, J. R., “A DNA microarray survey of gene expression in normal human tissues.”, Genome Biol, vol. 6, no. 3, p. R22, 2005.
S. J. Silverman, Petti, A. A., Slavov, N., Parsons, L., Briehof, R., Thiberge, S. Y., Zenklusen, D., Gandhi, S. J., Larson, D. R., Singer, R. H., and Botstein, D., “Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.”, Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O., “Genome-scale identification of membrane-associated human mRNAs.”, PLoS Genet, vol. 2, no. 1, p. e11, 2006.
J. R. Pollack, Sørlie, T., Perou, C. M., Rees, C. A., Jeffrey, S. S., Lonning, P. E., Tibshirani, R., Botstein, D., Børresen-Dale, A. - L., and Brown, P. O., “Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.”, Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12963-8, 2002.
RNA, Fungal
S. R McIsaac, Silverman, S. J., Parsons, L., Xu, P., Briehof, R., McClean, M. N., and Botstein, D., “Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae.”, J Vis Exp, no. 76, p. e50382, 2013.
M. Wyart, Botstein, D., and Wingreen, N. S., “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
O. Alter, Brown, P. O., and Botstein, D., “Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.”, Proc Natl Acad Sci U S A, vol. 100, no. 6, pp. 3351-6, 2003.
RNA
N. Novoradovskaya, Whitfield, M. L., Basehore, L. S., Novoradovsky, A., Pesich, R., Usary, J., Karaca, M., Wong, W. K., Aprelikova, O., Fero, M., Perou, C. M., Botstein, D., and Braman, J., “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
H. Zhao, Langerød, A., Ji, Y., Nowels, K. W., Nesland, J. M., Tibshirani, R., Bukholm, I. K., Kåresen, R., Botstein, D., Børresen-Dale, A. - L., and Jeffrey, S. S., “Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.”, Mol Biol Cell, vol. 15, no. 6, pp. 2523-36, 2004.
Risk Factors
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
Ribosomes
M. J. Brauer, Saldanha, A. J., Dolinski, K., and Botstein, D., “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
N. Slavov and Botstein, D., “Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.”, Mol Biol Cell, vol. 22, no. 12, pp. 1997-2009, 2011.
Ribosome Subunits, Large, Eukaryotic
A. Z. Welch, Gibney, P. A., Botstein, D., and Koshland, D. E., “TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
Ribosomal Proteins
A. J. Saldanha, Brauer, M. J., and Botstein, D., “Nutritional homeostasis in batch and steady-state culture of yeast.”, Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
Reverse Transcriptase Polymerase Chain Reaction
S. Y. Leung, Chen, X., Chu, K. M., Yuen, S. T., Mathy, J., Ji, J., S Y Chan, A., Li, R., Law, S., Troyanskaya, O. G., Tu, I. - P., Wong, J., So, S., Botstein, D., and Brown, P. O., “Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16203-8, 2002.
I. S. Lossos, Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., and Levy, R., “Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.”, N Engl J Med, vol. 350, no. 18, pp. 1828-37, 2004.
Retroviridae
K. S. Smith, Chanda, S. K., Lingbeek, M., Ross, D. T., Botstein, D., van Lohuizen, M., and Cleary, M. L., “Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1.”, Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
Response Elements
H. Yoshimoto, Saltsman, K., Gasch, A. P., Li, H. Xia, Ogawa, N., Botstein, D., Brown, P. O., and Cyert, M. S., “Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 34, pp. 31079-88, 2002.
Research Personnel
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
Research Design
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
K. Dolinski and Botstein, D., “Changing perspectives in yeast research nearly a decade after the genome sequence.”, Genome Res, vol. 15, no. 12, pp. 1611-9, 2005.
Research
K. Dolinski and Botstein, D., “Changing perspectives in yeast research nearly a decade after the genome sequence.”, Genome Res, vol. 15, no. 12, pp. 1611-9, 2005.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
D. Botstein, “Why we need more basic biology research, not less.”, Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 2012.
Reproduction, Asexual
G. I. Lang, Botstein, D., and Desai, M. M., “Genetic variation and the fate of beneficial mutations in asexual populations.”, Genetics, vol. 188, no. 3, pp. 647-61, 2011.
Reproduction
G. I. Lang, Murray, A. W., and Botstein, D., “The cost of gene expression underlies a fitness trade-off in yeast.”, Proc Natl Acad Sci U S A, vol. 106, no. 14, pp. 5755-60, 2009.
Reproducibility of Results
O. G. Troyanskaya, Garber, M. E., Brown, P. O., Botstein, D., and Altman, R. B., “Nonparametric methods for identifying differentially expressed genes in microarray data.”, Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
N. Novoradovskaya, Whitfield, M. L., Basehore, L. S., Novoradovsky, A., Pesich, R., Usary, J., Karaca, M., Wong, W. K., Aprelikova, O., Fero, M., Perou, C. M., Botstein, D., and Braman, J., “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
Repressor Proteins
M. J. Hickman, Petti, A. A., Ho-Shing, O., Silverman, S. J., R McIsaac, S., Lee, T. A., and Botstein, D., “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
K. S. Smith, Chanda, S. K., Lingbeek, M., Ross, D. T., Botstein, D., van Lohuizen, M., and Cleary, M. L., “Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1.”, Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
M. Ronen and Botstein, D., “Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.”, Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
Regulon
E. W. Trotter, Kao, C. M. - F., Berenfeld, L., Botstein, D., Petsko, G. A., and Gray, J. V., “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
Regulatory Sequences, Nucleic Acid
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
Regression Analysis
M. J. Brauer, Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., and Botstein, D., “Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.”, Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
Reference Values
O. G. Troyanskaya, Garber, M. E., Brown, P. O., Botstein, D., and Altman, R. B., “Nonparametric methods for identifying differentially expressed genes in microarray data.”, Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
Reference Standards
N. Novoradovskaya, Whitfield, M. L., Basehore, L. S., Novoradovsky, A., Pesich, R., Usary, J., Karaca, M., Wong, W. K., Aprelikova, O., Fero, M., Perou, C. M., Botstein, D., and Braman, J., “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
Recurrence
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
Recombination, Genetic
D. Gresham, Usaite, R., Germann, S. Manuela, Lisby, M., Botstein, D., and Regenberg, B., “Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.”, Proc Natl Acad Sci U S A, vol. 107, no. 43, pp. 18551-6, 2010.
Recombinant Fusion Proteins
S. R McIsaac, Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., and Noyes, M. B., “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
Receptors, IgE
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J., “Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”, BMC Immunol, vol. 3, p. 5, 2002.
Receptors, Estrogen
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., “Gene expression patterns in ovarian carcinomas.”, Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
S. R McIsaac, Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., and Noyes, M. B., “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
Receptors, Antigen, T-Cell
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Receptors, Androgen
H. Zhao, Whitfield, M. L., Xu, T., Botstein, D., and Brooks, J. D., “Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells.”, Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
Receptors, Adrenergic, beta-1
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
Receptor, Epidermal Growth Factor
T. O. Nielsen, Hsu, F. D., O'Connell, J. X., C Gilks, B., Sorensen, P. H. B., Linn, S., West, R. B., Liu, C. Long, Botstein, D., Brown, P. O., and van de Rijn, M., “Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology.”, Am J Pathol, vol. 163, no. 4, pp. 1449-56, 2003.
Rats
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A., “SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”, Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
N. Novoradovskaya, Whitfield, M. L., Basehore, L. S., Novoradovsky, A., Pesich, R., Usary, J., Karaca, M., Wong, W. K., Aprelikova, O., Fero, M., Perou, C. M., Botstein, D., and Braman, J., “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
ras Proteins
A. Z. Welch, Gibney, P. A., Botstein, D., and Koshland, D. E., “TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
Quaternary Ammonium Compounds
V. M. Boer, Crutchfield, C. A., Bradley, P. H., Botstein, D., and Rabinowitz, J. D., “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
Quality Control
J. Gollub, Ball, C. A., Binkley, G., Demeter, J., Finkelstein, D. B., Hebert, J. M., Hernandez-Boussard, T., Jin, H., Kaloper, M., Matese, J. C., Schroeder, M., Brown, P. O., Botstein, D., and Sherlock, G., “The Stanford Microarray Database: data access and quality assessment tools.”, Nucleic Acids Res, vol. 31, no. 1, pp. 94-6, 2003.
Pyrimidines
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Purines
M. Shakoury-Elizeh, Tiedeman, J., Rashford, J., Ferea, T., Demeter, J., Garcia, E., Rolfes, R., Brown, P. O., Botstein, D., and Philpott, C. C., “Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
Proto-Oncogene Proteins c-abl
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Proto-Oncogene Proteins
K. S. Smith, Chanda, S. K., Lingbeek, M., Ross, D. T., Botstein, D., van Lohuizen, M., and Cleary, M. L., “Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1.”, Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
Proteomics
R. Nash, Weng, S., Hitz, B., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Livstone, M. S., Oughtred, R., Park, J., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Dolinski, K., Botstein, D., and J Cherry, M., “Expanded protein information at SGD: new pages and proteome browser.”, Nucleic Acids Res, vol. 35, no. Database issue, pp. D468-71, 2007.
Proteome
E. M. Airoldi, Huttenhower, C., Gresham, D., Lu, C., Caudy, A. A., Dunham, M. J., Broach, J. R., Botstein, D., and Troyanskaya, O. G., “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
Proteins
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A., “SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”, Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
D. Botstein, “Genome-sequencing anniversary. Fruits of genome sequences for biology.”, Science, vol. 331, no. 6020, p. 1025, 2011.
M. L. Whitfield, Sherlock, G., Saldanha, A. J., Murray, J. I., Ball, C. A., Alexander, K. E., Matese, J. C., Perou, C. M., Hurt, M. M., Brown, P. O., and Botstein, D., “Identification of genes periodically expressed in the human cell cycle and their expression in tumors.”, Mol Biol Cell, vol. 13, no. 6, pp. 1977-2000, 2002.
Protein-Serine-Threonine Kinases
M. Ronen and Botstein, D., “Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.”, Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
Protein Transport
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O., “Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”, Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Protein Synthesis Inhibitors
E. W. Trotter, Kao, C. M. - F., Berenfeld, L., Botstein, D., Petsko, G. A., and Gray, J. V., “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
Protein Structure, Tertiary
S. R McIsaac, Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., and Noyes, M. B., “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
S. R. Engel, Balakrishnan, R., Binkley, G., Christie, K. R., Costanzo, M. C., Dwight, S. S., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Hong, E. L., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R., Oughtred, R., Park, J., Skrzypek, M. S., Weng, S., Wong, E. D., Dolinski, K., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database provides mutant phenotype data.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
Protein Sorting Signals
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O., “Genome-scale identification of membrane-associated human mRNAs.”, PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Protein Kinase C
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Protein Interaction Maps
D. Botstein and Fink, G. R., “Yeast: an experimental organism for 21st Century biology.”, Genetics, vol. 189, no. 3, pp. 695-704, 2011.
Protein Interaction Mapping
T. Reguly, Breitkreutz, A., Boucher, L., Breitkreutz, B. - J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., and Tyers, M., “Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.”, J Biol, vol. 5, no. 4, p. 11, 2006.
O. G. Troyanskaya, Dolinski, K., Owen, A. B., Altman, R. B., and Botstein, D., “A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8348-53, 2003.
Protein Folding
E. W. Trotter, Kao, C. M. - F., Berenfeld, L., Botstein, D., Petsko, G. A., and Gray, J. V., “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
Protein Engineering
S. R McIsaac, Oakes, B. L., Botstein, D., and Noyes, M. B., “Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters.”, J Vis Exp, no. 81, p. e51153, 2013.
Protein Conformation
E. S. Click, Stearns, T., and Botstein, D., “Systematic structure-function analysis of the small GTPase Arf1 in yeast.”, Mol Biol Cell, vol. 13, no. 5, pp. 1652-64, 2002.
Protein Binding
S. R McIsaac, Petti, A. A., Bussemaker, H. J., and Botstein, D., “Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 2993-3007, 2012.
Proteasome Endopeptidase Complex
K. M. Doherty, Pride, L. D., Lukose, J., Snydsman, B. E., Charles, R., Pramanik, A., Muller, E. G., Botstein, D., and Moore, C. Wood, “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), vol. 2, no. 8, pp. 943-59, 2012.
Prostatic Neoplasms
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
H. Zhao, Whitfield, M. L., Xu, T., Botstein, D., and Brooks, J. D., “Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells.”, Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
Prostate-Specific Antigen
H. Zhao, Whitfield, M. L., Xu, T., Botstein, D., and Brooks, J. D., “Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells.”, Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
Prospective Studies
T. Sørlie, Perou, C. M., Fan, C., Geisler, S., Aas, T., Nobel, A., Anker, G., Akslen, L. A., Botstein, D., Børresen-Dale, A. - L., and Lønning, P. Eystein, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
Promoter Regions, Genetic
N. D. Trinklein, Murray, J. I., Hartman, S. J., Botstein, D., and Myers, R. M., “The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response.”, Mol Biol Cell, vol. 15, no. 3, pp. 1254-61, 2004.
S. R McIsaac, Silverman, S. J., McClean, M. N., Gibney, P. A., Macinskas, J., Hickman, M. J., Petti, A. A., and Botstein, D., “Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 22, no. 22, pp. 4447-59, 2011.
H. Yoshimoto, Saltsman, K., Gasch, A. P., Li, H. Xia, Ogawa, N., Botstein, D., Brown, P. O., and Cyert, M. S., “Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 34, pp. 31079-88, 2002.
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
Programming Languages
E. I. Boyle, Weng, S., Gollub, J., Jin, H., Botstein, D., J Cherry, M., and Sherlock, G., “GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.”, Bioinformatics, vol. 20, no. 18, pp. 3710-5, 2004.
Prognosis
J. Lapointe, Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R., “Gene expression profiling identifies clinically relevant subtypes of prostate cancer.”, Proc Natl Acad Sci U S A, vol. 101, no. 3, pp. 811-6, 2004.
M. van de Rijn, Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, O., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Köchli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., and Brown, P., “Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.”, Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
H. Y. Chang, Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. - T., van de Rijn, M., Botstein, D., and Brown, P. O., “Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.”, PLoS Biol, vol. 2, no. 2, p. E7, 2004.
S. Y. Leung, Chen, X., Chu, K. M., Yuen, S. T., Mathy, J., Ji, J., S Y Chan, A., Li, R., Law, S., Troyanskaya, O. G., Tu, I. - P., Wong, J., So, S., Botstein, D., and Brown, P. O., “Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16203-8, 2002.
I. S. Lossos, Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., and Levy, R., “Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.”, N Engl J Med, vol. 350, no. 18, pp. 1828-37, 2004.
Probability
J. Akiko Heck, Gresham, D., Botstein, D., and Alani, E., “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.”, Genetics, vol. 174, no. 1, pp. 519-23, 2006.
Principal Component Analysis
M. Wyart, Botstein, D., and Wingreen, N. S., “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
Primary Cell Culture
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
Potassium
D. C. Hess, Lu, W., Rabinowitz, J. D., and Botstein, D., “Ammonium toxicity and potassium limitation in yeast.”, PLoS Biol, vol. 4, no. 11, p. e351, 2006.
Population Density
G. I. Lang, Botstein, D., and Desai, M. M., “Genetic variation and the fate of beneficial mutations in asexual populations.”, Genetics, vol. 188, no. 3, pp. 647-61, 2011.
Polymorphism, Single Nucleotide
D. Botstein and Risch, N., “Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease.”, Nat Genet, vol. 33 Suppl, pp. 228-37, 2003.
M. J. Hickman, Petti, A. A., Ho-Shing, O., Silverman, S. J., R McIsaac, S., Lee, T. A., and Botstein, D., “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
D. Gresham, Curry, B., Ward, A., D Gordon, B., Brizuela, L., Kruglyak, L., and Botstein, D., “Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.”, Proc Natl Acad Sci U S A, vol. 107, no. 4, pp. 1482-7, 2010.
D. Gresham, Ruderfer, D. M., Pratt, S. C., Schacherer, J., Dunham, M. J., Botstein, D., and Kruglyak, L., “Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray.”, Science, vol. 311, no. 5769, pp. 1932-6, 2006.

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