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

Filters: Keyword is Saccharomyces cerevisiae and Author is Botstein, David  [Clear All Filters]
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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.
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.
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.
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.
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.
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.
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. 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.
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. 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.
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.
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.
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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, 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.
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.
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.
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.
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.
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.
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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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.