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  [Clear All Filters]
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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.
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.
J. I. Kliegman, Fiedler, D., Ryan, C. J., Xu, Y. - F., Su, X. - Y., Thomas, D., Caccese, M. C., Cheng, A., Shales, M., Rabinowitz, J. D., Krogan, N. J., and Shokat, K. M., Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae., Cell Rep, vol. 5, no. 6, pp. 1725-36, 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.
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.
Y. Guan, Dunham, M. J., Troyanskaya, O. G., and Caudy, A. A., Comparative gene expression between two yeast species., BMC Genomics, vol. 14, p. 33, 2013.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., Comparing genomic expression patterns across species identifies shared transcriptional profile in aging., Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
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.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis., PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
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.
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.
N. S. Wingreen and Levin, S. A., Cooperation among microorganisms., PLoS Biol, vol. 4, no. 9, p. e299, 2006.
P. H. Bradley, Brauer, M. J., Rabinowitz, J. D., and Troyanskaya, O. G., Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
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.
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.
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.
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.
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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.
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.
J. S. Breunig, Hackett, S. R., Rabinowitz, J. D., and Kruglyak, L., Genetic basis of metabolome variation in yeast., PLoS Genet, vol. 10, no. 3, p. e1004142, 2014.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., The genetic landscape of a cell., Science, vol. 327, no. 5964, pp. 425-31, 2010.
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.
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.
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. 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, 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.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
J. M. Rossi, Burke, D. T., Leung, J. C., Koos, D. S., Chen, H., and Tilghman, S. M., Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts., Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
J. A. Brown, Sherlock, G., Myers, C. L., Burrows, N. M., Deng, C., H Wu, I., McCann, K. E., Troyanskaya, O. G., and J Brown, M., Global analysis of gene function in yeast by quantitative phenotypic profiling., Mol Syst Biol, vol. 2, p. 2006.0001, 2006.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., A global genetic interaction network maps a wiring diagram of cellular function., Science, vol. 353, no. 6306, 2016.
J. A. Capra, Paeschke, K., Singh, M., and Zakian, V. A., G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 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.
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J. S. Bloom, Khan, Z., Kruglyak, L., Singh, M., and Caudy, A. A., Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays., BMC Genomics, vol. 10, p. 221, 2009.
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.
W. Lu, Clasquin, M. F., Melamud, E., Amador-Noguez, D., Caudy, A. A., and Rabinowitz, J. D., Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer., Anal Chem, vol. 82, no. 8, pp. 3212-21, 2010.
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.
O. Troyanskaya, Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R. B., Missing value estimation methods for DNA microarrays., Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies., Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
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.
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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.
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.
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.
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, 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.
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, 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.
C. Huttenhower, Hibbs, M., Myers, C., and Troyanskaya, O. G., A scalable method for integration and functional analysis of multiple microarray datasets., Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
Y. Pritykin and Singh, M., Simple topological features reflect dynamics and modularity in protein interaction networks., PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
C. Y. Park, Hess, D. C., Huttenhower, C., and Troyanskaya, O. G., Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components., PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
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.
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, 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.
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.
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.
J. Choi, Rajagopal, A., Xu, Y. - F., Rabinowitz, J. D., and O'Shea, E. K., A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae., PLoS One, vol. 12, no. 5, p. e0176085, 2017.
Y. Guan, Dunham, M., Caudy, A., and Troyanskaya, O., Systematic planning of genome-scale experiments in poorly studied species., PLoS Comput Biol, vol. 6, no. 3, p. e1000698, 2010.
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.