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: Author is Botstein, David  [Clear All Filters]
2019
P. H. Bradley, Gibney, P. A., Botstein, D., Troyanskaya, O. G., and Rabinowitz, J. D., “Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.”, mSystems, vol. 4, no. 1, 2019.
2018
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. - 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.
2016
H. D. Møller, Bojsen, R. K., Tachibana, C., Parsons, L., Botstein, D., and Regenberg, B., “Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.”, J Vis Exp, no. 110, p. e54239 |, 2016.
S. R. Hackett, Zanotelli, V. R. T., Xu, W., Goya, J., Park, J. O., Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D., and Rabinowitz, J. D., “Systems-level analysis of mechanisms regulating yeast metabolic flux.”, Science, vol. 354, no. 6311, 2016.
2015
P. A. Gibney, Schieler, A., Chen, J. C., Rabinowitz, J. D., and Botstein, D., “Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter.”, Proc Natl Acad Sci U S A, 2015.
2014
D. Botstein, “Lasker∼Koshland to genetics pioneer.”, Cell, vol. 158, no. 6, pp. 1230-2, 2014.
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.
2013
K. Dolinski and Botstein, D., “Automating the construction of gene ontologies.”, Nat Biotechnol, vol. 31, no. 1, pp. 34-5, 2013.
N. Slavov and Botstein, D., “Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression.”, Mol Biol Cell, vol. 24, no. 2, pp. 157-68, 2013.
C. Reisser, Dick, C., Kruglyak, L., Botstein, D., Schacherer, J., and Hess, D., “Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case.”, G3 (Bethesda), 2013.
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.
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.
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.
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.
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.
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.
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.
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.
2012
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.
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.
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.
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, “Why we need more basic biology research, not less.”, Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 2012.
2011
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 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.
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.
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.
D. Botstein, “Genome-sequencing anniversary. Fruits of genome sequences for biology.”, Science, vol. 331, no. 6020, p. 1025, 2011.
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.
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.
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.
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.
D. Botstein and Fink, G. R., “Yeast: an experimental organism for 21st Century biology.”, Genetics, vol. 189, no. 3, pp. 695-704, 2011.
2010
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.
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.
D. Botstein, “It's the data!”, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 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.
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.
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.
D. Botstein, “Technological innovation leads to fundamental understanding in cell biology.”, Mol Biol Cell, vol. 21, no. 22, pp. 3791-2, 2010.
2009
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.
C. Hei Ho, Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., L Y Koh, J., Porter, J., Gray, C. A., Andersen, R. J., Giaever, G., Nislow, C., Andrews, B., Botstein, D., Graham, T. R., Yoshida, M., and Boone, C., “A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.”, Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 2009.
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.
L. Salwinski, Licata, L., Winter, A., Thorneycroft, D., Khadake, J., Ceol, A., Aryamontri, A. Chatr, Oughtred, R., Livstone, M., Boucher, L., Botstein, D., Dolinski, K., Berardini, T., Huala, E., Tyers, M., Eisenberg, D., Cesareni, G., and Hermjakob, H., “Recurated protein interaction datasets.”, Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.
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.
2008
D. Gresham, Dunham, M. J., and Botstein, D., “Comparing whole genomes using DNA microarrays.”, Nat Rev Genet, vol. 9, no. 4, pp. 291-302, 2008.
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.
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.
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.
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.
2007
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.
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.
K. Dolinski and Botstein, D., “Orthology and functional conservation in eukaryotes.”, Annu Rev Genet, vol. 41, pp. 465-507, 2007.
S. Heinicke, Livstone, M. S., Lu, C., Oughtred, R., Kang, F., Angiuoli, S. V., White, O., Botstein, D., and Dolinski, K., “The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.”, PLoS One, vol. 2, no. 8, p. e766, 2007.
2006
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.
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.
N. Wingreen and Botstein, D., “Back to the future: education for systems-level biologists.”, Nat Rev Mol Cell Biol, vol. 7, no. 11, pp. 829-32, 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.
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. 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.
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. 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.
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.
R. J. Pelham, Rodgers, L., Hall, I., Lucito, R., Nguyen, K. C. Q., Navin, N., Hicks, J., Mu, D., Powers, S., Wigler, M., and Botstein, D., “Identification of alterations in DNA copy number in host stromal cells during tumor progression.”, Proc Natl Acad Sci U S A, vol. 103, no. 52, pp. 19848-53, 2006.
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.
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.
D. Botstein, “Willing to do the math: an interview with David Botstein. Interview by Jane Gitschier.”, PLoS Genet, vol. 2, no. 5, p. e79, 2006.
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.
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.
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.
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A., “Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”, Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
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.
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.
2004
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.
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.
J. Isaac Murray, Whitfield, M. L., Trinklein, N. D., Myers, R. M., Brown, P. O., and Botstein, D., “Diverse and specific gene expression responses to stresses in cultured human cells.”, Mol Biol Cell, vol. 15, no. 5, pp. 2361-74, 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.
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. 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.
C. A. Rees, Demeter, J., Matese, J. C., Botstein, D., and Sherlock, G., “GeneXplorer: an interactive web application for microarray data visualization and analysis.”, BMC Bioinformatics, vol. 5, p. 141, 2004.
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.
W. Bialek and Botstein, D., “Introductory science and mathematics education for 21st-Century biologists.”, Science, vol. 303, no. 5659, pp. 788-90, 2004.
D. Botstein, “Ira Herskowitz: 1946-2003.”, Genetics, vol. 166, no. 2, pp. 653-60, 2004.
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J., “A method for detecting and correcting feature misidentification on expression microarrays.”, BMC Genomics, vol. 5, p. 64, 2004.
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.
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.
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.
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.
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.
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.
2003
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.
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.
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.
J. - T. Chi, Chang, H. Y., Haraldsen, G., Jahnsen, F. L., Troyanskaya, O. G., Chang, D. S., Wang, Z., Rockson, S. G., van de Rijn, M., Botstein, D., and Brown, P. O., “Endothelial cell diversity revealed by global expression profiling.”, Proc Natl Acad Sci U S A, vol. 100, no. 19, pp. 10623-8, 2003.
S. C. Linn, West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, iv, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., C Gilks, B., and van de Rijn, M., “Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.”, Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
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.
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.
K. Ranade, Hinds, D., Hsiung, C. Agnes, Chuang, L. - M., Chang, M. - S., Chen, Y. - T., Pesich, R., Hebert, J., Chen, Y. - D. I., Dzau, V., Olshen, R., Curb, D., Botstein, D., Cox, D. R., and Risch, N., “A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins.”, Am J Hypertens, vol. 16, no. 2, pp. 158-62, 2003.
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.
W. R. Uhlmann, Bennett, R., Botkin, J. R., Botstein, D., Boughman, J. A., Chakravarti, A., Clayton, E. Wright, Kahn, J., Koenig, B., Murray, T. H., Olson, M. V., Rowley, J., Terry, S., and Valle, D., “Planning the genome institute's future.”, Science, vol. 299, no. 5612, p. 1515; author reply 1515, 2003.
T. Sorlie, Tibshirani, R., Parker, J., Hastie, T., Marron, J. S., Nobel, A., Deng, S., Johnsen, H., Pesich, R., Geisler, S., Demeter, J., Perou, C. M., Lønning, P. E., Brown, P. O., Børresen-Dale, A. - L., and Botstein, D., “Repeated observation of breast tumor subtypes in independent gene expression data sets.”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8418-23, 2003.
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. 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.
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.
M. L. Whitfield, Finlay, D. R., Murray, J. Isaac, Troyanskaya, O. G., Chi, J. - T., Pergamenschikov, A., McCalmont, T. H., Brown, P. O., Botstein, D., and M Connolly, K., “Systemic and cell type-specific gene expression patterns in scleroderma skin.”, Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 2003.
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.
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.
S. P. Bohen, Troyanskaya, O. G., Alter, O., Warnke, R., Botstein, D., Brown, P. O., and Levy, R., “Variation in gene expression patterns in follicular lymphoma and the response to rituximab.”, Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 2003.
X. Chen, Leung, S. Y., Yuen, S. T., Chu, K. - M., Ji, J., Li, R., S Y Chan, A., Law, S., Troyanskaya, O. G., Wong, J., So, S., Botstein, D., and Brown, P. O., “Variation in gene expression patterns in human gastric cancers.”, Mol Biol Cell, vol. 14, no. 8, pp. 3208-15, 2003.
2002
J. R. Pollack, van de Rijn, M., and Botstein, D., “Challenges in developing a molecular characterization of cancer.”, Semin Oncol, vol. 29, no. 3, pp. 280-5, 2002.
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.
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.
S. S. Jeffrey, Fero, M. J., Børresen-Dale, A. - L., and Botstein, D., “Expression array technology in the diagnosis and treatment of breast cancer.”, Mol Interv, vol. 2, no. 2, pp. 101-9, 2002.
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.
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.
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.
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.
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.
J. Mulholland and Botstein, D., “Immunoelectron microscopy of aldehyde-fixed yeast cells.”, Methods Enzymol, vol. 351, pp. 50-81, 2002.
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.
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.
T. O. Nielsen, West, R. B., Linn, S. C., Alter, O., Knowling, M. A., O'Connell, J. X., Zhu, S., Fero, M., Sherlock, G., Pollack, J. R., Brown, P. O., Botstein, D., and van de Rijn, M., “Molecular characterisation of soft tissue tumours: a gene expression study.”, Lancet, vol. 359, no. 9314, pp. 1301-7, 2002.
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.
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.
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.
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.
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. 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.
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A., “Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
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.
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.
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.
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R., “Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”, Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.