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]
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
Databases, Protein
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.
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. 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.
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.
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.
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.
Databases, Nucleic Acid
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.
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.
Databases, Genetic
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.
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. 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Databases as Topic
D. Botstein, It's the data!, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
Culture Media
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.
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.
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. 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. 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.
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.
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.
Computer Graphics
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.
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.
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.
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.
Computational Biology
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.
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.
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. 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.
W. Bialek and Botstein, D., Introductory science and mathematics education for 21st-Century biologists., Science, vol. 303, no. 5659, pp. 788-90, 2004.
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.
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.
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.
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. 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.
Colony Count, Microbial
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.
Cluster Analysis
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.
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.
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.
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.
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.
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.
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. 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.
Chromosomes, Fungal
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. 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. 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.
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.
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.
Cell Division
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. 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.
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.
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.
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.
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.
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.
Cell Cycle
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.
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.
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.
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.
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.
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.
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. 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.
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.
Breast Neoplasms
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. 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. 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.
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.
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. 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.
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.
Biotechnology
D. Botstein, Why we need more basic biology research, not less., Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 2012.
Biology
D. Botstein, Why we need more basic biology research, not less., Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 2012.
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.
Biological Science Disciplines
W. Bialek and Botstein, D., Introductory science and mathematics education for 21st-Century biologists., Science, vol. 303, no. 5659, pp. 788-90, 2004.
Binding Sites
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, 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.
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.
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.
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.
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.
Bibliometrics
D. Botstein, It's the data!, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
Base Sequence
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.
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.
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.
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. 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.

Pages