List of Faculty Publications

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

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Journal Article
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.
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.
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.
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.
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. 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.
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 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. 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. 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.
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.
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.
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.
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.
S. R McIsaac, Silverman, S. J., McClean, M. N., Gibney, P. A., Macinskas, J., Hickman, M. J., Petti, A. A., and Botstein, D., “Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 22, no. 22, pp. 4447-59, 2011.
S. R McIsaac, Silverman, S. J., McClean, M. N., Gibney, P. A., Macinskas, J., Hickman, M. J., Petti, A. A., and Botstein, D., “Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 22, no. 22, pp. 4447-59, 2011.
S. 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.
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. 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.
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.
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. 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.
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. 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.
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.
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.
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. 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.
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.
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.
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.
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.
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.
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.
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.
G. I. Lang, Rice, D. P., Hickman, M. J., Sodergren, E., Weinstock, G. M., Botstein, D., and Desai, M. M., “Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.”, Nature, vol. 500, no. 7464, pp. 571-4, 2013.
S. 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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. 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.
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.
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.
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.
M. Ronen and Botstein, D., “Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.”, Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
S. 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.
D. Botstein, “Why we need more basic biology research, not less.”, Mol Biol Cell, vol. 23, no. 21, pp. 4160-1, 2012.