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. 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.
P. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies., BMC Bioinformatics, vol. 9, p. 458, 2008.
R. Godbout and Tilghman, S. M., Configuration of the alpha-fetoprotein regulatory domain during development., Genes Dev, vol. 2, no. 8, pp. 949-56, 1988.
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.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study., PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
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.
J. Song and Singh, M., From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization., PLoS Comput Biol, vol. 9, no. 2, p. e1002910, 2013.
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.
J. Mulholland and Botstein, D., Immunoelectron microscopy of aldehyde-fixed yeast cells., Methods Enzymol, vol. 351, pp. 50-81, 2002.
D. Botstein, Ira Herskowitz: 1946-2003., Genetics, vol. 166, no. 2, pp. 653-60, 2004.
C. A. Crutchfield, Lu, W., Melamud, E., and Rabinowitz, J. D., Mass spectrometry-based metabolomics of yeast., Methods Enzymol, vol. 470, pp. 393-426, 2010.
A. Baryshnikova, Costanzo, M., Kim, Y., Ding, H., Koh, J., Toufighi, K., Youn, J. - Y., Ou, J., San Luis, B. - J., Bandyopadhyay, S., Hibbs, M., Hess, D., Gingras, A. - C., Bader, G. D., Troyanskaya, O. G., Brown, G. W., Andrews, B., Boone, C., and Myers, C. L., Quantitative analysis of fitness and genetic interactions in yeast on a genome scale., Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
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.
P. T. Merrill, Sweeton, D., and Wieschaus, E., Requirements for autosomal gene activity during precellular stages of Drosophila melanogaster., Development, vol. 104, no. 3, pp. 495-509, 1988.
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.
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., Yeast cells can access distinct quiescent states., Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.