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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Ubiquitin
G. Liu, Rogers, J., Murphy, C. T., and Rongo, C., “EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan.”, EMBO J, vol. 30, no. 15, pp. 2990-3003, 2011.
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.
Ubiquitin Thiolesterase
L. J. Kurihara, Kikuchi, T., Wada, K., and Tilghman, S. M., “Loss of Uch-L1 and Uch-L3 leads to neurodegeneration, posterior paralysis and dysphagia.”, Hum Mol Genet, vol. 10, no. 18, pp. 1963-70, 2001.
L. J. Kurihara, Semenova, E., Levorse, J. M., and Tilghman, S. M., “Expression and functional analysis of Uch-L3 during mouse development.”, Mol Cell Biol, vol. 20, no. 7, pp. 2498-504, 2000.
E. Semenova, Wang, X. F., Jablonski, M. M., Levorse, J., and Tilghman, S. M., “An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina.”, Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
Ubiquitin-Protein Ligase Complexes
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.
Ubiquitin-Protein Ligases
D. Ghersi and Singh, M., “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
S. L. Grady, Hwang, J., Vastag, L., Rabinowitz, J. D., and Shenk, T., “Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase.”, J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
S. De Renzis, Yu, J., Zinzen, R., and Wieschaus, E., “Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway.”, Dev Cell, vol. 10, no. 2, pp. 257-64, 2006.
Ubiquitination
M. Anna Carbone, Ayroles, J. F., Yamamoto, A., Morozova, T. V., West, S. A., Magwire, M. M., Mackay, T. F. C., and Anholt, R. R. H., “Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma.”, PLoS One, vol. 4, no. 1, p. e4216, 2009.
Ultraviolet Rays
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.
United States
S. M. Tilghman, “Lessons learned, promises kept: a biologist's eye view of the Genome Project.”, Genome Res, vol. 6, no. 9, pp. 773-80, 1996.
D. Botstein, “Lasker∼Koshland to genetics pioneer.”, Cell, vol. 158, no. 6, pp. 1230-2, 2014.
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.
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.
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.
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W., “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
Universities
W. Bialek and Botstein, D., “Introductory science and mathematics education for 21st-Century biologists.”, Science, vol. 303, no. 5659, pp. 788-90, 2004.
Untranslated Regions
D. Papatsenko, Kislyuk, A., Levine, M., and Dubchak, I., “Conservation patterns in different functional sequence categories of divergent Drosophila species.”, Genomics, vol. 88, no. 4, pp. 431-42, 2006.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., “Positive and negative selection on noncoding DNA in Drosophila simulans.”, Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
Up-Regulation
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.
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., “The transcription/migration interface in heart precursors of Ciona intestinalis.”, Science, vol. 320, no. 5881, pp. 1349-52, 2008.
Uracil
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.
M. Louis Reaves, Young, B. D., Hosios, A. M., Xu, Y. - F., and Rabinowitz, J. D., “Pyrimidine homeostasis is accomplished by directed overflow metabolism.”, Nature, vol. 500, no. 7461, pp. 237-41, 2013.
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.
Uridine Monophosphate
M. Louis Reaves, Young, B. D., Hosios, A. M., Xu, Y. - F., and Rabinowitz, J. D., “Pyrimidine homeostasis is accomplished by directed overflow metabolism.”, Nature, vol. 500, no. 7461, pp. 237-41, 2013.
Uridine Triphosphate
J. D. Rabinowitz, Hsiao, J. J., Gryncel, K. R., Kantrowitz, E. R., Feng, X. - J., Li, G., and Rabitz, H., “Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase.”, Biochemistry, vol. 47, no. 21, pp. 5881-8, 2008.
Urochordata
A. Stolfi and Levine, M., “Neuronal subtype specification in the spinal cord of a protovertebrate.”, Development, vol. 138, no. 5, pp. 995-1004, 2011.
N. Harafuji, Keys, D. N., and Levine, M., “Genome-wide identification of tissue-specific enhancers in the Ciona tadpole.”, Proc Natl Acad Sci U S A, vol. 99, no. 10, pp. 6802-5, 2002.
A. Di Gregorio and Levine, M., “Analyzing gene regulation in ascidian embryos: new tools for new perspectives.”, Differentiation, vol. 70, no. 4-5, pp. 132-9, 2002.
Urodela
E. Schneidman, Berry, M. J., Segev, R., and Bialek, W., “Weak pairwise correlations imply strongly correlated network states in a neural population.”, Nature, vol. 440, no. 7087, pp. 1007-12, 2006.
G. Tkačik, Marre, O., Amodei, D., Schneidman, E., Bialek, W., and Berry, M. J., “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
User-Computer Interface
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.
R. S. G. Sealfon, Hibbs, M. A., Huttenhower, C., Myers, C. L., and Troyanskaya, O. G., “GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.”, BMC Bioinformatics, vol. 7, p. 443, 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.
C. L. Myers, Chen, X., and Troyanskaya, O. G., “Visualization-based discovery and analysis of genomic aberrations in microarray data.”, BMC Bioinformatics, vol. 6, p. 146, 2005.
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. A. Hibbs, Dirksen, N. C., Li, K., and Troyanskaya, O. G., “Visualization methods for statistical analysis of microarray clusters.”, BMC Bioinformatics, vol. 6, p. 115, 2005.
“The Gene Ontology in 2010: extensions and refinements.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D331-5, 2010.
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.
G. Wallace, Anshus, O. J., Bi, P., Chen, H., Chen, Y., Clark, D., Cook, P., Finkelstein, A., Funkhouser, T., Gupta, A., Hibbs, M., Li, K., Liu, Z., Samanta, R., Sukthankar, R., and Troyanskaya, O., “Tools and applications for large-scale display walls.”, IEEE Comput Graph Appl, vol. 25, no. 4, pp. 24-33, 2005.
C. Huttenhower, Schroeder, M., Chikina, M. D., and Troyanskaya, O. G., “The Sleipnir library for computational functional genomics.”, Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
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.
O. G. Troyanskaya, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 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.
C. S. Greene and Troyanskaya, O. G., “PILGRM: an interactive data-driven discovery platform for expert biologists.”, Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
Uterine Neoplasms
D. Munro, Ghersi, D., and Singh, M., “Two critical positions in zinc finger domains are heavily mutated in three human cancer types.”, PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.