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: Keyword is Genome  [Clear All Filters]
2013
M. Schumer, Cui, R., Boussau, B., Walter, R., Rosenthal, G., and Andolfatto, P., “An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.”, Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
R. B. Corbett-Detig, Zhou, J., Clark, A. G., Hartl, D. L., and Ayroles, J. F., “Genetic incompatibilities are widespread within species.”, Nature, vol. 504, no. 7478, pp. 135-7, 2013.
2012
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., “Genomic variation and its impact on gene expression in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
M. Lagha, Bothma, J. P., and Levine, M., “Mechanisms of transcriptional precision in animal development.”, Trends Genet, vol. 28, no. 8, pp. 409-16, 2012.
2011
K. C. Rowe, Singhal, S., Macmanes, M. D., Ayroles, J. F., Morelli, T. Lyn, Rubidge, E. M., Bi, K., and Moritz, C. C., “Museum genomics: low-cost and high-accuracy genetic data from historical specimens.”, Mol Ecol Resour, vol. 11, no. 6, pp. 1082-92, 2011.
2010
D. Hendrix, Levine, M., and Shi, W., “miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data.”, Genome Biol, vol. 11, no. 4, p. R39, 2010.
2009
C. L. Myers, Chiriac, C., and Troyanskaya, O. G., “Discovering biological networks from diverse functional genomic data.”, Methods Mol Biol, vol. 563, pp. 157-75, 2009.
J. F. Ayroles, Hughes, K. A., Rowe, K. C., Reedy, M. M., Rodriguez-Zas, S. L., Drnevich, J. M., Cáceres, C. E., and Paige, K. N., “A genomewide assessment of inbreeding depression: gene number, function, and mode of action.”, Conserv Biol, vol. 23, no. 4, pp. 920-30, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., “The sea squirt Ciona intestinalis.”, Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.emo138, 2009.
A. J. Butte, Sarkar, I. Neil, Ramoni, M., Lussier, Y., and Troyanskaya, O., “Selected proceedings of the First Summit on Translational Bioinformatics 2008.”, BMC Bioinformatics, vol. 10 Suppl 2, p. I1, 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.
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.
2005
D. J. Katz, Beer, M. A., Levorse, J. M., and Tilghman, S. M., “Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 25, no. 10, pp. 3855-63, 2005.
W. Shi, Levine, M., and Davidson, B., “Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis.”, Genome Res, vol. 15, no. 12, pp. 1668-74, 2005.
2004
A. Stathopoulos and Levine, M., “Whole-genome analysis of Drosophila gastrulation.”, Curr Opin Genet Dev, vol. 14, no. 5, pp. 477-84, 2004.
2002
M. Markstein and Levine, M., “Decoding cis-regulatory DNAs in the Drosophila genome.”, Curr Opin Genet Dev, vol. 12, no. 5, pp. 601-6, 2002.
B. P. Berman, Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B., “Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 757-62, 2002.
M. Markstein, Markstein, P., Markstein, V., and Levine, M. S., “Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 763-8, 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.
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.
O. G. Troyanskaya, Arbell, O., Koren, Y., Landau, G. M., and Bolshoy, A., “Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.”, Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
A. Stathopoulos, Van Drenth, M., Erives, A., Markstein, M., and Levine, M., “Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo.”, Cell, vol. 111, no. 5, pp. 687-701, 2002.
A. Stathopoulos and Levine, M., “Whole-genome expression profiles identify gene batteries in Drosophila.”, Dev Cell, vol. 3, no. 4, pp. 464-5, 2002.
2000
O. G. Vukmirovic and Tilghman, S. M., “Exploring genome space.”, Nature, vol. 405, no. 6788, pp. 820-2, 2000.
1998
T. Schupbach and Wieschaus, E., “Probing for gene specificity in epithelial development.”, Int J Dev Biol, vol. 42, no. 3, pp. 249-55, 1998.
1992
J. M. Rossi, Burke, D. T., Leung, J. C., Koos, D. S., Chen, H., and Tilghman, S. M., “Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts.”, Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
E. D. Schejter, Rose, L. S., Postner, M. A., and Wieschaus, E., “Role of the zygotic genome in the restructuring of the actin cytoskeleton at the cycle-14 transition during Drosophila embryogenesis.”, Cold Spring Harb Symp Quant Biol, vol. 57, pp. 653-9, 1992.