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 Amino Acid Sequence  [Clear All Filters]
2018
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.
2017
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
2012
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
2011
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S., “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
A. Ochoa, Llinás, M., and Singh, M., “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
2010
T. Mora, Walczak, A. M., Bialek, W., and Callan, C. G., “Maximum entropy models for antibody diversity.”, Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
2009
J. Doran Cande, Chopra, V. S., and Levine, M., “Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum.”, Development, vol. 136, no. 18, pp. 3153-60, 2009.
A. V. Persikov, Osada, R., and Singh, M., “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
2008
J. A. Capra and Singh, M., “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
L. R. Swem, Swem, D. L., Wingreen, N. S., and Bassler, B. L., “Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”, Cell, vol. 134, no. 3, pp. 461-73, 2008.
2007
J. A. Capra and Singh, M., “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
2005
C. L. Kingsford, Chazelle, B., and Singh, M., “Solving and analyzing side-chain positioning problems using linear and integer programming.”, Bioinformatics, vol. 21, no. 7, pp. 1028-36, 2005.
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.
D. H. Lenz, Mok, K. C., Lilley, B. N., Kulkarni, R. V., Wingreen, N. S., and Bassler, B. L., “The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.”, Cell, vol. 118, no. 1, pp. 69-82, 2004.
2002
C. Hunter, Sung, P., Schejter, E. D., and Wieschaus, E., “Conserved domains of the Nullo protein required for cell-surface localization and formation of adherens junctions.”, Mol Biol Cell, vol. 13, no. 1, pp. 146-57, 2002.
E. G. Emberly, Wingreen, N. S., and Tang, C., “Designability of alpha-helical proteins.”, Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
D. J. Brooks, Fresco, J. R., Lesk, A. M., and Singh, M., “Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.”, Mol Biol Evol, vol. 19, no. 10, pp. 1645-55, 2002.
J. A. Zallen, Cohen, Y., Hudson, A. M., Cooley, L., Wieschaus, E., and Schejter, E. D., “SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila.”, J Cell Biol, vol. 156, no. 4, pp. 689-701, 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.
2001
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
2000
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.
J. Grosshans and Wieschaus, E., “A genetic link between morphogenesis and cell division during formation of the ventral furrow in Drosophila.”, Cell, vol. 101, no. 5, pp. 523-31, 2000.
1997
S. Hayashi, Rubinfeld, B., Souza, B., Polakis, P., Wieschaus, E., and Levine, A. J., “A Drosophila homolog of the tumor suppressor gene adenomatous polyposis coli down-regulates beta-catenin but its zygotic expression is not essential for the regulation of Armadillo.”, Proc Natl Acad Sci U S A, vol. 94, no. 1, pp. 242-7, 1997.
1995
A. Bejsovec and Wieschaus, E., “Signaling activities of the Drosophila wingless gene are separately mutable and appear to be transduced at the cell surface.”, Genetics, vol. 139, no. 1, pp. 309-20, 1995.
1994
K. D. Irvine and Wieschaus, E., “fringe, a Boundary-specific signaling molecule, mediates interactions between dorsal and ventral cells during Drosophila wing development.”, Cell, vol. 79, no. 4, pp. 595-606, 1994.
P. Armand, Knapp, A. C., Hirsch, A. J., Wieschaus, E. F., and Cole, M. D., “A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.”, Mol Cell Biol, vol. 14, no. 6, pp. 4145-54, 1994.
M. Costa, Wilson, E. T., and Wieschaus, E., “A putative cell signal encoded by the folded gastrulation gene coordinates cell shape changes during Drosophila gastrulation.”, Cell, vol. 76, no. 6, pp. 1075-89, 1994.
1993
E. D. Schejter and Wieschaus, E., “bottleneck acts as a regulator of the microfilament network governing cellularization of the Drosophila embryo.”, Cell, vol. 75, no. 2, pp. 373-85, 1993.
C. Rauskolb, Peifer, M., and Wieschaus, E., “extradenticle, a regulator of homeotic gene activity, is a homolog of the homeobox-containing human proto-oncogene pbx1.”, Cell, vol. 74, no. 6, pp. 1101-12, 1993.
M. Peifer and Wieschaus, E., “The product of the Drosophila melanogaster segment polarity gene armadillo is highly conserved in sequence and expression in the housefly Musca domestica.”, J Mol Evol, vol. 36, no. 3, pp. 224-33, 1993.
1992
L. S. Rose and Wieschaus, E., “The Drosophila cellularization gene nullo produces a blastoderm-specific transcript whose levels respond to the nucleocytoplasmic ratio.”, Genes Dev, vol. 6, no. 7, pp. 1255-68, 1992.
M. Peifer, McCrea, P. D., Green, K. J., Wieschaus, E., and Gumbiner, B. M., “The vertebrate adhesive junction proteins beta-catenin and plakoglobin and the Drosophila segment polarity gene armadillo form a multigene family with similar properties.”, J Cell Biol, vol. 118, no. 3, pp. 681-91, 1992.
1991
S. Parks and Wieschaus, E., “The Drosophila gastrulation gene concertina encodes a G alpha-like protein.”, Cell, vol. 64, no. 2, pp. 447-58, 1991.
1990
D. E. Coulter, Swaykus, E. A., Beran-Koehn, M. A., Goldberg, D., Wieschaus, E., and Schedl, P., “Molecular analysis of odd-skipped, a zinc finger encoding segmentation gene with a novel pair-rule expression pattern.”, EMBO J, vol. 9, no. 11, pp. 3795-804, 1990.
C. I. Brannan, Dees, E. C., Ingram, R. S., and Tilghman, S. M., “The product of the H19 gene may function as an RNA.”, Mol Cell Biol, vol. 10, no. 1, pp. 28-36, 1990.
M. Peifer and Wieschaus, E., “The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin.”, Cell, vol. 63, no. 6, pp. 1167-76, 1990.
1989
B. Riggleman, Wieschaus, E., and Schedl, P., “Molecular analysis of the armadillo locus: uniformly distributed transcripts and a protein with novel internal repeats are associated with a Drosophila segment polarity gene.”, Genes Dev, vol. 3, no. 1, pp. 96-113, 1989.