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: First Letter Of Keyword is M and Author is Singh, Mona  [Clear All Filters]
Journal Article
E. Nabieva, Jim, K., Agarwal, A., Chazelle, B., and Singh, M., “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
E. Nabieva, Jim, K., Agarwal, A., Chazelle, B., and Singh, M., “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
A. Ochoa, Llinás, M., and Singh, M., “Using context to improve protein domain identification.”, BMC Bioinformatics, vol. 12, p. 90, 2011.
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.
S. Nadimpalli Kobren and Singh, M., “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
S. Nadimpalli Kobren and Singh, M., “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
P. Jiang and Singh, M., “SPICi: a fast clustering algorithm for large biological networks.”, Bioinformatics, vol. 26, no. 8, pp. 1105-11, 2010.
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.
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.
Z. Khan, Bloom, J. S., Amini, S., Singh, M., Perlman, D. H., Caudy, A. A., and Kruglyak, L., “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
Z. Khan, Bloom, J. S., Garcia, B. A., Singh, M., and Kruglyak, L., “Protein quantification across hundreds of experimental conditions.”, Proc Natl Acad Sci U S A, vol. 106, no. 37, pp. 15544-8, 2009.
J. H. Fong, Keating, A. E., and Singh, M., “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
J. A. Capra and Singh, M., “Predicting functionally important residues from sequence conservation.”, Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
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.
E. Banks, Nabieva, E., Chazelle, B., and Singh, M., “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
D. Ghersi and Singh, M., “Interaction-based discovery of functionally important genes in cancers.”, Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
Y. Pritykin, Brito, T., Schüpbach, T., Singh, M., and Pane, A., “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
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. 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. 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.
A. V. Persikov and Singh, M., “An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.”, Phys Biol, vol. 8, no. 3, p. 035010, 2011.
A. V. Persikov and Singh, M., “An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.”, Phys Biol, vol. 8, no. 3, p. 035010, 2011.
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.
D. Ghersi and Singh, M., “Disentangling function from topology to infer the network properties of disease genes.”, BMC Syst Biol, vol. 7, p. 5, 2013.
P. F. Przytycki and Singh, M., “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
P. F. Przytycki and Singh, M., “Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.”, Genome Med, vol. 9, no. 1, p. 79, 2017.
A. V. Persikov, Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B., “Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.”, Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
A. Pane, Jiang, P., Zhao, D. Yanling, Singh, M., and Schüpbach, T., “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
K. Jim, Parmar, K., Singh, M., and Tavazoie, S., “A cross-genomic approach for systematic mapping of phenotypic traits to genes.”, Genome Res, vol. 14, no. 1, pp. 109-15, 2004.
P. Jiang, Singh, M., and Coller, H. A., “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
P. Jiang, Singh, M., and Coller, H. A., “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
P. Jiang, Singh, M., and Coller, H. A., “Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.”, PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
J. A. Capra and Singh, M., “Characterization and prediction of residues determining protein functional specificity.”, Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
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.
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.