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Mona Singh, PhD

Publications since 2011

Nadimpalli, S. Persikov, A. V. Singh, M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet, 11:e1005011, . (PMID: 25748510)

Persikov, A. V. Wetzel, J. L. Rowland, E. F. Oakes, B. L. Xu, D. J. Singh, M. Noyes, M. B. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res, In process, . (PMID: 25593323)

Ghersi, D. Singh, M. molBLOCKS: Decomposing small molecule sets and uncovering enriched fragments. Bioinformatics, 30:2081-2083, . (PMID: 24681908, PMCID: PMC4080744)

Jiang, P. Singh, M. CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Res, 42:2833-2847, . (PMID: 24366875, PMCID: PMC3950699)

Persikov, A. V. Rowland, E. F. Oakes, B. L. Singh, M. 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, 42:1497-1508, . (PMID: 24214968, PMCID: PMC3919609)

Ghersi, D. Singh, M. Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Res, 42:e18, . (PMID: 24362839, PMCID: PMC3919581)

Persikov, A. V. Singh, M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res, 42:97-108, . (PMID: 24097433, PMCID: PMC3874201)

Jiang, P. Singh, M. Coller, H. A. Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay. PLoS Comput Biol, 9:e1003075, . (PMID: 23737738, PMCID: PMC3667768)

Berger, B. Peng, J. Singh, M. Computational solutions for omics data. Nat Rev Genet, 14:333-346, . (PMID: 23594911, PMCID: PMC3966295)

Song, J. 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, 9:e1002910, . (PMID: 23436988, PMCID: PMC3578755)

Ghersi, D. Singh, M. Disentangling function from topology to infer the network properties of disease genes. BMC Syst Biol, 7:5, . (PMID: 23324116, PMCID: PMC3614482)

Pritykin, Y. Singh, M. Simple topological features reflect dynamics and modularity in protein interaction networks. PLoS Comput Biol, 9:e1003243, . (PMID: 24130468, PMCID: PMC3794914)

Khan, Z. Bloom, J. S. Amini, S. Singh, M. Perlman, D. H. Caudy, A. A. Kruglyak, L. Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Mol Syst Biol, 8:602, . (PMID: 22893000, PMCID: PMC3435501)

Kingsford, C. Zaslavsky, E. Singh, M. A cost-aggregating integer linear program for motif finding. J Discrete Algorithms (Amst), 9:326-334, . (PMID: 22081765, PMCID: PMC3212737)

Pane, A. Jiang, P. Zhao, D. Y. Singh, M. Schupbach, T. The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. EMBO J, 30:4601-4615, . (PMID: 21952049, PMCID: PMC3243597)

Persikov, A. V. Singh, M. An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. Phys Biol, 8:035010, . (PMID: 21572177, PMCID: PMC3402046)

Khan, Z. Amini, S. Bloom, J. S. Ruse, C. Caudy, A. A. Kruglyak, L. Singh, M. Perlman, D. H. Tavazoie, S. Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. Genome Biol, 12:R122, . (PMID: 22182234, PMCID: PMC3334617)

Ochoa, A. Llinas, M. Singh, M. Using context to improve protein domain identification. BMC Bioinformatics, 12:90, . (PMID: 21453511, PMCID: PMC3090354)