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Mona Singh - Publications

Affiliations: 
Computer Science Princeton University, Princeton, NJ 
Area:
Computational molecular biology, as well as its interface with machine learning and algorithms.
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61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 King SB, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. Plos Computational Biology. 19: e1010966. PMID 36952575 DOI: 10.1371/journal.pcbi.1010966  0.794
2022 Wetzel JL, Zhang K, Singh M. Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings. Genome Research. PMID 36123148 DOI: 10.1101/gr.276606.122  0.785
2021 King SB, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. Plos Computational Biology. 17: e1009560. PMID 34793437 DOI: 10.1371/journal.pcbi.1009560  0.757
2021 Etzion-Fuchs A, Todd DA, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Research. PMID 33999210 DOI: 10.1093/nar/gkab356  0.74
2021 Marmion RA, Yang L, Goyal Y, Jindal GA, Wetzel JL, Singh M, Schüpbach T, Shvartsman SY. Molecular mechanisms underlying cellular effects of human MEK1 mutations. Molecular Biology of the Cell. mbcE20100625. PMID 33476180 DOI: 10.1091/mbc.E20-10-0625  0.73
2020 Munro D, Singh M. DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. Bioinformatics (Oxford, England). PMID 33325500 DOI: 10.1093/bioinformatics/btaa1030  0.682
2020 Kobren SN, Chazelle B, Singh M. PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. Cell Systems. 11: 63-74.e7. PMID 32711844 DOI: 10.1016/J.Cels.2020.06.005  0.782
2020 Hristov BH, Chazelle B, Singh M. uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. Cell Systems. 10: 470-479.e3. PMID 32684276 DOI: 10.1016/J.Cels.2020.05.008  0.352
2019 Wetzel JL, Singh M. Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination. Nucleic Acids Research. PMID 31777934 DOI: 10.1093/Nar/Gkz1087  0.801
2018 Kobren SN, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Research. PMID 30535108 DOI: 10.1093/Nar/Gky1224  0.802
2018 Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. Plos Computational Biology. 14: e1006290. PMID 29953437 DOI: 10.1371/Journal.Pcbi.1006290  0.706
2017 Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Systems. 5: 221-229.e4. PMID 28957656 DOI: 10.1016/J.Cels.2017.09.003  0.325
2017 Pritykin Y, Brito T, Schupbach T, Singh M, Pane A. Integrative analysis unveils new functions for the Drosophila Cutoff protein in non-coding RNA biogenesis and gene regulation. Rna (New York, N.Y.). PMID 28420675 DOI: 10.1261/Rna.058594.116  0.762
2017 Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics (Oxford, England). PMID 28407137 DOI: 10.1093/Bioinformatics/Btx221  0.362
2015 Ochoa A, Storey JD, Llinás M, Singh M. Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. Plos Computational Biology. 11: e1004509. PMID 26575353 DOI: 10.1371/Journal.Pcbi.1004509  0.399
2015 Pritykin Y, Ghersi D, Singh M. Genome-Wide Detection and Analysis of Multifunctional Genes. Plos Computational Biology. 11: e1004467. PMID 26436655 DOI: 10.1371/Journal.Pcbi.1004467  0.77
2015 Nadimpalli S, Persikov AV, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. Plos Genetics. 11: e1005011. PMID 25748510 DOI: 10.1371/Journal.Pgen.1005011  0.38
2015 Persikov AV, Wetzel JL, Rowland EF, Oakes BL, Xu DJ, Singh M, Noyes MB. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Research. 43: 1965-84. PMID 25593323 DOI: 10.1093/Nar/Gku1395  0.79
2014 Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics (Oxford, England). 30: 2081-3. PMID 24681908 DOI: 10.1093/Bioinformatics/Btu173  0.341
2014 Jiang P, Singh M. CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Research. 42: 2833-47. PMID 24366875 DOI: 10.1093/Nar/Gkt1302  0.369
2014 Ghersi D, Singh M. Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Research. 42: e18. PMID 24362839 DOI: 10.1093/Nar/Gkt1305  0.423
2014 Persikov AV, Rowland EF, Oakes BL, Singh M, Noyes MB. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Research. 42: 1497-508. PMID 24214968 DOI: 10.1093/Nar/Gkt1034  0.442
2014 Persikov AV, Singh M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Research. 42: 97-108. PMID 24097433 DOI: 10.1093/Nar/Gkt890  0.464
2013 Pritykin Y, Singh M. Simple topological features reflect dynamics and modularity in protein interaction networks. Plos Computational Biology. 9: e1003243. PMID 24130468 DOI: 10.1371/Journal.Pcbi.1003243  0.774
2013 Jiang P, Singh M, Coller HA. Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay. Plos Computational Biology. 9: e1003075. PMID 23737738 DOI: 10.1371/Journal.Pcbi.1003075  0.313
2013 Berger B, Peng J, Singh M. Computational solutions for omics data. Nature Reviews. Genetics. 14: 333-46. PMID 23594911 DOI: 10.1038/Nrg3433  0.523
2013 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 Computational Biology. 9: e1002910. PMID 23436988 DOI: 10.1371/Journal.Pcbi.1002910  0.651
2012 Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L. Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Molecular Systems Biology. 8: 602. PMID 22893000 DOI: 10.1038/Msb.2012.34  0.32
2011 Kingsford C, Zaslavsky E, Singh M. A cost-aggregating integer linear program for motif finding. Journal of Discrete Algorithms (Amsterdam, Netherlands). 9: 326-334. PMID 22081765 DOI: 10.1016/J.Jda.2011.04.001  0.763
2011 Pane A, Jiang P, Zhao DY, Singh M, Schüpbach T. The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. The Embo Journal. 30: 4601-15. PMID 21952049 DOI: 10.1038/Emboj.2011.334  0.348
2011 Persikov AV, Singh M. An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. Physical Biology. 8: 035010. PMID 21572177 DOI: 10.1088/1478-3975/8/3/035010  0.423
2011 Ochoa A, Llinás M, Singh M. Using context to improve protein domain identification. Bmc Bioinformatics. 12: 90. PMID 21453511 DOI: 10.1186/1471-2105-12-90  0.406
2010 Capra JA, Pollard KS, Singh M. Novel genes exhibit distinct patterns of function acquisition and network integration Genome Biology. 11. PMID 21187012 DOI: 10.1186/Gb-2010-11-12-R127  0.611
2010 Capra JA, Paeschke K, Singh M, Zakian VA. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. Plos Computational Biology. 6: e1000861. PMID 20676380 DOI: 10.1371/Journal.Pcbi.1000861  0.61
2009 Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. Plos Computational Biology. 5: e1000585. PMID 19997483 DOI: 10.1371/Journal.Pcbi.1000585  0.675
2009 Song J, Singh M. How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics (Oxford, England). 25: 3143-50. PMID 19770263 DOI: 10.1093/Bioinformatics/Btp551  0.608
2009 Khan Z, Bloom JS, Garcia BA, Singh M, Kruglyak L. Protein quantification across hundreds of experimental conditions. Proceedings of the National Academy of Sciences of the United States of America. 106: 15544-8. PMID 19717460 DOI: 10.1073/Pnas.0904100106  0.327
2009 Yanover C, Singh M, Zaslavsky E. M are better than one: an ensemble-based motif finder and its application to regulatory element prediction. Bioinformatics (Oxford, England). 25: 868-74. PMID 19223448 DOI: 10.1093/Bioinformatics/Btp090  0.695
2009 Persikov AV, Osada R, Singh M. Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics (Oxford, England). 25: 22-9. PMID 19008249 DOI: 10.1093/Bioinformatics/Btn580  0.72
2009 Banks E, Nabieva E, Chazelle B, Peterson R, Singh M. Analyzing and interrogating biological networks (abstract) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5462: 14-15. DOI: 10.1007/978-3-642-00727-9_2  0.51
2008 Banks E, Nabieva E, Chazelle B, Singh M. Organization of physical interactomes as uncovered by network schemas. Plos Computational Biology. 4: e1000203. PMID 18949022 DOI: 10.1371/Journal.Pcbi.1000203  0.63
2008 Banks E, Nabieva E, Peterson R, Singh M. NetGrep: fast network schema searches in interactomes. Genome Biology. 9: R138. PMID 18801179 DOI: 10.1186/Gb-2008-9-9-R138  0.636
2008 Capra JA, Singh M. Characterization and prediction of residues determining protein functional specificity. Bioinformatics (Oxford, England). 24: 1473-80. PMID 18450811 DOI: 10.1093/Bioinformatics/Btn214  0.649
2007 Capra JA, Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics (Oxford, England). 23: 1875-82. PMID 17519246 DOI: 10.1093/Bioinformatics/Btm270  0.668
2006 Zaslavsky E, Singh M. A combinatorial optimization approach for diverse motif finding applications. Algorithms For Molecular Biology : Amb. 1: 13. PMID 16916460 DOI: 10.1186/1748-7188-1-13  0.697
2006 Kingsford C, Zaslavsky E, Singh M. A compact mathematical programming formulation for DNA motif finding Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4009: 233-245. DOI: 10.1007/11780441_22  0.753
2005 Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics (Oxford, England). 21: i302-10. PMID 15961472 DOI: 10.1093/Bioinformatics/Bti1054  0.413
2005 Kingsford CL, Chazelle B, Singh M. Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics (Oxford, England). 21: 1028-36. PMID 15546935 DOI: 10.1093/Bioinformatics/Bti144  0.753
2004 Osada R, Zaslavsky E, Singh M. Comparative analysis of methods for representing and searching for transcription factor binding sites. Bioinformatics (Oxford, England). 20: 3516-25. PMID 15297295 DOI: 10.1093/Bioinformatics/Bth438  0.771
2004 Brooks DJ, Fresco JR, Singh M. A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor. Bioinformatics (Oxford, England). 20: 2251-7. PMID 15073018 DOI: 10.1093/Bioinformatics/Bth235  0.314
2004 Fong JH, Keating AE, Singh M. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biology. 5: R11. PMID 14759261 DOI: 10.1186/Gb-2004-5-2-R11  0.735
2004 Jim K, Parmar K, Singh M, Tavazoie S. A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Research. 14: 109-15. PMID 14707173 DOI: 10.1101/Gr.1586704  0.34
2004 Chazelle B, Kingsford C, Singh M. A semidefinite programming approach to side chain positioning with new rounding strategies Informs Journal On Computing. 16: 380-392. DOI: 10.1287/Ijoc.1040.0096  0.666
2003 Chazelle B, Kingsford C, Singh M. The Side-Chain Positioning Problem: A Semidefinite Programming Formulation with New Rounding Schemes Principles of Computing and Knowledge: Paris C. Kanellakis Memorial Workshop. 86-94.  0.61
2002 Brooks DJ, Fresco JR, Lesk AM, Singh M. Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Molecular Biology and Evolution. 19: 1645-55. PMID 12270892 DOI: 10.1093/Oxfordjournals.Molbev.A003988  0.312
2001 Malashkevich VN, Singh M, Kim PS. The trimer-of-hairpins motif in membrane fusion: Visna virus Proceedings of the National Academy of Sciences of the United States of America. 98: 8502-8506. PMID 11447278 DOI: 10.1073/Pnas.151254798  0.313
1999 Singh M, Berger B, Kim PS. LearnCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins Journal of Molecular Biology. 290: 1031-1041. PMID 10438601 DOI: 10.1006/Jmbi.1999.2796  0.557
1999 Awerbuch B, Betke M, Rivest RL, Singh M. Piecemeal Graph Exploration by a Mobile Robot Information & Computation. 152: 155-172. DOI: 10.1006/Inco.1999.2795  0.539
1998 Singh M, Berger B, Kim PS, Berger JM, Cochran AG. Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. Proceedings of the National Academy of Sciences of the United States of America. 95: 2738-43. PMID 9501159 DOI: 10.1073/Pnas.95.6.2738  0.565
1997 Berger B, Singh M. An iterative method for improved protein structural motif recognition. Journal of Computational Biology. 4: 261-273. PMID 9278059 DOI: 10.1089/Cmb.1997.4.261  0.577
1995 Betke M, Rivest RL, Singh M. Piecemeal Learning of an Unknown Environment Machine Learning. 18: 231-254. DOI: 10.1023/A:1022803514157  0.498
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