King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887

Wetzel J, Zhang K, Singh M. Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings. Genome Res. 2022;32(9):1776–86. PMCID: PMC9528988

Chacha P, Horie R, Kusakabe T, Sasakura Y, Singh M, Horie T, Levine M. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. Proc Natl Acad Sci U S A. 2022;119(4). PMCID: PMC8794889

King S, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol. 2021;17(11):e1009560. PMCID: PMC8601562

Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella A, Shen Y, Cowan A, McReynolds M, Kennedy B, Lato A, Campagna S, Singh M, Rabinowitz J. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods. 2021;18(11):1377–1385. PMCID: PMC8733904

Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948

Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics. 2021;37(Suppl_1):i133-i141. PMCID: PMC8275333

Marmion R, Yang L, Goyal Y, Jindal G, Wetzel J, Singh M, Schüpbach T, Shvartsman S. Molecular mechanisms underlying cellular effects of human MEK1 mutations. Mol Biol Cell. 2021;32(9):974–983. PMCID: PMC8108529

Munro D, Singh M. DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. Bioinformatics. 2021;36(22-23):5322–5329. PMCID: PMC8016454

Kobren S, Chazelle B, Singh M. PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. Cell Syst. 2020;11(1):63–74.e7. PMCID: PMC7493809

Hristov B, Chazelle B, Singh M. uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. Cell Syst. 2020;10(6):470–479.e3. PMCID: PMC7821437

Przytycki P, Singh M. Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. Cell Syst. 2020;10(2):193–203.e4. PMCID: PMC7457951

Wetzel J, Singh M. Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination. Nucleic Acids Res. 2020;48(2):e9. PMCID: PMC7028011

Kobren S, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019;47(2):582–593. PMCID: PMC6344845

Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol. 2018;14(6):e1006290. PMCID: PMC6040777

Przytycki P, Singh M. Correction to: Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes. Genome Med. 2018;10(1):35. PMCID: PMC5946516

Hristov B, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017;5(3):221–229.e4. PMCID: PMC5997485

Przytycki P, Singh M. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes. Genome Med. 2017;9(1):79. PMCID: PMC5574113

Pritykin Y, Brito T, Schüpbach T, Singh M, Pane A. Integrative analysis unveils new functions for the Cutoff protein in noncoding RNA biogenesis and gene regulation. RNA. 2017;23(7):1097–1109. PMCID: PMC5473144

Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017;33(16):2471–2478. PMCID: PMC5870623

Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics. 2014;30(14):2081–3. PMCID: PMC4080744

Persikov A, Wetzel J, Rowland E, Oakes B, Xu D, Singh M, Noyes M. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res. 2015;43(3):1965–84. PMCID: PMC4330361

Nadimpalli S, Persikov A, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 2015;11(3):e1005011. PMCID: PMC4351887

Pritykin Y, Ghersi D, Singh M. Genome-Wide Detection and Analysis of Multifunctional Genes. PLoS Comput Biol. 2015;11(10):e1004467. PMCID: PMC4593560

Ochoa A, Storey J, Llinás M, Singh M. Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PLoS Comput Biol. 2015;11(11):e1004509. PMCID: PMC4648515