Wang Family Professor in Computer Science and the Lewis Sigler Institute for Integrative Genomics

Areas of Research: Computational molecular biology, as well as its interface with machine learning and algorithms; molecular networks, cancer, disease mutations, protein sequence and structure analysis
  • Computer Science and the Lewis-Sigler Institute for Integrative Genomics
Research Lab
250 Carl Icahn Laboratory

Faculty Assistant:
Marybeth Fedele

Computational molecular biology

My group develops algorithms for a diverse set of problems in computational molecular biology. We are particularly interested in predicting specificity in protein interactions and uncovering how molecular interactions and functions vary across context, organisms and individuals. We leverage high-throughput biological datasets in order to develop data-driven algorithms for predicting protein interactions and specificity; for analyzing biological networks in order to uncover cellular organization, functioning, and pathways; for uncovering protein functions via sequences and structures; and for analyzing proteomics and sequencing data. An appreciation of protein structure guides much of our research.


Selected Publications

  • Chacha Paul PC, Horie R, Kusakabe T, Sasakura Y, Singh M, Horie T, Levine M. 2022. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. PNAS. 119(4): e2118817119. Pubmed

  • King SB and Singh M. 2021. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLOS Computational Biology.17: e1009560. Pubmed

  • Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella AD, Shen Y, Cowan A, McReynolds MR, Kennedy BJ, Lato AM, Campagna SR, Singh M, Rabinowitz JD. 2021. Metabolite discovery through global annotation of untargeted metabolomics data. Nature Methods. 18: 1377--1385. Pubmed

  • Aluru C and Singh M. 2021. Improved inference of tandem domain duplications. Bioinformatics. 37(Suppl_1): i333-i141. Pubmed

  • Etzion-Fuchs A, Todd DA, Singh M. 2021. dSPRINT: predicting DNA, RNA, ion, peptide, and small molecule interaction sites within protein domains. Nucleic Acids Research. 49:e78.Pubmed

  • Marmion RA, Yang L, Goyal Y, Jindal GA, Wetzel JL, Singh M, Schüpbach T, Shvartsman SY. 2021. Molecular mechanisms underlying cellular effects of human MEK1 mutations. Molecular Biology of the Cell. 32: 974. Pubmed

  • Munro D and Singh M. 2020. DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. Bioinformatics. 36: 5322-5329. Pubmed

View complete list of Publications.