Professor of 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
  • 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

  • Ochoa A, Storey J, Llinás M, Singh M. (2015) Beyond the E-value: Stratified statistics for protein domain prediction. PLOS Computational Biology. 11:e1004509 PubMed
  • Pritykin Y, Ghersi D, Singh M. (2015) Genome-wide detection and analysis of multifunctional genes. PLOS Computational Biology. 11:1004467. PubMed
  • Nadimpalli S, Persikov AV, Singh M. (2015) Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 11(3): e1005011. Pubmed
  • Persikov AV, Wetzel JL, Rowland EF, Oakes BL, Xu DJ, Singh M, Noyes MB. (2015) A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res. 43(3): 1965-84. Pubmed
  • Ghersi D, Singh M. (2014) molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics. 30: 2081-3. Pubmed
  • Jiang P, Singh M, Coller HA. (2013) Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay. PLoS Comput Biol. 9: e1003075. Pubmed
  • Jiang P, Singh M. (2013) CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Res. 42: 2833-47. Pubmed
  • Ghersi D, Singh M. (2013) Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Res. 42: e18. Pubmed
  • Persikov AV, Rowland EF, Oakes BL, Singh M, Noyes MB. (2013) Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res. 42: 1497-508. Pubmed
  • Pritykin Y, Singh M. (2013) Simple topological features reflect dynamics and modularity in protein interaction networks. PLoS Comput Biol. 9: e1003243. Pubmed
  • Persikov AV, Singh M. (2013) De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res. 42: 97-108. Pubmed
  • Ghersi D, Singh M. (2013) Disentangling function from topology to infer the network properties of disease genes. BMC Syst Biol. 7: 5. Pubmed
  • Jiang P, Singh M, Coller HA. (2013) Computational assessment of the cooperativity between RNA binding proteins and microRNAs in transcript decay. PLoS Comput Biol. 9: e1003075. Pubmed
  • Song J, Singh M. (2013) 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. Pubmed
  • Khan Z, Bloom JS, Amini S, Singh M,...Kruglyak L. (2012) Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Mol Syst Biol. 8: 602. Pubmed

View complete list of Publications.