While broadly interested in computational biology, we focus on biological questions pertaining to eukaryotic gene regulation and its evolution. We develop computational approaches to harness the huge amount of biological data (genomes, transcriptomes, proteomes, microarray, Chip-seq etc) to answer specific questions pertaining to gene regulation and molecular evolution. Within these parameters, anything is a fair game. Our current research activities include: (1) Characterizing transcription factor DNA interactions, (2) Identifying Cis-regulatory Modules (3) Modeling Modification-dependent activity of transcription factors, (4) Investigating the evolution of transcriptional regulation, and (5) Characterizing natural selection on regulatory elements.
Selected Publications
Rui Liu, Sridhar Hannenhalli*, Maja Bucan: Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons Genome Biology (in press), June 2009 Notes: * co-corresponding author.
Sridhar Hannenhalli and Klaus Kaestner: The evolution of FOX genes and their role in development and disease. Nature Review Genetics 10: 233-40, April 2009.
Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli: Mimosa – Mixture model of co-expression to detect modulators of regulatory interaction Algorithms in Mol Biology. Stephen Salzberg and Tandy Warnow (eds.). (in press), September 2009 Notes: Accepted at the conference 'Workshop on Algorithms in Bioinformics"
Putt, M., Hannenhalli, S., Lu, Y., Haines, P., Chandruptla, H., Morrisey, E.E., Margulies, K.B., Cappola, T.: Evidence for co-regulation of myocardial gene expression by MEF2 and NFAT in human heart failure. Circulation: Cardiovascular Genetics (in press), 2009.
Everett, L., Vo, A., Hannenhalli, S.: PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res 37(Database issue): D66-71, 2009.
P. Sethupathy, H. Giang, J. Plotkin, S. Hannenhalli: Genome-wide analysis of natural selection on human cis-elements. PLoS ONE 3(9): e3137, Aug 2008.
K. Essien, S. Hannenhalli, C.J. Stoeckert Jr: Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PLoS ONE 3(9): e3122, August 2008.
S. Hannenhalli, M. Putt, J. Gilmore, J. Wang, M. Parmacek, J. Epstein, E. Morrisey, K. Margulies and T. Cappola: Transcriptional genomics associates FOX transcription factors with human heart failure. Circulation 2006.
L. Everett , L.S. Wang, and S. Hannenhalli*: Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics 22(14): e117-e123, 2006.
S. Vardhanabhuti, J. Wang, S. Hannenhalli*: Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. NAR 35: 3339-3354, 2007.
Larry N. Singh, Li-San Wang, and Sridhar Hannenhalli: TREMOR – A tool for retrieving transcriptional modules by incorporating motif covariance. NAR 35(21): 7360-71, 2007.
Hannenhalli, S.: Eukaryotic transcription factor binding sites--modeling and integrative search methods. Bioinformatics 24(11): 1325-31, 2008.
L. Singh and S. Hannenhalli: Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. PLoS ONE 3(e2345), April 2008.
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Last updated: 11/17/2009
The Trustees of the University of Pennsylvania
