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Sridhar Hannenhalli, Ph.D.

Sridhar Hannenhalli, Ph.D.

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Department: Genetics

Contact information
3104G Biomolecular Sciences Building #296
College Park, MD 20742
Office: 301.405.8219
Fax: 301.314.1341
B.Tech. (Computer Science)
Institute of Technology, Varanasi, India, 1990.
M.S. (Computer Science)
University of Central Florida, Orlando, FL, 1992.
PhD (Computer Science)
Pennsylvania State University, University Park, PA, 1995.
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Description of Research Expertise

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

Diana K. Darnell, Li S. Zhang, Sridhar Hannenhalli and Sergey Yu. Yaklichkin: Developmental Expression of chicken FOXN1 and putative target genes during feather development. International Journal of Developmental Biology in press, 2014.

Yun Lu, Mary Putt, Sridhar Hannenhalli, Thomas Cappola: An Evaluation of MC Logic and logicFS Motivated by a Study of the Regulation of Gene Expression in Heart Failure. Journal of Applied Statistics (in press), 2014.

Sun Shim Choi, Sridhar Hannenhalli: Three Independent Determinants of Protein Evolutionary Rate. J Mol Evol 76(3): 98-111, February 2013.

Elfalem Alemu, Joseph W. Carl Jr., Hector Corrada-Bravo and Sridhar Hannenhalli: Determinants of expression variability. NAR in press, 2013.

Plasschaert, Robert; Vigneau, Sebatien; Tempera, Italo; Gupta, Ravi; Maksimoska, Jasna; Everett, Logan; Davuluri, Ramana; Marmorstein, Ronen; Lieberman, Paul; Schultz, David; Hannenhalli, Sridhar*; Bartolomei, Marisa: CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. NAR in press, 2013.

Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli and Carl Kingsford: Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. ACM BCB 2013 2013.

Robert Kim, Prakash Kulkarni and Sridhar Hannenhalli: Derepression of Cancer/Testis Antigens in Cancer is Associated with Distinct Patterns of DNA Hypomethylation. BMC Cancer 13: 144, 2013.

Malin, Justin; Aniba, Mohamed; Hannenhalli, Sridhar: Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. NAR 41(14): 6828-6838, 2013.

R. Mukherjee, L.N.S. Singh, P. Evans, S. Hannenhalli: Correlated evolution of positions within mammalian cis elements PLoS ONE 8(2): e55521, 2013.

Shrutii Sarda and Sridhar Hannenhalli: Next Generation Sequencing and Epigenomics research - A hammer in search of nails. Genomics and Informatics. Sangsoo Kim (eds.). in press, 2013.

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Last updated: 05/21/2014
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