Sridhar Hannenhalli

3236 Iribe Center
(301) 405-8219
Ph.D., Pennsylvania State University (Computer Science)

Sridhar Hannenhalli is a professor in the Department of Cell Biology and Molecular Genetics and holds joint appointments in the Center for Bioinformatics and Computational Biology (CBCB) and UMIACS. He also holds an affiliate position in the university's Department of Computer Science and the Department of Genetics at the University of Pennsylvania.

Hannenhalli served as the interim director of CBCB in 2013. He has previously held research positions at GlaxoSmithKline, Celera Genomics, and as assistant and then associate professor in the Department of Genetics at the University of Pennsylvania.

Hannenhalli's current research focuses on comparative genomics, transcriptional regulation, and evolution.

He has served on program committee for numerous bioinformatics conferences and chaired Workshop on Algorithms in Bioinformatics (WABI) and Research in Computational Molecular Biology (RECOMB) conferences. Hannenhalli has also served on several national and international grant review panels and as academic editor for PLOS ONE and BMC Genomics. He has co-authored more than 75 papers in computer science and bioinformatics.

Hannenhalli received his doctorate in computer science from Pennsylvania State University in 1996, where he developed combinatorial algorithms for genome rearrangement problems.

Go here to view Hannenhalli's academic publications on Google Scholar.



Everett LJ, Jensen ST, Hannenhalli S.  2011.  Transcriptional Regulation Via TF-Modifying Enzymes: An Integrative Model-Based Analysis. Nucleic Acids ResearchNucl. Acids Res.. 39(12):e78-e78-e78-e78.

Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S.  2011.  Genome-Wide Survey of Natural Selection on Functional, Structural, and Network Properties of Polymorphic Sites in Saccharomyces Paradoxus. Molecular Biology and EvolutionMol Biol Evol. 28(9):2615-2627.

Yaklichkin S Y, Darnell DK, Pier MV, Antin PB, Hannenhalli S.  2011.  Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1. BMC Evolutionary Biology. 11(1):302-302.

Tian Y, Zhang Y, Hurd L, Hannenhalli S, Liu F, Lu M M, Morrisey EE.  2011.  Regulation of Lung Endoderm Progenitor Cell Behavior by miR302/367. DevelopmentDevelopment. 138(7):1235-1245.

Dewey FE, Perez MV, Wheeler MT, Watt C, Spin J, Langfelder P, Horvath S, Hannenhalli S, Cappola TP, Ashley EA.  2011.  Gene Coexpression Network Topology of Cardiac Development, Hypertrophy, and FailureClinical Perspective. Circulation: Cardiovascular GeneticsCirc Cardiovasc Genet. 4(1):26-35.


Vishnoi A, Kryazhimskiy S, Bazykin GA, Hannenhalli S, Plotkin JB.  2010.  Young Proteins Experience More Variable Selection Pressures Than Old Proteins. Genome ResearchGenome Res.. 20(11):1574-1581.

Trivedi CM, Zhu W, Wang Q, Jia C, Kee H J, Li L, Hannenhalli S, Epstein JA.  2010.  Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation. Developmental Cell. 19(3):450-459.

Everett L, Hansen M, Hannenhalli S.  2010.  Regulating the Regulators: Modulators of Transcription Factor Activity. Computational Biology of Transcription Factor BindingComputational Biology of Transcription Factor Binding. 674:297-312.

Hansen M, Everett L, Singh L, Hannenhalli S.  2010.  Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. Algorithms for Molecular Biology. 5(1):4-4.


Shah R, Lu Y, Hinkle CC, McGillicuddy FC, Kim R, Hannenhalli S, Cappola TP, Heffron S, Wang XM, Mehta NN et al..  2009.  Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo. DiabetesDiabetes. 58(10):2211-2219.

Essien K, Vigneau S, Apreleva S, Singh LN, Bartolomei MS, Hannenhalli S.  2009.  CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biology. 10(11):R131-R131.

Putt ME, Hannenhalli S, Lu Y, Haines P, Chandrupatla HR, Morrisey EE, Margulies KB, Cappola TP.  2009.  Evidence for Coregulation of Myocardial Gene Expression by MEF2 and NFAT in Human Heart Failure / CLINICAL PERSPECTIVE. Circulation: Cardiovascular Genetics. 2(3):212-219.

Qasim AN, Metkus TS, Tadesse M, Lehrke M, Restine S, Wolfe ML, Hannenhalli S, Cappola T, Rader DJ, Reilly MP.  2009.  Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians. Clinical Endocrinology. 70(5):698-705.

Hannenhalli S, Kaestner KH.  2009.  The evolution of Fox genes and their role in development and disease. Nature reviews. GeneticsNat Rev Genet. 10(4):233-240.

Hansen M, Everett L, Singh L, Hannenhalli S.  2009.  Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Proceedings of the 9th international conference on Algorithms in bioinformatics.


Wan L-B, Pan H, Hannenhalli S, Cheng Y, Ma J, Fedoriw A, Lobanenkov V, Latham KE, Schultz RM, Bartolomei MS.  2008.  Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development. Development. 135(16):2729-2738.

Sethupathy P, Giang H, Plotkin JB, Hannenhalli S.  2008.  Genome-Wide Analysis of Natural Selection on Human Cis-Elements. PLoS ONEPLoS ONE. 3(9):e3137-e3137.

Giancarlo R, Hannenhalli S.  2008.  Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 5(4):482-483.

Fermin DR, Barac A, Lee S, Polster SP, Hannenhalli S, Bergemann TL, Grindle S, Dyke DB, Pagani F, Miller LW et al..  2008.  Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure. Circulation: Cardiovascular Genetics. 1(2):117-125.


Leparc GG, Mitra RD, Vardhanabhuti S, Wang J, Hannenhalli S, Smit S, Widmann J, Knight R, Wu S, Zhang Y et al..  2007.  COMPUTATIONAL BIOLOGY. Nucleic acids research. 35(9-12):3163-3163.

Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD.  2007.  Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Virology. 365(1):60-69.

Zhang Y, Rath N, Hannenhalli S, Wang Z, Cappola T, Kimura S, Atochina-Vasserman E, Lu M M, Beers MF, Morrisey EE.  2007.  GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo. Development. 134(1):189-198.


Wang J, Hannenhalli S.  2006.  A mammalian promoter model links cis elements to genetic networks. Biochemical and Biophysical Research Communications. 347(1):166-177.

Hadley D, Murphy T, Valladares O, Hannenhalli S, Ungar L, Kim J, Bućan M.  2006.  Patterns of sequence conservation in presynaptic neural genes. Genome Biology. 7(11):R105-R105.

Hannenhalli S, Putt ME, Gilmore JM, Wang J, Parmacek MS, Epstein JA, Morrisey EE, Margulies KB, Cappola TP.  2006.  Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. Circulation. 114(12):1269-1276.

Evans P, Donahue G, Hannenhalli S.  2006.  Conservation Patterns in cis-Elements Reveal Compensatory Mutations. Comparative GenomicsComparative Genomics. 4205:186-199.

Everett L, Wang L-S, Hannenhalli S.  2006.  Dense Subgraph Computation Via Stochastic Search: Application to Detect Transcriptional Modules. BioinformaticsBioinformatics. 22(14):e117-e123-e117-e123.

Hannenhalli S, Middleton RP, Levy S, Perroud B, Holzwarth JA, McDonald K, Hannah SS.  2006.  Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and Cartilage. 14(8):830-838.

Wang L-S, Jensen S, Hannenhalli S.  2006.  An Interaction-Dependent Model for Transcription Factor Binding. Systems Biology and Regulatory GenomicsSystems Biology and Regulatory Genomics. 4023:225-234.

Hannenhalli S.  2006.  Invited Talk: Deciphering Gene Regulatory Networks by in silico approaches. 6th International Workshop on Data Mining in Bioinformatics (BIOKDD06).

Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S et al..  2006.  Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection. PLoS PathogPLoS Pathog. 2(6):e60-e60.

Berry C, Hannenhalli S, Leipzig J, Bushman FD.  2006.  Selection of Target Sites for Mobile DNA Integration in the Human Genome. PLoS Comput BiolPLoS Comput Biol. 2(11):e157-e157.

Ross DA, Hannenhalli S, Tobias JW, Cooch N, Shiekhattar R, Kadesch T.  2006.  Functional Analysis of Hes-1 in Preadipocytes. Molecular EndocrinologyMolecular Endocrinology. 20(3):698-705.


Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C.  2005.  Genome-wide analysis of retroviral DNA integration. Nat Rev MicroNat Rev Micro. 3(11):848-858.

Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD.  2005.  Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription. Journal of VirologyJ. Virol.. 79(11):6610-6619.

Hannenhalli S, Wang L-S.  2005.  Enhanced position weight matrices using mixture models. Bioinformatics. 21(Suppl 1):i204-i212-i204-i212.


Bafna V, Gusfield D, Hannenhalli S, Yooseph S.  2004.  A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. Journal of Computational Biology. 11(5):858-866.



Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77:1-19.

Hannenhalli S, Levy S.  2002.  Predicting Transcription Factor Synergism. Nucleic Acids ResearchNucl. Acids Res.. 30(19):4278-4284.

Berman P, Hannenhalli S, Karpinski M.  2002.  1.375-Approximation Algorithm for Sorting by Reversals. Algorithms — ESA 2002Algorithms — ESA 2002. 2461:401-408.

Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77:1-19.


Hannenhalli S, Levy S.  2001.  Promoter prediction in the human genome. Bioinformatics. 17(Suppl 1):S90-S96-S90-S96.

Levy S, Hannenhalli S, Workman C.  2001.  Enrichment of Regulatory Signals in Conserved Non-Coding Genomic Sequence. BioinformaticsBioinformatics. 17(10):871-877.


Bafna V, Hannenhalli S, Rice K, Vawter L.  2000.  Ligand-Receptor Pairing Via Tree Comparison. Journal of Computational Biology. 7(1-2):59-70.


Hannenhalli S, Hayes WS, Hatzigeorgiou AG, Fickett JW.  1999.  Bacterial Start Site Prediction. Nucleic Acids ResearchNucl. Acids Res.. 27(17):3577-3582.


DANČÍK V, Hannenhalli S, Muthukrishnan S.  1997.  Hardness of flip-cut problems from optical mapping. Journal of Computational Biology. 4(2):119-125.