Sridhar Hannenhalli

3104G Bioscience Research Building
(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.



Agarwala R, Batzoglou S, DančíK V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan S, Skiena S.  1997.  Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. Journal of Computational Biology. 4(3):275-296.

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


Berman P, Hannenhalli S.  1996.  Fast sorting by reversal. Combinatorial Pattern MatchingCombinatorial Pattern Matching. 1075:168-185.

Hannenhalli S, Pevzner P.  1996.  To cut… or not to cut (applications of comparative physical maps in molecular evolution). Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms.

Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA.  1996.  Positional sequencing by hybridization. Computer applications in the biosciences : CABIOS. 12(1):19-24.


Hannenhalli S, Pevzner P.  1995.  Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000:184-202.

Hannenhalli S, Pevzner PA.  1995.  Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on.

Hannenhalli S, Pevzner P.  1995.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Proceedings of the twenty-seventh annual ACM symposium on Theory of computing.

Hannenhalli S.  1995.  Polynomial-time algorithm for computing translocation distance between genomes. Combinatorial Pattern MatchingCombinatorial Pattern Matching. 937:162-176.


Borah M, Bajwa RS, Hannenhalli S, Irwin MJ.  1994.  A SIMD solution to the sequence comparison problem on the MGAP. International Conference on Application Specific Array Processors, 1994. Proceedings.


Hannenhalli S, Perumalla K, Chandrasekharan N, Sridhar R.  1993.  A distributed algorithm for ear decomposition. , Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93.


Chandrasekharan N, Hannenhalli S.  1992.  Efficient algorithms for computing matching and chromatic polynomials on series-parallel graphs. , Fourth International Conference on Computing and Information, 1992. Proceedings. ICCI '92.


Hua KA, Hannenhalli S.  1991.  Parallel transitive closure computations using topological sort. , Proceedings of the First International Conference on Parallel and Distributed Information Systems, 1991.