Sridhar Hannenhalli

Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli: Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. Algorithms for Molecular Biology 5: 4 (2010)

Logan Everett, Antony Vo, Sridhar Hannenhalli: PTM-Switchboard - a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Research 37(Database-Issue): 66-71 (2009)

Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli: Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction. WABI 2009: 133-144

Praveen Sethupathy, Sridhar Hannenhalli: A Tutorial of the Poisson Random Field Model in Population Genetics. Adv. Bioinformatics 2008 (2008)

Sridhar Hannenhalli: Eukaryotic transcription factor binding sites - modeling and integrative search methods. Bioinformatics 24(11): 1325-1331 (2008)

Raffaele Giancarlo, Sridhar Hannenhalli: Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics. IEEE/ACM Trans. Comput. Biology Bioinform. 5(4): 482-483 (2008)

Raffaele Giancarlo, Sridhar Hannenhalli (Eds.): Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings. Lecture Notes in Computer Science 4645, Springer 2007, isbn 978-3-540-74125-1

Charles C. Berry, Sridhar Hannenhalli, Jeremy Leipzig, Frederic D. Bushman: Selection of Target Sites for Mobile DNA Integration in the Human Genome. PLoS Computational Biology 2(11) (2006)

Logan Everett, Li-San Wang, Sridhar Hannenhalli: Dense subgraph computation via stochastic search: application to detect transcriptional modules. ISMB (Supplement of Bioinformatics) 2006: 117-123

Perry Evans, Greg Donahue, Sridhar Hannenhalli: Conservation Patterns in cis-Elements Reveal Compensatory Mutations. Comparative Genomics 2006: 186-199

Junwen Wang, Sridhar Hannenhalli: Generalizations of Markov model to characterize biological sequences. BMC Bioinformatics 6: 219 (2005)

Sridhar Hannenhalli, Li-San Wang: Enhanced position weight matrices using mixture models. ISMB (Supplement of Bioinformatics) 2005: 204-212

Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli: An Interaction-Dependent Model for Transcription Factor Binding. Systems Biology and Regulatory Genomics 2005: 225-234

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

Piotr Berman, Sridhar Hannenhalli, Marek Karpinski: 1.375-Approximation Algorithm for Sorting by Reversals. ESA 2002: 200-210

Samuel Levy, Sridhar Hannenhalli, Christopher T. Workman: Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics 17(10): 871-877 (2001)

Sridhar Hannenhalli, Samuel Levy: Promoter prediction in the human genome. ISMB (Supplement of Bioinformatics) 2001: 90-96

Piotr Berman, Sridhar Hannenhalli, Marek Karpinski: 1.375-Approximation Algorithm for Sorting by Reversals. Electronic Colloquium on Computational Complexity (ECCC) 8(47) (2001)

Vineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter: Ligand-Receptor Pairing Via Tree Comparison. Journal of Computational Biology 7(1-2): 59-70 (2000)

Sridhar Hannenhalli, Pavel A. Pevzner: Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals. J. ACM 46(1): 1-27 (1999)

Vlado Dancík, Sridhar Hannenhalli, S. Muthukrishnan: Hardness of Flip-Cut Problems from Optical Mapping. Journal of Computational Biology 4(2): 119-125 (1997)

Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Sridhar Hannenhalli, Martin Farach, S. Muthukrishnan, Steven Skiena: Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. Journal of Computational Biology 4(3): 275-296 (1997)

Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, Steven Skiena: Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. RECOMB 1997: 1-2

Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena: Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. SODA 1997: 390-399

Sridhar Hannenhalli, W. Feldman, H. F. Lewis, Steven Skiena, Pavel A. Pevzner: Positional sequencing by hybridization. Computer Applications in the Biosciences 12(1): 19-24 (1996)

Sridhar Hannenhalli: Polynomial-time Algorithm for Computing Translocation Distance Between Genomes. Discrete Applied Mathematics 71(1-3): 137-151 (1996)

Piotr Berman, Sridhar Hannenhalli: Fast Sorting by Reversal. CPM 1996: 168-185

Sridhar Hannenhalli, Pavel A. Pevzner: To Cut... or Not to Cut (Applications of Comparative Physical Maps in Molecular Evolution). SODA 1996: 304-313

Sridhar Hannenhalli, Pavel A. Pevzner: Towards a Computational Theory of Genome Rearrangements. Computer Science Today 1995: 184-202

Sridhar Hannenhalli: Polynomial-time Algorithm for Computing Translocation Distance between Genomes. CPM 1995: 162-176

Sridhar Hannenhalli, Pavel A. Pevzner: Transforming Men into Mice (Polynomial Algorithm for Genomic Distance Problem). FOCS 1995: 581-592

Sridhar Hannenhalli, Pavel A. Pevzner: Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. STOC 1995: 178-189

Sridhar Hannenhalli, Kalyan S. Perumalla, N. Chandrasekharan, R. Sridhar: A Distributed Algorithm for Ear Decomposition. ICCI 1993: 180-184

N. Chandrasekharan, Sridhar Hannenhalli: Efficient Algorithms for Computing Matching and Chromatic Polynominals on Series-Parallel Graphs. ICCI 1992: 42-45

Kien A. Hua, Sridhar Hannenhalli: Parallel Transitive Closure Computations Using Topological Sort. PDIS 1991: 122-129