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ORCIDSridhar Hannenhalli
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2020 – today
- 2021
[j23]Narmada Sambaturu
, Vaidehi Pusadkar, Sridhar Hannenhalli, Nagasuma Chandra:
PathExt: a general framework for path-based mining of omics-integrated biological networks. Bioinform. 37(9): 1254-1262 (2021)- [j22]Gowthami Somepalli, Sarthak Sahoo, Arashdeep Singh, Sridhar Hannenhalli:
Prioritizing and characterizing functionally relevant genes across human tissues. PLoS Comput. Biol. 17(7) (2021)
2010 – 2019
- 2019
- [j21]Vishaka Datta, Sridhar Hannenhalli, Rahul Siddharthan:
ChIPulate: A comprehensive ChIP-seq simulation pipeline. PLoS Comput. Biol. 15(3) (2019) - 2017
- [j20]Sushant Patkar, Assaf Magen, Roded Sharan, Sridhar Hannenhalli:
A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PLoS Comput. Biol. 13(11) (2017) - 2015
- [j19]M. Senthil Kumar, Joshua B. Plotkin, Sridhar Hannenhalli:
Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution. PLoS Comput. Biol. 11(11) (2015) - [j18]Kun Wang, Avinash Das Sahu, Zheng-Mei Xiong, Kan Cao, Sridhar Hannenhalli:
Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. IEEE ACM Trans. Comput. Biol. Bioinform. 12(1): 30-39 (2015) - [c23]Kun Wang, Kan Cao, Sridhar Hannenhalli:
Chromatin and genomic determinants of alternative splicing. BCB 2015: 345-354 - 2013
- [j17]Joseph W. Carl, Joanne Trgovcich, Sridhar Hannenhalli:
Widespread evidence of viral miRNAs targeting host pathways. BMC Bioinform. 14(S-2): S3 (2013) - [j16]Jia Zeng, Sridhar Hannenhalli:
Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation. BMC Genom. 14(S-1): S15 (2013) - [c22]Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford:
Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. BCB 2013: 306 - [c21]Kun Wang, Avinash Das Sahu, Zheng-Mei Xiong, Kan Cao, Sridhar Hannenhalli:
Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing. BCB 2013: 377 - [c20]Avinash Das Sahu, Radhouane Aniba, Yen-Pei Christy Chang, Sridhar Hannenhalli:
Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association Studies. Pacific Symposium on Biocomputing 2013: 92-102 - 2010
- [j15]Matthew Hansen, Logan Everett, Larry N. Singh, Sridhar Hannenhalli:
Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. Algorithms Mol. Biol. 5: 4 (2010)
2000 – 2009
- 2009
- [j14]Logan Everett, Antony Vo, Sridhar Hannenhalli:
PTM-Switchboard - a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res. 37(Database-Issue): 66-71 (2009) - [c19]Matthew Hansen, Logan Everett, Larry N. Singh, Sridhar Hannenhalli:
Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction. WABI 2009: 133-144 - 2008
- [j13]Praveen Sethupathy, Sridhar Hannenhalli:
A Tutorial of the Poisson Random Field Model in Population Genetics. Adv. Bioinformatics 2008: 257864:1-257864:9 (2008) - [j12]Sridhar Hannenhalli:
Eukaryotic transcription factor binding sites - modeling and integrative search methods. Bioinform. 24(11): 1325-1331 (2008) - [j11]Raffaele Giancarlo, Sridhar Hannenhalli:
Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics. IEEE ACM Trans. Comput. Biol. Bioinform. 5(4): 482-483 (2008) - 2007
- [e2]Raffaele Giancarlo, Sridhar Hannenhalli:
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 [contents] - 2006
- [j10]Charles C. Berry, Sridhar Hannenhalli, Jeremy Leipzig, Frederic D. Bushman:
Selection of Target Sites for Mobile DNA Integration in the Human Genome. PLoS Comput. Biol. 2(11) (2006) - [c18]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 - [c17]Perry Evans, Greg Donahue, Sridhar Hannenhalli:
Conservation Patterns in cis-Elements Reveal Compensatory Mutations. Comparative Genomics 2006: 186-199 - 2005
- [j9]Junwen Wang, Sridhar Hannenhalli:
Generalizations of Markov model to characterize biological sequences. BMC Bioinform. 6: 219 (2005) - [c16]Sridhar Hannenhalli, Li-San Wang:
Enhanced position weight matrices using mixture models. ISMB (Supplement of Bioinformatics) 2005: 204-212 - [c15]Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli:
An Interaction-Dependent Model for Transcription Factor Binding. Systems Biology and Regulatory Genomics 2005: 225-234 - 2004
- [j8]Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph:
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. J. Comput. Biol. 11(5): 858-866 (2004) - 2002
- [c14]Piotr Berman, Sridhar Hannenhalli, Marek Karpinski:
1.375-Approximation Algorithm for Sorting by Reversals. ESA 2002: 200-210 - [e1]Gene Myers, Sridhar Hannenhalli, David Sankoff, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman:
Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002, Washington, DC, USA, April 18-21, 2002. ACM 2002, ISBN 1-58113-498-3 [contents] - 2001
- [j7]Samuel Levy, Sridhar Hannenhalli, Christopher T. Workman:
Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinform. 17(10): 871-877 (2001) - [c13]Sridhar Hannenhalli, Samuel Levy:
Promoter prediction in the human genome. ISMB (Supplement of Bioinformatics) 2001: 90-96 - [i1]Piotr Berman, Sridhar Hannenhalli, Marek Karpinski:
1.375-Approximation Algorithm for Sorting by Reversals. Electron. Colloquium Comput. Complex. TR01 (2001) - 2000
- [j6]Vineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter:
Ligand-Receptor Pairing Via Tree Comparison. J. Comput. Biol. 7(1-2): 59-70 (2000)
1990 – 1999
- 1999
- [j5]Sridhar Hannenhalli, Pavel A. Pevzner:
Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals. J. ACM 46(1): 1-27 (1999) - 1997
- [j4]Vlado Dancík, Sridhar Hannenhalli, S. Muthukrishnan:
Hardness of Flip-Cut Problems from Optical Mapping. J. Comput. Biol. 4(2): 119-125 (1997) - [j3]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. J. Comput. Biol. 4(3): 275-296 (1997) - [c12]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 - [c11]Vlado Dancík, Sridhar Hannenhalli, S. Muthukrishnan:
Hardness of flip-cut problems from optical mapping [DNA molecules application]. SEQUENCES 1997: 275-284 - [c10]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 - 1996
- [j2]Sridhar Hannenhalli, William Feldman, Herbert F. Lewis, Steven Skiena, Pavel A. Pevzner:
Positional sequencing by hybridization. Comput. Appl. Biosci. 12(1): 19-24 (1996) - [j1]Sridhar Hannenhalli:
Polynomial-time Algorithm for Computing Translocation Distance Between Genomes. Discret. Appl. Math. 71(1-3): 137-151 (1996) - [c9]Piotr Berman, Sridhar Hannenhalli:
Fast Sorting by Reversal. CPM 1996: 168-185 - [c8]Sridhar Hannenhalli, Pavel A. Pevzner:
To Cut... or Not to Cut (Applications of Comparative Physical Maps in Molecular Evolution). SODA 1996: 304-313 - 1995
- [c7]Sridhar Hannenhalli:
Polynomial-time Algorithm for Computing Translocation Distance between Genomes. CPM 1995: 162-176 - [c6]Sridhar Hannenhalli, Pavel A. Pevzner:
Transforming Men into Mice (Polynomial Algorithm for Genomic Distance Problem). FOCS 1995: 581-592 - [c5]Sridhar Hannenhalli, Pavel A. Pevzner:
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. STOC 1995: 178-189 - [p1]Sridhar Hannenhalli, Pavel A. Pevzner:
Towards a Computational Theory of Genome Rearrangements. Computer Science Today 1995: 184-202 - 1994
- [c4]Manjit Borah, Raminder Singh Bajwa, Sridhar Hannenhalli, Mary Jane Irwin:
A SIMD solution to the sequence comparison problem on the MGAP. ASAP 1994: 336-345 - 1993
- [c3]Sridhar Hannenhalli, Kalyan S. Perumalla, N. Chandrasekharan, R. Sridhar:
A Distributed Algorithm for Ear Decomposition. ICCI 1993: 180-184 - 1992
- [c2]N. Chandrasekharan, Sridhar Hannenhalli:
Efficient Algorithms for Computing Matching and Chromatic Polynominals on Series-Parallel Graphs. ICCI 1992: 42-45 - 1991
- [c1]Kien A. Hua, Sridhar Hannenhalli:
Parallel Transitive Closure Computations Using Topological Sort. PDIS 1991: 122-129
Coauthor Index
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