Parallel Transitive Closure Computations Using Topological Sort. - Kien A. Hua; Sridhar Hannenhalli (PDIS, 1991)

Efficient Algorithms for Computing Matching and Chromatic Polynominals on Series-Parallel Graphs. - N. Chandrasekharan; Sridhar Hannenhalli (ICCI, 1992)

A Distributed Algorithm for Ear Decomposition. - Sridhar Hannenhalli; Kalyan S. Perumalla; N. Chandrasekharan; R. Sridhar 001 (ICCI, 1993)

A SIMD solution to the sequence comparison problem on the MGAP. - Manjit Borah; Raminder Singh Bajwa; Sridhar Hannenhalli; Mary Jane Irwin (ASAP, 1994)

Towards a Computational Theory of Genome Rearrangements. - Sridhar Hannenhalli; Pavel A. Pevzner (Computer Science Today, 1995)

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

Fast Sorting by Reversal. - Piotr Berman; Sridhar Hannenhalli (CPM, 1996)

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

Positional sequencing by hybridization. - Sridhar Hannenhalli; William Feldman; Herbert F. Lewis; Steven Skiena; Pavel A. Pevzner (Comput. Appl. Biosci., 1996)

Polynomial-time Algorithm for Computing Translocation Distance Between Genomes. - Sridhar Hannenhalli (Discret. Appl. Math., 1996)

Hardness of flip-cut problems from optical mapping [DNA molecules application]. - Vlado Dancík; Sridhar Hannenhalli; S. Muthukrishnan 001 (SEQUENCES, 1997)

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

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. - Richa Agarwala; Serafim Batzoglou; Vlado Dancík; Scott E. Decatur; Sridhar Hannenhalli; Martin Farach; S. Muthukrishnan 001; Steven Skiena (J. Comput. Biol., 1997)

Hardness of Flip-Cut Problems from Optical Mapping. - Vlado Dancík; Sridhar Hannenhalli; S. Muthukrishnan 001 (J. Comput. Biol., 1997)

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

Ligand-Receptor Pairing Via Tree Comparison. - Vineet Bafna; Sridhar Hannenhalli; Ken Rice; Lisa Vawter (J. Comput. Biol., 2000)

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

Enrichment of regulatory signals in conserved non-coding genomic sequence. - Samuel Levy; Sridhar Hannenhalli; Christopher T. Workman (Bioinform., 2001)

1.375-Approximation Algorithm for Sorting by Reversals - Piotr Berman; Sridhar Hannenhalli; Marek Karpinski (Electron. Colloquium Comput. Complex., 2001)

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. - Vineet Bafna; Dan Gusfield; Sridhar Hannenhalli; Shibu Yooseph (J. Comput. Biol., 2004)

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

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

Generalizations of Markov model to characterize biological sequences. - Junwen Wang; Sridhar Hannenhalli (BMC Bioinform., 2005)

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

Conservation Patterns in cis-Elements Reveal Compensatory Mutations. - Perry Evans; Greg Donahue; Sridhar Hannenhalli (Comparative Genomics, 2006)

Selection of Target Sites for Mobile DNA Integration in the Human Genome. - Charles C. Berry; Sridhar Hannenhalli; Jeremy Leipzig; Frederic D. Bushman (PLoS Comput. Biol., 2006)

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

Eukaryotic transcription factor binding sites - modeling and integrative search methods. - Sridhar Hannenhalli (Bioinform., 2008)

Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics. - Raffaele Giancarlo; Sridhar Hannenhalli (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

PTM-Switchboard - a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. - Logan Everett; Antony Vo; Sridhar Hannenhalli (Nucleic Acids Res., 2009)

Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. - Matthew Hansen; Logan Everett; Larry N. Singh; Sridhar Hannenhalli (Algorithms Mol. Biol., 2010)

Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. - Hao Wang 024; Geet Duggal; Rob Patro; Michelle Girvan; Sridhar Hannenhalli; Carl Kingsford (BCB, 2013)

Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing. - Kun Wang; Avinash Das Sahu; Zheng-Mei Xiong; Kan Cao; Sridhar Hannenhalli (BCB, 2013)

Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association Studies. - Avinash Das Sahu; Radhouane Aniba; Yen-Pei Christy Chang; Sridhar Hannenhalli (Pacific Symposium on Biocomputing, 2013)

Widespread evidence of viral miRNAs targeting host pathways. - Joseph W. Carl; Joanne Trgovcich; Sridhar Hannenhalli (BMC Bioinform., 2013)

Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation. - Jia Zeng; Sridhar Hannenhalli (BMC Genom., 2013)

Chromatin and genomic determinants of alternative splicing. - Kun Wang; Kan Cao; Sridhar Hannenhalli (BCB, 2015)

Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution. - M. Senthil Kumar; Joshua B. Plotkin; Sridhar Hannenhalli (PLoS Comput. Biol., 2015)

Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. - Kun Wang; Avinash Das Sahu; Zheng-Mei Xiong; Kan Cao; Sridhar Hannenhalli (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. - Sushant Patkar; Assaf Magen; Roded Sharan; Sridhar Hannenhalli (PLoS Comput. Biol., 2017)

ChIPulate: A comprehensive ChIP-seq simulation pipeline. - Vishaka Datta; Sridhar Hannenhalli; Rahul Siddharthan (PLoS Comput. Biol., 2019)

PathExt: a general framework for path-based mining of omics-integrated biological networks. - Narmada Sambaturu; Vaidehi Pusadkar; Sridhar Hannenhalli; Nagasuma Chandra (Bioinform., 2021)

Prioritizing and characterizing functionally relevant genes across human tissues. - Gowthami Somepalli; Sarthak Sahoo; Arashdeep Singh; Sridhar Hannenhalli (PLoS Comput. Biol., 2021)