| 2013 | PSB | Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association Studies. | Avinash Das Sahu, Radhouane Aniba, Yen-Pei Christy Chang, Sridhar Hannenhalli |
| 2009 | WABI | Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction. | Matthew Hansen, Logan Everett, Larry N. Singh, Sridhar Hannenhalli |
| 2006 | ISMB | Dense subgraph computation via stochastic search: application to detect transcriptional modules. | Logan Everett, Li-San Wang, Sridhar Hannenhalli |
| 2006 | RECOMB | Conservation Patterns in | Perry Evans, Greg Donahue, Sridhar Hannenhalli |
| 2005 | ISMB | Enhanced position weight matrices using mixture models. | Sridhar Hannenhalli, Li-San Wang |
| 2005 | RECOMB | An Interaction-Dependent Model for Transcription Factor Binding. | Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli |
| 2002 | ESA | 1.375-Approximation Algorithm for Sorting by Reversals. | Piotr Berman, Sridhar Hannenhalli, Marek Karpinski |
| 2001 | ISMB | Promoter prediction in the human genome. | Sridhar Hannenhalli, Samuel Levy |
| 1997 | RECOMB | Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. | Richa Agarwala, Serafim Batzoglou, Vlado Danck, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, Steven Skiena |
| 1997 | SODA | Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. | Richa Agarwala, Serafim Batzoglou, Vlado Danck, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena |
| 1996 | CPM | Fast Sorting by Reversal. | Piotr Berman, Sridhar Hannenhalli |
| 1996 | SODA | To Cut... or Not to Cut (Applications of Comparative Physical Maps in Molecular Evolution). | Sridhar Hannenhalli, Pavel A. Pevzner |
| 1995 | CPM | Polynomial-time Algorithm for Computing Translocation Distance between Genomes. | Sridhar Hannenhalli |
| 1995 | FOCS | Transforming Men into Mice (Polynomial Algorithm for Genomic Distance Problem). | Sridhar Hannenhalli, Pavel A. Pevzner |
| 1995 | STOC | Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. | Sridhar Hannenhalli, Pavel A. Pevzner |
| 1993 | ICCI | A Distributed Algorithm for Ear Decomposition. | Sridhar Hannenhalli, Kalyan S. Perumalla, N. Chandrasekharan, R. Sridhar |
| 1992 | ICCI | Efficient Algorithms for Computing Matching and Chromatic Polynominals on Series-Parallel Graphs. | N. Chandrasekharan, Sridhar Hannenhalli |