| 2006 | ISMB | Dense subgraph computation via stochastic search: application to detect transcriptional modules. | Logan Everett, Li-San Wang, Sridhar Hannenhalli |
| 2006 | SODA | Weighted isotonic regression under the | Stanislav Angelov, Boulos Harb, Sampath Kannan, Li-San Wang |
| 2005 | BIBE | Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony. | Jijun Tang, Li-San Wang |
| 2005 | COCOON | RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. | Luay Nakhleh, Derek A. Ruths, Li-San Wang |
| 2005 | ICCS | Phylogenetic Networks, Trees, and Clusters. | Luay Nakhleh, Li-San Wang |
| 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 |
| 2004 | WABI | Genome Identification and Classification by Short Oligo Arrays. | Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, Li-San Wang |
| 2002 | ISMB | Statistically based postprocessing of phylogenetic analysis by clustering. | Cara Stockham, Li-San Wang, Tandy J. Warnow |
| 2002 | PSB | Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. | Li-San Wang, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Tandy J. Warnow |
| 2002 | WABI | Genome Rearrangement Phylogeny Using Weighbor. | Li-San Wang |
| 2001 | ISMB | New approaches for reconstructing phylogenies from gene order data. | Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman |
| 2001 | STOC | Estimating true evolutionary distances between genomes. | Li-San Wang, Tandy J. Warnow |
| 2001 | WABI | Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes. | Li-San Wang |
| 2000 | ISMB | A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. | Mary E. Cosner, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman |