| 2021 | CPM | Optimal Completion and Comparison of Incomplete Phylogenetic Trees Under Robinson-Foulds Distance. | Keegan Yao, Mukul S. Bansal |
| 2021 | PSB | TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. | Samuel Sledzieski, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal |
| 2018 | RECOMB | Linear-Time Algorithms for Some Phylogenetic Tree Completion Problems Under Robinson-Foulds Distance. | Mukul S. Bansal |
| 2013 | RECOMB | Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss. | Mukul S. Bansal, Eric J. Alm, Manolis Kellis |
| 2010 | RECOMB | Detecting Highways of Horizontal Gene Transfer. | Mukul S. Bansal, J. Peter Gogarten, Ron Shamir |
| 2008 | ISMB | The multiple gene duplication problem revisited. | Mukul S. Bansal, Oliver Eulenstein |
| 2008 | LATIN | Comparing and Aggregating Partially Resolved Trees. | Mukul S. Bansal, Jianrong Dong, David Fernndez-Baca |
| 2008 | RECOMB | Locating Multiple Gene Duplications through Reconciled Trees. | J. Gordon Burleigh, Mukul S. Bansal, Andr Wehe, Oliver Eulenstein |
| 2007 | RECOMB | Heuristics for the Gene-Duplication Problem: A | Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, Andr Wehe |
| 2007 | WABI | An | Mukul S. Bansal, Oliver Eulenstein |