| 2003 | BIBE | A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees. | Michael Hu, Paul E. Kearney, Jonathan H. Badger |
| 2003 | WABI | Efficient Generation of Uniform Samples from Phylogenetic Trees. | Paul E. Kearney, J. Ian Munro, Derek Phillips |
| 2001 | PSB | Phylogenetics in the Post-Genomic Era - Session Introduction. | Jennifer E. Steinbachs, Paul E. Kearney |
| 2001 | SAC | Picking fruit from the tree of life: comments on taxonomic sampling and quartet methods. | Jonathan H. Badger, Paul E. Kearney |
| 2000 | ISAAC | Phylogenetic | Guo-Hui Lin, Tao Jiang, Paul E. Kearney |
| 2000 | SODA | A practical algorithm for recovering the best supported edges of an evolutionary tree (extended abstract). | Vincent Berry, David Bryant, Tao Jiang, Paul E. Kearney, Ming Li, Todd Wareham, Haoyong Zhang |
| 2000 | SODA | Computing the quartet distance between evolutionary trees. | David Bryant, John Tsang, Paul E. Kearney, Ming Li |
| 1999 | ESA | Quartet Cleaning: Improved Algorithms and Simulations. | Vincent Berry, Tao Jiang, Paul E. Kearney, Ming Li, Todd Wareham |
| 1999 | SODA | Recovering Branches on the Tree of Life: An Approximation Algorithm. | Paul E. Kearney, Ming Li, John Tsang, Tao Jiang |
| 1998 | FOCS | Orchestrating Quartets: Approximation and Data Correction. | Tao Jiang, Paul E. Kearney, Ming Li |
| 1998 | RECOMB | The ordinal quartet method. | Paul E. Kearney |
| 1997 | SODA | Inferring Evolutionary Trees from Ordinal Data. | Paul E. Kearney, Ryan Hayward, Henk Meijer |
| 1994 | ECAI | Emergent Behaviour in a Multi-Agent Economic Situation. | Paul E. Kearney, Arvindra Sehmi, Robert M. Smith |