| 2003 | WABI | Distance Corrections on Recombinant Sequences. | David Bryant, Daniel H. Huson, Tobias H. Klpper, Kay Nieselt-Struwe |
| 2002 | WABI | NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. | David Bryant, Vincent Moulton |
| 2000 | CPM | A Lower Bound for the Breakpoint Phylogeny Problem. | David Bryant |
| 2000 | RECOMB | Early eukaryote evolution based on mitochondrial gene order breakpoints. | David Sankoff, David Bryant, Mlanie Deneault, B. Franz Lang, Gertraud Burger |
| 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 | RECOMB | Faster reliable phylogenetic analysis. | Vincent Berry, David Bryant |
| 1999 | RECOMB | Reconstructing the pre-doubling genome. | Nadia El-Mabrouk, David Bryant, David Sankoff |
| 1999 | SODA | Fast Algorithms for Constructing Optimal Trees from Quartets. | David Bryant, Mike A. Steel |