| 2019 | WABI | Weighted Minimum-Length Rearrangement Scenarios. | Pijus Simonaitis, Annie Chateau, Krister M. Swenson |
| 2019 | WABI | Rapidly Computing the Phylogenetic Transfer Index. | Jakub Truszkowski, Olivier Gascuel, Krister M. Swenson |
| 2018 | RECOMB | A General Framework for Genome Rearrangement with Biological Constraints. | Pijus Simonaitis, Annie Chateau, Krister M. Swenson |
| 2017 | RECOMB | Rearrangement Scenarios Guided by Chromatin Structure. | Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister M. Swenson |
| 2017 | WABI | Finding Local Genome Rearrangements. | Pijus Simonaitis, Krister M. Swenson |
| 2015 | WABI | Models and Algorithms for Genome Rearrangement with Positional Constraints. | Krister M. Swenson, Mathieu Blanchette |
| 2012 | RECOMB | Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. | Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk |
| 2012 | WABI | An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. | Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk |
| 2011 | WABI | OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. | Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff |
| 2010 | RECOMB | Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. | Ghada Badr, Krister M. Swenson, David Sankoff |
| 2010 | RECOMB | Ultra-Perfect Sorting Scenarios. | Ada Ouangraoua, Anne Bergeron, Krister M. Swenson |
| 2010 | RECOMB | An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. | Ada Ouangraoua, Krister M. Swenson, Cdric Chauve |
| 2010 | WABI | Listing All Sorting Reversals in Quadratic Time. | Krister M. Swenson, Ghada Badr, David Sankoff |
| 2009 | RECOMB | Sorting Signed Permutations by Inversions in O(nlogn) Time. | Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret |
| 2008 | APBC | Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. | Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret |
| 2008 | RECOMB | Hurdles Hardly Have to Be Heeded. | Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret |
| 2005 | ALENEX | Approximating the True Evolutionary Distance between Two Genomes. | Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret |
| 2005 | RECOMB | A Framework for Orthology Assignment from Gene Rearrangement Data. | Krister M. Swenson, Nicholas D. Pattengale, Bernard M. E. Moret |
| 2003 | COCOON | Genomic Distances under Deletions and Insertions. | Mark Marron, Krister M. Swenson, Bernard M. E. Moret |