Genomic Distances under Deletions and Insertions. - Mark Marron; Krister M. Swenson; Bernard M. E. Moret (Theor. Comput. Sci., 2004)

A Framework for Orthology Assignment from Gene Rearrangement Data. - Krister M. Swenson; Nicholas D. Pattengale; Bernard M. E. Moret (Comparative Genomics, 2005)

Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. - Krister M. Swenson; William Arndt; Jijun Tang; Bernard M. E. Moret (APBC, 2008)

Hurdles Hardly Have to Be Heeded. - Krister M. Swenson; Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (RECOMB-CG, 2008)

Approximating the true evolutionary distance between two genomes. - Krister M. Swenson; Mark Marron; Joel V. Earnest-DeYoung; Bernard M. E. Moret (ACM J. Exp. Algorithmics, 2008)

Sorting Signed Permutations by Inversions in O(nlogn) Time. - Krister M. Swenson; Vaibhav Rajan; Yu Lin 001; Bernard M. E. Moret (RECOMB, 2009)

Inversion-based genomic signatures. - Krister M. Swenson; Bernard M. E. Moret (BMC Bioinform., 2009)

Maximum independent sets of commuting and noninterfering inversions. - Krister M. Swenson; Yokuki To; Jijun Tang; Bernard M. E. Moret (BMC Bioinform., 2009)

Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. - Krister M. Swenson; Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (J. Comput. Biol., 2009)

Evolution of whole genomes through inversions - models and algorithms for duplicates, ancestors, and edit scenarios. - Krister M. Swenson (2009)

Uncovering Hidden Phylogenetic Consensus. - Nicholas D. Pattengale; Krister M. Swenson; Bernard M. E. Moret (ISBRA, 2010)

Ultra-Perfect Sorting Scenarios. - Aïda Ouangraoua; Anne Bergeron; Krister M. Swenson (RECOMB-CG, 2010)

An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. - Aïda Ouangraoua; Krister M. Swenson; Cédric Chauve (RECOMB-CG, 2010)

Estimating true evolutionary distances under rearrangements, duplications, and losses. - Yu Lin 001; Vaibhav Rajan; Krister M. Swenson; Bernard M. E. Moret (BMC Bioinform., 2010)

Heuristics for the inversion median problem. - Vaibhav Rajan; Andrew Wei Xu; Yu Lin 001; Krister M. Swenson; Bernard M. E. Moret (BMC Bioinform., 2010)

Sorting Signed Permutations by Inversions in O(nlogn) Time. - Krister M. Swenson; Vaibhav Rajan; Yu Lin 001; Bernard M. E. Moret (J. Comput. Biol., 2010)

The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths. - István Miklós; Bence Mélykúti; Krister M. Swenson (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. - Chunfang Zheng; Krister M. Swenson; Eric Lyons 002; David Sankoff (WABI, 2011)

Listing all sorting reversals in quadratic time. - Krister M. Swenson; Ghada Badr; David Sankoff (Algorithms Mol. Biol., 2011)

Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. - Ghada Badr; Krister M. Swenson; David Sankoff (J. Comput. Biol., 2011)

Theory and Practice of Ultra-Perfection. - Aïda Ouangraoua; Anne Bergeron; Krister M. Swenson (J. Comput. Biol., 2011)

A 2-Approximation for the Minimum Duplication Speciation Problem. - Aïda Ouangraoua; Krister M. Swenson; Cédric Chauve (J. Comput. Biol., 2011)

Uncovering Hidden Phylogenetic Consensus in Large Data Sets. - Nicholas D. Pattengale; Andre J. Aberer; Krister M. Swenson; Alexandros Stamatakis; Bernard M. E. Moret (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

On the Comparison of Sets of Alternative Transcripts. - Aïda Ouangraoua; Krister M. Swenson; Anne Bergeron (ISBRA, 2012)

Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. - Patrick Holloway; Krister M. Swenson; David H. Ardell; Nadia El-Mabrouk (RECOMB, 2012)

An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. - Manuel Lafond; Krister M. Swenson; Nadia El-Mabrouk (WABI, 2012)

Gene tree correction for reconciliation and species tree inference. - Krister M. Swenson; Andrea Doroftei; Nadia El-Mabrouk (Algorithms Mol. Biol., 2012)

A graph-theoretic approach for inparalog detection. - Olivier Tremblay Savard; Krister M. Swenson (BMC Bioinform., 2012)

Gene trees and species trees: irreconcilable differences. - Krister M. Swenson; Nadia El-Mabrouk (BMC Bioinform., 2012)

The Kernel of Maximum Agreement Subtrees. - Krister M. Swenson; Eric C. H. Chen; Nicholas D. Pattengale; David Sankoff (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Error Detection and Correction of Gene Trees. - Manuel Lafond; Krister M. Swenson; Nadia El-Mabrouk (Models and Algorithms for Genome Evolution, 2013)

Gene tree correction guided by orthology. - Manuel Lafond; Magali Semeria; Krister M. Swenson; Eric Tannier; Nadia El-Mabrouk (BMC Bioinform., 2013)

Reconstructing the modular recombination history of Staphylococcus aureus phages. - Krister M. Swenson; Paul Guertin; Hugo Deschênes; Anne Bergeron (BMC Bioinform., 2013)

Ancestral Genome Organization: An Alignment Approach. - Patrick Holloway; Krister M. Swenson; David H. Ardell; Nadia El-Mabrouk (J. Comput. Biol., 2013)

Gene tree correction for reconciliation and species tree inference: Complexity and algorithms. - Riccardo Dondi; Nadia El-Mabrouk; Krister M. Swenson (J. Discrete Algorithms, 2014)

Models and Algorithms for Genome Rearrangement with Positional Constraints. - Krister M. Swenson; Mathieu Blanchette (WABI, 2015)

Models and algorithms for genome rearrangement with positional constraints. - Krister M. Swenson; Pijus Simonaitis; Mathieu Blanchette (Algorithms Mol. Biol., 2016)

Aligning the unalignable: bacteriophage whole genome alignments. - Sèverine Bérard; Annie Chateau; Nicolas Pompidor; Paul Guertin; Anne Bergeron; Krister M. Swenson (BMC Bioinform., 2016)

Rearrangement Scenarios Guided by Chromatin Structure. - Sylvain Pulicani; Pijus Simonaitis; Eric Rivals; Krister M. Swenson (RECOMB-CG, 2017)

Finding local genome rearrangements. - Pijus Simonaitis; Krister M. Swenson (Algorithms Mol. Biol., 2018)

A framework for cost-constrained genome rearrangement under Double Cut and Join. - Pijus Simonaitis; Annie Chateau; Krister M. Swenson (CoRR, 2018)

Weighted Minimum-Length Rearrangement Scenarios. - Pijus Simonaitis; Annie Chateau; Krister M. Swenson (WABI, 2019)

Rapidly Computing the Phylogenetic Transfer Index. - Jakub Truszkowski; Olivier Gascuel; Krister M. Swenson (WABI, 2019)

A general framework for genome rearrangement with biological constraints. - Pijus Simonaitis; Annie Chateau; Krister M. Swenson (Algorithms Mol. Biol., 2019)

Rapid alignment-free phylogenetic identification of metagenomic sequences. - Benjamin Linard; Krister M. Swenson; Fabio Pardi (Bioinform., 2019)

Large-scale mammalian genome rearrangements coincide with chromatin interactions. - Krister M. Swenson; Mathieu Blanchette (Bioinform., 2019)

A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees. - Biing-Feng Wang; Krister M. Swenson (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

On the Comparison of Bacteriophage Populations. - Anne Bergeron; Marie-Jean Meurs; Romy Valiquette-Labonté; Krister M. Swenson (RECOMB-CG, 2022)

Quantifying Hierarchical Conflicts in Homology Statements. - Krister M. Swenson; Afif Elghraoui; Faramarz Valafar; Siavash Mirarab; Mathias Weller (RECOMB-CG, 2022)

Two Strikes Against the Phage Recombination Problem. - Manuel Lafond; Anne Bergeron; Krister M. Swenson (RECOMB-CG, 2023)

Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. - Afif Elghraoui; Siavash Mirarab; Krister M. Swenson; Faramarz Valafar (Bioinform., 2023)

A Simple and Efficient Algorithm for Sorting Signed Permutations by Reversals. - Krister M. Swenson (CoRR, 2024)