Krister M. Swenson

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 18

Top Topics

Conditional Distributions

Phylogenetic Analysis

Multiple Sequence Alignment

Genomic Sequences

Top Venues

Algorithms Mol. Biol.

Publications

Krister M. Swenson
A Simple and Efficient Algorithm for Sorting Signed Permutations by Reversals. CoRR (2024)
Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar
isolates. Bioinform. 39 (1) (2023)
Manuel Lafond, Anne Bergeron, Krister M. Swenson
Two Strikes Against the Phage Recombination Problem. RECOMB-CG (2023)
Krister M. Swenson, Afif Elghraoui, Faramarz Valafar, Siavash Mirarab, Mathias Weller
Quantifying Hierarchical Conflicts in Homology Statements. RECOMB-CG (2022)
Anne Bergeron, Marie-Jean Meurs, Romy Valiquette-Labonté, Krister M. Swenson
On the Comparison of Bacteriophage Populations. RECOMB-CG (2022)
Biing-Feng Wang, Krister M. Swenson
A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (2) (2021)
Pijus Simonaitis, Annie Chateau, Krister M. Swenson
A general framework for genome rearrangement with biological constraints. Algorithms Mol. Biol. 14 (1) (2019)
Pijus Simonaitis, Annie Chateau, Krister M. Swenson
Weighted Minimum-Length Rearrangement Scenarios. WABI (2019)
Krister M. Swenson, Mathieu Blanchette
Large-scale mammalian genome rearrangements coincide with chromatin interactions. Bioinform. 35 (14) (2019)
Jakub Truszkowski, Olivier Gascuel, Krister M. Swenson
Rapidly Computing the Phylogenetic Transfer Index. WABI (2019)
Benjamin Linard, Krister M. Swenson, Fabio Pardi
Rapid alignment-free phylogenetic identification of metagenomic sequences. Bioinform. 35 (18) (2019)
Pijus Simonaitis, Annie Chateau, Krister M. Swenson
A General Framework for Genome Rearrangement with Biological Constraints. RECOMB-CG (2018)
Pijus Simonaitis, Krister M. Swenson
Finding local genome rearrangements. Algorithms Mol. Biol. 13 (1) (2018)
Pijus Simonaitis, Annie Chateau, Krister M. Swenson
A framework for cost-constrained genome rearrangement under Double Cut and Join. CoRR (2018)
Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister M. Swenson
Rearrangement Scenarios Guided by Chromatin Structure. RECOMB-CG (2017)
Pijus Simonaitis, Krister M. Swenson
Finding Local Genome Rearrangements. WABI (2017)
Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron, Krister M. Swenson
Aligning the unalignable: bacteriophage whole genome alignments. BMC Bioinform. 17 (2016)
Krister M. Swenson, Pijus Simonaitis, Mathieu Blanchette
Models and algorithms for genome rearrangement with positional constraints. Algorithms Mol. Biol. 11 (2016)
Krister M. Swenson, Mathieu Blanchette
Models and Algorithms for Genome Rearrangement with Positional Constraints. WABI (2015)
Riccardo Dondi, Nadia El-Mabrouk, Krister M. Swenson
Gene tree correction for reconciliation and species tree inference: Complexity and algorithms. J. Discrete Algorithms 25 (2014)
Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk
Ancestral Genome Organization: An Alignment Approach. J. Comput. Biol. 20 (4) (2013)
Krister M. Swenson, Paul Guertin, Hugo Deschênes, Anne Bergeron
Reconstructing the modular recombination history of Staphylococcus aureus phages. BMC Bioinform. 14 (S-15) (2013)
Manuel Lafond, Magali Semeria, Krister M. Swenson, Eric Tannier, Nadia El-Mabrouk
Gene tree correction guided by orthology. BMC Bioinform. 14 (S-15) (2013)
Krister M. Swenson, Andrea Doroftei, Nadia El-Mabrouk
Gene tree correction for reconciliation and species tree inference. Algorithms Mol. Biol. 7 (2012)
Krister M. Swenson, Eric C. H. Chen, Nicholas D. Pattengale, David Sankoff
The Kernel of Maximum Agreement Subtrees. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
Krister M. Swenson, Nadia El-Mabrouk
Gene trees and species trees: irreconcilable differences. BMC Bioinform. 13 (S-19) (2012)
Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk
An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. WABI (2012)
Aïda Ouangraoua, Krister M. Swenson, Anne Bergeron
On the Comparison of Sets of Alternative Transcripts. ISBRA (2012)
Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk
Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. RECOMB (2012)
Olivier Tremblay Savard, Krister M. Swenson
A graph-theoretic approach for inparalog detection. BMC Bioinform. 13 (S-19) (2012)
Krister M. Swenson, Eric C. H. Chen, Nicholas D. Pattengale, David Sankoff
The Kernel of Maximum Agreement Subtrees. ISBRA (2011)
Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M. E. Moret
Uncovering Hidden Phylogenetic Consensus in Large Data Sets. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (4) (2011)
Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve
A 2-Approximation for the Minimum Duplication Speciation Problem. J. Comput. Biol. 18 (9) (2011)
Ghada Badr, Krister M. Swenson, David Sankoff
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. J. Comput. Biol. 18 (9) (2011)
Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff
OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. WABI (2011)
Aïda Ouangraoua, Anne Bergeron, Krister M. Swenson
Theory and Practice of Ultra-Perfection. J. Comput. Biol. 18 (9) (2011)
Krister M. Swenson, Ghada Badr, David Sankoff
Listing all sorting reversals in quadratic time. Algorithms Mol. Biol. 6 (2011)
Krister M. Swenson, Ghada Badr, David Sankoff
Listing All Sorting Reversals in Quadratic Time. WABI (2010)
Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret
Heuristics for the inversion median problem. BMC Bioinform. 11 (S-1) (2010)
Aïda Ouangraoua, Anne Bergeron, Krister M. Swenson
Ultra-Perfect Sorting Scenarios. RECOMB-CG (2010)
Ghada Badr, Krister M. Swenson, David Sankoff
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. RECOMB-CG (2010)
Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret
Estimating true evolutionary distances under rearrangements, duplications, and losses. BMC Bioinform. 11 (S-1) (2010)
István Miklós, Bence Mélykúti, Krister M. Swenson
The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (4) (2010)
Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret
) Time. J. Comput. Biol. 17 (3) (2010)
Nicholas D. Pattengale, Krister M. Swenson, Bernard M. E. Moret
Uncovering Hidden Phylogenetic Consensus. ISBRA (2010)
Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve
An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. RECOMB-CG (2010)
Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. J. Comput. Biol. 16 (10) (2009)
Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret
Sorting Signed Permutations by Inversions in O(nlogn) Time. RECOMB (2009)
Krister M. Swenson, Yokuki To, Jijun Tang, Bernard M. E. Moret
Maximum independent sets of commuting and noninterfering inversions. BMC Bioinform. 10 (S-1) (2009)
Krister M. Swenson, Bernard M. E. Moret
Inversion-based genomic signatures. BMC Bioinform. 10 (S-1) (2009)
Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Hurdles Hardly Have to Be Heeded. RECOMB-CG (2008)
Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret
Approximating the true evolutionary distance between two genomes. ACM J. Exp. Algorithmics 12 (2008)
Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret
Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. APBC (2008)
Krister M. Swenson, Nicholas D. Pattengale, Bernard M. E. Moret
A Framework for Orthology Assignment from Gene Rearrangement Data. Comparative Genomics (2005)
Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret
Approximating the True Evolutionary Distance between Two Genomes. ALENEX/ANALCO (2005)
Mark Marron, Krister M. Swenson, Bernard M. E. Moret
Genomic Distances under Deletions and Insertions. Theor. Comput. Sci. 325 (3) (2004)
Mark Marron, Krister M. Swenson, Bernard M. E. Moret
Genomic Distances under Deletions and Insertions. COCOON (2003)