Krister M. Swenson

Most-cited papers

Genomic Distances under Deletions and Insertions
Mark Marron, Krister M. Swenson, B. Moret
2003Theoretical Computer Science98 citations Open access
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Approximating the true evolutionary distance between two genomes
Krister M. Swenson, Mark Marron, J. V. Earnest-DeYoung, B. Moret
2008ALENEX/ANALCO82 citations Open access
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Rapid alignment-free phylogenetic identification of metagenomic sequences
Benjamin Linard, Krister M. Swenson, F. Pardi
2018bioRxiv48 citations Open access
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An Optimal Reconciliation Algorithm for Gene Trees with Polytomies
Manuel Lafond, Krister M. Swenson, N. El-Mabrouk
2012Workshop on Algorithms in Bioinformatics48 citations
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Uncovering Hidden Phylogenetic Consensus in Large Data Sets
N. Pattengale, A. Aberer, Krister M. Swenson, A. Stamatakis +1 more
2011IEEE/ACM Transactions on Computational Biology & Bioinformatics39 citations Open access
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Approximating the true evolutionary distance between genomes
Krister M. Swenson, Mark Marron, J. V. Earnest-DeYoung, B. Moret
200537 citations
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Sorting Signed Permutations by Inversions in O(nlogn) Time
Krister M. Swenson, Vaibhav Rajan, Yu Lin, B. Moret
2009Annual International Conference on Research in Computational Molecular Biology36 citations Open access
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OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations
Chun-Fang Zheng, Krister M. Swenson, E. Lyons, D. Sankoff
2011Workshop on Algorithms in Bioinformatics32 citations
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Gene tree correction guided by orthology
Manuel Lafond, M. Semeria, Krister M. Swenson, Eric Tannier +1 more
2013BMC Bioinformatics31 citations Open access
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Gene tree correction for reconciliation and species tree inference
Krister M. Swenson, A. Doroftei, N. El-Mabrouk
2012Algorithms for Molecular Biology31 citations Open access
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Diversity of bacteriophages encoding Panton-Valentine leukocidin in temporally and geographically related Staphylococcus aureus
G. Coombs, S. Baines, B. Howden, Krister M. Swenson +1 more
2020PLoS ONE27 citations Open access
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Heuristics for the inversion median problem
Vaibhav Rajan, A. W. Xu, Yu Lin, Krister M. Swenson +1 more
2010BMC Bioinformatics25 citations Open access
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Gene trees and species trees: irreconcilable differences
Krister M. Swenson, N. El-Mabrouk
2012BMC Bioinformatics24 citations Open access
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Uncovering Hidden Phylogenetic Consensus
N. Pattengale, Krister M. Swenson, B. Moret
2010International Symposium on Bioinformatics Research and Applications23 citations Open access
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Estimating true evolutionary distances under rearrangements, duplications, and losses
Yu Lin, Vaibhav Rajan, Krister M. Swenson, B. Moret
2010BMC Bioinformatics19 citations Open access
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Hurdles Hardly Have to Be Heeded
Krister M. Swenson, Yu Lin, Vaibhav Rajan, B. Moret
2008RECOMB Comparative Genomics Satellite Conference18 citations Open access
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Models and algorithms for genome rearrangement with positional constraints
Krister M. Swenson, Pijus Simonaitis, M. Blanchette
2015Algorithms for Molecular Biology17 citations Open access
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Inversion-based genomic signatures
Krister M. Swenson, B. Moret
2009BMC Bioinformatics16 citations Open access
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A Framework for Orthology Assignment from Gene Rearrangement Data
Krister M. Swenson, N. Pattengale, B. Moret
2005Comparative Genomics16 citations Open access
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Error Detection and Correction of Gene Trees
Manuel Lafond, Krister M. Swenson, N. El-Mabrouk
2013Models and Algorithms for Genome Evolution14 citations
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Ancestral Genome Organization: An Alignment Approach
Patrick Holloway, Krister M. Swenson, David H. Ardell, N. El-Mabrouk
2013J. Comput. Biol.14 citations Open access
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Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes
Krister M. Swenson, W. Arndt, Jijun Tang, B. Moret
2007Asia-Pacific Bioinformatics Conference13 citations Open access
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The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths
I. Miklós, B. Mélykúti, Krister M. Swenson
2010IEEE/ACM Transactions on Computational Biology & Bioinformatics12 citations Open access
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Assisted transcriptome reconstruction and splicing orthology
Samuel Blanquart, Jean-Stéphane Varré, Paul Guertin, A. Perrin +2 more
2016BMC Genomics11 citations Open access
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Evolution of Genome Organization by Duplication and Loss: An Alignment Approach
Patrick Holloway, Krister M. Swenson, David H. Ardell, N. El-Mabrouk
2012Annual International Conference on Research in Computational Molecular Biology10 citations
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Gene tree correction for reconciliation and species tree inference: Complexity and algorithms
R. Dondi, N. El-Mabrouk, Krister M. Swenson
2014J. Discrete Algorithms9 citations Open access
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Maximum independent sets of commuting and noninterfering inversions
Krister M. Swenson, Yokuki To, Jijun Tang, B. Moret
2009BMC Bioinformatics9 citations Open access
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Aligning the unalignable: bacteriophage whole genome alignments
S. Bérard, A. Chateau, N. Pompidor, Paul Guertin +2 more
2016BMC Bioinformatics8 citations Open access
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The Kernel of Maximum Agreement Subtrees
Krister M. Swenson, E. Chen, N. Pattengale, D. Sankoff
2011IEEE/ACM Transactions on Computational Biology & Bioinformatics8 citations
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Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives
G. Badr, Krister M. Swenson, D. Sankoff
2010RECOMB Comparative Genomics Satellite Conference7 citations
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Large-scale mammalian genome rearrangements coincide with chromatin interactions
Krister M. Swenson, M. Blanchette
2019Bioinform.6 citations Open access
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Finding local genome rearrangements
Pijus Simonaitis, Krister M. Swenson
2017Algorithms for Molecular Biology6 citations Open access
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Rearrangement Scenarios Guided by Chromatin Structure
Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister M. Swenson
2017bioRxiv6 citations Open access
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A graph-theoretic approach for inparalog detection
Olivier Tremblay-Savard, Krister M. Swenson
2012BMC Bioinformatics6 citations Open access
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A 2-Approximation for the Minimum Duplication Speciation Problem
Aïda Ouangraoua, Krister M. Swenson, C. Chauve
2011J. Comput. Biol.6 citations Open access
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Reconstructing the modular recombination history of Staphylococcus aureus phages
Krister M. Swenson, Paul Guertin, Hugo Deschênes, Anne Bergeron
2013BMC Bioinformatics5 citations Open access
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Listing all sorting reversals in quadratic time
Krister M. Swenson, G. Badr, D. Sankoff
2010Algorithms for Molecular Biology5 citations Open access
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A general framework for genome rearrangement with biological constraints
Pijus Simonaitis, A. Chateau, Krister M. Swenson
2018Algorithms for Molecular Biology4 citations Open access
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On the Comparison of Sets of Alternative Transcripts
Aïda Ouangraoua, Krister M. Swenson, Anne Bergeron
2012International Symposium on Bioinformatics Research and Applications4 citations
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Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results
Krister M. Swenson, Yu Lin, Vaibhav Rajan, B. Moret
2009J. Comput. Biol.4 citations Open access
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Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates
A. Elghraoui, S. Mirarab, Krister M. Swenson, F. Valafar
2023Bioinform.3 citations Open access
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Rapidly Computing the Phylogenetic Transfer Index
J. Truszkowski, O. Gascuel, Krister M. Swenson
2019bioRxiv3 citations Open access
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An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model
Aïda Ouangraoua, Krister M. Swenson, C. Chauve
2010RECOMB Comparative Genomics Satellite Conference3 citations Open access
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A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees
Biing-feng Wang, Krister M. Swenson
2019IEEE/ACM Transactions on Computational Biology & Bioinformatics2 citations Open access
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Theory and Practice of Ultra-Perfection
Aïda Ouangraoua, Anne Bergeron, Krister M. Swenson
2011J. Comput. Biol.2 citations
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Quantifying Hierarchical Conflicts in Homology Statements
Krister M. Swenson, A. Elghraoui, F. Valafar, S. Mirarab +1 more
2025Journal of Molecular Evolution1 citations
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Weighted Minimum-Length Rearrangement Scenarios
Pijus Simonaitis, A. Chateau, Krister M. Swenson
2019Workshop on Algorithms in Bioinformatics1 citations
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A framework for cost-constrained genome rearrangement under Double Cut and Join
Pijus Simonaitis, A. Chateau, Krister M. Swenson
2018Annual International Conference on Research in Computational Molecular Biology1 citations
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Gene trees and species trees: irreconcilable differences
Krister M. Swenson, N. El-Mabrouk
2012BMC Bioinformatics1 citations Open access
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Evolution of whole genomes through inversions - models and algorithms for duplicates, ancestors, and edit scenarios
Krister M. Swenson
20091 citations
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