@article{ElghraouiMSV23, author = {Elghraoui, Afif and Mirarab, Siavash and Swenson, Krister M and Valafar, Faramarz}, title = {Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using \emph{Mycobacterium tuberculosis} isolates}, journal = {Bioinformatics}, publisher = {Oxford Acedemic}, volume = 39, number = 1, year = 2023, month = 01, issn = {1367--4811}, doi = {10.1093/bioinformatics/btad024}, commentpdf = {../papers/2023-ElghraouiSSVImpactsSyntenyPhylogeny.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2023-ElghraouiSSVImpactsSyntenyPhylogeny.pdf}{PDF}} }
@article{CoombsBHSO20, title = {Diversity of bacteriophages encoding {Panton-Valentine} leukocidin in temporally and geographically related \emph{Staphylococcus aureus}}, author = {Coombs, G.W. and Baines, S.L. and Howden, B.P. and Swenson, K.M. and O'Brien, F.G.}, journal = {PloS one}, volume = {15}, number = {2}, pages = {e0228676}, year = {2020}, publisher = {Public Library of Science}, doi = {https://doi.org/10.1371/journal.pone.0228676}, commentpdf = {../papers/2020-CoombsBHSODiversityPVL.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2020-CoombsBHSODiversityPVL.pdf}{PDF}} }
@article{SwensonB19, author = {Swenson, K.M. and Blanchette, M.}, title = {{Large-scale mammalian genome rearrangements coincide with chromatin interactions}}, journal = {Bioinformatics}, volume = 35, number = 14, pages = {i117--i126}, year = 2019, month = 07, publisher = {Oxford Acedemic}, doi = {https://doi.org/10.1093/bioinformatics/btz343}, commentpdf = {../papers/2019-SwensonRearrangeInteractions.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2019-SwensonRearrangeInteractions.pdf}{PDF}} }
@article{WangS19, author = {Wang, B.-F. and Swenson, K.M.}, title = {A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees}, journal = {ACM/IEEE Trans.\ on Comput.\ Biology and Bioinformatics}, year = 2019, month = 6, publisher = {IEEE Computer Society}, doi = {https://doi.org/10.1109/TCBB.2019.2922955}, commentpdf = {../papers/2019-WangFasterKAST.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2019-WangFasterKAST.pdf}{PDF}} }
@article{LinardSP19, author = {Linard, B. and Swenson, K.M. and Pardi, F.}, title = {Rapid alignment-free phylogenetic identification of metagenomic sequences}, journal = {Bioinformatics}, year = 2019, month = 01, number = 18, volume = 35, pages = {3303--3312}, publisher = {Oxford Acedemic}, doi = {https://doi.org/10.1093/bioinformatics/btz068}, commentpdf = {../papers/2019-LinardRAPPAS.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2019-LinardRAPPAS.pdf}{PDF}} }
@article{SimonaitisCS19, author = {Simonaitis, P. and Chateau, A. and Swenson, K.M.}, title = {A general framework for genome rearrangement with biological constraints}, journal = {Algorithms for Mol.\ Biol.}, volume = 14, number = 15, year = 2019, publisher = {BioMed Central}, doi = {https://doi.org/10.1186/s13015-019-0149-4}, commentpdf = {../papers/2019-SimonaitisFrameworkRearrangementAMB.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2019-SimonaitisFrameworkRearrangementAMB.pdf}{PDF}} }
@article{SimonaitisS18, author = {Simonaitis, P. and Swenson, K.M.}, title = {Finding local genome rearrangements}, journal = {Algorithms for Mol.\ Biol.}, volume = 13, number = 1, pages = 9, year = 2018, publisher = {BioMed Central}, doi = {https://doi.org/10.1186/s13015-018-0127-2}, commentpdf = {../papers/2018-SimonaitisFindingLocalAMB.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2018-SimonaitisFindingLocalAMB.pdf}{PDF}} }
@article{BlanquartVGPBS16, author = {Blanquart, S. and Varré, J.-S. and Guertin, Paul and Perrin, A. and Bergeron, A. and Swenson, K.M.}, title = {Assisted transcriptome reconstruction and splicing orthology}, journal = {BMC Genomics}, volume = 17, number = 10, pages = {157--164}, year = 2016, publisher = {BioMed Central}, commentpdf = {../papers/2016-BlanquartTranscriptomeReconstruction.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2016-BlanquartTranscriptomeReconstruction.pdf}{PDF}}, issn = {1471-2164}, doi = {http://dx.doi.org/10.1186/s12864-016-3103-6} }
@article{SwensonSB16, author = {Swenson, K.M. and Simonaitis, P. and Blanchette, M.}, title = {Models and algorithms for genome rearrangement with positional constraints}, journal = {Algorithms for Molecular Biology}, year = 2016, volume = 11, number = 1, pages = {1--10}, issn = {1748-7188}, commentpdf = {../papers/2016-SwensonPositionalRearrangementsALMOB.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2016-SwensonPositionalRearrangementsALMOB.pdf}{PDF}}, doi = {http://dx.doi.org/10.1186/s13015-016-0065-9} }
@article{BerardCPGBS16, author = {B{\'e}rard, S. and Chateau, A. and Pompidor, N. and Guertin, P. and Bergeron, A. and Swenson, K.M.}, title = {Aligning the unalignable: bacteriophage whole genome alignments}, journal = {BMC Bioinformatics}, year = 2016, volume = 17, number = 1, pages = {1--13}, issn = {1471-2105}, commentpdf = {../papers/2016-BerardAligningUnalignable.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2016-BerardAligningUnalignable.pdf}{PDF}}, doi = {http://dx.doi.org/10.1186/s12859-015-0869-5} }
@article{DondiES14, author = {R. Dondi and N. El-Mabrouk and K.M. Swenson}, title = {Gene tree correction for reconciliation and species tree inference: complexity and algorithms}, journal = {J.\ Discrete Algorithms}, doi = {http://dx.doi.org/10.1016/j.jda.2013.06.001}, year = 2014, commentpdf = {../papers/2014-DondiReconciliationComplexityAlgorithms.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2014-DondiReconciliationComplexityAlgorithms.pdf}{PDF}}, issn = {1570-8667} }
@article{SwensonGDB13, author = {Swenson, K.M. and Guertin, P. and Deschenes, H. and Bergeron, A.}, title = {Reconstructing the modular recombination history of Staphylococcus aureus phages}, journal = {BMC Bioinformatics}, volume = 14, year = 2013, number = {Suppl 15}, pages = {S17}, doi = {10.1186/1471-2105-14-S15-S17}, commentpdf = {../papers/2013-SwensonModularRecombinationPhages.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2013-SwensonModularRecombinationPhages.pdf}{PDF}}, issn = {1471-2105} }
@article{LafondSSTE13, author = {Lafond, M. and Semeria, M. and Swenson, K.M. and Tannier, E. and El-Mabrouk, N.}, title = {Gene tree correction guided by orthology}, journal = {BMC Bioinformatics}, volume = 14, year = 2013, number = {Suppl 15}, pages = {S5}, commentpdf = {../papers/2013-LafondGeneTreeCorrectionOrthology.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2013-LafondGeneTreeCorrectionOrthology.pdf}{PDF}}, doi = {10.1186/1471-2105-14-S15-S5}, issn = {1471-2105} }
@article{HollowaySAEJ13, author = {P. Holloway and K.M. Swenson and D. Ardell and N. El-Mabrouk}, title = {Ancestral Genome Organization: an Alignment Approach}, journal = {J.\ Comput.\ Biology}, volume = 20, number = 4, year = 2013, pages = {280-295}, doi = {http://dx.doi.org/10.1089/cmb.2012.0292}, commentpdf = {../papers/2013-HollowayAncestralOrganization.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2013-HollowayAncestralOrganization.pdf}{PDF}} }
@article{SwensonE12, author = {K.M. Swenson and N. El-Mabrouk}, title = {Gene trees and species trees: irreconcilable differences}, journal = {BMC Bioinformatics}, volume = 13, number = {Suppl 19}, pages = {S15}, year = 2012, doi = {http://www.biomedcentral.com/1471-2105/13/S19/S15/}, commentpdf = {../papers/2012-SwensonIrreconcilableDifferences.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-SwensonIrreconcilableDifferences.pdf}{PDF}} }
@article{TremblaySavardS12, author = {O. Tremblay-Savard and K.M. Swenson}, title = {A graph-theoretic approach for inparalog detection}, journal = {BMC Bioinformatics}, volume = 13, number = {Suppl 19}, pages = {S16}, doi = {10.1186/1471-2105-13-S19-S16}, year = 2012, commentpdf = {../papers/2012-TremblaySavardInparalogDetection.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-TremblaySavardInparalogDetection.pdf}{PDF}} }
@article{SwensonDE12, author = {K.M. Swenson and A. Doroftei and N. El-Mabrouk}, title = {Gene tree correction for reconciliation and species tree inference}, journal = {Algorithms for Mol.\ Biol.}, volume = 7, number = 31, year = 2012, doi = {http://dx.doi.org/10.1186/1748-7188-7-31}, commentpdf = {../papers/2013-SwensonCorrectionReconciliationComplexity.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2013-SwensonCorrectionReconciliationComplexity.pdf}{PDF}} }
@article{SwensonCPS12, author = {K.M. Swenson and E. Chen and N.D. Pattengale and D. Sankoff}, title = {The Kernel of Maximum Agreement Subtrees}, journal = {ACM/IEEE Trans.\ on Comput.\ Biology and Bioinformatics}, volume = 9, number = 4, year = 2012, pages = {1023--1031}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, doi = {http://dx.doi.org/10.1109/TCBB.2012.11}, commentpdf = {../papers/2012-SwensonKAST.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-SwensonKAST.pdf}{PDF}} }
@article{PattengaleASSM11, author = {N.D. Pattengale and A.J. Aberer and K.M. Swenson and A. Stamatakis and B.M.E. Moret}, title = {Uncovering hidden phylogenetic consensus in large datasets}, journal = {ACM/IEEE Trans.\ on Comput.\ Biology and Bioinformatics}, volume = 8, number = 4, pages = {902-911}, year = 2011, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, doi = {http://dx.doi.org/10.1109/TCBB.2011.28}, commentpdf = {../papers/2011-PattengaleHiddenConsensus.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-PattengaleHiddenConsensus.pdf}{PDF}} }
@article{SwensonBS11, author = {K.M. Swenson and G. Badr and D. Sankoff}, title = {Listing all sorting reversals in quadratic time}, journal = {Algorithms for Mol.\ Biol.}, volume = 6, number = 11, year = 2011, doi = {http://dx.doi.org/10.1186/1748-7188-6-11}, commentpdf = {../papers/2011-SwensonAllSortingRevsALMOB.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-SwensonAllSortingRevsALMOB.pdf}{PDF}} }
@article{OuangraouaSC11, author = {A. Ouangraoua and K.M. Swenson and C. Chauve}, title = {A 2-approximation for the minimum duplication speciation problem}, journal = {J.\ Comput.\ Biology}, volume = 18, number = 9, year = 2011, doi = {http://dx.doi.org/10.1089/cmb.2011.0108}, commentpdf = {../papers/2011-Ouangraoua2ApproxMinDupSpec.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-Ouangraoua2ApproxMinDupSpec.pdf}{PDF}} }
@article{OuangraouaSB11, author = {A. Ouangraoua and K.M. Swenson and A. Bergeron}, title = {Theory and practice of ultra-perfection}, journal = {J.\ Comput.\ Biology}, volume = 18, number = 9, year = 2011, doi = {http://dx.doi.org/10.1089/cmb.2011.0086}, commentpdf = {../papers/2011-OuangraouaTheoryPracticeUPerfect.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-OuangraouaTheoryPracticeUPerfect.pdf}{PDF}} }
@article{BadrSS11, author = {G. Badr and K.M. Swenson and D. Sankoff}, title = {Listing all parsimonious reversal sequences: new algorithms and perspectives}, journal = {J.\ Comput.\ Biology}, volume = 18, number = 9, year = 2011, doi = {http://dx.doi.org/10.1089/cmb.2011.0133}, commentpdf = {../papers/2011-BadrListingParsimoniousRevSeqs.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-BadrListingParsimoniousRevSeqs.pdf}{PDF}} }
@article{SwensonRLM9, author = {K.M. Swenson and V. Rajan and Y. Lin and B.M.E. Moret}, title = {Sorting signed permutations by inversions in ${O}(n \log n)$ time}, journal = {J.\ Comput.\ Biology}, volume = 17, number = 3, year = 2010, pages = {489--501}, doi = {http://dx.doi.org/10.1089/cmb.2009.0184}, commentpdf = {../papers/2010-SwensonSortingFastJCB.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-SwensonSortingFastJCB.pdf}{PDF}} }
@article{LinRSM10, author = {Y. Lin and V. Rajan and K.M. Swenson and B.M.E. Moret}, title = {Estimating true evolutionary distances under rearrangements, duplications, and losses}, journal = {BMC Bioinformatics}, volume = 11, number = {Suppl 1}, year = 2010, pages = 54, doi = {http://dx.doi.org/10.1186/1471-2105-11-S1-S54}, commentpdf = {../papers/2010-LinEstimatingTrueDistance.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-LinEstimatingTrueDistance.pdf}{PDF}} }
@article{RajanXLSM10, author = {V. Rajan and A.W. Xu and Y. Lin and K M. Swenson and B.M.E. Moret}, title = {Heuristics for the inversion median problem}, journal = {BMC Bioinformatics}, volume = 11, number = {Suppl 1}, year = 2010, pages = 54, doi = {http://dx.doi.org/10.1186/1471-2105-11-S1-S30}, commentpdf = {../papers/2010-RajanHeuristicsForMedian.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-RajanHeuristicsForMedian.pdf}{PDF}} }
@article{MiklosSlow2009, author = {I. Mikl{\'o}s and B. M{\'e}lyk{\'u}ti and K.M. Swenson}, title = {The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths}, journal = {ACM/IEEE Trans.\ on Comput.\ Biology and Bioinformatics}, volume = 7, number = 4, issn = {763-767}, year = 2010, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.26}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, commentpdf = {../papers/2009-MiklosParISMixing.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2009-MiklosParISMixing.pdf}{PDF}} }
@article{SwensonLRM09, author = {K.M. Swenson and Y. Lin and V. Rajan and B.M.E. Moret}, title = {Hurdles and sorting by inversions: combinatorial, statistical, and experimental results}, journal = {J.\ Comput.\ Biology}, volume = 16, number = 10, year = 2009, pages = {1339--1351}, doi = {http://dx.doi.org/10.1089/cmb.2009.0156}, commentpdf = {../papers/2009-SwensonHurdlesSortingByInversions.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2009-SwensonHurdlesSortingByInversions.pdf}{PDF}} }
@article{SwensonTTM09, author = {K.M. Swenson and Y. To and J. Tang and B.M.E. Moret}, title = {Maximum independent sets of commuting and noninterfering inversions}, journal = {BMC Bioinformatics}, volume = 10, number = {Suppl 1}, year = 2009, doi = {http://dx.doi.org/10.1186/1471-2105-10-S1-S6}, commentpdf = {../papers/2009-SwensonMISNoninterfering.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2009-SwensonMISNoninterfering.pdf}{PDF}} }
@article{SwensonM09, author = {K.M. Swenson and B.M.E. Moret}, title = {Inversion-based genomic signatures}, journal = {BMC Bioinformatics}, volume = 10, number = {Suppl 1}, year = 2009, doi = {http://dx.doi.org/10.1186/1471-2105-10-S1-S7}, commentpdf = {../papers/2009-SwensonGenomicSignatures.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2009-SwensonGenomicSignatures.pdf}{PDF}} }
@article{swensonJEA2008, author = {K.M. Swenson and M. Marron and J.V Earnest-Deyoung and B.M.E. Moret}, title = {Approximating the true evolutionary distance between two genomes}, journal = {{ACM} J.\ Experimental Algorithmics}, volume = 12, year = 2008, issn = {1084-6654}, pages = {1--17}, doi = {http://doi.acm.org/10.1145/1227161.1402297}, publisher = {ACM}, address = {New York, NY, USA}, commentpdf = {../papers/2008-SwensonApproxTrueDistJEA.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2008-SwensonApproxTrueDistJEA.pdf}{PDF}} }
@article{Marron, author = {M. Marron and K.M. Swenson and B.M.E. Moret}, year = 2004, title = {Genomic distances under deletions and insertions}, journal = {Theor.\ Computer Science}, volume = 325, number = 3, pages = {347--360}, doi = {http://dx.doi.org/10.1016/j.tcs.2004.02.039}, commentpdf = {../papers/2004-MarronDistInsDel.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2004-MarronDistInsDel.pdf}{PDF}} }
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