@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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