@inproceedings{LafondBSStrikesAgainstPhageRecombination, author = {M. Lafond and A. Bergeron and K.M. Swenson}, title = {Two Strikes Against the Phage Recombination Problem}, booktitle = {Proc.\ 20th Workshop\ Comp.\ Genomics ({RECOMB-CG'23})}, pages = {68--83}, series = {Lecture Notes in Computer Science}, year = {2023}, volume = {13883}, doi = {10.1007/978-3-031-36911-7_5}, commentpdf = {../papers/2023-LafondBSStrikesAgainstPhageRecombination.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2023-LafondBSStrikesAgainstPhageRecombination.pdf}{PDF}} }
@inproceedings{SwensonEVMW2022, author = {K.M. Swenson and A. Elghraoui and F. Valafar and S. Mirarab and M. Weller}, title = {Quantifying Hierarchical Conflicts in Homology Statements}, booktitle = {Proc.\ 19th Workshop\ Comp.\ Genomics ({RECOMB-CG'22})}, pages = {146--167}, series = {Lecture Notes in Computer Science}, year = {2022}, volume = {13234}, doi = {10.1007/978-3-031-06220-9_9}, commentpdf = {../papers/2022-SwensonEVMWHierarchicalHomology.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2022-SwensonEVMWHierarchicalHomology.pdf}{PDF}} }
@inproceedings{BergeronMVS2022, author = {A. Bergeron and M-J. Meurs and R. Valiquette-Labont\'e and K.M. Swenson}, title = {On the Comparison of Bacteriophage Populations}, booktitle = {Proc.\ 19th Workshop\ Comp.\ Genomics ({RECOMB-CG'22})}, pages = {3--20}, series = {Lecture Notes in Computer Science}, year = {2022}, volume = {13234}, doi = {10.1007/978-3-031-06220-9_1}, commentpdf = {../papers/2022-BergeronMLSComparisonBacteriophages.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2022-BergeronMLSComparisonBacteriophages.pdf}{PDF}} }
@inproceedings{SimonaitisCS2019, author = {P. Simonaitis and A. Chateau and K.M. Swenson}, title = {Weighted Minimum-Length Rearrangement Scenarios}, booktitle = {Proc.\ 19th Int'l Workshop Algs.\ in Bioinformatics ({WABI'19})}, pages = {13:1--13:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, isbn = {978-3-95977-123-8}, issn = {1868-8969}, year = {2019}, volume = {143}, address = {Dagstuhl, Germany}, doi = {10.4230/LIPIcs.WABI.2019.13}, commentpdf = {../papers/2019-SimonaitisWeightedRearrangement.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2019-SimonaitisWeightedRearrangement.pdf}{PDF}} }
@inproceedings{TruszkowskiGS2019, author = {J. Truszkowski and O. Gascuel and K.M. Swenson}, title = {Rapidly Computing the Phylogenetic Transfer Index}, booktitle = {Proc.\ 19th Int'l Workshop Algs.\ in Bioinformatics ({WABI'19})}, pages = {20:1--20:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, isbn = {978-3-95977-123-8}, issn = {1868-8969}, year = {2019}, volume = {143}, address = {Dagstuhl, Germany}, doi = {10.4230/LIPIcs.WABI.2019.20}, commentpdf = {../papers/2019-TruszkowskiRapidTransferIndex.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2019-TruszkowskiRapidTransferIndex.pdf}{PDF}} }
@inproceedings{SimonaitisCS2018, author = {P. Simonaitis and A. Chateau and K.M. Swenson}, title = {A General Framework for Genome Rearrangement with Biological Constraints}, booktitle = {Proc.\ 16th Workshop\ Comp.\ Genomics ({RECOMB-CG'18})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Bioinformatics}, volume = 11183, year = 2018, pages = {49-71}, doi = {10.1007/978-3-030-00834-5_3}, commentpdf = {../papers/2018-SimonaitisFrameworkRearrangement.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2018-SimonaitisFrameworkRearrangement.pdf}{PDF}~$^*$} }
@inproceedings{PulicaniSRS2017, author = {S. Pulicani and P. Simonaitis and E. Rivals and K.M. Swenson}, title = {Rearrangement Scenarios Guided by Chromatin Structure}, booktitle = {Proc.\ 15th Workshop\ Comp.\ Genomics ({RECOMB-CG'17})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Bioinformatics}, volume = 10562, year = 2017, pages = {141-155}, doi = {10.1007/978-3-319-67979-2_8}, commentpdf = {../papers/2017-PulicaniGuidedRearrangements.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2017-PulicaniGuidedRearrangements.pdf}{PDF}} }
@inproceedings{SimonaitisS2017, author = {P. Simonaitis and K.M. Swenson}, title = {{Finding Local Genome Rearrangements}}, booktitle = {Proc.\ 17th Int'l Workshop Algs.\ in Bioinformatics ({WABI'17})}, pages = {24:1--24:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, isbn = {978-3-95977-050-7}, issn = {1868-8969}, year = {2017}, volume = {88}, address = {Dagstuhl, Germany}, doi = {10.4230/LIPIcs.WABI.2017.24}, commentpdf = {../papers/2017-SimonaitisFindingLocalWABI.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2017-SimonaitisFindingLocalWABI.pdf}{PDF}~$^*$} }
@inproceedings{SwensonB2015, title = {Models and Algorithms for Genome Rearrangement with Positional Constraints}, author = {K.M. Swenson and M. Blanchette}, booktitle = {Proc.\ 15th Int'l Workshop Algs.\ in Bioinformatics ({WABI'15})}, pages = {243-256}, year = 2015, publisher = {Springer Verlag, Berlin}, doi = {http://dx.doi.org/10.1007/978-3-662-48221-6_18}, commentpdf = {../papers/2015-SwensonPositionalRearrangements.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2015-SwensonPositionalRearrangements.pdf}{PDF}~$^*$} }
@inproceedings{LafondSE12, author = {M. Lafond and K.M. Swenson and N. El-Mabrouk}, title = {An optimal reconciliation algorithm for gene trees with polytomies}, booktitle = {Proc.\ 12th Int'l Workshop Algs.\ in Bioinformatics ({WABI'12})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 7534, year = 2012, pages = {106-122}, doi = {http://dx.doi.org/10.1007/978-3-642-33122-0_9}, commentpdf = {../papers/2012-LafondOptimalReconciliationPolytomies.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-LafondOptimalReconciliationPolytomies.pdf}{PDF}} }
@inproceedings{HollowaySAM12, author = {P. Holloway and K.M. Swenson and D. Ardell and N. El-Mabrouk}, title = {Evolution of genome organization by duplication and loss: an alignment approach}, booktitle = {Proc.\ 16th Ann.\ Int'l Conf.\ Comput.\ Mol.\ Biol.\ ({RECOMB'12})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 7262, year = 2012, isbn = {978-3-642-29626-0}, doi = {http://dx.doi.org/10.1007/978-3-642-29627-7_10}, pages = {94-112}, commentpdf = {../papers/2012-HollowayDupLossAlignment.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-HollowayDupLossAlignment.pdf}{PDF}~$^*$} }
@inproceedings{OuangraouaSB12, author = {A. Ouangraoua and K.M. Swenson and A. Bergeron}, title = {On the comparison of sets of alternative transcripts}, booktitle = {Proc.\ 8th Inter. Symp. on Bioinform. and Applic. ({ISBRA'12})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 7292, year = 2012, pages = {201-212}, doi = {http://dx.doi.org/10.1007/978-3-642-30191-9_19}, commentpdf = {../papers/2012-OuangraouaSetsOfTranscripts.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-OuangraouaSetsOfTranscripts.pdf}{PDF}} }
@inproceedings{SwensonCPS11, author = {K.M. Swenson and E. Chen and N.D. Pattengale and D. Sankoff}, title = {The kernel of maximum agreement subtrees}, booktitle = {Proc.\ 7th Inter. Symp. on Bioinform. and Applic. ({ISBRA'11})}, publisher = {Springer Verlag, Berlin}, volume = 6674, series = {Lecture Notes in Computer Science}, year = 2011, pages = {123-135}, doi = {http://dx.doi.org/10.1007/978-3-642-21260-4_15}, commentpdf = {../papers/2011-SwensonKAST.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-SwensonKAST.pdf}{PDF}~$^*$} }
@inproceedings{ZhengSLS11, author = {C. Zheng and K.M. Swenson and E. Lyons and D. Sankoff}, title = {{OMG}! orthologs in multiple genomes - competing graph-theoretical formulations}, booktitle = {Proc.\ 11th Int'l Workshop Algs.\ in Bioinformatics ({WABI'11})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 6833, year = 2011, pages = {364-375}, doi = {http://dx.doi.org/10.1007/978-3-642-23038-7_30}, commentpdf = {../papers/2011-ZhengOMG.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-ZhengOMG.pdf}{PDF}} }
@inproceedings{SwensonBS10, author = {K.M. Swenson and G. Badr and D. Sankoff}, title = {Listing all sorting reversals in quadratic time}, booktitle = {Proc.\ 10th Int'l Workshop Algs.\ in Bioinformatics ({WABI'10})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 6293, year = 2010, pages = {102-110}, doi = {http://dx.doi.org/10.1007/978-3-642-15294-8_9}, commentpdf = {../papers/2010-SwensonAllSortingRevs.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-SwensonAllSortingRevs.pdf}{PDF}~$^*$} }
@inproceedings{OuangraouaBS10, author = {A. Ouangraoua and A. Bergeron and K.M. Swenson}, title = {Ultra-perfect sorting scenarios}, booktitle = {Proc.\ 6th Workshop\ Comp.\ Genomics ({RECOMB-CG'10})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 6398, year = 2010, pages = {50-61}, doi = {http://dx.doi.org/10.1007/978-3-642-15294-8_9}, commentpdf = {../papers/2010-OuangraouaUltraPerfect.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-OuangraouaUltraPerfect.pdf}{PDF}~$^*$} }
@inproceedings{OuangraouaSC10, author = {A. Ouangraoua and K.M. Swenson and C. Chauve}, title = {An approximation algorithm for computing a parsimonious first speciation in the gene duplication model}, booktitle = {Proc.\ 6th Workshop\ Comp.\ Genomics ({RECOMB-CG'10})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 6398, year = 2010, pages = {290-302}, doi = {http://dx.doi.org/10.1007/978-3-642-15294-8_9}, commentpdf = {../papers/2010-OuangraouaParsimoniousFirstSpec.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-OuangraouaParsimoniousFirstSpec.pdf}{PDF}~$^*$} }
@inproceedings{PattengaleSM10, author = {N.D. Pattengale and K.M. Swenson and B.M.E. Moret}, title = {Uncovering Hidden Phylogenetic Consensus}, booktitle = {Proc. Bioinformatics Research and Applications, 6th International Symposium, ISBRA'10}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 6053, year = 2010, pages = {128-139}, doi = {http://dx.doi.org/10.1007/978-3-642-13078-6_16}, commentpdf = {../papers/2010-PattengaleUncoveringConsensus.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-PattengaleUncoveringConsensus.pdf}{PDF}~$^*$} }
@inproceedings{BadrSS10, author = {G. Badr and K.M. Swenson and D. Sankoff}, title = {Listing all parsimonious reversal sequences: new algorithms and perspectives}, booktitle = {Proc.\ 6th Workshop\ Comp.\ Genomics ({RECOMB-CG'10})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 6398, year = 2010, pages = {39-48}, doi = {http://dx.doi.org/10.1007/978-3-642-15294-8_9}, commentpdf = {../papers/2010-BadrAllParsimoniousSequences.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-BadrAllParsimoniousSequences.pdf}{PDF}~$^*$} }
@inproceedings{SwensonRLM09, 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}, booktitle = {Proc.\ 13th Ann.\ Int'l Conf.\ Comput.\ Mol.\ Biol.\ ({RECOMB'09})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 5541, year = 2009, pages = {386-399}, doi = {http://dx.doi.org/10.1007/978-3-642-02008-7_28}, commentpdf = {../papers/2009-SwensonSortingFastOLD.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2009-SwensonSortingFastOLD.pdf}{PDF}~$^*$} }
@inproceedings{Swe08, author = {K.M. Swenson and W. Arndt and J. Tang and B.M.E. Moret}, title = {Phylogenetic reconstruction from complete gene orders of whole genomes}, booktitle = {Proc.\ 6rd Asia Pacific Bioinformatics Conf.\ ({APBC'08})}, pages = {241-250}, year = 2008, commentpdf = {../papers/2008-SwensonPhyloCompleteGeneOrders.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2008-SwensonPhyloCompleteGeneOrders.pdf}{PDF}} }
@inproceedings{SwensonLRM08, author = {K.M. Swenson and Y. Lin and V. Rajan and B.M.E. Moret}, title = {Hurdles Hardly Have to Be Heeded}, booktitle = {Proc.\ 6th Workshop\ Comp.\ Genomics ({RECOMB-CG'08})}, publisher = {Springer Verlag, Berlin}, series = {Lecture Notes in Computer Science}, volume = 5267, year = 2008, pages = {241-251}, doi = {http://dx.doi.org/10.1007/978-3-540-87989-3_18}, commentpdf = {../papers/2008-SwensonHHHH.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2008-SwensonHHHH.pdf}{PDF}~$^*$} }
@inproceedings{SwensonF, author = {K.M. Swenson and N.D. Pattengale and B.M.E. Moret}, title = {A framework for orthology assignment from gene rearrangement data}, booktitle = {Proc.\ 3nd Workshop\ Comp.\ Genomics ({RECOMB-CG'05})}, publisher = {Springer Verlag, Berlin}, pages = {153-166}, year = 2005, doi = {http://dx.doi.org/10.1007/11554714_14}, commentpdf = {../papers/2005-SwensonFrameworkOrthologyAssignment.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2005-SwensonFrameworkOrthologyAssignment.pdf}{PDF}} }
@inproceedings{swenson2005, 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}, year = 2005, booktitle = {Proc.\ 7th SIAM Workshop on Algorithm Engineering \& Experiments ({ALENEX'05})}, publisher = {{SIAM Press, Philadelphia}}, pages = {121-129}, doi = {http://www.siam.org/meetings/alenex05/papers/11submission.pdf}, commentpdf = {../papers/2005-SwensonApproxTrueEvolDist.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2005-SwensonApproxTrueEvolDist.pdf}{PDF}~$^*$} }
@inproceedings{Marron-cocoon, author = {M. Marron and K.M. Swenson and B.M.E. Moret}, year = 2003, title = {Genomic distances under deletions and insertions}, booktitle = {Proc.\ 9th Int'l\ Conf.\ Computing and Combinatorics ({COCOON'03})}, pages = {537-547}, series = {Lecture Notes in Computer Science}, volume = 2697, publisher = {Springer Verlag, Berlin}, doi = {http://dx.doi.org/10.1007/3-540-45071-8_54}, commentpdf = {../papers/2004-MarronDistInsDel.pdf}, note = {\href{http://www2.lirmm.fr/~swenson/papers/2004-MarronDistInsDel.pdf}{PDF}~$^*$} }
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