M. Lafond, A. Bergeron, and K.M. Swenson. Two strikes against the phage recombination problem. In Proc. 20th Workshop Comp. Genomics (RECOMB-CG'23), volume 13883 of Lecture Notes in Computer Science, pages 68--83, 2023. PDF. [ bib | DOI ]

K.M. Swenson, A. Elghraoui, F. Valafar, S. Mirarab, and M. Weller. Quantifying hierarchical conflicts in homology statements. In Proc. 19th Workshop Comp. Genomics (RECOMB-CG'22), volume 13234 of Lecture Notes in Computer Science, pages 146--167, 2022. PDF. [ bib | DOI ]

A. Bergeron, M-J. Meurs, R. Valiquette-Labonté, and K.M. Swenson. On the comparison of bacteriophage populations. In Proc. 19th Workshop Comp. Genomics (RECOMB-CG'22), volume 13234 of Lecture Notes in Computer Science, pages 3--20, 2022. PDF. [ bib | DOI ]

P. Simonaitis, A. Chateau, and K.M. Swenson. Weighted minimum-length rearrangement scenarios. In Proc. 19th Int'l Workshop Algs. in Bioinformatics (WABI'19), volume 143 of Leibniz International Proceedings in Informatics (LIPIcs), pages 13:1--13:17, Dagstuhl, Germany, 2019. PDF. [ bib | DOI ]

J. Truszkowski, O. Gascuel, and K.M. Swenson. Rapidly computing the phylogenetic transfer index. In Proc. 19th Int'l Workshop Algs. in Bioinformatics (WABI'19), volume 143 of Leibniz International Proceedings in Informatics (LIPIcs), pages 20:1--20:12, Dagstuhl, Germany, 2019. PDF. [ bib | DOI ]

P. Simonaitis, A. Chateau, and K.M. Swenson. A general framework for genome rearrangement with biological constraints. In Proc. 16th Workshop Comp. Genomics (RECOMB-CG'18), volume 11183 of Lecture Notes in Bioinformatics, pages 49--71. Springer Verlag, Berlin, 2018. PDF ^*. [ bib | DOI ]

S. Pulicani, P. Simonaitis, E. Rivals, and K.M. Swenson. Rearrangement scenarios guided by chromatin structure. In Proc. 15th Workshop Comp. Genomics (RECOMB-CG'17), volume 10562 of Lecture Notes in Bioinformatics, pages 141--155. Springer Verlag, Berlin, 2017. PDF. [ bib | DOI ]

P. Simonaitis and K.M. Swenson. Finding Local Genome Rearrangements. In Proc. 17th Int'l Workshop Algs. in Bioinformatics (WABI'17), volume 88 of Leibniz International Proceedings in Informatics (LIPIcs), pages 24:1--24:13, Dagstuhl, Germany, 2017. PDF ^*. [ bib | DOI ]

K.M. Swenson and M. Blanchette. Models and algorithms for genome rearrangement with positional constraints. In Proc. 15th Int'l Workshop Algs. in Bioinformatics (WABI'15), pages 243--256. Springer Verlag, Berlin, 2015. PDF ^*. [ bib | DOI ]

M. Lafond, K.M. Swenson, and N. El-Mabrouk. An optimal reconciliation algorithm for gene trees with polytomies. In Proc. 12th Int'l Workshop Algs. in Bioinformatics (WABI'12), volume 7534 of Lecture Notes in Computer Science, pages 106--122. Springer Verlag, Berlin, 2012. PDF. [ bib | DOI ]

P. Holloway, K.M. Swenson, D. Ardell, and N. El-Mabrouk. Evolution of genome organization by duplication and loss: an alignment approach. In Proc. 16th Ann. Int'l Conf. Comput. Mol. Biol. (RECOMB'12), volume 7262 of Lecture Notes in Computer Science, pages 94--112. Springer Verlag, Berlin, 2012. PDF ^*. [ bib | DOI ]

A. Ouangraoua, K.M. Swenson, and A. Bergeron. On the comparison of sets of alternative transcripts. In Proc. 8th Inter. Symp. on Bioinform. and Applic. (ISBRA'12), volume 7292 of Lecture Notes in Computer Science, pages 201--212. Springer Verlag, Berlin, 2012. PDF. [ bib | DOI ]

K.M. Swenson, E. Chen, N.D. Pattengale, and D. Sankoff. The kernel of maximum agreement subtrees. In Proc. 7th Inter. Symp. on Bioinform. and Applic. (ISBRA'11), volume 6674 of Lecture Notes in Computer Science, pages 123--135. Springer Verlag, Berlin, 2011. PDF ^*. [ bib | DOI ]

C. Zheng, K.M. Swenson, E. Lyons, and D. Sankoff. OMG! orthologs in multiple genomes - competing graph-theoretical formulations. In Proc. 11th Int'l Workshop Algs. in Bioinformatics (WABI'11), volume 6833 of Lecture Notes in Computer Science, pages 364--375. Springer Verlag, Berlin, 2011. PDF. [ bib | DOI ]

K.M. Swenson, G. Badr, and D. Sankoff. Listing all sorting reversals in quadratic time. In Proc. 10th Int'l Workshop Algs. in Bioinformatics (WABI'10), volume 6293 of Lecture Notes in Computer Science, pages 102--110. Springer Verlag, Berlin, 2010. PDF ^*. [ bib | DOI ]

A. Ouangraoua, A. Bergeron, and K.M. Swenson. Ultra-perfect sorting scenarios. In Proc. 6th Workshop Comp. Genomics (RECOMB-CG'10), volume 6398 of Lecture Notes in Computer Science, pages 50--61. Springer Verlag, Berlin, 2010. PDF ^*. [ bib | DOI ]

A. Ouangraoua, K.M. Swenson, and C. Chauve. An approximation algorithm for computing a parsimonious first speciation in the gene duplication model. In Proc. 6th Workshop Comp. Genomics (RECOMB-CG'10), volume 6398 of Lecture Notes in Computer Science, pages 290--302. Springer Verlag, Berlin, 2010. PDF ^*. [ bib | DOI ]

N.D. Pattengale, K.M. Swenson, and B.M.E. Moret. Uncovering hidden phylogenetic consensus. In Proc. Bioinformatics Research and Applications, 6th International Symposium, ISBRA'10, volume 6053 of Lecture Notes in Computer Science, pages 128--139. Springer Verlag, Berlin, 2010. PDF ^*. [ bib | DOI ]

G. Badr, K.M. Swenson, and D. Sankoff. Listing all parsimonious reversal sequences: new algorithms and perspectives. In Proc. 6th Workshop Comp. Genomics (RECOMB-CG'10), volume 6398 of Lecture Notes in Computer Science, pages 39--48. Springer Verlag, Berlin, 2010. PDF ^*. [ bib | DOI ]

K.M. Swenson, V. Rajan, Y. Lin, and B. M. E. Moret. Sorting signed permutations by inversions in O(n log n) time. In Proc. 13th Ann. Int'l Conf. Comput. Mol. Biol. (RECOMB'09), volume 5541 of Lecture Notes in Computer Science, pages 386--399. Springer Verlag, Berlin, 2009. PDF ^*. [ bib | DOI ]

K.M. Swenson, W. Arndt, J. Tang, and B.M.E. Moret. Phylogenetic reconstruction from complete gene orders of whole genomes. In Proc. 6rd Asia Pacific Bioinformatics Conf. (APBC'08), pages 241--250, 2008. PDF. [ bib ]

K.M. Swenson, Y. Lin, V. Rajan, and B.M.E. Moret. Hurdles hardly have to be heeded. In Proc. 6th Workshop Comp. Genomics (RECOMB-CG'08), volume 5267 of Lecture Notes in Computer Science, pages 241--251. Springer Verlag, Berlin, 2008. PDF ^*. [ bib | DOI ]

K.M. Swenson, N.D. Pattengale, and B.M.E. Moret. A framework for orthology assignment from gene rearrangement data. In Proc. 3nd Workshop Comp. Genomics (RECOMB-CG'05), pages 153--166. Springer Verlag, Berlin, 2005. PDF. [ bib | DOI ]

K.M. Swenson, M. Marron, J.V. Earnest-DeYoung, and B.M.E. Moret. Approximating the true evolutionary distance between two genomes. In Proc. 7th SIAM Workshop on Algorithm Engineering & Experiments (ALENEX'05), pages 121--129. SIAM Press, Philadelphia, 2005. PDF ^*. [ bib | DOI ]

M. Marron, K.M. Swenson, and B.M.E. Moret. Genomic distances under deletions and insertions. In Proc. 9th Int'l Conf. Computing and Combinatorics (COCOON'03), volume 2697 of Lecture Notes in Computer Science, pages 537--547. Springer Verlag, Berlin, 2003. PDF ^*. [ bib | DOI ]

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