Afif Elghraoui, Siavash Mirarab, Krister M Swenson, and Faramarz Valafar. Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. Bioinformatics, 39(1), 01 2023. PDF. [ bib | DOI ]

G.W. Coombs, S.L. Baines, B.P. Howden, K.M. Swenson, and F.G. O'Brien. Diversity of bacteriophages encoding Panton-Valentine leukocidin in temporally and geographically related Staphylococcus aureus. PloS one, 15(2):e0228676, 2020. PDF. [ bib | DOI ]

K.M. Swenson and M. Blanchette. Large-scale mammalian genome rearrangements coincide with chromatin interactions. Bioinformatics, 35(14):i117--i126, 07 2019. PDF. [ bib | DOI ]

B.-F. Wang and K.M. Swenson. A faster algorithm for computing the kernel of maximum agreement subtrees. ACM/IEEE Trans. on Comput. Biology and Bioinformatics, 6 2019. PDF. [ bib | DOI ]

B. Linard, K.M. Swenson, and F. Pardi. Rapid alignment-free phylogenetic identification of metagenomic sequences. Bioinformatics, 35(18):3303--3312, 01 2019. PDF. [ bib | DOI ]

P. Simonaitis, A. Chateau, and K.M. Swenson. A general framework for genome rearrangement with biological constraints. Algorithms for Mol. Biol., 14(15), 2019. PDF. [ bib | DOI ]

P. Simonaitis and K.M. Swenson. Finding local genome rearrangements. Algorithms for Mol. Biol., 13(1):9, 2018. PDF. [ bib | DOI ]

S. Blanquart, J.-S. Varré, Paul Guertin, A. Perrin, A. Bergeron, and K.M. Swenson. Assisted transcriptome reconstruction and splicing orthology. BMC Genomics, 17(10):157--164, 2016. PDF. [ bib | DOI ]

K.M. Swenson, P. Simonaitis, and M. Blanchette. Models and algorithms for genome rearrangement with positional constraints. Algorithms for Molecular Biology, 11(1):1--10, 2016. PDF. [ bib | DOI ]

S. Bérard, A. Chateau, N. Pompidor, P. Guertin, A. Bergeron, and K.M. Swenson. Aligning the unalignable: bacteriophage whole genome alignments. BMC Bioinformatics, 17(1):1--13, 2016. PDF. [ bib | DOI ]

R. Dondi, N. El-Mabrouk, and K.M. Swenson. Gene tree correction for reconciliation and species tree inference: complexity and algorithms. J. Discrete Algorithms, 2014. PDF. [ bib | DOI ]

K.M. Swenson, P. Guertin, H. Deschenes, and A. Bergeron. Reconstructing the modular recombination history of staphylococcus aureus phages. BMC Bioinformatics, 14(Suppl 15):S17, 2013. PDF. [ bib | DOI ]

M. Lafond, M. Semeria, K.M. Swenson, E. Tannier, and N. El-Mabrouk. Gene tree correction guided by orthology. BMC Bioinformatics, 14(Suppl 15):S5, 2013. PDF. [ bib | DOI ]

P. Holloway, K.M. Swenson, D. Ardell, and N. El-Mabrouk. Ancestral genome organization: an alignment approach. J. Comput. Biology, 20(4):280--295, 2013. PDF. [ bib | DOI ]

K.M. Swenson and N. El-Mabrouk. Gene trees and species trees: irreconcilable differences. BMC Bioinformatics, 13(Suppl 19):S15, 2012. PDF. [ bib | DOI ]

O. Tremblay-Savard and K.M. Swenson. A graph-theoretic approach for inparalog detection. BMC Bioinformatics, 13(Suppl 19):S16, 2012. PDF. [ bib | DOI ]

K.M. Swenson, A. Doroftei, and N. El-Mabrouk. Gene tree correction for reconciliation and species tree inference. Algorithms for Mol. Biol., 7(31), 2012. PDF. [ bib | DOI ]

K.M. Swenson, E. Chen, N.D. Pattengale, and D. Sankoff. The kernel of maximum agreement subtrees. ACM/IEEE Trans. on Comput. Biology and Bioinformatics, 9(4):1023--1031, 2012. PDF. [ bib | DOI ]

N.D. Pattengale, A.J. Aberer, K.M. Swenson, A. Stamatakis, and B.M.E. Moret. Uncovering hidden phylogenetic consensus in large datasets. ACM/IEEE Trans. on Comput. Biology and Bioinformatics, 8(4):902--911, 2011. PDF. [ bib | DOI ]

K.M. Swenson, G. Badr, and D. Sankoff. Listing all sorting reversals in quadratic time. Algorithms for Mol. Biol., 6(11), 2011. PDF. [ bib | DOI ]

A. Ouangraoua, K.M. Swenson, and C. Chauve. A 2-approximation for the minimum duplication speciation problem. J. Comput. Biology, 18(9), 2011. PDF. [ bib | DOI ]

A. Ouangraoua, K.M. Swenson, and A. Bergeron. Theory and practice of ultra-perfection. J. Comput. Biology, 18(9), 2011. PDF. [ bib | DOI ]

G. Badr, K.M. Swenson, and D. Sankoff. Listing all parsimonious reversal sequences: new algorithms and perspectives. J. Comput. Biology, 18(9), 2011. 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. J. Comput. Biology, 17(3):489--501, 2010. PDF. [ bib | DOI ]

Y. Lin, V. Rajan, K.M. Swenson, and B.M.E. Moret. Estimating true evolutionary distances under rearrangements, duplications, and losses. BMC Bioinformatics, 11(Suppl 1):54, 2010. PDF. [ bib | DOI ]

V. Rajan, A.W. Xu, Y. Lin, K M. Swenson, and B.M.E. Moret. Heuristics for the inversion median problem. BMC Bioinformatics, 11(Suppl 1):54, 2010. PDF. [ bib | DOI ]

I. Miklós, B. Mélykúti, and K.M. Swenson. The metropolized partial importance sampling mcmc mixes slowly on minimum reversal rearrangement paths. ACM/IEEE Trans. on Comput. Biology and Bioinformatics, 7(4), 2010. PDF. [ bib | DOI ]

K.M. Swenson, Y. Lin, V. Rajan, and B.M.E. Moret. Hurdles and sorting by inversions: combinatorial, statistical, and experimental results. J. Comput. Biology, 16(10):1339--1351, 2009. PDF. [ bib | DOI ]

K.M. Swenson, Y. To, J. Tang, and B.M.E. Moret. Maximum independent sets of commuting and noninterfering inversions. BMC Bioinformatics, 10(Suppl 1), 2009. PDF. [ bib | DOI ]

K.M. Swenson and B.M.E. Moret. Inversion-based genomic signatures. BMC Bioinformatics, 10(Suppl 1), 2009. 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. ACM J. Experimental Algorithmics, 12:1--17, 2008. PDF. [ bib | DOI ]

M. Marron, K.M. Swenson, and B.M.E. Moret. Genomic distances under deletions and insertions. Theor. Computer Science, 325(3):347--360, 2004. PDF. [ bib | DOI ]

This file was generated by bibtex2html 1.99.