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ORCIDKrister M. Swenson
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2020 – today
- 2024
[i2]Krister M. Swenson:
A Simple and Efficient Algorithm for Sorting Signed Permutations by Reversals. CoRR abs/2403.20165 (2024)- 2023
- [j30]Afif Elghraoui
, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar:
Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. Bioinform. 39(1) (2023) - [c25]Manuel Lafond, Anne Bergeron, Krister M. Swenson:
Two Strikes Against the Phage Recombination Problem. RECOMB-CG 2023: 68-83 - 2022
- [c24]Anne Bergeron, Marie-Jean Meurs, Romy Valiquette-Labonté, Krister M. Swenson:
On the Comparison of Bacteriophage Populations. RECOMB-CG 2022: 3-20 - [c23]Krister M. Swenson, Afif Elghraoui, Faramarz Valafar, Siavash Mirarab, Mathias Weller:
Quantifying Hierarchical Conflicts in Homology Statements. RECOMB-CG 2022: 146-167 - 2021
- [j29]Biing-Feng Wang, Krister M. Swenson:
A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees. IEEE ACM Trans. Comput. Biol. Bioinform. 18(2): 416-430 (2021)
2010 – 2019
- 2019
- [j28]Pijus Simonaitis, Annie Chateau, Krister M. Swenson:
A general framework for genome rearrangement with biological constraints. Algorithms Mol. Biol. 14(1): 15:1-15:14 (2019) - [j27]Krister M. Swenson, Mathieu Blanchette:
Large-scale mammalian genome rearrangements coincide with chromatin interactions. Bioinform. 35(14): i117-i126 (2019) - [j26]Benjamin Linard, Krister M. Swenson, Fabio Pardi:
Rapid alignment-free phylogenetic identification of metagenomic sequences. Bioinform. 35(18): 3303-3312 (2019) - [c22]Pijus Simonaitis, Annie Chateau, Krister M. Swenson:
Weighted Minimum-Length Rearrangement Scenarios. WABI 2019: 13:1-13:17 - [c21]Jakub Truszkowski, Olivier Gascuel, Krister M. Swenson:
Rapidly Computing the Phylogenetic Transfer Index. WABI 2019: 20:1-20:12 - 2018
- [j25]Pijus Simonaitis, Krister M. Swenson:
Finding local genome rearrangements. Algorithms Mol. Biol. 13(1): 9:1-9:14 (2018) - [c20]Pijus Simonaitis, Annie Chateau, Krister M. Swenson:
A General Framework for Genome Rearrangement with Biological Constraints. RECOMB-CG 2018: 49-71 - [i1]Pijus Simonaitis, Annie Chateau, Krister M. Swenson:
A framework for cost-constrained genome rearrangement under Double Cut and Join. CoRR abs/1802.07515 (2018) - 2017
- [c19]Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister M. Swenson:
Rearrangement Scenarios Guided by Chromatin Structure. RECOMB-CG 2017: 141-155 - [c18]Pijus Simonaitis, Krister M. Swenson:
Finding Local Genome Rearrangements. WABI 2017: 24:1-24:13 - 2016
- [j24]Krister M. Swenson, Pijus Simonaitis, Mathieu Blanchette:
Models and algorithms for genome rearrangement with positional constraints. Algorithms Mol. Biol. 11: 13 (2016) - [j23]Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron, Krister M. Swenson:
Aligning the unalignable: bacteriophage whole genome alignments. BMC Bioinform. 17: 30 (2016) - 2015
- [c17]Krister M. Swenson, Mathieu Blanchette:
Models and Algorithms for Genome Rearrangement with Positional Constraints. WABI 2015: 243-256 - 2014
- [j22]Riccardo Dondi, Nadia El-Mabrouk, Krister M. Swenson:
Gene tree correction for reconciliation and species tree inference: Complexity and algorithms. J. Discrete Algorithms 25: 51-65 (2014) - 2013
- [j21]Krister M. Swenson, Paul Guertin, Hugo Deschênes, Anne Bergeron:
Reconstructing the modular recombination history of Staphylococcus aureus phages. BMC Bioinform. 14(S-15): S17 (2013) - [j20]Manuel Lafond, Magali Semeria, Krister M. Swenson, Eric Tannier, Nadia El-Mabrouk:
Gene tree correction guided by orthology. BMC Bioinform. 14(S-15): S5 (2013) - [j19]Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk:
Ancestral Genome Organization: An Alignment Approach. J. Comput. Biol. 20(4): 280-295 (2013) - [p1]Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk:
Error Detection and Correction of Gene Trees. Models and Algorithms for Genome Evolution 2013: 261-285 - 2012
- [j18]Krister M. Swenson, Andrea Doroftei, Nadia El-Mabrouk:
Gene tree correction for reconciliation and species tree inference. Algorithms Mol. Biol. 7: 31 (2012) - [j17]Krister M. Swenson, Nadia El-Mabrouk:
Gene trees and species trees: irreconcilable differences. BMC Bioinform. 13(S-19): S15 (2012) - [j16]Olivier Tremblay Savard, Krister M. Swenson:
A graph-theoretic approach for inparalog detection. BMC Bioinform. 13(S-19): S16 (2012) - [j15]Krister M. Swenson, Eric C. H. Chen, Nicholas D. Pattengale, David Sankoff:
The Kernel of Maximum Agreement Subtrees. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 1023-1031 (2012) - [c16]Aïda Ouangraoua, Krister M. Swenson, Anne Bergeron:
On the Comparison of Sets of Alternative Transcripts. ISBRA 2012: 201-212 - [c15]Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk:
Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. RECOMB 2012: 94-112 - [c14]Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk:
An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. WABI 2012: 106-122 - 2011
- [j14]Krister M. Swenson, Ghada Badr, David Sankoff:
Listing all sorting reversals in quadratic time. Algorithms Mol. Biol. 6: 11 (2011) - [j13]Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve:
A 2-Approximation for the Minimum Duplication Speciation Problem. J. Comput. Biol. 18(9): 1041-1053 (2011) - [j12]Ghada Badr, Krister M. Swenson, David Sankoff:
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. J. Comput. Biol. 18(9): 1201-1210 (2011) - [j11]Aïda Ouangraoua, Anne Bergeron, Krister M. Swenson:
Theory and Practice of Ultra-Perfection. J. Comput. Biol. 18(9): 1219-1230 (2011) - [j10]Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M. E. Moret:
Uncovering Hidden Phylogenetic Consensus in Large Data Sets. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 902-911 (2011) - [c13]Krister M. Swenson, Eric C. H. Chen, Nicholas D. Pattengale, David Sankoff:
The Kernel of Maximum Agreement Subtrees. ISBRA 2011: 123-135 - [c12]Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff:
OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. WABI 2011: 364-375 - 2010
- [j9]Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret:
Heuristics for the inversion median problem. BMC Bioinform. 11(S-1): 30 (2010) - [j8]Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret:
Estimating true evolutionary distances under rearrangements, duplications, and losses. BMC Bioinform. 11(S-1): 54 (2010) - [j7]Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret:
Sorting Signed Permutations by Inversions in O(nlogn) Time. J. Comput. Biol. 17(3): 489-501 (2010) - [j6]István Miklós, Bence Mélykúti, Krister M. Swenson:
The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths. IEEE ACM Trans. Comput. Biol. Bioinform. 7(4): 763-767 (2010) - [c11]Nicholas D. Pattengale, Krister M. Swenson, Bernard M. E. Moret:
Uncovering Hidden Phylogenetic Consensus. ISBRA 2010: 128-139 - [c10]Ghada Badr, Krister M. Swenson, David Sankoff:
Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. RECOMB-CG 2010: 39-49 - [c9]Aïda Ouangraoua, Anne Bergeron, Krister M. Swenson:
Ultra-Perfect Sorting Scenarios. RECOMB-CG 2010: 50-61 - [c8]Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve:
An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. RECOMB-CG 2010: 290-301 - [c7]Krister M. Swenson, Ghada Badr, David Sankoff:
Listing All Sorting Reversals in Quadratic Time. WABI 2010: 102-110
2000 – 2009
- 2009
- [b1]Krister M. Swenson:
Evolution of whole genomes through inversions - models and algorithms for duplicates, ancestors, and edit scenarios. EPFL, Switzerland, 2009 - [j5]Krister M. Swenson, Bernard M. E. Moret:
Inversion-based genomic signatures. BMC Bioinform. 10(S-1) (2009) - [j4]Krister M. Swenson, Yokuki To, Jijun Tang, Bernard M. E. Moret:
Maximum independent sets of commuting and noninterfering inversions. BMC Bioinform. 10(S-1) (2009) - [j3]Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. J. Comput. Biol. 16(10): 1339-1351 (2009) - [c6]Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret:
Sorting Signed Permutations by Inversions in O(nlogn) Time. RECOMB 2009: 386-399 - 2008
- [j2]Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret:
Approximating the true evolutionary distance between two genomes. ACM J. Exp. Algorithmics 12: 3.5:1-3.5:17 (2008) - [c5]Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret:
Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. APBC 2008: 241-250 - [c4]Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
Hurdles Hardly Have to Be Heeded. RECOMB-CG 2008: 241-251 - 2005
- [c3]Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret:
Approximating the True Evolutionary Distance between Two Genomes. ALENEX/ANALCO 2005: 121-129 - [c2]Krister M. Swenson, Nicholas D. Pattengale, Bernard M. E. Moret:
A Framework for Orthology Assignment from Gene Rearrangement Data. Comparative Genomics 2005: 153-166 - 2004
- [j1]Mark Marron, Krister M. Swenson, Bernard M. E. Moret:
Genomic Distances under Deletions and Insertions. Theor. Comput. Sci. 325(3): 347-360 (2004) - 2003
- [c1]Mark Marron, Krister M. Swenson, Bernard M. E. Moret:
Genomic Distances under Deletions and Insertions. COCOON 2003: 537-547
Coauthor Index
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