Recherche - Archive ouverte HAL Accéder directement au contenu

Filtrer vos résultats

27 résultats
Page :
triés par
Image document

Finding Local Genome Rearrangements

 Pijus Simonaitis , Krister M. Swenson
17th International Workshop on Algorithms in Bioinformatics (WABI 2017), Aug 2017, Boston, United States. pp.24:1--24:13, ⟨10.4230/LIPIcs.WABI.2017.24⟩
Communication dans un congrès lirmm-01794757v1
Image document

Weighted minimum-length rearrangement scenarios

 Pijus Simonaitis , Annie Chateau , Krister M. Swenson
WABI 2019 - 19th International Workshop on Algorithms in Bioinformatics, Sep 2019, Niagara Falls, NY, United States. pp.13:1-13:17, ⟨10.4230/LIPIcs.WABI.2019.13⟩
Communication dans un congrès lirmm-02410451v1
Image document

Quantifying Hierarchical Conflicts in Homology Statements

 Krister M. Swenson , Afif Elghraoui , Faramarz Valafar , Siavash Mirarab , Mathias Weller
RECOMB-CG 2022 - 19th International Conference on Comparative Genomics, May 2022, La Jolla, CA, United States. pp.146-167, ⟨10.1007/978-3-031-06220-9_9⟩
Communication dans un congrès hal-03875727v1
Image document

Two Strikes Against the Phage Recombination Problem

 Manuel Lafond , Krister M. Swenson , Anne Bergeron
RECOMB-CG 2023 - 20th International Conference on Comparative Genomics, Apr 2023, Istanbul, Turkey. pp.68-83, ⟨10.1007/978-3-031-36911-7_5⟩
Communication dans un congrès hal-04312199v1
Image document

On the Comparison of Bacteriophage Populations

 Anne Bergeron , Marie-Jean Meurs , Romy Valiquette-Labonté , Krister M. Swenson
RECOMB-CG 2022 - 19th International Conference on Comparative Genomics, May 2022, La Jolla, CA, United States. pp.3-20, ⟨10.1007/978-3-031-06220-9_1⟩
Communication dans un congrès hal-03875827v1
Image document

A General Framework for Genome Rearrangement with Biological Constraints

 Pijus Simonaitis , Annie Chateau , Krister M. Swenson
RECOMB-CG: Comparative Genomics, Oct 2018, Magog-Orford, QC, Canada. pp.49-71, ⟨10.1007/978-3-030-00834-5_3⟩
Communication dans un congrès lirmm-02067487v1
Image document

Large-scale mammalian genome rearrangements coincide with chromatin interactions

 Krister M. Swenson , Mathieu Blanchette
Bioinformatics, 2019, 35 (14), pp.i117-i126. ⟨10.1093/bioinformatics/btz343⟩
Article dans une revue lirmm-02410438v1
Image document

A general framework for genome rearrangement with biological constraints

 Pijus Simonaitis , Annie Chateau , Krister M. Swenson
Algorithms for Molecular Biology, 2019, 14 (1), ⟨10.1186/s13015-019-0149-4⟩
Article dans une revue lirmm-02410420v1

Rapid alignment-free phylogenec placement via ancestral k-mers

 Benjamin Linard , Krister M. Swenson , Fabio Pardi
MCEB: Mathematical and Computational Evolutionary Biology, Jun 2018, St Martin de Londres, France
Communication dans un congrès lirmm-01964481v1

Ultra-perfect Sorting Scenarios

 Aïda Ouangraoua , Anne Bergeron , Krister M. Swenson
RECOMB-Comparative Genomics, 2010, Canada. pp.50-61
Communication dans un congrès hal-00527625v1
Image document

Rapid alignment-free phylogenetic identification of metagenomic sequences

 Benjamin Linard , Krister M. Swenson , Fabio Pardi
Bioinformatics, 2019, 35 (18), pp.3303-3312. ⟨10.1093/bioinformatics/btz068⟩
Article dans une revue lirmm-02410441v1
Image document

Rapid alignment-free phylogenetic identification of metagenomic sequences

 Benjamin Linard , Krister M. Swenson , Fabio Pardi
2019
Pré-publication, Document de travail lirmm-01964474v2

On the comparison of sets of alternative transcripts

 Aïda Ouangraoua , Krister M. Swenson , Anne Bergeron
International Symposium on Bioinformatics Research and Applications, 2012, Dallas, Germany. pp.201-212
Communication dans un congrès hal-00750031v1
Image document

Rearrangement Scenarios Guided by Chromatin Structure

 Sylvain Pulicani , Pijus Simonaitis , Eric Rivals , Krister M. Swenson
RECOMB-CG: Comparative Genomics, Oct 2017, Barcelona, Spain. pp.141-155, ⟨10.1007/978-3-319-67979-2_8⟩
Communication dans un congrès hal-01791974v1
Image document

Aligning the unalignable: bacteriophage whole genome alignments

 Sèverine Bérard , Annie Chateau , Nicolas Pompidor , Paul Guertin , Anne Bergeron , et al.
BMC Bioinformatics, 2016, 17 (1), pp.30-43. ⟨10.1186/s12859-015-0869-5⟩
Article dans une revue lirmm-01275670v1

An approximation algorithm for computing a parsimonious first speciation in the gene duplication model

 Aïda Ouangraoua , Krister M. Swenson , Cedric Chauve
RECOMB-Comparative Genomics, 2010, Canada. pp.290-302
Communication dans un congrès hal-00527624v1

Theory and practice of ultra-perfection

 Aïda Ouangraoua , Anne Bergeron , Krister M. Swenson
Journal of Computational Biology, 2011, 18 (9), pp.1219-1230. ⟨10.1089/cmb.2011.0086⟩
Article dans une revue inria-00635033v1
Image document

Gene tree correction guided by orthology

 Manuel Lafond , Magali Semeria , Krister M. Swenson , Eric Tannier , Nadia El-Mabrouk
BMC Bioinformatics, 2013, 14 (Suppl 15), pp.S5
Article dans une revue hal-00873235v1
Image document

A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees

 Biing-Feng Wang , Krister M. Swenson
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021, 18 (2), pp.416-430. ⟨10.1109/TCBB.2019.2922955⟩
Article dans une revue lirmm-02410429v1
Image document

Rapidly computing the phylogenetic transfer index

 Jakub Truszkowski , Olivier Gascuel , Krister M. Swenson
WABI 2019 - 19th International Workshop on Algorithms in Bioinformatics, Sep 2019, Niagara Falls, NY, United States. pp.20:1--20:12, ⟨10.4230/LIPIcs.WABI.2019.20⟩
Communication dans un congrès lirmm-02410461v1
Image document

Diversity of bacteriophages encoding Panton-Valentine leukocidin in temporally and geographically related Staphylococcus aureus

 Geoffrey W. Coombs , Sarah L Baines , Benjamin Howden , Krister M. Swenson , Frances G. O'Brien
PLoS ONE, 2020, 15 (2), pp.e0228676. ⟨10.1371/journal.pone.0228676⟩
Article dans une revue hal-03064749v1
Image document

Models and algorithms for genome rearrangement with positional constraints

 Krister M. Swenson , Pijus Simonaitis , Mathieu Blanchette
Algorithms for Molecular Biology, 2016, 11 (1), pp.13-24. ⟨10.1186/s13015-016-0065-9⟩
Article dans une revue lirmm-01348502v1

A 2-Approximation for the Minimum Duplication Speciation Problem

 Aïda Ouangraoua , Krister M. Swenson , Cedric Chauve
Journal of Computational Biology, 2011, 18 (9), pp.1041-1053. ⟨10.1089/cmb.2011.0108⟩
Article dans une revue inria-00635025v1
Image document

Un siècle de réarrangements génomiques

 Anne Bergeron , Krister M. Swenson
Gilles Didier (IMAG); Stéphane Guindon (LIRMM). Modèles et méthodes pour l’évolution biologique, Chapitre 5, ISTE, pp.127-150, 2022, 9781789480696. ⟨10.51926/ISTE.9069.ch5⟩
Chapitre d'ouvrage hal-03875891v1
Image document

Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates

 Afif Elghraoui , Siavash Mirarab , Krister M. Swenson , Faramarz Valafar
Bioinformatics, 2023, 39 (1), pp.#btad024. ⟨10.1093/bioinformatics/btad024⟩
Article dans une revue hal-03875983v1
Image document

Assisted transcriptome reconstruction and splicing orthology

 Samuel Blanquart , Jean-Stéphane Varré , Paul Guertin , Amandine Perrin , Anne Bergeron , et al.
BMC Genomics, 2016, Proceedings of the 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: genomics, 17 (Suppl 10), pp.786. ⟨10.1186/s12864-016-3103-6⟩
Article dans une revue hal-01396410v1
Image document

Finding local genome rearrangements

 Krister M. Swenson , Pijus Simonaitis
Algorithms for Molecular Biology, 2018, 13, pp.9-23. ⟨10.1186/s13015-018-0127-2⟩
Article dans une revue lirmm-01794753v1
Page :