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42

Publications of Annie Duchateau


Journal articles12 documents

  • Pijus Simonaitis, Annie Chateau, Krister Swenson. A general framework for genome rearrangement with biological constraints. Algorithms for Molecular Biology, BioMed Central, 2019, 14 (1), ⟨10.1186/s13015-019-0149-4⟩. ⟨lirmm-02410420⟩
  • Adel Ferdjoukh, Florian Galinier, Eric Bourreau, Annie Chateau, Clémentine Nebut. Measurement and Generation of Diversity and Meaningfulness in Model Driven Engineering. International Journal On Advances in Software, IARIA, 2018, 11 (1/2), pp.131-146. ⟨lirmm-02067506⟩
  • Kleber Padovani de Souza, João Carlos Setubal, André Carlos Ponce de Leon F. de Carvalho, Guilherme Oliveira, Annie Chateau, et al.. Machine learning meets genome assembly. Briefings in Bioinformatics, Oxford University Press (OUP), 2018, pp.bby072. ⟨10.1093/bib/bby072⟩. ⟨lirmm-02067457⟩
  • Mathias Weller, Annie Chateau, Clément Dallard, Rodolphe Giroudeau. Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special Cases. Algorithmica, Springer Verlag, 2018, 80 (6), pp.1771-1803. ⟨10.1007/s00453-018-0405-x⟩. ⟨hal-01833303⟩
  • Benoit Darties, Nicolas Champseix, Annie Chateau, Rodolphe Giroudeau, Mathias Weller. Complexity and lowers bounds for Power Edge Set Problem. Journal of Discrete Algorithms, Elsevier, 2018, 52-53, pp.70-91. ⟨10.1016/j.jda.2018.11.006⟩. ⟨lirmm-01950398⟩
  • Mathias Weller, Annie Chateau, Rodolphe Giroudeau, Jean-Claude König, Valentin Pollet. On Residual Approximation in Solution Extension Problems. Journal of Combinatorial Optimization, Springer Verlag, 2018, 36 (4), pp.1195-1220. ⟨10.1007/s10878-017-0202-5⟩. ⟨lirmm-01889394⟩
  • Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron, et al.. Aligning the unalignable: bacteriophage whole genome alignments. BMC Bioinformatics, BioMed Central, 2016, 17 (1), pp.1-13. ⟨10.1186/s12859-015-0869-5⟩. ⟨lirmm-01275670⟩
  • Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, et al.. Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics, BioMed Central, 2015, 16 (Suppl 10), pp.S11. ⟨10.1186/1471-2164-16-S10-S11⟩. ⟨hal-01180303v2⟩
  • Mathias Weller, Annie Chateau, Rodolphe Giroudeau. Exact approaches for scaffolding. BMC Bioinformatics, BioMed Central, 2015, pp.S2. ⟨10.1186/1471-2105-16-S14-S2⟩. ⟨lirmm-01219627⟩
  • Annie Chateau, Rodolphe Giroudeau. A complexity and approximation framework for the maximization scaffolding problem. Theoretical Computer Science, Elsevier, 2015, 595, pp.92-106. ⟨10.1016/j.tcs.2015.06.023⟩. ⟨lirmm-01219622⟩
  • Romain Blanc Mathieu, Bram Verhelst, Evelyne Derelle, Stephane Rombauts, Francois-Yves Bouget, et al.. An improved genome of the model marine alga [i]Ostreococcus tauri[/i] unfolds by assessing Illumina [i]de novo[/i] assemblies. BMC Genomics, BioMed Central, 2014, 15, pp.1-11. ⟨10.1186/1471-2164-15-1103⟩. ⟨hal-01130514⟩
  • Sèverine Bérard, Annie Chateau, Cedric Chauve, Christophe Paul, Eric Tannier. Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes. Journal of Computational Biology, Mary Ann Liebert, 2009, 16 (10), pp.1287-1309. ⟨10.1089/cmb.2009.0088⟩. ⟨lirmm-00432670⟩

Conference papers28 documents

  • Tom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias Weller. Linearizing Genomes: Exact Methods and Local Search. SOFSEM, Jan 2020, Limassol, Cyprus. pp.505-518, ⟨10.1007/978-3-030-38919-2_41⟩. ⟨lirmm-02332049v2⟩
  • Pijus Simonaitis, Annie Chateau, Krister Swenson. Weighted minimum-length rearrangement scenarios. 19th International Workshop on Algorithms in Bioinformatics (WABI), Sep 2019, Niagara Falls, NY, United States. pp.13:1-13:17, ⟨10.4230/LIPIcs.WABI.2019.13⟩. ⟨lirmm-02410451⟩
  • Tom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias Weller. New Polynomial-Time Algorithm around the Scaffolding Problem. AlCoB: Algorithms for Computational Biology, May 2019, Berkeley, United States. pp.25-38, ⟨10.1007/978-3-030-18174-1_2⟩. ⟨lirmm-02047701⟩
  • Pierre Cazals, Benoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias Weller. Power Edge Set and Zero Forcing Set Remain Difficult in Cubic Graphs. 30th International Workshop on Combinatorial Algorithms (IWOCA), Jul 2019, Pisa, Italy. pp.122-135, ⟨10.1007/978-3-030-25005-8_11⟩. ⟨hal-02359076⟩
  • Pijus Simonaitis, Annie Chateau, Krister Swenson. A General Framework for Genome Rearrangement with Biological Constraints. RECOMB-CG: Comparative Genomics, Oct 2018, Magog-Orford, QC, Canada. pp.49-71, ⟨10.1007/978-3-030-00834-5_3⟩. ⟨lirmm-02067487⟩
  • Dorine Tabary, Tom Davot, Mathias Weller, Annie Chateau, Rodolphe Giroudeau. New Results About the Linearization of Scaffolds Sharing Repeated Contigs. COCOA: Conference on Combinatorial Optimization and Applications, Sep 2018, Atlanta, GA, United States. pp.94-107, ⟨10.1007/978-3-030-04651-4_7⟩. ⟨lirmm-01900389v2⟩
  • Tom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias Weller. On the hardness of approximating Linearization of Scaffolds sharing Repeated Contigs. RECOMB-CG: Comparative Genomics, Oct 2018, Magog-Orford, QC, Canada. pp.91-107, ⟨10.1007/978-3-030-00834-5_5⟩. ⟨lirmm-01900395v2⟩
  • Benoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias Weller. Improved Complexity for Power Edge Set Problem. IWOCA: International Workshop on Combinatorial Algorithms, Jul 2017, Newcastle, Australia. pp.128-141, ⟨10.1007/978-3-319-78825-8_11⟩. ⟨hal-01715909⟩
  • Adel Ferdjoukh, Florian Galinier, Eric Bourreau, Annie Chateau, Clémentine Nebut. Measuring Differences To Compare Sets Of Models And Improve Diversity In MDE. ICSEA: International Conference on Software Engineering Advances, Oct 2017, Athenes, Greece. ⟨hal-01586827⟩
  • Annie Chateau, Benoit Darties, Rodolphe Giroudeau, Mathias Weller. Surveiller un réseau électrique en plaçant des dispositifs sur ses liens : un problème difficile. AlgoTel: Aspects Algorithmiques des Télécommunications, May 2017, Quiberon, France. ⟨hal-01516931⟩
  • Eric Bourreau, Annie Chateau, Rodolphe Giroudeau, Clément Dallard. Une modélisation par Contrainte de graphe pour résoudre l’échafaudage de génome. ROADEF: Recherche Opérationnelle et Aide à la Décision, Feb 2017, Metz, France. ⟨lirmm-01875591⟩
  • Mathias Weller, Annie Chateau, Rodolphe Giroudeau. On the Linearization of Scaffolds Sharing Repeated Contigs. COCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.509-517, ⟨10.1007/978-3-319-71147-8_38⟩. ⟨lirmm-01672893⟩
  • Benoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias Weller. New Insights for Power Edge Set Problem. COCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.180-194, ⟨10.1007/978-3-319-71150-8_17⟩. ⟨lirmm-01672895⟩
  • Mathias Weller, Annie Chateau, Rodolphe Giroudeau, Jean-Claude König, Valentin Pollet. On Residual Approximation in Solution Extension Problems. COCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. pp.463-476, ⟨10.1007/978-3-319-48749-6_34⟩. ⟨lirmm-01378581⟩
  • Clément Dallard, Mathias Weller, Annie Chateau, Rodolphe Giroudeau. Instance Guaranteed Ratio on Greedy Heuristic for Genome Scaffolding. COCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. pp.294-308, ⟨10.1007/978-3-319-48749-6_22⟩. ⟨lirmm-01378584⟩
  • Eric Bourreau, Annie Chateau, Clément Dallard, Rodolphe Giroudeau. A Graph Constraints Formulation for Contigs Scaffolding. WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France. pp.136-149. ⟨lirmm-01360463⟩
  • Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, et al.. Comment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels. Journées Ouvertes Biologie Informatique Mathématiques, 2016, Lyon, France. ⟨hal-01394409⟩
  • Adel Ferdjoukh, Eric Bourreau, Annie Chateau, Clémentine Nebut. A Model-Driven Approach to Generate Relevant and Realistic Datasets. SEKE: Software Engineering and Knowledge Engineering, Jul 2016, Redwood City, San Francisco Bay, United States. pp.105-109, ⟨10.18293/SEKE2016-029⟩. ⟨lirmm-01397311⟩
  • Florian Galinier, Eric Bourreau, Annie Chateau, Adel Ferdjoukh, Clémentine Nebut. Genetic Algorithm to Improve Diversity in MDE. META: Metaheuristics and Nature Inspired Computing, Oct 2016, Marrakech, Morocco. ⟨lirmm-01397321⟩
  • Adel Ferdjoukh, Anne-Elisabeth Baert, Eric Bourreau, Annie Chateau, Remi Coletta, et al.. Instantiation of meta-models constrained with OCL: A CSP approach. MODELSWARD: Model-Driven Engineering and Software Development, Feb 2015, Angers, France. pp.213-222, ⟨10.5220/0005231402130222⟩. ⟨lirmm-01232891⟩
  • Mathias Weller, Annie Chateau, Rodolphe Giroudeau. On the Complexity of Scaffolding Problems: From Cliques to Sparse Graphs. COCOA: Conference on Combinatorial Optimization and Applications, Dec 2015, Houston, United States. pp.409-423, ⟨10.1007/978-3-319-26626-8_30⟩. ⟨lirmm-01250982⟩
  • Annie Chateau, Rodolphe Giroudeau. Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem. AlCoB: Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. pp.47-58, ⟨10.1007/978-3-319-07953-0_4⟩. ⟨lirmm-01007556⟩
  • Nicolas Briot, Annie Chateau, Remi Coletta, Simon de Givry, Philippe Leleux, et al.. An integer linear programming approach for genome scaffolding. WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2014, Lyon, France. 16 p. ⟨hal-01198359⟩
  • Adel Ferdjoukh, Anne-Elisabeth Baert, Annie Chateau, Remi Coletta, Clémentine Nebut. A CSP Approach for Metamodel Instantiation. ICTAI: International Conference on Tools with Artificial Intelligence, Nov 2013, Washington, United States. pp.1044-1051, ⟨10.1109/ICTAI.2013.156⟩. ⟨lirmm-01007571⟩
  • Pierre Riou, Eric Rivals, Annie Chateau. Approximate Common Intervals in Multiple Genome Comparison. BIBM'11: Bioinformatics and Biomedicine, Nov 2011, Atlanta, United States. pp.131-134, ⟨10.1109/BIBM.2011.96⟩. ⟨lirmm-00659473⟩
  • Annie Chateau, Cedric Chauve, Sèverine Bérard, Eric Tannier, Christophe Paul. Perfect DCJ rearrangement. RECOMB-CG: Comparative Genomics, Oct 2008, Paris, France. pp.158-169, ⟨10.1007/978-3-540-87989-3_12⟩. ⟨lirmm-00327258⟩
  • Mahdi Belcaid, Anne Bergeron, Annie Chateau, Cedric Chauve, Yannick Gingras, et al.. Exploring Genome Rearrangements using Virtual Hybridization. APBC'07: 5th Asia-Pacific Bioinformatics Conference, Jan 2007, Hong Kong, China. pp.205-214. ⟨lirmm-00203873⟩
  • Guillaume Blin, Annie Chateau, Cedric Chauve, Yannick Gingras. Inferring Positional Homologs with Common Intervals of Sequences. 4th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG'06), Sep 2006, Montreal, Canada. pp.24-38. ⟨hal-00620367⟩

Books1 document

  • Olivier Teytaud, Christophe Antonini, Pierre Borgnat, Annie Chateau, Edouard Lebeau. Mathématiques pour l'agrégation. Dunod, pp.736, 2007. ⟨inria-00173250⟩

Theses1 document

  • Annie Chateau. Utilisation des destinées pour la décision et sa complexité dans le cas de formules à profondeur de quantification bornée sur des structures logiques finies et infinies. Mathématiques [math]. Université d'Auvergne - Clermont-Ferrand I, 2003. Français. ⟨tel-00011983⟩