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Annie CHATEAU

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RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes

Clément Agret , Annie Chateau , Gaetan Droc , Gautier Sarah , Manuel Ruiz
Journal of Open Source Software, 2022, 7 (80), pp.4363. ⟨10.21105/joss.04363⟩
Journal articles lirmm-03920648v1
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On a greedy approach for genome scaffolding

Tom Davot , Annie Chateau , Rohan Fossé , Rodolphe Giroudeau , Mathias Weller
Algorithms for Molecular Biology, 2022, 17 (1), pp.16-46. ⟨10.1186/s13015-022-00223-x⟩
Journal articles lirmm-03835013v1
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BREC: An R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

Yasmine Mansour , Annie Chateau , Anna-Sophie Fiston-Lavier
BMC Bioinformatics, 2021, 22 (S6), pp.#396. ⟨10.1186/s12859-021-04233-1⟩
Journal articles lirmm-03475277v1
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Efficient assembly consensus algorithms for divergent contig sets

Annie Chateau , Tom Davot , Manuel Lafond
Computational Biology and Chemistry, 2021, 93, pp.#107516. ⟨10.1016/j.compbiolchem.2021.107516⟩
Journal articles lirmm-03244191v1
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Producing Genomic Sequences after Genome Scaffolding with Ambiguous Paths: Complexity, Approximation and Lower Bounds

Tom Davot , Annie Chateau , Rodolphe Giroudeau , Mathias Weller , Dorine Tabary
Algorithmica, 2021, 83, pp.2063-2095. ⟨10.1007/s00453-021-00819-6⟩
Journal articles lirmm-03218029v2

Machine learning meets genome assembly

Kleber Padovani de Souza , João Carlos Setubal , André Carlos Ponce de Leon F. de Carvalho , Guilherme Oliveira , Annie Chateau
Briefings in Bioinformatics, 2019, 20 (6), pp.2116-2129. ⟨10.1093/bib/bby072⟩
Journal articles lirmm-02067457v1
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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⟩
Journal articles lirmm-02410420v1
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Measurement and Generation of Diversity and Meaningfulness in Model Driven Engineering

Adel Ferdjoukh , Florian Galinier , Eric Bourreau , Annie Chateau , Clémentine Nebut
International Journal On Advances in Software, 2018, 11 (1/2), pp.131-146
Journal articles lirmm-02067506v1
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Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special Cases

Mathias Weller , Annie Chateau , Clément Dallard , Rodolphe Giroudeau
Algorithmica, 2018, 80 (6), pp.1771-1803. ⟨10.1007/s00453-018-0405-x⟩
Journal articles hal-01833303v1

Complexity and lowers bounds for Power Edge Set Problem

Benoit Darties , Nicolas Champseix , Annie Chateau , Rodolphe Giroudeau , Mathias Weller
Journal of Discrete Algorithms, 2018, 52-53, pp.70-91. ⟨10.1016/j.jda.2018.11.006⟩
Journal articles lirmm-01950398v1

On Residual Approximation in Solution Extension Problems

Mathias Weller , Annie Chateau , Rodolphe Giroudeau , Jean-Claude König , Valentin Pollet
Journal of Combinatorial Optimization, 2018, 36 (4), pp.1195-1220. ⟨10.1007/s10878-017-0202-5⟩
Journal articles lirmm-01889394v1
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Aligning the unalignable: bacteriophage whole genome alignments

Sèverine Bérard , Annie Chateau , Nicolas Pompidor , Paul Guertin , Anne Bergeron
BMC Bioinformatics, 2016, 17 (1), pp.30-43. ⟨10.1186/s12859-015-0869-5⟩
Journal articles lirmm-01275670v1
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Exact approaches for scaffolding

Mathias Weller , Annie Chateau , Rodolphe Giroudeau
BMC Bioinformatics, 2015, 16 (Suppl 14), pp.S2. ⟨10.1186/1471-2105-16-S14-S2⟩
Journal articles lirmm-01219627v1

A complexity and approximation framework for the maximization scaffolding problem

Annie Chateau , Rodolphe Giroudeau
Theoretical Computer Science, 2015, 595, pp.92-106. ⟨10.1016/j.tcs.2015.06.023⟩
Journal articles lirmm-01219622v1
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Ancestral gene synteny reconstruction improves extant species scaffolding

Yoann Anselmetti , Vincent Berry , Cedric Chauve , Annie Chateau , Eric Tannier
BMC Genomics, 2015, 16 (Suppl 10), pp.S11. ⟨10.1186/1471-2164-16-S10-S11⟩
Journal articles hal-01180303v2
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An improved genome of the model marine alga [i]Ostreococcus tauri[/i] unfolds by assessing Illumina [i]de novo[/i] assemblies

Romain Blanc Mathieu , Bram Verhelst , Evelyne Derelle , Stephane Rombauts , Francois-Yves Bouget
BMC Genomics, 2014, 15, pp.1-11. ⟨10.1186/1471-2164-15-1103⟩
Journal articles hal-01130514v1

Greffes de cornée automatisées par laser femtoseconde optimisé et système de contrôle aberrométrique

Karsten Plamann , Florent Aptel , N. Château , Caroline Crotti , Florent Deloison
Innovation and Research in BioMedical engineering, 2010, 31 (2), pp.97-100. ⟨10.1016/j.irbm.2010.02.011⟩
Journal articles hal-00526682v1

Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes

Sèverine Bérard , Annie Chateau , Cedric Chauve , Christophe Paul , Eric Tannier
Journal of Computational Biology, 2009, 16 (10), pp.1287-1309. ⟨10.1089/cmb.2009.0088⟩
Journal articles lirmm-00432670v1
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Linearizing Genomes: Exact Methods and Local Search

Tom Davot , Annie Chateau , Rodolphe Giroudeau , Mathias Weller
SOFSEM 2020 - 46th International Conference on Current Trends in Theory and Practice of Informatics, Jan 2020, Limassol, Cyprus. pp.505-518, ⟨10.1007/978-3-030-38919-2_41⟩
Conference papers lirmm-02332049v2
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New Polynomial-Time Algorithm around the Scaffolding Problem

Tom Davot , Annie Chateau , Rodolphe Giroudeau , Mathias Weller
AlCoB 2019 - 6th International Conference on Algorithms for Computational Biology, May 2019, Berkeley, United States. pp.25-38, ⟨10.1007/978-3-030-18174-1_2⟩
Conference papers lirmm-02047701v1

Power Edge Set and Zero Forcing Set Remain Difficult in Cubic Graphs

Pierre Cazals , Benoit Darties , Annie Chateau , Rodolphe Giroudeau , Mathias Weller
IWOCA 2019 - 30th International Workshop on Combinatorial Algorithms, Jul 2019, Pisa, Italy. pp.122-135, ⟨10.1007/978-3-030-25005-8_11⟩
Conference papers hal-02359076v1
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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⟩
Conference papers lirmm-02410451v1
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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⟩
Conference papers lirmm-02067487v1
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New Results About the Linearization of Scaffolds Sharing Repeated Contigs

Dorine Tabary , Tom Davot , Mathias Weller , Annie Chateau , Rodolphe Giroudeau
COCOA 2018 - 12th International Conference on Combinatorial Optimization and Applications, Sep 2018, Atlanta, GA, United States. pp.94-107, ⟨10.1007/978-3-030-04651-4_7⟩
Conference papers lirmm-01900389v2
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On the hardness of approximating Linearization of Scaffolds sharing Repeated Contigs

Tom Davot , Annie Chateau , Rodolphe Giroudeau , Mathias Weller
RECOMB-CG: Comparative Genomics, Oct 2018, Magog-Orford, QC, Canada. pp.91-107, ⟨10.1007/978-3-030-00834-5_5⟩
Conference papers lirmm-01900395v2
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Improved Complexity for Power Edge Set Problem

Benoit Darties , Annie Chateau , Rodolphe Giroudeau , Mathias Weller
IWOCA: International Workshop on Combinatorial Algorithms, Jul 2017, Newcastle, Australia. pp.128-141, ⟨10.1007/978-3-319-78825-8_11⟩
Conference papers hal-01715909v1
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Measuring Differences To Compare Sets Of Models And Improve Diversity In MDE

Adel Ferdjoukh , Florian Galinier , Eric Bourreau , Annie Chateau , Clémentine Nebut
ICSEA: International Conference on Software Engineering Advances, Oct 2017, Athenes, Greece
Conference papers hal-01586827v1
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Surveiller un réseau électrique en plaçant des dispositifs sur ses liens : un problème difficile

Annie Chateau , Benoit Darties , Rodolphe Giroudeau , Mathias Weller
AlgoTel: Aspects Algorithmiques des Télécommunications, May 2017, Quiberon, France
Conference papers hal-01516931v1

On the Linearization of Scaffolds Sharing Repeated Contigs

Mathias Weller , Annie Chateau , Rodolphe Giroudeau
COCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.509-517, ⟨10.1007/978-3-319-71147-8_38⟩
Conference papers lirmm-01672893v1
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Une modélisation par Contrainte de graphe pour résoudre l’échafaudage de génome

Eric Bourreau , Annie Chateau , Rodolphe Giroudeau , Clément Dallard
ROADEF 2017 - 18e Congrès de la Société Française de Recherche Opérationnelle et d'Aide à la Décision, Feb 2017, Metz, France
Conference papers lirmm-01875591v1

New Insights for Power Edge Set Problem

Benoit Darties , Annie Chateau , Rodolphe Giroudeau , Mathias Weller
COCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.180-194, ⟨10.1007/978-3-319-71150-8_17⟩
Conference papers lirmm-01672895v1
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A Graph Constraints Formulation for Contigs Scaffolding

Eric Bourreau , Annie Chateau , Clément Dallard , Rodolphe Giroudeau
WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France. pp.136-149
Conference papers lirmm-01360463v1

Instance Guaranteed Ratio on Greedy Heuristic for Genome Scaffolding

Clément Dallard , Mathias Weller , Annie Chateau , Rodolphe Giroudeau
COCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. pp.294-308, ⟨10.1007/978-3-319-48749-6_22⟩
Conference papers lirmm-01378584v1

On Residual Approximation in Solution Extension Problems

Mathias Weller , Annie Chateau , Rodolphe Giroudeau , Jean-Claude König , Valentin Pollet
COCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. pp.463-476, ⟨10.1007/978-3-319-48749-6_34⟩
Conference papers lirmm-01378581v1
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Comment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels

Yoann Anselmetti , Vincent Berry , Cedric Chauve , Annie Chateau , Eric Tannier
Journées Ouvertes Biologie Informatique Mathématiques, 2016, Lyon, France
Conference papers hal-01394409v1
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Genetic Algorithm to Improve Diversity in MDE

Florian Galinier , Eric Bourreau , Annie Chateau , Adel Ferdjoukh , Clémentine Nebut
META: Metaheuristics and Nature Inspired Computing, Oct 2016, Marrakech, Morocco
Conference papers lirmm-01397321v1
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A Model-Driven Approach to Generate Relevant and Realistic Datasets

Adel Ferdjoukh , Eric Bourreau , Annie Chateau , Clémentine Nebut
SEKE: Software Engineering and Knowledge Engineering, Jul 2016, Redwood City, San Francisco Bay, United States. pp.105-109, ⟨10.18293/SEKE2016-029⟩
Conference papers lirmm-01397311v1
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Instantiation of meta-models constrained with OCL: A CSP approach

Adel Ferdjoukh , Anne-Elisabeth Baert , Eric Bourreau , Annie Chateau , Remi Coletta
MODELSWARD: Model-Driven Engineering and Software Development, Feb 2015, Angers, France. pp.213-222, ⟨10.5220/0005231402130222⟩
Conference papers lirmm-01232891v1

On the Complexity of Scaffolding Problems: From Cliques to Sparse Graphs

Mathias Weller , Annie Chateau , Rodolphe Giroudeau
COCOA: Conference on Combinatorial Optimization and Applications, Dec 2015, Houston, United States. pp.409-423, ⟨10.1007/978-3-319-26626-8_30⟩
Conference papers lirmm-01250982v1

Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem

Annie Chateau , Rodolphe Giroudeau
AlCoB: Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. pp.47-58, ⟨10.1007/978-3-319-07953-0_4⟩
Conference papers lirmm-01007556v1
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An integer linear programming approach for genome scaffolding

Nicolas Briot , Annie Chateau , Remi Coletta , Simon de Givry , Philippe Leleux
WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2014, Lyon, France. 16 p
Conference papers hal-01198359v1
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A CSP Approach for Metamodel Instantiation

Adel Ferdjoukh , Anne-Elisabeth Baert , Annie Chateau , Remi Coletta , Clémentine Nebut
ICTAI: International Conference on Tools with Artificial Intelligence, Nov 2013, Washington, United States. pp.1044-1051, ⟨10.1109/ICTAI.2013.156⟩
Conference papers lirmm-01007571v1
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Approximate Common Intervals in Multiple Genome Comparison

Pierre Riou , Eric Rivals , Annie Chateau
BIBM'11: Bioinformatics and Biomedicine, Nov 2011, Atlanta, United States. pp.131-134, ⟨10.1109/BIBM.2011.96⟩
Conference papers lirmm-00659473v1
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Perfect DCJ rearrangement

Annie Chateau , Cedric Chauve , Sèverine Bérard , Eric Tannier , Christophe Paul
RECOMB-CG: Comparative Genomics, Oct 2008, Paris, France. pp.158-169, ⟨10.1007/978-3-540-87989-3_12⟩
Conference papers lirmm-00327258v1
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Exploring Genome Rearrangements using Virtual Hybridization

Mahdi Belcaid , Anne Bergeron , Annie Chateau , Cedric Chauve , Yannick Gingras
APBC'07: 5th Asia-Pacific Bioinformatics Conference, Jan 2007, Hong Kong, China. pp.205-214
Conference papers lirmm-00203873v1
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Inferring Positional Homologs with Common Intervals of Sequences

Guillaume Blin , Annie Chateau , Cedric Chauve , Yannick Gingras
4th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG'06), Sep 2006, Montreal, Canada. pp.24-38
Conference papers hal-00620367v1