AC

Annie CHATEAU

Publications of Annie Duchateau
53
Documents
Identifiants chercheurs

Présentation


Publications

22
8
6
3
3
2
2
1
1
1
1
1
1
1
6
4
3
3
2
2
2
2
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
22
18
7
7
6
6
6
5
5
5
5
4
4
4
4
4
3
3
3
2
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
3
2
2
2
1
1
1
1
1
1
1
1
1
1
3
5
2
6
8
5
7
5
3
1
1
1
1
2
1
1
3
3
1
1
1
1
1
45
7
6
1
1
1

Publications

Deposit thumbnail

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⟩

Article dans une revue lirmm-03835013v1
Deposit thumbnail

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 et al.

Journal of Open Source Software, 2022, 7 (80), pp.4363. ⟨10.21105/joss.04363⟩

Article dans une revue lirmm-03920648v1

Involving repetitive regions in scaffolding improvement

Quentin Delorme , Rémy Costa , Yasmine Mansour , Anna-Sophie Fiston-Lavier , Annie Chateau

Journal of Bioinformatics and Computational Biology, 2021, 19 (06), pp.2140016. ⟨10.1142/S0219720021400163⟩

Article dans une revue hal-04954688v1
Deposit thumbnail

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⟩

Article dans une revue lirmm-03218029v2
Deposit thumbnail

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⟩

Article dans une revue lirmm-03244191v1
Deposit thumbnail

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⟩

Article dans une revue lirmm-03475277v1

Machine learning meets genome assembly

Kleber Padovani de Souza , João Carlos Setubal , André Carlos Ponce de Leon F. de Carvalho , Guilherme Oliveira , Annie Chateau et al.

Briefings in Bioinformatics, 2019, 20 (6), pp.2116-2129. ⟨10.1093/bib/bby072⟩

Article dans une revue lirmm-02067457v1
Deposit thumbnail

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

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⟩

Article dans une revue lirmm-01889394v1

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⟩

Article dans une revue lirmm-01950398v1
Deposit thumbnail

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⟩

Article dans une revue hal-01833303v1
Deposit thumbnail

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

Article dans une revue lirmm-02067506v1
Deposit thumbnail

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
Deposit thumbnail

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⟩

Article dans une revue lirmm-01219627v1
Deposit thumbnail

Ancestral gene synteny reconstruction improves extant species scaffolding

Yoann Anselmetti , Vincent Berry , Cedric Chauve , Annie Chateau , Eric Tannier et al.

BMC Genomics, 2015, 16 (Suppl 10), pp.S11. ⟨10.1186/1471-2164-16-S10-S11⟩

Article dans une revue hal-01180303v2

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⟩

Article dans une revue lirmm-01219622v1
Deposit thumbnail

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 et al.

BMC Genomics, 2014, 15, pp.1-11. ⟨10.1186/1471-2164-15-1103⟩

Article dans une revue hal-01130514v1

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⟩

Article dans une revue lirmm-00432670v1
Deposit thumbnail

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⟩

Communication dans un congrès lirmm-02332049v2
Deposit thumbnail

South Green resources to manage Rice Big Genomics Data [W682]

Clément Agret , Celine Gottin , Alexis Dereeper , Christine Tranchant-Dubreuil , Annie Chateau et al.

Plant and Animal Genome, Jan 2020, San Diego, United States. pp.302-302

Communication dans un congrès hal-05174640v1
Deposit thumbnail

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⟩

Communication dans un congrès lirmm-02047701v1
Deposit thumbnail

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⟩

Communication dans un congrès hal-02359076v1
Deposit thumbnail

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
Deposit thumbnail

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
Deposit thumbnail

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⟩

Communication dans un congrès hal-01715909v1
Deposit thumbnail

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⟩

Communication dans un congrès lirmm-01900395v2
Deposit thumbnail

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⟩

Communication dans un congrès lirmm-01900389v2
Deposit thumbnail

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

Communication dans un congrès hal-01516931v1

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⟩

Communication dans un congrès lirmm-01672895v1
Deposit thumbnail

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

Communication dans un congrès hal-01586827v1
Deposit thumbnail

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

Communication dans un congrès lirmm-01875591v1

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⟩

Communication dans un congrès lirmm-01672893v1

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⟩

Communication dans un congrès lirmm-01378581v1
Deposit thumbnail

Comment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels

Yoann Anselmetti , Vincent Berry , Cedric Chauve , Annie Chateau , Eric Tannier et al.

Journées Ouvertes Biologie Informatique Mathématiques, 2016, Lyon, France

Communication dans un congrès hal-01394409v1
Deposit thumbnail

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

Communication dans un congrès 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⟩

Communication dans un congrès lirmm-01378584v1
Deposit thumbnail

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⟩

Communication dans un congrès lirmm-01397311v1
Deposit thumbnail

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

Communication dans un congrès lirmm-01397321v1
Deposit thumbnail

Instantiation of meta-models constrained with OCL: A CSP approach

Adel Ferdjoukh , Anne-Elisabeth Baert , Eric Bourreau , Annie Chateau , Remi Coletta et al.

MODELSWARD: Model-Driven Engineering and Software Development, Feb 2015, Angers, France. pp.213-222, ⟨10.5220/0005231402130222⟩

Communication dans un congrès 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⟩

Communication dans un congrès lirmm-01250982v1
Deposit thumbnail

An integer linear programming approach for genome scaffolding

Nicolas Briot , Annie Chateau , Remi Coletta , Simon de Givry , Philippe Leleux et al.

WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2014, Lyon, France. 16 p

Communication dans un congrès hal-01198359v1

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⟩

Communication dans un congrès lirmm-01007556v1
Deposit thumbnail

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⟩

Communication dans un congrès lirmm-01007571v1
Deposit thumbnail

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⟩

Communication dans un congrès lirmm-00659473v1
Deposit thumbnail

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⟩

Communication dans un congrès lirmm-00327258v1
Deposit thumbnail

Exploring Genome Rearrangements using Virtual Hybridization

Mahdi Belcaid , Anne Bergeron , Annie Chateau , Cedric Chauve , Yannick Gingras et al.

APBC'07: 5th Asia-Pacific Bioinformatics Conference, Jan 2007, Hong Kong, China. pp.205-214

Communication dans un congrès lirmm-00203873v1
Deposit thumbnail

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

Communication dans un congrès hal-00620367v1

Resources to manage Rice Big Genomics Data

Clément Agret , Celine Gottin , Alexis Dereeper , Christine Tranchant-Dubreuil , Annie Chateau et al.

International Symposium of Rice Functional Genomics, Nov 2019, Taipei, Taiwan. ISFRG, 2019

Poster de conférence hal-05174377v1