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Reconstructing the architecture of the ancestral amniote genome.

 Aïda Ouangraoua , Eric Tannier , Cedric Chauve
Bioinformatics, 2011, 27, 27 (19), pp.2664-2671. ⟨10.1093/bioinformatics/btr461⟩
Article dans une revue inria-00635016v1
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Local Similarity Between Quotiented Ordered Trees

 Pascal Ferraro , Aïda Ouangraoua , Laurent Tichit , Serge Dulucq
Journal of Discrete Algorithms, 2007, 5 (1), pp.23-35
Article dans une revue hal-00307119v1
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Deep transcriptome annotation suggests that small and large proteins encoded in the same genes often cooperate

 Sondos Samandi , Annie Roy , Vivian Delcourt , Jean-François Lucier , Jules Gagnon , et al.
2020
Pré-publication, Document de travail inserm-02940621v1

Un nouvel algorithme d alignement de structures secondaires d ARN

 Cedric Chauve , Aida Ouangraoua
8èmes Journées Ouvertes Biologie Informatique Mathématiques, 2007, France. pp.401-402
Communication dans un congrès hal-00306613v1

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

Comparison of Tree Architecture Using Tree Edit Distances: Application to Two-Year-Old Apple Tree

 Vincent Segura , Aida Ouangraoua , Pascal Ferraro , Evelyne Costes
XIII Eucarpia, biometrics in plant breeding section meeting, 2006, Austria. pp.21
Communication dans un congrès hal-00306607v1

Plant Architecture Comparison Methods: a Review of Existing Algorithms

 Aida Ouangraoua , Vincent Segura , Evelyne Costes , Pascal Ferraro
5th International Workshop on Functional Structural Plant Models, Nov 2007, Napier, New Zealand. pp.471--474
Communication dans un congrès hal-00306610v1

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
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Genome dedoubling by DCJ and reversal

 Antoine Thomas , Jean-Stéphane Varré , Aïda Ouangraoua
BMC Bioinformatics, 2011, 12 (Suppl 9), pp.S20. ⟨10.1186/1471-2105-12-S9-S20⟩
Article dans une revue hal-00784416v1
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Plant architecture comparison methods: A review of existing algorithms and examples of application

 Aïda Ouangraoua , Vincent Segura , Evelyne Costes , Pascal Ferraro
5th International Workshop on Functional-Structural Plant Models, 2007, Napier, New Zealand. pp.47, 1-4
Communication dans un congrès hal-00831826v1
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OpenAlea: An open-source platform for the integration of heterogeneous FSPM components

 Samuel Dufour-Kowalski , Christophe Pradal , Nicolas Dones , Pierre Barbier de Reuille , Frédéric Boudon , et al.
FSPM07 - 5th International Workshop on Functional-Structural Plant Models, Nov 2007, Napier, New Zealand. pp.P36:1-2
Communication dans un congrès hal-00831824v1

Genome Dedoubling by DCJ and Reversal

 Antoine Thomas , Jean-Stéphane Varré , Ouangraoua Aïda
BMC Bioinformatics, 2011, 12 (Supplement 9), ⟨10.1186/1471-2105-12-S9-S20⟩
Article dans une revue inria-00635003v1

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

PyTreeMatch : a Python Based Software for Comparing RNA Secondary Structure

 Ione Ituarte , Aïda Ouangraoua , Pascal Ferraro
JOBIM, 2006, Bordeaux, France. pp.127
Communication dans un congrès hal-00307001v1

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

Benchmarking RNA secondary structure comparison algorithms

 Julien Allali , Yves d'Aubenton-Carafa , Cedric Chauve , Alain Denise , Christine Drevet , et al.
JOBIM'08, 2008, Lille, France. pp.67-68
Communication dans un congrès hal-00375710v1
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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

 Julien Allali , Cédric Saule , Cedric Chauve , Yves d'Aubenton-Carafa , Alain Denise , et al.
Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩
Article dans une revue hal-00647725v1
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Tandem Halving Problems by DCJ

 Antoine Thomas , Aïda Ouangraoua , Jean-Stéphane Varré
Workshop on Algorithms in Bioinformatics, Sep 2012, Ljubljana, Slovenia. pp.417-429, ⟨10.1007/978-3-642-33122-0_33⟩
Communication dans un congrès hal-00749019v1
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Genome Halving by Block Interchange

 Antoine Thomas , Aïda Ouangraoua , Jean-Stéphane Varré
BIOINFORMATICS, Feb 2012, Lisboa, Portugal. pp.58-65
Communication dans un congrès hal-00749026v1

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
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A 3-approximation algorithm for computing a parsimonious first speciation in the gene duplication model

 Cedric Chauve , Aïda Ouangraoua
2009
Pré-publication, Document de travail hal-00374851v2
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Prediction of Contiguous Regions in the Amniote Ancestral Genome

 Aïda Ouangraoua , Frédéric Boyer , Andrew Mcpherson , Eric Tannier , Cedric Chauve
ISBRA 2009, 5th International Symposium on Bioinformatics Research and Applications,, May 2009, Fort Lauderdale, Florida, United States. ⟨10.1007/978-3-642-01551-9_18⟩
Communication dans un congrès hal-00368187v1

A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes

 Aïda Ouangraoua , Valentin Guignon , Hamel Sylvie , Cedric Chauve
Theoretical Computer Science, 2011, 412 (8-10), pp.753-764. ⟨10.1016/j.tcs.2010.11.020⟩
Article dans une revue istex inria-00635043v1
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ProCARs: Progressive Reconstruction of Ancestral Gene Orders

 Amandine Perrin , Jean-Stéphane Varré , Samuel Blanquart , Aïda Ouangraoua
BMC Genomics, 2015, 16 (Suppl 5), pp.S6. ⟨10.1186/1471-2164-16-S5-S6⟩
Article dans une revue hal-01217311v1
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Parking functions, labeled trees and DCJ sorting scenarios

 Aïda Ouangraoua , Anne Bergeron
Recomb Comparative Genomics 2009, 2009, Hungary. pp.24-35
Communication dans un congrès hal-00527614v1

Combinatorial structure of genome

 Aïda Ouangraoua , Anne Bergeron
Journal of Computational Biology, 2010, 17 (9), ⟨10.1089/cmb.2010.0126⟩
Article dans une revue hal-00527626v1
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OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes

 Marie A Brunet , Mylène Brunelle , Jean-François Lucier , Vivian Delcourt , Maxime Levesque , et al.
Nucleic Acids Research, 2019, 8 (47(D1)), pp.D403-D410. ⟨10.1093/nar/gky936⟩
Article dans une revue inserm-02941503v1

Yeast ancestral genome reconstructions: the possibilities of computational methods II.

 Cedric Chauve , Haris Gavranovic , Aida Ouangraoua , Eric Tannier
Journal of Computational Biology, 2010, 17 (9), pp.1097-112. ⟨10.1089/cmb.2010.0092⟩
Article dans une revue hal-00681091v1

On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction

 Aïda Ouangraoua , Mathieu Raffinot
Journal of Computational Biology, 2014, 21, 1, pp.64-79. ⟨10.1089/cmb.2013.0086⟩
Article dans une revue hal-00913212v1

Faster and Simpler Minimal Conflicting Set Identification.

 Aida Ouangraoua , Mathieu Raffinot
Combinatorial Pattern Matching, 2012, Helsinki, Finland. pp.41-55
Communication dans un congrès hal-00750028v1
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