Local similarity between quotiented ordered trees. - Aïda Ouangraoua; Pascal Ferraro; Laurent Tichit; Serge Dulucq (J. Discrete Algorithms, 2007)

Prediction of Contiguous Regions in the Amniote Ancestral Genome. - Aïda Ouangraoua; Frédéric Boyer; Andrew W. McPherson; Eric Tannier; Cédric Chauve (ISBRA, 2009)

Parking Functions, Labeled Trees and DCJ Sorting Scenarios. - Aïda Ouangraoua; Anne Bergeron (RECOMB-CG, 2009)

A 3-approximation algorithm for computing a parsimonious first speciation in the gene duplication model - Cédric Chauve; Aïda Ouangraoua (CoRR, 2009)

A new constrained edit distance between quotiented ordered trees. - Aïda Ouangraoua; Pascal Ferraro (J. Discrete Algorithms, 2009)

A constrained edit distance algorithm between semi-ordered trees. - Aïda Ouangraoua; Pascal Ferraro (Theor. Comput. Sci., 2009)

Ultra-Perfect Sorting Scenarios. - Aïda Ouangraoua; Anne Bergeron; Krister M. Swenson (RECOMB-CG, 2010)

An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. - Aïda Ouangraoua; Krister M. Swenson; Cédric Chauve (RECOMB-CG, 2010)

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II. - Cédric Chauve; Haris Gavranovic; Aïda Ouangraoua; Eric Tannier (J. Comput. Biol., 2010)

Combinatorial Structure of Genome Rearrangements Scenarios. - Aïda Ouangraoua; Anne Bergeron (J. Comput. Biol., 2010)

Reconstructing the architecture of the ancestral amniote genome. - Aïda Ouangraoua; Eric Tannier; Cédric Chauve (Bioinform., 2011)

Genome dedoubling by DCJ and reversal. - Antoine Thomas; Jean-Stéphane Varré; Aïda Ouangraoua (BMC Bioinform., 2011)

Theory and Practice of Ultra-Perfection. - Aïda Ouangraoua; Anne Bergeron; Krister M. Swenson (J. Comput. Biol., 2011)

A 2-Approximation for the Minimum Duplication Speciation Problem. - Aïda Ouangraoua; Krister M. Swenson; Cédric Chauve (J. Comput. Biol., 2011)

A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes. - Aïda Ouangraoua; Valentin Guignon; Sylvie Hamel; Cédric Chauve (Theor. Comput. Sci., 2011)

Genome Halving by Block Interchange. - Antoine Thomas; Aïda Ouangraoua; Jean-Stéphane Varré (BIOINFORMATICS, 2012)

Single Tandem Halving by Block Interchange. - Antoine Thomas; Aïda Ouangraoua; Jean-Stéphane Varré (BIOSTEC (Selected Papers), 2012)

Faster and Simpler Minimal Conflicting Set Identification - (Extended Abstract). - Aïda Ouangraoua; Mathieu Raffinot (CPM, 2012)

On the Comparison of Sets of Alternative Transcripts. - Aïda Ouangraoua; Krister M. Swenson; Anne Bergeron (ISBRA, 2012)

Tandem Halving Problems by DCJ. - Antoine Thomas; Aïda Ouangraoua; Jean-Stéphane Varré (WABI, 2012)

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. - Julien Allali; Cédric Saule; Cédric Chauve; Yves D'Aubenton-Carafa; Alain Denise; Christine Drevet; Pascal Ferraro; Daniel Gautheret; Claire Herrbach; Fabrice Leclerc; Antoine de Monte; Aïda Ouangraoua; et al. (Adv. Bioinformatics, 2012)

Faster and Simpler Minimal Conflicting Set Identification - Aïda Ouangraoua; Mathieu Raffinot (CoRR, 2012)

On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction. - Aïda Ouangraoua; Mathieu Raffinot (J. Comput. Biol., 2014)

Alignment of protein-coding sequences with frameshift extension penalties. - François Bélanger; Aïda Ouangraoua (CoRR, 2015)

Reconstructing the history of a WD40 beta-propeller tandem repeat using a phylogenetically informed algorithm. - Philippe Lavoie-Mongrain; Mahdi Belcaid; Aïda Ouangraoua; Anne Bergeron; Guylaine Poisson (PeerJ Comput. Sci., 2015)

Reconstructing a SuperGeneTree minimizing reconciliation. - Manuel Lafond; Aïda Ouangraoua; Nadia El-Mabrouk (BMC Bioinform., 2015)

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. - Nina Luhmann; Annelyse Thévenin; Aïda Ouangraoua; Roland Wittler; Cédric Chauve (ISBRA, 2016)

Reconstructing protein and gene phylogenies by extending the framework of reconciliation. - Esaie Kuitche; Aïda Ouangraoua (CoRR, 2016)

The SCJ small parsimony problem for weighted gene adjacencies (Extended version). - Nina Luhmann; Annelyse Thévenin; Aïda Ouangraoua; Roland Wittler; Cédric Chauve (CoRR, 2016)

A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation. - Nadia El-Mabrouk; Aïda Ouangraoua (WABI, 2017)

Aligning coding sequences with frameshift extension penalties. - Safa Jammali; Esaie Kuitche; Ayoub Rachati; François Bélanger; Michelle S. Scott; Aïda Ouangraoua (Algorithms Mol. Biol., 2017)

Improving spliced alignment for identification of ortholog groups and multiple CDS alignment. - Jean-David Aguilar; Safa Jammali; Esaie Kuitche; Aïda Ouangraoua (CoRR, 2017)

Reconstructing protein and gene phylogenies using reconciliation and soft-clustering. - Esaie Kuitche; Manuel Lafond; Aïda Ouangraoua (J. Bioinform. Comput. Biol., 2017)

aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences. - Jean-Pierre Séhi Glouzon; Aïda Ouangraoua (Bioinform., 2018)

Gene Tree Construction and Correction Using SuperTree and Reconciliation. - Manuel Lafond; Cédric Chauve; Nadia El-Mabrouk; Aïda Ouangraoua (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. - Safa Jammali; Jean-David Aguilar; Esaie Kuitche; Aïda Ouangraoua (BMC Bioinform., 2019)

SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution. - Esaie Kuitche; Safa Jammali; Aïda Ouangraoua (BMC Bioinform., 2019)

OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. - Marie A. Brunet; Mylène Brunelle; Jean-François Lucier; Vivian Delcourt; Maxime Levesque; Frédéric Grenier; Sondos Samandi; Sébastien Leblanc; Jean-David Aguilar; Pascal Dufour; Jean-Francois Jacques; Isabelle Fournier; et al. (Nucleic Acids Res., 2019)

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. - Nina Luhmann; Manuel Lafond; Annelyse Thévenin; Aïda Ouangraoua; Roland Wittler; Cédric Chauve (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Gene tree and species tree reconciliation with endosymbiotic gene transfer. - Yoann Anselmetti; Nadia El-Mabrouk; Manuel Lafond; Aïda Ouangraoua (Bioinform., 2021)

DoubleRecViz: a web-based tool for visualizing transcript-gene-species tree reconciliation. - Esaie Kuitche; Yanchun Qi; Nadia Tahiri; Jack Parmer; Aïda Ouangraoua (Bioinform., 2021)

OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. - Marie A. Brunet; Jean-François Lucier; Maxime Levesque; Sébastien Leblanc; Jean-Francois Jacques; Hassan R. H. Al-Saedi; Noé Guilloy; Frédéric Grenier; Mariano Avino; Isabelle Fournier; Michel Salzet; Aïda Ouangraoua; et al. (Nucleic Acids Res., 2021)

Inferring Clusters of Orthologous and Paralogous Transcripts. - Wend Yam Donald Davy Ouedraogo; Aïda Ouangraoua (RECOMB-CG, 2023)

GAIA: G-quadruplexes in alive creature database. - Anaïs Vannutelli; Lauriane lucienne noele Schell; Jean-Pierre Perreault; Aïda Ouangraoua (Nucleic Acids Res., 2023)

SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies. - Wend Yam Donald Davy Ouedraogo; Aïda Ouangraoua (BMC Bioinform., 2023)

Inferring Transcript Phylogenies from Transcript Ortholog Clusters. - Wend Yam Donald Davy Ouedraogo; Aïda Ouangraoua (RECOMB-CG, 2024)

Median and small parsimony problems on RNA trees. - Bertrand Marchand; Yoann Anselmetti; Manuel Lafond; Aïda Ouangraoua (Bioinform., 2024)

Orthology and Paralogy Relationships at Transcript Level. - Wend Yam Donald Davy Ouedraogo; Aïda Ouangraoua (J. Comput. Biol., 2024)