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- G-quadruplex occurrence and conservation: more than just a question of guanine–cytosine content
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- From pairwise to multiple spliced alignment
Safa Jammali, Abigaïl Djossou, Wend-Yam D D Ouédraogo, Yannis Nevers, Ibrahim Chegrane, and Aïda Ouangraoua. Bioinformatics Advances, Volume 2, Issue 1, 2022, vbab044. view.
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- DoubleRecViz: a Web-Based tool for visualizing Transcript-Gene-Species tree reconciliation
Esaie Kuitche, Yanchun Qi, Nadia Tahiri, Jack Parmer, Aida Ouangraoua. Bioinformatics, Volume 37, Issue 13, Pages 1920–1922, 2021, btaa882. view.
- Gene tree and species tree reconciliation with endosymbiotic gene transfer
Yoann Anselmetti, Nadia El-Mabrouk, Manuel Lafond, and Aïda Ouangraoua. Bioinformatics, Volume 37, Issue Supplement_1, Pages i120–i132, 2021. view.
- 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, Frederic Grenier, Mariano Avino, Isabelle Fournier, Michel Salzet, Aïda Ouangraoua, Michelle S Scott, François-Michel Boisvert, Xavier Roucou.
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- aliFreeFoldMulti: alignment-free method to predict secondary structures of multiple RNA homologs
Marc-Andre Bossanyi, Valentin Carpentier, Jean-Pierre S Glouzon, Aida Ouangraoua, Yoann Anselmetti. NAR Genomics and Bioinformatics, Volume 2, Issue 4, December 2020, lqaa086. view.
- Where are G-quadruplexes located in the human transcriptome ?
Anaïs Vannutelli, Sarah Belhamiti, Jean-Michel Garant, Aida Ouangraoua, Jean-Pierre Perreault. NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa035. view.
- Reconstructing the Phylogeny of Corynebacteriales While Accounting for Horizontal Gene Transfer.
Nilson Da Rocha Coimbra, Aristoteles Goes-Neto, Vasco Azevedo, Aïda Ouangraoua.
Genome Biology and Evolution, Volume 12, Issue 4, Pages 381–395, 2020, evaa058. view.
- SimSpliceEvol: Alternative Splicing-Aware Simulation of Biological Sequence Evolution.
Esaie Kuitche, Safa Jammali, Aïda Ouangraoua.
BMC Bioinformatics, 2019, volume 20. view.
- SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups.
Safa Jammali, Jean-David Aguilar, Esaie Kuitche, and Aida Ouangraoua.
BMC Bioinformatics, 2019, volume 20. view.
- 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, Aida Ouangraoua, Michelle S Scott, François-Michel Boisvert, Xavier Roucou.
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- Comparative Genomics – 16th International Conference, RECOMB-CG 2018, Proceedings.
Mathieu Blanchette, Aïda Ouangraoua
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Jean-Pierre Sehi GLOUZON and Aida OUANGRAOUA
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- Gene tree construction and correction using supertree and reconciliation.
Manuel LAFOND, Cedric CHAUVE, Nadia EL-MABROUK, Aida OUANGRAOUA
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Marie A. BRUNET, Mylène BRUNELLE, Jean-François LUCIER, …, Xavier ROUCOU
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- Reconstructing protein and gene phylogenies using reconciliation and soft-clustering.
Esaie KUITCHE, Manuel LAFOND and Aida OUANGRAOUA
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- Aligning coding sequences with frameshift extension penalties.
Safa JAMMALI, Esaie KUITCHE, Ayoub RACHATI, François BÉLANGER, Michelle SCOTT and Aida OUANGRAOUA
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- The SCJ small parsimony problem for weighted gene adjacencies.
Nina LUHMAN, Manuel LAFOND, Annelyse THEVENIN, Aida OUANGRAOUA, Roland WITTLER, Cedric CHAUVE
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- A general framework for gene tree correction based on duplication-loss reconciliation.
Nadia EL-MABROUK, Aida OUANGRAOUA.
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- Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins.
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- The SCJ small parsimony problem for weighted gene adjacencies.
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- Procars: Progressive reconstruction of ancestral gene orders.
Amandine PERRIN, Jean-Stéphane VARRÉ, Samuel BLANQUART, Aida OUANGRAOUA
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- Reconstructing a SuperGeneTree minimizing reconciliation.
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