• Complete publication lists of the team can be found on DBLP, Google  or PubMed.

  • 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.

  • DoubleRecViz: a Web-Based tool for visualizing Transcript-Gene-Species tree reconciliation
    Esaie Kuitche, Yanchun Qi, Nadia Tahiri, Jack Parmer, Aida Ouangraoua. Bioinformatics, October 2020, btaa882. 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, 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
    Nucleic Acids Research, 2019, volume 47, issue D1, pages D403-D410. view.

  • Comparative Genomics – 16th International Conference, RECOMB-CG 2018, Proceedings.
    Mathieu Blanchette, Aïda Ouangraoua 
    Lecture Notes in Computer Science 11183, Springer, 2018, ISBN 978-3-030-00833-8. view.

  • aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences.
    Jean-Pierre Sehi GLOUZON and Aida OUANGRAOUA 
    Bioinformatics, 2018, vol. 34, issue 13, p. i70–i78. view.

  • Gene tree construction and correction using supertree and reconciliation. 
    Manuel LAFOND, Cedric CHAUVE, Nadia EL-MABROUK, Aida OUANGRAOUA 
    IEEE/ACM transactions on computational biology and bioinformatics, 2018, vol. 15, no 5, p. 1560-1570.  view .

  • OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. 
    Marie A. BRUNET, Mylène BRUNELLE, Jean-François LUCIER, …, Xavier ROUCOU 
    Nucleic acids research, 2018. view .

  • Reconstructing protein and gene phylogenies using reconciliation and soft-clustering. 
    Esaie KUITCHE, Manuel LAFOND and Aida OUANGRAOUA 
    Journal of bioinformatics and computational biology, 2017, vol. 15, no 06, p. 1740007. view.

  • Aligning coding sequences with frameshift extension penalties. 
    Safa JAMMALI, Esaie KUITCHE, Ayoub RACHATI, François BÉLANGER, Michelle SCOTT and Aida OUANGRAOUA 
    Algorithms for Molecular Biology, 2017, vol. 12, no 1, p. 10. view .

  • The SCJ small parsimony problem for weighted gene adjacencies. 
    Nina LUHMAN, Manuel LAFOND, Annelyse THEVENIN, Aida OUANGRAOUA, Roland WITTLER, Cedric CHAUVE 
    IEEE/ACM transactions on computational biology and bioinformatics, 2017. view .

  • A general framework for gene tree correction based on duplication-loss reconciliation. 
    Nadia EL-MABROUK, Aida OUANGRAOUA. 
    In Proceedings of Algorithms in Bioinformatics, 17th International Workshop, LIPIcs-Leibniz, 2017.  view .

  • Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins. 
    Sondos SAMANDI, Annie ROY, Vivian DELCOURT, …, Xavier ROUCOU 
    Elife, 2017, vol. 6, p. e27860. view .

  • The SCJ small parsimony problem for weighted gene adjacencies. 
    Nina LUHMAN, Annelyse THEVENIN, Aida OUANGRAOUA, Roland WITTLER, Cedric CHAUVE 
    In Proceedings of Bioinformatics Research and Applications – 12th International Symposium, 2016, p. 200–210. view .

  • Procars: Progressive reconstruction of ancestral gene orders. 
    Amandine PERRIN, Jean-Stéphane VARRÉ, Samuel BLANQUART, Aida OUANGRAOUA 
    BMC genomics, 2015, vol. 16, no 5, p. S6.  view .

  • Reconstructing a SuperGeneTree minimizing reconciliation. 
    Manuel LAFOND, Aida OUANGRAOUA, Nadia EL-MABROUK. 
    BMC bioinformatics, 2015, vol. 16, no 14, p. S4.  view .