Search Results - "Ouangraoua, Aida"

SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies by Ouedraogo, Wend Yam D D, Ouangraoua, Aida

“…SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of…”
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Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins by Samandi, Sondos, Roy, Annie V, Delcourt, Vivian, Lucier, Jean-François, Gagnon, Jules, Beaudoin, Maxime C, Vanderperre, Benoît, Breton, Marc-André, Motard, Julie, Jacques, Jean-François, Brunelle, Mylène, Gagnon-Arsenault, Isabelle, Fournier, Isabelle, Ouangraoua, Aida, Hunting, Darel J, Cohen, Alan A, Landry, Christian R, Scott, Michelle S, Roucou, Xavier

“…Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames…”
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Median and small parsimony problems on RNA trees by Marchand, Bertrand, Anselmetti, Yoann, Lafond, Manuel, Ouangraoua, Aïda

“…Abstract Motivation Noncoding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a…”
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SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution by Kuitche, Esaie, Jammali, Safa, Ouangraoua, Aïda

“…It is now well established that eukaryotic coding genes have the ability to produce more than one type of transcript thanks to the mechanisms of alternative…”
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OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes by Brunet, Marie A, Lucier, Jean-François, Levesque, Maxime, Leblanc, Sébastien, Jacques, Jean-Francois, Al-Saedi, Hassan R H, Guilloy, Noé, Grenier, Frederic, Avino, Mariano, Fournier, Isabelle, Salzet, Michel, Ouangraoua, Aïda, Scott, Michelle S, Boisvert, François-Michel, Roucou, Xavier

“…Abstract OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a…”
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Gene tree and species tree reconciliation with endosymbiotic gene transfer by Anselmetti, Yoann, El-Mabrouk, Nadia, Lafond, Manuel, Ouangraoua, Aïda

“…Abstract Motivation It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α−proteobacterial genome…”
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DoubleRecViz: a web-based tool for visualizing transcript–gene–species tree reconciliation by Kuitche, Esaie, Qi, Yanchun, Tahiri, Nadia, Parmer, Jack, Ouangraoua, Aïda

“…Abstract Motivation A phylogenetic tree reconciliation is a mapping of one phylogenetic tree onto another which represents the co-evolution of two sets of taxa…”
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SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups by Jammali, Safa, Aguilar, Jean-David, Kuitche, Esaie, Ouangraoua, Aïda

“…The inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene…”
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OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes by Brunet, Marie A, Brunelle, Mylène, Lucier, Jean-François, Delcourt, Vivian, Levesque, Maxime, Grenier, Frédéric, Samandi, Sondos, Leblanc, Sébastien, Aguilar, Jean-David, Dufour, Pascal, Jacques, Jean-Francois, Fournier, Isabelle, Ouangraoua, Aida, Scott, Michelle S, Boisvert, François-Michel, Roucou, Xavier

“…Abstract Advances in proteomics and sequencing have highlighted many non-annotated open reading frames (ORFs) in eukaryotic genomes. Genome annotations,…”
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aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences by Glouzon, Jean-Pierre Séhi, Ouangraoua, Aïda

“…Abstract Motivation Predicting the conserved secondary structure of homologous ribonucleic acid (RNA) sequences is crucial for understanding RNA functions…”
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Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms by Vannutelli, Anaïs, Ouangraoua, Aïda, Perreault, Jean-Pierre

“…Background: G-quadruplexes (G4s) are secondary structures in DNA and RNA that impact various cellular processes, such as transcription, splicing, and…”
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Reconstructing a SuperGeneTree minimizing reconciliation by Lafond, Manuel, Ouangraoua, Aïda, El-Mabrouk, Nadia

“…Combining a set of trees on partial datasets into a single tree is a classical method for inferring large phylogenetic trees. Ideally, the combined tree should…”
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OpenProt 2.0 builds a path to the functional characterization of alternative proteins by Leblanc, Sébastien, Yala, Feriel, Provencher, Nicolas, Lucier, Jean-François, Levesque, Maxime, Lapointe, Xavier, Jacques, Jean-Francois, Fournier, Isabelle, Salzet, Michel, Ouangraoua, Aïda, Scott, Michelle S, Boisvert, François-Michel, Brunet, Marie A, Roucou, Xavier

“…Abstract The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or…”
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Reconstructing the architecture of the ancestral amniote genome by Ouangraoua, Aïda, Tannier, Eric, Chauve, Cedric

“…MOTIVATION: The ancestor of birds and mammals lived approximately 300 million years ago. Inferring its genome organization is key to understanding the…”
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G-quadruplex occurrence and conservation: more than just a question of guanine–cytosine content by Vannutelli, Anaïs, Perreault, Jean-Pierre, Ouangraoua, Aïda

“…Abstract G-quadruplexes are motifs found in DNA and RNA that can fold into tertiary structures. Until now, they have been studied experimentally mainly in…”
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The SCJ Small Parsimony Problem for Weighted Gene Adjacencies by Luhmann, Nina, Lafond, Manuel, Thevenin, Annelyse, Ouangraoua, Aida, Wittler, Roland, Chauve, Cedric

“…Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in…”
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Reconstructing protein and gene phylogenies using reconciliation and soft-clustering by Kuitche, Esaie, Lafond, Manuel, Ouangraoua, Aïda

“…The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods…”
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Gene Tree Construction and Correction Using SuperTree and Reconciliation by Lafond, Manuel, Chauve, Cedric, El-Mabrouk, Nadia, Ouangraoua, Aida

“…The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here,…”
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On the identification of conflicting contiguities in ancestral genome reconstruction by Ouangraoua, Aïda, Raffinot, Mathieu

“…In computional biology, up-to-date homology-based methods for the reconstruction of ancestral gene orders usually rely on two phases. First, potential…”
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Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer by Coimbra, Nilson Da Rocha, Goes-Neto, Aristoteles, Azevedo, Vasco, Ouangraoua, Aïda

“…Abstract Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for…”
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