Ouangraoua, Aïda

Professeure, Faculté des sciences
FAC. SCIENCES Informatique

Coordonnées

Courriel


819-821-8000, poste 62014


Site Web

Diplômes

(2009) Post-doctorate (Post-doctorate). Université du Québec à Montréal.

(2009) Post-doctorate (Post-doctorate). Simon Fraser University.

(2007) Modèles et algorithmes pour la comparaison de structures biologiques arborescentes. Doctorate (Doctorate). Université de Bordeaux I.

(2004) Master's Thesis (Master's Thesis). Université de Bordeaux I.

(2004) Master's Thesis (Master's Thesis). ENSEIRB.

Titres de compétence

(2004) Computer science engineer (2004) - Member of the order OIQ --Ordre des Ingénieurs du Québec-- as junior engineer (2014). Ecole Nationale Supérieure d'Electronique, Informatique et Radio-communication de Bordeaux (ENSEIRB).

Expérience académique

(2018) Professor. Université de Sherbrooke.

Présentation

Sujets de recherche

Bioinformatics, Algorithms.

Disciplines de recherche

Computer Science, Biology and Related Sciences.

Mots-clés

Algorithms, Computational Genomics, Data science, RNA structure, Alternative splicing.

Intérêts de recherche

Models and algorithms for the analysis of gene splicing structures and RNA structures, and evolutionary reconstruction.

Langues parlées et écrites

Anglais, Français

Prix et distinctions

  • (2020) CRC Tier 2. Canada Research Chairs (CRC). (Distinction).
  • (2020) New university researchers start up grant. Fonds de recherche du Québec - Nature et technologies (FRQNT). (Distinction).
  • (2009) Postdoctoral fellowship. Université du Québec à Montréal. (Distinction).
  • (2009) Postdoctoral fellowship. Université Bordeaux I. (Distinction).
  • (2009) Postdoctoral fellowship. Simon Fraser University. (Distinction).
  • (2009) Postdoctoral fellowship. Simon Fraser University. (Distinction).
  • (2007) Doctoral fellowship. Ministère de l’Enseignement supérieur et de la Recherche - France. (Distinction).

Financement

Grant. (Awarded). Principal Investigator. Structure-aware models and algorithms for reconstructing the evolution and ancestral states of genes and genomes. Natural Sciences and Engineering Research Council of Canada (NSERC). Discovery grants program. 100000 $ (2017-2022).

Grant. (Awarded). Co-applicant. Transcriptomique comparative des G-quadruplexes d’ARN à travers diverses espèces. Fonds de recherche du Québec - Nature et technologies (FRQNT). 153000 $ (2018-2021).

Grant. (Awarded). Principal Applicant. Faculty support for graduate student's scholarships (Soutien facultaire au recrutement d'étudiants gradués). Université de Sherbrooke - Faculté des Sciences. Soutien facultaire au recrutement d'étudiants gradués. 20000 $ (2019-2020).

Grant. (Awarded). Principal Applicant. Research support (Aide à la recherche). Université de Sherbrooke - Faculté des Sciences. Aide à la recherche. 20500 $ (2016-2020).

Grant. (Awarded). Principal Applicant. Visualization of gene structures, phylogenetic trees, and RNA structures. Mathematics of Information Technology and Complex Systems (MITACS). Acceleration. 80000 $ (2018-2020).

Grant. (Completed). Principal Applicant. Organization of the 16th "RECOMB Comparative Genomics" conference. Calcul Québec. 500 $ (2018-2019).

Publications

Articles de revue

  • N. Da Rocha Coimbra, A. Góes-Neto, V. Azevedo, A. Ouangraoua. (2020). CorynebacterialesReconstructing the phylogeny of while accounting for horizontal gene transfer. Genome Biology and Evolution, DOI. (Published).
  • M. A. Brunet, M. Brunelle, J-F. Lucier, V. Delcourt, M. Levesque, F. Grenier, S. Samandi, S. Leblanc, J-D. Aguilar, P. Dufour, J-F. Jacques, I. Fournier, A. Ouangraoua, M.S. Scott, F-M. Boivert, X. Roucou. (2019). OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. Nucleic Acids Research, 47(Database), 403-410. DOI. (Published).
  • E. Kuitche, S. Jammali, A. Ouangraoua. (2019). SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution. BMC bioinformatics, 20(20), 640. DOI. (In Press).
  • S. Jammali, J-D. Aguilar, E. Kuitche, A. Ouangraoua. (2019). SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. BMC Bioinformatics, 20(S3), 37-52. DOI. (Published).
  • N. Luhmann, M. Lafond, A. Thévenin, A. Ouangraoua, R. Wittler, C. Chauve. (2019). The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(4), 1364-1373. DOI. (Published).
  • Glouzon J-P S*, Ouangraoua A. (2018). aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences. Bioinformatics (Proceedings of ISMB 2018), (In Press).
  • Lafond M*, Chauve C, El-Mabrouk N, Ouangraoua A. (2017). Gene Tree Construction and Correction using SuperTree and Reconciliation. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Special issue of conference APBC 2017), (Published).
  • Kuitche E*, Lafond M*, Ouangraoua A*. (2017). Reconstructing protein and gene phylogenies using reconciliation and soft-clustering. Journal of Bioinformatics and Computational Biology, 15(6), 1-25. (Published).
  • Jammali S*, Kuitche E*, Rachati A*, Bélanger F*, Scott M, Ouangraoua A. (2016). Aligning coding sequences with frameshift extension penalties. Algorithms for Molecular Biology, 12(10), (Published).
  • Luhmann N*, Lafond M*, Thevenin A, Ouangraoua A, Wittler R, Chauve C. (2016). The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. IEEE/ACM Transactions on Computational Biology and Bioinformatics, (Published).
  • Perrin A*, Varré J-S, Blanquart , Ouangraoua A. (2015). ProCARs: Progressive Reconstruction of Ancestral Gene Orders. BMC Genomics (Special issue of conference ISCB-LA 2014), 16(Suppl 5)(S6), (Published).
  • Lafond M*, Ouangraoua A, El-Mabrouk N. (2015). Reconstructing a SuperGeneTree Minimizing Reconciliation. BMC Bioinformatics (Special issue of conference Recomb-CG 2015), 16(Suppl 14), S4. (Published).
  • Lavoie-Mongrain P*, Belcaid M, Ouangraoua A, Bergeron A, Poisson G. (2015). Reconstructing the history of a WD40 beta-propeller tandem repeat using a phylogenetically informed algorithm. PeerJ Computer Science, 1(e6), (Published).
  • Ouangraoua A , Raffinot M. (2014). On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction. Journal of Computational Biology, 21(1), 64--79. (Published).
  • Allali J , Saule C , Chauve C , d'Aubenton-Carafa Y , Denise A , Drevet C , Ferraro P , Gautheret D , Herrbach C , Leclerc F , de Monte A , Ouangraoua A , Sagot MF , Termier M , Thermes C , Touzet H. (2012). BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. Advances in bioinformatics, 2012, 893048. (Published).
  • Ouangraoua A , Swenson KM , Chauve C. (2011). A 2-Approximation for the Minimum Duplication Speciation Problem. Journal of Computational Biology, 18(9), 1041--1053. (Published).
  • Ouangraoua A , Guignon V , Hamel S , Chauve C. (2011). A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes. Theoretical Computer Science, 412(8-10), 753--764. (Published).
  • Thomas A* , Varré JS , Ouangraoua A. (2011). Genome dedoubling by DCJ and reversal. BMC bioinformatics (Special issue of conference Recomb-CG 2011), 12 Suppl 9, S20. (Published).
  • Ouangraoua A , Tannier E , Chauve C. (2011). Reconstructing the architecture of the ancestral amniote genome. Bioinformatics, 27(19), 2664--2671. (Published).
  • Ouangraoua A , Bergeron A , Swenson KM. (2011). Theory and Practice of Ultra-Perfection. Journal of Computational Biology, 18(9), 1219--1230. (Published).
  • Ouangraoua A , Bergeron A. (2010). Combinatorial Structure of Genome Rearrangements Scenarios. Journal of Computational Biology, 17(9), 1129--1144. (Published).
  • Chauve C , Gavranovic H , Ouangraoua A , Tannier E. (2010). Yeast ancestral genome reconstructions: the possibilities of computational methods II. Journal of computational biology, 17(9), 1097-112. (Published).
  • Ouangraoua A , Ferraro P. (2009). A constrained edit distance algorithm between semi-ordered trees. Theoretical Computer Science, 410(8-10), 837--846. (Published).
  • Ouangraoua A , Ferraro P. (2009). A new constrained edit distance between quotiented ordered trees. Journal of Discrete Algorithms, 7(1), 78--89. (Published).
  • Segura V , Ouangraoua A , Ferraro P , Costes E. (2008). Comparison of tree architecture using tree edit distances: application to two-year-old apple tree. Euphytica, 161(1-2), 55-164. (Published).
  • Ouangraoua A , Ferraro P , Tichit L , Dulucq S. (2007). Local similarity between quotiented ordered trees. J. Discrete Algorithms, 5(1), 23--35. (Published).

Livres

  • (2018). Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Magog-Orford, QC, Canada, October 9-12, 2018 (LNCS, 11183). Springer. (Published).

Rapports

  • Kuitche E*, Ouangraoua A. (2016). Reconstructing protein and gene phylogenies by extending the framework of reconciliation. Université de Sherbrooke. 10 p.
  • Bélanger F*, Ouangraoua A. (2015). Alignment of protein-coding sequences with frameshift extension penalties. arXiv:1508.04783 [cs.DS]. Université de Sherbrooke. 19 p.

Articles de conférence

  • El-Mabrouk N, Ouangraoua A. (2017). A general framework for genetree correction based on duplication-loss reconciliation. LIPICS 88, 8:1-8:14. (Published).
  • Kuitche E*, Ouangraoua A. (2017). Reconstructing protein and gene phylogenies by extending the framework of reconciliation. ISBN:9781510836679, 79-86. (Published).
  • Jammali S*, Kuitche E*, Rachati A*, Bélanger F*, Ouangraoua, A. (2016). Aligning coding sequences with frameshift extension penalties. RECOMB Comparative Genomics (RECOMB-CG 2016). (Published).
  • Da Rocha Coimbra N*, Azevedo V, Ouangraoua A. (2016). Highly resolved phylogeny for Corynebacteriales. ISCB-Latin America (ISCB-LA 2016). (Accepted).
  • Luhmann N, Thevenin A, Ouangraoua A, Wittler R, Chauve C. (2016). The SCJ small parsimony problem for weighted gene adjacencies. LNCS 9683, 200-210. (Published).
  • Ouangraoua A. (2013). Progressive reconstruction of ancestral gene orders. Models and Algorithms for Genome Evolution (MAGE 2013). (Published).
  • Belcaid M , Bergeron A , Ouangraoua A , Lavoie-Mongrain P* , Massoulier N* , Poisson G. (2012). Duplications in tape measure proteins. International conference on Research in Computational Molecular Biology (RECOMB 2012). (Published).
  • Ouangraoua A , Raffinot M. (2012). Faster and Simpler Minimal Conflicting Set Identification. LNCS 7354, 41--55. (Published).
  • Thomas A* , Ouangraoua A , Varre JS. (2012). Genome Halving by Block Interchange. ISBN 978-989-8425-90-4, 58-65. (Published).
  • Ouangraoua A , Swenson KM , Bergeron A. (2012). On the Comparison of Sets of Alternative Transcripts. LNCS 7292, 201--212. (Published).
  • Ouangraoua A , Swenson KM , Bergeron A. (2012). On the comparison of sets of alternative transcripts. International conference on Research in Computational Molecular Biology (RECOMB 2012). (Published).
  • Thomas A*, Ouangraoua A, Varré JS. (2012). Tandem Halving Problems by DCJ. LNCS 7534, 417-429. (Published).
  • Ouangraoua A, Swenson K , Chauve C. (2010). An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. LNBI 6398, 290--301. (Published).
  • Ouangraoua A , Bergeron A , Swenson KM. (2010). Ultra-Perfect Sorting Scenarios. LNBI 6398, 50--61. (Published).
  • Ouangraoua A , Bergeron A. (2009). Parking Functions, Labeled Trees and {DCJ} Sorting Scenarios. LNBI 5817, 24--35. (Published).
  • Ouangraoua A , Bergeron A. (2009). Parking functions, labeled trees and DCJ sorting scenarios. International Workshop on Algorithms in Bioinformatics (WABI 2009). (Published).
  • Ouangraoua A , Boyer F , McPherson A , Tannier E , Chauve C. (2009). Prediction of Contiguous Regions in the Amniote Ancestral Genome. LNBI 5542, 173-185. (Published).
  • Ouangraoua A , Segura V , Ferraro P , Costes E. (2007). A review of plant architecture comparison methods: Application to hybrids of apple trees. Proceedings of FSPM 2007, 471-474. (Published).
  • Ouangraoua A , Chauve C. (2007). Un nouvel algorithme d’alignement de structures secondaires d’ARN. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2007). (Published).
  • Segura V , Ouangraoua A , Ferraro P , Costes E. (2006). Comparison of tree architecture using tree edit distances: application to two-year-old apple tree. Eucarpia, biometrics in plant breeding section meeting (Eucarpia 2006). (Published).
  • Ituarte I , Ouangraoua A , Ferraro P. (2006). PyTreeMatch: a python based software for comparing RNA secondary structure. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2006). (Published).
  • Ouangraoua A , Ferraro P. (2004). Distance multi-échelles entre structures secondaires d’ARN. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2004). (Published).

Autres contributions

Cours enseignés

  • Datamining (Forage de données). IFT840. (2020-01-01 à 2020-04-30). Niveau : Graduate. (3CR).
  • Data structures (Structures de données). IFT339. (2020-01-01 à 2020-04-30). Niveau : Undergraduate. (3CR).
  • Data structures (Structures de données). IFT339. (2019-01-01 à 2019-04-30). Niveau : Undergraduate. (3CR).
  • Algorithms for bioinformatics (Algorithmes pour la bioinformatique). BIN702. (2018-01-01 à 2018-04-30). Niveau : Graduate. (3CR).
  • Data structures (Structures de données). IFT339. (2017-09-01 à 2017-12-31). Niveau : Undergraduate. (3CR).
  • Introduction to programming (Introduction à la programmation). CQP112. (2017-01-01 à 2017-04-30). Niveau : Undergraduate. (3CR).
  • Algorithms for bioinformatics (Algorithmes pour la bioinformatique). BIN702. (2016-09-01 à 2016-12-31). Niveau : Graduate. (3CR).
  • Introduction to programming (Introduction à la programmation). CQP112. (2016-01-01 à 2016-04-30). Niveau : Undergraduate. (4CR).
  • Introduction to programming (Introduction à la programmation). CQP112. (2015-01-01 à 2015-04-30). Niveau : Undergraduate.
  • Problem analysis and programming (Analyse et Programmation). IFT159. (2015-01-01 à 2015-04-30). Niveau : Undergraduate. (3CR).
  • Introduction à la programmation en génie mécanique. INF135. (2012-09-07 à 2012-12-07). Niveau : Undergraduate.
  • Mathématiques pour informaticiens. INF1130. (2012-09-05 à 2012-12-14). Niveau : Undergraduate.
  • Algorithmes et outils bioinformatique. MG8. (2011-01-13 à 2011-02-17). Niveau : Graduate.
  • Algorithmes et outils bioinformatique. MG8. (2010-01-14 à 2010-02-18). Niveau : Graduate.
  • Mathématiques pour informaticiens. INF1130. (2009-09-09 à 2009-12-16). Niveau : Undergraduate.
  • Programmation orientée-aspect. AP4. (2008-01-11 à 2008-04-18). Niveau : Undergraduate.
  • Réseaux et sécurité. ASR4. (2008-01-10 à 2008-04-24). Niveau : Undergraduate.
  • Bases de données avancées. OMGL3. (2007-09-12 à 2007-12-19). Niveau : Undergraduate.
  • Programmation orientée-objet. AP3. (2007-09-10 à 2007-12-17). Niveau : Undergraduate.
  • Probabilités et Statistiques. (2006-09-14 à 2006-12-21). Niveau : Graduate.
  • Introduction aux bases de données. (2006-01-10 à 2006-04-18). Niveau : Undergraduate.
  • Utilisation des systèmes informatiques. (2005-09-13 à 2005-12-13). Niveau : Undergraduate.

Gestion d'évènements

  • Area co-chair (Population Genomics and Molecular Evolution). (2020). Intelligent Systems for Molecular Biology (ISMB) 2020. (Conference).
  • Abstract chair (Evolution and Comparative Genomics). (2019). Intelligent Systems for Molecular Biology (ISMB) 2019. (Conference).
  • Organization and PC co-chair. (2018). 16th international RECOMB Comparative Genomics conference. (Conference).

Activités de collaboration internationale

  • Collaborator. (2016-2020). France. - Collaboration with Dr. Hélène Touzet (CNRS, Université de Lille) on the development of models for the comparison of non-coding RNAs. - Collaboration with Dr. Mathieu Raffinot (CNRS, Université de Bordeaux) and Drs. Jean-Stéphane Varré and Samuel Blanquart (INRIA, Université de Lille) on the development of algorithms for the reconstruction of ancestral gene orders, and genome rearrangement scenarios.
  • Collaborator and student supervisor. (2016-2019). Brazil. Collaboration and student co-supervision with the bioinformatics group of Professor Vasco Azevedo (Federal University of Minas Gerais) on the reconstruction of the evolution of Corybacteriales genomes and the impact on the evolution of pathogenic mechanisms.
  • Coordinator and Collaborator. (2014). France. Inria International associate team between Inria Lille and UQÀM on the development of comparative genomics models and methods for the analysis of eukaryotes gene structure evolution.