Section: Dissemination

Teaching - Supervision - Juries

Course and track responsibilities

F. Coste is coordinator of the track "From Data to Knowledge: Machine Learning, Modeling and Indexing Multimedia Contents and Symbolic Data" of the Master by research in Computer Science (2nd year), University of Rennes 1, France.

F. Coste is coordinator of the course “Extracting knowledge from symbolic data sequences” of the Master by research in Computer Science (2nd year), University of Rennes 1, France.

O. Dameron shares the coordination of the "Bioinformatique et génomique" Master degree, Univ. Rennes1, and of the "Méthodes et traitements de l'information biomédicale et hospitalière"

O. Dameron shares the coordination of the course "Bioinformatique expérimentale", Master1 in computer science, Univ. Rennes1 + ENS. He is the coordinator of the courses "Bases de mathématiques et probablité" and "Méthodes en informatique" in Master1 in public health (Univ. Rennes 1), "Représentation des connaissances biomédicales" in Master2 in public health (Univ. Rennes 1), "Principes de programmation et d'algorithmique" and "Gestion de projets informatiques" in Master1 in bioinformatics (Univ. Rennes 1), "Standardisation des connaissances et bio-ontologies" in Master2 in bioinformatics (Univ. Rennes1), as well as of the course "e-Santé et réseaux hospitaliers" in the last year if engineering school ESIR (Univ. Rennes 1).

Teaching

• Licence: C. Belleannée, Langages formels, 22h, L3 informatique, Univ. Rennes1, France.

• Licence: C. Belleannée, bureautique et C2i, 40h, L1 informatique, Univ. Rennes1, France.

• Licence: C. Belleannée, Algorithmique et Programmation Fonctionnelle, L1 informatique, Univ. Rennes1, France.

• Licence: V. Delannée, Optique, 4h, PACES, Univ. Rennes 1, France.

• Licence: V. Delannée, Biostatistiques, 24h, PACES, Univ. Rennes 1, France.

• Licence: J. Coquet, Algorithmique et Programmation Fonctionnelle, 20h, L1 informatique, Rennes1, France.

• Licence: J. Coquet, Bureautique, 10h, L1 informatique, Rennes1, France.

• Licence: O. Dameron, Biostatistiques, 12h, PACES, Univ. Rennes 1, France.

• Licence: V. Picard, Probability theory, 24h, L3, ENS Rennes, France.

• Master: J. Coquet, Principes de programmation et d'algorithmique, 32h, M1 BioInformatique et génomique, Rennes1, France.

• Master: A. Antoine-Lorquin, Principes de programmation et d'algorithmique, 32h, M1 BioInformatique et génomique, Univ. Rennes 1, France.

• Master: A. Antoine-Lorquin, Bases de mathématiques, probabilités et statistiques, 32h, M1 Master STS - Mention Santé publique, Univ. Rennes 1, France.

• Master: C. Belleannée, algorithmique du texte et bioinformatique, M1 informatique, Univ. Rennes1, France

• Master: C. Belleannée, Préférences Logique et contraintes, 32h, M1 informatique,Univ. Rennes1, France

• Master: F. Coste, Apprentissage Supervisé, 10h, M2 Informatique, Univ. Rennes 1, France

• Master: F. Coste, Données Séquentielles Symboliques, 10h, M2 Informatique, Univ. Rennes 1, France

• Master: O. Dameron, Bioinformatique expérimentale, 10h, M1 informatique, Univ. Rennes 1 and ENS Rennes, France

• Master: O. Dameron, Gestion de projets informatiques, 23h, M1 bioinformatique et génomique, Univ. Rennes 1, France.

• Master: O. Dameron, Standardisation des connaissances et bio-ontologies, 22h, M2 bioinformatique et génomique, Univ. Rennes 1, France.

• Master: C. Galiez, Compilation, 48h, M1 informatique, Rennes1 France

• Master: V. Picard, Formal methods for safe development, 16h, M1, Univ. Rennes 1, France

• Master: V. Picard, Agrégation de mathématiques option D, 16h, M1, ENS Rennes/Univ. Rennes 1, France.

• Master: A. Siegel, Integrative and Systems biology, 20h, M2, Univ. Rennes 1, France

• Engineer: O. Dameron, e-Santé et réseaux hospitaliers, ESIR, Rennes.

• Engineer: O. Dameron, Bio-ontologies et Web Sémantique, ENSTBr, Brest.

Supervision

• PhD : Clovis Galiez, Structural fragments : comparison, predictability from sequence and application to identification of viral proteins, 8 Dec. 2015, supervised by F. Coste and J. Nicolas. [11]

• PhD: Vincent Picard, Analyse dynamique d'algorithmes et dynamique symbolique pour l'étude de modèles semi-quantitatifs en biologie des systèmes,16 Dec. 2015, supervised by A. Siegel and J. Bourdon. [12]

• PhD in progress : Aymeric Antoine-Lorquin, Modèles grammaticaux au service de l’identification de marqueurs de régulation génétique dans les séquences biologiques, started in Oct. 2013, supervised by C. Belleannée

• PhD in progress : Jean Coquet, Semantic-based reasoning for biological pathways analysis, started in Oct. 2014, supervised by O. Dameron, N. Théret and J. Nicolas.

• PhD in progress : Victorien Delannée, Optimisation à différentes échelles pour étudier la variabilité de la toxicité de contaminants alimentaires, started in Oct. 2014, supervised by A. Siegel and N. Théret.

• PhD in progress : Julie Laniau, Méthodes d’optimisation combinatoire pour reconstruire et analyser les systèmes métaboliques de microalgues, started in Oct. 2013, supervised by A. Siegel and D. Eveillard.

• PhD in progress : Clémence Frioux, Using preferences in Answer Set Programming to decipher interactions within the species of an ecosystem at the genomic scale, started in Oct. 2015, supervised by A. Siegel.

Juries

• Member of Ph-D thesis jury. T. Nguyen, LABRI, Bordeaux [A. Siegel, rapporteure]. N. Mobillia, IMAG, Grenoble [A. Siegel, présidente].

• Member of medical thesis jury. V. Margot, Rennes [O. Dameron, examinateur].

Internships

• Internship, from February until July 2015. Supervised by A. Siegel. Student: Clémence Frioux. Subject: Iterative reconstruction of functional metabolic networks for non-model organisms

• Internship, from April until July 2015. Supervised by O. Dameron and J. Coquet. Student: Pierre Vignet. Subject: Evaluation of a knowledge-based selection strategy for candidate metabolic pathways

• Internship, from January until July 2015. Supervised by F. Coste. Student: Maud Jusot. Subject: Syntactic modelling of viral genomes

• Internship, from April until July 2015. Supervised by A. Siegel. Student: Meziane Aite. Subject: Tools for the reconstruction of the metabolic network of T. Lutea

• Internship, from April until July 2015. Supervised by J. Nicolas. Student: Lucas Bourneuf. Subject: Model reduction with power graph algorithms

• Internship, from April until Aug 2015. Supervised by C. Belleannée. Student: David Picard-Druet. Subject: Coupling pattern discovery and pattern matching to design a composite signature for the Yeast polyadenylation site