Section: Dissemination

Teaching - Supervision - Juries

Teaching track responsibilities

• Coordination of the doctoral school "Life, Agronomy and Health" of University of Rennes 1 [N. Théret]

• Coordination of the master degree "Bioinformatics and genomics", Univ. Rennes1 [O. Dameron]

• Coordination of the sub-domain "From Data to Knowledge: Machine Learning, Modeling and Indexing Multimedia Contents and Symbolic Data", Master in Computer Science, University of Rennes 1, France [F. Coste].

Course responsibilities

• "Atelier bioinformatique", Licence 2 informatique, Univ. Rennes 1 [O. Dameron]

• "Bioinformatique pour la génomique", 2nd year school of medicine, Univ. Rennes 1 [O. Dameron]

• "Bases de mathématiques et probablité" and "Méthodes en informatique", Master1 in public health, Univ. Rennes 1 [O. Dameron]

• "Big data and Semantic Web", Master 2 in public health, Univ. Rennes 1 [O. Dameron]

• "Intégration: Remise à niveau en informatique", Master 1 in bioinformatics, Univ. Rennes 1 [O. Dameron]

• "Programmation en Python", Master 1 in Public Health, Univ. Rennes 1 [O. Dameron]

• "Programmation impérative en Python", Master 1 in bioinformatics, Univ. Rennes 1 [O. Dameron]

• "Système informatique GNU/Linux", Master 1 in bioinformatics, Univ. Rennes 1 [O. Dameron]

• "Semantic Web and bio-ontologies", Master 2 in bioinformatics, Univ. Rennes 1 [O. Dameron]

• "e-Santé et réseaux hospitaliers", last year in engineering school ESIR, Univ. Rennes 1, [O. Dameron]

• "Equilibre Dynamique de la communication Cellulaire" Master 2 in Sciences cellulaire et Moléculaire du Vivant, Univ. Rennes 1 [N. Theret]

Teaching

• Licence: C. Belleannée, Langages formels, 20h, L3 informatique, Univ. Rennes1, France.

• Licence: C. Belleannée, Algorithmique et Programmation Fonctionnelle, 60, L1 informatique, Univ. Rennes1, France.

• Licence: J. Coquet, Module Programmation Scientifique 1, 20h, L1 informatique, Rennes1, France.

• Licence: O. Dameron, Biostatistiques, 12h, 1st year school of medicine, Univ. Rennes 1, France

• Licence: O. Dameron, C2i niveau 2, 2.5h, 2nd year school of medicine, Univ. Rennes 1, France

• Licence: O. Dameron, Bioinformatique pour la génomique, 5h, 2nd year school of medicine, Univ. Rennes 1, France

• Licence: C. Frioux, Programmation scientifique Python, 12h, L1, Rennes1, France.

• Licence: C. Frioux, LaTeX, 12h, L3 ENSAI, France.

• Licence: C. Frioux, Outils bureautiques pour le statisticien , 6h, L3 ENSAI, France.

• Licence: C. Frioux, Algorithmique et programmation Python, 6h, L3 ENSAI, France.

• Licence: L. Bourneuf, Ingénieurerie Systèmes et Réseaux, 10h, L3 INFO, France.

• Licence: L. Bourneuf, Algorithmique des graphes, 8h, L3 INFO, France.

• Licence: L. Bourneuf, Algorithmique des graphes, 2h, L3 MIAGE, France.

• Master: L. Bourneuf, Principes de Programmation et d'Algorithmique, 6h, M1 BIG, France.

• Master: L. Bourneuf, Projet, 10h, M1 BIG, France.

• Master: C. Belleannée, Programmation logique avec contraintes et algorithmes génétiques, 40h, M1 informatique, Univ. Rennes1, France.

• Master: C. Belleannée, Algorithmique du texte et bioinformatique, 10h, M1 informatique, Univ. Rennes1, France

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

• Master: O. Dameron, Object-oriented programing, 20h, M1 bioinformatique et génomique, Univ. Rennes 1, France

• Master: O. Dameron, Gestion de projet en informatique, 12h, M1 bioinformatique et génomique, Univ. Rennes 1, France

• Master: O. Dameron, Ontologies biomédicales, 6h, Engineering school Institut Mines-Télécom Bretagne-Atlantique Brest, France

• Master: O. Dameron, Internship jury, 25h, M1 bioinformatique et génomique, Univ. Rennes 1, France

• Master: O. Dameron, Internship jury, 7.5h, M2 bioinformatique et génomique, Univ. Rennes 1, France

• Master: O. Dameron, Intégration : remise à niveau en informatique, 14h, M1 bioinformatique, Univ. Rennes 1, France

• Master: O. Dameron, Programmation impérative en Python, 39.5h, M1 bioinformatique, Univ. Rennes 1, France

• Master: O. Dameron, Système informatique GNU/Linux, 12h, M1 bioinformatique, Univ. Rennes 1, France

• Master: O. Dameron, Programmation en Python, 24h, M1 in Public Health, Univ. Rennes 1 [O. Dameron]

• Master: O. Dameron, Semantic Web and bio-ontologies, 14h, M2 bioinformatique, Univ. Rennes 1, France

• Master: O. Dameron, Bases de mathématiques et probabilités, 15h, M1 santé publique, Univ. Rennes 1, France

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

• Master: A. Siegel, Introduction to integrative biology, 2h, M2, Univ. Rennes 1, France

Supervision

• PhD : Victorien Delannée, Intégrer les échelles moléculaires et cellulaires dans l’inférence de réseaux métaboliques. Application aux xénobiotiques., started in Oct. 2014, defensed in Nov. 2017, supervised by A. Siegel and N. Théret [14].

• PhD : Julie Laniau, Structure de réseaux biologiques : rôle des noeuds internes vis-à-vis de la production de composés, started in Oct. 2013, defended in Oct. 2017, supervised by A. Siegel and D. Eveillard. [15]

• PhD : Jean Coquet, Semantic-based reasoning for biological pathways analysis, started in Oct. 2014, defended in Dec. 2017, supervised by O. Dameron and N. Théret [12]/

• PhD in progress : Lucas Bourneuf, Justifiable graph decomposition to assist biological network understanding, started in Oct. 2016, supervised by J. Nicolas.

• 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.

• PhD in progress : Yann Rivault, Analyse de parcours de soins à  partir de bases de données médico-administratives en utilisant des outils du Web Sémantique: identification de complications et de leurs déterminants suite à  la pose chirurgicale de dispositif médical implantable en ambulatoire , started in Oct. 2015, supervised by O. Dameron and N. Lemeur.

• PhD in progress : Juliette Talibart, Learning grammars with long-distance correlations on proteins, started in Nov. 2017, supervised by F. Coste and J. Nicolas.

• PhD in progress : Mael Conan, Predictive approach to assess the genotoxicity of environmental contaminants during liver fibrosis, started in Oct. 2017, supervised by S. Langouet and A. Siegel.

• PhD in progress: Marine Louarn, Intégration de données génomiques massives et hétérogènes, application aux mutations non-codantes dans le lymphome folliculaire, started in Oct. 2017, supervised by A. Siegel, T. Fest (CHU) and O. Dameron.

• PhD in progress : Méline Wery, Methodology development in disease treatment projects. , started in Oct. 2017, supervised by O. Dameron, C. Bettembourg (Sanofi) and A. Siegel.

Juries

• Member of Ph-D thesis juries. J. Mercier, Univ. Evry/CEA [A. Siegel, reviewer]. C. Franay, INRA Toulouse [A. Siegel, reviewer]. W Bedhiafi, Univ. Pierre et Marie Curie Paris + UTM Tunis [O. Dameron]. V. Delannée, Univ. Rennes 1 [N. Theret, O. Dameron]. J. Coquet, Univ. Rennes 1 [O. Dameron, N. Theret]. P. Finet, Univ. Rennes 1 [O. Dameron]

• Member of habilitation thesis juries. E. Remy, Univ. Marseille [A. Siegel, president].

• Member of medicine doctorate juries G. Lebailly, Univ. Rennes 1 [O. Dameron].

Internships

• Internship, from Jun 2017 until Jul 2017. Supervised by J. Nicolas. Student: Alexis Baudin. Subject: Recherche d'attracteurs dans les réseaux booléens synchrones en ASP.

• Internship, from Jan until Jun 2017. Supervised by A. Siegel. Student: Mael Conan. Subject: Modélisation et caractérisation de la réponse au stress de la cyanobactérie marine Synechococcus sp. WH7803.

• Internship, from from Apr 2017 until Jul 2017. Supervised by Nathalie Théret and Olivier Dameron. Student: Kevin Courtet. Subject: Integration of genic regulatory interaction network by miRNAs from patients’ macrophages with cystic fibrosis.

• Internship, from Apr 2017 until Jul 2017. Supervised by J. Got. Student: Nicolas Guillaudeux Subject: Vérifications du réseau métabolique entier de Tisochrysis lutea.

• Internship, from Apr 2017 until Jul 2017. Supervised by J. Nicolas and F. Coste. Student: AliHassan Kachalo Subject: Annotation automatique en familles des séquences d’une superfamille d’enzymes, les HAD (haloacides déhalogénases) par Analyse de Concepts Formels (FCA).

• Internship, from from Apr 2017 until Jul 2017. Supervised by C. Frioux and C. Trottier. Student: Claire Lippold. Subject: Exploration et caractérisation du microbiome associé à Ectocarpus subulatus str. BFT.

• Internship, from Jan 2017 until Jun 2017. Supervised by O. Dameron and A. Siegel. Student: Marine Louarn. Subject: Analysis and integration of heterogeneous large-scale genomics data.

• Internship, from Apr 2017 until Jul 2017. Supervised by . Théret and J. Nicolas. Student: Aurelie Nicolas. Subject: Modeling of interaction networks from extracellular matrix components using formal concept analyses.

• Internship, from Apr 2017 until Jul 2017. Supervised by C. Belleannée. Student: Dimitri Pedron. Subject: Annotation et prédiction de transcriptome: validation d'ORF alternatifs prédits. Application au gène CREM chez l'humain, la souris et le chien.

• Internship, from Feb 2017 until Jun 2017. Supervised by F. Coste. Student: Manon Ruffini, Subject: Better scoring schemes for the recognition of functional proteins by protomata

• Internship, from Feb 2017 until Jun 2017. Supervised by J. Nicolas. Student: MarieSalmon, Subject: Biclustering: quantitative formal concept analysis in Answer Set Programming

• Internship, from Jan 2017 until Jun 2017. Supervised by A. Siegel and O. Dameron. Student: Meline Wery Subject: Formalizing and computing signatures of phenotypes within a biological network

• Internship, from May 2017 until Jul 2017. Supervised by C. Belleannée. Student: Mohamed Zemmouri Subject: Analyse de texte en bioinformatique : Modélisation grammaticale d’un site ADN, et recherche du site, même dégénéré, sur l’intégralité du génome humain