Section: Dissemination

Teaching - Supervision - Juries

Teaching track responsibilities

• Coordination of the doctoral school "Biology and Health" of University of Bretagne Loire, Rennes Site 1 [N. Théret]

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

Course responsibilities

• "Method", Master 2 in Computer Sciences, Univ. Rennes 1 [E. Becker]

• "Statistiques appliquées", 3rd year in Fundamental Computer Sciences, ENS Rennes [E. Becker]

• "Introduction to computational ecology", Master 2 in Ecology, Univ. Rennes 1 [E. Becker]

• "Object oriented programming", Master 1 in Bioinformatics, Univ. Rennes 1 [E. Becker]

• "Advanced R for data analysis", Master 1 in Ecology + Master 1 in Bioinformatics, Univ. Rennes 1 [E. Becker]

• "Insertion Professionnelle et tables rondes", Master 1 and Master 2 in Bioinformatics, Univ. Rennes 1 [E. Becker]

• "Atelier de Biostatistiques", 2nd year Biology, Univ Rennes 1 [E. Becker]

• "Internship", Master 1 in Computer Sciences, Univ. Rennes 1 [C. Belleannée]

• "Supervised machine learning", Master 2 in Computer Sciences, Univ Rennes 1 [F. Coste]

• "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", Master1 in public health, Univ. Rennes 1 [O. Dameron]

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

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

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

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

• "Internship", Master 2 in bioinformatics, Univ. Rennes 1 [O. Dameron]

• Master: A. Siegel, Integrative and Systems biology, Master 2 in bioinformatics, Univ. Rennes 1 [A. Siegel]

• Micro-environnement Cellulaire normal & pathologique, Master 2 in Biologie cellulaire et Moléculaire, Univ. Rennes 1 [N. Théret]

Teaching

• Licence : E. Becker, "TPs Python", 12h, 1st year in Biology, Univ. Rennes 1, France

• Licence : E. Becker, "Atelier de Biostatistiques", 34h, 2nd year in Biology, Univ. Rennes 1, France

• Licence : E. Becker, "Statistiques Appliquées", 20h, 3rd year in Fundamental Computer Sciences, ENS Rennes, France

• Master : E. Becker, "Object oriented programming", 43h, Master 1 in Bioinformatics, Univ. Rennes 1, France

• Master : E. Becker, "Advanced R for data analysis", 34h, Master 1 in Bioinformatics, Univ. Rennes 1, France

• Master : E. Becker, "Introduction to computational ecology", 34h, Master 2 in Ecology, Univ. Rennes 1, France

• Master : E. Becker, "Method", 15h, Master 2 in Computer Sciences, Univ. Rennes 1, France

• Master : E. Becker, "Insertion Professionnelle et tables rondes", 8h, Master 1 and Master 2 in Bioinformatics, Univ. Rennes 1, France

• Master : E. Becker, "Systems Biology : biological netorks", 27h, Master 2 in Bioinformatics, Univ. Rennes 1, France

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

• Licence: C. Belleannée, Projet professionnel et communication, 16h, L1 informatique, Univ. Rennes1, France.

• Licence: C. Belleannée, Enseignant référent, 20h, L1 informatique, Univ. Rennes1, France.

• Licence: C. Belleannée, Spécialité informatique : Functional and immutable programming , 42h, L1 informatique, Univ. Rennes1, France

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

• Master: S. Blanquart, Juries of Master 1 in bioinformatics, 5h, Univ. Rennes 1, France

• Master: L. Bourneuf, Projet, 25h, M1 Santé Publique, France.

• Master: F. Coste, Supervised machine learning, 20h, M2 + M1 Science Informatique, Univ. Rennes, France

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

• Licence: O. Dameron, "Atelier bioinformatique", 12h, Licence 2 informatique, Univ. Rennes 1, France

• Master: O. Dameron, "Intégration: Remise à niveau en informatique", 18h Master 1 in bioinformatics, Univ. Rennes 1, France

• Master: O. Dameron, "Programmation impérative en Python", 985h Master 1 in bioinformatics, Univ. Rennes 1, France

• Master: O. Dameron, "Système informatique GNU/Linux", 10h, Master 1 in bioinformatics, Univ. Rennes 1, France

• Master: O. Dameron, 5h, "Internship", Master 1 in bioinformatics, Univ. Rennes 1, France

• Master: O. Dameron, "Bases de mathématiques et probablité", 9h, Master1 in public health, Univ. Rennes 1, France

• Master: O. Dameron, "Programmation impérative en Python (2)", 3h Master 1 in public health, Univ. Rennes 1, France

• Master: O. Dameron, 20h, "Semantic Web and bio-ontologies", Master 2 in bioinformatics, Univ. Rennes 1, France

• Master: O. Dameron, 15h, "Internship", Master 2 in bioinformatics, Univ. Rennes 1, France

• Licence: N. Guillaudeux, Projet professionnel et communication, 16h, 1st year Computer Science, Univ. Rennes 1, France

• Licence: N. Guillaudeux, "TPs Python", 36h, 1st year in Biology, Univ. Rennes 1, France

• Licence: M. Louarn, Introduction à la BioInformatique, 6h, L2 Informatique, Univ. Rennes 1, France.

• Licence: M. Louarn, Informatique, 10h, L1 Physique Chimie, Univ. Rennes 1, France.

• Master: M. Louarn, Informatique Médicale Avancée, 2h, M1 Médecine, Univ. Rennes 1, France.

• Master: M. Louarn, Object-oriented programming, 25h, M2 bioinformatique et génomique, Univ. Rennes 1, France.

• Master: M. Louarn, Jury de stage, 6h, M1 bioinformatique et génomique, Univ. Rennes 1, France.

Supervision

• PhD: Yann Rivault, Analyse de trajectoires de soins à partir de bases de données médico-administratives : apport d'un enrichissement pas des connaissances biomédicales issues du Web des Données, defended 28th January 2019, supervised by O. Dameron and N. Lemeur  [64].

• PhD: Lucas Bourneuf, A search space of graph motifs for graph compression: From Powergraphs to triplet concepts, defended 17th december 2019, supervised by J. Nicolas [12].

• PhD in progress: Johanne Bakalara, Temporal models of care sequences for the exploration of medico-administrative data, started in Oct. 2018, supervised by T. Guyet (Lacodam), E. Oger (Repères) and O. Dameron.

• PhD in progress: Arnaud Belcour, Inferring Model metabolisms for bacterial ecosystems reduction, started in Oct. 2019, supervised by A. Siegel and S. Blanquart.

• 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: Olivier Dennler, Modular functional characterization of ADAMTL and ADAMTSL protein families, started in Oct. 2019, supervised by N. Theret, F. Coste and S. Blanquart.

• PhD in progress: Nicolas Guillaudeux, Compare gene structures to predict isoform transcripts, started in Oct. 2018, supervised by O. Dameron, S. Blanquart and C. Belleannée.

• PhD in progress: Virgilio Kmetzsch Multi-modal analysis of neuroimaging and transcriptomics data in genetically-induced fronto-temporal dementia, started in Oct. 2019, supervised by E. Becker and O. Colliot (Inria Aramis, ICM Paris)

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

• PhD in progress : Pierre Vignet, Identification et conception expérimentale de nouveaux agents thérapeutiques à partir d'un modèle informatique des réseaux d'influence du TGF-$\beta$ dans les pathologies hépatiques chroniques , started in Dec. 2018, supervised by N. Théret and A. Siegel.

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

Juries

• Referee of PhD thesis: Aarón Ayllón-Benítez, Univ. Bordeaux [O. Dameron] - A. Beica, ENS [A. Siegel, president] - F. Bridoux, Marseille [A. Siegel] - C. Hernandez, ENS [A. Siegel, president]

• Member of PhD thesis juries: Sandeep Manandhar, Univ. Rennes [O. Dameron] - A. Husson, Paris Diderot [A. Siegel] - Arran Hodgkinson, Univ. Montpellier [N. Théret]

• Referee of habilitation thesis: Fleur Mougin, Univ. Bordeaux [O. Dameron] - S. Peres, Orsay [A. Siegel]

• Member of habilitation thesis juries: Adrien Coulet, Univ. Lorraine [O. Dameron] - L. Calzone [A. Siegel, president]

Interns

• Internship, from Jan 2019 until Jun 2019. Supervised by O. Dameron and O. Corby (Wimmics team, Sophia-Antipolis) . Student: Antoine Abel (Master 2 bioinformatique, Univ. Rennes 1). Subject: Faster SPARQL federated queries [31]

• Internship, from Jan 2019 until Jun 2019, Supervised by O. Dameron and A. Duchene (Theranexus). Student: Pierre Beaudier (Master 2 bioinformatique, Rennes). Subject: Evaluation of the public databases' relevance as comprehensive tools for pharmalogical mechanisms [32]

• Internship, from Jan 2019 until Jun 2019, Supervised by E. Becker, Fabrice Legeai (IGEPP) and Julien Bobe (LPGP). Student: Fanny Casse (Master 2 bioinformatique, Rennes). Subject: MiRNA regulating genes responsible for fertility and early embryonic development in the Medaka fish [35].

• Internship, from April 2019 until July 2019, Supervised by P. Dabert (IRSTEA), A. Siegel and S. Blanquart. Student: Theo Combe (Master 1 bioinformatique, Rennes). Subject: Reconstructing metabolic pathways of methanogenic communities using metabarcoding data

• Internship, from May 2019 until Jun 2019, Supervised by F. Coste. Student: Arthur Correnson (Licence math-informatique, Université Paul Sabatier, Toulouse). Subject: Implementation of a new partial local multiple alignment algorithm.

• Internship, from Jan 2019 until Jun 2019, Supervised by F. Coste, N. Théret, S. Blanquart, C. Belleannée. Student: Olivier Dennler (Master 2 bioinformatique, Rennes). Subject: Functional module characterization of ADAMTS / ADAMTSL protein family [37]

• Internship, from Jan 2019 until Jun 2019, Supervised by A. Siegel. Student: Clara Emery (Master 2 bioinformatique, Rennes). Subject: Modeling of quorum sensing system by in silico approaches

• Internship, from May 2019 until Oct 2019, Supervised by E. Becker and G. Rabut (IGDR, Rennes). Student: Camille Juigne (ENSSAT, Lannion). Subject: Data integration and formal analysis of the network between ubiquitination enzymes.

• Internship, from Jan 2019 until Jun 2019, Supervised by F. Morrews. Student: Albane Lysiak (Master 2 bioinformatique, Rennes). Subject: Exploiting paralog genes for discovering genetic regulation by transcription factors.

• Internship, from Jul 2019 until Aug 2019, Supervised by C. Belleannée and N. Guillaudeux. Student: Pierre Alexis Odye (Master 1 informatique, Rennes). Subject: Design of a database on known and predicted transcriptomics data in humans, mice and dogs.

• Internship, from Jul 2019 until Aug 2019, Supervised by E. Becker and F. Moreews. Student: Hugo Simon (1st year Telecom Paris Tech). Subject: Large scale analysis of metabolic networks as biological graphs.

• Internship, from Jun 2019 until Jul 2019, Supervised by A. Siegel and R. Andonov. Student: Kerian Thuillier (ENS Rennes). Subject: Linear programming for metabolic network completion [41]

• Internship, from Jan 2019 until Jul 2019, Supervised by C. Frioux. Student: Margot Wagner (Master 2 écologie, Rennes). Subject: Discriminant analysis of transcriptomics and metagenomics of an alga and its microbiota in multiple culture conditions with genome-scale modelling.