Section: Dissemination

Teaching - Supervision - Juries

Teaching

We have and we will go on having trained a group of good multi-disciplinary students both at the Master and PhD level. Being part of this community as a serious training group is obviously an asset. Our project is also very much involved in two major student programs in France: the Master BIBS (Bioinformatique et Biostatistique) at Université Paris-Sud/École Polytechnique and the parcours d'Approfondissement en Bioinformatique at École Polytechnique. We are also involved in a student partnership with McGill University (partenariat France Quebec offering French and Canadian students co-supervised internships (short term -3 to 6 months- or long term -part of the PhD studies-). J.-M. Steyaert is involved in the development of an interdisciplinary cooperation between Polytechnique and AP-HP that will favor interships of Polytechnicians and Masters students in AP-HP operational services.

Ch. Froidevaux is a member of the Scientific Committee of the Computer Science Doctoral School of Paris-Sud University.

J.-M. Steyaert organizes Bibs (M1 and M2) at Ecole Polytechnique. Ch. Froidevaux is co-heading the Master (M1 and M2) at the University Paris Sud. Most team members are teaching in this master.

J.Bernauer was appointed Chargé d'enseignement in the Computer Science Department of École Polytechnique (DIX) in 2013.

• Master Bibs : J. Bernauer, Informatique théorique et Programmation Python, 20h, M2, Université Paris-Sud, France

• Cycle Ingénieur Polytechnicien: J. Bernauer, Modal Bioinformatique, 18h, 2ème année, École Polytechnique, France

• Cycle Ingénieur Polytechnicien: J. Bernauer, Algorithmes et Programmation INF421, 36h, 2ème année, Ecole Polytechnique, France

• Cycle Ingénieur Polytechnicien: J. Bernauer, Modal Web Tablette INF441a, 36h, 2ème année, Ecole Polytechnique, France

• Cycle Ingénieur Agro Paris Tech: J. Bernauer, Module AAB, cours invité, 3ème année, Agro Paris Tech, France

• Master Bibs : Y. Ponty, M. Regnier, J.-M. Steyaert, Combinatoire, Algorithmes, Séquences et Modélisation (Casm ), 32h, M2, Université Paris-Sud, France

• Master : J.-M. Steyaert, X cycle ingénieur INF582- Datamining, 35h, M1, Ecole Polytechnique, France

• Master : J.-M. Steyaert, X cycle ingénieur BioINF588- Algorithms for Bioinformatics, 35h, M1, Ecole Polytechnique, France

• Licence : J.-M. Steyaert, X cycle ingénieur Modal-BioInformatique, 45h, L3, Ecole Polytechnique, France

• Master : J.-M. Steyaert, Bibs Algorithmique avancée et optimisation, 25h, M2, X-Orsay, M2, Ecole Polytechnique, France

• Data Bases, 48h, M1 Bibs (Bioinformatics and BioStatistics), Paris-Sud University, France (C. Froidevaux)

• Advanced Algorithmics, 48h, M1 Bibs (Bioinformatics and BioStatistics), Paris-Sud University, France (C. Froidevaux)

• Integration and Analysis of heterogeneous data from the Web, 24h, M2 Bibs (Bioinformatics and BioStatistics), Paris-Sud University/École Polytechnique, France (J. Azé, S. Cohen Boulakia, C. Froidevaux)

• Advanced Data Bases and Data Mining, 42h, M2 Bibs (Bioinformatics and BioStatistics), Paris-Sud University/École Polytechnique, France (S. Cohen Boulakia, C. Froidevaux).

• Initiation to Research, 6h, M2 Bibs (Bioinformatics and BioStatistics), Paris-Sud University, France (C. Froidevaux)

• Software Engineering for Bioinformatics, 48h, M2 BIBS (Bioinformatics and BioStatistics), Paris-Sud University/École Polytechnique, France (P. Amar)

• Modelling and Simulation of Biological Processes, 24h, M2 BIBS (Bioinformatics and BioStatistics), Paris-Sud University/École Polytechnique, France (P. Amar)

• Biological Networks and Systems Biology, 9h, M1 BIBS (Bioinformatics and BioStatistics), Paris-Sud University/École Polytechnique, France (P. Amar)

• RNAomics and RNA Bioinformatics, 12h, M2 BIBS (Bioinformatics and BioStatistics), Paris-Sud University/École Polytechnique, France (A.Denise)

• Theoretical Computer Science, 30h, M2 BIBS (Bioinformatics and BioStatistics), Paris-Sud University/École Polytechnique, France (A.Denise)

Supervision

• HdR : Patrick Amar, Contributions à l'étude de la dynamique des systèmes biologiques et aux systèmes de calcul en biologie synthétique, Paris Sud University, 19/12/2013

• PhD : Jiuqiang Chen, Designing scientific workflows following a structure and provenance -aware strategy, Université Paris Sud, Defended on 10/10/2013, S. Cohen-Boulakia and C. Froidevaux.

• PhD in progress : Mélanie Boudard, Game theory and stochastic learning for predicting the three-dimensional structure of large RNA molecules , 15/10/2012, D. Barth (Univ. Versailles), J. Cohen (CNRS, LRI) and A. Denise.

• PhD in progress : Marc Bouffard, Étude de circuits logiques moléculaires et détection de portes logiques dans un réseau métabolique, Université Paris Sud, 01/10/2013, P. Amar and F. Molina.

• PhD in progress : Bryan Brancotte, Ranking biological and biomedical data: algorithms and applications, Université Paris Sud, 01/10/2012, S. Cohen-Boulakia and A. Denise.

• PhD in progress: Adrien Guilhot-Gaudeffroy, Modelling and scoring of protein-RNA complexes, 01/10/2011, J. Azé, J. Bernauer, C. Froidevaux.

• PhD in progress: Daria Iakovishina, A Combinatorial Approach to Assembly Algorithms, 01/11/2011, M. Régnier.

• PhD in progress : Adrien Rougny, Raisonnements sur des connaissances biologiques pour la construction et l'analyse des réseaux de signalisation, 01/10/2013, C. Froidevaux.

• PhD in progress : Antoine Soulé, Evolutionary study of RNA-RNA interactions in yeast, 01/09/2013, J.-M. Steyaert and J. Waldispühl (University McGill, Canada).

• PhD in progress : Bo Yang, Bioinformatics approaches for studying the relations between RNA structure and pre-messenger RNA splicing, 01/10/2011, A. Denise and Fu Xiangdong (Wuhan University, China)

• PhD in progress : Cong Zeng, Identification of structural motifs in messenger RNAs, 01/10/2011, A. Denise

Juries

• HDR

  • Ch. Froidevaux was a reviewer for an HDR (Montpellier).

  • J.-M. Steyaert served as a jury member for Hubert Lincet HDR defence (Caen).

• PhD

  • P. Amar served as a referee for Laurent Crepin's PhD defence (Brest University).

  • Ch. Froidevaux served as a referee for a PhD thesis in Rennes and was a member of the committee for J. Leblay.

  • M. Régnier served as a referee for O. Abdou Arbi's PhD defence (Rennes University).

• Funding agencies

  • ANR 2012-2013, SIMI2, J. Bernauer and S. Cohen-Boulakia

  • UEFISCDI 2011-2013 (Research Council Romania), Y. Ponty

• Selection committees

  • Cnrs CR/DR: comité national (Section 6 and CID 51), Y. Ponty.

  • Inria CR2/CR1 committee: Saclay, J. Bernauer;

  • Maitre de conférence: Paris-Sud, Computer science department, S. Cohen-Boulakia and J. Azé.

  • Maitre de conférence: Bordeaux I, A. Denise.

  • Ingénieur de recherche: LIP6 UPMC (Paris), Y. Ponty.

  • Chargés d'enseignement et Professeur : Ecole Polytechnique, M. Régnier et J.-M. Steyaert.