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Section: Dissemination

Teaching - Supervision - Juries

Teaching

Initial training in engineering at Ecole Polytechnique.

At the undergraduate level, AMIBio is essentially involved in Computer Science courses at Ecole Polytechnique, mainly in programming languages and Big Data processing (high-performance computing and machine learning). Notably, we are involved in the parcours d'Approfondissement en Bioinformatique at École Polytechnique.

Graduate-level programs and courses.

Our project is also very much involved in the AMI2B (Analyse, Modélisation et Ingénierie de l'Information Biologique et Médicale, formerly named BIBS – Bioinformatique et Biostatistique) Master program at Université Paris-Sud/École Polytechnique. Most AMIBio permanent members teach recurrent courses in AMI2B, and M. Regnier is in charge of the program at the M1 and M2 levels for Ecole Polytechnique.

Beyond the plateau de Saclay, AMIBio members participate in the BIM master program at Upmc , and regularly deliver PhD-level lectures in Summer/Winter schools.

• Bachelor (Licence & Ecole Ingénieur)

  • P. Chassignet, INF*, 100h, L2/L3, Ecole Polytechnique, France

  • Al. Héliou, INF*, 40h, L3, Ecole Polytechnique, France

• Master

  • P. Chassignet, INF*/Modal Bioinfo, 90h, M1/M2, Ecole Polytechnique, France

  • Al. Héliou, INF*, 7h, M1 AMI2B, Univ. Paris-Saclay, France

  • Am. Héliou, INF*, 44h, M1 AMI2B, Univ. Paris-Saclay, France

  • Y. Ponty, Bioinfo ARN, 12h AMI2B, M2, Univ. Paris-Saclay, France

  • Y. Ponty, Bioinfo ARN, 12h BIM, M2, UPMC, France

  • M. Regnier, Algo/Combinatoire, 12h AMI2B, M2, Univ. Paris-Saclay, France

  • J.-M. Steyaert, Algo/Combinatoire, 12h AMI2B, M2, Univ. Paris-Saclay, France

  • J.-M. Steyaert, Bioinformatics INF/BIO 588, 20h Majeure BioInfo, M1, Ecole Polytechnique,France

• Doctorat

  • Y. Ponty, Design ARN, 3h BIM, PhD, Univ. Tehran, Iran

Supervision

• PhD :

  • Wei Wang, Practical structure-sequence alignment of pseudoknotted RNAs, Univ. Paris-Saclay, December 2017, Y. Ponty, A. Denise

  • Alice Héliou, Analyse des séquences génomiques : Identification des ARNs circulaires et calcul de l’information négative, Univ. Paris-Saclay, July 2017, M. Regnier

  • Amélie Héliou, Théorie des jeux et échantillonnage de conformations pour l'amarrage macromoléculaire multi-corps et multi-échelle, Univ. Paris-Saclay, August 2017, J. Cohen

• PhD in progress

  • Afaf Saaidi, Differential analysis of RNA SHAPE probing data, Ecole Polytechnique, Encadrants: Yann Ponty and Mireille Régnier.

  • Antoine Soulé, Evolutionary study of RNA-RNA interactions in yeast , Ecole Polytechnique, Encadrants: Jean-Marc Steyaert and J. Waldispuhl (U. McGill, Canada);

  • Jorgelindo Moreira da Veiga, Caractérisation dynamique et optimisation des flux métaboliques , Ecole Polytechnique, Encadrants: L. Schwartz (AP-HP)Sabine Peres (U. Paris-Sud)

  • Juraj Michalik, Non-redundant sampling for the study of RNA kinetics, Inria Saclay, Encadrants: Y. Ponty and H. Touzet (Cristal, Univ. Lille I);

  • Pauline Pommeret, Étude de l’impact phénotypique de variants génétiques altérant la structure secondaire des ARNs chez le bovin : Méthodes algorithmiques et validations expérimentales, INRA Jouy & Ecole Polytechnique, Encadrants: Y. Ponty and D. Rocha (INRA Jouy);

  • Ha Thi Ngoc Nguyen, New computational strategies for analyzing the diversity of transcriptome sequence and structure, and their relationship to disease, I2BC (Univ. Paris-Sud) & Ecole Polytechnique, Encadrants: Y. Ponty and D. Gautheret (Univ. Paris-Sud);

Juries

• Y. Ponty participated in a hiring committee for an associate professor position in Discrete Mathematics at the University of Southern Denmark;

• Y. Ponty acted as an external opponent for the PhD defence of X. Pan at the University of Copenhagen;