Section: Dissemination

Teaching - Supervision - Juries

Teaching

France

The members of ERABLE teach both at the Department of Biology of the University of Lyon (in particular within the BISM (BioInformatics, Statistics and Modelling) specialty, and at the department of Bioinformatics of the Insa (National Institute of Applied Sciences). Cristina Vieira is responsible for the Master Biodiversity, Ecology and Evolution (https://www.bee-lyon-univ.fr/). She teaches genetics 192 hours per year at the University and at the ENS-Lyon. Hubert Charles is responsible for the Master of Modelling and Bioinformatics (BIM) at the Insa of Lyon (http://biosciences.insa-lyon.fr/). He teaches 192 hours per year in statistics and biology. Vincent Lacroix is responsible for the M1 master in bioinformatics (https://www.bioinfo-lyon.fr/) and of the following courses (L3: Advanced Bioinformatics, M1: Methods for Data Analysis in Genomics, M1: Methods for Data Analysis in Transcriptomics, M1: Bioinformatics Project, M2: Ethics). He taught 96 hours in 2018-2019 and 192 hours in 2019-2020. Arnaud Mary is responsible for three courses of the Bioinformatics Curriculum at the University (L2: Introduction to Bioinformatics and Biostatistics, M1: Object Oriented Programming, M2: new course on Advanced Algorithms for Bioinformatics) and one at Insa (Discrete Mathematics). He taught 198 hours in 2019. Blerina Sinaimeri taught 36 hours in 2019 on graph algorithms for the M1 students of the Master in Bioinformatics, and on Discrete Mathematics at Insa. Fabrice Vavre taught 20h at the Master level.

The ERABLE team regularly welcomes M1 and M2 interns from the bioinformatics Master.

Vincent Lacroix and Audric Cologne were instructors in the NGS data analysis training for the CNRS Formation, a course coordinated by Annabelle Haudry, LBBE (https://cnrsformation.cnrs.fr/stage-19026-Bioinformatique-pour-le-traitement-de-donnees-de-sequencage-%28NGS%29---Lyon.html).

All French members of the ERABLE team are affiliated to the doctoral school E2M2 (Ecology-Evolution-Microbiology-Modelling, http://e2m2.universite-lyon.fr/).

Italy & The Netherlands

Italian researchers teach between 90 and 140 hours per year, at both the undergraduate and at the Master levels. The teaching involves pure computer science courses (such as Programming foundations, Programming in C or in Java, Computing Models, Distributed Algorithms) and computational biology (such as Algorithms for Bioinformatics).

Dutch researchers teach between 60 and 100 hours per year, again at the undergraduate and Master levels, in applied mathematics (e.g. Operational Research, Advanced Linear Programming), machine learning (Deep Learning) and computational biology (e.g. Biological Network Analysis, Algorithms for Genomics).

Supervision

The following PhDs were defended in ERABLE in 2019:

• Jasmijn Baaijens, CWI (supervisor: Alexander Schönhuth), Sep 2019

• Annelieke Baller, Vrije Universiteit Amsterdam (co-supervisor: Leen Stougie), Nov 2019

• Thomas Bosman, Vrije Universiteit Amsterdam (co-supervisor: Leen Stougie), Nov 2019

• Audric Cologne, University of Lyon 1 (funded by Inserm and Inria, co-supervisors: Patrick Edery – Federation of Health Research of Lyon-Est, Vincent Lacroix), Oct 2019

• Leandro Ishi Soares de Lima, University of Lyon 1 (funded by the Brazilian “Science without Borders” program, co-supervisors: Giuseppe Italiano, Vincent Lacroix, Marie-France Sagot), Apr 2019

• Nikos Parotsidis, University of Rome Tor Vergata, supervisor: Giuseppe Italiano, Mar 2019

• Henri Taneli Pusa, University of Lyon 1 (funded by H2020-MSCA-ETN-2014 project MicroWine, co-supervisors: Alberto Marchetti-Spaccamela, Arnaud Mary, Marie-France Sagot), Feb 2019

The following are the PhDs in progress:

• Marianne Borderes, University Lyon 1 (funded by ANR Technology Spock, co-supervisors: Susana Vinga – Instituto Superior Técnico at Lisbon; Marie-France Sagot)

• Nicolas Homberg, Inra, Inria & University of Lyon 1 (funded by Inra & Inria, co-supervisors: Christine Gaspin at Inra; Marie-France Sagot)

• Carol Moraga Quinteros, University of Lyon 1 (funded by Conicyt Chile, co-supervisors: Rodrigo Gutierrez – Catholic University of Chile, Marie-France Sagot)

• Camille Sessegolo, University of Lyon 1 (funded by ANR Aster; co-supervisors: Vincent Lacroix, Arnaud Mary)

• Michelle Sweering, CWI (co-supervisors: Solon Pissis and Leen Stougie)

• Yishu Wang, University Lyon 1 (funded by Ministère de l?Enseignement supérieur, de la Recherche et de l?Innovation, co-supervisors: Mário Figueiredo – Instituto Superior Técnico at Lisbon; Marie-France Sagot; Blerina Sinaimeri)

• Irene Ziska, University Lyon 1 (funded by Inria Cordi-S, co-supervisors: Susana Vinga – Instituto Superior Técnico at Lisbon; Marie-France Sagot)

Juries

The following are the PhD or HDR juries to which members of ERABLE participated in 2019.

• Vincent Lacroix: External reviewer of the PhD of Patricia Sieber, supervised by Stefan Schuster at Friedrich-Schiller University of Jena, Germany; external reviewer of the PhD of Luca Denti, supervised by Paola Bonizzoni at University Bicocca of Milano, Italy.

• Arnaud Mary: External reviewer of the PhD of Karima Ennaoui, supervised by Lhouari Nourine at University of Clermont-Ferrand, France.

• Marie-France Sagot: External Reviewer of the PhD of Pierre Marijon, University of Lille, France, Dec 2019.

• Leen Stougie: Reading Committee of the PhD of Teun Janssen, TU Delft, Mar 2019; Chair Reading Committee of the PhD of Pieter Kleer, Vrije Universiteit Amsterdam, Sep 2019; Reading Committee of the PhD of Peter van der Gulik, Univ. of Amsterdam, Sep 2019; Chair Reading Committee of the PhD of Maaike Hoogeboom, Vrije Universiteit Amsterdam, Dec 2019.

• Cristina Vieira: Member of the PhD Committee of Olivier Tabone, Faculté de Médecine Rockfeller, Jan 2019; Member of the PhD Committee of Sébastien Lemaire, ENS Lyon, Mar 2019; External Reviewer of the PhD of Natalia Martinez, Université Paris Sud, Oct 2019.