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 several courses of the Master in Bioinformatics (https://www.bioinfo-lyon.fr/) (L3: Advanced Bioinformatics, M1: Methods for Data Analysis in Genomics, M1: Methods for Data Analysis in Transcriptomics, M1: Bioinformatics Project, M2: Ethics). He teaches 192 hours per year in bioinformatics. Arnaud Mary is responsible for two courses of the Bioinformatics Curriculum at the University (L2: Introduction to Bioinformatics and Biostatistics, M1: Object Oriented Programming) and one at Insa (Discrete Mathematics). He taught 198 hours in 2018. Blerina Sinaimeri taught 36 hours in 2018 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 was an instructor in NGS data analysis training for the CNRS Formation in the last 4 years since 2015, a course coordinated by Eric Rivals from the LIRMM, Montpellier (https://www.france-bioinformatique.fr/fr/formations/bioinformatique-pour-traitement-donn%C3%A9es-s%C3%A9quen%C3%A7age-ngs.

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 40 and 270 hours per year, again at the undergraduate and Master levels, in pure computer science (e.g. Algorithm Engineering, Randomised Algorithms), applied mathematics (e.g. Operational Research, Advanced Linear Programming) and computational biology (e.g. Biological Network Analysis).

Supervision

The following PhDs were defended in ERABLE in 2018:

• Damiano di Francesco Maesa, University of Pisa, co-supervisors: Laura Ricci and Andrea Marino, Oct 2018.

• Mattia Gastaldello, Sapienza University of Rome and University of Lyon 1 (funded by “Vinci Program-Université Franco-Italienne”, co-supervisors: Tiziana Calamoneri, Sapienza University of Rome; Marie-France Sagot), Feb 2018.

• Scheila Gabriele Mucha, Federal University of Rio Grande do Sul, Brazil (PhD scholarship from Brazil with one year spent as "sandwich PhD" in France funded by Capes, and 6 more months funded by a grant from ERABLE, co-supervisors: Arnaldo Zaha, Federal University of Rio Grande do Sul; Marie-France Sagot), Sept 2018.

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)

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

• 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)

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

• 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)

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

• 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)

Besides the PhD students indicated above, who are physically located within one of the premises of ERABLE, the project-team has PhD students in co-supervision who spend the majority or the whole of their time in the premises of other teams. These include: Rita Ramos (funded by Portuguese FCT, co-supervisors: Claudia Nunes dos Santos – ITQB Lisbon, Marie-France Sagot), and André Veríssimo (funded by Portuguese FCT, co-supervisors: Susana Vinga – Instituto Superior Técnico in Lisbon, Marie-France Sagot).

Juries

The following are the PhD or HDR juries to which members of ERABLE participated in 2018.

• Giuseppe Italiano: External Examiner of the PhD of Daniel Wolleb-Graf, ETH, Zurich, Switzerland, Dec 3, 2018.

• Marie-France Sagot: External Reviewer of the PhD of Clémence Frioux, University of Rennes 1, France, Nov 19, 2018.

• Leen Stougie: Member of the Committee of the PhD of Bart Kamphorst, Technical University Eindhoven, Netherlands, May 2018; Member of the Committee of Gregorios Koumoutsos, Technical University Eindhoven, Netherlands, Sept 2018.

• Fabrice Vavre: External Reviewer of the HDR Committee of Thierry Lefevre, Univ of Montpellier, France, March 3, 2018.