Emmanuelle Becker

Associate professor, Univ. Rennes 1
CNU Section 64, no HDR.
ORCID ID: 0000-0002-7673-0582
Researcher ID : H-2523-2015


Dyliss team, Irisa / Inria Rennes-Bretagne Atlantique,
Campus de Beaulieu, 35042 Rennes Cedex, France.
Tel: +33 (0) 2 99 84 75 95
Fax: +33 (0) 2 99 84 71 71
Email: [prenom.nom@irisa.fr or prenom.nom@univ-rennes1.fr]


Short presentation

Assistant professor at University Rennes 1 since 2009 and Dyliss member since 2019. I am co-head of the Bioinformatics master, with my colleague Olivier Dameron. My research interests are focused on bioinformatics : modelling knowledge, integrating heterogeneous data and reasonning on molecular biological data.

Keywords : -omic data integration ; protein-protein interactions ; applications for fundamental biology, environment and  health.

On-going collaborators outside Dyliss :

  • Institut de Génétique du Développement de Rennes (IGDR, institut CNRS), for the master thesis of Camille Juigne and the PhD of Marc Melkonian : Gwenaël Rabut
  • Laboratoire de Physiologie et Génomique des Poissons (LPGP, institut INRAE), for the master 2 of Fanny Casse and in the Phenomir project : Julien Bobe, Violette Thermes, Emilie Cardonna, Cervin Guyomard, Fabrice Legeai
  • Physiologie, Envionnement et Génétique pour l’Animal et les Systèmes d’Élevage (PEGASE, institut INRAE), for the master thesis of Quentin Delhon and the PhD of Camille Juigne : Florence Gondret, François Moreews
  • Paris Brain Institute (ICM, unité Inserm) & Aramis project team (INRIA), for the PhD of Virgilio Kmetzsch inside the IPL Neuromarker project : Olivier Colliot, Dr. Isabelle Le Ber, Dr. Dario Saracino
  • Sanofi, for the PhD of Méline Wery : Charles Bettembourg


Current PhD students

Camille Juigné (december 2020 – december 2023)

Title : “Analysis of heterogeneous biological data modelled with multiplex graphs applied to understand feeding efficiency”
Funding INRAe-Région Bretagne, co-supervized with Florence Gondret (50%, INRAe, HDR)

Virgilio Kmetzsch (october 2019 – october 2022)

Title : « Multimodal analysis of neuroimaging and transcriptomic data in genetic fronto-temporal dementia ».
INRIA IPL Neuromarker, co-supervized with Olivier Colliot (50%, INRIA et ICM, HDR).

    Plasma microRNA signature in presymptomatic and symptomatic subjects with C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis. Virgilio Kmetzsch, MSc; Vincent Anquetil, PhD; Dario Saracino, MD; Daisy Rinaldi, PhD; Agnès Camuzat, MSc; Thomas Gareau, MSc; Ludmila Jornea, MSc; Sylvie Forlani, PhD; Philippe Couratier, MD, PhD; David Wallon, MD, PhD; Florence Pasquier, MD, PhD; Noémie Robil, PhD; PREV-DEMALS study group; Pierre de la Grange, PhD; Ivan Moszer, PhD; Isabelle Le Ber, MD, PhD; Olivier Colliot, PhD; Emmanuelle Becker, PhD. (to be published).


Méline Wery (october 2017 – october 2020)

Title : « Data Integration and reasonning-based analysis : methodology at each step of drug development »
CIFRE Sanofi-IRISA, co-supervized with Olivier Dameron (25%, IRISA, HDR), Anne Siegel (25%, CNRS, HDR), and Charles Bettembourg (Sanofi).


Master students at Dyliss

Quentin Delhon (february 2020 – july 2020)

« Discovery of key genes in multi-layered biological graphs », co-supervized with François Moreews (ingénieur d’étude INRAe). Quentin was a second year master student in Bioinformatics, section Informatique et Biologie Intégrative (Univ Rennes).

Marc Melkonian (february 2020 – july 2020)

« Detection of redundancies in protein-protein interaction databases encoded by different PSI-MI identifiers using semantic web technologies ». Marc is a MD, and was a second year master student in Bioinformatics, section Informatique et Biologie Intégrative (Univ Rennes). Co-supervized with Olivier Dameron (IRISA). Marc will start a PhD in 2020.

Camille Juigné (may 2019 – october 2019)

« Intégration de données et analyse formelle du réseau d’interactions entre enzymes d’ubiquitination », co-supervized with Gwenaël Rabut (Institut de Génétique du Développement de Rennes). Camille was a last year student at ENSAT (École Nationale Supérieure des Sciences Appliquées et de Technologie). Camille will start a PhD in 2020.

Fanny Casse (january 2019 – july 2019)

« Régulation par les miARNs des gènes régulant la fécondité et le développement embryonnaire précoce chez le poisson médaka ». Fanny was a second year master student in Bioinformatics, section Informatique et Biologie Intégrative (Univ Rennes), co-supervized with Julien Bobe (LPGP INRAe) and Fabrice Legeai (IGEPP INRAe). Fanny found a contrat as a engineer at the ICM (Institut du Cerveau et de la Moëlle, Paris).

Hugo Simon (july 2019 – august 2019)

Intership for the Licence d’informatique de l’école Mines-Paris Tech.



Co-head of the Master in Bioinformatics, with my colleague Olivier Dameron.

Co-supervizer of  conferences dedicated to professional insertion (2019, 2018, 2017), with Stéphanie Le Bras.

Responsible of the courses (2017-2022) : 

  • Atelier de Biostatistiques (L2 Sciences de la Vie, 250 students) ;
  • Statistiques Appliquées (L3 Informatique ENS Rennes, 20 students,  up to 2019) ;
  • Advanced R for Data Analysis (M1 Bioinformatique + M1 Ecologues, 80 students) ;
  • Object Oriented Programming (M1 Bioinformatique, 50 students) ;
  • Introduction to Computational Ecology (M2 Ecologues, 45 students) ;
  • Systems Biology (M2 Bioinformatique, 35 students) ;
  • Method (since 2019, M2 Informatique, 20 students).

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