emmanuelle-becker

Emmanuelle Becker

Professor, Univ. Rennes
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: emmanuelle.becker@irisa.fr or emmanuelle.becker@univ-rennes.fr

Education and training

2000 – 2002 : Bs in Computer Sciences, Ecole Normale Supérieure de Lyon
2002 – 2003 : Ms in Bioinformatics, Université Paris Cité (former name Paris Diderot, Paris 7)
2003 – 2007 : PhD in Bioinformatics, CEA Saclay and Paris Sorbonne University (former name Pierre et Marie Curie, Paris 6)

Overview

2007 – 2009 : University of Aix-Marseille, post-doc with Christine Brun
2009 – 2023 : University of Rennes, Assistant professor in Bio-informatics. Research institutes : IRSET (2009 – 2018) and IRISA (2019 – …)
2017 – … : University of Rennes, co-head of Bioinformatics master degree
2023 – … : University of Rennes, Professor in Bio-informatics. Research institute : IRISA.

Short Presentation

Professor at Rennes University since 2023 (assistant professor 2009-2023) and Dyliss member since 2019. I am co-head of the Bioinformatics master, with my colleague Annabelle Monnier. My research interests are focused on bioinformatics : integrating homogeneous and heterogeneous data (-omics data, clinical data…), and extracting graphs from knowledge for systems biology.

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

Collaborators outside Dyliss :

Gwenaël Rabut at Institut de Génétique du Développement de Rennes : master thesis of Camille Juigne, Erasmus traineeship of Nancy D’Arminio
Olivier Colliot, Dr. Isabelle Le Ber, Dr. Dario Saracino at Paris Brain Institute (ICM) & Aramis project team (INRIA), for the PhD of Virgilio Kmetzsch inside the IPL Neuromarker project
Florence Gondret, François Moreews at institute Physiologie, Envionnement et Génétique pour l’Animal et les Systèmes d’Élevage : internship of Hugo Simon, master thesis of Quentin Delhon and PhD of Camille Juigne
Marc Aubry, Eric Ogier at Oncogenesis Stress Signalling Laboratory (Inserm) & Dr. Laurent Siprouhdis (CHU Rennes) : PhD of Corentin Lucas
Nathalie Volkoff, Fabrice Legeai at Institute of Genetics, Environnement and Plant Protection (Inrae) & Genscale project team (INRIA) for the PhD of Yaël Tirlet-Greiner inside the ANR Endovire project
Dr. Nicolas Jay, Dr. Aurélie Bannay at the LORIA, for a PhD starting in september 2024, inside de M4DI axis of the Numeric Health program (PEPR Santé Numérique)

Current PhD students

Yaël TIRLET-GREINER (may 2023 – may 2026)

Title : “Integrative method for multi-omics data analysis with application to the activation and regulation of a endogeneized viral genome in a parasitoid wasp”.
Funding ANR Endovire, co-supervized with Olivier Dameron (33%, IRISA) and Fabrice Legeai (33%, INRAe)

ORCID ID : 0009-0008-3713-2142
Pubmed author ID :

Major contributions during the PhD :

→ Generic and Queryable Data Integration Schema for Transcriptomics and Epigenomics studies. Yaël Tirlet, Matéo Boudet, Emmanuelle Becker, Fabrice Legeai and Olivier Dameron (submitted)

Corentin LUCAS (october 2023 – october 2026)

Title : “Integration of multi-modal data for longitudinal follow-up of Crohn’s disease patients”.
Funding INRIA, co-supervized with Yann Le Cunff (50%, IRISA)

ORCID ID : 0009-0006-5243-2931
Pubmed author ID :

Cécile BEUST (october 2023 – october 2026)

Title : “Knowledge-guided rules for generating context-specific views on a knowledge graph: application to biological networks”.
Funding Univ Rennes, co-supervized with Olivier Dameron (33%, IRISA) and Nathalie Théret (33%, IRISA / INSERM)

ORCID ID : 0009-0008-3660-7855
Pubmed author ID : 39123285

Major contributions during the PhD :

→ BioPAX in 2024: Where we are and where we are heading. Cécile Beust, Emmanuelle Becker, Nathalie Théret, Olivier Dameron (submitted)

Océane CARPENTIER (september 2024 – september 2027)

Title : “Integrating prior knowledge for better patient representation”.
Funding PEPR Santé Numérique, Axis Methods and Models for Multimodal and Multi-scale Data Integration (M4DI), co-supervized with Yann Le Cunff (25%, IRISA), Nicolas Jay (25%, LORIA) and Aurélie Bannay (25%, LORIA)

ORCID ID :
Researcher ID :

Former PhD students

Camille JUIGNE (december 2020 – december 2023)

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

ORCID ID : 0000-0003-1157-9030
Pubmed author ID : 37891507
DBLP key : 316/3937

Major contributions during the PhD :

→ Towards a reproducible interactome: semantic-based detection of redundancies to unify protein-protein interaction databases. Marc Melkonian, Camille Juigné, Olivier Dameron, Gwenaël Rabut* and Emmanuelle Becker*. Bioinformatics, 2022 [HAL][Pubmed]

→ Detection and correction of non-conformities and redundancies in complexes of molecules in BioPAX. Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret and Emmanuelle Becker. Actes JOBIM 2022, Rennes, 5-8 juillet 2022 [HAL]

→ A method to identify target molecules and extract the corresponding graph of interactions in BioPAX. Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret and Emmanuelle Becker. Bioinformatics and Computational Biology Conference (BBCC 2022), 13-15 Decembre 2022 [HAL]

→ Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using Semantic Web technologies. Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret and Emmanuelle Becker. Bioinformatics, 2023 [HAL][Pubmed]

→ Small networks of expressed genes in the whole blood and relationships to profiles in circulating metabolites provide insights in inter-individual variability of feed efficiency in growing pigs. Camille Juigné, Emmanuelle Becker and Florence Gondret. BMC Genomics, 2023 [HAL][Pubmed]

Virgilio KMETZSCH (october 2019 – october 2022)

Title : “Multimodal analysis of neuroimaging and transcriptomic data in genetic fronto-temporal dementia”. [link to PhD manuscript]
Funding : INRIA IPL Neuromarker, co-supervized with Olivier Colliot (50%, INRIA and ICM, HDR).
Current position : Virgilio works for Owkin, in Paris.

ORCID ID : 0000-0003-3691-0180
Pubmed author ID : 36264717
DBLP key : 266/7134

Major contributions during the PhD :

→ 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. JNNP 2020. [HAL][Pubmed]

→ Disease progression score estimation from multimodal imaging and microRNA data using supervised variational autoencoders. Virgilio Kmetzsch; Emmanuelle Becker; Dario Saracino; Vincent Anquetil; Daisy Rinaldi; Agnès Camuzat; Isabelle Le Ber; Olivier Colliot and the PREV-DEMALS study group. IEEE J Biomed Health Inform 2022 [HAL][Pubmed]

→ A multimodal variational autoencoder for estimating progression scores from imaging and microRNA data in neurodegenerative diseases. Virgilio Kmetzsch; Emmanuelle Becker; Dario Saracino; Vincent Anquetil; Daisy Rinaldi; Agnès Camuzat; Thomas Gareau; Isabelle Le Ber; Olivier Colliot and the PREV-DEMALS study group. SPIE Medical Imaging 2022 [HAL]

→ MicroRNA signatures in genetic frontotemporal dementia and amyotrophic lateral sclerosis. Virgilio Kmetzsch; Morwena Latouche; Dario Saracino; Daisy Rinaldi; Agnès Camuzat; Thomas Garreau; the French Research Network on FTD/ALS, Isabelle Le Ber; Olivier Colliot and Emmanuelle Becker. Annals of Clinical and Translational Neurology 2022 [HAL] [Pubmed]

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). [link to PhD manuscript]
Current position : Méline currently works at the CHU of Angers.

ORCID ID : 0000-0001-5306-4292
Pubmed author ID : link

Master students at Dyliss (internships)

Zoé Le Roux (feb 2024 – july 2024)

“Regulation network of EMX2, a tumor suppressor gene, in the context of glioblastoma”, co-supervized with Olivier Dameron, Marc Aubry, Annabelle Monnier and Jean Mosser. Zoé is a second year master student in Bioinformatics, section Informatique et Biologie Intégrative (Univ Rennes).

Sophia Pham (april 2023 – july 2023)

“Analyse de données transcriptomiques dans le cadre du projet Endovire”, co-supervized with Yael Tirlet-Greiner. Sophia was a first year student at ESIEE engineer school.

Océane Carpentier (april 2023 – july 2023)

“Joint analysis of transcriptomic and metabolomic data in BioPax metabolic networks”, co-supervized with Olivier Dameron and Camille Juigne. Océane was a first year master student in Bioinformatics, section Informatique et Biologie Intégrative (Univ Rennes).

Nancy D’Arminio (april 2021 – july 2021)

“Automatic extraction of relations between yeast ubiquitin ligases ans their substrate proteins based on litterature”. Nancy’s work is part of an Eramsus traineeship, and Nancy will start a PhD supervized by Pr. Anna Marrabotti in october 2021 (Salerno University, Italy). Co-supervized with Olivier Dameron and Gwenaël Rabut.

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).

→ Towards a reproducible interactome: semantic-based detection of redundancies to unify protein-protein interaction databases. Marc Melkonian, Camille Juigné, Olivier Dameron, Gwenaël Rabut* and Emmanuelle Becker* Bioinformatics, 2022 [HAL]

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.

→ PAX2GRAPHML : a python library for large-scale regulation network analysis using BIOPAX. François Moreews, Hugo Simon, Anne Siegel, Florence Gondret, Emmanuelle Becker
Bioinformatics, 2021 [HAL]

Teaching

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).
- Repeatability in computer science : [0]
- Publications to study in groups: [1] [2] [3] [4] [5] [6]
- R crashtest : [subject] [dataset] [cheatseet]
- Generating a synthetic dataset with signal : [subject]

Publication list 2020-…

Journal articles (2020 – …)

→ EXOSC10/Rrp6 is essential for the eight-cell embryo/morula transition. Fabrice Petit, Soazik Jamin, Pierre-Yves Kernarec, Emmanuelle Becker, Guillaume Hallet and Michael Primig. Dev Biol, 2022 [HAL][Pubmed]

→ PAX2GRAPHML : a python library for large-scale regulation network analysis using BIOPAX. François Moreews, Hugo Simon, Anne Siegel, Florence Gondret and Emmanuelle Becker. Bioinformatics, 2021 [HAL]

→ Exposure of human fetal kidneys to mild analgesics interferes with early nephrogenesis. Sabrina Leverrier-Penna, Alain Michel, Laetitia Lecante, Nathalie Costet, Antonio Suglia, Christèle Desdoits-Lethimonier, Hugoline Boulay, Roselyne Viel, Jonathan Chemouny, Emmanuelle Becker, Vincent Lavoué, Antoine D Rolland, Nathalie Dejucq-Rainsford, Cécile Vigneau, Séverine Mazaud-Guittot. FASEB J, 2021 [HAL][Pubmed]

Conference proceedings (2020 – …)