emmanuelle-becker

Emmanuelle Becker

Associate professor, Univ. Rennes 1
CNU Section 64, 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: emmanuelle.becker@irisa.fr or emmanuelle.becker@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 : 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.

On-going 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

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)

→ 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. submitted.

Past PhD students

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 and ICM, HDR).
Current position : Virgilio works for Owkin, in Paris.

→ 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]

→ 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]

→ 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]

→ Validation of circulating microRNA signatures as biomarkers 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).
Current position : Méline currently works at the CHU of Angers.

Master students at Dyliss

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

Publication list

2023

[S1]
Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret et Emmanuelle Becker
Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using Semantic Web technologies.
submitted.

2022

[36]

Virgilio Kmetzsch, Morwena Latouche, Dario Saracino, Daisy Rinaldi, Agnès Camuzat, Thomas Garreau, the French reserach network on FTD/ALS, Isabelle le Ber, Olivier Colliot and Emmanuelle Becker
Validation of miRNA signatures as biomarkers in genetic frontotemporal dementia and amyotrophic lateral sclerosis.
Annals of Clinical and Translational Neurology, 2022 [HAL]

[35]
Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret and Emmanuelle Becker
A method to identify target molecules and extract the corresponding graph of interactions in BioPAX.
Bioinformatics and Computational Biology Conference (BBCC 2022), 13-15 Decembre 2022

[34]
Virgilio Kmetzsch; Emmanuelle Becker; Dario Saracino; Vincent Anquetil; Daisy Rinaldi; Agnès Camuzat; Isabelle Le Ber; Olivier Colliot and the PREV-DEMALS study group
Disease progression score estimation from multimodal imaging and microRNA data using supervised variational autoencoders.
IEEE J Biomed Health Inform, 2022 [HAL]

[33]
Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret et Emmanuelle Becker,
Detection and correction of non-conformities and redundancies in complexes of molecules in BioPAX.
Actes JOBIM 2022, Rennes, 5-8 juillet 2022 [HAL]

[32]
Fabrice Petit, Soazic Jamin, Pierre-Yves Kernanec, Emmanuelle Becker, Guillaume Halet, and Mickaël Primig.
EXOSC10/Rrp6 is essential for the eight-cell embryo/morula transition.
Dev. Biol, 2022 [HAL] [Pubmed]

[31]
Marc Melkonian, Camille Juigné, Olivier Dameron, Gwenaël Rabut* and Emmanuelle Becker*
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein-protein interaction databases.
Bioinformatics, 2022 [HAL]

[30]
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
A multimodal variational autoencoder for estimating progression scores from imaging and microRNA data in neurodegenerative diseases.
SPIE Medical Imaging 2022. [HAL]

2021

[29]
François Moreews, Hugo Simon, Anne Siegel, Florence Gondret, Emmanuelle Becker
PAX2GRAPHML : a python library for large-scale regulation network analysis using BIOPAX
Bioinformatics, 2021 [HAL]

[28]
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.
Plasma microRNA signature in presymptomatic and symptomatic subjects with C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis
J Neurol Neurosurg Psychiatry, 2021 [HAL]

[27]
Leverrier-Penna S, Michel A, Lecante LL, Costet N, Suglia A, Desdoits-Lethimonier C, Boulay H, Viel R, Chemouny JM, Becker E, Lavoué V, Rolland AD, Dejucq-Rainsford N, Vigneau C, Mazaud-Guittot S.
Exposure of human fetal kidneys to mild analgesics interferes with early nephrogenesis
FASEB J, 2021

2019

[26]
Xie B, Becker E, Stuparevic I, Wery M , Descrimes M, Morillon A, and Primig M.
The anti-cancer drug 5-fluorouracil affects cell cycle regulators and long non-coding RNAs with regulatory potential in yeast.
RNA Biology, 2019

2018

[25]
Darde T, Gaudriault P, Beranger R, Lancien C, Caillarec-Joly A, Sallou O, Bonvallot N, Costet N, Chevrier C, Mazaud-Guittot S, Jégou B, Collin O, Becker E, Rolland A-D and Chalmel F.
TOXsIgN : A public repository for toxicological signatures at the IRSET.
Bioinformatics, 2018.

[24]
Leverrier-Penna S, Mitchell RT, Becker E, Lecante L, Ben Maamar M, Lavoué V, ristensen DM, Jégou B, Dejucq-Rainsford N, Mazaud-Gittot S.
Ibuprofen is deleterious for the development of first trimester human fetal ovary ex vivo.
Human Reprod, 2018.

[23]
Houzet L , Pérez-Losada M, Matusali G, Deleage C, Dereuddre-Bosquet N, Satie AP, Aubry F, Becker E, Jégou B, Le Grand R, Keele BF, Crandall KA and Dejucq-Rainsford N.
Seminal SIV in cynomolgus macaques is dominated by virus originating from multiple genital organs.
Journal of Virology, 2018.

2017

[22]
Dugay F, Llamas-Gutierrez F, Gournay M, Medane S, Mazet F, Christian-Chiforeanu D, Becker E, Lamy R, Léna H, Rioux-Leclercq N, Belaud-Rotureau MA and Cabilic F.
Clinicopathological characteristics of ROS1- and RET-rearranged NSCLC in caucasian patients. Data from a cohort of 713 non-squamous NSCLC lacking KRAS/EGFR/HER2/BRAF/PIK3CA/ALK alterations.
Oncotarget, 2017.

[21]
Becker E, Com E, Lavigne R, Guilleux M-H, Evard B, Pineau C and Primig M.
The protein expression landscape of mitosis and meiosis in diploid budding yeast.
J. Proteomics, 2017.

2016

[20]
Hao* C, Gely-Pernot* A, Kervarrec C, Boudjema M, Becker E, Khil P, Tevosian S, Jégou B and Smagulova F.
Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.
Nucleic Acids Research, 2016.

[19]
Xie B, Horecka J, Chu A, Davis RW, Becker E and Primig M.
Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae.
RNA Biology, 2016.

2015 and before

[18]
Chapple C E, Robisson B, Spinelli L, Guien C, Becker E, Brun C.
Extreme multifunctional proteins identified from a human protein interaction network.
Nature Communications, 2015.

[17]
Darde T, Sallou O, Becker E, Evrard B, Monjeau C, Le Bras Y, Jégou B, Collin O, Rolland A and Chalmel F.
The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community
Nucleic Acids Research, Web-Server issue, 2015.

[16]
Liu* Y, Stuparevic* I, Xie B, Becker E, Law M and Primig M.
The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1’s meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae.
Mol. Microbiology, 2015.
Corrected in Mol. Microbiology, 2015, Volume 99, Issue 1, 217.

[15]
Gely-Pernot* A, Hao* C, Becker E, Stuparevic I, Kervarrec C, Chalmel F, Primig M, Jégou B and Smagulova F. Worldwide used herbicide atrazine affects meiosis in male mice.
BMC Genomics, 2015.

[14]
Becker E, Liu Y, Lardenois A, Walther T, Horecka J, Stuparevic I, Law M, Lavigne R, Evrard E, Demougin P, Riffle M, Strich R, Davis R W, Pineau C and Primig M.
Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development.
J. of Proteomics, 2015.

[13]
Petit* F G, Kervarrec* C, Jamin* S P, Smagulova F, Hao C, Becker E, Jégou B, Chalmel F and Primig M.
Combining RNA- and Protein Profiling Data With Network Interactions Yields Clues About Gene Function in Mouse and Human Spermatogenesis
Biol. of Reproduction, 2015.

[12]
Stuparevic I, Becker E, Law M and Primig M.
The histone deacetylase Rpd3/Sin3/Ume6 complex represses an acetate inducible isoform of VTH2 in fermenting budding yeast cells.
FEBS Letters, 2015

[11]
Lardenois* A, Becker* E, Walther* T, Law M, Demougin P, Strich R and Primig M.
Global alterations of the transcriptional landscape during budding yeast growth and development in the absence of Ume6-dependant chromatin modification.
Mol. Genet. Genomics, 2015.

[10]
Lardenois A*, Stuparevic I*, Liu Y*, Law M J, Becker E, Smagulova F, Waern K, Guilleux M-H, Horecka J, Chu A, Kervarrec C, Strich R, Snyder M, Davis R W, Steinmetz L M, and Primig M.
The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development.
Nucleic Acids Research, 2014.

[09]
Lavigne R, Becker E, Liu Y, Evrard B, Lardenois A, Primig M and Pineau C.
Direct iterative protein profiling (DIPP) – an innovative method for large-scale protein detection applied to budding yeast mitosis.
Mol Cell Proteomics, 2012.

[08]
Becker E*, Robisson B*, Chapple CE, Guénoche A and Brun C.
Multifunctional proteins revealed by overlapping clustering in protein interaction network.
Bioinformatics, 2012.

[07]
Souiai O*, Becker E*, Prieto C, Benkahla A, De las Rivas J and Brun C.
Functional integrative levels in the human interactome recapitulate organ organization.
PLoS One, 2011.

[06]
Aucher W*, Becker E*, Ma E, Miron S, Martel A, Ochsenbein F, Marsolier-Kergoat M-C and Guerois R.
A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data.
Mol Cell Proteomics, 2010.

[05]
Becker E., Guénoche A. and Brun C. (2009).
Systèmes de classes chevauchantes pour la recherche de protéines multifonctionnelles.
Actes JOBIM 2009, p.49-54, Nantes, 9-11 juin 2009.

[04]
Becker E, Cotillard A, Meyer V, Madaoui H, Guerois R.
HmmKalign : a tool for generating sub-optimal HMM alignments.
Bioinformatics, 2007.

[03]
Becker E*, Meyer V*, Madaoui H, Guerois R.
Detection of a tandem BRCT in Xrs2 and Nbs1 with functional implications in the DNA damage response.
Bioinformatics, 2006.

[02]
Madaoui H, Becker E, Guérois R.
Sequence search methods and scoring functions for the design of protein structures.
Methods in Molecular Biology, 2006.

[01]
Mousson F, Lautrette A, Thuret JY, Agez M, Courbeyrette R, Amigues B, Becker E, Neumann JM, Guerois R, Mann C, Ochsenbein F.
Structural basis for the interaction of Asf1 with histone H3 and its functional implications.
Proc Natl Acad Sci U S A, 2005.