Emmanuel FAURE



Researcher, CNRS , Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier , ICAR Team



Associated Researcher, INRIA , MOSAIC Team



Associated Researcher, CNRS , Lemaire Team














LIRMM Batiment 5, Bureau 3/066
860 Rue de St - Priest
34090 Montpellier

(+33) 6 52 97 24 06
emmanuel.faure[at]lirmm.fr

News !!

PDF Nature Communications
MorphoNet: an interactive online morphological browser to explore complex multi-scale data
B. Leggio, J. laussu, A. Carlier, C. Godin, P. Lemaire, and E. Faure

Job Opportunities

Ingénieur Dévelopeur Unity
Ingénieur​-Développeur Unity (H/F) ​pour la visualisation de données 3D en ligne.
sur MorphoNet.
Location : LIRMM (Montpellier), Equipe ICAR
with Patrick Lemaire
Master 2 Intership - 2019-2020
Data Scientist
Deep Learning for Cell Tracking on 3D + time live embryos.
Location : LIRMM (Montpellier), Equipe ICAR
with Patrick Lemaire

Research Interests

Computational
Biology
from cells to embryos: multiscale morphogenesis reconstructions from 4D images datasets

genes : understanding genes interactions in the early embryogenesis using model of Genes Regulatory Network

A-C-G-T : DNA analysis to automatically detect transcription factors involving in the GRN

Approaches Image Processing : develop tools for 4D Images analysis

Simulation : simulate multi-agent models for understanding embryogenesis

Data Mining : create new protocols for manually annotated massive images dataset

Machine learning : apply neural networks, deep learning, active machine learning on big dataset

Complex System : using multiscale approach to understand complex interactions

Cognitive Sciences : develop methods based on neuroscience

Research Experiences

2015 - 2018
CNRS Researcher
Institut de Recherche en Informatique de Toulouse (CNRS UMR 5505) Toulouse - France
REVA Team
2014 - 2015
PostDoctoral Researcher
Computational Biology Institute - Virtual Plants (INRIA) - CRBM (CNRS UMR 5237) Montpellier - France
with Patrick Lemaire and Christophe Godin
Research topics: Morphogenesis multiscale modeling
2010 - 2014
Research Engineer ( permanent position )
Center for Research in Applied Epistemology - Ecole Polytechnique - CNRS (UMR 7656) - Paris - France
with Paul Bourgine
2012- 2014
Technical Director
BioEmergences Platform (IBISA) - CNRS (FRC 2118) - Gif sur Yvette - France
with Nadine Peyriéras
Research topics: Morphogenesis multi-scale dynamics reconstruction
2010 - 2012
PostDoctoral Researcher
Davidson Laboratory - California Institute of Technology - California - USA
with Eric Davidson
Research topics: Modeling the Gene Regulatory Network
2009 - 2010
PostDoctoral Researcher
Complex System Institute - Paris - France
with Paul Bourgine
Research topics: Machine Learning on Complex System Datas

Education

2005 - 2009

PhD in Complex Systems and Computer Science

PDF X Ecole Polytechnique - Paris - France
CREA Centre de recherche en épistémologie appliquée - Paris - France

Advisor: Paul Bourgine

Title: Automated reconstruction of the spatio-temporal lineage tree of the embryo
2004 - 2005

Master 2 in Cognitive Science

PDF EHESS Ecole des Hautes Etudes en Sciences Sociales - Paris - France
ENS Ecole Normale Supérieure - Paris - France
X Ecole Polytechnique - Paris - France
CREA Centre de recherche en épistémologie appliquée - Paris - France

Advisor: Paul Bourgine

Title: Creation, Design and Analysis of a new experimental platform for studying the influence of a group of standard reinforcement learning.
2000 - 2001

Master 2 in Artificial Intelligence

UT3 Paul Sabatier University - Toulouse - France
LAAS Laboratory for Analysis and Architecture of Systems - Toulouse - France

Advisor: Malik Ghallab

Title: Towards a synthesis task hierarchy and attributes hierarchy in planification.
1999 - 2000

Master 1 in Computer Science and Artificial Intelligence

UL Laval University - Quebec City - Canada
1996 - 1999

Licence in Math and Computer Science

UB1 Bordeaux 1 University - Bordeaux - France

Supplementary Training

10/2010 Gene Regulatory Networks for Development Marine Biological Laboratory - Woods Hole - USA
10/2008 Autumn School Interdisciplinary Systems Biology BIOSYS - Aspet - France
09/2008 School Interdisciplinary Topics in Functional Microscopy in Biology MIFOBIO - Carquerainne - France
09/2007 School on Parallel Computing CINECA - Bologna - Italy
09/2006 School of vision neuro-mathematical Scuola Normale Superiore - Pisa - Italy

Research Activities

10-2018
TSDL 2018
Symposium Organizer-- 2 days, 10 Speakers, 300 attendes
Toulouse Symposium on Deep Learning
03-2018
Spring School
Data Instructor -- Workshop organized by Patrick Lemaire and Christophe Godin
A multidisciplinary approach to animal and plant morphogenesis
03-2018
Workshop
Workshop co-organizer with Sylvain Cussat Blanc
Modélisation et Simulation pour les sciences du vivant
02-2018
Workshop
Workshop co-organizer with Josianne Mothe
Rencontres : Information médicale, Recherche d’information et Sciences des données
2016
Workshop
Workshop organizer
Rencontre des équipes VORTEX de l'IRIT et ICAR au LIRMM
2010
GridDay
Conference co-organizer
Multi-scale data mass and grid processing
Organizers: Arnaud Banos, Emmanuel Faure, Jean-Louis Giavitto, Romain Reuillon
2010
Contest
Dataset Organizer
Active Learning Challenge
Organizers : Isabelle Guyon - Berkeley - USA
2006-2009
Embryomics
Technical Coordinator
Embryomics European Project Reconstructing in space and time the cell lineage tree
Manager : Nadine Peyriéras
2008-2009
AFIA
Lecture Group Coordinator at the ISCPIF
Machine Learning Lecture Group
French Association for Artificial Intelligence
2007
Research internship
Department of Electrical, Electronic and Information Engineering, Bologna University - Italy
Advisor : Alexandro Sarti
Research topic: Cells tracking with high level features

Projects

2019 -
4DeepEmbryos
Labex Numev
Apprentissage profond pour la reconstruction d’images biologiques 4D
Manager : Emmanuel Faure
2010 -
MORPHOSCOPE
Equipex
Multi-scale imaging and reconstruction of morphogenesis
Manager : Emmanuel Beaurepaire
2013 - 2015
e-Laboratory
Designing and sharing new theoretical and methodological tools
e-Laboratory on Embryome Digital Campus
Manager : Nadine Peyriéras
2012 - 2013
GeNeTool
Dynamic Boolean model of endomesoderm gene regulatory network
Davidson Laboratory - California Institute of Technology - California - USA
2012 - 2014
ESEA - CLOUD
ANR Emergence
Massive parallel computing platform for cloud computing
Manager : Pierre Collet
2011 - 2014
TEFOR
Infrastructure Biologie Santé
Innovative services and tools for research on embryogenesis
Manager: Jean-Stéphane Joly
2011 - 2014
FBI
National Research Infrastructure
France Bio-Imaging
Manager : Maïté Coppey-Moisan

Collaborators

2018 - Dave Trinel - TisBio-UGSF - Université de Lille 1 - France
2016 - Axel Carlier, Sylvain Cussat-Blanc Josiane Mothe - IRIT - Toulouse - France
2016 - Pierre Brousset - Oncopole - Toulouse - France
2015 - Patrick Lemaire - CNRS - Centre de Recherche de Biochimie Macromoléculaire - Montpellier - France
2015 - Christophe Godin - INRIA - Virtual Plants - Montpellier - France
2012 - 2015 Eric Davidson - Caltech - Davidson Lab - Pasadena - USA
2010 - 2014 Nadine Peyriéras - CNRS - BioEmergences - Gif Sur Yvette - France
2010 - 2014 Paul Bourgine - CNRS - BioEmergences - Gif Sur Yvette - France

Teaching

2016 - 2017 - 2018
Master 2
Reconstruction d'embryons à partir d'images 4D
HMIN318M Imagerie 3D - Montpellier University - France
2016
Master / PhD
Reconstruction des dynamiques multi-échelles de la morphogenèse des organismes vivants.
Module Image - ICAR - LIRMM - Montpellier - France
2015
Master / PhD
GRN Boolean Model
Morphogenesis Summer School - Montpellier University - France
2010 , 2012
MIFOBIO
The BioEmergences workflow for the reconstruction of multiscale dynamics in multicellular organisms
Ecole de Microscopie fonctionnelle en biologie - France
2011
BIAT
Strategies for data reconstruction
Workshop Bio-Imaging Advanced Training - Lille - France
2009
Master 2
Dynamic multi-scale reconstruction in animal morphogenesis
Workshop Natural and Industrial Complex Systems Master - Rennes University - France
2007
Licence
Java : Object-Oriented Programming
Licence - LI230 - PARIS VI University - France
2007
Lesson
Machine Learning Introduction
Bologna University - Italy
2006
Summer School
Desde los pixeles hasta los campos morfo-genéticos : Analisis, modelacion y aprendizaje sobre embriogenesis
6th Summer School in Complex System - Valparaiso - Chile

Mentorship

2016 -
PhD
IRIT
ENSEEIHT - France co-supervised with Josiane Mothe (IRIT) and Pierre Brousset (Oncopole)
Sonia Mejbri
Deep Learning on multivariate medical data
2017
Master 2
CRBM
Bioinformatique et Génomique, Université Aix-Marseille
Franck Bonardi
Impact de la forme 3D et des paramètres physiques de l'hélice d'ADN sur l'activité des équences régulatrices.
2016
first year
IRIT
ENSEEIHT - France
Sacha Vanleene
4D Data streaming with Unity Game Engine
2016
Master 2
IRIT
École Nationale des ingénieurs de Tunis - Tunisia
Sonia Mejbri
Compression des données 4D de la morphogénèse animale
2016
Licence
IBC
Licence professionnelle image et son parcours 3D temps réel - Puy en Velay - France
Etienne Couturier
4D embryogenesis interface visualization
2013
Master 2
BioEmergences
ENS Cachan - Master Mathematics, Vision and Learning Track - France
Raphaël Gorrand
Cell Dynamics Reconstruction
2011
Caltech Student
SURF student - California Institute of Technology - USA
Jennifer Kang
4D Gene Expression of S. purpuratus throughout Embryogenesis
2010
Engeneer
ISCPIF
Computer Engineering - Compiègne University of Technology - France
Jonathan Denonain
Development of a Workflow Web application
2010
DUT
ISCPIF
University Degree in Technology, Computer Science - Limoges - France
Antoine Rougier co-supervised by Thierry Savy
Database workflow management

Publication

Journals

2019
link
Nature Communications
MorphoNet: an interactive online morphological browser to explore complex multi-scale data
B. Leggio, J. laussu, A. Carlier, C. Godin, P. Lemaire, and E. Faure
2018
PDF
Developmental Biology
Transcriptional regulation of the Ciona Gsx gene in the neural plate
C. Hudson, R. Esposito, A. Palladino, L. Staiano, D. Ferrier, E. Faure, P. Lemaire, H. Yasuo and A. Spanguolo
2018
PDF
Current Opinion in Systems Biology
The “computable egg”: Myth or useful concept?
K. Biasuz, B. Leggio, E. Faure and P. Lemaire
2017
PDF
bioRxiv and Science (under review )
Contact-dependent cell-cell communications drive morphological invariance during ascidian embryogenesis
L. Guignard*, U.M. Fiuza*, B. Leggio, E. Faure, J. Laussu, L. Hufnagel, G. Malandain, C. Godin and P. Lemaire(*equally contributing)
2017
PDF
Nuclei Acid Research
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
M. Brozovic,C. Dantec,J. Dardaillon,D. Dauga,E. Faure,M. Gineste,A. Louis,M. Naville,KR. Nitta,J. Piette,W. Reeves,C. Scornavacca,P. Simion,R. Vincentelli,M. Bellec,SB. Aicha,M. Fagotto,M. Guéroult-Bellone,M. Haeussler,E. Jacox,EK. Lowe,M. Mendez,A. Roberge,A. Stolfi,R. Yokomori, CT. Brown,C. Cambillau,L. Christiaen,F. Delsuc,E. Douzery,R. Dumollard,T. Kusakabe,K. Nakai,H. Nishida,Y. Satou,B. Swalla,M. Veeman,JN. Volff andP. Lemaire
2016
PDF
Nature Communication
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage
E. Faure*, T. Savy*, B. Rizzi*, C. Melani*, O. Strasova*, D. Fabrèges*, R. Spir, M. Hammons, R. Cunderlík, G. Recher, B. Lombardot, L. Duloquin, I. Colin, J. Kollár, S. Desnoulez, P. Affaticati, B. Maury, A. Boyreau, J.Y. Nief, P. Calvat,P. Vernier, M. Frain, G. Lutfalla, Y. Kergosien, P. Suret,M. Remesíková,R. Doursat, A. Sarti, K. Mikula, N. Peyriéras and P. Bourgine (*equally contributing)
2014
PDF
Applied Numerical Mathematics.
Nonlinear PDE based numerical methods for cell tracking in zebrafish embryogenesis
K. Mikula, R. Spir, M. Smisek, E. Faure and N. Peyriéras
2013
PDF
Journal of Computational Biology
A New Software Package for Predictive GRN Modeling and Redesign
E. Faure*, I.S. Peter* and E.H. Davidson (*equally contributing)
2012
PDF
Proceedings of the National Academy of Sciences identified by the Editorial Board as reporting findings of exceptional significance
Predictive computation of genomic logic processing functions in embryonic development
E. Faure*, I.S. Peter* and E.H. Davidson (*equally contributing)
2012
PDF
Transactions on Image Processing - IEEE
3D+t Morphological Processing: Applications to Embryogenesis Image Analysis
M.A. Luengo-Oroz, D. Pastor, C. Castro, E. Faure, T. Savy, B. Lombardot, J.L. Rubio-Guivernau, L. Duloquin, M.J. Ledesma-Carbayo, P. Bourgine, N. Peyriéras and A. Santos
2011
PDF
Transactions on Image Processing - IEEE
Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy
M.A. Luengo-Oroz, J.L. Rubio-Guivernau, E. Faure, T. Savy, L. Duloquin, N. Olivier, D. Pastor, M.J. Ledesma-Carbayo, D. Debarre, P. Bourgine, E. Beaurepaire, N. Peyriéras and A. Santos
2010
PDF
Science
Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy
N. Olivier*, M.A. Luengo-Oroz*, L. Duloquin*, E. Faure, T. Savy, I. Veilleux, X. Solina, D. Débarre, P. Bourgine, A. Santos, N. Peyriéras and E. Beaurepaire (*equally contributing)
2010
PDF
Development
Dual mechanism controls asymmetric spindle position in ascidian germ cell precursors
F. Prodon, J. Chenevert, C. Hébras, R. Dumollard, E. Faure, J. Gonzalz-Garcia, H. Nishida, C. Sarder and A. McDougall
2010
PDF
Image and Vision Computing Invited Paper : 8/97 for NICE-I challenge [nice1.di.ubi.pt]
Robust iris segmentation on uncalibrated noisy images using mathematical morphology
M.A Luengo-Oroz, E. Faure and J. Angulo

International conferences with proceedings and reviewing process

2019
link
BioImaging - Prague - Czech Republic
Deep Analysis of CNN Settings for New Cancer whole-slide Histological Images Segmentation: the Case of Small Training Sets
S. Mejbri, C. Franchet, R. Ismat-Ara, J. Mothe, P. Brousset, and E. Faure
2019
link
ASPAI - Barcelona - Spain
Training Set Class Distribution Analysis for Deep Learning Model – Application to Cancer Detection
R. Ismat-Ara, M. Gaspard, C. Franchet, P. Brousset, E. Faure, S. Mejbri and J. Mothe
2017
Abstract
ACM Multimedia, Mountain View - USA
Outlining Objects for Interactive Segmentation on Touch Devices
M. Pizenberg, A. Carlier, E. Faure, V. Charvillat
2017
Paper
Machine Learning for Health (ML4H 2017), Long Beach - USA
Cost-Effective Active Learning for Melanoma Segmentation
M. Gorriz Blanch, A. Carlier, E. Faure, X. Giro I Nieto
2017
9th International Tunicate Meeting- New York - USA
The 4D Cloud Embryos
B. Leggio, J. Laussu, C. Godin, P. Lemaire and E.Faure
2012
Abstract
Developmental Biology of the Sea Urchin XXI - Woods Hole - USA
A quantitative framework to define normal embryonic development and its range of variation
P. Villoutreix, L. Duloquin, B. Rizzi, E. Faure, T Savy and N. Peyriéras
2012
Abstract
Developmental Biology of the Sea Urchin XXI - Woods Hole - USA
Reconstruction of a Digital Sea Urchin Embryo during Early Development
B. Rizzi, L. Duloquin, T Savy, P. Villoutreix, E. Faure and N. Peyriéras
2011
Abstract
Annual International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology - Chicago - USA}
Processing pipeline for the digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging
M.A. Luengo-Oroz, J.L. Rubio-Guivernau, E. Faure, T Savy, L. Duloquin, N. Olivier, M.J. Ledesma-Carbayo, D. Debarre, P. Bourgine, E. Beaurepaire, N. Peyriéras and A. Santos
2010
Poster
Morphogenesis in Living Systems - Paris - France
Relevance of the SPIM/DSLM for in toto, in vivo imaging
V.V. Gurchenkov, J.L. Rubio, L. Duloquin, E. Faure, J.F. Gille, M. Frain, N. Peyriéras.
2010
Article
Advanced Information Networking and Applications - IEEE - Perth - Australie
Global Strategy of Active Machine Learning for Complex Systems : Embryogenesis Application on Cell Division Detection
E. Faure, C. Taramasco, J. Demongeot, L. Duloquin, B. Lombardot, N. Peyriéras and P. Bourgine
2010
Poster
ITMO Neurosciences, 10th Neurobiology Conferences Ladislav Tauc - Gif sur Yvette - France
BioEmergences Platform
L. Duloquin*, T. Savy*, E. Faure*, C. Melani*,P. Bourgine and N. Peyriéras (* equally contributing)
2009
Poster
Morphogenesis in Living Systems - Paris - France Best Poster Price for 4 Images
Multi-Scale Reconstruction
E. Faure, N.Peyriéras and P. Bourgine
2008
Article
Microscopic image analysis with application in biology - MIAAB08 workshop of IEEE - New-York - USA
Evaluation of four 3D non rigid registration methods applied to early zebrafish development sequences
B.Lombardot, M.A.Luengo-Oroz, C.Melani, E. Faure, A.Santos, N.Peyriéras, M.Ledesma-Carbayo and P. Bourgine
2008
Article
ISBI - Biomedical Imaging : From Nano to Macro - Paris
Can voronoi diagram model cell geometries in early sea-urchin embryogenesis ?
M.A. Luengo-Oroz, L. Duloquin, C. Castro, T. Savy, E. Faure, B. Lombardot, P. Bourgine, N. Peyriéras and A. Santos
2007
Article
European Conference on Complex Systems - Dresden - Germany
Active Learning For Embryogenesis
E. Faure, B. Lombardot, M.A. Luengo-Oroz, M. Campana, N. Peyriéras, R. Doursat and P. Bourgine
2007
Article
IEEE International Conference on Image Processing - San Antonio, Texas - USA
Twister segment morphological filtering. A new method for live Zebrafish embryos confocal images processing
M.A. Luengo-Oroz, E. Faure, B. Lombardot, R. Sance, P. Bourgine, N. Peyriéras and A. Santos
2007
Article
International Conference on Weblogs and Social Media - Boulder - USA
Intertemporal topic correlations in online media
J.P. Cointet, E. Faure and C. Roth
2007
Poster
System Complex National Network - Paris - France
Embryomics
E. Faure, B. Lombardot, and M.A. Luengo-Oroz

Invited Talk

2017
Bioinformatics Institute - A*STAR Singapore
Towards integrated modeling of animal morphogenesis by data-assimilation
E. Faure
2017
Institut de Biologie Computationnelle Annual Scientific Meeting - Montpellier - France
Méthodes de reconstructions de l’embryogenèse précoce : de l’acquisition à la visualisation de données 4D
E. Faure
2016
ppt
Modélisation biostatistique et biomathématique des données d'imagerie en cancérologie - Bordeaux - France
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage
E. Faure
2010
ppt
GridDay - Multi-scale data mass and grid processing - Paris - France
Automatic Multi-Scale Reconstruction of the spatio-temporal lineage tree of the embryo
E. Faure
2010
ppt
BioImage Analysis Workshop organized by Uwe Straehle - Karlsruhe Institute of Technology - Germany
Automatic Reconstruction of the spatio-temporal lineage tree
E. Faure, N. Péyrieras and P. Bourgine
2009
Epigenesis Workshop - Paris
Multi-agent modeling for embryogenesis: Heterogeneous collective motion or moving pattern formation ?
E. Faure, I. Junier and R. Doursat
2008
ppt
AFIA - Machine Learning and Causality Teleconference Seminars organized by Nicolas Brodu, Dominik Janzing, Isabelle Guyon and Michele Sebag - Paris - France
Active Learning For Embryogenesis
E. Faure
2008
ppt
Universidad de los Andes - Bogota - Colombia
Embryomics - BioEmergences European Project
E. Faure

Scientific Popularization

2014
journal
Le journal du CNRS
Incubateur de complexité
2007
article
Le Nouvel Observateur
De l’influence des blogs sur la presse
J.P. Cointet, E. Faure and C. Roth

&...

PhD Committee Carlos Castro (2013), Mathieu Bouyrie (2015), Alcia Madwwick (2016), Lijie Guo (2016), Nadia Amara (2017)
Reviewer Developmental Biology, IJCNN,Acta Biotheoretica,Idex...
Art & Science 2014 Futuroscope movie , article
2014 ISCPIF Inauguration article
2013 Cell Memories movie
2013 Modern Dance movie