Curriculum Vitæ
[Compact CV on Aviesan] [3-pages academic summary]
Employment history |
 |
| Since 2023 | Senior scientist | CNRS, European Genomic Institute for Diabetes, Lille, FR | PIs: Amélie BONNEFOND, Philippe FROGUEL |
| 2019-2023 | Consultant in data analysis, modelling, science copywriting, and language translation | aSciStance Limited, Cambridge, UK | Founder and director |
| 2012-2018 | Senior Group leader | Babraham Institute, Babraham, Cambridge, UK | |
| 2014-2015 | Chief Data Officer | Curie Institute, Paris, FR | |
| 2003-2012 | Group leader | EMBL-EBI, Hinxton, Cambridge, UK | |
| 2001-2003 | Researcher | CNRS URA 2182, Récepteurs et Cognition, Institut Pasteur, Paris, FR | PI: Jean-Pierre CHANGEUX |
| 1999-2001 | Post-doctoral fellow | Computational Cell Biology, University of Cambridge, Cambridge, UK | PI: Dennis BRAY |
| 1992-1999 | Undergraduate, PhD student, and post-doctoral fellow | CNRS URA D1284, Neurobiologie Moléculaire, Institut Pasteur, Paris, FR | PI: Jean-Pierre CHANGEUX |
| 1991 | Undergraduate student | INSERM 153, Service of Développement, Pathologie, Régénération du système neuromusculaire, Institut du fer à moulin, Paris, FR | PI: Michel FARDEAU |
Educational and professional qualifications |
|
| 2013 | Habilitation à diriger des recherches | University Bordeaux II Segalen |
| 2010-present | Directeur de Recherche (senior scientist) | CNRS |
| 2001-2010 | Chargé de Recherche (research fellow) | CNRS |
| 1994-1998 | PhD in Molecular and Cellular Pharmacology | University Paris VI Pierre et Marie Curie |
| 1992-1993 | Diploma of Advanced Studies (Master Degree) in Molecular and Cellular Pharmacology | University Paris VI Pierre et Marie Curie |
| 1990-1993 | Magistere in Biology-Biochemistry | École Normale Supérieure |
| 1991-1992 | Master of Cellular Biology [Evolution; Neuroendocrinology; Molecular Biophysics] | University Paris VI Pierre et Marie Curie and Paris XI |
| 1990-1991 | Licence (Bachelor) of Cellular Biology and Physiology | University Paris VI Pierre et Marie Curie |
| 1988-1990 | Advanced maths classes preparing for the Grandes Écoles | Lycée Camille Guérin of Poitier |
| 1988: | Scientific baccalaureate | Prytanée National Militaire of La Flèche |
Teaching and supervision |
|
Post-docs
Marwa Afnouch (2024-), Lu Li (2013-2018), Piero Dalle-Pezze (2016-2018), An Nguyen (2015-2018), Pınar Pir (2012-2015), Martina Froehlich (2012-2015), Junmei Zhu (2012), Vladimir Kiselev (2011-2015), Massimo Lai (2010-2015), Éric Fernandez (2004-2005),
PhD supervisions
PhD visitors
Lucas Marmiesse (2015), Anna Zhukova (2016), Youwei Zheng (2011), Nathan Skene (2010), Ron Henkel (2009), Koray Dağan Kaya (2008), Guillaume Guerlet (2008), Christian Knüpfer (2007), Dagmar Köhn (Waltemath) (2007)
PhD juries
Anwesha Bohler (2017), Lucas Marmiesse (2016), Sylvain Soliman Habilitation (2015), Samuel Croset (2014), Lukas Endler (2012), Allyson Lister (2011), Andrew Miller (2011), Dagmar Köhn (Waltemath) (2011), Aurelien Rizk (2011), Carito Guziolowski (2010), Sarala Wimalaratne (2009), Benjamin Hall (2007), Pim Van Nierop (2007), Stéphanie Weiss (2006), Anne-Sophie Villegier (2005), Geoffroy Golfier (2004)
Undergraduate interns
Arthur Six (2025), Sami Le Guilcher (2024), Adrien Leroy (2018), Stephen Cole (2017), Agathe Delaune (2017), Derya Sebukhan (2017), Letizia Vestito (2017), Katrīna Daila Neiburga (2016), Krutic Patel (2016), Hoa Le (2014), Ioana Olan (2014), Simon Delagneau (2014), John Gowers (2013), Grigalius Taukanska (2013), Marija Jankovic (2013), Yangyang Zhao (2012), Ishan Ajmera (2011), Denis Brun (2011), Michael Schubert (2011), Anna Zhukova (2011), Gael Jalowicki (2011), Jean-Baptiste Pettit (2010), Karim Tazibt (2010), Marine Dumousseau (2009), Ranjita Dutta-Roy (2008), Kedar Nath Natarajan (2008), David Marshall (2007), Antonia Mayer (2007), Anika Oellrich (2007), Enuo He (2006), Arnaud Henry (2006), Camille Laibe (2006), Renaud Schiappa (2006), Lu Li (2005), Alexander Broicher (2004), Marie-Ange Djite (2004).
Courses
Organiser (and lecturer)
EBI course In silico systems biology (2010-2018); Cajal Advanced Neuroscience Course Bioinformatics for the neuroscience (2015); WT/E-MeP Advanced Training Workshop in Bioinformatics of Membrane Proteins, Hinxton, UK (2008); Okinawa Computational Neuroscience Course 2006, OIST, JP (2006).
Lecturer
Graduate program Precision Health, Lille (2024), Master 2 Bioinformatique, Lille (2024); Part III Systems Biology, University of Cambridge, UK (2013-2018); Natural Science Tripos, University of Cambridge, UK (2017); Gebze Technical University Molecular Biology and Genetics Undergraduate program (2017); Cambridge University Technical College (2015, 2017); Advances in Systems and Synthetic Biology, Strasbourg (2015); EBI course "The Systems Biology Modelling Cycle", Hinxton, UK (2014); Instituto Gulbenkian de Ciência PhD student course, Lisbon, PT (2012); SystemsX.ch/SIB Summer School, Kandersteg, CH (2011); Summer school of the Center for Genomic Regulation, Barcelona, SP (2011); EBI-Wellcome Trust Summer School in Bioinformatics (2010, 2011, 2012); International Genetically Engineered Machine competition (iGEM) - Cambridge (2007, 2009); EBI training on Networks and Pathways (2009); APO-SYS data management workshop, Hinxton, UK (2008); SysBioMed Winter School, Tenerife, ES (2007); EMBL international PhD program, Heidelberg, DE. (2005, 2007); Symbionic course on Methods, data handling and standards in neuronal systems biology, Trieste, IT (2005); FEBS course 1st Advanced Course on Systems Biology: From Molecules & Modeling To Cells, Gosau, AT (2005); ESF course Modelling Metabolic and Signal Transduction Networks, Oxford, UK (2005); Diploma of Advanced Studies of Neurobiology and Pharmacology (École Normale Supérieure), Paris, FR (2002).
Awards and fellowships |
|
| 2003 | JM Le Goff Award | French Academy of Science (for bioinformatics analysis of the ligand-gated ion channels receptors of neurotransmitters) |
| 1999-2001 | long term fellowship | European Molecular Biology Organisation |
| 1998-1999 | Allocation Roux | Institut Pasteur |
| 1994-1997 | PhD scholarship | French Ministry of Research |
Professional memberships |
|
| 2017-2018 | Faculty of 1000 | Head of section Network and Systems Biology |
| 2014-2016 | International Society for Stem Cell Research | |
| 2010-2018 | International Society for Computational Biology | Senior member from 2016, Board of directors 2017-2018 |
| 2007-present | International Society of Systems Biology | Executive board |
| 1995 | The Society for Molecular Biology & Evolution |
Grants |
|
| IDEx University of Lille | NEXT-GENeration PRecIsion medicine in Inflammatory and MEtabolic diseases | co-I | 01/09/2025 - 30/08/2029 |
| ANR | Éclairer le métabolome obscur du microbiote intestinal humain avec la chimiométrie et la chémoinformatique adaptées à l'UHPLC-MS | co-I | 01/10/2024 - 31/09/2027 |
| Région Hauts-de-France | STaRS, Soutien à l’accueil de Talents de la Recherche Scientifique. AI models to reveal molecular networks underpinning the prediction of metabolic and inflammation disorders | PI | 01/09/2024 - 31/08/2026 |
| IHU2 PreciDIAB | Outils d’Apprentissage Profond pour appuyer la médecine de précision dans le diabète et affections apparentées | co-I | 01/02/2024 - 30/04/2026 |
| MRC | JPND - Intraneuronal transport-related pathways across neurodegenerative diseases | co-PI | 01/04/2018 - 30/06/2021 |
| BBSRC | Molecular and Cellular Mechanisms of Host Defence and Immunosenescence, a BBSRC Strategic Programme | co-I | 01/04/2017-31/03/2022. |
| BBSRC | Epigenetics and cellular heterogeneity in development and ageing, a BBSRC Strategic Programme | co-I | 01/04/2017-31/03/2022. |
| BBSRC | Molecular mechanisms underpinning healthy ageing, a BBSRC Strategic Programme | co-I | 01/04/2017-31/03/2022. |
| NIH | Continued support and development of SBML | co-I | 01/05/2016-30/04/2019. |
| BBSRC | MultiMod, flexible management for multi-scale multi-approach models in biology | co-PI | 01/06/2016-31/05/2019. |
| EU Commission | COST action CHARME | co-I | 2016-2018 |
| BBSRC | UK Multi-Scale Biology Network | co-I | 06/2015-05/2018. |
| BBSRC | Software hardening and training in epigenetics and systems biology | co-I | 2015-2017. |
| MRC | Modification of the host lipidome by Rhinovirus infection | co-I | 03/07/2014-2018 |
| BBSRC CASE | Systems Pharmacology Models of Druggable Pharmaceutical Targets and Disease Mechanisms | PI | 31/03/2014-30/03/2018. |
| EU commission | Systems biology of pathways involving brain ageing (AgedBrainSYSBIO) | co-PI | 01/01/2013-30/06/2017 |
| BBSRC ISP | A systems approach to understanding lipid, Ca2+ and MAPK signalling networks | co-I | 01/04/2012-31/07/2017. |
| BBSRC | Linking data with Identifiers.org | co-I | 08/2013-11/2014 |
| EU commission | Infrastructure for Systems Biology Europe (ISBE) | co-I | 27/09/2012- |
| BBSRC BBR | BioModels Database, the comprehensive resource for computational models in Biology | PI | 01/08/2012-30/07/2015 |
| IMI-JU | Open PHACTS | co-I | 01/02/2012 |
| BBSRC | How do cells shape and interpret PIP3 signals | co-I | 01/05/2011-30/04/2016. |
| IMI-JU | Drug Discovery Model Repository (DDMoRe) | co-I | 01/03/2011-28/02/2016. |
| BBSRC | First COMBINE meeting: Bridging model structure, semantics and representation. | PI | 06/10/2010-09/10/2010. |
| NIH | Continued support and development of SBML | co-I | 01/09/2010-31/12/2012. |
| EU commission | Synaptic Systems: dissecting brain function in health and disease (SynSys) | co-I | 01/07/2010-30/06/2014. |
| EU Commission | ELIXIR technical feasibility study 13.3 | co-I | 01/03/2008-31/08/2009 |
| BBSHDRRC BBR | BioModels Database: a unified resource for Systems Biology models. | PI | 01/01/2008-31/12/2011 |
| NIH | Continued support and development of SBML | co-I | 01/09/2007-31/08/2010. |
| BBSRC | Interfacing standards and ontologies in Systems Biology. | co-PI | 01/04/2007-31/03/2011 |
| BBSRC | Software infrastructure to support the standard of model curation and annotation MIRIAM. | PI | 01/09/2006-31/08/2007 |
| NEDO | Development of The Systems Biology Graphical Notation, a standard graphical notation for diagrams of computational models in biology | co-PI | 01/11/2005-30/06/2008 |
| NIH | Continued support and development of SBML | co-I | 01/09/2005-31/01/2007 |
| EU commission | The European Membrane Protein Consortium (e-MeP) | co-I | 01/07/2004-31/03/2009. |
| ESF | The Meso-telencephalic Dopamine Consortium (DopaNet). | PI | 01/01/2003-31/12/2005. |
Community involvement and management of science |
|
Member of the editorial board
NPJ Systems Biology and applications (associate editor 2014-2018), PeerJ (2012-2014), BMC Systems Biology (2006-2018, associate editor 2008-2018).
Meeting organisation
EMBO meeting 2015 special interest symposium on epigenetics and cell fate, COMBINE 2013, COMBINE 2012, COMBINE 2011, COMBINE 2010, HARMONY 2012, HARMONY 2011, SBGN 4, SBGN 3.5, SBGN 3, SBGN 2.5, SBGN 2, SBGN 1, SBML hackathon 2009, SBML hackathon 2004.
Member of conference scientific committee
Joint SysMod 2018, Joint SysMod 2017, Joint SysMod 2016, Joint SysMod/NetBio 2016, ISMB/ECCB 2017, ISMB/ECCB 2015 (chair of the "systems" theme) BioNetVisa 2017, BioNetVisa 2016, BioNetVisa 2015, BioNetVisa 2014, FMMB 2014, CBIBM 2014, ICBO 2013, ICBO 2012, CIBB 2009, BioSysBio 2009, BioSysBio2008, ECCB 2008, ICSB 2016, ICSB 2014, ICSB 2010, ICSB 2008, ICSB 2006, CMSB 2008, CMSB 2005.
Standardisation editorial boards
Simulation Experiment Description Markup Language (2008-2013), Systems Biology Graphical Notation (2008-2012), Systems Biology Markup Language - SBML (2006-2008, 2011-2013, 2016-2018), Co-chair of the IUPHAR sub-committee on the nomenclature of nicotinic acetylcholine receptors.
Grant panels
Swiss National Fund's Sinergia (2016-2018), ERC Advanced Grants (2015-2018), MRC Biomedical Informatics Fellowship (2014), FRM Bioinformatics (2013, 2014), Forschungszentrum Juelich GmbH (2013), agreenskills (2013), BMBF eBio (2011), BBSRC TRDF (2010) and STRDF (2011), ANR SYSCOMM (2008, 2009), ANR/BBSRC Systems Biology (2007)
Steering committee
UK Multi-Scale Biology community network (2015-), AgedBrainSYSBIO (2013-2017),The European Membrane Protein Consortium - E-MeP (2004-2007)
Scientific advisory committees
Toulouse's Centre of Integrative Biology (2016-2018), Cochin Institute (2016-2018), COPASI BBR (2013-2018), Heidelberg's Centre for Organismal Studies (2013-2018), Montpellier's Pôle Biosanté Rabelais (2013-2018), labex EpiGenMed (2013-2018), BioPAX (2010-), German Virtual Liver Network (2010-2014), Research Centre of the Institut Curie (2009-2018), BBSRC Plant Models Portal (PLaSMo, 2008-2010), EU IP ENFIN (2005-2010), UK Quantitative Systems Pharmacology Network, AERES.
Expert groups
Science Europe “Multidisciplinary career paths” (2015), BBSRC “Digital Organisms” (2012), EU “Systems Biology for Medical Applications” (2007), Inserm “Tobacco: Understand the addiction to act” (2003)