Jean-Loup Faulon
131
Documents
Présentation
**EDUCATION**
2007 Habilitation Chemistry, University of Strasbourg, France. Thesis title: The Signature Molecular Descriptor: Predicting Properties and Activities to Design Molecules and Biological Sequences.
1991 Ph.D. Computational Chemistry, Ecole des Mines, Paris, France. Thesis title: Prediction, Elucidation, and Molecular Modeling: Algorithms and Applications in Geochemistry.
1986 Master Computer Science, University of Paris VI, France. Thesis title: Hidden Surface Elimination.
1995 Engineering degree Computer Science, Institut d’Informatique d’Entreprise, Conservatoire National des Arts & Métiers, Paris, France.
1982 DEUG Chemistry, University of Dijon, France.
**RESEARCH, TEACHING AND ADMINISTRATIVE EXPERIENCE**
2022 ------ Senior Research Director (DREX) at MICALIS Institute. Head of the BioRetroSynth research team (~12 research staff).
2015-2022 Senior Research Director (DR1) at MICALIS Institute.
2014 ------- Addifilated Prof. Chair in Synthetic Biology and Systems Metabolic Engineering, School of Chemistry, The University of Manchester. SYNBIOCHEM cabinet member.
2010-2015 Director, Institute of Systems & Synthetic Biology (iSSB). iSSB is a CNRS research unit comprising 5 research teams, ~30 faculty and staff members and ~10 PhD students.
2010--- Head, Master in Systems & Synthtic Biology (mSSB). This master program has been ranked A+ by the French academic ranking agency (HCERES). The master has been running for 9 consecutive years and student have participated to the iGEM competition (gold medails in 2019, 2018, 2017, 2012, 2013, best model in 2012, best human practices in 2012 & 2013).
2009-2017 Consultant for Genopole ([www.genopole.fr](http://www.genopole.fr)). Advisor for the development of Synthetic Biology in Evry.
2008-2015 Full Professor, Biology Department, Évry University. Teaching Responsibility: bioinformatics, systems & synthetic biology, and metabolic engineering (undergraduate students first and 2nd-year graduate students).
Spring 2011 Visiting Scholar Institute for Pure and Applied Mathematics, UCLA, CA. Organized and chaired the long-term program « Navigating Chemical Compound Space for Materials and Bio Design ».
2007–2008 Director, Pretreatment Section, Deconstuction Division, Joint BioEnergy Institute, Emeryville, CA, USA. Research project: design of ionic liquids and cellulases for biofuel productions. Lead a group of 5 PhD staff scientists and post-docs (chemical engineers, analytical chemists, molecular biologists, and computational chemists).
2003–2008 Distinguished Member of the Systems Biology Dept., Sandia National Laboratories, Livermore, CA *(the distinguished scientist recognition is a peer-reviewed award given to the top 10% PhD employees).* Responsible of 9 research projects. Inference and dynamics of signaling and transcriptional networks (cf. MISL and GENET projects in funding sources lists). Prediction of protein-protein, enzyme-metabolite and drug-target interactions (GTL, PROTDESIGN and MLSC projects). Lead a group of 6 PhD staff scientists and post-docs in molecular biology, bioinformatics and computational biology.
1997–2003 Primary Member of Computational Biology Dept., Sandia National Laboratories *(25% of PhD staff scientists are primary members).* Research projects: structural biology (IBIG project), drug design and polymer design (MLSC, iQSAR and MICS projects). Lead a group of six polymer and materials staff scientists (ASCI project).
1995–1997 Senior Member of Computer-Aided Molecular Design group Sandia National Laboratories *(in 1995 I am one of the first non-US citizen to be hired by Sandia Labs on a tenured position).* Research projects: Structure and reaction network inference for hydrocarbon thermal cracking (funded by Chevron).
1993–1994 Research Associate in the Computer-Aided Molecular Design group at Sandia National Laboratories. Research: develop computational methods for molecular design and structure inference.
1991–1993 Post-doctoral Scientist in the Materials Science Dept. at Penn State Univ., PA, USA. Teaching: molecular modeling. Research: Molecular structure inference of natural products (lignin, humic substances).
1989–1991 Agent contractual, Ecole des Mines, Paris, France. Teaching: computer graphics, molecular modeling. Research: Molecular structure inference for petroleum precursors.
1985–1989 Adjunct Assistant Professor in Computer Science at the Conservatoire National Arts & Métiers, Paris, France. Teaching: computer graphics, computer systems, networks.
Publications
Galaxy-SynBioCAD — An Automated Pipeline for Synthetic Biology Design and EngineeringGlobal BioFoundries Alliance Meeting 2023 (GBA2023), Sep 2023, Copenaghen, Denmark
Communication dans un congrès
hal-04351679v1
|
|
Coupling retrosynthesis with automated in vitro and in vivo metabolic pathway engineeringBIOTRANS-2023, CBSO (Club Biocatalysis in Organic Synthesis), Jun 2023, La Rochelle, France
Communication dans un congrès
hal-04275856v1
|
|
Automated in vitro and in vivo metabolic pathway engineeringESAB WEBINAR - Biocatalysis meets Informatics, ESAB - European Society of Applied Biocatalysis, Aug 2023, Virtual, France
Communication dans un congrès
hal-04275883v1
|
|
in vitro and in vivo neural computations with metabolismAI, Engineering Biology & Beyond, The University of Edinburgh, Mar 2023, Edinburgh, United Kingdom
Communication dans un congrès
hal-04275865v1
|
|
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineeringIWBDA 14th International Workshop on Bio-Design Automation, Bio-Design Automation Consortium (BDAC), Oct 2022, Paris, France
Communication dans un congrès
hal-04275567v1
|
|
Hybrid models for neural computations with metabolismUniversity of Stuttgart seminatr series, University of Stuttgart, Jun 2022, Stuttgart, Germany
Communication dans un congrès
hal-04275845v1
|
|
Hybrid models enabling neural computation with metabolic networksSystem Biology Seminar Series, University of Stuttgart, Jun 2022, Stuttgart, Germany
Communication dans un congrès
hal-04275392v1
|
|
Artificial Metabolic NetworkSéminaire Centre de Biologie Structural, Centre de Biologie Structural, May 2022, Montpellier, France
Communication dans un congrès
hal-04275399v1
|
|
Artificial Metabolic Network for neural computation with metabolismAI-4-SynBio UK, Imperial College, Mar 2022, London, United Kingdom
Communication dans un congrès
hal-04275409v1
|
|
Artificial Metabolic NetworkAAAI Spring Symposium: Artificial Intelligence for Synthetic Biology, AAAI, Mar 2022, Stanford University (CA), United States
Communication dans un congrès
hal-04275418v1
|
|
Automated Pipeline for Synthetic Biology Design and EngineeringJBEI seminar series, JBEI (DOE), Oct 2022, Emeryville, CA, United States
Communication dans un congrès
hal-04275834v1
|
|
Biological Design and Engineering By and For machine LearningEngineering, Evolution & Design (SEED), AICHE, Jun 2021, Vitual, United States
Communication dans un congrès
hal-04275493v1
|
|
Synthetic Biology: past, present and futureBioket-2021, Bioket, Mar 2021, Lille, France
Communication dans un congrès
hal-04275511v1
|
|
Automated Workflows for Synthetic Biology and metabolic Engineering: the Galaxy-SynBioCAD PortalMicrobial Cell Factories Webinar Series, University of Manchester, Mar 2021, Manchester, United Kingdom
Communication dans un congrès
hal-04275504v1
|
|
Biocomputing with EnzymeFaulon JL, “Biocomputing with Enzyme”, International symposium on High Throughput Catalyst Design, HTCD-2021, HTCD, University of Lille, Jun 2021, Lille, France
Communication dans un congrès
hal-04275498v1
|
|
The Galaxy-SynBioCAD portal: tools and workflows for synthetic biology and metabolic engineeringJournées du PEPI IBIS 2021, Nov 2021, Toulouse, France
Communication dans un congrès
hal-04355490v1
|
|
Enzyme for BiocomputingSymposium « Chemistry goes Green », SANOFI, Sep 2020, Montpellier, France
Communication dans un congrès
hal-04275515v1
|
|
Intelligence Artificielle et BioSynthèseSéance Substances Naturelle, Académie nationale de Pharmacie, May 2020, Paris, France
Communication dans un congrès
hal-04275573v1
|
|
AI and Synthetic BiologyInvited Lecture EPFL, EPFL, Feb 2020, Lausane, Switzerland
Communication dans un congrès
hal-04275582v1
|
|
Machine Learning for and by Synthetic BiologyBeilstein Bozen Symposium, Beilstein Institute, Sep 2020, Rudesheime, Germany
Communication dans un congrès
hal-04275530v1
|
|
Design Automation Workflows for Synthetic Biology and Metabolic Engineering: The Galaxy SynBioCAD portalIWBDA, 12th International Workshop on Bio-Design Automation, Bio-Design Automation Consortium (BDAC), Aug 2020, Worcester, MA, United States
Communication dans un congrès
hal-04275555v1
|
|
A large-scale exploration of cell-free compositions to maximize protein production using reinforcement learningEMBO workshop “Creating is Understand-ing: Synthetic Biology Masters Complexity, EMBO, Sep 2019, Heildelberg, Germany
Communication dans un congrès
hal-04275652v1
|
|
Interfacing Machine Learning with Biological SystemsEMBO workshop “Creating is Under-standing: Synthetic Biology Masters Complexity”, EMBO, Sep 2019, Heidelberg, Germany
Communication dans un congrès
hal-04275642v1
|
|
Keynote lecture #2: Retrosynthesis and computer-aided design of metabolic pathwaysEMBO course Synthetic Biology in Action: Bridging Natural/NonNatural, EMBO, Sep 2019, Heidelberg, Germany
Communication dans un congrès
hal-04275688v1
|
|
Machine Learning in Synthetic Biology2nd Annual Synthetic Biology Congress, EBRC, Nov 2019, London, United Kingdom
Communication dans un congrès
hal-04275616v1
|
|
Design-Build-Test-Learn Paradigm in Synthetic BiologyJOBIM conference, JOBIM, Jul 2019, Nante, France
Communication dans un congrès
hal-04275697v1
|
|
Metabolic PerceptronSynthetic Biology UK 2019, Dec 2019, Warwick, UK, United Kingdom
Communication dans un congrès
hal-04275593v1
|
|
OptBioDes: an optimal design for the synbio toolchainIWBDA 11th In-ternational Workshop on Bio-Design Automation, Bio-Design Automation Consortium (BDAC), Jul 2019, Cambridge, UK, United Kingdom
Communication dans un congrès
hal-04275710v1
|
|
Retrosynthèse en BiologieColloque Chimie et biologie de synthèse : les applications, Maison de la Chimie, Feb 2018, Paris, France
Communication dans un congrès
hal-04275756v1
|
|
Retrosynthesis to design and engineer metabolic pathways BiologyCongress SCF 2018, SCF, Jul 2018, Montpellier, France
Communication dans un congrès
hal-04275730v1
|
|
Standard in Synthetic BiologyEU-US High Level Expert workshop on Biotechnology, Apr 2018, Bruxelles, Belgium
Communication dans un congrès
hal-04275741v1
|
|
Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensorsCongrés GDR BioSynSys, GDG BioSynSys, Oct 2018, Toulouse, France
Communication dans un congrès
hal-04275767v1
|
|
Microbial Biotechnology12th CeBiTec-Symposium, CeBiTec, Mar 2018, Bielefeld, Germany
Communication dans un congrès
hal-04275746v1
|
|
The Microbial Biotechnology ELIXIR communityAthens ELIXIR workshop, ELIXIR, Sep 2018, Athens, Greece
Communication dans un congrès
hal-04275722v1
|
|
Metabolic engineering for Natural ProductsIUPHAR Natural Products Meeting, IUPHAR, Apr 2018, Paris, France
Communication dans un congrès
hal-04275735v1
|
|
Cell-Free Biosensors and AI integrationCell-Free Gene Expression, 2433, Springer US, pp.303-323, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1998-8_19⟩
Chapitre d'ouvrage
hal-03545753v1
|
Cell-Free Biosensors and AI IntegrationCell-Free Gene Expression, 2433, Springer US, pp.303-323, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1998-8_19⟩
Chapitre d'ouvrage
hal-04275373v1
|
|
|
Cell-Free Biosensors and AI IntegrationAshty S. Karim; Michael C. Jewett. Cell-Free Gene Expression. Methods and Protocols, 2433, Springer US, pp.303-323, 2022, Methods in Molecular Biology, 978-1-0716-1997-1. ⟨10.1007/978-1-0716-1998-8_19⟩
Chapitre d'ouvrage
hal-03649323v1
|
Synthetic Biology at the Hand of Cell-Free SystemsAdvances in Synthetic Biology, Springer Singapore, pp. 275-288, 2020, ⟨10.1007/978-981-15-0081-7_16⟩
Chapitre d'ouvrage
hal-03852064v1
|
|
Enzyme discovery: Enzyme selection and pathway designMethods in Enzymology, 608, Elsevier Academic Press Inc., pp.25, 2018, Methods in Enzymology, 978-0-12-815148-8. ⟨10.1016/bs.mie.2018.04.005⟩
Chapitre d'ouvrage
hal-02789661v1
|
|
Enzyme Discovery: Enzyme Selection and Pathway DesignEnzymes in Synthetic Biology, 608, Elsevier, pp.3-27, 2018, Methods in Enzymology, ⟨10.1016/bs.mie.2018.04.005⟩
Chapitre d'ouvrage
hal-04275379v1
|
|
|
Extended metabolic space modelingSynthetic metabolic pathways, 1671, Springer, 394 p., 2017, Methods in Molecular Biology, 978-1-4939-7295-1
Chapitre d'ouvrage
hal-01603209v1
|
Retrosynthetic design of heterologous pathways 2013Systems Metabolic Engineering, 985, Humana Press, 2013, Methods in Molecular Biology, 978-1-62703-298-8. ⟨10.1007/978-1-62703-299-5_9⟩
Chapitre d'ouvrage
hal-01204312v1
|
|
|
Retrosynthetic design of heterologous pathwaysSystems metabolic engineering, 985, Springer, 474 p., 2013, Methods in Molecular Biology, 978-1-62703-298-8
Chapitre d'ouvrage
hal-01603740v1
|
Graphs: flexible representations of molecular structures and biological networksComputational Approaches in Cheminformatics and Bioinformatics, John Wiley and sons, 292 p., 2011, 978-0-470-38441-1. ⟨10.1002/9781118131411.ch6⟩
Chapitre d'ouvrage
hal-01602043v1
|
|
Artificial Metabolic Networks: enabling neural computation with metabolic networks2022
Pré-publication, Document de travail
hal-03613655v2
|
|
IBISBA-FR : Une infrastructure en soutien au développement de la biotechnologie industrielle comme technologie clef pour l’industrie du futur et pour accompagner la bioéconomie et l’économie circulaireINRAE; CNRS; CEA; INSA Toulouse; Université de nantes; Aix-Marseille Université (AMU). 2021
Rapport
hal-03153762v1
|
Synthèse du livre blanc des sciences de la vie du département des sciences de la vie de l'université Paris Saclay[0] 2015
Rapport
hal-02800505v1
|