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52

JEAN-LOUP FAULON


 

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

2015---     Senior Research Director (DR1) at MICALIS Institute. Head of the BioRetroSynth research team (~12 research staff).

2014---      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). 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.

 

 


Journal articles46 documents

  • Olivier Borkowski, Mathilde Koch, Agnes Zettor, Amir Pandi, Angelo Cardoso Batista, et al.. Large scale active-learning-guided exploration for in vitro protein production optimization. Nature Communications, Nature Publishing Group, 2020, 11 (1), pp.1872. ⟨10.1038/s41467-020-15798-5⟩. ⟨pasteur-02552065⟩
  • Sara Castaño-Cerezo, Mathieu Fournié, Philippe Urban, Jean-Loup Faulon, Gilles Truan. Development of a Biosensor for Detection of Benzoic Acid Derivatives in Saccharomyces cerevisiae. Frontiers in Bioengineering and Biotechnology, Frontiers, 2020, 7 (1), ⟨10.3389/fbioe.2019.00372⟩. ⟨hal-02905154⟩
  • Peter Voyvodic, Amir Pandi, Mathilde Koch, Ismael Conejero, Emmanuel Valjent, et al.. Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors. Nature Communications, Nature Publishing Group, 2019, 10 (1), ⟨10.1038/s41467-019-09722-9⟩. ⟨hal-02399479⟩
  • Amir Pandi, Ioana Grigoras, Olivier Borkowski, Jean-Loup Faulon. Optimizing Cell-Free Biosensors to Monitor Enzymatic Production. ACS Synthetic Biology, American Chemical Society, 2019, 8 (8), pp.1952-1957. ⟨10.1021/acssynbio.9b00160⟩. ⟨hal-02905163⟩
  • Adrian J. Jervis, Pablo Carbonell, Maria Vinaixa, Mark S. Dunstan, Katherine A. Hollywood, et al.. Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli. ACS Synthetic Biology, American Chemical Society, 2019, 8 (1), pp.127-136. ⟨10.1021/acssynbio.8b00398⟩. ⟨hal-02621980⟩
  • Manuel Salvador, Umar Abdulmutalib, Jaime Gonzalez, Juhyun Kim, Alex A Smith, et al.. Microbial genes for a circular and sustainable Bio-PET Economy.. Genes, MDPI, 2019, 10 (5), ⟨10.3390/genes10050373⟩. ⟨hal-02627201⟩
  • Amir Pandi, Ioana Grigoras, Olivier Borkowski, Jean-Loup Faulon. Optimizing cell-free biosensors to monitor enzymatic production.. ACS Synthetic Biology, American Chemical Society, 2019, 8 (8), pp.1952-1957. ⟨10.1021/acssynbio.9b00160⟩. ⟨hal-02625334⟩
  • Thomas Duigou, Melchior Du Lac, Pablo Carbonell, Jean-Loup Faulon. Retrorules: a database of reaction rules for engineering biology. Nucleic Acids Research, Oxford University Press, 2019, 47 (D1), pp.1-7. ⟨10.1093/nar/gky940⟩. ⟨hal-02619044⟩
  • Mathilde Koch, Amir Pandi, Olivier Borkowski, Angelo Cardoso Batista, Jean-Loup Faulon. Custom-made transcriptional biosensors for metabolic engineering.. Current Opinion in Biotechnology, Elsevier, 2019, 59, pp.78-84. ⟨10.1016/j.copbio.2019.02.016⟩. ⟨hal-02627127⟩
  • Mathilde Koch, Thomas Duigou, Jean-Loup Faulon. Reinforcement learning for bioretrosynthesis. ACS Synthetic Biology, American Chemical Society, 2019, 9 (1), pp.157-168. ⟨10.1021/acssynbio.9b00447⟩. ⟨hal-02905157⟩
  • Mathilde Koch, Amir Pandi, Olivier Borkowski, A.C. Batista, Jean-Loup Faulon. Custom-made transcriptional biosensors for metabolic engineering. Current Opinion in Biotechnology, Elsevier, 2019, 59, pp.78-84. ⟨10.1016/j.copbio.2019.02.016⟩. ⟨hal-02905165⟩
  • Pablo Carbonell, Jean-Loup Faulon, Rainer Breitling. Efficient learning in metabolic pathway designs through optimal assembling. IFAC-PapersOnLine, Elsevier, 2019, 52 (26), pp.7-12. ⟨10.1016/j.ifacol.2019.12.228⟩. ⟨hal-02905161⟩
  • Amir Pandi, Mathilde Koch, Peter Voyvodic, Paul Soudier, Jérôme Bonnet, et al.. Metabolic perceptrons for neural computing in biological systems. Nature Communications, Nature Publishing Group, 2019, 10 (1), ⟨10.1038/s41467-019-11889-0⟩. ⟨hal-02905160⟩
  • Amir Pandi, Mathilde Koch, Peter L. Voyvodic, Paul Soudier, Jérôme Bonnet, et al.. Metabolic perceptrons for neural computing in biological systems. Nature Communications, Nature Publishing Group, 2019, 10 (1), ⟨10.1038/s41467-019-11889-0⟩. ⟨hal-02275517⟩
  • Mathilde Koch, Amir Pandi, Baudoin Delepine, Jean-Loup Faulon. A dataset of small molecules triggering transcriptional and translational cellular responses. Data in Brief, Elsevier, 2018, 17, pp.1374-1378. ⟨10.1016/j.dib.2018.02.061⟩. ⟨hal-02622874⟩
  • Neil Swainston, Mark Dunstan, Adrian J. Jervis, Christopher J. Robinson, Pablo Carbonell, et al.. PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. Bioinformatics, Oxford University Press (OUP), 2018, 34 (13), pp.2327-2329. ⟨10.1093/bioinformatics/bty105⟩. ⟨hal-02622152⟩
  • Baudoin Delepine, Thomas Duigou, Pablo Carbonell, Jean-Loup Faulon. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, Elsevier, 2018, 45, pp.158-170. ⟨10.1016/j.ymben.2017.12.002⟩. ⟨hal-02625929⟩
  • Pablo Carbonell, Jerry Wong, Neil Swainston, Erika Takano, Nicholas J. Turner, et al.. Selenzyme: enzyme selection tool for pathway design. Bioinformatics, Oxford University Press (OUP), 2018, 34 (12), pp.2153-2154. ⟨10.1093/bioinformatics/bty065⟩. ⟨hal-02621189⟩
  • Mathilde Koch, Jean-Loup Faulon, Olivier Borkowski. Models for cell-free synthetic biology: Make prototyping easier, better, and faster. Frontiers in Bioengineering and Biotechnology, Frontiers, 2018, 6, pp.1-6. ⟨10.3389/fbioe.2018.00182⟩. ⟨hal-02621501⟩
  • Pablo Carbonell, Adrian J. Jervis, Christopher J. Robinson, Cunyu Yan, Mark Dunstan, et al.. An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals. Communications Biology, Nature Publishing Group, 2018, 1, ⟨10.1038/s42003-018-0076-9⟩. ⟨hal-02622177⟩
  • Heykel Trabelsi, Mathilde Koch, Jean-Loup Faulon. Building a minimal and generalizable model of transcription factor-based biosensors: Showcasing flavonoids. Biotechnology and Bioengineering, Wiley, 2018, 115 (9), pp.2292-2304. ⟨10.1002/bit.26726⟩. ⟨hal-02625459⟩
  • Mathilde Koch, Thomas Duigou, Pablo Carbonell, Jean-Loup Faulon. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, Chemistry Central Ltd. and BioMed Central, 2017, 9, pp.1-17. ⟨10.1186/s13321-017-0252-9⟩. ⟨hal-02623106⟩
  • Neil Swainston, Riza Batista Navarro, Pablo Carbonnell, Paul D. Dobson, Mark Dunstan, et al.. biochem4j: Integrated and extensible biochemical knowledge through graph databases. PLoS ONE, Public Library of Science, 2017, 12 (7), pp.e0179130. ⟨10.1371/journal.pone.0179130⟩. ⟨hal-01606003⟩
  • Jennifer Doudna, Roy Bar-Ziv, Johan Elf, Vincent Noireaux, Julien Berro, et al.. How will kinetics and thermodynamics inform our future efforts to understand and build biological systems?. Cell Systems, Elsevier, 2017, 4 (2), pp.144-146. ⟨10.1016/j.cels.2017.02.005⟩. ⟨hal-01530833⟩
  • Greg Wayne, Alex Graves, Demis Hassabis, Shambaditya Saha, Christoph A. Weber, et al.. Principles of Systems Biology, No. 11. Cell Systems, Elsevier, 2016, 3 (5), pp.406-410. ⟨hal-01531770⟩
  • Baudoin Delepine, Vincent Libis, Pablo Carbonell, Jean-Loup Faulon. SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic Acids Research, Oxford University Press, 2016, 44 (W1), pp.W226-W231. ⟨10.1093/nar/gkw305⟩. ⟨hal-02634192⟩
  • Pablo Carbonell, Andrew Currin, Mark Dunstan, Donal Fellows, Adrian J. Jervis, et al.. SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. Biochemical Society Transactions, Portland Press, 2016, 44 (3), pp.675-677. ⟨10.1042/BST20160009⟩. ⟨hal-01606550⟩
  • Joseph Mellor, Ioana Grigoras, Pablo Carbonell, Jean-Loup Faulon. Semisupervised Gaussian process for automated enzyme search. ACS Synthetic Biology, American Chemical Society, 2016, 5 (6), pp.518-528. ⟨10.1021/acssynbio.5b00294⟩. ⟨hal-02636917⟩
  • Vincent Libis, Baudoin Delepine, Jean-Loup Faulon. Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways. ACS Synthetic Biology, American Chemical Society, 2016, 5 (10), pp.1076-1085. ⟨10.1021/acssynbio.5b00225⟩. ⟨hal-01602231⟩
  • Rosalind A. Le Feuvre, Pablo Carbonell, Andrew Currin, Mark Dunstan, Donal Fellows, et al.. SYNBIOCHEM Synthetic Biology Research Centre, Manchester – A UK foundry for fine and speciality chemicals production. Synthetic and Systems Biotechnology, KeAi, 2016, 1 (4), pp.271-275. ⟨10.1016/j.synbio.2016.07.001⟩. ⟨hal-01602386⟩
  • Vincent Libis, Baudoin Delepine, Jean-Loup Faulon. Sensing new chemicals with bacterial transcription factors. Current Opinion in Microbiology, Elsevier, 2016, 33, pp.105-112. ⟨10.1016/j.mib.2016.07.006⟩. ⟨hal-01605043⟩
  • Pablo Carbonell, Abdullah Gok, Philip Shapira, Jean-Loup Faulon. Mapping the patent landscape of synthetic biology for fine chemical production pathways. Microbial Biotechnology, Wiley, 2016, 9 (5), pp.687-695. ⟨10.1111/1751-7915.12401⟩. ⟨hal-01607654⟩
  • Tamás Fehér, Vincent Libis, Pablo Carbonell, Jean-Loup Faulon. A sense of balance: experimental investigation and modeling of a malonyl-CoA sensor in Escherichia coli. Frontiers in Bioengineering and Biotechnology, Frontiers, 2015, 3, ⟨10.3389/fbioe.2015.0004⟩. ⟨hal-01601465⟩
  • Alfred Fernandez Castané, Tamás Fehér, Pablo Carbonell, Cyrille Pauthenier, Jean-Loup Faulon. Computer-aided design for metabolic engineering. Journal of Biotechnology, Elsevier, 2014, 192, pp.302-313. ⟨10.1016/j.jbiotec.2014.03.029⟩. ⟨hal-01606076⟩
  • Cyrille Pauthenier, Jean-Loup Faulon. PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling. Nucleic Acids Research, Oxford University Press, 2014, 42, pp.W205-W209. ⟨10.1093/nar/gku393⟩. ⟨hal-01607225⟩
  • Pablo Carbonell, Pierre Parutto, Joan Hérisson, Shashi Bhushan Pandit, Jean-Loup Faulon. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Research, Oxford University Press, 2014, 42, pp.W389-394. ⟨10.1093/nar/gku362⟩. ⟨hal-01608645⟩
  • Tamás Fehér, Anne-Gaëlle Planson, Pablo Carbonell, Alfred Fernández-Castané, Ioana Grigoras, et al.. Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.. Biotechnology Journal, Wiley-VCH Verlag, 2014, 9 (11), pp.1446-1457. ⟨10.1002/biot.201400055⟩. ⟨hal-02639677⟩
  • Pablo Carbonell, Pierre Parutto, Claire Baudier, Christophe Junot, Jean-Loup Faulon. Retropath: automated pipeline for embedded metabolic circuits. ACS Synthetic Biology, American Chemical Society, 2014, 3 (8), pp.565-577. ⟨10.1021/sb4001273⟩. ⟨hal-01608540⟩
  • Jaewok Joo, Steven J. Plimpton, Jean-Loup Faulon. Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κB signaling networks. BMC Systems Biology, BioMed Central, 2013, 7, ⟨10.1186/1752-0509-7-45⟩. ⟨hal-01601848⟩
  • Mohammad Mahdi Jaghoori, Sung-Shik T.Q. Jongmans, Frank de Boer, Julio Peironcely, Jean-Loup Faulon, et al.. PMG: Multi-core Metabolite Identification. Electronic Notes in Theoretical Computer Science, Elsevier, 2013, 299, pp.53-60. ⟨10.1016/j.entcs.2013.11.005⟩. ⟨hal-01601690⟩
  • Pablo Carbonell, Lars Carlsson, Jean-Loup Faulon. Stereo signature molecular descriptor. Journal of Chemical Information and Modeling, American Chemical Society, 2013, 53 (4), pp.887-897. ⟨10.1021/ci300584r⟩. ⟨hal-01601691⟩
  • Anne-Gaëlle Planson, Pablo Carbonell, Ioana Grigoras, Jean-Loup Faulon. A retrosynthetic biology approach to therapeutics: from conception to delivery. Current Opinion in Biotechnology, Elsevier, 2012, 23 (6), pp.948-956. ⟨10.1016/j.copbio.2012.03.009⟩. ⟨hal-02651873⟩
  • Anne-Gaëlle Planson, Pablo Carbonell, Elodie Paillard, Nicolas Pollet, Jean-Loup Faulon. Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnology and Bioengineering, Wiley, 2012, 109 (3), pp.846-850. ⟨10.1002/bit.24356⟩. ⟨hal-02941009⟩
  • Anne-Gaelle Planson, Pablo Carbonell, Elodie Paillard, Nicolas Pollet, Jean-Loup Faulon. Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnology and Bioengineering, Wiley, 2012, 109 (3), pp.846-850. ⟨10.1002/bit.24356⟩. ⟨hal-02341732⟩
  • Anne-Gaëlle Planson, Pablo Carbonell, Ioana Grigoras, Jean-Loup Faulon. Engineering antibiotic production and overcoming bacterial resistance. Biotechnology Journal, Wiley-VCH Verlag, 2011, 6 (7), pp.812-825. ⟨10.1002/biot.201100085⟩. ⟨hal-02647510⟩
  • Pablo Carbonell, Anne-Gaëlle Planson, Davide Fichera, Jean-Loup Faulon. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Systems Biology, BioMed Central, 2011, 5 (122), ⟨10.1186/1752-0509-5-122⟩. ⟨hal-02652758⟩

Book sections5 documents

  • Pablo Carbonell, Mathilde Koch, Thomas Duigou, Jean-Loup Faulon. Enzyme discovery: Enzyme selection and pathway design. Methods 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⟩. ⟨hal-02789661⟩
  • Pablo Carbonell, Baudoin Delepine, Jean-Loup Faulon. Extended metabolic space modeling. Synthetic metabolic pathways, 1671, Springer, 394 p., 2017, Methods in Molecular Biology, 978-1-4939-7295-1. ⟨hal-01603209⟩
  • Pablo Carbonell, Anne-Gaëlle Planson, Jean-Loup Faulon. Retrosynthetic design of heterologous pathways. Systems metabolic engineering, 985, Springer, 474 p., 2013, Methods in Molecular Biology, 978-1-62703-298-8. ⟨hal-01603740⟩
  • Pablo Carbonell, Anne-Gaëlle Planson, Jean-Loup Faulon. Retrosynthetic design of heterologous pathways 2013. Systems Metabolic Engineering, 985, Humana Press, 2013, Methods in Molecular Biology, 978-1-62703-298-8. ⟨10.1007/978-1-62703-299-5_9⟩. ⟨hal-01204312⟩
  • M. Misra, S. Martin, Jean-Loup Faulon. Graphs: flexible representations of molecular structures and biological networks. Computational Approaches in Cheminformatics and Bioinformatics, John Wiley and sons, 292 p., 2011, 978-0-470-38441-1. ⟨10.1002/9781118131411.ch6⟩. ⟨hal-01602043⟩

Reports1 document

  • Jacques Bittoun, Isabelle Bonnin, Jacques Capy, Gilles Chiocchia, Frédéric Dollé, et al.. Synthèse du livre blanc des sciences de la vie du département des sciences de la vie de l'université Paris Saclay. 2015. ⟨hal-02800505⟩