Access content directly

Jean-Loup Faulon

132
Documents

Presentation

**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

Image document

A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

Léon Faure , Bastien Mollet , Wolfram Liebermeister , Jean-Loup Faulon
Nature Communications, 2023, 14, pp.4669. ⟨10.1038/s41467-023-40380-0⟩
Journal articles hal-04178761v1
Image document

Cell-Free protein synthesis from exonuclease-deficient cellular extracts utilizing linear DNA templates

Mahnaz Sabeti Azad , Angelo Cardoso Batista , Jean-Loup Faulon , Chase L Beisel , Jérôme Bonnet
Journal of visualized experiments : JoVE, In press, ⟨10.3791/64236⟩
Journal articles hal-03748754v1
Image document

A versatile active learning workflow for optimization of genetic and metabolic networks

Amir Pandi , Christoph Diehl , Ali Yazdizadeh Kharrazi , Scott A Scholz , Elizaveta Bobkova
Nature Communications, 2022, 13 (1), pp.3876. ⟨10.1038/s41467-022-31245-z⟩
Journal articles hal-04099006v1

Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts

Angelo Cardoso Batista , Antoine Levrier , Paul Soudier , Peter Voyvodic , Tatjana Achmedov
ACS Synthetic Biology, 2022, 11 (2), pp 732-746. ⟨10.1021/acssynbio.1c00448⟩
Journal articles hal-04275284v1

Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts

Angelo Cardoso Batista , Antoine Levrier , Paul Soudier , Peter Voyvodic , Tatjana Achmedov
ACS Synthetic Biology, 2022, 11 (2), pp. 732-746. ⟨10.1021/acssynbio.1c00448⟩
Journal articles hal-03796457v1
Image document

The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Joan Hérisson , Thomas Duigou , Melchior Du Lac , Kenza Bazi-Kabbaj , Mahnaz Sabeti Azad
Nature Communications, 2022, 13 (1), pp.5082. ⟨10.1038/s41467-022-32661-x⟩
Journal articles hal-03649340v2

A versatile active learning workflow for optimization of genetic and metabolic networks

Amir Pandi , Christoph Diehl , Ali Yazdizadeh Kharrazi , Scott Scholz , Elizaveta Bobkova
Nature Communications, 2022, 13 (1), pp 3876. ⟨10.1038/s41467-022-31245-z⟩
Journal articles hal-04275269v1

Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates

Mahnaz Sabeti Azad , Angelo Cardoso Batista , Jean-Loup Faulon , Chase Beisel , Jerome Bonnet
Journal of visualized experiments : JoVE, 2022, 186, ⟨10.3791/64236⟩
Journal articles hal-04275276v1
Image document

PeroxiHUB : a modular cell-free biosensing platform using H2O2 as signal integrator

Paul Soudier , Ana Zúñiga , Thomas Duigou , Peter Voyvodic , Kenza Bazi-Kabbaj
ACS Synthetic Biology, 2022, 11 (8), pp 2578-2588. ⟨10.1021/acssynbio.2c00138⟩
Journal articles hal-03649349v2

In silico, in vitro, and in vivo machine learning in synthetic biology and metabolic engineering

Jean-Loup Faulon , Léon Faure
Current Opinion in Chemical Biology, 2021, 65, pp. 85-92. ⟨10.1016/j.cbpa.2021.06.002⟩
Journal articles hal-04275366v1

Optimising protein synthesis in cell‐free systems, a review

Angelo Batista , Paul Soudier , Manish Kushwaha , Jean‐loup Faulon
Engineering Biology, 2021, 5 (1), pp. 10-19. ⟨10.1049/enb2.12004⟩
Journal articles hal-04275290v1
Image document

Optimising protein synthesis in cell‐free systems, a review

Angelo C Batista , Paul Soudier , Manish Kushwaha , Jean‐loup Faulon
Engineering Biology, 2021, 5 (1), pp.10-19. ⟨10.1049/enb2.12004⟩
Journal articles hal-03545761v1
Image document

Differentially optimized cell-free buffer enables robust expression from unprotected linear DNA in exonuclease-deficient extracts

Angelo Cardoso Batista , Antoine Levrier , Paul Soudier , Peter L Voyvodic , Tatjana Achmedov
ACS Synthetic Biology, 2021, pp.acssynbio.1c00448. ⟨10.1101/2021.09.07.459228⟩
Journal articles hal-03545788v1
Image document

Development of a Biosensor for Detection of Benzoic Acid Derivatives in Saccharomyces cerevisiae

Sara Castaño-Cerezo , Mathieu Fournié , Philippe Urban , Jean-Loup Faulon , Gilles Truan
Frontiers in Bioengineering and Biotechnology, 2020, 7 (1), ⟨10.3389/fbioe.2019.00372⟩
Journal articles hal-02905154v1

Reinforcement Learning for Bioretrosynthesis

Mathilde Koch , Thomas Duigou , Jean-Loup Faulon
ACS Synthetic Biology, 2020, 9 (1), pp. 157-168. ⟨10.1021/acssynbio.9b00447⟩
Journal articles hal-04275305v1

Large scale active-learning-guided exploration for in vitro protein production optimization

Olivier Borkowski , Mathilde Koch , Agnès Zettor , Amir Pandi , Angelo Cardoso Batista
Nature Communications, 2020, 11 (1), pp. 1872. ⟨10.1038/s41467-020-15798-5⟩
Journal articles hal-04275293v1
Image document

Large scale active-learning-guided exploration for in vitro protein production optimization

Olivier Borkowski , Mathilde Koch , Agnes Zettor , Amir Pandi , Angelo Cardoso Batista
Nature Communications, 2020, 11 (1), pp.1872. ⟨10.1038/s41467-020-15798-5⟩
Journal articles pasteur-02552065v1

Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol

Mark Dunstan , Christopher Robinson , Adrian Jervis , Cunyu Yan , Pablo Carbonell
ACS Synthetic Biology, 2020, 5 (1), pp.ysaa012. ⟨10.1093/synbio/ysaa012⟩
Journal articles hal-04275306v1

Development of a Biosensor for Detection of Benzoic Acid Derivatives in Saccharomyces cerevisiae

Sara Castaño-Cerezo , Mathieu Fournié , Philippe Urban , Jean-Loup Faulon , Gilles Truan
Frontiers in Bioengineering and Biotechnology, 2020, 7 (7), pp.372. ⟨10.3389/fbioe.2019.00372⟩
Journal articles hal-04275297v1
Image document

Metabolic perceptrons for neural computing in biological systems

Amir Pandi , Mathilde Koch , Peter L. Voyvodic , Paul Soudier , Jérôme Bonnet
Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-11889-0⟩
Journal articles hal-02275517v1

Custom-made transcriptional biosensors for metabolic engineering

Mathilde Koch , Amir Pandi , Olivier Borkowski , A.C. Batista , Jean-Loup Faulon
Current Opinion in Biotechnology, 2019, 59, pp. 78-84. ⟨10.1016/j.copbio.2019.02.016⟩
Journal articles hal-04275369v1
Image document

Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors

Peter Voyvodic , Amir Pandi , Mathilde Koch , Ismael Conejero , Emmanuel Valjent
Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-09722-9⟩
Journal articles hal-02399479v1

Optimizing Cell-Free Biosensors to Monitor Enzymatic Production

Amir Pandi , Ioana Grigoras , Olivier Borkowski , Jean-Loup Faulon
ACS Synthetic Biology, 2019, 8 (8), pp. 1952-1957. ⟨10.1021/acssynbio.9b00160⟩
Journal articles hal-04275316v1

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli

Adrian J. Jervis , Pablo Carbonell , Maria Vinaixa , Mark S. Dunstan , Katherine A. Hollywood
ACS Synthetic Biology, 2019, 8 (1), pp.127-136. ⟨10.1021/acssynbio.8b00398⟩
Journal articles hal-02621980v1

Reinforcement learning for bioretrosynthesis

Mathilde Koch , Thomas Duigou , Jean-Loup Faulon
ACS Synthetic Biology, 2019, 9 (1), pp.157-168. ⟨10.1021/acssynbio.9b00447⟩
Journal articles hal-02905157v1
Image document

Microbial genes for a circular and sustainable Bio-PET Economy.

Manuel Salvador , Umar Abdulmutalib , Jaime Gonzalez , Juhyun Kim , Alex A Smith
Genes, 2019, 10 (5), ⟨10.3390/genes10050373⟩
Journal articles hal-02627201v1

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli

Adrian Jervis , Pablo Carbonell , Maria Vinaixa , Mark Dunstan , Katherine Hollywood
ACS Synthetic Biology, 2019, 8 (1), pp. 127-136. ⟨10.1021/acssynbio.8b00398⟩
Journal articles hal-04275329v1

Metabolic perceptrons for neural computing in biological systems

Amir Pandi , Mathilde Koch , Peter Voyvodic , Paul Soudier , Jerome Bonnet
Nature Communications, 2019, 10 (1), pp 3880. ⟨10.1038/s41467-019-11889-0⟩
Journal articles hal-04275311v1

RetroRules: a database of reaction rules for engineering biology

Thomas Duigou , Melchior Du Lac , Pablo Carbonell , Jean-Loup Faulon
Nucleic Acids Research, 2019, 47 (D1), pp.D1229-D1235. ⟨10.1093/nar/gky940⟩
Journal articles hal-04275325v1
Image document

Retrorules: a database of reaction rules for engineering biology

Thomas Duigou , Melchior Du Lac , Pablo Carbonell , Jean-Loup Faulon
Nucleic Acids Research, 2019, 47 (D1), pp.1-7. ⟨10.1093/nar/gky940⟩
Journal articles hal-02619044v1

Optimizing cell-free biosensors to monitor enzymatic production.

Amir Pandi , Ioana Grigoras , Olivier Borkowski , Jean-Loup Faulon
ACS Synthetic Biology, 2019, 8 (8), pp.1952-1957. ⟨10.1021/acssynbio.9b00160⟩
Journal articles hal-02625334v1

Efficient learning in metabolic pathway designs through optimal assembling

Pablo Carbonell , Jean-Loup Faulon , Rainer Breitling
IFAC-PapersOnLine, 2019, 52 (26), pp. 7-12. ⟨10.1016/j.ifacol.2019.12.228⟩
Journal articles hal-04275313v1

Microbial Genes for a Circular and Sustainable Bio-PET Economy

Manuel Salvador , Umar Abdulmutalib , Jaime Gonzalez , Juhyun Kim , Alex Smith
Genes, 2019, 10 (5), pp. 373. ⟨10.3390/genes10050373⟩
Journal articles hal-04275328v1

Efficient learning in metabolic pathway designs through optimal assembling

Pablo Carbonell , Jean-Loup Faulon , Rainer Breitling
IFAC-PapersOnLine, 2019, 52 (26), pp.7-12. ⟨10.1016/j.ifacol.2019.12.228⟩
Journal articles hal-02905161v1

Custom-made transcriptional biosensors for metabolic engineering.

Mathilde Koch , Amir Pandi , Olivier Borkowski , Angelo Cardoso Batista , Jean-Loup Faulon
Current Opinion in Biotechnology, 2019, 59, pp.78-84. ⟨10.1016/j.copbio.2019.02.016⟩
Journal articles hal-02627127v1

Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors

Peter Voyvodic , Amir Pandi , Mathilde Koch , Ismael Conejero , Emmanuel Valjent
Nature Communications, 2019, 10 (1), pp. 1697. ⟨10.1038/s41467-019-09722-9⟩
Journal articles hal-04275317v1
Image document

Selenzyme: enzyme selection tool for pathway design

Pablo Carbonell , Jerry Wong , Neil Swainston , Erika Takano , Nicholas J. Turner
Bioinformatics, 2018, 34 (12), pp.2153-2154. ⟨10.1093/bioinformatics/bty065⟩
Journal articles hal-02621189v1

Selenzyme: enzyme selection tool for pathway design

Pablo Carbonell , Jerry Wong , Neil Swainston , Eriko Takano , Nicholas Turner
Bioinformatics, 2018, 34 (12), pp. 2153-2154. ⟨10.1093/bioinformatics/bty065⟩
Journal articles hal-04275348v1

Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster

Mathilde Koch , Jean-Loup Faulon , Olivier Borkowski
Frontiers in Bioengineering and Biotechnology, 2018, 6 (182), ⟨10.3389/fbioe.2018.00182⟩
Journal articles hal-04275331v1

Building a minimal and generalizable model of transcription factor-based biosensors: Showcasing flavonoids

Heykel Trabelsi , Mathilde Koch , Jean-Loup Faulon
Biotechnology and Bioengineering, 2018, 115 (9), pp.2292-2304. ⟨10.1002/bit.26726⟩
Journal articles hal-02625459v1

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals

Pablo Carbonell , Adrian Jervis , Christopher Robinson , Cunyu Yan , Mark Dunstan
Communications Biology, 2018, 1, pp. 66. ⟨10.1038/s42003-018-0076-9⟩
Journal articles hal-04275335v1
Image document

RetroPath2.0: A retrosynthesis workflow for metabolic engineers

Baudoin Delepine , Thomas Duigou , Pablo Carbonell , Jean-Loup Faulon
Metabolic Engineering, 2018, 45, pp.158-170. ⟨10.1016/j.ymben.2017.12.002⟩
Journal articles hal-02625929v1

PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts

Neil Swainston , Mark Dunstan , Adrian Jervis , Christopher Robinson , Pablo Carbonell
Bioinformatics, 2018, 34 (13), pp. 2327-2329. ⟨10.1093/bioinformatics/bty105⟩
Journal articles hal-04275350v1
Image document

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals

Pablo Carbonell , Adrian J. Jervis , Christopher J. Robinson , Cunyu Yan , Mark Dunstan
Communications Biology, 2018, 1, ⟨10.1038/s42003-018-0076-9⟩
Journal articles hal-02622177v1
Image document

Models for cell-free synthetic biology: Make prototyping easier, better, and faster

Mathilde Koch , Jean-Loup Faulon , Olivier Borkowski
Frontiers in Bioengineering and Biotechnology, 2018, 6, pp.1-6. ⟨10.3389/fbioe.2018.00182⟩
Journal articles hal-02621501v1

PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts

Neil Swainston , Mark Dunstan , Adrian J. Jervis , Christopher J. Robinson , Pablo Carbonell
Bioinformatics, 2018, 34 (13), pp.2327-2329. ⟨10.1093/bioinformatics/bty105⟩
Journal articles hal-02622152v1

Building a minimal and generalizable model of transcription factor–based biosensors: Showcasing flavonoids

Heykel Trabelsi , Mathilde Koch , Jean‐loup Faulon
Biotechnology and Bioengineering, 2018, 115 (9), pp. 2292-2304. ⟨10.1002/bit.26726⟩
Journal articles hal-04275343v1
Image document

A dataset of small molecules triggering transcriptional and translational cellular responses

Mathilde Koch , Amir Pandi , Baudoin Delepine , Jean-Loup Faulon
Data in Brief, 2018, 17, pp.1374-1378. ⟨10.1016/j.dib.2018.02.061⟩
Journal articles hal-02622874v1
Image document

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Mathilde Koch , Thomas Duigou , Pablo Carbonell , Jean-Loup Faulon
Journal of Cheminformatics, 2017, 9, pp.1-17. ⟨10.1186/s13321-017-0252-9⟩
Journal articles hal-02623106v1
Image document

biochem4j: Integrated and extensible biochemical knowledge through graph databases

Neil Swainston , Riza Batista Navarro , Pablo Carbonnell , Paul D. Dobson , Mark Dunstan
PLoS ONE, 2017, 12 (7), pp.e0179130. ⟨10.1371/journal.pone.0179130⟩
Journal articles hal-01606003v1

How will kinetics and thermodynamics inform our future efforts to understand and build biological systems?

Jennifer Doudna , Roy Bar-Ziv , Johan Elf , Vincent Noireaux , Julien Berro
Cell Systems, 2017, 4 (2), pp.144-146. ⟨10.1016/j.cels.2017.02.005⟩
Journal articles hal-01530833v1

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Mathilde Koch , Thomas Duigou , Pablo Carbonell , Jean-Loup Faulon
Journal of Cheminformatics, 2017, 9 (1), pp.64. ⟨10.1186/s13321-017-0252-9⟩
Journal articles hal-04275352v1

Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways

Vincent Libis , Baudoin Delepine , Jean-Loup Faulon
ACS Synthetic Biology, 2016, 5 (10), pp.1076-1085. ⟨10.1021/acssynbio.5b00225⟩
Journal articles hal-01602231v1
Image document

Mapping the patent landscape of synthetic biology for fine chemical production pathways

Pablo Carbonell , Abdullah Gok , Philip Shapira , Jean-Loup Faulon
Microbial Biotechnology, 2016, 9 (5), pp.687-695. ⟨10.1111/1751-7915.12401⟩
Journal articles hal-01607654v1

SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals

Pablo Carbonell , Andrew Currin , Mark Dunstan , Donal Fellows , Adrian J. Jervis
Biochemical Society Transactions, 2016, 44 (3), pp.675-677. ⟨10.1042/BST20160009⟩
Journal articles hal-01606550v1

Semisupervised Gaussian process for automated enzyme search

Joseph Mellor , Ioana Grigoras , Pablo Carbonell , Jean-Loup Faulon
ACS Synthetic Biology, 2016, 5 (6), pp.518-528. ⟨10.1021/acssynbio.5b00294⟩
Journal articles hal-02636917v1

Sensing new chemicals with bacterial transcription factors

Vincent Libis , Baudoin Delepine , Jean-Loup Faulon
Current Opinion in Microbiology, 2016, 33, pp.105-112. ⟨10.1016/j.mib.2016.07.006⟩
Journal articles hal-01605043v1
Image document

SYNBIOCHEM Synthetic Biology Research Centre, Manchester – A UK foundry for fine and speciality chemicals production

Rosalind A. Le Feuvre , Pablo Carbonell , Andrew Currin , Mark Dunstan , Donal Fellows
Synthetic and Systems Biotechnology, 2016, 1 (4), pp.271-275. ⟨10.1016/j.synbio.2016.07.001⟩
Journal articles hal-01602386v1
Image document

SensiPath: computer-aided design of sensing-enabling metabolic pathways

Baudoin Delepine , Vincent Libis , Pablo Carbonell , Jean-Loup Faulon
Nucleic Acids Research, 2016, 44 (W1), pp.W226-W231. ⟨10.1093/nar/gkw305⟩
Journal articles hal-02634192v1

Principles of Systems Biology, No. 11

Greg Wayne , Alex Graves , Demis Hassabis , Shambaditya Saha , Christoph A. Weber
Cell Systems, 2016, 3 (5), pp.406-410
Journal articles hal-01531770v1
Image document

A sense of balance: experimental investigation and modeling of a malonyl-CoA sensor in Escherichia coli

Tamás Fehér , Vincent Libis , Pablo Carbonell , Jean-Loup Faulon
Frontiers in Bioengineering and Biotechnology, 2015, 3, ⟨10.3389/fbioe.2015.0004⟩
Journal articles hal-01601465v1

Computer-aided design for metabolic engineering

Alfred Fernandez Castané , Tamás Fehér , Pablo Carbonell , Cyrille Pauthenier , Jean-Loup Faulon
Journal of Biotechnology, 2014, 192, pp.302-313. ⟨10.1016/j.jbiotec.2014.03.029⟩
Journal articles hal-01606076v1
Image document

XTMS: pathway design in an eXTended metabolic space

Pablo Carbonell , Pierre Parutto , Joan Hérisson , Shashi Bhushan Pandit , Jean-Loup Faulon
Nucleic Acids Research, 2014, 42, pp.W389-394. ⟨10.1093/nar/gku362⟩
Journal articles hal-01608645v1
Image document

Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.

Tamás Fehér , Anne-Gaëlle Planson , Pablo Carbonell , Alfred Fernández-Castané , Ioana Grigoras
Biotechnology Journal, 2014, 9 (11), pp.1446-1457. ⟨10.1002/biot.201400055⟩
Journal articles hal-02639677v1

Retropath: automated pipeline for embedded metabolic circuits

Pablo Carbonell , Pierre Parutto , Claire Baudier , Christophe Junot , Jean-Loup Faulon
ACS Synthetic Biology, 2014, 3 (8), pp.565-577. ⟨10.1021/sb4001273⟩
Journal articles hal-01608540v1
Image document

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling

Cyrille Pauthenier , Jean-Loup Faulon
Nucleic Acids Research, 2014, 42, pp.W205-W209. ⟨10.1093/nar/gku393⟩
Journal articles hal-01607225v1
Image document

PMG: Multi-core Metabolite Identification

Mohammad Mahdi Jaghoori , Sung-Shik T.Q. Jongmans , Frank de Boer , Julio Peironcely , Jean-Loup Faulon
Electronic Notes in Theoretical Computer Science, 2013, 299, pp.53-60. ⟨10.1016/j.entcs.2013.11.005⟩
Journal articles hal-01601690v1

Stereo signature molecular descriptor

Pablo Carbonell , Lars Carlsson , Jean-Loup Faulon
Journal of Chemical Information and Modeling, 2013, 53 (4), pp.887-897. ⟨10.1021/ci300584r⟩
Journal articles hal-01601691v1
Image document

Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κB signaling networks

Jaewok Joo , Steven J. Plimpton , Jean-Loup Faulon
BMC Systems Biology, 2013, 7, ⟨10.1186/1752-0509-7-45⟩
Journal articles hal-01601848v1

Compound toxicity screening and structure-activity relationship modeling in Escherichia coli

Anne-Gaëlle Planson , Pablo Carbonell , Elodie Paillard , Nicolas Pollet , Jean-Loup Faulon
Biotechnology and Bioengineering, 2012, 109 (3), pp.846-850. ⟨10.1002/bit.24356⟩
Journal articles hal-02941009v1

Compound toxicity screening and structure-activity relationship modeling in Escherichia coli

Anne-Gaelle Planson , Pablo Carbonell , Elodie Paillard , Nicolas Pollet , Jean-Loup Faulon
Biotechnology and Bioengineering, 2012, 109 (3), pp.846-850. ⟨10.1002/bit.24356⟩
Journal articles hal-02341732v1
Image document

A retrosynthetic biology approach to therapeutics: from conception to delivery

Anne-Gaëlle Planson , Pablo Carbonell , Ioana Grigoras , Jean-Loup Faulon
Current Opinion in Biotechnology, 2012, 23 (6), pp.948-956. ⟨10.1016/j.copbio.2012.03.009⟩
Journal articles hal-02651873v1
Image document

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

Pablo Carbonell , Anne-Gaëlle Planson , Davide Fichera , Jean-Loup Faulon
BMC Systems Biology, 2011, 5 (122), ⟨10.1186/1752-0509-5-122⟩
Journal articles hal-02652758v1

Engineering antibiotic production and overcoming bacterial resistance

Anne-Gaëlle Planson , Pablo Carbonell , Ioana Grigoras , Jean-Loup Faulon
Biotechnology Journal, 2011, 6 (7), pp.812-825. ⟨10.1002/biot.201100085⟩
Journal articles hal-02647510v1

Galaxy-SynBioCAD — An Automated Pipeline for Synthetic Biology Design and Engineering

Joan Hérisson , Pablo Carbonell , Jean-Loup Faulon , Thomas Duigou
Global BioFoundries Alliance Meeting 2023 (GBA2023), Sep 2023, Copenaghen, Denmark
Conference papers hal-04351679v1

Coupling retrosynthesis with automated in vitro and in vivo metabolic pathway engineering

Jean-Loup Faulon
BIOTRANS-2023, CBSO (Club Biocatalysis in Organic Synthesis), Jun 2023, La Rochelle, France
Conference papers hal-04275856v1

Automated in vitro and in vivo metabolic pathway engineering

Jean-Loup Faulon
ESAB WEBINAR - Biocatalysis meets Informatics, ESAB - European Society of Applied Biocatalysis, Aug 2023, Virtual, France
Conference papers hal-04275883v1

in vitro and in vivo neural computations with metabolism

Jean-Loup Faulon
AI, Engineering Biology & Beyond, The University of Edinburgh, Mar 2023, Edinburgh, United Kingdom
Conference papers hal-04275865v1

Hybrid models enabling neural computation with metabolic networks

Jean-Loup Faulon
System Biology Seminar Series, University of Stuttgart, Jun 2022, Stuttgart, Germany
Conference papers hal-04275392v1

Hybrid models for neural computations with metabolism

Léon Faure , Bastien Mollet , Wolfram Liebermeister , Jean-Loup Faulon
University of Stuttgart seminatr series, University of Stuttgart, Jun 2022, Stuttgart, Germany
Conference papers hal-04275845v1

The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Joan Hérisson , Thomas Duigou , Jean-Loup Faulon
IWBDA 14th International Workshop on Bio-Design Automation, Bio-Design Automation Consortium (BDAC), Oct 2022, Paris, France
Conference papers hal-04275567v1

Artificial Metabolic Network

Jean-Loup Faulon
Séminaire Centre de Biologie Structural, Centre de Biologie Structural, May 2022, Montpellier, France
Conference papers hal-04275399v1

Artificial Metabolic Network for neural computation with metabolism

Léon Faure , Jean-Loup Faulon , Bastien Mollet
AI-4-SynBio UK, Imperial College, Mar 2022, London, United Kingdom
Conference papers hal-04275409v1

Artificial Metabolic Network

Léon Faure , Bastien Mollet , Jean-Loup Faulon
AAAI Spring Symposium: Artificial Intelligence for Synthetic Biology, AAAI, Mar 2022, Stanford University (CA), United States
Conference papers hal-04275418v1

Automated Pipeline for Synthetic Biology Design and Engineering

Jean-Loup Faulon , Thomas Duigou , Joan Hérisson
JBEI seminar series, JBEI (DOE), Oct 2022, Emeryville, CA, United States
Conference papers hal-04275834v1

Synthetic Biology: past, present and future

Jean-Loup Faulon
Bioket-2021, Bioket, Mar 2021, Lille, France
Conference papers hal-04275511v1

Biological Design and Engineering By and For machine Learning

Léon Faure , Manish Kushwaha , Thomas Duigou , Jean-Loup Faulon
Engineering, Evolution & Design (SEED), AICHE, Jun 2021, Vitual, United States
Conference papers hal-04275493v1

Biocomputing with Enzyme

Jean-Loup Faulon
Faulon JL, “Biocomputing with Enzyme”, International symposium on High Throughput Catalyst Design, HTCD-2021, HTCD, University of Lille, Jun 2021, Lille, France
Conference papers hal-04275498v1

Automated Workflows for Synthetic Biology and metabolic Engineering: the Galaxy-SynBioCAD Portal

Jean-Loup Faulon
Microbial Cell Factories Webinar Series, University of Manchester, Mar 2021, Manchester, United Kingdom
Conference papers hal-04275504v1

The Galaxy-SynBioCAD portal: tools and workflows for synthetic biology and metabolic engineering

Thomas Duigou , Joan Hérisson , Jean-Loup Faulon , Guillaume Gricourt , Kenza Bazi Kabbaj
Journées du PEPI IBIS 2021, Nov 2021, Toulouse, France
Conference papers hal-04355490v1

Machine Learning for and by Synthetic Biology

Jean-Loup Faulon
Beilstein Bozen Symposium, Beilstein Institute, Sep 2020, Rudesheime, Germany
Conference papers hal-04275530v1

Design Automation Workflows for Synthetic Biology and Metabolic Engineering: The Galaxy SynBioCAD portal

Melchior Du Lac , Thomas Duigou , Pablo Carbonell , Jean-Loup Faulon
IWBDA, 12th International Workshop on Bio-Design Automation, Bio-Design Automation Consortium (BDAC), Aug 2020, Worcester, MA, United States
Conference papers hal-04275555v1

Enzyme for Biocomputing

Jean-Loup Faulon
Symposium « Chemistry goes Green », SANOFI, Sep 2020, Montpellier, France
Conference papers hal-04275515v1

Intelligence Artificielle et BioSynthèse

Jean-Loup Faulon
Séance Substances Naturelle, Académie nationale de Pharmacie, May 2020, Paris, France
Conference papers hal-04275573v1

AI and Synthetic Biology

Jean-Loup Faulon
Invited Lecture EPFL, EPFL, Feb 2020, Lausane, Switzerland
Conference papers hal-04275582v1

Design-Build-Test-Learn Paradigm in Synthetic Biology

Jean-Loup Faulon
JOBIM conference, JOBIM, Jul 2019, Nante, France
Conference papers hal-04275697v1

Metabolic Perceptron

Amir Pandi , Mathilde Koch , Jean-Loup Faulon
Synthetic Biology UK 2019, Dec 2019, Warwick, UK, United Kingdom
Conference papers hal-04275593v1

Machine Learning in Synthetic Biology

Jean-Loup Faulon
2nd Annual Synthetic Biology Congress, EBRC, Nov 2019, London, United Kingdom
Conference papers hal-04275616v1

Interfacing Machine Learning with Biological Systems

Jean-Loup Faulon
EMBO workshop “Creating is Under-standing: Synthetic Biology Masters Complexity”, EMBO, Sep 2019, Heidelberg, Germany
Conference papers hal-04275642v1

Keynote lecture #2: Retrosynthesis and computer-aided design of metabolic pathways

Jean-Loup Faulon
EMBO course Synthetic Biology in Action: Bridging Natural/NonNatural, EMBO, Sep 2019, Heidelberg, Germany
Conference papers hal-04275688v1

OptBioDes: an optimal design for the synbio toolchain

Pablo Carbonell , Rainer Breitling , Jean-Loup Faulon
IWBDA 11th In-ternational Workshop on Bio-Design Automation, Bio-Design Automation Consortium (BDAC), Jul 2019, Cambridge, UK, United Kingdom
Conference papers hal-04275710v1

A large-scale exploration of cell-free compositions to maximize protein production using reinforcement learning

Olivier Borkowski , Mathilde Koch , Jean-Loup Faulon
EMBO workshop “Creating is Understand-ing: Synthetic Biology Masters Complexity, EMBO, Sep 2019, Heildelberg, Germany
Conference papers hal-04275652v1

Retrosynthèse en Biologie

Jean-Loup Faulon
Colloque Chimie et biologie de synthèse : les applications, Maison de la Chimie, Feb 2018, Paris, France
Conference papers hal-04275756v1

The Microbial Biotechnology ELIXIR community

Jean-Loup Faulon
Athens ELIXIR workshop, ELIXIR, Sep 2018, Athens, Greece
Conference papers hal-04275722v1

Metabolic engineering for Natural Products

Jean-Loup Faulon
IUPHAR Natural Products Meeting, IUPHAR, Apr 2018, Paris, France
Conference papers hal-04275735v1

Microbial Biotechnology

Jean-Loup Faulon
12th CeBiTec-Symposium, CeBiTec, Mar 2018, Bielefeld, Germany
Conference papers hal-04275746v1

Standard in Synthetic Biology

Jean-Loup Faulon
EU-US High Level Expert workshop on Biotechnology, Apr 2018, Bruxelles, Belgium
Conference papers hal-04275741v1

Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors

Peter Voyvodic , Amir Pandi , Mathilde Koch , Jean-Loup Faulon , Jérôme Bonnet
Congrés GDR BioSynSys, GDG BioSynSys, Oct 2018, Toulouse, France
Conference papers hal-04275767v1

Retrosynthesis to design and engineer metabolic pathways Biology

Jean-Loup Faulon
Congress SCF 2018, SCF, Jul 2018, Montpellier, France
Conference papers hal-04275730v1

Automated Bio-Production Pipeline

Joan Hérisson , Thomas Duigou , Guillaume Gricourt , Jean-Loup Faulon
The Automated Scientist, Mar 2024, Copenhagen, Denmark
Conference poster hal-04408969v1
Image document

Evaluation of information processing capacity of bacterial metabolism through regression problem solving

Ahavi Paul , Bastien Mollet , Antoine Cornuéjols , Evelyne Lutton , Alberto Tonda
BioSynSys 2023 - Symposium on Synthetic and Systems Biology, Jul 2023, Toulouse, France
Conference poster hal-04287846v1
Image document

Solving regression problems using bacterial metabolism

Paul Ahavi , Bastien Mollet , Antoine Cornuéjols , Evelyne Lutton , Alberto Tonda
2023 Living Machines @ Work day, Oct 2023, Gif-sur-Yvette, France.
Conference poster hal-04312498v1
Image document

Neural-like computation using bacterial metabolism to solve machine-learning problems

Paul Ahavi , Bastien Mollet , Antoine Cornuéjols , Evelyne Lutton , Alberto Tonda
DIM BioConvS - Innovation Day, Nov 2023, St-Ouen, France
Conference poster hal-04312782v1
Image document

Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering

Thomas Duigou , Joan Hérisson , Melchior Du Lac , Kenza Bazi-Kabbaj , Mahnaz Sabeti Azad
JOBIM 2022, Jul 2022, Rennes, France.
Conference poster hal-04302811v1
Image document

Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering

Thomas Duigou , Joan Hérisson , Melchior Du Lac , Kenza Bazi-Kabbaj , Mahnaz Sabeti Azad
BioSynSys 2022, Sep 2022, Paris, France.
Conference poster hal-04302912v1

Large scale active-learning-guided exploration for in vitro protein production optimization

Olivier Borkowski , Mathilde Koch , Agnès Zettor , Jean-Loup Faulon
Structural Biology and Chemistry Department days, Jun 2019, Paris, France
Conference poster hal-03852944v1

Metabolic Perceptrons for Neural Computing in Biological Systems.

Paul Soudier , Amir Pandi , Mathilde Koch , Peter Voyvodic , Manish Kushwaha
EMBO workshop “Creating is Understanding: Synthetic Biology Masters Complexity, Sep 2019, Heildelberg, Germany
Conference poster hal-04275677v1

Exploration, analyses, and design of heterologous pathways for the production of chemical compounds

Melchior Du Lac , Pablo Carbonell , Jean-Loup Faulon
EMBO workshop “Creating is Understanding: Synthetic Biology Masters Complexity, Sep 2019, Heidelberg, Germany
Conference poster hal-04275661v1
Image document

A large-scale exploration of cell-free compositions to maximize protein production using active learning

Olivier Borkowski , Mathilde Koch , Agnès Zettor , Amir Pandi , Angelo Cardoso Batista
Structural Biology and Chemistry Department days, Dec 2019, paris, France
Conference poster hal-04292156v1
Image document

Cell-Free Biosensors and AI integration

Paul Soudier , Léon Faure , Manish Kushwaha , Jean-Loup Faulon
Cell-Free Gene Expression, 2433, Springer US, pp.303-323, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1998-8_19⟩
Book sections hal-03545753v1

Cell-Free Biosensors and AI Integration

Paul Soudier , Léon Faure , Manish Kushwaha , Jean-Loup Faulon
Cell-Free Gene Expression, 2433, Springer US, pp.303-323, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1998-8_19⟩
Book sections hal-04275373v1
Image document

Cell-Free Biosensors and AI Integration

Paul Soudier , Léon Faure , Manish Kushwaha , Jean-Loup Faulon
Ashty 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⟩
Book sections hal-03649323v1

Synthetic Biology at the Hand of Cell-Free Systems

Amir Pandi , Olivier Borkowski , Jean-Loup Faulon
Advances in Synthetic Biology, Springer Singapore, pp. 275-288, 2020, ⟨10.1007/978-981-15-0081-7_16⟩
Book sections hal-03852064v1

Enzyme Discovery: Enzyme Selection and Pathway Design

Pablo Carbonell , Mathilde Koch , Thomas Duigou , Jean-Loup Faulon
Enzymes in Synthetic Biology, 608, Elsevier, pp.3-27, 2018, Methods in Enzymology, ⟨10.1016/bs.mie.2018.04.005⟩
Book sections hal-04275379v1

Enzyme discovery: Enzyme selection and pathway design

Pablo Carbonell , Mathilde Koch , Thomas Duigou , Jean-Loup Faulon
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⟩
Book sections hal-02789661v1
Image document

Extended metabolic space modeling

Pablo Carbonell , Baudoin Delepine , Jean-Loup Faulon
Synthetic metabolic pathways, 1671, Springer, 394 p., 2017, Methods in Molecular Biology, 978-1-4939-7295-1
Book sections hal-01603209v1

Retrosynthetic design of heterologous pathways 2013

Pablo Carbonell , Anne-Gaëlle Planson , Jean-Loup Faulon
Systems Metabolic Engineering, 985, Humana Press, 2013, Methods in Molecular Biology, 978-1-62703-298-8. ⟨10.1007/978-1-62703-299-5_9⟩
Book sections hal-01204312v1
Image document

Retrosynthetic design of heterologous pathways

Pablo Carbonell , Anne-Gaëlle Planson , Jean-Loup Faulon
Systems metabolic engineering, 985, Springer, 474 p., 2013, Methods in Molecular Biology, 978-1-62703-298-8
Book sections hal-01603740v1

Graphs: flexible representations of molecular structures and biological networks

M. Misra , S. Martin , Jean-Loup Faulon
Computational Approaches in Cheminformatics and Bioinformatics, John Wiley and sons, 292 p., 2011, 978-0-470-38441-1. ⟨10.1002/9781118131411.ch6⟩
Book sections hal-01602043v1