Jean-Loup Faulon

Présentation

Publications

Article dans une revue (61)

RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery Thomas Duigou,Philippe Meyer,Jean-Loup Faulon Nucleic Acids Research, 2026, 54 (D1), pp.D1799-D1806. ⟨10.1093/nar/gkaf1261⟩ Article dans une revue hal-05515316v1
Microbial computing: Review and Perspectives Paul Ahavi,Audrey Le Gouellec,Jean-Loup Faulon Biotechnology Advances, 2026, 87, pp.108766. ⟨10.1016/j.biotechadv.2025.108766⟩ Article dans une revue hal-05507127v1
BioRGroup dataset: R-group expansion of ChEBI molecules referenced in the Rhea database Guillaume Gricourt,Jean-Loup Faulon Scientific Data , 2025, 12 (1), pp.1692. ⟨10.1038/s41597-025-05983-w⟩ Article dans une revue hal-05333962v1
Machine learning in predictive biocatalysis: A comparative review of methods and applications Neha Tripathi,Joan Hérisson,Jean-Loup Faulon Biotechnology Advances, 2025, 84, pp.108698. ⟨10.1016/j.biotechadv.2025.108698⟩ Article dans une revue hal-05231537v1
Reverse engineering molecules from fingerprints through deterministic enumeration and generative models Philippe Meyer,Thomas Duigou,Guillaume Gricourt,Jean-Loup Faulon Journal of Cheminformatics, 2025, 17 (1), pp.157. ⟨10.1186/s13321-025-01074-5⟩ Article dans une revue hal-05507094v1
An AI-driven workflow for the accelerated optimization of cell-free protein synthesis Mostafa Khalil,Aisha Elsawah,An Hoang,Jean-Loup Faulon,Baptiste Panthuet al. iScience, 2025, 28 (10), pp.113599. ⟨10.1016/j.isci.2025.113599⟩ Article dans une revue hal-05315797v1
Reverse Engineering Molecules from Fingerprints through Deterministic Enumeration and Generative Models Philippe Meyer,Thomas Duigou,Guillaume Gricourt,Jean-Loup Faulon Journal of Cheminformatics, In press Article dans une revue hal-05281007v1
neo4jsbml: import systems biology markup language data into the graph database Neo4j Guillaume Gricourt,Thomas Duigou,Sandra Dérozier,Jean-Loup Faulon PeerJ, 2024, 12, pp.e16726. ⟨10.7717/peerj.16726⟩ Article dans une revue hal-04424418v1
Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review Guillaume Gricourt,Philippe Meyer,Thomas Duigou,Jean-Loup Faulon ACS Synthetic Biology, 2024, 13 (8), pp.2276-2294. ⟨10.1021/acssynbio.4c00091⟩ Article dans une revue hal-04673511v1
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⟩ Article dans une revue hal-04178761v1
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 Bonnetet al. Journal of visualized experiments : JoVE, In press, ⟨10.3791/64236⟩ Article dans une revue hal-03748754v1
A versatile active learning workflow for optimization of genetic and metabolic networks Amir Pandi,Christoph Diehl,Ali Yazdizadeh Kharrazi,Scott A Scholz,Elizaveta Bobkovaet al. Nature Communications, 2022, 13 (1), pp.3876. ⟨10.1038/s41467-022-31245-z⟩ Article dans une revue hal-04099006v1
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering Joan Hérisson,Thomas Duigou,Melchior Du Lac,Kenza Bazi-Kabbaj,Mahnaz Sabeti Azadet al. Nature Communications, 2022, 13 (1), pp.5082. ⟨10.1038/s41467-022-32661-x⟩ Article dans une revue hal-03649340v2
PeroxiHUB : a modular cell-free biosensing platform using H2O2 as signal integrator Paul Soudier,Ana Zúñiga,Thomas Duigou,Peter Voyvodic,Kenza Bazi-Kabbajet al. ACS Synthetic Biology, 2022, 11 (8), pp 2578-2588. ⟨10.1021/acssynbio.2c00138⟩ Article dans une revue 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⟩ Article dans une revue hal-04275366v1
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 Achmedovet al. ACS Synthetic Biology, 2021, pp.acssynbio.1c00448. ⟨10.1101/2021.09.07.459228⟩ Article dans une revue hal-03545788v1
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⟩ Article dans une revue (article de synthèse) hal-03545761v1
Large scale active-learning-guided exploration for in vitro protein production optimization Olivier Borkowski,Mathilde Koch,Agnes Zettor,Amir Pandi,Angelo Cardoso Batistaet al. Nature Communications, 2020, 11 (1), pp.1872. ⟨10.1038/s41467-020-15798-5⟩ Article dans une revue 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 Carbonellet al. ACS Synthetic Biology, 2020, 5 (1), pp.ysaa012. ⟨10.1093/synbio/ysaa012⟩ Article dans une revue 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⟩ Article dans une revue hal-04275297v1
Microbial genes for a circular and sustainable Bio-PET Economy. Manuel Salvador,Umar Abdulmutalib,Jaime Gonzalez,Juhyun Kim,Alex A Smithet al. Genes, 2019, 10 (5), pp.373. ⟨10.3390/genes10050373⟩ Article dans une revue hal-02627201v1
Reinforcement learning for bioretrosynthesis Mathilde Koch,Thomas Duigou,Jean-Loup Faulon ACS Synthetic Biology, 2019, 9 (1), pp.157-168. ⟨10.1021/acssynbio.9b00447⟩ Article dans une revue hal-02905157v1
Machine learning of designed translational control allows predictive pathway optimization in escherichia coli Adrian Jervis,Pablo Carbonell,Maria Vinaixa,Mark Dunstan,Katherine Hollywoodet al. ACS Synthetic Biology, 2019, 8 (1), pp. 127-136. ⟨10.1021/acssynbio.8b00398⟩ Article dans une revue hal-04275329v1
Metabolic perceptrons for neural computing in biological systems Amir Pandi,Mathilde Koch,Peter L. Voyvodic,Paul Soudier,Jérôme Bonnetet al. Nature Communications, 2019, 10 (1), pp.1-13. ⟨10.1038/s41467-019-11889-0⟩ Article dans une revue hal-02275517v1
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⟩ Article dans une revue 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⟩ Article dans une revue (article de synthèse) 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 Valjentet al. Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-09722-9⟩ Article dans une revue 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⟩ Article dans une revue hal-02625334v1
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⟩ Article dans une revue hal-02619044v1
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⟩ Article dans une revue hal-02625929v1
PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts Neil Swainston,Mark Dunstan,Adrian Jervis,Christopher Robinson,Pablo Carbonellet al. Bioinformatics, 2018, 34 (13), pp. 2327-2329. ⟨10.1093/bioinformatics/bty105⟩ Article dans une revue hal-04275350v1
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 Dunstanet al. Communications Biology, 2018, 1, ⟨10.1038/s42003-018-0076-9⟩ Article dans une revue hal-02622177v1
Selenzyme: enzyme selection tool for pathway design Pablo Carbonell,Jerry Wong,Neil Swainston,Erika Takano,Nicholas J. Turneret al. Bioinformatics, 2018, 34 (12), pp.2153-2154. ⟨10.1093/bioinformatics/bty065⟩ Article dans une revue hal-02621189v1
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⟩ Article dans une revue hal-04275343v1
Extended metabolic space modeling Pablo Carbonell,Baudoin Delépine,Jean-Loup Faulon Proceedings of the National Academy of Sciences of the United States of America, 2018, Methods in Molecular Biology, 1671 (28), pp. 83-96. ⟨10.1007/978-1-4939-7295-1_6⟩ Article dans une revue hal-04565190v1
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⟩ Article dans une revue (data paper) hal-02622874v1
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⟩ Article dans une revue (article de synthèse) hal-02621501v1
biochem4j: Integrated and extensible biochemical knowledge through graph databases Neil Swainston,Riza Batista Navarro,Pablo Carbonnell,Paul D. Dobson,Mark Dunstanet al. PLoS ONE, 2017, 12 (7), pp.e0179130. ⟨10.1371/journal.pone.0179130⟩ Article dans une revue 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 Berroet al. Cell Systems, 2017, 4 (2), pp.144-146. ⟨10.1016/j.cels.2017.02.005⟩ Article dans une revue 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, pp.1-17. ⟨10.1186/s13321-017-0252-9⟩ Article dans une revue hal-02623106v1
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. Jerviset al. Biochemical Society Transactions, 2016, 44 (3), pp.675-677. ⟨10.1042/BST20160009⟩ Article dans une revue hal-01606550v1
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⟩ Article dans une revue hal-01602231v1
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⟩ Article dans une revue hal-02636917v1
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⟩ Article dans une revue hal-01607654v1
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⟩ Article dans une revue istex hal-01605043v1
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 Fellowset al. Synthetic and Systems Biotechnology, 2016, 1 (4), pp.271-275. ⟨10.1016/j.synbio.2016.07.001⟩ Article dans une revue hal-01602386v1
Principles of Systems Biology, No. 11 Greg Wayne,Alex Graves,Demis Hassabis,Shambaditya Saha,Christoph A. Weberet al. Cell Systems, 2016, 3 (5), pp.406-410 Article dans une revue hal-01531770v1
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⟩ Article dans une revue hal-02634192v1
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⟩ Article dans une revue 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⟩ Article dans une revue hal-01606076v1
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⟩ Article dans une revue hal-01608645v1
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⟩ Article dans une revue hal-01608540v1
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⟩ Article dans une revue hal-01607225v1
Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering. Tamás Fehér,Anne-Gaëlle Planson,Pablo Carbonell,Alfred Fernández-Castané,Ioana Grigoraset al. Biotechnology Journal, 2014, 9 (11), pp.1446-1457. ⟨10.1002/biot.201400055⟩ Article dans une revue istex hal-02639677v1
PMG: Multi-core Metabolite Identification Mohammad Mahdi Jaghoori,Sung-Shik T.Q. Jongmans,Frank de Boer,Julio Peironcely,Jean-Loup Faulonet al. Electronic Notes in Theoretical Computer Science, 2013, 299, pp.53-60. ⟨10.1016/j.entcs.2013.11.005⟩ Article dans une revue hal-01601690v1
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⟩ Article dans une revue hal-01601848v1
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⟩ Article dans une revue hal-01601691v1
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⟩ Article dans une revue istex hal-02341732v1
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⟩ Article dans une revue istex hal-02651873v1
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⟩ Article dans une revue 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⟩ Article dans une revue istex hal-02647510v1

Communication dans un congrès (38)

Estimating the Learning Capacity of Bacterial Metabolic Networks Bastien Mollet,Paul Ahavi,Antoine Cornuéjols,Jean-Loup Faulon,Evelyne Luttonet al. Advances in Intelligent Data Analysis XXIII. IDA 2025, May 2025, Konstanz, Germany, Germany. pp.28-40, ⟨10.1007/978-3-031-91398-3_3⟩ Communication dans un congrès hal-05427376v1
Information processing circuits in cell-free systems: beyond gene expression regulation Manish Kushwaha,Amir Pandi,Mathilde Koch,Paul Soudier,Angelo Cardoso Batistaet al. International Conference on Engineering Synthetic Cells and Organelles, May 2023, Minneapolis, MN, USA, United States Communication dans un congrès hal-04563028v1
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 Communication dans un congrès hal-04275865v1
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 Communication dans un congrès hal-04275856v1
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 Communication dans un congrès hal-04351679v1
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 Communication dans un congrès hal-04275883v1
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 Communication dans un congrès hal-04275834v1
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 Communication dans un congrès hal-04275418v1
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 Communication dans un congrès hal-04275409v1
Artificial Metabolic Network Jean-Loup Faulon Séminaire Centre de Biologie Structural, Centre de Biologie Structural, May 2022, Montpellier, France Communication dans un congrès hal-04275399v1
Hybrid models enabling neural computation with metabolic networks Jean-Loup Faulon System Biology Seminar Series, University of Stuttgart, Jun 2022, Stuttgart, Germany Communication dans un congrès 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 Communication dans un congrès hal-04275845v1
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 Communication dans un congrès hal-04275498v1
Synthetic Biology: past, present and future Jean-Loup Faulon Bioket-2021, Bioket, Mar 2021, Lille, France Communication dans un congrès hal-04275511v1
The Galaxy-SynBioCAD portal: tools and workflows for synthetic biology and metabolic engineering Thomas Duigou,Joan Hérisson,Jean-Loup Faulon,Guillaume Gricourt,Kenza Bazi Kabbajet al. Journées du PEPI IBIS 2021, Nov 2021, Toulouse, France Communication dans un congrès hal-04355490v1
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 Communication dans un congrès hal-04275493v1
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 Communication dans un congrès hal-04275504v1
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 Communication dans un congrès hal-04275555v1
Machine Learning for and by Synthetic Biology Jean-Loup Faulon Beilstein Bozen Symposium, Beilstein Institute, Sep 2020, Rudesheime, Germany Communication dans un congrès hal-04275530v1
AI and Synthetic Biology Jean-Loup Faulon Invited Lecture EPFL, EPFL, Feb 2020, Lausane, Switzerland Communication dans un congrès hal-04275582v1
Intelligence Artificielle et BioSynthèse Jean-Loup Faulon Séance Substances Naturelle, Académie nationale de Pharmacie, May 2020, Paris, France Communication dans un congrès hal-04275573v1
Enzyme for Biocomputing Jean-Loup Faulon Symposium « Chemistry goes Green », SANOFI, Sep 2020, Montpellier, France Communication dans un congrès hal-04275515v1
Design-Build-Test-Learn Paradigm in Synthetic Biology Jean-Loup Faulon JOBIM conference, JOBIM, Jul 2019, Nante, France Communication dans un congrès hal-04275697v1
Metabolic Perceptron Amir Pandi,Mathilde Koch,Jean-Loup Faulon Synthetic Biology UK 2019, Dec 2019, Warwick, UK, United Kingdom Communication dans un congrès hal-04275593v1
Machine Learning in Synthetic Biology Jean-Loup Faulon 2nd Annual Synthetic Biology Congress, EBRC, Nov 2019, London, United Kingdom Communication dans un congrès 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 Communication dans un congrès hal-04275642v1
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 Batistaet al. Cell Free Systems Conference, Dec 2019, Boston (MA), United States Communication dans un congrès hal-04291932v1
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 Communication dans un congrès hal-04275688v1
Metabolic Perceptrons for Neural Computing in Cell Free Systems Amir Pandi,Mathilde Koch,Peter Voyvodic,Paul Soudier,Jerome Bonnetet al. AIChE Cell Free Systems Conference, American Institute of Chemical Engineers (AIChE), Dec 2019, Boston (MA), United States Communication dans un congrès hal-04563371v1
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 Communication dans un congrès 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 Communication dans un congrès hal-04275652v1
Metabolic engineering for Natural Products Jean-Loup Faulon IUPHAR Natural Products Meeting, IUPHAR, Apr 2018, Paris, France Communication dans un congrès hal-04275735v1
The Microbial Biotechnology ELIXIR community Jean-Loup Faulon Athens ELIXIR workshop, ELIXIR, Sep 2018, Athens, Greece Communication dans un congrès hal-04275722v1
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 Communication dans un congrès hal-04275767v1
Microbial Biotechnology Jean-Loup Faulon 12th CeBiTec-Symposium, CeBiTec, Mar 2018, Bielefeld, Germany Communication dans un congrès hal-04275746v1
Standard in Synthetic Biology Jean-Loup Faulon EU-US High Level Expert workshop on Biotechnology, Apr 2018, Bruxelles, Belgium Communication dans un congrès hal-04275741v1
Retrosynthèse en Biologie Jean-Loup Faulon Colloque 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 Biology Jean-Loup Faulon Congress SCF 2018, SCF, Jul 2018, Montpellier, France Communication dans un congrès hal-04275730v1

Poster de conférence (13)

Cell-free genome-wide transcriptomics through machine learning optimization Léa Wagner,An Hoang,Olivier Rue,Olivier Delumeau,Valentin Louxet al. SEED 2025, Jun 2025, Houston, United States Poster de conférence hal-05155548v1
Artificial Intelligence Methods and Models for Retro-Biosynthesis Guillaume Gricourt,Philippe Meyer,Thomas Duigou,Jean-Loup Faulon AI Methods and Models for (bio)catalysis and Synthetic Biology, Jun 2024, Montpellier, France Poster de conférence hal-04603192v1
Automated Bio-Production Pipeline Joan Hérisson,Thomas Duigou,Guillaume Gricourt,Jean-Loup Faulon The Automated Scientist, Mar 2024, Copenhagen, Denmark Poster de conférence hal-04408969v1
Solving regression problems using bacterial metabolism Paul Ahavi,Bastien Mollet,Antoine Cornuéjols,Evelyne Lutton,Alberto Tondaet al. 2023 Living Machines @ Work day, Oct 2023, Gif-sur-Yvette, France. Poster de conférence hal-04312498v1
Evaluation of information processing capacity of bacterial metabolism through regression problem solving Paul Ahavi,Bastien Mollet,Antoine Cornuéjols,Evelyne Lutton,Alberto Tondaet al. BioSynSys 2023 - Symposium on Synthetic and Systems Biology, Jul 2023, Toulouse, France Poster de conférence hal-04287846v1
Neural-like computation using bacterial metabolism to solve machine-learning problems Paul Ahavi,Bastien Mollet,Antoine Cornuéjols,Evelyne Lutton,Alberto Tondaet al. DIM BioConvS - Innovation Day, Nov 2023, St-Ouen, France Poster de conférence hal-04312782v1
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 Azadet al. JOBIM 2022, Jul 2022, Rennes, France. Poster de conférence hal-04302811v1
Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering Joan Hérisson,Thomas Duigou,Melchior Du Lac,Kenza Bazi Kabbaj,Mahnaz Sabeti Azadet al. Global BioFoundries Alliance Meeting 2022 (GBA2022), Oct 2022, Montréal, Canada Poster de conférence hal-04351669v1
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 Azadet al. BioSynSys 2022, Sep 2022, Paris, France. Poster de conférence hal-04302912v1
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 Batistaet al. Structural Biology and Chemistry Department days, Dec 2019, paris, France Poster de conférence hal-04292156v1
Metabolic Perceptrons for Neural Computing in Biological Systems. Paul Soudier,Amir Pandi,Mathilde Koch,Peter Voyvodic,Manish Kushwahaet al. EMBO workshop “Creating is Understanding: Synthetic Biology Masters Complexity, Sep 2019, Heildelberg, Germany Poster de conférence hal-04275677v1
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 Poster de conférence hal-03852944v1
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 Poster de conférence hal-04275661v1

Chapitre d'ouvrage (7)

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⟩ Chapitre d'ouvrage hal-03545753v1
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⟩ Chapitre d'ouvrage hal-03852064v1
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⟩ Chapitre d'ouvrage hal-02789661v1
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 Chapitre d'ouvrage hal-01603209v1
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 Chapitre d'ouvrage hal-01603740v1
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⟩ Chapitre d'ouvrage hal-01204312v1
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⟩ Chapitre d'ouvrage hal-01602043v1

Pré-publication, Document de travail (7)

What Makes a Bacterial Model a Good Reservoir Computer? Predicting Performance from Separability and Similarity Laura Alonso Bartolomé,Jean-Loup Faulon,Xavier Hinaut 2026 Pré-publication, Document de travail hal-05592447v1
RetroRules 2026: multi‑dataset combining chemistry and biochemistry for reaction templates Thomas Duigou,Philippe Meyer,Jean-Loup Faulon 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05267743v1
Cell-free genome-wide transcriptomics through machine learning optimization Léa Wagner,An Hoang,Olivier Rue,Olivier Delumeau,Valentin Louxet al. 2025 Pré-publication, Document de travail hal-05170246v1
dAMN: a genome scale neural-mechanistic hybrid model to predict bacterial growth dynamics Jean-Loup Faulon,Danilo Dursoniah,Paul Ahavi 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05233970v2
Microbial computing: review and perspectives Paul Ahavi,Audrey Le Gouellec,Jean-Loup Faulon 2025 Pré-publication, Document de travail hal-05281013v1
Living bacterial reservoir computers for information processing and sensing Paul Ahavi,Thi-Ngoc-An Hoang,Philippe Meyer,Sylvie Berthier,Federica Fioriniet al. 2026 Pré-publication, Document de travail hal-05500853v1
Artificial Metabolic Networks: enabling neural computation with metabolic networks Léon Faure,Bastien Mollet,Wolfram Liebermeister,Jean-Loup Faulon 2022 Pré-publication, Document de travail hal-03613655v2

Rapport (3)

EMBL-EBI Services Review Alan Archibald,Jürg Bähler,Jildau Bouwman,Robin Buell,Francesca Ciccarelliet al. EMBL-EBI. 2023 Rapport (rapport d’expertise collective) hal-04746697v1
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 circulaire Nicolas Bernet,Sophie Bozonnet,Fayza Daboussi,Véronique de Berardinis,Jean-Loup Faulonet al. INRAE; 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 Jacques Bittoun,Isabelle Bonnin,Jacques Capy,Gilles Chiocchia,Frédéric Dolléet al. [0] 2015 Rapport hal-02800505v1

Logiciel (1)

Artificial Metabolic Networks - Release Léon Faure,Bastien Mollet,Wolfram Liebermeister,Jean-Loup Faulon 2022, ⟨swh:1:dir:24e921bcc4d37caa4e0d275b9c4beae362945150;origin=https://hal.archives-ouvertes.fr/hal-05509239;visit=swh:1:snp:d30db40ea555413eb36ef565f5c92e62687bf901;anchor=swh:1:rel:b959c97c859ad2cc20ffffac1069b73e69c890b8;path=/⟩ Logiciel hal-05509239v1