Jean-Loup Faulon

121
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Publications

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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-04424418 v1

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-04673511 v1
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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-04178761 v1
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A versatile active learning workflow for optimization of genetic and metabolic networks

Amir Pandi , Christoph Diehl , Ali Yazdizadeh Kharrazi , Scott A Scholz , Elizaveta Bobkova et al.
Nature Communications, 2022, 13 (1), pp.3876. ⟨10.1038/s41467-022-31245-z⟩
Article dans une revue hal-04099006 v1
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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 et al.
Journal of visualized experiments : JoVE, In press, ⟨10.3791/64236⟩
Article dans une revue hal-03748754 v1
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The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Joan Hérisson , Thomas Duigou , Melchior Du Lac , Kenza Bazi-Kabbaj , Mahnaz Sabeti Azad et al.
Nature Communications, 2022, 13 (1), pp.5082. ⟨10.1038/s41467-022-32661-x⟩
Article dans une revue hal-03649340 v2
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PeroxiHUB : a modular cell-free biosensing platform using H2O2 as signal integrator

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

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 et al.
ACS Synthetic Biology, 2022, 11 (2), pp. 732-746. ⟨10.1021/acssynbio.1c00448⟩
Article dans une revue hal-04565201 v1
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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-04275366 v1
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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-03545761 v1
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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 et al.
ACS Synthetic Biology, 2021, pp.acssynbio.1c00448. ⟨10.1101/2021.09.07.459228⟩
Article dans une revue hal-03545788 v1
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Large scale active-learning-guided exploration for in vitro protein production optimization

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

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 et al.
ACS Synthetic Biology, 2020, 5 (1), pp.ysaa012. ⟨10.1093/synbio/ysaa012⟩
Article dans une revue hal-04275306 v1
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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-04275297 v1

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-02905157 v1
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Microbial genes for a circular and sustainable Bio-PET Economy.

Manuel Salvador , Umar Abdulmutalib , Jaime Gonzalez , Juhyun Kim , Alex A Smith et al.
Genes, 2019, 10 (5), ⟨10.3390/genes10050373⟩
Article dans une revue hal-02627201 v1

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⟩
Article dans une revue hal-04275369 v1
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Metabolic perceptrons for neural computing in biological systems

Amir Pandi , Mathilde Koch , Peter L. Voyvodic , Paul Soudier , Jérôme Bonnet et al.
Nature Communications, 2019, 10 (1), pp.1-13. ⟨10.1038/s41467-019-11889-0⟩
Article dans une revue hal-02275517 v1

Machine learning of designed translational control allows predictive pathway optimization in escherichia coli

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

Microbial Genes for a Circular and Sustainable Bio-PET Economy

Manuel Salvador , Umar Abdulmutalib , Jaime Gonzalez , Juhyun Kim , Alex Smith et al.
Genes, 2019, 10 (5), pp. 373. ⟨10.3390/genes10050373⟩
Article dans une revue hal-04275328 v1

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-02905161 v1

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-02627127 v1

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-04275316 v1
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Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors

Peter Voyvodic , Amir Pandi , Mathilde Koch , Ismael Conejero , Emmanuel Valjent et al.
Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-09722-9⟩
Article dans une revue hal-02399479 v1
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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-02619044 v1

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-02625334 v1

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

Neil Swainston , Mark Dunstan , Adrian Jervis , Christopher Robinson , Pablo Carbonell et al.
Bioinformatics, 2018, 34 (13), pp. 2327-2329. ⟨10.1093/bioinformatics/bty105⟩
Article dans une revue hal-04275350 v1
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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-02625929 v1
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Selenzyme: enzyme selection tool for pathway design

Pablo Carbonell , Jerry Wong , Neil Swainston , Erika Takano , Nicholas J. Turner et al.
Bioinformatics, 2018, 34 (12), pp.2153-2154. ⟨10.1093/bioinformatics/bty065⟩
Article dans une revue hal-02621189 v1
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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 et al.
Communications Biology, 2018, 1, ⟨10.1038/s42003-018-0076-9⟩
Article dans une revue hal-02622177 v1

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-04275343 v1
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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-02622874 v1

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-04565190 v1
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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-02621501 v1
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biochem4j: Integrated and extensible biochemical knowledge through graph databases

Neil Swainston , Riza Batista Navarro , Pablo Carbonnell , Paul D. Dobson , Mark Dunstan et al.
PLoS ONE, 2017, 12 (7), pp.e0179130. ⟨10.1371/journal.pone.0179130⟩
Article dans une revue hal-01606003 v1
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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-02623106 v1

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 et al.
Cell Systems, 2017, 4 (2), pp.144-146. ⟨10.1016/j.cels.2017.02.005⟩
Article dans une revue hal-01530833 v1

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⟩
Article dans une revue hal-04275352 v1

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 et al.
Biochemical Society Transactions, 2016, 44 (3), pp.675-677. ⟨10.1042/BST20160009⟩
Article dans une revue hal-01606550 v1
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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-01607654 v1

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-01602231 v1

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-02636917 v1
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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 et al.
Synthetic and Systems Biotechnology, 2016, 1 (4), pp.271-275. ⟨10.1016/j.synbio.2016.07.001⟩
Article dans une revue hal-01602386 v1

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 hal-01605043 v1

Principles of Systems Biology, No. 11

Greg Wayne , Alex Graves , Demis Hassabis , Shambaditya Saha , Christoph A. Weber et al.
Cell Systems, 2016, 3 (5), pp.406-410
Article dans une revue hal-01531770 v1
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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-02634192 v1
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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-01601465 v1

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-01606076 v1
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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-01608645 v1

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-01608540 v1
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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-01607225 v1
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Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.

Tamás Fehér , Anne-Gaëlle Planson , Pablo Carbonell , Alfred Fernández-Castané , Ioana Grigoras et al.
Biotechnology Journal, 2014, 9 (11), pp.1446-1457. ⟨10.1002/biot.201400055⟩
Article dans une revue istex hal-02639677 v1
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PMG: Multi-core Metabolite Identification

Mohammad Mahdi Jaghoori , Sung-Shik T.Q. Jongmans , Frank de Boer , Julio Peironcely , Jean-Loup Faulon et al.
Electronic Notes in Theoretical Computer Science, 2013, 299, pp.53-60. ⟨10.1016/j.entcs.2013.11.005⟩
Article dans une revue hal-01601690 v1
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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-01601848 v1

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-01601691 v1

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-02341732 v1

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⟩
Article dans une revue istex hal-02941009 v1
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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-02651873 v1
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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-02652758 v1

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-02647510 v1
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Information processing circuits in cell-free systems: beyond gene expression regulation

Manish Kushwaha , Pandi Amir , Koch Mathilde , Soudier Paul , Batista Angelo Cardoso et al.
International Conference on Engineering Synthetic Cells and Organelles, May 2023, Minneapolis, MN, USA, United States
Communication dans un congrès hal-04563028 v1

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-04275865 v1

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-04275856 v1

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-04351679 v1

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-04275883 v1

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-04275834 v1

Artificial Metabolic Network

Jean-Loup Faulon
Séminaire Centre de Biologie Structural, Centre de Biologie Structural, May 2022, Montpellier, France
Communication dans un congrès hal-04275399 v1

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-04275418 v1

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-04275409 v1

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-04275392 v1

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-04275845 v1

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
Communication dans un congrès hal-04275567 v1

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-04275498 v1

Synthetic Biology: past, present and future

Jean-Loup Faulon
Bioket-2021, Bioket, Mar 2021, Lille, France
Communication dans un congrès hal-04275511 v1

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 et al.
Journées du PEPI IBIS 2021, Nov 2021, Toulouse, France
Communication dans un congrès hal-04355490 v1

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-04275493 v1

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-04275504 v1

Machine Learning for and by Synthetic Biology

Jean-Loup Faulon
Beilstein Bozen Symposium, Beilstein Institute, Sep 2020, Rudesheime, Germany
Communication dans un congrès hal-04275530 v1

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-04275555 v1

Intelligence Artificielle et BioSynthèse

Jean-Loup Faulon
Séance Substances Naturelle, Académie nationale de Pharmacie, May 2020, Paris, France
Communication dans un congrès hal-04275573 v1

AI and Synthetic Biology

Jean-Loup Faulon
Invited Lecture EPFL, EPFL, Feb 2020, Lausane, Switzerland
Communication dans un congrès hal-04275582 v1

Enzyme for Biocomputing

Jean-Loup Faulon
Symposium « Chemistry goes Green », SANOFI, Sep 2020, Montpellier, France
Communication dans un congrès hal-04275515 v1

Metabolic Perceptron

Amir Pandi , Mathilde Koch , Jean-Loup Faulon
Synthetic Biology UK 2019, Dec 2019, Warwick, UK, United Kingdom
Communication dans un congrès hal-04275593 v1

Design-Build-Test-Learn Paradigm in Synthetic Biology

Jean-Loup Faulon
JOBIM conference, JOBIM, Jul 2019, Nante, France
Communication dans un congrès hal-04275697 v1

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-04275688 v1

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-04275642 v1

Machine Learning in Synthetic Biology

Jean-Loup Faulon
2nd Annual Synthetic Biology Congress, EBRC, Nov 2019, London, United Kingdom
Communication dans un congrès hal-04275616 v1

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 et al.
Cell Free Systems Conference, Dec 2019, Boston (MA), United States
Communication dans un congrès hal-04291932 v1

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-04275710 v1
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Metabolic Perceptrons for Neural Computing in Cell Free Systems

Amir Pandi , Mathilde Koch , Peter Voyvodic , Paul Soudier , Jerome Bonnet et al.
AIChE Cell Free Systems Conference, American Institute of Chemical Engineers (AIChE), Dec 2019, Boston (MA), United States
Communication dans un congrès hal-04563371 v1

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-04275652 v1

Metabolic engineering for Natural Products

Jean-Loup Faulon
IUPHAR Natural Products Meeting, IUPHAR, Apr 2018, Paris, France
Communication dans un congrès hal-04275735 v1

The Microbial Biotechnology ELIXIR community

Jean-Loup Faulon
Athens ELIXIR workshop, ELIXIR, Sep 2018, Athens, Greece
Communication dans un congrès hal-04275722 v1

Standard in Synthetic Biology

Jean-Loup Faulon
EU-US High Level Expert workshop on Biotechnology, Apr 2018, Bruxelles, Belgium
Communication dans un congrès hal-04275741 v1

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-04275767 v1

Microbial Biotechnology

Jean-Loup Faulon
12th CeBiTec-Symposium, CeBiTec, Mar 2018, Bielefeld, Germany
Communication dans un congrès hal-04275746 v1

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-04275756 v1

Retrosynthesis to design and engineer metabolic pathways Biology

Jean-Loup Faulon
Congress SCF 2018, SCF, Jul 2018, Montpellier, France
Communication dans un congrès hal-04275730 v1
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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-04603192 v1

Automated Bio-Production Pipeline

Joan Hérisson , Thomas Duigou , Guillaume Gricourt , Jean-Loup Faulon
The Automated Scientist, Mar 2024, Copenhagen, Denmark
Poster de conférence hal-04408969 v1
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Solving regression problems using bacterial metabolism

Paul Ahavi , Bastien Mollet , Antoine Cornuéjols , Evelyne Lutton , Alberto Tonda et al.
2023 Living Machines @ Work day, Oct 2023, Gif-sur-Yvette, France.
Poster de conférence hal-04312498 v1
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Evaluation of information processing capacity of bacterial metabolism through regression problem solving

Paul Ahavi , Bastien Mollet , Antoine Cornuéjols , Evelyne Lutton , Alberto Tonda et al.
BioSynSys 2023 - Symposium on Synthetic and Systems Biology, Jul 2023, Toulouse, France
Poster de conférence hal-04287846 v1
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Neural-like computation using bacterial metabolism to solve machine-learning problems

Paul Ahavi , Bastien Mollet , Antoine Cornuéjols , Evelyne Lutton , Alberto Tonda et al.
DIM BioConvS - Innovation Day, Nov 2023, St-Ouen, France
Poster de conférence hal-04312782 v1
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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 et al.
JOBIM 2022, Jul 2022, Rennes, France.
Poster de conférence hal-04302811 v1

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 Azad et al.
Global BioFoundries Alliance Meeting 2022 (GBA2022), Oct 2022, Montréal, Canada
Poster de conférence hal-04351669 v1
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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 et al.
BioSynSys 2022, Sep 2022, Paris, France.
Poster de conférence hal-04302912 v1

Metabolic Perceptrons for Neural Computing in Biological Systems.

Paul Soudier , Amir Pandi , Mathilde Koch , Peter Voyvodic , Manish Kushwaha et al.
EMBO workshop “Creating is Understanding: Synthetic Biology Masters Complexity, Sep 2019, Heildelberg, Germany
Poster de conférence hal-04275677 v1

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-03852944 v1
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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 et al.
Structural Biology and Chemistry Department days, Dec 2019, paris, France
Poster de conférence hal-04292156 v1

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-04275661 v1
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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-03545753 v1

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-03852064 v1

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-02789661 v1
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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-01603209 v1
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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-01603740 v1

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-01204312 v1

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-01602043 v1