Thomas Duigou

Publications

Article dans une revue (10)

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
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
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
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
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
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
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
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

Pré-publication, Document de travail (1)

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

Poster de conférence (4)

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
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 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

Communication dans un congrès (6)

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
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 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
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
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

Chapitre d'ouvrage (1)

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

Thèse (1)

Dynamique d'un réseau métabolique avec un modèle à base de contraintes : approche par échantillonnage des trajectoires solutions Thomas Duigou Bio-Informatique, Biologie Systémique [q-bio.QM]. Université Paris Sud - Paris XI, 2015. Français. ⟨NNT : 2015PA112061⟩ Thèse tel-01674162v1