Thomas Duigou

23
Documents

Publications

Publications

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-05507091v1

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
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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-03649340v2
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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-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
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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-02619044v1
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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-02625929v1
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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-02623106v1
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Information processing circuits in cell-free systems: beyond gene expression regulation

Manish Kushwaha , Amir Pandi , Mathilde Koch , Paul Soudier , Angelo Cardoso Batista et 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 Kabbaj et 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

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