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Simplification of Reaction Networks, Confluence and Elementary Modes

 Guillaume Madelaine , Elisa Tonello , Cédric Lhoussaine , Joachim Niehren
Computation, 2017, Multiscale and Hybrid Modeling of the Living Systems
Article dans une revue hal-01471074v1
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Supplementary material of condition for sustained oscillations in repressilator based on a hybrid modeling of gene regulatory networks

 Honglu Sun , Jean-Paul Comet , Maxime Folschette , Morgan Magnin
2022
Pré-publication, Document de travail hal-03890505v1

What population reveals about individual cell identity: Single-cell parameter estimation of models of gene expression in yeast

 Artémis Llamosi , Andres Gonzalez , Cristian Versari , Eugenio Cinquemani , Giancarlo Ferrari-Trecate , et al.
PLoS Computational Biology, 2016, 12 (2), pp.e1004706. ⟨10.1371/journal.pcbi.1004706⟩
Article dans une revue hal-01248298v1
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Core SBML Software Package

 Joachim Niehren
2024
Logiciel hal-04454979v2
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Limit cycle analysis of a class of hybrid gene regulatory networks

 Honglu Sun , Maxime Folschette , Morgan Magnin
20th International Conference on Computational Methods in Systems Biology (CMSB 2022), Sep 2022, Bucharest, Romania
Communication dans un congrès hal-03700025v2
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Exact Boolean Abstraction of Linear Equation Systems

 Emilie Allart , Joachim Niehren , Cristian Versari
Computation, 2021, 9 (11), pp.32. ⟨10.3390/COMPUTATION9110113⟩
Article dans une revue hal-03384058v2

Computational Methods in Systems Biology - 21st International Conference, CMSB 2023

 Jun Pang , Joachim Niehren
14137, Springer Nature Switzerland; Springer, 2023, Lecture Notes in Computer Science, ⟨10.1007/978-3-031-42697-1⟩
Proceedings/Recueil des communications hal-04325364v1
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A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma

 Maxime Folschette , Vincent Legagneux , Arnaud Poret , Lokmane Chebouba , Carito Guziolowski , et al.
BMC Bioinformatics, 2020, 21 (1), pp.18. ⟨10.1186/s12859-019-3316-1⟩
Article dans une revue hal-02095930v4
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Reachability analysis of a class of hybrid gene regulatory networks

 Honglu Sun , Maxime Folschette , Morgan Magnin
17th International Conference on Reachability Problems (RP'23), Oct 2023, Nice, France. pp.56-69, ⟨10.1007/978-3-031-45286-4_5⟩
Communication dans un congrès hal-04180870v1
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Automatic Modeling of Dynamical Interactions Within Marine Ecosystems

 Omar Iken , Maxime Folschette , Tony Ribeiro
1st International Joint Conference on Learning & Reasoning, Oct 2021, (virtual), Greece.
Poster de conférence hal-03347033v1
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pylfit

 Tony Ribeiro , Maxime Folschette , Morgan Magnin , Katsumi Inoue , Chiaki Sakama , et al.
2022, ⟨swh:1:dir:253fc595a7b0695e8b58396de8a0dbecfcc2d4f8;origin=https://hal.archives-ouvertes.fr/hal-04435180;visit=swh:1:snp:32e97fa297205b15881d7e629637ebaf1167a1f7;anchor=swh:1:rel:bd05bc079cbaec08139ca176051e66b656cd64ee;path=/⟩
Logiciel hal-04435180v1
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Structural simplification of chemical reaction networks preserving deterministic semantics

 Guillaume Madelaine , Cédric Lhoussaine , Joachim Niehren
Computational Methods in Systems Biology (CMSB), Jérémie BOURDON; Olivier ROUX, Sep 2015, Nantes, France. pp.133-144
Communication dans un congrès hal-01168038v1

Genetic engineering of the branched fatty acid metabolic pathway of Bacillus subtilis for the overproduction of surfactin C14 isoform

 Debarun Dhali , François Coutte , Anthony Argüelles Arias , Sandrine S. Auger , Vladimir V. Bidnenko , et al.
Biotechnology Journal, 2017, 12 (7), pp.23. ⟨10.1002/biot.201600574⟩
Article dans une revue hal-01502183v1
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Predicting Changes of Reaction Networks with Partial Kinetic Information

 Joachim Niehren , Cristian Versari , Mathias John , François Coutte , Philippe Jacques
BioSystems, 2016, Special Issue of CMSB 2015, 149, pp.113-124. ⟨10.1016/j.biosystems.2016.09.003⟩
Article dans une revue hal-01239198v3
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The surfactin-like lipopeptides from Bacillus spp.: natural biodiversity and synthetic biology for a broader application range

 Ariane Théatre , Carolina Cano-Prieto , Marco Bartolini , Yoann Laurin , Magali Deleu , et al.
Frontiers in Bioengineering and Biotechnology, 2021, ⟨10.3389/fbioe.2021.623701⟩
Article dans une revue hal-03158419v1
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Computing Difference Abstractions of Linear Equation Systems

 Emilie Allart , Joachim Niehren , Cristian Versari
Theoretical Computer Science, 2021, ⟨10.1016/j.tcs.2021.06.030⟩
Article dans une revue hal-03156136v3

The Challenges of Inferring Dynamic Models from Time Series

 Tony Ribeiro , Maxime Folschette , Laurent Trilling , Nicolas Glade , Katsumi Inoue , et al.
Symbolic Approaches to Modeling and Analysis of Biological Systems, Wiley, 2023, 9781789450293. ⟨10.1002/9781394229086.ch3⟩
Chapitre d'ouvrage hal-04279657v1
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Computing Difference Abstractions of Metabolic Networks Under Kinetic Constraints

 Emilie Allart , Cristian Versari , Joachim Niehren
CMSB 2019 - 17th International Conference on Computational Methods in Systems Biology, Luca Bortolussi; Guido Sanguinetti, Sep 2019, Trieste, Italy. pp.266-285, ⟨10.1007/978-3-030-31304-3_14⟩
Communication dans un congrès hal-02302463v1
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Bioinformatics Modelling and Metabolic Engineering of the Branched Chain Amino Acid Pathway for Specific Production of Microbial Biosurfactants and Biopesticides

 Jean-Sébastien Guez , Françoise Coucheney , Joany Guy , Max Béchet , Pierre Fontanille , et al.
BIOKET, Aug 2023, Montreal, Canada. pp.107, ⟨10.3390/metabo12020107⟩
Communication dans un congrès hal-04278771v1
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Bioinformatics modelling and metabolic engineering of the branched chain amino acid pathway for specific production of mycosubtilin isoforms in Bacillus subtilis

 Jean-Sébastien Guez , Françoise Coucheney , Joany Guy , Max Béchet , Pierre Fontanille , et al.
Metabolites, 2022, 12 (2), pp.107. ⟨10.3390/metabo12020107⟩
Article dans une revue hal-03498125v1
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Condition for periodic attractor in 4-dimensional repressilators

 Honglu Sun , Maxime Folschette , Morgan Magnin
21st International Conference on Computational Methods in Systems Biology (CMSB 2023), Sep 2023, Luxembourg City, Luxembourg. pp.184-201, ⟨10.1007/978-3-031-42697-1_13⟩
Communication dans un congrès hal-04135182v1
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Limit cycle analysis of a class of hybrid gene regulatory networks

 Honglu Sun , Maxime Folschette , Morgan Magnin
Journées Nationales de l’Informatique Mathématique (JNIM 2022), Mar 2022, Lille, France
Poster de conférence hal-03700402v1
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Modeling Leucine’s Metabolic Pathway and Knockout Prediction Improving the Production of Surfactin, a Biosurfactant from Bacillus Subtilis

 François Coutte , Joachim Niehren , Debarun Dhali , Mathias John , Cristian Versari , et al.
Biotechnology Journal, 2015, 10 (8), pp.1216-34. ⟨10.1002/biot.201400541⟩
Article dans une revue hal-01153704v1
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Abstract Simulation of Reaction Networks via Boolean Networks

 Joachim Niehren , Athénaïs Vaginay , Cristian Versari
CMSB 2022 - 20th International Conference on Computational Methods in Systems Biology, Sep 2022, Bucarest, Romania
Communication dans un congrès hal-02279942v9
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Attractor Equivalence: An Observational Semantics for Reaction Networks

 Guillaume Madelaine , Cédric Lhoussaine , Joachim Niehren
First International Conference on Formal Methods in Macro-Biology, Sep 2014, Nouméa, New Caledonia. pp.82-101
Communication dans un congrès hal-00990924v1
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Structural simplification of chemical reaction networks in partial steady states

 Guillaume Madelaine , Cédric Lhoussaine , Joachim Niehren , Elisa Tonello
BioSystems, 2016, Special Issue of CMSB'2015, 149, pp.34--49. ⟨10.1016/j.biosystems.2016.08.003⟩
Article dans une revue hal-01350517v1
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Core SBML and its Formal Semantics

 Joachim Niehren , Cédric Lhoussaine , Athénaïs Vaginay
CMSB 2023 - 21th International Conference on Computational Methods in Systems Biology, Sep 2023, Luxembourg, Luxembourg
Communication dans un congrès hal-04125922v2

Bioinformatics Modelling and Metabolic Engineering of the Branched Chain Amino Acid Pathway for Specific Production of Microbial Biosurfactants and Biopesticides

 François Coutte , Jean-Sebastien Guez , Joany Castéra-Guy , Cristian Versari , Joachim Niehren , et al.
Congrès BIOKET dédié aux procédés et technologies appliqués à la biomasse, May 2023, Trois Rivieres, Canada
Communication dans un congrès hal-04551935v1
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Condition for sustained oscillations in repressilator based on a hybrid modeling of gene regulatory networks

 Honglu Sun , Jean-Paul Comet , Maxime Folschette , Morgan Magnin
International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2023), Feb 2023, Lisbon, Portugal. pp.29-40, ⟨10.5220/0011614300003414⟩
Communication dans un congrès hal-03902156v1
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Les enjeux de l'inférence de modèles dynamiques des systèmes biologiques à partir de séries temporelles

 Tony Ribeiro , Maxime Folschette , Laurent Trilling , Nicolas Glade , Katsumi Inoue , et al.
Approches symboliques de la modélisation et de l’analyse des systèmes biologiques, 2022
Chapitre d'ouvrage hal-02634235v2
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