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A modular, qualitative modelling of regulatory networks using Petri nets

 Hanna Klaudel , Claudine Chaouiya , Franck Pommereau
Modeling in Systems Biology, pp.253-279, 2011, ⟨10.1007/978-1-84996-474-6_12⟩
Chapitre d'ouvrage hal-02309999v1

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

 Michael Hucka , Frank Bergmann , Claudine Chaouiya , Andreas Dräger , Stefan Hoops , et al.
Journal of Integrative Bioinformatics, 2019, 16 (2), ⟨10.1515/jib-2019-0021⟩
Article dans une revue hal-02564234v1

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

 Andreas Dräger , Tomáš Helikar , Matteo Barberis , Marc Birtwistle , Laurence Calzone , et al.
Bioinformatics, 2021, ⟨10.1093/bioinformatics/btab229⟩
Article dans une revue hal-03344134v1

Model checking to assess T-helper cell plasticity

 Wassim Abou-Jaoudé , Pedro T. Monteiro , Aurélien Naldi , Maximilien Grandclaudon , Vassili Soumelis , et al.
Frontiers in Bioengineering and Biotechnology, 2014, Computational methods for understanding complexity: the use of formal methods in biology, pp.22. ⟨10.3389/fbioe.2014.00086⟩
Article dans une revue hal-01099490v1

Impact of changing cell-cell communication network in models of epithelial pattern formation

 Pedro Varela , Pedro Monteiro , Claudine Chaouiya
IFAC-PapersOnLine, 2019, 52 (26), pp.38-44. ⟨10.1016/j.ifacol.2019.12.233⟩
Article dans une revue hal-02564340v1
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SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

 Andreas Dräger , Tomáš Helikar , Matteo Barberis , Marc Birtwistle , Laurence Calzone , et al.
Bioinformatics, 2021, 37 (21), pp.3702 - 3706. ⟨10.1093/bioinformatics/btab229⟩
Article dans une revue hal-03515692v2

Logical Modelling of Regulatory Networks, Methods and Applications

 Claudine Chaouiya , Elisabeth Remy
Bulletin of Mathematical Biology, 2013, 75 (6), pp.891-5. ⟨10.1007/s11538-013-9863-0⟩
Article dans une revue hal-01282925v1
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Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

 Anna Niarakis , Martin Kuiper , Marek Ostaszewski , Rahuman Malik Sheriff , Cristina Casals-Casas , et al.
Briefings in Bioinformatics, 2021, 22 (2), pp.1848--1859. ⟨10.1093/bib/bbaa046⟩
Article dans une revue hal-02549796v1

Extended kanban control systems for assembly manufacturing systems

 Claudine Chaouiya , George Liberopoulos , Yves Dallery
International Conference on Industrial Engineering and Production Management, Oct 1997, Lyon, France
Communication dans un congrès hal-01645551v1
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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

 Claudine Chaouiya , Duncan Bérenguier , Sarah Keating , Aurélien Naldi , Martijn van Iersel , et al.
BMC Systems Biology, 2013, 7 (1), pp.135. ⟨10.1186/1752-0509-7-135⟩
Article dans une revue hal-00926033v1

Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors

 Gianluca Selvaggio , Sara Canato , Archana Pawar , Pedro Monteiro , Patrícia Guerreiro , et al.
Cancer Research, 2020, pp.canres.3147.2019. ⟨10.1158/0008-5472.CAN-19-3147⟩
Article dans une revue hal-02563962v1

Quantification of reachable attractors in asynchronous discrete dynamics

 Nuno D. Mendes , Pedro T. Monteiro , Jorge Carneiro , Elisabeth Remy , Claudine Chaouiya
2014
Pré-publication, Document de travail hal-01266262v1
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The Extended Kanban System for Production Control of Assembly Systems

 Claudine Chaouiya , George Liberopoulos , Yves Dallery
[Research Report] lip6.1998.024, LIP6. 1998
Rapport hal-02547737v1
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Modelling molecular networks: relationships between different formalisms and levels of details

 Sylvain Soliman , Claudine Chaouiya , Grégory Batt , Francois Fages , Élisabeth Remy , et al.
[Research Report] RR-7221, INRIA. 2010
Rapport inria-00461084v1

Dynamically consistent reduction of logical regulatory graphs

 Aurélien Naldi , Elisabeth Remy , Denis Thieffry , Claudine Chaouiya
Theoretical Computer Science, 2011, 412 (21), ⟨10.1016/j.tcs.2010.10.021⟩
Article dans une revue hal-01284743v1

EpiLog: A software for the logical modelling of epithelial dynamics

 Pedro Varela , Camila Ramos , Pedro Monteiro , Claudine Chaouiya
F1000Research, 2018, 7, pp.1145. ⟨10.12688/f1000research.15613.2⟩
Article dans une revue hal-02564252v1
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Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling.

 Aurélien Naldi , Jorge Carneiro , Claudine Chaouiya , Denis Thieffry
PLoS Computational Biology, 2010, 6 (9), pp.e1000912. ⟨10.1371/journal.pcbi.1000912⟩
Article dans une revue inserm-00704876v1
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

 Aurélien Naldi , Céline Hernandez , Nicolas Levy , Gautier Stoll , Pedro Monteiro , et al.
Frontiers in Physiology, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩
Article dans une revue hal-01794294v2

Model Checking logical regulatory networks

 Pedro T. Monteiro , Wassim Abou-Jaoudé , Denis Thieffry , Claudine Chaouiya
WODES'14, 12th IFAC - IEEE International Workshop on Discrete Event Systems, Jean-Marc Faure, May 2014, Cachan, France. ⟨10.3182/20140514-3-FR-4046.00135⟩
Communication dans un congrès hal-01099489v1
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Composition and abstraction of logical regulatory modules: application to multicellular systems

 Nuno D Mendes , Frédéric Lang , Yves-Stan Le Cornec , Radu Mateescu , Grégory Batt , et al.
Bioinformatics, 2013, 29 (6), pp.749-757. ⟨10.1093/bioinformatics/btt033⟩
Article dans une revue hal-00785564v1
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SBML Level 3: an extensible format for the exchange and reuse of biological models

 Sarah Keating , Frank Bergmann , Tomáš Helikar , Rahuman Malik‐sheriff , Ion Moraru , et al.
Molecular Systems Biology, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Article dans une revue hal-02924909v1
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Problemes d'ordonnancement d'une superposition de flux periodiques sous contrainte temps-reel

 Sophie Lefebvre-Barbaroux , Alain Jean-Marie , Claudine Chaouiya
[Rapport de recherche] RR-1576, INRIA. 1992
Rapport inria-00074984v1

A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis.

 Elisabeth Remy , Sandra Rebouissou , Claudine Chaouiya , Andrei Zinovyev , François Radvanyi , et al.
Cancer Research, 2015, 75 (19), pp.4042-52
Article dans une revue hal-01285974v1
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Mapping multivalued onto Boolean dynamics

 Gilles Didier , Elisabeth Remy , Claudine Chaouiya
Journal of Theoretical Biology, 2011, 270 (1), pp.177. ⟨10.1016/j.jtbi.2010.09.017⟩
Article dans une revue hal-00656334v1

Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components

 Elisa Tonello , Etienne Farcot , Claudine Chaouiya
SIAM Journal on Applied Dynamical Systems, 2019, 18 (1), pp.68-79. ⟨10.1137/18M1173988⟩
Article dans une revue hal-02564212v1
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Estimating Attractor Reachability in Asynchronous Logical Models

 Nuno Mendes , Rui Henriques , Elisabeth Rémy , Jorge Carneiro , Pedro Monteiro , et al.
Frontiers in Physiology, 2018, 9, pp.1161. ⟨10.3389/fphys.2018.01161⟩
Article dans une revue hal-02075322v1
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Logical modelling of cellular decision processes with GINsim

 Claudine Chaouiya , Aurélien Naldi , Lionel Spinelli , Pedro Monteiro , Duncan Berenguier , et al.
JOBIM 2012, Jul 2012, Rennes, France
Communication dans un congrès hal-01261855v1
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Dynamical modeling and analysis of large cellular regulatory networks

 D Bérenguier , Claudine Chaouiya , Pedro T. Monteiro , A Naldi , Élisabeth Remy , et al.
Chaos: An Interdisciplinary Journal of Nonlinear Science, 2013, 23 (2), ⟨10.1063/1.4809783⟩
Article dans une revue hal-01261849v1
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Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

 Anna Niarakis , Dagmar Waltemath , James Glazier , Falk Schreiber , Sarah Keating , et al.
Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩
Article dans une revue hal-03690604v1
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