A description of dynamical graphs associated to elementary regulatory circuits. - Elisabeth Remy; Brigitte Mossé; Claudine Chaouiya; Denis Thieffry (ECCB, 2003)

Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. - Claudine Chaouiya; Elisabeth Remy; Brigitte Mossé; Denis Thieffry (POSTA, 2003)

Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. - Claudine Chaouiya; Elisabeth Remy; Paul Ruet; Denis Thieffry (ICATPN, 2004)

Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli. - E. Simão; Elisabeth Remy; Denis Thieffry; Claudine Chaouiya (ECCB/JBI, 2005)

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. - Adrien Fauré; Aurélien Naldi; Claudine Chaouiya; Denis Thieffry (ISMB (Supplement of Bioinformatics), 2006)

Qualitative Petri Net Modelling of Genetic Networks. - Claudine Chaouiya; Elisabeth Remy; Denis Thieffry (Trans. Comp. Sys. Biology, 2006)

From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits. - Elisabeth Remy; Paul Ruet; Luis Eduardo Mendoza; Denis Thieffry; Claudine Chaouiya (Trans. Comp. Sys. Biology, 2006)

Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. - Aurélien Naldi; Denis Thieffry; Claudine Chaouiya (CMSB, 2007)

Petri net modelling of biological networks. - Claudine Chaouiya (Briefings Bioinform., 2007)

Logical modelling and analysis of the budding yeast cell cycle. - Adrien Fauré; Claudine Chaouiya; Andrea Ciliberto; Denis Thieffry (BMC Bioinform., 2007)

Chronique : Réseaux de Petri et modélisation en biologie moléculaire. - Claudine Chaouiya (Tech. Sci. Informatiques, 2007)

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. - Aitor González; Claudine Chaouiya; Denis Thieffry (ECCB, 2008)

Petri net modelling of biological regulatory networks. - Claudine Chaouiya; Elisabeth Remy; Denis Thieffry (J. Discrete Algorithms, 2008)

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. - Aurélien Naldi; Elisabeth Remy; Denis Thieffry; Claudine Chaouiya (CMSB, 2009)

Logical modelling of regulatory networks with GINsim 2.3. - Aurélien Naldi; Duncan Bérenguier; Adrien Fauré; Fabrice Lopez; Denis Thieffry; Claudine Chaouiya (Biosyst., 2009)

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. - Özgür Sahin; Holger Fröhlich; Christian Löbke; Ulrike Korf; Sara Burmester; Meher Majety; Jens Mattern; Ingo Schupp; Claudine Chaouiya; Denis Thieffry; Annemarie Poustka; Stefan Wiemann; et al. (BMC Syst. Biol., 2009)

Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. - Claudine Chaouiya; Aurélien Naldi; Elisabeth Remy; Denis Thieffry (CCA, 2010)

Introduction. - Claudine Chaouiya; Monika Heiner (ACSD/Petri Nets Workshops, 2010)

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. - Aurélien Naldi; Jorge Carneiro; Claudine Chaouiya; Denis Thieffry (PLoS Comput. Biol., 2010)

Relating Formalisms for the Qualitative Modelling of Regulatory Networks. - Beatriz Luna; Claudine Chaouiya (PACBB, 2011)

Petri net representation of multi-valued logical regulatory graphs. - Claudine Chaouiya; Aurélien Naldi; Elisabeth Remy; Denis Thieffry (Nat. Comput., 2011)

Dynamically consistent reduction of logical regulatory graphs. - Aurélien Naldi; Elisabeth Remy; Denis Thieffry; Claudine Chaouiya (Theor. Comput. Sci., 2011)

Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. - Aurélien Naldi; Pedro T. Monteiro 001; Claudine Chaouiya (CMSB, 2012)

Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data. - Fabien Corblin; Eric Fanchon; Laurent Trilling; Claudine Chaouiya; Denis Thieffry (IPCAT, 2012)

Efficient Verification for Logical Models of Regulatory Networks. - Pedro T. Monteiro 001; Claudine Chaouiya (PACBB, 2012)

Composition and abstraction of logical regulatory modules: application to multicellular systems. - Nuno D. Mendes; Frédéric Lang; Yves-Stan Le Cornec; Radu Mateescu 001; Grégory Batt; Claudine Chaouiya (Bioinform., 2013)

Path2Models: large-scale generation of computational models from biochemical pathway maps. - Finja Büchel; Nicolas Rodriguez 001; Neil Swainston; Clemens Wrzodek; Tobias Czauderna; Roland Keller; Florian Mittag; Michael Schubert; Mihai Glont; Martin Golebiewski; Martijn P. van Iersel; Sarah M. Keating; et al. (BMC Syst. Biol., 2013)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Claudine Chaouiya; Duncan Bérenguier; Sarah M. Keating; Aurélien Naldi; Martijn P. van Iersel; Nicolas Rodriguez 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

Model Checking Logical Regulatory Networks. - Pedro T. Monteiro 001; Wassim Abou-Jaoudé; Denis Thieffry; Claudine Chaouiya (WODES, 2014)

Quantification of reachable attractors in asynchronous discrete dynamics. - Nuno D. Mendes; Pedro T. Monteiro 001; Jorge Carneiro; Elisabeth Remy; Claudine Chaouiya (CoRR, 2014)

A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects. - Adrien Fauré; Barbara M. I. Vreede; Élio Sucena; Claudine Chaouiya (PLoS Comput. Biol., 2014)

Cooperative development of logical modelling standards and tools with CoLoMoTo. - Aurélien Naldi; Pedro T. Monteiro 001; Christoph Müssel; Hans A. Kestler; Denis Thieffry; Ioannis Xenarios; Julio Saez-Rodriguez; Tomás Helikar; Claudine Chaouiya (Bioinform., 2015)

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. - Claudine Chaouiya; Sarah M. Keating; Duncan Bérenguier; Aurélien Naldi; Denis Thieffry; Martijn P. van Iersel; Nicolas Le Novère; Tomás Helikar (J. Integr. Bioinform., 2015)

Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells. - Lucas Sánchez; Claudine Chaouiya (BMC Syst. Biol., 2016)

A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets. - Claudine Chaouiya; Hanna Klaudel; Franck Pommereau (Modeling in Systems Biology, The Petri Net Approach, 2016)

Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids. - Pedro L. Varela; Inês Lynce; Vasco Manquinho; Claudine Chaouiya; Pedro T. Monteiro 001 (SASB, 2018)

EpiLog: A software for the logical modelling of epithelial dynamics. - Pedro L. Varela; Camila V. Ramos; Pedro T. Monteiro 001; Claudine Chaouiya (F1000Research, 2018)

Partial Order on the set of Boolean Regulatory Functions. - José E. R. Cury; Pedro T. Monteiro 001; Claudine Chaouiya (CoRR, 2019)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. - Michael Hucka; Frank T. Bergmann; Claudine Chaouiya; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Matthias König 003; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; et al. (J. Integr. Bioinform., 2019)

Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components. - Elisa Tonello; Etienne Farcot; Claudine Chaouiya (SIAM J. Appl. Dyn. Syst., 2019)

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 S. Malik-Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C. Freeman; Paul D. Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; et al. (Briefings Bioinform., 2021)

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. - Andreas Dräger; Tomás Helikar; Matteo Barberis; Marc R. Birtwistle; Laurence Calzone; Claudine Chaouiya; Jan Hasenauer; Jonathan R. Karr; Anna Niarakis; María Rodríguez Martínez; Julio Saez-Rodriguez; Juilee Thakar (Bioinform., 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - Vasundra Touré; Steven Vercruysse; Marcio Luis Acencio; Ruth C. Lovering; Sandra E. Orchard; Glyn Bradley; Cristina Casals-Casas; Claudine Chaouiya; Noemi del-Toro; Åsmund Flobak; Pascale Gaudet; Henning Hermjakob; et al. (Bioinform., 2021)

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. - Anna Niarakis; Dagmar Waltemath; James A. Glazier; Falk Schreiber; Sarah M. Keating; David P. Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomás Helikar; Sylvain Soliman; et al. (Briefings Bioinform., 2022)

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. - Anna Niarakis; Juilee Thakar; Matteo Barberis; María Rodríguez Martínez; Tomás Helikar; Marc R. Birtwistle; Claudine Chaouiya; Laurence Calzone; Andreas Dräger (Bioinform., 2022)

YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. - Miguel Cacho Teixeira; Romeu Viana; Margarida Palma; Jorge Oliveira; Mónica Galocha; Marta Neves Mota; Diogo Couceiro; Maria Galhardas Pereira; Miguel Antunes; Inês V. Costa; Pedro Pais; Carolina Parada; et al. (Nucleic Acids Res., 2023)

Logical Modelling, Some Recent Methodological Advances Illustrated. - Claudine Chaouiya; Pedro T. Monteiro 001; Elisabeth Remy (AUTOMATA, 2024)

Immediate Neighbours of Monotone Boolean Functions. - José E. R. Cury; Patrícia Tenera Roxo; Vasco Manquinho; Claudine Chaouiya; Pedro T. Monteiro 001 (CoRR, 2024)

On Model Reductions of Boolean Networks. - Claudine Chaouiya; Jérôme Feret; Patrícia Tenera Roxo (CMSB, 2025)

Computation of Immediate Neighbours of Monotone Boolean Functions. - José E. R. Cury; Patrícia Tenera Roxo; Vasco Manquinho; Claudine Chaouiya; Pedro T. Monteiro 001 (CMSB, 2025)