Claudine Chaouiya

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 15

Top Topics

Neighborhood Sequences

Qualitative Models

Monotone Boolean Functions

Systems Biology

Top Venues

Briefings Bioinform.

J. Integr. Bioinform.

Publications

José E. R. Cury, Patrícia Tenera Roxo, Vasco Manquinho, Claudine Chaouiya, Pedro T. Monteiro
Immediate Neighbours of Monotone Boolean Functions. CoRR (2024)
Claudine Chaouiya, Pedro T. Monteiro, Elisabeth Remy
Logical Modelling, Some Recent Methodological Advances Illustrated. AUTOMATA (2024)
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, Claudine Chaouiya, Isabel Sá-Correia, Pedro Tiago Monteiro
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. Nucleic Acids Res. 51 (D1) (2023)
Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. Bioinform. 38 (21) (2022)
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone
. Briefings Bioinform. 23 (4) (2022)
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, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36 (24) (2021)
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, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone
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. Briefings Bioinform. 22 (2) (2021)
Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37 (21) (2021)
Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16 (2) (2019)
José E. R. Cury, Pedro T. Monteiro, Claudine Chaouiya
Partial Order on the set of Boolean Regulatory Functions. CoRR (2019)
Elisa Tonello, Etienne Farcot, Claudine Chaouiya
Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components. SIAM J. Appl. Dyn. Syst. 18 (1) (2019)
Pedro L. Varela, Inês Lynce, Vasco M. Manquinho, Claudine Chaouiya, Pedro T. Monteiro
Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids. SASB 335 (2018)
Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro, Claudine Chaouiya
EpiLog: A software for the logical modelling of epithelial dynamics. F1000Research 7 (2018)
Elisa Tonello, Etienne Farcot, Claudine Chaouiya
Local negative circuits and cyclic attractors in Boolean networks with at most five components. CoRR (2018)
Lucas Sánchez, Claudine Chaouiya
Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells. BMC Syst. Biol. 10 (2016)
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. 31 (7) (2015)
Claudine Chaouiya, Sarah M. Keating, Duncan Bérenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomás Helikar
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. J. Integr. Bioinform. 12 (2) (2015)
Nuno D. Mendes, Pedro T. Monteiro, Jorge Carneiro, Elisabeth Remy, Claudine Chaouiya
Quantification of reachable attractors in asynchronous discrete dynamics. CoRR (2014)
Pedro T. Monteiro, Wassim Abou-Jaoudé, Denis Thieffry, Claudine Chaouiya
Model Checking Logical Regulatory Networks. WODES (2014)
Adrien Fauré, Barbara M. I. Vreede, Élio Sucena, Claudine Chaouiya
Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects. PLoS Comput. Biol. 10 (3) (2014)
Nuno D. Mendes, Frédéric Lang, Yves-Stan Le Cornec, Radu Mateescu, Grégory Batt, Claudine Chaouiya
Composition and abstraction of logical regulatory modules: application to multicellular systems. Bioinform. 29 (6) (2013)
Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7 (2013)
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7 (2013)
Aurélien Naldi, Pedro T. Monteiro, Claudine Chaouiya
Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. CMSB (2012)
Fabien Corblin, Eric Fanchon, Laurent Trilling, Claudine Chaouiya, Denis Thieffry
Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data. IPCAT (2012)
Pedro T. Monteiro, Claudine Chaouiya
Efficient Verification for Logical Models of Regulatory Networks. PACBB (2012)
Beatriz Luna, Claudine Chaouiya
Relating Formalisms for the Qualitative Modelling of Regulatory Networks. PACBB (2011)
Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
Dynamically consistent reduction of logical regulatory graphs. Theor. Comput. Sci. 412 (21) (2011)
Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
Petri net representation of multi-valued logical regulatory graphs. Nat. Comput. 10 (2) (2011)
Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. CCA (2010)
Claudine Chaouiya, Monika Heiner
Introduction. ACSD/Petri Nets Workshops (2010)
Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. PLoS Comput. Biol. 6 (9) (2010)
Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. CMSB (2009)
Aurélien Naldi, Duncan Bérenguier, Adrien Fauré, F. Lopez, Denis Thieffry, Claudine Chaouiya
Logical modelling of regulatory networks with GINsim 2.3. Biosyst. 97 (2) (2009)
Özgür Sahin, Holger Fröhlich, Christian Löbke, Ulrike Korf, Sara Burmester, Meher Majety, Jens Mattern, Ingo Schupp, Claudine Chaouiya, Denis Thieffry, Annemarie Poustka, Stefan Wiemann, Tim Beißbarth, Dorit Arlt
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol. 3 (2009)
Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
Petri net modelling of biological regulatory networks. J. Discrete Algorithms 6 (2) (2008)
Aitor González, Claudine Chaouiya, Denis Thieffry
wing disc. ECCB (2008)
Adrien Fauré, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry
Logical modelling and analysis of the budding yeast cell cycle. BMC Bioinform. 8 (S-8) (2007)
Claudine Chaouiya
Petri net modelling of biological networks. Briefings Bioinform. 8 (4) (2007)
Claudine Chaouiya
Chronique : Réseaux de Petri et modélisation en biologie moléculaire. Tech. Sci. Informatiques 26 (1-2) (2007)
Aurélien Naldi, Denis Thieffry, Claudine Chaouiya
Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. CMSB (2007)
Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
Qualitative Petri Net Modelling of Genetic Networks. Trans. Comp. Sys. Biology 6 (2006)
Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. ISMB (Supplement of Bioinformatics) (2006)
Elisabeth Remy, Paul Ruet, Luis Eduardo Mendoza, Denis Thieffry, Claudine Chaouiya
From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits. Trans. Comp. Sys. Biology 7 (2006)
E. Simão, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
. ECCB/JBI (2005)
Claudine Chaouiya, Elisabeth Remy, Paul Ruet, Denis Thieffry
Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. ICATPN (2004)
Elisabeth Remy, Brigitte Mossé, Claudine Chaouiya, Denis Thieffry
A description of dynamical graphs associated to elementary regulatory circuits. ECCB (2003)
Claudine Chaouiya, Elisabeth Remy, Brigitte Mossé, Denis Thieffry
Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. POSTA (2003)