Claudine Chaouiya

51 papers C 3Misc 2Journal 31Unranked 14

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Computation of Immediate Neighbours of Monotone Boolean Functions. CMSB José E. R. Cury, Patrícia Tenera Roxo, Vasco Manquinho, Claudine Chaouiya, Pedro T. Monteiro
2025	—	`conf`	On Model Reductions of Boolean Networks. CMSB Claudine Chaouiya, Jérôme Feret, Patrícia Tenera Roxo
2024	J	`jnl`	Immediate Neighbours of Monotone Boolean Functions. CoRR José E. R. Cury, Patrícia Tenera Roxo, Vasco Manquinho, Claudine Chaouiya, Pedro T. Monteiro
2024	—	`conf`	Logical Modelling, Some Recent Methodological Advances Illustrated. AUTOMATA Claudine Chaouiya, Pedro T. Monteiro, Elisabeth Remy
2023	J	`jnl`	YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. Nucleic Acids Res. 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
2022	J	`jnl`	Addressing Briefings Bioinform. 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, Laurence Calzone
2022	J	`jnl`	Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. Bioinform. Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
2021	J	`jnl`	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. 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
2021	J	`jnl`	SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 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
2021	J	`jnl`	The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 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
2019	J	`jnl`	Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components. SIAM J. Appl. Dyn. Syst. Elisa Tonello, Etienne Farcot, Claudine Chaouiya
2019	J	`jnl`	Partial Order on the set of Boolean Regulatory Functions. CoRR José E. R. Cury, Pedro T. Monteiro, Claudine Chaouiya
2019	J	`jnl`	The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 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
2018	J	`jnl`	EpiLog: A software for the logical modelling of epithelial dynamics. F1000Research Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro, Claudine Chaouiya
2018	J	`jnl`	Local negative circuits and cyclic attractors in Boolean networks with at most five components. CoRR Elisa Tonello, Etienne Farcot, Claudine Chaouiya
2018	—	`conf`	Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids. SASB Pedro L. Varela, Inês Lynce, Vasco Manquinho, Claudine Chaouiya, Pedro T. Monteiro
2016	—	`ch.`	A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets. Modeling in Systems Biology, The Petri Net Approach Claudine Chaouiya, Hanna Klaudel, Franck Pommereau
2016	J	`jnl`	Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells. BMC Syst. Biol. Lucas Sánchez, Claudine Chaouiya
2015	J	`jnl`	Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
2015	J	`jnl`	The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. J. Integr. Bioinform. Claudine Chaouiya, Sarah M. Keating, Duncan Bérenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomás Helikar
2014	J	`jnl`	A Discrete Model of PLoS Comput. Biol. Adrien Fauré, Barbara M. I. Vreede, Élio Sucena, Claudine Chaouiya
2014	—	`conf`	Model Checking Logical Regulatory Networks. WODES Pedro T. Monteiro, Wassim Abou-Jaoudé, Denis Thieffry, Claudine Chaouiya
2014	J	`jnl`	Quantification of reachable attractors in asynchronous discrete dynamics. CoRR Nuno D. Mendes, Pedro T. Monteiro, Jorge Carneiro, Elisabeth Remy, Claudine Chaouiya
2013	J	`jnl`	Composition and abstraction of logical regulatory modules: application to multicellular systems. Bioinform. Nuno D. Mendes, Frédéric Lang, Yves-Stan Le Cornec, Radu Mateescu, Grégory Batt, Claudine Chaouiya
2013	J	`jnl`	Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 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
2013	J	`jnl`	SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 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
2012	—	`conf`	Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data. IPCAT Fabien Corblin, Eric Fanchon, Laurent Trilling, Claudine Chaouiya, Denis Thieffry
2012	—	`conf`	Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. CMSB Aurélien Naldi, Pedro T. Monteiro, Claudine Chaouiya
2012	Misc	`conf`	Efficient Verification for Logical Models of Regulatory Networks. PACBB Pedro T. Monteiro, Claudine Chaouiya
2011	J	`jnl`	Dynamically consistent reduction of logical regulatory graphs. Theor. Comput. Sci. Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
2011	J	`jnl`	Petri net representation of multi-valued logical regulatory graphs. Nat. Comput. Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
2011	Misc	`conf`	Relating Formalisms for the Qualitative Modelling of Regulatory Networks. PACBB Beatriz Luna, Claudine Chaouiya
2010	J	`jnl`	Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. PLoS Comput. Biol. Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry
2010	—	`conf`	Introduction. ACSD/Petri Nets Workshops Claudine Chaouiya, Monika Heiner
2010	C	`conf`	Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. CCA Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
2009	—	`conf`	A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. CMSB Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
2009	J	`jnl`	Logical modelling of regulatory networks with GINsim 2.3. Biosyst. Aurélien Naldi, Duncan Bérenguier, Adrien Fauré, Fabrice Lopez, Denis Thieffry, Claudine Chaouiya
2009	J	`jnl`	Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol. 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
2008	C	`conf`	Logical modelling of the role of the Hh pathway in the patterning of the ECCB Aitor González, Claudine Chaouiya, Denis Thieffry
2008	J	`jnl`	Petri net modelling of biological regulatory networks. J. Discrete Algorithms Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
2007	J	`jnl`	Chronique : Réseaux de Petri et modélisation en biologie moléculaire. Tech. Sci. Informatiques Claudine Chaouiya
2007	—	`conf`	Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. CMSB Aurélien Naldi, Denis Thieffry, Claudine Chaouiya
2007	J	`jnl`	Logical modelling and analysis of the budding yeast cell cycle. BMC Bioinform. Adrien Fauré, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry
2007	J	`jnl`	Petri net modelling of biological networks. Briefings Bioinform. Claudine Chaouiya
2006	—	`conf`	Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. ISMB (Supplement of Bioinformatics) Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry
2006	J	`jnl`	From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits. Trans. Comp. Sys. Biology Elisabeth Remy, Paul Ruet, Luis Eduardo Mendoza, Denis Thieffry, Claudine Chaouiya
2006	J	`jnl`	Qualitative Petri Net Modelling of Genetic Networks. Trans. Comp. Sys. Biology Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
2005	—	`conf`	Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in ECCB/JBI E. Simão, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
2004	—	`conf`	Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. ICATPN Claudine Chaouiya, Elisabeth Remy, Paul Ruet, Denis Thieffry
2003	C	`conf`	A description of dynamical graphs associated to elementary regulatory circuits. ECCB Elisabeth Remy, Brigitte Mossé, Claudine Chaouiya, Denis Thieffry
2003	—	`conf`	Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. POSTA Claudine Chaouiya, Elisabeth Remy, Brigitte Mossé, Denis Thieffry