Claudine CHAOUIYA CHANTEGREL

See web pages of my group Network Modelling at the Instituto Gulbenkian de Ciência

Journals Conferences


In international journals

[1] Elisa Tonello, Etienne Farcot, and Claudine Chaouiya. Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components. SIAM Journal on Applied Dynamical Systems, 18(1):68-79, jan 2019. [ DOI | http ]
[2] Lucas Sánchez and Claudine Chaouiya. Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads. J R Soc Interface, 15(142), May 2018. [ DOI ]
[3] Nuno D Mendes, Rui Henriques, Elisabeth Remy, Jorge Carneiro, Pedro T Monteiro, and Claudine Chaouiya. Estimating attractor reachability in asynchronous logical models. Front Physiol, 9:1161, 2018. [ DOI ]
[4] Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, and Loïc Paulevé. The colomoto interactive notebook: Accessible and reproducible computational analyses for qualitative biological networks. Front Physiol, 9:680, 2018. [ DOI ]
[5] Aurélien Naldi, Céline Hernandez, Wassim Abou-Jaoudé, Pedro T Monteiro, Claudine Chaouiya, and Denis Thieffry. Logical modeling and analysis of cellular regulatory networks with ginsim 3.0. Front Physiol, 9:646, 2018. [ DOI ]
[6] Pedro L Varela, Camila V Ramos, Pedro T Monteiro, and Claudine Chaouiya. Epilog: A software for the logical modelling of epithelial dynamics. F1000Res, 7:1145, 2018. [ DOI ]
[7] Wassim Abou-Jaoudé, Pauline Traynard, Pedro T Monteiro, Julio Saez-Rodriguez, Tomáš Helikar, Denis Thieffry, and Claudine Chaouiya. Logical modeling and dynamical analysis of cellular networks. Front Genet, 7:94, 2016. [ DOI ]
[8] Lucas Sánchez and 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(1):37, 05 2016. [ DOI ]
[9] Claudine Chaouiya, Sarah M Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P van Iersel, Nicolas Le Novère, and Tomá s Helikar. The systems biology markup language (sbml) level 3 package: Qualitative models, version 1, release 1. J Integr Bioinform, 12(2):270, Sep 2015. [ DOI ]
[10] Aurélien Naldi, Pedro T Monteiro, Christoph Müssel, Consortium for Logical Models and Tools, Hans A Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomas Helikar, and Claudine Chaouiya. Cooperative development of logical modelling standards and tools with colomoto. Bioinformatics, 31(7):1154-9, Apr 2015. [ DOI ]
[11] Elisabeth Remy, Sandra Rebouissou, Claudine Chaouiya, Andrei Zinovyev, Fran cois Radvanyi, and Laurence Calzone. A modeling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis. Cancer Res, 75(19):4042-52, Oct 2015. [ DOI ]
[12] Wassim Abou-Jaoudé, Pedro T Monteiro, Aurélien Naldi, Maximilien Grandclaudon, Vassili Soumelis, Claudine Chaouiya, and Denis Thieffry. Model checking to assess t-helper cell plasticity. Front Bioeng Biotechnol, 2:86, 2014. [ DOI ]
[13] Adrien Fauré, Barbara M I Vreede, Elio Sucena, and Claudine Chaouiya. A discrete model of drosophila eggshell patterning reveals cell-autonomous and juxtacrine effects. PLoS Comput Biol, 10(3):e1003527, Mar 2014. [ DOI ]
[14] José C M Mombach, Cristhian A Bugs, and Claudine Chaouiya. Modelling the onset of senescence at the g1/s cell cycle checkpoint. BMC Genomics, 15 Suppl 7:S7, 2014. [ DOI ]
[15] D Bérenguier, C Chaouiya, P T Monteiro, A Naldi, E Remy, D Thieffry, and L Tichit. Dynamical modeling and analysis of large cellular regulatory networks. Chaos, 23(2):025114, Jun 2013. [ DOI ]
[16] Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah 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, and Nicolas Le Novère. Path2models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol, 7:116, Nov 2013. [ DOI ]
[17] Rui Castanhinha, Ricardo Araújo, Luís C Júnior, Kenneth D Angielczyk, Gabriel G Martins, Rui M S Martins, Claudine Chaouiya, Felix Beckmann, and Fabian Wilde. Bringing dicynodonts back to life: paleobiology and anatomy of a new emydopoid genus from the upper permian of mozambique. PLoS One, 8(12):e80974, 2013. [ DOI ]
[18] Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gon calves, 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, and Tomáš Helikar. Sbml qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol, 7:135, Dec 2013. [ DOI ]
[19] Claudine Chaouiya, Ouerdia Ourrad, and Ricardo Lima. Majority rules with random tie-breaking in boolean gene regulatory networks. PLoS One, 8(7):e69626, 2013. [ DOI ]
[20] Claudine Chaouiya and Elisabeth Remy. Logical modelling of regulatory networks, methods and applications. Bull Math Biol, 75(6):891-5, Jun 2013. [ DOI ]
[21] Nuno D Mendes, Frédéric Lang, Yves-Stan Le Cornec, Radu Mateescu, Gregory Batt, and Claudine Chaouiya. Composition and abstraction of logical regulatory modules: application to multicellular systems. Bioinformatics, 29(6):749-57, Mar 2013. [ DOI ]
[22] Claudine Chaouiya, Aurélien Naldi, and Denis Thieffry. Logical modelling of gene regulatory networks with ginsim. Methods Mol Biol, 804:463-79, 2012. [ DOI ]
[23] Aurélien Naldi, Elisabeth Remy, Denis Thieffry, and Claudine Chaouiya. Dynamically consistent reduction of logical regulatory graphs. Theoretical Computer Science, 412(21):2207 - 2218, 2011. Selected Papers from the 7th International Conference on Computational Methods in Systems Biology. [ DOI | http ]
[24] C. Chaouiya, A. Naldi, E. Remy, and D. Thieffry. Petri net representation of multi-valued logical regulatory graphs. Natural Computing, 10(2):727-750, Jun 2011. [ DOI | http ]
[25] Gilles Didier, Elisabeth Remy, and Claudine Chaouiya. Mapping multivalued onto boolean dynamics. J Theor Biol, 270(1):177-84, Feb 2011. [ DOI ]
[26] Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, and Denis Thieffry. Diversity and plasticity of th cell types predicted from regulatory network modelling. PLoS Comput Biol, 6(9):e1000912, Sep 2010. [ DOI ]
[27] Adrien Fauré, Aurélien Naldi, Fabrice Lopez, Claudine Chaouiya, Andrea Ciliberto, and Denis Thieffry. Modular logical modelling of the budding yeast cell cycle. Mol Biosyst, 5(12):1787-96, Dec 2009. [ DOI ]
[28] A Naldi, D Berenguier, A Fauré, F Lopez, D Thieffry, and C Chaouiya. Logical modelling of regulatory networks with ginsim 2.3. Biosystems, 97(2):134-9, Aug 2009. [ DOI ]
[29] Ozgür 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, and Dorit Arlt. Modeling erbb receptor-regulated g1/s transition to find novel targets for de novo trastuzumab resistance. BMC Syst Biol, 3:1, Jan 2009. [ DOI ]
[30] Claudine Chaouiya, Elisabeth Remy, and Denis Thieffry. Petri net modelling of biological regulatory networks. Journal of Discrete Algorithms, 6(2):165 - 177, 2008. Selected papers from CompBioNets 2004. [ DOI | http ]
[31] Aitor González, Claudine Chaouiya, and Denis Thieffry. Logical modelling of the role of the hh pathway in the patterning of the drosophila wing disc. Bioinformatics, 24(16):i234-40, Aug 2008. [ DOI ]
[32] Lucas Sánchez, Claudine Chaouiya, and Denis Thieffry. Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module. Int J Dev Biol, 52(8):1059-75, 2008. [ DOI ]
[33] Claudine Chaouiya. Petri net modelling of biological networks. Brief Bioinform, 8(4):210-9, Jul 2007. [ DOI ]
[34] Claudine Chaouiya, Hidde de Jong, and Denis Thieffry. Dynamical modeling of biological regulatory networks. Biosystems, 84(2):77-80, May 2006. [ DOI ]
[35] A Gonzalez Gonzalez, A Naldi, L Sánchez, D Thieffry, and C Chaouiya. Ginsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems, 84(2):91-100, May 2006. [ DOI ]
[36] Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, and Denis Thieffry. Dynamical analysis of a generic boolean model for the control of the mammalian cell cycle. Bioinformatics, 22(14):e124-31, Jul 2006. [ DOI ]
[37] Aitor González, Claudine Chaouiya, and Denis Thieffry. Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the drosophila wing imaginal disc. Genetics, 174(3):1625-34, Nov 2006. [ DOI ]
[38] E Simão, E Remy, D Thieffry, and C Chaouiya. Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in e.coli. Bioinformatics, 21 Suppl 2:ii190-6, Sep 2005. [ DOI ]
[39] E Remy, B Mossé, C Chaouiya, and D Thieffry. A description of dynamical graphs associated to elementary regulatory circuits. Bioinformatics, 19 Suppl 2:ii172-8, Oct 2003.
[40] Claudine Chaouiya, George Liberopoulos, and Yves Dallery. The extended kanban control system for production coordination of assembly manufacturing systems. IIE Transactions, 32(10):999-1012, Oct 2000. [ DOI | http ]

In proceedings of international conferences

[1] Pedro L. Varela, Inês Lynce, Vasco M. Manquinho, Claudine Chaouiya, and Pedro T. Monteiro. Stable states of boolean regulatory networks composed over hexagonal grids. Electr. Notes Theor. Comput. Sci., 335:113-130, 2018. [ DOI | http ]
[2] Pedro T. Monteiro, Wassim Abou-Jaoudé, Denis Thieffry, and Claudine Chaouiya. Model checking logical regulatory networks. In 12th International Workshop on Discrete Event Systems, WODES 2014, Cachan, France, May 14-16, 2014., pages 170-175, 2014. [ DOI | http ]
[3] Pedro T. Monteiro and Claudine Chaouiya. Efficient verification for logical models of regulatory networks. In 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, Salamanca, Spain, pages 259-267, 2012. [ DOI | http ]
[4] Fabien Corblin, Eric Fanchon, Laurent Trilling, Claudine Chaouiya, and Denis Thieffry. Automatic inference of regulatory and dynamical properties from incomplete gene interaction and expression data. In Information Processign in Cells and Tissues - 9th International Conference, IPCAT 2012, Cambridge, UK, March 31 - April 2, 2012. Proceedings, pages 25-30, 2012. [ DOI | http ]
[5] Aurélien Naldi, Pedro T. Monteiro, and Claudine Chaouiya. Efficient handling of large signalling-regulatory networks by focusing on their core control. In Computational Methods in Systems Biology - 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings, pages 288-306, 2012. [ DOI | http ]
[6] Beatriz Luna and Claudine Chaouiya. Relating formalisms for the qualitative modelling of regulatory networks. In 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2011, April 6-8, 2011, Salamanca, Spain, pages 293-302, 2011. [ DOI | http ]
[7] Aurélien Naldi, Elisabeth Remy, Denis Thieffry, and Claudine Chaouiya. A reduction of logical regulatory graphs preserving essential dynamical properties. In Computational Methods in Systems Biology, 7th International Conference, CMSB 2009, Bologna, Italy, August 31-September 1, 2009. Proceedings, pages 266-280, 2009. [ DOI | http ]
[8] C. Chaouiya. Qualitative modelling of biological regulatory networks combining a logical multi-valued formalism and petri nets. In 2008 9th International Workshop on Discrete Event Systems, pages 263-268, May 2008. [ DOI ]
[9] Aurélien Naldi, Denis Thieffry, and Claudine Chaouiya. Decision diagrams for the representation and analysis of logical models of genetic networks. In Computational Methods in Systems Biology, International Conference, CMSB 2007, Edinburgh, Scotland, September 20-21, 2007, Proceedings, pages 233-247, 2007. [ DOI | http ]
[10] Claudine Chaouiya, Elisabeth Remy, and Denis Thieffry. Qualitative petri net modelling of genetic networks. In Corrado Priami and Gordon Plotkin, editors, Transactions on Computational Systems Biology VI, pages 95-112, Berlin, Heidelberg, 2006. Springer Berlin Heidelberg.
[11] Elisabeth Remy, Paul Ruet, Luis Mendoza, Denis Thieffry, and Claudine Chaouiya. From logical regulatory graphs to standard petri nets: Dynamical roles and functionality of feedback circuits. In Corrado Priami, Anna Ingólfsdóttir, Bud Mishra, and Hanne Riis Nielson, editors, Transactions on Computational Systems Biology VII, pages 56-72, Berlin, Heidelberg, 2006. Springer Berlin Heidelberg.
[12] Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, and Denis Thieffry. Dynamical analysis of a generic boolean model for the control of the mammalian cell cycle. In Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006, pages 124-131, 2006. [ DOI | http ]
[13] Claudine Chaouiya, Elisabeth Remy, Paul Ruet, and Denis Thieffry. Qualitative modelling of genetic networks: From logical regulatory graphs to standard petri nets. In Applications and Theory of Petri Nets 2004, 25th International Conference, ICATPN 2004, Bologna, Italy, June 21-25, 2004, Proceedings, pages 137-156, 2004. [ DOI | http ]
[14] Claudine Chaouiya, Elisabeth Remy, Brigitte Mossé, and Denis Thieffry. Qualitative analysis of regulatory graphs: A computational tool based on a discrete formal framework. In Positive Systems, Proceedings of the First Multidisciplinary International Symposium on Positive Systems: Theory and Applications (POSTA 2003), Rome, Italy, August 28-30, 2003, pages 119-126, 2003. [ DOI | http ]
[15] Michel Occello, Claudine Chaouiya, and Marie-Claude Thomas. A Parallel Blackboard Model for Mobile Robotics control, pages 439-447. Springer Netherlands, Dordrecht, 1992. [ DOI | http ]

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