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Book chapters

C. Chaouiya, A. Naldi and D. Thieffry, Logical Modelling of Gene Regulatory Networks with GINsim, Methods in Molecular Biology, 1, Volume 804, Bacterial Molecular Networks, Part 3, Pages 463-479, 2012 DOI

C. Chaouiya, H. Klaudel, and F. Pommereau, A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets, In Modeling in Systems Biology, the Petri Net Approach. I.Koch, W. Reisig, F. Schreiber (Eds.). Springer, 2010 DOI

I. Koch and C. Chaouiya, Discrete Modelling: Petri Net and Logical Approaches, in Systems Biology for Signaling Networks. Sangdun Choi (Ed.) Springer, pp. 821-855, 2010 DOI

D. Thieffry, C. Chaouiya, L. Sánchez, From gradients to stripes: a logical analysis of Drosophila Segmentation genetic network, In N. Kolchanov, R. Hofestaedt, L. Milanesi (Eds.), Bioinformatics of Genome Regulation and Structure II, Springer, 279-390, 2006

C.Chaouiya, S.Lefebvre-Barbaroux, A.Jean-Marie, Real Time Scheduling of Periodic Tasks, in Scheduling Theory and its Applications, P.Chretienne, E.G.Coffman, J.K.Lenstra, Z.Liu (Eds), J.Wiley, pp. 167-91., 1995

Papers in international journals

E. Tonello, E. Farcot, and C. Chaouiya , Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components , SIAM J. Appl. Dyn. Syst. 18-1, pp. 68-79, 2019 DOI pdf

Hucka, Michael and Bergmann, Frank T and Chaouiya, Claudine and Dräger, Andreas and Hoops, Stefan and Keating, Sarah M and König, Matthias and Novère, Nicolas Le and Myers, Chris J and Olivier, Brett G and Sahle, Sven and Schaff, James C and Sheriff, Rahuman and Smith, Lucian P and Waltemath, Dagmar and Wilkinson, Darren J and Zhang, Fengkai, The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2, J Integr Bioinform 16(2), 2019 DOI

José E. R. Cury, Pedro T. Monteiro, Claudine Chaouiya, Partial Order on the set of Boolean Regulatory Functions, arXiv:1901.07623 [cs.DM], 2019

A. Naldi, C. Hernandez, N. Levy, G. Stoll, P.T. Monteiro, C. Chaouiya, T. Helikar, A. Zinovyev, L. Calzone, S. Cohen-Boulakia, D. Thieffry, L. Paulevé, The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks, Front. Physiol., 9, pp. 680, 2018 DOI

A. Naldi, C. Hernandez, W. Abou-Jaoudé, P.T. Monteiro, C. Chaouiya, D. Thieffry, Logical modelling and analysis of cellular regulatory networks with GINsim 3.0, Front. Physiol., 9, pp. 646, 2018 DOI

L. Sánchez, C. Chaouiya, Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads, Journal of The Royal Society Interface, 15(142), 2018 DOI

Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro, Claudine Chaouiya, EpiLog: A software for the logical modelling of epithelial dynamics, F1000Research, 7:1145 , 2018 DOI

L. Sánchez, C. Chaouiya, Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells, BMC Systems Biology, 10:37, 2016 DOI

W. Abou-Jaoudé, P. Traynard, P.T. Monteiro, J. Saez Rodriguez, T. Helikar, D. Thieffry, C. Chaouiya , Logical modeling and dynamical analysis of cellular networks, Frontiers in Genetics, 7:00094, 2016 DOI

Abou-Jaoudé W. Monteiro P.T., Naldi A. Grandclaudon M. Soumelis V. Chaouiya C. Thieffry D., Model checking to assess T-helper cell plasticity, Frontiers in Bioengineering and Biotechnology, 2:00086., 2015 DOI

Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, the 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., 2015 DOI

C. Chaouiya, S. M. Keating, D. Berenguier, A. Naldi, D. Thieffry, M. P. van Iersel, N. Le Novere, T. Helikar, SBML Level 3 package: Qualitative Models, Version 1, Release 1, Journal of Integrative Bioinformatics, 12(2):270 , 2015 pdf

E Remy, S Rebouissou, C Chaouiya, A Zinovyev, F Radvanyi, L Calzone, A modelling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis, Cancer Res. 75(19):4042-52, 2015 DOI

Dagmar Waltemath, Frank T Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Mickael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I Moraru, Chris J Myers, David Nickerson, Brett G Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet, Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE), Standards in Genomic Sciences (SIGS ) Vol 9, No 3 , 2014 DOI

Fauré A, Vreede BMI, Sucena É, Chaouiya C , A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects, PLoS Comput Biol 10(3): e1003527, 2014 DOI

JCM Mombach, CA Bugs, C Chaouiya, Modelling the onset of senescence at the G1/S cell cycle checkpoint, BMC Genomics, 15(Suppl 7):S7, 2014 DOI

Castanhinha R, Araújo R, Júnior LC, Angielczyk KD, Martins GG, Martins RM, Chaouiya C, Beckmann F, Wilde F., 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

Chaouiya C, Ourrad O, Lima R, Majority Rules with Random Tie-Breaking in Boolean Gene Regulatory Networks, PLoS ONE 8(7): e69626, 2013 DOI

Chaouiya C, Remy E., Logical modelling of regulatory networks, methods and applications (Editorial), Bull Math Biol. 2013 Jun;75(6):891-5., 2013 DOI

 Claudine Chaouiya, Duncan Berenguier, Sarah M Keating, Aurelien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel 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 and Tomás Helikar , SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools, BMC Systems Biology, 7:135, 2013 DOI

 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, 025114, 2013 DOI

 F. Büchel, N. Rodriguez, N. Swainston, C. Wrzodek, T. Czauderna, R. Keller, F. Mittag, M. Schubert, M. Glont, M. Golebiewski, M. van Iersel, S. Keating, M. Rall, M. Wybrow, H. Hermjakob, M. Hucka, D. Kell, W. Müller, P. Mendes, A. Zell, C. Chaouiya, J. Saez-Rodriguez, F. Schreiber, C. Laibe, A. Dräger, N. Le Novère, Path2Models: large-scale generation of computational models from biochemical pathway maps, BMC Systems Biology 2013 7:116 , 2013 DOI

N.D. Mendes, F. Lang, Y-S. Le Cornec, R. Mateescu, G. Batt, C. Chaouiya, Composition and abstraction of logical regulatory modules: application to multicellular systems, Bioinformatics, 29(6): 749-757, 2013 DOI

A. Naldi, E. Remy, D. Thieffry, and C. Chaouiya, Dynamically consistent reduction of logical regulatory graphs, Theoretical Computer Science 412(21):2207-18, 2011 DOI

C. Chaouiya, A. Naldi, E. Remy, D. Thieffry, Petri net representation of multi-valued logical regulatory graphs, Natural Computing Volume 10, Number 2, 727-750, 2011 DOI

G. Didier, E. Remy, C. Chaouiya, Mapping multivalued onto Boolean dynamics, Journal of Theoretical Biology, 270:177–184, 2011 DOI

A. Naldi, J. Carneiro, C. Chaouiya, D. Thieffry , Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling, PLoS Comput Biol 6(9): e1000912, 2010 DOI

Ö. Sahin, H. Fröhlich, C. Löbke, U. Korf, S. Burmester, M. Majety, J. Mattern, I. Schupp, C. Chaouiya, D. Thieffry, A. Poustka, S. Wiemann, T. Beissbarth, D. Arlt , Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance , BMC Systems Biology 2009, 3:1, 2009 DOI

A. Fauré, A. Naldi, F. Lopez, C. Chaouiya, A. Ciliberto, D. Thieffry, Modular logical modelling of the budding yeast cell cycle, Molecular BioSystems, 5:1787-96, 2009 DOI

 A. Naldi, D. Berenguier, A. Fauré, F. Lopez, D. Thieffry, C. Chaouiya , Logical modelling of regulatory networks with GINsim 2.3, Biosystems, 97(2):134-9, 2009 DOI

A. González, C. Chaouiya, D. Thieffry, Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc, Bioinformatics, 24(16):i234-40, 2008 DOI

 C. Chaouiya, E. Remy, D. Thieffry, Petri net modelling of biological regulatory networks, Journal of Discrete Algorithms, 6,2:165-77, 2008 DOI

L. Sánchez, C. Chaouiya, D. Thieffry, Segmenting the fly embryo: logical analysis of the role of the Segment Polarity cross-regulatory module, Int. J. Dev. Biol. 52:1059-75, 2008 DOI

C. Chaouiya , Petri net modelling of biological networks, Briefings in Bioinformatics, 8:210-219, 2007 DOI

A. Gonzalez, C. Chaouiya, D. Thieffry, Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disk, Genetics, 174:1625-34, 2006 DOI

A.Fauré, A.Naldi, C.Chaouiya, D.Thieffy , Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle, Bioinformatics, ISMB'06 Special Issue, 22(14):124-131, 2006 DOI

 A.Gonzalez, A. Naldi, L.Sánchez, D.Thieffry, C.Chaouiya, GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks, BioSystems, 84(2):91-100, 2006 DOI

E.Simão, E.Remy, D.Thieffry, C.Chaouiya , Qualitative Modelling of Regulated Metabolic Pathways: Application to the Tryptophan Biosynthesis in E.Coli. , Bioinformatics, ECCB'05 Special Issue 21: ii190-196, 2005 DOI

E. Remy, B. Mossé, C. Chaouiya, D. Thieffry, A description of dynamical graphs associated to elementary regulatory circuits, Bioinformatics ECCB'03 Special Issue, 19 Suppl. 2:172-178, 2003 DOI

C.Chaouiya, G.Liberopoulos, Y.Dallery , The extended kanban control system for production coordination of assembly manufacturing systems , IIE Transactions 32, 999-1012, 2000 DOI

Conference papers

P. L.Varela, P.T.Monteiro, C. Chaouiya, Impact of changing cell-cell communication network in models of epithelial pattern formation, IFAC-PapersOnLine ,Volume 52, Issue 26, Pages 38-44, 2019 DOI

P.L. Varela, I. Lynce, V. Manquinho, C. Chaouiya, P.T. Monteiro, Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids, Proc. 7th Int. Workshop on Static Analysis and Systems Biology (SASB 2016), ENTCS, 335: 113–130, 2018 DOI

P.T. Monteiro, W. Abou-Jaoudé, D. Thieffry, C. Chaouiya, Model Checking Logical Regulatory Networks, Proc. of the 12th IFAC - IEEE International Workshop on Discrete Event Systems, WODES'14 pp. 170-175, 2014 DOI pdf

A. Naldi, P. Monteiro, C. Chaouiya, Efficient handling of large signalling-regulatory networks by focusing on their core control, CMSB, Lecture Notes in Computer Science, 2012:288-306., 2012 DOI

F Corblin, E Fanchon, L Trilling, C Chaouiya, D Thieffry, Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data, IPCAT'12 Proc. LNCS 7223:25-30, 2012 DOI

P. T. Monteiro, C. Chaouiya, Efficient verification for logical models of regulatory networks, In PACBB'12 proc. Advances in Intelligent and Soft Computing, Vol. 154:259-267, 2012 DOI

B. Luna, C. Chaouiya, Relating Formalisms for the Qualitative Modelling of Regulatory Networks, 5th In. Conf on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011) in Advances in Intelligent and Soft Computing, Vol 93, pp. 293-302, 2011 DOI

C. Chaouiya, A. Naldi, E. Remy, D. Thieffry, Reduction of logical models of regulatory networks yields insight into dynamical properties , In 2010 IEEE International Conference on Control Applications (CCA), IEEE Xplore, pp. 524-29 , 2010 DOI

A. Naldi,E. Remy, D. Thieffry, C. Chaouiya, A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties, CMSB 2009, LNCS/LNBI: 5688:266-80, 2009 DOI

C. Chaouiya, Qualitative Modelling of Biological Regulatory Networks Combining a Logical Multi-Valued Formalism and Petri Nets, 9th Int. Workshop on Discrete Events Systems, WODES'08, pp. 263-68, 2008 DOI

A. Naldi, D. Thieffry, C. Chaouiya , Decision diagrams for the representation and analysis of logical models of genetic networks, CMSB 2007. LNCS/LNBI 4695:233-247, 2007 DOI

C. Chaouiya, E. Remy, D. Thieffry , Qualitative Petri Net Modelling of Genetic Networks , CMSB 2005 Transactions on Computation Systems Biology VI 4220:95-112, 2006 DOI

E. Remy, P. Ruet, L. Mendoza, D. Thieffry, and C. Chaouiya, From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits, BioConcur 2004. Transactions on Computation Systems Biology VII (TCSB) 4230: 55-72, 2006 DOI

C. Chaouiya, E. Remy, P. Ruet, D. Thieffry, Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets, in ICATPN'04, LNCS 3099: 137-156, 2004 DOI pdf

C. Chaouiya, E. Remy, B. Mossé and D. Thieffry, Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework, POSTA 2003, LNCIS 294 : 119-126. , 2003 DOI pdf

C.Chaouiya, Y.Dallery, Throughput Comparisons Concerning Discrete and Continuous Fork Join Queuing Networks with Finite Buffers, 4th Int. Workshop On Queueing Networks With Finite Capacity (QNETs 2000), Ilkley, U.K., 2000

Preprints (arXiv)

A. Naldi, C. Hernandez, N. Levy, G. Stoll, P.T. Monteiro, C. Chaouiya, T. Helikar, A. Zinovyev, L. Calzone, S. Cohen-Boulakia, D. Thieffry, L. Paulev&eactue;, The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks bioRxiv 290411, 2018

A. Naldi, CC. Hernandez, W. Abou-Jaoudé, P.T. Monteiro, C. Chaouiya, D. Thieffry, Logical modelling and analysis of cellular regulatory networks with GINsim 3.0 bioRxiv 289298, 2018

Elisa Tonello, Etienne Farcot, Claudine Chaouiya, Local negative circuits and cyclic attractors in Boolean networks with at most five components arXiv:1803.02095, 2018


C. Chaouiya, Réseaux de Petri et modelisation en biologie moleculaire, Technique et Science Informatiques, TSI 26(1-2):229-36, 2007

H. de Jong, D. Ropers, C. Chaouiya, D. Thieffry, Modélisation, analyse et simulation de réseaux de régulation génique, Biofutur, 252:36-40, 2005