Journals Conferences

In international journals

List of bibtex references
[1] 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, and Pedro Tiago Monteiro. YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. Nucleic Acids Research, 11 2022. gkac1041. [ DOI | http ]
[2] Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, and Laurence Calzone. Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings in Bioinformatics, 2022. [ DOI | http ]
[3] Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S Malik Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C Freeman, Paul Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomáš Helikar, and 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 in Bioinformatics, 2021. bbaa046. [ DOI | http ]
[4] Gianluca Selvaggio, Claudine Chaouiya, and Florence Janody. In silico logical modelling to uncover cooperative interactions in cancer. International Journal of Molecular Sciences, 22(9), 2021. [ DOI | http ]
[5] Andreas Dräger, Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, and Juilee Thakar. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics, 2021. btab229. [ DOI | http ]
[6] Pedro T. Monteiro, Tiago Pedreira, Monica Galocha, Miguel C. Teixeira, and Claudine Chaouiya. Assessing regulatory features of the current transcriptional network of saccharomyces cerevisiae. Scientific Reports, 10(1), oct 2020. [ DOI ]
[7] Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik-Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier-Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, and SBML Level 3 Community members. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, 16(8):e9110, 2020. [ DOI | http ]
[8] Gianluca Selvaggio, Sara Canato, Archana Pawar, Pedro T Monteiro, Patrícia S. Guerreiro, M. Manuela Brás, Florence Janody, and Claudine Chaouiya. Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors. Cancer Research, 2020. [ DOI | http ]
[9] Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C Lovering, Sandra Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del Toro, Asmund 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, and Martin Kuiper. The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics, 2020. btaa622. [ DOI | http ]
[10] 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 ]
[11] 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 Sheriff, Lucian P Smith, Dagmar Waltemath, Darren J Wilkinson, and Fengkai Zhang. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J Integr Bioinform, 16(2), Jun 2019. [ DOI ]
[12] 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 ]
[13] 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 ]
[14] 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 ]
[15] 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 ]
[16] 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 ]
[17] 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 ]
[18] 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 ]
[19] Elisabeth Remy, Sandra Rebouissou, Claudine Chaouiya, Andrei Zinovyev, François 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 ]
[20] 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 ]
[21] Claudine Chaouiya, Sarah M Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P van Iersel, Nicolas Le Novère, and Tomáš 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 ]
[22] 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 ]
[23] 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 ]
[24] 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 ]
[25] 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 ]
[26] Claudine Chaouiya and Elisabeth Remy. Logical modelling of regulatory networks, methods and applications. Bull Math Biol, 75(6):891--5, Jun 2013. [ DOI ]
[27] 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 ]
[28] 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 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 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 ]
[29] 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 ]
[30] 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 ]
[31] 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 ]
[32] Claudine Chaouiya, Aurélien Naldi, and Denis Thieffry. Logical modelling of gene regulatory networks with ginsim. Methods Mol Biol, 804:463--79, 2012. [ DOI ]
[33] Gilles Didier, Elisabeth Remy, and Claudine Chaouiya. Mapping multivalued onto Boolean dynamics. J Theor Biol, 270(1):177--84, Feb 2011. [ DOI ]
[34] 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 ]
[35] 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 ]
[36] 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 ]
[37] 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 ]
[38] 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 ]
[39] 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 ]
[40] 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 ]
[41] 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 ]
[42] 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 ]
[43] Claudine Chaouiya. Petri net modelling of biological networks. Brief Bioinform, 8(4):210--9, Jul 2007. [ DOI ]
[44] 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 ]
[45] Claudine Chaouiya, Hidde de Jong, and Denis Thieffry. Dynamical modeling of biological regulatory networks. Biosystems, 84(2):77--80, May 2006. [ DOI ]
[46] 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 ]
[47] 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 ]
[48] 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 ]
[49] 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.
[50] 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 ]

Conference proceedings

[1] Hannes Klarner, Elisa Tonello, Laura Fontanals, Florence Janody, Claudine Chaouiya, and Heike Siebert. Detection of markers for discrete phenotypes. In The 12th International Conference on Computational Systems-Biology and Bioinformatics, CSBio2021, page 64–68, New York, NY, USA, 2021. Association for Computing Machinery. [ DOI | http ]
[2] Pedro L. Varela, Pedro T. Monteiro, and Claudine Chaouiya. Impact of changing cell-cell communication network in models of epithelial pattern formation. IFAC-PapersOnLine, 52(26):38 -- 44, 2019. 8th Conference on Foundations of Systems Biology in Engineering FOSBE 2019. [ DOI | http ]
[3] 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 ]
[4] 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 ]
[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] 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 ]
[7] 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 ]
[8] 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 ]
[9] 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 ]
[10] 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 ]
[11] 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 ]
[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] 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.
[14] 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.
[15] 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 ]
[16] 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 ]
[17] 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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