Publications list

Bibliographies

Publications

Sylvain Soliman and Andrei Zinovyev. Reduction of differential models. deliverable D1.2, ANR CALAMAR (ANR-08-SYSC-003), September 2011. [ bib ]

Laurence Calzone and Sylvain Soliman. Quantitative modelling of the RB/E2F network. deliverable D3.2, ANR CALAMAR (ANR-08-SYSC-003), September 2011. [ bib ]

Steven Gay, Thierry Martinez, Sylvain Soliman, and François Fages. A constraint program for subgraph epimorphisms with application to identifying model reductions in systems biology. In Proceedings of the seventh Workshop on Constraint Based Methods for Bioinformatics WCB'11, colocated with CP 2011, pages 59-66, September 2011. [ bib ]

Aurélien Rizk, Grégory Batt, François Fages, and Sylvain Soliman. Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures. Theoretical Computer Science, 412(26):2827-2839, June 2011. [ bib | DOI ]

Elisabetta De Maria, François Fages, Aurélien Rizk, and Sylvain Soliman. Design, optimization, and predictions of a coupled model of the cell cycle, circadian clock, dna repair system, irinotecan metabolism and exposure control under temporal logic constraints. Theoretical Computer Science, 412(21):2108-2127, May 2011. [ bib | DOI ]

Sylvain Soliman. Constraint programming for the dynamical analysis of biochemical systems - a survey. deliverable D1.6, ANR CALAMAR (ANR-08-SYSC-003), February 2011. [ bib | PDF ]

Laurence Calzone, Claudine Chaouiya, Élisabeth Remy, and Sylvain Soliman. Qualitative modelling of the RB/E2F network. deliverable D3.1, ANR CALAMAR (ANR-08-SYSC-003), February 2011. [ bib | PDF ]

Steven Gay, François Fages, Thierry Martinez, Sylvain Soliman, and Christine Solnon. On the subgraph epimorphism problem. Discrete Applied Mathematics, 2011. [ bib ]

François Fages, Philip Robin, and Sylvain Soliman. Simulations hybrides. deliverable INR-04-L3-D14, OSEO project BioIntelligence, 2011. [ bib ]

François Fages, Dragana Jovanovska, Aurélien Rizk, and Sylvain Soliman. BIOCHAM v3.3 Reference Manual. INRIA, 2011. [ bib | link ]

Sylvain Soliman and Monika Heiner. A unique transformation from ordinary differential equations to reaction networks. PLoS One, 5(12):e14284, December 2010. [ bib | DOI ]

Steven Gay, François Fages, and Sylvain Soliman. From models to metamodels. In IPG'10 Integrative Post-Genomique. University of Lyon, France, November 2010. [ bib ]

Faten Nabli and Sylvain Soliman. Steady-state solution of biochemical systems, beyond S-Systems via T-invariants. In Paola Quaglia, editor, CMSB'10: Proceedings of the 8th International Conference on Computational Methods in Systems Biology, pages 14-22. CoSBi, ACM, October 2010. [ bib | DOI | link ]

Dragana Jovanovska, François Fages, and Sylvain Soliman. SBGN support in BIOCHAM. In the COmputational Modeling in BIology NEtwork, (invited talk), University of Edinburgh, UK, October 2010. Nature Precedings. [ bib | DOI ]

François Fages and Sylvain Soliman. New computational methods for systems biology (tutorial). In ICSB'10 11th International Conference on Systems Biology: abstract of tutorials. University of Edinburgh, UK, October 2010. [ bib ]

Steven Gay, Sylvain Soliman, and François Fages. A graphical method for reducing and relating models in systems biology. In Graphical models for reasoning on biological systems: computational challenges (Satellite workshop), ISCTE Lisbon University Institute, Portugal, September 2010. Complex Systems Society. [ bib ]

François Fages, Grégory Batt, Elisabetta De Maria, Dragana Jovanovska, Aurélien Rizk, and Sylvain Soliman. Computational systems biology in biocham. ERCIM News, 82, July 2010. [ bib | link ]

Dragana Jovanovska, François Fages, and Sylvain Soliman. Modelling molecular networks with the biocham graphical user interface (poster). In Evry Spring School on Modelling Complex Biological Systems in the Context of Genomics, Evry, France, May 2010. [ bib ]

Faten Nabli, Sylvain Soliman, and François Fages. Bipartite graph properties and systems biology (poster). In Evry Spring School on Modelling Complex Biological Systems in the Context of Genomics, Evry, France, May 2010. [ bib ]

Sylvain Soliman, Claudine Chaouiya, Grégory Batt, François Fages, Élisabeth Remy, Franck Pommereau, and Laurence Calzone. Modelling molecular networks: relationships between different formalisms and levels of details. Research Report RR-7221, INRIA, 2010. [ bib | OAI ]

Steven Gay, Sylvain Soliman, and François Fages. A graphical method for reducing and relating models in systems biology. Bioinformatics, 26(18):i575-i581, 2010. [ bib | DOI ]

Elisabetta De Maria, François Fages, Aurélien Rizk, and Sylvain Soliman. Design, optimization, and predictions of a coupled model of the cell cycle, circadian clock, dna repair system, irinotecan metabolism and exposure control under temporal logic constraints (poster). In European Conference on Computational Biology ECCB'10, Gent, Belgium, 2010. [ bib ]

Elisabetta De Maria, François Fages, and Sylvain Soliman. A coupled model of cell cycle, circadian clock, dna repair system, irinotecan metabolism, and exposure control. In 42ème congrès de la société Francophone de Chronobiologie, 2010. [ bib ]

Aurélien Rizk, Grégory Batt, François Fages, and Sylvain Soliman. A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics, 12(25):il69-il78, June 2009. [ bib | DOI ]

Elisabetta De Maria, François Fages, and Sylvain Soliman. Model-based predictions of the influence of circadian clock genes knock-outs on the cell cycle. INRIA Research Report RR-7064, INRIA, June 2009. [ bib | OAI ]

Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordan, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, and Paolo Ballarini. Analyzing various models of circadian clock and cell cycle coupling. In Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami, editors, Formal Methods in Molecular Biology, number 09091 in Dagstuhl Seminar Proceedings, Dagstuhl, Germany, May 2009. Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany. [ bib | link ]

Sylvain Soliman. Modelling biochemical reaction networks with biocham extracting qualitative and quantitative information from the structure. In Proceedings of the 6th Vienna Conference on Mathematical Modelling MATHMOD'09, volume 35, pages 2304-2312. ARGESIM, February 2009. [ bib | PDF ]

Sriram Krishnamachari, Sylvain Soliman, and François Fages. Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in candida albicans. Journal of Theoretical Biology, 258(1):71-88, 2009. [ bib | DOI ]

François Fages, Sylvain Soliman, and Aurélien Rizk. BIOCHAM v2.8 user's manual. INRIA, 2009. [ bib | link ]

Elisabetta De Maria, François Fages, and Sylvain Soliman. On coupling models using model-checking: Effects of irinotecan injections on the mammalian cell cycle. In CMSB'09: Proceedings of the seventh international conference on Computational Methods in Systems Biology, volume 5688 of Lecture Notes in BioInformatics, pages 142-157. Springer-Verlag, 2009. [ bib | DOI ]

Aurélien Rizk, Grégory Batt, François Fages, and Sylvain Soliman. On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology. In Monika Heiner and Adeline Uhrmacher, editors, CMSB'08: Proceedings of the fourth international conference on Computational Methods in Systems Biology, volume 5307 of Lecture Notes in Computer Science, pages 251-268. Springer-Verlag, October 2008. [ bib | DOI ]

Sylvain Soliman. Finding minimal P/T-invariants as a CSP. In Proceedings of the fourth Workshop on Constraint Based Methods for Bioinformatics WCB'08, associated to CPAIOR'08, May 2008. [ bib | PDF ]

François Fages and Sylvain Soliman. From reaction models to influence graphs and back: a theorem. In Proceedings of Formal Methods in Systems Biology FMSB'08, number 5054 in Lecture Notes in Computer Science. Springer-Verlag, February 2008. [ bib | DOI ]

François Fages and Sylvain Soliman. Formal cell biology in BIOCHAM. In M. Bernardo, P. Degano, and G. Zavattaro, editors, 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology SFM'08, volume 5016 of Lecture Notes in Computer Science, pages 54-80, Bertinoro, Italy, February 2008. Springer-Verlag. [ bib | DOI ]

François Fages, Francesca Rossi, and Sylvain Soliman, editors. Recent Advances in Constraints, 12th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming CSCLP'07, volume 5129 of Lecture Notes in Artificial Intelligence. Springer-Verlag, Rocquencourt, France, 2008. [ bib | DOI ]

François Fages and Sylvain Soliman. Abstract interpretation and types for systems biology. Theoretical Computer Science, 403(1):52-70, 2008. [ bib | DOI ]

Aurélien Rizk, Grégory Batt, François Fages, and Sylvain Soliman. Towards a general computational method for robustness analysis. In International Conference Frontiers in Synthetic Biology, Boston, 2008. [ bib ]

Aurélien Rizk, Grégory Batt, François Fages, and Sylvain Soliman. Towards a general computational method for robustness analysis (poster). In International Conference Synthetic Biology 4.0, Hong Kong, 2008. [ bib ]

Domitille Heitzler, Guillaume Durand, Laurence Dupuy, Christophe Gauthier, Vincent Piketty, Pascale Crépieux, Aurélien Rizk, Sylvain Soliman, François Fages, Frédérique Clément, and Eric Reiter. Modelling of fshr-induced signalling network. In Poster, International Conference on Gonadotropins and Receptors IGCR'08, London, UK, 2008. [ bib ]

François Fages and Sylvain Soliman. Model revision from temporal logic properties in systems biology. In Probabilistic Inductive Logic Programming, volume 4911 of Lecture Notes in Computer Science, pages 287-304. Springer-Verlag, 2008. [ bib | DOI ]

Sylvain Soliman. Langages formels pour la biologie systémique dans la machine abstraite biochimique BIOCHAM. Avancées en Sciences de l'Information, October 2007. [ bib | realplayer | PDF ]

François Fages and Sylvain Soliman, editors. Actes des 3ièmes Journées Francophones de Programmation par Contraintes JFPC'07, Rocquencourt, France, June 2007. INRIA. [ bib | link ]

Jean Clairambault, François Fages, and Sylvain Soliman. Patient-tailored cancer therapeutics - the tempo project. ERCIM News, 69:24-25, April 2007. [ bib | link ]

Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, and Sylvain Soliman. Langages formels dans la machine abstraite biochimique BIOCHAM. Techniques et Sciences Informatiques, 26(1-2):47-72, 2007. [ bib | DOI ]

Rémy Haemmerlé, François Fages, and Sylvain Soliman. Closures and modules within linear logic concurrent constraint programming. In V. Arvind and Sanjiva Prasad, editors, Proceedings of FSTTCS 2007, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, volume 4855 of Lecture Notes in Computer Science, pages 544-556. Springer-Verlag, 2007. [ bib | DOI ]

Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, and Sylvain Soliman. Machine learning biochemical networks from temporal logic properties. In Gordon Plotkin, editor, Transactions on Computational Systems Biology VI, volume 4220 of Lecture Notes in BioInformatics, pages 68-94. Springer-Verlag, November 2006. [ bib | DOI ]

Laurence Calzone and Sylvain Soliman. Coupling the cell cycle and the circadian cycle. Research Report 5835, INRIA, February 2006. [ bib | OAI ]

Rémy Haemmerlé, François Fages, and Sylvain Soliman. On internalizing modules as agents in concurrent constraint programming. Technical Report RR-5981, INRIA, 2006. [ bib | OAI ]

Laurence Calzone, François Fages, and Sylvain Soliman. BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics, 22(14):1805-1807, 2006. [ bib | DOI ]

François Fages and Sylvain Soliman. Type inference in systems biology. In Corrado Priami, editor, CMSB'06: Proceedings of the fourth international conference on Computational Methods in Systems Biology, volume 4210 of Lecture Notes in Computer Science. Springer-Verlag, 2006. [ bib | DOI ]

Laurence Calzone and Sylvain Soliman. BIOCHAM: une approche langage de la biologie des systèmes. Conférence OUEST-genopole, September 2005. [ bib | PDF ]

Rolf Backofen, Liviu Badea, Pedro Barahona, Mikael Berndtsson, Albert Burger, Gihan Dawelbait, Andreas Doms, François Fages, Anca Hotaran, Vaida Jakoniene, Ludwig Krippahl, Patrick Lambrix, Kenneth McLeod, Werner Nutt, Bjorn Olsson, Michael Schroeder, Anna Schroiff, Loic Royer, Sylvain Soliman, He Tan, Doina Tilivea, and Sebastian Will. Requirements and specification of bioinformatics use cases. deliverable A2-D3, Dresden, August 2005. [ bib | PDF ]

Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, and Sylvain Soliman. Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle. In Guy Perrière, Alain Guénoche, and Christophe Geourjon, editors, Actes de JOBIM'05, pages 183-192, Lyon, July 2005. [ bib | OAI ]

Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman, and Laurence Calzone. Learning transition rules from temporal logic properties. Research Report 5543, INRIA, April 2005. [ bib | OAI ]

Rolf Backofen, Liviu Badea, Pedro Barahona, Albert Burger, Gihan Dawelbait, Andreas Doms, François Fages, Anca Hotaran, Vaida Jakoniene, Ludwig Krippahl, Patrick Lambrix, Kenneth McLeod, Steffen Möller, Werner Nutt, Bjorn Olsson, Michael Schroeder, Sylvain Soliman, He Tan, Doina Tilivea, and Sebastian Will. Usage of bioinformatics tools and identification of information sources. deliverable A2-D2, Lisbon, March 2005. [ bib | PDF ]

François Fages and Sylvain Soliman, editors. Proceedings of PPSWR'05, Third International Workshop on Principles and Practice of Sematic Web Reasoning, volume 3703 of Lecture Notes in Computer Science, Dagstuhl Castle, Germany, 2005. Springer-Verlag. [ bib | DOI ]

Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Lucie Gentils, and Sylvain Soliman. Machine learning bio-molecular interactions from temporal logic properties. In Gordon Plotkin, editor, CMSB'05: Proceedings of the third international conference on Computational Methods in Systems Biology, 2005. [ bib | OAI ]

Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, and Sylvain Soliman. A machine learning approach to biochemical reaction rules discovery. In Francis J. Doyle III, editor, Proceedings of Foundations of Systems Biology and Engineering FOSBE'05, pages 375-379, Santa Barbara, 2005. [ bib | OAI ]

François Fages, Sylvain Soliman, and Nathalie Chabrier-Rivier. Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM. Journal of Biological Physics and Chemistry, 4(2):64-73, October 2004. [ bib | .ps.gz ]

François Fages, Sylvain Soliman, and Rémi Coolen. CLPGUI: a generic graphical user interface for constraint logic programming. Journal of Constraints, Special Issue on User-Interaction in Constraint Satisfaction, 9(4):241-262, October 2004. [ bib | DOI ]

Nathalie Chabrier-Rivier, François Fages, and Sylvain Soliman. The biochemical abstract machine BIOCHAM. In Proceedings of the 5th International Conference on Systems Biology ICSB'04, October 2004. [ bib ]

Rolf Backofen, Mike Badea, Pedro Barahona, Liviu Badea, François Bry, G. Dawelbait, Andreas Doms, François Fages, C. Goble, A. Henschel, A. Hotaran, B. Huang, L. Krippahl, Patrick Lambrix, Werner Nutt, Michael Schroeder, Sylvain Soliman, and Sebastian Will. Poster: Towards a semantic web for bioinformatics. In Proceedings of Bioinformatics 2004, Linköping, Sweden, June 2004. SocBIN - Society for Bioinformatics in the Nordic countries. [ bib ]

Sylvain Soliman. Pi-calcul et LCC, une odyssée de l'espace. In Fred Mesnard, editor, Programmation en logique avec contraintes (Actes de JFPLC 2004), pages 201-218, Angers (France), June 2004. Hermès. [ bib | PDF ]

Étienne Parizot, Sylvain Soliman, and François Fages. La programmation par contraintes. Dossier algorithmique du site web de vulgarisation interstices.info, February 2004. [ bib | link ]

Rolf Backofen, Mike Badea, Albert Burger, François Fages, Patrick Lambrix, Werner Nutt, Michael Schroeder, Sylvain Soliman, and Sebastian Will. State-of-the-art in bioinformatics. deliverable A2-D1, Dresden, 2004. [ bib | PDF ]

Nathalie Chabrier, François Fages, and Sylvain Soliman. BIOCHAM user's manual. INRIA, 2004. [ bib | link ]

Nathalie Chabrier-Rivier, François Fages, and Sylvain Soliman. The biochemical abstract machine BIOCHAM. In Patrick Amar, Jean-Paul Cornet, François Képès, and Victor Norris, editors, Proceedings of the Evry Spring School on Modelling and Simulation of Biological Processes in the Context of Genomics, pages 35-49. Platypus Press, 2004. [ bib | .ps.gz ]

Nathalie Chabrier-Rivier, François Fages, and Sylvain Soliman. The biochemical abstract machine BIOCHAM. In Vincent Danos and Vincent Schächter, editors, CMSB'04: Proceedings of the second international workshop on Computational Methods in Systems Biology, volume 3082 of Lecture Notes in BioInformatics, pages 172-191. Springer-Verlag, 2004. [ bib | DOI ]

Sylvain Soliman and François Fages. CMBSlib: a library for comparing formalisms and models of biological systems. In Vincent Danos and Vincent Schächter, editors, CMSB'04: Proceedings of the second international workshop on Computational Methods in Systems Biology, volume 3082 of Lecture Notes in BioInformatics, pages 231-235. Springer-Verlag, 2004. [ bib | DOI ]

Sylvain Soliman. Pi-calculus and LCC, a space odyssey. Research Report RR-4855, INRIA, June 2003. [ bib | OAI ]

Sylvain Soliman. CLP implementation of a phase model checker. LICS'02: 17th Annual IEEE Symposium on Logic In Computer Science, Short Session, 2002. [ bib | .ps.gz ]

Sylvain Soliman. Phase model checking for some linear logic calculi. In Hans de Nivelle and Stephan Schultz, editors, Proceedings of the Second International Workshop of the Implementation of Logics, Havana, Cuba, MPI-I-2001-2-006, pages 60-80. Max-Planck-Institut für Informatik, December 2001. [ bib | .ps.gz ]

Sylvain Soliman. Programmation concurrente avec contraintes et logique linéaire. PhD thesis, Université Paris 7, Denis Diderot, April 2001. [ bib | .ps.gz ]

François Fages, Paul Ruet, and Sylvain Soliman. Linear concurrent constraint programming: operational and phase semantics. Information and Computation, 165(1):14-41, February 2001. [ bib | DOI ]

François Fages, Paul Ruet, and Sylvain Soliman. Phase semantics and verification of concurrent constraint programs. In Proceedings of the 13thAnnual IEEE Symposium on Logic In Computer Science, pages 141-152, Indianapolis, 1998. IEEE Computer Society. [ bib | DOI ]

François Fages, Paul Ruet, and Sylvain Soliman. Linear concurrent constraint programming: operational and phase semantics. In Proc. COMPULOG Workshop associated to Constraint Programming Conf. CP'97, Linz, Austria, October 1997. [ bib ]

Sylvain Soliman. Preuves sémantiques pour les programmes concurrents avec contraintes. Rapport de stage de DEA, INRIA, 1997. [ bib ]