Selected publications

2017

François Fages. AI in Biological Modeling. In A Guided Tour of Artificial Intelligence Research. Springer-Verlag, 2017. [ preprint ]

François Fages, Le Guludec, Guillaume. Programmation biochimique et algorithmes mixtes analogiques-digitaux dans la cellule. In Sciences du vivant, science de l'information. Hermes, 2017. [ preprint ]

Cristian Versari, Szymon Stoma, Kirill Batmatov , Artémis Llamosi, Filip Moroz, Adam Kaczmarek , Matt Deyell, Cédric Lhoussaine, P. Hersen and G. Batt. Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform. Royal Society Interface, 14, 2017.

2016

Abderrahmane Aggoun, Nicolas Beldiceanu, Gilles Chabert, François Fages. Packing with Complex Shapes. ERCIM News, 2016(105), 2016. [ preprint ]

Abder Aggoun, Ahmed Rhiat, François Fages. Panorama of real-life applications in logistics embedding bin packing optimization algorithms, robotics and cloud computing technologies. In Proc. 3rd IEEE International Conference on Logistics Operations Management, GOL'16, 2016. [ preprint ]

François Bertaux. Cell-based multi-scale modeling for systems and synthetic biology: from stochastic gene expression in single cells to spatially organized cell populations. Thèse de doctorat, Université Paris - Diderot, 2016. [ preprint ]

François Fages, Thierry Martinez, David Rosenblueth, Sylvain Soliman. Influence Systems vs Reaction Systems. In CMSB'16: Proceedings of the fourteenth international conference on Computational Methods in Systems Biology, pages 98–115, volume 9859 of Lecture Notes in BioInformatics. Springer-Verlag, 2016. [ preprint ]

A. Llamosi, A.M. Gonzales-Vargas, E. Cinquemani , G. Ferrari-Trecate, P. Hersen, G. Batt. What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast. PLOS Computational Biology, 9(12), 2016.

Thierry Martinez, François Fages, Abder Aggoun. A Stochastic Continuous Optimization Backend for MiniZinc with Applications to Geometrical Placement Problems. In Proceedings of the 13th International Conference on Integration of Artificial Intelligence and Operations Research Techniques in Constraint Programming, CPAIOR'16, 2016. [ preprint ]

Thierry Martinez, François Fages, Abder Aggoun. Un solveur d'optmization stochastique pour MiniZinc avec des applications à des problèmes de placements géométriques. In Douzièmes Journées Francophones de Programmation par Contraintes JFPC'16, 2016. [ preprint ]

Faten Nabli, Thierry Martinez, François Fages, Sylvain Soliman. On Enumerating Minimal Siphons in Petri nets using CLP and SAT solvers: Theoretical and Practical Complexity. Constraints, 21(2):251–276, 2016. [ preprint ]

Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry. Logical model specification aided by model- checking techniques: application to the mammalian cell cycle regulation. Bioinformatics, 32(17):i772-i780, 2016. [ preprint ]

Pauline Traynard, Céline Feillet, Sylvain Soliman, Franck Delaunay, François Fages. Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-alpha Up-Regulation during Mitosis. Biosystems, 149:59–69, 2016. [ preprint ]

Pauline Traynard. Model Building by Temporal Logic Constraint Solving: Investigation of the Coupling between the Cell Cycle and the Circadian Clock. Thèse de doctorat, Université Paris - Diderot, 2016. [ preprint ]

2015

Tai-Yin Chiu, Hui-Ju K. Chiang, Ruei-Yang Huang , Jie-Hong R. Jiang, François Fages. Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications. PLoS ONE, 10(9), 2015.

Hui-Ju Chiang, François Fages, Jie-Hong Jiang, Sylvain Soliman. Hybrid Simulations of Heterogeneous Biochemical Models in SBML. ACM Transactions on Modeling and Computer Simulation (TOMACS), 25(2):14:1–14:22, 2015. [ preprint ]

Hui-Ju Katherine Chiang. Biomolecular System Design: Architecture, Synthesis, and Simulation. Thèse de doctorat, National Taiwan University, Taiwan, 2015. [ preprint ]

Hui-Ju Chiang, Jie-Hong Jiang, François Fages. Reconfigurable Neuromorphic Computation in Biochemical Systems. In Proc. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society EMBC, 2015. [ preprint ]

François Fages. Machinerie cellulaire et programmation biochimique: vers une informatique de la cellule (exposé invité). In Actes 11ièmes Journèes Francophones de Programmation par Contraintes JFPC'15, 2015.

François Fages, Steven Gay, Sylvain Soliman. Inferring Reaction Systems from Ordinary Differential Equations. Theoretical Computer Science, 599:64–78, 2015. [ preprint ]

Steven Gay. Subgraph Epimorphisms: Theory and Application to Model Reductions in Systems Biology. Thèse de doctorat, Université Paris - Diderot, 2015. [ preprint ]

Artemis Llamosi. Effects of repeated osmotic stress on gene expression and growth: from cell-to-cell variability to cellular individuality in the budding yeast Saccharomyces cerevisiae. Thèse de doctorat, Université Denis Diderot, Paris, 2015. [ preprint ]

Thierry Martinez. Execution models for Constraint Programming: kernel language design through semantics equivalence. Thèse de doctorat, Université Denis Diderot, Paris, 2015. [ preprint ]

Thierry Martinez, François Fages. On Translating MiniZinc Constraint Models into Fitness Function for Evolutionary Algorithms: Application to Continuous Placement Problems. In Proceedings of the sixth Workshop on Bin Packing and Placement Constraints BPPC'15, associated to CP'15, 2015. [ preprint ]

Thierry Martinez, François Fages, Sylvain Soliman. Search by Constraint Propagation. In Proceedings of the 17th International Conference on Principles and Practice of Declarative Programming, PPDP'15, pages 173–183. ACM, 2015. [ preprint ]

Pauline Traynard, François Fages, Sylvain Soliman. Model-based Investigation of the Effect of the Cell Cycle on the Circadian Clock through Transcription Inhibition during Mitosis. In CMSB'15: Proceedings of the thirteenth international conference on Computational Methods in Systems Biology, pages 208–221, volume 9308 of Lecture Notes in BioInformatics. Springer-Verlag, 2015. [ preprint ]

2014

Abder Aggoun, François Fages, Nicolas Beldiceanu, Gilles Chabert. Packing with complex shapes in Supply Chain Networked Warehouse Management Systems. In Int. Conf. on Metaheuristics and Nature Inspired Computing, 2014. [ preprint ]

Grégory Batt. Design, Optimization and Control in Systems and Synthetic Biology. Habilitation à Diriger des Recherches, Université Paris-Diderot, 2014. [ preprint ]

D. Bikard, W. Euler, W. Jiang, N. Philip, G. Goldberg, X. Duportet, V. Fischetti, L. Marraffini. Exploiting CRISP-Cas nucleases to produce sequence-specific antimicrobials. Nature Biotechnologies, 32(11), 2014. [ preprint ]

F. Bertaux, S. Stoma, D. Drasdo, G. Batt. Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance. PLoS Computational Biology, 10(10):e1003893, 2014.

Tai-Yin Chiu, Ruei-Yang Huang, Hui-Ju Katherine Chiang, Jie-Hong Jiang, François Fages. Configurable Linear Control of Biochemical Systems. In IWBDA'14: Proceedings of the sixth International Workshop on Bio-Design Automation, 2014. [ preprint ]

Katherine Chiang, Jie-Hong Jiang, François Fages. Building Reconfigurable Circuitry in a Biochemical World. In BioCAS'14: IEEE Biomedical Circuits and Systems Conference. IEEE, 2014. [ preprint ]

Xavier Duportet. Developing new tools and platforms for mammalian synthetic biology: from the assembly and chromosomal integration of large genetic circuits to the engineering of artificial intercellular communication systems. Thèse de doctorat, Université Paris - Diderot, 2014. [ preprint ]

X. Duportet, L. Wroblewska, P. Guye, Y. Li and J. Eyquem, J. Rieders, G. Batt, R. Weiss. A platform for rapid prototyping of synthetic gene networks in mammalian cells. Nucleic Acids Research, 42(21), 2014. [ preprint ]

François Fages. Cells as Machines: towards Deciphering Biochemical Programs in the Cell (Keynote Talk). In 21st European Conference on Artificial Intelligence ECAI'14, 2014. [ slides ]

François Fages. Cells as Machines: towards Deciphering Biochemical Programs in the Cell (Invited Talk). In Proc. 10th International Conference on Distributed Computing and Internet Technology ICDCIT'14, pages 50–67, volume 8337 of Lecture Notes in Computer Science. Springer-Verlag, 2014. [ preprint ]

David Fournier, François Fages, Denis Mulard. A Greedy Heuristic for Optimizing Metro Regenerative Energy Usage. In Proceedings of the second international conference on railway technology: research, development and maintenance. Civil-Comp Press, 2014. [ preprint ]

David Fournier. Metro Regenerative Braking Energy Optimization through Rescheduling: Mathematical Model and Greedy Heuristics Compared to MILP and CMA-ES. Thèse de doctorat, Université Paris - Diderot, 2014. [ preprint ]

François Fages, Pauline Traynard. Temporal Logic Modeling of Dynamical Behaviors: First-Order Patterns and Solvers. In Logical Modeling of Biological Systems, pages 291–323. John Wiley Sons, Inc., 2014. [ preprint ]

Steven Gay, François Fages, Thierry Martinez, Sylvain Soliman, Christine Solnon. On the subgraph Epimorphism Problem. Discrete Applied Mathematics, 162:214–228, 2014. [ preprint ]

L. Maruthi, I. Tkachev, A. Carta, E. Cinquemani , P. Hersen, G. Batt, A. Abate. Towards real-time control of gene expression at the single cell level: a stochastic control approach. In Proceedings of the 12th International Conference on Computational Methods in Systems Biology, pages 155–172, CMSB '14. Springer, 2014.

A. Oyarzun, J.-B. Lugagne, G.-B. Stan. Noise propagation in synthetic gene circuits for metabolic control. ACS Synthetic Biology, 2014. [ preprint ]

Sylvain Soliman, François Fages, Ovidiu Radulescu. A constraint solving approach to model reduction by tropical equilibration. Algorithms for Molecular Biology, 9(24), 2014.

Pauline Traynard, François Fages, Sylvain Soliman. Trace Simplifications preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock (best student paper award). In CMSB'14: Proceedings of the twelth international conference on Computational Methods in Systems Biology, pages 114–128, Lecture Notes in BioInformatics. Springer-Verlag, 2014. [ preprint ] [ slides ]

J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages, S. Bottani, P. Hersen, G. Batt. In silico control of biomolecular processes. In Computational Methods in Synthetic Biology. Humana Press, Springer, 2014.

2013

Stefano Bistarelli, Francesco Santini. Coalitions of Arguments: An Approach with Constraint Programming. Fundamenta Informaticae, IOS Press, 124(4), 2013.

Katherine Chiang, François Fages, Jie-Hong Jiang, Sylvain Soliman. On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models. In CMSB'13: Proceedings of the eleventh international conference on Computational Methods in Systems Biology, pages 192–205, volume 8130 of Lecture Notes in BioInformatics. Springer-Verlag, 2013. [ preprint ]

Steven Gay, François Fages, Francesco Santini, Sylvain Soliman. Solving Subgraph Epimorphism Problems using CLP and SAT. In Proceedings of the ninth Workshop on Constraint Based Methods for Bioinformatics WCB'13, colocated with CP 2013, pages 67–74, 2013. [ preprint ]

A.M. Gonzalez, J. Uhlendorf, J. Schaul, E. Cinquemani, G. Batt, G. Ferrari-Trecate. Identification of biological models from single-cell data: a comparison between mixed-effects and moment-based inference. In ECC'13: Proceedings of the 12th European Control Conference, 2013.

Ruei-Yang Huang, De-An Huang, Hui-Ju Katherine Chiang, Jie-Hong Jiang, François Fages. Species Minimization in Computation with Biochemical Reactions. In IWBDA'13: Proceedings of the fifth International Workshop on Bio-Design Automation, 2013. [ preprint ]

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.

Thierry Martinez, Lumadaiara Vitorino, François Fages, Abderrahmane Aggoun. On Solving Mixed Shapes Packing Problems by Continuous Optimization with the CMA Evolution Strategy. In Proceedings of the first Computational Intelligence BRICS Congress BRICS-CCI'13, pages 515–521. IEEE Press, 2013. [ preprint ]

Faten Nabli. Approches de programmation par contraintes pour l'analyse des propriétés structurelles des réseaux de Petri et application aux réseaux biochimiques. Thèse de doctorat, Université Paris - Diderot, 2013. [ preprint ]

Szymon Stoma, Alexandre Donzé, François Bertaux, Oded Maler, Grégory Batt. STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification. PLoS Computational Biology, 9(5):e1003056, 2013.

Sylvain Soliman, François Fages, Ovidiu Radulescu. A Constraint Solving Approach to Tropical Equilibration and Model Reduction. In Proceedings of the ninth Workshop on Constraint Based Methods for Bioinformatics WCB'13, colocated with CP 2013, pages 27–36, 2013. [ preprint ]

Sylvain Soliman. A stronger necessary condition for the multistationarity of chemical reaction networks. Bulletin of Mathematical Biology, 75(11):2289–2303, 2013. [ preprint ]

Jannis Uhlendorf. Real-time feedback control of gene expression. Thèse de doctorat, Université Paris - Diderot, 2013. [ preprint ]

2012

G. Batt, B. Besson, P.E. Ciron, H. de Jong and E. Dumas, J. Geiselmann, R. Monte, P.T. Monteiro , M. Page, F. Rechenmann, D. Ropers. Genetic Network Analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks. In Bacterial Molecular Networks, pages 439–462. Springer, 2012.

François Fages, Steven Gay, Sylvain Soliman. Inferring Reaction Models from ODEs. In CMSB'12: Proceedings of the tenth international conference on Computational Methods in Systems Biology, pages 370–373, volume 7605 of Lecture Notes in BioInformatics. Springer-Verlag, 2012. [ preprint ]

David Fournier, Denis Mulard, François Fages. Energy optimization of metro timetables: a hybrid approach. In Doctoral Programme Proceedings of the 18th International Conference on Principles and Practive of Constraint Programming CP'12, pages 7–12, 2012.

David Fournier, Denis Mulard, François Fages. Optimisation énergétique de tables horaires de métros: une approche hybride. In Actes de Journées Francophones de Programmation par Contraintes JFPC'12, pages 127–130, 2012.

Domitille Heitzler, Guillaume Durand, Nathalie Gallay, Aurélien Rizk, Seungkirl Ahn, Jihee Kim, Jonathan D. Violin, Laurence Dupuy and Christophe Gauthier, Vincent Piketty, Pascale Crépieux, Anne Poupon, Frédérique Clément, François Fages, Robert J. Lefkowitz, Eric Reiter. Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling. Molecular Systems Biology, 8(590), 2012.

Anthony Lins, Fernando Buarque, François Fages , Carmelo Filho. A Comparative Analysis of FSS with CMA-ES and S-PSO in Ill-Conditioned Problems. In Intelligent Data Engineering and Automated Learning - 13th International Conference IDEAL, pages 416–422, volume 7435 of Lecture Notes in Computer Science. Springer, 2012. [ preprint ]

Faten Nabli, François Fages, Thierry Martinez, Sylvain Soliman. A Boolean Model for Enumerating Minimal Siphons and Traps in Petri-nets. In Proceedings of CP'2012, 18th International Conference on Principles and Practice of Constraint Programming, pages 798–814, volume 7514 of Lecture Notes in Computer Science. Springer-Verlag, 2012. [ preprint ] [ slides ] [ poster ]

Faten Nabli, François Fages, Thierry Martinez, Sylvain Soliman. Un modèle Booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri. In Actes de Journées Francophones de Programmation par Contraintes JFPC'12, 2012. [ preprint ]

Sylvain Soliman. Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem. Algorithms for Molecular Biology, 7(15), 2012.

Jannis Uhlendorf, Agnés Miermont, Thierry Delaveau, Gilles Charvin, François Fages and Samuel Bottani, Gregory Batt, Pascal Hersen. Long-term model predictive control of gene expression at the population and single-cell levels. Proceedings of the National Academy of Sciences USA, 109(35):14271–14276, 2012.

2011

Elisabetta De Maria, François Fages, Aurélien Rizk, 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, 2011. [ preprint ]

Radu Grosu, Grégory Batt, F. Fenton, J. Glimm , Colas Le Guernic, S.A. Smolka, E. Bartocci. From cardiac cells to genetic regulatory networks. In 23rd International Conference on Computer Aided Verification, CAV'11, 2011.

Steven Gay, Thierry Martinez, Sylvain Soliman, 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, 2011. [ preprint ]

Domitille Heitzler. Modélisation dynamique des mécanismes de signalisation cellulaire induits par l'hormone folliculo-stimulante et l'angiotensine. Thèse de doctorat, Univ. François Rabelais de Tours, 2011.

Julien Martin, Thierry Martinez, François Fages. Static Expansion vs Procedural Code Generation in Rule-based Modeling Languages. In Recent Advances in Constraints, pages 38–58, LNAI. Springer-Verlag, 2011. [ preprint ]

A. Miermont, Jannis Uhlendorf, M. McClean, P. Hersen. The dynamical systems properties of the HOG signaling cascade. Journal of Signal Transduction, 2011.

Faten Nabli. Finding minimal siphons as a CSP. In CP'11: The Seventeenth International Conference on Principles and Practice of Constraint Programming, Doctoral Program, pages 67–72, 2011.

Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. Continuous Valuations of Temporal Logic Specifications with applications to Parameter Optimization and Robustness Measures. Theoretical Computer Science, 412(26):2827–2839, 2011. [ preprint ]

A. Randall, P. Guye, S. Gupta, X. Duportet and R. Weiss. Design and connection of robust genetic circuits. In Methods in Enzymology, pages 159–186. Elsevier, 2011.

Aurélien Rizk. Résolution de contraintes temporelles pour l'analyse de systèmes biologiques. Thèse de doctorat, Université Denis Diderot, Paris, 2011.

Jannis Uhlendorf, Samuel Bottani, François Fages, Pascal Hersen, Grégory Batt. Towards real-time control of gene experession: controlling the HOG signaling cascade. In Proceedings of the 16th Pacific Symposium on Biocomputing (PSB 2011), pages 338–349, 2011. [ preprint ]

Jannis Uhlendorf, Pascal Hersen, Grégory Batt. Towards real-time control of gene expression: in silico analysis. In 18th IFAC World Congress, WC'11, 2011.

2010

Abder Aggoun, Nicolas Beldiceanu, Mats Carlsson , François Fages. Integrating Rule-Based Modelling and Constraint Programming for Solving Industrial Packing Problems. ERCIM News, 81, 2010. [ preprint ]

Grégory Batt, Michel Page, Irene Cantone and Gregor Goessler, Pedro Monteiro, Hidde de Jong. Efficient parameter search for qualitative models of regulatory networks using symbolic model checking. Bioinformatics, 26(18):i603-i610, 2010.

François Fages. A Logical Paradigm for Systems Biology (Invited Talk). In Technical Communications of the 26th International Conference on Logic Programming, pages 2–3, volume 7 of Leibniz International Proceedings in Informatics (LIPIcs). Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2010. [ preprint ]

François Fages. A graphical method for reducing and relating models in systems biology (invited talk). In ICSB'10 11th International Conference on Systems Biology. University of Edinburgh, UK, 2010. [ preprint ]

François Fages, Grégory Batt, Elisabetta De Maria, Dragana Jovanovska, Aurélien Rizk, Sylvain Soliman. Computational Systems Biology in BIOCHAM. ERCIM News, 82, 2010. [ preprint ]

François Fages, 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, 2010.

Steven Gay, Sylvain Soliman, François Fages. A Graphical Method for Reducing and Relating Models in Systems Biology. Bioinformatics, 26(18):i575–i581, 2010.

Julien Martin. Un langage de modélisation à base de règles pour la programmation par contraintes. Thèse de doctorat, Université Pierre et Marie Curie, Paris, 2010.

Thierry Martinez. Semantics-preserving translations between Linear Concurrent Constraint Programming and Constraint Handling Rules. In Proceedings of PPDP'10, International Conference on Principles and Practice of Declarative Programming, Edinburgh, UK, pages 57–66. ACM, 2010. [ preprint ]

Faten Nabli, Sylvain Soliman. Steady-state solution of biochemical systems, beyond S-Systems via T-invariants. In CMSB'10: Proceedings of the 8th International Conference on Computational Methods in Systems Biology, pages 14–22. ACM, 2010.

Sylvain Soliman, Monika Heiner. A Unique Transformation from Ordinary Differential Equations to Reaction Networks. PLoS One, 5(12):e14284, 2010.

2009

Elisabetta De Maria, François Fages, 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, pages 142–157, volume 5688 of Lecture Notes in BioInformatics. Springer-Verlag, 2009. [ preprint ]

François Fages, Julien Martin. Modelling search strategies in Rules2CP. In Proceedings of CPAIOR'09, pages 321–322, volume 5547 of Lecture Notes in Computer Science. Springer-Verlag, 2009. [ preprint ]

François Fages, Julien Martin. From Rules to Constraint Programs with the Rules2CP Modelling language. In Recent Advances in Constraints, Revised Selected Papers of the 13th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP'08, pages 66–83, volume 5655 of Lecture Notes in Artificial Intelligence. Springer-Verlag, 2009. [ preprint ]

François Fages, Thierry Martinez, Cleyton Mario de Oliveira Rodrigues. CHR modulaire avec ask et tell. In Actes de Journées Francophones de Programmation par Contraintes JFPC'09, 2009. [ preprint ]

François Fages, Aurélien Rizk. From Model-Checking to Temporal Logic Constraint Solving. In Proceedings of CP'2009, 15th International Conference on Principles and Practice of Constraint Programming, pages 319–334, Lecture Notes in Computer Science. Springer-Verlag, 2009. [ preprint ]

Domitille Heitzler, Pascale Crépieux, Anne Poupon, Frédérique Clément, François Fages, Eric Reiter. Towards a systems biology approach to G protein-coupled receptor signalling: challenges and expectations. C.R. Biologies, 332:947–957, 2009.

Sriram Krishnamachari, Sylvain Soliman, 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. [ preprint ]

Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics, 12(25):il69–il78, 2009.

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, pages 2304–2312, volume 35 of . ARGESIM, 2009.

2008

François Fages, Julien Martin. Des règles aux contraintes avec le langage de modélisation Rules2CP. In Actes de Journées Francophones de Programmation par Contraintes JFPC'08, 2008.

François Fages, Aurélien Rizk. Analyse de Séries Temporelles par Résolution de Contraintes de Logique Temporelle. In Actes de Journées Francophones de Programmation par Contraintes JFPC'08, 2008.

François Fages, Aurélien Rizk. On Temporal Logic Constraint Solving for the Analysis of Numerical Data Time series. Theoretical Computer Science, 408(1):55–65, 2008. [ preprint ]

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

François Fages, Sylvain Soliman. Model Revision from Temporal Logic Properties in Systems Biology. In Probabilistic Inductive Logic Programming, pages 287–304, volume 4911 of Lecture Notes in Computer Science. Springer-Verlag, 2008. [ preprint ]

François Fages, Sylvain Soliman. Formal Cell Biology in BIOCHAM. In 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology SFM'08, pages 54–80, volume 5016 of Lecture Notes in Computer Science. Springer-Verlag, 2008. [ preprint ]

François Fages, Sylvain Soliman. Abstract Interpretation and Types for Systems Biology. Theoretical Computer Science, 403(1):52–70, 2008. [ preprint ]

Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology. In CMSB'08: Proceedings of the fourth international conference on Computational Methods in Systems Biology, pages 251–268, volume 5307 of Lecture Notes in Computer Science. Springer-Verlag, 2008. [ preprint ]

2007

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

Jean Clairambault, François Fages, Sylvain Soliman. Patient-tailored cancer therapeutics - The TEMPO Project. ERCIM News, 69:24–25, 2007. [ preprint ]

Alessandro Dal Palu, Agostino Dovier, François Fages, Sebastian Will. Constraint-based Methods in Bioinformatics. In Future and trends of Constraint Programming: the next ten years. Hermès, 2007. [ preprint ]

François Fages. Des contraintes au programme. Revue littéraire de l'Institut Universitaire de France, Actes de Savoirs, PUF, 2007. [ preprint ]

François Fages, Aurélien Rizk. On the Analysis of Numerical Data Time Series in Temporal Logic. In CMSB'07: Proceedings of the fifth international conference on Computational Methods in Systems Biology, pages 48–63, volume 4695 of Lecture Notes in Computer Science. Springer-Verlag, 2007. [ preprint ]

Rémy Haemmerlé, François Fages. Abstract Critical Pairs and Confluence of Arbitrary Binary Relations. In Proceedings of th 18th International Conference on Rewriting Techniques and Applications, RTA'07, Lecture Notes in Computer Science. Springer-Verlag, 2007. [ preprint ]

Rémy Haemmerlé, François Fages, Sylvain Soliman. Closures and Modules within Linear Logic Concurrent Constraint Programming. In Proceedings of FSTTCS 2007, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, pages 544–556, volume 4855 of Lecture Notes in Computer Science. Springer-Verlag, 2007. [ preprint ]

2006

Nadia Busi, Roberto Gorrieri. On the Computational Power of Brane Calculi. In Transactions on Computational Systems Biology VI, pages 16–43, volume 4220 of Lecture Notes in BioInformatics. Springer-Verlag, 2006.

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

Emmanuel Coquery, François Fages. A type system for CHR. In Recent Advances in Constaints, revised selected papers from CSCLP'05, pages 100–117, Lecture Notes in Artificial Intelligence. Springer-Verlag, 2006. [ preprint ]

Laurence Calzone, François Fages, Sylvain Soliman. BIOCHAM: An Environment for Modeling Biological Systems and Formalizing Experimental Knowledge. Bioinformatics, 22(14):1805–1807, 2006. [ preprint ]

François Fages. From Syntax to Semantics in Systems Biology - Towards Automated Reasoning Tools. Transactions on Computational Systems Biology IV, 3939:68–70, 2006. [ preprint ]

François Fages. Programmation logique et contraintes. In Encyclopédie d'informatique, pages 151–162. Vuibert, 2006. [ preprint ]

François Fages, Akash Lal. A Constraint Programming Approach to Cutset Problems. Journal Computers and Operations Research, 33:10:2852–2865, 2006. [ preprint ]

François Fages, Sylvain Soliman. Type Inference in Systems Biology. In 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. [ preprint ]

Rémy Haemmerlé, François Fages. Modules for Prolog Revisited. In Proceedings of International Conference on Logic Programming ICLP 2006, pages 41–55, Lecture Notes in Computer Science. Springer-Verlag, 2006. [ preprint ]

2005

Sacha Berger, Emmanuel Coquery, Wlodzimierz Drabent, Artur Wilk. Descriptive Typing Rules for Xcerpt. In , .

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

Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman. A Machine Learning approach to Biochemical Reaction Rules Discovery. In Proceedings of Foundations of Systems Biology and Engineering FOSBE'05, pages 375–379, 2005. [ preprint ]

Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman. Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle. In Actes de JOBIM'05, pages 183–192, 2005.

Emmanuel Coquery, François Fages. A prescriptive type system for CHR (short paper). In Proceedings of International Conference on Logic Programming ICLP 2005, pages 402–403, volume 3668 of Lecture Notes in Computer Science. Springer-Verlag, 2005.

Emmanuel Coquery, François Fages. Un système de types pour CHR. In Actes de Journées Francophones de Programmation par Contraintes JFPC'05, 2005.

François Fages. Temporal logic constraints in the biochemical abstract machine BIOCHAM (invited talk). In Proceedings of Logic Based Program Synthesis and Transformation, LOPSTR'05, Lecture Notes in Computer Science, 2005. [ preprint ]

Rémy Haemmerlé, François Fages. Un système de modules fermé pour la PLC. In Actes de Journées Francophones de Programmation par Contraintes JFPC'05, 2005.

2004

Nathalie Chabrier-Rivier, Marc Chiaverini, Vincent Danos, François Fages, Vincent Schächter. Modeling and querying biochemical interaction networks. Theoretical Computer Science, 325(1):25–44, 2004. [ preprint ]

Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman. The Biochemical Abstract Machine BIOCHAM. In CMSB'04: Proceedings of the second international workshop on Computational Methods in Systems Biology, pages 172–191, volume 3082 of Lecture Notes in BioInformatics. Springer-Verlag, 2004. [ preprint ]

François Fages. Automated reasoning tools for molecular biology (invited talk). In Proceedings of the 27th Annual German Conference on AI, KI'04, pages 1–2, volume 3238 of Lecture Notes in Artificial Intelligence. Springer-Verlag, 2004.

François Fages, Sylvain Soliman, 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, 2004. [ preprint ]

François Fages, Sylvain Soliman, Nathalie Chabrier-Rivier. Modelling and Querying Interaction Networks in the Biochemical Abstract Machine BIOCHAM. Journal of Biological Physics and Chemistry, 4(2):64–73, 2004. [ preprint ]

Ludovic Langevine, Pierre Deransart, Mireille Ducassé. A Generic Trace Schema for the Portability of CP(FD) Debugging Tools. In , .

Sylvain Soliman, François Fages. CMBSlib: a Library for Comparing Formalisms and Models of Biological Systems. In CMSB'04: Proceedings of the second international workshop on Computational Methods in Systems Biology, pages 231–235, volume 3082 of Lecture Notes in BioInformatics. Springer-Verlag, 2004. [ preprint ]

Sylvain Soliman. Pi-calcul et LCC, une odyssée de l'espace. In Programmation en logique avec contraintes (Actes de JFPLC 2004), pages 201–218. Hermès, 2004.

2003

Nathalie Chabrier, François Fages. Symbolic model checking of biochemical networks. In CMSB'03: Proceedings of the first workshop on Computational Methods in Systems Biology, pages 149–162, volume 2602 of Lecture Notes in Computer Science. Springer-Verlag, 2003. [ preprint ]

Emmanuel Coquery, François Fages. Subtyping constraints in quasi-lattices. In Proceedings of the 23rd conference on foundations of software technology and theoretical computer science, FSTTCS'2003, pages 136–148, volume 2914 of Lecture Notes in Computer Science. Springer-Verlag, 2003. [ preprint ]

Emmanuel Coquery, François Fages. Contraintes de sous-typage dans les quasi-treillis. In Actes des Journées Francophones de la Programmation en Logique avec Contraintes JFPLC'2003, pages 253–266, special issue of RSTI. Hermès, 2003. [ preprint ]

Nathalie Chabrier, François Fages. "Model-checking" symbolique de réseaux biochimiques. In Actes des Journées Francophones de la Programmation en Logique avec Contraintes JFPLC'2003, pages 155–168, special issue of RSTI. Hermès, 2003. [ preprint ]

François Fages. Symbolic model checking for biochemical systems (invited talk). In Proceedings of International Conference on Logic Programming ICLP'03, pages 102, volume 2916 of Lecture Notes in Computer Science. Springer-Verlag, 2003. [ preprint ]

François Fages, Akash Lal. A Global Constraint for Cutset Problems. In Proceedings of Fifth International Workshop on Integration of AI and OR techniques in constraint programming for combinatorial optimization problems CPAIOR'03, 2003. [ preprint ]

2002

Emmanuel Coquery, François Fages. TCLP: overloading, subtyping and parametric polymorphism made practical for constraint logic programming. In Proceedings of International Conference on Logic Programming ICLP 2002, pages 480, volume 2401 of Lecture Notes in Computer Science. MIT Press, 2002. [ preprint ]

Emmanuel Coquery, François Fages. Surcharge et sous-typage dans TCLP. In Actes des Journées Francophones de Programmation en Logique et programmation par Contraintes, JFPLC'2002. Hermès, 2002.

2001

Emmanuel Coquery, François Fages. Programmes logiques avec contraintes typés. In Actes des Journées Francophones de la Programmation en Logique avec Contraintes JFPLC'2001, pages 223–237, 2001. [ preprint ]

François Fages, Emmanuel Coquery. Typing Constraint Logic Programs. Journal of Theory and Practice of Logic Programming, 1(6):751–777, 2001. [ preprint ]

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

Sylvain Soliman. Phase Model Checking for some Linear Logic Calculi. In Proceedings of the Second International Workshop of the Implementation of Logics, Havana, Cuba, pages 60–80, MPI-I-2001-2-006. Max-Planck-Institut für Informatik, 2001.

2000

François Fages. Concurrent constraint programming and linear logic (invited talk). In Proceedings of ACM Sigplan conference on Principles and Practice of Declarative Programming PPDP'2000. ACM Publishing Company, 2000. [ preprint ]

Jan-Georg Smaus, François Fages, Pierre Deransart. Using Modes to Ensure Subject Reduction for Typed Logic Programs with Subtyping. In Proceedings of FSTTCS '2000, Lecture Notes in Computer Science. Springer-Verlag, 2000. [ preprint ]