- "I hear and I forget. I see and I remember. I do and I understand." Confucius
Selected publications
2024
François Fages. A Constraint-based Mathematical Modeling Library in Prolog with Answer Constraint Semantics. In 17th International Symposium on Functional and Logic Programming, FLOPS 2024, LNCS. Springer-Verlag, 2024. [ preprint ]
Hemery, Mathieu, Fages, François. On a model of online analog computation in the cell with absolute functional robustness: algebraic characterization, function compiler and error control. Theoretical Computer Science, 991:114432, 2024. [ preprint ]
2023
Aghakhani, Sahar. Computational modeling of metabolic reprogramming in rheumatoid arthritis synovial fibroblasts and cancer- associated fibroblasts. Theses, Université Paris-Saclay, 2023. [ preprint ]
Aghakhani, Sahar, Silva-Saffar, Sacha E, Soliman, Sylvain, Niarakis, Anna. Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts. Computational and Structural Biotechnology Journal, 21:4196–4206, 2023. [ preprint ]
Collery, Marine, Bonnard, Philippe, Fages, François, Kusters, Remy. Neural-based classification rule learning for sequential data. In ICLR 2023 - The Eleventh International Conference on Learning Representations, 2023. [ preprint ]
Collery, Marine. Expressive classification rule learning with an emphasis on learning from sequential data. Theses, Institut Polytechnique de Paris, 2023. [ preprint ]
Fages, François, Molina, Franck. The Cell, a Chemical Analog Calculator. In Symbolic Approaches to Modeling and Analysis of Biological Systems, pages 235–254. John Wiley Sons, Ltd, 2023. [ preprint ]
Hemery, Mathieu, Fages, François. On Estimating Derivatives of Input Signals in Biochemistry. In CMSB 2023 - 21st International Conference on Computational Methods in Systems Biology, volume 14137 of LNCS. Springer-Verlag, 2023. [ preprint ]
Ruess, Jakob, Ballif, Guillaume, Aditya, Chetan. Stochastic chemical kinetics of cell fate decision systems: from single cells to populations and back. Journal of Chemical Physics, 159(18), 2023. [ preprint ]
Singh, Vidisha, Naldi, Aurélien, Soliman, Sylvain, Niarakis, Anna. A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint. npj Systems Biology and Applications, 9(33), 2023. [ preprint ]
Trinh, Van-Giang, Benhamou, Belaid, Soliman, Sylvain. Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming. In 29th International Conference on Principles and Practice of Constraint Programming (CP 2023), pages 35:1–35:19, volume 280 of . Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. [ preprint ]
Trinh, Van-Giang, Benhamou, Belaid, Soliman, Sylvain. Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding. Theoretical Computer Science, 971:114073, 2023. [ preprint ]
Thibault Greugny, Eléa, Fages, François and Radulescu, Ovidiu, Szmolyan, Peter, Stamatas, Georgios. A Skin Microbiome Model with AMP interactions and Analysis of Quasi-Stability vs Stability in Population Dynamics. Theoretical Computer Science, 983:114294, 2023. [ preprint ]
2022
Aghakhani, Sahar, Soliman, Sylvain, Niarakis, Anna. Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach. PLoS Computational Biology, 18(12):e1010408, 2022. [ preprint ]
François Fages, Franck Molina. La cellule, un calculateur analogique chimique. In Approches symboliques de la modélisation et de l'analyse des systèmes biologiques, pages 255–273. ISTE group, Ed Ltd, London, 2022. [ preprint ] [ video ]
E. Greugny, J. Bensaci, F. Fages, G. Stamatas. Computational modeling predicts impaired barrier function and higher sensitivity to skin inflammation following pH elevation. Journal of Experimental Dermatology, 2022. [ preprint ]
Van-Giang Trinh, Belaid Benhamou, Kunihiko Hiraishi, Sylvain Soliman. Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding. In CMSB'22: Proceedings of the twentieth international conference on Computational Methods in Systems Biology, volume 13447 of LNCS. Springer-Verlag, 2022. [ preprint ]
Jeremy Grignard, Véronique Lamamy, Eva Vermersch, Philippe Delagrange, Jean-Philippe Stephan, Thierry Dorval, François Fages. Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design. PLOS Computational Biology, 18(6), 2022.
Elea Thibault-Greugny. Computational modeling approaches to multifactorial aspects of atopic dermatitis. PhD Thesis, Institut Polytechnique de Paris, 2022. [ preprint ]
Jeremy Grignard. Méthodes computationnelles pour améliorer les phases primaires de recherche de nouveaux médicaments. PhD Thesis, Institut Polytechnique de Paris, 2022. [ preprint ]
Eléa Thibault Greugny, Georgios N Stamatas and François Fages. Stability versus Meta-stability in a Skin Microbiome Model. In CMSB'22: Proceedings of the twentieth international conference on Computational Methods in Systems Biology, volume 13447 of LNCS. Springer-Verlag, 2022. [ preprint ] [ slides ]
Mathieu Hemery, François Fages. Algebraic Biochemistry: a Framework for Analog Online Computation in Cells. In CMSB'22: Proceedings of the twentieth international conference on Computational Methods in Systems Biology, volume 13447 of LNCS. Springer-Verlag, 2022. [ preprint ] [ slides ] [ video ]
Lüders, Christoph, Bellot, Eléonore and Fages, François, Radulescu, Ovidiu, Soliman, Sylvain. Symbolic Methods for Biological Networks D2.1 Report on Scalable Methods for Tropical Solutions (T1.2). . Inria Saclay, 2022. [ preprint ]
Laubenbacher, Reinhard, Niarakis, A., Helikar, Tomáv s, An, Gary, Shapiro, Bruce and Malik-Sheriff, Rahuman, Sego, Timothy, Knapp, Adam , Macklin, Paul, Glazier, James. Building digital twins of the human immune system: toward a roadmap. npj Digital Medicine, 5(64), 2022. [ preprint ]
Julien Martinelli. On learning mechanistic models from time series data with applications to personalised chronotherapies. PhD Thesis, Institut Polytechnique de Paris, 2022. [ preprint ]
Niarakis, Anna, Waltemath, Dagmar, Glazier, James , Schreiber, Falk, Keating, Sarah, Nickerson, David, Chaouiya, Claudine, Siegel, Anne and Noël, Vincent, Hermjakob, Henning, Helikar, Tomáv s, Soliman, Sylvain, Calzone, Laurence. Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings in Bioinformatics, 23(4):1–11, 2022. [ preprint ]
Stoll, Gautier, Naldi, Aurélien, Noël, Vincent, Viara, Eric, Barillot, Emmanuel and Kroemer, Guido, Thieffry, Denis, Calzone, Laurence. UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling. Frontiers in Molecular Biosciences, 9, 2022. [ preprint ]
Shaikh, Bilal, Smith, Lucian, Vasilescu, Dan and Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran , Agnew, Henry, Andrews, Steven, Anwar, Azraf and Beber, Moritz et al. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research, 2022. [ preprint ]
Zerrouk, Naouel, Aghakhani, Sahar, Singh, Vidisha , Augé, Franck, Niarakis, Anna. A Mechanistic Cellular Atlas of the Rheumatic Joint. Frontiers in Systems Biology, 2022. [ preprint ]
2021
Alizon, Samuel, Cazals, Frédéric, Guindon, Stéphane, Lemaitre, Claire, Mary-Huard, Tristan , Niarakis, Anna, Salson, Mikaël and Scornavacca, Celine, Touzet, Hélène. SARS-CoV-2 Through the Lens of Computational Biology:How bioinformatics is playing a key role in the study of the virus and its origins. . CNRS, 2021. [ preprint ]
Aghakhani, Sahar, Zerrouk, Naouel, Niarakis, Anna. Metabolic Reprogramming of Fibroblasts as Therapeutic Target in Rheumatoid Arthritis and Cancer: Deciphering Key Mechanisms Using Computational Systems Biology Approaches. Cancers, 2021. [ preprint ]
Buffard, Marion, Desoeuvres, Aurélien, Naldi, Aurélien, Requilé, Clément, Zinovyev, Andrei, Radulescu, Ovidiu. LNetReduce: tool for reducing linear dynamic networks with separated time scales. In Computational Methods in Systems Biology, 2021. [ preprint ]
Buffard, Marion, Naldi, Aurélien, Freiss, Gilles Gf, Deckert, Marcel, Radulescu, Ovidiu and Coopman, Peter, Larive, Romain M.. Comparison of SYK Signaling Networks Reveals the Potential Molecular Determinants of Its Tumor-Promoting and Suppressing Functions. Biomolecules, 11(2):308, 2021. [ preprint ]
Collery, Marine, Bonnard, Philippe, Fages, François. Apprentissage de règles pour la détection de fraudes. In RJCIA 2021 - Dix-neuvièmes Rencontres des Jeunes Chercheurs en Intelligence Artificielle, pages 77–78, 2021. [ preprint ]
Marine Collery. Rule Learning from Time-Dependent Data Applied to Fraud Detection. In RuleML'21: The Fifthth International Conference on Rules and Reasoning and RuleML, Doctoral Program, 2021.
Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert and Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis et al. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology, 17(10):e10387, 2021. [ preprint ]
Dräger, Andreas, Helikar, Tomáv s and Barberis, Matteo, Birtwistle, Marc, Calzone, Laurence, Chaouiya, Claudine, Hasenauer, Jan and Karr, Jonathan R, Niarakis, Anna, Rodríguez Martínez, María, Saez-Rodriguez, Julio and Thakar, Juilee. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics, 37(21):3702–3706, 2021. [ preprint ]
Mathieu Hemery, François Fages, Sylvain Soliman. Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs. In CMSB'21: Proceedings of the nineteenth international conference on Computational Methods in Systems Biology, volume 12881 of LNCS. Springer-Verlag, 2021. [ preprint ]
Hesse, Janina, Martinelli, Julien, Aboumanify, Ouda, Ballesta, Annabelle, Relógio, Angela. A mathematical model of the circadian clock and drug pharmacology to optimize irinotecan administration timing in colorectal cancer. Computational and Structural Biotechnology Journal, 19:5170–5183, 2021. [ preprint ]
Hall, Benjamin A, Niarakis, Anna. Data integration in logic-based models of biological mechanisms. Current Opinion in Systems Biology, 28:100386, 2021. [ preprint ]
Julien Martinelli, Sandrine Dulong, Xiao-Mei Li , Michèle Teboul, Sylvain Soliman, Francis Lévi, François Fages, Annabelle Ballesta. Model learning to identify systemic regulators of the peripheral circadian clock. Bioinformatics, 37:i401-i409, 2021. [ preprint ] [ slides ] [ video ]
Miagoux, Quentin, Singh, Vidisha, de Mézquita, Dereck, Chaudru, Valérie, Elati, Mohamed and Petit-Teixeira, Elisabeth, Niarakis, Anna. Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map. Journal of Personalized Medicine, 11(8):785, 2021. [ preprint ]
2020
Aghamiri, Sara Sadat, Singh, Vidisha, Naldi, Aurélien, Helikar, Tomas, Soliman, Sylvain and Niarakis, Anna. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics, 2020. [ preprint ]
Elisabeth Degrand, François Fages, Sylvain Soliman. Graphical Conditions for Rate Independence in Chemical Reaction Networks. In CMSB'20: Proceedings of the eighteenth international conference on Computational Methods in Systems Biology, volume 12314 of LNCS. Springer-Verlag, 2020. [ preprint ] [ slides ] [ video ]
François Fages. Artificial Intelligence in Biological Modeling. In A Guided Tour of Artificial Intelligence Research, Volume III: Interfaces and Applications of AI. Springer-Verlag, 2020. [ preprint ]
Mathieu Hemery, François Fages, Sylvain Soliman. On the Complexity of Quadratization for Polynomial Differential Equations. In CMSB'20: Proceedings of the eighteenth international conference on Computational Methods in Systems Biology, LNCS. Springer-Verlag, 2020. [ preprint ]
Niarakis, Anna, Helikar, Tomáv s. A practical guide to mechanistic systems modeling in biology using a logic-based approach. Briefings in Bioinformatics, 2020. [ preprint ]
Anna Niarakis, Martin Kuiper, Marek Ostaszewski , Malik Rahuman S. Sheriff, Cristina Casals-Casas , Denis Thieffry, Tom C. Freeman, Paul Thomas and Vasundra Touré et al. 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, 2020. [ preprint ]
Francisco Santos Schneider, Patrick Amar, Asma Bahri, Julien Espeut, Julie Baptiste, Mellis Alali, François Fages, Franck Molina. Biomachines for Medical Diagnosis. Advanced Materials Letters, 11(4):1535–1558, 2020.
Sarah M. Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger and Claudine Chaouiya, Frank T. Bergmann, Andrew Finney , Colin S. Gillespie et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, 16(8):1–21, 2020. [ preprint ]
Touré, Vasundra, Flobak, AAsmund, Niarakis, Anna, Vercruysse, Steven, Kuiper, Martin. The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Briefings in Bioinformatics, 2020. [ preprint ]
2019
Orianne Bargain. Graph matching, theory and SAT implementation. . Master's Thesis Technische Universität Dresden, Germany, 2019. [ preprint ]
Cepeda-Humerez, Sarah Anhala, Ruess, Jakob and Tkavcik, Gavsper. Estimating information in time-varying signals. PLoS Computational Biology, 15(9):e1007290, 2019. [ preprint ]
Elisabeth Degrand. Evolving Chemical Reaction Networks. . Master's Thesis, KTH Royal Institute of Technology, Stockholm, Sweden, Inria Saclay Ile de France, 2019. [ preprint ]
Elisabeth Degrand, Mathieu Hemery, François Fages. On Chemical Reaction Network Design by a Nested Evolution Algorithm. In CMSB'19: Proceedings of the seventeenth international conference on Computational Methods in Systems Biology, volume 11773 of LNCS. Springer-Verlag, 2019. [ preprint ]
François Fages. Information Leakage in a Music Score. In The Art of Modeling Computational Systems - A Journey from Logic and Concurrency Theory to Security and Privacy - Essays Dedicated to Catuscia Palamidessi on the Occasion of Her 60th Birthday. Springer-Verlag, 2019. [ preprint ]
Hemery, Mathieu, François, Paul. In Silico Evolution of Biochemical Log-Response. The Journal of Physical Chemistry B, 2019. [ preprint ]
Huang, Wei-Chih, Jiang, Jie-Hong, Fages, François, Molina, Franck. Biochemical Threshold Function Implementation with Zero-Order Ultrasensitivity. In 15th IEEE Biomedical Circuits and Systems Conference, 2019. [ preprint ]
Kryukov, Maxim, Carcano, Arthur, Batt, Grégory, Ruess, Jakob. Can optimal experimental design serve as a tool to characterize highly non-linear synthetic circuits?. In ECC 2019 - European Control Conference, 2019. [ preprint ]
Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages. On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics. In CMSB'19: Proceedings of the seventeenth international conference on Computational Methods in Systems Biology, volume 11773 of LNCS. Springer-Verlag, 2019. [ preprint ]
Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages. A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data. In ICML Workshop on Computational Biology, 2019. [ preprint ]
Ruess, Jakob, Plevska, Marovs, Guet, Cvalin C, Tkavcik, Gavsper. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology, 2019. [ preprint ]
2018
Boulier, François, Fages, François and Radulescu, Ovidiu, Samal, Satya S, Schuppert, Andreas, Seiler, Werner M., Sturm, Thomas and Walcher, Sebastian, Weber, Andreas. The SYMBIONT Project: Symbolic Methods for Biological Networks. ACM Communications in Computer Algebra, 52(3), 2018.
Adrien Baudier, François Fages, Sylvain Soliman. Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. Journal of Theoretical Biology, 459:79–89, 2018. [ preprint ]
Alexis Courbet, Patrick Amar, François Fages, Eric Renard, Franck Molina. Computer-aided biochemical programming of synthetic microreactors as diagnostic devices. Molecular Systems Biology, 14(4), 2018. [ preprint ]
François Fages, Le Guludec, Guillaume. Biochemical Programs and Analog-Digital Mixed Algorithms in the Cell. In Life Sciences, Information Sciences, pages 201–216. Wiley, 2018.
François Fages, Thierry Martinez, David Rosenblueth, Sylvain Soliman. Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018. [ preprint ]
Fages, François, Soliman, Sylvain. On Robustness Computation and Optimization in BIOCHAM-4. In CMSB'18: Proceedings of the sixteenth international conference on Computational Methods in Systems Biology, LNCS. Springer-Verlag, 2018. [ preprint ]
Lugagne, Jean-Baptiste, Jain, Srajan, Ivanovitch, Pierre, Ben Meriem, Zacchary, Vulin, Clément and Fracassi, Chiara, Batt, Grégory, Hersen, Pascal. Identification of individual cells from z-stacks of bright-field microscopy images. Scientific Reports, 8(1):11455, 2018.
Meredith, Hannah, Andreani, Virgile, Ma, Helena , Lopatkin, Allison, Lee, Anna, Anderson, Deverick, Batt, Gregory, You, Lingchong. Applying ecological resistance and resilience to dissect bacterial antibiotic responses. Science Advances, 4(12):eaau1873, 2018. [ preprint ]
2017
Carcano, Arthur, Fages, François, Soliman, Sylvain. Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. In CMSB'17: Proceedings of the fifteenth international conference on Computational Methods in Systems Biology, pages 74–90, volume 10545 of , 2017. [ preprint ]
Remy Chait, Jakob Ruess, Tobias Bergmiller and Gavsper Tkavcik, Cvalin Guet. Shaping bacterial population behavior through computer-interfaced control of individual cells. Nature Communications, 8(1):1535, 2017.
François Fages, Le Guludec, Guillaume. Programmation biochimique et algorithmes mixtes analogiques-digitaux dans la cellule. In Sciences du vivant, sciences de l'information. ISTE Ed. Ltd, London, 2017. [ preprint ]
Fages, François, Le Guludec, Guillaume and Bournez, Olivier, Pouly, Amaury. Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs. In CMSB'17: Proceedings of the fiveteen international conference on Computational Methods in Systems Biology, pages 108–127, volume 10545 of LNCS. Springer-Verlag, 2017. [ preprint ]
Lai, Chun-Ning, Jiang, Jie-Hong, Fages, François. Recombinase-Based Genetic Circuit Optimization. In 13th IEEE Biomedical Circuits and Systems Conference, 2017. [ preprint ] [ preprint ]
Jean-Baptiste Lugagne, Sebastian Sosa Carrillo and Melanie Kirch, Agnes Köhler, Gregory Batt and Pascal Hersen. Balancing a genetic toggle switch by real-time feedback control and periodic forcing. Nature Communications, 8(1):1671, 2017.
Palaniappan, Sucheendra K., Bertaux, François and Pichené, Matthieu, Fabre, Eric, Batt, Gregory , Genest, Blaise. Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway. Bioinformatics, 33(13):1980–1986, 2017. [ preprint ]
Jakob Ruess, Heinz Koeppl, Christoph Zechner. Sensitivity estimation for stochastic models of biochemical reaction networks in the presence of extrinsic variability. The Journal of Chemical Physics, 146(12):124122, 2017.
Sofia Triantafillou, Vincenzo Lagani, Christina Heinze-Deml, Angelika Schmidt, Jesper Tegner and Ioannis Tsamardinos. Predicting Causal Relationships from Biological Data: Applying Automated Causal Discovery on Mass Cytometry Data of Human Immune Cells. Scientific Reports, 7:12724, 2017.
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 ]
Fournier, David, Martinez, Thierry, Fages, François, Mulard, Denis. Metro Energy Optimization through Rescheduling: Mathematical Models and Heuristic Algorithm Compared to MILP and CMA-ES. . Inria Saclay Ile de France, 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 LNCS. 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.
Lugagne, Jean-Baptiste. Real-time control of a genetic toggle switch. Theses, Université Paris 7, 2016. [ preprint ]
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 ]
Sylvain Soliman. A structural perspective on the dynamics of biochemical systems. Habilitation Thesis, Université Paris Sud - Orsay, 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):e0137442, 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 ]
Hemery, Mathieu. Modeles d'evolution de proteeines en environnement variable.. Thèse de doctorat, Universite Pierre et Marie Curie, 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, 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 LNCS. Springer-Verlag, 2015. [ preprint ]
2014
Grégory Batt. Design, Optimization and Control in Systems and Synthetic Biology. Habilitation Thesis, 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.
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 ] [ video ]
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. In CMSB'14: Proceedings of the twelth international conference on Computational Methods in Systems Biology, pages 114–128, LNCS. 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. [ preprint ]
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 LNCS. Springer-Verlag, 2013. [ preprint ]
François Fages, Simon de Givry, Christine Solnon. Preface, Special Section of JFPC 2012. In , pages 89–90, volume 47 of RAIRO - Operations Research. EDP Sciences, 2013.
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 ]
François Fages, Sylvain Soliman. Special Section on Computational Methods in Systems Biology, second part. In , pages 308–351, volume 10 of Transactions on Computational Biology and Bioinformatics. IEEE/ACM, 2013.
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 LNCS. 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 et al. 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 LNCS. 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.
François Fages, Sylvain Soliman. Special Section on Computational Methods in Systems Biology. In , pages 1314–1378, volume 9 of Transactions on Computational Biology and Bioinformatics. IEEE/ACM, 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.
Zechner, Christoph, Ruess, Jakob, Krenn, Peter and Pelet, Serge, Peter, Matthias, Lygeros, John and Koeppl, Heinz. Moment-based inference predicts bimodality in transient gene expression. Proceedings of the National Academy of Sciences USA, 109(21):8340–8345, 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 ]
François Fages. Proc. of the 9th International Conference on Computational Methods in Systems Biology CMSB'11. In , ACM in cooperation Conference Proceedings. ACM Digital Libray, 2011.
David Fournier. Constraint Modeling of Trains Supervision and Timetabling. . Chalmers University, Sweden, Ecole des Mines d'Alès, INRIA, France, 2011.
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.
Dragana Jovanovska, François Fages, Sylvain Soliman. SBGN support in BIOCHAM. Nature Precedings, 2010. [ preprint ]
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. [ preprint ]
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 LNCS. Springer-Verlag, 2009. [ preprint ]
François Fages, Julien Martin. Modelling search strategies in Rules2CP. In Proceedings of CPAIOR'09, pages 321–322, volume 5547 of LNCS. 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 LNAI. 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, LNCS. 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 ]
Angelo Oddi, François Fages, Francesca Rossi. Recent Advances in Constraints, post-proceedings of 13th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming CSCLP'08. In , volume 5655 of LNAI. Springer-Verlag, 2009.
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, LNCS. 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 LNCS. 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 LNCS. Springer-Verlag, 2008. [ preprint ]
François Fages, Sylvain Soliman. Abstract Interpretation and Types for Systems Biology. Theoretical Computer Science, 403(1):52–70, 2008. [ preprint ]
François Fages, Francesca Rossi, Sylvain Soliman. Recent Advances in Constraints, post-proceedings of 12th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming CSCLP'07. In , volume 5129 of LNAI. Springer-Verlag, 2008.
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 LNCS. 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 LNCS. 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, LNCS. 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 LNCS. Springer-Verlag, 2007. [ preprint ]
Stephano Spaccapietra, Paolo Atzeni, François Fages, Mohand-Said Hacid, Michael Kifer, John Mylopoulos, Barbara Pernici, Pavel Shvaiko, Juan Trujillo, Ilya Zaihrayeu. Journal on Data Semantics IX. In , volume 4601 of LNCS. Springer-Verlag, 2007.
Stephano Spaccapietra, Paolo Atzeni, François Fages, Mohand-Said Hacid, Michael Kifer, John Mylopoulos, Barbara Pernici, Pavel Shvaiko, Juan Trujillo, Ilya Zaihrayeu. Journal on Data Semantics VIII. In , volume 4380 of LNCS. Springer-Verlag, 2007.
Francisco Azevedo, Pedro Barahona, François Fages, Francesca Rossi. Recent Advances in Constraints, post-proceedings of 11th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming CSCLP'06. In , volume 4651 of LNAI. Springer-Verlag, 2007.
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 LNBI. 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 LNBI. Springer-Verlag, 2006. [ preprint ]
Emmanuel Coquery, François Fages. A type system for CHR. In Recent Advances in Constraints, revised selected papers from CSCLP'05, pages 100–117, LNAI. 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 ]
Laurence Calzone, Sylvain Soliman. Coupling the Cell cycle and the Circadian Cycle. . INRIA, 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 LNCS. 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, LNCS. Springer-Verlag, 2006. [ preprint ]
Brahim Hnich, Mats Carlsson, François Fages, Francesca Rossi. Recent Advances in Constraints, selected papers from the 10th Joint ERCIM/Colognet Workshop CSCLP'05. In , volume 3978 of LNAI. Springer-Verlag, 2006.
François Fages, Narendra Jussien, Christine Solnon. Journées Francophones de Programmation par Contraintes 2005. In , volume 40 of RAIRO Operations Research. Hermès, 2006.
Seelig, Georg, Soloveichik, David, Zhang, David Yu , Winfree, Erik. Enzyme-Free Nucleic Acid Logic Circuits. Science, 314(5805):1585–1588, 2006.
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 LNCS. 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. [ preprint ]
François Fages. Temporal logic constraints in the biochemical abstract machine BIOCHAM (invited talk). In Proceedings of Logic Based Program Synthesis and Transformation, LOPSTR'05, LNCS, 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.
Boi Faltings, Adrian Petcu, François Fages, Francesca Rossi. Recent Advances in Constraints, selected papers from the 9th Joint ERCIM/Colognet Workshop CSCLP'04. In , volume 3419 of LNAI. Springer-Verlag, 2005.
2004
Krzysztof Apt, François Fages, Francesca Rossi, Peter Szeredi, Jozsef Vancza. Recent Advances in Constraints, selected papers from the 8th Joint ERCIM/Colognet Workshop CSCLP'03. In Recent Advances in Constraints, selected papers from the 8th Joint ERCIM/Colognet Workshop CSCLP'03, LNAI. Springer-Verlag, 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 LNCS. 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 LNAI. 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 LNCS. 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 LNCS. 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 LNCS. 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 LNCS. 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 LNCS. Springer-Verlag, 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, LNCS. Springer-Verlag, 2000. [ preprint ]