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François Fages
,
Mathieu Hemery
,
Sylvain Soliman
.
On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry
. In
ISSAC 2024 - 49th International Symposium on Symbolic and Algebraic Computation
, 2024.
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Giang Trinh
,
Belaid Benhamou
,
Samuel Pastva
,
Sylvain Soliman
.
Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming
. In
AAAI 2024 - The 38th Annual Conference on Artificial Intelligence
, pages 10714-10722, 2024.
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DOI
Sahar Aghakhani
,
Anna Niarakis
,
Sylvain Soliman
.
MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps
.
Journal of Integrative Bioinformatics
, 21 (1):20230048, 2024.
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DOI
Anna Niarakis et al
.
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
.
Frontiers in Immunology
, 14, 2024.
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DOI
Van-Giang Trinh
,
Belaid Benhamou
,
Sylvain Soliman
.
Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding
.
Theoretical Computer Science
, 971:114073, 2023.
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DOI
Sahar Aghakhani
,
Sacha E Silva-Saffar
,
Sylvain Soliman
,
Anna Niarakis
.
Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts
.
Computational and Structural Biotechnology Journal
, 21:4196-4206, 2023.
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DOI
Van-Giang Trinh
,
Belaid Benhamou
,
Sylvain Soliman
.
Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming
. In Roland H. C. Yap, editor,
29th International Conference on Principles and Practice of Constraint Programming (CP 2023)
, pages 35:1–35:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
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DOI
Vidisha Singh
,
Aurélien Naldi
,
Sylvain Soliman
,
Anna Niarakis
.
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.
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DOI
Sahar Aghakhani
,
Sylvain Soliman
,
Anna Niarakis
.
Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach
.
PLoS Computational Biology
, 18 (12):e1010408, 2022.
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DOI
Van-Giang Trinh
,
Belaid Benhamou
,
Kunihiko Hiraishi
,
Sylvain Soliman
.
Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding
. In Ion Petre, Andrei Păun, editor,
CMSB 2022 - International Conference on Computational Methods in Systems Biology
, volume 13447 of
Lecture Notes in Computer Science
, pages 158–176, Springer, 2022.
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Anna Niarakis et al
.
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
.
Briefings in Bioinformatics
, 23 (4):1-11, 2022.
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DOI
Christoph Lüders
,
Eléonore Bellot
,
François Fages
,
Ovidiu Radulescu
,
Sylvain Soliman
.
Symbolic Methods for Biological Networks D2.1 Report on Scalable Methods for Tropical Solutions (T1.2)
. Research Report, 2022.
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Anna Niarakis 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
, 22 (2):1848–1859, 2021.
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Marek Ostaszewski et al
.
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
.
Molecular Systems Biology
, 17 (10):e10387, 2021.
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DOI
Mathieu Hemery
,
François Fages
,
Sylvain Soliman
.
Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs
. In
CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology
, 2021.
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Mathieu Hemery
,
François Fages
,
Sylvain Soliman
.
A Polynomialization Algorithm for Elementary Functions and ODEs, and their Compilation into Chemical Reaction Networks
. In
CASC'21 - Computer Algebra in Scientific Computing.
, 2021.
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Julien Martinelli et al
.
Model learning to identify systemic regulators of the peripheral circadian clock
.
Bioinformatics
, 37 (Supplement_1):9, 2021.
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Mathieu Hemery
,
François Fages
,
Sylvain Soliman
.
On the Complexity of Quadratization for Polynomial Differential Equations
. In
CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology
, 2020.
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Elisabeth Degrand
,
François Fages
,
Sylvain Soliman
.
Graphical Conditions for Rate Independence in Chemical Reaction Networks
. In
CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology
, 2020.
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Sarah Keating et al
.
SBML Level 3: an extensible format for the exchange and reuse of biological models
.
Molecular Systems Biology
, 16 (8):1-21, 2020.
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Sara Sadat Aghamiri et al
.
Automated inference of Boolean models from molecular interaction maps using CaSQ
.
Bioinformatics
, 36 (16):4473-4482, 2020.
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Julien Martinelli
,
Jeremy Grignard
,
Sylvain Soliman
,
François Fages
.
On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics
. In Luca Bortolussi, Guido Sanguinetti, editor,
CMSB 2019 - 17th Computational Methods in Systems Biology
,
LNCS
, Springer-Verlag, 2019.
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Julien Martinelli
,
Jeremy Grignard
,
Sylvain Soliman
,
François Fages
.
A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data
. In
ICML 2019 - Workshop on Computational Biology
, 2019.
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François Fages
,
Thierry Martinez
,
David A Rosenblueth
,
Sylvain Soliman
.
Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors
.
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, PP (99):1-14, 2018.
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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.
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François Fages
,
Sylvain Soliman
.
On Robustness Computation and Optimization in BIOCHAM-4
. In
16th Int. Conf. on Computational Methods in Systems Biology
, 2018.
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DOI
Vidisha Singh et al
.
Executable Disease Networks: Adding dynamics to molecular maps
. In
ECCB 2018 - 17th European Conference on Computational Biology
, 2018.
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Arthur Carcano
,
François Fages
,
Sylvain Soliman
.
Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data
. In J. Feret, H. Koeppl, editor,
CMSB'17 - 15th International Conference on Computational Methods for Systems Biology
, pages 74-90, 2017.
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Pauline Traynard
,
Celine 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-α Up-regulation During Mitosis
. In
Dynamics Days 2017 - XXXVII Dynamics Days Europe International Conference
, 2017.
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Sylvain Soliman
.
A structural perspective on the dynamics of biochemical systems
. Habilitation à diriger des recherches, Université Paris Sud - Orsay, 2016.
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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-α up-regulation during mitosis
.
BioSystems
, 149:59–69, 2016.
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François Fages
,
Thierry Martinez
,
David Rosenblueth
,
Sylvain Soliman
.
Influence Systems vs Reaction Systems
. In Ezio Bartocci, Pietro Lio, Nicola Paoletti, editor,
CMSB'16: Proceedings of the fourteenth international conference on Computational Methods in Systems Biology
, volume 9859 of
Lecture Notes in Computer Science
, pages 98-115, Springer-Verlag, 2016.
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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.
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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 Olivier Roux, Jérémie Bourdon, editor,
CMSB'15 - Proceedings of the thirteenth international conference on Computational Methods in Systems Biology
, volume 9308 of
Lecture Notes in BioInformatics
, pages 208–221, Springer-Verlag, 2015.
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François Fages
,
Steven Gay
,
Sylvain Soliman
.
Inferring reaction systems from ordinary differential equations
.
Theoretical Computer Science
, 599:64–78, 2015.
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DOI
Thierry Martinez
,
François Fages
,
Sylvain Soliman
.
Search by Constraint Propagation
. In ACM, editor,
PPDP ‘15- 17th International Symposium on Principles and Practice of Declarative Programming
, pages 173–183, 2015.
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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
, 25 (2):14:1-14:22, 2015.
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Sylvain Soliman
,
François Fages
,
Ovidiu Radulescu
.
A constraint solving approach to model reduction by tropical equilibration
.
Algorithms for Molecular Biology
, 9 (1):24, 2014.
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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 Prize)
. In
CMSB'14: Proceedings of the twelth international conference on Computational Methods for Systems Biology
,
LNBI
, pages 114–128, Springer Verlag, 2014.
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Steven Gay
,
François Fages
,
Thierry Martinez
,
Sylvain Soliman
,
Christine Solnon
.
On the subgraph Epimorphism Problem
.
Discrete Applied Mathematics
, 162:214–228, 2014.
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Sylvain Soliman
.
A stronger necessary condition for the multistationarity of chemical reaction networks
.
Bulletin of Mathematical Biology
, 75 (11):2289-2303, 2013.
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Steven Gay
,
François Fages
,
Francesco Santini
,
Sylvain Soliman
.
Solving Subgraph Epimorphism Problems using CLP and SAT
. In
WCB - ninth Workshop on Constraint Based Methods for Bioinformatics, colocated with CP 2013 (2013)
, pages 67–74, 2013.
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Katherine Chiang
,
François Fages
,
Jie-Hong Jiang
,
Sylvain Soliman
.
On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models
. In Gupta, Ashutosh, Henzinger, Thomas A., editor,
CMSB - 11th International Conference on Computational Methods for Systems Biology - 2013
, volume 8130 of
Lecture Notes in Computer Science
, pages 192–205, Springer, 2013.
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Sylvain Soliman
,
François Fages
,
Ovidiu Radulescu
.
A Constraint Solving Approach to Tropical Equilibration and Model Reduction
. In
WCB - ninth Workshop on Constraint Based Methods for Bioinformatics, colocated with CP 2013
, pages 27–36, 2013.
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Sylvain Soliman
.
Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem
.
Algorithms for Molecular Biology
, 7 (1):15, 2012.
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Francois Fages
,
Sylvain Soliman
.
Reifying Global Constraints
. Research Report, 2012.
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Francois Fages
,
Steven Gay
,
Sylvain Soliman
.
Inferring Reaction Models from ODEs
. In
CMSB 2012: Computational Methods in Systems Biology
, pages 370-373, 2012.
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Faten Nabli
,
Francois Fages
,
Thierry Martinez
,
Sylvain Soliman
.
A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets
. In
CP 2012: Principles and Practice of Constraint Programming
, pages 798-814, 2012.
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Francois Fages
,
Steven Gay
,
Sylvain Soliman
.
Automatic Curation of SBML Models based on their ODE Semantics
. Research Report, 2012.
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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
JFPC 2012 - Huitièmes Journées Francophones de Programmation par Contraintes
, 2012.
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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.
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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.
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Faten Nabli
,
Sylvain Soliman
.
Steady-state Solution of Biochemical Systems, Beyond S-systems via T-invariants
. In
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
,
CMSB ‘10
, pages 14–22, ACM, 2010.
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Sylvain Soliman
,
Monika Heiner
.
A Unique Transformation from Ordinary Differential Equations to Reaction Networks
.
PLoS ONE
, 5 (12):e14284, 2010.
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Dragana Jovanovska
,
Francois Fages
,
Sylvain Soliman
.
SBGN support in BIOCHAM
.
Nature Precedings
, 2010.
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Steven Gay
,
Sylvain Soliman
,
François Fages
.
A graphical method for reducing and relating models in systems biology
.
Bioinformatics
, 26 (18):i575–i581, 2010.
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Sylvain Soliman et al
.
Modelling molecular networks: relationships between different formalisms and levels of details
. Research Report, 2010.
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Elisabetta de Maria
,
Francois Fages
,
Sylvain Soliman
.
On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle
. In Degano, Pierpaoloand Gorrieri, Roberto, editor,
Computational Methods in Systems Biology
, pages 142–157, Springer Berlin Heidelberg, 2009.
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Elisabetta de Maria
,
Francois Fages
,
Sylvain Soliman
.
Model-based Predictions of the Influence of Circadian Clock Genes Knock-Outs on the Cell Cycle
. Research Report, 2009.
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Krishnamachari Sriram
,
Sylvain Soliman
,
Francois 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.
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Elisabetta de Maria
,
Francois Fages
,
Sylvain Soliman
.
On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle
. In
CMSB 2009: Computational Methods in Systems Biology
, pages 142-157, 2009.
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Aurélien Rizk
,
Grégory Batt
,
Francois Fages
,
Sylvain Soliman
.
A general computational method for robustness analysis with applications to synthetic gene networks
.
Bioinformatics
, 25 (12):il69–il78, 2009.
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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, ARGESIM, 2009.
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Francois Fages
,
Sylvain Soliman
.
Model Revision from Temporal Logic Properties in Computational Systems Biology
. 2008.
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Aurélien Rizk
,
Grégory Batt
,
Francois Fages
,
Sylvain Soliman
.
On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology
. In Springer-Verlag, editor,
CMSB'08: Proceedings of the fourth international conference on Computational Methods in Systems Biology
, volume 5307 of
Lecture Notes in Computer Science
, pages 251–268, 2008.
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François Fages
,
Sylvain Soliman
.
Abstract interpretation and types for systems biology
.
Theoretical Computer Science
, 403 (1):52–70, 2008.
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Domitille Heitzler et al
.
Modelling of FSHR-induced signalling network
. In
International Conference for Gonadotropins & their Receptors
, pages n.p., 2008.
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Francois Fages
,
Sylvain Soliman
.
Formal Cell Biology in Biocham
. In
SFM 2008: Formal Methods for Computational Systems Biology
, volume 5016 of
Lecture Notes in Computer Science
, pages 54-80, Springer Berlin Heidelberg, 2008.
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Francois Fages
,
Sylvain Soliman
.
From reaction models to influence graphs and back: a theorem
. In Springer-Verlag, editor,
Proceedings of Formal Methods in Systems Biology FMSB'08
, volume 5054 of
LNCS
, 2008.
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Francois Fages
,
Francesca Rossi
,
Sylvain Soliman
.
Proceedings of CSCLP 2007: Annual ERCIM Workshop on Constraint Solving and Constraint Logic Programming
. 2007.
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Laurence Calzone
,
Nathalie Chabrier-Rivier
,
François Fages
,
Loïc Fosse
,
Sylvain Soliman
.
Langages formels dans la machine abstraite biochimique BIOCHAM
.
Revue des Sciences et Technologies de l’Information - Série TSI : Technique et Science Informatiques
, 26 (1-2):47–72, 2007.
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Rémy Haemmerlé
,
François Fages
,
Sylvain Soliman
.
Closures and Modules Within Linear Logic Concurrent Constraint Programming
. In Arvind, V. and Prasad, Sanjiva, editor,
FSTTCS 2007: Foundations of Software Technology and Theoretical Computer Science
, pages 544–556, Springer Berlin Heidelberg, 2007.
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Remy Haemmerle
,
Francois Fages
,
Sylvain Soliman
.
On Internalizing Modules as Agents in Concurrent Constraint Programming
. Research Report, 2006.
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Laurence Calzone
,
Nathalie Chabrier-Rivier
,
François Fages
,
Sylvain Soliman
.
Machine Learning Biochemical Networks from Temporal Logic Properties
. In Priami, Corradoand Plotkin, Gordon, editor,
Transactions on Computational Systems Biology VI
, pages 68–94, Springer Berlin Heidelberg, 2006.
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Laurence Calzone
,
Sylvain Soliman
.
Coupling the Cell cycle and the Circadian Cycle
. Research Report, 2006.
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Laurence Calzone
,
François Fages
,
Sylvain Soliman
.
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
.
Bioinformatics
, 22 (14):1805–1807, 2006.
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Nathalie Chabrier-Rivier
,
Francois Fages
,
Sylvain Soliman
,
Laurence Calzone
.
Learning Transition Rules from Temporal Logic Properties
. Research Report, 2005.
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Laurence Calzone
,
Nathalie Chabrier-Rivier
,
Francois Fages
,
Sylvain Soliman
.
A Machine Learning approach to Biochemical Reaction Rules Discovery
. In Francis J. Doyle III, editor,
Proceedings of Foundations of Systems Biology and Engineering FOSBE'05
, pages 375–379, 2005.
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Laurence Calzone
,
Nathalie Chabrier-Rivier
,
Francois Fages
,
Sylvain Soliman
.
Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle
. In Alain Guénoche et Christophe Geourjon Guy Perrière, editor,
Actes de JOBIM'05
, pages 183–192, 2005.
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Laurence Calzone
,
Nathalie Chabrier-Rivier
,
Francois Fages
,
Lucie Gentils
,
Sylvain Soliman
.
Machine Learning Bio-molecular Interactions from Temporal Logic Properties
. In Gordon Plotkin, editor,
Third Workshop on Computational Methods in Systems Biology
, 2005.
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Nathalie Chabrier-Rivier
,
Francois Fages
,
Sylvain Soliman
.
The Biochemical Abstract Machine BIOCHAM
. In Vincent Danos, Vincent Schächter, editor,
CMSB'04: Proceedings of the second Workshop on Computational Methods in Systems Biology
, pages 172–191, Springer-Verlag, 2004.
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Francois 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.
HAL
François Fages
,
Sylvain Soliman
,
Rémi Coolen
.
CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming
.
Constraints
, 9 (4):241 - 262, 2004.
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Sylvain Soliman
,
Francois Fages
.
La programmation par contraintes
.
Interstices
, 2004.
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Sylvain Soliman
.
Pi-calculus and LCC, a Space Odyssey
. Research Report, 2003.
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Sylvain Soliman
.
Concurrent constraint programming and linear logic
. Theses, Université Paris Diderot - Paris 7, 2001.
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François Fages
,
Paul Ruet
,
Sylvain Soliman
.
Linear Concurrent Constraint Programming: Operational and Phase Semantics
.
Information and Computation
, 165 (1):14–41, 2001.
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