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Machine Learning Bio-molecular Interactions from Temporal Logic Properties

Laurence Calzone , Nathalie Chabrier-Rivier , Francois Fages , Lucie Gentils , Sylvain Soliman
Third Workshop on Computational Methods in Systems Biology, Apr 2005, Edinburgh, Scotland
Conference papers inria-00000117v1
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On Internalizing Modules as Agents in Concurrent Constraint Programming

Remy Haemmerle , Francois Fages , Sylvain Soliman
[Research Report] RR-5981, INRIA. 2006
Reports inria-00096644v3
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Learning Transition Rules from Temporal Logic Properties

Nathalie Chabrier-Rivier , Francois Fages , Sylvain Soliman , Laurence Calzone
[Research Report] RR-5543, INRIA. 2005, pp.19
Reports inria-00070464v1

Formal Cell Biology in Biocham

Francois Fages , Sylvain Soliman
SFM 2008: Formal Methods for Computational Systems Biology, Jun 2008, Bertinoro, Italy. pp.54-80, ⟨10.1007/978-3-540-68894-5_3⟩
Conference papers hal-02308547v1

Model-based Investigation of the Effect of the Cell Cycle on the Circadian Clock through Transcription Inhibition during Mitosis

Pauline Traynard , François Fages , Sylvain Soliman
CMSB'15 - Proceedings of the thirteenth international conference on Computational Methods in Systems Biology, 2015, Nantes, France. pp.208--221, ⟨10.1007/978-3-319-23401-4_18⟩
Conference papers hal-01236264v1
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Model-based Predictions of the Influence of Circadian Clock Genes Knock-Outs on the Cell Cycle

Elisabetta de Maria , Francois Fages , Sylvain Soliman
[Research Report] RR-7064, INRIA. 2009
Reports inria-00424950v2
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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

Elisabetta de Maria , François Fages , Aurélien Rizk , Sylvain Soliman
Theoretical Computer Science, 2011, 412 (21), pp.2108--2127. ⟨10.1016/j.tcs.2010.10.036⟩
Journal articles hal-01285815v2
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A Unique Transformation from Ordinary Differential Equations to Reaction Networks

Sylvain Soliman , Monika Heiner
PLoS ONE, 2010, 5 (12), pp.e14284. ⟨10.1371/journal.pone.0014284⟩
Journal articles hal-01431261v1

Closures and Modules Within Linear Logic Concurrent Constraint Programming

Rémy Haemmerlé , François Fages , Sylvain Soliman
FSTTCS 2007: Foundations of Software Technology and Theoretical Computer Science, 2007, Berlin, Heidelberg, Unknown Region. pp.544--556
Conference papers hal-01779531v1
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Pi-calculus and LCC, a Space Odyssey

Sylvain Soliman
[Research Report] RR-4855, INRIA. 2003
Reports inria-00071728v1
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Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach

Sahar Aghakhani , Sylvain Soliman , Anna Niarakis
PLoS Computational Biology, 2022, 18 (12), pp.e1010408. ⟨10.1371/journal.pcbi.1010408⟩
Journal articles hal-03880870v2

On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology

Aurélien Rizk , Grégory Batt , Francois Fages , Sylvain Soliman
CMSB'08: Proceedings of the fourth international conference on Computational Methods in Systems Biology, Monika Heiner and Adeline Uhrmacher, Oct 2008, Rostock, Germany. pp.251--268, ⟨10.1007/978-3-540-88562-7_19⟩
Conference papers istex inria-00419781v1
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On Robustness Computation and Optimization in BIOCHAM-4

François Fages , Sylvain Soliman
16th Int. Conf. on Computational Methods in Systems Biology, Sep 2018, Brno, Czech Republic. ⟨10.1007/978-3-319-99429-1_18⟩
Conference papers hal-01814854v1
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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

Anna Niarakis , Martin Kuiper , Marek Ostaszewski , Rahuman Malik Sheriff , Cristina Casals-Casas , et al.
Briefings in Bioinformatics, 2021, 22 (2), pp.1848--1859. ⟨10.1093/bib/bbaa046⟩
Journal articles hal-02549796v1
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Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs

Mathieu Hemery , François Fages , Sylvain Soliman
CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France
Conference papers hal-03220725v3
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Graphical Conditions for Rate Independence in Chemical Reaction Networks

Elisabeth Degrand , François Fages , Sylvain Soliman
CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology, Sep 2020, Konstanz / Online, Germany
Conference papers hal-02900758v1
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Automated inference of Boolean models from molecular interaction maps using CaSQ

Sara Sadat Aghamiri , Vidisha Singh , Aurélien Naldi , Tomáš Helikar , Sylvain Soliman , et al.
Bioinformatics, 2020, 36 (16), pp.4473-4482. ⟨10.1093/bioinformatics/btaa484⟩
Journal articles hal-02590714v1
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Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis

Pauline Traynard , Céline Feillet , Sylvain Soliman , Franck Delaunay , François Fages
BioSystems, 2016, 149, pp.59--69. ⟨10.1016/j.biosystems.2016.07.003⟩
Journal articles hal-01378466v1
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Model learning to identify systemic regulators of the peripheral circadian clock

Julien Martinelli , Sandrine Dulong , Xiao-Mei Li , Michèle Teboul , Sylvain Soliman , et al.
Bioinformatics, 2021, 37 (Supplement_1), pp.9. ⟨10.1093/bioinformatics/btab297⟩
Journal articles hal-03183579v1
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On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics

Julien Martinelli , Jeremy Grignard , Sylvain Soliman , François Fages
CMSB 2019 - 17th Computational Methods in Systems Biology, Sep 2019, Trieste, Italy
Conference papers hal-02173721v1

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)

Pauline Traynard , François Fages , Sylvain Soliman
CMSB'14: Proceedings of the twelth international conference on Computational Methods for Systems Biology, Nov 2014, Manchester, United Kingdom. pp.114--128, ⟨10.1007/978-3-319-12982-2⟩
Conference papers hal-01098529v1
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A structural perspective on the dynamics of biochemical systems

Sylvain Soliman
Bioinformatics [q-bio.QM]. Université Paris Sud - Orsay, 2016
Habilitation à diriger des recherches tel-01403712v1

Steady-state Solution of Biochemical Systems, Beyond S-systems via T-invariants

Faten Nabli , Sylvain Soliman
Proceedings of the 8th International Conference on Computational Methods in Systems Biology, 2010, New York, NY, USA, Unknown Region. pp.14--22, ⟨10.1145/1839764.1839768⟩
Conference papers hal-01779507v1

Machine Learning Biochemical Networks from Temporal Logic Properties

Laurence Calzone , Nathalie Chabrier-Rivier , François Fages , Sylvain Soliman
Transactions on Computational Systems Biology VI, 2006, Berlin, Heidelberg, Unknown Region. pp.68--94
Conference papers hal-01779529v1

Executable Disease Networks: Adding dynamics to molecular maps

Vidisha Singh , Saran Pankaew , Marek Ostaszewski , George D. Kalliolias , Sylvain Soliman , et al.
ECCB 2018 - 17th European Conference on Computational Biology, Sep 2018, Athens, Greece
Poster communications hal-01875418v1

Modelling and Querying Interaction Networks in the Biochemical Abstract Machine BIOCHAM

Francois Fages , Sylvain Soliman , Nathalie Chabrier-Rivier
Journal of Biological Physics and Chemistry, 2004, 4 (2), pp.64--73
Journal articles hal-01431345v1
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COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms

Marek Ostaszewski , Anna Niarakis , Alexander Mazein , Inna Kuperstein , Robert Phair , et al.
Molecular Systems Biology, 2021, 17 (10), pp.e10387. ⟨10.15252/msb.202110387⟩
Journal articles hal-03385317v2
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Automatic Curation of SBML Models based on their ODE Semantics

Francois Fages , Steven Gay , Sylvain Soliman
[Research Report] RR-8014, INRIA. 2012
Reports hal-00723554v1

La programmation par contraintes

Sylvain Soliman , Francois Fages
Interstices, 2004
Journal articles inria-00000571v1
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Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle

Laurence Calzone , Nathalie Chabrier-Rivier , Francois Fages , Sylvain Soliman
Actes de {JOBIM}'05, Jul 2005, Lyon, pp.183--192
Conference papers inria-00000813v1