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Sylvain Soliman
Sylvain Soliman
Inria Saclay Île-de-France, Lifeware team
Verified email at inria.fr - Homepage
Title
Cited by
Cited by
Year
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
L Calzone, F Fages, S Soliman
Bioinformatics 22 (14), 1805-1807, 2006
3232006
Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM
F Fages, S Soliman, N Chabrier-Rivier
Journal of Biological Physics and Chemistry 4, 64-73, 2004
2152004
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
1962020
Machine learning biochemical networks from temporal logic properties
L Calzone, N Chabrier-Rivier, F Fages, S Soliman
Transactions on Computational Systems Biology VI, 68-94, 2006
1472006
A general computational method for robustness analysis with applications to synthetic gene networks
A Rizk, G Batt, F Fages, S Soliman
Bioinformatics 25 (12), i169, 2009
1462009
On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology
A Rizk, G Batt, F Fages, S Soliman
Computational Methods in Systems Biology, 251-268, 2008
1232008
The biochemical abstract machine BIOCHAM
N Chabrier-Rivier, F Fages, S Soliman
Computational Methods in Systems Biology, 172-191, 2005
1142005
Linear concurrent constraint programming: operational and phase semantics
F Fages, P Ruet, S Soliman
Information and Computation 165 (1), 14-41, 2001
1112001
Abstract interpretation and types for systems biology
F Fages, S Soliman
Theoretical Computer Science 403 (1), 52-70, 2008
1072008
Formal cell biology in biocham
F Fages, S Soliman
Formal Methods for Computational Systems Biology, 54-80, 2008
912008
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ...
Molecular systems biology 17 (10), e10387, 2021
792021
A graphical method for reducing and relating models in systems biology
S Gay, S Soliman, F Fages
Bioinformatics 26 (18), i575-i581, 2010
792010
Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures
A Rizk, G Batt, F Fages, S Soliman
Theoretical Computer Science, 2010
712010
Automated inference of Boolean models from molecular interaction maps using CaSQ
SS Aghamiri, V Singh, A Naldi, T Helikar, S Soliman, A Niarakis
Bioinformatics 36 (16), 4473-4482, 2020
602020
Inferring reaction systems from ordinary differential equations
F Fages, S Gay, S Soliman
Theoretical Computer Science 599, 64-78, 2015
572015
A unique transformation from ordinary differential equations to reaction networks
S Soliman, M Heiner
PloS one 5 (12), e14284, 2010
562010
From reaction models to influence graphs and back: a theorem
F Fages, S Soliman
Formal Methods in Systems Biology, 90-102, 2008
532008
On the subgraph epimorphism problem
S Gay, F Fages, T Martinez, S Soliman, C Solnon
Discrete Applied Mathematics 162, 214-228, 2014
412014
Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans
K Sriram, S Soliman, F Fages
Journal of Theoretical Biology 258 (1), 71-88, 2009
342009
Invariants and other structural properties of biochemical models as a constraint satisfaction problem
S Soliman
Algorithms for Molecular Biology 7, 1-9, 2012
312012
Phase semantics and verification of concurrent constraint programs
F Fages, P Ruet, S Soliman
Logic in Computer Science, 1998. Proceedings. Thirteenth Annual IEEE …, 1998
311998
CLPGUI: a generic graphical user interface for constraint logic programming
F Fages, S Soliman, R Coolen
Constraints 9 (4), 241-262, 2004
302004
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 …
E De Maria, F Fages, A Rizk, S Soliman
Theoretical Computer Science 412 (21), 2108-2127, 2011
272011
Machine learning bio-molecular interactions from temporal logic properties
L Calzone, N Chabrier-Rivier, F Fages, L Gentils, S Soliman
262005
Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis
P Traynard, C Feillet, S Soliman, F Delaunay, F Fages
Biosystems 149, 59-69, 2016
242016
On coupling models using model-checking: effects of irinotecan injections on the mammalian cell cycle
E De Maria, F Fages, S Soliman
Computational Methods in Systems Biology, 142-157, 2009
242009
A constraint solving approach to model reduction by tropical equilibration
S Soliman, F Fages, O Radulescu
Algorithms for Molecular Biology 9, 1-11, 2014
212014
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
A Niarakis, M Kuiper, M Ostaszewski, RS Malik Sheriff, C Casals-Casas, ...
Briefings in bioinformatics 22 (2), 1848-1859, 2021
202021
On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity
F Nabli, T Martinez, F Fages, S Soliman
Constraints 21, 251-276, 2016
172016
Closures and modules within linear logic concurrent constraint programming
R Haemmerlé, F Fages, S Soliman
FSTTCS 2007: Foundations of Software Technology and Theoretical Computer …, 2007
172007
Coupling the cell cycle and the circadian cycle
L Calzone, S Soliman
162006
A machine learning approach to biochemical reaction rules discovery
L Calzone, N Chabrier-Rivier, F Fages, S Soliman
Proceedings of Foundations of Systems Biology and Engineering FOSBE 5, 375–379, 2005
162005
BIOCHAM Reference Manual
F Fages, D Jovanovska, A Rizk, S Soliman
15*2003
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
A Niarakis, D Waltemath, J Glazier, F Schreiber, SM Keating, D Nickerson, ...
Briefings in bioinformatics 23 (4), bbac212, 2022
132022
Finding minimal P/T-invariants as a CSP
S Soliman
Proceedings of the fourth Workshop on Constraint Based Methods for …, 2008
132008
On the complexity of quadratization for polynomial differential equations
M Hemery, F Fages, S Soliman
Computational Methods in Systems Biology: 18th International Conference …, 2020
122020
Minimal trap spaces of logical models are maximal siphons of their petri net encoding
VG Trinh, B Benhamou, K Hiraishi, S Soliman
International Conference on Computational Methods in Systems Biology, 158-176, 2022
112022
A stronger necessary condition for the multistationarity of chemical reaction networks
S Soliman
Bulletin of mathematical biology 75, 2289-2303, 2013
112013
A boolean model for enumerating minimal siphons and traps in petri nets
F Nabli, F Fages, T Martinez, S Soliman
International Conference on Principles and Practice of Constraint …, 2012
112012
On robustness computation and optimization in BIOCHAM-4
F Fages, S Soliman
Computational Methods in Systems Biology: 16th International Conference …, 2018
102018
CMBSlib: a library for comparing formalisms and models of biological systems
S Soliman, F Fages
Computational Methods in Systems Biology, 231-235, 2005
102005
Model learning to identify systemic regulators of the peripheral circadian clock
J Martinelli, S Dulong, XM Li, M Teboul, S Soliman, F Lévi, F Fages, ...
Bioinformatics 37 (Supplement_1), i401-i409, 2021
92021
Compiling elementary mathematical functions into finite chemical reaction networks via a polynomialization algorithm for ODEs
M Hemery, F Fages, S Soliman
Computational Methods in Systems Biology: 19th International Conference …, 2021
92021
Graphical requirements for multistationarity in reaction networks and their verification in BioModels
A Baudier, F Fages, S Soliman
Journal of Theoretical Biology 459, 79-89, 2018
92018
Model revision from temporal logic properties in computational systems biology
F Fages, S Soliman
Probabilistic inductive logic programming, 287-304, 2008
92008
Influence networks compared with reaction networks: Semantics, expressivity and attractors
F Fages, T Martinez, DA Rosenblueth, S Soliman
IEEE/ACM Transactions on Computational Biology and Bioinformatics 15 (4 …, 2018
82018
Constraint logic programming
S Soliman, F Fages
82017
Steady-state solution of biochemical systems, beyond S-Systems via T-invariants
F Nabli, S Soliman
Proceedings of the 8th International Conference on Computational Methods in …, 2010
82010
Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach
S Aghakhani, S Soliman, A Niarakis
PLoS Computational Biology 18 (12), e1010408, 2022
72022
Influence systems vs reaction systems
F Fages, T Martinez, DA Rosenblueth, S Soliman
Computational Methods in Systems Biology: 14th International Conference …, 2016
72016
Modelling biochemical reaction networks with biocham extracting qualitative and quantitative information from the structure
S Soliman
Proceedings of the 6th Vienna Conference on Mathematical Modelling MATHMOD 9 …, 2009
72009
A constraint solving approach to tropical equilibration and model reduction
S Soliman, F Fages, O Radulescu
arXiv preprint arXiv:1401.6337, 2014
62014
Automatic curation of SBML models based on their ODE semantics
F Fages, S Gay, S Soliman
INRIA, 2012
62012
Type inference in systems biology
F Fages, S Soliman
Computational Methods in Systems Biology, 48-62, 2006
62006
Learning transition rules from temporal logic properties
N Chabrier-Rivier, F Fages, S Soliman, L Calzone
62005
Phase model checking for some linear logic calculi
S Soliman
Proceedings of the Second International Workshop of the Implementation of …, 2001
62001
Graphical conditions for rate independence in chemical reaction networks
E Degrand, F Fages, S Soliman
International Conference on Computational Methods in Systems Biology, 61-78, 2020
52020
Search by constraint propagation
T Martinez, F Fages, S Soliman
Proceedings of the 17th International Symposium on Principles and Practice …, 2015
52015
Model-based investigation of the effect of the cell cycle on the circadian clock through transcription inhibition during mitosis
P Traynard, F Fages, S Soliman
Computational Methods in Systems Biology: 13th International Conference …, 2015
52015
A statistical unsupervised learning algorithm for inferring reaction networks from time series data
J Martinelli, J Grignard, S Soliman, F Fages
ICML 2019-Workshop on Computational Biology, 2019
42019
Hybrid simulations of heterogeneous biochemical models in SBML
HJK Chiang, F Fages, JHR Jiang, S Soliman
ACM Transactions on Modeling and Computer Simulation (TOMACS) 25 (2), 1-22, 2015
42015
Trace simplifications preserving temporal logic formulae with case study in a coupled model of the cell cycle and the circadian clock
P Traynard, F Fages, S Soliman
Computational Methods in Systems Biology: 12th International Conference …, 2014
42014
Inferring reaction models from ODEs
F Fages, S Gay, S Soliman
International Conference on Computational Methods in Systems Biology, 370-373, 2012
42012
Expressiveness and complexity of concurrent constraint programming: a finite model theoretic approach
F Fages, S Soliman, V Vianu
41998
The Biochemical abstract machine BIOCHAM
F Fages, A Rizk, S Soliman
4
Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding
VG Trinh, B Benhamou, S Soliman
Theoretical Computer Science 971, 114073, 2023
32023
A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint
V Singh, A Naldi, S Soliman, A Niarakis
NPJ systems biology and applications 9 (1), 33, 2023
32023
Probably approximately correct learning of regulatory networks from time-series data
A Carcano, F Fages, S Soliman
Computational Methods in Systems Biology: 15th International Conference …, 2017
32017
Computational methods in systems biology
P Traynard, C Feillet, S Soliman, F Delaunay
BioSystems 149, 1-2, 2016
32016
Solving subgraph epimorphism problems using CLP and SAT
S Gay, F Fages, F Santini, S Soliman
WCB-ninth Workshop on Constraint Based Methods for Bioinformatics, colocated …, 2013
32013
Reifying global constraints
F Fages, S Soliman
INRIA, 2012
32012
A Constraint Program For Subgraph Epimorphisms with Application to Identifying Model Reductions in Systems Biology
S Gay, F Fages, T Martinez, S Soliman
Proceedings of WCB11 - Workshop on Constraint Based Methods for …, 2011
32011
Modelling molecular networks: relationships between different formalisms and levels of details
S Soliman, C Chaouiya, G Batt, F Fages, E Remy, F Pommereau, ...
32010
Principles and Practice of Semantic Web Reasoning: Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005, Proceedings
F Fages, S Soliman
Springer, 2005
32005
Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle
L Calzone, N Chabrier-Rivier, F Fages, S Soliman
Actes de {JOBIM}'05, 183--192, 2005
32005
State-of-the-art in Bioinformatics
R Backofen, M Badea, A Burger, F Fages, P Lambrix, W Nutt, ...
REWERSE, 2004
32004
Pi-calcul et LCC, une odyssée de l'espace.
S Soliman
JFPLC, 2004
32004
Towards a Semantic Web for bioinformatics
R Backofen, M Badea, P Barahona, L Badea, F Bry, G Dawelbait, A Doms, ...
32004
Pi-calculus and LCC, a Space Odyssey
S Soliman
INRIA, 2003
32003
Programmation Concurrente avec Contraintes et Logique Lineaire
S Soliman
Ph.D. thesis, Université Paris 7, Denis Diderot, 2001
32001
PhysiBoSS-COVID: the Boolean modelling of COVID-19 signalling pathways in a multicellular simulation framework allows for the uncovering of mechanistic insights
V Noël, J Carbonell, MP de Leon, S Soliman, A Niarakis, L Calzone, ...
Google Scholar Google Scholar Cross Ref Cross Ref, 2020
22020
Search as constraint satisfaction
T Martinez, F Fages, P Morignot, S Soliman
Technical Report TR-***, INRIA Rocquencourt, Le Chesnay, France, 2014
22014
Modelling of FSHR-induced signalling network
D Heitzler, G Durand, L Dupuy, C Gauthier, V Piketty, P Crépieux, A Rizk, ...
International Conference for Gonadotropins & their Receptors, np, 2008
22008
Langages formels dans la machine abstraite biochimique BIOCHAM
L Calzone, N Chabrier-Rivier, F Fages, L Fosse, S Soliman
Revue des Sciences et Technologies de l'Information-Série TSI: Technique et …, 2007
22007
Requirements and specification of bioinformatics use cases
R Backofen, L Badea, P Barahona, M Berndtsson, A Burger, G Dawelbait, ...
22005
Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts
S Aghakhani, SE Silva-Saffar, S Soliman, A Niarakis
Computational and Structural Biotechnology Journal 21, 4196-4206, 2023
12023
A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms
A Niarakis, M Ostaszewski, A Mazein, I Kuperstein, M Kutmon, ...
bioRxiv, 2022.12. 17.520865, 2022
12022
On inferring reactions from data time series by a statistical learning greedy heuristics
J Martinelli, J Grignard, S Soliman, F Fages
Computational Methods in Systems Biology: 17th International Conference …, 2019
12019
BIOCHAM 3.7. 3 Reference Manual
F Fages, FM Floch, S Gay, D Jovanovska, A Rizk, S Soliman, P Traynard, ...
Institut National de Recherche en Informatique et Automatique EPI Lifeware …, 2015
12015
On the hybrid composition and simulation of heterogeneous biochemical models
K Chiang, F Fages, JH Jiang, S Soliman
Computational Methods in Systems Biology: 11th International Conference …, 2013
12013
Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology
F Fages, S Soliman
IEEE/ACM transactions on computational biology and bioinformatics 9 (05 …, 2012
12012
Constraint programming for the dynamical analysis of biochemical systems–a survey
S Soliman
Technical Report Deliverable 1.6, ANR CALAMAR, ANR-08-SYSC-003, 2011
12011
SBGN support in BIOCHAM
D Jovanovska, F Fages, S Soliman
Nature Precedings, 1-1, 2010
12010
Analyzing various models of Circadian Clock and Cell Cycle coupling
A Csikász-Nagy, A Faure, R Larcher, P Lecca, I Mura, F Jordan, ...
Dagstuhl Seminar Proceedings, 2009
12009
Model-based predictions of the influence of circadian clock genes knock-outs on the cell cycle
E De Maria, F Fages, S Soliman
12009
On Internalizing Modules as Agents in Concurrent Constraint Programming
R Haemmerle, F Fages, S Soliman
INRIA, 2006
12006
Usage of bioinformatics tools and identification of information sources
R Backofen, B Mike, P Barahona, A Burger, G Dawelbait, A Doms, ...
REWERSE, 2005
12005
Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming
G Trinh, B Benhamou, S Pastva, S Soliman
Proceedings of the AAAI Conference on Artificial Intelligence 38 (9), 10714 …, 2024
2024
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
A Niarakis, M Ostaszewski, A Mazein, M Kutmon, ME Gillespie, ...
Frontiers in Immunology 14, 1282859, 2024
2024
MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps
S Aghakhani, A Niarakis, S Soliman
Journal of Integrative Bioinformatics, 20230048, 2024
2024
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