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ORCIDSylvain Soliman
Person information
- affiliation: Inria, Lifeware Group, Palaiseau, France
- affiliation (PhD 2001): Paris Diderot University, Paris, France
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Books and Theses
- 2016
[b2]Sylvain Soliman:
A structural perspective on the dynamics of biochemical systems. (Une perspective structurelle sur la dynamique des systèmes biochimiques). University of Paris-Sud, Orsay, France, 2016- 2001
- [b1]Sylvain Soliman:
Concurrent constraint programming and linear logic. Paris Diderot University, France, 2001
Journal Articles
- 2023
- [j27]Van-Giang Trinh
, Belaid Benhamou, Sylvain Soliman:
Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding. Theor. Comput. Sci. 971: 114073 (2023) - 2022
- [j26]Anna Niarakis, Dagmar Waltemath, James A. Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone:
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings Bioinform. 23(4) (2022) - [j25]Sahar Aghakhani, Sylvain Soliman, Anna Niarakis:
Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach. PLoS Comput. Biol. 18(12): 1010408 (2022) - 2021
- [j24]Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik-Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C. Freeman, Paul D. Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone:
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 Bioinform. 22(2): 1848-1859 (2021) - [j23]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. Bioinform. 37(Supplement): 401-409 (2021) - 2020
- [j22]Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu:
Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinform. 36(16): 4473-4482 (2020) - 2018
- [j21]François Fages, Thierry Martinez, David A. Rosenblueth, Sylvain Soliman:
Influence Networks Compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE ACM Trans. Comput. Biol. Bioinform. 15(4): 1138-1151 (2018) - 2016
- [j20]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. Biosyst. 149: 59-69 (2016) - [j19]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 An Int. J. 21(2): 251-276 (2016) - 2015
- [j18]François Fages, Steven Gay, Sylvain Soliman:
Inferring reaction systems from ordinary differential equations. Theor. Comput. Sci. 599: 64-78 (2015) - [j17]Hui-Ju Katherine Chiang, François Fages, Jie-Hong Roland Jiang, Sylvain Soliman:
Hybrid Simulations of Heterogeneous Biochemical Models in SBML. ACM Trans. Model. Comput. Simul. 25(2): 14:1-14:22 (2015) - 2014
- [j16]Sylvain Soliman, François Fages, Ovidiu Radulescu:
A constraint solving approach to model reduction by tropical equilibration. Algorithms Mol. Biol. 9: 24 (2014) - [j15]Steven Gay, François Fages, Thierry Martinez, Sylvain Soliman, Christine Solnon:
On the subgraph epimorphism problem. Discret. Appl. Math. 162: 214-228 (2014) - 2013
- [j14]François Fages, Sylvain Soliman:
Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 10(2): 308-309 (2013) - 2012
- [j13]Sylvain Soliman:
Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem. Algorithms Mol. Biol. 7: 15 (2012) - [j12]François Fages, Sylvain Soliman:
Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1314-1315 (2012) - 2011
- [j11]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. Theor. Comput. Sci. 412(21): 2108-2127 (2011) - [j10]Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman:
Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures. Theor. Comput. Sci. 412(26): 2827-2839 (2011) - 2010
- [j9]Steven Gay, Sylvain Soliman, François Fages:
A graphical method for reducing and relating models in systems biology. Bioinform. 26(18) (2010) - 2009
- [j8]Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman:
A general computational method for robustness analysis with applications to synthetic gene networks. Bioinform. 25(12) (2009) - [j7]Sylvain Soliman:
Modelling Biochemical Reaction Networks with BIOCHAM Extracting Qualitative and Quantitative Information from the Structure. Simul. Notes Eur. 19(3-4): 33-40 (2009) - 2008
- [j6]François Fages, Sylvain Soliman:
Abstract interpretation and types for systems biology. Theor. Comput. Sci. 403(1): 52-70 (2008) - 2007
- [j5]Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, L. Fosse, Sylvain Soliman:
Langages formels dans la machine abstraite biochimique BIOCHAM. Tech. Sci. Informatiques 26(1-2): 47-72 (2007) - 2006
- [j4]Laurence Calzone, François Fages, Sylvain Soliman:
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinform. 22(14): 1805-1807 (2006) - [j3]Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman:
Machine Learning Biochemical Networks from Temporal Logic Properties. Trans. Comp. Sys. Biology 6: 68-94 (2006) - 2004
- [j2]François Fages, Sylvain Soliman, Rémi Coolen:
CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming. Constraints An Int. J. 9(4): 241-262 (2004) - 2001
- [j1]François Fages, Paul Ruet, Sylvain Soliman:
Linear Concurrent Constraint Programming: Operational and Phase Semantics. Inf. Comput. 165(1): 14-41 (2001)
Conference and Workshop Papers
- 2024
- [c27]Giang V. Trinh, Belaid Benhamou, Samuel Pastva, Sylvain Soliman:
Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming. AAAI 2024: 10714-10722 - 2023
- [c26]Van-Giang Trinh, Belaid Benhamou, Sylvain Soliman:
Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming. CP 2023: 35:1-35:19 - 2022
- [c25]Van-Giang Trinh, Belaid Benhamou, Kunihiko Hiraishi, Sylvain Soliman:
Minimal Trap Spaces of Logical Models are Maximal Siphons of Their Petri Net Encoding. CMSB 2022: 158-176 - 2021
- [c24]Mathieu Hemery, François Fages, Sylvain Soliman:
Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs. CMSB 2021: 74-90 - 2020
- [c23]Elisabeth Degrand, François Fages, Sylvain Soliman:
Graphical Conditions for Rate Independence in Chemical Reaction Networks. CMSB 2020: 61-78 - [c22]Mathieu Hemery, François Fages, Sylvain Soliman:
On the Complexity of Quadratization for Polynomial Differential Equations. CMSB 2020: 120-140 - 2019
- [c21]Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages:
On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics. CMSB 2019: 352-355 - 2018
- [c20]François Fages, Sylvain Soliman:
On Robustness Computation and Optimization in BIOCHAM-4. CMSB 2018: 292-299 - 2017
- [c19]Arthur Carcano, François Fages, Sylvain Soliman:
Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. CMSB 2017: 74-90 - 2016
- [c18]François Fages, Thierry Martinez, David A. Rosenblueth, Sylvain Soliman:
Influence Systems vs Reaction Systems. CMSB 2016: 98-115 - 2015
- [c17]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. CMSB 2015: 208-221 - [c16]Thierry Martinez, François Fages, Sylvain Soliman:
Search by constraint propagation. PPDP 2015: 173-183 - 2014
- [c15]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. CMSB 2014: 114-128 - 2013
- [c14]Hui-Ju Katherine Chiang, François Fages, Jie-Hong R. Jiang, Sylvain Soliman:
On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models. CMSB 2013: 192-205 - 2012
- [c13]François Fages, Steven Gay, Sylvain Soliman:
Inferring Reaction Models from ODEs. CMSB 2012: 370-373 - [c12]Faten Nabli, François Fages, Thierry Martinez, Sylvain Soliman:
A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets. CP 2012: 798-814 - 2010
- [c11]Faten Nabli, Sylvain Soliman:
Steady-state solution of biochemical systems, beyond S-systems via T-invariants. CMSB 2010: 14-22 - 2009
- [c10]Elisabetta De Maria, François Fages, Sylvain Soliman:
On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle. CMSB 2009: 142-157 - 2008
- [c9]Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman:
On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology. CMSB 2008: 251-268 - [c8]François Fages, Sylvain Soliman:
From Reaction Models to Influence Graphs and Back: A Theorem. FMSB 2008: 90-102 - [c7]François Fages, Sylvain Soliman:
Formal Cell Biology in Biocham. SFM 2008: 54-80 - 2007
- [c6]Rémy Haemmerlé, François Fages, Sylvain Soliman:
Closures and Modules Within Linear Logic Concurrent Constraint Programming. FSTTCS 2007: 544-556 - 2006
- [c5]François Fages, Sylvain Soliman:
Type Inference in Systems Biology. CMSB 2006: 48-62 - 2004
- [c4]Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman:
The Biochemical Abstract Machine BIOCHAM. CMSB 2004: 172-191 - [c3]Sylvain Soliman, François Fages:
CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems. CMSB 2004: 231-235 - [c2]Sylvain Soliman:
Pi-calcul et LCC, une odyssée de l'espace. JFPLC 2004 - 1998
- [c1]François Fages, Paul Ruet, Sylvain Soliman:
Phase Semantics and Verification of Concurrent Constraint Programs. LICS 1998: 141-152
Parts in Books or Collections
- 2008
- [p1]François Fages, Sylvain Soliman:
Model Revision from Temporal Logic Properties in Computational Systems Biology. Probabilistic Inductive Logic Programming 2008: 287-304
Editorship
- 2008
- [e2]François Fages, Francesca Rossi, Sylvain Soliman:
Recent Advances in Constraints, 12th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2007, Rocquencourt, France, June 7-8, 2007, Revised Selected Papers. Lecture Notes in Computer Science 5129, Springer 2008, ISBN 978-3-540-89811-5 [contents] - 2005
- [e1]François Fages, Sylvain Soliman:
Principles and Practice of Semantic Web Reasoning, Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005, Proceedings. Lecture Notes in Computer Science 3703, Springer 2005, ISBN 3-540-28793-0 [contents]
Informal and Other Publications
- 2020
- [i7]Mathieu Hemery, François Fages, Sylvain Soliman:
On the Complexity of Quadratization for Polynomial Differential Equations. CoRR abs/2007.08910 (2020) - [i6]Elisabeth Degrand, François Fages, Sylvain Soliman:
Graphical Conditions for Rate Independence in Chemical Reaction Networks. CoRR abs/2007.15642 (2020) - 2018
- [i5]Adrien Baudier, François Fages, Sylvain Soliman:
Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. CoRR abs/1809.08891 (2018) - 2013
- [i4]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. CoRR abs/1304.2948 (2013) - 2010
- [i3]François Fages, Grégory Batt, Elisabetta De Maria, Dragana Jovanovska, Aurélien Rizk, Sylvain Soliman:
Computational Systems Biology in BIOCHAM. ERCIM News 2010(82): 36 (2010) - 2009
- [i2]Attila Csikász-Nagy, Adrien Fauré, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordán, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, Paolo Ballarini:
Analyzing various models of Circadian Clock and Cell Cycle coupling. Formal Methods in Molecular Biology 2009 - 2007
- [i1]Jean Clairambault, François Fages, Sylvain Soliman:
Patient-Tailored Cancer Therapeutics - The Tempo Project. ERCIM News 2007(69) (2007)
Coauthor Index
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