Sylvain Soliman

Latest

• On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry
• MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps
• Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming
• Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding
• Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming
• Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts
• A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint
• Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach
• Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding
• Symbolic Methods for Biological Networks D2.1 Report on Scalable Methods for Tropical Solutions (T1.2)
• A Polynomialization Algorithm for Elementary Functions and ODEs, and their Compilation into Chemical Reaction Networks
• Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs
• Graphical Conditions for Rate Independence in Chemical Reaction Networks
• On the Complexity of Quadratization for Polynomial Differential Equations
• On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics
• A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data
• Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels
• Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors
• On Robustness Computation and Optimization in BIOCHAM-4
• Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data
• Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-α Up-regulation During Mitosis
• A structural perspective on the dynamics of biochemical systems
• Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis
• Influence Systems vs Reaction Systems
• On Enumerating Minimal Siphons in Petri nets using CLP and SAT solvers: Theoretical and Practical Complexity
• Model-based Investigation of the Effect of the Cell Cycle on the Circadian Clock through Transcription Inhibition during Mitosis
• Inferring reaction systems from ordinary differential equations
• Search by Constraint Propagation
• Hybrid Simulations of Heterogeneous Biochemical Models in SBML
• A constraint solving approach to model reduction by tropical equilibration
• 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)
• On the subgraph Epimorphism Problem
• A stronger necessary condition for the multistationarity of chemical reaction networks
• A Constraint Solving Approach to Tropical Equilibration and Model Reduction
• On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models
• Solving Subgraph Epimorphism Problems using CLP and SAT
• Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem
• A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets
• Inferring Reaction Models from ODEs
• Reifying Global Constraints
• Automatic Curation of SBML Models based on their ODE Semantics
• Un modèle booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri
• Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures
• 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
• A Unique Transformation from Ordinary Differential Equations to Reaction Networks
• Steady-state Solution of Biochemical Systems, Beyond S-systems via T-invariants
• SBGN support in BIOCHAM
• A graphical method for reducing and relating models in systems biology
• Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans
• Model-based Predictions of the Influence of Circadian Clock Genes Knock-Outs on the Cell Cycle
• On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle
• On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle
• A general computational method for robustness analysis with applications to synthetic gene networks
• Modelling Biochemical Reaction Networks with BIOCHAM Extracting Qualitative and Quantitative Information from the Structure
• Model Revision from Temporal Logic Properties in Computational Systems Biology
• On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology
• Abstract interpretation and types for systems biology
• Formal Cell Biology in Biocham
• From reaction models to influence graphs and back: a theorem
• Closures and Modules Within Linear Logic Concurrent Constraint Programming
• Langages formels dans la machine abstraite biochimique BIOCHAM
• Proceedings of CSCLP 2007: Annual ERCIM Workshop on Constraint Solving and Constraint Logic Programming
• Coupling the Cell cycle and the Circadian Cycle
• Machine Learning Biochemical Networks from Temporal Logic Properties
• On Internalizing Modules as Agents in Concurrent Constraint Programming
• BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
• A Machine Learning approach to Biochemical Reaction Rules Discovery
• Learning Transition Rules from Temporal Logic Properties
• Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle
• Machine Learning Bio-molecular Interactions from Temporal Logic Properties
• The Biochemical Abstract Machine BIOCHAM
• CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming
• Modelling and Querying Interaction Networks in the Biochemical Abstract Machine BIOCHAM
• La programmation par contraintes
• Pi-calculus and LCC, a Space Odyssey
• Concurrent constraint programming and linear logic
• Linear Concurrent Constraint Programming: Operational and Phase Semantics