François Fages

Latest

• On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry
• 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
• 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 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
• 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 graphical method for reducing and relating models in systems biology
• Abstract interpretation and types for systems biology
• Closures and Modules Within Linear Logic Concurrent Constraint Programming
• Langages formels dans la machine abstraite biochimique BIOCHAM
• Machine Learning Biochemical Networks from Temporal Logic Properties
• BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
• CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming
• Linear Concurrent Constraint Programming: Operational and Phase Semantics