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    • Graphical conditions for the existence, unicity and number of regular models
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    • 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
    • Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
    • Symbolic Methods for Biological Networks D2.1 Report on Scalable Methods for Tropical Solutions (T1.2)
    • 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
    • COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
    • 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
    • Model learning to identify systemic regulators of the peripheral circadian clock
    • Graphical Conditions for Rate Independence in Chemical Reaction Networks
    • On the Complexity of Quadratization for Polynomial Differential Equations
    • SBML Level 3: an extensible format for the exchange and reuse of biological models
    • Automated inference of Boolean models from molecular interaction maps using CaSQ
    • 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
    • Executable Disease Networks: Adding dynamics to molecular maps
    • 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
    • Modelling molecular networks: relationships between different formalisms and levels of details
    • 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
    • Modelling of FSHR-induced signalling network
    • 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
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SBGN support in BIOCHAM

Mon, Nov 1, 2010·
Dragana Jovanovska
,
Francois Fages
,
Sylvain Soliman
· 0 min read
HAL DOI
Type
Journal article
Publication
Nature Precedings
Last updated on Mon, Nov 1, 2010
← Steady-state Solution of Biochemical Systems, Beyond S-systems via T-invariants Wed, Dec 1, 2010
A graphical method for reducing and relating models in systems biology Wed, Sep 1, 2010 →

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