Computational Methods in Systems Biology

Chemical Reaction Networks Algebraic Biochemistry: a Framework for On-line Analog Computation in Cells.- Abstract Simulation of Reaction Networks via Boolean Networks.- Abstraction-Based Segmental Simulation of Chemical Reaction Networks.- Qualitative dynamics of chemical reaction networks: an investigation using partial tropical equilibrations.- Boolean Networks Prioritization of candidate genes through Boolean networks.- Variable Stabilisation in Boolean Monotonic Model Pools.- Variable-Depth Simulation of Most Permissive Boolean Networks.- Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding.- Continuous and Hybrid Models Stability versus Metastability in a Model of Skin Fages Exact linear reduction for rational dynamical systems.- Limit cycle analysis of a class of hybrid gene regulatory networks.- Machine Learning Bayesian learning of effective chemical master equations in crowded intracellular conditions.- Probabilistic Multivariate Early Warning Signals.- A Meta-Species Language for Chemical Reaction Networks.- Automated Generation of Conditional Moment Equations for Stochastic Reaction Networks.- An Extension of ERODE to Reduce Boolean Networks by Backward Boolean Equivalence.- 2.0: Modelling and Analysis of Regulated Rule-based Systems.