Computational Methods in Systems Biology

On the Use of the Moment Equations for Parameter Inference, Control and Experimental Design in Stochastic Biochemical Reaction Networks.- Numerical Approximation of Rare Event Probabilities in Biochemically Reacting Systems.- An Approximate Execution of Rule-Based Multi-level Models.- Computing Cumulative Rewards Using Fast Adaptive Uniformisation.- Linking Discrete and Stochastic Models: The Chemical Master Equation as a Bridge between Process Hitting and Proper Generalized Decomposition.- Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models.- Modelling and Analysis of Phase Variation in Bacterial Colony Growth.- Using Probabilistic Strategies to Formalize and Compare -Synuclein Aggregation and Propagation under Different Scenarios.- Dynamic Image-Based Modelling of Kidney Branching Morphogenesis.- Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models.- Constraint Programming in Community-Based Gene Regulatory Network Inference.- ABC-Fun: A Probabilistic Programming Language for Biology.- A Temporal Logic Approach to Modular Design of Synthetic Biological Circuits.- A Lattice-Theoretic Framework for Metabolic Pathway Analysis.- On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models.- On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology.- Context-Sensitive Flow Analyses: A Hierarchy of Model Reductions.- Posters Backmatter).- ARNI: Abductive Inference of Complex Regulatory Network Structures.- A Systems Biology and Ecology Framework for POPs Bioaccumulation in Marine Ecosystems.- A Symbolic Approach Based on Model Checking and Constraint Solving Techniques for Reverse Engineering of Thomas Networks Parameters.- Compositionality Results for Cardiac Cell Dynamics.- Quantification of Biological Network Perturbations: Impact Assessment Using Causal Biological Networks.- Deciphering the Transcriptional Landscape of Caulobacter crescentus at Base Pair Resolution.-Identifiablity