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 Analysis and Improved Parameter Estimation of a Human Blood Glucose Control System Model.- RNA Interference in Cancer and Cell Cycle Networks: A Case Study of E2F Proteins.- A Balancing Act: Parameter Estimation for Biological Models with Steady-State Measurements.- A Fusion Approach Linking Signaling Logic and Metabolic Mass-Flow Kinetics in Hepatocytes.- Esther: Introducing an Online Platform for Parameter Identification of Boolean Networks.- Identifying Latent Dynamic Components in Biological Systems.- Next-Newtomics: The Next Generation Repository for Bioinformatical Interpreted Omics Datasets from the Newt Notophthalmus viridescens.- MiRNA Expression Analysis during Heart Regeneration of N. viridescens.- Algorithm to Predict G-Quadruplex Folding through Score Computing.- Optimization Based Inference of Metabolic Networks from Metabolome Data.- PHISTO: A New Web Platform for Pathogen-Human Interactions.- Frameshift Correction in De Novo Assembled Transcriptome Data Using Peptide Data, Blast Sequence Alignments and Hidden Markov Models.- From Prokaryote Genome Sequencing to Pan-Genomic Modeling.- A Simulation Approach to Detect Oscillating Behaviour in Stochastic Population Models.- On Bistability Causing Structures in Escherichia Coli's Metabolism.- Mathematical Modelling of the Function of Ubiquitylation in TNFR1-MediatedNF- B Signalling.- Organizing SIV Gene Network Modules into Graph Database.