Computational Methods in Systems Biology

Qualitative Modeling and Simulation of Bacterial Regulatory Networks.- Integrated Analysis from Abstract Stochastic Process Algebra Models.- An Exact Brownian Dynamics Method for Cell Simulation.- Multiscale Modelling of Neuronal Signalling.- Systems Biology of Halophilic Archaea.- A Partial Granger Causality Approach to Explore Causal Networks Derived From Multi-parameter Data.- Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe.- Component-Based Modelling of RNA Structure Folding.- A Language for Biochemical Systems.- The Attributed Pi Calculus.- The Continuous ?-Calculus: A Process Algebra for Biochemical Modelling.- Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems.- Formal Analysis of Abnormal Excitation in Cardiac Tissue.- The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock.- SED-ML – An XML Format for the Implementation of the MIASE Guidelines.- On Parallel Stochastic Simulation of Diffusive Systems.- Large-Scale Design Space Exploration of SSA.- Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway.- On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology.- A Model Checking Approach to the Parameter Estimation of Biochemical Pathways.- Compositional Definitions of Minimal Flows in Petri Nets.- On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network.- A Combinatorial Approach to Reconstruct Petri Nets from Experimental Data.- An Exact Brownian Dynamics Method for Cell Simulation.- Stochastic Analysis of Amino Acid Substitution in Protein Synthesis.- A Stochastic Single Cell Based Model of BrdU Measured Hematopoietic Stem Cell Kinetics.- Erratum: Analyzing a Discrete Model of Aplysia Central Pattern Generator.