Computational Methods in Systems Biology

Chemical Master Equation and Langevin Regimes for a Gene Transcription Model.- Simultaneous Stochastic Simulation of Multiple Perturbations in Biological Network Models.- Modelling Yeast Pre-rRNA Processing.- On the Analysis of Numerical Data Time Series in Temporal Logic.- Context Sensitivity in Logical Modeling with Time Delays.- Stochastic Simulation of Biological Systems with Dynamical Compartment Structure.- Computational Simulation of Optical Tracking of Cell Populations Using Quantum Dot Fluorophores.- A Formal and Integrated Framework to Simulate Evolution of Biological Pathways.- Reconstruction of Mammalian Cell Cycle Regulatory Network from Microarray Data Using Stochastic Logical Networks.- An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra.- Expressive Models for Synaptic Plasticity.- Modelization and Simulation of Nano Devices in nano ? Calculus.- Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus.- A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets.- Reconstructing Metabolic Pathways by Bidirectional Chemical Search.- Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks.