Computational Methods in Systems Biology

Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks.- The Equivalence between Biology and Computation.- BlenX4Bio – BlenX for Biologists.- Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network.- Quantitative Pathway Logic for Computational Biology.- A Prize-Collecting Steiner Tree Approach for Transduction Network Inference.- Formal Analysis of the Genetic Toggle.- Control Strategies for the Regulation of the Eukaryotic Heat Shock Response.- Computing Reachable States for Nonlinear Biological Models.- On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle.- The ?-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages.- Approximation of Event Probabilities in Noisy Cellular Processes.- Equivalence and Discretisation in Bio-PEPA.- Improved Parameter Estimation for Completely Observed Ordinary Differential Equations with Application to Biological Systems.- A Bayesian Approach to Model Checking Biological Systems.- Dynamic Compartments in the Imperative ?-Calculus.- Probabilistic Approximations of Signaling Pathway Dynamics.- A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties.- On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process.- CSL Model Checking of Biochemical Networks with Interval Decision Diagrams.- Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models.