Computational Methods in Systems Biology

Modal Logics for Brane Calculus.- Deciding Behavioural Properties in Brane Calculi.- Probabilistic Model Checking of Complex Biological Pathways.- Type Inference in Systems Biology.- Stronger Computational Modelling of Signalling Pathways Using Both Continuous and Discrete-State Methods.- A Formal Approach to Molecular Docking.- Feedbacks and Oscillations in the Virtual Cell VICE.- Modelling Cellular Processes Using Membrane Systems with Peripheral and Integral Proteins.- Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets.- Regulatory Network Reconstruction Using Stochastic Logical Networks.- Identifying Submodules of Cellular Regulatory Networks.- Incorporating Time Delays into the Logical Analysis of Gene Regulatory Networks.- A Computational Model for Eukaryotic Directional Sensing.- Modeling Evolutionary Dynamics of HIV Infection.- Compositional Reachability Analysis of Genetic Networks.- Randomization and Feedback Properties of Directed Graphs Inspired by Gene Networks.- Computational Model of a Central Pattern Generator.- Rewriting Game Theory as a Foundation for State-Based Models of Gene Regulation.- Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast.- An In Silico Analogue of In Vitro Systems Used to Study Epithelial Cell Morphogenesis.- A Numerical Aggregation Algorithm for the Enzyme-Catalyzed Substrate Conversion.- Possibilistic Approach to Biclustering: An Application to Oligonucleotide Microarray Data Analysis.