Computational Methods in Systems Biology

Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia coli.- Deep Abstractions of Chemical Reaction Networks.- Derivation of A Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models.- Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data.- Characterization of the Experimentally Observed Clustering of VEGF Receptors.- Synthesis for Vesicle Traffic Systems.- Formal Analysis of Network Motifs.- Buffering Gene Expression Noise by microRNA Based Feed Forward Regulation.- Stochastic Rate Parameter Inference Using the Cross-Entropy Method.- Experimental Biological Protocols with Formal Semantics.- Robust Data-Driven Control of Artificial Pancreas Systems Using Neural Networks.- Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks.- A Trace Query Language for Rule-based Models.- Inferring Mechanism of Action of an Unknown Compound from Time Series Omics Data.- Composable Rate-Independent Computation in Continuous Chemical Reaction Networks.- ASSA-PBN 3.0: Analysing Context-sensitive Probabilistic Boolean Networks.- KaSa: A Static Analyzer for Kappa.- On Robustness Computation and Optimization in BIOCHAM-4.- LNA++: Linear Noise Approximation with First and Second Order Sensitivities.- Reparametrizing the Sigmoid Model of Gene Regulation for Bayesian Inference.- On the Full Control of Boolean Networks.- Systems Metagenomics: Applying Systems Biology Thinking to Human Microbiome Analysis.