Computational Methods in Systems Biology, 1st ed. 2018 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings Lecture Notes in Bioinformatics Series

This book constitutes the refereed proceedings of the 16th International Conference on Computational Methods in Systems Biology, CMSB 2018, held in BRNO, Czech Republic, in September 2018.

The 15 full and 7 short papers presented together with 5 invited talks were carefully reviewed and selected from 46 submissions. Topics of interest include formalisms for modeling  biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology; parameter and model inference from experimental data; automated parameter and model synthesis; model integration and biological databases; multi-scale modeling and analysis methods; design, analysis, and verification methods for synthetic biology; methods for biomolecular computing and engineered molecular devices.

Chapters 3, 9 and 10 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

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.