Computational Methods in Systems Biology: 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings (Lecture Notes in Computer Science Book 11095)

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. Front Matter ....Pages I-XXIII Front Matter ....Pages 1-1 Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia Coli (Samuel M. D. Oliveira, Mohamed N. M. Bahrudeen, Sofia Startceva, Vinodh Kandavalli, Andre S. Ribeiro)....Pages 3-20 Deep Abstractions of Chemical Reaction Networks (Luca Bortolussi, Luca Palmieri)....Pages 21-38 Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models (Timothy Self, David Gilbert, Monika Heiner)....Pages 39-58 Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data (Misbah Razzaq, Roland Kaminski, Javier Romero, Torsten Schaub, Jeremie Bourdon, Carito Guziolowski)....Pages 59-74 Characterization of the Experimentally Observed Clustering of VEGF Receptors (Emine Güven, Michael J. Wester, Bridget S. Wilson, Jeremy S. Edwards, Ádám M. Halász)....Pages 75-92 Synthesis for Vesicle Traffic Systems (Ashutosh Gupta, Somya Mani, Ankit Shukla)....Pages 93-110 Formal Analysis of Network Motifs (Hillel Kugler, Sara-Jane Dunn, Boyan Yordanov)....Pages 111-128 Buffering Gene Expression Noise by MicroRNA Based Feedforward Regulation (Pavol Bokes, Michal Hojcka, Abhyudai Singh)....Pages 129-145 Stochastic Rate Parameter Inference Using the Cross-Entropy Method (Jeremy Revell, Paolo Zuliani)....Pages 146-164 Experimental Biological Protocols with Formal Semantics (Alessandro Abate, Luca Cardelli, Marta Kwiatkowska, Luca Laurenti, Boyan Yordanov)....Pages 165-182 Robust Data-Driven Control of Artificial Pancreas Systems Using Neural Networks (Souradeep Dutta, Taisa Kushner, Sriram Sankaranarayanan)....Pages 183-202 Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks (Keenan Breik, Cameron Chalk, David Doty, David Haley, David Soloveichik)....Pages 203-219 A Trace Query Language for Rule-Based Models (Jonathan Laurent, Hector F. Medina-Abarca, Pierre Boutillier, Jean Yang, Walter Fontana)....Pages 220-237 Inferring Mechanism of Action of an Unknown Compound from Time Series Omics Data (Akos Vertes, Albert-Baskar Arul, Peter Avar, Andrew R. Korte, Hang Li, Peter Nemes et al.)....Pages 238-255 Composable Rate-Independent Computation in Continuous Chemical Reaction Networks (Cameron Chalk, Niels Kornerup, Wyatt Reeves, David Soloveichik)....Pages 256-273 Front Matter ....Pages 275-275 ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks (Andrzej Mizera, Jun Pang, Hongyang Qu, Qixia Yuan)....Pages 277-284 KaSa: A Static Analyzer for Kappa (Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jérôme Feret, Kim Quyên Lý, Nathalie Theret et al.)....Pages 285-291 On Robustness Computation and Optimization in BIOCHAM-4 (François Fages, Sylvain Soliman)....Pages 292-299 LNA++: Linear Noise Approximation with First and Second Order Sensitivities (Justin Feigelman, Daniel Weindl, Fabian J. Theis, Carsten Marr, Jan Hasenauer)....Pages 300-306 Front Matter ....Pages 307-307 Reparametrizing the Sigmoid Model of Gene Regulation for Bayesian Inference (Martin Modrák)....Pages 309-312 On the Full Control of Boolean Networks (Soumya Paul, Jun Pang, Cui Su)....Pages 313-317 Systems Metagenomics: Applying Systems Biology Thinking to Human Microbiome Analysis (Golestan Sally Radwan, Hugh Shanahan)....Pages 318-321 Back Matter ....Pages 323-326