Computational Methods in Systems Biology

1. Front Matter

   Pages I-XXIII

   PDF

2. Regular Papers

   1. Front Matter

      Pages 1-1

      PDF

   2. 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

   3. Deep Abstractions of Chemical Reaction Networks

      • Luca Bortolussi, Luca Palmieri

      Pages 21-38

   4. Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models

      • Timothy Self, David Gilbert, Monika Heiner

      Pages 39-58Open Access

   5. Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data

      • Misbah Razzaq, Roland Kaminski, Javier Romero, Torsten Schaub, Jeremie Bourdon, Carito Guziolowski

      Pages 59-74

   6. 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

   7. Synthesis for Vesicle Traffic Systems

      • Ashutosh Gupta, Somya Mani, Ankit Shukla

      Pages 93-110

   8. Formal Analysis of Network Motifs

      • Hillel Kugler, Sara-Jane Dunn, Boyan Yordanov

      Pages 111-128

   9. Buffering Gene Expression Noise by MicroRNA Based Feedforward Regulation

      • Pavol Bokes, Michal Hojcka, Abhyudai Singh

      Pages 129-145

   10. Stochastic Rate Parameter Inference Using the Cross-Entropy Method

       • Jeremy Revell, Paolo Zuliani

       Pages 146-164Open Access

   11. Experimental Biological Protocols with Formal Semantics

       • Alessandro Abate, Luca Cardelli, Marta Kwiatkowska, Luca Laurenti, Boyan Yordanov

       Pages 165-182Open Access

   12. Robust Data-Driven Control of Artificial Pancreas Systems Using Neural Networks

       • Souradeep Dutta, Taisa Kushner, Sriram Sankaranarayanan

       Pages 183-202

   13. Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks

       • Keenan Breik, Cameron Chalk, David Doty, David Haley, David Soloveichik

       Pages 203-219

   14. A Trace Query Language for Rule-Based Models

       • Jonathan Laurent, Hector F. Medina-Abarca, Pierre Boutillier, Jean Yang, Walter Fontana

       Pages 220-237

   15. 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

   16. Composable Rate-Independent Computation in Continuous Chemical Reaction Networks

       • Cameron Chalk, Niels Kornerup, Wyatt Reeves, David Soloveichik

       Pages 256-273

3. Tool Papers

   1. Front Matter

      Pages 275-275

      PDF

   2. ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks

      • Andrzej Mizera, Jun Pang, Hongyang Qu, Qixia Yuan

      Pages 277-284

   3. KaSa: A Static Analyzer for Kappa

      • Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jérôme Feret, Kim Quyên Lý, Nathalie Theret et al.

      Pages 285-291

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 CreativeCommons Attribution 4.0 International License via link.springer.com.

• Agent / Discrete Models
• Artificial intelligence
• Computational Systems Biology
• Continuous Models
• Data Processing
• Formal logic
• Formal Methods
• Machine Learning
• Model Development and Analysis
• Model Verification and Validation
• Network Science
• Parallel Computing Methodologies
• Semantics
• Signal processing
• Software engineering
• Systems Theory

• Brno University of Technology, Brno, Czech Republic

  Milan Češka

• Masaryk University, Brno, Czech Republic

  David Šafránek

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