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Computational Methods in Systems Biology

16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings

  • Conference proceedings
  • © 2018

Overview

Editors:
  1. Milan Češka

    1. Brno University of Technology, Brno, Czech Republic

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  2. David Šafránek

    1. Masaryk University, Brno, Czech Republic

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    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Lecture Notes in Computer Science (LNCS, volume 11095)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: CMSB 2018.

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About this book

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.

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Table of contents (22 papers)

  1. Front Matter

    Pages I-XXIII
    Download chapter PDF

  2. Regular Papers

    1. Front Matter

      Pages 1-1
      Download chapter 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
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    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
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Other volumes

  1. Computational Methods in Systems Biology

Editors and Affiliations

  • Brno University of Technology, Brno, Czech Republic

    Milan Češka

  • Masaryk University, Brno, Czech Republic

    David Šafránek

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