Computational Methods in Systems Biology

1. Front Matter

   Pages I-XIII

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2. Invited Paper

   1. Front Matter

      Pages 1-1

      PDF

   2. Bio-Curation for Cellular Signalling: The KAMI Project

      • Russ Harmer, Yves-Stan Le Cornec, Sébastien Légaré, Ievgeniia Oshurko

      Pages 3-19

3. Regular Papers

   1. Front Matter

      Pages 21-21

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   2. Quantitative Regular Expressions for Arrhythmia Detection Algorithms

      • Houssam Abbas, Alena Rodionova, Ezio Bartocci, Scott A. Smolka, Radu Grosu

      Pages 23-39

   3. Detecting Attractors in Biological Models with Uncertain Parameters

      • Jiří Barnat, Nikola Beneš, Luboš Brim, Martin Demko, Matej Hajnal, Samuel Pastva et al.

      Pages 40-56

   4. Abduction Based Drug Target Discovery Using Boolean Control Network

      • Célia Biane, Franck Delaplace

      Pages 57-73

   5. Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data

      • Arthur Carcano, François Fages, Sylvain Soliman

      Pages 74-90

   6. Identifying Functional Families of Trajectories in Biological Pathways by Soft Clustering: Application to TGF-\(\beta \) Signaling

      • Jean Coquet, Nathalie Theret, Vincent Legagneux, Olivier Dameron

      Pages 91-107

   7. Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs

      • François Fages, Guillaume Le Guludec, Olivier Bournez, Amaury Pouly

      Pages 108-127

   8. A Scheme for Adaptive Selection of Population Sizes in Approximate Bayesian Computation - Sequential Monte Carlo

      • Emmanuel Klinger, Jan Hasenauer

      Pages 128-144

   9. Methods to Expand Cell Signaling Models Using Automated Reading and Model Checking

      • Kai-Wen Liang, Qinsi Wang, Cheryl Telmer, Divyaa Ravichandran, Peter Spirtes, Natasa Miskov-Zivanov

      Pages 145-159

   10. A Stochastic Model for the Formation of Spatial Methylation Patterns

       • Alexander Lück, Pascal Giehr, Jörn Walter, Verena Wolf

       Pages 160-178

   11. Temporal Reprogramming of Boolean Networks

       • Hugues Mandon, Stefan Haar, Loïc Paulevé

       Pages 179-195

   12. Detecting Toxicity Pathways with a Formal Framework Based on Equilibrium Changes

       • Benjamin Miraglio, Gilles Bernot, Jean-Paul Comet, Christine Risso-de Faverney

       Pages 196-213

   13. Data-Driven Robust Control for Type 1 Diabetes Under Meal and Exercise Uncertainties

       • Nicola Paoletti, Kin Sum Liu, Scott A. Smolka, Shan Lin

       Pages 214-232

   14. Graph Representations of Monotonic Boolean Model Pools

       • Robert Schwieger, Heike Siebert

       Pages 233-248

   15. Explaining Response to Drugs Using Pathway Logic

       • Carolyn Talcott, Merrill Knapp

       Pages 249-264

   16. Automated Property Synthesis of ODEs Based Bio-pathways Models

       • Jun Zhou, R. Ramanathan, Weng-Fai Wong, P. S. Thiagarajan

       Pages 265-282

4. Tool Papers

   1. Front Matter

      Pages 283-283

      PDF

This book constitutes the refereed proceedings of the 15th International Conference on Computational Methods in Systems Biology, CMSB 2017, held in Darmstadt, Germany, in September 2017. The 15 full papers, 4 tool papers and 4 posters presented together with 1 invited talk were carefully reviewed and selected from 41  regular paper submissions. Topics of interest include formalisms for modeling  biological processes; models and their biological applications; frameworks for model verication, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology.

• formal methods
• live and medical sciences
• model checking
• simulation and modeling uncertainty
• quantification
• approximation
• automated static analysis
• big data
• computational biology
• dynamic analysis
• dynamic modeling
• game theory
• logical frameworks
• model verification and validation
• semantics
• genes
• temporal logic
• numeric methods

• Inria & École normale supérieure, Paris, France

  Jérôme Feret

• Technische Universität Darmstadt, Darmstadt, Germany

  Heinz Koeppl

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