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Computational Methods in Systems Biology

11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, Proceedings

  • Conference proceedings
  • © 2013

Overview

Editors:
  1. Ashutosh Gupta

    1. IST Austria, Klosterneuburg, Austria

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  2. Thomas A. Henzinger

    1. IST Austria, Klosterneuburg, Austria

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  • Conference proceedings of the International Conference on Computational Methods in Systems Biology

Part of the book series: Lecture Notes in Computer Science (LNCS, volume 8130)

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

Included in the following conference series:

Conference proceedings info: CMSB 2013.

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Table of contents (17 papers)

  1. Front Matter

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  2. Regular Papers

    1. On the Use of the Moment Equations for Parameter Inference, Control and Experimental Design in Stochastic Biochemical Reaction Networks

      • Jakob Ruess, John Lygeros
      Pages 1-4

    2. Numerical Approximation of Rare Event Probabilities in Biochemically Reacting Systems

      • Linar Mikeev, Werner Sandmann, Verena Wolf
      Pages 5-18

    3. An Approximate Execution of Rule-Based Multi-level Models

      • Tobias Helms, Martin Luboschik, Heidrun Schumann, Adelinde M. Uhrmacher
      Pages 19-32

    4. Computing Cumulative Rewards Using Fast Adaptive Uniformisation

      • Frits Dannenberg, Ernst Moritz Hahn, Marta Kwiatkowska
      Pages 33-49

    5. Linking Discrete and Stochastic Models: The Chemical Master Equation as a Bridge between Process Hitting and Proper Generalized Decomposition

      • Courtney Chancellor, Amine Ammar, Francisco Chinesta, Morgan Magnin, Olivier Roux
      Pages 50-63

    6. Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models

      • Michael Klann, Loïc Paulevé, Tatjana Petrov, Heinz Koeppl
      Pages 64-77

    7. Modelling and Analysis of Phase Variation in Bacterial Colony Growth

      • Ovidiu Pârvu, David Gilbert, Monika Heiner, Fei Liu, Nigel Saunders
      Pages 78-91

    8. Using Probabilistic Strategies to Formalize and Compare α-Synuclein Aggregation and Propagation under Different Scenarios

      • Lucian Bentea, Peter Csaba Ölveczky, Eduard Bentea
      Pages 92-105

    9. Dynamic Image-Based Modelling of Kidney Branching Morphogenesis

      • Srivathsan Adivarahan, Denis Menshykau, Odyssé Michos, Dagmar Iber
      Pages 106-119

    10. Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models

      • Sucheendra K. Palaniappan, Benjamin M. Gyori, Bing Liu, David Hsu, P. S. Thiagarajan
      Pages 120-134

    11. Constraint Programming in Community-Based Gene Regulatory Network Inference

      • Ferdinando Fioretto, Enrico Pontelli
      Pages 135-149

    12. ABC–Fun: A Probabilistic Programming Language for Biology

      • Anastasis Georgoulas, Jane Hillston, Guido Sanguinetti
      Pages 150-163

    13. A Temporal Logic Approach to Modular Design of Synthetic Biological Circuits

      • Ezio Bartocci, Luca Bortolussi, Laura Nenzi
      Pages 164-177

    14. A Lattice-Theoretic Framework for Metabolic Pathway Analysis

      • Yaron A. B. Goldstein, Alexander Bockmayr
      Pages 178-191

    15. On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models

      • Katherine Chiang, François Fages, Jie-Hong Jiang, Sylvain Soliman
      Pages 192-205

    16. On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology

      • Attila Gábor, Katalin M. Hangos, Gábor Szederkényi, Julio R. Banga
      Pages 206-219

    17. Context-Sensitive Flow Analyses: A Hierarchy of Model Reductions

      • Ferdinanda Camporesi, Jérôme Feret, Jonathan Hayman
      Pages 220-233

  3. Back Matter

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Other volumes

  1. Computational Methods in Systems Biology

Keywords

About this book

This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms.

Editors and Affiliations

  • IST Austria, Klosterneuburg, Austria

    Ashutosh Gupta, Thomas A. Henzinger

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