Computational Methods in Systems Biology

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