Computational Methods in Systems Biology

1. Front Matter

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2. Invited Talks

   1. Differential and Integral Views of Gene-Phenotype Relations: A Systems Biological Insight

      • Denis Noble

      Pages 1-1

   2. Resolving the Three-Dimensional Histology of the Heart

      • Matthew Gibb, Rebecca A. B. Burton, Christian Bollensdorff, Carlos Afonso, Tahir Mansoori, Ulrich Schotten et al.

      Pages 2-16

   3. Bimodal Protein Distributions in Heterogeneous Oscillating Systems

      • Maciej Dobrzyński, Dirk Fey, Lan K. Nguyen, Boris N. Kholodenko

      Pages 17-28

3. Regular Papers

   1. Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics

      • Paolo Ballarini, Jarno Mäkelä, Andre S. Ribeiro

      Pages 29-48

   2. Symmetry-Based Model Reduction for Approximate Stochastic Analysis

      • Kirill Batmanov, Celine Kuttler, Francois Lemaire, Cédric Lhoussaine, Cristian Versari

      Pages 49-68

   3. Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum

      • Laura Bennett, Artem Lysenko, Lazaros G. Papageorgiou, Martin Urban, Kim Hammond-Kosack, Chris Rawlings et al.

      Pages 69-86

   4. Predicting Phenotype from Genotype through Automatically Composed Petri Nets

      • Mary Ann Blätke, Monika Heiner, Wolfgang Marwan

      Pages 87-106

   5. A Simple Model to Control Growth Rate of Synthetic E. coli during the Exponential Phase: Model Analysis and Parameter Estimation

      • Alfonso Carta, Madalena Chaves, Jean-Luc Gouzé

      Pages 107-126

   6. Multi-objective Optimisation, Sensitivity and Robustness Analysis in FBA Modelling

      • Jole Costanza, Giovanni Carapezza, Claudio Angione, Pietro Liò, Giuseppe Nicosia

      Pages 127-147

   7. Analysis of Modular Organisation of Interaction Networks Based on Asymptotic Dynamics

      • Franck Delaplace, Hanna Klaudel, Tarek Melliti, Sylvain Sené

      Pages 148-165

   8. Concretizing the Process Hitting into Biological Regulatory Networks

      • Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, Olivier Roux

      Pages 166-186

   9. Abstraction of Graph-Based Models of Bio-molecular Reaction Systems for Efficient Simulation

      • Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano, Masami Hagiya

      Pages 187-206

   10. Parameter Identification and Model Ranking of Thomas Networks

       • Hannes Klarner, Adam Streck, David Šafránek, Juraj Kolčák, Heike Siebert

       Pages 207-226

   11. Investigating Co-infection Dynamics through Evolution of Bio-PEPA Model Parameters: A Combined Process Algebra and Evolutionary Computing Approach

       • David Marco, Erin Scott, David Cairns, Andrea Graham, Judi Allen, Simmi Mahajan et al.

       Pages 227-246

   12. Population Dynamics P Systems on CUDA

       • Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado, Adolfo Gastalver-Rubio, Anne C. Elster, Mario J. Pérez-Jiménez

       Pages 247-266

   13. Approximate Bisimulations for Sodium Channel Dynamics

       • Abhishek Murthy, Md. Ariful Islam, Ezio Bartocci, Elizabeth M. Cherry, Flavio H. Fenton, James Glimm et al.

       Pages 267-287

   14. Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control

       • Aurélien Naldi, Pedro T. Monteiro, Claudine Chaouiya

       Pages 288-306

   15. Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks

       • Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja, Andre Ribeiro

       Pages 307-321

   16. Simulating Insulin Infusion Pump Risks by In-Silico Modeling of the Insulin-Glucose Regulatory System

       • Sriram Sankaranarayanan, Georgios Fainekos

       Pages 322-341

This book constitutes the thoroughly refereed conference proceedings of the 10th International Conference on Computational Methods in Systems Biology, CMSB 2012, held in London, UK, during October 3-5, 2012. The 17 revised full papers and 8 flash posters presented together with the summaries of 3 invited papers were carefully reviewed and selected from 62 submissions. The papers cover the analysis of biological systems, networks, and data ranging from intercellular to multiscale. Topics included high-performance computing, and for the first time papers on synthetic biology.

• Petri nets
• cellular systems
• gene networks
• model checking
• population dynamics

• School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, UK

  David Gilbert

• Computer Science Institute, University of Technology, Cottbus, Germany

  Monika Heiner

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