Transactions on Computational Systems Biology XIII

1. Front Matter

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2. Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene

   • Antti Häkkinen, Fred G. Biddle, Olli-Pekka Smolander, Olli Yli-Harja, Andre S. Ribeiro

   Pages 1-12

3. Translation from the Quantified Implicit Process Flow Abstraction in SBGN-PD Diagrams to Bio-PEPA Illustrated on the Cholesterol Pathway

   • Laurence Loewe, Maria Luisa Guerriero, Steven Watterson, Stuart Moodie, Peter Ghazal, Jane Hillston

   Pages 13-38

4. Impulse-Based Dynamic Simulation of Deformable Biological Structures

   • Rhys Goldstein, Gabriel Wainer

   Pages 39-60

5. Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach

   • Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo

   Pages 61-84

6. Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis

   • Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Elena Grassi, Mike Guether, Angelo Troina

   Pages 85-109

7. Genetically Regulated Metabolic Networks: Gale-Nikaido Modules and Differential Inequalities

   • Ovidiu Radulescu, Anne Siegel, Elisabeth Pécou, Clément Chatelain, Sandrine Lagarrigue

   Pages 110-130

8. Cultural Epigenetics: On the Heritability of Complex Diseases

   • Rodrick Wallace, Deborah Wallace

   Pages 131-170

9. Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework

   • Loïc Paulevé, Morgan Magnin, Olivier Roux

   Pages 171-191

10. Back Matter

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The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This, the 13th Transactions on Computational Systems Biology volume, guest edited by Ralph-Johan Back, Ion Petre, and Erik de Vink, focuses on Computational Models for Cell Processes and features a number of carefully selected and enhanced contributions initially presented at the CompMod workshop, which took place in Eindhoven, The Netherlands, in November 2009. From different points of view and following various approaches, the papers cover a wide range of topics in systems biology, addressing the dynamics and the computational principles of this emerging field.

• brane calculus
• computational modeling
• continuous time Markov chains
• differential equations
• gene expression
• genetic regulation
• metabolic control
• metabolic pathways
• ordinary differential equations
• parameterised modules
• process algebra
• qualitative constraints
• qualitative networks
• stochastic programming
• univalence property
• algorithm analysis and problem complexity

From the reviews:

“This collection of papers offers a great synopsis of the actual trends in systems biology. In this book, researchers, students, and computational biologists will find examples of various modern time- and space-dependent prediction and simulation methods and models. … The wealth of methods and approaches presented in this collection is clear evidence that great progress has been made in modeling many particular aspects of systems biology.” (Adrian Pasculescu, ACM Computing Reviews, April, 2012)

• Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Povo (TN), Italy

  Corrado Priami

• Department of Information Technologies, Åbo Akademi University, Turku, Finland

  Ralph-Johan Back, Ion Petre

• Technische Universiteit Eindhoven, Eindhoven, The Netherlands

  Erik Vink

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