Computational Methods in Systems Biology

1. Front Matter

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2. Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks

   • Lisa Bartoli, Pier Luigi Martelli, Ivan Rossi, Piero Fariselli, Rita Casadio

   Pages 1-17

3. The Equivalence between Biology and Computation

   • John K. Heath

   Pages 18-25

4. BlenX4Bio – BlenX for Biologists

   • Corrado Priami, Paolo Ballarini, Paola Quaglia

   Pages 26-51

5. Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network

   • Ozgur E. Akman, Federica Ciocchetta, Andrea Degasperi, Maria Luisa Guerriero

   Pages 52-67

6. Quantitative Pathway Logic for Computational Biology

   • Michele Baggi, Demis Ballis, Moreno Falaschi

   Pages 68-82

7. A Prize-Collecting Steiner Tree Approach for Transduction Network Inference

   • Marc Bailly-Bechet, Alfredo Braunstein, Riccardo Zecchina

   Pages 83-95

8. Formal Analysis of the Genetic Toggle

   • Giampaolo Bella, Pietro Liò

   Pages 96-110

9. Control Strategies for the Regulation of the Eukaryotic Heat Shock Response

   • Elena Czeizler, Eugen Czeizler, Ralph-Johan Back, Ion Petre

   Pages 111-125

10. Computing Reachable States for Nonlinear Biological Models

    • Thao Dang, Colas Le Guernic, Oded Maler

    Pages 126-141

11. On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle

    • Elisabetta De Maria, François Fages, Sylvain Soliman

    Pages 142-157

12. The κ-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages

    • Giorgio Delzanno, Cinzia Di Giusto, Maurizio Gabbrielli, Cosimo Laneve, Gianluigi Zavattaro

    Pages 158-172

13. Approximation of Event Probabilities in Noisy Cellular Processes

    • Frédéric Didier, Thomas A. Henzinger, Maria Mateescu, Verena Wolf

    Pages 173-188

14. Equivalence and Discretisation in Bio-PEPA

    • Vashti Galpin, Jane Hillston

    Pages 189-204

15. Improved Parameter Estimation for Completely Observed Ordinary Differential Equations with Application to Biological Systems

    • Peter Gennemark, Dag Wedelin

    Pages 205-217

16. A Bayesian Approach to Model Checking Biological Systems

    • Sumit K. Jha, Edmund M. Clarke, Christopher J. Langmead, Axel Legay, André Platzer, Paolo Zuliani

    Pages 218-234

17. Dynamic Compartments in the Imperative π-Calculus

    • Mathias John, Cédric Lhoussaine, Joachim Niehren

    Pages 235-250

18. Probabilistic Approximations of Signaling Pathway Dynamics

    • Bing Liu, P. S. Thiagarajan, David Hsu

    Pages 251-265

19. A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties

    • Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya

    Pages 266-280

20. On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process

    • Lucia Napione, Daniele Manini, Francesca Cordero, András Horváth, Andrea Picco, Massimiliano De Pierro et al.

    Pages 281-295

This volume contains the proceedings of the 7th Conference on Computational Methods in Systems Biology (CMSB 2009), held in Bologna, from August 31 to September 1, 2009. The ?rst CMSB was held in Trento in 2003, bringing together life scientists, computer scientists, engineers and physicists. The goal was to promote the c- vergence of di?erent disciplines aiming at a new understanding and description of biological systems, ?rmly ground in formal models, supported by compu- tionallanguagesandtools,ando?eringnew methodsofanalysis.The conference then moved to Paris in 2004, Edinburgh in 2005, Trento in 2006, Edinburgh in 2007 and Rostock/Warnemunde ¨ in 2008. This year the conference attracted about 45 submissions form 18 countries, mainly from Europe and North America, but also from Asia and Australia. We wish to thank all authors for their interest in CMSB 2009. After careful disc- sions, the Programme Committee eventually selected 18 papers for presentation at the conference. Each of them was accurately refereed by at least three - viewers, who delivered detailed and insightful comments and suggestions. The Conference Chairmen warmly thank all the members of the Programme C- mittee and all their sub-referees for the excellent support they gave, as well as for the friendly and constructive discussions. We also would like to thank the authorsfor havingrevisedtheir papers to addressthe comments andsuggestions by the referees.

• angiogenesis
• biological clocks
• biological models
• biological systems
• biology
• cell cylce
• cell models
• computational biology
• model checking
• modeling
• protein interaction
• signaling pathways

• Dipartimento di Informatica, Università di Pisa, Pisa, Italy

  Pierpaolo Degano

• Dipartimento di Scienze dell’Informazione, Università degli Studi di Bologna, Bologna, Italy

  Roberto Gorrieri

Policies and ethics