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Computational Methods in Systems Biology

7th International Conference, CMSB 2009, Bologna, Italy, August 31-September 1, 2009. Proceedings

  • Pierpaolo Degano
  • Roberto Gorrieri
Conference proceedings CMSB 2009

Part of the Lecture Notes in Computer Science book series (LNCS, volume 5688)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 5688)

Table of contents

  1. Front Matter
    PDF
  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
  21. CSL Model Checking of Biochemical Networks with Interval Decision Diagrams
    Martin Schwarick, Monika Heiner
    Pages 296-312
  22. Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models
    Hayssam Soueidan, Grégoire Sutre, Macha Nikolski
    Pages 313-327
  23. Back Matter
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About these proceedings

Introduction

This book constitutes the refereed proceedings of the 7th International Conference on Computational Methods in Systems Biology, CMSB 2009, held in Bologna, Italy, August 31 - September 1, 2009.

The 18 revised full papers presented together with the summaries of 3 invited papers were carefully reviewed and selected from more than 45 submissions. The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.

Keywords

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

Editors and affiliations

  • Pierpaolo Degano
    • 1
  • Roberto Gorrieri
    • 2
  1. 1.Dipartimento di InformaticaUniversità di PisaPisaItaly
  2. 2.Dipartimento di Scienze dell’InformazioneUniversità degli Studi di BolognaBolognaItaly

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-642-03845-7
  • Copyright Information Springer-Verlag Berlin Heidelberg 2009
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-642-03844-0
  • Online ISBN 978-3-642-03845-7
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site
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