Computational Methods in Systems Biology

First International Workshop, CMSB 2003 Rovereto, Italy, February 24–26, 2003 Proceedings

  • Corrado Priami
Conference proceedings CMSB 2003

DOI: 10.1007/3-540-36481-1

Part of the Lecture Notes in Computer Science book series (LNCS, volume 2602)

Table of contents

  1. Front Matter
    Pages I-IX
    PDF

  2. Invited Papers

    1. Cells as Computation
      Amitai Regev, Ehud Shapiro
      Pages 1-3
    2. Formal Modeling of C. elegans Development: A Scenario-Based Approach
      Na’aman Kam, David Harel, Hillel Kugler, Rami Marelly, Amir Pnueli, E. Jane Albert Hubbard et al.
      Pages 4-20

  3. Regular Papers

    1. Causal π-Calculus for Biochemical Modelling
      Michele Curti, Pierpaolo Degano, Cosima Tatiana Baldari
      Pages 21-34
    2. Graphs for Core Molecular Biology
      Vincent Danos, Cosimo Laneve
      Pages 34-46
    3. Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa
      Sabine Peres, Jean-Paul Comet
      Pages 47-56
    4. Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing
      Marco Antoniotti, Bhubaneswar Mishra, Carla Piazza, Alberto Policriti, Marta Simeoni
      Pages 57-74
    5. Multiscale Modeling of Alternative Splicing Regulation
      Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant, Alexander Bockmayr
      Pages 75-87
    6. A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information
      Juho Rousu, Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Katja Saarela, Esko Ukkonen
      Pages 88-103
    7. Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data
      SunYong Kim, Seiy Imoto, Satoru Miyano
      Pages 104-113
    8. Discrete Event Simulation for a Better Understanding of Metabolite Channeling - A System Theoretic Approach
      Daniela Degenring, Mathias Röhl, Adelinde M. Uhrmacher
      Pages 114-126
    9. Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway
      Kwang-Hyun Cho, Sung-Young Shin, Hyun-Woo Kim, Olaf Wolkenhauer, Brian McFerran, Walter Kolch
      Pages 127-141
    10. A Method to Identify Essential Enzymes in the Metabolism: Application to Escherichia Coli
      Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos, José C. M. Mombach
      Pages 142-148
    11. Symbolic Model Checking of Biochemical Networks
      Nathalie Chabrier, François Fages
      Pages 149-162

  4. Presentation Abstracts

    1. Coupled Oscillator Models for a Set of Communicating Cells
      Will Casey
      Pages 163-163
    2. Representing and Simulating Protein Functional Domains in Signal Transduction Using Maude
      Steven Eker, Keith Laderoute, Patrick Lincoln, M.G. Sriram, Carolyn Talcott
      Pages 164-165
    3. A Core Modeling Language for the Working Molecular Biologist (Abstract)
      Marc Chiaverini, Vincent Danos
      Pages 166-166
    4. Integrating Simulation Packages via Systems Biology Mark-Up Language
      Manuel Corpas
      Pages 167-167
    5. Recreating Biopathway Databases towards Simulation
      Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
      Pages 168-169
    6. How to Synthesize an Optimized Genetic λ-Switching System? A System-Theoretic Approach Based on SQP
      Kwang-Hyun Cho, Jong-Ho Cha, Olaf Wolkenhauer
      Pages 170-170

About these proceedings

Keywords

Bisimulation Evolution Simulation automata bioinformatics cellular communication cellular networks computational biology computational molecular biology computer simulation databases genes genome genome sequ petri net

Editors and affiliations

  • Corrado Priami
    • 1
  1. 1.Dipartimento di Informatica e TelecomunicazioniUniversità di TrentoPovo (TN)Italy

Bibliographic information

  • Copyright Information Springer-Verlag Berlin Heidelberg 2003
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Springer Book Archive
  • Print ISBN 978-3-540-00605-3
  • Online ISBN 978-3-540-36481-8
  • Series Print ISSN 0302-9743