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Computational Methods in Systems Biology

First International Workshop, CMSB 2003, Roverto, Italy, February 24–26, 2003

  • Conference proceedings
  • © 2003

Overview

Editors:
  1. Corrado Priami

    1. Dipartimento di Informatica e Telecomunicazioni, Università di Trento, Povo (TN), Italy

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

Included in the following conference series:

Conference proceedings info: CMSB 2003.

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Table of contents (31 papers)

  1. Front Matter

    Pages I-IX
    Download chapter 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
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  1. Computational Methods in Systems Biology

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Editors and Affiliations

  • Dipartimento di Informatica e Telecomunicazioni, Università di Trento, Povo (TN), Italy

    Corrado Priami

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