Table of Contents

November 2003; 13 (11)

Preface

  • The Logic of Life

    • Måns Ehrenberg,
    • Erik Aurell,
    • Johan Elf,
    • Rickard Sandberg,
    • and Jesper Tegnér
    Genome Res. November 2003 13: 2375-2376; doi:10.1101/gr.1765703

COMMENTARY

  • Systems Biology Is Taking Off

    • Måns Ehrenberg,
    • Johan Elf,
    • Erik Aurell,
    • Rickard Sandberg,
    • and Jesper Tegnér
    Genome Res. November 2003 13: 2377-2380; doi:10.1101/gr.1763203

ARTICLES

  • A Biophysical Approach to Transcription Factor Binding Site Discovery

    • Marko Djordjevic,
    • Anirvan M. Sengupta,
    • and Boris I. Shraiman
    Genome Res. November 2003 13: 2381-2390; doi:10.1101/gr.1271603

  • Limitations of Quantitative Gene Regulation Models: A Case Study

    • Philip M. Kim and
    • Bruce Tidor
    Genome Res. November 2003 13: 2391-2395; doi:10.1101/gr.1207003

  • Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network

    • Daniel E. Zak,
    • Gregory E. Gonye,
    • James S. Schwaber,
    • and Francis J. Doyle III
    Genome Res. November 2003 13: 2396-2405; doi:10.1101/gr.1198103

  • Signal Processing and Flagellar Motor Switching During Phototaxis of Halobacterium salinarum

    • Torsten Nutsch,
    • Wolfgang Marwan,
    • Dieter Oesterhelt,
    • and Ernst Dieter Gilles
    Genome Res. November 2003 13: 2406-2412; Published in Advance January 1, 2003, doi:10.1101/gr.1241903

LETTERS

  • Investigations Into the Analysis and Modeling of the TNFα-Mediated NF-κB-Signaling Pathway

    • Kwang-Hyun Cho,
    • Sung-Young Shin,
    • Hyeon-Woo Lee,
    • and Olaf Wolkenhauer
    Genome Res. November 2003 13: 2413-2422; Published in Advance January 1, 2003, doi:10.1101/gr.1195703

  • Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures

    • Markus J. Herrgård,
    • Markus W. Covert,
    • and Bernhard ø. Palsson
    Genome Res. November 2003 13: 2423-2434; Published in Advance January 1, 2003, doi:10.1101/gr.1330003

  • Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles

    • Rosa María Gutiérrez-Ríos,
    • David A. Rosenblueth,
    • José Antonio Loza,
    • Araceli M. Huerta,
    • Jeremy D. Glasner,
    • Fred R. Blattner,
    • and Julio Collado-Vides
    Genome Res. November 2003 13: 2435-2443; doi:10.1101/gr.1387003

  • Functionality of System Components: Conservation of Protein Function in Protein Feature Space

    • Lars Juhl Jensen,
    • David W. Ussery,
    • and Søren Brunak
    Genome Res. November 2003 13: 2444-2449; Published in Advance January 1, 2003, doi:10.1101/gr.1190803

  • Bioinformatics Analysis of Experimentally Determined Protein Complexes in the Yeast Saccharomyces cerevisiae

    • Zoltán Dezső,
    • Zoltán N. Oltvai,
    • and Albert-László Barabási
    Genome Res. November 2003 13: 2450-2454; Published in Advance January 1, 2003, doi:10.1101/gr.1073603

Methods

  • In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia coli Intermediary Metabolism

    • Masanori Arita
    Genome Res. November 2003 13: 2455-2466; Published in Advance January 1, 2003, doi:10.1101/gr.1212003

  • Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods

    • Carmen G. Moles,
    • Pedro Mendes,
    • and Julio R. Banga
    Genome Res. November 2003 13: 2467-2474; Published in Advance January 1, 2003, doi:10.1101/gr.1262503

  • Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation

    • Johan Elf and
    • Måns Ehrenberg
    Genome Res. November 2003 13: 2475-2484; doi:10.1101/gr.1196503

RESOURCES

  • Toward Rigorous Comprehension of Biological Complexity: Modeling, Execution, and Visualization of Thymic T-Cell Maturation

    • Sol Efroni,
    • David Harel,
    • and Irun R. Cohen
    Genome Res. November 2003 13: 2485-2497; doi:10.1101/gr.1215303

  • Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

    • Paul Shannon,
    • Andrew Markiel,
    • Owen Ozier,
    • Nitin S. Baliga,
    • Jonathan T. Wang,
    • Daniel Ramage,
    • Nada Amin,
    • Benno Schwikowski,
    • and Trey Ideker
    Genome Res. November 2003 13: 2498-2504; doi:10.1101/gr.1239303
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This Issue

November 2003; 13 (11)
Cover
  1. Preface
  2. COMMENTARY
  3. ARTICLES
  4. LETTERS
  5. Methods
  6. RESOURCES

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