Volume 13, Issue 11 | November 2003

Preface
- - The Logic of Life
    Måns Ehrenberg
    Erik Aurell
    Johan Elf
    Rickard Sandberg
    Jesper Tegnér
    First Published November 3, 2003
COMMENTARY
- - Systems Biology Is Taking Off
    Måns Ehrenberg
    Johan Elf
    Erik Aurell
    Rickard Sandberg
    Jesper Tegnér
    First Published November 3, 2003
ARTICLES
- - A Biophysical Approach to Transcription Factor Binding Site Discovery
    Marko Djordjevic
    Anirvan M. Sengupta
    Boris I. Shraiman
    First Published November 3, 2003
  - Limitations of Quantitative Gene Regulation Models: A Case Study
    Philip M. Kim
    Bruce Tidor
    First Published November 3, 2003
  - 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
    Francis J. Doyle
    First Published November 3, 2003
  - Signal Processing and Flagellar Motor Switching During Phototaxis of Halobacterium salinarum
    Torsten Nutsch
    Wolfgang Marwan
    Dieter Oesterhelt
    Ernst Dieter Gilles
    First Published January 1, 2003
LETTERS
- - Investigations Into the Analysis and Modeling of the TNFα-Mediated NF-κB-Signaling Pathway
    Kwang-Hyun Cho
    Sung-Young Shin
    Hyeon-Woo Lee
    Olaf Wolkenhauer
    First Published January 1, 2003
  - Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures
    Markus J. Herrgård
    Markus W. Covert
    Bernhard ø. Palsson
    First Published January 1, 2003
  - 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
    First Published November 3, 2003
  - Functionality of System Components: Conservation of Protein Function in Protein Feature Space
    Lars Juhl Jensen
    David W. Ussery
    Søren Brunak
    First Published January 1, 2003
  - Bioinformatics Analysis of Experimentally Determined Protein Complexes in the Yeast Saccharomyces cerevisiae
    Zoltán Dezső
    Zoltán N. Oltvai
    Albert-László Barabási
    First Published January 1, 2003
Methods
- - In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia coli Intermediary Metabolism
    Masanori Arita
    First Published January 1, 2003
  - Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
    Carmen G. Moles
    Pedro Mendes
    Julio R. Banga
    First Published January 1, 2003
  - Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation
    Johan Elf
    Måns Ehrenberg
    First Published November 3, 2003
RESOURCES
- - Toward Rigorous Comprehension of Biological Complexity: Modeling, Execution, and Visualization of Thymic T-Cell Maturation
    Sol Efroni
    David Harel
    Irun R. Cohen
    First Published November 3, 2003
  - Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
    Paul Shannon
    Andrew Markiel
    Owen Ozier
    Nitin S. Baliga
    Jonathan T. Wang
    First Published November 3, 2003

Table of Contents

Volume 13, Issue 11 | November 2003

Preface

The Logic of Life

COMMENTARY

Systems Biology Is Taking Off

ARTICLES

A Biophysical Approach to Transcription Factor Binding Site Discovery

Limitations of Quantitative Gene Regulation Models: A Case Study

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

Signal Processing and Flagellar Motor Switching During Phototaxis of Halobacterium salinarum

LETTERS

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

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

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

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

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

Methods

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

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

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

RESOURCES

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

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

Table of Contents

Volume 13, Issue 11 | November 2003

Share this issue

Preface

COMMENTARY

ARTICLES

LETTERS

Methods

RESOURCES