Genome Research -- Table of Contents (13 [11])

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Volume 13, Issue 11: November 2003 [Index by Author] [Cover Caption]

Other Issues:

PREFACE

COMMENTARY

ARTICLES

LETTERS

METHODS

RESOURCES

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PREFACE:

Måns Ehrenberg, Erik Aurell, Johan Elf, Rickard Sandberg, and Jesper Tegnér: The Logic of Life
Genome Res. 2003 13: 2375-2376. [Full Text]

COMMENTARY:

Måns Ehrenberg, Johan Elf, Erik Aurell, Rickard Sandberg, and Jesper Tegnér: Systems Biology Is Taking Off
Genome Res. 2003 13: 2377-2380. [Full Text]

ARTICLES:

Marko Djordjevic, Anirvan M. Sengupta, and Boris I. Shraiman: A Biophysical Approach to Transcription Factor Binding Site Discovery
Genome Res. 2003 13: 2381-2390. [Abstract] [Full Text] [Supplemental Research Data]

Philip M. Kim and Bruce Tidor: Limitations of Quantitative Gene Regulation Models: A Case Study
Genome Res. 2003 13: 2391-2395. [Abstract] [Full Text]

Daniel E. Zak, Gregory E. Gonye, James S. Schwaber, and Francis J. Doyle, III: 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
Genome Res. 2003 13: 2396-2405. [Abstract] [Full Text] [Supplemental Research Data]

Torsten Nutsch, Wolfgang Marwan, Dieter Oesterhelt, and Ernst Dieter Gilles: Signal Processing and Flagellar Motor Switching During Phototaxis of Halobacterium salinarum
Genome Res. 2003 13: 2406-2412. Published in Advance October 14, 2003, 10.1101/gr.1241903 [Abstract] [Full Text] [Supplemental Research Data]

LETTERS:

Kwang-Hyun Cho, Sung-Young Shin, Hyeon-Woo Lee, and Olaf Wolkenhauer: Investigations Into the Analysis and Modeling of the TNF ${alpha}$ -Mediated NF- ${kappa}$ B-Signaling Pathway
Genome Res. 2003 13: 2413-2422. Published in Advance October 14, 2003, 10.1101/gr.1195703 [Abstract] [Full Text]

Markus J. Herrgård, Markus W. Covert, and Bernhard ø. Palsson: Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures
Genome Res. 2003 13: 2423-2434. Published in Advance October 14, 2003, 10.1101/gr.1330003 [Abstract] [Full Text] [Supplemental Research Data]

Rosa María Gutiérrez-Ríos, David A. Rosenblueth, José Antonio Loza, Araceli M. Huerta, Jeremy D. Glasner, Fred R. Blattner, and Julio Collado-Vides: Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles
Genome Res. 2003 13: 2435-2443. [Abstract] [Full Text] [Supplemental Research Data]

Lars Juhl Jensen, David W. Ussery, and Søren Brunak: Functionality of System Components: Conservation of Protein Function in Protein Feature Space
Genome Res. 2003 13: 2444-2449. Published in Advance October 14, 2003, 10.1101/gr.1190803 [Abstract] [Full Text]

Zoltán Dezso, Zoltán N. Oltvai, and Albert-László Barabási: Bioinformatics Analysis of Experimentally Determined Protein Complexes in the Yeast Saccharomyces cerevisiae
Genome Res. 2003 13: 2450-2454. Published in Advance October 14, 2003, 10.1101/gr.1073603 [Abstract] [Full Text] [Supplemental Research Data]

METHODS:

Masanori Arita: In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia coli Intermediary Metabolism
Genome Res. 2003 13: 2455-2466. Published in Advance October 14, 2003, 10.1101/gr.1212003 [Abstract] [Full Text]

Carmen G. Moles, Pedro Mendes, and Julio R. Banga: Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
Genome Res. 2003 13: 2467-2474. Published in Advance October 14, 2003, 10.1101/gr.1262503 [Abstract] [Full Text]

Johan Elf and Måns Ehrenberg: Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation
Genome Res. 2003 13: 2475-2484. [Abstract] [Full Text] [Supplemental Research Data]

RESOURCES:

Sol Efroni, David Harel, and Irun R. Cohen: Toward Rigorous Comprehension of Biological Complexity: Modeling, Execution, and Visualization of Thymic T-Cell Maturation
Genome Res. 2003 13: 2485-2497. [Abstract] [Full Text] [Supplemental Research Data]

Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S. Baliga, Jonathan T. Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, and Trey Ideker: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Genome Res. 2003 13: 2498-2504. [Abstract] [Full Text]

Cover Caption:

Cover Cover A static view of reactive animation: An approach to modeling complex systems, in which the mathematical execution of a precise model of behavior generates a simulation viewed as a moving picture of molecules and cells. Here we illustrate thymocytes developing in the thymus lobule: surface molecules, differentiation, migration, proliferation, apoptosis, molecular gradients, anatomical compartments, etc. The upper rectangle represents a thymocyte's statechart; the lower rectangle shows a front-end animation (self-organization of anatomical zones); the middle rectangle zooms into the animation (differentiating thymocytes interacting with epithelial cells). This simulation makes it possible to observe emergent properties and to experiment in silico. (For details, see Efroni etal., pp. 2485-2497. Cover art designed by Shlomit Davidson.)