Networks in Cell Biology

by Edited by Mark Buchanan , Guido Caldarelli , Paolo De Los Rios , Francesco Rao , Michele Vendruscolo

• ISBN13: 9780521882736
• ISBN10: 0521882737
• Format: Hardcover
• Copyright: 2010-06-28
• Publisher: Cambridge University Press

Summary

The science of complex biological networks is transforming research in areas ranging from evolutionary biology to medicine. This is the first book on the subject, providing a comprehensive introduction to complex network science and its biological applications. With contributions from key leaders in both network theory and modern cell biology, this book discusses the network science that is increasingly foundational for systems biology and the quantitative understanding of living systems. It surveys studies in the quantitative structure and dynamics of genetic regulatory networks, molecular networks underlying cellular metabolism, and other fundamental biological processes. The book balances empirical studies and theory to give a unified overview of this interdisciplinary science. It is a key introductory text for graduate students and researchers in physics, biology and biochemistry, and presents ideas and techniques from fields outside the reader's own area of specialization.

Author Biography

Mark Buchanan is a physicist and an independent author. He writes a monthly column for the journal nature physics. Guido Caldarelli is Associate Professor in the Centre for Statistical Mechanics, CNR-INFM, Rome, and collaborates with the Research Centre 'E. Fermi', the Laboratory LINKALAB and the London Institute for Mathematical Sciences. Paolo De Los Rios is a Professor in the Laboratory of Statistical Biophysics, Institute of Theoretical Physics, Ecole Polytechnique Federale de Lausanne (EPFL). Francesco Rao researches in the Laboratoire de Chimie Biophysique at the University of Strasbourg and at the Research Centre 'E. Fermi' Rome. Michele Vendruscolo is a Reader in Theoretical Chemical Biology in the Department of Chemistry at the University of Cambridge.

Table of Contents

List of contributors	p. viii
Introduction	p. 1
Network views of the cell	p. 4
The network hypothesis	p. 4
The central dogma and gene regulatory networks	p. 5
Protein-protein interaction networks	p. 7
Metabolic networks	p. 9
Signaling networks	p. 11
Networked networks and cell functionality	p. 12
Concluding remarks	p. 13
Transcriptional regulatory networks	p. 14
Introduction	p. 14
Transcriptional regulation in prokaryotes and eukaryotes	p. 19
Structure of transcriptional regulatory networks	p. 20
Evolution of transcriptional regulatory networks	p. 25
Dynamics of transcriptional regulatory networks	p. 29
Conclusions	p. 34
Transcription factors and gene regulatory networks	p. 36
Introduction	p. 36
Promoters' complexity/eukaryotic gene promoters	p. 37
Transcription factors	p. 41
Bioinformatics of regulatory networks	p. 46
Experimental methods for protein interaction identification	p. 53
Introduction	p. 53
Protein complementation techniques	p. 57
Affinity purification methods	p. 62
Protein complex purification and mass spectrometry	p. 65
Protein and peptide chips	p. 73
Other methods for interaction detection and functional analysis	p. 74
Quality of large-scale interaction data	p. 75
Comparison of methods	p. 77
Conclusions	p. 80
Modeling protein interaction networks	p. 83
Introduction	p. 83
Scaling laws and network topology	p. 85
Predicting protein interactions	p. 87
Towards models at an atomic level of resolution	p. 88
Concluding remarks	p. 90
Dynamics and evolution of metabolic networks	p. 93
Introduction	p. 93
Cellular metabolism and its regulation	p. 93
Metabolism across disciplines	p. 96
Dynamics of a metabolic system	p. 98
Stoichiometric analysis	p. 100
Constraint-based modeling: feasible states and optimality	p. 103
Predicting genetic perturbations	p. 108
Double perturbations and epistatic interactions	p. 109
The ancient history of metabolism: from cell-scale to biosphere-scale	p. 112
Conclusions	p. 116
Hierarchical modularity in biological networks: the case of metabolic networks	p. 117
Introduction	p. 117
Modularity and hubs in biological networks	p. 119
Scaling of the clustering coefficient: a signature of hierarchy	p. 121
Method for finding network modules	p. 123
A case study: the E. coli metabolic network	p. 126
Hierarchy, fractality and the small world of networks	p. 131
Conclusions	p. 134
Signalling networks	p. 135
Introduction	p. 135
Chemical signalling: many pathways following a few general themes	p. 136
Cross-talks among signal transduction pathways	p. 159
Signalling networks, system organization and modelling	p. 166
Conclusions and outlook	p. 169
Complex networks: from local to global properties	p. 170
Modelling the local structure of networks	p. 188
Higher-order topological properties	p. 210
Elementary mathematical concepts	p. 219
References	p. 235
Index	p. 269
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