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E-raamat: Networks in Cell Biology

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Edited by , Edited by (Consiglio Nazionale delle Ricerche (CNR), Rome), Edited by (University of Cambridge), Edited by , Edited by
  • Formaat: PDF+DRM
  • Ilmumisaeg: 13-May-2010
  • Kirjastus: Cambridge University Press
  • Keel: eng
  • ISBN-13: 9780511731181
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Networks in Cell BiologySuurem pilt
  • Formaat: PDF+DRM
  • Ilmumisaeg: 13-May-2010
  • Kirjastus: Cambridge University Press
  • Keel: eng
  • ISBN-13: 9780511731181
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"Biologists now have access to a virtually complete map of all the genes in thehuman genome, and in the genomes of many other species. They are aggressivelyassembling a similarly detailed knowledge of the proteome, the full collection ofproteins encoded by those genes, and the transcriptome, the diverse set of mRNA"--Provided by publisher.

"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"--Provided by publisher.

Arvustused

'Network science has experienced a spectacular explosion in the past decade, influencing a wide range of fields, from computer science to sociology. Yet, nowhere is the impact of the new theoretical framework as promising as it is in cell biology - many of the difficult open questions cannot be understood without a network based approach. Networks in Cell Biology offers an excellent introduction to this frontier, at the same time capturing the current state of research. With contributions from the best in the field, it is a valuable addition to the shelf of anyone interested in this exciting area.' Albert-László Barabási, Northeastern University and Harvard Medical School 'This book describes the state of the art in understanding cellular networks through contributions by leaders in modern cell biology and network theory. It is clearly organized and exhibits an excellent balance between empirical studies and theory. The biological underpinnings are explained clearly and comprehensively, and the appendices give a great primer to the key mathematical concepts necessary for network analysis and modeling. This book will be of great use as a course textbook or for self-study.' Reka Albert, Pennsylvania State University

Muu info

Key introductory text for graduate students and researchers in physics, biology and biochemistry.
List of contributors
viii
Introduction 1(3)
M. Buchanan
G. Caldarelli
P. De Los Rios
F. Rao
M. Vendruscolo
1 Network views of the cell
4(10)
Paolo De Los Rios
Michele Vendruscolo
1.1 The network hypothesis
4(1)
1.2 The central dogma and gene regulatory networks
5(2)
1.3 Protein---protein interaction networks
7(2)
1.4 Metabolic networks
9(2)
1.5 Signaling networks
11(1)
1.6 Networked networks and cell functionality
12(1)
1.7 Concluding remarks
13(1)
2 Transcriptional regulatory networks
14(22)
Sarath Chandra Janga
M. Madan Babu
2.1 Introduction
14(5)
2.2 Transcriptional regulation in prokaryotes and eukaryotes
19(1)
2.3 Structure of transcriptional regulatory networks
20(5)
2.4 Evolution of transcriptional regulatory networks
25(4)
2.5 Dynamics of transcriptional regulatory networks
29(5)
2.6 Conclusions
34(2)
3 Transcription factors and gene regulatory networks
36(17)
Matteo Brilli
Elisa Calistri
Pietro Lio
3.1 Introduction
36(1)
3.2 Promoters' complexity/eukaryotic gene promoters
37(4)
3.3 Transcription factors
41(5)
3.4 Bioinformatics of regulatory networks
46(7)
4 Experimental methods for protein interaction identification
53(30)
Peter Uetz
Bjorn Titz
Seesandra V. Rajagopala
Gerard Cagney
4.1 Introduction
53(4)
4.2 Protein complementation techniques
57(5)
4.3 Affinity purification methods
62(3)
4.4 Protein complex purification and mass spectrometry
65(8)
4.5 Protein and peptide chips
73(1)
4.6 Other methods for interaction detection and functional analysis
74(1)
4.7 Quality of large-scale interaction data
75(2)
4.8 Comparison of methods
77(3)
4.9 Conclusions
80(3)
5 Modeling protein interaction networks
83(10)
Francesco Rao
5.1 Introduction
83(2)
5.2 Scaling laws and network topology
85(2)
5.3 Predicting protein interactions
87(1)
5.4 Towards models at an atomic level of resolution
88(2)
5.5 Concluding remarks
90(3)
6 Dynamics and evolution of metabolic networks
93(24)
Daniel Segre
6.1 Introduction
93(1)
6.2 Cellular metabolism and its regulation
93(3)
6.3 Metabolism across disciplines
96(2)
6.4 Dynamics of a metabolic system
98(2)
6.5 Stoichiometric analysis
100(3)
6.6 Constraint-based modeling: feasible states and optimality
103(5)
6.7 Predicting genetic perturbations
108(1)
6.8 Double perturbations and epistatic interactions
109(3)
6.9 The ancient history of metabolism: from cell-scale to biosphere-scale
112(4)
6.10 Conclusions
116(1)
7 Hierarchical modularity in biological networks: the case of metabolic networks
117(18)
Erzsebet Ravasz Regan
7.1 Introduction
117(2)
7.2 Modularity and hubs in biological networks
119(2)
7.3 Scaling of the clustering coefficient: a signature of hierarchy
121(2)
7.4 Method for finding network modules
123(3)
7.5 A case study: the E. coli metabolic network
126(5)
7.6 Hierarchy, fractality and the small world of networks
131(3)
7.7 Conclusions
134(1)
8 Signalling networks
135(35)
Gian Paolo Rossini
8.1 Introduction
135(1)
8.2 Chemical signalling: many pathways following a few general themes
136(23)
8.3 Cross-talks among signal transduction pathways
159(7)
8.4 Signalling networks, system organization and modelling
166(3)
8.5 Conclusions and outlook
169(1)
Appendix A Complex networks: from local to global properties 170(18)
D. Garlaschelli
G. Caldarelli
Appendix B Modelling the local structure of networks 188(22)
D. Garlaschelli
G. Caldarelli
Appendix C Higher-order topological properties 210(9)
S. Ahnert
T. Fink
G. Caldarelli
Appendix D Elementary mathematical concepts 219(16)
A. Gabrielli
G. Caldarelli
References 235(34)
Index 269
Mark Buchanan is a physicist and independent author. He writes a monthly column for the journal Nature Physics. Guido Caldarelli is Associate Professor in the Centre for Statistical Mechanics, University of Rome 'Sapienza', Italy. Paolo De Los Rios is a Professor in the Laboratory of Statistical Biophysics, Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL). Francesco Rao researches in the Laboratoire de Chimie Biophysique, University of Strasbourg. Michele Vendruscolo is a Reader in Theoretical Chemical Biology at the Department of Chemistry, University of Cambridge.
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