Analysis of Biological Networks
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Reviews / Votes
"This book is a wonderful text for biological network analysis. Itcomprehensively presents a numbers of analysis tools and theirapplications for understanding real biological problems. This bookis a must-read for entry-level students and researchers, and acomplete reference source for experts." (Computing Reviews,March 6, 2009) "This book is an excellent introduction to the analysis ofbiological networks. The exercise provided after each chaptermake the book suitable for self-study, and the extensive referencesprovide the interested reader with good sources for furtherreading." (Computing Reviews, August 21, 2008)More details
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Content
Preface xv
Contributors xix
PART I INTRODUCTION 1
1 Networks in Biology 3
Bjorn H. Junker
1.1 Introduction 3
1.2 Biology 101 4
1.3 Systems Biology 8
1.4 Properties of Biological Networks 8
1.5 Summary 12
1.6 Exercises 12
2 Graph Theory 15
Falk Schreiber
2.1 Introduction 15
2.2 Basic Notation 16
2.3 Special Graphs 19
2.4 Graph Representation 23
2.5 Graph Algorithms 24
2.6 Summary 27
2.7 Exercises 27
PART II NETWORK ANALYSIS 29
3 Global Network Properties 31
Ralf Steuer and Gorka Zamora Lopez
3.1 Introduction 31
3.2 Global Properties of Complex Networks 33
3.3 Models of Complex Networks 43
3.4 Additional Properties of Complex Networks 48
3.5 Statistical Testing of Network Properties 52
3.6 Summary 57
3.7 Exercises 58
4 Network Centralities 65
Dirk Koschutzki
4.1 Introduction 65
4.2 Centrality Definition and Fundamental Properties 67
4.3 Degree and Shortest Path-Based Centralities 69
4.4 Feedback-Based Centralities 77
4.5 Tools 80
4.6 Summary 80
4.7 Exercises 81
5 Network Motifs 85
Henning Schwobbermeyer
5.1 Introduction 85
5.2 Definitions and Basic Concepts 86
5.3 Motif Statistics and Motif-Based Network Distance 89
5.4 Complexity of Network Motif Detection 94
5.5 Methods and Tools for Network Motif Analysis 96
5.6 Analyses and Applications of Network Motifs 97
5.7 Summary 106
5.8 Exercises 108
6 Network Clustering 113
Balabhaskar Balasundaram and Sergiy Butenko
6.1 Introduction 113
6.2 Notations and Definitions 115
6.3 Network Clustering Problem 118
6.4 Clique-Based Clustering 119
6.5 Center-Based Clustering 125
6.6 Conclusion 131
6.7 Summary 133
6.8 Exercises 133
7 Petri Nets 139
Ina Koch and Monika Heiner
7.1 Introduction 139
7.2 Qualitative Modeling 141
7.3 Qualitative Analysis 152
7.4 Quantitative Modeling and Analysis 169
7.5 Tool Support 171
7.6 Case Studies 172
7.7 Summary 174
7.8 Exercises 175
PART III BIOLOGICAL NETWORKS 181
8 Signal Transduction and Gene Regulation Networks 183
Anatolij P. Potapov
8.1 Introduction 183
8.2 Decisive Role of Regulatory Networks in the Evolution and Existence of Organisms 184
8.3 Gene Regulatory Network as a System of Many Subnetworks 186
8.4 Databases on Gene Regulation and Software Tools for Network Analysis 187
8.5 Peculiarities of Signal Transduction Networks 188
8.6 Topology of Signal Transduction Networks 190
8.7 Topology of Transcription Networks 191
8.8 Intercellular Molecular Regulatory Networks 198
8.9 Summary 200
8.10 Exercises 201
9 Protein Interaction Networks 207
Frederik Bornke
9.1 Introduction 207
9.2 Detecting Protein Interactions 209
9.3 Establishing Protein Interaction Networks 220
9.4 Analyzing Protein Interaction Networks 223
9.5 Summary 225
9.6 Exercises 226
10 Metabolic Networks 233
Marcio Rosa da Silva, Jibin Sun, Hongwu Ma, Feng He, and An-Ping Zeng
10.1 Introduction 233
10.2 Visualization and Graph Representation 234
10.3 Reconstruction of Genome-Scale Metabolic Networks 234
10.4 Connectivity and Centrality in Metabolic Networks 239
10.5 Modularity and Decomposition of Metabolic Networks 242
10.6 Elementary Flux Modes and Extreme Pathways 246
10.7 Summary 249
10.8 Exercises 249
11 Phylogenetic Networks 255
Birgit Gemeinholzer
11.1 Introduction 255
11.2 Character Selection, Character Coding, and Matrices for Phylogenetic Reconstruction 257
11.3 Tree Reconstruction Methodologies 260
11.4 Phylogenetic Networks 264
11.5 Summary 276
11.6 Exercises 276
12 Ecological Networks 283
Ursula Gaedke
12.1 Introduction 283
12.2 Binary Food Webs 289
12.3 Quantitative Trophic Food Webs 293
12.4 Ecological Information Networks 298
12.5 Summary 300
12.6 Exercises 301
13 Correlation Networks 305
Dirk Steinhauser, Leonard Krall, Carsten Mussig, Dirk Bussis, and Bjorn Usadel
13.1 Introduction 305
13.2 General Remarks 306
13.3 Basic Notation 307
13.4 Construction and Analyses of Correlation Networks 314
13.5 Biological Use of Correlation Networks 321
13.6 Summary 328
13.7 Exercises 329
References 330
Index 335
