Analysis of Biological Networks / Edition 1

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Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks.

Analysis of Biological Networks is a self-contained introduction to this important research topic, assumes no expert knowledge in computer science or biology, and is accessible to professionals and students alike. Each chapter concludes with a summary of main points and with exercises for readers to test their understanding of the material presented. Additionally, an FTP site with links to author-provided data for the book is available for deeper study.

This book is suitable as a resource for researchers in computer science, biology, bioinformatics, advanced biochemistry, and the life sciences, and also serves as an ideal reference text for graduate-level courses in bioinformatics and biological research.

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Editorial Reviews

From the Publisher

"This book is a wonderful text for biological network analysis. It comprehensively presents a numbers of analysis tools and their applications for understanding real biological problems. This book is a must-read for entry-level students and researchers, and a complete reference source for experts." (Computing Reviews, March 6, 2009)

"This book is an excellent introduction to the analysis of biological networks.  The exercise provided after each chapter make the book suitable for self-study, and the extensive references provide the interested reader with good sources for further reading." (Computing Reviews, August 21, 2008)

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Product Details

  • ISBN-13: 9780470041444
  • Publisher: Wiley
  • Publication date: 3/7/2008
  • Series: Wiley Series in Bioinformatics Series , #2
  • Edition description: New Edition
  • Edition number: 1
  • Pages: 368
  • Product dimensions: 6.46 (w) x 9.43 (h) x 0.55 (d)

Table of Contents

Foreword     xiii
Preface     xv
Contributors     xix
Introduction     1
Networks in Biology   Bjorn H. Junker     3
Introduction     3
Biology 101     4
Biochemistry and Molecular Biology     4
Cell Biology     6
Ecology and Evolution     7
Systems Biology     8
Properties of Biological Networks     8
Networks on a Microscopic Scale     9
Networks on a Macroscopic Scale     11
Other Biological Networks     11
Summary     12
Exercises     12
References     12
Graph Theory   Falk Schreiber     15
Introduction     15
Basic Notation     16
Sets     16
Graphs     16
Graph Attributes     19
Special Graphs     19
Undirected, Directed, Mixed, and Multigraphs     19
Hypergraphs and Bipartite Graphs     20
Trees     21
Graph Representation     23
Adjacency Matrix     23
Adjacency List     23
Graph Algorithms     24
Running Times of Algorithms     24
Traversal     25
Summary     27
Exercises     27
References     28
Network Analysis     29
Global Network Properties   Ralf Steuer   Gorka Zamora Lopez     31
Introduction     31
Global Properties of Complex Networks     33
Distance, Average Path Length, and Diameter     33
Six Degrees of Separation: Concepts of a Small World     35
The Degree Distribution     35
Assortative Mixing and Degree Correlations     38
The Clustering Coefficient     39
The Matching Index     41
Network Centralities     42
Eigenvalues and Spectral Properties of Networks     43
Models of Complex Networks     43
The Erdos-Renyi Model     44
The Watts-Strogatz Model     45
The Barabasi-Albert Model     46
Extensions of the BA Model     48
Additional Properties of Complex Networks     48
Structural Robustness and Attack Tolerance     49
Modularity, Community Structures and Hierarchies     50
Subgraphs and Motifs in Networks      51
Statistical Testing of Network Properties     52
Generating Networks and Null Models     53
The Conceptualization of Cellular Networks     54
Bipartite Graphs     55
Correlation Networks     57
Summary     57
Exercises     58
References     59
Network Centralities   Dirk Koschutzki     65
Introduction     65
Centrality Definition and Fundamental Properties     67
Comparison of Centrality Values     68
Disconnected Networks     68
Degree and Shortest Path-Based Centralities     69
Degree Centrality     69
Eccentricity Centrality     71
Closeness Centrality     72
Shortest Path Betweenness Centrality     73
Algorithms     74
Example     76
Feedback-Based Centralities     77
Katz's Status Index     77
Bonacich's Eigenvector Centrality     78
PageRank     79
Tools     80
Summary     80
Exercises     81
References     81
Network Motifs   Henning Schwobbermeyer      85
Introduction     85
Definitions and Basic Concepts     86
Definitions     86
Modeling of Biological Networks     88
Concepts of Motif Frequency     88
Motif Statistics and Motif-Based Network Distance     89
Determination of Statistical Significance of Network Motifs     89
Randomization Algorithm for Generation of Null Model Networks     90
Influence of the Null Model on Motif Significance     91
Limitations of the Null Model on Motif Detection     91
Measures of Motif Significance and for Network Comparison     91
Complexity of Network Motif Detection     94
Aspects Affecting the Complexity of Network Motif Detection     94
Frequency Estimation by Motif Sampling     96
Methods and Tools for Network Motif Analysis     96
Pajek     96
Mfinder     96
MAVisto     97
FANMOD     97
Analyses and Applications of Network Motifs     97
Network Motifs in Complex Networks     97
Dynamic Properties of Network Motifs     98
Higher Order Structures Formed by Network Motifs     102
Network Comparison Based on Network Motifs     104
Evolutionary Origin of Network Motifs     106
Summary     106
Exercises     108
References     108
Network Clustering   Balabhaskar Balasundaram   Sergiy Butenko     113
Introduction     113
Notations and Definitions     115
Network Clustering Problem     118
Clique-Based Clustering     119
Minimum Clique Partitioning     120
Min-Max k-Clustering     122
Center-Based Clustering     125
Clustering with Dominating Sets     126
k-Center Clustering     129
Conclusion     131
Summary     133
Exercises     133
References     134
Petri Nets   Ina Koch   Monika Heiner     139
Introduction     139
Qualitative Modeling     141
The Model     141
The Behavioral Properties     148
Qualitative Analysis     152
Structural Analysis     152
Invariant Analysis     155
MCT-Sets     162
Dynamic Analysis of General Properties     164
Dynamic Analysis of Special Properties      166
Model Validation Criteria     168
Quantitative Modeling and Analysis     169
Tool Support     171
Case Studies     172
Summary     174
Exercises     175
References     177
Biological Networks     181
Signal Transduction and Gene Regulation Networks   Anatolij P. Potapov     183
Introduction     183
Decisive Role of Regulatory Networks in the Evolution and Existence of Organisms     184
Gene Regulatory Network as a System of Many Subnetworks     186
Databases on Gene Regulation and Software Tools for Network Analysis     187
Peculiarities of Signal Transduction Networks     188
Topology of Signal Transduction Networks     190
Topology of Transcription Networks     191
Intercellular Molecular Regulatory Networks     198
Summary     200
Exercises     201
References     202
Protein Interaction Networks   Frederik Bornke     207
Introduction     207
Detecting Protein Interactions     209
The Yeast Two-Hybrid System     211
Affinity Capture of Protein Complexes      216
Computational Methods to Predict Protein Interactions     218
Other Ways to Identify Protein Interactions     219
Establishing Protein Interaction Networks     220
Data Storage and Network Generation     220
Benchmarking High-Throughput Interaction Data     222
Analyzing Protein Interaction Networks     223
Network Topology and Functional Implications     223
Functional Modules in Protein Interaction Networks     223
Evolution of Protein Interaction Networks     224
Comparative Interactomics     225
Summary     225
Exercises     226
References     227
Metabolic Networks   Marcio Rosa da Silva   Jibin Sun   Hongwu Ma   Feng He   An-Ping Zeng     233
Introduction     233
Visualization and Graph Representation     234
Reconstruction of Genome-Scale Metabolic Networks     234
Connectivity and Centrality in Metabolic Networks     239
Modularity and Decomposition of Metabolic Networks     242
Modularity Coefficient     244
Modularity-Based Decomposition     245
Elementary Flux Modes and Extreme Pathways      246
Summary     249
Exercises     249
References     251
Phylogenetic Networks   Birgit Gemeinholzer     255
Introduction     255
Character Selection, Character Coding, and Matrices for Phylogenetic Reconstruction     257
Tree Reconstruction Methodologies     260
Phylogenetic Networks     264
Galled Trees     266
Statistical Parsimony     267
Median Network     269
Median-Joining Networks     270
Pyramids     271
Example of a Pyramidal Clustering Model     271
Split Decomposition     274
Summary     276
Exercises     276
References     277
Ecological Networks   Ursula Gaedke     283
Introduction     283
Binary Food Webs     289
Introduction and Definitions     289
Descriptors of the Network     289
Operational Problems     291
Aims and Results     291
Conclusion     293
Quantitative Trophic Food Webs     293
Introduction, Definitions, and Database     293
Multiple Commodities      295
Descriptors of the Network and Information to be Gained     295
Conclusion     298
Ecological Information Networks     298
Summary     300
Exercises     301
References     301
Correlation Networks   Dirk Steinhauser   Leonard Krall   Carsten Mussig   Dirk Bussis   Bjorn Usadel     305
Introduction     305
General Remarks     306
Basic Notation     307
Data, Unit, Variable, and Observation     307
Sample, Profiles, and Replica Set     308
Measures of Association     309
Simple Correlation Measures     310
Complex Correlation and Association Measures     311
Probability, Confidence, and Power     313
Matrices     314
Construction and Analyses of Correlation Networks     314
Data and Profiles     315
Data Set and Matrix     316
Correlation Matrix     318
Network Matrix     318
Correlation Network Analysis     319
Interpretation and Validation     321
Biological Use of Correlation Networks     321
The Global Analysis Approach     321
The Guide Gene Approach     322
A Simple Coregulation Test: Photosynthesis     324
A Complex Coregulation Test: Brassinosteroids     327
Summary     328
Exercises     329
References     330
Index     335

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