Analysis of Biological Networks

Foreword. Preface. Contributors. PART I INTRODUCTION 1 1 Networks in Biology (Bjorn H. Junker). 1.1 Introduction. 1.2 Biology. 1.3 Systems Biology. 1.4 Properties of Biological Networks. 1.5 Summary. 1.6 Exercises. References. 2 Graph Theory (Falk Schreiber). 2.1 Introduction. 2.2 Basic Notation. 2.3 Special Graphs. 2.4 Graph Representation. 2.5 Graph Algorithms. 2.6 Summary. 2.7 Exercises. References. PART II NETWORK ANALYSIS. 3 Global Network Properties (Ralf Steuer and Gorka Zamora Lopez). 3.1 Introduction. 3.2 Global Properties of Complex Networks. 3.3 Models of Complex Networks. 3.4 Additional Properties of Complex Networks. 3.5 Statistical Testing of Network Properties. 3.6 Summary. 3.7 Exercises. References. 4 Network Centralities (Dirk Koschutzki). 4.1 Introduction. 4.2 Centrality Definition and Fundamental Properties. 4.3 Degree and Shortest Path-Based Centralities. 4.4 Feedback-Based Centralities. 4.5 Tools. 4.6 Summary. 4.7 Exercises. References. 5 Network Motifs (Henning Schwobbermeyer). 5.1 Introduction. 5.2 Definitions and Basic Concepts. 5.3 Motif Statistics and Motif-Based Network Distance. 5.4 Complexity of Network Motif Detection. 5.5 Methods and Tools for Network Motif Analysis. 5.6 Analyses and Applications of Network Motifs. 5.7 Summary. 5.8 Exercises. References. 6 Network Clustering (Balabhaskar Balasundaram and Sergiy Butenko). 6.1 Introduction. 6.2 Notations and Definitions. 6.3 Network Clustering Problem. 6.4 Clique-Based Clustering. 6.5 Center-Based Clustering. 6.6 Conclusion. 6.7 Summary. 6.8 Exercises. References. 7 Petri Nets (Ina Koch and Monika Heiner). 7.1 Introduction. 7.2 Qualitative Modeling. 7.3 Qualitative Analysis. 7.4 Quantitative Modeling and Analysis. 7.5 Tool Support. 7.6 Case Studies. 7.7 Summary. 7.8 Exercises. References. PART III BIOLOGICAL NETWORKS. 8 Signal Transduction and Gene Regulation Networks (Anatolij P. Potapov). 8.1 Introduction. 8.2 Decisive Role of Regulatory Networks in the Evolution and Existence of Organisms. 8.3 Gene Regulatory Network as a System of Many Subnetworks. 8.4 Databases on Gene Regulation and Software Tools for Network Analysis. 8.5 Peculiarities of Signal Transduction Networks. 8.6 Topology of Signal Transduction Networks. 8.7 Topology of Transcription Networks. 8.8 Intercellular Molecular Regulatory Networks. 8.9 Summary. 8.10 Exercises. References. 9 Protein Interaction Networks (Frederik Bornke). 9.1 Introduction. 9.2 Detecting Protein Interactions. 9.3 Establishing Protein Interaction Networks. 9.4 Analyzing Protein Interaction Networks. 9.5 Summary. 9.6 Exercises. References. 10 Metabolic Networks (Marcio Rosa da Silva, Jibin Sun, Hongwu Ma, Feng He, and An-Ping Zeng). 10.1 Introduction . 10.2 Visualization and Graph Representation. 10.3 Reconstruction of Genome-Scale Metabolic Networks. 10.4 Connectivity and Centrality in Metabolic Networks. 10.5 Modularity and Decomposition of Metabolic Networks. 10.6 Elementary Flux Modes and Extreme Pathways. 10.7 Summary. 10.8 Exercises. References. 11 Phylogenetic Networks (Birgit Gemeinholzer). 11.1 Introduction. 11.2 Character Selection, Character Coding, and Matrices for Phylogenetic Reconstruction. 11.3 Tree Reconstruction Methodologies. 11.4 Phylogenetic Networks. 11.5 Summary. 11.6 Exercises. References. 12 Ecological Networks (Ursula Gaedke). 12.1 Introduction. 12.2 Binary Food Webs. 12.3 Quantitative Trophic Food Webs. 12.4 Ecological Information Networks. 12.5 Summary. 12.6 Exercises. References. 13 Correlation Networks (Dirk Steinhauser, Leonard Krall, Carsten Mussig, Dirk Bussis, and Bjorn Usadel). 13.1 Introduction. 13.2 General Remarks. 13.3 Basic Notation. 13.4 Construction and Analyses of Correlation Networks. 13.5 Biological Use of Correlation Networks. 13.6 Summary. 13.7 Exercises. References. Index.