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

Björn H. Junker is a biologist with a strong background in bioinformatics. His current research activities include the quantitative analysis and modeling of metabolic networks, as well as pathway databases and visual data mining. Mr. Junker has been at the Leibniz Institute of Plant Genetics and Crop Plant Research in Germany since 2003. He worked at Brookhaven National Laboratory in New York during 2006 and was appointed as project leader at the Leibniz Institute in 2007.

Falk Schreiber is a computer scientist who has worked in bioinformatics for more than ten years. His current research areas include modeling, analysis, and visualization of biological networks; graph algorithms; and data exploration and information visualization in the life sciences. Since 2003, he has been head of the Network Analysis Research Group at the Leibniz Institute of Plant Genetics and Crop Plant Research. He was appointed professor of bioinformatics at the Martin Luther University Halle-Wittenberg, Germany, in 2007.

"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)