Biomolecular Networks : Methods and Applications in Systems Biology

by Luonan Chen; Rui-Sheng Wang; Xiang-Sun Zhang

• ISBN13: 9780470488058
• ISBN10: 0470488050
• Format: eBook
• Copyright: 2009-06-01
• Publisher: Wiley

Summary

The study of biomolecular networks is gaining much attention from both biology and engineering communities to show the principles or fundamental mechanisms of cellular systems. Focusing on computational methods for analyzing biomolecular networks, Biomolecular Networks helps researchers and graduate students understand state-of-the-art techniques in bioinformatics and systems biology, in particular, the theory and application of molecular networks. Concepts from several disciplines (optimization, differential equations, graph theory, network analysis, complex systems, and probability) provide the foundation of these techniques and tools.

Table of Contents

Preface

Acknowledgments

List of Illustrations

Acronyms

Introduction

Basic Concepts in Molecular Biology

Biomolecular Networks in Cells

Network Systems Biology

About This Book

I

Transcription Regulation: Networks and Models

Transcription Regulation and Gene Expression

Networks in Transcription Regulation

Nonlinear Models Based on Biochemical Reactions

Integrated Models for Regulatory Networks

Summary

Reconstruction of Gene Regulatory Networks

Mathematical Models of Gene Regulatory Network

Reconstructing Gene Regulatory Networks

Inferring Gene Networks from Multiple Datasets

Gene Network-Based Drug Target Identification

Summary

Inference of Transcriptional Regulatory Networks

Predicting TF Binding Sites and Promoters

Inference of Transcriptional Interactions

Identifying Combinatorial Regulations of TFs

Inferring Cooperative Regulatory Networks

Prediction of Transcription Factor Activity

Summary

Protein Interaction Networks

Prediction of Protein-Protein Interactions

Experimental Protein-Protein Interactions

Prediction of Protein-Protein Interactions

Protein Interaction Prediction Based on Multidomain Pairs

Domain Interaction Prediction Methods

Summary

Topological Structure of Biomolecular Networks

Statistical Properties of Biomolecular Networks

Evolution of Protein Interaction Networks

Hubs, Motifs, and Modularity in Biomolecular Networks

Explorative Roles of Hubs and Network Motifs

Modularity Evaluation of Biomolecular Networks

Summary

Alignment of Biomolecular Networks

Biomolecular Networks from Multiple Species

Pairwise Alignment of Biomolecular Networks

Network Alignment by Mathematical Programming

Multiple Alignment of Biomolecular Networks

Subnetwork and Pathway Querying

Summary

Network-Based Prediction of Protein Function

Protein Function and Annotation

Protein Functional Module Detection

Functional Linkage for Protein Function Annotation

Protein Function Prediction from High-Throughput Data

Function Annotation Methods for Domains

Summary

Metabolic Networks and Signaling Networks

Metabolic Networks: Analysis, Reconstruction, and Application

Cellular Metabolism and Metabolic Pathways

Metabolic Network Analysis and Modeling

Reconstruction of Metabolic Networks

Drug Target Detection in Metabolic Networks

Summary

Signaling Networks: Modeling and Inference

Signal Transduction in Cellular Systems

Modeling of Signal Transduction Pathways

Inferring Signaling Networks from High-Throughput Data

Inferring Signaling Networks by Linear Programming

Inferring Signaling Networks from Experimental Evidence

Summary

Other Topics and New Trends

Network-Based Protein Structural Analysis

Integration of Biomolecular Networks

Posttranscriptional Regulation of Noncoding RNAs

Biomolecular Interactions and Human Diseases

Summary

References

Index

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