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Introduction to Biological Networks

By Alpan Raval, Animesh Ray

Chapman and Hall/CRC – 2013 – 335 pages

Series: Chapman & Hall/CRC Mathematical and Computational Biology

Purchasing Options:

  • Add to CartHardback: $79.95
    978-1-58488-463-7
    April 23rd 2013

Description

The new research area of genomics-inspired network biology lacks an introductory book that enables both physical/computational scientists and biologists to obtain a general yet sufficiently rigorous perspective of current thinking. Filling this gap, Introduction to Biological Networks provides a thorough introduction to genomics-inspired network biology for physical scientists and biologists involved in interdisciplinary research.

The book focuses on the concept of molecular and genetic interaction networks as a paradigm for interpreting the complexity of molecular biology at a genomic scale. The authors describe the experimental methods used to discover and test networks of interaction among biological molecules. They also present computational methods for predicting the interaction networks, discuss general mechanisms of network formation and evolution, and explore the application of network approaches to important problems in biology and medicine.

With many examples throughout and clear explanations of key concepts, this book is the first to offer a broad treatment of genomics-inspired network biology with sufficient mathematical and biological rigor. It gives readers a conceptual understanding of this burgeoning scientific field.

Reviews

"Raval and Ray provide a comprehensive and modern exposition of a rapidly evolving field: network biology. This text will help biology, mathematics, and computer science students alike to become acquainted with the history and frontiers of research in this exciting area."

—Joshua B. Plotkin, University of Pennsylvania

"Finally a book has arrived that describes the basics of biological complexity. Written by leading scientists Raval and Ray, it provides a scholarly account of the concepts of network theory. It describes in great detail the experimental and computational methods for identifying and predicting biological networks and reveals how network analysis can be applied to solve fundamental questions in biology and medicine. Introduction to Biological Networks is easily the best read available on this important and rapidly developing field."

—Cornelis Murre, University of California-San Diego, La Jolla, USA

Contents

The Living Interactome

Biological Function Depends on Context

The Nature of Interactions

Network as a Metaphor in Biology

Metabolic Networks

Robustness at the Network Level

Experimental Inference of Interactions

Direct versus Indirect Inference of Interactions

Physical versus Genetic Interactions

The Two-Hybrid Interaction

Affinity Co-Purification

DNA-Protein Interactions

Classification and Interpretation of Genetic Interactions

Inference of Genetic Interactions

Prediction of Physical Interactions

Entropy and Information

Boolean Networks REVEAL Regulatory Interactions

Variants of the REVEAL Method

Dynamic Bayesian Networks

Predicting Protein-Protein Interactions

Data Integration to Improve Prediction Performance

Metabolic Networks and Genetic Interactions

Optimal Metabolic States and Flux Balance Analysis

Minimization of Metabolic Adjustment and Gene Deletions

Predicting Genetic Interactions among Metabolic Genes

General Methods for Predicting Genetic Interactions

Approaches for Integrated Prediction of Networks

Testing Inferred Networks

Co-Expression as a Test of Physical Interaction

An Experimental Test of Predicted Protein-Protein Interactions

Combining Protein Interactions Discovered by High-Throughput Experiments

From Curated Protein-Protein Interactions to Protein Complexes

Testing DNA-Protein Interactions

Congruence of Biological Function among Interacting Partners

Testing Genetic Interactions

Structure-Based Tests of Interaction

Small Model Networks

Life Cycle of the Lambda Phage

Interaction Network in the Lysis-Lysogeny Decision

Recruitment of Proteins as a Theme in Regulatory Networks

The Network of Cell Cycle Regulation

Tractable Models of Large Networks

Models of Regular Networks

Random Network Models

Evolving Networks by Preferential Attachment

Evolving Networks Based on Gene Duplication

Reconstruction of Ancient Networks from Modern Ones

Large-Scale Biophysics-Inspired Models for Protein Interaction Networks

Network Modularity and Robustness

Modularity Implies Robustness in the Drosophila Segment Polarity Network

Topological and Functional Aspects of Network Modularity

Robustness Implications of Topology of Biological Networks

Robustness and Network Dynamics

Network Robustness by Rewiring

Networks and Disease

Disease Loci Identification and Mapping

Network as a Paradigm for Linking Diseases and Disease Genes

Network-Based Prediction of Disease Genes

Network Analysis of Disease Mechanisms and Disease Response

Network-Based Prediction of Disease Comorbidity

Cancer and Synthetic Lethality

Name: Introduction to Biological Networks (Hardback)Chapman and Hall/CRC 
Description: By Alpan Raval, Animesh Ray. The new research area of genomics-inspired network biology lacks an introductory book that enables both physical/computational scientists and biologists to obtain a general yet sufficiently rigorous perspective of current thinking. Filling this gap,...
Categories: Algorithms & Complexity, Bioinformatics