Introduction to Genomic Signal Processing with Control: 1st Edition (Hardback) book cover

Introduction to Genomic Signal Processing with Control

1st Edition

By Aniruddha Datta, Edward R. Dougherty

CRC Press

288 pages | 32 Color Illus. | 123 B/W Illus.

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pub: 2006-11-14
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Description

Studying large sets of genes and their collective function requires tools that can easily handle huge amounts of information. Recent research indicates that engineering approaches for prediction, signal processing, and control are well suited for studying multivariate interactions. A tutorial guide to the current engineering research in genomics, Introduction to Genomic Signal Processing with Control provides a state-of-the-art account of the use of control theory to obtain intervention strategies for gene regulatory networks.

The book builds up the necessary molecular biology background with a basic review of organic chemistry and an introduction of DNA, RNA, and proteins, followed by a description of the processes of transcription and translation and the genetic code that is used to carry out the latter. It discusses control of gene expression, introduces genetic engineering tools such as microarrays and PCR, and covers cell cycle control and tissue renewal in multi-cellular organisms.

The authors then delineate how the engineering approaches of classification and clustering are appropriate for carrying out gene-based disease classification. This leads naturally to expression prediction, which in turn leads to genetic regulatory networks. The book concludes with a discussion of control approaches that can be used to alter the behavior of such networks in the hope that this alteration will move the network from a diseased state to a disease-free state.

Written by recognized leaders in this emerging field, the book provides the exact amount of molecular biology required to understand the engineering applications. It is a self-contained resource that spans the diverse disciplines of molecular biology and electrical engineering.

Table of Contents

INTRODUCTION

REVIEW OF ORGANIC CHEMISTRY

Electrovalent and Covalent Bonds

Some Chemical Bonds and Groups Commonly Encountered in Biological Molecules

Building Blocks for Common Organic Molecules

ENERGY CONSIDERATIONS IN BIOCHEMICAL REACTIONS

Some Common Biochemical Reactions

Role of Enzymes

Feasibility of Chemical Reactions

Activated Carrier Molecules and Their Role in Biosynthesis

PROTEINS

Protein Structure and Function

Levels of Organization in Proteins

Protein Ligand Interactions

Isolating Proteins from Cells

Separating a Mixture of Proteins

Protein Structure Determination

Proteins That Are Enzymes

DNA

TRANSCRIPTION AND TRANSLATION

Transcription

Translation

CHROMOSOMES AND GENE REGULATION

Organization of DNA into Chromosomes

Gene Regulation

GENETIC VARIATION

Genetic Variation in Bacteria

Sources of Genetic Change in Eucaryotic Genomes

DNA TECHNOLOGY

Techniques for Analyzing DNA Molecules

Nucleic Acid Hybridization and Associated Techniques

Construction of Human Genomic and cDNA Libraries

Polymerase Chain Reaction (PCR)

Genetic Engineering

CELL DIVISION

Mitosis and Cytokinesis

Meiosis

CELL CYCLE CONTROL, CELL DEATH AND CANCER

Cyclin-Dependent Kinases and Their Role

Control of Cell Numbers in Multicellular Organisms

Programmed Cell Death

Cancer as the Breakdown of Cell Cycle Control

EXPRESSION MICROARRAYS

cDNA Microarrays

Synthetic Oligonucleotide Arrays

CLASSIFICATION

Classifier Design

Feature Selection

Error Estimation

CLUSTERING

Examples of Clustering Algorithms

Clustering Accuracy

Cluster Validation

GENETIC REGULATORY NETWORKS

Nonlinear Dynamical Modeling of Gene Networks

Boolean Networks

Probabilistic Boolean Networks

Network Inference

INTERVENTION

PBN Notation

Intervention by Flipping the Status of a Single Gene

Intervention to Alter the Steady-State Behavior

EXTERNAL INTERVENTION BASED ON OPTIMAL CONTROL THEORY

Finite Horizon Control

External Intervention in the Imperfect Information Case

External Intervention in the Context-Sensitive Case

External Intervention for a Family of Boolean Networks

External Intervention in the Infinite Horizon Case

Concluding Remarks

References

Index

Subject Categories

BISAC Subject Codes/Headings:
SCI049000
SCIENCE / Life Sciences / Biology / Molecular Biology
TEC007000
TECHNOLOGY & ENGINEERING / Electrical