Datta / Dougherty Introduction to Genomic Signal Processing with Control

Erscheinungsjahr 2006
ISBN: 978-1-4200-0667-4
Verlag: Taylor & Francis
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 288 Seiten

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.

Zielgruppe

Engineers interested in genomics; molecular biology; bioinformatics; signal processing; and controls.

Autoren/Hrsg.

Datta, Aniruddha

Dougherty, Edward R.

Fachgebiete

• Naturwissenschaften Biowissenschaften Biowissenschaften

Inhaltsverzeichnis

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