1st Edition
Introduction to Genomic Signal Processing with Control
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.
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
Biography
Aniruddha Datta, Edward R. Dougherty
