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