Introduction to Genomic Signal Processing with Control

by Datta; Aniruddha

• ISBN13: 9780849371981
• ISBN10: 0849371988
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-11-14
• Publisher: CRC Press

Summary

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

1 Introduction	1	(4)
2 Review of Organic Chemistry	5	(22)
2.1 Electrovalent and Covalent Bonds	6	(3)
2.2 Some Chemical Bonds and Groups Commonly Encountered in Biological Molecules	9	(4)
2.3 Building Blocks for Common Organic Molecules	13	(14)
2.3.1 Sugars	13	(4)
2.3.2 Fatty Acids	17	(1)
2.3.3 Amino Acids	18	(2)
2.3.4 Nucleotides	20	(7)
3 Energy Considerations in Biochemical Reactions	27	(10)
3.1 Some Common Biochemical Reactions	28	(2)
3.1.1 Photosynthesis	28	(1)
3.1.2 Cellular Respiration	29	(1)
3.1.3 Oxidation and Reduction	29	(1)
3.2 Role of Enzymes	30	(2)
3.3 Feasibility of Chemical Reactions	32	(2)
3.4 Activated Carrier Molecules and Their Role in Biosynthesis	34	(3)
4 Proteins	37	(16)
4.1 Protein Structure and Function	37	(4)
4.1.1 The a-helix and the 0-sheet	38	(3)
4.2 Levels of Organization in Proteins	41	(2)
4.3 Protein Ligand Interactions	43	(2)
4.4 Isolating Proteins from Cells	45	(1)
4.5 Separating a Mixture of Proteins	46	(2)
4.5.1 Column Chromatography	47	(1)
4.5.2 Gel Electrophoresis	47	(1)
4.6 Protein Structure Determination	48	(1)
4.7 Proteins That Are Enzymes	49	(4)
5 DNA	53	(10)
6 Transcription and Translation	63	(14)
6.1 Transcription	64	(5)
6.2 Translation	69	(8)
7 Chromosomes and Gene Regulation	77	(12)
7.1 Organization of DNA into Chromosomes	78	(4)
7.2 Gene Regulation	82	(7)
8 Genetic Variation	89	(12)
8.1 Genetic Variation in Bacteria	89	(5)
8.1.1 Bacterial Mating	90	(2)
8.1.2 Gene Transfer by Bacteriophages	92	(1)
8.1.3 Transposons	93	(1)
8.2 Sources of Genetic Change in Eucaryotic Genomes	94	(7)
8.2.1 Gene Duplication	94	(2)
8.2.2 Transposable Elements and Viruses	96	(2)
8.2.3 Sexual Reproduction and the Reassortment of Genes	98	(3)
9 DNA Technology	101	(16)
9.1 Techniques for Analyzing DNA Molecules	101	(4)
9.2 Nucleic Acid Hybridization and Associated Techniques	105	(2)
9.3 Construction of Human Genomic and cDNA Libraries	107	(2)
9.4 Polymerase Chain Reaction (PCR)	109	(3)
9.5 Genetic Engineering	112	(7)
9.5.1 Engineering DNA Molecules, Proteins and RNAs	112	(1)
9.5.2 Engineering Mutant Haploid Organisms	112	(2)
9.5.3 Engineering Transgenic Animals	114	(3)
10 Cell Division	117	(10)
10.1 Mitosis and Cytokinesis	119	(4)
10.2 Meiosis	123	(4)
11 Cell Cycle Control, Cell Death and Cancer	127	(10)
11.1 Cyclin-Dependent Kinases and Their Role	128	(3)
11.2 Control of Cell Numbers in Multicellular Organisms	131	(1)
11.3 Programmed Cell Death	132	(1)
11.4 Cancer as the Breakdown of Cell Cycle Control	133	(4)
12 Expression Microarrays	137	(10)
12.1 cDNA Microarrays	138	(7)
12.1.1 Normalization	140	(2)
12.1.2 Ratio Analysis	142	(3)
12.2 Synthetic Oligonucleotide Arrays	145	(2)
13 Classification	147	(20)
13.1 Classifier Design	147	(11)
13.1.1 Bayes Classifier	148	(1)
13.1.2 Classification Rules	148	(3)
13.1.3 Constrained Classifier Design	151	(3)
13.1.4 Regularization for Quadratic Discriminant Analysis	154	(3)
13.1.5 Regularization by Noise Injection	157	(1)
13.2 Feature Selection	158	(3)
13.3 Error Estimation	161	(7)
13.3.1 Error Estimation Using the Training Data	162	(1)
13.3.2 Performance Issues	163	(4)
14 Clustering	167	(14)
14.1 Examples of Clustering Algorithms	168	(5)
14.1.1 k-means	168	(1)
14.1.2 Fuzzy k-means	169	(1)
14.1.3 Self-Organizing Maps	170	(1)
14.1.4 Hierarchical Clustering	171	(2)
14.2 Clustering Accuracy	173	(3)
14.2.1 Model-Based Clustering Error	173	(1)
14.2.2 Application to Real Data	174	(2)
14.3 Cluster Validation	176	(5)
15 Genetic Regulatory Networks	181	(16)
15.1 Nonlinear Dynamical Modeling of Gene Networks	182	(2)
15.2 Boolean Networks	184	(4)
15.2.1 Boolean Model	184	(3)
15.2.2 Coefficient of Determination	187	(1)
15.3 Probabilistic Boolean Networks	188	(4)
15.4 Network Inference	192	(5)
16 Intervention	197	(10)
16.1 PBN Notation	198	(1)
16.2 Intervention by Flipping the Status of a Single Gene	199	(4)
16.3 Intervention to Alter the Steady-State Behavior	203	(4)
17 External Intervention Based on Optimal Control Theory	207	(46)
17.1 Finite-Horizon-Control	208	(12)
17.1.1 Solution Using Dynamic Programming	211	(1)
17.1.2 A Simple Illustrative Example	212	(3)
17.1.3 Melanoma Example	215	(5)
17.2 External Intervention in the Imperfect Information Case	220	(6)
17.2.1 Melanoma Example	221	(5)
17.3 External Intervention in the Context-Sensitive Case	226	(6)
17.3.1 Melanoma Example	229	(3)
17.4 External Intervention for a Family of Boolean Networks	232	(6)
17.4.1 Melanoma Example	235	(3)
17.5 External Intervention in the Infinite Horizon Case	238	(10)
17.5.1 Optimal Control Solution	240	(4)
17.5.2 Melanoma Example	244	(4)
17.6 Concluding Remarks	248	(5)
References	253	(12)
Index	265