Bioinformatics: An Introduction

by Ramsden, Jeremy J.

• ISBN13: 9781848002562
• ISBN10: 1848002564
• Edition: 2nd
• Format: Hardcover
• Copyright: 2009-05-01
• Publisher: SPRINGER

Summary

The Computational Biology series publishes the very latest, high-quality research devoted to specific issues in computer-assisted analysis of biological data. The main emphasis is on current scientific developments and innovative techniques in computational biology (bioinformatics), bringing to light methods from mathematics, statistics and computer science that directly address biological problems currently under investigation.

Table of Contents

Introduction	p. 1
What is Bioinformatics?	p. 2
What Can Bioinformatics Do?	p. 3
Information
The Nature of Information	p. 9
Structure and Quantity	p. 15
The Generation of Information	p. 15
Conditional and Unconditional Information	p. 15
Experiments and Observations	p. 16
Constraint	p. 17
The Value of Information	p. 22
The Quality of Information	p. 23
Accuracy, Meaning, and Effect	p. 23
Accuracy	p. 23
Meaning	p. 24
Effect	p. 27
Significs	p. 28
Further Remarks on Information Generation	p. 28
Summary	p. 29
The Transmission of Information	p. 31
The Capacity of a Channel	p. 33
Coding	p. 35
Decoding	p. 37
Compression	p. 38
Use of Compression to Measure Distance	p. 41
Ergodicity	p. 41
Noise	p. 42
Error Correction	p. 44
Summary	p. 46
Sets and Combinatorics	p. 47
The Notion of Set	p. 47
Combinatorics	p. 47
Ordered Sampling With Replacement	p. 48
Ordered Sampling Without Replacement	p. 48
Unordered Sampling Without Replacement	p. 49
Unordered Sampling With Replacement	p. 51
The Binomial Theorem	p. 51
Probability and Likelihood	p. 53
The Notion of Probability	p. 53
Fundamentals	p. 54
Generalized Union	p. 56
Conditional Probability	p. 57
Bernoulli Trials	p. 59
Moments of Distributions	p. 61
Runs	p. 62
The Hypergeometric Distribution	p. 63
Multiplicative Processes	p. 64
Likelihood	p. 65
The Maximum Entropy Method	p. 68
Randomness and Complexity	p. 69
Random Processes	p. 72
Markov Chains	p. 73
Random Walks	p. 75
Noise	p. 77
Complexity	p. 78
Systems, Networks, and Circuits	p. 83
General Systems Theory	p. 84
Automata	p. 86
Cellular Automata	p. 88
Percolation	p. 88
Networks (graphs)	p. 89
Trees	p. 91
Complexity Parameters	p. 92
Dynamical Properties	p. 92
Synergetics	p. 93
Some Examples	p. 94
Reception and Generation of Information	p. 96
Evolutionary Systems	p. 96
Algorithms	p. 99
Evolutionary Computing	p. 100
Pattern Recognition	p. 101
Botryology	p. 102
Clustering	p. 103
Principal Component and Linear Discriminant Analyses	p. 105
Wavelets	p. 106
Multidimensional Scaling and Seriation	p. 107
Visualization	p. 110
Biology
Introduction to Part II	p. 115
Genotype, Phenotype, and Species	p. 115
Adaptation	p. 117
Timescales of Adaptation	p. 118
The R&ohat;le of Memory	p. 119
The Integrating R&ohat;le of Directive Correlation	p. 119
Regulation	p. 120
The Concept of Machine	p. 121
The Architecture of Functional Systems	p. 122
The Nature of Living Things	p. 123
The Cell	p. 123
The Structure of a Cell	p. 125
Observational Overview	p. 125
Metabolism	p. 127
The Cell Cycle	p. 128
The Chromosome	p. 130
The Structure of Genome and Genes	p. 133
The C-Value Paradox	p. 136
The Structure of the Chromosome	p. 139
The Immune System	p. 140
Molecular Mechanisms	p. 141
Replication	p. 141
Proofreading and Repair	p. 142
Recombination	p. 143
Summary of Sources of Genome Variation	p. 145
Gene Expression	p. 145
Transcription	p. 146
Regulation of Transcription	p. 146
Prokaryotic Transcriptional Regulation	p. 147
Eukaryotic Transcriptional Regulation	p. 147
mRNA Processing	p. 149
Translation	p. 150
Ontogeny (Development)	p. 151
Stem Cells	p. 152
Epigenesis	p. 153
r and K Selection	p. 154
Homeotic Genes	p. 155
Phylogeny and Evolution	p. 155
Models of Evolution	p. 158
Sources of Genome Variation	p. 160
The Origin of Proteins	p. 160
Geological Eras and Taxonomy	p. 161
The Molecules of Life	p. 163
Molecules and Supramolecular Structure	p. 163
Water	p. 165
DNA	p. 166
RNA	p. 171
Proteins	p. 172
Amino Acids	p. 173
Protein Folding and Interaction	p. 175
Experimental Techniques for Protein Structure Determination	p. 178
Protein Structure Overview	p. 179
Polysaccharides	p. 179
Lipids	p. 180
Applications
Introduction to Part III	p. 185
Genomics	p. 189
DNA Sequencing	p. 190
Extraction of Nucleic Acids	p. 190
The Polymerase Chain Reaction	p. 191
Sequencing	p. 191
Expressed Sequence Tags	p. 192
DNA Methylation Profiling	p. 193
Gene Identification	p. 193
Extrinsic Methods	p. 194
Database Reliability	p. 194
Sequence Comparison and Alignment	p. 194
Dynamic Programming Algorithms	p. 196
Intrinsic Methods	p. 197
Signals	p. 198
Hidden Markov Models	p. 199
Beyond Sequence	p. 199
Minimalist Approaches	p. 200
Nucleotide Frequencies	p. 200
Word Occurrences	p. 201
Phylogenies	p. 202
Proteomics	p. 205
Transcriptomics	p. 206
Limitations	p. 210
Proteomics	p. 211
Two-Dimensional Gel Electrophoresis	p. 212
Column Chromatography	p. 213
Other Kinds of Electrophoresis	p. 214
Protein Identification	p. 214
Isotope-Coded Affinity Tags	p. 215
Protein Microarrays	p. 216
Protein Expression Patterns	p. 217
The Kinome	p. 218
Interactomics: Interactions and Regulatory Networks	p. 221
Inference of Regulatory Networks	p. 225
The Physical Chemistry of Interactions	p. 226
Intermolecular Interactions	p. 228
Time-Dependent Rate "Constants"	p. 229
Specificity	p. 230
Nonspecific Interactions	p. 230
Cooperative Binding	p. 230
Sustained Activation	p. 231
In vivo Experimental Methods	p. 232
The Yeast Two-Hybrid Assay	p. 232
Crosslinking	p. 233
Correlated Expression	p. 233
Other Methods	p. 234
In vitro Experimental Methods	p. 234
Chromatography	p. 235
Direct Affinity Measurement	p. 235
Protein Chips	p. 237
Interactions from Sequence	p. 237
Global Statistics of Interactions	p. 238
Metabolomics and Metabonomics	p. 239
Data Collection	p. 240
Data Analysis	p. 241
Metabolic Regulation	p. 242
Metabolic Control Analysis	p. 242
The Metabolic Code	p. 243
Metabolic Networks	p. 243
Medical Applications	p. 245
The Genetic Basis of Disease	p. 246
Cancer	p. 247
Toward Automated Diagnosis	p. 249
Drug Discovery and Testing	p. 249
Personalized Medicine	p. 251
The Organization of Knowledge	p. 253
Ontology	p. 254
Knowledge Representation	p. 255
The Problem of Bacterial Identification	p. 256
Text Mining	p. 257
Bibliography	p. 259
Index	p. 267
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