Ramsden Bioinformatics

An Introduction
2. Auflage 2009
ISBN: 978-1-84800-257-9
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 10, 272 Seiten

Reihe: Computational Biology

The field of bioinformatics continues to develop energetically. This second edition covers new findings using the formula of the original text. It is self-contained, bringing together the multiple disciplines necessary for a profound grasp of the field.

Autoren/Hrsg.

Ramsden, Jeremy

Inhaltsverzeichnis

1;Preface to the Second Edition;7
2;Preface;9
3;Contents;11
4;Introduction;17
4.1;1.1 What is Bioinformatics?;18
4.2;1.2 What Can Bioinformatics Do?;19
5;Part I Information;22
5.1;The Nature of Information;23
5.1.1;2.1 Structure and Quantity;29
5.1.2;2.2 Constraint;31
5.1.3;2.3 Accuracy, Meaning, and Effect;37
5.1.4;2.4 Further Remarks on Information Generation;42
5.1.5;2.5 Summary;43
5.2;The Transmission of Information;45
5.2.1;3.1 The Capacity of a Channel;47
5.2.2;3.2 Coding;49
5.2.3;3.3 Decoding;51
5.2.4;3.4 Compression;52
5.2.5;3.5 Noise;56
5.2.6;3.6 Error Correction;58
5.2.7;3.7 Summary;60
5.3;Sets and Combinatorics;61
5.3.1;4.1 The Notion of Set;61
5.3.2;4.2 Combinatorics;61
5.3.3;4.3 The Binomial Theorem;65
5.4;Probability and Likelihood;66
5.4.1;5.1 The Notion of Probability;66
5.4.2;5.2 Fundamentals;67
5.4.3;5.3 Moments of Distributions;74
5.4.4;5.4 Likelihood;78
5.4.5;5.5 The Maximum Entropy Method;81
5.5;Randomness and Complexity;82
5.5.1;6.1 Random Processes;85
5.5.2;6.2 Markov Chains;86
5.5.3;6.3 Random Walks;88
5.5.4;6.4 Noise;90
5.5.5;6.5 Complexity;91
5.6;Systems, Networks, and Circuits;96
5.6.1;7.1 General Systems Theory;97
5.6.2;7.2 Networks (graphs);102
5.6.3;7.3 Synergetics;106
5.6.4;7.4 Evolutionary Systems;109
5.7;Algorithms;111
5.7.1;8.1 Evolutionary Computing;112
5.7.2;8.2 Pattern Recognition;113
5.7.3;8.3 Botryology;114
5.7.4;8.4 Multidimensional Scaling and Seriation;119
5.7.5;8.5 Visualization;122
6;Part II Biology;124
6.1;Introduction to Part II;125
6.1.1;9.1 Genotype, Phenotype, and Species;125
6.1.2;9.2 Adaptation;127
6.1.3;9.3 Timescales of Adaptation;128
6.1.4;9.4 Regulation;130
6.1.5;9.5 The Concept of Machine;131
6.1.6;9.6 The Architecture of Functional Systems;132
6.2;The Nature of Living Things;133
6.2.1;10.1 The Cell;133
6.2.2;10.2 Metabolism;137
6.2.3;10.3 The Cell Cycle;138
6.2.4;10.4 The Immune System;150
6.2.5;10.5 Molecular Mechanisms;151
6.2.6;10.6 Gene Expression;155
6.2.7;10.7 Ontogeny (Development);161
6.2.8;10.8 Phylogeny and Evolution;165
6.3;The Molecules of Life;172
6.3.1;11.1 Molecules and Supramolecular Structure;172
6.3.2;11.2 Water;174
6.3.3;11.3 DNA;175
6.3.4;11.4 RNA;180
6.3.5;11.5 Proteins;181
6.3.6;11.6 Polysaccharides;188
6.3.7;11.7 Lipids;189
7;Part III Applications;191
7.1;Introduction to Part III;192
7.2;Genomics;195
7.2.1;13.1 DNA Sequencing;196
7.2.2;13.2 DNA Methylation Profiling;199
7.2.3;13.3 Gene Identification;199
7.2.4;13.4 Extrinsic Methods;200
7.2.5;13.5 Intrinsic Methods;203
7.2.6;13.6 Beyond Sequence;205
7.2.7;13.7 Minimalist Approaches;206
7.2.8;13.8 Phylogenies;208
7.3;Proteomics;211
7.3.1;14.1 Transcriptomics;212
7.3.2;14.2 Proteomics;217
7.3.3;14.3 Protein Identification;220
7.3.4;14.4 Isotope-Coded Affinity Tags;221
7.3.5;14.5 Protein Microarrays;222
7.3.6;14.6 Protein Expression Patterns;223
7.3.7;14.7 The Kinome;224
7.4;Interactomics: Interactions and Regulatory Networks;226
7.4.1;15.1 Inference of Regulatory Networks;230
7.4.2;15.2 The Physical Chemistry of Interactions;231
7.4.3;15.3 Intermolecular Interactions;233
7.4.4;15.4 In vivo Experimental Methods;237
7.4.5;15.5 In vitro Experimental Methods;239
7.4.6;15.6 Interactions from Sequence;242
7.4.7;15.7 Global Statistics of Interactions;243
7.5;Metabolomics and Metabonomics;244
7.5.1;16.1 Data Collection;245
7.5.2;16.2 Data Analysis;246
7.5.3;16.3 Metabolic Regulation;247
7.5.4;16.4 Metabolic Networks;248
7.6;Medical Applications;250
7.6.1;17.1 The Genetic Basis of Disease;251
7.6.2;17.2 Cancer;252
7.6.3;17.3 Toward Automated Diagnosis;254
7.6.4;17.4 Drug Discovery and Testing;254
7.6.5;17.5 Personalized Medicine;256
7.7;The Organization of Knowledge;257
7.7.1;18.1 Ontology;258
7.7.2;18.2 Knowledge Representation;259
7.7.3;18.3 The Problem of Bacterial Identification;260
7.7.4;18.4 Text Mining;261
8;Bibliography;263
9;Index;270