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Introduction to genomics / Arthur M. Lesk. — 2nd ed. — Oxford : Oxford University Press, c2012. – (58.1481/L629/2nd ed.) |
Contents
CONTENTS
Preface to the first edition
Preface to the second edition
Plan of the second edition
New to this edition
Recommended reading
Introduction to genomics on the web
Acknowledgements
Sections marked with * are clinically related
1 Introduction to Genomics
The human genome
Contents of the human genome
Genes that encode the proteome
Varieties of genome organization
Genome sequencing projects
Variations within and between populations
Human genome sequencing
The human genome and medicine*
The evolution and development of databases
Protein evolution: divergence of sequences and structures within and between species
Ethical, legal, and social issues (*, partly)
Recommended Reading
Exercises, Problems, and Weblems
2 Genomes are the Hub of Biology
Individuals, populations, the biosphere: past, present, and future
The central dogma, and peripheral ones
Expression patterns
Populations
Genetic diseases - some examples of their causes and treatment*
Species
The biosphere
Recommended Reading
Exercises, Problems, and Weblems
3 Mapping, Sequencing, Annotation, and Databases
Classical genetics as background
Maps and tour guides
Discovery of the structure of DNA
DNA sequencing
Organizing a large-scale sequencing project
Databanks in molecular biology
Recommended Reading
Exercises, Problems, and Weblems
4 Comparative Genomics
Introduction
Unity and diversity of life
Sizes and organization of genomes
Viral genomes
Genome organization in prokaryotes
Genome organization in eukaryotes
How genomes differ
What makes us human?
Genomes of chimpanzees and humans
Genomes of mice and rats
Model organisms for study of human diseases*
The ENCODE project
Recommended Reading
Exercises, Problems, and Weblems
5 Evolution and Genomic Change
Evolution is exploration
Biological systematics
Homologues and families
Pattern matching - the basic tool of bioinformatics
Evolution of protein sequences, structures, and functions
Phylogeny
Short-circuiting evolution: genetic engineering
Recommended Reading
Exercises, Problems, and Weblems
6 Genomes of Prokaryotes
Evolution and phylogenetic relationships in prokaryotes
Archaea
Bacteria
Metagenomics: the collection of genomes in a coherent environmental sample
Recommended Reading
Exercises, Problems, and Weblems
7 Genomes of Eukaryotes
The origin and evolution of eukaryotes
Evolution and phylogenetic relationships in eukaryotes
Palaeosequencing - ancient DNA
DNA from extinct birds
High-throughput sequencing of mammoth DNA
Recommended Reading
Exercises, Problems, and Weblems
8 Genomics and Human Biology
Genomics in personal identification
The domestication of crops
Genomics in anthropology
Genomics and language
Recommended Reading
Exercises, Problems, and Weblems
9 Microarrays and Transcriptomics
Introduction
Analysis of microarray data
Expression patterns in different physiological states
Expression pattern changes in development
Expression patterns in learning and memory: long-term potentiation
Evolutionary changes in expression patterns
Applications of microarrays in medicine*
Whole transcriptome shotgun sequencing: RNA-seq
Recommended Reading
Exercises, Problems, and Weblems
10 Proteomics
Introduction
Protein nature and types
Protein structure
Post-translational modifications
Separation and analysis of proteins
Classification of protein structures
Many proteins change conformation as part of the mechanism of their function
Protein structure prediction and modelling
Directed evolution and protein design
Protein complexes and aggregates
Recommended Reading
Exercises, Problems, and Weblems
11 Systems Biology
Introduction to systems biology
Pictures of networks as graphs
Sources of ideas for systems biology
The metabolome
Regulatory networks
Dynamics, stability, and robustness
Protein interaction networks
Protein-DNA interactions
Gene regulation
The genetic regulatory network of Saccharomyces cerevisiae
Recommended Reading
Exercises, Problems, and Weblems
Epilogue
Index