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