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| Preface | |
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| Genome Projects: Organization and Objectives | |
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| The Core Aims of Genome Science | |
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| Mapping Genomes | |
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| Genetic Maps | |
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| Physical Maps | |
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| Cytological Maps | |
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| Comparative Genomics | |
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| The Human Genome Project | |
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| Objectives | |
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| The Content of the Human Genome | |
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| Internet resources | |
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| Animal Genome Projects | |
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| Mouse Genome Projects | |
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| Other Vertebrate Biomedical Models | |
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| Animal Breeding Projects | |
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| Invertebrate Model Organisms | |
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| Plant Genome Projects | |
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| Arabidopsis thaliana | |
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| Grasses and Legumes | |
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| Other Flowering Plants | |
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| Genome Projects | |
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| The Minimal Genome | |
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| Bacteria and Archaea | |
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| Yeast | |
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| Parasite Genomics | |
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| Summary | |
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| Discussion Questions | |
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| Literature Cited | |
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| Genome Sequencing and Annotation | |
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| Automated DNA Sequencing | |
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| The Principle of Sanger Sequencing | |
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| High-Throughput Sequencing | |
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| Reading Sequence Traces | |
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| Contig Assembly | |
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| Emerging Sequencing Methods | |
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| Genome Sequencing | |
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| Hierarchical Sequencing | |
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| Shotgun Sequencing | |
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| Sequence Verification | |
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| Genome Annotation | |
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| EST Sequencing | |
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| Ab initio Gene Discovery | |
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| Non-Protein Coding Genes | |
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| Structural Features of Genome Sequences | |
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| Functional Annotation and Gene Family Clusters | |
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| Clustering of Genes by Sequence Similarity | |
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| Clusters of Orthologous Genes | |
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| Phylogenetic Classification of Genes | |
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| Gene Ontology | |
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| Summary | |
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| Discussion Questions | |
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| Web Site Exercises | |
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| Literature Cited | |
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| Gene Expression and the Transcriptome | |
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| Parallel Analysis of Gene Expression: Microarrays | |
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| cDNA Microarray Technology | |
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| Statistical Analysis of cDNA Microarray Data and Experimental Design | |
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| Oligonucleotide Microarray Technology | |
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| Microarray Data Mining | |
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| SAGE, Microbeads, and Differential Display | |
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| Serial Analysis of Gene Expression | |
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| Microbead Technology | |
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| Differential Display | |
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| Single-Gene Analyses | |
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| Northern Blots and RNAse Protection | |
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| Quantitative PCR | |
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| Properties of Transcriptomes | |
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| Yeast | |
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| Cancer | |
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| Model Organisms | |
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| Gene Expression Databases | |
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| Summary | |
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| Discussion Questions | |
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| Web Site Exercises | |
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| Literature Cited | |
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| Proteomics and Functional Genomics | |
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| Functional Proteomics | |
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| Protein Annotation | |
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| Protein Separation and 2D-PAGE | |
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| Mass Spectrometry and Protein Identification | |
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| Protein Microarrays | |
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| Protein Interaction Maps | |
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| Structural Proteomics | |
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| Objectives of Structural Proteomics | |
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| Protein Structure Determination | |
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| Protein Structure Prediction and Threading | |
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| Functional Genomics | |
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| Saturation Forward Genetics | |
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| High-Throughput Reverse Genetics | |
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| Fine-Structure Genetics | |
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| Genetic Fingerprinting | |
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| Summary | |
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| Discussion Questions | |
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| Web Site Exercises | |
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| Literature Cited | |
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| SNPs and Variation | |
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| The Nature of Single Nucleotide Polymorphisms | |
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| Classification | |
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| Distribution of SNPs | |
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| Applications of SNP Technology | |
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| Population Genetics | |
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| Recombination Mapping | |
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| QTL Mapping | |
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| Linkage Disequilibrium Mapping | |
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| SNP Discovery | |
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| Resequencing | |
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| Sequence-Free Polymorphism Detection | |
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| SNP Genotyping | |
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| Low-Technology Methods | |
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| Hybridization-Based Methods | |
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| Minisequencing Methods | |
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| Homogeneous Fluorogenic Dye-Based Methods | |
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| Haplotype phasing methods | |
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| Summary | |
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| Discussion Questions | |
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| Web Site Exercises | |
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| Literature Cited | |
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| Integrative Genomics | |
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| Metabolomics | |
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| Analysis of Cellular Constituents | |
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| Metabolic and Biochemical Databases | |
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| In silico Genomics | |
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| Metabolic Control Analysis | |
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| Systems-Level Modeling of Gene Networks | |
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| Summary | |
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| Discussion Questions | |
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| Literature Cited | |
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| Glossary | |
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| List of Abbreviations | |
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| Index | |