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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 | |