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Copyright, iv
Preface, xi
1. Genome Projects: Organization and Objectives, 1
The Core Aims of Genome Science, 1
Mapping Genomes, 4
Genetic Maps, 4
EXERCISE 1.1 Constructing a genetic map, 7
Physical Maps, 8
Cytological Maps, 8
Comparative Genomics, 10
The Human Genome Project, 13
Objectives, 13
The Content of the Human Genome, 16
BOX 1.1 The Ethical, Legal, and Social Implications of the Human Genome Project, 18
EXERCISE 1.2 Use the NCBI and Ensembl genome browsers to examine a human disease gene, 22
Internet Resources, 22
BOX 1.2 GenBank Files, 26
Animal Genome Projects, 28
Primate Genome Projects, 28
Rodent Genome Projects, 30
EXERCISE 1.3 Compare the structure of a gene in a mouse and a human, 33
Other Vertebrate Biomedical Models, 34
Animal Breeding Projects, 35
Invertebrate Model Organisms, 36
BOX 1.3 Managing and Distributing Genome Data, 40
Plant Genome Projects, 40
Arabidopsis thaliana, 40
Grasses and Legumes, 44
Other Flowering Plants, 46
Microbial Genome Projects, 48
The Minimal Genome, 48
Sequenced Microbial Genomes, 51
EXERCISE 1.4 Compare two microbial genomes using the CMR, 53
Yeast, 54
EXERCISE 1.5 Examining a gene in the Saccharomyces Genome Database, 56
Metagenomics, 59
Summary, 60
Discussion Questions, 61
Literature Cited, 62
2. Genome Sequencing and Annotation, 65
Automated DNA Sequencing, 65
The Principle of Sanger Sequencing, 65
High-Throughput Sequencing, 68
Reading Sequence Traces, 68
EXERCISE 2.1 Reading a sequence trace, 71
Contig Assembly, 71
BOX 2.1 Pairwise Sequence Alignment, 74
EXERCISE 2.2 Computing an optimal sequence alignment, 78
Emerging Sequencing Methods: The Next Generation, 79
Genome Sequencing, 83
Hierarchical Sequencing, 84
Shotgun Sequencing, 88
BOX 2.2 Searching Sequence Databases Using BLAST, 90
Sequence Verification, 94
Genome Annotation, 95
EST Sequencing, 95
Ab Initio Gene Discovery, 98
BOX 2.3 Hidden Markov Models and Gene Finding, 100
Regulatory Sequences, 103
Non-Protein Coding Genes, 104
Structural Features of Genome Sequences, 107
Functional Annotation and Clusters of Gene Families, 113
EXERCISE 2.3 Perform a BLAST search, 114
Clustering of Genes by Sequence Similarity, 114
Clusters of Orthologous Genes, 116
Phylogenetic Classification of Genes, 119
BOX 2.4 Phylogenetics, 120
EXERCISE 2.4 A simple phylogenetic analysis, 123
Gene Ontology, 124
BOX 2.5 Gene Ontologies, 126
Summary, 128
Discussion Questions, 130
Web Site Exercises, 130
Literature Cited, 131
3. Genomic Variation, 133
The Nature of Single Nucleotide Polymorphisms, 133
Classification of SNPs, 133
Distribution of SNPs, 136
Linkage Disequilibrium and Haplotype Maps, 138
BOX 3.1 Disequilibrium between Alleles at Two Loci, 139
EXERCISE 3.1 Quantifying heterozygosity and LD, 143
Applications of SNP Technology, 146
Population Genetics, 146
BOX 3.2 The Coalescent, 148
Recombination Mapping, 152
EXERCISE 3.2 Inferring haplotype structure, 154
QTL Mapping, 155
Linkage Disequilibrium Mapping, 158
BOX 3.3 Case-Control Association Studies, 164
BOX 3.4 Family-Based Association Tests, 167
EXERCISE 3.3 Perform a case-control association test, 170
BOX 3.5 Genome-Wide Association Studies, 173
SNP Genotyping, 177
SNP Discovery, 177
SNP Genotyping, 178
EXERCISE 3.4 Designing a genotyping assay for a double polymorphism, 183
High-throughput genotyping platforms, 183
Haplotype phasing methods, 185
Summary, 186
Discussion Questions, 187
Web Site Exercises, 187
Literature Cited, 188
4. Gene Expression and the Transcriptome, 191
Parallel Analysis of Gene Expression: Microarrays, 191
Applications of Microarray Technology, 192
Experimental Design, 194
EXERCISE 4.1 Design a microarray experiment, 196
Microarray Technologies, 198
Labeling and Hybridization of cDNAs, 205
Statistical Analysis of cDNA Microarray Data, 207
EXERCISE 4.2 Calculate which genes are differentially exposed, 209
BOX 4.1 Microarray Image Processing, 211
BOX 4.2 Basic Statistical Methods, 214
EXERCISE 4.3 Evaluate the significance of the following gene expression differences, 217
Microarray Data Mining, 220
BOX 4.3 Clustering Methods, 221
EXERCISE 4.4 Perform a cluster analysis on gene expression profiles, 224
ChIP Chips and Gene Regulation, 225
DNA Applications of Microarrays, 227
BOX 4.4 Motif Detection in Promoter Sequences, 228
Parallel Analysis of Gene Expression: RNA Sequencing, 231
Serial Analysis of Gene Expression, 231
RNA-Seq, 234
Single-Gene Analyses, 236
Northern Blots, 236
Quantitative PCR, 237
Properties of Transcriptomes, 239
Microbial Transcriptomics, 239
Cancer and Clinical Applications, 243
Development, Physiology, and Behavior, 246
Evolutionary and Ecological Functional Genomics, 248
Gene Expression Databases, 252
Summary, 253
Discussion Questions, 255
Web Site Exercises, 255
Literature Cited, 256
5. Proteomics and Functional Genomics, 259
Functional Proteomics, 259
Protein Annotation, 259
EXERCISE 5.1 Structural annotation of a protein, 262
BOX 5.1 Hidden Markov Models in Domain Profiling, 264
Protein Separation and 2D-PAGE, 267
Mass Spectrometry, 270
EXERCISE 5.2 Identification of a protein on the basis of a mass spectrometry profile, 273
Immunochemistry, 276
Protein Microarrays, 277
Protein Interaction Maps, 280
EXERCISE 5.3 Formulating a network of protein interactions, 281
BOX 5.2 Biological Networks in Genome Science, 283
Structural Proteomics, 286
Objectives of Structural Proteomics, 286
Protein Structure Determination, 288
Protein Structure Prediction and Threading, 291
Functional Genomics, 294
Saturation Forward Genetics, 295
High-Throughput Reverse Genetics, 300
BOX 5.3 Transgenic Animals and Plants, 304
Fine-Structure Genetics, 308
EXERCISE 5.4 Designing a genetic screen, 309
Genetic Fingerprinting, 314
Summary, 317
Discussion Questions, 318
Web Site Exercises, 319
Literature Cited, 319
6. Integrative Genomics, 323
Metabolomics, 325
Analysis of Cellular Constituents, 325
Metabolic Profiling, 328
Metabolic and Biochemical Databases, 331
In Silico Genomics, 333
Metabolic Control Analysis, 333
Systems-Level Modeling of Gene Networks, 338
Summary, 342
Discussion Questions, 343
Literature Cited, 343
Glossary, 345
List of Abbreviations, 355
Index, 357

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