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Paperback: 370 pages
1. Genome Projects: Organization and Objectives

The Core Aims of Genome Science
Mapping Genomes
Genetic Maps
Exercise 1.1. Constructing a genetic map
Physical Maps
Cytological Maps
Comparative Genomics
The Human Genome Project
Objectives
The Content of the Human Genome
Internet Resources
Exercise 1.2. Use the NCBI and Ensembl Genome Browsers to examine a human disease gene
Animal Genome Projects
Primate Genome Projects
Rodent Genome Projects
Exercise 1.3. Compare the structure of a gene in mouse and human
Other Vertebrate Biomedical Models
Animal Breeding Projects
Invertebrate Model Organisms
Plant Genome Projects
Arabidopsis thaliana
Grasses and Legumes
Other Flowering Plants
Microbial Genome Projects
The Minimal Genome
Sequenced Microbial Genomes
Exercise 1.4. Compare two microbial genomes using the CMR
Metagenomics
Yeast
Exercise 1.5. Examining a gene in the Saccharomyces Genome Database
Parasite Genomics
Summary
Discussion Questions
Literature Cited
BOXES
Ethical, Legal, and Social Implications of the Human Genome Project
GenBank Files
Managing and Distributing Genome Data

2. Genome Sequencing and Annotation

Automated DNA Sequencing
The Principle of Sanger Sequencing
High-Throughput Sequencing
Reading Sequence Traces
Exercise 2.1. Reading a sequence trace
Contig Assembly
Exercise 2.2. Computing an optimal sequence alignment
Emerging “Next Generation” Sequencing Methods
Genome Sequencing
Hierarchical Sequencing
Shotgun Sequencing
Sequence Verification
Genome Annotation
EST Sequencing
Ab initio Gene Discovery
Regulatory Sequences
Non-Protein Coding Genes
Structural Features of Genome Sequences
Functional Annotation and Clusters of Gene Families
Exercise 2.3. Perform a BLAST search
Clustering of Genes by Sequence Similarity
Clusters of Orthologous Genes
Phylogenetic Classification of Genes
Exercise 2.4. Simple phylogenetic analysis of a short sequence
Gene Ontology
Summary
Discussion Questions
Web Site Exercises
Literature Cited
BOXES
Pairwise Sequence Alignment
Searching Sequence Databases Using BLAST
Hidden Markov Models and Gene Finding
Phylogenetics
Gene Ontologies

3. Genomic Variation

The Nature of Single Nucleotide Polymorphisms
Classification
Distribution of SNPs
Linkage Disequilibrium and Haplotype Maps
Exercise 3.1. Quantitfying heterozygosity and LD
Applications of SNP technology
Population Genetics
Recombination Mapping
Exercise 3.2. Inferring haplotype structure
QTL Mapping
Linkage Disequilibrium Mapping
Exercise 3.3. Perform a case-control association test
SNP Genotyping
SNP Discovery
SNP Genotyping
Exercise 3.4. Design a genotyping assay for a double polymorphism
High-Throughput Genotyping Platforms
Haplotype Phasing Methods
Summary
Discussion Questions
Web Site Exercises
Literature Cited
BOXES
Disequilibrium between Alleles at Two Loci
The Coalescent
Case-Control Association Studies
Family-Based Association Tests

4. Gene Expression and the Transcriptome

Parallel Analysis of Gene Expression: Microarrays
Applications of Microarray Technology
Experimental Design
Exercise 4.1. Design a microarray experiment
Microarray Technologies
Labeling and Hybridization of cDNAs
Statistical Analysis of cDNA Microarray Data
Exercise 4.2. Calculate which of the following genes are differentially expressed
Exercise 4.3. Evaluate the significance of the following gene expression differences
Microarray Data Mining
Exercise 4.4. Perform a cluster analysis on gene expression profiles
ChIP Chips and Gene Regulation
DNA Applications of Microarrays
Parallel Analysis of Gene Expression: RNA-Sequencing
Serial Analysis of Gene Expression
RNA-Seq
Single-Gene Analyses
Northern Blots
Quantitative PCR
Properties of Transcriptomes
Microbial Transcriptomics
Cancer and Clinical Applications
Development, Physiology, and Behavior
Evolutionary and Ecological Functional Genomics
Gene Expression Databases
Summary
Discussion Questions
Web Site Exercises
Literature Cited
BOXES
Microarray Image Processing
Basis Statistics
Clustering Methods
Motif Detection in Promoter Sequences of Gene Clusters

5. Proteomics and Functional Genomics

Functional Proteomics
Protein Annotation
Exercise 4.1. Structural annotation of a protein
Protein Separation and 2D-PAGE
Mass Spectrometry
Exercise 4.2. Identification of a protein on the basis of a MS profile
Immunochemistry
Protein Microarrays
Protein Interaction Maps
Exercise 4.3. Formulating a network of protein interactions
Structural Proteomics
Objectives of Structural Proteomics
Protein Structure Determination
Protein Structure Prediction and Threading
Functional Genomics
Saturation Forward Genetics
High-Throughput Reverse Genetics
Fine-Structure Genetics
Exercise 4.4. Designing a genetic screen
Genetic Fingerprinting
Summary
Discussion Questions
Web Site Exercises
Literature Cited
BOXES
Hidden Markov Models in Domain Profiling
Network Theory
Transgenic Animals and Plants

6. Integrative Genomics

Metabolomics
Analysis of Cellular Constituents
Metabolic profiling
Metabolic and Biochemical Databases
In silico Genomics
Metabolic Control Analysis
Systems-Level Modeling of Gene Networks
Summary
Discussion Questions
Literature Cited
BOXES
Mathematical Modeling of Biochemical Pathways
Genome-wide Association Studies

Glossary
Index