• eukaryotic genomes
• epigenomics
• translational genomics and biomarker development

Genes and Genomes

1. Fundamentals of Structure-Function Analysis of Eukaryotic Protein-Coding Genes

• Structure and Function of Typical Eukaryotic Protein-Coding Gene

2. The Eukaryotic Genome: A Brief Overview of Structure, Function, and Evolution

• Introduction—The Scope of Genomics
• Nucleoprotein Organization of the Genome
• Genomic DNA as a Mosaic of Isochores
• Genomic Landscape as Revealed by Genome Sequencing
• Chromosomal Synteny and Synthenic Maps in Comparative Genomics

• Molecular Basis of Epigenetic Regulation
• Examples of Epigenetic Regulation of Gene and Genome Expression

4. Principles of Functional Genomic Analysis

• Sequencing by Synthesis—Sanger Method
• Sequencing by Chemical Cleavage—Maxam and Gilbert Method
• Sequencing by Hybridization—ED Southern Method
• Sequencing by Synthesis—Pal Nyren's Pyrosequencing Method
• Applications of Pyrosequencing
• Next Generation Sequencing—$1,000 Per Genome?
• Principles of Protein Separation
• Principles of Protein Identification
• Principles of Protein Structure and Determination

5. Toxicogenomics in Non-Clinical Safety Studies: Models of Animal and Human Tissues to Assess Target Organ Injury

• Introduction—Translational Research and Research Models
• New Approaches and Models for Mechanistic Insight
• Value of In Vitro Models
• Toxicogenomics in Translational Research—Animal and Human Models (in Vivo and In Vitro)

• Identification of Disease-Related Genes by Database Mining

7. Functional Genomic Approaches for Studying Genotoxicity and Carcinogenesis

• Transcriptomics
• Functional Genomics

8. Human Genomics in Hypertension

• Intermediate Phenotypes and Heritability in Hypertension
• Systematic Polymophism Discovery at the Candidate Genetic Loci Susceptible for Hypertension
• Genome-Wide Linkage Studies in Hypertension
• Genome-Wide Association Studies in Hypertension
• Gene-by-Sex Interaction in Hypertension
• Adrenergic Pathway Polymorphisms and Hypertension
• Renin-Angiotensin-Aldosterone System and Hypertension
• Metabolic Syndrome and Hypertension
• Endothelium and Vascular Dysfunction in Hypertension
• Cardio-Renal Target Organ Susceptibility Genes and Hypertension
• Pleiotropy and Hypertension
• Epistasis and Hypertension
• Heterosis and Hypertension
• Pharmacogenetics—Antihypertensive Drugs
• Mechanistic Studies on Trait-Associated Genetic Variants
• Transcriptomics in Hypertension
• Perspectives and Strategies

• Immune Suppression
• Specific Application of Genomics Techniques as a Discovery Tool to Investigate Targeted Pathways in Immune Suppression
• Screening for Dermal Sensitizers
• Relating Genetic Variability and Host Susceptibility to Immune-Mediated Diseases
• Genomics Applications in Discovery—a Tool in the Development of Immunomdulatory Therapeutics
• Hazard Identification and Risk Characterization

10. Statistical Methods for Functional Anaylsis of 'Omics Experimental Data

• Enrichment Analysis of High-Content Data
• Analyzing Condition-Specific Networks
• Network Meaures

• Public Toxicogenomics Databases
• Types of Data
• Archiving 'Omics Data
• Cheminformatics Data
• Sharing Data
• Characteristics of "Ideal" Database

12. Phenotypic Microarray Approaches to the Study of Prokaryotes

• The Phenotypic Microarray System
• Phenotypic Mcroarray Studies with E. coli K-12 Mutants Deleted for all Two-Component Systems
• Deciphering the Function of the b1012 Operon in E. Coli K-12
• Investigation of Phenotypic Changes in Rifampicin-Resistant rpoB Mutants of Bacillus Subtilis
• Identifying Phenotypic Markers to Distinguish Foodborne Enteric Pathogens

13. Functional Analysis and Genomics of G-Protein-Coupled Receptors

• GPCR Structural Features and Pharmacology
• Receptor Functional Screening Strategies
• Functional Genomics and Characterization of Orphan GPCRs
• GPCR Dimerization and Allosteric Activation
• GPCR Mutations in Human Diseases and Natural Variants

14. Nutrigenomics: A Genomic Approach to Human Nutrition

• Applied Genomics—Pharmacogenomics and Nutrigenomics in Health Care
• Nutrient-Gene Interactions
• Paradigm Shift from Health-Care to Self-Care and the Current State of Personalized Nutrition
• Public Perceptions and the Future of Nutrigenomics
• New Applications of Genomic Technologies
• Moving Forward

Use of Genomics Data by the Regulatory Agencies

15. Collaborations Lay the Critical Path to Acceptance of Genomics in Drug Safety Assessment

• Forums for Collaboration
• Microarray Technology Performance
• Microarray Applications in Risk Assessment and Regulatory Concerns
• Advancing the Science

16. Application of Pharmacogenetics and Pharmacogenomics in Drug Development and Regulatory Review

• Type of Genomic Data that Qualifies as Valid Biomarkers
• Drug Interactions
• Voluntary Versus Required Submissions
• Qualification of Biomarkers
• Genetic Tests
• Drug/Test Codevelpment
• Clinical Study Design
• Labeling Implications

17. Potential Use of Microarray Technology at the U.S. Environmental Protection Agency

• Applicability of Gneomics Tehcnology in Regulatory Application
• The Potential of Microarray Data
• limitations of Microarray Technology
• Data Submission condierations
• Research Utilizing Microarrray Technology
• Potential Integration of Microarray Data into EPA'S Regulatory Applications
• Microarray Applications and Challenges in Risk Assessment
• Collaborations to Standardized the Field of Microarray Technology
• Outlook on Microarray Technology

The Promise of Genomics

18. Genomics: The State of the Science

• From Genes to Genomics
• Genomic Data, Databases, and Statistical Analysis
• Current Applications and Future Promises of Genomics
• Genomics and Regulatory Agencies
• Genomics—The State of the Science

Index