Bioinformatics and Computational Biology: Bottlenecks and Options

Table of Contents

Chapter One

• INTRODUCTION TO BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
• 1.1. Definitions; Principle and Applications
• What are Bioinformatics and Computational Biology?
• What Is an Algorithm?
• Heuristics
• Approximation Algorithms for Parsimony Models
• Neural Networks
• Markov Chains
• B&CB Application of Markov Chain Modeling
• B&CB Application of Markov Chain Modeling to Timing of Antiretroviral Therapy
• Markov Chain Monte Carlo Algorithms
• 1.2. Scope of the Fields
• Overview of Presently Available Software Tools
• Managing Terabytes of Data
• 1.3. Product Categories
• Content Databases
• Data Mining
• Analytical Software and Services
• 1.4. Subsequent Chapters

Chapter Two

• TEAMING BIOINFORMATICS AND POWERFUL HARDWARE
• 2.1. Biomedical Imagery Hardware
• Computerized Axial Tomography
• Magnetic Resonance Imaging
• Positron Emission Tomography
• Ultrasonography
• 2.2. Mass Spectrometry
• Theoretical Basis
• Bioinformatics Applications
• Sample Preparation for Mass Spectrometry
• 2.3. X-ray Crystallography
• 2.4. High-throughput Image Analysis
• 2.5. Sequencing
• 2.6. Microarrays
• 2.7. The Future of Imaging and B&CB

Chapter Three

• OVERVIEW OF BIOINFORMATICS-DRIVEN APPLICATIONS
• 3.1. Genes, Genomes and Genomics
• 3.2. The Human Genome
• DNA Sequence Analysis
• Alignment
• Databases
• 3.3. Disease Determination
• Alzheimer' s Disease
• Other Genomes
• Comparative Genomics
• 3.4. Gene Regulation
• The Proteome and Proteomics
• Protein Structure Alignment
• Protein Structure Prediction
• Protein-Protein Interactions
• Clustering Algorithms
• The Future of the Proteome
• 3.5. Systems Biology
• 3.6. Biomedical Informatics
• Infectious Diseases and B&CB
• Epidemiology
• Institutional Support for Infectious Disease B&CB
• Population Dynamics of Drug Resistance
• Immunoinformatics
• 3.7. The Nature of Cancer and the Contributions of B&CB to its Elucidation
• Analysis of Mutations in Cancer
• Cancer Biomarkers
• Analysis of Bladder Cancer
• 3.8. Pharma Investigations
• Cheminformatics
• Drug Discovery
• New Uses for Existing Drugs
• Chiral Pharmaceuticals
• Natural Products as New Therapeutics
• In Silico Drug Development
• In Silico Prediction Tools
• Online Drug Resources
• Pharmacogenomics
• 3.9. Forensic Investigations

Chapter Four

• THE DILEMMA AHEAD FOR BIOINFORMATICS
• 4.1. Data Proliferation: The Good News and Challenges
• 4.2. Some Storage Solutions
• 4.3. Product and Market Implications
• 4.4. Personalized Medicine
• Single-Gene Mutations and the Concept of Personalized Medicine
• Box 4.1. A company based on a paradigm of personalized medicine
• Genetic Determination by Multiple Factors and the Development of Personalized Medicine
• 4.5. Are GRID Networks the Answer?

Chapter Five

• INTERVIEWS WITH BIOINFORMATICS SPECIALISTS
• 5.1. Interview with Tim Riley of Waters Corporation
• 5.2. Interview with Nasri G. Nahas, Chief Executive Officer, Geneva Bioinformatics (GeneBio) S.A.
• 5.3. Interview with Ruedi Aebersold, Chairman, Scientific Executive Board, SystemsX.ch Project, Zurich Switzerland
• 5.4. Interview with John Pestian, PhD, MBA, Director, Computational Medicine Center, Cincinnati Children' s Medical Center and the University of Cincinnati
• 5.5. Interview with Kevin Davies, Editor in Chief, BioIT World

Chapter Six

• CONCLUSIONS
• 6.1. B&CB Progress is Driven by Hardware Improvements
• 6.2. Old, Simplistic Models of Biomedicine Needs to be Critically Reexamined
• 6.3. Why Has So Little Progress been Made on the "War on Cancer"?
• 6.4. Toward a Cancer Program Based on B&CB
• 6.5. The Limitations of In Silico Pharmacology
• 6.6. The Limitations of B&CB