Length 134 pages

Date published June 2009

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Bioinformatics and Computational Biology: Bottlenecks and Options Table of Contents

 

Author: K. John Morrow, Jr., PhD

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

References

Company Index with Web Addresses