Bioinformatics Computing

by Bryan P. Bergeron

Publisher: Prentice Hall PTR
ISBN: 0131008250

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Book Description

The complete, practical guide to bioinformatics for molecular biologists and life scientists

• Gives an overview of bioinformatics from a computer science perspective.
• Makes the computer science aspects of bioinformatics more understandable for life scientists.
• Presents a ready reference for current and future online and standalone tools.

In Bioinformatics Computing, Harvard Medical School and MIT faculty member Bryan Bergeron presents a comprehensive and practical guide to bioinformatics for life scientists at every level of training and practice. After an up-to-the-minute overview of the entire field, he illuminates every key bioinformatics technology, offering practical insights into the full range of bioinformatics applications-both new and emerging. Coverage includes:

• Technologies that enable researchers to collaborate more effectively
• Fundamental concepts, state-of-the-art tools, and "on the horizon" advances
• Bioinformatics information infrastructure, including GENBANK and other Web-based resources
• Very large biological databases: object-oriented database methods, data mining/warehousing, knowledge management, and more
• 3D visualization: exploring the inner workings of complex biological structures
• Advanced pattern matching techniques, including microarray research and gene prediction
• Event-driven, time-driven, and hybrid simulation techniques

Bioinformatics Computing combines practical insight for assessing bioinformatics technologies, practical guidance for using them effectively, and intelligent context for understanding their rapidly evolving roles.

Table of Contents

1. The Central Dogma.
   The Killer Application. Parallel Universes. Watson's Definition. Top-Down Versus Bottom-Up. Information Flow. Convergence. Endnote.
2. Databases.
   Definitions. Data Management. Data Life Cycle. Database Technology. Interfaces. Implementation. Endnote.
3. Networks.
   Geographical Scope. Communications Models. Transmissions Technology. Protocols. Bandwidth. Topology. Hardware. Contents. Security. Ownership. Implementation. Management. On the Horizon. Endnote.
4. Search Engines.
   The Search Process. Search Engine Technology. Searching and Information Theory. Computational Methods. Search Engines and Knowledge Management. On the Horizon. Endnote.
5. Data Visualization.
   Sequence Visualization. Structure Visualization. User Interface. Animation Versus Simulation. General-Purpose Technologies. One the Horizon. Endnote.
6. Statistics.
   Statistical Concepts. Microarrays. Imperfect Data. Basics. Quantifying Randomness. Data Analysis. Tool Selection. Statistics of Alignment. Clustering and Classification. On the Horizon. Endnote.
7. Data Mining.
   Methods. Technology Overview. Infrastructure. Pattern Recognition and Discovery. Machine Learning. Text Mining. Tools. On the Horizon. Endnote.
8. Pattern Matching.
   Fundamentals. Dot Matrix Analysis. Substitution Matrices. Dynamic Programming. Word Methods. Multiple Sequence Alignment. Tools. On the Horizon. Endnote.
9. Modeling and Simulation.
   Drug Discovery. Fundamentals. Protein Structure. Systems Biology. Tools. On the Horizon. Endnote.
10. Collaboration.
    Collaboration and Communications. Standards. Issues. On the Horizon. Endnote.

About the Author

BRYAN BERGERON is a faculty member at both Harvard Medical School and MIT, Editor-in-Chief of e.MD, editorial board member of Healthcare Informatics, and Fellow of the American College of Medical Informatics. He has authored more than 300 publications on topics ranging from AI to computers in medicine.

Customer Reviews

This book was a pleasant surprise. It's one of the few books on bioinformatics that I've read that doesn't assume the reader has a PhD in biochemistry or mathematics. It's a gentle but thorough introduction to many of the problems faced by life scientists who are trying to get a handle on this thing called bioinformatics. I've been working in the life sciences for years, and this is the first book I've read that explains how I can make use of the various search engines, genomic analysis tools, and the dozens of genomics databases worldwide in my day-to-day life.

I especially appreciate the author's frank analysis of the state of the art at the end of each chapter. He seems to put a balanced spin on the field, pointing out the vast potential of bioinformatics computing in practical medicine and materials synthesis, while grounding the reader in current political and economic realities that are limiting many aspects of the field.

I consider it a must read.

Dr, Beregeron ofers a sensible yet visionary exposition of the field. For me, the future direction of this field is most compelling. It is a primer that can be challenging to the most sophisticated afficionado, also.