Bioinformatics: A Practical Guide to the Analysisof Genes and Proteins, Third Edition
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Reviews of the Second Edition
"In this book, Andy Baxevanis and Francis Ouellette . . . have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt."
--Eric Lander, from the Foreword to the Second Edition
"The editors and the chapter authors of this book are to be applauded for providing biologists with lucid and comprehensive descriptions of essential topics in bioinformatics. This book is easy to read, highly informative, and certainly timely. It is most highly recommended for students and for established investigators alike, for anyone who needs to know how to access and use the information derived in and from genomic sequencing projects."
--Trends in Genetics
"It is an excellent general bioinformatics text and reference, perhaps even the best currently available . . . Congratulations to the authors, editors, and publisher for producing a weighty, authoritative, readable, and attractive book."
--Briefings in Bioinformatics
"This book, written by the top scientists in the field of bioinformatics, is the perfect choice for every molecular biology laboratory."
--The Quarterly Review of Biology
This fully revised version of a world-renowned bestseller provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. Using relevant biological examples, the book provides background on and strategies for using many of the most powerful and commonly used computational approaches for biological discovery. This Third Edition reinforces key concepts that have stood the test of time while making the reader aware of new and important developments in this fast-moving field. With a new full-color and enlarged page design, Bioinformatics, Third Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists.
This new edition features:
* New chapters on genomic databases, predictive methods using RNA sequences, sequence polymorphisms, protein structure prediction, intermolecular interactions, and proteomic approaches for protein identification
* Detailed worked examples illustrating the strategic use of the concepts presented in each chapter, along with a collection of expanded,more rigorous problem sets suitable for classroom use
* Special topic boxes and appendices highlighting experimental strategies and advanced concepts
* Annotated reference lists, comprehensive lists of relevant Web resources, and an extensive glossary of commonly used terms in bioinformatics, genomics, and proteomics
Bioinformatics, Third Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, clinical research, proteomics, and computational biology.


Andreas D. Baxevanis, Ph.D. is the Deputy Director for Intramural Research and the Director of the Computational Genomics Program at the National Human Genome Research Institute, National Institutes of Health. He is currently the editor-in-chief of Current Protocols in Bioinformatics, senior editor of Molecular Cancer Therapeutics, and associate editor of Proteins: Structure, Function, and Bioinformatics. His involvement in educational activities include teaching bioinformatics at The Johns Hopkins University, serving as adjunct faculty at Boston University, lecturing in numerous courses, and developing materials intended to facilitate the use of genomic sequence data. He is the recipient of the Bodossaki Foundation's 2000 Academic Prize in Medicine and Biology.

Dr. B. F. Francis Ouellette is Director of the University of British Columbia Bioinformatics Centre and Director for the Canadian Genetic Disease Network (CGDN) Bioinformatics Facility, where he coordinates the Canadian Bioinformatics Workshop series. His research includes work on the Biomolecular Interaction Network Database (BIND), development of gene prediction tools, and use of comparative genomics approaches to help identify human genes. Dr. Ouellette has worked on yeast genome sequencing and analysis, and has previously served as GenBank coordinator at the National Center for Biotechnology Information (NCBI), NIH.


Foreword (Lee Hood).




1. Sequence Databases (Rolf Apweiler).

2. Mapping Databases (Peter S. White and Tara C. Matise).

3. Information Retrieval from Biological Databases (Andreas D. Baxevanis).

4. Genomic Databases (Tyra G. Wolfsberg).


5. Predictive Methods Using DNA Sequences (Enrique Blanco and Roderic Guigó).

6. Predictive Methods Using RNA Sequences (David Mathews and Michael Zuker).

7. Sequence Polymorphisms (James C. Mullikin and Stephen T. Sherry).


8. Predictive Methods Using Protein Sequences (Yanay Ofran and Burkhard Rost).

9. Protein Structure Prediction and Analysis (David Wishart).

10. Intermolecular Interactions and Biological Pathways (Gary D. Bader and Anton J. Enright).


11. Assessing Pairwise Sequence Similarity: BLAST and FASTA (Andreas D. Baxevanis).

12. Creation and Analysis of Protein Multiple Sequence Alignments (Geoffrey J. Barton).

13. Sequence Assembly and Finishing Methods (Nancy F. Hansen, Pamela Jacques Thomas and Gerard G. Bouffard).

14. Phylogenetic Analysis (Fiona S. L. Brinkman).

15. Computational Approaches in Comparative Genomics (Andreas D. Baxevanis).

16. Using DNA Microarrays to Assay Gene Expression (John Quackenbush).

17. Proteomics and Protein Identification (Mark R. Holmes, Kevin R. Ramkissoon and Morgan C. Giddings).


18. Using Perl to Facilitate Biological Analysis (Lincoln D. Stein).


Glossary. Index.


"…an outstanding achievement and will be a sound resource for bioengineers, cellular and molecular biotechnologists, and bioinformatists." (Annals of Biomedical Engineering, June 2006)

"…does an excellent job of tracking developments and providing an account that will be accessible to working biologists. This should be on the bookshelf of every molecular biologist." (The Quarterly Review of Biology, December 2005)

"...fully delivers on its promise of providing a useful and practical guide...I found it to be the most useful book on bioinformatics I have seen and recommend it very highly." (ASM News, September 2005)

“…not only an excellent guidebook … but also a supreme teaching and reference material.” (ChemBioChem, 2005; Vol. 6, 6)

"…not only an excellent guidebook for bioinformatics users but also…a supreme teaching and reference material." (ChemBioChem, July 4, 2005)

"…the most updated bioinformatics book that offers expert insights into cutting-edge tools of modern computational biology and stands out from many current texts on the subject." (American Journal of Human Biology, May/June 2005)

"…The book and the attached web links together give readers a rich resource of topics covered..." (Statistical Methods in Medical Research, Vol.14, No.1, 2005)