Bioinformatics and Functional Genomics
PART I: ANALYZING DNA, RNA, AND PROTEIN SEQUENCES IN DATABASES.
2. Access to Sequence Data and Literature Information.
3. Pairwise Sequence Alignment.
4. Basic Local Alignment Search Tool (BLAST).
5. Advanced BLAST Searching.
PART II: GENOMEWIDE ANALYSIS OF RNA AND PROTEIN.
6. Bioinformatic Approaches to Gene Expression.
7. Gene Expression: Microarray Data Analysis.
8. Protein Analysis and Proteomics.
9. Protein Structure.
10. Multiple Sequence Alignment.
11. Molecular Phylogeny and Evolution.
PART III: GENOME ANALYSIS.
12. Completed Genomes and the Tree of Life.
13. Completed Genomes: Viruses.
14. Completed Genomes: Bacteria and Archaea.
15. Eukaryotic Genomes: Fungi.
16. Eukaryotic Genomes: From Parasites to Primates.
17. Human Genome.
18. Human Disease.
Appendix: GCG for Protein and DNA Analysis.
Solutions to Self-Test Quizzes.
- Attractive two-color page design throughout, along with a section of full color figures
- Features 375 figures and 170 tables
- Each chapter includes a Problem Set, Pitfalls section, Boxes explaining key techniques and math/stats principles, Summary, Recommended Reading, and a list of freely available software
- Companion website at www.bioinfbook.org, including answers to problem sets and complete PowerPoint presentations organized by chapter
- Consistent use of breast cancer, retinal-binding protein (RBP), and HIV-1 as real-life illustrative examples
- Key terms are highlighted in boldface and defined in the Glossary
"...ideal both for biologists who want to master the application of bioinformatics to real-world problems and for computer scientists who need to understand the biological questions that motivate algorithms." (Quarterly Review of Biology, March-May 2005)
"…this appears to be an excellent textbook for graduate students and upper level undergraduate students." (Annals of Biomedical Engineering, July 2004, 32, 7)
"…highly recommended for academic and medical libraries, and for researchers as an introduction and reference…" (E-Streams, Vol. 7, No. 4)
“...an intriguing work targeted toward biologists wanting to solve problems...provides a compendium of many biological insights and breakthroughs and will be a useful resource...highly recommended.” (Choice, Vol. 41, No. 7, March 2004)"I was particularly impressed by the comprehensible and comprehensive treatment of BLAST - the best that I have seen. One is guided from choosing the appropriate type of BLAST program, database and search parameters through to refining and analysing the significance of the search results--all illustrated with clear examples."
--David P. Leader, University of Glasgow
"I would not hesitate for a moment to propose Jonathan Pevsner’s new book as a standard course for biologists who need a serious, practical knowledge of modern bioinformatics. Dr. Pevsner does a masterful job at presenting virtually every major topic in bioinformatics and computational genomics, from the basics of sequence analysis, to microarray data classification, accurately and at a considerable level of detail but without any complex mathematics. In addition to being an extremely useful textbook, Pevsner’s book is a very nice read, due in large part, to carefully constructed questions and suggestions for discussion, and wonderful historical vignettes. In short, a great bioinformatics book for biologists!"
--Eugene V. Koonin, Ph.D., National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland