Bioinformatics and Functional Genomics (eBook)

Jonathan Pevsner received his Ph.D. in Pharmacology and Molecular Sciences at the Johns Hopkins School of Medicine (1989). There, he identified an odorant-binding protein in nasal secretions. He completed postdoctoral training as a Helen Hay Whitney fellow in the Department of Molecular Physiology at the Stanford University Medical Center. At Stanford he identified proteins that function in neurotransmitter release at nerve terminals. In 1995 he joined the faculty in the Department of Neurology at the Kennedy Krieger Institute and the Department of Neuroscience at the Johns Hopkins School of Medicine. He began teaching bioinformatics in 1996, and introduced a ten-week course in 2000. In 2001 the graduate students voted him Teacher of the Year, and in 2003 the Johns Hopkins faculty gave him the Professor's Award for Excellence in Teaching. His lab studies the molecular basis of childhood neurological disorders including autism and Down Syndrome, and develops bioinformatics software.

PART I: ANALYZING DNA, RNA, AND PROTEIN SEQUENCES IN DATABASES.

1. Introduction.

2. Access to Sequence Data and Literature Information.

3. Pairwise Sequence Alignment.

4. Basic Local Alignmnet Search Tool (BLAST).

5. Advanced BLAST Searching.

PART II: GENOMEWIDE ANALYSIS OF RNA AND PROTEIN.

6. Bioinformatic Approaches to Gene Expression.

7. Gene Expression: Microarrays 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. The Human Genome.

18. Human Disease.

Epilogue.

Appendix: GCG for Protein and DNA Analysis.

Glossary.

Solutions to Self-Test Quizzes.

Subject Index.

Author Index.

"...provides non-trivial tools and biological motivations to
learn bioinformatics." (Journal of Statistical Computation &
Simulation, January 2005)

"...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