There are no required texts for this course. However, some students will want to purchase a book on Unix, Emacs or vi, and additional texts are on reserve in the Health Sciences Library.
The course makes extensive use of lectures, slides, and computational resources on the WWW. You must have access to a recent WWW browser (Netscape4 or Internet Explorer 4.0or later) and Adobe Acrobat.
BIOINFORMATICS: Sequence and Genome Analysis, D. W. Mount (2001) Cold Spring Harbor Press ISBN 0-879-69608-7 New, very comprehensive text on sequence analysis. (Newcomb Hall Bookstore)
Bioinformatics for Dummies, J.-M. Claverie, C. Notredame (2003) Wiley ISBN 0-764-51696-5 Comprehensive mix of practical approaches
BIOINFORMATICS 2nd ed., A. D. Baxevanis and B. F. Ouellette (2001) Wiley-Interscience ISBN 0-471-38391-0 Excellent overview of databases and sequence analysis, stronger on "How To" than fundamentals. (Newcomb Hall Bookstore, on reserve, HSL)
Biological Sequence Analysis: Probabilistic Models Of Proteins And Nucleic Acids (1998) Durbin, Richard (Ed), Eddy, R., Krogh, A., Mitchison, G., Durbin, R., ISBN: 0-521-629-713 - Outstanding book on the statistical foundations of alignment and pattern finding methods, particularly Hidden Markov Models. Very mathematical. (Newcomb Hall Bookstore, on reserve, HSL)
Bioinformatics; The Machine Learning Approach (1998) Baldi, Pierre and Brunak, Soren ISBN: 026202442X - Strongest on Hidden Markov Models and Neural Nets. (requested for reserve)
Computer methods for macromolecular sequence analysis (1996) Russ Doolittle, ed. Methods in Enzymology v. 266 (on reserve, HSL) Excellent recent reviews on advanced methods.
DNA and Protein Sequence Analysis - A practical approach (1997) Bishop and Rawlings, eds. (on reserve, HSL)
Algorithms on strings, trees, and sequences : computer science and computational biology (1997) Dan Gusfield - Strong computer science orientation on algorithms.
Sequence Analysis in Molecular Biology von Heijne (1986) Academic Press - This one is short, comprehensive, and reasonably accurate, but out of date (1986).
Algorithms on strings, trees, and sequences : computer science and computational biology (1997) Dan Gusfield - Strong computer science orientation on algorithms.
Complete documentation for GCG is available on-line:
http://www.med.Virginia.EDU/achs/molbio/gcg/gcg.html
Fundamentals of Molecular Evolution 2nd ed Li and Graur (2000) Sinauer - Evolution is a much larger discipline that we can begin to cover in this course, but this book will be used for the evolution lectures, and it provides an excellent general background to phylogenetic methods and evolutionary problems in general. Recommended strongly. (on reserve, HSL in March)
Molecular Systematics 2nd ed. Hillis, Moritz, and Mable (eds) (1996) Sinauer - Excellent comprehensive overview of molecular phylogenetics. See Chapt. 11, Phylogenetic Inference for the a current review of methods and programs for constructing evolutionary trees. (on reserve in HSL in March)
Learning the UNIX Operating System O'Reilly & Associates - Excellent quick introduction to unix. Contains many short examples that should be tried.
Learning GNU Emacs O'Reilly & Associates - To get the most out of this course, and the Unix computers, you MUST learn a Unix text editor, and emacs is a power choice. This is an excellent introduction that covers the most common emacs commands in 100 pages.