Classes will be held twice-weekly, one meeting in a classroom (Room 327or Kettering Auditorium) with an Internet connection and projector, and the other in a computer classroom (usually 442 or 444 University Hall).

Grades will be awarded on the basis of

    (i) Consistent attendance in class, including final presentation sessions

    (ii) A written examination at the end of the quarter

    (iii) An  individual original presentation based on

(a) discussion of a Web site not discussed in the class or

(b) a journal article in which computing methods were used extensively or

(c) description of the application of computing methods to solution of  problems in your own research. 

In all cases discussion and criticism of the methods used is expected.
   

Links to related resources and other materials will be provided for each lecture.

CATALOGS OF DATABASES

The Molecular Biology Database Collection.  Nucleic Acids Research, annually

2006.  M.Y. Galperin NAR 34, January 1st issue.

2004. M.Y. Galperin NAR (2004) 32, D3-D22  

2002. A.D. Baxevanis.  NAR (2002) 30, 1-12

Books

Recent:

Campbell, A.M. and Heyer, L.J. (2002) Discovering Genomics, Proteomics and Bioinformatics. CSHL Press/Benjamin Cummings, San Francisco CA

Misener, S. and Krawetz, S.A. (2000) Bioinformatics Methods and Protocols. Humana Press, Totowa, NJ
 
Baldi, P. and Brunak, S. (1998). Bioinformatics: The Machine Learning Approach (1st ed.). Cambridge, MA: The
MIT Press.

*Brown, T. A. (1999) Genomes. New York : Wiley-Liss, 1999

*Durbin, R., Eddy, S., Krogh, A. and Michison, G. (1998). Biological Sequence Analysis (1st ed.). Cambridge, UK:
Cambridge University Press.

Salzberg, S. L., Searls, D. B. and Kasif, S. (1998). Computational Methods in Molecular Biology. Amsterdam:
Elsevier, 371.

Older

Adams, M. D., Fields, C. and Venter, J. C. (1994). Automated DNA Sequencing and Analysis. New York: Academic Press,
368 pages.

Bishop, M. J. (1994). Guide to Human Genome Computing. London: Academic Press, 350 pages.

Creighton, T. E. (1993). Proteins: Structures and Molecular Properties (Second Edition ed.). New York: Freeman.

Cover, T. M. and Thomas, J. A. (1991). Elements of Information Theory (1st ed.). New York NY: John Wiley and Sons Inc.

Doolittle, R. F. (1986). Of Urfs and Orfs: A Primer on How to Analyze Derived Amino Acid Sequences. University Science
Books, Mill Valley, California.

Doolittle, R. F. (1990). Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences (1 ed.). Methods in
Enzymology Volume 183, New York: Academic Press.

Doolittle, R. F. (1996). Computer Methods for Macromolecular Sequence Analysis. Methods in Enzymology, Vol.
266. New York: Academic Press. 711 Pages.

Fasman, G. D. (1989). Prediction of Protein Structure and the Principles of Protein Conformation. New York NY: Plenum
Press,

Gribskov, M. and Devereux, J. (1991). Sequence Analysis Primer. New York: Stockton Press, 279 pages.

Gusfield, D. (1997). Algorithms on Strings, Trees and Sequences. (1st. ed.). Cambridge, UK: Cambridge University
Press, 534 pages.

Hunter, L. (1993). Artificial Intelligence and Molecular Biology. Menlo Park, CA: AAAI Press, 470 pages.

Hunter, L., Searls, D. and Shavlik, J. (1993). First International Conference on Intelligent Systems for Molecular Biology.
Menlo Park, CA.: AAAI Press.

Lander, E. S. and Waterman, M. S. (1995). Calculating the Secrets of Life: Applications of the Mathematical Sciences in
Molecular Biology. Washington D. C.: National Academy Press, 285 pages.

Lesk, A. (1991). Protein Architecture: A Practical Approach . Oxford: IRL Press at Oxford University Press. 287 pages
 

Schultze-Kremer, S. (1994). Advances in Molecular Bioinformatics. Washington D.D.: IOS PRess, 259 pages.

* Recommended as Molecular Biologist - friendly

Trade Publications (occasional articles interesting to molecular biologists)

Genome Technology: www.GenomeWeb.com

American Genomic/Proteomic Technology: www.iscpubs.com

Drug Discovery & Development: www.ddmag.com