UCSC CMP243 Bioniformatics: Text and reserve list

CMP243 Text and reserve list

The text is R. Durbin and S. Eddy and A. Krogh and G. Mitchison's Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. from Cambridge University Press. It is a tutorial introduction to the use of hidden Markov models and other probabilistic models for sequence analysis problems in computational molecular biology, and should be for sale at Baytree Bookstore.

In addition to this text, a number of books have been put on reserve in the Science Library, from which there may be required reading assignments. These are also available to students for further research into the topic they choose for their project.

The following are available as postscript files (some html too)

Tutorial on hidden Markov models for biosequence analysis by Melissa Cline, Christian Barrett, and Kevin Karplus.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs by Altschul et al. (1997, Nucleic Acids Res., 25, 3389-3402)
Information Theory Primer by Tom Schneider, written for molecular biologists.
Sequence Logos: a new way to display consensus sequences Tom Schneider and R. Michael Stephens.
Weight matrices for sequence similarity scoring David Wheeler. A tutorial on score matrices for biosequence comparison. Postsript version or html version.
Pairwise Sequence Alignment by Robert Giegerich and David Wheeler. Postscript version or html version.
Paper on mapping genes in human DNA before the sequence is finished. html version only.

The following are (soon to be?) on reserve in the Science Library:

R. Durbin and S. Eddy and A. Krogh and G. Mitchison.: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. (Library must order.)
Waterman, Michael S.: Introduction to computational biology : maps, sequences and genomes. UCSC Science QH438.4.M33.
Russell F. Doolittle, editor.: Computer methods for macromolecular sequence analysis. UCSC Science QP601.A1 M4 v.266.
Schulze-Kremer, Steffen.: Molecular bioinformatics : algorithms and applications UCSC Science QH506 .S346.
Douglas W. Smith, editor.: Biocomputing : informatics and genome projects. UCSC Science QH447.B56.
M.J. Bishop and C.J. Rawlings, editor.: DNA and protein sequence analysis; a practical approach. IRL Press at Oxford University Press, 1997. UCSC Science QP620 .D58 1997.
Lawrence Hunter, Teri E. Klein, editors.: Pacific Symposium on Biocomputing, 1998 and 1999 UCSC Science QH323.5 .P33.
C. Branden and J. Tooze.: Introduction to Protein Structure (second edition) (First edition was UCSC Science QP551.B7635. Need to order new edition. It is also a text for Chem 200A this quarter.)
Michael Gribskov and John Devereux, editors.: Sequence analysis primer. UCSC Science QP620 .S47.
Campbell, Neil.: Biology. 5th Edition. 1999. (Text used for "From Gene to Protein" handout) UCSC Science QH308.2 .C34.
Harvey Lodish et al..: Molecular cell biology, 3rd ed., 1995 (or latest edition). UCSC Science QH581.2 .D37.
Sheldon Ross.: A first course in Probability 5th Edition. UCSC Science QA273.R83.
John Rice: Mathematical Statistics and Data Analysis UCSC Science QA276.12 .R53 1995 (second edition)
Andrew Gelman et al.: Bayesian data analysis UCSC Science QA279.5 .B39
Rabiner, Lawrence R.,: Fundamentals of speech recognition. UCSC Science TK7895.S65. (Note: this has basic material on Hidden Markov Models)
Lewin, Benjamin.: Genes VI. 1997. UCSC Science QH430 .L487 1997.
Setubal, Joao Carlos.: Introduction to computational molecular biology. 1997. UCSC Science QH506 .S49.
N. Cooper (ed.).: The human genome project: deciphering the blueprint of heredity. 1994. UCSC Science QH431.H87.
D. Clark and L. Russell.: Molecular Biology made simple and fun. 1997. UCSC Science QH506 .C535.
Gonick and Wheelis.: Cartoon Guide to Genetics. 1991. UCSC Science QH436.G66.
M. Sternberg.: Protein Structure Prediction--A Practical Approach. 1996. UCSC Science QP551 .P69764.
D. Gusfield.: Algorithms on strings, trees, and sequences : computer science and computational biology. 1997. UCSD S & E QA76.9.A43 G87.
Andreas Baxevanis and B.F.Francis Ouellette, Eds.: Bioinformatics : A Practical Guide to the Analysis of Genes and Proteins. (Library must order) Wiley, 1998. ISBN: 0471191965.
Pierre Baldi and Soren Brunak: Bioinformatics : The Machine Learning Approach (Adaptive Computation and Machine Learning). 1998. UCSC Science QH506 .B35.
Steven L. Salzberg, David B. Searls, Simon Kasif, Eds.: Computational methods in molecular biology. 1998. UCSC Science QH506 .C7375.
Various editors.: Proceedings of the sixth and seventh International Conference on Intelligent Systems for Molecular Biology AAAI Press, 1998 and 1999. (Library needs to order. Previous editions were UCSC Science QH506 .I487)
Various editors.: Proceedings of the First, Second and Third International Conference on Computational Molecular Biology ACM Press. 1997, 1998 and 1999. (Library needs to order).

Questions regarding about page content should be directed to haussler@cse.ucsc.edu.
Last modified Sept. 10, 1999.

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