BSCI 348S — Bioinformatics in Genomics and Evolution

Supplementary Reading


Atwood, T.K., and Parry-Smith, D.J. 1999. Introduction to Bioinformatics. Prentice Hall, London.

* Baxevanis, A.D., and B.F. Ouellette. 1998. Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins. Wiley Interscience, New York. [Recommended for a good overview of GenBank structure and design].

* Durbin, R., S. Eddy, A. Krogh, and G. Mitchison. 1998. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. CambridgeUniversity Press, Cambridge. [Recommended for more advanced students interested in understanding the underlying models and their probabilistic basis].

Gibas, C., and Jambeck, P. 2001. Developing Bioinformatics Computer Skills. O'Reilly & Associates, Sebastopol, CA. [A good, practical introduction]

Krane, D.E, and Raymer, M. L. 2003. Fundamental Concepts of Bioinformatics. Benjamin Cummings, San Francisco.

* Mount, D.W. 2001. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

* Pevsner, J. 2003. Bioinformatics and Functional Genomics. John Wiley & Sons, Hoboken, New Jersey.


Campbell, A. M., and Heyer, L. J. 2003. Discovering Genomics, Proteomics, & Bioinformatics. Benjamin Cummings, San Francisco.

* Gibson, G., and Muse, S. V. 2002. A primer of genome science. Sinauer Associates, Sunderland MA.

Hunt, S. P., and Livesey, F. J. 2000. Functional Genomics, A Practical Approach. Oxford University Press, Oxford.

Primrose, S.B. 1998. Principles of Genome Analysis, 2nd Ed. Blackwell Science, Oxford.

Molecular Biology and Molecular Evolution

* Alberts, B., D. , Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. 2002. Molecular Biology of the Cell, 4th Edition. Garland Publishing, New York.

Freeman, S. and Herron, J. C. 2001. Evolutionary Analysis. Prentice-Hall, Inc., Upper Saddle River, New Jersey.

Li, W.-H., and D. Grauer. 1991. Fundamentals of Molecular Evolution. Sinauer Associates, Inc., Sunderland MA.

Li, W.-H. 1997. Molecular Evolution. Sinauer Associates, Inc., Sunderland MA.

Osawa, S. 1995. Evolution of the Genetic Code. Oxford Scientific Publications, Oxford, UK.

* Page, R. D. M., and Holmes, E. C. 1998. Molecular Evolution, a Phylogenetic Approach. Blackwell Science Ltd., Oxford, UK.

Schrödinger, E. 1944. What is Life? Cambridge University Press, Cambridge, England. [Reprinted in 1992 as a combined volume with Mind and Matter, Autobiographical Sketches, and a forward by Roger Penrose. A classic in information theory applied to genetics and heredity].

Math and Computer Science

Friedl, J.E.F. 1997. Mastering Regular Expressions. O'Reilly and Associates, Sebastopol CA.

Gilly, D., and the staff of O'Reilly & Associates, inc. 1992. UNIX in a nutshell. O'Reilly and Associates, Sebastopol. [available for several flavors of UNIX]

Todino, G., J. Strang, and J. Peek. 1993. Learning the UNIX operating system. O'Reilly and Associates, Sebastopol CA.

* Tisdall, J. 2001. Beginning PERL for Bioinformatics. O'Reilly and Associates, Sebastopol CA.


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