**Mathematics and the Genome: Annotated Bibliography (07/17/2005)**

Prepared by:

Joseph Malkevitch

Department of Mathematics

York College (CUNY)

Jamaica, New York 11451

Email: malkevitch@york.cuny.edu (for additions, suggestions, and corrections)

web page:

http://www.york.cuny.edu/~malk

Gusfield, D., Algorithms on Strings, Trees, and Sequences, Cambridge U. Press, New York, 1997.

*A very readable introduction to pattern matching algorithms for strings in a biological context. Also, a nice treatment of evolutionary trees. (No Calculus required.)*

Jones, N. and P. Pevzner, An Introduction to Bioinformatics Algorithms,MIT Press, Cambridge, 2004.

*An elementary, leisurely and well written integrated treatment of algorithm design and the mathematics to attack computational biology problems. (No Calculus.)*

Page, R., and E. Holmes, Molecular Evolution: A Phylogenetic Approach, Blackwell Science, Oxford, 1998.

*This book, written by two biologists, has a relatively light overlay of mathematics but clearly addresses the places where mathematical tools can be put to use.*

Patterson, C., Evolution, Second Edition, Comstock Publishing (Cornell University Press), Ithaca, New York, 1999.

*A biologist's account of evolution using examples and data that help clarify the development of mathematical methods that have occurred to get insight into the problems faced by biologists.*

Pevzner, P., Computational Molecular Biology, MIT Press, Cambridge, 20001.

*Many topics in computational biology including sorting and transforming string sequences by "reversing" a portion of a string. Some parts are quite technical. (No Calculus.) *

Sankoff, D., and J. Kruskal, (eds.), Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, Addison-Wesley, Reading, 1983.

*This book is now a classic (but dated in parts) and was written before many of the dramatic uses to which the ideas developed here were put to use.*

Waterman, M., Introduction to Computational Biology, Chapman and Hall, New York, 1995.

*A very comprehensive treatment of using mathematical tools in molecular biology by one of the pioneers in this area. (Parts require Calculus.)*

Note: All of these books, including Jones and Pevzner, which is probably the most "user friendly," are worth taking a look at. To master this material will take careful reading and rereading. Many of the books have parts that are fairly independent of what comes at the start and so the later parts of the books are worth looking at to get a feel for the problems which are addressed and the methods used to attack them. Most of the books review or outline the biology necessary to understand the development. There are also excellent more advanced books.

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