Harvard University, fas   
Fall 2002   

Biophysics 101

Genomics and Computational Biology

George Church, Ph.D. (HMS)

         

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Texts for Background Reference

Please note: These "recommended texts" etc. are not required. They are rough order of decreasing relevance. They do not perfectly cover key topics of interest including quantitative functional-genomics, linkage/population genomics, and biosystem modeling. Beginning after the first problem set we will assign readings from primary bioinformatics articles. These will focus on those subjects and help teach the important skills of reading cutting-edge research, but will cover only part of the lecture material.

Beginning Perl for Bioinformatics , James Tisdall; O'Reilly & Assoc. 2001 . $32 B&N , $28 Amazon. See also www.bookpool.com.

Bioinformatics: Sequence and Genome Analysis , David Mount; CSHL 2001 . $75 B&N , $75 Amazon.

Molecular Biology for Computer Scientists ed. L. Hunter, MIT Press. (Out-of-print but see this PDF) Recommended for all non-biologists.

Genomes by T.A. Brown. $70 A good biology reference.

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids by Richard Durbin, S. Eddy, A. Krogh & G. Mitchison $35
This book covers basic and advanced models for sequence analysis.

Introductory Statistics, Neil A. Weiss, 5th edition, Addison-Wesley 1999. $93

Mathematica 4.2 free for all students of this course (Check with your TF if you are not a full time Harvard student) Or more permanently: $140 student price.

MATLAB $99 Since not free for some students this will not be used (but will be accepted for the problem sets if you already use it).

Developing Bioinformatics Computer Skills , Cynthia Gibas & Per Jambeck, O'Reilly 2001 . $28

The Perl CD Bookshelf, Linda Walsh (Editor) from O'Reilly $72.  
This CD contains 6 "books" that might supplement numerous free resources on the web: General Perl documents & download , Perl for biologists: , Perl tutorials.

Articles

(The TFs will assist in getting access to electronic versions (pdf) as needed). Additional references will be embedded in the class lecture notes and problem sets:

Primer on molecular biology @ http://www.ornl.gov/hgmis/publicat/primer/intro.html

See Syllabus for a week-by-week set of readings.

Please send comments to bphys101@fas.harvard.edu

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