Review form for text and other reading for CMP243
The authors of our text were very kind in providing a
preliminary version free for our class. In return, it
is our duty to give them feedback. Please save this file
as plain text, edit it to add your comments, and email it back to
me. Your comments will be saved and used to improve the reading
selections for future editions of CMP243. I will also strip
off the mail headers and forward the reviews anonymously to
the authors, so that they can improve the text.
This is not optional. All students must complete the review form.
I expect all students to report at least one typo in the text,
preferably about 5 typos.
However, it is ok to leave blank or say "no comment"
for some of the questions about
the other reading material, apart from the text. I don't expect that you
have read all the other material, and many of these were hardly covered
at all in class.
General comments about the text
Comments on specific chapters of the text
- Chapter 1.
- Chapter 3.
- Chapter 4.
- Chapter 7.
- Chapter 8.
Comments on xeroxed materials
- Tooze chapter on proteins
- Campbell chapter on the central dogma and chapter on "tour of the cell"
- Science paper on Methanococcus jannaschii complete genome
- ENTREZ paper
- BLAST paper
- Altschul Amino acid substitution matrices paper
- Judea Pearl's chapter on Bayes rule
- Eisenberg's profiles paper
- CLUSTAL paper
- Rumelhart, Widrow and Lehr intro to neural nets
- Bishop and Jordan review paper on neural nets
- GRAIL paper
- PHD paper
- Genie paper
- HMM paper from JMB
- Grate, Kaplus, Hughey, Sjolander HMM tutorial
- EcoParse paper
- Rabiner HMM tutorial paper
- slides for HMM lectures
- Searls' paper on grammars
- SCFGs for tRNA paper
- slides for SCFG lecture
- protein fold recognition paper by Jones and Thornton
- Mapping the protein Universe by Holm and Sander
Comments on postscript/html papers
- Tom Schneider's primer on Information Theory
- David Wheeler's tutorial on score matricies for biosequence comparison
- Tutorial on pairwise sequence alignment by Georg Fuellen and Robert Giegerich.
- Science paper on human transcript map
Comments on reserve materials
- Waterman, Michael S.
Introduction to computational biology : maps, sequences and genomes
- Computer methods for macromolecular sequence analysis, edited by Russell F.
Doolittle.
- Schulze-Kremer, Steffen.
Molecular bioinformatics : algorithms and applications
- Biocomputing : informatics and genome projects,
edited by Douglas W. Smith.
- Pacific Symposium on Biocomputing, 1996, editors, Lawrence Hunter, Teri E.
Klein.
- C. Branden and J. Tooze.
Introduction to Protein Structure
- Sequence analysis primer, edited by Michael Gribskov and John Devereux.
- Campbell, Neil. Biology. 4th Edition. 1996.
(Text used for "From Gene to Protein" handout)
- Lehninger, Albert L.
Principles of biochemistry (1993 edition)
- Molecular cell biology, Harvey Lodish ... [et al.]. 3rd ed., 1995.
- Sheldon Ross. A first course in probability. 2nd edition.
- Andrew Gelman ... [et al.].
Bayesian data analysis
- Rabiner, Lawrence R., Fundamentals of speech recognition.