ECS 124
Paperlist for Bioinformatics
Gusfield

This page lists various journal articles that we may use during the course. When possible, it will just give the web link to the on-line article for you to read on-line or download. Sometimes the link only leads to a table of contents where you then have to click on the appropriate entry to bring up a pdf copy of the article. Note that on-line papers might only be available via an on-campus machine. When an article is not available online, but xeroxing is permitted, the paper will be distributed in class.

Distribution List

1. Chapter 1 - Molecular Biology for Computer Scientists by L. Hunter A good place to start if you haven't had an in-depth course in molecular biology. Good for others to scan.
   
2. Chapter 13 - Afterword by Joshua Lederberg. This chapter has a strange title, but is very instructive and connects to the issue of implicit models that are extracted from limited available data.
   
3. GENOMICS: Journey to the Center of Biology Eric S. Lander and Robert A. Weinberg March 10, 2000 Science A review of the history of biology leading to Genomics and beyond.
   
4. DOE Primer on Molecular Genetics The introduction is good for people without an in-depth background in molecular biology. The remainder of the primer is spotty and dated (particularly on sequencing).
   
5. COMPUTERS AND BIOLOGY: Bioinformatics in the Information Age, Sylvia J. Spengler Science 2000 February 18; 287: 1221-1223.
   
6. The Emerging Paradigm and Open Problems in Comparative Genomics, E. Koonin, Vol. 15, no. 4, 1999, Bioinformatics
   
7. The New Genomics: Global Views of Biology, Eric Lander Science, Vol. 274, 25 October 1996
   
8. Gene Mutation Provides More Meat on the Hoof by S. Dickman. A News article showing a typical use of (partial) sequence data used for gene finding. I like this story.
   
9. Trends in Biochemical Sciences Vol. 25, Issue 1, Jan. 2000, p.11-12
   Cell-cycle regulatory proteins Hsl7p/Skb1p belong to the protein methyltransferase superfamily An example of typical use of bioinformatics tools to find new (surprising) members of a protein family.
   
10. Identification of Vaccine Candidates Against Serogroup B Meningococcus by Whole-Genome Sequencing. March 10, 2000 Science An example of sequence data and phylogenetics used to find vaccine candidates.
    
11. Bioinformatics Online Home Page
    
12. The eMOTIF Database. Nucleic Acids Research (29) 1 (2001) p. 202-204. J.Y. Huang and D. Brutlag.
13. Highly Specific Protein Sequence Motifs for Genome Analysis. Nevill-Manning, C. G, Wu, T. D., Brutlag, D. L.
    
14. UCSC Tutorial on Hidden Markov Models We will dip into this tutorial at different times during the class.
    
15. Four Evolutionary Strata on the Human X Chromosome
    Bruce T. Lahn and David C. Page
    Science Oct 29 1999: 964-967. [Abstract] [Full Text]
    
16. Evolution of the carabid ground beetles,
    Syozo Osawa, Zhi-Hui Su, Choonggon Kim, Munehiro Okamoto, Osamu Tominaga and Yûki Imura
    Advances in Biophysics Pages 65-106
    [Full Text-PDF (1521 K)]
    
17. Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. S. Altschul and E. Koonin TIBS article on PSI-Blast
18. Reaping the plant gene harvest, Science vol. 287, 21 Jan. 2000, p. 412-414. This is the article that has the crop circle figure I showed in class. However, this online version of the article lacks that figure. Still a good article to read for bioinformatics and genomics. Reaping the plant harvest
19. A short poster-paper on dinucleotide frequencies. Dinucleotide Frequencies
20. A Recent Nature Paper showing many aspects of the use of bioinformatics tools for genomic analysis and discovery. Comparison of Yeast Species
21. ELVIS is Everywhere
    The Scientist, Vol. 18, Issue 1, 64, Jan. 19, 2004
    You should be able to get this online through the campus library site, but it was not working when I last tried.