BIO/CSC 295 2011F Bioinformatics

Readings

Further details on a variety of readings. For many of these readings, you will write a short response paper.

Altshcul et al. 1990
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic Local Alignment Search Tool. J. Mol. Bio 215, pp. 403-410.
Asara et al. 2007
Asara, J. M., Schweitzer, M. H., Freimark, L. M., Phillips, M., Cantley, L. C. (2007). Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry. Science 13 April 2007: Vol. 316. no. 5822, pp. 280 - 285 DOI: 10.1126/science.1137614.
http://www.sciencemag.org/cgi/content/full/316/5822/280
Baggerly 2010
Baggerly, K. A. (2010). The Importance of Reproducibility in High-Throughput Biology: Case Studies in Forensic Bioinformatics. PASCAL 2 Cancer Bioinformatics Workshop. Presentation, 4 September 2010.
http://videolectures.net/cancerbioinformatics2010_baggerly_irrh/
Kellis et al. 2003
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., & Lander, E. S. (2003). Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, Vol. 432, pp. 241-254. 15 May 2003.
PDF: http://web.mit.edu/manoli/www/publications/Kellis_Nature_03.pdf
Supp. Info: http://www.nature.com/nature/journal/v423/n6937/suppinfo/nature01644.html
Supp. Info: http://www.broadinstitute.org/annotation/fungi/comp_yeasts/
Krings et al. 1997
Krings, M; Stone, A; Schmitz, R W; Krainitzki, H; Stoneking, M; Paabo, S. (1997). Neandertal DNA sequences and the origin of modern humans. Cell 90 (1): 19-30.
Markham et al. 1998
Markham, R.B., Wang, W.C., Weisstein, A. E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., Yu, X. F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12568-73.
http://www.pnas.org/content/95/21/12568.full
Needleman & Wunsch 1970
Needleman, S. B. and Wunsch, C. D. (1970). A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins. J. Mol. Biol. 48 pp. 443-453.
http://www-helix.stanford.edu/bmi214/articles/NeedlemanWunsch1970.pdf
Pevzner et al. 2008
Pevzner, P. A., Kim, S., and Ng, J. Comment on Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry Science 22 August 2008: Vol. 321. no. 5892, p. 1040 DOI: 10.1126/science.1155006
http://www.sciencemag.org/cgi/content/full/321/5892/1040b
Ratliff 2009
Ratliff, E. (2009). Origin of a Species: How a T. Rex Femur Sparked a Scientific Smackdown. Wired 17.07.
http://www.wired.com/medtech/genetics/magazine/17-07/ff_originofspecies
Schweitzer et al. 2009.
Mary H. Schweitzer, Wenxia Zheng, Chris L. Organ, Recep Avci, Zhiyong Suo, Lisa M. Freimark, Valerie S. Lebleu, Michael B. Duncan, Matthew G. Vander Heiden, John M. Neveu, William S. Lane, John S. Cottrell, John R. Horner, Lewis C. Cantley, Raghu Kalluri, John M. Asara (2009). Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis. Science 1 May 2009: Vol. 324. no. 5927, pp. 626 - 631 DOI: 10.1126/science.1165069
http://www.sciencemag.org/cgi/content/full/324/5927/626

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