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