Graduate Bioinformatics: Comparative Methods
Reading 2007
For the Final Exam (Friday, May 18, 1:30 - 3:30 pm, 1229 HJ Patterson)
Collins, S. R., K. M. Miller, N. L. Maas, A. Roguev, J. Fillingham, C. S. Chu, M. Schuldiner, M. Gebbia, J. Recht, M. Shales, H. M. Ding, H. Xu, J. H. Han, K. Ingvarsdottir, B. Cheng, B. Andrews, C. Boone, S. L. Berger, P. Hieter, Z. G. Zhang, G. W. Brown, C. J. Ingles, A. Emili, C. D. Allis, D. P. Toczyski, J. S. Weissman, J. F. Greenblatt, and N. J. Krogan. 2007. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446:806-810.
Advice on writing reviews is here: http://www.life.umd.edu/labs/delwiche/MSyst/misc/review.html
For Wednesday, May 2:
HMMs
• Pedersen, J.S., and Hein, J. 2003. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics 19:219-227.
A general introduction to HMMs, specific to bioinformatics: http://www.nature.com/nbt/journal/v22/n10/abs/nbt1004-1315.html
Eddy, S. 2004. What is a hidden markov model? Nature Biotechnology 22, 1315 - 1316
An excellent, but old tutorial on speech recognition: http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=698&arnumber=18626&type=ref
Rabiner, L. R. 1989. A Tutorial on Hidden Markov-Models and Selected Applications in Speech Recognition. Proceedings of the IEEE 77:257-286.
Microarrays
• Gresham D, Ruderfer DM, Pratt SC, et al. 2006. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray Science 311: 1932-1936 (MAR 31 2006)
Schena, M., Shalon, D., Davis, R.W., et al. 1995. Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 270:467-470. (Oct. 20, 1995).
Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863-14868. (Dec. 8, 1998)
For Monday, April 30:
Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-34.
For Wednesday, April 25:
Review of DNA sequencing technologies:
Sanger
454
Solexa
ABI's next generation (if information is available)
For Monday, April 23:
Nagaraj SH, Gasser RB, Ranganathan S. 2007. A hitchhiker's guide to expressed sequence tag (EST) analysis. Briefings in Bioinformatics 2007 Jan;8(1):6-21. Epub 2006 May 23. Review.
Bailey LC Jr, Searls DB, Overton GC. 1998. Analysis of EST-driven gene annotation in human genomic sequence. Genome Res. 1998 Apr;8(4):362-76.
Burke J, Davison D, Hide W. 1999. d2_cluster: a validated method for clustering EST and full-length cDNA sequences. Genome Res. 1999 Nov;9(11):1135-42.
No Class Wednesday April 18
For Monday, April 16:
Amino Acid Scoring Matrices:
Henikoff, S., & Henikoff, J. G. (1992). Amino-acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences of the United States of America, 89(22), 10915-10919.
Dayhoff, M. O., Schwartz, R. M., & Orcutt, B. C. (1978). A model of evolutionary change in proteins. In M. O. Dayhoff (Ed.), Atlas of protein sequece and structure, supplement 3 (Vol. 5, pp. 345-352). Washington, DC: National Biomedical Research Foundation.
Whelan, S., & Goldman, N. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution, 18(5), 691-699. [primary paper]
COG and related databases.
Kaufmann, M. 2006. The role of the COG database in comparative and functional genomics. CURRENT BIOINFORMATICS 1 (3): 291-300. [primary paper]
Tatusov, RL; Fedorova, ND; Jackson, JD; Jacobs, AR; Kiryutin, B; Koonin, EV; Krylov, DM; Mazumder, R; Mekhedov, SL; Nikolskaya, AN; Rao, BS; Smirnov, S; Sverdlov, AV; Vasudevan, S; Wolf, YI; Yin, JJ; Natale, DA. 2003. The COG database: an updated version includes eukaryotes. BMC BIOINFORMATICS 4: doi:.
For Wednesday, April 11:
Pearson, W. R., & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85(8), 2444-2448.
For Monday, April 9:
Altschul, SF, W Gish, W Miller, EW Myers, and DJ Lipman. Basic local alignment search tool. J Mol Biol 215(3):403-10, 1990.
Altschul, SF, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, and DJ Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database
search. Nucleic Acids Res 25(17):3389-3402, 1997.For Monday, April 2:
Pearson, W. R., & Miller, W. (1992). Dynamic-programming algorithms for biological sequence comparison. Methods in Enzymology, 210, 575-601.
Assigned March 26:
Platt, J. R. 1964. Strong inference - certain systematic methods of scientific thinking may produce much more rapid progress than others. Science 146:347-.
Nelson, K. E., et al. 1999. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329.
For Monday 2/26/2007 we will read:
Wetterbom, A., et al., 2006. Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution. Journal of Molecular Evolution. 63:682-690.
and
Karro JE, Yan YP, Zheng DY, et al. 2007.
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
NUCLEIC ACIDS RESEARCH 35: D55-D60 Sp. Iss. SI