CBB752/CPSC452/CPSC752/MBB452/MBB752/MCDB452/MCDB752

http://www.gersteinlab.org/courses/452/

Discussion sections

Sept
18(7:00-8:00pm, 405 BASS) or 21(5:30-6:30pm, 405 BASS)
Section 1
 Hutchison C.A.et al. (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science, 286(5447), 2165-9. PMID: 10591650
Vetsigian K., Woese C. and Goldenfeld N. (2006) Collective evolution and the genetic code. PNAS, 103(28), 10696-701. PMID: 16818880
25(7:00-8:00pm, 405 BASS) or 28(5:30-6:30pm, 405 BASS)
Section 2
 Doolittle W.F. (1999) Phylogenetic classification and the universal tree. Science, 284(5423), 2124-9. PMID: 10381871
Sali A. et al. (2003) From words to literature in structural proteomics. Nature, 422(6928), 216-25. PMID: 12634795
Oct
3(7:00-8:00pm, 326 BASS) or 5(5:30-6:30pm, 405 BASS)
Section 3
 DeRisi J.L., Iyer V.R. and Brown P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278(5338), 680-6. PMID: 9381177
Golub T.R. et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286(5439), 531-7. PMID: 10521349
10(7:00-8:00pm, 405 BASS) or 12(5:30-6:30pm, 405 BASS)
Section 4
 Hannon G.J. (2002) RNA interference. Nature, 418(6894), 244-51. PMID: 12110901
Hughes T.R. et al. (2000) Functional Discovery via a Compendium of Expression Profiles. Cell, 102(1), 109-26. PMID: 10929718
16(8:00-9:30pm, 405 BASS)
Midterm Review Section
 Midterm Review.
24(7:00-8:00pm, 405 BASS) or 26(5:30-6:30pm, 405 BASS)
Section 5
 Luscombe N.M., Greenbaum D. and Gerstein M. (2001) What is bioinformatics? A proposed definition and overview of the field. Methods Inf Med., 40(4), 346-58. PMID: 11552348
Greenbaum D. et al. (2001) Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res., 11(9), 1463-8. PMID: 11544189
Nov
Oct 31(7:00-8:00pm, 405 BASS) or 2(5:30-6:30pm, 405 BASS)
Section 6
 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(3), 443-53. PMID: 5420325
Roberts L. (2001) Controversial From the Start. Science, 291, 1182-8. link
7(7:00-8:00pm, 326 BASS) or 9(5:30-6:30pm, 405 BASS)
Section 7
 Altschul S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25(17), 3389-402. PMID: 9254694
Altschul S.F. et al. (1994) Issues in searching molecular sequence databases. Nat Genet., 6(2), 119-29. PMID: 8162065
14(7:00-8:00pm, 405 BASS) or 16(5:30-6:30pm, 405 BASS)
Section 8
 Eddy S.R. (1998) Profile hidden Markov models. Bioinformatics, 14(9), 755-63. PMID: 9918945
Thompson J.D., Higgins D.G. and Gibson T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22(22), 4673-80. PMID: 7984417
28(7:00-8:00pm, 405 BASS) or 30(5:30-6:30pm, 405 BASS)
Section 9
 Levitt M. and Gerstein M. (1998) A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci U S A., 95(11), 5913-20. PMID: 9600892
Garnier J., Gibrat J.F. and Robson B. (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol., 266, 540-53. PMID: 8743705 ScienceDirect link
Dec
5(7:00-8:00pm, 308A Gibbs)
Section 10
 Review section for quiz 2; Q&A for final projects.

Related pages

Outline of Topics