CBB752/CPSC452/CPSC752/MBB452/MBB752/MCDB452/MCDB752
http://www.gersteinlab.org/courses/452/Discussion sections
| Jan | 1/21/2009 (5 PM and 8 PM) Bass 205 |
T.F. Smith and M.S. Waterman. (1981) Identification of common molecular subsequences. Journal of Molecular Biology,147(1): 195-7. PMID: 7265238. Article |
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| Myers G. (1999) A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming. Journal of the ACM, 46, 395-415. Article | |||
1/28/2009 (5 PM and 8 PM) Bass 205 |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215(3):403-10. PMID: 2231712. Article | ||
| Garnier J, Gibrat JF, Robson B. (1996) GOR method for predicting protein secondary structure from amino acid sequence.Methods in Enzymology,266: 540-53. PMID: 8743705. Article | |||
| Feb | 2/04/2009 (5 PM and 8 PM) Bass 205 |
Michael Levitt and Mark Gerstein. (1998) A unified statistical framework for sequence comparison and structure comparison. Proc. Nat. Sci.,95(11): 5913-20. PMID: 9600892. Article |
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| Liisa Holm and Chris Sander. (1993) Protein Structure Comparison by Alignment of Distance Matrices. J. Mol. Biol., 233, 123-138. PMID: 8377180. Article | |||
2/11/2009 (5 PM and 8 PM) Bass 205 |
ML Connolly. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science, 221(4612): 709-13. PMID: 6879170. Article |
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| Martin Karplus and J. Andrew McCammon. (2002) Molecular dynamics simulations of biomolecules. Nature Structural Biology,9, 646-52. PMID: 12198485. Article | |||
2/18/2009 No Meeting This Week (To be held at later date) |
S Stephens, D LaVigna, M DiLascio, J Luciano. (2006) Aggregation of Bioinformatics Data Using Semantic Web Technology. Web Semantics: Science, Services and Agents on the World Wide Web, 4(3): 216-21. Article |
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| X Zhu, M Gerstein, M Snyder. (2007) Getting connected: analysis and principles of biological networks. Genes and Development, 21, 1010-24. Article | |||
2/25/2009 (5 PM and 8 PM) Bass 205
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JC Venter, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304(5667): 66-74. PMID: 15001713. Article |
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| CR Woese, O Kandler, ML Wheelis. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.Proc. Nat. Acad. Sci.,87(12): 4576-9. Article | |||
| Mar | 3/04/2009 (5 PM and 8 PM) Bass 205 |
Tarca AL, Carey VJ, Chen XW, Romero R, Drăghici S. (2007) Machine learning and its applications to biology. PLoS Comput Biol.,26: e116. PMID: 17604446. Article |
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| Kingsford C and Salzberg SL. (2008) What are decision trees? Nature Biotech,26, 1011-1013. Article | 3/25/2009 |
Alter O, Brown PO, Botstein D. (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Nat Acad Sci USA,29:97(18), 10101-6. PMID: 10963673. Article |
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| van 't Veer et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature,415, 530-6. Article | |||
| April | 4/01/2009 (6 PM and 8 PM) Bass 205 |
DeRisi JL, Iyer VR, and Brown PO. (1997) Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science, 278(5338): 680-6. Article |
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| Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, and Brown PO. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature,409, 533-8. Article | 4/08/2009 (5 PM and 8 PM) Bass 205 |
Zhu H, et al. (2001) Global analysis of protein activities using proteome chips. Science, 293(5537): 2101-5. PMID: 11474067. Article |
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| Hughes TR, et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102(1): 109-26. Article | 4/15/2009 (5 PM and 8 PM) Bass 205 |
Pop M, Phillippy A, Delcher AL, Salzberg SL. (2004) Comparative genome assembly. Brief Bioinform., 5(3): 237-48. PMID: 15383210. Article |
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| Mardis ER. (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet., 9: 387-402. Article |
Programming Assignments
Assignment 1: Due 02/05/2009 by 5 PM
Input File, Assignment
Assignment 2: Due 02/25/2009 by 5 PM
Training Set, Test Set, Assignment
Related pages
Outline of Topics