Molecular, Cell and Developmental Biology 172 Genomics ... - UCLA

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Week 726 Nov 10, Transcriptional regulation: cis motifs27 Nov 12, Transcriptional regulation: regulatory networks28 Nov 14, MIDTERM29 LAB: Prepare for midtermWeek 830 Nov 17, Transcriptional regulation: gene set analysis31 Nov 19, Epigenomics: DNA methylation32 Nov 21, Student presentations33 LAB: Chlamydomonas transcription analysis34Week 935 Nov 24, Epigenomics: the histone code36 Nov 26, Epigenomics: nucleosome positioning37 Nov 28, Thanksgiving holiday38 LAB: Chlamydomonas transcription analysispresentationsWeek 1039 Dec 1, Systems biology: yeast metabolic cycle40 Dec 3, Systems biology: network motifs41 Dec 5, Student presentations42 LAB: Chlamydomonas transcription analysispresentationsWeek 1122 FinalsCourse Reading List:Textebook: noneAdditional reading:Week 0Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409,860-921 (2001).Week 1Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563-7 (1996).
Blattner, F. R. et al. The complete genome sequence of Escherichia coli K-12. Science277, 1453-74 (1997).Week 2Needleman, S. B. & Wunsch, C. D. A general method applicable to the search forsimilarities in the amino acid sequence of two proteins. J Mol Biol 48, 443-53 (1970).Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic localalignment search tool. J Mol Biol 215, 403-10 (1990).Dayhoff, M.O., Schwartz, R.M. & Orcutt, B.C. A model of evolutionary change inproteins. Atlas of protein sequence and structure 1978.Sneath, P. H. & Sokal, R. R. Numerical taxonomy. Nature 193, 855-60 (1962).Week 3Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O.Assigning protein functions by comparative genome analysis: protein phylogeneticprofiles. Proc Natl Acad Sci U S A 96, 4285-8 (1999)Bowers, P. M. et al. Prolinks: a database of protein functional linkages derived fromcoevolution. Genome Biol 5, R35 (2004).Lee, I., Date, S. V., Adai, A. T. & Marcotte, E. M. A probabilistic functional network ofyeast genes. Science 306, 1555-8 (2004).Week 4Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature418, 387-91 (2002).Giaever, G. et al. Chemogenomic profiling: identifying the functional interactions ofsmall molecules in yeast. Proc Natl Acad Sci U S A 101, 793-8 (2004).Kamath, R. S. et al. Systematic functional analysis of the Caenorhabditis elegans genomeusing RNAi. Nature 421, 231-7 (2003).Tong, A. H. et al. Global mapping of the yeast genetic interaction network. Science 303,808-13 (2004).Week 5
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