演讲人：
Michael Q. Zhang Cold Spring Harbor Laboratory, USA
时间： 2005-11-04 09:30-2005-11-29 11:30
地点：FIT-1-101
内容：
Course focus: (1)What is the questions;
(2) Biological backgrounds;
(3)Current approaches;
(4)Open challenges.
Topics not covered: (1) Sequence alignment and database search;
(2) Phylogenetic trees;
(3) RNA folding;
(4) Protein structure-function;
(5) Molecular evolution;
(6) Population genetics; etc.
Next year topics: (1) Alternative splicing;
(2) Translational regulation;
(3) RNAi and miRNAs;
(4) Epigenomics;
(5) Cancer and Aging.
Tentative course outline on genomic sequence and microarray data analyses: (1)Overview: Genomics, revolution in biology and life sciences;
(2)Finding protein coding genes in Eukaryotic genomes;
(3)Transciptional regulation and promoter prediction;(4)Identification of cis-regulatory motifs and modules;
(5)Expression microarrays and transcriptome analysis;
(6)ChIP-chip and protein localization analysis;
(7)Genomic arrays and CNP analysis;
(8)Gene expression networks in systems biology;
Recommended references: 1 Overview: Genomics, revolution in biology and life sciences
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Watson JD, Gilman M, Witkowski J, Zoller M (1992) Recombinant DNA, 2nd Ed. New York
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Gerhardt J, Kirschner M. (1997) Cells, Embryos, and Evolution (Blackwell Scientific, Malden, MA)
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Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. & Walter, P. (2002) Molecular Biology of the Cell (Garland, New York).
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Lander E, et al. Nature. 2001 Feb 15;409(6822):860-921. Erratum in: Nature 2001 Aug 2;412(6846):565.
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Venter C, et al. The sequence of the human genome. Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838.
2 Finding protein coding genes in Eukaryotic genomes
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Zhang MQ (2002) Computational Prediction of Eukaryotic Protein-Coding Genes - Nat Rev Genet 3(9):698-709
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Solovyev VV (2002) Finding genes by computer: probabilistic and discriminative approaches. – Chapter 9, Current Topics in Computational Molecular Biology (Jiang T, Xu Y & Zhang MQ, eds.) pp201-248 MIT Press, Cambridge, Massachusetts.
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Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol. 268:78-94.
3 Transciptional regulation and promoter prediction
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Carey M, Smale S (2000) Transcriptional regulation in Eukaryotes: Concepts, Strategies and techniques.CSHL Press.
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Zhang MQ (2003) Prediction, Annotation and Analysis of Human Promoters - CSHL Quantitative Biology Symposium 68. pp217-225 Cold Spring Harb Symp Quant Biol 2003;68:217-225
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Zhang MQ (2002) Computational Methods for Promoter Recognition - Chapter 10, Current TopITCS in Computational Molecular Biology (Jiang T, Xu Y & Zhang MQ, eds.) pp249-268 MIT Press, Cambridge, Massachusetts
4 Identification of cis-regulatory motifs and modules
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Zhang MQ (2002) Computational Methods for Promoter Recognition - Chapter 10, Current Topics in Computational Molecular Biology (Jiang T, Xu Y & Zhang MQ, eds.) pp249-268 MIT Press, Cambridge, Massachusetts
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Stormo GD, Fields DS (1998) Trends Biochem. Sci. 23, 109–113.
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Berg, O. G. & von Hippel, P. H. (1987) J. Mol. Biol. 193, 723–750
5 Expression microarrays and transcriptome analysis
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Zhang MQ (1999) Large Scale Gene Expression Data Analysis: A New Challenge to Computational Biologists - Genome Res 9(8):681-688
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Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998) Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization - Mol Biol Cell 9(12):3273-3297
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Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet. Suppl:496-501
6 ChIP-chip and protein localization analysis
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Ren B, Dynlacht BD (2004) Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol. 376:304-15.
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Horak CE, Snyder M (2002) ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol. 350:469-83.
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Van Steensel B (2005) Mapping of genetic and epigenetic regulatory networks using microarrays.Nat Genet. Suppl:S18-24.
7 Genomic arrays and CNP analysis
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Thompson CT, Gray JW (1993) Cytogenetic profiling using fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). J Cell Biochem Suppl. 17G:139-43.
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Pinkel D, Albertson DG (2005) Array comparative genomic hybridization and its applications in cancer.Nat Genet. Suppl:S11-7.
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Lucito R, et al. (2003) Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13:2291-305.
8 Gene expression networks in systems biology
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Levine M, Davidson EH (2005) Gene regulatory networks for development. Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4936-42.
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Davidson EH et al (2002)A genomic regulatory network for development. Science. 295:1669-78.
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Davidson, E. H. (2001) Genomic Regulatory Systems (Academic, San Diego)
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Bar-Joseph Z, et al. (2003) Computational discovery of gene modules and regulatory networks. Nat Biotechnol. 21:1337-42
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Segal E, Friedman N, Kaminski N, Regev A, Koller D. (2005) From signatures to models: understanding cancer using microarrays. Nat Genet. Suppl:S38-45.
