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Mount, David W. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2001. ISBN: 0879695978.
| 1 |
绪论/序列比对与动态规划 |
Mount. pp. 1-7, 29-35, 45-48, 51-64. |
| 2 |
多序列比对 I |
Mount. pp. 8-9, 65-89, 96-115, 140-155, 161-170. |
| 3 |
多序列比对 II |
Mount. pp. 139-150, 152-157, 161-171, 185-198. |
| 4 |
亲缘分析 |
Mount. pp. 237-280, 283-286, 291-308. |
| 5 |
文献讨论 |
Pellegrini, M., E. M. Marcotte, M. J. Thompson, D. Eisenberg, and T. O. Yeates. "Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles." Proc. Natl. Acad. Sci. USA. 96, no. 8 (13 Apr 1999): 4285-8.
Suel, G. M., S. W. Lockless, M. A. Wall, and R. Ranganathan. "Evolutionarily Conserved Networks of Residues Mediate Allosteric Communication in Proteins." Nat. Struct. Biol. 10, no. 1 (Jan 2003): 59-69. |
| 6 |
基因组序列与DNA序列分析 |
Woolf, Peter, Christopher Burge, Amy Keating, and Michael Yaffe. "Statistics and Probabilty Primer for Computational Biologists." MIT. BE.490/7.91 Spring 2004. (PDF)
Bork, Peer, and Richard Copley. "Genome Speak." Nature 409 (15 Feb 2001): 815. |
| 7 |
DNA序列比较与比对 |
Mount. Chap. 7. |
| 8 |
DNA模体建模与识别 |
Mount. Chap. 4. |
| 9 |
DNA序列分析中的马尔科夫模型与隐马尔科夫模型 |
Mount. Chap. 4. |
| 10 |
DNA序列进化 |
Mount. Chap. 4. |
| 11 |
RNA二级结构预测 |
Mount. Chap. 4. |
| 12 |
DNA/RNA序列功能预测的相关文献讨论 |
Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander. "Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Elements." Nature 423, no. 6937 (15 May 2003): 241-54.
Rivas, E., R. J. Klein, T. A. Jones, and S. R. Eddy. "Computational Identification of Noncoding RNAs in E. Coli by Comparative Genomics." Curr. Biol. 11, no. 17 (4 Sep 2001): 1369-73. |
| 13 |
期中考试 – 随堂 – 蛋白质和DNA序列分析 |
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| 14 |
蛋白质二级结构预测 |
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| 15 |
蛋白质结构与分类导论 |
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| 16 |
蛋白质结构比较
分子建模：方法及应用 |
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| 17 |
利用计算方法分析、预测和设计蛋白质序列及其结构
利用X射线晶体衍射图及核磁共振谱解析结构 |
Marti-Renom, et. al. Annu. Rev. Biophys. Biomol. Struct. 29 (2000): 291-325. |
| 18 |
利用X射线晶体衍射图及核磁共振谱解析结构 (续前节)
同源建模 |
Marti-Renom, et. al. Annu. Rev. Biophys. Biomol. Struct. 29 (2000): 291-325. |
| 19 |
蛋白质结构预测方法：同源建模与折叠识别 |
Bonneau, and Baker. Annu. Rev. Biophys. Biomol. Struct. 30 (2001): 173-189. |
| 20 |
指认方法和从头算 结构预测
基于计算的蛋白质设计 |
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| 21 |
系统生物学导论 |
Ideker, and Lauffenburger. TRENDS in Biotechnology 21 (2003): 255-262. |
| 22 |
反馈系统与耦合微分方程 |
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| 23 |
DNA微阵列与聚类分析 |
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| 24 |
DNA微阵列与聚类分析相关文献讨论 |
Segal, E., et. al. "Module Networks: Identifying Regulatory Modules and their Condition-specific Regulators from Gene Expression Data." Nature Genetics (2003).
Beer, M., and S. Tavazoie. "Predicting Gene expression from Sequence." Cell (2004).
Background Reading
Friedman, N. "Inferring Cellular Networks Using Probabilistic Graphical Models." Science (2004).
Appendix of Probability and Statistics Primer. |
| 25 |
基于计算的蛋白质组注释 |
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| 26 |
与基于计算的蛋白质组注释相关的文献讨论 |
Bader, J. S., A. Chaudhuri, J. M. Rothberg, and J. Chant. "Gaining Confidence in High-throughput Protein Interaction Networks." Nat Biotechnol. 22, no. 1 (Jan 2004): 78-85. Epub (14 Dec 2003).
Jansen, R., H. Yu, D. Greenbaum, Y. Kluger, N. J. Krogan, S. Chung, A. Emili, M. Snyder, J. F. Greenblatt, and M. Gerstein. "A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data." Science 302, no. 5644 (17 Oct 2003): 449-53. |
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