下表列出了专业参考读物。另外，在表格后还列出了本课程的相关文献。

文章

阅读列表

ses #	主题	阅读内容
1	引言 课程介绍， 现代生物学综述 I Abstraction Level 1: 序列 生物信息学实验/生物信息学在计算机业中的应用	Course Introduction, Review of Modern Biology I Alterovitz, G., E. Afkhami, and M. Ramoni. "Robotics, Automation, and Statistical Learning for Proteomics." In Focus on Robotics and Intelligent Systems Research. Edited by F. Columbus. Vol. 1. New York: Nova Science Publishers, Inc., 2005, sections I-II. (In press) Introduction to Bioinformatics Laboratory / Bioinformatics in the Computer Industry Moormans, M. W. Matlab on Athena, Technical Publication AC-71. Cambridge, MA: Massachusetts Institute of Technology, 2001. Pochet, N., et al. "Systematic benchmarking of microarray data classification: assessing the role of nonlinearity and dimensionality reduction." Bioinformatics, 2004. Kasturi, J., R. Acharya, and M. Ramanathan. "An information theoretic approach for analyzing temporal patterns of gene expression." Bioinformatics 19, no. 4 (2003): 449-58.
2	Abstraction Level 1: 序列 现代生物学 综述II 序列分析：基序和调控	Review of Modern Biology II Alterovitz, G., E. Afkhami, and M. Ramoni. "Robotics, Automation, and Statistical Learning for Proteomics." In Focus on Robotics and Intelligent Systems Research. Edited by F. Columbus. Vol. 1. New York: Nova Science Publishers, Inc., 2005, sections I-II. (In press) Sequence Analysis: Motif and Regulation Kellis, M., et al. "Sequencing and comparison of yeast species to identify genes and regulatory elements." Nature 423, no. 6937 (2003): 241-54. Kellis, M., et al. "Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery." Journal of Computational Biology 11, no. 2-3 (2004): 319-55.
3	Abstraction Level 1: 序列 序列分析：基因和基因组 序列分析：基因进化	Sequence Analysis: Genes and Genome Kellis, M., B. W. Birren, and E. S. Lander. "Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae." Nature 428, no. 6983 (2004): 617-24. Jaillon, O., et al. "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, no. 7011 (2004): 946-57. Sequence Analysis: Gene Evolution Kellis, M., B. W. Birren, and E. S. Lander. "Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae." Nature 428, no. 6983 (2004): 617-24.
4	Abstraction Level 2: 表达 微阵列表达数据分析 机器学习：贝叶斯判别方法	Microarray Expression Data Analysis Sebastiani, P., I. S. Kohane, and M. F. Ramoni. "The role of machine learning in the post-genomic era." Mach Learning 52, no. 1-2 (2003): 5-9. Machine Learning: Bayesian Methodologies Ramoni, M.F., P. Sebastiani, and I.S. Kohane. "Cluster analysis of gene expression dynamics." Proc Natl Acad Sci U S A 99, no. 14 (2002): 9121-6.
5	Abstraction Level 2: 表达 生物技术业中的生物信息学 Abstraction Level 4: 系统/Misc 系统控制与前馈	Bioinformatics in the Biotech Industry Kramer, R., and D. Cohen. "Functional genomics to new drug targets." Nature Reviews Drug Discovery 3, no. 11 (2004): 965-72. Lawler, A. "Diabetes research. Broad-Novartis venture promises a no-strings, public gene database." Science 306, no. 5697 (2004): 795. Control and Feedback in Systems Rangel, C., et al. "Modeling T-cell activation using gene expression profiling and state-space models." Bioinformatics 20, no. 9 (2004): 1361-72.
6	Abstraction Level 4: 系统/Misc 无尺度网络 I 无尺度网络 II	Scale-free Networks I Goh, K. I., et al. "Classification of scale-free networks." Proc Natl Acad Sci U S A 99, no. 20 (2002): 12583-8. Bilke, S., and C. Peterson. "Topological properties of citation and metabolic networks." Phys Rev E Stat Nonlin Soft Matter Phys 64, no. 3 Pt 2 (2001): 036106. Scale-free Networks II Goh, K. I., et al. "Classification of scale-free networks." Proc Natl Acad Sci U S A 99, no. 20 (2002): 12583-8. Rzhetsky, A., and S. M. Gomez. "Birth of scale-free molecular networks and the number of distinct DNA and protein domains pergenome." Bioinformatics 17, no. 10 (2001): 988-96.
7	Abstraction Level 3: 蛋白质组学 蛋白质组学中的统计模型和随机处理 蛋白质组学的信号处理	Statistical Models and Stochastic Processes in Proteomics Alterovitz, G., E. Afkhami, and M. Ramoni. "Robotics, Automation, and Statistical Learning for Proteomics." In Focus on Robotics and Intelligent Systems Research. Edited by F. Columbus. Vol. 1. New York: Nova Science Publishers, Inc., 2005, sections IV-V. (In press) Signal Processing for Proteomics Baggerly, K. A., J. S. Morris, and K. R. Coombes. "Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments." Bioinformatics 20, no. 5 (2004): 777-85.
8	Abstraction Level 3: 蛋白质组学s 生物学方法、自动化操作和机器人技术 结论 项目讨论与总结	Biological Methods, Automation, Robotics Alterovitz, G., E. Afkhami, and M. Ramoni. "Robotics, Automation, and Statistical Learning for Proteomics." In Focus on Robotics and Intelligent Systems Research. Edited by F. Columbus. Vol. 1. New York: Nova Science Publishers, Inc., 2005, section III. (In press)

参考文献

Book Chapter

Alterovitz, G., E. Afkhami, and M. Ramoni. "Robotics, Automation, and Statistical Learning for Proteomics." In Focus on Robotics and Intelligent Systems Research. Edited by F. Columbus. Vol. 1. New York: Nova Science Publishers, Inc., 2005. (In press).

Texts

Oppenheim, A. V., A. S. Willsky, and H. Nawab. Signals and Systems. 3rd ed. Englewood Cliffs, NJ: Prentice Hall, 1997.

Papoulis, A., and S. U. Pillai. Probability, Random Variables and Stochastic Processes: Sanitary and Water Resources Engineering (Sanitary & Water Resources Engineering S). New York, NY: McGraw-Hill, 2002.

Kohane, I. S., A. T. Kho, and A. J. Butte. Microarrays for an Integrative Genomics. Cambridge, MA: MIT Press, 2002. ISBN: 026211271X.

Links

Hunter, Lawrence. Introduction to Molecular Biology for the Computer Scientist. (PDF)