系统生物学选讲（2022春季学期） 

课号：08411207    学分：3

主持人：汤超

授课老师：齐志，林一瀚，宋晨，罗春雄，林杰，李志远，汤超，张磊，欧阳颀，罗冬根，来鲁华，韩敬东

助教：蔡之远（2001111552@pku.edu.cn）

时间：周二 15:10 - 17:00（第7-8节课）

地点：三教305

本课以深度文献阅读为主，重点介绍生物学中理论与实验相结合而产生的概念、原理、方法，及其当前的发展趋势和面临的挑战。每堂课针对一个方面，深入讨论一篇文章，适当参考第二篇文章。学生在课前应仔细阅读要讨论的文章，并在课堂上积极参与讨论。指导老师介绍背景知识，启发、引导讨论。

课程涉及的内容包括：生物系统中的随机性和噪声、双稳态、协同性、鲁棒性、能耗与精确性，细菌生长中的定量规律，图灵斑图，定量神经生物学，合成生物学，从生物网络的角度来理解疾病、衰老及药物相互作用等。本课为定量生物学中心研究生必修课。欢迎其它院系的研究生及本科生选修。

参考书：

  ●  Bruce Alberts et al. Molecular Biology of the Cell.

  ●  Daniel L. Hartl and Elizabeth W. Jones. Genetics: Analysis of Genes and Genomes.

  ●  Uri Alon. An introduction to systems biology: design principles of biological circuits.

课程网站：http://cqb.pku.edu.cn/xtswxxj/

评分方式：

阅读报告 40％,  课堂参与 30％，Project 30％

阅读报告：每堂课开始前提交关于该课将要讨论的文章的阅读报告，可以包括：该文章讨论了什么科学问题，用了什么方法，得到了什么结论，有什么意义，对你有什么启发，你有什么问题等内容。长度在一页纸左右。

课堂参与：包括发言，提问，回答问题，互动 ，感想，体会，辩论，上黑板讲解，推公式等。

Project：学生自己分组（3-5人），其中两组讲最后两次课，其它组自选一个project进行展示，不能讲与自己研究有关的内容。

课程安排

课程文献合集下载

 Class 1  Course Introduction（汤超）2月22日

 Class 2  DNA-Protein Interactions: Transcription factor search and binding（齐志）3月1日

    Wang, F. et al. The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion. Nat. Struct. Mol. Biol. 20: 174-181 (2013).

    Riggs, A. D., Bourgeois, S. & Cohn, M. The lac repressor-operator interaction. III. Kinetic studies. J. Mol. Biol. 53: 401-417 (1970).

 Class 3  Fluctuations and noise - Gene products（林一瀚）3月8日

    Elowitz MB, Levine AJ, Siggia ED, Swain PS. 2002. Stochastic gene expression in a single cell. Science 297: 1183-6. (Supplementary Material will also be discussed)

    Maamar H, Raj A, Dubnau D. 2007. Noise in gene expression determines cell fate in Bacillus subtilis. Science 317: 526-9.

 Class 4  All-or-none transition I - Cooperativity（宋晨）3月15日

    Monod J, Wyman J, and Changeux J-P. 1965. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12: 88-118.

    Duke TAJ, Bray D. 1999. Heightened sensitivity of a lattice of membrane receptors. PNAS 96: 10104-10108.

 Class 5  All-or-none transition II - Bistability（罗春雄）3月22日 （两篇文章都要阅读、讨论）

    Novick A, Wiener M. 1957. Enzyme induction as an all-or-none phenomenon. PNAS 43:553-66.

    Paul J. Choi, Long Cai, Kirsten Frieda, X. Sunney Xie.2008. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322: 442-5.

 Class 6  Bacterial growth law（林杰）3月29日

    Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T. 2010. Interdependence of cell growth and gene expression: origins and consequences. Science 330: 1099-1102.

    Monod J. 1949. The growth of bacterial cultures. Ann Rev Microbiol 3: 371-394.

4月5日清明节假期

 Class 7  Microbial community（李志远）4月12日

    Goldford, Joshua E., et al. "Emergent simplicity in microbial community assembly." Science 361.6401 (2018): 469-474.

    Ratzke, Christoph, Julien Barrere, and Jeff Gore. "Strength of species interactions determines biodiversity and stability in microbial communities." Nature ecology & evolution 4.3 (2020): 376-383.

 Class 8  Energy-accuracy relation（汤超）4月19日

    Hopfield JJ. 1974. Kinetic proofreading: a new mechanism for reducing errors inbiosynthetic processes requiring high specificity. PNAS71: 4135-9.

    Lan G,Sartori P, Neumann S, Sourjik V, Tu Y. 2012. The energy-speed-accuracy trade-off in sensory adaptation. Nature Physics 8: 422-428.

 Class 9  Turing Pattern（张磊）4月26日

    Kondo,S., & Miura, T. (2010). Reaction-diffusion model as a framework forunderstanding biological pattern formation. Science, 329:1616-1620.

    J.D. Murray, Mathematical Biology II (Springer Verlag, Berlin, 2003) Chapter2: Spatial Pattern Formation with Reaction Diffusion Systems

5月3日劳动节假期

 Class 10  Synthetic Biology（欧阳颀）5月10日

    Gardner, Timothy S., Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-42.

    Elowitz M, Leibler S. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-8.

 Class 11  Neuroscience: Efficient Sensory Coding（罗冬根） 5月17日

    Barlow, Horace B. "Possible principles underlying the transformation of sensory messages." Sensory communication 1.01 (1961).

    Cao, LH., Yang, D., Wu, W. et al. Odor-evoked inhibition of olfactory sensory neurons drives olfactory perception in Drosophila . Nat Commun 8, 1357 (2017).

 Class 12  Disease and drug networks（来鲁华）5月24日

    Behar M, Barken D, Werner SL, Hoffmann A. 2013. The dynamics of signaling as a pharmacological target. Cell 155: 448-461.

    Yang K et al. 2008. Finding multiple target optimal intervention in disease-related molecular network. Mol. Sys. Biol. 4: 228.

 Class 13  Systems biology of aging and development（韩敬东） 5月31日 

    Ahadi S, et al. 2020. Personal aging markers and ageotypes revealed by deep longitudinal profiling. Nature Medicine 26: 83-90.

    Xia, Xian, et al. Three-dimensional facial-image analysis to predict heterogeneity of the human ageing rate and the impact of lifestyle. Nature Metabolism 2.9 (2020): 946-957.

    Lehallier, Benoit, et al. Undulating changes in human plasma proteome profiles across the lifespan. Nature medicine 25.12 (2019): 1843-1850.

 Class 14  Robustness（学生）6月7日

    Barkai N, Leibler S. 1997. Robustness in simple biochemical networks. Nature 387: 913-7.

    Li F, Long T, Lu Y, Ouyang Q, and Tang C. 2004. The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA. 101: 4781–4786.

 Class 15  Mutation: lessons from phage（学生）

    Luria SE, Delbruck M. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491-511.

    The phage group. https://en.wikipedia.org/wiki/Phage_group

 Project Presentation  6月14日