CSSS 2008 Beijing-Readings-Week-Two

CSSS 2008 Beijing Home Faculty Participants Highlights Photos Schedule Readings and Lecture Notes Week One Week Two Week Three Week Four Projects T-Shirt Chinese Visa Information Travel Details and Logistics Final Papers

Aaron Clauset

• Power Laws
• Introduction to Networks I
• Introduction to Networks II

Background Reading

The following references cover background material for the three lectures.

• "The Structure and function of complex networks." M. E. J. Newman, SIAM Review 45, 167-256 (2003)
• "Power-law distributions in empirical data." A. Clauset, C. R. Shalizi and M. E. J. Newman. arXiv:0706.1062 (2007).

DI Zhengru

Introduction to Weighted Networks

Background Reading

• Ying Fan, Menghui Li, Peng Zhang, Jinshan Wub, Zengru Di. Accuracy and precision of methods for community identification in weighted networks. Physica A 377 (2007) 363­372.
• S. Boccaletti, , V. Latora, Y. Moreno, M. Chavef , D.-U. Hwang. Complex networks: Structure and dynamics. Physics Reports 424 (2006) 175 ­ 308.
• Menghui Li, Ying Fan, Dahui Wang, Daqing Li, Jinshan Wu, Zengru D. Small-world effect induced by weight randomization on regular networks. Physics Letters A 364 (2007) 488­493.
• Menghui Li, Dahui Wang, Ying Fan, Zengru Di, and Jinshan Wu1. Modelling weighted networks using connection count. New Journal of Physics 8 (2006) 72.

HAO Bai-lin

• Lecture 2: Visualization of DNA data and a few nice math therefrom (A PPT that contains more than used in class

Background Reading

Lecture 1：Symbolic Dynamics in Action or Applied Symbolic Dynamics

1. Bailin Hao, Elementary Symbolic Dyanmics and Chaos in Dissipative Systems,

  a monograph, World Scientific, 1989. Downloadable from Hao's webpage:
  http://www.itp.ac.cn/~hao/ESDCDS-hao.pdf
  Hao's apology: Since not all figures in this book were Postscript files and
  I have not made them into .eps yet, I have put an image of my personal copy
  in my website. It is a file of more than 20MB. That is why I did not put it
  in the SFI Wiki. I hope I will be able to do it in not-distant future. The
  symbolic dynamics chapters of this book are somehow outdated. For those who
  want to learn more about symbolic dynamics I suggest the following book.

2. Bailin Hao and Weimou Zheng, Applied Symbolic Dynamics and Chaos, WSPC, 1989,

  430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: Visualization of real DNA data and a few nice math therefrom

1. Shen Junjie at al., SeeDNA: a visualization tool for long DNA sequences and complete genomes It runs on RedHat Linux with GTK support. Its C source may be downloaded from Hao's website: http://www.itp.ac.cn/~hao/SeeDNA.tar.gz.

2. Bailin Hao and Huimin Xie, Factorizable Language: From Dyanmics to Biology

3. Xiaoli Shi et al., Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language

4. Bailin Hao and Lei Gao, Prokaryotic branch of tree of life: a composition vector approach

Dan Hruschka

• Models of Cultural Diversity
• Simple Models of Social Learning
• Neutral Models of Language Change

ZHAO Liping

• Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology Four slides on each page.
• Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology One slide on each page.

Background Reading

1. Pang et al., Inter-species transplantation of gut microbiota from human to pigs, The ISME J. 1(2007): 156-162)
2. Wei Jia, Houkai Li, Liping Zhao, and Jeremy K. Nicholson, Got microbiota: a potential new territory for drug targeting, Nature Reviews Drug Discovery, 7 (Feb 2008): 123-129.
3. Min Li et al., Symbiotic gut microbes modulate human metabolic phenotypes, Prod. Natl. Acad. Sci. USA 105(6) (Feb 2008): 2117-2122.