计算系统生物学简介

1、计算系统生物学简介崔庆华2008-3-14Outline 计算系统生物学简介网络的数学模型网络可视化工具Pajek无尺度网络和小世界网络生物信息学的分支Bioinformatics is defined as a scientific discipline that encompasses all aspects of biological information acquisition, processing, storage, distribution, analysis and interpretation, that combines the tools and techniques

2、of mathematics, computer science and biology with the aim of understanding the biological significance of a variety of data.生物信息学的兴起Data Large-scale and high-throughput High-dimensional Non-linear Noisy Unequally distributedWhat is Systems Biology?Not a new concept!Systems biology is an emergent fie

3、ld that aims at system-level understanding of biological systems (Kitano 2002).To understand biology at the system level, we must examine the structure and dynamics and cellular organismal function, rather than the characteristics of isolated parts of a cell or organism. Systems的层次性Why Systems Biolo

4、gy?/background/images/elephant.gif+_0ABCDEWhy Computational Systems Biology?Golden opportunity, now! More than 16 international meetings in 2006 More than 10 books in the past two years Journals: Molecular systems biology (Nature & EMBO), BMC systems biology, IET systems biology, EURASIP Journal on

5、Bioinformatics and Systems Biology etc.Large-scale, high-throughput dataFields of Computational Systems Biology?Biological networks construction, such as gene regulatory networks, cellular signaling networks, metabolic networks, protein-protein interaction networks, genetic interaction networks, gen

6、e co-expression networks, literature networks.Fields of Computational Systems Biology?Properties of systems, such as topology, robustness, tolerance. Albert et al., Nature 2000Fields of Computational Systems Biology?Goh et al., PNAS 2007P53 regionTGF regionRas regionCui et al., MSB 2007Biological qu

7、estions on systems-levels, such as diseases, evolution, medicine etc.生物复杂网络的数学模型0ABCDE图论(graph theory)中的一个图(graph)：两个集合V(A,B,C,D,E)和E(AB,AC,AB,BC,CD,DE)ABCDE网络可视化软件PajekAEFDCB有向网络AEFDCB*Vertices*Edges*Arcs自组织临界性 (self organization criticality)幂律分布 power law钟形分布钟形分布成年人身高、体重跳远的距离苹果大小。幂律分布城镇人口：纽约800万，D

8、uffield 52个 地震战争人类语言词汇的使用频率音乐年薪网站点击量论文引用率。How about networks?网络节点的度 (degree)度的分布ABCDE随机网络真实网络-无尺度网络真实网络社会网络电话calling网络通信网络交通网络河道电网。真实网络-hubs (top 15% degree)真实网络-小世界属性真实网络-小世界属性地球上任意两个人之间的平均距离是6，6度分离(six degrees of separation)。2001， Watts internet小世界网络实验小世界属性的度量+_0ABCDEShortest path AE: A-B(C)-D-ENetwork distance: 3Average shortest path(network distance)Clustering coefficient (CC)小世界属性的度量-例子构建和研究网络的一个模型：二部图(bipartite gr