计算系统生物学简介

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，Duffield 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 。。。。。。。
计算系统生物学简介
崔庆华 2008-3-14
Outline
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 of mathematics, computer science and biology with the aim of understanding the biological significance of a variety of data.
Large-scale, high-throughput data ★ 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 Bioinformatics and Systems Biology etc.
Fields of Computational Systems Biology?
Properties of systems,
such as topology, robustness, tolerance.
Albert et al., Nature 2000
Fields of Computational Systems Biology?
Fields of Computational Systems Biology?
Biological networks construction, such as gene regulatory networks,
cellular signaling wenku.baidu.cometworks, metabolic networks, protein-protein interaction networks, genetic interaction networks, gene co-expression networks, literature networks.
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.
生物复杂网络的数学模型
E
B
D
1 2 3 4 5
A B C D E
A C 0
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)
网络可视化软件Pajek
A F E D
B C
有向网络
A F E D B C
*Vertices *Edges *Arcs
生物信息学的兴起
★ Large-scale and high-throughput ★ High-dimensional ★ Non-linear ★ Noisy ★ Unequally distributed
Data……
What is Systems Biology?
Not a new concept! Systems biology is an emergent field that
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， 度分离 度分离(six 地球上任意两个人之间的平均距离是 ，6度分离 degrees of separation)。 。 2001， Watts internet小世界网络实验 ， 小世界网络实验
小世界属性的度量
Average shortest path(network distance) Clustering coefficient (CC)
How about networks?
E
网络节点的度 (degree) 度的分布
A
B
D
C
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
E _ B + D
+ A 0
+
Shortest path A~E: A-B(C)-D-E
C
Network distance: 3
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 graph)
D1 D2 D3 M1 M2 M3 M4 D1 D2
D3
二部图： 一些例子
作者-文章(author-literature) 演员-电影(actor-film) 基因-疾病(gene-disease) 药物-靶标(drug-protein target) 基础医学和临床中的数据？ 。。。。。。。。
Systems的层次性
Why Systems Biology?
E _ B + D + C
+ A 0
http://www.newvisions.ucsb.edu/background/images/elephant.gif
Why Computational Systems Biology?
Golden opportunity, now!
Biological questions on systems-levels,
such as diseases, evolution, medicine etc.
Ras region TGFβ region
P53 region
Goh et al., PNAS 2007
Cui et al., MSB 2007