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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Bioinformaticsisdefinedasascientificdisciplinethatencompassesallaspectsofbiologicalinformationacquisition,processing,storage,distribution,analysisandinterpretation,thatcombinesthetoolsandtechniquesofmathematics,computerscienceandbiologywiththeaimofunderstandingthebiologicalsignificanceofavarietyofdata.生物信息学的兴起Data……★Large-scaleandhigh-throughput★High-dimensional★Non-linear★Noisy★UnequallydistributedWhatisSystemsBiology?•Notanewconcept!•Systemsbiologyisanemergentfieldthataimsatsystem-levelunderstandingofbiologicalsystems(Kitano2002).•Tounderstandbiologyatthesystemlevel,wemustexaminethestructureanddynamicsandcellularorganismalfunction,ratherthanthecharacteristicsofisolatedpartsofacellororganism.Systems的层次性WhySystemsBiology?•Goldenopportunity,now!★Morethan16internationalmeetingsin2006★Morethan10booksinthepasttwoyears★Journals:Molecularsystemsbiology(Nature&EMBO),BMCsystemsbiology,IETsystemsbiology,EURASIPJournalonBioinformaticsandSystemsBiologyetc.Large-scale,high-throughputdataFieldsofComputationalSystemsBiology?•Biologicalnetworksconstruction,suchasgeneregulatorynetworks,cellularsignalingnetworks,metabolicnetworks,protein-proteininteractionnetworks,geneticinteractionnetworks,geneco-expressionnetworks,literaturenetworks.FieldsofComputationalSystemsBiology?•Propertiesofsystems,suchastopology,robustness,tolerance.Albertetal.,Nature2000FieldsofComputationalSystemsBiology?Gohetal.,PNAS2007P53regionTGFβregionRasregionCuietal.,MSB2007•Biologicalquestionsonsystems-levels,suchasdiseases,evolution,medicineetc.生物复杂网络的数学模型0ABCDE•图论(graphtheory)中的一个图(graph)：两个集合V(A,B,C,D,E)和E(AB,AC,AB,BC,CD,DE)1A2B3C4D5E网络可视化软件PajekAEFDCB有向网络AEFDCB*Vertices*Edges*Arcs自组织临界性(selforganizationcriticality)幂律分布powerlaw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，Duffield52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•。。。。。。。Howaboutnetworks?•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(top15%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(sixdegreesofseparation)。2001，Wattsinternet小世界网络实验小世界属性的度量+++_0ABCDEShortestpathA~E:A-B(C)-D-ENetworkdistance:3•Averageshortestpath(networkdistance)•Clusteringcoefficient(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(bipartitegraph)D3D1D2D1D2M1M2M3M4D3二部图：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-proteintarget)•基础医学和临床中的数据？•。。。。。。。。