Turning genomics data into Biology课件
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分子生物学课件(第二章)
Cytoplasm(90%), Nucleus(10%),viruses
tRNA
rRNA
mRNA
1.1.2.1 mRNA
Life time is short
Each polypeptide has corresponding mRNA，the difference among different mRNA is quite big (in length and molecular weight)；
♬ Experimental basis
① X~ray photograph of DNA with high quality：
DNA specimens from different species have
the same results（constant width; 3.4nm）；
② Chargaff rules：the rule of the composition of
Double helix stairway in the Vatican Museum
2.2.1 key notes of DNA double helix
Two polynucleotide chains in a DNA double helix antiparallel（one strand runs in the 5 ’ → 3 ’ direction, whlie its partner runs 3’→5’）
Every Aa at least has a correspnding tRNA（tRNA、 tRNAAla）。
Different tRNA has almost the same big，73-98 Nts
系统生物学简介systemsbiology
Database, schema standards
Modelling; ODEs, Constraint-based optimisation, Solving inverse problems, Novel strategies
Iteration between theory and experiment
一个自稳态系统是一个开放系统，通过由相互依赖的调控 机制严格控制的多重动态平衡来维持其结构和功能
History
• Term coined at 1960s, however theoretical people and experimental biologists diverged • Renaissance at 1990s
Genome-wide protein-metabolite binding constants Regulatory interactions Genome-wide protein-protein binding constants
Experimentation Analysis
Genome-wide high-throughput enzyme kinetics
Model organism/ system of choice
Transcriptome Proteome Metabolome
New theory
New methodology
Genome-wide protein-inhibitor binding constants (Chemical genetics)
E. Schrödinger (1944) What is life? Cambridge University Press
生物化学及分子生物学(人卫第九版)-27组学与系统生物学 ppt课件
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第五节
其他组学
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一、糖组学研究生命体聚糖多样性及其生物学功能
（一）糖组学分为结构糖组学与功能糖组学两个分支 （二）色谱分离/质谱鉴定和糖微阵列技术是糖组学研究的主要技术 （三）糖组学与肿瘤的关系密切
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二、脂组学揭示生命体脂质多样性及其代谢调控
（一）脂组学是代谢组学的一个分支 （二）脂组学研究的三大步骤——分离、鉴定和数据库检索
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（三）MPSS是以序列测定为基础的基因表达谱高通量分析新技术
大规模平行信号测序系统(MPSS)
https:///probe/docs/techmpss/
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三、转录组测序和单细胞转录组分析是转录组学的核心任务
（一）高通量转录组测序是获得基因表达调控信息的基础 （二）单细胞转录组有助于解析单个细胞行为的分子基础
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2.物理作图就是描绘杂交图、限制性酶切图及克隆系图
物理作图（physical mapping）以物理尺度（bp或kb）标示遗传标志 在染色体上的实际位置和它们间的距离，是在遗传作图基础上绘制的更为 详细的基因组图谱。
常用的物理作图方法
荧光原位杂交图（fluorescent in situ hybridization map，FISH map） 限制性酶切图（restriction map） 连续克隆系图（clone contig map）
第27章
组学与系统生物医学
作者 : 杨生生 焦炳华
单位 : 海军军医大学
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目录
第一节 基因组学 第二节 转录组学
课件1-系统生物学与合成生物学
S5
S6
X1
Typical replies: 1. Nothing happens. 2. Nothing happens unless it is the rate-limiting step. 3. The rate v goes down, but that’s all. 4. S3 goes up. 5. S4 goes down. 6. Species downstream of v go down. 7. Steady State flow changes but species levels don’t. 8. Xo and X1 change
Technologies to study systems at different levels
Genomics (HT-DNA sequencing) (HTMutation detection (SNP methods) Transcriptomics (Gene/Transcript measurement, SAGE, gene chips, microarrays) Proteomics (MS, 2D-PAGE, protein 2Dchips, Yeast-2-hybrid, X-ray, NMR) YeastXMetabolomics (NMR, X-ray, capillary Xelectrophoresis)
So where do we start?
Feedback loops
So where do we start?
So where do we start?
autoregulation
So where do we start?
X Y
– 转录因子X调控基因Y 转录因子X调控基因Y
Bioinformatics
Bioinformatics
Chien-Yu Chen Graduate school of biotechnology and bioinformatics, Yuan Ze University
Course Information
Web page
– .tw/~cychen/course/922BioInfo/922-BioInfo-CourseInformation.htm
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Functional Genomics – Research Issues
Which genes are expressed in which tissues? How is the expression of a gene affected by extracellular influences? Which genes are expressed during the development of an organism? What is the effect of misregulated expression of a gene? What patterns of gene expression cause a disease or lead to disease progression? What patterns of gene expression influence response to treatmen Reading Frames
Consider the double-stranded DNA sequence below
5' CAATGGCTAGGTACTATGTATGAGATCATGATCTTTACAAATCCGAG 3' 3' GTTACCGATCCATGATACATACTCTAGTACTAGAAATGTTTAGGCTC 5'
Chien-Yu Chen Graduate school of biotechnology and bioinformatics, Yuan Ze University
Course Information
Web page
– .tw/~cychen/course/922BioInfo/922-BioInfo-CourseInformation.htm
12
Functional Genomics – Research Issues
Which genes are expressed in which tissues? How is the expression of a gene affected by extracellular influences? Which genes are expressed during the development of an organism? What is the effect of misregulated expression of a gene? What patterns of gene expression cause a disease or lead to disease progression? What patterns of gene expression influence response to treatmen Reading Frames
Consider the double-stranded DNA sequence below
5' CAATGGCTAGGTACTATGTATGAGATCATGATCTTTACAAATCCGAG 3' 3' GTTACCGATCCATGATACATACTCTAGTACTAGAAATGTTTAGGCTC 5'
北京大学细胞生物学课件
Assembly of the Individual Sequences
Individual sequencing reads are compared to each other and where they overlap can be assembled to create contigs
Assembly of the Individual Sequences
• BAC（Bacterial artificial chromosome），用细菌的F质 粒及其调控基因构建了细菌染色体克隆载体，其克隆 能力在125~150 Kbp左右。以BAC为基础的克隆载体 形成嵌合体的频率较低，转化效率高，而且以环状结 构存在于细菌体内，易于分辨和分离纯化，已被科学 界广泛接受。
• 人类基因组计划（Human Genome Project，HGP）： 90年代提出并已基本完成，同40年代原子弹爆炸，60 年代人类登月一起被认为是二十世纪科技发展史上的 三大创举。
History of the Human Genome Project
1990 Official start of HGP with 3 billion $ and a 15 year horizon. 1999 Sanger Centre publishes chromosome 22 2001 Draft Genome published: Celera & Public 2003 Completion (almost) of Human Genome
基因组计划
• 基因组（genome）是生物体内遗传信息的集合，是某 个特定物种细胞内全部DNA分子的总和。
• 基因组学（genomics）是指研究并解析生物体整个基 因组的所有遗传信息的学科。
中国科技大学课件系列：《生物信息学》01
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科研机构及网络资源中心
Bioinformatics Links Directory： 各种数据库等
如 PDB (Protein Data Bank) UniProt 数据库 软件资源：
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国内生物信息中心举例
CBIPKU：北京大学生物信息中心 BioSino：中国生物信息
中国科学院上海生命科学院生物信息中心 上海生物信息技术研究中心
1. 1970年，Gibbs AJ 和 McIntyre GA，点阵法进行氨 基酸和核酸的序列比较：当相同的字母在两条序列中 同时出现时，在交叉处置点。
2. 1970年，Needleman-Wunsch，全局优化的序列比 对算法：允许匹配、错配和缺失。动态规划的算法： 任务可分割，分成更小的子问题进行解决。
生物信息学 (Bioinformatics)
1
背景
人类基因组计划(Human Genome Project, HGP)：1990年正式启动，旨在完成人类基 因组约30亿个碱基的全序列测定。
海量生物数据的迅速膨胀：DNA、RNA和 蛋白质序列，蛋白质二级结构和三维结构数 据，蛋白质相互作用数据等。
2.数学知识：概率论与统计学等 3.算法及编程能力：JAVA, Perl/Python，
PHP+MySQL, …
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生物信息学的常用算法与方法
动态规划算法(Dynamic programming)； 贝叶斯统计(bayesian statistic)； 人工神经网络(ANNs)； 马尔可夫模型和隐马尔科夫模型(HMM)； 遗传算法(Genetic Algorithm)； 蒙特卡洛方法(Monte Carlo)； 模拟退火算法(Simulated Annealing)； 支持向量机(SVM); …
科研机构及网络资源中心
Bioinformatics Links Directory： 各种数据库等
如 PDB (Protein Data Bank) UniProt 数据库 软件资源：
34
国内生物信息中心举例
CBIPKU：北京大学生物信息中心 BioSino：中国生物信息
中国科学院上海生命科学院生物信息中心 上海生物信息技术研究中心
1. 1970年，Gibbs AJ 和 McIntyre GA，点阵法进行氨 基酸和核酸的序列比较：当相同的字母在两条序列中 同时出现时，在交叉处置点。
2. 1970年，Needleman-Wunsch，全局优化的序列比 对算法：允许匹配、错配和缺失。动态规划的算法： 任务可分割，分成更小的子问题进行解决。
生物信息学 (Bioinformatics)
1
背景
人类基因组计划(Human Genome Project, HGP)：1990年正式启动，旨在完成人类基 因组约30亿个碱基的全序列测定。
海量生物数据的迅速膨胀：DNA、RNA和 蛋白质序列，蛋白质二级结构和三维结构数 据，蛋白质相互作用数据等。
2.数学知识：概率论与统计学等 3.算法及编程能力：JAVA, Perl/Python，
PHP+MySQL, …
31
生物信息学的常用算法与方法
动态规划算法(Dynamic programming)； 贝叶斯统计(bayesian statistic)； 人工神经网络(ANNs)； 马尔可夫模型和隐马尔科夫模型(HMM)； 遗传算法(Genetic Algorithm)； 蒙特卡洛方法(Monte Carlo)； 模拟退火算法(Simulated Annealing)； 支持向量机(SVM); …
植物学及园艺学英文版 botany and horticulture (66)
Jan 16,2012 SBL201 Lec 6-7 2
What is the genome?
Entire genetic complement of an organism
Jan 16,2012
SBL201 Lec 6-7
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How many types of genomes are there in this world?
– e.g., DNA sequencing, making libraries and PCRs
• High-throughput technology
– e.g., robotics for sequencing
• Computers are essential for processing and analyzing the large quantities of data generated
• High-throughput genetics
Jan 16,2012
SBL201 Lec 6-7
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Technology Revolution
Sequencing by‘synthesis nanotechnology’approach
Sequencing genomes in Months and Years Sequencing genomes in Minutes (14 min precisely)!!
Jan 16,2012 SBL201 Lec 6-7 5
Genome sequence can tell us…
• • • • • Everything about the organism's life Its developmental program Disease resistance or susceptibility How do we struggle, survive and die? Where are we going and where we came from? • How similar are we to apes, trees, and yeast?
What is the genome?
Entire genetic complement of an organism
Jan 16,2012
SBL201 Lec 6-7
3
How many types of genomes are there in this world?
– e.g., DNA sequencing, making libraries and PCRs
• High-throughput technology
– e.g., robotics for sequencing
• Computers are essential for processing and analyzing the large quantities of data generated
• High-throughput genetics
Jan 16,2012
SBL201 Lec 6-7
15
Technology Revolution
Sequencing by‘synthesis nanotechnology’approach
Sequencing genomes in Months and Years Sequencing genomes in Minutes (14 min precisely)!!
Jan 16,2012 SBL201 Lec 6-7 5
Genome sequence can tell us…
• • • • • Everything about the organism's life Its developmental program Disease resistance or susceptibility How do we struggle, survive and die? Where are we going and where we came from? • How similar are we to apes, trees, and yeast?
ch8 evolutionary genomics-基因组学
Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
8.2 Acquisition of new gene
8.2.1 DNA duplication(p465~473) By duplication of the entire genome; By duplication of a single chromosome or part of a chromosome; By duplication of a single gene or group of genes. 8.2.2 Horizontal gene transfer
Genomics
Chapter 8 Genomes and Evolution
Content
8.1 The molecular basis for evolution 8.2 Acquisition of new gene 8.3 Expansion of non-coding DNA 8.4 model organisms and comparative genomics 8.5 Molecular phylogenetics
Nothing in biology makes sense without evolution.
Theodosius Dobzhansky (1900～1975) 美国进化遗 传学家。代表著作 “Genetics and the Origin of Species”. New York, Columbia University Press, 1937.
8.4 model organisms and comparative genomics 基因共线性 基因岛和基因协同进化 直系同源集簇 常见模式生物
生物信息学-欢迎光临浙江大学生命科学学院
Dennis Ritchie发明C语言; NCSA developed Telnet
FTP
Bill Gates和Paul Allen成立微软; Bill Joy developed C
shell (csh) and Vi text editor David Boggs invent Ethernet; Stephen Wozniak et al found Apple
算(manuipulation)，分析(analysis)，模拟 (simulation)，预测(prediction)等等的一门新兴学科，
是21世纪科学发展的热点之一。
Biology, Bioinformatics, Systems Biology
3
Genetics & Genomics
4
Genomic achievements since HGP
Apple introduce macintosh System 3.0
Larry Wall推出Perl语言
Apple introduce macintosh System 4.0; Windows 2.0
Compact Disk Recordable (CD-R); Pearson实现FASTA程序
Arpanet ceases to exist (INTERNET). Archie by Alan Emtage created.
Gopher by Paul Lindner. Python by Guido van Rossum; Tim BernersLee announce the WWW project; Linus Torvalds releases Linux versions 0.01.
FTP
Bill Gates和Paul Allen成立微软; Bill Joy developed C
shell (csh) and Vi text editor David Boggs invent Ethernet; Stephen Wozniak et al found Apple
算(manuipulation)，分析(analysis)，模拟 (simulation)，预测(prediction)等等的一门新兴学科，
是21世纪科学发展的热点之一。
Biology, Bioinformatics, Systems Biology
3
Genetics & Genomics
4
Genomic achievements since HGP
Apple introduce macintosh System 3.0
Larry Wall推出Perl语言
Apple introduce macintosh System 4.0; Windows 2.0
Compact Disk Recordable (CD-R); Pearson实现FASTA程序
Arpanet ceases to exist (INTERNET). Archie by Alan Emtage created.
Gopher by Paul Lindner. Python by Guido van Rossum; Tim BernersLee announce the WWW project; Linus Torvalds releases Linux versions 0.01.