Bioinformatics Lab 陳博現 老師 吳謂勝 博二生 陳泓竹 碩二生 林立協 劉家榮...
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Transcript of Bioinformatics Lab 陳博現 老師 吳謂勝 博二生 陳泓竹 碩二生 林立協 劉家榮...
Bioinformatics Lab 陳博現 老師 吳謂勝 博二生 陳泓竹 碩二生
林立協 劉家榮 張文杰 碩一生
執行計畫• 國科會 基因體醫學國家型科技計畫• 統計模型與訊號處理在蛋白質酵素功能活性部位偵測上之應用
Bioinformatics
• a new emerging interdisciplinary research area
• interface between biological and computational sciences
(math, ee, cs,…)
• computational management of all kinds of biological information
Biological information is hierarchical in nature
• DNA mRNA protein protein
interactions informational pathways
informational networks cells tissues
or networks of cells an organism
populations ecologies
Research topics
• DNA level:
DNA sequence alignment; gene prediction;
gene evolution;…
• RNA level:
gene expression study; transcription mechanism; post-transcription modification;…
• Protein level: protein 2D, 3D structure prediction; protein active site pre
diction; protein-protein interactions; protein-DNA interactions;…
• System level: (pathways, networks) Genome 基因體學 (gene-gene interactions) ex. use gene chips to study gene regulatory network
Proteome 蛋白體學 (protein-protein interactions) ex. use protein chips to study protein interaction network
Microarray
• a kind of gene chips
• record the gene expression profiles (in time series) of the whole genome
• with large amount of biological information imbedded
• need to develop data mining methodology to extract this biological information
112/04/18
Principle of Microarray
在 slide 上點上已知的單股 DNA片段 (probe), 做成檢驗用的 slide 。
取得待檢的單股 cDNA(target), 並標示螢光染劑放在 slide 上和 probe 作用。
使用螢光顯微鏡觀察染色的情形。
Printing
Hybridization
Scanning
Analysis 分析染色的 pattern 便可進一步研究待檢DNA/RNA 的資訊。
傳統方法 基因晶片
見樹不見林 見樹又見林
大海撈針 一網打盡
下一代生物晶片 (3D)
•多功能•高靈敏度•較易檢測及操作•可重複使用
研發成功後可廣泛應用於 :•癌症研究、診斷、治療•高血壓、糖尿病、老化等複雜症狀之研究•快速之各種病毒感染檢測
史丹福大學
清華大學
清華特色
光電
微機電
生技生化
國立清華大學
分子生醫光電實驗室基因晶片及新型生物晶片之研發與應用
20,100 點 在 2 cm x 2 cm
Affymetrix GeneChip
Analysis
Microarray data
Gene expression profiles
Construct the gene regulatory network
• cells regulate their gene expression during development or in response to the change of the environment
• use the expression profiles of the yeast cell cycle (about 6,000 genes) as data sets
• develop computational algorithms to construct the gene regulatory network
Requirement of students
• preliminary courses: genetics, biological database, introduction to microarray, statistics, …
• weekly meeting to present bio-related papers
• be familiar with Matlab software package
• wish to do bioinformatics research in your master career