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課程名稱 |
高通量基因體資料分析的統計方法和演算法
Statistical Methods and Algorithms in High-Throughput Genomic Data Analysis |
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開課學期 |
101-2 |
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授課對象 |
生命科學院 基因體與系統生物學學位學程 |
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授課教師 |
阮雪芬 |
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課號 |
GenSys5007 |
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課程識別碼 |
B48 U0220 |
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班次 |
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學分 |
3 |
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全/半年 |
半年 |
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必/選修 |
選修 |
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上課時間 |
星期三3,4(10:20~12:10)星期五5,6(12:20~14:10) |
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上課地點 |
生科3C生科419 |
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備註 |
本課程中文授課,使用英文教科書。合授老師：楊欣洲、黃宣誠、曾建城。
總人數上限：20人 |
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Ceiba 課程網頁 |
http://ceiba.ntu.edu.tw/1012sma |
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課程簡介影片 |
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核心能力關聯 |
核心能力與課程規劃關聯圖 |
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課程大綱
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課程概述 |
高通量基因體學已經變成現代生物醫學研究的常規。在這門課中我們將會介紹目前被普遍使用在基因體資料分析的統計分法和演算法。這門課主要可以讓兩群學生修習：(1) 生物背景學生想要學習更紮實的統計方法，(2) 數學、統計或電腦科學背景的學生學習如何應用在基因體科學上。除了正規的課程外，這門課更鼓勵學生跨領域溝通及經由一連串電腦實驗課、回家作業和期末計畫來獲得合作經驗。生物背景學生和數學、統計或電腦科學背景的學生將會聚在一起腦力激盪並互相學習。Analysis of high-throughput genomic data has now become a routine in modern biomedical research. In this course, we will go over statistical methods and algorithms that are commonly used in genomic data analysis. The course is targeted to two categories of students: (1) biological background students who want to obtain more solid training of statistical methods (2) quantitative students (e.g. math, statistics or computer science) who are interested in genomic applications. In addition to formal lectures, the class atmosphere is to encourage interdisciplinary communications and collaboration experiences through a series of computing labs, homework problem sets and a final project. Biological students and quantitative students will be paired to brainstorm and learn from each other in these dynamic course activities. |
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課程目標 |
1. 幫助學生熟悉基因體資料分析常用的統計方法及其原理。
2. 幫助學生有能力獨立編程解決基因體資料分析常見的問題。
3. 幫助生物和數理背景的學生學習跨領域的溝通和合作。
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課程要求 |
預修課程: 一學年的統計推論或統計方法
生物學生: 基本編程經驗 (R, C++ 或 Matlab). 或者需要在開學三個星期內學會R的編程 (授課老師會提供教材).
數理學生: 基本基因學或分子生物學經驗. 或者需要在開學三個星期內自學 (授課老師會提供教材)
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預期每週課後學習時數 |
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Office Hours |
另約時間 |
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指定閱讀 |
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參考書目 |
授課老師會提供每堂課的投影片和課程筆記. |
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評量方式
(僅供參考) |
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No. |
項目 |
百分比 |
說明 |
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1. |
Final project |
40% |
(mid-term progress report due 4/10 for 10%; final presentation for 15%; final paper due on 6/19 for 15%)
Final projects are conducted by groups of 2-3 students. We will encourage/enforce mixture of quantitative (statisticians) and qualitative (biologists) students in the final projects. The lecturer will provide a list of topics/references at the beginning of the semester and the major goal is to apply statistical techniques learned in class to analyze the real data sets and solve the problems. A presentation and a final report are expected from each group in the end of the semester. |
2. |
Homework 1~5 |
60% |
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週次 |
日期 |
單元主題 |
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第1週 |
2/20,2/22 |
Introduction of basic molecular biology and genetics; Introduction of next-generation sequencing technology (阮雪芬) |
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第2週 |
2/27,3/01 |
Introduction of array technology (gene expression array, SNP array, miRNA array, methylation array and protein adrray) ; Human Genome Project => Hapmap=>1000 Genome Project (楊欣洲) |
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第3週 |
3/06,3/08 |
Basic concept in statistical genetics and linkage analysis; (Lab1) Examples and exercises of Bioconductor and NCBI databases. Homework 1 distributed (楊欣洲) |
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第4週 |
3/13,3/15 |
Genetic association analysis (楊欣洲) |
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第5週 |
3/20,3/22 |
Rare variant analysis and gene-gene/gene-environment interaction analysis; (Lab2) Examples and exercises for the last four lectures. Homework 2 distributed. (楊欣洲) |
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第6週 |
3/27,3/29 |
Proteomic data analysis; (Lab3-1) Examples and exercises for the last two lectures (阮雪芬) |
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第7週 |
4/03,4/05 |
4/3溫書假; 4/5放假 |
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第8週 |
4/10,4/12 |
Biological network analysis; (Lab3-2) Examples and exercises for the last two lectures. Homework 3 distributed. (黃宣誠) |
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第9週 |
4/17,4/19 |
Experimental design; Data Preprocessing (normalization, transformation, filtering, missing value imputation etc) ; Dimension reduction (曾建城) |
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第10週 |
4/24,4/26 |
dimension reduction (PCA, MDS, FDA, PLS); Lab 4 (曾建城) |
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第11週 |
5/01,5/03 |
DE gene detection; Lab 5 and HW 4 (曾建城) |
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第12週 |
5/08,5/10 |
Suupervised machine learning (曾建城) |
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第13週 |
5/15,5/17 |
Supervised machine learning; Lab 6 (曾建城) |
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第14週 |
5/22,5/24 |
Unsupervised machine learning, Lab7 and HW5 (曾建城) |
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第15週 |
5/29,5/31 |
Pathway analysis; genomic meta-analysis (曾建城) |
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第16週 |
6/05,6/07 |
Case study in psychiatric research (曾建城, 張倫境); Student final project presentation I (阮雪芬、楊欣洲、黃宣誠、曾建城) |
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第17週 |
6/12,6/14 |
端午節; Student final project presentation II (阮雪芬、楊欣洲、黃宣誠、曾建城) |
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