課程資訊
課程名稱
基因體學
Genomics 
開課學期
103-1 
授課對象
生命科學院  生命科學系  
授課教師
丁照棣 
課號
LS5080 
課程識別碼
B21EU2240 
班次
 
學分
全/半年
半年 
必/選修
必修 
上課時間
星期二3,4,@(10:20~) 
上課地點
生科4B 
備註
本課程以英語授課。B群選擇必修。先修科目:遺傳學。
總人數上限:40人 
Ceiba 課程網頁
http://ceiba.ntu.edu.tw/1031LS5080_Genomics 
課程簡介影片
 
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課程概述

Recent advances in genomics have significantly revolutionized the ways which we do science in the 21st century. With the completion of the human draft genome, the new genome technologies have transformed our ability to understand the structure and function of genomes and allow scientists to explore the genomes of multicellular organisms. This course is designed to introduce undergraduate students, who are interested in this exciting and rapidly evolving field, the basic knowledge of genome and the state-of-the-art genome technologies. The lectures will cover an introduction on genome projects, sequencing technologies, genetic variation, transcriptomics, proteomics, functional genomics, comparative genomics, metagenomics and epigenomics. This semester, we are part of the Genome Education Partnership (GEP) and students taking this course will work on an annotation project under the guidance of the instructors. The goal is to provide opportunities for undergraduate students to participate in genomic research. Students will learn to annotate genes and other features, leading to analysis of a question in genomics and research publication. More information about GEP can be found at http://gep.wustl.edu and the 2014 project is described at http://gep.wustl.edu/projects/dot_chromosome. 

課程目標
The aim for this course is to provide students an up-to-date knowledge in genome science at the introductory level and act as a bridging course to the more advanced levels. In addition to basic genome science, participating undergraduates will learn to annotate genes and other features, leading to address scientific questions in genomics and research publication. 
課程要求
All students should have taken introductory level of genetics. The instructors will assume that all participants are familiar with basic terminologies in genetics (http://gep.wustl.edu/repository/introduction_to_genomics/GEP_Glossary.pdf). Students should read the assigned materials and/or watch the online lectures every week prior to lecture. Attendance at all course sessions is expected and is essential for finishing homework and assigned project. In-class discussion, homework, annotation project and student presentation will be the main activities in the classroom. Keeping electronic notes as a Google documents sharing with instructors is required. Your notes will help us to guide you throughout the project. An example of electronic notes will be provided in class. At the end of the semester, students will present their projects and write a scientific report on their project. Example of student’s report can be viewed online at http://gep.wustl.edu/curriculum/student_work. 
預期每週課後學習時數
 
Office Hours
每週二 08:30~10:30 
指定閱讀
All required readings and online lectures will be listed at the course website. 
參考書目
Major References:
Introduction to Genomics by Arthur M. Lesk (2nd Edition, Oxford University Press, 2011)
A Primer of Genome Science by G. Gibson and S. V. Muse (3rd Edition, Sinauer, 2009)

Other References:
Dictionary of DNA and genome technology by P. Singleton (Wiley-Blackwell, 2010)
Evolutionary Genomics and Proteomics Edited by M. Pagel and A. Pomiankowski (Sinauer Associates, 2007)
From Genes to Genomes: Concepts and Applications of DNA Technology by J. W. Dale and M. van Schantz (John Wiley & Sons, 2007) [2002 Ed. available through NTU library]
Foundations of comparative genomics by Arcady R. Mushegian (Academic Press, 2007)
Genome Science: A Practical and Conceptual Introduction to Molecular Genetic Analysis in Eukaryotes by David Micklos (CSHL Press, 2012)
Genomes 3 by T. A. Brown (Garland Science, 2007) [2nd Ed. available at NCBI, http://www.ncbi.nlm.nih.gov/books/NBK21128/]
 
評量方式
(僅供參考)
 
No.
項目
百分比
說明
1. 
Homework 
30% 
 
2. 
GEP annotation project 
30% 
 
3. 
Presentation/ Term paper 
20% 
 
4. 
In class participation 
20% 
 
 
課程進度
週次
日期
單元主題
第1週
9/16  Introduction/ Genome and Genome Projects
Homework: History of Genomics I (Class wiki project) 
第2週
9/23  High throughput reverse genetics
(Guest lecture by You-Tzung Chen, Ph.D., Institute of Medical Genomics and Proteomics, NTUCM)
Homework: History of Genomics II (Class wiki project) 
第3週
9/30  Genome Databases, Introduction to NCBI
Homework: Blast Problem Set 
第4週
10/07  Sequencing Technologies (online lectures) 
第5週
10/14  Genome projects: Experimental Design and beyond
Project Demo: Closing the gaps 
第6週
10/21  Genome Annotation (I)
Homework: Chimp project 
第7週
10/28  Genome Annotation (II)
Project Demo: Annotating Drosophila genes 
第8週
11/04  Gene Expression and Transcriptome
Homework: Annotation project I
Meeting with Prof. Sarah Elgin (Viktor Hamburger Professor of Arts & Sciences, Department of Biology, Washington University in St. Louis) 
第9週
11/11  SNPs and Variation
Homework: Annotation project II  
第10週
11/18  Cancer Genomics
Homework: Annotation project III 
第11週
11/25  Evolution and comparative genomics
Homework: Annotation project IV 
第12週
12/02  Proteomics – protein identification, annotation and protein interactomics
Student’s presentation slides due 
第13週
12/09  Student Presentation (I) 
第14週
12/16  Student Presentation (II) 
第15週
12/23  Epigenomics
Full draft of term paper due 
第16週
12/30  Systems Biology
Revision of term paper 
第17週
1/06  Final Discussion
Revision of term paper 
第18週
1/13  Final version of term paper due