課程資訊
課程名稱
基因體學
Genomics 
開課學期
104-2 
授課對象
生命科學院  生命科學所  
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
選修 
上課時間
星期四2,3,4(9:10~12:10) 
上課地點
生科419 
備註
本課程以英語授課。必須先修習過遺傳學。
總人數上限:30人 
Ceiba 課程網頁
http://ceiba.ntu.edu.tw/1042Genomics 
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
另約時間 備註: by appointment 
指定閱讀
 
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)
   
課程進度
週次
日期
單元主題
Week 1
2/25  Lecture 1. DNA Sequencing Technologies
DNA sequencing technologies by Adams, J. (2008) Nature Education 1(1):193.
Sequencing technologies — the next generation by Metzker (2010) Nat Rev Genet 11:31-46.
Next-Generation Sequencing: Methodology and Application by Grada and Weinbrecht (2013) J Inv Dermatology 133, e11; doi:10.1038/jid.2013.248. 
Week 2
3/03  Lecture 2. Human Genome Project
DNA sequencing technologies key to the human genome project by Chial (2008) Nature Education 1(1):219.
Sequencing Human Genome: the Contributions of Francis Collins and Craig Venter by Adams (2008) Nature Education 1(1):133. 
Week 3
3/10  Lecture 3. Genome Resources
Genomic Data Resources: Challenges and Promises by Lathe, Williams, Mangan & Karolchik (2008) Nature Education 1(3):2. 
Week 4
3/17  Lecture 4. Transcriptome
Transcriptome: Connecting the Genome to Gene Function by Adams, J. (2008) Nature Education 1(1):195.
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs by The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team Nature 420:563-573.
The amazing complexity of the human transcriptome by Frith, Pheasant and Mattick (2005) European Journal of Human Genetics 13:894–897.
RNA-Seq: a revolutionary tool for transcriptomics by Wang, Gerstein and Snyder (2009) Nat Rev Genet 10:59-63.
 
Week 5
3/24  Lecture 5. Gene Annotation
Genome annotation past, present, and future: How to define an ORF at each locus by Brent Genome Res. 2005. 15: 1777-1786.
A beginner's guide to eukaryotic genome annotation by Yandell & Ence (2012) Nat Rev Genet 13:329-342. 
Week 6
3/31  Spring Break 
Week 7
4/07  Lecture 6. Genome Variation (I) Human
The International HapMap Project by The International HapMap Consortium* Nature 426:789.
A Map of Human Genome Variation from Population-scale Sequencing by The 1000 Genomes Project Consortium* Nature 467:1061 (doi:10.1038/nature09534)
Genetic variation and the de novo assembly of human genomes by Chaisson, Wilson and Eichler (2015) Nat Rev Genet 16:627-640. 
Week 8
4/14  [Lecture 7] Functional Genomics 
Week 9
4/23  Midterm Break 
Week 10
4/28  [Student Presentation] Genomic Resources of Model Organisms
 
Week 11
5/05  Lecture 8. Metagenomics
Genomes of Other Organisms: DNA Barcoding and Metagenomics by Zhaurova (2008) Nature Education 1(1):89. 
Week 12
5/12  Lecture 9. Cancer Genomics
(http://www.nytimes.com/2015/09/27/opinion/sunday/elizabeth-wurtzel-the-breast-cancer-gene-and-me.html; http://www.nytimes.com/2016/03/12/health/breast-cancer-brca-genetic-testing.html; http://www.nytimes.com/2013/05/14/opinion/my-medical-choice.html) 
Week 13
5/19  Epigenomics: The New Tool in Studying Complex Diseases by Laura (2008) Nature Education 1(1):178. 
Week 14
5/26  Epigenomics: The New Tool in Studying Complex Diseases by Laura (2008) Nature Education 1(1):178. 
Week 15
6/02  Final report outline due [no class] 
Week 16
6/09  Final report draft due [Holiday] 
Week 17
6/16  Student's Presentation