NGS course (G788/I590) - Yunlong Liu Lab |
The video collections for the 2011 lectures are now available at Youtube and Youku. The slides can also be downloaded.
Please address all the feedback to: yunliu@iupui.edu.
MGEN-G788 (INFO-I590) Introduction to Next Generation Sequencing
Time: 3PM-6PM, Fridays (Fall 2013 Semester)
Location: HS 1110 (Map)
Course materials:
- Course materials are available in the oncourse system. If you need access, please email the course TA (Haoyu Cheng: haoychen@iupui.edu) for access. If you do NOT have an IU university ID, please acquire an IU guest user ID following instruction: https://kb.iu.edu/data/alqu.html.
- Podcast of the lectures is now available in the oncourse system.
Registration:
- School of Medicine (MGEN-G788): http://registrar.iupui.edu/enrollment/4118/classes/MGEN/MGEN-G788.html
- School of Informatics (INFO-I590): http://registrar.iupui.edu/enrollment/4118/classes/INFO/INFO-I590.html
Goal:
Understanding the basic principles of next generation sequencing technology. This includes basic biological applications, basics in data processing, statistical and informatics theories in data analysis, advantages, limitations, and assumptions of different methodologies, and biological interpretation of the results.
Expected outcomes:
For School of Informatics students: know how to do the analysis
- Understand the basics of biological questions
- Implement different analysis tools (such as alignment, alternative splicing, variant call, ...)
- Fully understand the standard data structure; capable of retrieve relevant information throug basic programming
- Understand statistical/computational models to solve different biological questions
For School of Medicine students: know how to interpret the results, and know how to creatively design an experiment using NGS technology
- Understand the basics of informatics theories
- Understand the standard data structure (what information is included in each file)
- Appreciate the advantages, limitations, and assumptions of standard stantistical/bioinformatics methods
- Interpret the analysis results
- Creativly design an experiement for solving the problem of your own research interest
For faculty and staff sitting in the class: due to the expected heterogeneous nature of the class, some of the lectures may provide more informatics/statisitics details than you need. If you have any suggestions on the class contents, please feel free to contact me at yunliu@iupui.edu.
If you want to officially audit the class, please read and follow the IUPUI audit policy on the IUPUI Office of Registrar. If no credit is needed, please just drop me a message indicating you are interested in auditing.
Syllabus:
*** Lab tour to the Center for Medical Genomics will be separately arranged
Week |
Date |
Lecture |
1 |
Aug 23 |
Overview of next generation sequencing technology
|
2 |
Aug 30 |
Data processing
|
3 |
Sep 6 |
DNA-seq I
|
4 |
Sep 13
|
DNA-seq II – Bioinformatics topics for DNA-seq data analysis
|
5 |
Sep 20 @BRTC |
Guest Lecture - Drs. Howard Edenberg and Xiaoling Xuei
|
6 |
Sep 27 |
Guest lecture – Dr. Tatiana Foroud
DNA-seq III
|
7 |
Oct 4 |
RNA-seq I
|
8 |
Oct 11 |
Guest lecture - Dr. Sarath Janga
RNA-seq II
|
9 |
Oct 18 |
RNA-seq III
|
10 |
Oct 25 |
ChIP-seq I
|
11 |
Nov 1 |
Guest lecture - Dr. Milan Radovich
Guest lecture - Dr. Matteo Vatta
|
12 |
Nov 8 |
ChIP-seq II - Bioinformatics topics in ChIP-seq analysis
|
13 |
Nov 15 |
ChIP-seq III: Epigenetics
|
14 |
Nov 22 |
Student presentation |
15 |
Nov 29 |
Thanksgiviing recess |
16 |
Dec 6 |
final exam |