This elective course will cover the latest advances in bioinformatics in the context of human diseases. Students will be provided with the practical skills to implement what they have learned in class. Specifically, when the course is finished, students will be able to analyze multi-omics data to understand human disease.
- Number: MED263, Bioinformatics Applications to Human Disease
- Quarter: Winter 2018
- Units: 4
- Directors: Lucila Ohno-Machado ([email protected]) and Jihoon Kim ([email protected])
- TA: Andre Fonseca Faustino ([email protected])
- Place: Room 304, Medical Education Telemedicine (MET) building
- Time: 2-3:30 pm, Tuesdays and Thursdays (Jan 9 - Mar 8, 2018)
- Grading: Homework 60%, Final presentation/report 40% (no mid-term)
- Class start date: Tuesday January 9, 2018
- Class end date: Thursday March 8, 2018
- Submission deadline for final exam report: 11:59 pm Sunday March 18, 2018
- Student presentation (for final exam) date: Thursday March 8, 2018
| Week | Date | Topic | Instructor |
|---|---|---|---|
| 1 | Tuesday 1/9 | Overview & Bootcamp part 1 (docker and linux) | Lucila Ohno-Machado ([email protected]) and Jihoon Kim ([email protected]) |
| 1 | Thursday 1/11 | Bootcamp part 2 (conda, Jupyter notebok, and R) | Jihoon Kim ([email protected]) |
| 2 | Tuesday 1/16 | Network Biology lecture | Hannah Carter ([email protected]) |
| 2 | Thursday 1/18 | Network Biology hands-on session | Hannah Carter ([email protected]) |
| 3 | Tuesday 1/23 | Exome-seq and variant analysis lecture | Olivier Harismendy ([email protected]) |
| 3 | Thursday 1/25 | Exome-seq and variant analysis hands-on session | Olivier Harismendy ([email protected]) |
| 4 | Tuesday 1/30 | Classification model and survival analysis in biomedicine | Xiaoqian Jiang ([email protected]) |
| 4 | Thursday 2/1 | Classification model and survival analysis in biomedicine hands-on session | Xiaoqian Jiang ([email protected]) |
| 5 | Tuesday 2/6 | RNA-seq lecture | Katie Fisch ([email protected]) |
| 5 | Thursday 2/8 | RNA-seq hands-on session | Katie Fisch ([email protected]) |
| 6 | Tuesday 2/13 | Prioritizing disease mutations using DNA sequence data lecture | Vikas Bansal ([email protected]) |
| 6 | Thursday 2/15 | Prioritizing disease mutations using DNA sequence data hands-on session | Vikas Bansal ([email protected]) |
| 7 | Tuesday 2/20 | Chip-Seq lecture | Sven Heinz ([email protected]) |
| 7 | Thursday 2/22 | Chip-Seq hands-on session | Sven Heinz ([email protected]) |
| 8 | Tuesday 2/27 | GRO-seq lecture | Chris Benner ([email protected]) |
| 9 | Thursday 3/1 | GRO-seq hands-on session | Chris Benner ([email protected]) |
| 9 | Tuesday 3/6 | Ethics, Privacy, and Policy lecture | Cinnamon Bloss ([email protected]) |
| 9 | Thursday 3/8 | Student Presentation | Jihoon Kim ([email protected]) |
- 3:30-4:30 pm after class Tuesdays and Thursdays at room 304, MET building
- If these hours don't work you, email to Andre ([email protected]) or Jihoon ([email protected]) to schdedule different hours, preferrably on Tuesdays and Thursdays.
- You will get a homework every Thursday.
- The expected level of homework is that whoever attended and followed well on the Thursday hands-on course should be able to answer the homework questions in a few hours.
- Homework is due by the following Thursday right before class (1:59 pm Thursdays).
- Turn in the homework to TA Andre([email protected]) by email.
- Show all codes with answers to the questions.
- Create a hands-on session document to perform data analysis with your own data (public or private data) similar to MED 263 class
- Following this document, students (or others) should be able to conduct a data analysis in the context of bioinformatics
- Turn in the hands-on session document to TA ([email protected]) prior to the last class (deadline 11:59 pm Sunday March 18, 2018)
- Present the hands-on session during the class Thursday March 8, 2018 (10-minute presetation each)