Course website for CSE 284 Spring 2020
This page is no longer being maintained. All material will be updated on Canvas this quarter. Note: for Spring 2020, due to the COVID-19 situation, this entire course will be held remotely. No in-person attendance is required.
Under construction!
See the course syllabus for more details.
Lecture slides and zoom recordings will be posted here and on Canvas throughout the quarter.
Assignments will be posted on our course JupyterHub at datahub.ucsd.edu.
We will use Piazza for discussions about assignments.
Grades will be posted on Canvas.
To see material from a previous offering of this course, see http://gymreklab.com/teaching/personal_genomics/personal_genomics_2017.html
See
- Jupyter Assignment Instructions to get started with the problem sets.
- Journal Club Instructions for instructions on journal club assignments.
- Final Project Guidelines for information about final projects.
- Resources for more helpful resources each week.
| Module | Week | Date | Lecture | Problem Sets | Journal Club |
|---|---|---|---|---|---|
| Intro | 1 | 03/30/20 (M) | Introduction to your genome | ||
| Ancestry | 1 | 04/01/20 (W) | Basic population genetics | JC1 questions due | |
| 2 | 04/06/20 (M) | Phasing and imputation | ps1 due | ||
| 2 | 04/08/20 (W) | Determining ancestry | |||
| 3 | 04/13/20 (M) | Relative finding | |||
| 3 | 04/15/20 (W) | Genetic Genealogy, Web 2.0 Genomics | ps2 due | ||
| Trait prediction | 4 | 04/20/20 (M) | Mendelian(ish) traits | ||
| 4 | 04/22/20 (W) | Intro to GWAS | JC2 questions due | ||
| 5 | 04/27/20 (M) | Risk prediction | |||
| 5 | 04/29/20 (W) | Missing heritability | ps3 due | ||
| Next-generation sequencing | 6 | 05/04/20 (M) | Introduction to NGS | ||
| 6 | 05/06/20 (W) | Short read alignment and variant calling | JC3 questions due | ||
| 7 | 05/11/20 (M) | Filtering and prioritizing variants | |||
| 7 | 05/13/20 (W) | Functional genomics | Project proposal due | ||
| 8 | 05/18/20 (M) | Clinical genome sequencing | |||
| 8 | 05/20/20 (W) | Long read technologies | ps4 due | ||
| 9 | 05/25/20 (M) | No lecture - Memorial Day | |||
| Special topics | 9 | 05/27/20 (W) | Improving diversity in genomics | JC4 questions due | |
| 10 | 06/01/20 (M) | Ethical considerations in personal genomics | |||
| 10 | 06/03/20 (W) | Project presentations | Project due |