CSE284 - Home

UCSD CSE 284

Personal Genomics for Bioinformaticians

Welcome to CSE284!

Note: for Spring 2021, this entire course will be held remotely and all materials will be available asynchronously. No in-person attendance is required.

See the Course Syllabus for more details. You can join lectures through Zoom via this link Links to an external site..

Resources

Lecture slides and zoom recordings will be posted here throughout the quarter. You can also find recordings in this Google Drive folder Links to an external site..

Assignments will be posted on our course JupyterHub at datahub.ucsd.edu

We will use Piazza for discussions about assignments: http://piazza.com/ucsd/spring2021/cse284 Links to an external site. (access code: SP21CSE284)

Grades will be posted on Canvas.

To see material from previous offerings of this course, see http://gymreklab.com/teaching/personal_genomics/personal_genomics_2017.html and https://canvas.ucsd.edu/courses/12840.

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
Additional resources and readings!

Schedule

Module	Week	Date	Lecture	Problem Sets	Journal Club
Intro	1	03/29/21 (M)	Introduction to your genome Download Introduction to your genome [Zoom Links to an external site.]
Ancestry	1	03/31/21 (W)	Basic population genetics Download Basic population genetics [Zoom Links to an external site.]		JC1 questions due 10am 3/31
	2	04/05/21 (M)	Phasing, imputation, and HMMs Download Phasing, imputation, and HMMs [Zoom Links to an external site.]	PS1 due 4/05
	2	04/07/21 (W)	Relative finding Download Relative finding [Zoom Links to an external site.]
	3	04/12/21 (M)	Determining ancestry Download Determining ancestry [Zoom Links to an external site.]
	3	04/14/21 (W)	Genetic Genealogy/Ethics part 1 Download Genetic Genealogy/Ethics part 1 [Zoom Links to an external site.]	PS2 due 4/16
Trait prediction	4	04/19/21 (M)	Mendelian vs. Complex Traits Download Mendelian vs. Complex Traits [Zoom Links to an external site.]
	4	04/21/21 (W)	Risk prediction Download Risk prediction [Zoom Links to an external site.]		JC2 questions due 10am 4/21
	5	04/26/21 (M)	Controlling for confounding Download Controlling for confounding [Zoom Links to an external site.]
	5	04/28/21 (W)	Missing heritability Download Missing heritability [Zoom Links to an external site.]	PS3 due 4/30
NGS	6	05/03/21 (M)	Intro to NGS Download Intro to NGS [Zoom Links to an external site.]
	6	05/05/21 (W)	Short read alignment and variant calling Download Short read alignment and variant calling [Zoom Links to an external site.]	Proposal due
	7	05/10/21 (M)	Clinical genome sequencing Download Clinical genome sequencing [Zoom Links to an external site.]		JC3 questions due
	7	05/12/21 (W)	Long reads Download Long reads [Zoom Links to an external site.]
Special topics	8	05/17/21 (M)	Deep learning in genomics Download Deep learning in genomics [Zoom Links to an external site.]
	8	05/19/21 (W)	Ethics part 2 Download Ethics part 2 [Zoom Links to an external site.]	PS4 due 5/21	JC4 questions due
	9	05/24/21 (M)	No lecture - Project OH Links to an external site.
	9	05/26/21 (W)	Project presentations
	10	05/31/21 (M)	No class - Memorial Day
	10	06/02/21 (W)	Project presentations	Project due (06/04)

This course content is offered under a CC Attribution Non-Commercial Share Alike Links to an external site. license. Content in this course can be considered under this license unless otherwise noted.