Contact us

Lead Instructor Dr. Gene Yeo
Teaching Assistant Olga Botvinnik
Teaching Assistant Jamison McCorrison
All other lecturer contact info provided below.

Course Description

Quantitative Methods in Genetics and Genomics is designed to teach experimental and analytical approaches in modern genetics and genomics, from experimental design through data analysis in each of several topic areas. Lecturers this year include Gene Yeo, Scott Rifkin, Bruce Hamilton, Rob Knight, Olivier Harismendy, Nicholas Schork, Aaron Chang and Hannah Carter.

This course is a requirement for students in the UCSD Genetics Training Program. 4 units.


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Module Num. Tues Thurs Lecturer Topic
1 1/5/16 1/7/16 Olga Botvinnik, Gene Yeo (contact) TSCC Setup, UNIX, Git/Github, and Python introduction Lecture Homework Solution
2 1/12/16 1/14/16 Scott Rifkin (contact) Statistic; logic of testing hypotheses; estimation Lecture
conda install R fix
Homework Solution
3 1/19/16 1/21/16 Bruce Hamilton (contact) Low throughput methodology, qRT PCR Lecture Homework Solution
4 1/26/16 1/28/16 Olga Botvinnik, Gene Yeo NGS Technology, RNA-seq tools and analyses, IGV Lecture Powerpoint Lecture Homework Solution
5 2/2/16 2/4/16 Rob Knight (contact) Microbiome Lecture Additional Materials Homework Solution
6 2/9/16 2/11/16 Olivier Harismendy (contact) NGS sequencing. Analysis file standards. SNPs and SNVs in cancer. Querying public databases. Variant annotation, filtering and statistical associations. Lectures: NGS Tools, Practice - Day 1 Practice - Day 2 Homework Solution
7 2/16/16 2/18/16 Gene Yeo, Olga Botvinnik, Jamison McCorrison Review of class materials. Lecture Homework Solution
8 2/23/16 2/25/16 Nicholas Schork (contact) Modern Applied Population Genetics. Applied Population Genetic. Admixture Mapping. Lecture 1 Exercise 1 : Python/PLINK Exercise 1 : R/Plots Homework Solution
9 3/1/16 3/3/16 Hannah Carter (contact) Genome-wide associations studies. Lectures: Exercise 1, Exercise 2, Exercise 3, Exercise 4, Powerpoint 1, Powerpoint 2, Data Homework Solution
10 3/8/16 3/10/16 Hannah Carter Prioritizing genetic variation. Inherited variation. Somatic variation. Lectures: Exercise 1, Week 2 Lecture, pptx Homework Solution

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Class Location

All lectures throughout the quarter will be held in the Sanford Consortium for Regenerative Medicine (SCRM) building.


Take home exam due Monday March 14, 2016