Genetics 211: Genomics : Winter 2019

About Genomics (Genetics 211) | Course Description | Course Schedule & Assignments

Goals

The goal of this course is to explore different genomic approaches and technologies, to learn how they work from a molecular biology view point, and to understand how they can be applied to understanding biological systems. In addition, we teach material on how the data generated from these approaches can be analyzed, from an algorithmic perspective. The papers that are discussed are a mixture of algorithmic papers, and technological papers. Finally, the course has a strong programming component, with Python being the language that we teach. All of our problem sets require Python programming - while beginning programmers succeed in our course, it is a steep learning curve, and the problem sets can require a significant time investment.

Piazza used for announcements, logistics, and to contact instuctors

https://piazza.com/stanford/winter2019/gene211

Instuctors

Lecturers

Teaching Assistants

TA Office Hours:

Meeting Times & Locations

Discussion Sections

Sections will be defined the first class meeting.

Course Description

About Genomics (Genetics 211) | Course Description | Course Schedule & Assignments

Format

Each week faculty will provide a two hour lecture on a current topic within Genomics, a two hour discussion section exploring a significant paper, and a two hour lecture on the Python programming language.

Course Grade

The overall course grade will be based four problem sets that require the creation of Python scripts to process biological data (40%), on participation in discussion sections including four write-ups (30%), and a final exam (30%). The take home final exam will consist a project of your design analyzing a question of your choice and requires the use of Python to process the data.

Preparing for Python

In this course you will be learning and using the scripting language Python. We assume that many of you have no experience with Python or any programming language. The Friday lectures will teach you everything you need to know about Python to be successful in this course. If you have not been exposed to Python, or if you have no experience with programming we suggest that you do one of the many online courses. This will give you a head start on the course and the first couple of weeks will not as time consuming. Most online courses teach Python version 2. We teach Python version 3.

Python Lecture & Discussion Video

The Friday lecture and discussion are recorded an available from Stanford Medicine Media Dropbox

Course Schedule - Winter 2019

About Genomics (Genetics 211) | Course Description | Course Schedule & Assignments
Tues 1/8 (M112) Course Overview (30 minutes)
Lecture #1 -- Sherlock : Genome Sequencing           [PDF]
Thurs 1/10 Discussion
CANCELLED
Fri 1/11 (M112) disc:M208
Python - Data Types PS0 - Due 1/11/2019 at 9:00AM: Problem Set 0
Tues 1/15 (M112) Lecture #2 -- Sherlock : Short Read Genome (Re)sequencing           [PDF]
Thurs 1/17 (M212|M214) Discussion - Exon Sequencing and Capturing Haplotype Information
1. Ng, S. B. et al (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272-278
2. Amini, S. et al (2014). Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nature Genetics 46, 1343-1349
Fri 1/18 (M112) disc:M214
Python - Loops & Logic PS1 - Due 1/18/2019 at 9:00AM: Problem Set 1
Tues 1/22 (M112) Lecture #3 -- Sherlock : Functional Genomics           [PDF]
Thurs 1/24 (M212|M214) Discussion - 3D Map of Human Genome
Rao, S.S.P. et al. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell 159, 1665-1680
Fri 1/25 (M112) disc:M214
Python - Functions PS2 - Part 1 Due 1/25/2019 at 9:00AM: Problem Set 2
Tues 1/29 (M112) Lecture #4 -- Sherlock : RNA Expression           [PDF]
Thurs 1/31 Discussion
CANCELLED
Fri 2/1 (M112) disc:M214
Python - Pattern matching PS2 - Part 2 Due 2/1/2019 at 9:00AM: Problem Set 2
Tues 2/5 (M112) Lecture #5 -- Cherry : Sequence Comparision and Analysis           [PDF]
Thurs 2/7 (M212|M214) Discussion - Single cell RNA-seq and Expression Compendium
1. Macosko, et al (2015). Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161:1202–1214
2. Hughes, et al (2000) Functional Discovery via a Compendium of Expression Profiles. Cell 102:109-126
Fri 2/8 (LK101) disc:LK102
Python - File I/O & CLI arguments PS3 - Part 1 Due 2/8/2019 at 9:00AM: Problem Set 3
Tues 2/12 (M112) Lecture #6 -- Snyder : Personalized Genomics: Disease and Health           [PDF]
Thurs 2/14 (M212|M214) Discussion - Sequence Alignment
1. Henikoff, S. & Henikoff, J. (1992) Amino Acid substitution matrices from protein blocks. PNAS 89:10915-10919
2. Notredame, C., Higgins, D.G & Heringa, J (2000) T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment JMB 302:205-217
Fri 2/15 (M112) disc:M214
Python - matplotlib and biopython PS3 - Part 2 Due 2/15/2019 at 9:00AM: Problem Set 3
Tues 2/19 (M112) Lecture #7 -- Snyder : Epigenomics           [PDF]
Thurs 2/21 (M212|M214) Discussion
CANCELLED
Fri 2/22 (M112) disc:M214
Python - Object-oriented python and classes PS4 - Part 1 Due 2/22/2019 at 9:00AM: Problem Set 4
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Take Home Final Project Abstract - Due Monday 2/25/2019 at 5:00pm:
Final Project Specifications
Tues 2/26 (M112) Lecture #8 -- Snyder : Microbiome           [PDF]
Thurs 2/28 Discussion
CANCELLED prospective grad student interviews
Fri 3/1
Python
CANCELLED prospective grad student interviews
Tues 3/5 (M112) Lecture #9 -- Cherry : Functional Annotation & Open Science           [PDF]
Thurs 3/7 (M212|M214) Discussion - Microbiome
1. Lim, et al (2015) Early life dynamics of the human gut virome and bacterial microbiome in infants. Nature Medicine 211228-1236
2. Lim, et al (2015) supplementary Information
Fri 3/8 (LK101)
Python - Numpy, pandas, more matplotlib PS4 - Part 2 Due 3/8/2019 at 9:00AM: Problem Set 4
Tues 3/12 (M112) Lecture #10 -- Snyder : Proteomics           [PDF]
Thurs 3/14 (M212|M214) Discussion - Proteomics
Markmiller,S et al (2018) Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules. Cell 172590-604
We will also discuss the supplemental figures.
Fri 3/15 (LK101)
Seth Strattan - Running ENCODE pipelines at Google Cloud.     [Video]     [Slides] Final Project - Due Sunday 3/17/2019 at noon