Bioinformatics

I've been teaching bioinformatics since 2014, and I really enjoy this work! Below are course materials I've written over the last few years. Please feel free to use with attribution!

In April of 2024, I taught an updated Medical and Population Genetics Primer session on bulk RNA-seq analysis, the youtube video is linked below.

• A Practical guide to bulk RNA-seq, including guidelines for eQTL analysis (2024)

In December of 2023, I co-taught a breakout session (with Allie Cliffe and Nicole Rockweiler) at the 19th Annual Broad Retreat, the publically accessible Terra workspace is linked below:

• So you’ve generated the data … now what? Bioinformatics and data science for the bench scientist

In May of 2023, I was invited to the American Heart Association's Vascular Discovery Conference for a session on single cell RNA-seq design and analysis. Course materials are linked below:

• Single cell and single nucleus RNA sequencing experiments: an updated practical guide to design and analysis
• Link to the Terra walkthrough for scanpy (Jupyter notebook)
• An ipython notebook of the scanpy walkthrough
• ArchR tutorial
• An ipython notebook of the ArchR tutorial (in pdf format)

In the fall of 2021 into early 2022, I did another version of my informal computational biology course. We covered the previous material but also went through plotting in ggplot2, and single cell ATAC-seq analysis using ArchR. Links to public access Terra Jupyter notebooks are below.

• ggplot2 examples and tutorial
• ArchR tutorial

In September of 2021, I developed material for a course on single cell RNA-seq experimental design and analysis for the American Heart Association's Vascular Discovery conference. Course materials are linked below:

• Single cell and single nucleus RNA sequencing experiments: a practical guide to design and analysis
• Zoom video of me narrating this lecture (mp4 format)
• Zip archive containing a pdf and jupyter notebook of the code walkthrough
• Link to the Terra walkthrough (Jupyter notebook)
• Zoom video of me narrating this code walkthrough (mp4 format)
• Zoom video of a discussion with Anwar Chahal, Jennie Lin, Mete Civelek and myself on the code walkthrough (mp4 format)

In October 2020, I was fortunate to be able to do two primers for the Medical and Population Genetics group at the Broad Institute on bulk RNA-sequencing best practices! Youtube videos are linked below:

• A Practical Guide To Differential Gene Expression and Pathway Analysis
• Using tximport and DEseq2 to identify differentially expressed genes: Terra tutorial

The Terra tutorial mentioned is located here, and should be open access with a gmail email address.

During the Fall of 2019, and over the first half of 2020, I informally taught a course on computational biology with several people from the 10th floor of 75 Ames st. During those sessions, we covered the following topics (links are to overview PDFs, you can use these if you credit me!):

• Big data and genomics
• Session I: Intro to NGS/Genomics
• Session II: Alignment to a genome, and QC
• single cell RNA-seq analysis using ScanPy, including subclustering
• Including using Jupyer notebooks on Terra
• History of single cell genomics
• An overview of a script I wrote to demonstrate analysis of single cell data

Since I work with clinicians in my day to day work, Dr. Emelia Benjamin requested that I write and present a talk on "Epigenomics for Everyone", which is linked here.

For several years at UT Austin, I was a co-instructor (with the wonderful Anna Battenhouse) for the Big Data Summer School course "Core Next Generation Sequencing Tools." I've also co-taught courses on ChIP-seq and MySQL.