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 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 (link requires a Broad email address to access). 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.