Single Cell Epigenomics at the Gene Regulation Observatory

I only recently moved into this new role, but I'll be updating this space frequently with wet-lab and computational efforts.

Functional Genomics: Cardiovascular Genetics

In the Ellinor laboratory, I worked on a variety of projects, many of which are now being published! Many of these projects also have results viewable at the Broad Cardiovascular Disease knowledge portal. A selection of publications in which I've been involved include:
There are several currently under review or revision, and more entering the pipeline all the time!


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:
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!): 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.

Functional Genomics: Glioblastoma multiforme

In the Iyer lab, I worked on several projects that relate to the genomics of glioblastoma multiforme (GBM).
The culmination of my work there was to profile histone PTMs in several primary GBM lesions. We also did RNA-seq from these same samples, and found that common bivalent chromatin state regions (marked by active and repressive histone PTMs at the same locus) revealed a striking enrichment for genes involved in GBM "stemness" which is thought to relate to the strong reistant GBM has to most chemotherapies. We also found that enhancers and bivalent regions clustered based on their gene expression based molecular subtype, with proneural samples forming a group, and classical/mesenchymal samples forming a second group.

In my other work during graduate school, I worked on quantifying allele specific bias in ChIP-seq. I also participated in an eQTL analysis of the GBM genome, derived from array data. In my first foray into atrial fibrillation, I did some selective genotyping of individuals undergoing cardiac ablation for treatment of AF.

Finally, I continued to work with the Aldrich laboratory, and we did some really cool studies of amino acid conservation across many phyla for the highly conserved calcium signaling protein calmodulin.