I am currently a fifth-year Ph.D. student at University of California,
Santa Cruz, studying biomolecular engineering
and bioinformatics in the labs of Drs Russell Corbett-Detig and Todd Lowe.
- tRNA Activity Predictor - This pipeline uses DNA data to
predict tRNA expression with 94% accuracy. As a n input, it minimally requires a reference genome, but is
aided by genome annotations and multiple sequence alignments. I applied tRAP to a Cactus graph spanning 29
placental mammal species. Details are available in this publication
as well as in this talk from RNA 2020. tRNA-level data is available
- tRNA Gene Simulation - This individual-based simulation engine
adapts theory from this publication to finite populations. I fit several parameters to human tRNA genes, including expression, germline mutation rate, and the relationship between these two values. Importantly, this simulation engine makes many assumptions about tRNA gene evolution and is not meant to perfectly model reality, but is useful as an exploration of the evolution of duplicate genes more generally. Options for usage and installation instructions are provided at the link.
- UCSC RMI Poster Workshop - I was invited to give a presentation on making a scientific poster for presentation at a conference as an undergraduate student. Here I include my slides from this presentation, which cover the very basics of creating a poster as well as advice and guidelines that I have picked up on over the course of my time as a graduate student.
- RNA 2020 - One perk of online meetings is that talks are pre-recorded. I gave this talk at the 2020 RNA virtual conference where I describe tRAP, its motivation, application, and a scenario in which its resulting data is useful.
- Evolution 2019 - I also gave a talk on my tRNA gene simulation project at the Evolution conference in Providence in 2019. This simulation has a lot of moving parts, so I cover the framework in detail, along with its motivating theory, and our preliminary results upon fitting to human tRNA gene distributions.
Last Updated: September 12, 2021
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