I spent much of 2023 as a visiting scientist with Dr. Nicolas Alcala in the Rare Cancer Genomics Group at IARC. During my visit, we developed signature variability analysis, a framework to quantify the diversity of mutational signatures within tumors and the heterogeneity of signatures across tumors in a population. We found that carcinogen exposure increases the diversity of mutational signatures present in a tumor—even in cases when carcinogens were thought not to have genomic effects!

This work is now available as a preprint on medRxiv!

With Drs. Noah Rosenberg and Katherine Xue, I developed FAVA, an Fst-based Assessment of Variability across vectors of relative Abundances. We used FAVA to quantify the temporal stability of microbiomes following an antibiotic perturbation and the heterogeneity of microbiomes across ruminant host species at different regions of the gastrointestinal tract.

Check out our R package on GitHub and preprint on bioRxiv!

Dr. Noah Rosenberg and I derived the upper and lower bounds on the popular biodiversity statistic Shannon entropy when the abundance of the ith most abundant community member is fixed. This project extends previous work which established these bounds conditional on only the first most abundant taxon.

Check out our paper in Journal of Mathematical Biology!

With Drs. Noah Rosenberg and Nicolas Alcala, I developed an $F_{ST}$-based tool, called FSTruct, for quantifying the variability of a population’s estimated ancestry.

Check out our R package on GitHub and paper in Molecular Ecology Resources!

Dr. Lauren Ancel Meyers, Dr. Spencer Fox, Tanvi Ingle, and I modeled demand for COVID-19 isolation beds for the Austin homeless population based on epidemic projections. This work was done in collaboration with public health leaders from the City of Austin.

This project is now published in PLOS One! See this link for the open-access paper.

I wrote an honors mathematics thesis with the supervision of Dr. Stephen Walker as part of my degree through the Dean’s Scholars Honors Program.

You can view an abridged copy of my thesis here!

As part of the UCSF Summer Research Training Program and the Amgen Scholars Program, I worked with Dr. John Witte, Dr. Linda Kachuri, and Dr. Sara Rashkin to conduct genome-wide association studies of immune response strength to 22 distinct antigens.

We identified many interesting and novel single-nucleotide polymorphisms that are implicated in immune response variability.

This work is now published in Genome Medicine! You can find the open-access paper here and my poster here!

As part of The Mathematical Biosciences Institute NSF REU Program, I worked with Dr. Ephraim Hanks and Emily Strong to explore the dynamics of disease spread over patchy terrain through an extensive simulation study.

We found that terrain heterogeneity (i.e. resource selection) can cause population dispersal to be heavy tailed, creating accelerating epidemic waves.

You can view our poster here and a recording of our final presentation here!

Under Dr. Mark Kirkpatrick, I evaluated the performance of Bayesian Phylogenetics and Phylogeography (an MCMC program for analyzing DNA alignments under the multispecies coalescent model) when applied to prokaryotic genomic data.

I have used this tool to identify independently evolving lineages, or ecotypes, within a superabundant marine cyanobacteria responsible for 5% of global oxygen production, Prochlorococcus marinus.

You can access my poster from the 2019 Evolution Meeting here and our preprint on bioRxiv here!

With the guidance Dr. Lauren Ancel Meyers and Dr. Lauren Castro, I analyzed the Texas counties and school districts most at risk of an outbreak due to high conscientious vaccination exemption rates and fit an array of models to identify sociodemographic predictors of these exemptions.

This work is now published in PLOS Medicine! You can find the open-access paper here.