Biography

Hi, welcome to my website! I am graduate of the MIT-Woods Hole Oceanographic Institution Joint Program in Biological Oceanography. During my PhD, I studied the biogeochemistry and ecophysiology of chemoautotrophic Campylobacteria (prev. Epsilonproteobacteria) under the guidance of Dr. Stefan Sievert.

Currently, I am working as a Postdoc at the University of Southern California with Dr. Jed Fuhrman. This position is part of a larger project funded by the Simons Foundation (CBIOMES) to model the biogeochemistry of oceans on basin scales. I am contributing to this effort by generating new amplicon datasets from materials shared by collaborators using the Fuhrman Lab’s universal (16S/18S) primers. Since the resulting data provide a comprehensive profile of the entire community, they can be used to better understand microbial biogeography and help contribute to model validation and development. During my time in the Fuhrman lab, I’ve also become interested in reproducible data analysis. My first foray into this area was to develop a simple pipeline for amplicon data derived from the 515Y/926R primers. When trying to apply the same kind of bash scripting to a more complex/less linear task, it quickly became too unweildy. This led me to buckle down and learn how to use the workflow management tool snakemake which is an incredibly powerful tool to answer scientific questions that are not straightforward computationally (see for example my MGPrimerEval pipeline). As a huge bonus, snakemake has conda/docker support “baked in” so that sharing your pipelines with others should be relatively painless.

Before coming to USC, I worked for one year at the Chinese University of Hong Kong with Dr. Haiwei Luo where I focused mainly on microbial isolation and single-cell genomic analyses. Part of that work involved isolating novel Campylobacteria from shallow-water hydrothermal vents at Kueishan island, Taiwan (pictured in the background of my photo). This work is in preparation for publication, and involves the pangenomic/population genetic analysis of pure culture genomes from 3 genera of Campylobacteria, including a novel genus awaiting scientific description. Before my PhD, I worked with the National Research Council of Canada on algal biofuels research in Halifax, NS, Canada under the tutelage of Dr. Patrick McGinn. There, I harvested kilogram quantities of microalgal biomass, isolated new microalgae, and developed lipid extraction and quantification techniques. Before NRC, I completed my undergraduate degree in Biology on Canada’s east coast at Mount Allison University in Sackville, NB where among the many amazing teachers I encountered my most important mentors were Felix Bärlocher, Robert Thompson, Zoe Finkel, and Jack Stewart. I am originally from Kingston, Ontario, Canada. My hobbies include gardening, board games, spending time in the great outdoors, listening to great music (check my twitter for some #songsofcomfort apropos to this difficult time we are living through), playing around on linux systems, and fermenting things.