Barney Potter

Research assistant
Twitter
GitHub
Email
barney.potter.24obfuscate@gmail.com

I just joined the Bedford lab as a research assistant, where I am contributing to nextstrain and nextflu. Soon, I will also begin working on applying deep learning to try to predict flu success. I am interested in developing new algorithms that can efficiently reason with large amounts of sequence data.

I received my bachelor's from Reed College in Portland, Oregon where I majored in mathematics and biology. My undergraduate thesis was about extending the Prize-Collecting Steiner Tree problem to directed hypergraphs, which I used to model dysregulations in cell signaling networks. I have also studied the effects of whole genome duplication in synthetic polyploid Arabidopsis thaliana. I plan on applying to graduate school to begin in Fall 2018, where I hope to pursue a PhD in computer science or computational biology.

Papers

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

Seasonal influenza circulation patterns and projections for September 2019 to September 2020

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

Nextstrain: real-time tracking of pathogen evolution

Genetic characterization of the Zika virus epidemic in the US Virgin Islands

Projects

fauna - RethinkDB database to support real-time virus analysis

h3n2-reassortment - Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

zika-seq - Pipelines to do MinION sequencing of Zika virus

nextflu - Real-time tracking of influenza evolution

sacra - Cleaning scripts for real-time pathogen analysis