Barney Potter

Research assistant

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

Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes

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

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

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

nextflu - Real-time tracking of influenza evolution

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

sacra - Cleaning scripts for real-time pathogen analysis