John Huddleston

PhD student
Google Scholar

I am a second-year MCB student in the Bedford Lab. I am generally interested in evolutionary biology, genomics, and bioinformatics. My interests in these fields developed while studying genetic algorithms during a master's program for computer science at Western Washington University (WWU). This research motivated me to return to school to study evolution where I explored prezygotic reproductive isolation between species in the apple maggot species group (Rhagoletis). During my master's in biology at WWU, I had the opportunity to join Evan Eichler's lab in University of Washington's Genome Sciences as a bioinformatics specialist where I studied structural variation and genome assembly in primates.


Cryptic transmission of SARS-CoV-2 in Washington State

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

dms-view: Interactive visualization tool for deep mutational scanning data

Limited predictability of amino acid substitutions in seasonal influenza viruses

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

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

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

Nextstrain: real-time tracking of pathogen evolution


augur - Pipeline components for real-time phylodynamic analysis

baltic - baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

janus - Build and deploy Nextstrain

nextflu - Real-time tracking of influenza evolution


Deep mutational scanning helps predict evolutionary fates of human H3N2 influenza variants