John Huddleston

Staff scientist
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As a staff scientist in the Bedford Lab, my work includes independent research, software development, and educational outreach and mentorship. I study the evolution of seasonal influenza viruses, develop computational models to predict the composition of future influenza populations, and contribute to reports to the World Health Organization’s vaccine composition meetings. I am also a core developer of Nextstrain’s real-time pathogen surveillance tools including the Augur bioinformatics toolkit and the SARS-CoV-2 genomic epidemiology workflow. This work builds on my previous professional roles as a bioinformatics specialist and software developer and my previous educational experiences including master’s degrees in computer science and biology.

Papers

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

Limited predictability of amino acid substitutions in seasonal influenza viruses

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

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

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

Projects

augur - Pipeline components for real-time phylodynamic analysis

nextflu - Real-time tracking of influenza evolution

fauna - RethinkDB database to support real-time virus analysis

cli - The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.

ncov - Nextstrain build for novel coronavirus SARS-CoV-2

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).

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

janus - Build and deploy Nextstrain

Posts

Predicting seasonal influenza evolution

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