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

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition

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

nextflu - Real-time tracking of influenza evolution

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

Posts

Predicting seasonal influenza evolution

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