James Hadfield

Postdoc / Programmer
Google Scholar

I work on all aspects of nextstrain, including a mixture of programming, data visualization, modeling, phylogenetics and communication. I have ongoing research projects on Influenza and viral reassortment detection.

I received my BSc(hons) in mathematics from Canterbury University, New Zealand and my PhD in bacterial genomics from the Sanger Institute (University of Cambridge) supervised by Julian Parkhill and Nick Thomson. I’ve previously worked in virology with Arvind Varsani and in RNA bioinformatics with Paul Gardner.

During my PhD I built phandango, a web-based visualization tool for interpreting the genomics of bacterial populations.


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

Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Ebola virus transmission initiated by relapse of systemic Ebola virus disease

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics

Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context

The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

Cryptic transmission of SARS-CoV-2 in Washington State

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

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

Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain

Nextstrain: real-time tracking of pathogen 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.

nextstrain.org - The Nextstrain website

augur - Pipeline components for real-time phylodynamic analysis

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

auspice - Web app for visualizing pathogen evolution

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).

sacra - Cleaning scripts for real-time pathogen analysis

janus - Build and deploy Nextstrain


Using Nextstrain narratives to explain WNV spread and evolution

Preliminary analysis of the fifth epidemic of avian influenza A/H7N9