James Hadfield

Postdoc / Programmer
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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.

Papers

Nextstrain: real-time tracking of pathogen evolution

Projects

augur - Pipeline components for real-time virus analysis

auspice - Web app for visualizing pathogen evolution

fauna - RethinkDB database to support real-time virus analysis

baltic - BALTIC - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation

sacra - Cleaning scripts for real-time pathogen analysis

janus - Build and deploy Nextstrain

Posts

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