Thomas Sibley

Software engineer

I joined the Bedford Lab in mid 2018 as a computing generalist focused on software engineering. I work on all aspects of Nextstrain, including backend systems, the website frontend, new features for sharing and collaboration, data management, and operational processes. My focus, as of late 2021, is reducing the barriers to entry to use Nextstrain in public health and research settings.

From late 2018 to mid 2021, I was focused on the Seattle Flu Study, where I started as the sole engineer for the informatics group. I designed and built the Study’s central informatics system and staffed up and lead the software development team to build and maintain the many software systems which support the ever-changing work of the Study.


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

Trends in risk factors and symptoms associated with SARS-CoV-2 and rhinovirus test positivity in King County, Washington: A test-negative design study of the greater Seattle Coronavirus Assessment Network

Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

SARS-CoV-2 epidemiology on a public university campus in Washington State

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study

Evaluating specimen quality and results from a community-wide, home-based respiratory surveillance study

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

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

Characteristics of COVID-19 in homeless shelters: A community-based surveillance study

Cryptic transmission of SARS-CoV-2 in Washington State

Ten recommendations for supporting open pathogen genomic analysis in public health

Early detection of Covid-19 through a citywide pandemic surveillance platform


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. - The Nextstrain website

augur - Pipeline components for real-time phylodynamic analysis

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

id3c - Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.

auspice - Web app for visualizing pathogen evolution

id3c-customizations - Extensions of ID3C for the Seattle Flu Study

nextflu - Real-time tracking of influenza evolution

sacra - Cleaning scripts for real-time pathogen analysis


Full-stack developer and bioinformatician for an open-source genomic epidemiology research platform