I’m a Professor at the Fred Hutchinson Cancer Research Center in the Vaccine and Infectious Disease Division and the Computational Biology Program, affiliate faculty in the Department of Genome Sciences and the Department of Epidemiology at the University of Washington, and an Investigator at the Howard Hughes Medical Institute.
My research program focuses on using viral genome sequences to understand virus evolution and to gain insight into factors driving viral outbreaks, epidemics and pandemics.
Much of this work has been instantiated in the Nextstrain platform to conduct real-time genomic epidemiology and to share results broadly.
This platform has seen substantial public health adoption to improve seasonal influenza vaccines, combat Ebola outbreaks and to understand and curb SARS-CoV-2 transmission.
More broadly, I’ve sought to progress genomic surveillance and with the Seattle Flu Study, lead the design and implementation of a next-generation infectious disease surveillance system that greatly impacted state and local response to the COVID-19 pandemic.
Papers
An atlas of adaptive evolution in endemic human viruses
Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences
Tracking the horizontal transfer of plasmids in Shigella sonnei and Shigella flexneri using phylogenetics
Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition
State-dependent evolutionary models reveal modes of solid tumor growth
Fitting stochastic epidemic models to gene genealogies using linear noise approximation
Sentinel surveillance system implementation and evaluation for SARS-CoV-2 genomic data, Washington, USA, 2020–2021
Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county
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
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus
SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus
A Bayesian approach to infer recombination patterns in coronaviruses
Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2
Diagnostic accuracy of an at-home, rapid self-test for influenza: prospective comparative accuracy study
Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data
SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing
Tracing the origin, spread, and molecular evolution of Zika virus, Puerto Rico, 2016–2017
SARS-CoV-2 epidemiology on a public university campus in Washington State
Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York
Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks
SARS-CoV-2 variants in patients with immunosuppression
Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State
Comparison of symptoms and RNA levels in children and adults With SARS-CoV-2 infection in the community setting
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse
Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State
A remote household-based approach to influenza self-testing and antiviral treatment
Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State
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
Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study
Limited predictability of amino acid substitutions in seasonal influenza viruses
Evaluating specimen quality and results from a community-wide, home-based respiratory surveillance study
Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
Remote household observation for non-influenza respiratory viral illness
Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes
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
Characteristics of COVID-19 in homeless shelters: A community-based surveillance study
Cryptic transmission of SARS-CoV-2 in Washington State
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
Cross-sectional prevalence of SARS-CoV-2 among skilled nursing facility employees and residents across facilities in Seattle
dms-view: Interactive visualization tool for deep mutational scanning data
Ten recommendations for supporting open pathogen genomic analysis in public health
Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California
Evidence for limited early spread of COVID-19 within the United States, January–February 2020
Early detection of Covid-19 through a citywide pandemic surveillance platform
CpG-creating mutations are costly in many human viruses
High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters
Early prediction of antigenic transitions for influenza A/H3N2
Quantifying within-host evolution of H5N1 influenza in humans and poultry in Cambodia
The ability of single genes vs full genomes to resolve time and space in outbreak analysis
Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season
Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia
Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain
Seasonal influenza circulation patterns and projections for September 2019 to September 2020
Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin
Dengue genetic divergence generates within-serotype antigenic variation, but serotypes dominate evolutionary dynamics
Clustered mutations at the murine and human IgH locus exhibit significant linkage consistent with templated mutagenesis
Comprehensive mapping of avian influenza polymerase adaptation to the human host
Estimating vaccine-driven selection in seasonal influenza
Real-time analysis and visualization of pathogen sequence data
Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants
Nextstrain: real-time tracking of pathogen evolution
Massive iatrogenic outbreak of human immunodeficiency virus type 1 in rural Cambodia, 2014-2015
Within-host evolution of human influenza virus
Seasonal influenza circulation patterns and projections for Feb 2018 to Feb 2019
Predictive modeling of influenza shows the promise of applied evolutionary biology
MERS-CoV spillover at the camel-human interface
Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza
Genome-wide evolutionary dynamics of influenza B viruses on a global scale
Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018
Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Virus genomes reveal factors that spread and sustained the Ebola epidemic
Genetic characterization of the Zika virus epidemic in the US Virgin Islands
Seasonal influenza circulation patterns and projections for 2017-2018
Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus
Viral factors in influenza pandemic risk assessment
Did a single amino acid change make Ebola virus more virulent?
Seasonal influenza circulation patterns and projections for 2016-2017
Explaining the geographical origins of seasonal influenza A (H3N2)
Identification of low- and high-impact hemagglutinin amino acid substitutions that drive antigenic drift of influenza A(H1N1) viruses
Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses
Quantifying and mitigating the effect of preferential sampling on phylodynamic inference
Persistent HIV-1 replication maintains the tissue reservoir during therapy
Genetic diversity and protective efficacy of the RTS,S/AS01 malaria vaccine
Positive selection in CD8+ T-cell epitopes of influenza nucleoprotein revealed by a comparative analysis of human and swine viral lineages
Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak
Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
Quantifying evolutionary constraints on B cell affinity maturation
nextflu: real-time tracking of seasonal influenza virus evolution in humans
Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone
Global circulation patterns of seasonal influenza viruses vary with antigenic drift
Eight challenges in phylodynamic inference
Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution
Reassortment between influenza B lineages and the emergence of a co-adapted PB1-PB2-HA gene complex
Seasonality in the migration and establishment of H3N2 influenza lineages with epidemic growth and decline
Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak
The early spread and epidemic ignition of HIV-1 in human populations
Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses
Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2
Integrating influenza antigenic dynamics with molecular evolution
Phylowood: interactive web-based animations of biogeographic and phylogeographic histories
Viral phylodynamics
The roles of competition and mutation in shaping antigenic and genetic diversity in influenza
Canalization of the evolutionary trajectory of the human influenza virus
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
Spatial guilds in the Serengeti food web revealed by a Bayesian group model
Strength and tempo of selection revealed in viral gene genealogies
Global migration dynamics underlie evolution and persistence of human influenza A (H3N2)
Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster
Optimization of gene expression by natural selection
Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster
Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila
Overdispersion of the molecular clock varies between yeast, Drosophila and mammals
Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum
Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites
Gene conversion as a source of nucleotide diversity in Plasmodium falciparum
Evolvability of Hsp70 expression under artificial selection for inducible thermotolerance in independent populations of Drosophila melanogaster
Projects
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
id3c - Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.
auspice - Web app for visualizing pathogen evolution
flu-forecasting - Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 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).
nextflu - Real-time tracking of influenza evolution
sismid - Pathogen evolution, selection and immunity
sacra - Cleaning scripts for real-time pathogen analysis
mitii - Pathogen evolution, selection and immunity
phylodynamics-lecture - Lecture on viral phylodynamics
ncov-wa-phylodynamics - Analyses of the hCoV-19 outbreak in Washington State
ncov-wa-d614g -
zika-usvi - Evolutionary analysis of USVI Zika epidemic
ncov-cryptic-transmission - Cryptic transmission of SARS-CoV-2 in Washington State
gs541-phylodynamics - Lectures and materials for GS541 Introduction to Computational Molecular Biology
janus - Build and deploy Nextstrain
ncov-phylodynamics - Phylodynamic estimation of nCoV incidence and prevalence
genomic-horizon - Temporal horizons of genomic epidemiology
h5n1-cambodia - Within-host diversity in H5N1-infected humans and poultry in Cambodia
h3n2-reassortment - Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season
zika-colombia - Genetic analysis of the Zika epidemic in Colombia
dengue-antigenic-dynamics - Dengue antigenic variation and evolutionary dynamics
zika-seq - Pipelines to do MinION sequencing of Zika virus
global-migration - Analysis of global migration patterns of seasonal influenza viruses
mers-structure - Looking into MERS-CoV dynamics through the structured coalescent lens
roka - Evolutionary and epidemiological analysis of Roka HIV outbreak
unsampled - Estimating unsampled viral diversity
siv-cst - Dynamics of cross-species transmission in SIV
yellow-fever - Evolutionary dynamics of yellow fever virus
chikv - Evolutionary dynamics of chikungunya virus
medium-data - Talk on data and visualization
infectious-pulse - Many-strain SIR epidemiological model
sctrace - Simulating migration patterns using charged particles
flutrace - Visualizing influenza global circulation patterns
PACT - Posterior Analysis of Coalescent Trees
coaltrace - Simulating genealogies using charged particles
antigen - Simulating virus evolution and epidemiology
haplotypes - Visualizing evolution as a network of shared mutations
ancestry - Tracing coalescent histories
stem - Picking influenza stem strains
dynamics-practical - Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data
divergence - Illustration of Darwin's Principle of Divergence
Posts
Openings for bioinformatician and full-stack developer to contribute to Nextstrain platform
Cryptic transmission of novel coronavirus revealed by genomic epidemiology
Early warnings of novel coronavirus from genomic epidemiology and the global open scientific response
Forecasting influenza virus evolution to Sep 2020
Developer for real-time genomic epidemiology platform Nextstrain.org
Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018
Establishment and spread of Zika in the Americas
Zika in the USVI genome announcement
Seasonal influenza circulation patterns and projections for 2017-2018
Open Science Prize and nextstrain.org relaunch
The Open Science Prize and a shared scientific endeavor
Seasonal influenza circulation patterns and projections for 2016-2017
Summer 2016
Zika sequencing in Brazil (or Trevor does fieldwork)
Programmer for real-time phylodynamic analysis
Seasonal influenza circulation patterns and future projections
Strain-specific vaccine efficacy in the RTS,S malaria vaccine
Analysis and visualization of influenza antigenic evolution
Seasonal influenza circulation patterns and future projections
Pathogen evolution, selection and immunity
New recruits
On scientific publishing practices in the face of public health crises
Ebola transmission and evolution revealed through genomic analysis
Tracking down the sneeze that started seasonal flu
Global circulation patterns of seasonal influenza viruses
Real-time analysis of Ebola evolution and geographic spread
Postdoc in immune repertoire dynamics
Observations of recent influenza evolution and predictions for the 2015-2016 flu season
Real-time tracking of influenza virus evolution
Seasonal migration of influenza lineages
Is Ebola adapting?
Bayesian estimation of phylogenetic signal
Reassortment between influenza B lineages
Uncovering the "hidden history" of HIV emergence and spread
Challenges in phylodynamics
Avian influenza diversity and persistence
Assessing correlated trait evolution
Molecular evolution of the human B cell repertoire
Reassortment patterns between influenza B lineages
Predicting flu migration patterns
Publishing with eLife
Postdoc in viral phylogenetics and evolution
Identifying sites responsible for antigenic change in influenza
Comparing amino acid distance to BLOSUM as a predictor of antigenic drift
Phylowood phylogeographic visualization
Version 2.0
Newton Institute presentation
Issue tracking reviewer criticisms
Integrating influenza antigenic dynamics with molecular evolution
Tutorial on inferring spatiotemporal dynamics from sequence data
Wikipedia x PLoS topics page on viral phylodynamics
Fixation of new alleles
Influenza diversity across spatial scales
Visualizing evolution as a network of shared mutations
What limits the rate of virus adaptation?
Plotting interpretable phylogenies
Comparing performance of Processing.js and D3.js
Simulating virus evolution and epidemiology
Running the numbers for Contagion... they don't come out well
Model comparison through path sampling and AICM
Visualizing the global circulation of the human influenza virus
Some thoughts on a GitHub of Science
Estimating global flu diversity
LaTeX manuscript template with web display
Interactive visualization of the Serengeti food web
Spatial guilds in the Serengeti food web revealed by a Bayesian group model
Reproducible peer review
Canalization of the evolutionary trajectory of the human influenza virus
Visualizing mortality data
Estimating the effective population size of swine flu
Illustrating Darwin's Principle of Divergence
Wright-Fisher population genetic simulation
Strength and tempo of selection revealed in viral gene genealogies
Matching R0 to cumulative prevalence in the H1N1 influenza pandemic
Counting parameters in a phylogeny
Multi-strain multi-deme model with SIRS dynamics
Updating coaltrace to use Javascript
Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster
Reuters: "Who to blame for flu? Maybe the US, study finds"
Global migration dynamics underlie evolution and persistence of human influenza A (H3N2)
Presentation on phyloseminar.org
Population genetic simulation on a mutational landscape
Compilation of most interesting Wikipedia articles
PACT: Posterior Analysis of Coalescent Trees
Basic coalescent simulation with physics-based layout
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