Trevor Bedford

Principal investigator
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trevorobfuscate@bedford.io

I'm an Assistant Member at the Fred Hutch in the Vaccine and Infectious Disease Division and the Computational Biology Program. I'm also an Affiliate Assistant Professor in the Department of Epidemiology at the University of Washington School of Public Health. I study the dynamics of virus populations. How do strains spread through the world? How do strains evolve in response to immune pressure? And ultimately, what makes a strain successful?

I received my bachelor's degree from the University of Chicago and my PhD from Harvard University, advised by Dan Hartl. Following my PhD I worked for Wolfram Research on Wolfram|Alpha, worked on infectious disease dynamics at the University of Michigan with Mercedes Pascual and worked on viral phylogenetics with Andrew Rambaut at the University of Edinburgh.

Papers

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

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza

Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission

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 - Rethink database to support real-time virus analysis

zika-seq - Pipelines to do MinION sequencing of Zika virus

auspice - Web app for visualizing pathogen evolution

nextflu - Real-time tracking of influenza evolution

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

siv-cst - Dynamics of cross-species transmission in SIV

augur - Pipeline components for real-time virus analysis

mitii - Pathogen evolution, selection and immunity

zika-usvi - Evolutionary analysis of USVI Zika epidemic

yellow-fever - Evolutionary dynamics of yellow fever virus

chikv - Evolutionary dynamics of chikungunya virus

unsampled - Estimating unsampled viral diversity

sismid - Pathogen evolution, selection and immunity

global-migration - Analysis of global migration patterns of seasonal influenza viruses

medium-data - Talk on data and visualization

phylodynamics-lecture - Lecture on viral phylodynamics

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

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

Welcome