265 citations · 600 across the 13 of their papers we have counts for
14 papers
Fitting stochastic epidemic models to gene genealogies using linear noise approximation
Mingwei Tang, Gytis Dudas, Trevor Bedford +1
Phylodynamics is a set of population genetics tools that aim at reconstructing demographic history of a population based on molecular sequences of individuals sampled from the popu…
Explaining the geographic origins of seasonal influenza A (H3N2)
Frank Wen, Trevor Bedford, Sarah Cobey
Most antigenically novel and evolutionarily successful strains of seasonal influenza A (H3N2) originate in East, South, and Southeast Asia. To understand this pattern, we simulated…
Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses
Richard A. Neher, Trevor Bedford, Rodney S. Daniels +2
Human seasonal influenza viruses evolve rapidly, enabling the virus population to evade immunity and re-infect previously infected individuals. Antigenic properties are largely det…
Quantifying and mitigating the effect of preferential sampling on phylodynamic inference
Michael D. Karcher, Julia A. Palacios, Trevor Bedford +2
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this tas…
Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak
Marta Łuksza, Trevor Bedford, Michael Lässig
The 2014 epidemic of the Ebola virus is governed by a genetically diverse viral population. In the early Sierra Leone outbreak, a recent study has identified new mutations that gen…
Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline
Daniel Zinder, Trevor Bedford, Edward B. Baskerville +3
Background: Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonali…
Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
Gabriela B. Cybis, Janet S. Sinsheimer, Trevor Bedford +3
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate…
Identifying the genetic basis of antigenic change in influenza A(H1N1)
William T. Harvey, Victoria Gregory, Donald J. Benton +7
Determining phenotype from genetic data is a fundamental challenge. Influenza A viruses undergo rapid antigenic drift and identification of emerging antigenic variants is critical…
Quantifying evolutionary constraints on B cell affinity maturation
Connor O. McCoy, Trevor Bedford, Vladimir N. Minin +3
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain de…
Nonparametric Bayesian grouping methods for spatial time-series data
Edward B. Baskerville, Trevor Bedford, Robert C. Reiner +1
We describe an approach for identifying groups of dynamically similar locations in spatial time-series data based on a simple Markov transition model. We give maximum-likelihood, e…
Integrating influenza antigenic dynamics with molecular evolution
Trevor Bedford, Marc A. Suchard, Philippe Lemey +7
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed thr…
The seasonal flight of influenza: a unified framework for spatiotemporal hypothesis testing
Philippe Lemey, Andrew Rambaut, Trevor Bedford +8
Global mobility flow data are at the heart of spatial epidemiological models used to predict infectious disease behavior but this wealth of data on human mobility has been largely…
Canalization of the evolutionary trajectory of the human influenza virus
Trevor Bedford, Andrew Rambaut, Mercedes Pascual
Since its emergence in 1968, influenza A (H3N2) has evolved extensively in genotype and antigenic phenotype. Antigenic evolution occurs in the context of a two-dimensional 'antigen…
Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model
Edward B. Baskerville, Andy P. Dobson, Trevor Bedford +2
Food webs, networks of feeding relationships among organisms, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. Despite long-standing…