Trevor Bedford

The paper introduces a simulator called antigen-prime to model influenza virus evolution and benchmarks methods for variant assignment and growth rate estimation.

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

This paper directly measures viral fitness flux in SARS-CoV-2 and influenza H3N2 by tracking variant frequency dynamics and finds it correlates with fitness variance, matching Fisher's fundamental theorem.

This study identifies recurrent saltational events in SARS-CoV-2 evolution, linking them to persistent human infections rather than zoonotic sources.

This study compares neutralizing antibody titers from egg-derived and recombinant protein influenza vaccines against diverse H1N1 strains, finding that egg-derived vaccines induce less boost against a new clade with specific antigenic mutations.

A sequencing-based neutralization assay across 78 H3N2 HA strains and 150 sera shows strain growth in 2023 tracks the fraction of sera with low titers, but not pooled-serum titers.

Sequencing-based neutralization of 91 H3N2 and H1N1 hemagglutinins against 302 human sera (27,409 titers) shows reduced titers to H3N2 subclade K and H1N1 D.3.1.1.

The paper introduces a hidden Markov model to detect recombination in SARS-CoV-2 sequences and identifies parental lineages without user-specified parameters, finding 1.73% of sequences are recombinant.

MASCOT-Skyline jointly infers spatial and temporal transmission dynamics of infectious diseases using a structured coalescent skyline approach, revealing biases in existing phylogeographic methods.

The paper examines adaptive mutations in seasonal influenza viruses grown in chicken eggs, finding most mutations cluster around the HA receptor-binding pocket and show varying background dependence across subtypes.

The paper quantifies neutralizing antibody responses to influenza strains using sera collected in 2024-2025 to inform vaccine-strain selection for 2025.

This study develops a high-throughput sequencing-based neutralization assay to measure antibody titers against multiple influenza strains and finds that vaccination effects vary by individual and prior vaccination history.

The paper tests dimensionality reduction methods on viral genomes to capture genetic relationships without phylogenetic analysis, finding MDS and t-SNE accurately represent known clusters in influenza and SARS-CoV-2.

SwabExpress is a simplified COVID-19 testing protocol that eliminates the need for transport media and nucleic acid extraction, achieving high sensitivity and specificity.

dms-view is a web-based tool for visualizing DMS data in the context of 3-D protein structures and natural sequence variation.

The paper uses genomic data to show multiple ZIKV introductions and cryptic transmission in Colombia, with most transmission occurring locally.

The paper identifies a reassortant A(H3N2) virus, A2/re, which became dominant in the 2017-2018 influenza season despite lacking HA mutations and showing no antigenic difference from previous strains.

The paper analyzes seasonal influenza circulation patterns from Feb 2018 to Feb 2019 and projects future trends to inform vaccine strain selection.

The paper analyzes seasonal influenza circulation patterns from Sep 2017 to Sep 2018, identifying clade dynamics and antigenic evolution in A/H3N2, A/H1N1pdm, and B/VicA viruses.

This paper describes a method to sequence Zika and other virus genomes directly from clinical samples using multiplex PCR and portable sequencing technologies, achieving complete genomes in 1-2 days.

This study analyzes 1600 Ebola virus genomes to show viral spread followed a gravity model, with cross-border transmission before border closures contributing to an international epidemic.

The paper uses ZIKV genomes to estimate the origin and spread of Zika virus in Brazil and the Americas, providing a timeframe for baseline microcephaly rates.

The paper analyzes seasonal influenza circulation patterns and projections for 2017-2018, identifying genetic and antigenic dynamics of H3N2, H1N1pdm, B/Vic, and B/Yam clades.

The paper observes and projects seasonal influenza circulation patterns for 2016-2017 using data from the GISAID database.

The paper analyzes the 2014 Ebola virus outbreak in Sierra Leone, finding that different viral clades have varying growth rates and reproduction numbers, which affect epidemic dynamics.