John Huddleston

This study reports neutralization titers from 355 human sera against 148 influenza strains, showing reduced neutralization of new H3N2 and H1N1 variants.

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 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 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.

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 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.