Richard A. Neher

The paper analyzes SARS-CoV-2 genomic data to show how mutational fitness costs change over time and introduces a model of pairwise epistasis to explain these changes.

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.

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 analyzes the evolution of 3425 actinobacteriophage genomes, finding conserved synteny and varying linkage decay patterns due to homologous recombination.

The paper investigates the evolutionary origin and functional diversification of plant GBF1-type ARF-GEFs, showing how AtGNOM and AtGNL1 orthologs evolved distinct roles in membrane trafficking.

The paper estimates mutation rates across SARS-CoV-2 genome sites and identifies factors influencing these rates, finding significant variability and patterns related to gene boundaries, sequence context, and RNA structure.

The paper introduces Aionostat, an automated device for high-throughput bacteriophage evolution studies, demonstrating its ability to accelerate and standardize phage adaptation and recombination experiments.

This paper shows that shifting habitats can lead to biased and overconfident phylogeographic inferences due to local density regulation and population dynamics.

The paper develops datasets for Nextclade to enable rapid and accurate clade assignment of avian influenza A(H5) viruses, validated against existing tools.

The paper analyzes genome evolution in closely related E. coli ST131 strains, finding more accessory genome structural changes than core genome mutations, with most structural changes being short-lived and deleterious.

The paper introduces a method to visualize and quantify structural diversity around mobile resistance genes using pangraph, applied to beta-lactamase genes to show correlations between mutational and structural evolution.

PanGraph constructs a scalable pan-genome graph from whole-genome assemblies to capture structural and nucleotide polymorphisms across bacterial populations.

TreeKnit infers ancestral reassortment graphs from segment trees of influenza viruses, showing high accuracy and speed compared to Bayesian methods.

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 uses single molecule sequencing to analyze genomic diversity of carbapenemase-producing bacteria and identifies patterns of carbapenemase movement and recombination.

The paper analyzes the phylodynamics of rapidly evolving pathogens, showing how extinction and speciation rates depend on evolutionary parameters and cross-immunity dynamics in Red Queen states.

The paper estimates evolutionary rates and optimizes tree roots using covariance-aware regression on phylogenetic trees with linear computational cost.

The paper shows that partial inhibition of HIV transmission can increase live infected lymph node cells by reducing cell death, even with fewer HIV DNA copies per cell.

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.

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.