R. A. Neher

The paper estimates fitness effects of SARS-CoV-2 mutations using phylogenetic data, finding most mutations are neutral or deleterious, with some accessory proteins under weak selection.

This study analyzes changes in the mutation spectrum of SARS-CoV-2 across millions of sequences, finding shifts in mutation rates, particularly a decrease in G[->]T mutations in Omicron compared to early clades.

This paper introduces a pseudovirus system for deep mutational scanning of SARS-CoV-2 spike protein mutations, showing how they affect antibody neutralization and infection.

This study estimates synonymous and non-synonymous mutation rates in SARS-CoV-2 over 2.5 years, finding accelerated non-synonymous evolution suggesting adaptive processes.

The paper uses genetic sequence data and patient metadata to analyze local influenza transmission dynamics in Basel, Switzerland, finding that temperature trends correlate with transmission and that elderly and school children drive different transmission networks.

This study analyzes the evolution and geographic spread of EV-D68 using genomic data from 2018, revealing distinct subclades and age-related patterns in infection.

The paper surveys Pseudomonas in Arabidopsis thaliana over multiple years and sites, finding that pathogenic sublineages coexist without a single dominant strain overtaking populations.

Nextstrain provides real-time tracking of pathogen evolution by integrating viral genome data with other public health data through a database, bioinformatics pipeline, and visualization platform.

This study shows that colistin resistance in Pseudomonas aeruginosa evolves rapidly and consistently in morbidostat cultures, with mutations targeting specific genes involved in lipopolysaccharide synthesis and signaling.

panX is a pipeline and visualization tool for analyzing pan-genomes, enabling exploration of gene clusters, phylogenetic trees, and evolutionary history.