Yang Liu

The paper analyzes 6,895 Enterobacteriaceae genomes to show plasmid-borne antibiotic resistance genes (pARGs) have species-dependent evolutionary dynamics and are associated with chromosomal resistance genes.

The paper analyzes DEF and anti-DEF gene dynamics across Enterobacteriaceae genomes, finding differences in turnover rates between chromosomal and mobile genetic elements.

This study identifies over 1,500 viral histones and histone-fold proteins in dsDNA viruses, revealing their structural and functional diversity beyond nucleocytoplasmic large DNA viruses.

The paper examines how defense systems affect horizontal gene transfer (HGT) across different timescales and finds that CRISPR-Cas most often reduces MGE abundance and gene acquisition, but this effect is masked by recent co-transfer events.

This study compares gene clustering criteria in prokaryotic pangenomes, showing that clustering methods significantly affect functional characterization and core genome inference, with methodological inconsistencies often exceeding ecological and phylogenetic effects.