Yang Liu

Gain and loss of plasmid-borne antibiotic resistance genes are associated with chromosomal resistance presence in Enterobacteriaceae

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.

Co-evolutionary dynamics of defense systems and anti-defense genes in chromosomes and mobile genetic elements of Enterobacteriaceae

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

Metagenomic mining reveals novel viral histones in dsDNA viruses

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.

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses

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.