Yan Shao

MxSure: a mixture model for inferring within-host substitution rates and transmission SNP thresholds

MxSure estimates within-host substitution rates and transmission SNP thresholds from pairwise SNP distances, addressing challenges in microbial genome evolution analysis.

Discovery, functionality and global dynamics of Bifidobacterium longum subsp. nexti : a novel starch-degrading subspecies in the infant gut

The paper identifies a novel subspecies of Bifidobacterium longum, BL. nexti, in infant gut microbiomes, showing its association with formula feeding and vertical transmission.

Human milk oligosaccharide metabolism by Clostridium species suppresses inflammation and pathogen growth

The paper identifies Clostridium species that metabolize human milk oligosaccharides, producing beneficial metabolites and suppressing inflammation and pathogen growth in preterm infants.

Enhanced metagenomics-enabled transmission inference with TRACS

TRACS improves transmission inference by accurately estimating SNP-level genetic distances, outperforming existing methods in multiple datasets and revealing species-specific transmission rates between mothers and infants.

In vitro demonstration of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome

The paper demonstrates broad host range mobile genetic elements transferring antibiotic resistance from human gut commensals to enteropathogens.

PlasmidTron: assembling the cause of phenotypes from NGS data

PlasmidTron identifies mobile genetic elements linked to phenotypes by analyzing short read WGS data and phenotypic metadata from bacterial populations.