Ming Yan

The paper introduces MODIFI, a tool for detecting DNA modifications in metagenomes, and identifies ECE-host linkages in environmental and human samples.

The paper uses single-cell genomics to analyze MGE-host interactions in microbiomes, revealing widespread MGE presence and host range diversity across microbial lineages.

This study reveals alternative nitrogen assimilation pathways in rumen microbes and shows that dietary concentrate levels, not protein content, influence N assimilation gene expression.

The paper develops GutEuk, a deep-learning classifier, and curated protein databases to improve identification and functional analysis of eukaryotic microbes in ruminant gut metagenomes.