Yifeng Yuan

This study examines how tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis across growth phases.

This study maps tRNA modifications in Streptococcus mutans and S. pneumoniae, revealing shared losses and clade-specific adaptations in modification genes and metabolic strategies.

The paper identifies new phosphorothioate DNA modification systems in the human gut microbiome using genomic and mass spectrometric analysis.

The paper evaluates machine-learning models' ability to predict enzymatic functions for uncharacterized proteins and finds they fail to integrate scientific reasoning and make logic errors.

The paper profiles tRNA modifications in Pseudomonas aeruginosa to uncover regulatory networks and validate gene annotations.

This paper identifies SLC35F2 as a high-specificity transporter for queuine and queuosine in multiple species and shows its role in regulating intracellular levels of these micronutrients.

The paper characterizes phosphorothioate (PT) modifications in the human gut microbiome using metagenomics and mass spectrometry, revealing temporal dynamics and species-specific patterns.

This study identifies genetic interactions among tRNA modification genes in E. coli K12, revealing synthetic lethal pairs and condition-dependent phenotypes.

PT-seq is a high-sensitivity method for mapping phosphorothioate DNA modifications in complex microbial communities and metagenomic identification of PT-containing microbes.