Zeyu Zhu

Virus-assisted directed evolution of enhanced suppressor tRNAs in mammalian cells

This paper develops VADER, a virus-assisted directed evolution method for improving suppressor tRNAs in mammalian cells, resulting in more active and orthogonal tRNA mutants.

Entropy of a bacterial stress response is a generalizable predictor for fitness and antibiotic sensitivity.

This paper introduces transcriptomic entropy as a generalizable predictor of bacterial fitness and antibiotic sensitivity across species and stress conditions using RNA-Seq and experimental evolution data.

The landscape of intrinsic and evolved fluoroquinolone resistance in Acinetobacter baumannii includes suppression of drug-induced prophage replication

This paper identifies mutations that alter fluoroquinolone sensitivity in Acinetobacter baumannii and shows that preferential Topo IV poisoning leads to prophage induction and SOS response activation.

Forecasting bacterial survival-success and adaptive evolution through multi-omics stress response-mapping, network analyses and machine learning

This paper predicts bacterial survival and adaptive evolution using multi-omics data, network analysis, and machine learning to identify coordinated responses and gene adaptation.