Margaret L. Barry

The paper identifies 21 novel pseudouridine sites in S. cerevisiae tRNAs using DRS and BACS, and maps their modifying enzymes.

The paper introduces tRNAZAP, a deep learning method using nanopore ionic current signals to classify tRNA isodecoders, achieving better alignment results than BWA-MEM in E. coli and S. cerevisiae.

The paper uses single-molecule techniques to study tRNA structural dynamics before and during interaction with the pseudouridine synthase Pus4, revealing conformational changes and remodeling effects.

The paper examines how codon bias and mRNA folding strength interact to affect protein expression in yeast using genomic, transcriptomic, and proteomic data.