Yixin Zhao

The paper identifies how hidden assumptions in nascent RNA sequencing pipelines lead to structured divergence in transcriptional profiles across datasets.

The paper introduces a model-based framework to compare promoter-proximal pausing dynamics across biological contexts, revealing kinetic and distributional variations in pausing.

This study shows that FKS1-S639 mutations confer caspofungin resistance in C. auris but cause moderate fitness trade-offs without reducing virulence.

This paper identifies TkeA, a T6SS DNase effector from Yersinia pseudotuberculosis, which induces host apoptosis via the cGAS-STING-TNF axis and promotes bacterial competition.

The paper investigates DNA-sequence and epigenomic factors influencing local transcription elongation rates.

The paper develops a probabilistic model to estimate transcription initiation and pause-escape rates from nascent RNA sequencing data, showing pause-escape is often more rate-limiting than previously thought.

This study shows that reduced miRNA levels in Drosophila lead to developmental instability and reduced longevity, highlighting miRNAs' role in stabilizing gene regulatory networks against weak environmental perturbations.

The paper shows that RNA Pol II pausing is essential for proper pluripotency transitions in mouse embryos by maintaining balance between gene expression states.

The paper introduces a method to estimate RNA half-lives using PRO-seq and RNA-seq data, finding correlations between RNA stability and splicing, miRNA binding, DNA methylation, and histone modifications.