Swastik Mishra

The paper introduces an improved protocol and software for sequence-specific direct RNA sequencing of non-polyadenylated RNAs, validated on human rRNA and other RNA species.

The paper analyzes bacterial genomes to show that horizontally acquired genes are mostly lost quickly but some persist long-term, often involved in transport and metabolism.

QutRNA2 improves tRNA modification detection using Nanopore sequencing with GPU acceleration, achieving faster performance and identifying modifications in human and mouse tRNAs.

This study compares HGT inference methods, finding that gene presence-absence analysis outperforms gene tree-based approaches in detecting horizontal gene transfer.

The paper finds that bacteria entering new environments have smaller genomes and lower horizontal gene transfer rates, challenging the assumption that genomic plasticity drives adaptation.