Yanwen Shao

The paper investigates the genomic basis of metamorphosis in orbicular batfish, identifying gene family expansions and differentially expressed genes involved in developmental reprogramming during life-history transition.

The paper identifies a shared A-to-G and G-to-A substitution bias in nanopore sequencing, amplified by bacterial DNA methylation, and shows this bias is concentrated around methylation motifs.

This study identifies epigenetic changes in Flavobacterium columnare under prolonged starvation using DNA methylation profiling, revealing motif-specific demethylation patterns linked to adaptation.

The paper develops ANASFV, a pipeline for ASFV whole genome sequencing, assembly, and evaluation, addressing challenges like contamination, error rates, and recombination analysis.

The paper evaluates RNA modification detection in E. coli using nanopore RNA004 technology, introduces nanoSundial for improved detection, and identifies 190 modified CDS regions.

This study uses direct RNA sequencing to compare TGEV with and without gene 7, revealing changes in RNA modifications and polyA tails, and their impact on viral replication and host immunity.

Giraffe is a tool for comparative analysis and visualization of long-read sequencing data across multiple samples and platforms, showing Oxford Nanopore duplex reads outperform PacBio HiFi in homopolymer identification and GC evenness.