Ting Yu

WattmaMod enables high-resolution and extensible RNA modification profiling for nanopore direct RNA sequencing

WattmaMod detects multiple RNA modifications from nanopore sequencing data using deep learning, achieving high accuracy and extending to low-resource modifications.

Viral haplotype reconstruction from long reads with virCHap

virCHap reconstructs viral haplotypes from long-read sequencing data, outperforming existing methods in recall, abundance estimation, and read clustering.

GLASS: A Graph Learning Algorithm for Screening Splice-Aware Alignments of Long-Read RNA-seq

GLASS filters erroneous splice-aware alignments from long-read RNA-seq data, improving transcriptome reconstruction accuracy across multiple species.

De novo annotation of centromere with centroAnno

centroAnno is a de novo algorithm for centromere annotation that outperforms existing tools in accuracy and efficiency on simulated and real datasets.

An integrated Asian human SNV and indel benchmark combining multiple sequencing methods

The paper constructs a high-confidence Asian variant benchmark using multiple sequencing methods and identifies novel variants in challenging regions.