Fan Nie

PECAT improves diploid genome assembly from long noisy reads by correcting errors and resolving haplotypes, achieving high contiguity in cattle and human genomes.

The paper introduces ccsmeth, a deep-learning method for detecting DNA 5mCpGs using PacBio CCS, achieving high accuracy and AUC, and presents ccsmethphase for haplotype-aware methylation detection.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

This study introduces a deep learning pipeline to detect 5mC in CpG and non-CpG contexts from Nanopore sequencing data in plants, achieving high accuracy compared to bisulfite sequencing.

NECAT improves Nanopore read error correction and de novo assembly, achieving higher accuracy and faster performance for genome assembly.