Peng Ni

Unimeth: A unified transformer framework for accurate DNA methylation detection from nanopore reads

Unimeth improves DNA methylation detection from nanopore reads across species and modification types by using a transformer framework with multi-phase training.

de novo diploid genome assembly using long noisy reads

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

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing

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.

Genome-wide Detection of Cytosine Methylations in Plant from Nanopore sequencing data using Deep Learning

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.

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

DeepSignal detects DNA methylation sites from Nanopore sequencing reads using deep learning, achieving higher accuracy than HMM-based methods across multiple organisms and methylation types.