Chuan‐Le Xiao

High accuracy methylation identification tools on single molecular level for PacBio HiFi data

The paper introduces hifimeth, a deep learning model that improves 5mC detection accuracy on PacBio HiFi data by using 400 bp context, achieving higher accuracy and F1 score than existing methods.

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.

High-resolution diploid 3D genome reconstruction using Pore-C data

This paper introduces Dip3D, a method to reconstruct high-resolution diploid 3D human genomes from Pore-C data, achieving better performance than existing methods.

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.

An efficient error correction and accurate assembly tool for noisy long reads

NextDenovo corrects noisy Nanopore reads faster and more accurately than Canu and Necat; its maize and 35 human-genome assemblies are more contiguous, with fewer misassemblies, than Flye's.

Falign: An effective alignment tool for long noisy 3C data

Falign improves alignment of fragmented long noisy 3C data by addressing fragment boundary issues and increasing data utilization.

Automated assembly of high-quality diploid human reference genomes

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.

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.

HIT-scISOseq: High-throughput and High-accuracy Single-cell Full-length Isoform Sequencing for Corneal Epithelium

HIT-scISOseq improves single-cell isoform sequencing throughput and accuracy, revealing novel transcriptomic features in corneal epithelium injury.

Fast and accurate assembly of Nanopore reads via progressive error correction and adaptive read selection

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

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.

N6-Methyladenine DNA Modification in Human Genome

This study identifies widespread N6-methyladenine (6mA) modification in the human genome, links it to gene expression, and shows its role in cancer by demonstrating reduced 6mA levels in tumors.

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

MECAT provides an ultra-fast tool for mapping, error correction, and de novo assembly of single-molecule sequencing reads, achieving high-quality assemblies with reduced computational cost.