Feng Luo

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.

HapBridge: A Methylation-Guided Approach for Correcting Switch Errors and Bridging Phased Blocks in Long-Read Phasing

HapBridge improves haplotype phasing by correcting switch errors and bridging phased blocks using DNA methylation signals, achieving higher accuracy and contiguity in long-read sequencing.

Transposon activities drive the selection and diversification of sweet orange (Citrus sinensis) cultivars in the last 500 years

This study identifies transposon activities as key drivers of sweet orange cultivar selection and diversification over the last 500 years.

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.

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.

Genome-wide Comparative Analysis Reveals Possible Common Ancestors of NBS Domain Containing Genes in Hybrid Citrus sinensis Genome and Original Citrus clementina Genome

The paper identifies and re-annotates NBS genes in three citrus genomes, revealing shared ancestral origins and evolutionary patterns among NBS genes in hybrid and original citrus species.