Neng Huang

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

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

The paper introduces longcallR, a tool for SNP calling, haplotype phasing, and allele-specific analysis using long RNA-seq reads, achieving high accuracy and identifying significant allele-specific splicing events in human samples.

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.

miniBUSCO improves genome assembly completeness evaluation by being faster and more accurate than BUSCO.

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