Depeng Wang

gSV: a general structural variant detector using the third-generation sequencing data

gSV improves structural variant detection in long-read sequencing data by integrating alignment and assembly approaches, showing better sensitivity for complex variants and uncovering new SVs in breast cancer.

NextPolish2: a repeat-aware polishing tool for genomes assembled using HiFi long reads

NextPolish2 improves genome accuracy by fixing base errors in HiFi assemblies without overcorrections or haplotype switch errors.

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance

This paper introduces Quartet DNA reference materials to comprehensively evaluate germline variant calling accuracy across the genome, including difficult regions and batch effects.

Large scale interrogation of retinal cell functions by 1-photon light-sheet microscopy

This paper introduces a 1-photon light-sheet microscopy system for high-throughput, high-resolution functional analysis of retinal neurons.

Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration

This paper introduces ratio-based multiomics profiling using universal reference materials to improve data integration across omics types and batches.

Structural variant selection for high-altitude adaptation using single-molecule long-read sequencing

The paper uses single-molecule long-read sequencing to identify structural variants driving high-altitude adaptation in Tibetans, revealing their role in gene regulation and biological functions.

Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies

The paper establishes high-confidence structural variant calls in an Asian individual using long-read sequencing technologies and validates them through PCR and Sanger sequencing.

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacbio Sequel II system and ultralong reads of Oxford Nanopore

This study compares genome assemblies from Pacbio HiFi and Oxford Nanopore ultralong reads in rice, finding that ONT provides better contiguity but more errors, while PB offers fewer errors but lower contiguity.

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.

Localization of balanced chromosome translocation breakpoints by long-read sequencing on the Oxford Nanopore platform

This study uses Oxford Nanopore long-read sequencing to precisely localize breakpoints in balanced translocations and inversions, achieving single-base resolution for some cases.

The Tung Tree (Vernicia Fordii) Genome Provides A Resource for Understanding Genome Evolution and Oil Improvement

The paper presents a high-quality tung tree genome, identifies oil-related genes, and provides insights into genome evolution and oil biosynthesis mechanisms.

Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD)

This paper develops a single-molecule optical mapping method for quantitative D4Z4 repeat analysis in FSHD, showing concordance with Southern blot and improved haplotype resolution.

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.

Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis

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.

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

NextSV is a meta-caller for structural variants from low-coverage long-read sequencing data, providing sensitive and stringent call sets with balanced performance.