Luyao Ren

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

A high-resolution human pangenome structural variant resource for improved disease association

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

Pangenome discovery and characterization of human protein-coding duplicated genes

The paper identifies and characterizes human protein-coding duplicated genes using long-read genomic and transcriptomic data, revealing new gene models and constraint patterns.

Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

NPEPPS segmental duplication drives position effect expression of TBC1D3 in the human brain

The paper identifies a segmental duplication that drives position effect expression of TBC1D3 in the human brain, explaining its high structural heterozygosity.

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

This study generates haplotype-resolved assemblies and a variant benchmark for a Chinese monozygotic twin quartet using advanced sequencing and computational methods.

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.

The Quartet Data Portal: integration of community-wide resources for multiomics quality control

The Quartet Data Portal provides access to multi-omics reference materials and datasets, along with tools for quality control and community integration.

Correcting batch effects in large-scale multiomic studies using a reference-material-based ratio method

The paper evaluates seven batch-effect correction algorithms for multiomic data and finds the ratio-based method is more effective, especially when batch effects are confounded with biological factors.

Quartet metabolite reference materials for assessing inter-laboratory reliability and data integration of metabolomic profiling

The paper establishes reference materials and methods to assess inter-laboratory reliability and data integration in metabolomic profiling.

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.

Quartet RNA reference materials and ratio-based reference datasets for reliable transcriptomic profiling

The paper introduces RNA reference materials and ratio-based datasets to improve the reliability and benchmarking of transcriptomic profiling.

Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study

The paper presents whole-genome and whole-exome sequencing datasets from a multi-center, cross-platform study to benchmark NGS technologies and bioinformatics pipelines in cancer genomics.

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing

This study evaluates reproducibility and accuracy of cancer mutation detection using whole-genome and whole-exome sequencing across multiple sequencing centers and bioinformatics pipelines.