Ying Yu

Plasma titration provides a physical ruler for cross-platform proteomics

The paper introduces Plasmix, a plasma reference suite, to improve cross-platform proteomics integration by identifying proteins with consistent titration responses across platforms.

A comprehensive personal omics clinical interpreter based on genomic and transcriptomic profiles

The paper introduces POI, a tool that integrates genomic and transcriptomic data to suggest personalized therapies by matching patients to treatments using PreMedKB and predictive algorithms.

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 protein reference materials and datasets for multi-platform assessment of label-free proteomics

The paper develops Quartet, a proteome reference material with built-in truths, to assess label-free proteomics reproducibility across platforms and labs.

Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples

This study compares transcriptomic profiles of whole blood, plasma-free blood, and serum-free blood samples, finding that plasma-free blood is more similar to whole blood in gene expression and immune characterization.

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.

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.