Qingwang Chen

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 ratio-based framework using Quartet reference materials for integrating long- and short-read RNA-seq

This paper develops a ratio-based framework using Quartet reference materials to integrate long- and short-read RNA-seq data, showing hybrid-seq achieves the highest quantification accuracy.

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.

Toward Best Practice in Identifying Subtle Differential Expression with RNA-seq: A Real-World Multi-Center Benchmarking Study Using Quartet and MAQC Reference Materials

This study benchmarks RNA-seq methods across 45 labs to identify sources of variation in detecting subtle differential expression, highlighting experimental and bioinformatics factors affecting reliability.

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.

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.

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.