Leming M. Shi

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 Telomere-to-Telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

The paper presents a telomere-to-telomere diploid reference genome for the Chinese Quartet, improving centromere structure annotation and enabling population-specific structural variant analysis.

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.

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.

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.

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.

BEdeepon: an in silico tool for prediction of base editor efficiencies and outcomes

BEdeepon predicts base editor efficiencies and outcome sequences using deep learning models trained on high-throughput screening data.

BEdeepoff: an in silico tool for off-target prediction of ABE and CBE base editors

BEdeepoff predicts off-target editing efficiencies for ABE and CBE base editors using deep learning models trained on high-throughput screening data.