Qian Qin

This paper introduces a method for improving long-read somatic structural variant calling by integrating pangenome and de novo personal genome assembly, reducing false positives while maintaining sensitivity.

FuFiHLA is a tool for full-field HLA typing from long-read data, achieving high accuracy in allele typing and consensus sequence construction.

LongcallD jointly calls and phases small, structural, and mosaic variants from long reads, improving SV discovery and mosaic variant accuracy.

The paper identifies fibroblast-derived neurotrophin signaling as a driver of abnormal vascular maturation in RA synovia and shows that neurotrophin inhibitors can reverse this process.

This study uses spatial transcriptomics to identify CD8+ T cell-driven mechanisms of kidney damage in ICI-AIN, showing increased IFN-γ signaling and proinflammatory myeloid cell activation.

This study evaluates diploid donor-specific assemblies for improving somatic structural variant detection in cancer genomes, finding they identify more variants and reduce artifacts compared to standard references.

This study identifies tonic signaling as a key factor in CAR-T cell efficacy for diffuse midline glioma, showing that restrained tonic signaling improves therapeutic outcomes.

This paper introduces colorSV, a method for calling long-range somatic structural variants using co-assembly graphs, achieving high precision and sensitivity in translocation detection.

CTAT-LR-fusion detects fusion transcripts from long and short read RNA-seq data, improving accuracy in bulk and single cell transcriptomes.

Pyro-Velocity improves RNA velocity inference by modeling raw sequencing counts with synchronized cell time across genes to better estimate cell fate and trajectory dynamics.

singlecellVR provides an accessible VR tool for visualizing single-cell data, supporting various modalities and offering a companion package for data conversion and pre-analyzed datasets.

Lisa predicts transcriptional regulators of gene sets by integrating chromatin accessibility and ChIP-seq data to identify relevant regulators.