Yonghe Xia

Rho: A Purpose-Driven Workspace for Human-AI Collaborative Analysis

Rho is a collaborative analysis environment that organizes materials by scientific purpose to support human-AI judgment in bioinformatics.

Unravelling genome-wide mosaic microsatellite mutations at single-cell resolution

The paper develops BayesMonSTR to detect mosaic STR mutations at single-cell resolution and finds increased STR indels in aging cells, particularly in prefrontal cortex neurons.

Accurate detection of mosaic mutations at short tandem repeats from bulk sequencing data

BulkMonSTR detects mosaic STR mutations in bulk sequencing data with improved precision and F1 scores compared to existing methods.

Detection of Somatic Point Mutations Directly from Spatial Transcriptomics Enables in vivo Spatiotemporal Lineage Tracing

SpaceTracer detects somatic SNVs from spatial transcriptomics data to enable lineage tracing in human tissues, revealing tumor progression and immune cell migration.

PhyloSOLID: Robust phylogeny reconstruction from single-cell data despite inherent error and sparsity

PhyloSOLID improves phylogenetic reconstruction from single-cell data by addressing error and sparsity, achieving better accuracy than existing methods.