Xiaoyu Wei

Single-nucleus chromatin accessibility time course of excisional wound repair in rat skin

The paper presents a time-course single-nucleus ATAC-seq dataset from rat skin wounds, revealing chromatin accessibility changes across repair phases.

Spatiotemporal atlas resolves the mesenchymal-epithelial stem cell axis governing human hair follicle aging and pathology

This study creates a spatiotemporal atlas to understand mesenchymal-epithelial stem cell dynamics in human hair follicle aging and androgenetic alopecia, identifying PTN as a key regenerative factor.

SPARKLE: evidence-constrained correction of local RNA leakage in high-resolution spatial transcriptomics

SPARKLE corrects local RNA leakage in spatial transcriptomics by using spatial evidence within each sample, improving cell-type localization and communication inference.

Ribonucleotide Reductase Inhibition Overcomes FLT3 Inhibitor Resistance in Acute Myeloid Leukemia

This paper identifies RNR inhibition as a strategy to overcome FLT3 inhibitor resistance in FLT3ITD+ AML by reversing resistance mechanisms and enhancing therapeutic efficacy.

Targeting Cellular Pseudo-Senescence to Overcome PARP inhibitors Resistance in BRCA1 -Mutated Breast Cancer

This study identifies ZNF251 deficiency as a driver of PARP inhibitor resistance in BRCA1-mutant breast cancer, showing that targeting pseudo-senescence with senomorphic or senolytic therapies can overcome resistance.

Cell Type Architecture and Positional Gene Gradients in an Adult Animal at Subcellular Resolution

This study reconstructs 3D spatial transcriptomic models of planarians to map cell type distribution and positional gene regulation, identifying candidate genes involved in regeneration.

4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians

This study constructs a 4D spatiotemporal transcriptomic map of planarian regeneration using Stereo-seq, identifying dynamic gradients and an injury-induced regenerative zone.

Inferring cell trajectories of spatial transcriptomics via optimal transport analysis

spaTrack infers spatial cell trajectories using optimal transport, revealing spatiotemporal dynamics in regeneration and tumor development.

A spatiotemporal transcriptomic atlas of the mouse placenta reveals glycogen cell-mediated metabolic support essential for fetal viability

Mutant forms of DDX3X with diminished catalysis form hollow condensates that exhibit sex-specific regulation

This study shows that specific DDX3X mutants form hollow condensates, impairing catalytic activity and interacting differently with WT DDX3X and DDX3Y, which may explain sex-specific disease biases.

Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics

Spateo provides a framework for spatiotemporal modeling of single-cell spatial transcriptomics data to study cell-cell interactions and organ development in 3D space.

Spatiotemporal transcriptome at single-cell resolution reveals key radial glial cell population in axolotl telencephalon development and regeneration

The paper uses Stereo-seq to map single-cell transcriptomes of axolotl telencephalon during development and regeneration, identifying a key radial glial cell subtype involved in early wound healing.

A portable and cost-effective microfluidic system for massively parallel single-cell transcriptome profiling

The DNBelab C4 portable, negative-pressure microfluidic device performs high-throughput single-cell transcriptome profiling, resolving species-specific cells and tissue heterogeneity in murine lung and cerebral cortex comparably to existing platforms.

An ATAC-seq atlas of chromatin accessibility in mouse tissues

The paper creates an ATAC-seq atlas of chromatin accessibility in adult mouse tissues, identifying tissue-specific accessible elements and transcription factor motifs.

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

The paper introduces scCAT-seq, a method to simultaneously assay chromatin accessibility and transcriptome in single cells, and demonstrates its application in human pre-implantation embryos to reveal regulatory heterogeneity.