Jie Wang

CSOA improves gene set enrichment analysis in single-cell data by accurately distinguishing enriched cells from background, outperforming existing methods in multiple benchmarks.

This study identifies ATOH7+ nascent cone precursors as the earliest cell-of-origin for human retinoblastoma using RB1-deficient retinal organoids and scRNA-seq.

This study constructs a cross-etiological HSC atlas to reveal HSC heterogeneity and spatiotemporal dynamics in liver injury, identifying a novel apoptosis-prone HSC subtype and a 531-gene fibrosis signature.

scRetinaDB aggregates single-cell and spatial omics data from retinas across species to enable cross-species analysis and resource sharing.

ScReNI integrates scRNA-seq and scATAC-seq data to infer cell-specific regulatory networks and identify cell-enriched regulators.

CACIMAR identifies conserved cell types, markers, regulations, and interactions across species using scRNA-seq data.

This study identifies key transcription factors that regulate the epigenetic landscape during retinal cell differentiation using scATAC-seq and CUT&Tag.

The paper characterizes RNA content in individual phase-separated coacervate microdroplets using high-throughput sequencing and identifies sequence motifs associated with RNA accumulation.

LRLoop identifies bidirectional ligand-receptor feedback loops in cell-cell communication, reducing false positives and revealing new interactions in retinal development.

IReNA integrates scRNA-seq and scATAC-seq data to infer regulatory networks, outperforming existing methods in identifying known regulators.

This study defines mouse iris cell types and their transcriptomic changes during pupil dilation using single nucleus RNA sequencing.

The paper organizes a DREAM challenge to benchmark predictive models of single-cell signaling using mass cytometry data from breast cancer cell lines.

The paper uses single-cell RNA-seq to analyze retinal ganglion cell lineage development in wild-type and Atoh7-null retinas, revealing a transitional cell state and revised understanding of Atoh7's role.

This study shows that Zfp36l1 and Zfp36l2 regulate retinal development by balancing proliferation and differentiation, with their loss causing reduced proliferation and increased differentiation in the retina.

This study identifies gene regulatory networks controlling proliferative and neurogenic competence in retinal Muller glia.

This study shows Foxd1 is required for sustained expression of genes in mature anterior hypothalamic neurons, but not for initial patterning.

This study identifies global decreases in chromatin accessibility in AMD patients, linking epigenetic changes to disease progression and suggesting HDAC11 as a potential therapeutic target.