Zhaojun Zhang

This paper introduces 3D-Omics-Flow, a method that reconstructs 3D molecular volumes from 2D spatial proteomics sections by repairing damaged sections and interpolating between them.

CoPro identifies spatially coordinated gene expression programs across tissues, revealing distinct cellular states and their interactions in colon, brain, liver, and kidney.

Thermostable RNaseH release of barcoded cDNA keeps sections intact for CODEX imaging, yielding same-section whole-transcriptome and protein maps plus CODEX-guided spot deconvolution in FFPE tissues.

The paper analyzes ex vivo human erythropoiesis at single-cell chromatin accessibility and transcriptome levels to identify discrepancies and constraints in erythrocyte regeneration.

EryDB is a database that collects and integrates transcriptomic data for erythropoiesis and erythroid-related diseases, enabling analysis and visualization of gene expression across species and tissues.

This paper introduces CellANOVA, a statistical model to recover biological signals lost during single-cell data integration by distinguishing batch effects from true biological variation.

The paper introduces TRIPOD, a nonparametric method to detect TF-target gene-accessibility relationships in multiomic data, validated across multiple datasets.

This study maps the single-cell landscape of acral melanoma and analyzes the molecular regulatory network of its tumor microenvironment, identifying nine cell types and key interactions.

This study maps the differentiation trajectory of iPSC-derived erythroid cells using single-cell transcriptomics, identifying key transcription factors and cell types.

The paper investigates the interaction between long non-coding RNAs and chromatin accessibility during erythroid differentiation, identifying stage-specific regulatory networks and key lncRNAs involved in the process.

SAVERCAT improves batch correction and denoising in single-cell RNA sequencing by adjusting for observed confounding variables, outperforming existing methods in high-dimensional data.