Kun Zhang

High-resolution retrospective single cell lineage tracing with mutable homopolymers

RETrace2 enables high-resolution retrospective lineage tracing and cell-type identification using mutable homopolymers, achieving resolution below five cell divisions in microsatellite-unstable organisms.

Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality

The paper uses multiomic single-cell and spatial data to identify gene regulatory networks and transcription factors driving cortical regionality in the human brain.

A cross-species single-cell epigenome kidney atlas identifies epithelial cells as a driver of epigenetic aging

The paper builds a cross-species single-cell multi-omics kidney atlas to identify epithelial cells as a driver of epigenetic aging in diseased kidneys.

Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney

The paper presents a multi-modal atlas of human kidney disease, identifying cellular and spatial mechanisms of injury resolution or failure and linking them to clinical outcomes.

Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization

The paper introduces DART-FISH, a multiplexed RNA in situ hybridization technique for high-resolution profiling of human tissues, demonstrating its application on brain and kidney samples.

Gene panel selection for targeted spatial transcriptomics

This paper introduces gpsFISH, a method for selecting gene panels in spatial transcriptomics that outperforms existing methods by accounting for platform effects and incorporating cell type hierarchies.

The chromatin landscape of healthy and injured cell types in the human kidney

The paper defines the chromatin landscape of healthy and injured kidney cells using multi-omics data, identifying regulatory elements and transcription factor networks involved in injury response.

A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury and matrix remodeling in patients with stone disease

This study maps the spatial transcriptomic landscape of the human kidney papilla in stone disease, identifying immune injury and matrix remodeling as key features.

A reference tissue atlas for the human kidney

The paper constructs a reference tissue atlas of the human kidney using multi-omics data to identify cell types, pathways, and genes across nephron segments and interstitium.

Temporal Analyses of Postnatal Liver Development and Maturation by Single Cell Transcriptomics

The paper uses single-cell transcriptomics to analyze liver development in mice, identifying cell types, metabolic zonation, and a transient macrophage population.

A multimodal cell census and atlas of the mammalian primary motor cortex

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of cell types.

Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas

The paper develops a method to screen oncogenic genes across multiple lineages using teratomas and identifies drivers of proliferation in specific cell types.

Revealing the transcription factor regulatory context of human specific cortical development using single-cell multi-omics

The paper uses single-cell multi-omics to analyze HARs and HGEs in fetal human brain development, identifying regulatory networks and key transcription factors involved in human-specific neurodevelopment.

Linking transcriptome and chromatin accessibility in nanoliter droplets for single-cell sequencing

The paper introduces SNARE-seq, a droplet-based method for simultaneous transcriptome and chromatin accessibility profiling in single cells, and applies it to study neurogenesis in mouse cerebral cortices.

Visualizing and interpreting single-cell gene expression datasets with Similarity Weighted Nonnegative Embedding

The paper introduces SWNE, a method for visualizing single-cell gene expression data that improves local and global structure preservation compared to t-SNE.

Single nucleus analysis of the chromatin landscape in mouse forebrain development

The paper uses single nucleus ATAC-seq to analyze chromatin accessibility in mouse forebrain development, identifying cell-type-specific regulatory sequences and transcriptional regulators.

Integrative Single-Cell Analysis By Transcriptional And Epigenetic States In Human Adult Brain

The paper develops two single-cell methods to analyze human brain cells, identifies neuronal subtypes and non-neuronal cell types, and links genetic risk factors to specific cell types.

Ultra-Accurate Genome Sequencing And Haplotyping Of Single Human Cells

This paper introduces a method for accurate single-cell genome sequencing and haplotyping with low error rates and long haplotype assembly.

Assessing the measurement transfer function of single-cell RNA sequencing

This study evaluates the performance of three scRNA-seq methods through controlled experiments, finding they reliably detect genes above 5-10 molecules with linear measurement transfer functions.

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

This study introduces PAGODA, a method to detect transcriptional heterogeneity by analyzing pathway and gene set overdispersion, and applies it to characterize neuronal progenitors in the developing mouse cortex.