Rongxin Fang

This paper introduces a 3D MERFISH method for imaging thick tissues, demonstrating its application on mouse brain sections with high accuracy.

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

The paper develops a multi-omic single-nucleus sequencing method and framework to analyze regulatory genome diversity in human cortical cells and link it to disease risk variants.

This study compares cellular organization and interactions in human and mouse cortex using single-cell transcriptome imaging, finding conserved laminar organization but divergent cell-cell interactions in humans.

The paper compares cellular diversity in the primary motor cortex across human, marmoset, and mouse using single-nucleus transcriptomics and epigenomics, finding conserved cell types and species-specific adaptations.

The paper identifies 491,818 candidate cis regulatory elements in adult mouse brain sub-types and links them to target genes and transcriptional regulators involved in various pathways.

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

The paper uses single-cell chromatin accessibility to identify cell type- and state-specific regulatory programs associated with type 2 diabetes risk.

SnapATAC is a software package for analyzing scATAC-seq data, revealing regulatory elements and transcriptional regulators in mouse brain cells.

SnapHiC identifies high-resolution chromatin loops from scHi-C data and demonstrates cell-type-specific chromatin architecture in mouse and human cells.

The paper maps DNA methylation changes across 12 mouse tissues at 8 developmental stages, identifying methylation variant regions and tissue-specific enhancers linked to human genetic diseases.

The paper investigates chromatin architecture changes during human cardiomyocyte differentiation and identifies HERV-H retrotransposons as key regulators of TAD boundaries and gene regulation.

MAPS processes PLAC-seq and HiChIP data to identify long-range chromatin interactions by removing biases and analyzing contact frequencies.

The paper introduces Methyl-HiC, a method that simultaneously profiles DNA methylation and chromatin architecture, revealing coordinated methylation and dynamic chromatin contacts in mouse embryonic stem cells.

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

This study shows that MLL3/4 proteins regulate chromatin interactions at enhancers by depositing H3K4me1, which recruits Cohesin to facilitate chromatin looping.

The paper introduces a method combining proximity ligation with chromatin immunoprecipitation and sequencing to map long-range chromatin interactions in eukaryotic cells, showing improved sensitivity and accuracy in mouse embryonic stem cells.