Mengnan Cheng

Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis

The paper uses single-cell multiomics to study gene regulatory programs in mouse embryonic skin, identifying cis-regulatory elements and transcription factors involved in development.

Genomic evolution reshapes cell type diversification in the amniote brain

The paper creates a single-cell atlas of amniote brains to study cell type diversification and identifies species-specific gene expression patterns and novel cell subtypes.

Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Stereopy provides a framework for analyzing multi-sample spatial transcriptomics data to model comparative and spatiotemporal cellular heterogeneity through three key algorithms.

Three-dimension transcriptomics maps of whole mouse embryo during organogenesis

The paper fills a gap in 3D spatial transcriptomics by providing data from E9.5 and E11.5 mouse embryos, enabling detailed analysis of organogenesis with a new open-access database.

Spatially resolved molecular and cellular atlas of the mouse brain

The paper creates a high-resolution spatial transcriptomic atlas of the mouse brain using snRNA-seq and Stereo-seq, identifying new cell clusters, region-specific genes, and transcription factor regulons.

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.

High-resolution spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae

This study uses Stereo-seq to generate high-resolution spatiotemporal transcriptomic maps of Drosophila embryos and larvae, revealing new subregions and gene regulatory networks.

Spatially resolved gene regulatory and disease vulnerability map of the adult Macaque cortex

The paper integrates single-cell ATAC and transcriptomic data with spatial transcriptomics to map regulatory features and disease vulnerabilities in macaque cortex.

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.