Ying Gu

This study creates a spatiotemporal atlas to understand mesenchymal-epithelial stem cell dynamics in human hair follicle aging and androgenetic alopecia, identifying PTN as a key regenerative factor.

This study reconstructs 3D spatial transcriptomic models of planarians to map cell type distribution and positional gene regulation, identifying candidate genes involved in regeneration.

The paper introduces CIMA, a multi-omics atlas of human immune cells, identifying regulatory mechanisms and genetic associations across sex, age, and genetic factors.

This study constructs a 4D spatiotemporal transcriptomic map of planarian regeneration using Stereo-seq, identifying dynamic gradients and an injury-induced regenerative zone.

The paper constructs a multimodal brain cell atlas of adult macaques across their lifespan, revealing aging-related molecular changes and identifying aging hotspots and regulatory loci.

The paper constructs a near-complete genome assembly for the bearded dragon Pogona vitticeps and characterizes the Z sex chromosome, identifying key genes involved in sex determination.

The paper uses single cell transcriptomes to study how regulatory networks change during the development of Kranz anatomy in C4 grasses.

The paper uses single-cell long-read transcriptome sequencing to study transcript diversity and alternative splicing in zebrafish embryos, identifying cell populations with distinct splicing regulations during early development.

This paper introduces an improved nanopore sequencing platform called CycloneSEQ, demonstrating long-duration sequencing and high yield with applications in genomics.

The paper constructs a 3D spatiotemporal multi-omics atlas of Drosophila development, revealing gene regulatory networks and cell type dynamics across embryogenesis to metamorphosis.

Spateo provides a framework for spatiotemporal modeling of single-cell spatial transcriptomics data to study cell-cell interactions and organ development in 3D space.

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.

The paper introduces DocMF, a high-throughput method to profile protein-DNA interactions, identifying PAM sequences for CRISPR systems and other DNA-binding proteins.

This study shows that gene conversion and NHEJ are major DNA repair mechanisms in human embryos, with gene conversion potentially useful for gene correction but also causing extensive loss of heterozygosity.

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

The paper compares human and mouse neocortical development using scRNA-seq, finding differences in excitatory neuron trajectories and gene expression but conservation in glial and inhibitory neuron development.

The paper derives and characterizes XEN cells from pig embryos, showing their ability to contribute to chimerism and serve as nuclear donors for cloning.

This paper develops CRISPR systems to target and deplete an oncogenic KRAS mutant allele, leading to tumor regression in vitro and in vivo.

This study introduces qCas9, a modified CRISPR/Cas9 system that enhances genome editing efficiency and reduces off-target effects in zebrafish and mammalian cells.

The paper sequences and compares three Chlorella genomes to identify genetic factors contributing to wastewater tolerance and nutrient removal.

This study validates the use of exosomal DNA from maternal plasma for noninvasive prenatal detection of fetal trisomy and single gene disease.