Qianhui Yu

Modeling host-microbe interactions in immunocompetent engineered human gut tissues

The paper develops engineered human gut tissues to study host-microbe interactions and identifies an epithelial gene regulatory network in response to Salmonella Typhimurium infection.

Human Lung Alveolar Model with an Autologous Innate and Adaptive Immune Compartment

This paper develops human lung alveolar immuno-organoids with autologous immune cells to model immune-epithelial interactions and study inflammation-related pulmonary side effects.

A Development-Inspired Niche for Homeostatic Human Mini-Intestines

The paper identifies EPIREGULIN as a niche factor that enables spatial organization in human intestinal organoids, mimicking the native intestine's structure and gene expression.

Multimodal spatiotemporal phenotyping of human organoid development

This paper develops a multimodal approach to study human retinal organoid development, integrating spatial, transcriptomic, and chromatin accessibility data to create a virtual atlas of retinal development.

In vitro and in vivo development of the human intestine at single cell resolution

This study uses scRNA-seq to analyze human intestinal development, identifying cell sources of niche factors and their functional roles in stem cell maintenance.

Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model

The paper uses ChRO-seq to study chromatin dynamics during human small intestinal development, identifying enhancer activity and transcription patterns at HOX gene loci.

An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine

The paper uses human intestinal organoids to create a single-cell transcriptome atlas, revealing molecular mechanisms of cell fate specification in the intestine.

Basal stem cell fate specification is mediated by SMAD signaling in the developing human lung

The paper identifies SMAD signaling as a regulator of basal cell fate specification in the developing human lung using single-cell transcriptomics and organoid models.

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

The paper identifies 33 functional modules associated with human neuron maturation and develops a model to quantify neuron maturity states across species.

Comprehensive investigation of temporal and autism-associated cell type composition-dependent and independent gene expression changes in human brains

The paper quantifies how cell type composition and independent gene expression changes contribute to age-related transcriptome changes in human brains.