Xingjie Pan

MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue

The paper introduces an imaging-based pooled screening method to identify genetic perturbations and their effects on cell states and neighboring cells in intact tissues.

Whole-transcriptome-scale and isoform-resolved spatial imaging of single cells in complex tissues

The paper introduces a spatial transcriptomics method for whole-transcriptome and isoform-resolved analysis of single cells in mouse brain tissue, revealing spatial diversity and cell-type-specific isoform usage.

Global cell-state and gene-program representations reveal conserved and context-specific perturbation responses of cells

The paper develops a contrastive learning model to integrate scRNA-seq data and perturbation responses, revealing conserved and cell-type-specific cellular responses to genetic perturbations.

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

The paper develops a platform combining imaging and sequencing to study genetic perturbations in mouse liver, identifying regulators of hepatocyte zonation and liver unfolded protein response.

A molecularly defined and spatially resolved cell atlas of the whole mouse brain

MERFISH profiling of >1,100 genes in ~8 million cells spanning the whole mouse brain, integrated with scRNA-seq, maps >5,000 clusters into the Allen Common Coordinate Framework.