Xiaowei Zhuang

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.

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

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.

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.

This paper introduces a spatial omics method that combines high spatial resolution with genome-wide profiling through optical barcoding and sequencing.

PEtracer maps cell state and lineage dynamics in vivo with high spatial resolution using prime editing and multimodal imaging.

The paper maps molecular and spatial organization of the mouse primary olfactory system in response to social odors using MERFISH and identifies spatial domains of sensory responses.

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

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.

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.

This paper creates a high-resolution transcriptomic and spatial cell type atlas of the whole adult mouse brain, revealing spatial organization and transcription factor codes for cell types.

SCHAF generates spatially resolved single-cell transcriptomes from H&E histology images using vision transformers and adversarial learning, showing good agreement with ground-truth data.

This paper introduces a method for spatially resolved epigenomic profiling in single cells and generates a high-resolution spatial atlas of active promoters and enhancers in mouse brains.

This study maps age-related changes in mouse brain cellular and molecular organization using spatial transcriptomics, revealing significant shifts in non-neuronal cells and glial activation patterns.

The paper uses spatially resolved single-cell transcriptomics to map transcriptional heterogeneity and spatial organization of cell types in the periaqueductal gray during instinctive behaviors.

The paper identifies and validates MPS-interacting proteins in neurons, showing their periodic distribution and functional roles in axon interactions and diameter regulation.

This study uses electron microscopy to analyze dopaminergic axon connections in the Nucleus Accumbens before and after cocaine exposure, revealing non-synaptic communication and axonal remodeling.

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 introduces Tangram, a method that aligns single-nucleus RNA-seq data with spatial data to create an anatomically integrated spatial map of the mouse brain.

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of cell types.

This study uses scRNA-seq and MERFISH to reveal the molecular and spatial heterogeneity of mouse nucleus accumbens cells and their functional implications.

This study investigates how CTCF binding sites mediate transcriptional insulation in mouse embryonic stem cells, showing that insulation depends on CTCF site number, sequence context, and TAD boundary location.

MERFISH imaging of ~300,000 mouse primary motor cortex cells yields 95 clusters, layered inhibitory as well as excitatory, with intratelencephalic neurons forming a depth-linked expression gradient.

The paper introduces a high-throughput screening method to identify genetic variants with desired phenotypes by imaging barcoded mutants in individual cells.

The paper investigates the prevalence of the actin-spectrin-based membrane skeleton (MPS) across neuronal types and species, finding it widespread in axons and some glial processes but absent in presynaptic boutons.