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Xiaowei Zhuang's Lab

@zhuanglab.bsky.social

Xiaowei Zhuang's Lab at Harvard University and Howard Hughes Medical Institute

Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 17/07/2026

RT&T-AMP-MERFISH opens new ways to study tissues at whole-transcriptome-scale with high spatial resolution, revealing how transcript diversity, gene and isoform regulation, and cell-cell interactions contribute tissue function in health and disease

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 17/07/2026

These data further revealed brain structures with especially rich isoform specificity. For example, the choroid plexus and hippocampus showed specific or preferential isoform expression across many genes.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 17/07/2026

Our isoform-resolved single-cell spatial transcriptomics data revealed widespread spatial and cell-type-specific isoform usage across the brain, with many genes showing distinct isoform enrichment in different anatomical regions and/or cell types.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 17/07/2026

Our whole-transcriptome-scale imaging data revealed spatially organized gene programs, cell-type- and region-specific differential expression, and ligand-receptor-based cell-cell communication patterns across the brain.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 17/07/2026

Integrating RT&T-AMP with multiplexed error-robust fluorescence in situ hybridization, (MERFISH), we imaged ~23,000 genes and ~10,000 isoforms in single cells in brain tissues with high spatial resolution.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 17/07/2026

We developed an in situ RNA amplification method, RT&T-AMP, that uses reverse transcription followed by transcription to generate amplicons at original transcript sites with uniform transcript body coverage, enabling to imaging of short RNA sequences anywhere along transcripts.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 17/07/2026

Excited to share our recent paper (doi.org/10.1016/j.ce...)! In this multi-year effort, we developed RT&T-AMP-MERFISH, enabling whole-transcriptome-scale, isoform-resolved single-cell spatial transcriptomics and imaging ~33,000 RNAs in the brain.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 28/05/2026

Explore the Global Pattern Browser: xingjiepan.github.io/SCMG/ Code: github.com/xingjiepan/S...

xingjiepan.github.io

Global Pattern Browser

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 28/05/2026

Moreover, we perform a genome-scale Perturb-seq screen in human embryonic stem cells, validating and extending these findings and uncovering a class of mesenchymal transitions induced by diverse perturbations to cellular stress-response pathways.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 28/05/2026

Applying this framework across Perturb-seq datasets on different cell types reveals conserved cellular responses to perturbations, as well as cell-type-specific rewiring of stress responses.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 28/05/2026

We introduce SCMG, a machine learning framework that integrates diverse scRNA-seq datasets into a global, interpretable cell-state manifold. We identify gene-expression programs that define axes of cell-state transitions and functional embeddings of genes that define perturbation classes.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 28/05/2026

What is the global structure of cell-state space—and how do perturbations drive transitions within it? Excited to share our new preprint (www.biorxiv.org/content/10.6...), a work in collaboration with @weissmanlab.bsky.social.

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Xiaowei Zhuang's Lab @zhuanglab.bsky.social · 25/11/2024

Check out this preprint on Perturb-multi (doi.org/10.1101/2024...), a multi-year collaborative effort that enabled multi-modal in vivo genotype-phenotype mapping by pooled genetic perturbations and high-dimensionality phenotype readout by imaging and sequencing. bsky.app/profile/weal...

doi.org

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

Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the...

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