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.

bioRxiv · Oct 6, 2026 · PreprintGenomics

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

Limor Cohen, Aaron R. Halpern, Timothy R. Blosser, Z. Phil Che, Xingjie Pan, Xiaowei Zhuang

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.

Cell · Jul 16, 2026Peer-reviewedGenomics

Three-dimensional single-cell transcriptome imaging of thick tissues

Rongxin Fang, Aaron R. Halpern, Mohammed Mostafizur Rahman, Zhengkai Huang, Zhiyun Lei, Sebastian J Hell, Catherine G. Dulac, Xiaowei Zhuang

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

eLife · Dec 27, 2024Peer-reviewedNeuroscience

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

Meng Zhang, Xingjie Pan, Won Jung, Aaron R. Halpern, Stephen W. Eichhorn, Zhiyun Lei, Limor Cohen, Kimberly A. Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Xiaowei Zhuang

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.

Nature · Dec 13, 2023Peer-reviewedNeuroscience✦ In-depth digest

Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy

Marcus A. Woodworth, Kenneth K.H. Ng, Aaron R. Halpern, Nicholas A. Pease, Phuc Hong Nguyen, Hao Yuan Kueh, Joshua C. Vaughan

The paper introduces SCEPTRE, a method combining expansion microscopy with histone modification analysis to study chromatin states in single cells at high resolution.

Nucleic Acids Research · May 7, 2021Peer-reviewedGenomics