Publications

Browse our recent published articles in peer-reviewed journals.

2026

  1. The temporal architecture of the seminiferous epithelial cycle revealed by spatial transcriptomics

    Arun Chakravorty, Jina Yun1, Henry Amrhein, Katsuya L. Colón1, Toshiyuki Sato, Benjamin D. Simons, Shosei Yoshida, Long Cai

    Cell, 2026

    Cell

2025

  1. Spatial multi-omics reveals cell-type-specific nuclear compartments

    Yodai Takei, Yujing Yang, Jonathan White, Isabel N. Goronzy, Jina Yun, Meera Prasad, Lincoln J. Ombelets, Simone Schindler, Prashant Bhat, Mitchell Guttman & Long Cai

    Nature, 2025

    Nature Spatial multi-omics of nuclear architecture with two-layer seqFISH+

2024

  1. Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease

    Michal Polonsky, Louisa M. S. Gerhardt, Jina Yun, Kari Koppitch, Katsuya Lex Colón, Henry Amrhein, Shiwei Zheng, Guo-Cheng Yuan, Matt Thomson, Long Cai, Andrew P. McMahon

    Nature Communications, 2024

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2023

  1. High-resolution spatial multi-omics reveals cell-type specific nuclear compartments

    Yodai Takei, Yujing Yang, Jonathan White, Jina Yun, Meera Prasad, Lincoln J Ombelets, Simone Schindler, Long Cai

    BioRxiv (2023)

    Preprint

2021

  1. Single-cell nuclear architecture across cell types in the mouse brain

    Yodai Takei , Shiwei Zheng , Jina Yun , Sheel Shah , Nico Pierson , Jonathan White , Simone Schindler , Carsten Tischbirek , Guo-Cheng Yuan , Long Cai

    Science (2021)

    Science Preprint (2021) at biorxiv.org

  2. Integrated spatial genomics reveals global architecture of single nuclei

    Yodai Takei, Jina Yun, Shiwei Zheng, Noah Ollikainen, Nico Pierson, Jonathan White, Sheel Shah, Julian Thomassie, Shengbao Suo, Chee-Huat Linus Eng, Mitchell Guttman, Guo-Cheng Yuan & Long Cai

    Nature, (2021)

    Nature Preprint

2020

  1. Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)

    Yandong Zhang, Changho Sohn, Seoyeon Lee, Heejeong Ahn, Jinyoung Seo, Junyue Cao and Long Cai

    Nature, Communications Biology (2020)

    Nature

2019

  1. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

    Chee-Huat Linus Eng, Michael Lawson, Qian Zhu, Ruben Dries, Noushin Koulena, Yodai Takei, Jina Yun, Christopher Cronin, Christoph Karp, Guo-Cheng Yuan and Long Cai

    Nature (2019)

    Nature

2018

  1. Identification of spatially associated subpopulations by combiningscRNAseq and sequential fluorescence in situ hybridization data

    Zhu Q, Shah S, Dries R, Cai L*, Yuan GC*

    Nature Biotechnology (2018)

    Nature

  2. Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

    Sheel Shah, Yodai Takei, Wen Zhou, Eric Lubeck, Jina Yun, Chee-Huat Linus Eng, Noushin Koulena, Christopher Cronin, Christoph Karp, Eric J. Liaw, Mina Amin and Long Cai

    Cell (2018)

    Cell

2017

  1. Identification of a neural crest stem cell niche by Spatial Genomic Analysis

    Antti Lignell, Laura Kerosuo, Sebastian J. Streichan, Long Cai and Marianne E. Bronner

    Nature Communications (2017)

    Nature

  2. Profiling the transciptome with RNA SPOTs

    CH. L. Eng, S. Shah, J. Thomassie and L. Cai

    Nature Methods (2017)

    Nature

  3. seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

    CH. L. Eng, S. Shah, J. Thomassie and L. Cai

    Neuron (2017)

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  4. Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH

    Y. Takei, S. Shah, S. Harvey, L. S. Qi and L. Cai

    Biophysical Journal (2017)

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2016

  1. Synthetic recording and in situ readout of lineage information in single cells

    K.L. Frieda+, J.M. Linton+, S. Hormoz+, J. Choi, K.-H.K. Chow, Z.S. Singer, M.W. Budde, M.B. Elowitz* and L. Cai*

    Nature (2016)

    Nature

  2. In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

    S. Shah+, E. Lubeck+, W. Zhou and L. Cai

    Neuron (2016)

    Cell

  3. Noncommutative Biology: Sequential Regulation of Complex Networks

    W. Letsou and L. Cai

    PLOS Computational Biology (2016)

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  4. Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

    S. Shah+, E. Lubeck+, M. Schwarzkopf+, T. He+, A. Greenbaum+, C. H. Sohn, A. Lignell, H. M. T. Choi, V. Gradinaru*, N. A. Pierce* and L. Cai*

    Development (2016)

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  5. Dense transcript profiling in single cells by image correlation decoding

    A.F. Coskun and L. Cai

    Nature Methods (2016)

    Nature

2015

  1. Combinatorial gene regulation by modulation of relative pulse timing

    Y. Lin, C.H. Sohn, C.K. Dalal, L. Cai, M.B. Elowitz

    Nature 527, 54-58 (2015)

    Nature

  2. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

    J.B. Treweek,K.Y.Chan,N.C. Flytzanis, B. Yang, B.E. Deverman, A. Greenbaum, A. Lignell, C. Xiao, L.Cai, M.S. Ladinsky,P.J. Bjorkman, C.C. Fowlkes, and V. Gradinaru

    Nature Protocols 10, 1860–1896 (2015)

    Nature

2014

  1. Single-cell phenotyping within transparent intact tissue through whole-body clearing

    B. Yang, J.B. Treweek, R.J. Kulkarni, B.E. Deverman, C. Chen, E. Lubeck,S. Shah, L. Cai, and V. Gradinaru

    Cell 158, 945 (2014)

    Cell

  2. Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

    Z. S. Singer, J. Yong, J. Tischler, J. A. Hackett, A. Altinok, M. A. Surani, L. Cai, and M.B. Elowitz

    Molecular Cell 55, 319 (2014)

    Cell

  3. Single-cell in situ RNA profiling by sequential hybridization

    E. Lubeck*, A. F. Coskun*, T. Zhiyentayev, M. Ahmad, and L. Cai

    Nature Methods 11, 360 (2014)

    Nature

2013

  1. Turning single cells into microarrays by super-resolution barcoding

    L. Cai

    Briefings in Functional Genomics 12, 75 (2013)

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