Publications
Browse our recent published articles in peer-reviewed journals.2023
![Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease](https://spatial.caltech.edu/files/2024/02/F_pVnEJa4AA9d3V.jpg)
Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease
BioRxiv (2023)
![High-resolution spatial multi-omics reveals cell-type specific nuclear compartments](https://spatial.caltech.edu/files/2024/02/FvtofkTaQAAM00D-scaled-e1706840164239.jpg)
High-resolution spatial multi-omics reveals cell-type specific nuclear compartments
BioRxiv (2023)
2021
![Single-cell nuclear architecture across cell types in the mouse brain](https://spatial.caltech.edu/files/2021/04/Neuro-DNAseqFISH-01.jpg)
Single-cell nuclear architecture across cell types in the mouse brain
Science (2021)
![Integrated spatial genomics reveals global architecture of single nuclei](https://spatial.caltech.edu/files/2021/02/Integrated-spatial-genomics-1024x429.jpg)
Integrated spatial genomics reveals global architecture of single nuclei
Nature, (2021)
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
Preprint (2020) at biorxiv.org
2020
![Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)](https://spatial.caltech.edu/files/2020/08/2019_blog_DUET.jpg)
Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)
Nature, Communications Biology (2020)
Yandong Zhang, Changho Sohn, Seoyeon Lee, Heejeong Ahn, Jinyoung Seo, Junyue Cao and Long Cai
2019
![Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+](https://spatial.caltech.edu/files/2020/07/fig_1_seqFISH.png)
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
Nature (2019)
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
2018
![Identification of spatially associated subpopulations by combiningscRNAseq and sequential fluorescence in situ hybridization data](https://spatial.caltech.edu/files/2020/09/nat_biotech.png)
Identification of spatially associated subpopulations by combiningscRNAseq and sequential fluorescence in situ hybridization data
Nature Biotechnology (2018)
Zhu Q, Shah S, Dries R, Cai L*, Yuan GC*
![Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH](https://spatial.caltech.edu/files/2020/07/sheel-1.png)
Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH
Cell (2018)
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
2017
![Identification of a neural crest stem cell niche by Spatial Genomic Analysis](https://spatial.caltech.edu/files/2020/08/Antti-1.png)
Identification of a neural crest stem cell niche by Spatial Genomic Analysis
Nature Communications (2017)
Antti Lignell, Laura Kerosuo, Sebastian J. Streichan, Long Cai and Marianne E. Bronner
![Profiling the transciptome with RNA SPOTs](https://spatial.caltech.edu/files/2020/08/Linus1.png)
Profiling the transciptome with RNA SPOTs
Nature Methods (2017)
CH. L. Eng, S. Shah, J. Thomassie and L. Cai
![seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus](https://spatial.caltech.edu/files/2020/09/neuron.png)
seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus
Neuron (2017)
CH. L. Eng, S. Shah, J. Thomassie and L. Cai
![Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH](https://spatial.caltech.edu/files/2020/08/BJ-slider.jpg)
Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH
Biophysical Journal (2017)
Y. Takei, S. Shah, S. Harvey, L. S. Qi and L. Cai
2016
Synthetic recording and in situ readout of lineage information in single cells
Nature (2016)
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*
In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus
Neuron (2016)
S. Shah+, E. Lubeck+, W. Zhou and L. Cai
Noncommutative Biology: Sequential Regulation of Complex Networks
PLOS Computational Biology (2016)
W. Letsou and L. Cai
Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing
Development (2016)
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*
![Dense transcript profiling in single cells by image correlation decoding](https://spatial.caltech.edu/files/2020/08/corrfish.png)
Dense transcript profiling in single cells by image correlation decoding
Nature Methods (2016)
A.F. Coskun and L. Cai
2015
![Combinatorial gene regulation by modulation of relative pulse timing](https://spatial.caltech.edu/files/2020/08/pb10.png)
Combinatorial gene regulation by modulation of relative pulse timing
Nature 527, 54-58 (2015)
Y. Lin, C.H. Sohn, C.K. Dalal, L. Cai, M.B. Elowitz
![Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping](https://spatial.caltech.edu/files/2020/08/pb9.jpg)
Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping
Nature Protocols 10, 1860–1896 (2015)
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
2014
![Single-cell phenotyping within transparent intact tissue through whole-body clearing](https://spatial.caltech.edu/files/2020/08/pb8.png)
Single-cell phenotyping within transparent intact tissue through whole-body clearing
Cell 158, 945 (2014)
B. Yang, J.B. Treweek, R.J. Kulkarni, B.E. Deverman, C. Chen, E. Lubeck,S. Shah, L. Cai, and V. Gradinaru
![Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells](https://spatial.caltech.edu/files/2020/08/pb7.png)
Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells
Molecular Cell 55, 319 (2014)
Z. S. Singer, J. Yong, J. Tischler, J. A. Hackett, A. Altinok, M. A. Surani, L. Cai, and M.B. Elowitz
![Single-cell in situ RNA profiling by sequential hybridization](https://spatial.caltech.edu/files/2020/08/SeqFISH.png)
Single-cell in situ RNA profiling by sequential hybridization
Nature Methods 11, 360 (2014)
E. Lubeck*, A. F. Coskun*, T. Zhiyentayev, M. Ahmad, and L. Cai
2013
![Turning single cells into microarrays by super-resolution barcoding](https://spatial.caltech.edu/files/2020/08/pb6.png)
Turning single cells into microarrays by super-resolution barcoding
Briefings in Functional Genomics 12, 75 (2013)
L. Cai
*denotes equal contribution