Publications

Browse our recent published articles in peer-reviewed journals.

2021

Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture

Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture

Preprint

Yodai Takei, Shiwei Zheng, Jina Yun, Sheel Shah, Nico Pierson, Jonathan White, Simone Schindler, Carsten Tischbirek, Guo-Cheng Yuan, Long Cai
Integrated spatial genomics reveals global architecture of single nuclei

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)

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+

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

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

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

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

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

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

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

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

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

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

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

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

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

Turning single cells into microarrays by super-resolution barcoding

Briefings in Functional Genomics 12, 75 (2013)

L. Cai

*denotes equal contribution