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
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
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 Nature Methods (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 Biophysical Journal (2017) Y. Takei, S. Shah, S. Harvey, L. S. Qi and L. Cai
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. Nature Methods (2016) A.F. Coskun and L. Cai
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. 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.
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. 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. Nature Methods 11, 360 (2014) E. Lubeck*, A. F. Coskun*, T. Zhiyentayev, M. Ahmad, and L. Cai
Turning single cells into microarrays by super-resolution barcoding. Briefings in Functional Genomics 12, 75 (2013) L. Cai
Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nature Methods 9, 743 (2012) E. Lubeck and L. Cai
Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 445, 485 (2008) L. Cai*, C. Dalal*, and M.E. Elowitz
A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322, 422 (2008) P. Choi*, L. Cai*, K. Frieda, and X.S. Xie
Studying stochastic protein expression in individual cells with single molecule sensitivity. Nature 440, 358 (2006) L.Cai*, N. Friedman*, and X.S. Xie
Linking stochastic dynamics to population distribution: an analytical framework of gene expression. Phys. Rev. Lett, 97, 168302 (2006) N. Friedman, L.Cai, and X.S. Xie
*denotes equal contribution