Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
Rodriques, S. G., Stickels, R. R., Goeva, A., Martin, C. A., Murray, E., Vanderburg, C. R., … & Macosko, E. Z. (2019). Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science, 363(6434), 1463-1467.
Multiplex digital spatial profiling of proteins and RNA in fixed tissue
Merritt, C.R., Ong, G.T., Church, S.E. et al. Multiplex digital spatial profiling of proteins and RNA in fixed tissue. Nat Biotechnol 38, 586–599 (2020).
MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure
Keren, L., Bosse, M., Thompson, S., Risom, T., Vijayaragavan, K., McCaffrey, E., Marquez, D., Angoshtari, R., Greenwald, N. F., Feinberg, H., Wang, J., Kambhan, N., Kirkwood, D., Nolan, G., Montine, T. J., Galli, S. J., West, R., Bendall, S. C., Angelo, M. (2018). MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure. Science Advances, 5(10),
Keren, L., Bosse, M., Marquez, D., Angoshtari, R., Jain, S., Varma, S., Yang, S., Kurian, A., Van Valen, D., West, R., Bendall, S. C., Angelo, M. (2018). A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging. Cell, 174(6), 1373–1387.
Multiplexed ion beam imaging of human breast tumors
Angelo, M., Bendall, S. C., Finck, R., Hale, M. B., Hitzman, C., Borowsky, A. D., Levenson, R. M., Lowe, J.B., Liu, S. D., Zhao, S., Natkunam, Y., Nolan, G. P. (2014). Multiplexed ion beam imaging of human breast tumors. Nature Medicine, 20(4), 436–442.
Spatially resolved, highly multiplexed RNA profiling in single cells
K.H. Chen, A.N. Boettiger, J.R. Moffitt, S. Wang, X. Zhuang. Science, 348, aaa6090 (2015)
High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization
J.R. Moffitt, J. Hao, G. Wang, K.H. Chen, H.P. Babcock, X. Zhuang. PNAS, 113, 11046 (2016)
High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing
J.R. Moffitt, J. Hao, D. Bambah-Mukkua, T. Lu, C. Dulac, X. Zhuang. PNAS 113, 14456 (2016)
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. BronnerSynthetic 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
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
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
The Single-Cell Pathology Landscape of Breast Cancer
Jackson HW, Fischer JR, Zanotelli VRT, Ali HR, Mechera R, Soysal SD, Moch H, Muenst S, Varga Z, Weber WP, Bodenmiller B
Nature (2020).
HistoCAT: Analysis of Cell Phenotypes and Interactions in Multiplex Image Cytometry Data
Schapiro D, Jackson HW, Raghuraman S, Fischer JR, Zanotelli VRT, Schulz D, Giesen C, Catena R, Varga Z, Bodenmiller B
Nature Methods. 2017 Aug 7.
Highly Multiplexed Imaging of Tumor Tissues with Subcellular Resolution by Mass Cytometry
Giesen C, Wang HAO, Schapiro D, Zivanovic N, Jacobs A, Hattendorf B, Schüffler PJ, Grolimund D, Buhmann JM, Brandt S, Varga Z, Wild PJ, Günther D and Bodenmiller B Nature Methods. 2014 Apr; 11(4):417-22.
Imaging Mass Cytometry Analysis of the Natural History of Type 1 Diabetes
Damond N, Engler S, Zanotelli VRT, Schapiro D, Wasserfall CH, Kusmartseva I, Nick HS, Thorel F, Herrera PL, Atkinson MA, Bodenmiller B
Cell Metabolism. 2019 Mar 5;29(3):755-768.e5.
Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.
Schulz D, Zanotelli VRT, Fischer JR, Schapiro D, Engler S, Lun XK, Jackson HW, Bodenmiller B
Cell Systems. 2018 Jan 24;6(1):25-36.e5.