Multiplexed spatial transcriptomics methods and the application of expansion microscopy

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., et al. (2014) · Science · doi:10.1126/science.1254257 · Cited by 5,063 · see citing works

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Ståhl, P. L., Salmén, F., Vickovic, S., Lundmark, A., Navarro, J. F., Magnusson, J., Giacomello, S., Asp, M., Westholm, J. O., Huss, M., et al. (2016) · Science · doi:10.1126/science.aaf2403 · Cited by 3,834 · see citing works

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015) · Science · doi:10.1126/science.aaa6090 · Cited by 2,969 · see citing works

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., Welch, J., Chen, L. M., Chen, F., & Macosko, E. Z. (2019) · Science · doi:10.1126/science.aaw1219 · Cited by 2,424 · see citing works

Imaging individual mRNA molecules using multiple singly labeled probes

Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A., & Tyagi, S. (2008) · Nature Methods · doi:10.1038/nmeth.1253 · Cited by 2,028 · see citing works

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

Chen, A., Liao, S., Cheng, M., Ma, K., Wu, L., Lai, Y., Qiu, X., Yang, J., Xu, J., Hao, S., et al. (2022) · Cell · doi:10.1016/j.cell.2022.04.003 · Cited by 1,784 · see citing works

Exploring tissue architecture using spatial transcriptomics

Rao, A., Barkley, D., França, G. S., & Yanai, I. (2021) · Nature · doi:10.1038/s41586-021-03634-9 · Cited by 1,700 · see citing works

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

Wang, X., Allen, W. E., Wright, M. A., Sylwestrak, E. L., Samusik, N., Vesuna, S., Evans, K., Liu, C., Ramakrishnan, C., Liu, J., et al. (2018) · Science · doi:10.1126/science.aat5691 · Cited by 1,620 · see citing works

The Technology and Biology of Single-Cell RNA Sequencing

Kolodziejczyk, A. A., Kim, J. K., Svensson, V., Marioni, J. C., & Teichmann, S. A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.005 · Cited by 1,487 · see citing works

Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome

Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D., & Church, G. M. (2005) · Science · doi:10.1126/science.1117389 · Cited by 1,402 · see citing works

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

Moffitt, J. R., Bambah-Mukku, D., Eichhorn, S. W., Vaughn, E., Shekhar, K., Perez, J. D., Rubinstein, N. D., Hao, J., Regev, A., Dulac, C., et al. (2018) · Science · doi:10.1126/science.aau5324 · Cited by 1,365 · see citing works

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

Stickels, R. R., Murray, E., Kumar, P., Li, J., Marshall, J. L., Di Bella, D. J., Arlotta, P., Macosko, E. Z., & Chen, F. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0739-1 · Cited by 1,295 · see citing works

Museum of spatial transcriptomics

Moses, L., & Pachter, L. (2022) · Nature Methods · doi:10.1038/s41592-022-01409-2 · Cited by 1,255 · see citing works

Methods and applications for single-cell and spatial multi-omics

Vandereyken, K., Sifrim, A., Thienpont, B., & Voet, T. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00580-2 · Cited by 1,244 · see citing works

Super-resolution microscopy demystified

Schermelleh, L., Ferrand, A., Huser, T. R., Eggeling, C., Sauer, M., Biehlmaier, O., & Drummen, G. P. C. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0251-8 · Cited by 1,224 · see citing works

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Yao, Z., van Velthoven, C. T. J., Kunst, M., Zhang, M., McMillen, D., Lee, C., Jung, W., Goldy, J., Abdelhak, A., Aitken, M., et al. (2023) · Nature · doi:10.1038/s41586-023-06812-z · Cited by 1,194 · cited 1× · see citing works

Single-cell in situ RNA profiling by sequential hybridization

Lubeck, E., Coskun, A. F., Zhiyentayev, T., Ahmad, M., & Cai, L. (2014) · Nature Methods · doi:10.1038/nmeth.2892 · Cited by 985 · see citing works

Highly Multiplexed Subcellular RNA Sequencing in Situ

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S. F., Li, C., Amamoto, R., et al. (2014) · Science · doi:10.1126/science.1250212 · Cited by 973 · see citing works

In situ sequencing for RNA analysis in preserved tissue and cells

Ke, R., Mignardi, M., Pacureanu, A., Svedlund, J., Botling, J., Wählby, C., & Nilsson, M. (2013) · Nature Methods · doi:10.1038/nmeth.2563 · Cited by 934 · see citing works

Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer

Galeano Niño, J. L., Wu, H., LaCourse, K. D., Kempchinsky, A. G., Baryiames, A., Barber, B., Futran, N., Houlton, J., Sather, C., Sicinska, E., et al. (2022) · Nature · doi:10.1038/s41586-022-05435-0 · Cited by 887 · see citing works

An introduction to spatial transcriptomics for biomedical research

Williams, C. G., Lee, H. J., Asatsuma, T., Vento‐Tormo, R., & Haque, A. (2022) · Genome Medicine · doi:10.1186/s13073-022-01075-1 · Cited by 859 · see citing works

Next-Generation Sequencing: From Basic Research to Diagnostics

Voelkerding, K. V., Dames, S. A., & Durtschi, J. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2008.112789 · Cited by 846 · see citing works

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

Xia, C., Fan, J., Emanuel, G., Hao, J., & Zhuang, X. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912459116 · Cited by 755 · see citing works

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

Asp, M., Giacomello, S., Larsson, L., Wu, C., Fürth, D., Qian, X., Wärdell, E., Custodio, J., Reimegård, J., Salmén, F., et al. (2019) · Cell · doi:10.1016/j.cell.2019.11.025 · Cited by 740 · see citing works

Spatial omics and multiplexed imaging to explore cancer biology

Lewis, S. M., Asselin-Labat, M.-L., Nguyen, Q. H., Berthelet, J., Tan, X., Wimmer, V. C., Mérino, D., Rogers, K. L., & Naik, S. H. (2021) · Nature Methods · doi:10.1038/s41592-021-01203-6 · Cited by 609 · see citing works

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioningPreprint

Valouev, A., Ichikawa, J. K., Tonthat, T., Stuart, J., Ranade, S., Peckham, H. E., Zeng, K., Malek, J. A., Costa, G. L., McKernan, K. J., et al. (2008) · Genome Research · doi:10.1101/gr.076463.108 · Cited by 580 · see citing works

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

Su, J.-H., Zheng, P., Kinrot, S. S., Bintu, B., & Zhuang, X. (2020) · Cell · doi:10.1016/j.cell.2020.07.032 · Cited by 562 · see citing works

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

Moffitt, J. R., Hao, J., Wang, G., Chen, K. H., Babcock, H. P., & Zhuang, X. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612826113 · Cited by 557 · see citing works

The expanding vistas of spatial transcriptomics

Tian, L., Chen, F., & Macosko, E. Z. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01448-2 · Cited by 539 · see citing works

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Ferrante, T. C., Terry, R., Turczyk, B. M., Yang, J. L., Lee, H. S., Aach, J., et al. (2015) · Nature Protocols · doi:10.1038/nprot.2014.191 · Cited by 529 · see citing works

Microscopic examination of spatial transcriptome using Seq-Scope

Cho, C.-S., Xi, J., Si, Y., Park, S.-R., Hsu, J.-E., Kim, M., Jun, G., Kang, H. M., & Lee, J. H. (2021) · Cell · doi:10.1016/j.cell.2021.05.010 · Cited by 520 · see citing works

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

Zhang, M., Pan, X., Jung, W., Halpern, A. R., Eichhorn, S. W., Lei, Z., Cohen, L., Smith, K. A., Tasic, B., Yao, Z., et al. (2023) · Nature · doi:10.1038/s41586-023-06808-9 · Cited by 506 · see citing works

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

Zhang, M., Eichhorn, S. W., Zingg, B., Yao, Z., Cotter, K., Zeng, H., Dong, H., & Zhuang, X. (2021) · Nature · doi:10.1038/s41586-021-03705-x · Cited by 498 · see citing works

Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer

Jia, Q., Wu, W., Wang, Y., Alexander, P. B., Sun, C., Gong, Z., Cheng, J.-N., Sun, H., Guan, Y., Xia, X., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07767-w · Cited by 483 · see citing works

Expansion microscopy: principles and uses in biological research

Wassie, A. T., Zhao, Y., & Boyden, E. S. (2018) · Nature Methods · doi:10.1038/s41592-018-0219-4 · Cited by 464 · see citing works

Single-cell systems biology by super-resolution imaging and combinatorial labeling

Lubeck, E., & Cai, L. (2012) · Nature Methods · doi:10.1038/nmeth.2069 · Cited by 462 · see citing works

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

Frieda, K. L., Linton, J. M., Hormoz, S., Choi, J., Chow, K.-H. K., Singer, Z. S., Budde, M. W., Elowitz, M. B., & Cai, L. (2017) · Nature · doi:10.1038/nature20777 · Cited by 440 · see citing works

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Maniatis, S., Äijö, T., Vickovic, S., Braine, C., Kang, K., Mollbrink, A., Fagegaltier, D., Andrusivová, Ž., Saarenpää, S., Saiz-Castro, G., et al. (2019) · Science · doi:10.1126/science.aav9776 · Cited by 429 · see citing works

Molecular and spatial signatures of mouse brain aging at single-cell resolution

Allen, W. E., Blosser, T. R., Sullivan, Z. A., Dulac, C., & Zhuang, X. (2023) · Cell · doi:10.1016/j.cell.2022.12.010 · Cited by 423 · see citing works

The emerging landscape of spatial profiling technologies

Moffitt, J. R., Lundberg, E., & Heyn, H. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00515-3 · Cited by 419 · see citing works

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

Alon, S., Goodwin, D., Sinha, A., Wassie, A. T., Chen, F., Daugharthy, E. R., Bando, Y., Kajita, A., Xue, A. G., Marrett, K., et al. (2021) · Science · doi:10.1126/science.aax2656 · Cited by 413 · see citing works

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

Moffitt, J. R., Hao, J., Bambah-Mukku, D., Lu, T., Dulac, C., & Zhuang, X. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617699113 · Cited by 308 · see citing works

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

Fang, R., Xia, C., Close, J. L., Zhang, M., He, J., Huang, Z., Halpern, A. R., Long, B., Miller, J. A., Lein, E. S., et al. (2022) · Science · doi:10.1126/science.abm1741 · Cited by 277 · see citing works

High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing

Chen, X., Sun, Y.-C., Zhan, H., Kebschull, J. M., Fischer, S., Matho, K. S., Huang, Z. J., Gillis, J. A., & Zador, A. M. (2019) · Cell · doi:10.1016/j.cell.2019.09.023 · Cited by 273 · see citing works

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

Wang, G., Moffitt, J. R., & Zhuang, X. (2018) · Scientific Reports · doi:10.1038/s41598-018-22297-7 · Cited by 259 · see citing works

Spatially resolved single-cell genomics and transcriptomics by imaging

Zhuang, X. (2021) · Nature Methods · doi:10.1038/s41592-020-01037-8 · Cited by 243 · see citing works

Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy

Zhao, Y., Bucur, O., Irshad, H., Chen, F., Weins, A., Stancu, A. L., Oh, E.-Y., DiStasio, M., Torous, V. F., Glass, B., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3892 · Cited by 224 · see citing works

Soluble TREM2 levels reflect the recruitment and expansion of TREM2+ macrophages that localize to fibrotic areas and limit NASH

Hendrikx, T., Porsch, F., Kiss, M. G., Rajcic, D., Papac-Miličević, N., Hoebinger, C., Goederle, L., Hladik, A., Shaw, L. E., Horstmann, H., et al. (2022) · Journal of Hepatology · doi:10.1016/j.jhep.2022.06.004 · Cited by 220 · see citing works

Delineating the dynamic evolution from preneoplasia to invasive lung adenocarcinoma by integrating single-cell RNA sequencing and spatial transcriptomics

Zhu, J., Fan, Y., Xiong, Y., Wang, W., Chen, J., Xu, S., Xia, Y., Jiang, R., Ma, S., Lei, J., et al. (2022) · Experimental & Molecular Medicine · doi:10.1038/s12276-022-00896-9 · Cited by 211 · see citing works

Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

Cheng, M., Jiang, Y., Xu, J., Mentis, A. A., Wang, S., Zheng, H., Sahu, S. K., Liu, L., & Xu, X. (2023) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2023.03.011 · Cited by 190 · see citing works

A preoptic neuronal population controls fever and appetite during sickness

Osterhout, J. A., Kapoor, V., Eichhorn, S. W., Vaughn, E., Moore, J. D., Liu, D., Lee, D., DeNardo, L. A., Luo, L., Zhuang, X., et al. (2022) · Nature · doi:10.1038/s41586-022-04793-z · Cited by 177 · see citing works

A molecularly defined and spatially resolved cell atlas of the whole mouse brainPreprint

Zhang, M., Pan, X., Jung, W., et al. (2023) · bioRxiv · doi:10.1101/2023.03.06.531348 · Cited by 167 · see citing works

Single-cell analysis of ploidy and the transcriptome reveals functional and spatial divergency in murine megakaryopoiesis

Sun, S. F., Jin, C., Si, J., Lei, Y., Chen, K., Cui, Y., Liu, Z., Liu, J., Zhao, M. L., Zhang, X., et al. (2021) · Blood · doi:10.1182/blood.2021010697 · Cited by 162 · see citing works

Multiplexed detection of RNA using MERFISH and branched DNA amplification

Xia, C., Babcock, H. P., Moffitt, J. R., & Zhuang, X. (2019) · Scientific Reports · doi:10.1038/s41598-019-43943-8 · Cited by 160 · see citing works

Excised linear introns regulate growth in yeast

Morgan, J. T., Fink, G. R., & Bartel, D. P. (2019) · Nature · doi:10.1038/s41586-018-0828-1 · Cited by 157 · see citing works

Spatial Transcriptomic Technologies

Chen, T.-Y., You, L., Hardillo, J. A., & Chien, M. (2023) · Cells · doi:10.3390/cells12162042 · Cited by 153 · see citing works

Analysis of Donor Pancreata Defines the Transcriptomic Signature and Microenvironment of Early Neoplastic Lesions

Carpenter, E. S., Elhossiny, A. M., Kadiyala, P., Li, J., McGue, J. J., Griffith, B. D., Zhang, Y., Edwards, J., Nelson, S., Lima, F., et al. (2023) · Cancer Discovery · doi:10.1158/2159-8290.cd-23-0013 · Cited by 152 · see citing works

Genome-wide spatial expression profiling in formalin-fixed tissues

Gracia Villacampa, E., Larsson, L., Mirzazadeh, R., Kvastad, L., Andersson, A., Mollbrink, A., Kokaraki, G., Monteil, V., Schultz, N., Appelberg, K. S., et al. (2021) · Cell Genomics · doi:10.1016/j.xgen.2021.100065 · Cited by 132 · see citing works

Mammalian gene expression variability is explained by underlying cell state

Foreman, R., & Wollman, R. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199146 · Cited by 126 · see citing works

Fluorescence In Situ Hybridization ( FISH )

Bayani, J., & Squire, J. A. (2004) · Current Protocols in Cell Biology · doi:10.1002/0471143030.cb2204s23 · Cited by 125 · see citing works

Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling

Cadinu, P., Sivanathan, K. N., Misra, A., Xu, R. J., Mangani, D., Yang, E., Rone, J. M., Tooley, K., Kye, Y.-C., Bod, L., et al. (2024) · Cell · doi:10.1016/j.cell.2024.03.013 · Cited by 120 · see citing works

Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization

Wang, C., Lu, T., Emanuel, G., Babcock, H. P., & Zhuang, X. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1903808116 · Cited by 111 · see citing works

The spatial landscape of gene expression isoforms in tissue sections

Lebrigand, K., Bergenstråhle, J., Thrane, K., Mollbrink, A., Meletis, K., Barbry, P., Waldmann, R., & Lundeberg, J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad169 · Cited by 105 · see citing works

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium

Vicković, S., Schapiro, D., Carlberg, K., Lötstedt, B., Larsson, L., Hildebrandt, F., Korotkova, M., Hensvold, A. H., Catrina, A. I., Sorger, P. K., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03050-3 · Cited by 87 · see citing works

Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis

Vu, T., Vallmitjana, A., Gu, J., La, K., Xu, Q., Flores, J., Zimak, J., Shiu, J., Hosohama, L., Wu, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27798-0 · Cited by 78 · see citing works

Single Molecule Fluorescence In Situ Hybridization (smFISH) Analysis in Budding Yeast Vegetative Growth and Meiosis

Chen, J., McSwiggen, D. T., & Ünal, E. (2018) · Journal of Visualized Experiments · doi:10.3791/57774 · Cited by 76 · see citing works

Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics

Carlberg, K., Korotkova, M., Larsson, L., Catrina, A. I., Ståhl, P. L., & Malmström, V. (2019) · Scientific Reports · doi:10.1038/s41598-019-55441-y · Cited by 73 · see citing works

Localization of T cell clonotypes using the Visium spatial transcriptomics platform

Hudson, W. H., & Sudmeier, L. J. (2022) · STAR Protocols · doi:10.1016/j.xpro.2022.101391 · Cited by 72 · see citing works

Spatial genomic, biochemical and cellular mechanisms underlying meningioma heterogeneity and evolution

Lucas, C. G., Mirchia, K., Seo, K., Najem, H., Chen, W., Zakimi, N., Foster, K. J., Eaton, C. D., Cady, M. A., Choudhury, A., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01747-1 · Cited by 72 · see citing works

Spatial organization of the mouse retina at single cell resolution by MERFISH

Choi, J., Li, J., Ferdous, S., Liang, Q., Moffitt, J. R., & Chen, R. (2023) · Nature Communications · doi:10.1038/s41467-023-40674-3 · Cited by 71 · see citing works

Spatially resolved transcriptomics of high-grade serous ovarian carcinoma

Stur, E., Corvigno, S., Xu, M., Chen, K., Tan, Y., Lee, S., Liu, J., Ricco, E., Kraushaar, D. C., Castro, P. D., et al. (2022) · iScience · doi:10.1016/j.isci.2022.103923 · Cited by 70 · see citing works

Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture

Lu, Y., Liu, M., Yang, J., Weissman, S. M., Pan, X., Katz, S. G., & Wang, S. (2021) · Cell Discovery · doi:10.1038/s41421-021-00266-1 · Cited by 68 · see citing works

Expansion spatial transcriptomics

Fan, Y., Andrusivová, Ž., Wu, Y., Chai, C., Larsson, L., He, M., Luo, L., Lundeberg, J., & Wang, B. (2023) · Nature Methods · doi:10.1038/s41592-023-01911-1 · Cited by 68 · see citing works

Spatial Transcriptomics-correlated Electron Microscopy maps transcriptional and ultrastructural responses to brain injury

Androvic, P., Schifferer, M., Perez Anderson, K., Cantuti-Castelvetri, L., Jiang, H., Ji, H., Liu, L., Gouna, G., Berghoff, S. A., Besson-Girard, S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39447-9 · Cited by 67 · see citing works

Fourth Generation of Next‐Generation Sequencing Technologies: Promise and Consequences

Ke, R., Mignardi, M., Hauling, T., & Nilsson, M. F. (2016) · Human Mutation · doi:10.1002/humu.23051 · Cited by 65 · see citing works

Expansion Microscopy: Scalable and Convenient Super-Resolution Microscopy

Tillberg, P. W., & Chen, F. (2019) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100818-125320 · Cited by 58 · see citing works

Neuroblastoma Formation Requires Unconventional CD4 T Cells and Arginase-1–Dependent Myeloid Cells

de Velde, L.-A. V., Allen, E. K., Crawford, J. C., Wilson, T. L., Guy, C. S., Russier, M., Zeitler, L., Bahrami, A., Finkelstein, D., Pelletier, S. W., et al. (2021) · Cancer Research · doi:10.1158/0008-5472.can-21-0691 · Cited by 50 · see citing works

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

Гарафутдинов, Р. Р., Sakhabutdinova, A. R., Gilvanov, A. R., & Chemeris, A. V. (2021) · Russian Journal of Bioorganic Chemistry · doi:10.1134/s1068162021060078 · Cited by 46 · see citing works

Single-cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2R47H Alzheimer’s risk gene mutation

Johnston, K. G., Berackey, B. T., Tran, K. M., Gelber, A., Yu, Z., MacGregor, G. R., Mukamel, E. A., Tan, Z., Green, K. N., & Xu, X. (2024) · Molecular Psychiatry · doi:10.1038/s41380-024-02651-0 · Cited by 44 · see citing works

Spatial transcriptomics identifies spatially dysregulated expression of GRM3 and USP47 in amyotrophic lateral sclerosis

Gregory, J. M., McDade, K., Livesey, M. R., Croy, I., de Procé, S. M., Aitman, T. J., Chandran, S., & Smith, C. (2020) · Neuropathology and Applied Neurobiology · doi:10.1111/nan.12597 · Cited by 41 · see citing works

Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology

Bucur, O., Fu, F., Calderon, M., Mylvaganam, G., Ly, N. L., Day, J., Watkin, S. W., Walker, B. D., Boyden, E. S., & Zhao, Y. (2020) · Nature Protocols · doi:10.1038/s41596-020-0300-1 · Cited by 39 · see citing works

Asymmetric Hapln1a drives regionalized cardiac ECM expansion and promotes heart morphogenesis in zebrafish development

Derrick, C. J., Sánchez-Posada, J., Hussein, F., Tessadori, F., Pollitt, E. J. G., Savage, A. M., Wilkinson, R. N., Chico, T., van Eeden, F. J., Bakkers, J., et al. (2021) · Cardiovascular Research · doi:10.1093/cvr/cvab004 · Cited by 38 · see citing works

Single-cell and spatial heterogeneity landscapes of mature epicardial cells

Du, J., Yuan, X. H., Deng, H., Huang, R., Liu, B., Xiong, T., Long, X., Zhang, L., Li, Y., & She, Q. (2023) · Journal of Pharmaceutical Analysis · doi:10.1016/j.jpha.2023.07.011 · Cited by 36 · see citing works

Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections

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Fate specification is spatially intermingled across planarian stem cells

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Integrated analysis on transcriptome and behaviors defines HTT repeat-dependent network modules in Huntington's disease

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Nanoscale Imaging of Kidney Glomeruli Using Expansion Pathology

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Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

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Single cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2R47H Alzheimer’s risk gene mutationPreprint

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Modeling Tumor Microenvironment Complexity In Vitro: Spheroids as Physiologically Relevant Tumor Models and Strategies for Their Analysis

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Applications and development of in situ nucleic acid visualization techniques

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Spatial organization of intratumoral microbiome and regional tumor immunity

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Артеріальна гіпертензія, асоційована із застосуванням комбінованих оральних контрацептивів: фактори ризику та патогенетичні механізми

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ExSeq: Expansion Sequencing for Single-Cell Spatial Transcriptomics

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Seq-Scope-eXpanded: spatial omics beyond optical resolution

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Spatially resolved transcriptomes—next generation tools for tissue exploration

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Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

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