Highly multiplexed in situ protein imaging with signal amplification by Immuno-SABER

Deep Residual Learning for Image Recognition

He, K., Zhang, X., Ren, S., & Sun, J. (2016) · 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) · doi:10.1109/cvpr.2016.90 · Cited by 235,474 · see citing works

U-Net: Convolutional Networks for Biomedical Image Segmentation

Ronneberger, O., Fischer, P., & Brox, T. (2015) · Lecture notes in computer science · doi:10.1007/978-3-319-24574-4_28 · Cited by 99,404 · see citing works

Fiji: an open-source platform for biological-image analysis

Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890 · see citing works

Tissue-based map of the human proteome

Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286 · see citing works

Global quantification of mammalian gene expression control

Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works

CellProfiler: image analysis software for identifying and quantifying cell phenotypes

Carpenter, A. E., Jones, T. R., Lamprecht, M. R., Clarke, C., Kang, I. H., Friman, O., Guertin, D. A., Chang, J. H., Lindquist, R. A., Moffat, J., et al. (2006) · Genome biology · doi:10.1186/gb-2006-7-10-r100 · Cited by 5,172 · see citing works

Simultaneous epitope and transcriptome measurement in single cells

Stoeckius, M., Hafemeister, C., Stephenson, W., Houck-Loomis, B., Chattopadhyay, P. K., Swerdlow, H., Satija, R., & Smibert, P. (2017) · Nature Methods · doi:10.1038/nmeth.4380 · Cited by 3,098 · 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

Untitled work

(2012) · doi:10.1016/j.jmoldx.2011.08.002 · Cited by 2,567 · see citing works

The human cell atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232 · see citing works

Triggered amplification by hybridization chain reaction

Dirks, R. M., & Pierce, N. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407024101 · Cited by 2,077 · see citing works

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

Giesen, C., Wang, H. A. O., Schapiro, D., Zivanovic, N., Jacobs, A., Hattendorf, B., Schüffler, P. J., Grolimund, D., Buhmann, J. M., Brandt, S., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2869 · Cited by 1,951 · see citing works

NUPACK: Analysis and design of nucleic acid systems

Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., & Pierce, N. A. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21596 · Cited by 1,670 · 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

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

Amir, E.-A. D., Davis, K. L., Tadmor, M. D., Simonds, E. F., Levine, J. H., Bendall, S. C., Shenfeld, D. K., Krishnaswamy, S., Nolan, G. P., & Pe'er, D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2594 · Cited by 1,550 · see citing works

Expansion microscopy

Chen, F., Tillberg, P. W., & Boyden, E. S. (2015) · Science · doi:10.1126/science.1260088 · Cited by 1,531 · see citing works

Deep profiling of mouse splenic architecture with CODEX multiplexed imaging

Goltsev, Y., Samusik, N., Kennedy-Darling, J., Bhate, S., Hale, M., Vazquez, G., Black, S., & Nolan, G. P. (2018) · Cell · doi:10.1016/j.cell.2018.07.010 · Cited by 1,501 · see citing works

Third-generation <i>in situ</i> hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

Choi, H. M. T., Schwarzkopf, M., Fornace, M. E., Acharya, A., Artavanis, G., Stegmaier, J., Cunha, A., & Pierce, N. A. (2018) · Development · doi:10.1242/dev.165753 · Cited by 1,495 · see citing works

The Human Cell Atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., & al, E. (2017) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-162597 · Cited by 1,457 · see citing works

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

Jungmann, R., Avendaño, M. S., Woehrstein, J. B., Dai, M., Shih, W. M., & Yin, P. (2014) · Nature Methods · doi:10.1038/nmeth.2835 · Cited by 1,137 · see citing works

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., et al. (2014) · Nature Medicine · doi:10.1038/nm.3488 · Cited by 1,108 · 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

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

Bendall, S. C., Davis, K. L., Amir, E.-A. D., Tadmor, M. D., Simonds, E. F., Chen, T. J., Shenfeld, D. K., Nolan, G. P., & Pe’er, D. (2014) · Cell · doi:10.1016/j.cell.2014.04.005 · Cited by 906 · see citing works

The quantitative proteome of a human cell line

Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., & Aebersold, R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.82 · Cited by 816 · see citing works

Multiplexed immunohistochemistry, imaging, and quantitation: A review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis

Stack, E. C., Wang, C., Roman, K., & Hoyt, C. C. (2014) · Methods · doi:10.1016/j.ymeth.2014.08.016 · Cited by 779 · see citing works

Catalyzed reporter deposition, a novel method of signal amplification application to immunoassays

Bobrow, M. N., Harris, T. D., Shaughnessy, K. J., & Litt, G. J. (1989) · Journal of Immunological Methods · doi:10.1016/0022-1759(89)90104-x · Cited by 774 · see citing works

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

Gerdes, M. J., Sevinsky, C. J., Sood, A., Adak, S., Bello, M. O., Bordwell, A., Can, A. B., Corwin, A. D., Dinn, S. R., Filkins, R. J., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1300136110 · Cited by 733 · see citing works

Programmable in situ amplification for multiplexed imaging of mRNA expression

Choi, H. M. T., Chang, J. Y., Trinh, L. A., Padilla, J. E., Fraser, S. E., & Pierce, N. A. (2010) · Nature Biotechnology · doi:10.1038/nbt.1692 · Cited by 720 · see citing works

Superresolution Imaging of Chemical Synapses in the Brain

Dani, A., Huang, B., Bergan, J. F., Dulac, C. G., & Zhuang, X. (2010) · Neuron · doi:10.1016/j.neuron.2010.11.021 · Cited by 718 · see citing works

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

Shah, S., Lubeck, E., Zhou, W., & Cai, L. (2016) · Neuron · doi:10.1016/j.neuron.2016.10.001 · Cited by 671 · see citing works

OMERO: flexible, model-driven data management for experimental biology

Allan, C., Burel, J.-M., Moore, J., Blackburn, C., Linkert, M., Loynton, S., MacDonald, D., Moore, W. J., Neves, C., Patterson, A., et al. (2012) · Nature Methods · doi:10.1038/nmeth.1896 · Cited by 653 · see citing works

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

Schapiro, D., Jackson, H. W., Raghuraman, S., Fischer, J. R., Zanotelli, V. R., Schulz, D., Giesen, C., Catena, R., Varga, Z., & Bodenmiller, B. (2017) · Nature Methods · doi:10.1038/nmeth.4391 · Cited by 643 · see citing works

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

Choi, H. M. T., Beck, V. A., & Pierce, N. A. (2014) · ACS Nano · doi:10.1021/nn405717p · Cited by 634 · see citing works

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

Lin, J.-R., Izar, B., Wang, S., Yapp, C., Mei, S.-L., Shah, P., Santagata, S., & Sorger, P. (2018) · eLife · doi:10.7554/elife.31657 · Cited by 631 · see citing works

Immunoassays with rolling circle DNA amplification: A versatile platform for ultrasensitive antigen detection

Schweitzer, B. I., Wiltshire, S., Lambert, J., O'Malley, S. M., Kukanskis, K. A., Zhu, Z., Kingsmore, S. F., Lizardi, P. M., & Ward, D. C. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.170237197 · Cited by 597 · see citing works

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

HuBMAP Consortium, Writing Group, Snyder, M. P., Lin, S., Posgai, A., Atkinson, M., Regev, A., Rood, J., Rozenblatt-Rosen, O., Gaffney, L., et al. (2019) · Nature · doi:10.1038/s41586-019-1629-x · Cited by 595 · see citing works

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

Lin, J., Fallahi‐Sichani, M., & Sorger, P. K. (2015) · Nature Communications · doi:10.1038/ncomms9390 · 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

Super-multiplex vibrational imaging

Wei, L., Chen, Z., Shi, L., Long, R., Anzalone, A. V., Zhang, L., Hu, F., Yuste, R., Cornish, V. W., & Min, W. (2017) · Nature · doi:10.1038/nature22051 · Cited by 514 · see citing works

Multiplexed protein maps link subcellular organization to cellular states

Gut, G., Herrmann, M. D., & Pelkmans, L. (2018) · Science · doi:10.1126/science.aar7042 · Cited by 510 · see citing works

Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues

Ku, T., Swaney, J., Park, J. Y., Albanese, A., Murray, E. M., Cho, J. H., Park, Y.-G., Mangena, V., Chen, J., & Chung, K. (2016) · Nature Biotechnology · doi:10.1038/nbt.3641 · Cited by 466 · see citing works

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

Kishi, J. Y., Lapan, S. W., Beliveau, B. J., West, E. R., Zhu, A., Sasaki, H. M., Saka, S. K., Wang, Y., Cepko, C. L., & Yin, P. (2019) · Nature Methods · doi:10.1038/s41592-019-0404-0 · Cited by 440 · see citing works

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

Chen, Y., Zhang, Y., Wang, Y., Zhang, L., Brinkman, E. K., Adam, S. A., Goldman, R. D., van Steensel, B., Ma, J., & Belmont, A. S. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201807108 · Cited by 435 · see citing works

Nanoscale imaging of RNA with expansion microscopy

Chen, F., Wassie, A. T., Coté, A., Sinha, A., Alon, S., Asano, S. M., Daugharthy, E. R., Chang, J., Marblestone, A. H., Church, G. M., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3899 · Cited by 411 · see citing works

A partition function algorithm for nucleic acid secondary structure including pseudoknots

Dirks, R. M., & Pierce, N. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10296 · Cited by 403 · see citing works

Iterative expansion microscopy

Chang, J., Chen, F., Yoon, Y., Jung, E. E., Babcock, H. P., Kang, J. S., Asano, S. M., Suk, H., Pak, N., Tillberg, P. W., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4261 · Cited by 390 · see citing works

Defining the transcriptome and proteome in three functionally different human cell lines

Lundberg, E., Fagerberg, L., Klevebring, D., Matic, I., Geiger, T., Cox, J., Älgenäs, C., Lundeberg, J., Mann, M., & Uhlen, M. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.106 · Cited by 373 · see citing works

Programmable autonomous synthesis of single-stranded DNA

Kishi, J. Y., Schaus, T. E., Gopalkrishnan, N., Xuan, F., & Yin, P. (2017) · Nature Chemistry · doi:10.1038/nchem.2872 · Cited by 321 · see citing works

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry

Schulz, D., Zanotelli, V. R., Fischer, J. R., Schapiro, D., Engler, S., Lun, X., Jackson, H. W., & Bodenmiller, B. (2017) · Cell Systems · doi:10.1016/j.cels.2017.12.001 · Cited by 279 · see citing works

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Battich, N., Stoeger, T., & Pelkmans, L. (2013) · Nature Methods · doi:10.1038/nmeth.2657 · Cited by 269 · see citing works

Super-Resolution Microscopy: From Single Molecules to Supramolecular Assemblies

Sydor, A. M., Czymmek, K. J., Puchner, E. M., & Mennella, V. (2015) · Trends in Cell Biology · doi:10.1016/j.tcb.2015.10.004 · Cited by 251 · see citing works

Correction: Corrigendum: Global quantification of mammalian gene expression control

Schwanhäußer, B., Busse, D., Li, N., Dittmar, G. A. G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2013) · Nature · doi:10.1038/nature11848 · Cited by 249 · see citing works

Morphology and immunology of the human palatine tonsil

Nave, H., Gebert, A., & Pabst, R. (2001) · Anatomy and Embryology · doi:10.1007/s004290100210 · Cited by 248 · see citing works

X10 expansion microscopy enables 25‐nm resolution on conventional microscopes

Truckenbrodt, S., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., & Rizzoli, S. O. (2018) · EMBO Reports · doi:10.15252/embr.201845836 · Cited by 242 · see citing works

Rapid and Precise Quantification of HIV-1 RNA in Plasma Using a Branched DNA Signal Amplification Assay

Pachl, C. A., Todd, J. A., Kern, D. G., Sheridan, P. J., Fong, S.-J., Stempien, M. M., Hoo, B., Besemer, D. J., Yeghiazarian, T., Irvine, B. D., et al. (1995) · Journal of Acquired Immune Deficiency Syndromes & Human Retrovirology · doi:10.1097/00042560-199504120-00003 · Cited by 232 · see citing works

The challenge of the proteome dynamic range and its implications for in‐depth proteomics

Zubarev, R. A. (2013) · PROTEOMICS · doi:10.1002/pmic.201200451 · Cited by 230 · see citing works

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

Shah, S., Lubeck, E., Schwarzkopf, M., He, T.-F., Greenbaum, A., Sohn, C. H., Lignell, A., Choi, H. M. T., Gradinaru, V., Pierce, N. A., et al. (2016) · Development · doi:10.1242/dev.138560 · Cited by 210 · see citing works

DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging

Agasti, S. S., Wang, Y., Schueder, F., Sukumar, A., Jungmann, R., & Yin, P. (2017) · Chemical Science · doi:10.1039/c6sc05420j · Cited by 200 · see citing works

Single-copy Gene Detection Using Branched DNA (bDNA) In Situ Hybridization

Player, A. N., Shen, L., Kenny, D. A., Antao, V., & Kolberg, J. A. (2001) · Journal of Histochemistry & Cytochemistry · doi:10.1177/002215540104900507 · Cited by 196 · see citing works

DNA-Sequence-Encoded Rolling Circle Amplicon for Single-Cell RNA Imaging

Deng, R., Zhang, K., Wang, L., Ren, X., Sun, Y., & Li, J. (2018) · Chem · doi:10.1016/j.chempr.2018.03.003 · Cited by 185 · see citing works

Amplification Methods to Increase the Sensitivity of In Situ Hybridization: Play CARD(S)

Speel, E. M., Hopman, A. H. N., & Komminoth, P. (1999) · Journal of Histochemistry & Cytochemistry · doi:10.1177/002215549904700302 · Cited by 184 · see citing works

An algorithm for computing nucleic acid base‐pairing probabilities including pseudoknots

Dirks, R. M., & Pierce, N. A. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20057 · Cited by 171 · see citing works

The use of catalyzed reporter deposition as a means of signal amplification in a variety of formats

Bobrow, M. N., Litt, G. J., Shaughnessy, K. J., Mayer, P., & Conlon, J. S. (1992) · Journal of Immunological Methods · doi:10.1016/0022-1759(92)90073-3 · Cited by 159 · see citing works

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak, E., Rajasethupathy, P., Wright, M. A., Jaffe, A., & Deisseroth, K. A. (2016) · Cell · doi:10.1016/j.cell.2016.01.038 · Cited by 151 · see citing works

Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues

Wang, Y., Woehrstein, J. B., Donoghue, N. D., Dai, M., Avendaño, M. S., Schackmann, R. C. J., Zoeller, J. J., Wang, S. S. H., Tillberg, P. W., Park, D., et al. (2017) · Nano Letters · doi:10.1021/acs.nanolett.7b02716 · Cited by 151 · see citing works

An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma

Kern, D., Collins, M., Fultz, T. J., Detmer, J. J., Hamren, S., Peterkin, J. J., Sheridan, P., Urdea, M. S., White, R., Yeghiazarian, T., et al. (1996) · Journal of Clinical Microbiology · doi:10.1128/jcm.34.12.3196-3202.1996 · Cited by 151 · see citing works

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

Rouhanifard, S. H., Mellis, I. A., Dunagin, M. C., Bayatpour, S., Jiang, C., Dardani, I. P., Symmons, O., Emert, B. L., Torre, E. A., Coté, A., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4286 · Cited by 147 · see citing works

A hybridization-chain-reaction-based method for amplifying immunosignals

Lin, R., Feng, Q., Li, P., Zhou, P., Wang, R., Liu, Z., Wang, Z., Qi, X., Tang, N., Shao, F., et al. (2018) · Nature Methods · doi:10.1038/nmeth.4611 · Cited by 125 · see citing works

The pros and cons of vertebrate animal models for functional and therapeutic research on inherited retinal dystrophies

Slijkerman, R. W. N., Song, F., Astuti, G., Huynen, M. A., van Wijk, E., Stieger, K., & Collin, R. W. J. (2015) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2015.04.004 · Cited by 114 · see citing works

Regional and cellular distribution of neural visinin-like protein immunoreactivities (VILIP-1 and VILIP-3) in human brain

Bernstein, H., Baumann, B., Dános, P., Diekmann, S., Bogerts, B., Gundelfinger, E. D., & Braunewell, K. (1999) · Journal of Neurocytology · doi:10.1023/a:1007056731551 · Cited by 113 · see citing works

Immunohistochemistry and mass spectrometry for highly multiplexed cellular molecular imaging

Levenson, R. M., Borowsky, A. D., & Angelo, M. R. (2015) · Laboratory Investigation · doi:10.1038/labinvest.2015.2 · Cited by 112 · see citing works

Automated cell-type classification in intact tissues by single-cell molecular profiling

Nagendran, M., Riordan, D. P., Harbury, P. B., & Desai, T. (2018) · eLife · doi:10.7554/elife.30510 · Cited by 105 · see citing works

Universal Super‐Resolution Multiplexing by DNA Exchange

Schueder, F., Strauss, M. T., Hörl, D., Schnitzbauer, J., Schlichthaerle, T., Strauss, S., Yin, P., Harz, H., Leonhardt, H., & Jungmann, R. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201611729 · Cited by 95 · see citing works

Evidence for an association between CD8 molecules and the T cell receptor complex on cytotoxic T cells.

Takada, S., & Engleman, E. G. (1987) · The Journal of Immunology · doi:10.4049/jimmunol.139.10.3231 · Cited by 82 · see citing works

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

Trivedi, V., Choi, H. M. T., Fraser, S. E., & Pierce, N. A. (2018) · Development · doi:10.1242/dev.156869 · Cited by 62 · see citing works

Strength in numbers: quantitative single‐molecule RNA detection assays

Gáspár, I., & Ephrussi, A. (2015) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.170 · Cited by 58 · see citing works

Tyramide signal amplification for analysis of kinase activity by intracellular flow cytometry

Clutter, M. R., Heffner, G. C., Krutzik, P. O., Sachen, K. L., & Nolan, G. P. (2010) · Cytometry Part A · doi:10.1002/cyto.a.20970 · Cited by 49 · see citing works

Machine-based method for multiplex in situ molecular characterization of tissues by immunofluorescence detection

Yarilin, D. A., Xu, K., Turkekul, M., Fan, N., Romin, Y., Fijisawa, S., Barlas, A., & Manova-Todorova, K. O. (2015) · Scientific Reports · doi:10.1038/srep09534 · Cited by 43 · see citing works

Multiplexed tissue biomarker imaging

Stack, E. C., Foukas, P. G., & Lee, P. P. (2016) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-016-0115-3 · Cited by 36 · see citing works

Expression of the IgLON cell adhesion molecules kilon and OBCAM in hypothalamic magnocellular neurons

Miyata, S., Funatsu, N., Matsunaga, W., Kiyohara, T., Sokawa, Y., & Maékawa, S. (2000) · The Journal of Comparative Neurology · doi:10.1002/1096-9861(20000814)424:1 · Cited by 35 · see citing works

Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactionsPreprint

Wang, Y., Zeng, Y., Saka, S. K., Xie, W., Goldaracena, I., Kohman, R. E., Yin, P., & Church, G. M. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/274456 · Cited by 19 · see citing works

Novel Application of Tyramide Signal Amplification (TSA): Ultrastructural Visualization of Double-labeled Immunofluorescent Axonal Profiles

Büki, A., Walker, S. A., Stone, J. R., & Povlishock, J. T. (2000) · Journal of Histochemistry & Cytochemistry · doi:10.1177/002215540004800116 · Cited by 19 · see citing works

KSHV cell attachment sites revealed by ultra sensitive tyramide signal amplification (TSA) localize to membrane microdomains that are up-regulated on mitotic cells

Garrigues, H. J., Rubinchikova, Y. E., & Rose, T. M. (2014) · Virology · doi:10.1016/j.virol.2014.01.006 · Cited by 12 · see citing works

Multiplexed confocal and super-resolution fluorescence imaging of cytoskeletal and neuronal synapse proteinsPreprint

Guo, S.-M., Veneziano, R., Gordonov, S., Li, L., Park, D., Kulesa, A. B., Blainey, P. C., Cottrell, J. R., Boyden, E. S., & Bathe, M. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/111625 · Cited by 7 · see citing works

A Hybridization Chain Reaction-based Method for Amplifying Immunosignals

Lin, R., Lin, R., Feng, Q., Li, P., Zhou, P., Wang, R., Liu, Z., Wang, Z., Qi, X., Tang, N., et al. (2018) · Protocol Exchange · doi:10.1038/protex.2018.014 · Cited by 3 · see citing works

Eleven grand challenges in single-cell data science

Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-1926-6 · Cited by 1,327 · 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

Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front

Schürch, C. M., Bhate, S. S., Barlow, G. L., Phillips, D. J., Noti, L., Zlobec, I., Chu, P., Black, S., Demeter, J., McIlwain, D. R., et al. (2020) · Cell · doi:10.1016/j.cell.2020.07.005 · Cited by 1,058 · see citing works

CODEX multiplexed tissue imaging with DNA-conjugated antibodies

Black, S. A., Phillips, D. J., Hickey, J. W., Kennedy‐Darling, J., Venkataraaman, V. G., Samusik, N., Goltsev, Y., Schürch, C. M., & Nolan, G. P. (2021) · Nature Protocols · doi:10.1038/s41596-021-00556-8 · Cited by 668 · 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

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

HuBMAP Consortium, Writing Group, Snyder, M. P., Lin, S., Posgai, A., Atkinson, M., Regev, A., Rood, J., Rozenblatt-Rosen, O., Gaffney, L., et al. (2019) · Nature · doi:10.1038/s41586-019-1629-x · Cited by 595 · see citing works

Spatial profiling technologies illuminate the tumor microenvironment

Elhanani, O., Ben-Uri, R., & Keren, L. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.01.010 · Cited by 525 · see citing works

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

Kishi, J. Y., Lapan, S. W., Beliveau, B. J., West, E. R., Zhu, A., Sasaki, H. M., Saka, S. K., Wang, Y., Cepko, C. L., & Yin, P. (2019) · Nature Methods · doi:10.1038/s41592-019-0404-0 · Cited by 440 · see citing works

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure

Keren, L., Bosse, M. M., Thompson, S., Risom, T., Vijayaragavan, K., McCaffrey, E., Marquez, D. M., Angoshtari, R., Greenwald, N. F., Fienberg, H. G., et al. (2019) · Science Advances · doi:10.1126/sciadv.aax5851 · Cited by 441 · 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

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

Hickey, J. W., Neumann, E. K., Radtke, A. J., Camarillo, J. M., Beuschel, R. T., Albanese, A., McDonough, E., Hatler, J. M., Wiblin, A. E., Fisher, J., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01316-y · Cited by 317 · see citing works

Spatial and temporal scales of dopamine transmission

Liu, C., Goel, P., & Kaeser, P. S. (2021) · Nature reviews. Neuroscience · doi:10.1038/s41583-021-00455-7 · Cited by 302 · see citing works

An end-to-end workflow for multiplexed image processing and analysis

Windhager, J., Zanotelli, V. R., Schulz, D., Meyer, L., Daniel, M., Bodenmiller, B., & Eling, N. (2023) · Nature Protocols · doi:10.1038/s41596-023-00881-0 · Cited by 290 · see citing works

Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer

Lin, J., Wang, S., Coy, S., Chen, Y., Yapp, C., Tyler, M., Nariya, M. K., Heiser, C. N., Lau, K. S., Santagata, S., et al. (2023) · Cell · doi:10.1016/j.cell.2022.12.028 · Cited by 284 · see citing works

Explainable multiview framework for dissecting spatial relationships from highly multiplexed data

(2022) · doi:10.1186/s13059-022-02663-5 · Cited by 297 · see citing works

Presynaptic calcium channels: specialized control of synaptic neurotransmitter release

DOLPHIN, A. C., & Lee, A. (2020) · Nature reviews. Neuroscience · doi:10.1038/s41583-020-0278-2 · Cited by 284 · see citing works

Advances in spatial transcriptomic data analysisPreprint

Dries, R., Chen, J. G., Rossi, N. D., Khan, M. M., Sistig, A., & Yuan, G. (2021) · Genome Research · doi:10.1101/gr.275224.121 · Cited by 236 · see citing works

MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

Schapiro, D., Sokolov, A., Yapp, C., Chen, Y., Muhlich, J. L., Hess, J. M., Creason, A., Nirmal, A. J., Baker, G. J., Nariya, M. K., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01308-y · Cited by 229 · see citing works

CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues

Stoltzfus, C. R., Filipek, J., Gern, B. H., Olin, B. E., Leal, J. M., Wu, Y., Lyons‐Cohen, M. R., Huang, J. Y., Paz-Stoltzfus, C. L., Plumlee, C. R., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107523 · Cited by 241 · see citing works

Spatiotemporal omics for biology and medicine

Liu, L., Chen, A., Li, Y., Mulder, J., Heyn, H., & Xu, X. (2024) · Cell · doi:10.1016/j.cell.2024.07.040 · Cited by 238 · see citing works

Single-cell analysis targeting the proteome

Labib, M., & Kelley, S. O. (2020) · Nature Reviews Chemistry · doi:10.1038/s41570-020-0162-7 · Cited by 233 · see citing works

Electrochemical biosensor for ultrasensitive exosomal miRNA analysis by cascade primer exchange reaction and MOF@Pt@MOF nanozyme

Li, X., Li, X., Li, D., Zhao, M., Wu, H., Shen, B., Liu, P., & Ding, S. (2020) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2020.112554 · Cited by 218 · see citing works

Spatial biology of cancer evolution

Seferbekova, Z., Lomakin, A., Yates, L. R., & Gerstung, M. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00553-x · Cited by 208 · see citing works

Light microscopy of proteins in their ultrastructural context

M’Saad, O., & Bewersdorf, J. (2020) · Nature Communications · doi:10.1038/s41467-020-17523-8 · Cited by 206 · see citing works

Spatial multi-omics analyses of the tumor immune microenvironment

Hsieh, W.-C., Budiarto, B. R., Wang, Y., Lin, C., Gwo, M.-C., So, D. K., Tzeng, Y.-S., & Chen, S.-Y. (2022) · Journal of Biomedical Science · doi:10.1186/s12929-022-00879-y · Cited by 215 · see citing works

Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the future

Akhoundova, D., & Rubin, M. A. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.08.011 · Cited by 188 · see citing works

Decoding the tumor microenvironment with spatial technologies

Walsh, L. A., & Quail, D. F. (2023) · Nature Immunology · doi:10.1038/s41590-023-01678-9 · Cited by 184 · see citing works

Prospects and challenges of dynamic DNA nanostructures in biomedical applications

Tian, T., Li, Y., & Lin, Y. (2022) · Bone Research · doi:10.1038/s41413-022-00212-1 · Cited by 171 · see citing works

Magnify is a universal molecular anchoring strategy for expansion microscopy

Klimas, A., Gallagher, B. R., Wijesekara, P., Fekir, S., DiBernardo, E. F., Cheng, Z., Stolz, D. B., Cambi, F., Watkins, S. C., Brody, S. L., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01546-1 · Cited by 150 · see citing works

Joint single-cell measurements of nuclear proteins and RNA in vivo

Chung, H., Parkhurst, C. N., Magee, E. M., Phillips, D., Habibi, E., Chen, F., Yeung, B. Z., Waldman, J., Artis, D., & Regev, A. (2021) · Nature Methods · doi:10.1038/s41592-021-01278-1 · Cited by 144 · see citing works

IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues

Radtke, A. J., Chu, C. J., Yaniv, Z., Li, Y., Marr, J., Beuschel, R. T., Ichise, H., Gola, A., Kabát, J., Lowekamp, B., et al. (2022) · Nature Protocols · doi:10.1038/s41596-021-00644-9 · Cited by 144 · see citing works

Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data

Hickey, J. W., Tan, Y., Nolan, G. P., & Goltsev, Y. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.727626 · Cited by 137 · see citing works

Spatial proteomics in three-dimensional intact specimens

Bhatia, H. S., Brunner, A.-D., Öztürk, F., Kapoor, S., Rong, Z., Mai, H., Thielert, M., Ali, M., Al-Maskari, R., Paetzold, J. C., et al. (2022) · Cell · doi:10.1016/j.cell.2022.11.021 · Cited by 129 · see citing works

Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics

Rivest, F., Eroglu, D., Pelz, B., Kowal, J., Kehren, A., Navikas, V., Procopio, M. G., Bordignon, P., Pérès, E., Ammann, M., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-43435-w · Cited by 123 · see citing works

Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization

Schwarzkopf, M., Liu, M. C., Schulte, S. J., Ives, R., Husain, N., Choi, H. M. T., & Pierce, N. A. (2021) · Development · doi:10.1242/dev.199847 · Cited by 118 · see citing works

Super-resolving Microscopy in Neuroscience

Werner, C. D., Sauer, M., & Geis, C. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c01174 · Cited by 111 · see citing works

Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes

Ko, J., Wilkovitsch, M., Oh, J., Köhler, R. H., Bolli, E., Pittet, M. J., Vinegoni, C., Sykes, D. B., Mikula, H., Weissleder, R., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01339-6 · Cited by 111 · see citing works

Highly-multiplexed volumetric mapping with Raman dye imaging and tissue clearing

Shi, L., Wei, M., Miao, Y., Qian, N., Shi, L., Singer, R. A., Benninger, R. K. P., & Min, W. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-01041-z · Cited by 110 · see citing works

PICASSO allows ultra-multiplexed fluorescence imaging of spatially overlapping proteins without reference spectra measurements

Seo, J., Sim, Y., Kim, J., Kim, H., Cho, I., Nam, H., Yoon, Y., & Chang, J. (2022) · Nature Communications · doi:10.1038/s41467-022-30168-z · Cited by 110 · see citing works

Label-retention expansion microscopy

Shi, X., Li, Q., Dai, Z., Tran, A. A., Feng, S., Ramirez, A. D., Lin, Z., Wang, X., Chow, T. T., Chen, J., et al. (2021) · The Journal of Cell Biology · doi:10.1083/jcb.202105067 · Cited by 108 · see citing works

Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases

Kießling, P., & Kuppe, C. (2024) · Genome Medicine · doi:10.1186/s13073-024-01282-y · Cited by 108 · see citing works

CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images

Lee, M. Y., Bedia, J. S., Bhate, S. S., Barlow, G. L., Phillips, D. J., Fantl, W. J., Nolan, G. P., & Schürch, C. M. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04570-9 · Cited by 107 · see citing works

Basic principles of hydrogel-based tissue transformation technologies and their applications

Choi, S. W., Guan, W., & Chung, K. (2021) · Cell · doi:10.1016/j.cell.2021.07.009 · Cited by 105 · see citing works

Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction

Kennedy‐Darling, J., Bhate, S. S., Hickey, J. W., Black, S., Barlow, G. L., Vazquez, G., Venkataraaman, V. G., Samusik, N., Goltsev, Y., Schürch, C. M., et al. (2021) · European Journal of Immunology · doi:10.1002/eji.202048891 · Cited by 104 · see citing works

Quantification of tumor heterogeneity: from data acquisition to metric generation

Kashyap, A., Rapsomaniki, M., Barros, V., Khartchenko, A. F., Martinelli, A. L., Foncubierta–Rodríguez, A., Gabrani, M., Rosen‐Zvi, M., & Kaigala, G. V. (2021) · Trends in biotechnology · doi:10.1016/j.tibtech.2021.11.006 · Cited by 104 · see citing works

Deep-tissue transcriptomics and subcellular imaging at high spatial resolution

Gandin, V., Kim, J., Yang, L.-Z., Lian, Y., Kawase, T., Hu, A., Rokicki, K., Fleishman, G. M., Tillberg, P. W., Aguilera-Castrejon, A., et al. (2025) · Science · doi:10.1126/science.adq2084 · Cited by 100 · see citing works

Single Extracellular Vesicle Protein Analysis Using Immuno‐Droplet Digital Polymerase Chain Reaction Amplification

Ko, J., Wang, Y., Carlson, J., Marquard, A. N., Gungabeesoon, J., Charest, A., Weitz, D. A., Pittet, M. J., & Weissleder, R. (2020) · Advanced Biosystems · doi:10.1002/adbi.201900307 · Cited by 97 · see citing works

Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma

Coy, S., Wang, S., Stopka, S. A., Lin, J., Yapp, C., Ritch, C. C., Salhi, L., Baker, G. J., Rashid, R., Baquer, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32430-w · Cited by 98 · see citing works

Multiplex protein imaging in tumour biology

de Souza, N., Zhao, S., & Bodenmiller, B. (2024) · Nature reviews. Cancer · doi:10.1038/s41568-023-00657-4 · Cited by 93 · see citing works

Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments

Jiang, S., Chan, C. N., Clavé, X. R., Chen, H. M., Bai, Y., Zhu, B., McCaffrey, E., Greenwald, N. F., Liu, C. C., Barlow, G. L., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.03.020 · Cited by 94 · see citing works

Sensitive detection of multiple blood biomarkers via immunomagnetic exosomal PCR for the diagnosis of Alzheimer’s disease

Shun, H., Zhang, L., Su, Y., Liang, X., Yang, J., Luo, Q., & Luo, H. (2024) · Science Advances · doi:10.1126/sciadv.abm3088 · Cited by 94 · see citing works

Multiplex Immunofluorescence: A Powerful Tool in Cancer Immunotherapy

Sheng, W., Zhang, C., Mohiuddin, T. M., Al-Rawe, M., Zeppernick, F. A., Falcone, F. H., Meinhold-Heerlein, I. M., & Hussain, A. F. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043086 · Cited by 93 · see citing works

CellSighter: a neural network to classify cells in highly multiplexed images

Amitay, Y., Bussi, Y., Feinstein, B., Bagon, S., Milo, I., & Keren, L. (2023) · Nature Communications · doi:10.1038/s41467-023-40066-7 · Cited by 93 · see citing works

Multiplex bioimaging of single-cell spatial profiles for precision cancer diagnostics and therapeutics

Allam, M., Cai, S., & Coskun, A. F. (2020) · npj Precision Oncology · doi:10.1038/s41698-020-0114-1 · Cited by 91 · see citing works

Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors

Bhate, S. S., Barlow, G. L., Schürch, C. M., & Nolan, G. P. (2021) · Cell Systems · doi:10.1016/j.cels.2021.09.012 · Cited by 87 · see citing works

Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering

Liu, C. C., Greenwald, N. F., Kong, A., McCaffrey, E., Leow, K. X., Mrdjen, D., Cannon, B. J., Rumberger, J. L., Varra, S. R., & Angelo, M. (2023) · Nature Communications · doi:10.1038/s41467-023-40068-5 · Cited by 81 · see citing works

Spatially resolved transcriptomics and its applications in cancer

Maniatis, S., Petrescu, J., & Phatnani, H. P. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.12.002 · Cited by 86 · see citing works

Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy

Sarkar, D., Kang, J., Wassie, A. T., Schroeder, M. E., Peng, Z., Tarr, T. B., Tang, A., Niederst, E. D., Young, J. Z., Su, H., et al. (2022) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00912-3 · Cited by 86 · see citing works

MITI minimum information guidelines for highly multiplexed tissue images

Schapiro, D., Yapp, C., Sokolov, A., Reynolds, S. M., Chen, Y.-A., Sudar, D., Xie, Y., Muhlich, J. L., Arias-Camison, R., Arena, S., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01415-4 · Cited by 84 · see citing works

Immunology in the Era of Single-Cell Technologies

Efremova, M., Vento‐Tormo, R., Park, J.-E., Teichmann, S. A., & James, K. R. (2020) · Annual Review of Immunology · doi:10.1146/annurev-immunol-090419-020340 · Cited by 77 · see citing works

In Situ Genetically Cascaded Amplification for Imaging RNA Subcellular Locations

Ren, K., Wu, R., Mudiyanselage, A. P. K. K. K., Yu, Q., Zhao, B., Xie, Y., Bagheri, Y., Tian, Q., & You, M. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.9b11748 · Cited by 77 · see citing works

cytomapper : an R/Bioconductor package for visualization of highly multiplexed imaging data

Eling, N., Damond, N., Hoch, T., & Bodenmiller, B. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1061 · Cited by 76 · see citing works

Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing

Kishi, J. Y., Liu, N., West, E. R., Sheng, K., Jordanides, J. J., Serrata, M. P., Cepko, C. L., Saka, S. K., & Yin, P. (2022) · Nature Methods · doi:10.1038/s41592-022-01604-1 · Cited by 78 · see citing works

Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry

Su, P., McGee, J., Durbin, K. R., Hollas, M., Yang, M.-X., Neumann, E. K., Allen, J. L., Drown, B. S., Butun, F., Greer, J. B., et al. (2022) · Science Advances · doi:10.1126/sciadv.abp9929 · Cited by 67 · see citing works

Engineered Tools to Study Intercellular Communication

Yang, B. A., Westerhof, T. M., Sabin, K., Merajver, S. D., & Aguilar, C. A. (2020) · Advanced Science · doi:10.1002/advs.202002825 · Cited by 73 · see citing works

Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 severity

Inde, Z., Croker, B. A., Yapp, C., Joshi, G. N., Spetz, J. K. E., Fraser, C. S., Qin, X., Xu, L., Deskin, B., Ghelfi, E., et al. (2021) · Science Advances · doi:10.1126/sciadv.abf8609 · Cited by 72 · see citing works

Computer-aided design of reversible hybridization chain reaction (CAD-HCR) enables multiplexed single-cell spatial proteomics imaging

Liu, X., Mao, D., Song, Y., Zhu, L., Isak, A. N., Lu, C., Deng, G., Chen, F., Sun, F., Yang, Y. P., et al. (2022) · Science Advances · doi:10.1126/sciadv.abk0133 · Cited by 70 · see citing works

Super‐Resolution Vibrational Imaging Using Expansion Stimulated Raman Scattering Microscopy

Shi, L., Klimas, A., Gallagher, B. R., Cheng, Z., Fu, F., Wijesekara, P., Miao, Y., Ren, X., Zhao, Y., & Min, W. (2022) · Advanced Science · doi:10.1002/advs.202200315 · Cited by 69 · see citing works

A Cleavable C2-Symmetric trans -Cyclooctene Enables Fast and Complete Bioorthogonal Disassembly of Molecular Probes

Wilkovitsch, M., Haider, M., Sohr, B., Herrmann, B., Klubnick, J., Weissleder, R., Carlson, J., & Mikula, H. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c07922 · Cited by 66 · see citing works

Current Progress in Expansion Microscopy: Chemical Strategies and Applications

Wen, G., Leen, V., Rohand, T., Sauer, M., & Hofkens, J. (2023) · Chemical Reviews · doi:10.1021/acs.chemrev.2c00711 · Cited by 65 · see citing works

A framework for multiplex imaging optimization and reproducible analysis

Eng, J. R., Bucher, E., Hu, Z., Zheng, T., Gibbs, S. L., Chin, K., & Gray, J. W. (2022) · Communications Biology · doi:10.1038/s42003-022-03368-y · Cited by 64 · see citing works

Exploring single cells in space and time during tissue development, homeostasis and regeneration

Mayr, U., Serra, D., & Liberali, P. (2019) · Development · doi:10.1242/dev.176727 · Cited by 63 · see citing works

Rolling circle amplification for single cell analysis and in situ sequencing

Gao, H., Zhang, K., Teng, X., & Li, J. (2019) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2019.115700 · Cited by 63 · see citing works

Temporal and spatial topography of cell proliferation in cancer

Gaglia, G., Kabraji, S. K., Rammos, D., Dai, Y., Verma, A., Wang, S., Mills, C. E., Chung, M., Bergholz, J. S., Coy, S., et al. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-00860-9 · Cited by 62 · see citing works

Enablers and challenges of spatial omics, a melting pot of technologies

Alexandrov, T., Sáez-Rodríguez, J., & Saka, S. K. (2023) · Molecular Systems Biology · doi:10.15252/msb.202110571 · Cited by 64 · see citing works

Application of single-cell and spatial omics in deciphering cellular hallmarks of cancer drug response and resistance

Cheng, X., Peng, T., Chu, T., Yang, Y., Liu, J., Gao, Q., Cao, C., & Wei, J. (2025) · Journal of Hematology & Oncology · doi:10.1186/s13045-025-01722-1 · Cited by 64 · see citing works

Single-cell biology: beyond the sum of its parts

Schier, A. F. (2020) · Nature Methods · doi:10.1038/s41592-019-0693-3 · Cited by 56 · see citing works

Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies

Vries, N. L. D., Mahfouz, A. E., Koning, F., & de Miranda, N. F. C. C. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.01254 · Cited by 58 · see citing works

Simultaneous detection of cancerous exosomal miRNA-21 and PD-L1 with a sensitive dual-cycling nanoprobe

Qin, X., Xiang, Y., Li, N., Wei, B., Chen, Y., Fang, D., Fang, M., Li, Q., Liu, J., Tang, Y., et al. (2022) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2022.114636 · Cited by 60 · see citing works

Unbiased discovery of autoantibodies associated with severe COVID-19 via genome-scale self-assembled DNA-barcoded protein libraries

Credle, J. J., Gunn, J., Sangkhapreecha, P., Monaco, D. R., Zheng, X. A., Tsai, H.-J., Wilbon, A., Morgenlander, W. R., Rastegar, A. T., Dong, Y. W., et al. (2022) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00925-y · Cited by 60 · see citing works

Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields

Agbleke, A. A., Amitai, A., Buenrostro, J. D., Chakrabarti, A., Chu, L., Hansen, A. S., Koenig, K. M., Labade, A. S., Liu, S., Nozaki, T., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.07.003 · Cited by 59 · see citing works

Pooled genetic perturbation screens with image-based phenotypes

Feldman, D., Funk, L., Le, A., Carlson, R. J., Leiken, M. D., Tsai, F., Soong, B., Singh, A., & Blainey, P. C. (2022) · Nature Protocols · doi:10.1038/s41596-021-00653-8 · Cited by 59 · see citing works

Preparation of single- and double-oligonucleotide antibody conjugates and their application for protein analytics

Wiener, J., Kokotek, D., Rosowski, S., Lickert, H., & Meier, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-58238-6 · Cited by 58 · see citing works

Programmable DNA-Fueled Electrochemical Analysis of Lung Cancer Exosomes

Sha, L., Bo, B., Yang, F., Li, J., Cao, Y., & Zhao, J. T. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c01318 · Cited by 58 · see citing works

Imaging dendritic cell functions*

Bošnjak, B., Do, K. T. H., Förster, R., & Hammerschmidt, S. I. (2021) · Immunological Reviews · doi:10.1111/imr.13050 · Cited by 58 · see citing works

Mapping the Proteoform Landscape of Five Human Tissues

Drown, B. S., Jooss, K., Melani, R., Lloyd-Jones, C., Camarillo, J., & Kelleher, N. L. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00034 · Cited by 47 · see citing works

Light microscopy based approach for mapping connectivity with molecular specificity

Shen, F. Y., Harrington, M. M., Walker, L. A., Cheng, H. P. J., Boyden, E. S., & Cai, D. (2020) · Nature Communications · doi:10.1038/s41467-020-18422-8 · Cited by 57 · see citing works

Spatial proteomics for understanding the tissue microenvironment

Mao, Y., Wang, X., Huang, P., & Tian, R. (2021) · The Analyst · doi:10.1039/d1an00472g · Cited by 53 · see citing works

DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging

Hosogane, T., Casanova, R., & Bodenmiller, B. (2023) · Nature Methods · doi:10.1038/s41592-023-01976-y · Cited by 55 · see citing works

An Integrated Multi‐Function Heterogeneous Biochemical Circuit for High‐Resolution Electrochemistry‐Based Genetic Analysis

Dai, Y., Xu, W. L., Somoza, R. A., Welter, J. F., Caplan, A. I., & Liu, C.-C. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.202010648 · Cited by 54 · see citing works

UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues

Yapp, C., Novikov, E., Jang, W.-D., Vallius, T., Chen, Y., Cicconet, M., Maliga, Z., Jacobson, C. A., Wei, D., Santagata, S., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-04076-3 · Cited by 54 · see citing works

The Intriguing Landscape of Single‐Cell Protein Analysis

Xie, H., & Ding, X. (2022) · Advanced Science · doi:10.1002/advs.202105932 · Cited by 52 · see citing works

Spatial Transcriptomics for Tumor Heterogeneity Analysis

Li, Q., Zhang, X., & Ke, R. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.906158 · Cited by 52 · see citing works

Expansion microscopy: A powerful nanoscale imaging tool for neuroscientists

Gallagher, B. R., & Zhao, Y. (2021) · Neurobiology of Disease · doi:10.1016/j.nbd.2021.105362 · Cited by 50 · see citing works

MAUI (MBI Analysis User Interface)—An image processing pipeline for Multiplexed Mass Based Imaging

Baranski, A., Milo, I., Greenbaum, S., Oliveria, J. P., Mrdjen, D., Angelo, M., & Keren, L. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008887 · Cited by 49 · see citing works

Engineering Functional DNA–Protein Conjugates for Biosensing, Biomedical, and Nanoassembly Applications

Zhao, D., Kong, Y., Zhao, S., & Xing, H. (2020) · Topics in Current Chemistry · doi:10.1007/s41061-020-00305-7 · Cited by 49 · see citing works

Ultra‐fast Cycling for Multiplexed Cellular Fluorescence Imaging

Ko, J., Oh, J., Ahmed, M. S., Carlson, J., & Weissleder, R. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.201915153 · Cited by 48 · see citing works

Highly Multiplexed Tissue Imaging in Precision Oncology and Translational Cancer Research

Bollhagen, A., & Bodenmiller, B. (2024) · Cancer Discovery · doi:10.1158/2159-8290.cd-23-1165 · Cited by 49 · see citing works

Structure and dynamics of photoreceptor sensory cilia

Wensel, T. G., Potter, V. L., Moye, A. R., Zhang, Z., & Robichaux, M. A. (2021) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-021-02564-9 · Cited by 46 · see citing works

Next-Generation Pathology Using Multiplexed Immunohistochemistry: Mapping Tissue Architecture at Single-Cell Level

Bosisio, F. M., Herck, Y. V., Messiaen, J., Bolognesi, M. M., Marcelis, L., Haele, M. V., Cattoretti, G., Antoranz, A., & Smet, F. D. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.918900 · Cited by 46 · see citing works

Impact of Implementing an Elaborated CT Perfusion Protocol for Aneurysmal SAH on Functional Outcome: CTP Protocol for SAH

Malinova, V., Döring, K., Psychogios, M., Rohde, V., & Mielke, D. (2021) · American Journal of Neuroradiology · doi:10.3174/ajnr.a7279 · Cited by 12 · see citing works

Highly Multiplexed in Situ Protein Imaging Using DNA-Exchange-Imaging and Immuno-SABER

Wang, Y. (2019) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)

Advancing multiplexed imaging for enhanced tissue complexity analysis

Ijsselsteijn, M. E., & de Miranda, N. F. C. C. (2023) · Nature Methods · doi:10.1038/s41592-023-01935-7 · Cited by 2 · see citing works

DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging

Hosogane, T., Casanova, R., & Bodenmiller, B. (2023) · Nature Methods · doi:10.1038/s41592-023-01976-y · Cited by 55 · see citing works

Combining Qdot Nanotechnology and DNA Nanotechnology for Sensitive Single‐Cell Imaging

Zhou, W. J., Han, Y., Beliveau, B. J., & Gao, X. (2020) · Advanced Materials · doi:10.1002/adma.201908410 · Cited by 40 · see citing works