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

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314 · see citing works

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110 · see citing works

Spatial reconstruction of single-cell gene expression data

Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055 · see citing works

Role of YAP/TAZ in mechanotransduction

Dupont, S., Morsut, L., Aragona, M., Enzo, E., Giulitti, S., Cordenonsi, M., Zanconato, F., Le Digabel, J., Forcato, M., Bicciato, S., et al. (2011) · Nature · doi:10.1038/nature10137 · Cited by 5,979 · see citing works

Reversed graph embedding resolves complex single-cell trajectories

Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A., & Trapnell, C. (2017) · Nature Methods · doi:10.1038/nmeth.4402 · Cited by 5,070 · 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

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells

Klein, A. M., Mazutis, L., Akartuna, I., Tallapragada, N., Veres, A., Li, V., Peshkin, L., Weitz, D. A., & Kirschner, M. W. (2015) · Cell · doi:10.1016/j.cell.2015.04.044 · Cited by 3,356 · see citing works

On the Dependency of Cellular Protein Levels on mRNA Abundance

Liu, Y., Beyer, A., & Aebersold, R. (2016) · Cell · doi:10.1016/j.cell.2016.03.014 · Cited by 3,221 · 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

Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules

Han, M., Gao, X., Su, J. Z., & Nie, S. (2001) · Nature Biotechnology · doi:10.1038/90228 · Cited by 2,632 · see citing works

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

Sato, T., van Es, J. H., Snippert, H. J., Stange, D. E., Vries, R. G., van den Born, M., Barker, N., Shroyer, N. F., van de Wetering, M., & Clevers, H. (2011) · Nature · doi:10.1038/nature09637 · Cited by 2,510 · 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

Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy

Huisken, J., Swoger, J., Bene, F. D., Wittbrodt, J., & Stelzer, E. H. K. (2004) · Science · doi:10.1126/science.1100035 · Cited by 2,370 · see citing works

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

Picelli, S., Björklund, Å. K., Faridani, O. R., Sagasser, S., Winberg, G., & Sandberg, R. (2013) · Nature Methods · doi:10.1038/nmeth.2639 · Cited by 2,358 · see citing works

Imaging individual mRNA molecules using multiple singly labeled probes

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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

Single-cell RNA sequencing to explore immune cell heterogeneity

Papalexi, E., & Satija, R. (2018) · Nature Reviews Immunology · doi:10.1038/nri.2017.76 · Cited by 1,806 · see citing works

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Elefant, N., Paul, F., Zaretsky, I., Mildner, A., Cohen, N., Jung, S., Tanay, A., et al. (2014) · Science · doi:10.1126/science.1247651 · Cited by 1,795 · see citing works

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH

Eng, C.-H. L., Lawson, M., Zhu, Q., Dries, R., Koulena, N., Takei, Y., Yun, J., Cronin, C., Karp, C., Yuan, G.-C., et al. (2019) · Nature · doi:10.1038/s41586-019-1049-y · Cited by 1,754 · see citing works

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Wolf, F. A., Hamey, F. K., Plass, M., Solana, J., Dahlin, J. S., Göttgens, B., Rajewsky, N., Simon, L., & Theis, F. J. (2019) · Genome Biology · doi:10.1186/s13059-019-1663-x · Cited by 1,698 · 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

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

Ramsköld, D., Luo, S., Wang, Y.-C., Li, R., Deng, Q., Faridani, O. R., Daniels, G. A., Khrebtukova, I., Loring, J. F., Laurent, L. C., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2282 · Cited by 1,609 · 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

Mechanobiology of YAP and TAZ in physiology and disease

Panciera, T., Azzolin, L., Cordenonsi, M., & Piccolo, S. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.87 · Cited by 1,461 · see citing works

Designer matrices for intestinal stem cell and organoid culture

Gjorevski, N., Sachs, N., Manfrin, A., Giger, S., Bragina, M. E., Ordóñez-Morán, P., Clevers, H., & Lutolf, M. P. (2016) · Nature · doi:10.1038/nature20168 · Cited by 1,426 · see citing works

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

Rosenberg, A. B., Roco, C. M., Muscat, R. A., Kuchina, A., Sample, P., Yao, Z., Graybuck, L. T., Peeler, D. J., Mukherjee, S., Chen, W., et al. (2018) · Science · doi:10.1126/science.aam8999 · Cited by 1,422 · see citing works

Diffusion pseudotime robustly reconstructs lineage branching

Haghverdi, L., Büttner, M., Wolf, F. A., Buettner, F., & Theis, F. J. (2016) · Nature Methods · doi:10.1038/nmeth.3971 · Cited by 1,385 · see citing works

CEL-seq: single-cell RNA-seq by multiplexed linear amplification

Hashimshony, T., Wagner, F., Sher, N., & Yanai, I. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.003 · Cited by 1,231 · see citing works

The intestinal crypt, a prototype stem cell compartment

Clevers, H. (2013) · Cell · doi:10.1016/j.cell.2013.07.004 · Cited by 1,223 · see citing works

Cellular Heterogeneity: Do Differences Make a Difference?

Altschuler, S. J., & Wu, L. F. (2010) · Cell · doi:10.1016/j.cell.2010.04.033 · Cited by 1,214 · see citing works

Mass Cytometry: Single Cells, Many Features

Spitzer, M. H., & Nolan, G. P. (2016) · Cell · doi:10.1016/j.cell.2016.04.019 · Cited by 1,199 · see citing works

A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable

Tian, H., Biehs, B., Warming, S., Leong, K. G., Rangell, L. K., Klein, O. D., & de Sauvage, F. J. (2011) · Nature · doi:10.1038/nature10408 · Cited by 1,194 · see citing works

Quantitative single-cell RNA-seq with unique molecular identifiers

Islam, S., Zeisel, A., Joost, S., La Manno, G., Zajac, P., Kasper, M., Lönnerberg, P., & Linnarsson, S. (2014) · Nature Methods · doi:10.1038/nmeth.2772 · Cited by 1,183 · see citing works

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

Keren, L., Bosse, M., Marquez, D., Angoshtari, R., Jain, S., Varma, S., Yang, S.-R., Kurian, A., Van Valen, D., West, R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.039 · Cited by 1,183 · see citing works

Computational and analytical challenges in single-cell transcriptomics

Stegle, O., Teichmann, S. A., & Marioni, J. C. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3833 · Cited by 1,170 · see citing works

Growing Self-Organizing Mini-Guts from a Single Intestinal Stem Cell: Mechanism and Applications

Sato, T., & Clevers, H. (2013) · Science · doi:10.1126/science.1234852 · Cited by 1,170 · see citing works

CEL-seq2: sensitive highly-multiplexed single-cell RNA-Seq

Hashimshony, T., Senderovich, N., Avital, G., Klochendler, A., de Leeuw, Y., Anavy, L., Gennert, D., Li, S., Livak, K. J., Rozenblatt-Rosen, O., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0938-8 · Cited by 1,125 · see citing works

Applying systems-level spectral imaging and analysis to reveal the organelle interactome

Valm, A. M., Cohen, S., Legant, W. R., Melunis, J., Hershberg, U., Wait, E., Cohen, A. R., Davidson, M. W., Betzig, E., & Lippincott-Schwartz, J. (2017) · Nature · doi:10.1038/nature22369 · Cited by 1,113 · 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

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

Halpern, K. B., Shenhav, R., Matcovitch-Natan, O., Tóth, B., Lemze, D., Golan, M., Massasa, E. E., Baydatch, S., Landen, S., Moor, A. E., et al. (2017) · Nature · doi:10.1038/nature21065 · Cited by 1,059 · see citing works

Yap1 acts downstream of α-catenin to control epidermal proliferation

Schlegelmilch, K., Mohseni, M., Kirak, O., Pruszak, J., Rodriguez, J. R., Zhou, D., Kreger, B. T., Vasioukhin, V., Avruch, J., Brummelkamp, T. R., et al. (2011) · Cell · doi:10.1016/j.cell.2011.02.031 · Cited by 1,036 · see citing works

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

Spencer, S. L., Gaudet, S., Albeck, J. G., Burke, J. M., & Sorger, P. K. (2009) · Nature · doi:10.1038/nature08012 · Cited by 1,023 · 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

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

Hippo pathway effector Yap promotes cardiac regeneration

Xin, M., Kim, Y., Sutherland, L. B., Murakami, M., Qi, X., McAnally, J., Porrello, E. R., Mahmoud, A. I., Tan, W., Shelton, J. M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313192110 · Cited by 895 · see citing works

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

Wagner, D. E., Weinreb, C., Collins, Z. M., Briggs, J. A., Megason, S. G., & Klein, A. M. (2018) · Science · doi:10.1126/science.aar4362 · Cited by 849 · see citing works

Characterization of cell fate probabilities in single-cell data with Palantir

Setty, M., Kiseliovas, V., Levine, J., Gayoso, A., Mazutis, L., & Pe’er, D. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0068-4 · Cited by 833 · cited 1× · see citing works

Reproducibility crisis: Blame it on the antibodies

Baker, M. (2015) · Nature · doi:10.1038/521274a · Cited by 830 · see citing works

Scaling single-cell genomics from phenomenology to mechanism

Tanay, A., & Regev, A. (2017) · Nature · doi:10.1038/nature21350 · Cited by 792 · see citing works

From cells to organs: building polarized tissue

Bryant, D. M., & Mostov, K. E. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2523 · Cited by 788 · see citing works

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

Shin, J., Berg, D. A., Zhu, Y., Shin, J. Y., Song, J., Bonaguidi, M. A., Enikolopov, G., Nauen, D. W., Christian, K. M., Ming, G.-L., et al. (2015) · Cell Stem Cell · doi:10.1016/j.stem.2015.07.013 · Cited by 784 · see citing works

Dll1+ secretory progenitor cells revert to stem cells upon crypt damage

van Es, J. H., Sato, T., van de Wetering, M., Lyubimova, A., Nee, A. N. Y., Gregorieff, A., Sasaki, N., Zeinstra, L. M., van den Born, M., Korving, J., et al. (2012) · Nature Cell Biology · doi:10.1038/ncb2581 · Cited by 781 · see citing works

Intestinal label-retaining cells are secretory precursors expressing Lgr5

Buczacki, S. J. A., Zecchini, H. I., Nicholson, A. M., Russell, R., Vermeulen, L., Kemp, R., & Winton, D. J. (2013) · Nature · doi:10.1038/nature11965 · Cited by 761 · 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

YAP/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration

Yui, S., Azzolin, L., Maimets, M., Pedersen, M. T., Fordham, R. P., Hansen, S. L., Larsen, H. L., Guiu, J., Alves, M. R. P., Rundsten, C. F., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.11.001 · Cited by 678 · 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

Dedifferentiation of committed epithelial cells into stem cells in vivo

Tata, P. R., Mou, H., Pardo–Saganta, A., Zhao, R., Prabhu, M., Law, B. M., Vinarsky, V., Cho, J. L., Breton, S., Sahay, A., et al. (2013) · Nature · doi:10.1038/nature12777 · Cited by 657 · see citing works

Spatial organization of the somatosensory cortex revealed by osmFISH

Codeluppi, S., Borm, L. E., Zeisel, A., Manno, G. L., van Lunteren, J. A., Svensson, C. I., & Linnarsson, S. (2018) · Nature Methods · doi:10.1038/s41592-018-0175-z · Cited by 649 · see citing works

Yap-dependent reprogramming of Lgr5+ stem cells drives intestinal regeneration and cancer

Gregorieff, A., Liu, Y., Inanlou, M. R., Khomchuk, Y., & Wrana, J. L. (2015) · Nature · doi:10.1038/nature15382 · Cited by 647 · 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

Revealing the vectors of cellular identity with single-cell genomics

Wagner, A., Regev, A., & Yosef, N. (2016) · Nature Biotechnology · doi:10.1038/nbt.3711 · Cited by 632 · 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

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

Raj, B., Wagner, D. E., McKenna, A., Pandey, S., Klein, A. M., Shendure, J., Gagnon, J. A., & Schier, A. F. (2018) · Nature Biotechnology · doi:10.1038/nbt.4103 · Cited by 622 · see citing works

Multilineage communication regulates human liver bud development from pluripotency

Camp, J. G., Sekine, K., Gerber, T., Loeffler-Wirth, H., Binder, H., Gac, M., Kanton, S., Kageyama, J., Damm, G., Seehofer, D., et al. (2017) · Nature · doi:10.1038/nature22796 · Cited by 621 · see citing works

The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity

Pauklin, S., & Vallier, L. (2013) · Cell · doi:10.1016/j.cell.2013.08.031 · Cited by 611 · see citing works

Building epithelial architecture: insights from three-dimensional culture models

O'Brien, L. E., Zegers, M. M. P., & Mostov, K. E. (2002) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm859 · Cited by 596 · see citing works

Clonal analysis of lineage fate in native haematopoiesis

Rodriguez-Fraticelli, A. E., Wolock, S. L., Weinreb, C. S., Panero, R., Patel, S. H., Jankovic, M., Sun, J., Calogero, R. A., Klein, A. M., & Camargo, F. D. (2018) · Nature · doi:10.1038/nature25168 · Cited by 596 · see citing works

Replacement of lost Lgr5-positive stem cells through plasticity of their enterocyte-lineage daughters

Tetteh, P. W., Basak, O., Farin, H. F., Wiebrands, K., Kretzschmar, K., Begthel, H., van den Born, M., Korving, J., de Sauvage, F., van Es, J. H., et al. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.01.001 · Cited by 575 · see citing works

Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung

Zepp, J. A., Zacharias, W. J., Frank, D. B., Cavanaugh, C. A., Zhou, S., Morley, M. P., & Morrisey, E. E. (2017) · Cell · doi:10.1016/j.cell.2017.07.034 · Cited by 567 · see citing works

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms

Liu, T., Upadhyayula, S., Milkie, D. E., Singh, V. P., Wang, K., Swinburne, I. A., Mosaliganti, K. R., Collins, Z. M., Hiscock, T. W., Shea, J., et al. (2018) · Science · doi:10.1126/science.aaq1392 · Cited by 567 · see citing works

Cdk4/CyclinD1 Overexpression in Neural Stem Cells Shortens G1, Delays Neurogenesis, and Promotes the Generation and Expansion of Basal Progenitors

Lange, C. M., Huttner, W. Β., & Calegari, F. (2009) · Cell stem cell · doi:10.1016/j.stem.2009.05.026 · Cited by 565 · 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

Self-organization and symmetry breaking in intestinal organoid development

Serra, D., Mayr, U., Boni, A., Lukonin, I., Rempfler, M., Challet Meylan, L., Stadler, M. B., Strnad, P., Papasaikas, P., Vischi, D., et al. (2019) · Nature · doi:10.1038/s41586-019-1146-y · Cited by 561 · see citing works

Wishbone identifies bifurcating developmental trajectories from single-cell data

Setty, M., Tadmor, M. D., Reich-Zeliger, S., Angel, O., Salame, T. M., Kathail, P., Choi, K., Bendall, S., Friedman, N., & Pe'er, D. (2016) · Nature Biotechnology · doi:10.1038/nbt.3569 · Cited by 558 · 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

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

Spanjaard, B., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., Ninov, N., & Junker, J. P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4124 · Cited by 531 · see citing works

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

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Interplay between metabolic identities in the intestinal crypt supports stem cell function

Rodríguez-Colman, M. J., Schewe, M., Meerlo, M., Stigter, E., Gerrits, J., Pras-Raves, M., Sacchetti, A., Hornsveld, M., Oost, K. C., Snippert, H. J., et al. (2017) · Nature · doi:10.1038/nature21673 · Cited by 522 · see citing works

In toto imaging and reconstruction of post-implantation mouse development at the single-cell level

McDole, K., Guignard, L., Amat, F., Berger, A., Malandain, G., Royer, L. A., Turaga, S. C., Branson, K., & Keller, P. J. (2018) · Cell · doi:10.1016/j.cell.2018.09.031 · Cited by 522 · 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

Differentiated Troy+ Chief Cells Act as Reserve Stem Cells to Generate All Lineages of the Stomach Epithelium

Stange, D. E., Koo, B., Huch, M., Sibbel, G., Başak, O., Lyubimova, A., Kujala, P., Bartfeld, S., Köster, J., Geahlen, J. H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.09.008 · Cited by 509 · see citing works

Spatially resolved transcriptomics and beyond

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Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

Ounkomol, C., Seshamani, S., Maleckar, M. M., Collman, F., & Johnson, G. R. (2018) · Nature Methods · doi:10.1038/s41592-018-0111-2 · Cited by 495 · see citing works

Gene‐specific correlation of RNA and protein levels in human cells and tissues

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