A combined approach for single-cell mRNA and intracellular protein expression analysis
Open accessAbstract
Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation.
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mRNA abundance from transcriptomics alone is insufficient to infer protein abundance.
“For example, mRNA abundance from transcriptomics alone is insufficient to infer protein abundance [Chen et al., 2020; Reimegård et al., 2021]”
From Cell signaling pathways discovery from multi-modal data (2025) · cites this paper as Reimegård et al., 2021
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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw377 · Cited by 10,799 · 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 · cited 1× · see citing works
“05); and (2) reported as bound by POU5F1 in vicinity of the TSS by the curated set of ChIP-seq data described in the section below.”
BackgroundScenic: single-cell regulatory network inference and clustering.
Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520 · see citing works
La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0414-6 · Cited by 4,118 · 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
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
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
Raj, A., & van Oudenaarden, A. (2008) · Cell · doi:10.1016/j.cell.2008.09.050 · Cited by 2,593 · 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
Assarsson, E., Lundberg, M., Holmquist, G., Björkesten, J., Bucht Thorsen, S., Ekman, D., Eriksson, A., Rennel Dickens, E., Ohlsson, S., Edfeldt, G., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0095192 · Cited by 1,874 · see citing works
Stochastic mRNA Synthesis in Mammalian Cells
Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y., & Tyagi, S. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040309 · Cited by 1,737 · see citing works
Regulation of noise in the expression of a single gene
Özbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D., & van Oudenaarden, A. (2002) · Nature Genetics · doi:10.1038/ng869 · Cited by 1,559 · see citing works
Multiplexed quantification of proteins and transcripts in single cells
Peterson, V. M., Zhang, K. X., Kumar, N., Wong, J., Li, L., Wilson, D. C., Moore, R., McClanahan, T. K., Sadekova, S., & Klappenbach, J. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3973 · Cited by 832 · see citing works
ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
Oki, S., Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., & Meno, C. (2018) · The EMBO Reports · doi:10.15252/embr.201846255 · Cited by 763 · see citing works
Design and Analysis of Single-Cell Sequencing Experiments
Grün, D., & van Oudenaarden, A. (2015) · Cell · doi:10.1016/j.cell.2015.10.039 · Cited by 536 · see citing works
Genomic encoding of transcriptional burst kinetics
Larsson, A. J. M., Johnsson, P., Hagemann-Jensen, M., Hartmanis, L., Faridani, O. R., Reinius, B., Segerstolpe, Å., Rivera, C. M., Ren, B., & Sandberg, R. (2019) · Nature · doi:10.1038/s41586-018-0836-1 · Cited by 534 · see citing works
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2
Specht, H., Emmott, E., Petelski, A. A., Huffman, R. G., Perlman, D. H., Serra, M., Kharchenko, P., Koller, A., & Slavov, N. (2021) · Genome Biology · doi:10.1186/s13059-021-02267-5 · Cited by 493 · see citing works
Dynamic profiling of the protein life cycle in response to pathogens
Jovanovic, M., Rooney, M. S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., et al. (2015) · Science · doi:10.1126/science.1259038 · Cited by 460 · see citing works
Padovan-Merhar, O. M., Nair, G. P., Biaesch, A. G., Mayer, A., Scarfone, S., Foley, S. W., Wu, A. R., Churchman, L. S., Singh, A., & Raj, A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.03.005 · Cited by 434 · see citing works
Highly multiplexed simultaneous detection of RNAs and proteins in single cells
Frei, A. P., Bava, F.-A., Zunder, E. R., Hsieh, E. W. Y., Chen, S.-Y., Nolan, G. P., & Gherardini, P. F. (2016) · Nature Methods · doi:10.1038/nmeth.3742 · Cited by 330 · see citing works
A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
Lee, M. V., Topper, S. E., Hubler, S. L., Hose, J., Wenger, C. D., Coon, J. J., & Gasch, A. P. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.48 · Cited by 290 · see citing works
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
Proteomic and phosphoproteomic comparison of human ES and iPS cells
Phanstiel, D. H., Brumbaugh, J., Wenger, C. D., Tian, S., Probasco, M. D., Bailey, D. J., Swaney, D. L., Tervo, M. A., Bolin, J. M., Ruotti, V., et al. (2011) · Nature Methods · doi:10.1038/nmeth.1699 · Cited by 257 · see citing works
Post-transcriptional regulation across human tissues
Franks, A., Airoldi, E., & Slavov, N. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005535 · Cited by 219 · see citing works
Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells
Darmanis, S., Gallant, C. J., Marinescu, V. D., Niklasson, M., Segerman, A., Flamourakis, G., Fredriksson, S., Assarsson, E., Lundberg, M., Nelander, S., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2015.12.021 · Cited by 219 · see citing works
Self-citationDissecting neural differentiation regulatory networks through epigenetic footprinting
Ziller, M. J., Edri, R., Yaffe, Y., Donaghey, J., Pop, R., Mallard, W., Issner, R., Gifford, C. A., Goren, A., Xing, J. C., et al. (2014) · Nature · doi:10.1038/nature13990 · Cited by 197 · see citing works
Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe
Qiu, X., Rahimzamani, A., Wang, L., Ren, B., Mao, Q., Durham, T., McFaline-Figueroa, J. L., Saunders, L., Trapnell, C., & Kannan, S. (2020) · Cell Systems · doi:10.1016/j.cels.2020.02.003 · Cited by 185 · see citing works
Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Genshaft, A. S., Li, S., Gallant, C. J., Darmanis, S., Prakadan, S. M., Ziegler, C. G. K., Lundberg, M., Fredriksson, S., Hong, J., Regev, A., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-1045-6 · Cited by 175 · see citing works
Self-citationSCORPIUS improves trajectory inference and identifies novel modules in dendritic cell developmentPreprint
Cannoodt, R., Saelens, W., Sichien, D., Tavernier, S. J., Janssens, S., Guilliams, M., Lambrecht, B. N., Preter, K. D., & Saeys, Y. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/079509 · Cited by 159 · see citing works
Controlling nuclear RNA levels
Schmid, M., & Jensen, T. H. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0013-2 · Cited by 155 · see citing works
Comparative analysis of sequencing technologies for single-cell transcriptomics
Natarajan, K. N., Miao, Z., Jiang, M., Huang, X., Zhou, H., Xie, J., Wang, C., Qin, S., Zhao, Z., Wu, L. L., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1676-5 · Cited by 114 · see citing works
Weibrecht, I., Lundin, E., Kiflemariam, S., Mignardi, M., Grundberg, I., Larsson, C., Koos, B., Nilsson, M. F., & Söderberg, O. (2013) · Nature Protocols · doi:10.1038/nprot.2013.006 · Cited by 108 · see citing works
Gerlach, J. P., van Buggenum, J. A. G., Tanis, S. E. J., Hogeweg, M., Heuts, B. M. H., Muraro, M. J., Elze, L., Rivello, F., Rakszewska, A., van Oudenaarden, A., et al. (2019) · Scientific Reports · doi:10.1038/s41598-018-37977-7 · Cited by 104 · see citing works
ProteinSeq: High-Performance Proteomic Analyses by Proximity Ligation and Next Generation Sequencing
Darmanis, S., Nong, R. Y., Vänelid, J., Siegbahn, A., Ericsson, O., Fredriksson, S., Bäcklin, C. L., Gut, M., Heath, S. C., Gut, I. G., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025583 · Cited by 101 · see citing works
Delayed Protein Synthesis Reduces the Correlation between mRNA and Protein Fluctuations
Gedeon, T., & Bokes, P. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.06.025 · Cited by 95 · see citing works
Protein velocity and acceleration from single-cell multiomics experiments
Gorin, G., Svensson, V., & Pachter, L. S. (2020) · Genome biology · doi:10.1186/s13059-020-1945-3 · Cited by 85 · see citing works
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneityPreprint
Specht, H., Emmott, E., Petelski, A. A., Huffman, R. G., Perlman, D. H., Serra, M., Kharchenko, P. V., Koller, A. A., & Slavov, N. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/665307 · Cited by 51 · see citing works
Schulz, D., Zanotelli, V. R., Fischer, J. R., Schapiro, D., Engler, S., Lun, X., Jackson, H. W., & Bodenmiller, B. (2018) · Cell Systems · doi:10.1016/j.cels.2018.04.004 · Cited by 48 · see citing works
Ogris, C., Guala, D., Helleday, T., & Sonnhammer, E. L. L. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw849 · Cited by 41 · see citing works
Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells
Popovic, D., Koch, B., Kueblbeck, M., Ellenberg, J., & Pelkmans, L. (2018) · Cell Systems · doi:10.1016/j.cels.2018.09.001 · Cited by 33 · see citing works
The interdependence of transcript and protein abundance: new data–new complexities
Liu, Y., & Aebersold, R. H. (2016) · Molecular Systems Biology · doi:10.15252/msb.20156720 · Cited by 32 · see citing works
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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
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry
Bennett, H. M., Stephenson, W., Rose, C. M., & Darmanis, S. (2023) · Nature Methods · doi:10.1038/s41592-023-01791-5 · Cited by 351 · see citing works
Proteomics technologies for cancer liquid biopsies
Ding, Z., Wang, N., Ji, N., & Chen, Z. (2022) · Molecular Cancer · doi:10.1186/s12943-022-01526-8 · Cited by 250 · see citing works
Advances in single-cell omics and multiomics for high-resolution molecular profiling
Lim, J., Park, C., Kim, M., Kim, H., Kim, J., & Lee, D.-S. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01186-2 · Cited by 193 · 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
Chen, A. F., Parks, B., Kathiria, A. S., Ober-Reynolds, B., Goronzy, J. J., & Greenleaf, W. J. (2022) · Nature Methods · doi:10.1038/s41592-022-01461-y · Cited by 139 · see citing works
Alsafran, M. H. S. A., Usman, K., Ahmed, B., Rizwan, M., Saleem, M. H., & Jabri, H. M. S. J. A. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.881242 · Cited by 134 · see citing works
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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
Le, J., Dian, Y., Zhao, D., Guo, Z., Luo, Z., Chen, X., Zeng, F., & Deng, G. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02426-3 · Cited by 109 · see citing works
Klebes, A., Ates, H. C., Verboket, R. D., Urban, G. A., von Stetten, F., Dincer, C., & Früh, S. M. (2023) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2023.115800 · Cited by 90 · see citing works
Into the multiverse: advances in single-cell multiomic profiling
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Lin, Y. H., Duong, H. G., Limary, A. E., Kim, E. S., Hsu, P. W., Patel, S. A., Wong, W. H., Indralingam, C. S., Liu, Y. C., Yao, P., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.12.007 · Cited by 74 · see citing works
Exploring the untapped potential of single‐cell and spatial omics in plant biology
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Wang, J., Ye, F., Chai, H., Jiang, Y., Wang, T., Ran, X., Xia, Q., Xu, Z., Fu, Y., Zhang, G., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2770-x · Cited by 69 · see citing works
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Xie, H., & Ding, X. (2022) · Advanced Science · doi:10.1002/advs.202105932 · Cited by 52 · see citing works
Cheng, R. Y.-H., de Rutte, J. M., Ito, C. E., Ott, A. R., Bosler, L., Kuo, W.-Y., Liang, J., Hall, B. E., Rawlings, D. J., Carlo, D. D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39367-8 · Cited by 52 · see citing works
Single-cell sorting based on secreted products for functionally defined cell therapies
Miwa, H., Dimatteo, R., de Rutte, J. M., Ghosh, R., & Carlo, D. D. (2022) · Microsystems & Nanoengineering · doi:10.1038/s41378-022-00422-x · Cited by 49 · see citing works
Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99
Mattisson, J., Danielsson, M., Hammond, M., Davies, H., Gallant, C. J., Nordlund, J., Raine, A., Edén, M., Kilander, L., Ingelsson, M., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-94588-5 · Cited by 48 · see citing works
Self-citationFetal brain response to maternal inflammation requires microglia
Lessi, M., Iturza, N. D., Stogsdill, J., Faits, T., Kim, K., Levin, J. Z., & Arlotta, P. (2024) · Development · doi:10.1242/dev.202252 · Cited by 46 · see citing works
Gupta, A., Martin-Rufino, J. D., Jones, T. R., Subramanian, V., Qiu, X., Grody, E. I., Bloemendal, A., Weng, C., Niu, S.-Y., Min, K. H., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2207392119 · Cited by 42 · see citing works
Cellular control of protein levels: A systems biology perspective
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Pathway dynamics can delineate the sources of transcriptional noise in gene expression
Ham, L., Jackson, M., & Stumpf, M. P. (2021) · eLife · doi:10.7554/elife.69324 · Cited by 37 · see citing works
Current annotation strategies for T cell phenotyping of single-cell RNA-seq data
Mullan, K. A., de Vrij, N., Valkiers, S., & Meysman, P. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1306169 · Cited by 31 · see citing works
Caron, D. P., Specht, W. L., Chen, D., Wells, S. B., Szabo, P. A., Jensen, I. J., Färber, D. L., & Sims, P. A. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100938 · Cited by 31 · see citing works
Li, Z., Sun, C., Wang, F., Wang, X., Zhu, J., Luo, L., Ding, X., Zhang, Y., Ding, P., Wang, H., et al. (2022) · Clinical and Translational Medicine · doi:10.1002/ctm2.689 · Cited by 30 · see citing works
Revealing microRNA regulation in single cells
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Wu, X., Ying, H., Yang, Q., Yang, Q., Liu, H., Ding, Y., Zhao, H., Chen, Z., Zheng, R., Lin, H., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53621-7 · Cited by 31 · see citing works
Trends in Mass Spectrometry-Based Single-Cell Proteomics
Sanchez-Avila, X., de Oliveira, R. M., Huang, S., Wang, C., & Kelly, R. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c00661 · Cited by 29 · see citing works
Chalazonitis, A., Rao, M., & Sulzer, D. L. (2022) · npj Parkinson s Disease · doi:10.1038/s41531-022-00308-9 · Cited by 25 · see citing works
Keeler, A. B., Deusen, A. L. V., Gadani, I. C., Williams, C. M., Goggin, S. M., Hirt, A. K., Vradenburgh, S. A., Fread, K., Puleo, E. A., Jin, L., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01181-8 · Cited by 26 · see citing works
Owen, T. M., Carpino, G., Chen, L., Kundu, D., Wills, P. G., Ekser, B., Onori, P., Gaudio, E., Alpini, G. D., Francis, H., et al. (2023) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2023.06.005 · Cited by 23 · see citing works
El‐Sayed, K. M. F., Bittner, A., Schlicht, K., Mekhemar, M. K., Enthammer, K., Höppner, M. P., Es‐Souni, M., Schulz, J. C., Laudes, M., Graetz, C., et al. (2021) · Cells · doi:10.3390/cells10123310 · Cited by 22 · see citing works
Wu, R., Veličković, M., & Burnum-Johnson, K. (2024) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2024.103174 · Cited by 21 · see citing works
Gong, Q., Lv, X., Liao, C., Liang, A., Luo, C., Wu, J., Zhou, Y., Huang, Y., & Tong, Z. (2024) · Journal of Advanced Research · doi:10.1016/j.jare.2024.01.018 · Cited by 21 · see citing works
Boss, A. L., Damani, T. T., Wickman, T. J., Chamley, L., James, J. L., & Brooks, A. E. S. (2022) · eLife · doi:10.7554/elife.76622 · Cited by 17 · see citing works
Hong, Y., Li, J., Xu, N., Shu, W., Chen, F., Mi, Y., Geng, H., & Li, Q. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1604154 · Cited by 17 · see citing works
Hong, Y., Wang, Y., Shu, W., Li, J., Mi, Y., Chen, H., & Chen, C. (2025) · Ageing Research Reviews · doi:10.1016/j.arr.2025.102835 · Cited by 17 · see citing works
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Single-cell metabolome and RNA-seq multiplexing on single plant cells
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Hamel, R., Peruzzotti‐Jametti, L., Ridley, K., Testa, V., Yu, B., Rowitch, D. H., Marioni, J. C., & Pluchino, S. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e18339 · Cited by 19 · see citing works
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Lairikyengbam, D., Wetterauer, B., Schmiech, M., Jahraus, B., Kirchgessner, H., Wetterauer, P., Berschneider, K. M., Beier, V., Niesler, B., Balta, E., et al. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1388962 · Cited by 14 · see citing works
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Wu, L., & de Perrot, M. E. (2023) · Biomolecules · doi:10.3390/biom13071103 · Cited by 12 · see citing works
Single-cell epigenomics and proteomics methods integrated in multiomics
Bi, H., & Weng, X. (2024) · Fundamental Research · doi:10.1016/j.fmre.2023.11.014 · Cited by 12 · see citing works
de Clauser, L., Kappert, C., Sondermann, J. R., Gómez‐Varela, D., Flatters, S. J. L., & Schmidt, M. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.818690 · Cited by 11 · see citing works
Harmanci, A. O., Harmancı, A. S., Klisch, T. J., & Patel, A. J. (2022) · BMC Genomics · doi:10.1186/s12864-022-09004-7 · Cited by 11 · see citing works
Decoding Human Biology and Disease Using Single-Cell Omics Technologies
Shi, Q., Chen, X., & Zhang, Z. (2023) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2023.06.003 · Cited by 10 · see citing works
Lv, X., Luo, C., Wu, J., Huang, Y., Quan, J., Gong, Q., & Tong, Z. (2024) · International Endodontic Journal · doi:10.1111/iej.14080 · Cited by 10 · see citing works
Repertoire-based mapping and time-tracking of T helper cell subsets in scRNA-Seq
Lukyanov, D. K., Kriukova, V., Ladell, K., Shagina, I. A., Staroverov, D. B., Минасян, Б. Э., Fedosova, A. S., Shelyakin, P. V., Suchalko, O. N., Komkov, A. Y., et al. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1536302 · Cited by 8 · see citing works
Caprioli, C., Nazari, I., Milovanovic, S., & Pelicci, P. G. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2021.796477 · Cited by 9 · see citing works
Yao, Z., Li, M., & Lv, G. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1058296 · Cited by 9 · see citing works
Gu, R., Cui, T., Guo, Y., Luan, Y., Wang, X., Liu, R., & Yin, C. (2023) · Molecular Biology Reports · doi:10.1007/s11033-023-08544-9 · Cited by 9 · see citing works
Suarez‐Arnedo, A., Caston, E. L. P., Liu, Y., Bai, H., Muddiman, D. C., & Segura, T. (2025) · Biomaterials · doi:10.1016/j.biomaterials.2025.123667 · Cited by 8 · see citing works
Transcriptomic and proteomic profiling of NaV1.8-expressing mouse nociceptors
Schmidt, M., Sondermann, J. R., Gómez‐Varela, D., Çubuk, C., Millet, Q., Lewis, M., Wood, J. N., & Zhao, J. (2022) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2022.1002842 · Cited by 8 · see citing works
SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling AnalysisPreprint
Opzoomer, J. W., O’Sullivan, R., Sufi, J., Madsen, R. R., Qin, X., Basiarz, E., & Tape, C. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.23.581433 · Cited by 8 · see citing works
Raven, N., Klaassen, M., Madsen, T. R. L., Frédéric Thomas, A., Hamede, R., & Újvári, B. (2022) · Molecular Ecology · doi:10.1111/mec.16408 · Cited by 7 · see citing works
Ballasch, I., López-Molina, L., Galán-Ganga, M., Sancho‐Balsells, A., Rodríguez-Navarro, I., Borràs‐Pernas, S., Rabadán, M. A., Chen, W., Pastó-Pellicer, C., Flotta, F., et al. (2024) · Journal of Neuroinflammation · doi:10.1186/s12974-024-03320-3 · Cited by 6 · see citing works
Single-Cell RNA Sequencing and Combinatorial Approaches for Understanding Heart Biology and Disease
Wang, L., & Jin, B. (2024) · Biology · doi:10.3390/biology13100783 · Cited by 7 · see citing works
Mesquita, L. A., Bailão, A. M., de Curcio, J. S., da Silva, K. L. P., Fernandes, G. D. R., Bailão, M. G. S., Novaes, E., & Soares, C. M. D. A. (2023) · Journal of Fungi · doi:10.3390/jof9030281 · Cited by 6 · see citing works
Zhang, Y., Liu, Y., Xue, S., Zhang, Y., Li, Z., Zhang, M., Kai, G., & Li, J. (2024) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.18303 · Cited by 6 · see citing works
Deciphering cellular complexity: advances and future directions in single-cell protein analysis
Zhao, Q., Li, S., Krall, L., Li, Q., Sun, R., Yin, Y., Fu, J., Zhang, X. D., Wang, Y., & Yang, M. (2025) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2024.1507460 · Cited by 5 · see citing works
Shahzaib, M., Aprile, D., Squillaro, T., Alessio, N., Peluso, G., Bernardo, G. D., & Galderisi, U. (2025) · Ageing Research Reviews · doi:10.1016/j.arr.2025.102916 · Cited by 5 · see citing works
Ye, H., Huang, Y., Wang, C., Jin, J., Jiang, C., Fang, J., & Xu, Q.-H. (2025) · The Journal of Headache and Pain · doi:10.1186/s10194-025-02241-7 · Cited by 5 · see citing works
Ramelow, C. C., Dammer, E. B., Xiao, H., Cheng, L., Kumar, P., Espinosa‐García, C., Sampson, M. M., Kour, D., Nelson, R. S., Malepati, S., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-71098-4 · Cited by 5 · see citing works
Proteome-wide copy-number estimation from transcriptomics
Sweatt, A. J., Griffiths, C. D., Groves, S. M., Paudel, B. B., Wang, L., Kashatus, D. F., & Janes, K. A. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00064-3 · Cited by 5 · see citing works
Korbonits, L., Kleinwort, K. J. H., Amann, B., Didier, A., Märtlbauer, E. P., Hauck, S. M., & Deeg, C. A. (2022) · Metabolites · doi:10.3390/metabo12100924 · Cited by 5 · see citing works
Liu, C., Li, Z., Ji, J.-J., Liu, K., Samsom, J., Li, T., Qi, L., & Liu, F. (2025) · Neuropsychopharmacology · doi:10.1038/s41386-025-02273-2 · Cited by 4 · see citing works
Dissecting autonomous enzymatic variability in single cells
Gnann, C., Sigaeva, A., Le, T., Cesnik, A. J., Sariyar, S., Mahdessian, D., Schutten, R., Raghavan, P., Leonetti, M. D., Lindskog, C., et al. (2025) · bioRxiv · doi:10.1038/s41467-026-74172-z · Cited by 3 · see citing works
Repapi, E., Agarwal, D., Napolitani, G., Sims, D., & Taylor, S. (2023) · F1000Research · doi:10.12688/f1000research.121829.3 · Cited by 4 · see citing works
Lin, H., Makhlouf, A., Echegaray, C. V., Zawada, D. M., & Simões, F. C. (2023) · Development · doi:10.1242/dev.202300 · Cited by 4 · see citing works
DNA mismatch repair system regulates the expression of PD-L1 through DNMTs in cervical cancer
Guo, F., Lu, R., Kong, W., Anwar, M., & Feng, Y. (2024) · Cancer Cell International · doi:10.1186/s12935-024-03214-7 · Cited by 4 · see citing works
Soni, J., Chattopadhyay, P., Mehta, P., Mohite, R., Tardalkar, K., Joshi, M. G., & Pandey, R. (2024) · Frontiers in Medicine · doi:10.3389/fmed.2024.1297001 · Cited by 4 · see citing works
Kim, Y. J., Tarashansky, A. J., Liang, K., Urisko, M., Dorman, L. C., Borja, M., Neff, N. F., Pisco, A. O., & Granados, A. A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.11.548639 · Cited by 4 · see citing works
Cell signaling pathways discovery from multi-modal data
He, C., Simpson, C., Cossentino, I., Zhang, B., Tkachev, S., Eddins, D. J., Kosters, A., Yang, J., Sheth, S., Levy, T., et al. (2025) · doi:10.1101/2025.02.06.636961 · Cited by 3 · see citing works
Higher-order interactions in neuronal function: from genes to ionic currents in biophysical models
Reva, M., Arnaudon, A., Zbili, M., Makkeh, A., Markram, H., Goaillard, J.-M., & Van Geit, W. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2500048122 · Cited by 3 · see citing works
Hansberg, W. (2022) · Differentiation · doi:10.1016/j.diff.2022.02.005 · Cited by 3 · see citing works
Sequencing-based methods for single-cell multi-omics studies
Qin, S., Liu, S., & Weng, X. (2023) · Science China Chemistry · doi:10.1007/s11426-023-1793-7 · Cited by 2 · see citing works
Marhamati, S., Ali, Z., Zargar, A. M., & Mohagheghi, S. (2025) · Molecular Biology Reports · doi:10.1007/s11033-025-10780-0 · Cited by 2 · see citing works
Alternative Matrices for Protein Biomarker Analysis by qPCR Using Proximity Extension Assay (PEA)
Llamas-Urbano, A., Martinez-Moreno, J. M., Pérez-Sánchez, C., & Barbarroja, N. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4595-6_14 · Cited by 2 · see citing works
Zhong, S., Zeng, Z., Jin, Z., Zhang, L., Ye, G., He, W., Sun, J., Wang, L., Song, L., Cai, J., et al. (2025) · Journal of Medical Virology · doi:10.1002/jmv.70572 · Cited by 2 · see citing works
Huang, Y.-L., Lin, Z., Song, Y.-Q., Wang, Z.-K., Weng, L. L., Yang, G.-H., Zhong, N., Guang-hong, Z., & Zheng, Y. (2025) · Current Research in Food Science · doi:10.1016/j.crfs.2025.101253 · Cited by 2 · see citing works
Ardissino, M., Morley, A. P., Truong, B. M. T., Schuermans, A., Reddy, R. K., Milani, M., Sacco, A., Ware, J. S., Burgess, S., Halliday, B. P., et al. (2026) · Circulation Genomic and Precision Medicine · doi:10.1161/circgen.125.005330 · Cited by 2 · see citing works
Mass spectrometry-based single-cell proteomics technologies, trends, and biological insights
Hu, R., Montes, C., & Walley, J. W. (2026) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2026.04.011 · Cited by 3 · see citing works
Single‐cell analytical technologies: uncovering the mechanisms behind variations in immune responses
Kashima, Y., Reteng, P., Haga, Y., Yamagishi, J., & Suzuki, Y. (2022) · FEBS Journal · doi:10.1111/febs.16622 · Cited by 2 · see citing works
Recent progress in co-detection of single-cell transcripts and proteins
Huang, S., Fan, Q., Wang, Y., Huang, Z., Shi, W., Gong, Y., Yang, T., Wang, J., Wu, L., & Yang, C. J. (2023) · Nano Research · doi:10.1007/s12274-023-5924-3 · Cited by 2 · see citing works
He, L., Wang, W., Dang, K., Zhang, W., Ye, K., Wang, H., Huang, Y., & Zhao, X. (2025) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2025.118418 · Cited by 2 · see citing works
Al-Abbasi, Z., Bhuiyan, S. A., Renthal, W. R., & Molliver, D. C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.03.643725 · Cited by 2 · see citing works
Global quantification of mammalian gene expression noisePreprint
Welter, A. S., Mutschler, F., Simon, M. C., Giacomelli, C., Branscheid, A.-C., Manukyan, A., Alves, L. G. T., Gerwien, M., Kerridge, R., Landthaler, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.11.724258 · Cited by 4 · see citing works
Ph-chromosome-negative myeloproliferative neoplasms: clonal dynamics are the name of the game
Noorafrooz, M., Noorafrooz, R., Barosi, G., & Gale, R. P. (2026) · Blood Reviews · doi:10.1016/j.blre.2026.101385 · Cited by 1 · see citing works
Alnuaimi, N. S., Lößlein, L., Mousa, M., Khader, T. A., Alkhaaldi, A., Azzam, S. K., Craenenbroeck, A. H. V., Ashraf, S. M., Carmeliet, P., & AlSafar, H. S. (2026) · Cardiovascular Diabetology · doi:10.1186/s12933-026-03187-z · Cited by 1 · see citing works
Kamarulzaman, L., Kim, S., Hidaka, T., Tsuchida, M., & Taniguchi, Y. (2026) · Nature Communications · doi:10.1038/s41467-026-74840-0 · Cited by 2 · see citing works
Single-cell multi-omics sequencing and its applications in studying the nervous system
Chaoyang, W., & Xiaoying, F. (2021) · Biophysics Reports · doi:10.52601/bpr.2021.210031 · Cited by 1 · see citing works
Repapi, E., Agarwal, D., Napolitani, G., Sims, D., & Taylor, S. (2022) · F1000Research · doi:10.12688/f1000research.121829.2 · Cited by 1 · see citing works
Boahen, C. K., Oelen, R., Le, K. T. T., Netea, M. G., Franke, L., van der Wijst, M. G. P., & Kumar, V. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1069379 · Cited by 1 · see citing works
Statistical and Computational Methods for Proteogenomic Data Analysis
Song, X. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-2986-4_13 · Cited by 1 · see citing works
Das, S., & Srivastava, D. K. (2023) · Genetic Epidemiology · doi:10.1002/gepi.22536 · Cited by 1 · see citing works
- Authors
- Reimegård, J., Tarbier, M., Danielsson, M., Schuster, J., Baskaran, S., Panagiotou, S., Dahl, N., Friedländer, M. R., & Gallant, C. J.
- Affiliations
- Uppsala University (SE)
- Stockholm University (SE)
- Corresponding author
- Gallant, Caroline J.
- ORCID
- Venue
- Communications Biology
- Published
- 2021-05-25
- Volume
- 4
- Issue
- 1
- Pages
- 624-624
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC8149646
- OpenAlex
- W3164706810
- Cited by
- 129
- References
- 39
- Citations by year
- 2026: 25 · 2025: 26 · 2024: 22 · 2023: 23 · 2022: 28 · 2021: 5
- FWCI
- 6.12
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Communications Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Vetenskapsrådet (2017-05229)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- single-cell transcriptomics, single-cell proteomics, proximity extension assay, SPARC, intracellular protein expression, neuronal differentiation, transcription factor activity, mRNA-protein correlation, protein localization
- MeSH terms
- Humans, Proteins, RNA, Messenger, Transcription, Genetic, Sequence Analysis, RNA, Gene Expression Profiling, Proteomics, Single-Cell Analysis
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