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Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

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Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

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Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

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

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NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells

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A combined approach for single-cell mRNA and intracellular protein expression analysis

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From bench to bedside: Single-cell analysis for cancer immunotherapy

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Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis

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Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment

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Emerging multianalyte biosensors for the simultaneous detection of protein and nucleic acid biomarkers

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Into the multiverse: advances in single-cell multiomic profiling

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Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective

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Single-cell omics: experimental workflow, data analyses and applications

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Time-resolved single-cell RNA-seq using metabolic RNA labelling

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Advances and applications in single-cell and spatial genomics

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Gene regulatory network inference in single-cell biology

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SCITO-seq: single-cell combinatorial indexed cytometry sequencing

Hwang, B., Lee, D. S., Tamaki, W., Sun, Y., Ogorodnikov, A., Hartoularos, G. C., Winters, A. F., Yeung, B. Z., Nazor, K. L., Song, Y. S., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01222-3 · Cited by 65

Single‐Cell Sequencing Methodologies: From Transcriptome to Multi‐Dimensional Measurement

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Signalling dynamics in embryonic development

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Integrated multi-omics with machine learning to uncover the intricacies of kidney disease

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Neurodegeneration cell per cell

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Human placental methylome in the interplay of adverse placental health, environmental exposure, and pregnancy outcome

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Heterogeneity and plasticity in healthy and atherosclerotic vasculature explored by single-cell sequencing

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Single-cell intracellular epitope and transcript detection reveals signal transduction dynamics

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Progress in single-cell multimodal sequencing and multi-omics data integration

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X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation ModelsPreprint

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Computational Methods for Single-Cell Imaging and Omics Data Integration

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Single-Cell Multi-Omics: Insights into Therapeutic Innovations to Advance Treatment in Cancer

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Gene expression and protein abundance: Just how associated are these molecular traits?

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Microfluidics-based single cell analysis: from transcriptomics to spatiotemporal multi-omics

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Epigenetic Regulations in Mammalian Cells: Roles and Profiling Techniques

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FixNCut: single-cell genomics through reversible tissue fixation and dissociation

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scTrends: A living review of commercial single-cell and spatial 'omic technologies

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Decoding Expression Dynamics of Protein and Transcriptome at the Single-Cell Level in Paired Picoliter Chambers.

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Microfluidic single‐cell multiomics analysis

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Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research: recent advances and future opportunities

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Epigenetically regulated RNA-binding proteins signify malaria hypnozoite dormancy

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The role of single-cell genomics in human genetics

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ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study

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Single-cell technologies in multiple myeloma: new insights into disease pathogenesis and translational implications

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Scalable, multimodal profiling of chromatin accessibility and protein levels in single cellsPreprint

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Droplet-based mRNA sequencing of fixed and permeabilized cells by CLInt-seq allows for antigen-specific TCR cloning

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Integration of single‐cell transcriptome and proteome technologies: Toward spatial resolution levels

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Key Considerations on CITE‐Seq for Single‐Cell Multiomics

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Advanced sequencing-based high-throughput and long-read single-cell transcriptome analysis

Huang, S., Shi, W., Li, S., Fan, Q., Yang, C. J., Cao, J., & Wu, L. (2024) · Lab on a Chip · doi:10.1039/d4lc00105b · Cited by 14

Advances in Single Cell Technologies in Immunology

Choi, J. R. (2020) · BioTechniques · doi:10.2144/btn-2020-0047 · Cited by 15

Single‐Cell and Spatial Omics: Methods and Applications

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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

Large-scale datasets uncovering cell signalling networks in cancer: context matters

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The Application of Single-Cell Technologies in Cardiovascular Research

Chen, Y., Liu, Y., & Gao, X. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.751371 · Cited by 11

Single-Cell Molecular Barcoding to Decode Multimodal Information Defining Cell States

Kim, I. S. (2023) · Molecules and Cells · doi:10.14348/molcells.2023.2168 · Cited by 11

Single-cell approaches to dissect adaptive immune responses involved in autoimmunity: the case of celiac disease

Lindeman, I., & Sollid, L. M. (2021) · Mucosal Immunology · doi:10.1038/s41385-021-00452-0 · Cited by 11

Inducible MLL-AF9 Expression Drives an AML Program during Human Pluripotent Stem Cell-Derived Hematopoietic Differentiation

Heuts, B. M. H., Arza-Apalategi, S., Alkema, S. G., Tijchon, E. J. H., Jussen, L., Bergevoet, S. M., van der Reijden, B. A., & Martens, J. H. A. (2023) · Cells · doi:10.3390/cells12081195 · Cited by 10

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 11

Multimodal detection of protein isoforms and nucleic acids from mouse pre-implantation embryos

Rosàs, E., Modzelewski, A. J., Geldert, A., He, L., & Herr, A. E. (2021) · Nature Protocols · doi:10.1038/s41596-020-00449-2 · Cited by 8

Single-Cell Technologies to Decipher the Immune Microenvironment in Myeloid Neoplasms: Perspectives and Opportunities

Caprioli, C., Nazari, I., Milovanovic, S., & Pelicci, P. G. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2021.796477 · Cited by 9

Transcriptional Profiling of CD8+ CMV-Specific T Cell Functional Subsets Obtained Using a Modified Method for Isolating High-Quality RNA From Fixed and Permeabilized Cells

Healy, Z. R., Weinhold, K. J., & Murdoch, D. M. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.01859 · Cited by 9

Integrated Single-Cell (Phospho-)Protein and RNA Detection Uncovers Phenotypic Characteristics and Active Signal Transduction of Human Antibody-Secreting Cells

van Buijtenen, E., Janssen, W., Vink, P. M., Habraken, M., Wingens, L., van Elsas, A., Huck, W. T. S., van Buggenum, J. A. G. L., & van Eenennaam, H. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100492 · Cited by 10

Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development

Pregizer, S. K., Vreven, T., Mathur, M., & Robinson, L. N. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1176856 · Cited by 9

Reverse Phase Protein Arrays in cancer stem cells

Signore, M., & Manganelli, V. (2022) · Methods in cell biology · doi:10.1016/bs.mcb.2022.04.004 · Cited by 8

An Innovative Approach to Tissue Processing and Cell Sorting of Fixed Cells for Subsequent Single-Cell RNA Sequencing

Mutisheva, I., Robatel, S., Bäriswyl, L., & Schenk, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231810233 · Cited by 10

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 10

How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification

Mircea, M., & Semrau, S. (2021) · Biochemical Society Transactions · doi:10.1042/bst20210135 · Cited by 9

Single-cell RNA-Sequencing in Neuroscience

Mayer, S., Khakipoor, S., Droemer, M. A., & Cozetto, D. A. (2019) · e-Neuroforum · doi:10.1515/nf-2019-0021 · Cited by 6

Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARCPreprint

Reimegård, J., Danielsson, M., Tarbier, M., Schuster, J., Baskaran, S., Panagiotou, S., Dahl, N., Friedländer, M. R., & Gallant, C. J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/749473 · Cited by 6

Multiplexed multimodal single-cell technologies: From observation to perturbation analysis

Lee, S.-H., Park, J., & Hwang, B. (2024) · Molecules and Cells · doi:10.1016/j.mocell.2024.100147 · Cited by 4

Single-Cell Transcriptome Sequencing Using Microfluidics

Chen, Y., Jung, S., Choi, Y., & Yoon, E. (2021) · Springer eBooks · doi:10.1007/978-981-10-8953-4_42 · Cited by 4

Applications of Single-Cell Omics Technologies for Induced Pluripotent Stem Cell-Based Cardiovascular Research

Kim, H., Choi, S., Heo, H., Cho, S. H., Lee, Y., Kim, D., Jung, K. O., & Rhee, S. (2024) · International Journal of Stem Cells · doi:10.15283/ijsc23183 · Cited by 3

Single-Cell Transcriptomics and Computational Frameworks for Target Discovery in Cancer

Tarozzi, M. E., Derus, N. R., Polizzi, S., Sala, C., & Castellani, G. (2026) · Targets · doi:10.3390/targets4010006 · Cited by 3

Cell-State-Specific Drug Responses are Associated With Differences in Signaling Network Wiring

Krämer, N., van Eijl, R. A. P. M., Stohn, T., Tanis, S. E. J., Wessels, L. F. A., Bosdriesz, E., & Mulder, K. W. (2026) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2026.101529 · Cited by 3

The role of single-cell sequencing in studying tumour evolution

Mossner, M., Baker, A., & Graham, T. A. (2021) · Faculty Reviews · doi:10.12703/r/10-49 · Cited by 5

Simultaneous Quantification of Single-Cell Proteomes and Transcriptomes in Integrated Fluidic Circuits

Wong, M. H., Kosman, C., Takahashi, L., & Ramalingam, N. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1771-7_15 · Cited by 3

Brain-wide monosynaptic single-neuron connectivity with ROInet-seqPreprint

Lin, Z., Ophir, O., Trimbuch, T., Brokowski, B., Tibi, M., Schmidt, H., Rosenmund, C., Hochgerner, H., & Zeisel, A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.04.588058 · Cited by 3

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

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

Deciphering single-cell protein secretion and gene expressions by constructing cell-antibody conjugates

Li, Y., Li, W., Chen, J., Qiu, S., Liu, Y., Xu, L., Tian, T., & Li, J. P. (2023) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2023.106987 · Cited by 2

Total-mRNA-Aware Analysis for Droplet-Based Single Cell SequencingPreprint

Lian, Q., Ma, J., Hua, K., Rong, Z., Cai, J., Jiang, X., Zhou, J., Xu, J., Zhang, Z., Fan, L., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-2211167/v1 · Cited by 2

Signalling-state dependent drug-tolerance in head and neck squamous cell carcinomaPreprint

Karjosukarso, D. W., Dini, A., Wingens, L., Liu, R., Joosten, L. A. B., Bussink, J., & Mulder, K. W. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.05.570063 · Cited by 2

Stochastic variation in the FOXM1 transcription program mediates replication stress tolerance

Segeren, H. A., Wierenga, K. A., Riemers, F. M., van Liere, E. A., & Westendorp, B. (2025) · Molecular Oncology · doi:10.1002/1878-0261.13819 · Cited by 1

Identification of immunosuppressive neutrophils using multi-omics: why functional testing remains key

van Oosterom, F., Gankema, A. A. F., Rojas-Rodríguez, F., Hoogendijk, A. J., & Kuijpers, T. W. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1814355 · Cited by 1

Understanding developing kidneys and Wilms tumors one cell at a time

Pop, N. S., Dolt, K. S., & Hohenstein, P. (2025) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2024.11.005 · Cited by 1

TIP-seq: A Single-cell Multiomics Approach for Simultaneous Transcriptome and Intracellular Protein ProfilingPreprint

Xue, Y., Qi, J., Xie, G., Wang, M., Xu, W., Ma, C., Xu, X., Yang, Y., He, Y., Guo, Y. L., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.26.653374 · Cited by 1

Single-Cell Transcriptome Sequencing Using Microfluidics

Chen, Y., Jung, S., Choi, Y., & Yoon, E. (2020) · Springer eBooks · doi:10.1007/978-981-10-4857-9_42-1

Single Cell Sequencing, Its Application and Future Challenges

Saleem, M., Alam, S., Kainat, I., Iftikhar, R., & Ijaz, A. (2021) · Current Trends in OMICS · doi:10.32350/cto.11.05

Handbuch der politischen Ikonographie von Uwe Fleckner, Martin Warnke und Hendrik Ziegler (Hg.) München: C.H. Beck Verlag, 2011

Bouwers, E. G. (2011) · PUB – Publications at Bielefeld University (Bielefeld University)

Integrated single-cell (phospho-)protein and RNA detection uncovers phenotypic characteristics of human antibody secreting cellsPreprint

van Buijtenen, E., Janssen, W., Vink, P. M., Habraken, M., Wingens, L. J. A., van Elsas, A., Huck, W. T. S., van Buggenum, J. A. G. L., & van Eenennaam, H. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.31.486501

The effect of intra- and extracellular challenges on cellular responses in atherosclerosis

van Kuijk, K. (2021) · Research Publications (Maastricht University) · doi:10.26481/dis.20210604kk

Single-Cell Technologies: Advances in Single-Cell Migration and Multi-Omics

Moarefian, M., Capossela, A. M., Eom, R., & Aran, K. (2022) · GEN Biotechnology · doi:10.1089/genbio.2022.0014

The current state of methods, models and algorithms for gene regulatory networks validation and simulation

Liakh, I., Durnyak, B., & Babichev, S. A. (2021) · Printing and Publishing · doi:10.32403/0554-4866-2021-2-82-92-103

Tools for Kidney Tissue Analysis

Melk, A. (2023) · Springer eBooks · doi:10.1007/978-3-031-11665-0_5

Assessing the Influence of Selected Permeabilization Methods on Lymphocyte Single-Cell Multi-Omics

Ding, S., Lu, N., & Abolhassani, H. (2025) · Antibodies · doi:10.3390/antib14010015

A Unified Multiplex Digital PCR-based Platform for Multi-class Biomarker Quantification from Low-volume BloodPreprint

Hu, J., Park, J. S., Lei, H., Akarapipad, P., Sun, J., Park, D. J., Cui, W., & Wang, T. (2025) · medRxiv · doi:10.1101/2025.08.31.25334810

Additional file 12 of FixNCut: single-cell genomics through reversible tissue fixation and dissociation

Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699438

Additional file 8 of FixNCut: single-cell genomics through reversible tissue fixation and dissociation

Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699426

Additional file 1 of FixNCut: single-cell genomics through reversible tissue fixation and dissociation

Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25511855

Additional file 14 of FixNCut: single-cell genomics through reversible tissue fixation and dissociation

Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699444

Additional file 5: Figure S4. of 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) · Figshare · doi:10.6084/m9.figshare.c.3617903_d13

Single-cell intracellular epitope and transcript detection reveals signal transduction dynamics

Rivello, F., van Buijtenen, E., Matuła, K., van Buggenum, J. A. G. L., Vink, P. M., van Eenennaam, H., Mulder, K. W., & Huck, W. T. S. (2021) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100070 · Cited by 46

Additional file 7: Figure S6. of 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) · Figshare · doi:10.6084/m9.figshare.4384061

An integrated single-cell multiomics approach to characterize mRNA, intracellular, and surface proteins using intracellular AbSeq and BD® AbSeq Immune Discovery Panel

Song, H.-W., Hatami, E., Vadrevu, S., Martin, J. W., Snowden, E., Zhu, T. Z., Wright, A. T., Nakamoto, M. A., Dillmore, S., & Ayer, A. (2022) · The Journal of Immunology · doi:10.4049/jimmunol.208.supp.173.04

Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARCPreprint

Reimegård, J., Danielsson, M., Tarbier, M., Schuster, J., Baskaran, S., Panagiotou, S., Dahl, N., Friedländer, M. R., & Gallant, C. J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/749473 · Cited by 6