Shao, X., Lu, X., Liao, J., Chen, H. & Fan, X. New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data. Protein Cell 11, 866–880 (2020).Article
PubMed
PubMed Central
CAS
Google Scholar
Armingol, E., Officer, A., Harismendy, O. & Lewis, N. E. Deciphering cell–cell interactions and communication from gene expression. Nat. Rev. Genet. 22, 71–88 (2021).Article
PubMed
CAS
Google Scholar
Almet, A. A., Cang, Z., Jin, S. & Nie, Q. The landscape of cell–cell communication through single-cell transcriptomics. Curr. Opin. Syst. Biol. 26, 12–23 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Armingol, E., Baghdassarian, H. M. & Lewis, N. E. The diversification of methods for studying cell-cell interactions and communication. Nat. Rev. Genet. 25, 381–400 (2024).Article
PubMed
CAS
Google Scholar
Jin, S. et al. Inference and analysis of cell–cell communication using CellChat. Nat. Commun. 12, 1088 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Kanemaru, K. et al. Spatially resolved multiomics of human cardiac niches. Nature 619, 801–810 (2023).Article
PubMed
PubMed Central
CAS
Google Scholar
Zhao, W., Johnston, K. G., Ren, H., Xu, X. & Nie, Q. Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nat. Commun. 14, 1128 (2023).Article
PubMed
PubMed Central
CAS
Google Scholar
Vu, R. et al. Wound healing in aged skin exhibits systems-level alterations in cellular composition and cell–cell communication. Cell Rep. 40, 111155 (2022).Article
PubMed
PubMed Central
CAS
Google Scholar
Hao, M., Zou, X. & Jin, S. Identification of intercellular signaling changes across conditions and their influence on intracellular signaling response from multiple single-cell datasets. Front. Genet. 12, 751158 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Dimitrov, D. et al. Comparison of methods and resources for cell–cell communication inference from single-cell RNA-Seq data. Nat. Commun. 13, 3224 (2022).Article
PubMed
PubMed Central
Google Scholar
Liu, Z., Sun, D. & Wang, C. Evaluation of cell–cell interaction methods by integrating single-cell RNA sequencing data with spatial information. Genome Biol. 23, 218 (2022).Article
PubMed
PubMed Central
Google Scholar
Efremova, M., Vento-Tormo, M., Teichmann, S. A. & Vento-Tormo, R. CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand–receptor complexes. Nat. Protoc. 15, 1484–1506 (2020).Article
PubMed
CAS
Google Scholar
Garcia-Alonso, L. et al. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nat. Genet. 53, 1698–1711 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Hou, R., Denisenko, E., Ong, H. T., Ramilowski, J. A. & Forrest, A. R. R. Predicting cell-to-cell communication networks using NATMI. Nat. Commun. 11, 5011 (2020).Article
PubMed
PubMed Central
CAS
Google Scholar
Noel, F. et al. Dissection of intercellular communication using the transcriptome-based framework ICELLNET. Nat. Commun. 12, 1089 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Raredon, M. S. B. et al. Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome. Sci. Rep. 12, 4187 (2022).Article
PubMed
PubMed Central
CAS
Google Scholar
Armingol, E. et al. Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. Nat. Commun. 13, 3665 (2022).Article
PubMed
PubMed Central
CAS
Google Scholar
Luo, J., Deng, M., Zhang, X. & Sun, X. ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods. Genome Res. 33, 1788–1805 (2023).Article
PubMed
PubMed Central
Google Scholar
Vento-Tormo, R. et al. Single-cell reconstruction of the early maternal-fetal interface in humans. Nature 563, 347–353 (2018).Article
PubMed
PubMed Central
CAS
Google Scholar
Garcia-Alonso, L. et al. Single-cell roadmap of human gonadal development. Nature 607, 540–547 (2022).Article
PubMed
PubMed Central
CAS
Google Scholar
Browaeys, R. et al. MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data. Preprint at bioRxiv https://doi.org/10.1101/2023.06.13.544751 (2023).Jin, S. & Ramos, R. Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data. Biochem. Soc. Trans. 50, 297–308 (2022).Article
PubMed
PubMed Central
CAS
Google Scholar
Yang, A. C. et al. Dysregulation of brain and choroid plexus cell types in severe COVID-19. Nature 595, 565–571 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Wendisch, D. et al. SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis. Cell 184, 6243–6261 e6227 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Winkler, E. A. et al. A single-cell atlas of the normal and malformed human brain vasculature. Science 375, eabi7377 (2022).Article
PubMed
PubMed Central
CAS
Google Scholar
Lake, B. B. et al. An atlas of healthy and injured cell states and niches in the human kidney. Nature 619, 585–594 (2023).Article
PubMed
PubMed Central
CAS
Google Scholar
Cheng, Y. T. et al. Inhibitory input directs astrocyte morphogenesis through glial GABA(B)R. Nature 617, 369–376 (2023).Article
PubMed
PubMed Central
CAS
Google Scholar
Ortiz-Munoz, G. et al. In situ tumour arrays reveal early environmental control of cancer immunity. Nature 618, 827–833 (2023).Article
PubMed
PubMed Central
CAS
Google Scholar
Li, J. et al. Remodeling of the immune and stromal cell compartment by PD-1 blockade in mismatch repair-deficient colorectal cancer. Cancer Cell 41, 1152–1169 e1157 (2023).Article
PubMed
CAS
Google Scholar
Longo, S. K., Guo, M. G., Ji, A. L. & Khavari, P. A. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nat. Rev. Genet. 22, 627–644 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Wang, X., Almet, A. A. & Nie, Q. The promising application of cell-cell interaction analysis in cancer From single-cell and spatial transcriptomics. Semin. Cancer Biol., (2023).Perkel, J. M. Single-cell proteomics takes centre stage. Nature 597, 580–582 (2021).Article
PubMed
CAS
Google Scholar
Jin, S., Zhang, L. & Nie, Q. scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles. Genome Biol. 21, 25 (2020).Article
PubMed
PubMed Central
Google Scholar
Zhang, L., Zhang, J. & Nie, Q. DIRECT-NET: an efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data. Sci. Adv. 8, eabl7393 (2022).Article
PubMed
PubMed Central
CAS
Google Scholar
Troulé, K. et al. CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data. Preprint at https://doi.org/10.48550/arXiv.2311.04567 (2023).Cang, Z. & Nie, Q. Inferring spatial and signaling relationships between cells from single cell transcriptomic data. Nat. Commun. 11, 2084 (2020).Article
PubMed
PubMed Central
CAS
Google Scholar
Shao, X. et al. Knowledge-graph-based cell–cell communication inference for spatially resolved transcriptomic data with SpaTalk. Nat. Commun. 13, 4429 (2022).Article
PubMed
PubMed Central
CAS
Google Scholar
Cang, Z. et al. Screening cell–cell communication in spatial transcriptomics via collective optimal transport. Nat. Methods 20, 218–228 (2023).Article
PubMed
PubMed Central
CAS
Google Scholar
Li, H. et al. Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics. Brief. Bioinform. 24, bbad359 (2023).Article
PubMed
Google Scholar
Wang, S., Karikomi, M., MacLean, A. L. & Nie, Q. Cell lineage and communication network inference via optimization for single-cell transcriptomics. Nucleic Acids Res. 47, e66 (2019).Article
PubMed
PubMed Central
CAS
Google Scholar
Browaeys, R., Saelens, W. & Saeys, Y. NicheNet: modeling intercellular communication by linking ligands to target genes. Nat. Methods 17, 159–162 (2020).Article
PubMed
CAS
Google Scholar
Hu, Y., Peng, T., Gao, L. & Tan, K. CytoTalk: de novo construction of signal transduction networks using single-cell transcriptomic data. Sci. Adv. 7, eabf1356 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang, Y. et al. CellCall: integrating paired ligand–receptor and transcription factor activities for cell-cell communication. Nucleic Acids Res. 49, 8520–8534 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Cheng, J., Zhang, J., Wu, Z. & Sun, X. Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19. Brief. Bioinform. 22, 988–1005 (2021).Article
PubMed
CAS
Google Scholar
Landherr, A., Friedl, B. & Heidemann, J. A critical review of centrality measures in social networks. Bus. Inform. Syst. Eng. 2, 371–385 (2010).Article
Google Scholar
He, H. et al. Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis. J. Allergy Clin. Immunol. 145, 1615–1628 (2020).Article
PubMed
CAS
Google Scholar
Gupta, K. et al. Single-cell analysis reveals a hair follicle dermal niche molecular differentiation trajectory that begins prior to morphogenesis. Dev. Cell 48, 17–31 e16 (2019).Article
PubMed
CAS
Google Scholar
Reynolds, G. et al. Developmental cell programs are co-opted in inflammatory skin disease. Science 371, eaba6500 (2021).Article
PubMed
PubMed Central
CAS
Google Scholar
Jin, S. Datasets and CellChat objects for running cell-cell communication analysis using CellChat. Figshare https://figshare.com/projects/Example_data_for_cell-cell_communication_analysis_using_CellChat/157272 (2023).Shao, X. et al. CellTalkDB: a manually curated database of ligand–receptor interactions in humans and mice. Brief. Bioinform. 22, bbaa269 (2021).Article
PubMed
Google Scholar