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