Mittelbrunn M, Sánchez-Madrid F. Intercellular communication: diverse structures for exchange of genetic information. Nat Rev Mol Cell Biol. 2012;13(5):328–35.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Scadden DT. Nice neighborhood: emerging concepts of the stem cell niche. Cell. 2014;157(1):41–50.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Douam F, Gaska JM, Winer BY, Ding Q, Schaewen MV, Ploss A. Genetic dissection of the host tropism of human-tropic pathogens. Annu Rev Genet. 2015;49(1):21–45.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li Y, Wang C, Miao Z, Bi X, Wu D, Jin N, Wang L, Wu H, Qian K, Li C, Zhang T, Zhang C, Yi Y, Lai H, Hu Y, Cheng L, Leung KS, Li X, Zhang F, Li K, Li X, Wang D. ViRBase: a resource for virus-host ncRNA-associated interactions. Nucleic Acids Res. 2015;43(Database issue):D578–82.

Article  CAS  PubMed  Google Scholar 

Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res. 2020;30(6):492–506.

Article  PubMed  PubMed Central  Google Scholar 

Hantak MP, Einstein J, Kearns RB, Shepherd JD. Intercellular communication in the nervous system goes viral. Trends Neurosci. 2021;44(4):248–59.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sonnen KF, Janda CY. Signalling dynamics in embryonic development. Biochem J. 2021;478(23):4045–70.

Article  CAS  PubMed  Google Scholar 

Massagué J, Obenauf AC. Metastatic colonization by circulating tumour cells. Nature. 2016;529(7586):298–306.

Article  PubMed  PubMed Central  Google Scholar 

Ning L, Cui T, Zheng B, Wang N, Luo J, Yang B, et al. MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation. Nucleic Acids Res. 2021;49(D1):D160–D4.

Polyakova N, Kalashnikova M, Belyavsky A. Non-classical intercellular communications: basic mechanisms and roles in biology and medicine. Int J Mol Sci. 2023;24(7):6455.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park J-E, Stephenson E, Polański K, Goncalves A, Gardner L, Holmqvist S, Henriksson J, Zou A, Sharkey AM, Millar B, Innes B, Wood L, Wilbrey-Clark A, Payne RP, Ivarsson MA, Lisgo S, Filby A, Rowitch DH, Bulmer JN, Wright GJ, Stubbington MJT, Haniffa M, Moffett A, Teichmann SA. Single-cell reconstruction of the early maternal–fetal interface in humans. Nature. 2018;563(7731):347–53.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang Q, He Y, Luo N, Patel SJ, Han Y, Gao R, Modak M, Carotta S, Haslinger C, Kind D, Peet GW, Zhong G, Lu S, Zhu W, Mao Y, Xiao M, Bergmann M, Hu X, Kerkar SP, Vogt AB, Pflanz S, Liu K, Peng J, Ren X, Zhang Z. Landscape and dynamics of single immune cells in hepatocellular carcinoma. Cell. 2019;179(4):829–45.e20.

Article  CAS  PubMed  Google Scholar 

Popescu D-M, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park J-E, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani A-C, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M. Decoding human fetal liver haematopoiesis. Nature. 2019;574(7778):365–71.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang M, Liu X, Chang G, Chen Y, An G, Yan L, Gao S, Xu Y, Cui Y, Dong J, Chen Y, Fan X, Hu Y, Song K, Zhu X, Gao Y, Yao Z, Bian S, Hou Y, Lu J, Wang R, Fan Y, Lian Y, Tang W, Wang Y, Liu J, Zhao L, Wang L, Liu Z, Yuan R, Shi Y, Hu B, Ren X, Tang F, Zhao XY, Qiao J. Single-cell RNA sequencing analysis reveals sequential cell fate transition during human spermatogenesis. Cell Stem Cell. 2018;23(4):599–614.e4.

Article  CAS  PubMed  Google Scholar 

Sharma A, Seow JJW, Dutertre C-A, Pai R, Blériot C, Mishra A, Wong RMM, Singh GSN, Sudhagar S, Khalilnezhad S, Erdal S, Teo HM, Khalilnezhad A, Chakarov S, Lim TKH, Fui ACY, Chieh AKW, Chung CP, Bonney GK, Poh BGK, Chan JKY, Chow PKH, Ginhoux F, DasGupta R. Onco-fetal reprogramming of endothelial cells drives immunosuppressive macrophages in hepatocellular carcinoma. Cell. 2020;183(2):377–394.e21.

Article  CAS  PubMed  Google Scholar 

Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan C-H, Myung P, Plikus MV, Nie Q. Inference and analysis of cell-cell communication using Cell Chat. Nat Commun. 2021;12(1):1088.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Efremova M, Vento-Tormo M, Teichmann SA, Vento-Tormo R. Cell PhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes. Nat Protoc. 2020;15(4):1484–506.

Article  CAS  PubMed  Google Scholar 

Cabello-Aguilar S, Alame M, Kon-Sun-Tack F, Fau C, Lacroix M, Colinge J. SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics. Nucleic Acids Res. 2020;48(10):e55.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hou R, Denisenko E, Ong HT, Ramilowski JA, Forrest ARR. Predicting cell-to-cell communication networks using NATMI. Nat Commun. 2020;11(1):5011.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Noël F, Massenet-Regad L, Carmi-Levy I, Cappuccio A, Grandclaudon M, Trichot C, Kieffer Y, Mechta-Grigoriou F, Soumelis V. Dissection of intercellular communication using the transcriptome-based framework ICELLNET. Nat Commun. 2021;12(1):1089.

Article  PubMed  PubMed Central  Google Scholar 

Zhang Y, Liu T, Hu X, Wang M, Wang J, Zou B, Tan P, Cui T, Dou Y, Ning L, Huang Y, Rao S, Wang D, Zhao X. CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication. Nucleic Acids Res. 2021;49(15):8520–34.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choi H, Sheng J, Gao D, Li F, Durrans A, Ryu S, Lee SB, Narula N, Rafii S, Elemento O, Altorki NK, Wong ST, Mittal V. Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model. Cell Rep. 2015;10(7):1187–201.

Article  CAS  PubMed  Google Scholar 

Browaeys R, Saelens W, Saeys Y. NicheNet: modeling intercellular communication by linking ligands to target genes. Nat Methods. 2020;17(2):159–62.

Article  CAS  PubMed  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. 2021;7(16):eabf1356.

Article  CAS  PubMed  PubMed Central  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. 2021;22(2):988–1005.

Article  CAS  PubMed  Google Scholar 

Armingol E, Ghaddar A, Joshi CJ, Baghdassarian H, Shamie I, Chan J, Her HL, Berhanu S, Dar A, Rodriguez-Armstrong F, Yang O, O’Rourke EJ, Lewis NE. Inferring a spatial code of cell-cell interactions across a whole animal body. PLoS Comput Biol. 2022;18(11):e1010715.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cang Z, Nie Q. Inferring spatial and signaling relationships between cells from single cell transcriptomic data. Nat Commun. 2020;11(1):2084.

Article  CAS  PubMed