[2512.03497] Cell-cell Communication Inference and Analysis: Biological Mechanisms, Computational Approaches, and Future Opportunities

Quantitative Biology > Quantitative Methods arXiv:2512.03497 (q-bio) [Submitted on 3 Dec 2025 (v1), last revised 21 Mar 2026 (this version, v3)] Title:Cell-cell Communication Inference and Analysis: Biological Mechanisms, Computational Approaches, and Future Opportunities Authors:Xiangzheng Cheng, Haili Huang, Ye Su, Qing Nie, Xiufen Zou, Suoqin Jin View a PDF of the paper titled Cell-cell Communication Inference and Analysis: Biological Mechanisms, Computational Approaches, and Future Opportunities, by Xiangzheng Cheng and 5 other authors View PDF HTML (experimental) Abstract:In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics technologies provide unprecedented opportunities to systematically infer and analyze CCC from these omics data, either by integrating prior knowledge of ligand-receptor interactions (LRIs) or through de novo approaches. A variety of computational methods have been developed, focusing on methodological innovations, accurate modeling of complex signaling mechanisms, and investigation of broader biological questions. These advances have greatly enhanced our ability to analyze CCC and generate biological hypotheses. Here, we introduce the biological mechanisms and modeling strategies of CCC, and provide a focused overview of more than 140 computational methods for inferring CCC f...