Published papers

Research articles | Reviews | Comments
• Shao X#*, Yu L#, Li C, Qian J, Yang X, Yang H, Liao J, Fan, X, Xu X*, Fan X*. Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data with miRTalk. Genome Biol. 2025 April 14;26:95. doi: 10.1186/s13059-025-03566-x.
• Qian J#, Shao X#*, Bao H#, Fang Y, Guo W, Li C, Li A, Hua H*, Fan X*. Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution. Nat Commun (Editor Highlights). 2025 Feb 16;16(1):1693. doi: 10.1038/s41467-025-57029-9.
• Dai Y#, Shao X#*, Zhang J#, Chen Y, Chen Q, Liao J, Chi F, Zhang J*, Fan X*. TCMChat: A generative large language model for traditional Chinese medicine. Pharmacol Res. 2024 Dec;210:107530. doi: 10.1016/j.phrs.2024.107530.
• Sun F#, Li H#, Sun D#, Fu S#, Gu L#, Shao X#, Wang Q#, Dong X#, Duan B#, Xing F#, Wu J#, Xiao M*, Zhao F*, Han JJ*, Liu Q*, Fan X*, Li C*, Wang C*, Shi T*. Single-cell omics: experimental workflow, data analyses and applications. Sci China Life Sci (Cover). 2025 Jan;68(1):5-102. doi: 10.1007/s11427-023-2561-0.
• Li C#, Shao X#*, Zhang S, Wang Y, Jin K, Yang P, Lu X, Fan X*, Wang Y*. scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network. Cell Rep Med. 2024 Jun 18;5(6):101568. doi: 10.1016/j.xcrm.2024.101568.
• Shao X#, Wang Z#, Wang K#, Lu X#, Zhang P, Guo R, Liao J, Yang P, Zheng S, Xu X*, Fan X*. A Single-Cell Landscape of Human Liver Transplantation Reveals a Pathogenic Immune Niche Associated with Early Allograft Dysfunction. Engineering. 2024 May;36:193-208. doi: 10.1016/j.eng.2023.12.004.
• Shao X#, Li C#, Yang H#, Lu X, Liao J, Qian J, Wang K, Cheng J, Yang P, Chen H*, Xu X*, Fan X*. Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk. Nat Commun (Editor Highlights). 2022 Jul 30;13(1):4429. doi: 10.1038/s41467-022-32111-8.
• Shao X#, Yang H#, Zhuang X, Liao J, Yang P, Cheng J, Lu X, Chen H*, Fan X*. scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network. Nucleic Acids Res. 2021 Dec 2;49(21):e122. doi: 10.1093/nar/gkab775.
• Shao X#, Liao J#, Li C#, Lu X, Cheng J, Fan X*. CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice. Brief Bioinform (ESI highly cited paper). 2021 Jul 20;22(4):bbaa269. doi: 10.1093/bib/bbaa269.
• 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. 2020 Dec;11(12):866-880. doi: 10.1007/s13238-020-00727-5.
• Shao X#, Wang Y#, Lu X#, Hu Y, Liao J, Li J, Chen X, Yu Y, Ai N, Ying M, Fan X*. A Clinical Genomics-Guided Prioritizing Strategy Enables Selecting Proper Cancer Cell Lines for Biomedical Research. iScience. 2020 Oct 28;23(11):101748. doi: 10.1016/j.isci.2020.101748.
• Shao X, Liao J, Lu X, Xue R, Ai N, Fan X*. scCATCH: Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data. iScience. 2020 Mar 27;23(3):100882. doi: 10.1016/j.isci.2020.100882.
• Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D*, Fan X*. Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC Med Genet. 2019 Nov 9;20(1):175. doi: 10.1186/s12881-019-0909-5.
• Shao X, Ai N*, Xu D*, Fan X. Exploring the interaction between Salvia miltiorrhiza and human serum albumin: Insights from herb-drug interaction reports, computational analysis and experimental studies. Spectrochim Acta A Mol Biomol Spectrosc. 2016 May 15;161:1-7. doi: 10.1016/j.saa.2016.02.015.