REFERENCES

1. Rai A, Claridge B, Lozano J, Greening DW. The discovery of extracellular vesicles and their emergence as a next-generation therapy. Circ Res. 2024;135:198-221.

2. Su X, Wang H, Li Q, Chen Z. Extracellular vesicles: a review of their therapeutic potentials, sources, biodistribution, and administration routes. Int J Nanomedicine. 2025;20:3175-99.

3. Visnovitz T. Extracellular vesicles: biology and therapeutic applications. Int J Mol Sci. 2024;25:13034.

4. Wang F, Feng J, Jin A, et al. Extracellular vesicles for disease treatment. Int J Nanomedicine. 2025;20:3303-37.

5. Nowak M, Górczyńska J, Kołodzińska K, Rubin J, Choromańska A. Extracellular vesicles as drug transporters. Int J Mol Sci. 2023;24:10267.

6. Moya-Guzmán MJ, de Solminihac J, Padilla C, et al. Extracellular vesicles from immune cells: a biomedical perspective. Int J Mol Sci. 2023;24:13775.

7. Yang C, Xue Y, Duan Y, Mao C, Wan M. Extracellular vesicles and their engineering strategies, delivery systems, and biomedical applications. J Control Release. 2024;365:1089-123.

8. Chen L, Li Q, Nasif KFA, et al. AI-driven deep learning techniques in protein structure prediction. Int J Mol Sci. 2024;25:8426.

9. Cui H, Wang C, Maan H, et al. scGPT: toward building a foundation model for single-cell multi-omics using generative AI. Nat Methods. 2024;21:1470-80.

10. Greenberg ZF, Graim KS, He M. Towards artificial intelligence-enabled extracellular vesicle precision drug delivery. Adv Drug Deliv Rev. 2023;199:114974.

11. Greening DW, Xu R, Rai A, Suwakulsiri W, Chen M, Simpson RJ. Clinical relevance of extracellular vesicles in cancer - therapeutic and diagnostic potential. Nat Rev Clin Oncol. 2025;22:924-52.

12. Bunne C, Roohani Y, Rosen Y, et al. How to build the virtual cell with artificial intelligence: Priorities and opportunities. Cell. 2024;187:7045-63.

13. Jiang H, Huang X, Bi X, et al. Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunities. Brief Bioinform. 2026;27:bbag104.

14. Wu J, Song D, Li Z, et al. Immunity-and-matrix-regulatory cells derived from human embryonic stem cells safely and effectively treat mouse lung injury and fibrosis. Cell Res. 2020;30:794-809.

15. Su Y, He Z, Wang K, et al. Immunity-and-matrix-regulatory cells promote hyaline-like cartilage repair in osteoarthritis. Bioact Mater. 2026;65:905-23.

16. Laubenbacher R, Mehrad B, Shmulevich I, Trayanova N. Digital twins in medicine. Nat Comput Sci. 2024;4:184-91.

17. Aliper A, Kudrin R, Polykovskiy D, et al. Prediction of clinical trials outcomes based on target choice and clinical trial design with multi-modal artificial intelligence. Clin Pharmacol Ther. 2023;114:972-80.

18. Chou WC, Lin Z. Machine learning and artificial intelligence in physiologically based pharmacokinetic modeling. Toxicol Sci. 2023;191:1-14.

19. Dudas B, Miteva MA. Computational and artificial intelligence-based approaches for drug metabolism and transport prediction. Trends Pharmacol Sci. 2024;45:39-55.

20. Kale M, Wankhede N, Pawar R, et al. AI-driven innovations in Alzheimer’s disease: Integrating early diagnosis, personalized treatment, and prognostic modelling. Ageing Res Rev. 2024;101:102497.

21. Kumar H, Kim P. Artificial intelligence in fusion protein three-dimensional structure prediction: review and perspective. Clin Transl Med. 2024;14:e1789.

22. Lu H, Zhang J, Shen T, Jiang W, Liu H, Su J. Harnessing artificial intelligence for engineering extracellular vesicles. Extracell Vesicles Circ Nucl Acids. 2025;6:522-46.

23. Liu H, Li S, Wang J, Su J. Artificial intelligence virtual extracellular vesicles (AIVEVs). Bioact Mater. 2026;61:34-55.

24. Hu M, Han Y, Zhang X, et al. Extracellular vesicles for targeted drug delivery: advances in surface modification strategies and therapeutic applications. J Transl Med. 2025;23:1028.

25. Rapp JT, Bremer BJ, Romero PA. Self-driving laboratories to autonomously navigate the protein fitness landscape. Nat Chem Eng. 2024;1:97-107.

26. Welsh JA, Goberdhan DCI, O’Driscoll L, et al. ; MISEV Consortium. Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches. J Extracell Vesicles. 2024;13:e12404.

27. Cheng CA. Before translating extracellular vesicles into personalized diagnostics and therapeutics: what we could do. Mol Pharm. 2024;21:2625-36.

28. Lotfollahi M, Klimovskaia Susmelj A, De Donno C, et al. Predicting cellular responses to complex perturbations in high-throughput screens. Mol Syst Biol. 2023;19:e11517.

29. Miceli RT, Chen TY, Nose Y, et al. Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations. J Extracell Vesicles. 2024;13:e70005.

30. Zhang O, Lin H, Zhang X, et al. Graph neural networks in modern AI-aided drug discovery. Chem Rev. 2025;125:10001-103.

31. Kim J, Hwang YH, Nam GH, Kim IS. Breaking barriers: engineering extracellular vesicles for enhanced endosomal escape and therapeutic delivery. J Control Release. 2026;389:114462.

32. Watson JL, Juergens D, Bennett NR, et al. De novo design of protein structure and function with RFdiffusion. Nature. 2023;620:1089-100.

33. Bergqvist M, Park KS, Karimi N, Yu L, Lässer C, Lötvall J. Extracellular vesicle surface engineering with integrins (ITGAL & ITGB2) to specifically target ICAM-1-expressing endothelial cells. J Nanobiotechnology. 2025;23:64.

34. Hao D, Lu L, Song H, et al. Engineered extracellular vesicles with high collagen-binding affinity present superior in situ retention and therapeutic efficacy in tissue repair. Theranostics. 2022;12:6021-37.

35. Rädler J, Gupta D, Zickler A, Andaloussi SE. Exploiting the biogenesis of extracellular vesicles for bioengineering and therapeutic cargo loading. Mol Ther. 2023;31:1231-50.

36. Villarroya-Beltri C, Gutiérrez-Vázquez C, Sánchez-Cabo F, et al. Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs. Nat Commun. 2013;4:2980.

37. Shurtleff MJ, Temoche-Diaz MM, Karfilis KV, Ri S, Schekman R. Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction. Elife. 2016;5:e19276.

38. Mekki YM, Luijten G, Hagert E, et al. Digital twins for the era of personalized surgery. NPJ Digit Med. 2025;8:283.

39. Sverchkov Y, Craven M. A review of active learning approaches to experimental design for uncovering biological networks. PLoS Comput Biol. 2017;13:e1005466.

40. Sun C, Teng F, Xia Y. Extracellular vesicles in osteoarthritis: mechanisms, therapeutic potential, and diagnostic applications. Front Immunol. 2025;16:1595095.

41. Xia W, Tan Y, Liu Y, Xie N, Zhu H. Prospect of extracellular vesicles in tumor immunotherapy. Front Immunol. 2025;16:1525052.

42. Liao Z, Tong B, Ke W, Yang C, Wu X, Lei M. Extracellular vesicles as carriers for mitochondria: biological functions and clinical applications. Mitochondrion. 2024;78:101935.

43. Li J, Wen T, Li X, et al. Harnessing extracellular vesicles to tame inflammation: a new strategy for atherosclerosis therapy. Front Immunol. 2025;16:1625958.

44. Ai X, Yu H, Cai Y, Guan Y. Interactions between extracellular vesicles and autophagy in neuroimmune disorders. Neurosci Bull. 2024;40:992-1006.

45. Habibi A, Zarei-Behjani Z, Falamarzi K, et al. Extracellular vesicles as a new horizon in the diagnosis and treatment of inflammatory eye diseases: a narrative review of the literature. Front Immunol. 2023;14:1097456.

46. Mazahir F, Yadav AK. Recent progress in engineered extracellular vesicles and their biomedical applications. Life Sci. 2024;350:122747.

47. Richter M, Vader P, Fuhrmann G. Approaches to surface engineering of extracellular vesicles. Adv Drug Deliv Rev. 2021;173:416-26.

48. Jia Y, Yu L, Ma T, et al. Small extracellular vesicles isolation and separation: current techniques, pending questions and clinical applications. Theranostics. 2022;12:6548-75.

49. Dave KM, Pinky PP, Manickam DS. Molecular engineering of extracellular vesicles for drug delivery: Strategies, challenges, and perspectives. J Control Release. 2025;386:114068.

50. Li X, Yuan H, Wu X, et al. MultiDS-MDA: integrating multiple data sources into heterogeneous network for predicting novel metabolite-drug associations. Comput Biol Med. 2023;162:107067.

51. Yang B, Meng T, Wang X, et al. CAT Bridge: an efficient toolkit for gene-metabolite association mining from multiomics data. Gigascience. 2024;13:giae083.

52. Veličković P. Everything is connected: graph neural networks. Curr Opin Struct Biol. 2023;79:102538.

53. Jiang X, Tan L, Zou Q. DGCL: dual-graph neural networks contrastive learning for molecular property prediction. Brief Bioinform. 2024;25:bbae474.

54. Gu S, Jiang M, Guzzi PH, Milenković T. Modeling multi-scale data via a network of networks. Bioinformatics. 2022;38:2544-53.

55. Recanatini M, Menestrina L. Network modeling helps to tackle the complexity of drug-disease systems. WIREs Mech Dis. 2023;15:e1607.

56. Dixson AC, Dawson TR, Di Vizio D, Weaver AM. Context-specific regulation of extracellular vesicle biogenesis and cargo selection. Nat Rev Mol Cell Biol. 2023;24:454-76.

57. Ripoll L, Zickler AM, Vader P, El Andaloussi S, Verweij FJ, van Niel G. Biology and therapeutic potential of extracellular vesicle targeting and uptake. Nat Rev Mol Cell Biol. 2026;27:358-76.

58. Ngo JM, Williams JK, Zhang C, et al. Extracellular vesicles and cellular homeostasis. Annu Rev Biochem. 2025;94:587-609.

59. Xing Y, Sun X, Dou Y, et al. The immuno-modulation effect of macrophage-derived extracellular vesicles in chronic inflammatory diseases. Front Immunol. 2021;12:785728.

60. You DG, Lim GT, Kwon S, et al. Metabolically engineered stem cell-derived exosomes to regulate macrophage heterogeneity in rheumatoid arthritis. Sci Adv. 2021;7:eabe0083.

61. Zhang J, Song H, Dong Y, et al. Surface engineering of HEK293 cell-derived extracellular vesicles for improved pharmacokinetic profile and targeted delivery of IL-12 for the treatment of hepatocellular carcinoma. Int J Nanomedicine. 2023;18:209-23.

62. Sui J, Qin H, Zhang Z, et al. Engineering extracellular vesicles for tumor targeted therapy: source optimization, modification, and clinical application. Int J Nanomedicine. 2026;21:592579.

63. Yang S, Ge S, Liu Z, et al. Exosome-enabled bone defect repair: mechanistic foundations, bioengineered delivery, and artificial intelligence-driven translation. J Nanobiotechnology. 2026;24:320.

64. Fischer RP, Volpert A, Antonino P, Ahrens TD. Digital patient twins for personalized therapeutics and pharmaceutical manufacturing. Front Digit Health. 2023;5:1302338.

65. Corrado C, Fontana S. Exosomes/extracellular vesicles and targeted tumor immunotherapy. Int J Mol Sci. 2024;25:5458.

66. Liu Y, Zhang Z, Wang B, et al. Inflammation-stimulated MSC-derived small extracellular vesicle miR-27b-3p regulates macrophages by targeting CSF-1 to promote temporomandibular joint condylar regeneration. Small. 2022;18:e2107354.

67. Fu M, Gao Q, Xiao M, et al. Extracellular vesicles containing circMYBL1 induce CD44 in adenoid cystic carcinoma cells and pulmonary endothelial cells to promote lung metastasis. Cancer Res. 2024;84:2484-500.

68. Yang M, Guo J, Li J, et al. Platycodon grandiflorum-derived extracellular vesicles suppress triple-negative breast cancer growth by reversing the immunosuppressive tumor microenvironment and modulating the gut microbiota. J Nanobiotechnology. 2025;23:92.

69. Eguchi T, Sheta M, Fujii M, Calderwood SK. Cancer extracellular vesicles, tumoroid models, and tumor microenvironment. Semin Cancer Biol. 2022;86:112-26.

70. Belényesi SK, Patmore S, O’Driscoll L. Extracellular vesicles and the tumour microenvironment. Biochim Biophys Acta Rev Cancer. 2025;1880:189275.

71. Tiwari A, Widodo, Krisnawati DI, Tzou KY, Kuo TR. Machine learning for extracellular vesicles enables diagnostic and therapeutic nanobiotechnology. J Nanobiotechnology. 2026;24:153.

72. Budhkar A, Song Q, Su J, Zhang X. Demystifying the black box: a survey on explainable artificial intelligence (XAI) in bioinformatics. Comput Struct Biotechnol J. 2025;27:346-59.

73. Thakur A, Rai D. Global requirements for manufacturing and validation of clinical grade extracellular vesicles. J Liq Biopsy. 2024;6:100278.

74. Wang CK, Tsai TH, Lee CH. Regulation of exosomes as biologic medicines: Regulatory challenges faced in exosome development and manufacturing processes. Clin Transl Sci. 2024;17:e13904.

75. Warraich HJ, Tazbaz T, Califf RM. FDA perspective on the regulation of artificial intelligence in health care and biomedicine. JAMA. 2025;333:241-7.

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