{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T19:08:38Z","timestamp":1791832118942,"version":"4.3.4"},"reference-count":247,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,7,29]],"date-time":"2025-07-29T00:00:00Z","timestamp":1753747200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100021207","name":"Bronx Council on the Arts","doi-asserted-by":"publisher","award":["42,43,160"],"award-info":[{"award-number":["42,43,160"]}],"id":[{"id":"10.13039\/100021207","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100021207","name":"Bronx Council on the Arts","doi-asserted-by":"publisher","award":["117,207"],"award-info":[{"award-number":["117,207"]}],"id":[{"id":"10.13039\/100021207","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021171","name":"Basic and Applied Basic Research Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2022A1515110379"],"award-info":[{"award-number":["2022A1515110379"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021171","name":"Basic and Applied Basic Research Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2022A1515111092"],"award-info":[{"award-number":["2022A1515111092"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002402","name":"Sun Yat-sen University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002402","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82301134"],"award-info":[{"award-number":["82301134"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Bioactive Materials"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1016\/j.bioactmat.2025.07.047","type":"journal-article","created":{"date-parts":[[2025,8,8]],"date-time":"2025-08-08T21:02:36Z","timestamp":1754686956000},"page":"1-33","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":10,"special_numbering":"C","title":["Biomaterial-mediated Cell Atlas: an insight from single-cell and spatial transcriptomics"],"prefix":"10.1016","volume":"54","author":[{"given":"Xiaokun","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingshu","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingtao","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8600-9206","authenticated-orcid":false,"given":"Jiahao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiannan","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0782-6713","authenticated-orcid":false,"given":"Ping","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.bioactmat.2025.07.047_bib1","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1038\/s41578-022-00426-z","article-title":"Design of therapeutic biomaterials to control inflammation","volume":"7","author":"Tu","year":"2022","journal-title":"Nat. Rev. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib2","doi-asserted-by":"crossref","DOI":"10.1093\/rb\/rbac098","article-title":"Recent advances in regenerative biomaterials","volume":"9","author":"Cao","year":"2022","journal-title":"Regen. Biomater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib3","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/s41578-020-0209-x","article-title":"Engineered biomaterials for in situ tissue regeneration","volume":"5","author":"Gaharwar","year":"2020","journal-title":"Nat. Rev. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib4","article-title":"Piezoelectric biomaterials inspired by nature for applications in biomedicine and nanotechnology","volume":"36","author":"Chen","year":"2024","journal-title":"Adv. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib5","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1038\/s41578-020-0204-2","article-title":"Materials design for bone-tissue engineering","volume":"5","author":"Koons","year":"2020","journal-title":"Nat. Rev. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib6","article-title":"Beyond tissue replacement: the emerging role of smart implants in healthcare","volume":"22","author":"Abyzova","year":"2023","journal-title":"Mater. Today Bio"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib7","doi-asserted-by":"crossref","DOI":"10.1002\/adhm.202202766","article-title":"Bone tissue engineering scaffolds: function of multi-material hierarchically structured scaffolds","volume":"12","author":"Koushik","year":"2023","journal-title":"Adv. Healthc. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib8","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.biomaterials.2018.03.020","article-title":"Understanding interactions between biomaterials and biological systems using proteomics","volume":"167","author":"Othman","year":"2018","journal-title":"Biomaterials"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib9","series-title":"Advanced Polymers in Medicine","first-page":"91","article-title":"Overview on cell-biomaterial interactions","author":"Gon\u00e7alves","year":"2015"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib10","series-title":"Biomaterials and Tissue Engineering","first-page":"239","article-title":"Cell-materials interaction","author":"Buitrago","year":"2023"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.actbio.2022.02.027","article-title":"Biomaterialomics: data science-driven pathways to develop fourth-generation biomaterials","volume":"143","author":"Basu","year":"2022","journal-title":"Acta Biomater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib12","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.mattod.2023.01.018","article-title":"Omics-based approaches to guide the design of biomaterials","volume":"64","author":"Kersey","year":"2023","journal-title":"Mater. Today"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib13","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1038\/s41581-021-00463-x","article-title":"Multi-omics integration in the age of million single-cell data","volume":"17","author":"Miao","year":"2021","journal-title":"Nat. Rev. Nephrol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib14","doi-asserted-by":"crossref","first-page":"1430","DOI":"10.1038\/s41592-024-02353-z","article-title":"Transformers in single-cell omics: a review and new perspectives","volume":"21","author":"Sza\u0142ata","year":"2024","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib15","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/s41580-023-00615-w","article-title":"The technological landscape and applications of single-cell multi-omics","volume":"24","author":"Baysoy","year":"2023","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib16","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/s41580-024-00756-6","article-title":"Harnessing the deep learning power of foundation models in single-cell omics","volume":"25","author":"Ma","year":"2024","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib17","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/s44222-023-00132-7","article-title":"Single-cell transcriptomics in tissue engineering and regenerative medicine","volume":"2","author":"Ruta","year":"2024","journal-title":"Nat. Rev. Bioeng."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib18","first-page":"45","article-title":"Advances in single-cell sequencing: insights from organ transplantation","volume":"8","author":"Wang","year":"2021","journal-title":"Mil. Med. Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib19","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1038\/s41551-021-00739-4","article-title":"The surface topography of silicone breast implants mediates the foreign body response in mice, rabbits and humans","volume":"5","author":"Doloff","year":"2021","journal-title":"Nat. Biomed. Eng."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib20","article-title":"Combinatorial photothermal 3D-printing scaffold and checkpoint blockade inhibits growth\/metastasis of breast cancer to bone and accelerates osteogenesis","volume":"31","author":"He","year":"2020","journal-title":"Adv. Funct. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib21","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/s41587-022-01528-3","article-title":"Wireless, closed-loop, smart bandage with integrated sensors and stimulators for advanced wound care and accelerated healing","volume":"41","author":"Jiang","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib22","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.mattod.2021.11.028","article-title":"Magnesium facilitates the healing of atypical femoral fractures: a single-cell transcriptomic study","volume":"52","author":"Zheng","year":"2022","journal-title":"Mater. Today"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib23","first-page":"404","article-title":"Remodeling of the osteoimmune microenvironment after biomaterials implantation in murine tibia: single-cell transcriptome analysis","volume":"22","author":"Li","year":"2023","journal-title":"Bioact. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib24","doi-asserted-by":"crossref","first-page":"3447","DOI":"10.1016\/j.matt.2024.05.041","article-title":"Stiff hydrogel encapsulation retains mesenchymal stem cell stemness for regenerative medicine","volume":"7","author":"Li","year":"2024","journal-title":"Matter"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib25","doi-asserted-by":"crossref","DOI":"10.1016\/j.biomaterials.2024.122685","article-title":"Integrated-omics profiling unveils the disparities of host defense to ECM scaffolds during wound healing in aged individuals","volume":"311","author":"Chen","year":"2024","journal-title":"Biomaterials"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib26","article-title":"Silk gel recruits specific cell populations for scarless skin regeneration","volume":"23","author":"Liang","year":"2021","journal-title":"Appl. Mater. Today"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib27","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1016\/j.tig.2021.03.007","article-title":"Towards a human cell atlas: taking notes from the past","volume":"37","author":"Lindeboom","year":"2021","journal-title":"Trends Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib28","doi-asserted-by":"crossref","first-page":"2486","DOI":"10.1038\/s41591-022-02104-7","article-title":"Impact of the human cell atlas on medicine","volume":"28","author":"Rood","year":"2022","journal-title":"Nat. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib29","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/s41586-021-03620-1","article-title":"A roadmap for the human developmental cell atlas","volume":"597","author":"Haniffa","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib30","doi-asserted-by":"crossref","DOI":"10.1126\/science.aba7721","article-title":"A human cell atlas of fetal gene expression","volume":"370","author":"Cao","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib31","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1038\/s41586-024-08172-8","article-title":"An integrated transcriptomic cell atlas of human neural organoids","volume":"635","author":"He","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib32","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s41580-024-00768-2","article-title":"Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics","volume":"26","author":"Gulati","year":"2025","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib33","article-title":"Mass cytometry and single-cell RNA-seq profiling of the heterogeneity in human peripheral blood mononuclear cells interacting with silver nanoparticles","volume":"16","author":"Ha","year":"2020","journal-title":"Small"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib34","doi-asserted-by":"crossref","DOI":"10.1016\/j.nantod.2021.101332","article-title":"Systemically administered silica nanoparticles result in diminished T cell response in lung","volume":"42","author":"Dai","year":"2022","journal-title":"Nano Today"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib35","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/j.jconrel.2023.07.037","article-title":"Single-cell RNA transcriptome landscape of murine liver following systemic administration of mesoporous silica nanoparticles","volume":"361","author":"Zheng","year":"2023","journal-title":"J. Control. Release"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib36","doi-asserted-by":"crossref","DOI":"10.1016\/j.biomaterials.2023.122137","article-title":"DLP printed hDPSC-loaded GelMA microsphere regenerates dental pulp and repairs spinal cord","volume":"299","author":"Qian","year":"2023","journal-title":"Biomaterials"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib37","doi-asserted-by":"crossref","DOI":"10.1002\/advs.202308986","article-title":"Mgp high-expressing MSCs orchestrate the osteoimmune microenvironment of collagen\/nanohydroxyapatite-mediated bone regeneration","volume":"11","author":"Wan","year":"2024","journal-title":"Adv. Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib38","doi-asserted-by":"crossref","DOI":"10.1016\/j.biomaterials.2021.121116","article-title":"Single-cell RNA-seq reveals functionally distinct biomaterial degradation-related macrophage populations","volume":"277","author":"Huang","year":"2021","journal-title":"Biomaterials"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib39","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/s41563-023-01689-9","article-title":"Pro-regenerative biomaterials recruit immunoregulatory dendritic cells after traumatic injury","volume":"23","author":"Lokwani","year":"2024","journal-title":"Nat. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib40","doi-asserted-by":"crossref","first-page":"1419","DOI":"10.1038\/s41551-023-01091-5","article-title":"Allometrically scaling tissue forces drive pathological foreign-body responses to implants via Rac2-activated myeloid cells","volume":"7","author":"Padmanabhan","year":"2023","journal-title":"Nat. Biomed. Eng."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib41","doi-asserted-by":"crossref","DOI":"10.1016\/j.celbio.2025.100099","article-title":"Spatial and single-cell transcriptomics unravel the complex interplay between the body and medical implants","author":"Farbehi","year":"2025","journal-title":"Cell Biomater"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib42","first-page":"580","article-title":"Vascular restoration through local delivery of angiogenic factors stimulates bone regeneration in critical size defects","volume":"36","author":"Fang","year":"2024","journal-title":"Bioact. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib43","doi-asserted-by":"crossref","DOI":"10.1002\/adma.202410962","article-title":"A single-cell RNA sequencing guided multienzymatic hydrogel design for self-regenerative repair in diabetic mandibular defects","volume":"36","author":"Lin","year":"2024","journal-title":"Adv. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib44","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.actbio.2016.02.015","article-title":"Stepping into the omics era: opportunities and challenges for biomaterials science and engineering","volume":"34","author":"Groen","year":"2016","journal-title":"Acta Biomater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib45","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/s41576-021-00370-8","article-title":"Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics","volume":"22","author":"Longo","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib46","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/nrg3542","article-title":"Single-cell sequencing-based technologies will revolutionize whole-organism science","volume":"14","author":"Shapiro","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib47","doi-asserted-by":"crossref","first-page":"3737","DOI":"10.1016\/j.molcel.2024.08.002","article-title":"Spatial omics advances for in situ RNA biology","volume":"84","author":"Ren","year":"2024","journal-title":"Mol. Cell"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib48","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/s41592-025-02617-2","article-title":"Optimizing xenium in situ data utility by quality assessment and best-practice analysis workflows","volume":"22","author":"Marco Salas","year":"2025","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib49","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaa6090","article-title":"Spatially resolved, highly multiplexed RNA profiling in single cells","volume":"348","author":"Chen","year":"2015","journal-title":"Science"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib50","doi-asserted-by":"crossref","DOI":"10.1002\/pmic.201900226","article-title":"Deep profiling of cellular heterogeneity by emerging single-cell proteomic technologies","volume":"20","author":"Yang","year":"2020","journal-title":"Proteomics"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib51","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/s41368-021-00146-0","article-title":"From bulk, single-cell to spatial RNA sequencing","volume":"13","author":"Li","year":"2021","journal-title":"Int. J. Oral Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib52","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.copbio.2019.03.001","article-title":"Beyond bulk: a review of single cell transcriptomics methodologies and applications","volume":"58","author":"Kulkarni","year":"2019","journal-title":"Curr. Opin. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib53","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1038\/s41587-021-01091-3","article-title":"Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data","volume":"40","author":"Sun","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib54","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.ejca.2021.03.005","article-title":"Applications of single-cell and bulk RNA sequencing in onco-immunology","volume":"149","author":"Kuksin","year":"2021","journal-title":"Eur. J. Cancer"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib55","doi-asserted-by":"crossref","first-page":"3224","DOI":"10.1038\/s41467-022-30755-0","article-title":"Comparison of methods and resources for cell-cell communication inference from single-cell RNA-seq data","volume":"13","author":"Dimitrov","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib56","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20178046","article-title":"Using single-cell genomics to understand developmental processes and cell fate decisions","volume":"14","author":"Griffiths","year":"2018","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib57","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1042\/BST20210863","article-title":"Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data","volume":"50","author":"Jin","year":"2022","journal-title":"Biochem. Soc. Trans."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib58","doi-asserted-by":"crossref","first-page":"1864","DOI":"10.1038\/s41467-023-37439-3","article-title":"Cellcano: supervised cell type identification for single cell ATAC-seq data","volume":"14","author":"Ma","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib59","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nri.2017.76","article-title":"Single-cell RNA sequencing to explore immune cell heterogeneity","volume":"18","author":"Papalexi","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib60","doi-asserted-by":"crossref","first-page":"5874","DOI":"10.1016\/j.csbj.2021.10.027","article-title":"Automatic cell type identification methods for single-cell RNA sequencing","volume":"19","author":"Xie","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib61","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbaf253","article-title":"ScInfeR: an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics","volume":"26","author":"Kumar Swain","year":"2025","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib62","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1186\/s13059-025-03639-x","article-title":"scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration","volume":"26","author":"Wu","year":"2025","journal-title":"Genome Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib63","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","article-title":"Single-cell chromatin state analysis with signac","volume":"18","author":"Stuart","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib64","series-title":"Ctenophores: Methods and Protocols","first-page":"383","article-title":"Analysis and visualization of single-cell sequencing data with scanpy and MetaCell: a tutorial","author":"Li","year":"2024"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib65","doi-asserted-by":"crossref","first-page":"4100","DOI":"10.1093\/bioinformatics\/btab404","article-title":"Interfacing seurat with the R tidy universe","volume":"37","author":"Mangiola","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib66","doi-asserted-by":"crossref","first-page":"2749","DOI":"10.1038\/s41596-021-00534-0","article-title":"Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods","volume":"16","author":"Clarke","year":"2021","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib67","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1038\/s41467-022-28803-w","article-title":"Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data","volume":"13","author":"Ianevski","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib68","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib69","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/nprot.2009.97","article-title":"Mapping identifiers for the integration of genomic datasets with the R\/Bioconductor package biomaRt","volume":"4","author":"Durinck","year":"2009","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib70","doi-asserted-by":"crossref","first-page":"6820","DOI":"10.1038\/s41467-024-50072-y","article-title":"Hydrogel crosslinking modulates macrophages, fibroblasts, and their communication, during wound healing","volume":"15","author":"Butenko","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib71","doi-asserted-by":"crossref","first-page":"2044","DOI":"10.1093\/bib\/bby067","article-title":"Interpretation of differential gene expression results of RNA-Seq data: review and integration","volume":"20","author":"McDermaid","year":"2019","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib72","doi-asserted-by":"crossref","first-page":"W90","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib73","doi-asserted-by":"crossref","DOI":"10.1155\/2022\/9717599","article-title":"Identification of human retinal organoid cell differentiation-related genes via single-cell sequencing data analysis","volume":"2022","author":"Dong","year":"2022","journal-title":"Comput. Math. Methods Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib74","first-page":"575","article-title":"Gene co-expression analysis for functional classification and gene-disease predictions","volume":"19","author":"van Dam","year":"2018","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib75","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib76","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/s41596-018-0103-9","article-title":"Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, cytoscape and EnrichmentMap","volume":"14","author":"Reimand","year":"2019","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib77","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/s13059-024-03183-0","article-title":"A comparison of marker gene selection methods for single-cell RNA sequencing data","volume":"25","author":"Pullin","year":"2024","journal-title":"Genome Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib78","doi-asserted-by":"crossref","unstructured":"G. Protti, R. Spreafico, A primer on single-cell RNA-Seq analysis using dendritic cells as a case study, FEBS Lett. n\/a https:\/\/doi.org\/10.1002\/1873-3468.15009.","DOI":"10.1002\/1873-3468.15009"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib79","first-page":"D331","article-title":"Expansion of the gene ontology knowledgebase and resources","volume":"45","author":"Consortium","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib80","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac143","article-title":"On the influence of several factors on pathway enrichment analysis","volume":"23","author":"Mubeen","year":"2022","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib81","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btac757","article-title":"GSEApy: a comprehensive package for performing gene set enrichment analysis in python","volume":"39","author":"Fang","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib82","article-title":"Improving gene set enrichment analysis (GSEA) by using regulation directionality","volume":"12","author":"Wang","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib83","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1002\/jbm.a.37090","article-title":"GSVA score reveals molecular signatures from transcriptomes for biomaterials comparison","volume":"109","author":"Ferreira","year":"2021","journal-title":"J. Biomed. Mater. Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib84","first-page":"318","article-title":"Interfacial delivery of carbon monoxide via smart titanium implant coating for enhanced soft tissue integration with switchable antibacterial and immunomodulatory properties","volume":"40","author":"Zhou","year":"2024","journal-title":"Bioact. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib85","article-title":"Inference of high-resolution trajectories in single-cell RNA-Seq data by using RNA velocity","volume":"1","author":"Zhang","year":"2021","journal-title":"Cell Rep. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib86","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/s41587-019-0071-9","article-title":"A comparison of single-cell trajectory inference methods","volume":"37","author":"Saelens","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib87","doi-asserted-by":"crossref","first-page":"684","DOI":"10.12688\/f1000research.134078.1","article-title":"Unraveling the timeline of gene expression: a pseudotemporal trajectory analysis of single-cell RNA sequencing data","volume":"12","author":"Cheng","year":"2023","journal-title":"F1000Res"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib88","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.copbio.2019.12.005","article-title":"The emergence and promise of single-cell temporal-omics approaches","volume":"63","author":"Lederer","year":"2020","journal-title":"Curr. Opin. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib89","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1134\/S0006297923020074","article-title":"Complex analysis of single-cell RNA sequencing data","volume":"88","author":"Khozyainova","year":"2023","journal-title":"Biochemistry (Mosc)."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib90","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","article-title":"The single-cell transcriptional landscape of Mammalian organogenesis","volume":"566","author":"Cao","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib91","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib92","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1038\/nrg.2016.98","article-title":"Transition states and cell fate decisions in epigenetic landscapes","volume":"17","author":"Moris","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib93","doi-asserted-by":"crossref","first-page":"2442","DOI":"10.1038\/s41467-018-04696-6","article-title":"Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data","volume":"9","author":"Campbell","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib94","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1038\/nmeth.4402","article-title":"Reversed graph embedding resolves complex single-cell trajectories","volume":"14","author":"Qiu","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib95","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abn1958","article-title":"Recombinant DT\u03b24-inspired porous 3D vascular graft enhanced antithrombogenicity and recruited circulating CD93(+)\/CD34(+) cells for endothelialization","volume":"8","author":"Xiao","year":"2022","journal-title":"Sci. Adv."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib96","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1186\/s13059-023-03065-x","article-title":"Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates","volume":"24","author":"Zheng","year":"2023","journal-title":"Genome Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib97","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"La Manno","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib98","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41587-020-0591-3","article-title":"Generalizing RNA velocity to transient cell states through dynamical modeling","volume":"38","author":"Bergen","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib99","doi-asserted-by":"crossref","first-page":"5211","DOI":"10.1038\/s41467-022-32868-y","article-title":"Msx1+ stem cells recruited by bioactive tissue engineering graft for bone regeneration","volume":"13","author":"Zhang","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib100","doi-asserted-by":"crossref","first-page":"6586","DOI":"10.1038\/s41467-022-34188-7","article-title":"UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference","volume":"13","author":"Gao","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib101","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1010492","article-title":"RNA velocity unraveled","volume":"18","author":"Gorin","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib102","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1038\/s41592-024-02471-8","article-title":"Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations","volume":"21","author":"Lederer","year":"2024","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib103","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.molcel.2018.09.026","article-title":"RNA velocity: molecular kinetics from single-cell RNA-seq","volume":"72","author":"Svensson","year":"2018","journal-title":"Mol. Cell"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib104","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/s41592-023-01994-w","article-title":"Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells","volume":"21","author":"Gayoso","year":"2024","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib105","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/s41592-021-01346-6","article-title":"CellRank for directed single-cell fate mapping","volume":"19","author":"Lange","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib106","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1038\/s41592-024-02303-9","article-title":"CellRank 2: unified fate mapping in multiview single-cell data","volume":"21","author":"Weiler","year":"2024","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib107","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/s41392-024-01888-z","article-title":"Cell\u2013cell communication: new insights and clinical implications","volume":"9","author":"Su","year":"2024","journal-title":"Signal Transduct. Targeted Ther."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib108","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/s41576-023-00685-8","article-title":"The diversification of methods for studying cell-cell interactions and communication","volume":"25","author":"Armingol","year":"2024","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib109","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41576-020-00292-x","article-title":"Deciphering cell\u2013cell interactions and communication from gene expression","volume":"22","author":"Armingol","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib110","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/s41587-023-01782-z","article-title":"Comparative analysis of cell\u2013cell communication at single-cell resolution","volume":"42","author":"Wilk","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib111","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaa183","article-title":"SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics","volume":"48","author":"Cabello-Aguilar","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib112","doi-asserted-by":"crossref","first-page":"8520","DOI":"10.1093\/nar\/gkab638","article-title":"CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication","volume":"49","author":"Zhang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib113","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/s41596-024-01045-4","article-title":"CellChat for systematic analysis of cell\u2013cell communication from single-cell transcriptomics","volume":"20","author":"Jin","year":"2025","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib114","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib115","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/s41592-019-0667-5","article-title":"NicheNet: modeling intercellular communication by linking ligands to target genes","volume":"17","author":"Browaeys","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib116","first-page":"1","article-title":"Unraveling cell\u2013cell communication with NicheNet by inferring active ligands from transcriptomics data","author":"Sang-Aram","year":"2025","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib117","article-title":"Enhancing endogenous hyaluronic acid in osteoarthritic joints with an anti-inflammatory supramolecular nanofiber hydrogel delivering HAS2 lentivirus","volume":"20","author":"Zhou","year":"2024","journal-title":"Small"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib118","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1109\/TCBB.2021.3138142","article-title":"Community detection in protein-protein interaction networks and applications","volume":"20","author":"Manipur","year":"2023","journal-title":"IEEE ACM Trans. Comput. Biol. Bioinf"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib119","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1016\/j.cell.2021.04.011","article-title":"Dual proteome-scale networks reveal cell-specific remodeling of the human interactome","volume":"184","author":"Huttlin","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib120","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbad076","article-title":"Machine learning on protein-protein interaction prediction: models, challenges and trends","volume":"24","author":"Tang","year":"2023","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib121","doi-asserted-by":"crossref","first-page":"3932","DOI":"10.1021\/acs.chemrev.3c00550","article-title":"Computational approaches to predict protein\u2013protein interactions in crowded cellular environments","volume":"124","author":"Grassmann","year":"2024","journal-title":"Chem. Rev."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib122","doi-asserted-by":"crossref","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The STRING database in 2021: customizable protein\u2013protein networks, and functional characterization of user-uploaded gene\/measurement sets","volume":"49","author":"Szklarczyk","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib123","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib124","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aax4783","article-title":"Interleukin-36\u03b3\u2013producing macrophages drive IL-17\u2013mediated fibrosis","volume":"4","author":"Sommerfeld","year":"2019","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib125","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/s13045-024-01596-9","article-title":"Spatial multi-omics: deciphering technological landscape of integration of multi-omics and its applications","volume":"17","author":"Liu","year":"2024","journal-title":"J. Hematol. Oncol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib126","doi-asserted-by":"crossref","first-page":"5995","DOI":"10.1038\/s41467-023-41608-9","article-title":"Tracing immune cells around biomaterials with spatial anchors during large-scale wound regeneration","volume":"14","author":"Yang","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib127","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/s41587-022-01448-2","article-title":"The expanding vistas of spatial transcriptomics","volume":"41","author":"Tian","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib128","doi-asserted-by":"crossref","first-page":"2663","DOI":"10.7150\/ijbs.43887","article-title":"Encoding method of single-cell spatial transcriptomics sequencing","volume":"16","author":"Zhou","year":"2020","journal-title":"Int. J. Biol. Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib129","doi-asserted-by":"crossref","first-page":"3085","DOI":"10.1038\/s41596-024-01001-2","article-title":"A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract","volume":"19","author":"Monasterio","year":"2024","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib130","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1038\/s41540-024-00462-1","article-title":"Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology","volume":"10","author":"Juwayria","year":"2024","journal-title":"npj Syst. Biol. Appl."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib131","doi-asserted-by":"crossref","first-page":"2501","DOI":"10.1038\/s41596-018-0045-2","article-title":"Barcoded solid-phase RNA capture for spatial transcriptomics profiling in mammalian tissue sections","volume":"13","author":"Salm\u00e9n","year":"2018","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib132","article-title":"Internal oligo(dT) priming introduces systematic bias in bulk and single-cell RNA sequencing count data, optimization of FFPE preparation and identification of gene attributes associated with RNA degradation, NAR genom","volume":"4","author":"Svoboda","year":"2022","journal-title":"Bioinform"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib133","first-page":"295","article-title":"Integration tools for scRNA-seq data and spatial transcriptomics sequencing data, integration tools for scRNA-seq data and spatial transcriptomics sequencing data, brief. Funct","volume":"23","author":"Yan","year":"2024","journal-title":"Genomics"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib134","doi-asserted-by":"crossref","DOI":"10.1038\/s41576-025-00845-y","article-title":"Cell-type deconvolution methods for spatial transcriptomics","author":"Gaspard-Boulinc","year":"2025","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib135","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkab043","article-title":"SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes","volume":"49","author":"Elosua-Bayes","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib136","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1038\/s42003-023-04761-x","article-title":"SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning","volume":"6","author":"Coleman","year":"2023","journal-title":"Commun. Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib137","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib138","doi-asserted-by":"crossref","first-page":"D1138","DOI":"10.1093\/nar\/gkac889","article-title":"SPASCER: spatial transcriptomics annotation at single-cell resolution","volume":"51","author":"Fan","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib139","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1038\/s41592-022-01409-2","article-title":"Museum of spatial transcriptomics","volume":"19","author":"Moses","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib140","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/s41587-021-01044-w","article-title":"Cell segmentation in imaging-based spatial transcriptomics","volume":"40","author":"Petukhov","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib141","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaf087","article-title":"Precise gene expression deconvolution in spatial transcriptomics with STged","volume":"53","author":"Tu","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib142","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1186\/s12915-024-02085-8","article-title":"Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data","volume":"22","author":"Huang","year":"2024","journal-title":"BMC Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib143","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/s41592-021-01171-x","article-title":"The triumphs and limitations of computational methods for scRNA-seq","volume":"18","author":"Kharchenko","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib144","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/s41587-020-00812-4","article-title":"Building a high-quality human cell atlas","volume":"39","author":"Rozenblatt-Rosen","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib145","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/s41587-020-0739-1","article-title":"Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2","volume":"39","author":"Stickels","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib146","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/s13059-018-1603-1","article-title":"Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics","volume":"19","author":"Stoeckius","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib147","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1039\/D2MO00060A","article-title":"Omics technologies for high-throughput-screening of cell\u2013biomaterial interactions","volume":"18","author":"Sari","year":"2022","journal-title":"Mol. Omics"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib148","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1016\/j.tibtech.2020.02.013","article-title":"Integrative methods and practical challenges for single-cell multi-omics","volume":"38","author":"Ma","year":"2020","journal-title":"Trends Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib149","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/s44222-024-00264-4","article-title":"Multi-omics approaches to decipher the interactions of nanoparticles and biological systems","volume":"3","author":"Wang","year":"2025","journal-title":"Nat. Rev. Bioeng."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib150","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1007\/978-1-0716-1831-8_3","article-title":"Single-cell analysis of the transcriptome and epigenome","volume":"2399","author":"Mazan-Mamczarz","year":"2022","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib151","article-title":"Three differential expression analysis methods for RNA sequencing: limma, EdgeR, DESeq2","author":"Liu","year":"2021","journal-title":"J. Vis. Exp."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib152","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad547","article-title":"PyDESeq2: a python package for bulk RNA-Seq differential expression analysis","volume":"39","author":"Muzellec","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib153","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s13059-022-02648-4","article-title":"Exaggerated false positives by popular differential expression methods when analyzing human population samples","volume":"23","author":"Li","year":"2022","journal-title":"Genome Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib154","doi-asserted-by":"crossref","DOI":"10.1016\/j.bbapap.2023.140889","article-title":"Analysis and prediction of protein stability based on interaction network, gene ontology, and KEGG pathway enrichment scores","volume":"1871","author":"Huang","year":"2023","journal-title":"Biochim. Biophys. Acta Proteins Proteom"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib155","series-title":"Proc. IEEE\/CVF Conf. Comput. Vis. Pattern Recognit. (CVPR)","first-page":"3858","article-title":"GSVA: generalized segmentation via multimodal large language models","author":"Xia","year":"2024"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib156","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-024-80534-8","article-title":"Dual gene set enrichment analysis (dualGSEA); an R function that enables more robust biological discovery and pre-clinical model alignment from transcriptomics data","volume":"14","author":"Bull","year":"2024","journal-title":"Sci. Rep."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib157","doi-asserted-by":"crossref","DOI":"10.1016\/j.cej.2022.135814","article-title":"Single-cell transcriptomics uncovers the impacts of titanium dioxide nanoparticles on human bone marrow stromal cells","volume":"440","author":"Xiang","year":"2022","journal-title":"Chem. Eng. J."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib158","article-title":"Single-cell RNA sequencing reveals multiple immune cell subpopulations promote the formation of abnormal bone microenvironment in osteoporosis","volume":"14","author":"Yang","year":"2024","journal-title":"Sci. Rep."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib159","doi-asserted-by":"crossref","DOI":"10.36922\/OR025040007","article-title":"Organoid research: theory, technology, and therapeutics","volume":"1","author":"Bai","year":"2025","journal-title":"Organoid Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib160","article-title":"Targeting YAP1-regulated glycolysis in fibroblast-like synoviocytes impairs macrophage infiltration to ameliorate diabetic osteoarthritis progression","volume":"11","author":"Yang","year":"2024","journal-title":"Adv. Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib161","first-page":"281","article-title":"A single-cell transcriptome of mesenchymal stromal cells to fabricate bioactive hydroxyapatite materials for bone regeneration","volume":"9","author":"Guo","year":"2022","journal-title":"Bioact. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib162","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1038\/s41551-021-00770-5","article-title":"Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics","volume":"5","author":"Cherry","year":"2021","journal-title":"Nat. Biomed. Eng."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib163","doi-asserted-by":"crossref","DOI":"10.1016\/j.biomaterials.2022.121928","article-title":"Substrate stiffness enhances human regulatory T cell induction and metabolism","volume":"292","author":"Shi","year":"2023","journal-title":"Biomaterials"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib164","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2406787121","article-title":"Hydrogel biomaterials that stiffen and soften on demand reveal that skeletal muscle stem cells harbor a mechanical memory","volume":"121","author":"Madl","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib165","doi-asserted-by":"crossref","DOI":"10.1002\/adhm.202400134","article-title":"Eosinophils respond to extracellular matrix treated muscle injuries but are not required for macrophage polarization","volume":"14","author":"Lokwani","year":"2025","journal-title":"Adv. Healthc. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib166","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1007\/s10311-021-01307-7","article-title":"Engineered nanomaterials for biomedical applications and their toxicity: a review","volume":"20","author":"Umapathi","year":"2022","journal-title":"Environ. Chem. Lett."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib167","article-title":"Nanomaterials: types, properties, recent advances, and toxicity concerns","volume":"25","author":"Sajid","year":"2022","journal-title":"Curr. Opin. Environ. Sci. Health"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib168","doi-asserted-by":"crossref","DOI":"10.1002\/mco2.327","article-title":"Nanoparticles-induced potential toxicity on human health: applications, toxicity mechanisms, and evaluation models","volume":"4","author":"Xuan","year":"2023","journal-title":"MedComm"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib169","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/j.jconrel.2022.05.035","article-title":"Recent trends in the application of nanoparticles in cancer therapy: the involvement of oxidative stress","volume":"348","author":"Sanati","year":"2022","journal-title":"J. Control. Release"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib170","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.mrgentox.2012.08.007","article-title":"In vitro and in vivo genotoxicity of silver nanoparticles","volume":"749","author":"Ghosh","year":"2012","journal-title":"Mutat. Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib171","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1021\/nn800596w","article-title":"Cytotoxicity and genotoxicity of silver nanoparticles in human cells","volume":"3","author":"AshaRani","year":"2009","journal-title":"ACS Nano"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib172","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.redox.2017.12.011","article-title":"TiO2 nanoparticles cause mitochondrial dysfunction, activate inflammatory responses, and attenuate phagocytosis in macrophages: a proteomic and metabolomic insight","volume":"15","author":"Chen","year":"2018","journal-title":"Redox Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib173","doi-asserted-by":"crossref","DOI":"10.3390\/ijms232012353","article-title":"TiO2 nanoparticles and their effects on eukaryotic cells: a double-edged sword","volume":"23","author":"Gojznikar","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib174","doi-asserted-by":"crossref","first-page":"1821","DOI":"10.1039\/D0MA00807A","article-title":"Nanomaterials: a review of synthesis methods, properties, recent progress, and challenges","volume":"2","author":"Baig","year":"2021","journal-title":"Mater. Adv."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib175","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s12943-023-01797-9","article-title":"Nanomaterials in tumor immunotherapy: new strategies and challenges","volume":"22","author":"Zhu","year":"2023","journal-title":"Mol. Cancer"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib176","first-page":"425","article-title":"Future perspectives: advances in bone\/cartilage organoid technology and clinical potential","volume":"5","author":"Huang","year":"2024","journal-title":"Biomater. Trans."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib177","doi-asserted-by":"crossref","DOI":"10.36922\/OR025040003","article-title":"A trabeculae-like biomimetic bone-filling material as a potential organoid for bone defect treatment","volume":"1","author":"Meng","year":"2025","journal-title":"Organoid Res.: Theory, Technol. Therapeu."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib178","doi-asserted-by":"crossref","DOI":"10.1002\/adfm.202208639","article-title":"Bone repair biomaterials: a perspective from immunomodulation","volume":"32","author":"Wang","year":"2022","journal-title":"Adv. Funct. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib179","doi-asserted-by":"crossref","DOI":"10.1016\/j.biomaterials.2022.121604","article-title":"Immunomodulatory strategies for bone regeneration: a review from the perspective of disease types","volume":"286","author":"Su","year":"2022","journal-title":"Biomaterials"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib180","first-page":"65","article-title":"The role of the immune microenvironment in bone, cartilage, and soft tissue regeneration: from mechanism to therapeutic opportunity","volume":"9","author":"Xiong","year":"2022","journal-title":"Mil. Med. Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib181","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1111\/exd.14547","article-title":"Single\u2010cell transcriptomics in human skin research: available technologies, technical considerations and disease applications","volume":"31","author":"Theocharidis","year":"2022","journal-title":"Exp. Dermatol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib182","first-page":"345","article-title":"3D bioprinting of engineered exosomes secreted from M2-polarized macrophages through immunomodulatory biomaterial promotes in vivo wound healing and angiogenesis","volume":"45","author":"Dutta","year":"2025","journal-title":"Bioact. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib183","doi-asserted-by":"crossref","first-page":"3655","DOI":"10.7150\/thno.85823","article-title":"LncRNAs associated with oxidative stress in diabetic wound healing: regulatory mechanisms and application prospects","volume":"13","author":"Yang","year":"2023","journal-title":"Theranostics"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib184","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2023.1216321","article-title":"Exploring the contribution of pro-inflammatory cytokines to impaired wound healing in diabetes","volume":"14","author":"Nirenjen","year":"2023","journal-title":"Front. Immunol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib185","article-title":"Tracing immunological interaction in trimethylamine N-Oxide hydrogel-derived zwitterionic microenvironment during promoted diabetic wound regeneration","volume":"36","author":"Li","year":"2024","journal-title":"Adv. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib186","doi-asserted-by":"crossref","first-page":"2190","DOI":"10.1111\/iwj.14097","article-title":"Mechanisms underlying pathological scarring by fibroblasts during wound healing","volume":"20","author":"Ma","year":"2023","journal-title":"Int. Wound J."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib187","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.1028410","article-title":"Mechanotransduction in skin wound healing and scar formation: potential therapeutic targets for controlling hypertrophic scarring","volume":"13","author":"Yin","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib188","doi-asserted-by":"crossref","first-page":"897","DOI":"10.3390\/ijms22020897","article-title":"Molecular changes underlying hypertrophic scarring following burns involve specific deregulations at all wound healing stages (inflammation, proliferation and maturation)","volume":"22","author":"\u010coma","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib189","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.abj9152","article-title":"Disrupting mechanotransduction decreases fibrosis and contracture in split-thickness skin grafting","volume":"14","author":"Chen","year":"2022","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib190","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.1016\/j.joen.2022.06.013","article-title":"Determinants of dental pulp stem cell heterogeneity","volume":"48","author":"Nel","year":"2022","journal-title":"J. Endod."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib191","first-page":"258","article-title":"Dental pulp regeneration strategies: a review of status quo and recent advances","volume":"38","author":"Li","year":"2024","journal-title":"Bioact. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib192","doi-asserted-by":"crossref","first-page":"1544","DOI":"10.1177\/0022034515601658","article-title":"Pulp-dentin regeneration: current state and future prospects","volume":"94","author":"Cao","year":"2015","journal-title":"J. Dent. Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib193","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1146\/annurev-physiol-031120-103629","article-title":"Cardiac regeneration: new hope for an old dream","volume":"83","author":"Weinberger","year":"2021","journal-title":"Annu. Rev. Physiol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib194","doi-asserted-by":"crossref","first-page":"4636","DOI":"10.1039\/C9BM01003C","article-title":"Cardiomyocyte dedifferentiation and remodeling in 3D scaffolds to generate the cellular diversity of engineering cardiac tissues","volume":"7","author":"Wang","year":"2019","journal-title":"Biomater. Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib195","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1038\/s41536-024-00365-z","article-title":"Anti-inflammatory prowess of endothelial progenitor cells in the realm of biology and medicine","volume":"9","author":"Hassanpour","year":"2024","journal-title":"NPJ Regen. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib196","doi-asserted-by":"crossref","DOI":"10.1002\/adhm.202200045","article-title":"Immunomodulation strategies for the successful regeneration of a tissue\u2010engineered vascular graft","volume":"11","author":"Zhang","year":"2022","journal-title":"Adv. Healthc. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib197","doi-asserted-by":"crossref","DOI":"10.1002\/adfm.202209471","article-title":"Repair strategies and bioactive functional materials for intervertebral disc","volume":"32","author":"Wu","year":"2022","journal-title":"Adv. Funct. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib198","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.actbio.2023.06.012","article-title":"Emerging tissue engineering strategies for annulus fibrosus therapy","volume":"167","author":"Zhang","year":"2023","journal-title":"Acta Biomater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib199","first-page":"350","article-title":"Decoding the annulus fibrosus cell atlas by scRNA-seq to develop an inducible composite hydrogel: a novel strategy for disc reconstruction","volume":"14","author":"Wang","year":"2022","journal-title":"Bioact. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib200","first-page":"231","article-title":"3D-printed advanced scaffold armed with exosomes derived from human skeletal stem cell identified by single-cell RNA sequencing enhances osteochondral regeneration, bioact","volume":"51","author":"Lou","year":"2025","journal-title":"Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib201","article-title":"Injectable body temperature responsive hydrogel for encephalitis treatment via sustained release of nano-anti-inflammatory agents","volume":"5","author":"Gai","year":"2024","journal-title":"Biomater. Transl."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib202","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1016\/j.it.2023.04.005","article-title":"Engineered treg cells as putative therapeutics against inflammatory diseases and beyond","volume":"44","author":"Bittner","year":"2023","journal-title":"Trends Immunol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib203","doi-asserted-by":"crossref","DOI":"10.4028\/b-XDTcg5","article-title":"ROS-activated nanohydrogel scaffolds with multi-factors controlled release for targeted dual-lineage repair of osteochondral defects","volume":"12","author":"Wang","year":"2025","journal-title":"Adv. Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib204","doi-asserted-by":"crossref","DOI":"10.1002\/adma.202311646","article-title":"Immunoengineering biomaterials for musculoskeletal tissue repair across lifespan","volume":"36","author":"Han","year":"2024","journal-title":"Adv. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib205","doi-asserted-by":"crossref","DOI":"10.1002\/adfm.202213066","article-title":"Immunomodulatory hydrogels: advanced regenerative tools for diabetic foot ulcer","volume":"33","author":"Xiong","year":"2023","journal-title":"Adv. Funct. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib206","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1021\/acscentsci.3c01169","article-title":"Single-cell analysis reveals Cxcl14(+) fibroblast accumulation in regenerating diabetic wounds treated by hydrogel-delivering carbon monoxide","volume":"10","author":"Li","year":"2024","journal-title":"ACS Cent. Sci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib207","doi-asserted-by":"crossref","first-page":"540","DOI":"10.3390\/biology13070540","article-title":"Understanding the foreign body response via single-cell meta-analysis","volume":"13","author":"Liang","year":"2024","journal-title":"Biology"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib208","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.cmi.2019.08.006","article-title":"Pathogenesis and management of fracture-related infection","volume":"26","author":"Depypere","year":"2020","journal-title":"Clin. Microbiol. Infect."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib209","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.ensm.2020.12.008","article-title":"An interface-reinforced rhombohedral Prussian blue analogue in semi-solid state electrolyte for sodium-ion battery","volume":"36","author":"Xie","year":"2021","journal-title":"Energy Storage Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib210","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1056\/NEJMra2203477","article-title":"Periprosthetic joint infection","volume":"388","author":"Patel","year":"2023","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib211","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s10020-023-00632-7","article-title":"Single-cell transcriptome reveals Staphylococcus aureus modulating fibroblast differentiation in the bone-implant interface","volume":"29","author":"Yu","year":"2023","journal-title":"Mol. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib212","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1111\/jcpe.13982","article-title":"Single-cell analysis reveals a unique microenvironment in peri-implantitis","volume":"51","author":"Li","year":"2024","journal-title":"J. Clin. Periodontol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib213","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/s41572-021-00289-8","article-title":"Non-union bone fractures","volume":"7","author":"Wildemann","year":"2021","journal-title":"Nat. Rev. Dis. Primers"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib214","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/s12891-024-07283-7","article-title":"Dnmt3b ablation affects fracture repair process by regulating apoptosis","volume":"25","author":"Wang","year":"2024","journal-title":"BMC Musculoskelet. Disord."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib215","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1172\/JCI80672","article-title":"NOTCH signaling in skeletal progenitors is critical for fracture repair","volume":"126","author":"Wang","year":"2016","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib216","doi-asserted-by":"crossref","first-page":"2307","DOI":"10.1002\/jbmr.2373","article-title":"The convergence of fracture repair and stem cells: interplay of genes, aging, environmental factors and disease","volume":"29","author":"Hadjiargyrou","year":"2014","journal-title":"J. Bone Miner. Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib217","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.immuni.2021.12.013","article-title":"Inflammation in obesity, diabetes, and related disorders","volume":"55","author":"Rohm","year":"2022","journal-title":"Immunity"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib218","doi-asserted-by":"crossref","DOI":"10.1016\/j.bone.2020.115618","article-title":"Abnormal macrophage polarization impedes the healing of diabetes-associated tooth sockets","volume":"143","author":"Shen","year":"2021","journal-title":"Bone"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib219","doi-asserted-by":"crossref","DOI":"10.1002\/adfm.202009432","article-title":"Recent advances in design of functional biocompatible hydrogels for bone tissue engineering","volume":"31","author":"Xue","year":"2021","journal-title":"Adv. Funct. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib220","article-title":"A single-cell atlas-inspired hitchhiking therapeutic strategy for acute pancreatitis by restricting ROS in neutrophils","author":"Zhang","year":"2025","journal-title":"Adv. Mater."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib221","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s41576-019-0093-7","article-title":"Integrative single-cell analysis","volume":"20","author":"Stuart","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib222","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1038\/s12276-020-0420-2","article-title":"Single-cell multiomics: technologies and data analysis methods","volume":"52","author":"Lee","year":"2020","journal-title":"Exp. Mol. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib223","doi-asserted-by":"crossref","first-page":"2742","DOI":"10.1038\/s41596-018-0073-y","article-title":"Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies","volume":"13","author":"Lafzi","year":"2018","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib224","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1093\/biostatistics\/kxx053","article-title":"Missing data and technical variability in single\u2010cell RNA\u2010sequencing experiments","volume":"19","author":"Hicks","year":"2018","journal-title":"Biostatistics"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib225","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nmeth.4437","article-title":"Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations","volume":"14","author":"van den Brink","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib226","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/s13059-020-02048-6","article-title":"Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows","volume":"21","author":"Denisenko","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib227","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2019.00317","article-title":"Single-cell RNA-seq technologies and related computational data analysis","volume":"10","author":"Chen","year":"2019","journal-title":"Front. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib228","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2022.994069","article-title":"From multitude to singularity: an up-to-date overview of scRNA-seq data generation and analysis","volume":"13","author":"Carangelo","year":"2022","journal-title":"Front. Genet."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib229","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s13059-020-1926-6","article-title":"Eleven grand challenges in single-cell data science","volume":"21","author":"L\u00e4hnemann","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib230","doi-asserted-by":"crossref","DOI":"10.3389\/fnins.2021.591122","article-title":"Single-cell transcriptomics: current methods and challenges in data acquisition and analysis","volume":"15","author":"Adil","year":"2021","journal-title":"Front. Neurosci."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib231","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkz826","article-title":"Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data","volume":"47","author":"Cheng","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib232","doi-asserted-by":"crossref","DOI":"10.1002\/ctm2.694","article-title":"Single-cell RNA sequencing technologies and applications: a brief overview","volume":"12","author":"Jovic","year":"2022","journal-title":"Clin. Transl. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib233","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/s41587-020-0469-4","article-title":"Benchmarking single-cell RNA-sequencing protocols for cell atlas projects","volume":"38","author":"Mereu","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib234","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baaa073","article-title":"A curated database reveals trends in single-cell transcriptomics","author":"Svensson","year":"2020","journal-title":"Database"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib235","first-page":"470","article-title":"Advances in bulk and single-cell multi-omics approaches for systems biology and precision medicine","volume":"22","author":"Li","year":"2021","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib236","article-title":"Integrating bulk and single-cell sequencing reveals the phenotype-associated cell subpopulations in sepsis-induced acute lung injury","volume":"13","author":"Wang","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib237","series-title":"Biobanks and Tissue Research: the Public, the Patient and the Regulation","first-page":"37","article-title":"Biobanks and research: scientific potential and regulatory challenge","author":"Elger","year":"2011"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib238","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.aca.2020.10.038","article-title":"Multi-omics integration in biomedical research - a metabolomics-centric review","volume":"1141","author":"W\u00f6rheide","year":"2021","journal-title":"Anal. Chim. Acta"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib239","doi-asserted-by":"crossref","first-page":"1458","DOI":"10.1038\/s41587-022-01284-4","article-title":"Multi-omics single-cell data integration and regulatory inference with graph-linked embedding","volume":"40","author":"Cao","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib240","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.cell.2012.05.044","article-title":"A whole-cell computational model predicts phenotype from genotype","volume":"150","author":"Karr","year":"2012","journal-title":"Cell"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib241","doi-asserted-by":"crossref","first-page":"7045","DOI":"10.1016\/j.cell.2024.11.015","article-title":"How to build the virtual cell with artificial intelligence: priorities and opportunities","volume":"187","author":"Bunne","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib242","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib243","article-title":"AI-driven construction of digital cell model","volume":"28","author":"Yang","year":"2024","journal-title":"J. Cell Mol. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib244","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/S0167-7799(01)01740-1","article-title":"The virtual cell: a software environment for computational cell biology","volume":"19","author":"Loew","year":"2001","journal-title":"Trends Biotechnol."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib245","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1038\/s41586-024-08338-4","article-title":"The human cell atlas from a cell census to a unified foundation model","volume":"637","author":"Rood","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.bioactmat.2025.07.047_bib246","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/s41746-024-01188-4","article-title":"From virtual patients to digital twins in immuno-oncology: lessons learned from mechanistic quantitative systems pharmacology modeling","volume":"7","author":"Wang","year":"2024","journal-title":"npj Digit. Med."},{"key":"10.1016\/j.bioactmat.2025.07.047_bib247","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13073-025-01435-7","article-title":"Digital twins as global learning health and disease models for preventive and personalized medicine","volume":"17","author":"Li","year":"2025","journal-title":"Genome Med."}],"container-title":["Bioactive Materials"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2452199X25003470?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2452199X25003470?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T19:44:08Z","timestamp":1772912648000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2452199X25003470"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12]]},"references-count":247,"alternative-id":["S2452199X25003470"],"URL":"https:\/\/doi.org\/10.1016\/j.bioactmat.2025.07.047","relation":{},"ISSN":["2452-199X"],"issn-type":[{"value":"2452-199X","type":"print"}],"subject":[],"published":{"date-parts":[[2025,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Biomaterial-mediated Cell Atlas: an insight from single-cell and spatial transcriptomics","name":"articletitle","label":"Article Title"},{"value":"Bioactive Materials","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.bioactmat.2025.07.047","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd.","name":"copyright","label":"Copyright"}]}}