{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T12:59:59Z","timestamp":1790600399658,"version":"4.1.0"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"vor","delay-in-days":27,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"\u201cPioneer\u201d and \u201cLeading Goose\u201d R&D Program of Zhejiang","award":["2024C03106"],"award-info":[{"award-number":["2024C03106"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82474160"],"award-info":[{"award-number":["82474160"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Identification of new cell subtypes in single-cell RNA sequencing (scRNA-seq) data is critically crucial in accurately understanding the mechanisms of disease occurrence and development, which provides unprecedented insights into the development of therapeutic strategies, however, despite the abundance of existing methods, most heavily rely on the reference with the fixed cell labels, which fail to uncover new cell subtypes. Herein, we propose Subtypist, a fully data-driven multiscale iterative algorithm for cell subtype identification in scRNA-seq data without relying on external prior references. The benchmarking evaluation on both simulated and real datasets demonstrates its superior performance over other existing methods, and Subtypist was further applied to three disease scenarios, uncovering novel biologically meaningful cell subtypes and revealing their in-depth cell\u2013cell communicative mechanisms underlying hepatocellular carcinoma, esophageal squamous cell carcinoma, and myocardial infarction. In summary, Subtypist enables the data-driven and reproducible identification of cell subtypes, providing an invaluable tool for accurately characterizing the cellular and molecular heterogeneity underlying disease pathogenesis.<\/jats:p>","DOI":"10.1093\/bib\/bbag529","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T11:46:50Z","timestamp":1789127210000},"source":"Crossref","is-referenced-by-count":0,"title":["Data-driven identification of cell subtypes for single-cell transcriptomic data with Subtypist"],"prefix":"10.1093","volume":"27","author":[{"given":"Yue","family":"Yao","sequence":"first","affiliation":[{"name":"Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang ,","place":["China"]},{"name":"State Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University , Xiangfudang Sci-tech Innovation Green Valley, Jiashan County, Jiaxing 314103 ,","place":["Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1928-3878","authenticated-orcid":false,"given":"Xin","family":"Shao","sequence":"additional","affiliation":[{"name":"Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang ,","place":["China"]},{"name":"State Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University , Xiangfudang Sci-tech Innovation Green Valley, Jiashan County, Jiaxing 314103 ,","place":["Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renjie","family":"Chen","sequence":"additional","affiliation":[{"name":"Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang ,","place":["China"]},{"name":"State Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University , Xiangfudang Sci-tech Innovation Green Valley, Jiashan County, Jiaxing 314103 ,","place":["Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingyang","family":"Qian","sequence":"additional","affiliation":[{"name":"Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang ,","place":["China"]},{"name":"State Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University , Xiangfudang Sci-tech Innovation Green Valley, Jiashan County, Jiaxing 314103 ,","place":["Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Gao","sequence":"additional","affiliation":[{"name":"Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang ,","place":["China"]},{"name":"State Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University , Xiangfudang Sci-tech Innovation Green Valley, Jiashan County, Jiaxing 314103 ,","place":["Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiyang","family":"Peng","sequence":"additional","affiliation":[{"name":"Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang ,","place":["China"]},{"name":"State Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University , Xiangfudang Sci-tech Innovation Green Valley, Jiashan County, Jiaxing 314103 ,","place":["Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Gynecology & Scientific Research Department, The First Affiliated Hospital of Guangzhou University of Chinese Medicine , 16 Jichang Road, Baiyun District, Guangzhou 510405, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6336-3007","authenticated-orcid":false,"given":"Xiaohui","family":"Fan","sequence":"additional","affiliation":[{"name":"Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang ,","place":["China"]},{"name":"State Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University , Xiangfudang Sci-tech Innovation Green Valley, Jiashan County, Jiaxing 314103 ,","place":["Zhejiang, China"]},{"name":"Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine , 1 Xueshi Road, Shangcheng District, Hangzhou 310006, Zhejiang ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,28]]},"reference":[{"key":"2026092808242963000_ref1","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1038\/nbt.3711","article-title":"Revealing the vectors of cellular identity with single-cell genomics","volume":"34","author":"Wagner","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2026092808242963000_ref2","doi-asserted-by":"publisher","first-page":"eabi7377","DOI":"10.1126\/science.abi7377","article-title":"A single-cell atlas of the normal and malformed human brain vasculature","volume":"375","author":"Winkler","year":"2022","journal-title":"Science"},{"key":"2026092808242963000_ref3","doi-asserted-by":"publisher","first-page":"971","DOI":"10.1038\/s41590-022-01215-0","article-title":"Single-cell RNA sequencing reveals evolution of immune landscape during glioblastoma progression","volume":"23","author":"Yeo","year":"2022","journal-title":"Nat Immunol"},{"key":"2026092808242963000_ref4","doi-asserted-by":"publisher","first-page":"4790","DOI":"10.1016\/j.cell.2024.06.038","article-title":"Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes","volume":"187","author":"Yang","year":"2024","journal-title":"Cell"},{"key":"2026092808242963000_ref5","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1038\/nature21350","article-title":"Scaling single-cell genomics from phenomenology to mechanism","volume":"541","author":"Tanay","year":"2017","journal-title":"Nature"},{"key":"2026092808242963000_ref6","first-page":"1","article-title":"Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq","volume":"5","author":"Brandon","year":"2021","journal-title":"Journal of Translational Genetics and Genomics"},{"key":"2026092808242963000_ref7","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1016\/j.cell.2017.10.044","article-title":"Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer","volume":"171","author":"Puram","year":"2017","journal-title":"Cell"},{"key":"2026092808242963000_ref8","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1016\/j.cell.2019.10.003","article-title":"Landscape and dynamics of single immune cells in hepatocellular carcinoma","volume":"179","author":"Zhang","year":"2019","journal-title":"Cell"},{"key":"2026092808242963000_ref9","doi-asserted-by":"publisher","first-page":"4235","DOI":"10.1016\/j.cell.2023.07.034","article-title":"A pan-cancer single-cell panorama of human natural killer cells","volume":"186","author":"Tang","year":"2023","journal-title":"Cell"},{"key":"2026092808242963000_ref10","doi-asserted-by":"publisher","first-page":"1207","DOI":"10.1002\/cac2.12486","article-title":"Interactions of indoleamine 2,3-dioxygenase-expressing LAMP3(+) dendritic cells with CD4(+) regulatory T cells and CD8(+) exhausted T cells: synergistically remodeling of the immunosuppressive microenvironment in cervical cancer and therapeutic implications","volume":"43","author":"Qu","year":"2023","journal-title":"Cancer Commun (Lond)"},{"key":"2026092808242963000_ref11","doi-asserted-by":"publisher","first-page":"eabl5197","DOI":"10.1126\/science.abl5197","article-title":"Cross-tissue immune cell analysis reveals tissue-specific features in humans","volume":"376","author":"Dom\u00ednguez Conde","year":"2022","journal-title":"Science"},{"key":"2026092808242963000_ref12","doi-asserted-by":"publisher","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":"2026092808242963000_ref13","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab775","article-title":"scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network","volume":"49","author":"Shao","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026092808242963000_ref14","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2020.100882","article-title":"ScCATCH: automatic annotation on cell types of clusters from single-cell RNA sequencing data","volume":"23","author":"Shao","year":"2020","journal-title":"iScience"},{"key":"2026092808242963000_ref15","doi-asserted-by":"publisher","first-page":"490","DOI":"10.3389\/fgene.2020.00490","article-title":"SCSA: a cell type annotation tool for single-cell RNA-seq data","volume":"11","author":"Cao","year":"2020","journal-title":"Front Genet"},{"key":"2026092808242963000_ref16","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1186\/s13059-019-1795-z","article-title":"A comparison of automatic cell identification methods for single-cell RNA sequencing data","volume":"20","author":"Abdelaal","year":"2019","journal-title":"Genome Biol"},{"key":"2026092808242963000_ref17","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1038\/s41592-019-0529-1","article-title":"Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling","volume":"16","author":"Zhang","year":"2019","journal-title":"Nat Methods"},{"key":"2026092808242963000_ref18","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/s11427-023-2561-0","article-title":"Single-cell omics: experimental workflow, data analyses and applications","volume":"68","author":"Sun","year":"2024","journal-title":"Sci China Life Sci"},{"key":"2026092808242963000_ref19","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1016\/j.csbj.2021.01.015","article-title":"Automated methods for cell type annotation on scRNA-seq data","volume":"19","author":"Pasquini","year":"2021","journal-title":"Comput Struct Biotechnol J"},{"key":"2026092808242963000_ref20","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20188746","article-title":"Current best practices in single-cell RNA-seq analysis: a tutorial","volume":"15","author":"Luecken","year":"2019","journal-title":"Mol Syst Biol"},{"key":"2026092808242963000_ref32","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1073\/pnas.0605965104","article-title":"Resolution limit in community detection","volume":"104","author":"Fortunato","year":"2007","journal-title":"Proc Natl Acad Sci"},{"key":"2026092808242963000_ref21","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1038\/s41576-018-0088-9","article-title":"Challenges in unsupervised clustering of single-cell RNA-seq data","volume":"20","author":"Kiselev","year":"2019","journal-title":"Nat Rev Genet"},{"key":"2026092808242963000_ref22","doi-asserted-by":"publisher","first-page":"1196","DOI":"10.1038\/s41592-023-01933-9","article-title":"Significance analysis for clustering with single-cell RNA-sequencing data","volume":"20","author":"Grabski","year":"2023","journal-title":"Nat Methods"},{"key":"2026092808242963000_ref23","first-page":"37","article-title":"Use of \"default\" parameter settings when analyzing single cell RNA sequencing data using Seurat: a biologist's perspective","volume":"5","author":"Isaac","year":"2021","journal-title":"Journal of Translational Genetics and Genomics"},{"key":"2026092808242963000_ref24","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1016\/j.jhep.2023.01.011","article-title":"Identification of a tumour immune barrier in the HCC microenvironment that determines the efficacy of immunotherapy","volume":"78","author":"Liu","year":"2023","journal-title":"J Hepatol"},{"key":"2026092808242963000_ref25","doi-asserted-by":"publisher","first-page":"5291","DOI":"10.1038\/s41467-021-25539-x","article-title":"Dissecting esophageal squamous-cell carcinoma ecosystem by single-cell transcriptomic analysis","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat Commun"},{"key":"2026092808242963000_ref26","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1038\/s41586-022-05060-x","article-title":"Spatial multi-omic map of human myocardial infarction","volume":"608","author":"Kuppe","year":"2022","journal-title":"Nature"},{"key":"2026092808242963000_ref27","doi-asserted-by":"publisher","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":"2026092808242963000_ref28","doi-asserted-by":"publisher","first-page":"2374","DOI":"10.1093\/bioinformatics\/btab116","article-title":"ESCO: single cell expression simulation incorporating gene co-expression","volume":"37","author":"Tian","year":"2021","journal-title":"Bioinformatics"},{"key":"2026092808242963000_ref29","author":"Liu","year":"2012"},{"key":"2026092808242963000_ref30","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2026092808242963000_ref31","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1038\/nmeth.4236","article-title":"SC3: consensus clustering of single-cell RNA-seq data","volume":"14","author":"Kiselev","year":"2017","journal-title":"Nat Methods"},{"key":"2026092808242963000_ref33","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1016\/j.immuni.2020.08.004","article-title":"Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver","volume":"53","author":"Remmerie","year":"2020","journal-title":"Immunity"},{"key":"2026092808242963000_ref34","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1016\/j.eng.2023.12.004","article-title":"A single-cell landscape of human liver transplantation reveals a pathogenic immune niche associated with early allograft dysfunction","volume":"36","author":"Shao","year":"2024","journal-title":"Engineering"},{"key":"2026092808242963000_ref35","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/j.cell.2021.12.018","article-title":"Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches","volume":"185","author":"Guilliams","year":"2022","journal-title":"Cell"},{"key":"2026092808242963000_ref36","doi-asserted-by":"publisher","first-page":"5226","DOI":"10.1038\/s41467-023-40895-6","article-title":"Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype","volume":"14","author":"Oh","year":"2023","journal-title":"Nat Commun"},{"key":"2026092808242963000_ref37","doi-asserted-by":"publisher","first-page":"4506","DOI":"10.1038\/s41467-023-40156-6","article-title":"Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease","volume":"14","author":"Garrido-Trigo","year":"2023","journal-title":"Nat Commun"},{"key":"2026092808242963000_ref38","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/j.immuni.2024.01.006","article-title":"An atlas of cells in the human tonsil","volume":"57","author":"Massoni-Badosa","year":"2024","journal-title":"Immunity"},{"key":"2026092808242963000_ref39","doi-asserted-by":"publisher","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":"2026092808242963000_ref40","doi-asserted-by":"publisher","first-page":"1470","DOI":"10.1038\/s41592-024-02201-0","article-title":"scGPT: toward building a foundation model for single-cell multi-omics using generative AI","volume":"21","author":"Cui","year":"2024","journal-title":"Nat Methods"},{"key":"2026092808242963000_ref41","doi-asserted-by":"publisher","first-page":"9996","DOI":"10.1038\/s41598-019-45593-2","article-title":"Hepatic triglyceride content does not affect circulating CETP: lessons from a liraglutide intervention trial and a population-based cohort","volume":"9","author":"Eyk","year":"2019","journal-title":"Sci Rep"},{"key":"2026092808242963000_ref42","doi-asserted-by":"publisher","first-page":"2725","DOI":"10.7314\/APJCP.2015.16.7.2725","article-title":"S100A12 and RAGE expression in human bladder transitional cell carcinoma: a role for the ligand\/RAGE axis in tumor progression?","volume":"16","author":"Khorramdelazad","year":"2015","journal-title":"Asian Pac J Cancer Prev"},{"key":"2026092808242963000_ref43","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1002\/art.41813","article-title":"Expansion of Fc\u03b3 receptor IIIa-positive macrophages, ficolin 1-positive monocyte-derived dendritic cells, and plasmacytoid dendritic cells associated with severe skin disease in systemic sclerosis","volume":"74","author":"Xue","year":"2022","journal-title":"Arthritis Rheumatol"},{"key":"2026092808242963000_ref44","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1038\/s41587-022-01233-1","article-title":"Spatial charting of single-cell transcriptomes in tissues","volume":"40","author":"Wei","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2026092808242963000_ref45","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.cytogfr.2016.03.010","article-title":"HES1 in immunity and cancer","volume":"30","author":"Rani","year":"2016","journal-title":"Cytokine Growth Factor Rev"},{"key":"2026092808242963000_ref46","doi-asserted-by":"publisher","first-page":"2802","DOI":"10.7150\/jca.19142","article-title":"HES1 promotes colorectal cancer cell resistance to 5-fu by inducing of EMT and ABC transporter proteins","volume":"8","author":"Sun","year":"2017","journal-title":"J Cancer"},{"key":"2026092808242963000_ref47","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1186\/s13046-023-02625-0","article-title":"HES1-mediated down-regulation of miR-138 sustains NOTCH1 activation and promotes proliferation and invasion in renal cell carcinoma","volume":"42","author":"Liu","year":"2023","journal-title":"J Exp Clin Cancer Res"},{"key":"2026092808242963000_ref48","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1007\/s12029-014-9648-1","article-title":"HES1 as an independent prognostic marker in esophageal squamous cell carcinoma","volume":"45","author":"Taleb","year":"2014","journal-title":"J Gastrointest Cancer"},{"key":"2026092808242963000_ref49","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/s41586-019-0979-8","article-title":"Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction","volume":"567","author":"Liu","year":"2019","journal-title":"Nature"},{"key":"2026092808242963000_ref50","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1186\/s12885-021-08520-1","article-title":"Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer","volume":"21","author":"Gao","year":"2021","journal-title":"BMC Cancer"},{"key":"2026092808242963000_ref51","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1016\/j.imbio.2017.11.006","article-title":"Cardiac CD68+ and stabilin-1+ macrophages in wound healing following myocardial infarction: from experiment to clinic","volume":"223","author":"Ryabov","year":"2018","journal-title":"Immunobiology"},{"key":"2026092808242963000_ref52","doi-asserted-by":"publisher","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":"2026092808242963000_ref53","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1055\/a-0794-6163","article-title":"Free IGF-1, intact IGFBP-4, and PicoPAPP-A are altered in acute myocardial infarction compared to stable coronary artery disease and healthy controls","volume":"51","author":"Anastasilakis","year":"2019","journal-title":"Horm Metab Res"},{"key":"2026092808242963000_ref54","doi-asserted-by":"publisher","first-page":"4785","DOI":"10.3892\/mmr.2018.8456","article-title":"miR-483-3p regulates acute myocardial infarction by transcriptionally repressing insulin growth factor 1 expression","volume":"17","author":"Sun","year":"2018","journal-title":"Mol Med Rep"},{"key":"2026092808242963000_ref55","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.ymthe.2018.10.020","article-title":"IGF1 treatment improves cardiac remodeling after infarction by targeting myeloid cells","volume":"27","author":"Heinen","year":"2019","journal-title":"Mol Ther"},{"key":"2026092808242963000_ref56","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1038\/s41420-024-02169-y","article-title":"Extracellular vesicles containing GAS6 protect the liver from ischemia-reperfusion injury by enhancing macrophage efferocytosis via MerTK-ERK-COX2 signaling","volume":"10","author":"Miao","year":"2024","journal-title":"Cell Death Discov"},{"key":"2026092808242963000_ref57","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/s41592-022-01728-4","article-title":"Screening cell-cell communication in spatial transcriptomics via collective optimal transport","volume":"20","author":"Cang","year":"2023","journal-title":"Nat Methods"},{"key":"2026092808242963000_ref58","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1038\/s41588-024-01993-3","article-title":"Consensus prediction of cell type labels in single-cell data with popV","volume":"56","author":"Ergen","year":"2024","journal-title":"Nat Genet"},{"key":"2026092808242963000_ref59","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-021-01336-8","article-title":"Benchmarking atlas-level data integration in single-cell genomics","volume":"19","author":"Luecken","year":"2022","journal-title":"Nat Methods"},{"key":"2026092808242963000_ref60","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaa6090","article-title":"RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells","volume":"348","author":"Chen","year":"2015","journal-title":"Science"},{"key":"2026092808242963000_ref61","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1038\/nmeth.2892","article-title":"Single-cell in situ RNA profiling by sequential hybridization","volume":"11","author":"Lubeck","year":"2014","journal-title":"Nat Methods"},{"key":"2026092808242963000_ref62","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","article-title":"Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression","volume":"20","author":"Hafemeister","year":"2019","journal-title":"Genome Biol"},{"key":"2026092808242963000_ref63","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"2026092808242963000_ref64","doi-asserted-by":"publisher","first-page":"4429","DOI":"10.1038\/s41467-022-32111-8","article-title":"Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk","volume":"13","author":"Shao","year":"2022","journal-title":"Nat Commun"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/5\/bbag529\/71438181\/bbag529.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/5\/bbag529\/71438181\/bbag529.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T12:24:43Z","timestamp":1790598283000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag529\/8841210"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":64,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag529","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,9,1]]},"article-number":"bbag529"}}