{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T21:10:55Z","timestamp":1789506655019,"version":"build-2803163510"},"reference-count":75,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,12,1]],"date-time":"2026-12-01T00:00:00Z","timestamp":1796083200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["The International Journal of Biochemistry &amp; Cell Biology"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1016\/j.biocel.2026.107027","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T07:10:51Z","timestamp":1789024251000},"page":"107027","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Annotation of cell types in single-cell sequencing for cardiovascular disease: Concepts, workflows, challenges, and best practices"],"prefix":"10.1016","volume":"201","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9631-1270","authenticated-orcid":false,"given":"Lu","family":"Sun","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lizhi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqian","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianrui","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaihua","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaiyu","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingqi","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib1","doi-asserted-by":"crossref","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."},{"issue":"7867","key":"10.1016\/j.biocel.2026.107027_bib2","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/s41586-021-03674-1","article-title":"A transcriptional switch governs fibroblast activation in heart disease","volume":"595","author":"Alexanian","year":"2021","journal-title":"Nature"},{"issue":"2","key":"10.1016\/j.biocel.2026.107027_bib3","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."},{"issue":"12","key":"10.1016\/j.biocel.2026.107027_bib4","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1038\/nrg.2016.127","article-title":"The origin and evolution of cell types","volume":"17","author":"Arendt","year":"2016","journal-title":"Nat. Rev. Genet."},{"issue":"7","key":"10.1016\/j.biocel.2026.107027_bib5","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1016\/j.cell.2019.11.025","article-title":"A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart","volume":"179","author":"Asp","year":"2019","journal-title":"Cell"},{"issue":"17","key":"10.1016\/j.biocel.2026.107027_bib6","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/s12859-017-1977-1","article-title":"Cell type discovery and representation in the era of high-content single cell phenotyping","volume":"18","author":"Bakken","year":"2017","journal-title":"BMC Bioinforma."},{"key":"10.1016\/j.biocel.2026.107027_bib7","article-title":"Dimensionality reduction for visualizing scRNA-seq using UMAP","author":"Becht","year":"2018","journal-title":"Nat. Biotechnol."},{"issue":"11","key":"10.1016\/j.biocel.2026.107027_bib8","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1038\/s41592-021-01264-7","article-title":"Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram","volume":"18","author":"Biancalani","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.biocel.2026.107027_bib9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-3-030-02601-1_1","article-title":"Pericyte biology: development, homeostasis, and disease","volume":"1109","author":"Birbrair","year":"2018","journal-title":"Adv. Exp. Med. Biol."},{"issue":"11","key":"10.1016\/j.biocel.2026.107027_bib10","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1038\/s44161-022-00160-3","article-title":"Single-cell and spatial transcriptomics of the infarcted heart define the dynamic onset of the border zone in response to mechanical destabilization","volume":"1","author":"Calcagno","year":"2022","journal-title":"Nat. Cardiovasc. Res."},{"issue":"11","key":"10.1016\/j.biocel.2026.107027_bib11","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1038\/s44161-022-00160-3","article-title":"Single-cell and spatial transcriptomics of the infarcted heart define the dynamic onset of the border zone in response to mechanical destabilization","volume":"1","author":"Calcagno","year":"2022","journal-title":"Nat. Cardiovasc. Res."},{"issue":"7745","key":"10.1016\/j.biocel.2026.107027_bib12","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"},{"issue":"7924","key":"10.1016\/j.biocel.2026.107027_bib13","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/s41586-022-05060-x","article-title":"Spatial multi-omic map of human myocardial infarction","volume":"608","author":"Christoph","year":"2022","journal-title":"Nature"},{"issue":"7","key":"10.1016\/j.biocel.2026.107027_bib14","doi-asserted-by":"crossref","first-page":"1934","DOI":"10.1016\/j.celrep.2019.01.079","article-title":"Single-cell transcriptome analysis maps the developmental track of the human heart","volume":"26","author":"Cui","year":"2019","journal-title":"Cell. Rep."},{"issue":"D1","key":"10.1016\/j.biocel.2026.107027_bib15","doi-asserted-by":"crossref","first-page":"D886","DOI":"10.1093\/nar\/gkae1142","article-title":"CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data","volume":"53","author":"CZI Cell Science Program","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.biocel.2026.107027_bib16","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1016\/j.csbj.2025.03.051","article-title":"Mapping Cell Identity from scRNA-seq: a primer on computational methods","volume":"27","author":"Daniele","year":"2025","journal-title":"Comput. Struct. Biotechnol. J."},{"issue":"7767","key":"10.1016\/j.biocel.2026.107027_bib17","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41586-019-1414-x","article-title":"Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects","volume":"572","author":"de Soysa","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.biocel.2026.107027_bib18","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2023.1027346","article-title":"Manual cell selection in single cell transcriptomics using scSELpy supports the analysis of immune cell subsets","volume":"14","author":"Dedden","year":"2023","journal-title":"Front. Immunol."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib19","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."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib20","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/s41590-018-0272-2","article-title":"Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction","volume":"20","author":"Dick","year":"2019","journal-title":"Nat. Immunol."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib21","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/s13326-016-0088-7","article-title":"The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability","volume":"7","author":"Diehl","year":"2016","journal-title":"J. Biomed. Semant."},{"issue":"6594","key":"10.1016\/j.biocel.2026.107027_bib22","doi-asserted-by":"crossref","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"},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib23","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.immuni.2013.11.019","article-title":"Embryonic and adult-derived resident cardiac macrophages are maintained through distinct mechanisms at steady state and during inflammation","volume":"40","author":"Epelman","year":"2014","journal-title":"Immunity"},{"key":"10.1016\/j.biocel.2026.107027_bib24","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s42256-022-00534-z","article-title":"scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data","volume":"4","author":"Fan","year":"2022","journal-title":"Nat. Mach. Intell."},{"key":"10.1016\/j.biocel.2026.107027_bib25","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.43882","article-title":"Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury","volume":"8","author":"Farbehi","year":"2019","journal-title":"Elife"},{"issue":"9","key":"10.1016\/j.biocel.2026.107027_bib26","doi-asserted-by":"crossref","first-page":"3149","DOI":"10.1016\/j.celrep.2020.02.008","article-title":"Dynamic interstitial cell response during myocardial infarction predicts resilience to rupture in genetically diverse mice","volume":"30","author":"Forte","year":"2020","journal-title":"Cell. Rep."},{"issue":"2","key":"10.1016\/j.biocel.2026.107027_bib27","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1161\/CIRCULATIONAHA.117.030742","article-title":"Single-cell sequencing of the healthy and diseased heart reveals cytoskeleton-associated protein 4 as a new modulator of fibroblasts activation","volume":"138","author":"Gladka","year":"2018","journal-title":"Circulation"},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib28","doi-asserted-by":"crossref","first-page":"4566","DOI":"10.1038\/s41467-023-40173-5","article-title":"Guided construction of single cell reference for human and mouse lung","volume":"14","author":"Guo","year":"2023","journal-title":"Nat. Commun."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib29","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","article-title":"Normalization and variance stabilization of scRNA-seq data using regularized negative binomial regression","volume":"20","author":"Hafemeister","year":"2019","journal-title":"Genome Biol."},{"issue":"13","key":"10.1016\/j.biocel.2026.107027_bib30","doi-asserted-by":"crossref","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":"10.1016\/j.biocel.2026.107027_bib31","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.65921","article-title":"Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted murine heart","volume":"10","author":"Hesse","year":"2021","journal-title":"Elife"},{"issue":"8","key":"10.1016\/j.biocel.2026.107027_bib32","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/s41576-023-00586-w","article-title":"Best practices for single-cell analysis across modalities","volume":"24","author":"Heumos","year":"2023","journal-title":"Nat. Rev. Genet."},{"issue":"15","key":"10.1016\/j.biocel.2026.107027_bib33","doi-asserted-by":"crossref","first-page":"2739","DOI":"10.1016\/j.cell.2022.06.031","article-title":"What is a cell type and how to define it?","volume":"185","author":"Hongkui","year":"2022","journal-title":"Cell"},{"issue":"17","key":"10.1016\/j.biocel.2026.107027_bib34","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/s13059-016-0888-1","article-title":"Classification of low quality cells from single-cell RNA-seq data","volume":"17","author":"Ilicic","year":"2016","journal-title":"Genome Biol."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib35","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/s40364-024-00696-5","article-title":"CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases","volume":"12","author":"Jiang","year":"2024","journal-title":"Biomark. Res."},{"issue":"12","key":"10.1016\/j.biocel.2026.107027_bib36","doi-asserted-by":"crossref","first-page":"2128","DOI":"10.1038\/s12276-022-00892-z","article-title":"Comparison of cell type distribution between single-cell and single-nucleus RNA sequencing: enrichment of adherent cell types in single-nucleus RNA sequencing","volume":"54","author":"Jin","year":"2022","journal-title":"Exp. Mol. Med."},{"issue":"8038","key":"10.1016\/j.biocel.2026.107027_bib37","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/s41586-024-08008-5","article-title":"Targeting immune\u2013fibroblast cell communication in heart failure","volume":"635","author":"Junedh","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.biocel.2026.107027_bib38","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1016\/j.cell.2020.01.015","article-title":"Single-cell transcriptome atlas of murine endothelial cells","volume":"180","author":"Kalucka","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.biocel.2026.107027_bib39","doi-asserted-by":"crossref","first-page":"5890","DOI":"10.1038\/s41467-021-25957-x","article-title":"Efficient and precise single-cell reference atlas mapping with Symphony","volume":"12","author":"Kang","year":"2021","journal-title":"Nat. Commun."},{"issue":"3","key":"10.1016\/j.biocel.2026.107027_bib40","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/s44161-022-00028-6","article-title":"Single-cell transcriptomics reveals cell-type-specific diversification in human heart failure","volume":"1","author":"Koenig","year":"2022","journal-title":"Nat. Cardiovasc. Res."},{"issue":"12","key":"10.1016\/j.biocel.2026.107027_bib41","doi-asserted-by":"crossref","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"},{"issue":"7924","key":"10.1016\/j.biocel.2026.107027_bib42","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/s41586-022-05060-x","article-title":"Spatial multi-omic map of myocardial infarction","volume":"608","author":"Kuppe","year":"2022","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib43","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/nbt.4038","article-title":"Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain","volume":"36","author":"Lake","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.biocel.2026.107027_bib44","doi-asserted-by":"crossref","first-page":"2768","DOI":"10.1038\/s41467-020-16264-y","article-title":"Cellular census of human fibrosis defines functionally distinct stromal cell types and states","volume":"11","author":"Layton","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.biocel.2026.107027_bib45","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1038\/s41586-020-2797-4","article-title":"Cells of the adult human heart","volume":"588","author":"Litvi\u0148ukov\u00e1","year":"2020","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib46","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/s41587-021-01001-7","article-title":"Mapping single-cell data to reference atlases by transfer learning","volume":"40","author":"Lotfollahi","year":"2022","journal-title":"Nat. Biotechnol."},{"issue":"10","key":"10.1016\/j.biocel.2026.107027_bib47","doi-asserted-by":"crossref","first-page":"2343","DOI":"10.1016\/j.cell.2024.03.009","article-title":"The future of rapid and automated single-cell data analysis using reference mapping","volume":"187","author":"Lotfollahi","year":"2024","journal-title":"Cell"},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib48","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/s41587-021-01001-7","article-title":"Mapping single-cell data to reference atlases by transfer learning","volume":"40","author":"Lotfollahi","year":"2021","journal-title":"Nat. Biotechnol."},{"issue":"6","key":"10.1016\/j.biocel.2026.107027_bib49","doi-asserted-by":"crossref","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."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib50","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/s13059-019-1662-y","article-title":"EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data","volume":"20","author":"Lun","year":"2019","journal-title":"Genome Biol."},{"issue":"4","key":"10.1016\/j.biocel.2026.107027_bib51","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell. Syst."},{"issue":"15","key":"10.1016\/j.biocel.2026.107027_bib52","doi-asserted-by":"crossref","first-page":"1448","DOI":"10.1161\/CIRCULATIONAHA.119.045115","article-title":"High-resolution transcriptomic profiling of the heart during chronic stress reveals cellular drivers of cardiac fibrosis and hypertrophy","volume":"142","author":"McLellan","year":"2020","journal-title":"Circulation"},{"issue":"12","key":"10.1016\/j.biocel.2026.107027_bib53","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1161\/CIRCRESAHA.124.323672","article-title":"Revisiting cardiac biology in the era of single-cell and spatial Omics","volume":"134","author":"Palmer","year":"2024","journal-title":"Circ. Res."},{"issue":"25","key":"10.1016\/j.biocel.2026.107027_bib54","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adk8501","article-title":"Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies","volume":"10","author":"Patrick","year":"2024","journal-title":"Sci. Adv."},{"issue":"10","key":"10.1016\/j.biocel.2026.107027_bib55","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/s41592-019-0535-3","article-title":"Supervised classification enables rapid annotation of cell atlases","volume":"16","author":"Pliner","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.biocel.2026.107027_bib56","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.27041","article-title":"The human cell atlas","volume":"6","author":"Regev","year":"2017","journal-title":"Elife"},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib57","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/s41467-017-00319-8","article-title":"Single cardiomyocyte nuclear transcriptomes reveal a lincRNA-regulated de-differentiation and cell cycle stress-response in vivo","volume":"8","author":"See","year":"2017","journal-title":"Nat. Commun."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib58","doi-asserted-by":"crossref","first-page":"6495","DOI":"10.1038\/s41467-023-41855-w","article-title":"Benchmarking strategies for cross-species integration of single-cell RNA sequencing data","volume":"14","author":"Song","year":"2023","journal-title":"Nat. Commun."},{"issue":"7","key":"10.1016\/j.biocel.2026.107027_bib59","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"issue":"18","key":"10.1016\/j.biocel.2026.107027_bib60","doi-asserted-by":"crossref","first-page":"4817","DOI":"10.1093\/bioinformatics\/btaa611","article-title":"Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data","volume":"36","author":"Sturm","year":"2020","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib61","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/s44161-022-00205-7","article-title":"Current and future perspectives of single-cell multi-omics technologies in cardiovascular research","volume":"2","author":"Tan","year":"2023","journal-title":"Nat. Cardiovasc. Res."},{"issue":"2","key":"10.1016\/j.biocel.2026.107027_bib62","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.cels.2019.06.004","article-title":"SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species","volume":"9","author":"Tan","year":"2019","journal-title":"Cell. Syst."},{"issue":"12","key":"10.1016\/j.biocel.2026.107027_bib63","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1038\/s44161-023-00367-y","article-title":"Single cell multimodal analyses reveal epigenomic and transcriptomic basis for birth defects in maternal diabetes","volume":"2","author":"Tomohiro","year":"2023","journal-title":"Nat. Cardiovasc. Res."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib64","doi-asserted-by":"crossref","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci. Rep."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib65","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13059-019-1850-9","article-title":"A benchmark of batch-effect correction methods for single-cell RNA sequencing data","volume":"21","author":"Tran","year":"2020","journal-title":"Genome Biol."},{"issue":"5","key":"10.1016\/j.biocel.2026.107027_bib66","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1161\/CIRCULATIONAHA.119.045401","article-title":"Transcriptional and cellular diversity of the human heart","volume":"142","author":"Tucker","year":"2020","journal-title":"Circulation"},{"issue":"10","key":"10.1016\/j.biocel.2026.107027_bib67","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"},{"issue":"6335","key":"10.1016\/j.biocel.2026.107027_bib68","doi-asserted-by":"crossref","DOI":"10.1126\/science.aah4573","article-title":"Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes and progenitors","volume":"356","author":"Villani","year":"2017","journal-title":"Science"},{"issue":"5","key":"10.1016\/j.biocel.2026.107027_bib69","doi-asserted-by":"crossref","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":"Vladimir","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.biocel.2026.107027_bib70","doi-asserted-by":"crossref","first-page":"641","DOI":"10.2147\/VHRM.S288090","article-title":"Single-cell RNA sequencing (scRNA-seq) in cardiac tissue: applications and limitations","volume":"17","author":"Wang","year":"2021","journal-title":"Vasc. Health Risk Manag."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib71","doi-asserted-by":"crossref","first-page":"5556","DOI":"10.1038\/s41467-021-25725-x","article-title":"Leveraging the cell ontology to classify unseen cell types","volume":"12","author":"Wang","year":"2021","journal-title":"Nat. Commun."},{"issue":"8","key":"10.1016\/j.biocel.2026.107027_bib72","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1038\/s41591-019-0512-5","article-title":"Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis","volume":"25","author":"Wirka","year":"2019","journal-title":"Nat. Med."},{"issue":"4","key":"10.1016\/j.biocel.2026.107027_bib73","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: computational identification of cell doublets in Single-Cell Transcriptomic Data","volume":"8","author":"Wolock","year":"2019","journal-title":"Cell. Syst."},{"issue":"1","key":"10.1016\/j.biocel.2026.107027_bib74","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20209620","article-title":"Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models","volume":"17","author":"Xu","year":"2021","journal-title":"Mol. Syst. Biol."},{"issue":"12","key":"10.1016\/j.biocel.2026.107027_bib75","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa151","article-title":"SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data","volume":"9","author":"Young","year":"2020","journal-title":"Gigascience"}],"container-title":["The International Journal of Biochemistry &amp; Cell Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1357272526001378?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1357272526001378?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T20:35:07Z","timestamp":1789504507000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1357272526001378"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,12]]},"references-count":75,"alternative-id":["S1357272526001378"],"URL":"https:\/\/doi.org\/10.1016\/j.biocel.2026.107027","relation":{},"ISSN":["1357-2725"],"issn-type":[{"value":"1357-2725","type":"print"}],"subject":[],"published":{"date-parts":[[2026,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Annotation of cell types in single-cell sequencing for cardiovascular disease: Concepts, workflows, challenges, and best practices","name":"articletitle","label":"Article Title"},{"value":"The International Journal of Biochemistry & Cell Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.biocel.2026.107027","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"107027"}}