{
  "abstract": "The updated CellMarker 3.0 resource (http://bio-bigdata.hrbmu.edu.cn/CellMarker) offers a comprehensive resource, integrating experimentally validated and robustly algorithm-predicted marker genes for diverse cell types across human and mouse tissues. In addition, web tools for analyzing single-cell RNA-seq (scRNA-seq) and spatial transcriptomics (ST) data are described. CellMarker 3.0 was updated with more data and new features, including (i) appending 274 tissues, 1877 cell types, 64 040 markers, and 1 245 923 tissue–cell type–marker entries over the previous version. The current release contains 930 tissues, 4455 cell types, and 90 955 cell markers, resulting in a total of 1 329 284 tissue–cell type–marker entries. (ii) Expanding the resource to include computationally predicted cell-type markers derived from six algorithms, namely Spapros, Seurat::FindAllMarkers, SEMITONES, Cepo, CelliD, and COSG. (iii) New marker information was incorporated from 168 sequencing technologies, such as CEL-Seq2 and SNARE-seq. (iv) Covering 35 types of cell markers, including protein–coding genes, rRNAs, and pseudogenes. (v) The cell tool module was comprehensively restructured and upgraded, with the original six scRNA-seq analysis modules systematically optimized and two new spatial transcriptomics modules, Spatial Expression, and Spatial Chat, added. CellMarker 3.0 is a valuable resource that integrates cell identity identification, single-cell transcriptomics, and spatial transcriptomics analysis.",
  "abstract_shown": true,
  "affiliations": [
    "College of Bioinformatics Science and Technology, Harbin Medical University , Harbin, Heilongjiang 150081 ,",
    "School of Intelligent Medicine and Technology (Big Data Research Center), Hainan Medical University , Haikou 571199 ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 16,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Congxue Hu",
      "orcid": "0009-0001-3279-9457"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Tengyue Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Minghui Zhu"
    },
    {
      "affs": [
        0
      ],
      "name": "Liyuan Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Bolin Ren"
    },
    {
      "affs": [
        0
      ],
      "name": "Kuan Yang"
    },
    {
      "affs": [
        1
      ],
      "name": "Zhenzhen Wang",
      "orcid": "0009-0000-5724-0118"
    },
    {
      "affs": [
        0
      ],
      "name": "Maohao Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Baobin Qi"
    },
    {
      "affs": [
        0
      ],
      "name": "Yongjin Long"
    },
    {
      "affs": [
        0
      ],
      "name": "Na Lv"
    },
    {
      "affs": [
        0
      ],
      "name": "Xiaoxu Yang"
    },
    {
      "affs": [
        0
      ],
      "name": "Rui Fu"
    },
    {
      "affs": [
        0
      ],
      "name": "Jing Bai"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Xia Li",
      "orcid": "0000-0002-9794-2648"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Yunpeng Zhang",
      "orcid": "0000-0002-3709-3656"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/01b4wbss5jdsy.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag1040",
  "fulltext_url": null,
  "id": "01b4wbss5jdsy",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1040/9002626",
  "language": null,
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7223949284",
  "pdf_url": "https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkag1040/72531511/gkag1040.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-27",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/01b4wbss5jdsy.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:50Z",
      "native_id": "10.1093/nar/gkag1040",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1040/9002626"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "CellMarker 3.0: an updated resource of manually curated and computationally predicted cell markers in human/mouse and interactive web tools for single-cell and spatial transcriptomics analysis",
  "title_text": "CellMarker 3.0: an updated resource of manually curated and computationally predicted cell markers in human/mouse and interactive web tools for single-cell and spatial transcriptomics analysis",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:50Z",
  "url": "https://research.draconitic.com/paper/01b4wbss5jdsy",
  "venue": "Nucleic Acids Research",
  "versions": []
}