{
  "abstract": "R-loops are non-canonical nucleic acid structures implicated in diverse cellular processes and diseases. We previously developed R-loopBase to address the pressing challenges of inaccurate R-loop maps and the limited understanding of the R-loop regulatory network. However, R-loopBase provided only human R-loop maps with categorical confidence and did not account for cell type specificity. These limitations, coupled with the emerging R-loop profiling technologies and advances in R-loop regulatory mechanisms, have motivated the development of R-loopBase v2.0 (https://rloopbase.nju.edu.cn). After uniformly re-analysing 358 R-loop mapping datasets generated by 16 technologies, we introduce a quantitative R-loop scoring framework that assesses genome-wide R-loop confidence in human, demonstrating strong concordance with known R-loop biology. We further extend the framework to specific cell types and mouse, fruit fly, and yeast. In parallel, we substantially expand the collection of R-loop regulators across species, enabling the inference of changes in R-loop homeostasis. Building on these expanded datasets, we implement several new interactive features and analytical tools, including an expanded multi-species genome browser, deep learning-based R-loop prediction, R-loop homeostasis analysis, and a streamlined data download portal. We anticipate that R-loopBase v2.0 will serve as an enhanced, up-to-date one-stop resource for the R-loop research community.",
  "abstract_shown": true,
  "affiliations": [
    "State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Department of Laboratory Medicine at Nanjing Drum Tower Hospital, Nanjing University , Nanjing 210023 ,",
    "Center of Excellence for Leukemia Studies, Department of Pathology, St. Jude Children’s Research Hospital , Memphis, TN 38105 ,",
    "Nanchuang (Jiangsu) Institute of Chemistry and Health , Nanjing 210032 ,",
    "State Key Laboratory of Natural Medicines, China Pharmaceutical University , Nanjing 211198 ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 12,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Rongchen Gu"
    },
    {
      "affs": [
        0
      ],
      "name": "Jiyun Hu"
    },
    {
      "affs": [
        0
      ],
      "name": "Yajie Gao"
    },
    {
      "affs": [
        0
      ],
      "name": "Hongbing Yang"
    },
    {
      "affs": [
        0
      ],
      "name": "Ruoyao Lin"
    },
    {
      "affs": [
        1
      ],
      "name": "Xiaoming Zhong"
    },
    {
      "affs": [
        0
      ],
      "name": "Kui-Xing Zhang"
    },
    {
      "affs": [
        0
      ],
      "name": "Wenjun Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Qingxi Hu"
    },
    {
      "affs": [
        0
      ],
      "name": "Luojie Wei"
    },
    {
      "affs": [
        0
      ],
      "name": "Zetong Xing"
    },
    {
      "affs": [
        0,
        2,
        3
      ],
      "name": "Jia-Yu Chen",
      "orcid": "0000-0001-9449-9321"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8h3nyv3mqftra.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag1103",
  "fulltext_url": null,
  "id": "8h3nyv3mqftra",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1103/9012871",
  "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": null,
  "pdf_url": "https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkag1103/73053499/gkag1103.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-05",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/8h3nyv3mqftra.ris",
  "sources": [
    {
      "first_seen": "2026-11-05T12:20:58Z",
      "native_id": "10.1093/nar/gkag1103",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1103/9012871"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "issn:0305-1048",
      "subfield": "molecular-biology"
    }
  ],
  "title": "R-loopBase v2.0: species- and cell type-resolved quantitative R-loop maps and R-loop regulatory resources",
  "title_text": "R-loopBase v2.0: species- and cell type-resolved quantitative R-loop maps and R-loop regulatory resources",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T00:21:10Z",
  "url": "https://research.draconitic.com/paper/8h3nyv3mqftra",
  "venue": "Nucleic Acids Research",
  "versions": []
}