{
  "abstract": "Genomic DNA used as a template for in vitro transcription of RNA can serve as a true negative control for benchmarking RNA modification detection by Nanopore direct RNA sequencing (DRS) models. We generated DRS data for in vitro transcribed (IVT) RNA composed of canonical nucleotides using genomic DNA from a human cell line. We applied Dorado modification calling models to these data, and calculated 9-mer specific false-positive rates for eight RNA modifications as a comparison point for future development of RNA modification models.",
  "abstract_shown": true,
  "affiliations": [
    "Northeastern University Department of Bioengineering, , Boston, MA ,",
    "Northeastern University Department of Electrical & Computer Engineering, , Boston, MA ,",
    "Northeastern University Department of Physics, , Boston, MA ,",
    "Khoury College of Computer Sciences, Northeastern University , Boston, MA ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Talia Tzadikario",
      "orcid": "0009-0000-6795-0340"
    },
    {
      "affs": [
        0
      ],
      "name": "Stuart Akeson",
      "orcid": "0009-0008-8008-2486"
    },
    {
      "affs": [
        0
      ],
      "name": "Sally Dorer"
    },
    {
      "affs": [
        0
      ],
      "name": "Neda Ghohabi Esfahani",
      "orcid": "0000-0003-0539-4603"
    },
    {
      "affs": [
        0
      ],
      "name": "Andrew J Stein",
      "orcid": "0009-0001-6525-6512"
    },
    {
      "affs": [
        1
      ],
      "name": "Pooria Daneshvar Kakhaki",
      "orcid": "0009-0001-3030-836X"
    },
    {
      "affs": [
        0
      ],
      "name": "Urja Choudhary",
      "orcid": "0009-0007-8829-278X"
    },
    {
      "affs": [
        0
      ],
      "name": "Kshitij Amar",
      "orcid": "0000-0002-8365-7942"
    },
    {
      "affs": [
        0,
        2,
        3
      ],
      "name": "Miten Jain",
      "orcid": "0000-0002-4571-3982"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/e1fvmjs3xh107.bib",
  "cited_by": 8,
  "doi": "10.1093/gigascience/giag098",
  "fulltext_url": null,
  "id": "e1fvmjs3xh107",
  "issns": [
    "2047-217X"
  ],
  "landing_url": "https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giag098/9002150",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|RNA modifications and cancer"
    ]
  ],
  "openalex": "W7223650608",
  "pdf_url": "https://academic.oup.com/gigascience/advance-article-pdf/doi/10.1093/gigascience/giag098/72522379/giag098.pdf",
  "pmcid": "PMC13277973",
  "pmid": "42327118",
  "published": "2026-10-20",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/e1fvmjs3xh107.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:42Z",
      "native_id": "10.1093/gigascience/giag098",
      "source": "crossref",
      "url": "https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giag098/9002150"
    },
    {
      "first_seen": "2026-11-02T13:20:38Z",
      "native_id": "W4409865845",
      "source": "openalex",
      "url": "https://doi.org/10.1093/gigascience/giag098"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|RNA modifications and cancer",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line",
  "title_text": "Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line",
  "type": "peer-reviewed",
  "updated_at": "2026-11-04T13:21:07Z",
  "url": "https://research.draconitic.com/paper/e1fvmjs3xh107",
  "venue": "GigaScience",
  "versions": []
}