{
  "abstract": "Ambient RNA contamination confounds expression analysis in droplet-based single-cell and single-nucleus RNA sequencing. Here we present AmbiDose, which combines an ambient profile estimated from empty droplets with cell-specific nominal removal budgets and expression-based protection of lineage-enriched genes. Its ambient dose guides count removal rather than estimating a calibrated contamination fraction. In a held-out human-mouse GEM-X mixture, AmbiDose removed 92.0% of cross-species UMIs while retaining 99.6% of same-species UMIs. It reduced off-target marker expression in kidney-tumor and fetal-liver cohorts and yielded the lowest proximal-tubule marker leakage among the tested methods across five strain-mixed kidney libraries. Simulations supported the contribution of cell-specific dose estimates but identified reduced endogenous retention or incomplete removal when ambient and endogenous expression overlapped. AmbiDose is available as a Python package compatible with Scanpy.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Pathology, Johns Hopkins University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Z. Li"
    },
    {
      "name": "A. W. James"
    },
    {
      "affs": [
        0
      ],
      "name": "S. Li"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/34wcaakmf889z.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.27.754849",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.27.754849v1.full",
  "id": "34wcaakmf889z",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.27.754849v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7216495730",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.27.754849v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-27",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/34wcaakmf889z.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:26:25Z",
      "native_id": "10.64898/2026.09.27.754849",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.27.754849v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "AmbiDose: per-cell removal budgets for ambient RNA contamination",
  "title_text": "AmbiDose: per-cell removal budgets for ambient RNA contamination",
  "type": "preprint",
  "updated_at": "2026-10-30T12:26:25Z",
  "url": "https://research.draconitic.com/paper/34wcaakmf889z",
  "venue": "bioRxiv",
  "versions": []
}