{
  "abstract": "Single-cell RNA sequencing is revolutionizing our understanding of cell state dynamics, allowing researchers to capture and quantify the transcriptomic profile of a single cell at a specific timepoint. Among the computational techniques used to predict cellular trajectories, RNA velocity has emerged as a predominant tool for modeling transcriptional dynamics. RNA velocity leverages the mRNA maturation process to generate velocity vectors that predict the likely future state of a cell, offering insights into cellular differentiation, aging, and disease progression. Although this technique has shown promise across biological fields, the performance accuracy varies depending on the RNA velocity method and dataset. We established a comparative pipeline and analyzed the performance of five RNA velocity methods on three datasets based on local consistency, method agreement, identification of driver genes, and robustness to sequencing depth. This benchmark provides a resource for scientists to understand the strengths and limitations of different RNA velocity methods.",
  "abstract_shown": true,
  "affiliations": [
    "Biohub, San Francisco, United States of America",
    "Present address Biological and Medical Informatics Graduate Program, University of California, San Francisco, California, United States of America",
    "Chan Zuckerberg Biohub SF",
    "University of California, San Francisco, United States of America",
    "Calico Life Sciences LLC",
    "Present address Calico Life Sciences LLC, South San Francisco, California, United States of America",
    "Institut de la Vision, Sorbonne Universite´, INSERM, CNRS, Paris, France"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Sarah Ancheta",
      "orcid": "0009-0004-2198-2821"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Leah C. Dorman",
      "orcid": "0000-0002-5511-887X"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Guillaume Le Treut",
      "orcid": "0000-0002-9842-2804"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Abel Gurung",
      "orcid": "0009-0008-7282-9252"
    },
    {
      "affs": [
        0,
        3,
        2
      ],
      "name": "Greg Huber",
      "orcid": "0000-0001-8565-3067"
    },
    {
      "affs": [
        0,
        4
      ],
      "name": "Löıc A. Royer",
      "orcid": "0000-0002-9991-9724"
    },
    {
      "affs": [
        0,
        5,
        2
      ],
      "name": "Alejandro A. Granados",
      "orcid": "0000-0002-6275-9800"
    },
    {
      "affs": [
        0,
        6
      ],
      "name": "Merlin Lange",
      "orcid": "0000-0003-0534-4374"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/d5fxzs56eqzx5.bib",
  "cited_by": 10,
  "doi": "10.1371/journal.pcbi.1014303",
  "fulltext_url": null,
  "id": "d5fxzs56eqzx5",
  "issns": [
    "1553-734X",
    "1553-7358"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pcbi.1014303",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W4400152666",
  "pdf_url": "https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1014303&type=printable",
  "pmcid": "PMC13252846",
  "pmid": "42224352",
  "published": "2026-06-01",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/d5fxzs56eqzx5.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:46Z",
      "native_id": "W4400152666",
      "source": "openalex",
      "url": "https://doi.org/10.1371/journal.pcbi.1014303"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Challenges and progress in RNA velocity: Comparative analysis across multiple biological contexts",
  "title_text": "Challenges and progress in RNA velocity: Comparative analysis across multiple biological contexts",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T13:21:07Z",
  "url": "https://research.draconitic.com/paper/d5fxzs56eqzx5",
  "venue": "PLoS Computational Biology",
  "versions": []
}