{
  "abstract": "Multiple single nuclei RNA-sequencing (snRNA-seq) studies of the vulnerable brain regions of Parkinson’s Disease (PD) have revealed alterations in brain cell populations and cell type specific transcriptomes. However, a systematic analysis of cell-type–resolved gene regulatory architecture in PD is lacking. Here, we develop an integrative, meta-cell based multiscale network analysis (MCMNA) of snRNA-seq data from the substantia nigra to systematically uncover molecular mechanisms and identify potential therapeutic targets for PD. MCMNA overcomes the inherent sparsity of single cell data by leveraging metacell-based aggregation, enabling construction of robust gene regulatory networks. Gene co-expression network analysis identifies cell-type specific gene modules associated with PD. Integration of meta-cell based differential gene expression and a Bayesian causal network systematically reveals putative driver genes and their hierarchies. Our multiscale network models provide a framework for prioritizing candidate molecular regulators and pathways for further investigation of disease mechanisms and therapeutic targets.",
  "abstract_shown": true,
  "affiliations": [
    "Icahn School of Medicine at Mount Sinai Department of Genetics and Genomic Sciences, , 1425 Madison Avenue, NY 10029 ,",
    "Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai , 1470 Madison Avenue, NY 10029 ,",
    "Icahn School of Medicine at Mount Sinai Department of Neurology, , 1425 Madison Avenue, NY 10029 ,",
    "Icahn School of Medicine at Mount Sinai Department of Pharmacological Sciences, , 1425 Madison Avenue, NY 10029 ,",
    "Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, NY 10029 ,",
    "Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai , 1470 Madison Avenue, NY 10029 ,",
    "Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , 1470 Madison Avenue, NY 10029 ,",
    "Center of Parkinson’s Disease Neurobiology, Icahn School of Medicine at Mount Sinai , 1470 Madison Avenue, New York, NY ,",
    "Icahn School of Medicine at Mount Sinai Department of Artificial Intelligence & Human Health, , 1470 Madison Avenue, NY 10029 ,"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0,
        1,
        2,
        3
      ],
      "name": "Linh Chu",
      "orcid": "0000-0001-7463-5947"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Gefei Yu",
      "orcid": "0009-0001-4238-5100"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Xianxiao Zhou",
      "orcid": "0000-0001-9350-4467"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Minghui Wang",
      "orcid": "0000-0001-9171-4962"
    },
    {
      "affs": [
        2,
        5,
        6,
        7
      ],
      "name": "Zhenyu Yue",
      "orcid": "0000-0001-8730-8515"
    },
    {
      "affs": [
        0,
        1,
        3,
        4,
        8
      ],
      "name": "Bin Zhang",
      "orcid": "0000-0002-9549-5653"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3fsm8vxtg84jy.bib",
  "cited_by": 0,
  "doi": "10.1093/gigascience/giag096",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13723071/",
  "id": "3fsm8vxtg84jy",
  "issns": [
    "2047-217X"
  ],
  "landing_url": "https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giag096/8868918",
  "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": [
    [
      "heading",
      "AcademicSubjects/SCI00960"
    ],
    [
      "heading",
      "AcademicSubjects/SCI02254"
    ],
    [
      "heading",
      "Research"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7220722725",
  "pdf_url": "https://academic.oup.com/gigascience/advance-article-pdf/doi/10.1093/gigascience/giag096/71626537/giag096.pdf",
  "pmcid": "PMC13723071",
  "pmid": "42836551",
  "published": "2026-10-06",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/3fsm8vxtg84jy.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:42Z",
      "native_id": "10.1093/gigascience/giag096",
      "source": "crossref",
      "url": "https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giag096/8868918"
    },
    {
      "first_seen": "2026-11-04T12:21:44Z",
      "native_id": "PMC13723071",
      "source": "pmc",
      "url": "https://doi.org/10.1093/gigascience/giag096"
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  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Multiscale Transcriptomic Network Models of Parkinson’s Disease at the Single Cell Level",
  "title_text": "Multiscale Transcriptomic Network Models of Parkinson’s Disease at the Single Cell Level",
  "type": "peer-reviewed",
  "updated_at": "2026-11-04T12:21:44Z",
  "url": "https://research.draconitic.com/paper/3fsm8vxtg84jy",
  "venue": "GigaScience",
  "versions": []
}