{
  "abstract": "Short-read (SR) single-cell and spatial transcriptomics characterize gene expression but provide limited resolution of within-gene isoform usage. Here we present IsoPrism, a structure-guided competitive allocation framework that predicts isoform proportions from gene-level expression. IsoPrism combines individual expression and local expression context with transcript structural annotations, using shared iterative updates to preserve non-negative, gene-normalized proportions. Joint supervision from individual long-read (LR) counts and group-level isoform usage enables prediction in samples without matched LR measurements. Across five transfer scenarios derived from three paired transcriptomic resources, IsoPrism achieved the highest mean dominant isoform accuracy, compositional similarity, and cluster-level allocation correlation among eight evaluated methods. Ablation analyses supported complementary contributions from structural queries, expression context, iterative allocation, and dual-resolution supervision. Applied to a developing mouse cortex atlas, IsoPrism identified stage- and cell-type-associated isoform-usage patterns, including variation in the predicted relative usage of two Pkm transcripts. IsoPrism enables isoform-usage analysis of SR transcriptomes by transferring information from paired LR references, extending the analytical value of existing single-cell and spatial gene-expression atlases.",
  "abstract_shown": true,
  "affiliations": [
    "Faculty of Computing, Harbin Institute of Technology, 92 West Dazhi Street, Nangang District, Harbin 150001, China.",
    "Department of Orthopedic Surgery, The Second Affiliated Hospital, Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin 150086, China.",
    "Department of Orthopedics, Changzheng Hospital, 415 Fengyang Road, Huangpu District, Shanghai 200003, China.",
    "College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin 150081, China.",
    "NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin 150081, China."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Peiyi Yan",
      "orcid": "0009-0008-4407-6134"
    },
    {
      "affs": [
        1
      ],
      "name": "Jingchen Liu"
    },
    {
      "affs": [
        0
      ],
      "name": "Xuejian Cui"
    },
    {
      "affs": [
        1
      ],
      "name": "Xiaoqi Liu"
    },
    {
      "affs": [
        2
      ],
      "name": "Lei Shi"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Liang Cheng",
      "orcid": "0000-0002-6665-6710"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/cgkvh3dc99zxh.bib",
  "cited_by": 0,
  "doi": "10.1093/bib/bbag621",
  "fulltext_url": "https://europepmc.org/articles/PMC13725926",
  "id": "cgkvh3dc99zxh",
  "issns": [
    "1467-5463",
    "1477-4054"
  ],
  "landing_url": "https://europepmc.org/article/MED/42969855",
  "language": "eng",
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI01060"
    ],
    [
      "heading",
      "Position Article"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7225092830",
  "pdf_url": "https://europepmc.org/articles/PMC13725926?pdf=render",
  "pmcid": "PMC13725926",
  "pmid": "42969855",
  "published": "2026-11-01",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/cgkvh3dc99zxh.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T15:20:53Z",
      "native_id": "MED:42969855",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42969855"
    },
    {
      "first_seen": "2026-11-05T12:22:22Z",
      "native_id": "PMC13725926",
      "source": "pmc",
      "url": "https://doi.org/10.1093/bib/bbag621"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "IsoPrism predicts isoform usage from short-read transcriptomes through structure-guided competitive allocation.",
  "title_text": "IsoPrism predicts isoform usage from short-read transcriptomes through structure-guided competitive allocation.",
  "type": "peer-reviewed",
  "updated_at": "2026-11-06T12:22:00Z",
  "url": "https://research.draconitic.com/paper/cgkvh3dc99zxh",
  "venue": "Briefings in bioinformatics",
  "versions": []
}