{
  "abstract": "Matched single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) profiles from the same cells remain limited in hepatocellular carcinoma (HCC), hindering cell-resolved integration of transcriptional programs and regulatory chromatin states. To address this challenge, we developed single-cell Liver-adapted Alignment and Pseudo-pairing (scLAP), a liver-adapted contrastive shared-latent framework for cross-study RNA-ATAC pseudo-pairing. scLAP was trained on a paired liver single-nucleus multiome reference using 2000 highly variable RNA features and 697 ATAC features, including 647 transcription factor motif activity scores and 50 latent semantic indexing components. On a prespecified cell-level test partition (n = 3235), scLAP achieved an ATAC-to-RNA Top 10 exact-pair retrieval rate of 21.48% and a mean fraction of samples closer than the true match (FOSCTTM) of 0.0431. In six leave-one-sample-out folds, the corresponding macro means were 5.23% and 0.2278, respectively, indicating above-random ranking but limited exact-pair transfer to unseen samples. A validation-selected scButterfly configuration using 20,000 native ATAC peaks achieved 8.93% Top 10 retrieval and a mean FOSCTTM of 0.0811 on the same test cells; comparisons with Con-AAE and scMODAL remained study-specific adaptations. Applying reciprocal retrieval, a validation-derived cosine-similarity threshold, and greedy one-to-one assignment to independent HCC datasets yielded 4007 similarity-filtered candidate RNA-ATAC pseudo-pairs. Downstream analyses identified an NRCAM-associated accessibility candidate and separate exploratory MET-, CAV1-, and AP-1-associated observations.",
  "abstract_shown": true,
  "affiliations": [
    "Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China",
    "Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Hongfei Li"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Jiechen Wang"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Huan Yang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1jhgnayg6epxw.bib",
  "cited_by": 0,
  "doi": "10.3390/ijms27219888",
  "fulltext_url": null,
  "id": "1jhgnayg6epxw",
  "issns": [
    "1422-0067"
  ],
  "landing_url": "https://www.mdpi.com/1422-0067/27/21/9888",
  "language": null,
  "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": null,
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-04",
  "publisher": "MDPI AG",
  "ris": "https://research.draconitic.com/paper/1jhgnayg6epxw.ris",
  "sources": [
    {
      "first_seen": "2026-11-05T00:20:58Z",
      "native_id": "10.3390/ijms27219888",
      "source": "crossref",
      "url": "https://www.mdpi.com/1422-0067/27/21/9888"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "issn:1422-0067",
      "subfield": "general"
    }
  ],
  "title": "scLAP: A Liver-Adapted Contrastive Shared-Latent Framework for Pseudo-Pairing Single-Cell Transcriptomes and Chromatin Accessibility Profiles",
  "title_text": "scLAP: A Liver-Adapted Contrastive Shared-Latent Framework for Pseudo-Pairing Single-Cell Transcriptomes and Chromatin Accessibility Profiles",
  "type": "peer-reviewed",
  "updated_at": "2026-11-06T00:21:14Z",
  "url": "https://research.draconitic.com/paper/1jhgnayg6epxw",
  "venue": "International Journal of Molecular Sciences",
  "versions": []
}