{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T19:44:10Z","timestamp":1792266250592,"version":"4.4.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62102294"],"award-info":[{"award-number":["62102294"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62673377"],"award-info":[{"award-number":["62673377"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Basic Research Program of Shaanxi","award":["2026JC-YBQN-0777"],"award-info":[{"award-number":["2026JC-YBQN-0777"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Single-cell RNA sequencing and single-cell ATAC sequencing provide complementary views of transcriptional output and chromatin regulatory potential, but integrating unpaired profiles remains challenging because the modalities differ in feature space, sparsity and noise. Existing approaches often frame integration as distribution matching, which can over-align biologically distinct, condition-specific or modality-specific cell states. We present scHPGT, a single-cell Heterogeneous Prior-Guided Transformer for regulatory-prior-guided integration of unpaired RNA and chromatin accessibility profiles. scHPGT uses modality-specific encoders to model RNA and ATAC signals, a prior-guided cross-modal Transformer to constrain gene\u2013peak attention using regulatory links, and a domain-adversarial objective to reduce modality-specific discrepancies in a shared latent space.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Across PBMC3k, mouse spleen, CITE-seq\/ASAP-seq PBMC and PBMC10k benchmarks, scHPGT improves clustering agreement, label transfer and biological structure preservation while maintaining effective modality alignment. In partial-overlap and condition-shift settings, scHPGT aligns shared populations without forcing unmatched or condition-specific states into inappropriate correspondence. Attention-derived links recover regulatory relationships, highlight marker-gene regulatory regions, recover transcription factor programs and produce regulatory activity profiles consistent with cell-type-specific transcriptional programs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>Code and datasets are released at https:\/\/github.com\/zlCreator\/scHPGT.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag696","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T19:20:16Z","timestamp":1789672816000},"source":"Crossref","is-referenced-by-count":0,"title":["Regulatory-prior-guided attention preserves biological structure during unpaired single-cell RNA\u2013ATAC integration"],"prefix":"10.1093","volume":"42","author":[{"given":"Zhenglong","family":"Cheng","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Xidian University , Xi\u2019an, Shaanxi 710126,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8218-3688","authenticated-orcid":false,"given":"Jiao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Texas Children\u2019s Cancer and Hematology Center, Texas Children\u2019s Hospital , Houston, TX 77030,","place":["United States"]},{"name":"Division of Hematology and Oncology, Department of Pediatrics, Baylor College of Medicine , Houston, TX 77030,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0314-9199","authenticated-orcid":false,"given":"Shixiong","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and 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