{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T19:44:11Z","timestamp":1792266251839,"version":"4.4.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62432011"],"award-info":[{"award-number":["62432011"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62372390"],"award-info":[{"award-number":["62372390"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Provincial Natural Science Foundation of China","award":["2025J010001"],"award-info":[{"award-number":["2025J010001"]}]}],"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>Gene expression prediction benefits from integrating DNA sequences and epigenomic signals. Existing approaches typically combine these modalities using simple operations such as concatenation or summation, without explicitly modeling fine-grained token-level cross-modal interactions. Establishing precise cross-modal correspondences remains challenging due to (1) inter-modal discrepancies, and (2) intra-modal structural preservation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To address these challenges, we propose OrchAlign, an orchestrated multimodal alignment framework that establishes fine-grained cross-modal alignment while preserving intra-modal structure. Our approach first disentangles each modality into shared and specific representations. We then perform focused cross-modal alignment on the shared subspace within a key regulatory region, producing aligned representations with token-level correspondences. Moreover, we enforce consistency between relational structures of the aligned shared representations and their corresponding modality-specific counterparts, enhancing intra-modal structural coherence. Finally, the aligned shared representations and modality-specific representations are passed to the BiMamba backbone for further multimodal fusion. Our experimental results show that OrchAlign achieves state-of-the-art performance in gene expression prediction.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>All resources are available at https:\/\/github.com\/XMUDM\/OrchAlign<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag711","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T11:39:40Z","timestamp":1790681980000},"source":"Crossref","is-referenced-by-count":0,"title":["OrchAlign: orchestrated multimodal alignment for gene expression prediction"],"prefix":"10.1093","volume":"42","author":[{"given":"Li","family":"Liu","sequence":"first","affiliation":[{"name":"School of Informatics, National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen 361005,","place":["China"]},{"name":"School of Information Engineering, Sanming University , Sanming 365004,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guipeng","family":"Xv","sequence":"additional","affiliation":[{"name":"School of Informatics, National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen 361005,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shujie","family":"Liu","sequence":"additional","affiliation":[{"name":"Microsoft Research Asia, Microsoft , Beijing 100080,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeyun","family":"Gong","sequence":"additional","affiliation":[{"name":"Microsoft Research Asia, Microsoft , Beijing 100080,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2275-997X","authenticated-orcid":false,"given":"Chen","family":"Lin","sequence":"additional","affiliation":[{"name":"School of Informatics, National 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