{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T13:24:03Z","timestamp":1790861043409,"version":"4.1.0"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T00:00:00Z","timestamp":1773878400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32270688"],"award-info":[{"award-number":["32270688"]}],"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":["31801117"],"award-info":[{"award-number":["31801117"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Program for Changjiang Scholars and Innovative Research Team in University in China","award":["IRT_14R40"],"award-info":[{"award-number":["IRT_14R40"]}]},{"name":"Chinese National Key Research and Development Project","award":["2018YFC1315600"],"award-info":[{"award-number":["2018YFC1315600"]}]},{"name":"Tianjin Science and Technology Committee Foundation","award":["17JCYBJC25300"],"award-info":[{"award-number":["17JCYBJC25300"]}]},{"name":"Tianjin Key Medical Discipline Construction Project","award":["TJYXZDXK-3-016C"],"award-info":[{"award-number":["TJYXZDXK-3-016C"]}]},{"name":"Tianjin Key Medical Discipline Construction Project","award":["TJYXZDXK-3-003A"],"award-info":[{"award-number":["TJYXZDXK-3-003A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Foundation models have demonstrated exceptional performance across diverse downstream tasks. However, in genomics and transcriptomics, the integration of nucleotide sequences with their rich annotations remains underexplored, potentially limiting model generalizability across species and biological contexts. Here, we introduce OmniNA (Omni-applicable foundation model for nucleic acid), a self-supervised generative foundation model trained on 91.7 million nucleotide sequences and their associated annotations, totaling 1076.2 billion bases and 197 million words spanning diverse species. Unlike most existing approaches that focus solely on functional genomic element recognition, OmniNA jointly learns from both sequences and annotations, leveraging their complementarity to enhance semantic understanding and representation learning. We demonstrate that OmniNA captures sequence grammar and annotation semantics, facilitating robust transfer across nucleotide-level tasks. OmniNA can be fine-tuned under natural language paradigms and achieves state-of-the-art or competitive performance in 23 benchmarks, including sequence detection and species classification. Its learned representations also help reveal mutation effects on DNA and RNA processing. We release the model publicly as a community resource for genomics and transcriptomics research. OmniNA represents a step toward advancing foundational modeling by integrating annotation-aware learning, offering a powerful tool for genomics and transcriptomics research.<\/jats:p>","DOI":"10.1093\/nar\/gkag083","type":"journal-article","created":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T09:28:25Z","timestamp":1773912505000},"source":"Crossref","is-referenced-by-count":4,"title":["A foundation model for nucleotide sequences"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3897-695X","authenticated-orcid":false,"given":"Xilin","family":"Shen","sequence":"first","affiliation":[{"name":"Tianjin Cancer Institute, Key Laboratory of Cancer Prevention and Therapy, Tianjin\u2019s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin Medical University , Tianjin 300060 ,","place":["China"]},{"name":"Department of Pathology, Tianjin\u2019s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital , Tianjin 300060 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia Xin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Pathology, Tianjin\u2019s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital , Tianjin 300060 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng","family":"Yang","sequence":"additional","affiliation":[{"name":"Tianjin Cancer Institute, Key Laboratory of Cancer Prevention and Therapy, Tianjin\u2019s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin Medical University , Tianjin 300060 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1679-3618","authenticated-orcid":false,"given":"Lei","family":"Shi","sequence":"additional","affiliation":[{"name":"Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Tianjin\u2019s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin Medical University , Tianjin 300060 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kexin","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Key Laboratory of Prevention and Control of Major Diseases in the Population Ministry of Education, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin\u2019s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin Medical University , Tianjin 300060 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2230-2152","authenticated-orcid":false,"given":"Xiangchun","family":"Li","sequence":"additional","affiliation":[{"name":"Tianjin Cancer Institute, Key Laboratory of Cancer Prevention and Therapy, Tianjin\u2019s Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin Medical University , Tianjin 300060 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,3,19]]},"reference":[{"key":"2026031905422754200_B1","article-title":"On the opportunities and risks of foundation models","author":"Bommasani"},{"key":"2026031905422754200_B2","doi-asserted-by":"publisher","first-page":"2307","DOI":"10.1038\/s41591-023-02504-3","article-title":"A visual\u2013language foundation model for pathology image analysis using medical Twitter","volume":"29","author":"Huang","year":"2023","journal-title":"Nat Med"},{"key":"2026031905422754200_B3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1109\/jbhi.2024.3505955","article-title":"BioMedGPT: open multimodal 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