{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T18:53:57Z","timestamp":1767380037646,"version":"3.48.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T00:00:00Z","timestamp":1754956800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation International Cooperation and Exchange Projects","award":["62120106011"],"award-info":[{"award-number":["62120106011"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62176146"],"award-info":[{"award-number":["62176146"]}],"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":["U2468206"],"award-info":[{"award-number":["U2468206"]}],"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":["U2341271"],"award-info":[{"award-number":["U2341271"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Basic Research Program of Shaanxi","award":["2024JC-YBMS-484"],"award-info":[{"award-number":["2024JC-YBMS-484"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Gene expression plays a crucial role in cell function, and enhancers can regulate gene expression precisely. Therefore, accurate prediction of enhancers is particularly critical. However, existing prediction methods have low accuracy or rely on fixed multiple epigenetic signals, which may not always be available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a two-stage framework that accurately predicts enhancers by flexibly combining multiple epigenetic signals. In the first stage, we designed a Blending-KAN model, which integrates the results of various base classifiers and employs Kolmogorov\u2013Arnold Networks (KAN) as a meta-classifier to predict enhancers based on flexible combinations of multiple epigenetic signals. In the second stage, we developed a Stacking-Auto model, which extracted sequence features using DNABERT-2 and located the enhancers based on the Stacking strategy and AutoGluon framework. The accuracy of the Blending-KAN model reached 99.69\u2009\u00b1\u20090.11% when five epigenetic signals were used. In cross-cell line prediction, the accuracy was more significant than or equal to 93.72%. With Gaussian noise, it still maintains an accuracy of 98.74\u2009\u00b1\u20090.03%. In the second stage, the accuracy of the Stacking-Auto model is 80.50%, which is better than the existing 17 methods. The results show that our models can be flexibly used to predict and locate enhancers utilizing a combination of multiple epigenetic signals.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code is available at https:\/\/github.com\/emanlee\/Hi-Enhancer and https:\/\/doi.org\/10.6084\/m9.figshare.29262158.v1.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf441","type":"journal-article","created":{"date-parts":[[2025,8,11]],"date-time":"2025-08-11T11:25:54Z","timestamp":1754911554000},"source":"Crossref","is-referenced-by-count":0,"title":["Hi-Enhancer: a two-stage framework for prediction and localization of enhancers based on Blending-KAN and Stacking-Auto models"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6983-2310","authenticated-orcid":false,"given":"Aimin","family":"Li","sequence":"first","affiliation":[{"name":"Shaanxi Key Laboratory for Network Computing and Security Technology, Xi\u2019an University of Technology , Xi\u2019an, Shaanxi 710048,","place":["China"]}]},{"given":"Haotian","family":"Zhou","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory for Network Computing and Security Technology, Xi\u2019an University of Technology , Xi\u2019an, Shaanxi 710048,","place":["China"]}]},{"given":"Rong","family":"Fei","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory for Network Computing and Security Technology, Xi\u2019an University of Technology , Xi\u2019an, Shaanxi 710048,","place":["China"]}]},{"given":"Juntao","family":"Zou","sequence":"additional","affiliation":[{"name":"Department of Materials Science and Engineering, Xi\u2019an University of Technology , Xi\u2019an, Shaanxi 710048,","place":["China"]}]},{"given":"Xiguo","family":"Yuan","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xidian University , Xi\u2019an, Shaanxi 710071,","place":["China"]}]},{"given":"Yajun","family":"Liu","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory for Network Computing and Security Technology, Xi\u2019an University of Technology , Xi\u2019an, Shaanxi 710048,","place":["China"]}]},{"given":"Saurav","family":"Mallik","sequence":"additional","affiliation":[{"name":"Department of Environmental Health, Harvard University T.H. Chan School of Public Health , Boston, MA 02115,","place":["United States"]}]},{"given":"Xinhong","family":"Hei","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory for Network Computing and Security Technology, Xi\u2019an University of Technology , Xi\u2019an, Shaanxi 710048,","place":["China"]}]},{"given":"Lei","family":"Wang","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory for Network Computing and Security Technology, Xi\u2019an University of Technology , Xi\u2019an, Shaanxi 710048,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,12,8]]},"reference":[{"key":"2026010213513099700_btaf441-B1","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1007\/978-3-030-63836-8_4","volume-title":"Neural Information Processing: 27th International Conference, ICONIP 2020, Bangkok, Thailand, November 23\u201327, 2020, Proceedings, Part III 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