{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T22:41:58Z","timestamp":1785796918868,"version":"3.56.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,6]],"date-time":"2019-09-06T00:00:00Z","timestamp":1567728000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61701340"],"award-info":[{"award-number":["61701340"]}],"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":["61472333"],"award-info":[{"award-number":["61472333"]}],"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":["61772441"],"award-info":[{"award-number":["61772441"]}],"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":["61472335"],"award-info":[{"award-number":["61472335"]}],"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":["61272152"],"award-info":[{"award-number":["61272152"]}],"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":["61872309"],"award-info":[{"award-number":["61872309"]}],"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":["41476118"],"award-info":[{"award-number":["41476118"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Project of marine economic innovation and development in Xiamen","award":["16PFW034SF02"],"award-info":[{"award-number":["16PFW034SF02"]}]},{"name":"Natural Science Foundation of the Higher Education Institutions of Fujian Province","award":["JZ160400"],"award-info":[{"award-number":["JZ160400"]}]},{"DOI":"10.13039\/501100003392","name":"Natural Science Foundation of Fujian Province","doi-asserted-by":"publisher","award":["2017J01099"],"award-info":[{"award-number":["2017J01099"]}],"id":[{"id":"10.13039\/501100003392","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006606","name":"Natural Science Foundation of Tianjin City","doi-asserted-by":"publisher","award":["18JCQNJC00500"],"award-info":[{"award-number":["18JCQNJC00500"]}],"id":[{"id":"10.13039\/501100006606","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2017YFE0130600"],"award-info":[{"award-number":["2017YFE0130600"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Identification of enhancer\u2013promoter interactions (EPIs) is of great significance to human development. However, experimental methods to identify EPIs cost too much in terms of time, manpower and money. Therefore, more and more research efforts are focused on developing computational methods to solve this problem. Unfortunately, most existing computational methods require a variety of genomic data, which are not always available, especially for a new cell line. Therefore, it limits the large-scale practical application of methods. As an alternative, computational methods using sequences only have great genome-scale application prospects.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this article, we propose a new deep learning method, namely EPIVAN, that enables predicting long-range EPIs using only genomic sequences. To explore the key sequential characteristics, we first use pre-trained DNA vectors to encode enhancers and promoters; afterwards, we use one-dimensional convolution and gated recurrent unit to extract local and global features; lastly, attention mechanism is used to boost the contribution of key features, further improving the performance of EPIVAN. Benchmarking comparisons on six cell lines show that EPIVAN performs better than state-of-the-art predictors. Moreover, we build a general model, which has transfer ability and can be used to predict EPIs in various cell lines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code and data are available at: https:\/\/github.com\/hzy95\/EPIVAN.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz694","type":"journal-article","created":{"date-parts":[[2019,9,4]],"date-time":"2019-09-04T19:28:55Z","timestamp":1567625335000},"page":"1037-1043","source":"Crossref","is-referenced-by-count":183,"title":["Identifying enhancer\u2013promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism"],"prefix":"10.1093","volume":"36","author":[{"given":"Zengyan","family":"Hong","sequence":"first","affiliation":[{"name":"Department of Computer Science, Xiamen University , Xiamen 361005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangxiang","family":"Zeng","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Hunan University , Changsha 410076, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1444-190X","authenticated-orcid":false,"given":"Leyi","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Software, Shandong University , Jinan 250000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9885-1978","authenticated-orcid":false,"given":"Xiangrong","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Xiamen University , Xiamen 361005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,9,6]]},"reference":[{"key":"2023013110105670000_btz694-B1","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/j.tcb.2014.07.004","article-title":"In search of the determinants of enhancer\u2013promoter interaction specificity","volume":"24","author":"Arensbergen","year":"2014","journal-title":"Trends Cell Biol"},{"key":"2023013110105670000_btz694-B2","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nrg3163","article-title":"Metazoan promoters: emerging characteristics and insights into transcriptional regulation","volume":"13","author":"Boris","year":"2012","journal-title":"Nat. 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