{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T18:35:15Z","timestamp":1780079715041,"version":"3.54.0"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2019,8,14]],"date-time":"2019-08-14T00:00:00Z","timestamp":1565740800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1356524"],"award-info":[{"award-number":["1356524"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1661414"],"award-info":[{"award-number":["1661414"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1149955"],"award-info":[{"award-number":["1149955"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["R15GM123407"],"award-info":[{"award-number":["R15GM123407"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The identification of enhancer\u2013promoter interactions (EPIs), especially condition-specific ones, is important for the study of gene transcriptional regulation. Existing experimental approaches for EPI identification are still expensive, and available computational methods either do not consider or have low performance in predicting condition-specific EPIs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a novel computational method called EPIP to reliably predict EPIs, especially condition-specific ones. EPIP is capable of predicting interactions in samples with limited data as well as in samples with abundant data. Tested on more than eight cell lines, EPIP reliably identifies EPIs, with an average area under the receiver operating characteristic curve of 0.95 and an average area under the precision\u2013recall curve of 0.73. Tested on condition-specific EPIPs, EPIP correctly identified 99.26% of them. Compared with two recently developed methods, EPIP outperforms them with a better accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The EPIP tool is freely available at http:\/\/www.cs.ucf.edu\/\u02dcxiaoman\/EPIP\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz641","type":"journal-article","created":{"date-parts":[[2019,8,11]],"date-time":"2019-08-11T19:12:03Z","timestamp":1565550723000},"page":"3877-3883","source":"Crossref","is-referenced-by-count":42,"title":["EPIP: a novel approach for condition-specific enhancer\u2013promoter interaction prediction"],"prefix":"10.1093","volume":"35","author":[{"given":"Amlan","family":"Talukder","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Central Florida , Orlando, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samaneh","family":"Saadat","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Central Florida , Orlando, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoman","family":"Li","sequence":"additional","affiliation":[{"name":"Burnett School of Biomedical Science, College of Medicine, University of Central Orlando , Orlando, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiyan","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Central Florida , Orlando, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,13]]},"reference":[{"key":"2023020108351874000_btz641-B1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nature12787","article-title":"An atlas of active enhancers across human samples and tissues","volume":"507","author":"Andersson","year":"2014","journal-title":"Nature"},{"key":"2023020108351874000_btz641-B2","doi-asserted-by":"crossref","first-page":"567.","DOI":"10.1186\/1471-2164-11-567","article-title":"Systematic identification of conserved motif modules in the human genome","volume":"11","author":"Cai","year":"2010","journal-title":"BMC Genomics"},{"key":"2023020108351874000_btz641-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.164079.113","article-title":"Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits","volume":"24","author":"Corradin","year":"2014","journal-title":"Genome Res"},{"key":"2023020108351874000_btz641-B4","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1126\/science.1067799","article-title":"Capturing chromosome conformation","volume":"295","author":"Dekker","year":"2002","journal-title":"Science"},{"key":"2023020108351874000_btz641-B5","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nature12753","article-title":"Topology of mammalian developmental enhancers and their regulatory landscapes","volume":"502","author":"De Laat","year":"2013","journal-title":"Nature"},{"key":"2023020108351874000_btz641-B6","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopaedia of DNA elements in the human genome","volume":"489","author":"Dunham","year":"2012","journal-title":"Nature"},{"key":"2023020108351874000_btz641-B7","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat. 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