{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T22:07:02Z","timestamp":1776204422763,"version":"3.50.1"},"reference-count":26,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T00:00:00Z","timestamp":1572393600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["EY024580, GM111514, EY029548, and EY001765"],"award-info":[{"award-number":["EY024580, GM111514, EY029548, and EY001765"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007436","type":"journal-article","created":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T13:28:34Z","timestamp":1572442114000},"page":"e1007436","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue\/cell type-specific enhancer-gene interactions"],"prefix":"10.1371","volume":"15","author":[{"given":"Tianshun","family":"Gao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0476-3596","authenticated-orcid":true,"given":"Jiang","family":"Qian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2019,10,30]]},"reference":[{"issue":"7493","key":"pcbi.1007436.ref001","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nature12787","article-title":"An atlas of active enhancers across human cell types and tissues","volume":"507","author":"R Andersson","year":"2014","journal-title":"Nature"},{"issue":"4","key":"pcbi.1007436.ref002","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1016\/j.cell.2013.09.053","article-title":"Super-enhancers in the control of cell identity and disease","volume":"155","author":"D Hnisz","year":"2013","journal-title":"Cell"},{"issue":"7231","key":"pcbi.1007436.ref003","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1038\/nature07730","article-title":"ChIP-seq accurately predicts tissue-specific activity of enhancers","volume":"457","author":"A Visel","year":"2009","journal-title":"Nature"},{"issue":"50","key":"pcbi.1007436.ref004","doi-asserted-by":"crossref","first-page":"21931","DOI":"10.1073\/pnas.1016071107","article-title":"Histone H3K27ac separates active from poised enhancers and predicts developmental state","volume":"107","author":"MP Creyghton","year":"2010","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7414","key":"pcbi.1007436.ref005","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature11232","article-title":"The accessible chromatin landscape of the human genome","volume":"489","author":"RE Thurman","year":"2012","journal-title":"Nature"},{"issue":"8","key":"pcbi.1007436.ref006","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1101\/gr.232488.117","article-title":"An atlas of chromatin accessibility in the adult human brain","volume":"28","author":"JF Fullard","year":"2018","journal-title":"Genome research"},{"issue":"5","key":"pcbi.1007436.ref007","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/nmeth.3329","article-title":"Identification of active transcriptional regulatory elements from GRO-seq data","volume":"12","author":"CG Danko","year":"2015","journal-title":"Nature methods"},{"issue":"21","key":"pcbi.1007436.ref008","doi-asserted-by":"crossref","first-page":"E2191","DOI":"10.1073\/pnas.1320308111","article-title":"Global view of enhancer-promoter interactome in human cells","volume":"111","author":"B He","year":"2014","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"18","key":"pcbi.1007436.ref009","doi-asserted-by":"crossref","first-page":"8694","DOI":"10.1093\/nar\/gkv865","article-title":"A predictive modeling approach for cell line-specific long-range regulatory interactions","volume":"43","author":"S Roy","year":"2015","journal-title":"Nucleic acids research"},{"issue":"5","key":"pcbi.1007436.ref010","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1038\/ng.3539","article-title":"Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin","volume":"48","author":"S Whalen","year":"2016","journal-title":"Nature genetics"},{"issue":"10","key":"pcbi.1007436.ref011","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1038\/ng.3950","article-title":"Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines","volume":"49","author":"Q Cao","year":"2017","journal-title":"Nature genetics"},{"issue":"7","key":"pcbi.1007436.ref012","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"SS Rao","year":"2014","journal-title":"Cell"},{"issue":"7269","key":"pcbi.1007436.ref013","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nature08497","article-title":"An oestrogen-receptor-alpha-bound human chromatin interactome","volume":"462","author":"MJ Fullwood","year":"2009","journal-title":"Nature"},{"issue":"7345","key":"pcbi.1007436.ref014","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature09906","article-title":"Mapping and analysis of chromatin state dynamics in nine human cell types","volume":"473","author":"J Ernst","year":"2011","journal-title":"Nature"},{"issue":"1","key":"pcbi.1007436.ref015","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":"O Corradin","year":"2014","journal-title":"Genome research"},{"issue":"7414","key":"pcbi.1007436.ref016","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nature11279","article-title":"The long-range interaction landscape of gene promoters","volume":"489","author":"A Sanyal","year":"2012","journal-title":"Nature"},{"issue":"1","key":"pcbi.1007436.ref017","doi-asserted-by":"crossref","first-page":"2237","DOI":"10.1038\/s41467-017-02386-3","article-title":"Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains","volume":"8","author":"G Ron","year":"2017","journal-title":"Nature communications"},{"issue":"23","key":"pcbi.1007436.ref018","doi-asserted-by":"crossref","first-page":"3543","DOI":"10.1093\/bioinformatics\/btw495","article-title":"EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell\/tissue types","volume":"32","author":"T Gao","year":"2016","journal-title":"Bioinformatics"},{"issue":"5","key":"pcbi.1007436.ref019","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1016\/j.cell.2016.09.018","article-title":"Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution","volume":"167","author":"HK Long","year":"2016","journal-title":"Cell"},{"issue":"3","key":"pcbi.1007436.ref020","doi-asserted-by":"crossref","first-page":"e0118432","DOI":"10.1371\/journal.pone.0118432","article-title":"The precision-recall plot is more informative than the ROC plot when evaluating binary classifiers on imbalanced datasets","volume":"10","author":"T Saito","year":"2015","journal-title":"PloS one"},{"issue":"6","key":"pcbi.1007436.ref021","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The Genotype-Tissue Expression (GTEx) project","volume":"45","author":"Consortium GT","year":"2013","journal-title":"Nature genetics"},{"issue":"7","key":"pcbi.1007436.ref022","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1038\/ng.154","article-title":"Combinatorial patterns of histone acetylations and methylations in the human genome","volume":"40","author":"Z Wang","year":"2008","journal-title":"Nature genetics"},{"issue":"6","key":"pcbi.1007436.ref023","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1016\/j.cell.2013.02.029","article-title":"CTCF and cohesin: linking gene regulatory elements with their targets","volume":"152","author":"M Merkenschlager","year":"2013","journal-title":"Cell"},{"issue":"3","key":"pcbi.1007436.ref024","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"J Ernst","year":"2012","journal-title":"Nature methods"},{"issue":"7479","key":"pcbi.1007436.ref025","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/nature12716","article-title":"Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations","volume":"504","author":"Y Zhang","year":"2013","journal-title":"Nature"},{"key":"pcbi.1007436.ref026","first-page":"2016","article-title":"CCSI: a database providing chromatin-chromatin spatial interaction information","author":"X Xie","year":"2016","journal-title":"Database: the journal of biological databases and curation"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007436","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T04:16:22Z","timestamp":1695356182000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007436"}},"subtitle":[],"editor":[{"given":"Ilya","family":"Ioshikhes","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,10,30]]},"references-count":26,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2019,10,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007436","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/781427","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,10,30]]}}}