{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T03:00:32Z","timestamp":1767927632607,"version":"3.49.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2018,4,25]],"date-time":"2018-04-25T00:00:00Z","timestamp":1524614400000},"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":["61772531"],"award-info":[{"award-number":["61772531"]}],"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":["11631014"],"award-info":[{"award-number":["11631014"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Doctor Startup Foundation"},{"name":"Liaoning province","award":["20170520217"],"award-info":[{"award-number":["20170520217"]}]},{"name":"Education Department of Liaoning Province","award":["LT2015011"],"award-info":[{"award-number":["LT2015011"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31570160"],"award-info":[{"award-number":["31570160"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Important Scientific and Technical Achievements Transformation Project","award":["Z17-5-078"],"award-info":[{"award-number":["Z17-5-078"]}]},{"name":"Large-scale Equipment Shared Services","award":["F15165400"],"award-info":[{"award-number":["F15165400"]}]},{"name":"Applied Basic Research Project","award":["F16205151"],"award-info":[{"award-number":["F16205151"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>A large number of resources have been devoted to exploring the associations between microRNAs (miRNAs) and diseases in the recent years. However, the experimental methods are expensive and time-consuming. Therefore, the computational methods to predict potential miRNA\u2013disease associations have been paid increasing attention.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this paper, we proposed a novel computational model of Bipartite Network Projection for MiRNA\u2013Disease Association prediction (BNPMDA) based on the known miRNA\u2013disease associations, integrated miRNA similarity and integrated disease similarity. We firstly described the preference degree of a miRNA for its related disease and the preference degree of a disease for its related miRNA with the bias ratings. We constructed bias ratings for miRNAs and diseases by using agglomerative hierarchical clustering according to the three types of networks. Then, we implemented the bipartite network recommendation algorithm to predict the potential miRNA\u2013disease associations by assigning transfer weights to resource allocation links between miRNAs and diseases based on the bias ratings. BNPMDA had been shown to improve the prediction accuracy in comparison with previous models according to the area under the receiver operating characteristics (ROC) curve (AUC) results of three typical cross validations. As a result, the AUCs of Global LOOCV, Local LOOCV and 5-fold cross validation obtained by implementing BNPMDA were 0.9028, 0.8380 and 0.8980 \u00b1 0.0013, respectively. We further implemented two types of case studies on several important human complex diseases to confirm the effectiveness of BNPMDA. In conclusion, BNPMDA could effectively predict the potential miRNA\u2013disease associations at a high accuracy level.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>BNPMDA is available via http:\/\/www.escience.cn\/system\/file?fileId=99559.<\/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\/bty333","type":"journal-article","created":{"date-parts":[[2018,4,24]],"date-time":"2018-04-24T11:13:12Z","timestamp":1524568392000},"page":"3178-3186","source":"Crossref","is-referenced-by-count":274,"title":["BNPMDA: Bipartite Network Projection for MiRNA\u2013Disease Association prediction"],"prefix":"10.1093","volume":"34","author":[{"given":"Xing","family":"Chen","sequence":"first","affiliation":[{"name":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China"}]},{"given":"Di","family":"Xie","sequence":"additional","affiliation":[{"name":"School of Mathematics, Liaoning University, Shenyang, China"}]},{"given":"Lei","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China"}]},{"given":"Qi","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Mathematics, Liaoning University, Shenyang, China"},{"name":"Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning Province, Shenyang, China"}]},{"given":"Zhu-Hong","family":"You","sequence":"additional","affiliation":[{"name":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, \u00dcr\u00fcmqi, China"}]},{"given":"Hongsheng","family":"Liu","sequence":"additional","affiliation":[{"name":"Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning Province, Shenyang, China"},{"name":"School of Life Science, Liaoning University, Shenyang, China"}]}],"member":"286","published-online":{"date-parts":[[2018,4,25]]},"reference":[{"key":"2023012704190620000_bty333-B1","doi-asserted-by":"crossref","first-page":"1914","DOI":"10.1111\/j.1349-7006.2007.00618.x","article-title":"Downregulation of microRNAs-143 and -145 in B-cell malignancies","volume":"98","author":"Akao","year":"2007","journal-title":"Cancer Sci"},{"key":"2023012704190620000_bty333-B2","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/35000501","article-title":"Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling","volume":"403","author":"Alizadeh","year":"2000","journal-title":"Nature"},{"key":"2023012704190620000_bty333-B3","doi-asserted-by":"crossref","first-page":"6.","DOI":"10.1186\/1758-907X-1-6","article-title":"Development of the human cancer microRNA network","volume":"1","author":"Bandyopadhyay","year":"2010","journal-title":"Silence"},{"key":"2023012704190620000_bty333-B4","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","article-title":"MicroRNAs: target recognition and regulatory functions","volume":"136","author":"Bartel","year":"2009","journal-title":"Cell"},{"key":"2023012704190620000_bty333-B5","doi-asserted-by":"crossref","first-page":"2792","DOI":"10.1039\/c2mb25180a","article-title":"RWRMDA: predicting novel human microRNA\u2013disease associations","volume":"8","author":"Chen","year":"2012","journal-title":"Mol. 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