{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T13:35:39Z","timestamp":1781789739717,"version":"3.54.5"},"reference-count":77,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,8,18]],"date-time":"2021-08-18T00:00:00Z","timestamp":1629244800000},"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":["61972399"],"award-info":[{"award-number":["61972399"]}],"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":["11931008"],"award-info":[{"award-number":["11931008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Mounting evidence has demonstrated the significance of taking microRNAs (miRNAs) as the target of small molecule (SM) drugs for disease treatment. Given the fact that exploring new SM\u2013miRNA associations through biological experiments is extremely expensive, several computing models have been constructed to reveal the possible SM\u2013miRNA associations. Here, we built a computing model of Bounded Nuclear Norm Regularization for SM\u2013miRNA Associations prediction (BNNRSMMA). Specifically, we first constructed a heterogeneous SM\u2013miRNA network utilizing miRNA similarity, SM similarity, confirmed SM\u2013miRNA associations and defined a matrix to represent the heterogeneous network. Then, we constructed a model to complete this matrix by minimizing its nuclear norm. The Alternating Direction Method of Multipliers was adopted to minimize the nuclear norm and obtain predicted scores. The main innovation lies in two aspects. During completion, we limited all elements of the matrix within the interval of (0,1) to make sure they have practical significance. Besides, instead of strictly fitting all known elements, a regularization term was incorporated to tolerate the noise in integrated similarities. Furthermore, four kinds of cross-validations on two datasets and two types of case studies were performed to evaluate the predictive performance of BNNRSMMA. Finally, BNNRSMMA attained areas under the curve of 0.9822 (0.8433), 0.9793 (0.8852), 0.8253 (0.7350) and 0.9758\u2009\u00b1\u20090.0029 (0.8759\u2009\u00b1\u20090.0041) under global leave-one-out cross-validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and 5-fold cross-validation based on Dataset 1(Dataset 2), respectively. With regard to case studies, plenty of predicted associations have been verified by experimental literatures. All these results confirmed that BNNRSMMA is a reliable tool for inferring associations.<\/jats:p>","DOI":"10.1093\/bib\/bbab328","type":"journal-article","created":{"date-parts":[[2021,7,27]],"date-time":"2021-07-27T11:08:46Z","timestamp":1627384126000},"source":"Crossref","is-referenced-by-count":77,"title":["Predicting potential small molecule\u2013miRNA associations based on bounded nuclear norm regularization"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9297-7174","authenticated-orcid":false,"given":"Xing","family":"Chen","sequence":"first","affiliation":[{"name":"Artificial Intelligence Research Institute, China University of Mining and Technology, Xuzhou 221116, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6795-4007","authenticated-orcid":false,"given":"Chun-Chun","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,8,18]]},"reference":[{"key":"2021110815092155700_ref1","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: genomics, biogenesis, mechanism, and function","volume":"116","author":"Bartel","year":"2004","journal-title":"Cell"},{"key":"2021110815092155700_ref2","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/0092-8674(93)90529-Y","article-title":"The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14","volume":"75","author":"Lee","year":"1993","journal-title":"Cell"},{"key":"2021110815092155700_ref3","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1038\/35002607","article-title":"The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans","volume":"403","author":"Reinhart","year":"2000","journal-title":"Nature"},{"key":"2021110815092155700_ref4","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1126\/science.1080372","article-title":"Vertebrate microRNA genes","volume":"299","author":"Lim","year":"2003","journal-title":"Science"},{"key":"2021110815092155700_ref5","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1038\/nature02871","article-title":"The functions of animal microRNAs","volume":"431","author":"Ambros","year":"2004","journal-title":"Nature"},{"key":"2021110815092155700_ref6","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1101\/gad.1004402","article-title":"MicroRNAs in plants","volume":"16","author":"Reinhart","year":"2002","journal-title":"Genes Dev"},{"key":"2021110815092155700_ref7","doi-asserted-by":"crossref","first-page":"D155","DOI":"10.1093\/nar\/gky1141","article-title":"miRBase: from microRNA sequences to function","volume":"47","author":"Kozomara","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2021110815092155700_ref8","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1126\/science.1065329","article-title":"An extensive class of small RNAs in Caenorhabditis elegans","volume":"294","author":"Lee","year":"2001","journal-title":"Science"},{"key":"2021110815092155700_ref9","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1126\/science.1066315","article-title":"Molecular biology. 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