{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T02:00:06Z","timestamp":1783044006657,"version":"3.54.6"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,5,27]],"date-time":"2024-05-27T00:00:00Z","timestamp":1716768000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62372143"],"award-info":[{"award-number":["62372143"]}],"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":["62072145"],"award-info":[{"award-number":["62072145"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province","doi-asserted-by":"publisher","award":["LH2019C042"],"award-info":[{"award-number":["LH2019C042"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Micro ribonucleic acids (miRNAs) play a pivotal role in governing the human transcriptome in various biological phenomena. Hence, the accumulation of miRNA expression dysregulation frequently assumes a noteworthy role in the initiation and progression of complex diseases. However, accurate identification of dysregulated miRNAs still faces challenges at the current stage. Several bioinformatics tools have recently emerged for forecasting the associations between miRNAs and diseases. Nonetheless, the existing reference tools mainly identify the miRNA-disease associations in a general state and fall short of pinpointing dysregulated miRNAs within a specific disease state. Additionally, no studies adequately consider miRNA\u2013miRNA interactions (MMIs) when analyzing the miRNA-disease associations. Here, we introduced a systematic approach, called IDMIR, which enabled the identification of expression dysregulated miRNAs through an MMI network under the gene expression context, where the network\u2019s architecture was designed to implicitly connect miRNAs based on their shared biological functions within a particular disease context. The advantage of IDMIR is that it uses gene expression data for the identification of dysregulated miRNAs by analyzing variations in MMIs. We illustrated the excellent predictive power for dysregulated miRNAs of the IDMIR approach through data analysis on breast cancer and bladder urothelial cancer. IDMIR could surpass several existing miRNA-disease association prediction approaches through comparison. We believe the approach complements the deficiencies in predicting miRNA-disease association and may provide new insights and possibilities for diagnosing and treating diseases. The IDMIR approach is now available as a free R package on CRAN (https:\/\/CRAN.R-project.org\/package=IDMIR).<\/jats:p>","DOI":"10.1093\/bib\/bbae258","type":"journal-article","created":{"date-parts":[[2024,5,27]],"date-time":"2024-05-27T15:42:44Z","timestamp":1716824564000},"source":"Crossref","is-referenced-by-count":8,"title":["IDMIR: identification of dysregulated miRNAs associated with disease based on a miRNA\u2013miRNA interaction network constructed through gene expression data"],"prefix":"10.1093","volume":"25","author":[{"given":"Jiashuo","family":"Wu","sequence":"first","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xilong","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yalan","family":"He","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bingyue","family":"Pan","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiyin","family":"Lai","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miao","family":"Ji","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyuan","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junling","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3276-0819","authenticated-orcid":false,"given":"Junwei","family":"Han","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang Province , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,5,27]]},"reference":[{"key":"2024052715422717800_ref1","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/nrc3932","article-title":"MicroRNA biogenesis pathways in cancer","volume":"15","author":"Lin","year":"2015","journal-title":"Nat Rev Cancer"},{"key":"2024052715422717800_ref2","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","article-title":"MicroRNAs: target recognition and regulatory 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