{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T03:17:14Z","timestamp":1768447034734,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013665","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000}}],"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T00:00:00Z","timestamp":1762387200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62372303,62002234"],"award-info":[{"award-number":["62372303,62002234"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"crossref","award":["2024A1515010113"],"award-info":[{"award-number":["2024A1515010113"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Shenzhen Science and Technology Program","award":["RCYX20231211090244048"],"award-info":[{"award-number":["RCYX20231211090244048"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12371382"],"award-info":[{"award-number":["12371382"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fujian Provincial Natural Science Foundation of China","award":["2025J01030"],"award-info":[{"award-number":["2025J01030"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62131004"],"award-info":[{"award-number":["62131004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    <jats:bold>Motivation:<\/jats:bold>\n                    Epithelial-mesenchymal transition (EMT) plays a key role in cancer metastasis by promoting changes in adhesion and motility. RNA-binding proteins (RBPs) regulate alternative splicing (AS) during EMT, enabling a single gene to produce multiple protein isoforms that affect tumor progression. Disruption of RBP-AS interactions may disrupt the progress of diseases like cancer. Despite the importance of RBP-AS relationships in EMT, few computational methods predict these associations. Existing models struggle in sparse settings with limited known associations. To improve performance, we incorporate both sparsity constraints and heterogeneous biological data to infer RBP\u2013AS associations.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Result:<\/jats:bold>\n                    We propose a new method based on\n                    <jats:underline>A<\/jats:underline>\n                    ccelerated\n                    <jats:underline>P<\/jats:underline>\n                    roximal\n                    <jats:underline>DC<\/jats:underline>\n                    <jats:underline>A<\/jats:underline>\n                    lgorithm (APDCA) for predicting RBP\u2013AS associations. In particular, APDCA combines sparse low-rank matrix factorization with a Difference-of-Convex (DC) optimization framework and uses extrapolation to improve convergence. A key feature of APDCA is the use of a sparsity constraint, which filters out noise and highlights key associations. In addition, integrating multiple related data sources with direct or indirect relationships can help in reaching a more comprehensive view of RBPs and AS events and to reduce the impact of false positives associated with individual data sources. we prove that our proposed algorithm is convergent under some conditions and the experimental results have illustrated that APDCA outperforms six baseline methods in both AUC and AUPR. A case study on the RBP QKI shows that the top predictions are verified by the OncoSplicing database. Thus, APDCA provides a fast, interpretable, and scalable tool for discovering post-transcriptional regulatory interactions.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1013665","type":"journal-article","created":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T18:45:28Z","timestamp":1762454728000},"page":"e1013665","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["APDCA: An accurate and effective method for predicting associations between RBPs and AS-events during epithelial-mesenchymal transition"],"prefix":"10.1371","volume":"21","author":[{"given":"Yangsong","family":"He","sequence":"first","affiliation":[]},{"given":"Zheng-Jian","family":"Bai","sequence":"additional","affiliation":[]},{"given":"Wai-Ki","family":"Ching","sequence":"additional","affiliation":[]},{"given":"Quan","family":"Zou","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9393-3648","authenticated-orcid":true,"given":"Yushan","family":"Qiu","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2025,11,6]]},"reference":[{"issue":"11","key":"pcbi.1013665.ref001","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1038\/nrm2777","article-title":"Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches","volume":"10","author":"M Chen","year":"2009","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"10","key":"pcbi.1013665.ref002","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1038\/nrg3778","article-title":"Context-dependent control of alternative splicing by RNA-binding proteins","volume":"15","author":"X-D Fu","year":"2014","journal-title":"Nat Rev Genet"},{"issue":"2","key":"pcbi.1013665.ref003","doi-asserted-by":"crossref","first-page":"893","DOI":"10.3390\/biom5020893","article-title":"RNA-binding proteins: splicing factors and disease","volume":"5","author":"AM Fredericks","year":"2015","journal-title":"Biomolecules"},{"issue":"8","key":"pcbi.1013665.ref004","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1002218","article-title":"An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype","volume":"7","author":"IM Shapiro","year":"2011","journal-title":"PLoS Genet"},{"issue":"5","key":"pcbi.1013665.ref005","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1016\/j.cell.2009.11.007","article-title":"Epithelial-mesenchymal transitions in development and disease","volume":"139","author":"JP Thiery","year":"2009","journal-title":"Cell"},{"key":"pcbi.1013665.ref006","doi-asserted-by":"crossref","unstructured":"Bebee TW, Cieply BW, Carstens RP, et al. 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