{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:22Z","timestamp":1753875862257,"version":"3.41.2"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,14]],"date-time":"2024-12-14T00:00:00Z","timestamp":1734134400000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61972002"],"award-info":[{"award-number":["61972002"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>RNA N$^{6}$-methyladenosine (m$^{6}$A) is a critical epigenetic modification closely related to rice growth, development, and stress response. m$^{6}$A accurate identification, directly related to precision rice breeding and improvement, is fundamental to revealing phenotype regulatory and molecular mechanisms. Faced on rice m$^{6}$A variable-length sequence, to input into the model, the maximum length padding and label encoding usually adapt to obtain the max-length padded sequence for prediction. Although this can retain complete sequence information, resulting in sparse information and invalid padding, reducing feature extraction accuracy. Simultaneously, existing rice-specific m$^{6}$A prediction methods are still at an early stage. To address these issues, we develop a new end-to-end deep learning framework, MFDm$^{6}$ARice, for predicting rice m$^{6}$A sites. In particular, to alleviate sparseness, we construct a multi-kernel feature fusion module to mine essential information in max-length padded sequences by multi-kernel feature extraction function and effectively transfer information through global\u2013local dynamic fusion function. Concurrently, considering the complexity and computational efficiency of high-dimensional features caused by invalid padding, we design a downsampling residual feature embedding module to optimize feature space compression and achieve accurate feature expression and efficient computational performance. Experiments show that MFDm$^{6}$ARice outperforms comparison methods in cross-validation, same- and cross-species independent test sets, demonstrating good robustness and generalization. The application on maize m$^{6}$A indicates the MFDm$^{6}$ARice\u2019s scalability. Further investigations have shown that combining different kernel features, focusing on global channel-local spatial, and employing reasonable downsampling and residual connections can improve feature representation and extraction, ensure effective information transfer, and significantly enhance model performance.<\/jats:p>","DOI":"10.1093\/bib\/bbae647","type":"journal-article","created":{"date-parts":[[2024,12,14]],"date-time":"2024-12-14T22:52:32Z","timestamp":1734216752000},"source":"Crossref","is-referenced-by-count":0,"title":["Multi-kernel feature extraction with dynamic fusion and downsampled residual feature embedding for predicting rice RNA <i>N<\/i>6-methyladenine sites"],"prefix":"10.1093","volume":"26","author":[{"given":"Mengya","family":"Liu","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Anhui University , Hefei 230601,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhan-Li","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Electrical Engineering and Automation, Anhui University , Hefei 230601,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhigang","family":"Zeng","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence and Automation, Huazhong University of Science and Technology , Wuhan 430074,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kin-Man","family":"Lam","sequence":"additional","affiliation":[{"name":"Department of Electronic and Information Engineering, The Hong Kong Polytechnic University , Hong Kong,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,12,14]]},"reference":[{"key":"2024121422522400700_ref1","doi-asserted-by":"publisher","first-page":"D303","DOI":"10.1093\/nar\/gkx1030","article-title":"MODOMICS: a database of RNA modification pathways. 2017 update","volume":"46","author":"Boccaletto","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2024121422522400700_ref2","doi-asserted-by":"publisher","first-page":"D195","DOI":"10.1093\/nar\/gkq1028","article-title":"The RNA modification database, RNAMDB: 2011 update","volume":"39","author":"Cantara","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2024121422522400700_ref3","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1016\/j.tplants.2020.04.005","article-title":"m6A editing: new tool to improve crop quality?","volume":"25","author":"Zheng","year":"2020","journal-title":"Trends Plant Sci"},{"key":"2024121422522400700_ref4","doi-asserted-by":"publisher","first-page":"e1008120","DOI":"10.1371\/journal.pgen.1008120","article-title":"The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice","volume":"15","author":"Zhang","year":"2019","journal-title":"PLoS Genet"},{"key":"2024121422522400700_ref5","doi-asserted-by":"publisher","first-page":"1982","DOI":"10.1111\/jipb.13167","article-title":"OsEDM2L mediates m6A of EAT1 transcript for proper alternative splicing and polyadenylation regulating rice tapetal degradation","volume":"63","author":"Ma","year":"2021","journal-title":"J Integr Plant Biol"},{"key":"2024121422522400700_ref6","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.3390\/plants10061101","article-title":"OseIF3h regulates plant growth and pollen development at translational level presumably through interaction with OsMTA2","volume":"10","author":"Huang","year":"2021","journal-title":"Plants"},{"key":"2024121422522400700_ref7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-021-02410-2","article-title":"The dynamics of N6-methyladenine RNA modification in interactions between rice and plant viruses","volume":"22","author":"Zhang","year":"2021","journal-title":"Genome Biol"},{"key":"2024121422522400700_ref8","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fny286","article-title":"N6-methyladenosine RNA methylation is involved in virulence of the rice blast fungus Pyricularia oryzae (syn. 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