{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T16:14:41Z","timestamp":1777047281658,"version":"3.51.4"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T00:00:00Z","timestamp":1731974400000},"content-version":"vor","delay-in-days":57,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Open Fund of Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information","award":["BDSY2023001"],"award-info":[{"award-number":["BDSY2023001"]}]},{"name":"Anhui Province Excellent Young Teacher Training Project","award":["YQYB2024007"],"award-info":[{"award-number":["YQYB2024007"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62102004"],"award-info":[{"award-number":["62102004"]}],"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":["62472005"],"award-info":[{"award-number":["62472005"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Rice consistently faces significant threats from biotic stresses, such as fungi, bacteria, pests, and viruses. Consequently, accurately and rapidly identifying previously unknown single-nucleotide polymorphisms (SNPs) in the rice genome is a critical challenge for rice research and the development of resistant varieties. However, the limited availability of high-quality rice genotype data has hindered this research. Deep learning has transformed biological research by facilitating the prediction and analysis of SNPs in biological sequence data. Convolutional neural networks are especially effective in extracting structural and local features from DNA sequences, leading to significant advancements in genomics. Nevertheless, the expanding catalog of genome-wide association studies provides valuable biological insights for rice research. Expanding on this idea, we introduce RiceSNP-BST, an automatic architecture search framework designed to predict SNPs associated with rice biotic stress traits (BST-associated SNPs) by integrating multidimensional features. Notably, the model successfully innovates the datasets, offering more precision than state-of-the-art methods while demonstrating good performance on an independent test set and cross-species datasets. Additionally, we extracted features from the original DNA sequences and employed causal inference to enhance the biological interpretability of the model. This study highlights the potential of RiceSNP-BST in advancing genome prediction in rice. Furthermore, a user-friendly web server for RiceSNP-BST (http:\/\/rice-snp-bst.aielab.cc) has been developed to support broader genome research.<\/jats:p>","DOI":"10.1093\/bib\/bbae599","type":"journal-article","created":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T01:35:03Z","timestamp":1732066503000},"source":"Crossref","is-referenced-by-count":4,"title":["RiceSNP-BST: a deep learning framework for predicting biotic stress\u2013associated SNPs in rice"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-0712-0167","authenticated-orcid":false,"given":"Jiajun","family":"Xu","sequence":"first","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujia","family":"Gao","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6802-0443","authenticated-orcid":false,"given":"Quan","family":"Lu","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Renyi","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianfeng","family":"Gui","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoshuang","family":"Liu","sequence":"additional","affiliation":[{"name":"Research Center for Biological Breeding Technology , Advance Academy, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Advance Academy, , 130, Changjiang West Road, Hefei, Anhui Province 230036 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