{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T20:39:56Z","timestamp":1792096796338,"version":"4.4.0"},"reference-count":29,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2024,6,15]],"date-time":"2024-06-15T00:00:00Z","timestamp":1718409600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,6,15]],"date-time":"2024-06-15T00:00:00Z","timestamp":1718409600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82002144"],"award-info":[{"award-number":["82002144"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["iMeta"],"published-print":{"date-parts":[[2024,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Rapid and accurate diagnostic tests are fundamental for improving patient outcomes and combating infectious diseases. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas12a\u2010based detection system has emerged as a promising solution for on\u2010site nucleic acid testing. Nonetheless, the effective design of CRISPR RNA (crRNA) for Cas12a\u2010based detection remains challenging and time\u2010consuming. In this study, we propose an enhanced crRNA design system with deep learning for Cas12a\u2010mediated diagnostics, referred to as EasyDesign. This system employs an optimized convolutional neural network (CNN) prediction model, trained on a comprehensive data set comprising 11,496 experimentally validated Cas12a\u2010based detection cases, encompassing a wide spectrum of prevalent pathogens, achieving Spearman's\n                    <jats:italic>\u03c1<\/jats:italic>\n                    \u2009=\u20090.812. We further assessed the model performance in crRNA design for four pathogens not included in the training data: Monkeypox Virus, Enterovirus 71, Coxsackievirus A16, and\n                    <jats:italic>Listeria monocytogenes<\/jats:italic>\n                    . The results demonstrated superior prediction performance compared to the traditional experiment screening. Furthermore, we have developed an interactive web server (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/crispr.zhejianglab.com\/\">https:\/\/crispr.zhejianglab.com\/<\/jats:ext-link>\n                    ) that integrates EasyDesign with recombinase polymerase amplification (RPA) primer design, enhancing user accessibility. Through this web\u2010based platform, we successfully designed optimal Cas12a crRNAs for six human papillomavirus (HPV) subtypes. Remarkably, all the top five predicted crRNAs for each HPV subtype exhibited robust fluorescent signals in CRISPR assays, thereby suggesting that the platform could effectively facilitate clinical sample testing. In conclusion, EasyDesign offers a rapid and reliable solution for crRNA design in Cas12a\u2010based detection, which could serve as a valuable tool for clinical diagnostics and research applications.\n                  <\/jats:p>","DOI":"10.1002\/imt2.214","type":"journal-article","created":{"date-parts":[[2024,6,15]],"date-time":"2024-06-15T09:20:14Z","timestamp":1718443214000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":67,"title":["Deep learning enhancing guide RNA design for CRISPR\/Cas12a\u2010based diagnostics"],"prefix":"10.1002","volume":"3","author":[{"given":"Baicheng","family":"Huang","sequence":"first","affiliation":[{"name":"Zhejiang Lab Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling","family":"Guo","sequence":"additional","affiliation":[{"name":"Zhejiang Lab Hangzhou 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Hangzhou China"},{"name":"Institute of Laboratory Medicine Zhejiang University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhimin","family":"Ai","sequence":"additional","affiliation":[{"name":"Zhejiang Lab Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiqiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Zhejiang Lab Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingchi","family":"Kan","sequence":"additional","affiliation":[{"name":"Zhejiang Lab Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Yu","sequence":"additional","affiliation":[{"name":"Zhejiang Lab Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shimin","family":"Du","sequence":"additional","affiliation":[{"name":"Zhejiang Lab Hangzhou 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China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,6,15]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2020.02.024"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra2208860"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2207323"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2279-8"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aar6245"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2020.1793689"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.09.038"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-022-04968-5"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-022-01213-5"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.3389\/fbioe.2023.1226182"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29268-7"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00407-0"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4061"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-2939-6"},{"key":"e_1_2_11_16_1","volume-title":"International 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