{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:46:32Z","timestamp":1792784792467,"version":"4.5.0"},"reference-count":35,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"name":"The Fundamental Research Funds for the Central Universities","award":["D5000230363"],"award-info":[{"award-number":["D5000230363"]}]},{"name":"The Fundamental Research Funds for the Central Universities","award":["D5000250279"],"award-info":[{"award-number":["D5000250279"]}]},{"name":"National Natural Science Foundation of China (NSFC)","award":["62002388"],"award-info":[{"award-number":["62002388"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Natural Science Foundation of China (NSFC)","award":["62433016"],"award-info":[{"award-number":["62433016"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Accurate identification and classification of CRISPR-Cas systems are crucial for understanding microbial immune mechanisms and developing novel genome-editing tools. However, traditional homology-based mining methods face severe computational bottlenecks and assembly fragmentation challenges when processing massive metagenomic data. Here, we present DeepCRISPR-Typer, a comprehensive computational framework integrating a large protein language model (TEMC-Cas), a deep sequence feature extractor (CRISPR-RepTyper), and an adaptive targeted HMM profiling strategy. DeepCRISPR-Typer integrates array and Cas evidence and significantly reduces computational overhead by dynamically invoking subtype-specific HMM subsets. In metagenomic dataset evaluations, DeepCRISPR-Typer achieved a classification accuracy of 94.26% and demonstrated a significant acceleration of approximately 1 orders of magnitude compared to existing mainstream tools. This research provides a robust and scalable engine for metagenome-scale CRISPR system discovery, significantly expanding the mining toolbox for genome engineering applications.<\/jats:p>","DOI":"10.1021\/acssynbio.6c00398","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T16:03:45Z","timestamp":1786550625000},"page":"3738-3749","source":"Crossref","is-referenced-by-count":0,"title":["DeepCRISPR-Typer: Accurate CRISPR-Cas Identification and Subtyping in Metagenomes via Integrated Deep Learning"],"prefix":"10.1021","volume":"15","author":[{"given":"Long","family":"Wen","sequence":"first","affiliation":[{"name":"Northwestern Polytechnical University (NPU) , , , ,","place":["Xi\u2019an, Shaanxi, P. R. China, 710072"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minghui","family":"Jing","sequence":"additional","affiliation":[{"name":"Northwestern Polytechnical University (NPU) , , , ,","place":["Xi\u2019an, Shaanxi, P. R. China, 710072"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanyan","family":"Li","sequence":"additional","affiliation":[{"name":"Northwestern Polytechnical University (NPU) , , , ,","place":["Xi\u2019an, Shaanxi, P. R. China, 710072"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuequn","family":"Shang","sequence":"additional","affiliation":[{"name":"Northwestern Polytechnical University (NPU) , , , ,","place":["Xi\u2019an, Shaanxi, P. R. China, 710072"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0061-1317","authenticated-orcid":true,"given":"Xingyu","family":"Liao","sequence":"additional","affiliation":[{"name":"Northwestern Polytechnical University (NPU) , , , ,","place":["Xi\u2019an, Shaanxi, P. R. 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Rev. Microbiol."},{"issue":"7640","key":"2026091815065628800_cit8","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/nature21059","article-title":"New CRISPR\u2212Cas systems from uncultivated microbes","volume":"542","author":"Burstein","year":"2017","journal-title":"Nature"},{"issue":"6416","key":"2026091815065628800_cit9","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1126\/science.aav4294","article-title":"Programmed DNA destruction by miniature CRISPR-Cas14 enzymes","volume":"362","author":"Harrington","year":"2018","journal-title":"Science"},{"issue":"5","key":"2026091815065628800_cit10","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41592-021-01124-4","article-title":"Programmable RNA editing with compact CRISPR\u2212Cas13 systems from uncultivated microbes","volume":"18","author":"Xu","year":"2021","journal-title":"Nat. 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Microbiol."},{"issue":"4","key":"2026091815065628800_cit32","doi-asserted-by":"publisher","first-page":"2000","DOI":"10.1093\/nar\/gkz1197","article-title":"Type IV CRISPR-Cas Systems Are Highly Diverse and Involved in Competition Between Plasmids","volume":"48","author":"Pinilla-Redondo","year":"2020","journal-title":"Nucleic Acids Res."},{"issue":"D1","key":"2026091815065628800_cit33","doi-asserted-by":"publisher","first-page":"D134","DOI":"10.1093\/nar\/gkad903","article-title":"GenBank 2024 Update","volume":"52","author":"Sayers","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"2026091815065628800_cit34","doi-asserted-by":"crossref","unstructured":"Chen, T.\n          ; Xgboost: A Scalable Tree Boosting System. In Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining; ACM Digital Library, 2016.","DOI":"10.1145\/2939672.2939785"},{"key":"2026091815065628800_cit35","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1109\/tkde.2009.191","article-title":"A survey on transfer learning","volume":"22","author":"Pan","year":"2010","journal-title":"IEEE Trans. Knowl. Data Eng."}],"container-title":["ACS Synthetic Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acssynbio.6c00398","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/asbcd6\/article-pdf\/15\/9\/3738\/66515660\/sb6c00398.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/asbcd6\/article-pdf\/15\/9\/3738\/66515660\/sb6c00398.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T19:31:16Z","timestamp":1789759876000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/asbcd6\/article\/15\/9\/3738\/5253663\/DeepCRISPR-Typer-Accurate-CRISPR-Cas"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,12]]},"references-count":35,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,8,12]]},"published-print":{"date-parts":[[2026,9,18]]}},"URL":"https:\/\/doi.org\/10.1021\/acssynbio.6c00398","relation":{},"ISSN":["2161-5063"],"issn-type":[{"value":"2161-5063","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,12]]}}}