{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T02:58:35Z","timestamp":1771210715943,"version":"3.50.1"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T00:00:00Z","timestamp":1709251200000},"content-version":"vor","delay-in-days":39,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDA26030301"],"award-info":[{"award-number":["XDA26030301"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970609"],"award-info":[{"award-number":["31970609"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Top Talents Program in Science and Technology\u2019 from Yunnan Province"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>CRISPR\/Cas9 is a promising RNA-guided genome editing technology, which consists of a Cas9 nuclease and a single-guide RNA (sgRNA). So far, a number of sgRNA prediction softwares have been developed. However, they were usually designed for protein-coding genes without considering that long non-coding RNA (lncRNA) genes may have different characteristics. In this study, we first evaluated the performances of a series of known sgRNA-designing tools in the context of both coding and non-coding datasets. Meanwhile, we analyzed the underpinnings of their varied performances on the sgRNA\u2019s specificity for lncRNA including nucleic acid sequence, genome location and editing mechanism preference. Furthermore, we introduce a support vector machine-based machine learning algorithm named CRISPRlnc, which aims to model both CRISPR knock-out (CRISPRko) and CRISPR inhibition (CRISPRi) mechanisms to predict the on-target activity of targets. CRISPRlnc combined the paired-sgRNA design and off-target analysis to achieve one-stop design of CRISPR\/Cas9 sgRNAs for non-coding genes. Performance comparison on multiple datasets showed that CRISPRlnc was far superior to existing methods for both CRISPRko and CRISPRi mechanisms during the lncRNA-specific sgRNA design. To maximize the availability of CRISPRlnc, we developed a web server (http:\/\/predict.crisprlnc.cc) and made it available for download on GitHub.<\/jats:p>","DOI":"10.1093\/bib\/bbae066","type":"journal-article","created":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T10:54:58Z","timestamp":1709290498000},"source":"Crossref","is-referenced-by-count":8,"title":["CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR\/Cas9 system"],"prefix":"10.1093","volume":"25","author":[{"given":"Zitian","family":"Yang","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Tropical Plant Resources and Sustainable Use , Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223 , China"},{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"given":"Zexin","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Tropical Plant Resources and Sustainable Use , Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223 , China"}]},{"given":"Jing","family":"Li","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Tropical Plant Resources and Sustainable Use , Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223 , China"}]},{"given":"Wen","family":"Chen","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Laboratory of Vascular Biology and Translational Medicine , School of Medicine, Hunan University of Chinese Medicine, Changsha 410208 , China"}]},{"given":"Changning","family":"Liu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Tropical Plant Resources and Sustainable 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