DeepCRISPR: optimized CRISPR guide RNA design by deep learning
Chuai, Guohui1,2; Ma, Hanhui5; Yan, Jifang1,2; Chen, Ming4; Hong, Nanfang1,2; Xue, Dongyu1,2; Zhou, Chi1,2; Zhu, Chenyu1,2; Chen, Ke1,2; Duan, Bin1,2
2018-06-26
发表期刊GENOME BIOLOGY
ISSN1474-760X
卷号19
发表状态已发表
DOI10.1186/s13059-018-1459-4
摘要A major challenge for effective application of CRISPR systems is to accurately predict the single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would facilitate the optimized design of sgRNAs with high sensitivity and specificity. Here we present DeepCRISPR, a comprehensive computational platform to unify sgRNA on-target and off-target site prediction into one framework with deep learning, surpassing available state-of-the-art in silico tools. In addition, DeepCRISPR fully automates the identification of sequence and epigenetic features that may affect sgRNA knockout efficacy in a data-driven manner. DeepCRISPR is available at http://www.deeperispr.net/.
关键词CRISPR system Gene knockout Deep learning On-targets Off-targets
收录类别SCI ; SCIE
语种英语
资助项目Shanghai Natural Science Foundation Program[17ZR1449400]
WOS研究方向Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号WOS:000436514600001
出版者BMC
WOS关键词OFF-TARGET CLEAVAGE ; GENOME ; SEQ ; DNA ; SPECIFICITIES ; PREDICTION ; NUCLEASES ; SELECTION ; SGRNAS
原始文献类型Article
引用统计
文献类型期刊论文
条目标识符https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/27450
专题生命科学与技术学院
生命科学与技术学院_PI研究组_马涵慧组
通讯作者Huang, Deshuang; Wei, Jia; Liu, Qi
作者单位1.Tongji Univ, Dept Endocrinol & Metab, Shanghai Peoples Hosp 10, Shanghai 20009, Peoples R China
2.Tongji Univ, Sch Life Sci & Technol, Bioinformat Dept, Shanghai 20009, Peoples R China
3.Tongji Univ, Sch Elect & Informat Engn, Machine Learning & Syst Biol Lab, Shanghai 201804, Peoples R China
4.AstraZeneca, Innovat Ctr China, R&D Informat, 199 Liangjing Rd, Shanghai 201203, Peoples R China
5.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China
6.Wenzhou Med Univ, State Key Lab Cultivat Base, Eye Hosp, Wenzhou 325027, Zhejiang, Peoples R China
7.Wenzhou Med Univ, Key Lab Vis Sci, Minist Hlth, Eye Hosp, Wenzhou 325027, Zhejiang, Peoples R China
8.Wenzhou Med Univ, Zhejiang Prov Key Lab Ophthalmol & Optometry, Sch Ophthalmol & Optometry, Eye Hosp, Wenzhou 325027, Zhejiang, Peoples R China
推荐引用方式
GB/T 7714
Chuai, Guohui,Ma, Hanhui,Yan, Jifang,et al. DeepCRISPR: optimized CRISPR guide RNA design by deep learning[J]. GENOME BIOLOGY,2018,19.
APA Chuai, Guohui.,Ma, Hanhui.,Yan, Jifang.,Chen, Ming.,Hong, Nanfang.,...&Liu, Qi.(2018).DeepCRISPR: optimized CRISPR guide RNA design by deep learning.GENOME BIOLOGY,19.
MLA Chuai, Guohui,et al."DeepCRISPR: optimized CRISPR guide RNA design by deep learning".GENOME BIOLOGY 19(2018).
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