DeepCRISPR: optimized CRISPR guide RNA design by deep learning

doi:10.1186/s13059-018-1459-4

	DeepCRISPR: optimized CRISPR guide RNA design by deep learning
	Chuai, Guohui 1,2; Ma, Hanhui5 ; Yan, Jifang 1,2; Chen, Ming 4; Hong, Nanfang 1,2; Xue, Dongyu 1,2; Zhou, Chi 1,2; Zhu, Chenyu 1,2; Chen, Ke 1,2; Duan, Bin 1,2; Gu, Feng 6,7,8; Qu, Sheng 1,2; Huang, Deshuang 3; Wei, Jia 4; Liu, Qi 1,2
	2018-06-26
发表期刊	GENOME BIOLOGY
ISSN	1474-760X
卷号	19
发表状态	已发表
DOI	10.1186/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).