CRISPR-DO for genome-wide CRISPR design and optimization

Bioinformatics

Volumn 32, Issue 21, 2016, Pages 3336-3338

  Ma, Jian ^a   Köster, Johannes ^b,c,d   Qin, Qian ^a   Hu, Shengen ^a   Li, Wei ^b,c   Chen, Chenhao ^b,c   Cao, Qingyi ^e   Wang, Jinzeng ^a   Mei, Shenglin ^a   Liu, Qi ^a   Xu, Han ^b,c   Liu, Xiaole Shirley ^a,b,c  

^a TONGJI UNIVERSITY   (China)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GUIDE RNA;

ANIMAL; BIOLOGY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; EXON; GENE EDITING; GENOME; HUMAN; MOUSE;

ANIMALS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; COMPUTATIONAL BIOLOGY; DNA; EXONS; GENE EDITING; GENOME; HUMANS; MICE; RNA, GUIDE;

EID: 84994666838     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw476     Document Type: Article

References (19)

1. Bae, S. et al. (2014) Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics, 30, 1473-1475.
2. Cho, S. W. et al. (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol., 31, 230-232.
3. Cong, L. et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819-823.
4. Consortium, E. P. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
5. Doench, J. G. et al. (2016) Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol., 34, 184-191.
6. Fu, Y. et al. (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol., 32, 279-284.
7. Heigwer, F. et al. (2014) E-CRISP: fast CRISPR target site identification. Nat. Methods, 11, 122-123.
8. Hsu, P. D. et al. (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol., 31, 827-832.
9. Hsu, P. D. et al. (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157, 1262-1278.
10. Jinek, M. et al. (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337, 816-821.
11. Lei, Y. et al. (2014) CRISPR-P: A web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol. Plant, 7, 1494-1496.
12. Li, H. And Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
13. Liu, H. et al. (2015) CRISPR-ERA: A comprehensive design tool for CRISPRmediated gene editing, repression and activation. Bioinformatics, 31, 3676-3678.
14. Mali, P. et al. (2013) RNA-guided human genome engineering via Cas9. Science, 339, 823-826.
15. Shi, J. et al. (2015) Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat. Biotechnol., 33, 661-667.
16. Wang, T. et al. (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science, 343, 80-84.
17. Xiao, A. et al. (2014) CasOT: A genome-wide Cas9/gRNA off-target searching tool. Bioinformatics, [Epub ahead of print].
18. Xu, H. et al. (2015) Sequence determinants of improved CRISPR sgRNA design. Genome Res., 25, 1147-1157.
19. Zhou, X. et al. (2011) The human epigenome Browser at Washington University. Nat. Methods, 8, 989-990.