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Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting.
Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi MB, Kost-Alimova M, Gill S, Xu H, Ali LD, Jiang G, Pantel S, Lee Y, Goodale A, Cherniack AD, Oh C, Kryukov G, Cowley GS, Garraway LA, Stegmaier K, Roberts CW, Golub TR, Meyerson M, Root DE, Tsherniak A, Hahn WC. Aguirre AJ, et al. Among authors: xu h. Cancer Discov. 2016 Aug;6(8):914-29. doi: 10.1158/2159-8290.CD-16-0154. Epub 2016 Jun 3. Cancer Discov. 2016. PMID: 27260156 Free PMC article.
Sequence determinants of improved CRISPR sgRNA design.
Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS. Xu H, et al. Genome Res. 2015 Aug;25(8):1147-57. doi: 10.1101/gr.191452.115. Epub 2015 Jun 10. Genome Res. 2015. PMID: 26063738 Free PMC article.
CRISPR-DO for genome-wide CRISPR design and optimization.
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS. Ma J, et al. Among authors: xu h. Bioinformatics. 2016 Nov 1;32(21):3336-3338. doi: 10.1093/bioinformatics/btw476. Epub 2016 Jul 10. Bioinformatics. 2016. PMID: 27402906 Free PMC article.
Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, Dharia NV, Montgomery PG, Cowley GS, Pantel S, Goodale A, Lee Y, Ali LD, Jiang G, Lubonja R, Harrington WF, Strickland M, Wu T, Hawes DC, Zhivich VA, Wyatt MR, Kalani Z, Chang JJ, Okamoto M, Stegmaier K, Golub TR, Boehm JS, Vazquez F, Root DE, Hahn WC, Tsherniak A. Meyers RM, et al. Among authors: xu h. Nat Genet. 2017 Dec;49(12):1779-1784. doi: 10.1038/ng.3984. Epub 2017 Oct 30. Nat Genet. 2017. PMID: 29083409 Free PMC article.
Improved design and analysis of CRISPR knockout screens.
Chen CH, Xiao T, Xu H, Jiang P, Meyer CA, Li W, Brown M, Liu XS. Chen CH, et al. Among authors: xu h. Bioinformatics. 2018 Dec 1;34(23):4095-4101. doi: 10.1093/bioinformatics/bty450. Bioinformatics. 2018. PMID: 29868757 Free PMC article.
Benchmarking CRISPR on-target sgRNA design.
Yan J, Chuai G, Zhou C, Zhu C, Yang J, Zhang C, Gu F, Xu H, Wei J, Liu Q. Yan J, et al. Among authors: xu h. Brief Bioinform. 2018 Jul 20;19(4):721-724. doi: 10.1093/bib/bbx001. Brief Bioinform. 2018. PMID: 28203699
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