Xu H - Search Results

1

MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes.

Zheng X, Zhao Q, Wu HJ, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P, Li F, Hou Y, He J, Wang J, Wang J, Zhang P, Zhang Y, Liu XS. Zheng X, et al. Among authors: xu h. Genome Biol. 2014 Aug 7;15(8):419. doi: 10.1186/s13059-014-0419-x. Genome Biol. 2014. PMID: 25103624 Free PMC article.

2

Computational inference of mRNA stability from histone modification and transcriptome profiles.

Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS. Wang C, et al. Among authors: xu h. Nucleic Acids Res. 2012 Aug;40(14):6414-23. doi: 10.1093/nar/gks304. Epub 2012 Apr 10. Nucleic Acids Res. 2012. PMID: 22495509 Free PMC article.

3

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.

He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. He HH, et al. Among authors: xu h. Nat Methods. 2014 Jan;11(1):73-78. doi: 10.1038/nmeth.2762. Epub 2013 Dec 8. Nat Methods. 2014. PMID: 24317252 Free PMC article.

4

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.

Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS. Li W, et al. Among authors: xu h. Genome Biol. 2014;15(12):554. doi: 10.1186/s13059-014-0554-4. Genome Biol. 2014. PMID: 25476604 Free PMC article.

5

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.

6

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression.

Xu H, Xu K, He HH, Zang C, Chen CH, Chen Y, Qin Q, Wang S, Wang C, Hu S, Li F, Long H, Brown M, Liu XS. Xu H, et al. Among authors: xu k. Mol Cancer Res. 2016 Feb;14(2):163-172. doi: 10.1158/1541-7786.MCR-15-0313. Epub 2015 Dec 9. Mol Cancer Res. 2016. PMID: 26659825 Free PMC article.

7

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.

Li W, Köster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS. Li W, et al. Among authors: xu h. Genome Biol. 2015 Dec 16;16:281. doi: 10.1186/s13059-015-0843-6. Genome Biol. 2015. PMID: 26673418 Free PMC article.

8

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.

9

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.

Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, Long HW, Liu XS. Qin Q, et al. Among authors: xu h. BMC Bioinformatics. 2016 Oct 3;17(1):404. doi: 10.1186/s12859-016-1274-4. BMC Bioinformatics. 2016. PMID: 27716038 Free PMC article.

10

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.

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