| Year |
Citation |
Score |
| 2023 |
Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Zhang Z, Liu W, Lee HRL, Tang X, He W, Islam N, Jain A, Chiu Y, ... ... Xu H, et al. CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nature Structural & Molecular Biology. PMID 37932451 DOI: 10.1038/s41594-023-01117-1 |
0.491 |
|
| 2023 |
Zhang L, He W, Fu R, Wang S, Chen Y, Xu H. Guide-specific loss of efficiency and off-target reduction with Cas9 variants. Nucleic Acids Research. PMID 37615574 DOI: 10.1093/nar/gkad702 |
0.423 |
|
| 2023 |
Zheng C, Wei Y, Zhang Q, Sun M, Wang Y, Hou J, Zhang P, Lv X, Su D, Jiang Y, Gumin J, Sahni N, Hu B, Wang W, Chen X, ... ... Xu H, et al. Multiomics analyses reveal /YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Science Advances. 9: eadf3984. PMID 37540752 DOI: 10.1126/sciadv.adf3984 |
0.453 |
|
| 2023 |
Zheng C, Wei Y, Zhang P, Xu L, Zhang Z, Lin K, Hou J, Lv X, Ding Y, Chiu Y, Jain A, Islam N, Malovannaya A, Wu Y, Ding F, ... Xu H, et al. CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer. The Journal of Clinical Investigation. 133. PMID 36856111 DOI: 10.1172/JCI159940 |
0.508 |
|
| 2022 |
Fu R, He W, Dou J, Villarreal OD, Bedford E, Wang H, Hou C, Zhang L, Wang Y, Ma D, Chen Y, Gao X, Depken M, Xu H. Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity. Nature Communications. 13: 474. PMID 35078987 DOI: 10.1038/s41467-022-28028-x |
0.442 |
|
| 2022 |
Liao Y, Chen CH, Xiao T, de la Peña Avalos B, Dray EV, Cai C, Gao S, Shah N, Zhang Z, Feit A, Xue P, Liu Z, Yang M, Lee JH, Xu H, et al. Inhibition of EZH2 transactivation function sensitizes solid tumors to genotoxic stress. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35031563 DOI: 10.1073/pnas.2105898119 |
0.377 |
|
| 2021 |
Sun M, Wang Y, Zheng C, Wei Y, Hou J, Zhang P, He W, Lv X, Ding Y, Liang H, Hon CC, Chen X, Xu H, Chen Y. Systematic functional interrogation of human pseudogenes using CRISPRi. Genome Biology. 22: 240. PMID 34425866 DOI: 10.1186/s13059-021-02464-2 |
0.436 |
|
| 2021 |
He W, Wang H, Wei Y, Jiang Z, Tang Y, Chen Y, Xu H. GuidePro: A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. Bioinformatics (Oxford, England). PMID 33394026 DOI: 10.1093/bioinformatics/btaa1068 |
0.396 |
|
| 2018 |
Xiao T, Li W, Wang X, Xu H, Yang J, Wu Q, Huang Y, Geradts J, Jiang P, Fei T, Chi D, Zang C, Liao Q, Rennhack J, Andrechek E, et al. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. Proceedings of the National Academy of Sciences of the United States of America. PMID 29987050 DOI: 10.1073/Pnas.1722617115 |
0.641 |
|
| 2018 |
Chen CH, Xiao T, Xu H, Jiang P, Meyer CA, Li W, Brown M, Liu XS. Improved design and analysis of CRISPR knockout screens. Bioinformatics (Oxford, England). PMID 29868757 DOI: 10.1093/Bioinformatics/Bty450 |
0.42 |
|
| 2017 |
Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, Dharia NV, Montgomery PG, Cowley GS, Pantel S, Goodale A, Ali LD, Jiang G, Lubonja R, Harrington WF, et al. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics. PMID 29083409 DOI: 10.1038/Ng.3984 |
0.41 |
|
| 2017 |
Cao Q, Ma J, Chen CH, Xu H, Chen Z, Li W, Liu XS. CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. Plos One. 12: e0184281. PMID 28873439 DOI: 10.1371/Journal.Pone.0184281 |
0.62 |
|
| 2017 |
Rosenbluh J, Xu H, Harrington W, Gill S, Wang X, Vazquez F, Root DE, Tsherniak A, Hahn WC. Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression. Nature Communications. 8: 15403. PMID 28534478 DOI: 10.1038/Ncomms15403 |
0.426 |
|
| 2017 |
Meyers RM, Aguirre AJ, Weir BA, Vazquez F, Zhang C, Ben-David U, Cook A, Ha G, Harrington WF, Doshi M, Gill S, Xu H, Ali LD, Jiang G, Pantel S, et al. Abstract B39: Genomic copy number alterations introduce a gene-independent viability bias in CRISPR-Cas9 knock-out screens of cancer cell lines Clinical Cancer Research. 23. DOI: 10.1158/1557-3265.Pmccavuln16-B39 |
0.424 |
|
| 2017 |
Xiao T, Li W, Wang X, Xu H, Wu Q, Jiang P, Yang J, Fei T, Zang C, Liao Q, Rennhack J, Andrechek E, Li N, Jeselsohn R, Liu SX, et al. Abstract PR06: CRISPR screens identified drivers of endocrine resistance and synthetic lethal vulnerabilities in breast cancer Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-Pr06 |
0.571 |
|
| 2016 |
Zhu S, Li W, Liu J, Chen CH, Liao Q, Xu P, Xu H, Xiao T, Cao Z, Peng J, Yuan P, Brown M, Liu XS, Wei W. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nature Biotechnology. PMID 27798563 DOI: 10.1038/Nbt.3715 |
0.606 |
|
| 2016 |
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, et al. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. Bmc Bioinformatics. 17: 404. PMID 27716038 DOI: 10.1186/S12859-016-1274-4 |
0.631 |
|
| 2016 |
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS. CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics (Oxford, England). PMID 27402906 DOI: 10.1093/Bioinformatics/Btw476 |
0.606 |
|
| 2016 |
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, et al. Genomic copy number dictates a gene-independent cell response to CRISPR-Cas9 targeting. Cancer Discovery. PMID 27260156 DOI: 10.1158/2159-8290.Cd-16-0154 |
0.414 |
|
| 2016 |
Aguirre AJ, Shao W, Xu H, Weir B, Vazquez F, Meyers R, Zhang C, Doshi M, Cowley GS, Ewachiw T, Rasheed Z, Golub TR, Stegmaier K, Roberts CW, Garraway LA, et al. Abstract PR05: Genome-scale CRISPR-Cas9 screening to identify essential genes and pathways in pancreatic cancer Cancer Research. 76. DOI: 10.1158/1538-7445.Panca16-Pr05 |
0.373 |
|
| 2015 |
Li W, Köster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS. Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biology. 16: 281. PMID 26673418 DOI: 10.1186/S13059-015-0843-6 |
0.4 |
|
| 2015 |
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. Integrative analysis reveals the transcriptional collaboration between EZH2 and E2F1 in the regulation of cancer-related gene expression. Molecular Cancer Research : McR. PMID 26659825 DOI: 10.1158/1541-7786.Mcr-15-0313 |
0.706 |
|
| 2015 |
Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh PR, Anttila V, Xu H, Zang C, Farh K, Ripke S, Day FR, et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nature Genetics. PMID 26414678 DOI: 10.1038/Ng.3404 |
0.557 |
|
| 2015 |
Trynka G, Westra HJ, Slowikowski K, Hu X, Xu H, Stranger BE, Klein RJ, Han B, Raychaudhuri S. Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci. American Journal of Human Genetics. 97: 139-52. PMID 26140449 DOI: 10.1016/J.Ajhg.2015.05.016 |
0.386 |
|
| 2015 |
Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS. Sequence determinants of improved CRISPR sgRNA design. Genome Research. PMID 26063738 DOI: 10.1101/Gr.191452.115 |
0.611 |
|
| 2014 |
Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology. 15: 554. PMID 25476604 DOI: 10.1186/S13059-014-0554-4 |
0.62 |
|
| 2014 |
Gusev A, Lee SH, Trynka G, Finucane H, Vilhjálmsson BJ, Xu H, Zang C, Ripke S, Bulik-Sullivan B, Stahl E, Kähler AK, Hultman CM, Purcell SM, et al. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. American Journal of Human Genetics. 95: 535-52. PMID 25439723 DOI: 10.1016/J.Ajhg.2014.10.004 |
0.536 |
|
| 2014 |
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, et al. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biology. 15: 419. PMID 25103624 DOI: 10.1186/S13059-014-0419-X |
0.642 |
|
| 2014 |
He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nature Methods. 11: 73-8. PMID 24317252 DOI: 10.1038/Nmeth.2762 |
0.636 |
|
| 2013 |
Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, Raychaudhuri S. Chromatin marks identify critical cell types for fine mapping complex trait variants Nature Genetics. 45: 124-130. PMID 23263488 DOI: 10.1038/Ng.2504 |
0.542 |
|
| 2012 |
Xu K, Wu ZJ, Groner AC, He HH, Cai C, Lis RT, Wu X, Stack EC, Loda M, Liu T, Xu H, Cato L, Thornton JE, Gregory RI, Morrissey C, et al. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science (New York, N.Y.). 338: 1465-9. PMID 23239736 DOI: 10.1126/Science.1227604 |
0.593 |
|
| 2012 |
Orlov Y, Xu H, Afonnikov D, Lim B, Heng JC, Yuan P, Chen M, Yan J, Clarke N, Orlova N, Huss M, Gunbin K, Podkolodnyy N, Ng HH. Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell. Journal of Integrative Bioinformatics. 9: 211. PMID 22987856 DOI: 10.2390/Biecoll-Jib-2012-211 |
0.37 |
|
| 2012 |
Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS. Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Research. 40: 6414-23. PMID 22495509 DOI: 10.1093/Nar/Gks304 |
0.531 |
|
| 2012 |
Xu H, Sung WK. Identifying differential histone modification sites from ChIP-seq data. Methods of Molecular Biology. 802: 293-303. PMID 22130888 DOI: 10.1007/978-1-61779-400-1_19 |
0.371 |
|
| 2011 |
Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nature Genetics. 43: 630-8. PMID 21685913 DOI: 10.1038/Ng.857 |
0.384 |
|
| 2011 |
Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CWH, Ye C, Ping JLH, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, et al. Erratum: CTCF-mediated functional chromatin interactome in pluripotent cells Nature Genetics. 43: 815-815. DOI: 10.1038/Ng0811-815A |
0.306 |
|
| 2010 |
Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics (Oxford, England). 26: 1199-204. PMID 20371496 DOI: 10.1093/Bioinformatics/Btq128 |
0.316 |
|
| 2010 |
Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei C, Ruan Y, Sung W. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing Genome Biology. 11: 1-13. PMID 20181287 DOI: 10.1186/Gb-2010-11-2-R22 |
0.319 |
|
| 2009 |
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 462: 58-64. PMID 19890323 DOI: 10.1038/Nature08497 |
0.36 |
|
| 2009 |
Lee WH, Narang V, Xu H, Lin F, Chin KC, Sung WK. DREAM2 challenge: Integrated multi-array supervised learning algorithm for BCL6 transcriptional targets prediction Annals of the New York Academy of Sciences. 1158: 196-204. PMID 19348641 DOI: 10.1111/J.1749-6632.2008.03755.X |
0.329 |
|
| 2008 |
Xu H, Wei CL, Lin F, Sung WK. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics (Oxford, England). 24: 2344-9. PMID 18667444 DOI: 10.1093/Bioinformatics/Btn402 |
0.387 |
|
| 2008 |
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 133: 1106-17. PMID 18555785 DOI: 10.1016/J.Cell.2008.04.043 |
0.375 |
|
| 2007 |
Lim CA, Yao F, Wong JJ, George J, Xu H, Chiu KP, Sung WK, Lipovich L, Vega VB, Chen J, Shahab A, Zhao XD, Hibberd M, Wei CL, Lim B, et al. Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Molecular Cell. 27: 622-35. PMID 17707233 DOI: 10.1016/J.Molcel.2007.06.038 |
0.304 |
|
| 2007 |
Chiu KP, Ariyaratne P, Xu H, Tan A, Ng P, Liu ET, Ruan Y, Wei C, Sung WK. Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. Bmc Cancer. 7: 109-109. PMID 17594473 DOI: 10.1186/1471-2407-7-109 |
0.319 |
|
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