Publications

2017 - Present

Srour N, Villarreal OD, Hardikar S, Yu Z, Preston S, Miller WH Jr, Szewczyk MM, Barsyte-Lovejoy D, Xu H, Chen T, Del Rincón SV, Richard S. PRMT7 ablation stimulates anti-tumor immunity and sensitizes melanoma to immune checkpoint blockade.  Cell Rep. 2022 Mar 29;38(13):110582. PMID: 35354055

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. Nat Commun. 2022 Jan 25;13(1):474. PMID: 35078987 PMCID: PMC8789861 (^#equal contributions)

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, Li W, Mei S, Pierre RS, Shu S, Fei T, Duarte M, Zhao J, Bradner JE, Polyak K, Kantoff PW, Long H, Balk SP, Liu XS, Brown M, Xu K. Inhibition of EZH2 transactivation function sensitizes solid tumors to genotoxic stress. Proc Natl Acad Sci U S A. 2022 Jan 18;119(3):e2105898119 PMID: 35031563 PMCID: PMC8784159

Sun M^#, Wang Y^#, Zheng C^#, Wei Y, Hou J, Zhang P, He W, Lv X, Ding Y, Liang H, Hon CC, Xu H*, Chen Y*. Systematic functional interrogation of human pseudogenes using CRISPRi. Genome Biol. 2021 Aug 23;22(1):240, PMID: 34425866 PMCID: PMC8381491. (*Co-corresponding authors, ^#equal contributions)

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. 2021 (In press) PMID: 33394026

Veazey KJ, Cheng D, Lin K, Villarreal OD, Gao G, Perez-Oquendo M, Van HT, Stratton SA, Green M, Xu H, Lu Y, Bedford MT, Santos MA. CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300-mutated lymphomas. Leukemia. 2020 Dec;34(12):3269-3285. PMID: 32576962 PMCID: PMC7688486

He W, Zhang L, Villarreal OD, Fu R, Bedford E, Dou J, Patel AY, Bedford MT, Shi X, Chen T, Bartholomew B, Xu H. De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun. 2019 Oct 4;10(1):4541. 10/2019. PMID: 31586052 PMCID: PMC6778102

Gao G^#, Zhang L^#, Villarreal OD, He W, Su D, Bedford E, Moh P, Shen J, Shi X, Bedford MT, Xu H. PRMT1 loss sensitizes cells to PRMT5 inhibition. Nucleic Acids Res. 2019 Jun 4;47(10):5038-5048. 6/2019. PMID: 30916320 PMCID: PMC6547413 (^#equal contributions)

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. 2018 Dec 1;34(23):4095-4101. PMID: 29868757  PMCID: PMC6247926.

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, Li N, Detre S, Dowsett M, Jeselsohn RM, Liu XS, Brown M. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):7869-7878. PMID: 29987050 PMCID: PMC6077722.

Yan J, Chuai G, Zhou C, Zhu C, Yang J, Zhang C, Gu F, Xu H, Wei J, Liu Q. Benchmarking CRISPR on-target sgRNA design. Brief Bioinform. 2018 Jul 20;19(4):721-724 PMID: 28203699.

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. 2017 Sep 5;12(9):e0184281. PMID: 28873439 PMCID: PMC5584922.

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. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet. 2017 Dec;49(12):1779-1784. PMID: 29083409 PMCID: PMC5709193.

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. Nat Commun. 2017 May 23;8:15403. PMID: 28534478  PMCID: PMC5457492 (*co-first author).

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 32(21):3336-3338, 11/2016. e-Pub 7/2016. PMID: 27402906 (*co-corresponding author).

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. Mol Cancer Res 14(2):163-72, 2/2016. e-Pub 12/2015. PMCID: PMC4828727 (*co-first author).

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 Res 25(8):1147-57, 8/2015. e-Pub 6/2015. PMCID: PMC4509999 (*co-first author).

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 Biol 15(12):554, 2014. PMCID: PMC4290824 (*co-first author).

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, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 43(7):630-8, 6/2011. e-Pub 6/2011. PMCID: PMC3436933 (*co-first author).

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 26(9):1199-204, 5/2010. e-Pub 4/2010. PMID: 20371496.

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 24(20):2344-9, 10/2008. e-Pub 7/2008. PMID: 18667444.

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, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133(6):1106-17, 6/2008. PMID: 18555785 (*co-first author).

Zhao XD*, Han X*, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, Bourque G, Oh S, Ruan Y, Ng HH, Wei CL. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1(3):286-98, 9/2007. PMID: 18371363 (*co-first author).