Han Xu, Ph.D.

Peer-Reviewed Articles

1. Xu, L, Peng, F, Luo, Q, Ding, Y, Yuan, F, Zheng, L, He, W, Zhang, SS, Fu, X, Liu, J, Mutlu, AS, Wang, S, Nehring, RB, Li, X, Tang, Q, Li, C, Lyu, X, Dobrolecki, LE, Zhang, W, Han, D, Zhao, N, Jaehnig, EJ, Wang, J, Wu, W, Graham, DA, Li, Y, Chen, R, Peng, W, Chen, Y, Catic, A, Zhang, Z, Zhang, B, Mustoe, AM, Koong, A, Miles, G, Lewis, MT, Wang, MC, Rosenberg, SM, O'Malley, BW, Westbrook, TF, Xu, H, Zhang, XH, Osborne, CK, Li, JB, Ellis, MJ, Rimawi, MF, Rosen, JM, Chen, X. IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer. Cell 187(25):7248-7266.e34, 2024. e-Pub 2024. PMID: 39419025.
2. Chen, S, Hou, J, Jaffery, R, Guerrero, AM, Fu, R, Shi, L, Zheng, N, Bohat, R, Egan, NA, Yu, C, Sharif, S, Lu, Y, He, W, Wang, S, Gjuka, D, Stone, E, Shah, P, Rodon Ahnert, J, Chen, T, Liu, X, Bedford, MT, Xu, H, Peng, W. MTA-cooperative PRMT5 inhibitors enhance T cell-mediated antitumor activity in MTAP-loss tumors. Journal for immunotherapy of cancer 12(9), 2024. e-Pub 2024. PMID: 39313308.
3. Samer, EK, Morris, SA, Hutter, CM, Gilchrist, DA, Calluori, S, Bly, Z, Osorio, D, Zhang, L, He, W, Fu, R, Xu, H, Wittibschlager, S, Kutschat, AP, Seruggia, D, Morris, JA, Caragine, C, Sanjana, NE, Ho, CH, Harten, IA, Ray, JP, Whalen, S, Drusinsky, S, Pollard, KS, Visel, A, Slaven, N, Mannion, B, Kosicki, M, Kato, M, Pennacchio, LA, Spiro, A, Sasse, A, Mostafavi, S, Song, S, Roberts, E, Murphy, M, Donnard, E, Jones, TR, Losert, C, Heinig, M, Lee-Kim, V, Fang, S, Gupta, R, Salomonis, N, Grimes, HL, Kim, A, Ali, TA, Dey, KK, McGrail, DJ, Jain, A, Sahni, N. Deciphering the impact of genomic variation on function. Nature 633(8028):47-57, 2024. e-Pub 2024. PMID: 39232149.
4. Wang, Y, Zhou, J, He, W, Fu, R, Shi, L, Dang, NK, Liu, B, Xu, H, Cheng, X, Bedford, MT. SART3 reads methylarginine-marked glycine- and arginine-rich motifs. Cell Reports 43(7), 2024. e-Pub 2024. PMID: 38985674.
5. Xuan, F, Xuan, H, Huang, M, He, W, Xu, H, Shi, X, Wen, H. The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation. Journal of Molecular Biology 436(7), 2024. e-Pub 2024. PMID: 38141874.
6. Zheng, C, Wei, Y, Zhang, P, Lin, K, He, D, Teng, H, Manyam, GC, Zhang, Z, Liu, W, Lee, HL, Tang, X, He, W, Islam, N, Jain, A, Chiu, Y, Cao, S, Diao, Y, Meyer-Gauen, S, Hook, M, Malovannaya, A, Li, W, Hu, M, Wang, W, Xu, H, Kopetz, S, Chen, Y. CRISPR–Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nature Structural and Molecular Biology 30(12):1878-1892, 2023. e-Pub 2023. PMID: 37932451.
7. Xu, L, Xuan, H, He, W, Zhang, L, Huang, M, Li, K, Wen, H, Xu, H, Shi, X. TAZ2 truncation confers overactivation of p300 and cellular vulnerability to HDAC inhibition. Nature communications 14(1), 2023. e-Pub 2023. PMID: 37660055.
8. 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 51(18):9880-9893, 2023. e-Pub 2023. PMID: 37615574.
9. 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, McGrail, DJ, Zhang, C, Huang, S, Xu, H, Chen, J, Lang Jr, FF, Hu, J, Chen, Y. Multiomics analyses reveal DARS1-AS1/YBX1–controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Science Advances 9(31), 2023. e-Pub 2023. PMID: 37540752.
10. 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, Sun M, Chen X, Chen Y. CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer. J Clin Invest 133(5), 2023. e-Pub 2023. PMID: 36856111.
11. Zhang L, He W, Fu R, Xu H. Guide-specific loss of efficiency and off-target reduction with Cas9 variants. bioRxiv, 2023. e-Pub 2023. PMID: 36993488.
12. Srour N, Villarreal OD, Hardikar S, Yu Z, Preston S, Miller WH, 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 38(13):110582, 2022. e-Pub 2022. PMID: 35354055.
13. 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 119(3), 2022. e-Pub 2022. PMID: 35031563.
14. 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 13(1):474, 2022. e-Pub 2022. PMID: 35078987.
15. 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(1), 2021. e-Pub 2021. PMID: 34425866.
16. Sun M, Wang Y, Zheng C, Wei Y, Hou J, Zhang P, He W, Lv X, Ding Y, Liang H, Hon CC, Chen X, H* X, Y* C. Systematic functional interrogation of human pseudogenes using CRISPRi. Genome Biol 22(1):240, 2021. e-Pub 2021.
17. 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 37(1):134-136, 2021. e-Pub 2021. PMID: 33394026.
18. 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 34(12):3269-3285, 2020. e-Pub 2020. PMID: 32576962.
19. 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 10(1):4541, 2019. e-Pub 2019. PMID: 31586052.
20. Gao G, Zhang L, Villarreal OD, He W, Su D, Bedford E, Moh P, Shen J, Shi X, MT* B, H* X. PRMT1 loss sensitizes cells to PRMT5 inhibition. Nucleic Acids Res 47(10):5038-5048, 2019. e-Pub 2019.
21. 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 34(23):4095-4101, 2018. e-Pub 2018. PMID: 29868757.
22. 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 19(4):721-724, 2018. e-Pub 2018. PMID: 28203699.
23. 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 115(31):7869-7878, 2018. e-Pub 2018. PMID: 29987050.
24. 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 49(12):1779-1784, 2017. e-Pub 2017. PMID: 29083409.
25. J* R, H* X, 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 8:15403, 2017. e-Pub 2017.
26. 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(9):e0184281, 2017. e-Pub 2017. PMID: 28873439.
27. 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. Nat Biotechnol 34(12):1279-1286, 2016. e-Pub 2016. PMID: 27798563.
28. Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, H* X, XS* L. CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics 32(21):3336-3338, 2016. e-Pub 2016.
29. 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. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC Bioinformatics 17(1):404, 2016. e-Pub 2016. PMID: 27716038.
30. 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. Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting. Cancer Discov 6(8):914-29, 2016. e-Pub 2016. PMID: 27260156.
31. H* X, K* X, 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, 2016. e-Pub 2016.
32. 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 Biol 16:281, 2015. e-Pub 2015. PMID: 26673418.
33. 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, Consortium R, Genomics Consortium SWGOTP, Consortium R, Purcell S, Stahl E, Lindstrom S, Perry JR, Okada Y, Raychaudhuri S, Daly MJ, Patterson N, Neale BM, Price AL. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat Genet 47(11):1228-35, 2015. e-Pub 2015. PMID: 26414678.
34. H* X, T* X, 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, 2015. e-Pub 2015.
35. 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. Am J Hum Genet 97(1):139-52, 2015. e-Pub 2015. PMID: 26140449.
36. Gusev A, Lee SH, Trynka G, Finucane H, Vilhjálmsson BJ, Xu H, Zang C, Ripke S, Bulik-Sullivan B, Stahl E, Genomics Consortium SWGOTP, Consortium S, Kähler AK, Hultman CM, Purcell SM, McCarroll SA, Daly M, Pasaniuc B, Sullivan PF, Neale BM, Wray NR, Raychaudhuri S, Price AL, Genomics Consortium SWGOTP, Consortium S. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Am J Hum Genet 95(5):535-52, 2014. e-Pub 2014. PMID: 25439723.
37. 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. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol 15(8):419, 2014. e-Pub 2014. PMID: 25103624.
38. 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. Nat Methods 11(1):73-8, 2014. e-Pub 2014. PMID: 24317252.
39. W* L, H* X, 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. e-Pub 2014.
40. 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. Nat Genet 45(2):124-30, 2013. e-Pub 2013. PMID: 23263488.
41. 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, Vessella RL, Montironi R, Magi-Galluzzi C, Kantoff PW, Balk SP, Liu XS, Brown M. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science 338(6113):1465-9, 2012. e-Pub 2012. PMID: 23239736.
42. 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. J Integr Bioinform 9(2):211, 2012. e-Pub 2012. PMID: 22987856.
43. 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 Res 40(14):6414-23, 2012. e-Pub 2012. PMID: 22495509.
44. Xu H, Sung WK. Identifying differential histone modification sites from ChIP-seq data. Methods Mol Biol 802:293-303, 2012. e-Pub 2012. PMID: 22130888.
45. L* H, H* X, G* L, 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, 2011. e-Pub 2011.
46. 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, 2010. e-Pub 2010. PMID: 20371496.
47. G* L, MJ* F, H* X, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11(2):R22, 2010. e-Pub 2010. PMID: 20181287.
48. 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, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462(7269):58-64, 2009. e-Pub 2009. PMID: 19890323.
49. Lee WH, Narang V, Xu H, Lin F, Chin KC, Sung WK. DREAM2 challenge. Ann N Y Acad Sci 1158:196-204, 2009. e-Pub 2009. PMID: 19348641.
50. 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, 2008. e-Pub 2008. PMID: 18667444.
51. X* C, H* X, 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, 2008. e-Pub 2008.
52. XD* Z, X* H, 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, 2007. e-Pub 2007.
53. 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, Ng HH, Ruan Y, Chin KC. Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol Cell 27(4):622-35, 2007. e-Pub 2007. PMID: 17707233.
54. Chiu KP, Ariyaratne P, Xu H, Tan A, Ng P, Liu ET, Ruan Y, Wei CL, Sung WK. Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. BMC Cancer 7:109, 2007. e-Pub 2007. PMID: 17594473.
55. Han X, Sung WK, Feng L. Identifying differentially expressed genes in time-course microarray experiment without replicate. J Bioinform Comput Biol 5(2a):281-96, 2007. e-Pub 2007. PMID: 17589962.
56. Rodrigues F, Sarkar-Tyson M, Harding SV, Sim SH, Chua HH, Lin CH, Han X, Karuturi RK, Sung K, Yu K, Chen W, Atkins TP, Titball RW, Tan P. Global map of growth-regulated gene expression in Burkholderia pseudomallei, the causative agent of melioidosis. J Bacteriol 188(23):8178-88, 2006. e-Pub 2006. PMID: 16997946.

Abstracts

1. Han X, Sung WK, Feng L. Pem: a general statistical approach for identifying differentially expressed genes in time-course cDNA microarray experiment without replicate. Comput Syst Bioinformatics Conf:123-32, 2006. e-Pub 2006. PMID: 17369631.