Assistant Professor, Department of Epigenetics and Molecular Carcinogenesis, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Smithville, TX
Faculty Member, Graduate School of Biomedical Sciences (GSBS), The University of Texas Health Science Center, Houston, TX
I am interested in developing computational algorithms for the design and analysis of high-throughput biological experiments, with a focus on applications in the field of transcriptional and epigenetic regulation. The advent of Next-Generation Sequencing has facilitated the development of a number of high-throughput biotechnologies in the past decade, which have greatly accelerated biomedical research. Innovative computational methods are in demand, not only for standardized data processing, but also for rational design and unbiased interpretation of these experiments. We have developed a series of bioinformatics tools for applications with ChIP-seq, DNase-seq, RNA-seq, and 3D chromatin interaction experiments. These tools have enabled in-depth collaborations leading to the elucidation of transcriptional and epigenetic regulatory mechanisms in cancer cells and embryonic stem cells. My current research interest is mainly on the optimization, design, and analysis of CRISPR-based genetic or epigenetic perturbation screens. We are developing machine-learning and statistical methods to boost the performance of CRISPR screens, and are using these approaches for systematic functional characterization of coding and non-coding genomic regions. We are also developing novel algorithms to integrate information from CRISPR screens and other heterogeneous “-omic” datasets. Working with molecular biologists and clinical researchers, my group combines our computational expertise with cutting-edge biotechnologies to address fundamental questions in cancer epigenetics and to decipher the genetic and epigenetic “codes” underlying various cancer phenotypes.
|2010||Nanyang Technological University, Singapore, SGP, PHD, Bioinformatics|
|1999||Zhejiang University, Zhejiang, CHN, ME, Information Systems|
|1996||Zhejiang University, Zhejiang, CHN, BE, Computer Science|
|2010-2015||Postdoctoral Research Fellowship, Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA|
- 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.
- 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. PMID: 28203699.
- 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.
- 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 8:15403, 2017. e-Pub 2017. PMID: 28534478.
- 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.
- 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, 2016. e-Pub 2016. PMID: 27402906 (* co-corresponding author).
- 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.
- 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, 2016. e-Pub 2015. PMID: 26659825.
- 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, 2015. e-Pub 2015. PMID: 26063738.
- 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. PMID: 25476604.
- Xu H, Sung WK. Identifying differential histone modification sites from ChIP-seq data. Methods Mol Biol 802:293-303, 2012. PMID: 22130888.
- 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, 2011. e-Pub 2011. PMID: 21685913.
- 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.
- 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.
- 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, 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, 2007. PMID: 18371363 (* co-first author).
- 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. e-Pub 2018. PMID: 29868757.
|Title:||Recruitment of First-time, Tenure-Track Faculty - Dr. Han Xu|
|Funding Source:||Cancer Prevention & Research Institute of Texas (CPRIT)|
|Title:||Integrative Approaches to Identifying Epigenetic Regulatory Networks in Cancer|
|Funding Source:||UTMDACC Rising STARS|