Han Xu, Ph.D.
Present Title & Affiliation
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.
1808 Park Road 1C
P.O. Box 389
Unit Number: 116
Smithville, TX 78957
Room Number: SRA1.114
Education & Training
|2010||Nanyang Technological University, Singapore, Singapore, PHD, Bioinformatics|
|1999||Zhejiang University, Zhejiang, China, ME, Information Systems|
|1996||Zhejiang University, Zhejiang, China, BE, Computer Science|
|12/2010-4/2015||Postdoctoral Research Fellowship, Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA|
Peer-Reviewed Original Research Articles
|1.||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).|
|2.||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).|
|3.||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).|
|4.||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).|
|5.||Xu H, Sung WK. Identifying differential histone modification sites from ChIP-seq data. Methods Mol Biol 802:293-303, 2012. PMID: 22130888.|
|6.||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).|
|7.||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.|
|8.||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.|
|9.||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).|
|10.||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).|
Grant & Contract Support
|Title:||Recruitment of First-time, Tenure-Track Faculty - Dr. Han Xu|
|Funding Source:||Cancer Prevention & Research Institute of Texas (CPRIT)|
|Duration:||12/1/2016 - 11/30/2020|
Last updated: 3/13/2017