Dr. Han Xu
The University of Texas MD Anderson Cancer Center
Department of Epigenetics and Molecular Carcinogenesis
The Virginia Harris Cockrell Cancer Research Center
My laboratory is located in Smithville, Texas, at UT Science Park
Our laboratory is 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 (NGS) 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. To address these needs, we have developed a series of bioinformatics tools for applications with ChIP-seq, DNase-seq, RNA-seq, and 3D chromatin interaction experiments. Our 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. Potential projects for graduate students include but not limited to the following: i) Development of computational solutions for the optimization and analysis of high-throughput CRISPR-Cas9 and -dCas9 functional screens; ii) Identifying synthetic lethal epigenetic regulators using high-throughput CRISPR functional screens; iii) Development of integrative methods to identify epigenetic drug targets and biomarkers for the treatment of small-cell lung cancer; iv) Reconstruction and visualization of 3D chromatin interactome in normal and cancer cells.