The University of Texas MD Anderson Cancer Center
Department of Epigenetics and Molecular Carcinogenesis
I have provided the collaborative support for departmental research labs on epigenetic studies involving in the next generation sequencing data. One of the studies focuses on the chromatin accessibility and nascent RNA synthesis during the stem cell development. We are performing the integrative analysis of the ATAC-seq, Pro-seq and HiChIP-seq to identify the landscapes of transcription initiation and elongation in gene regions and the profiling of chromatin structures and RNA transcripts (eRNA) in enhancer regions. The additional differential evaluation will identify the dynamic genomic changes at different stages of the stem cells. Furthermore, we are going to correlate above results with other genomic information from multiple platforms such as different ChIP-seq assays characterizing histone modifications.
Additional collaborative projects are involving in functional genomics studies, such as evaluation of immunoglobulins repertoire in virus infected germline centers, gene expression profiling during B lymphocytes in response to antigen stimulation, pathway regulations involving in the DNA damages, and gene signature classification of cells in thymus development.
We also developed new analytical tools for identification of cryptic splicing and introns retention and have constructed multiple bioinformatics pipelines for RNA-seq, ChIP-seq, Exome-seq, Pro-seq, ATAC-seq, Whole Genome sequencing, miRNA-seq and microarrays. Different bioinformatics software have been integrated in the pipelines such as GATK, Mutect, Pindel, Bowtie1/2, BWA, Tophat, DESeq2, MACS, MEME-ChIP, CrispRVariants, limma, samtools, picard, bedtools, vcftools, fastqc and et al. HPC (High Performance Computing) servers with multi-thread programming have been utilized for the analysis.
Education & Training
PhD, MD Anderson UTHealth Graduate School, 2000