Our research focused on the application of algorithm to solve biology problems. We develop new computational tools to address a range of topics, including genome assembly, pathogen detection, phylogenetic, transcription factor binding sites finding, DNA motif prediction, and genomic sequence indexing. Currently, my research focus is on designing the pathogen chip, understanding the promoter/enhancer structure, and reconstructing the transcriptome. Below, we briefly describe the various projects.
- Understanding promoter and enhancer structures: It is well-known that enhancer will work with promoter to regulate the expression of genes. However, we still have little understanding of the mechanism. Using the exprimental data ChIP-seq and ChIA-PET, we aim to discover how the transcription factors on the promoters and the enhancers work together.
- Pathogen chip: Pathogen chip is a microarray which allows us to detect pathogen. We have developed the version 1 pathogen chip in 2007. Currently, we would like to enhance the chip so that we can covers more different pathogens while we can improve the sensitivity.
- Reconstructing the transcriptome: The aim of this project is to reconstruct the transcriptome uisng the RNA-seq data.