Bioinformatics is an interdisciplinary field that combines computer science and biology to analyze biological data. My research interests are functional genomics and pest bioinformatics. For functional genomics, I am interested in understanding the dynamic interactions between cis- and trans-regulatory elements and the evolutionary signatures of genomes. Our recent progresses include (1) transcriptional regulatory mechanism and evolution, (2) epigenetics and enhancer function, and (3) discovery of non-coding RNA (ncRNA) and mRNA isoforms. We recently develop a statistical method to identify the novel factors involving in the transcriptional buffering during S phase in the budding yeast, which are validated by the biological experiments. By integrating multi-omics data, we are able to show that the divergent transcription factor (TF)-binding motifs tend to be introduced in the edges of cis-regulatory regions across evolutionary time. In addition, we have employed machine learning techniques to investigate the TF binding site prediction and the combinatorial effect of TFs on alternative splicing of gene transcripts. As emergence of long ncRNAs (lncRNAs) through evolution may hold the potential role in transcriptional regulation, we have demonstrated that a notable portion of lncRNAs were derived from pseudogenized protein-coding genes. Besides, we have constructed the database related to splicing isoforms in different organisms and a novel splicing annotation tool. For pest bioinformatics, we apply bioinformatics approaches to help the pest control management. Our applications cover the discovery of gene isoforms in mosquitoes, image classification of urban pest insects (e.g. termites and red imported fire ants), and the metagenome diversity in the invasive yellow crazy ant. In addition, our team could not only analyze the large amount of biological data but also conduct the interdisciplinary and collaborative research with different biology experts, who experimentally validating novel hypotheses generated by our analyses.