研究內容為分析定序技術 (Second/Third generation sequencing) 產生的巨量基因體資訊來做物種間的比較及族群分析。
研究材料著重於醫學，林業，農業，畜牧業，及台灣生態環境上有重要地位的真菌及線蟲。主要研究方向如下：

• 亞洲環境相關的線蟲及真菌基因體研究
• 酵母菌的生態與演化
• 真核病原寄生及感染動植物宿主的機制
• Oxford nanopore定序技術分析及相關新實驗的設計

The principal objective of our research lies in the fundamental mechanisms and evolution or pathogenicity and parasitism. We are mainly interested in fungi and nematodes that are of medical, agricultural, forestry, and Taiwan biodiversity importance.

Can you guess which is which?

Comparative population genomics of microbes in nature

Microbes can survive in almost any environment and play a major role in shaping their surroundings. Comparing genomes between and within populations of microbes allows us to understand the process of evolution of one of the most diverse and dominant life forms on earth. Additionally, insights regarding their impact on their environment or hosts such as human health can also be achieved.

Evolution and biology of microbial life cycle dynamics

Although vast amounts of information are being gathered from the various genome projects on similarities and differences between species that are very different to each other, virtually nothing is known about differences at the genomic level between individuals from the same species or from very closely related species. Yet such variability forms the basis for evolutionary change. One of our main focuses of was to quantify the life cycle of microbes undergoing different modes of reproduction in nature. Measures of DNA sequence variation as a result of fundamental cellular processes at different stages of life cycle, for example, mutation and recombination, were calculated. Some of these variations are influenced by processes that only occur in certain stages of the life cycle.

Evolution of parasitic pathogens.

Parasitism is a common way of life and coexists with almost every species including humans. Parasites are interesting for two reasons: (1) for the disease burdens that they incur on humans, and the plants and animals of economic importance that we depend on, and (2) their diverse strategies of infection. We have been trying to identify the unique evolutionary signatures that have made a parasite what it is and have studied pathogens across many ecological niches (helminths, fungi, viruses and cockroaches) as well as different hosts (mammals and plants). The genomes of parasites are very interesting because they tend to lose genes of which the corresponding traits are no longer needed. Existing genes, however, may be duplicated, providing extra copies for the evolution of new functions.

Bioinformatics

Recognizing that important pathogens still lag far behind in terms of genome research compared to model species, we started developing informatics tools with the aim of building up genomic resources to provide analysis tools both for my own research and for the wider research community.