The motivation of our research is to perform IT innovations on deciphering the secret of life, e.g. differentiation of stem cells (regenerative medicine) and infection mechanism among host and pathogens. Meanwhile, all of our results will be converted into useful web applications / Databases for research communities worldwide not only presented in the form of publications. In pasted eight years, we have published 18 SCI papers (11, first / corresponding author by me) with 3 web databases, 6 web applications, 2 patents and 2 technology transfers. In recent years, my research has focused on following important issues:
(1) Network analysis of human protein interactions for Tumorigenesis and infectious diseases in systems biology: In our current work, we are constructing eukaryotic protein-protein interaction networks from recently high though-put interactome studies of various species. Meanwhile we have also integrated a statistical model into our protein interaction database for validation of two-hybrid assays of Helicobacter pylori, and the prediction of putative protein interactions not yet discovered experimentally (hp-DPI, http://dpi.nhri.org.tw/hp/, Bioinformatics 2005). Using a more sophisticated statistical method with expression profile, we integrated a database called flydpi for the interactome of Drosophila Melanogaster (http://flydpi.nhri.org.tw, BMC Bioinfo, 2006). And we also constructed a topological analyzer to extract hubs and motifs from complex network named as Hubba and HUNTER (http://hubba.iis.sinica.edu.tw, NAR, 2008, http://hub.iis.sinica.edu.tw/hunter, BMC Bioinformatics, 2010, respectively). Objectives of our work are to improve understanding of the puzzle during development stage, carcinogenesis, infectious mechanism and co-infection, and then to furthermore introduce a new paradigm for the diagnosis and treatment of human disease to revolutionize current medical services delivered.
(2) Developing value-added databases and web applications for biomedical research communities: We have developed several web applications and databases related to bioinformatics for the biomedical research community. For example, the web application Primer Design Assistant (PDA, http://dbb.nhri.org.tw/primer/) can be helpful for large scale PCR in high throughput experiments, such as microarray experiments. From July 2003 to May 2010, the numbers of accumulated website visits and processed sequences were more than 165,000 and 900,000, respectively. In addition to its use by research groups, PDA has been used to develop several diagnostic kits and get patents. For example, in 2004, the Center for Disease Control (CDC), Taiwan used PDA to develop a rapid diagnostic kit for SARS. Based on a similar idea, we have developed a platform called "Unique Probe Selector” (UPS) (http://array.iis.sinica.edu.tw/ups, BMC Bioinformatics 2008) with various uses in hybridization, such as microarrays and blots. Arrays designed by UPS were validated by experiments for specificity and sensitivity. In 2005, we implemented a phylogenetic platform, called POWER (http://power.nhri.org.tw, Nucleic Acid Research, 2005), for topology construction and visualization. Recently, we have published our work to select the best model automatically, and help several biomedical research groups to conquer the reconstruction of phylogenetic tree with large dataset (PALM, http://palm.iis.sinica.edu.tw/, PLoS ONE, 2009).
(3) Metagenomics: According to the advance in sequencing technology, time for sequencing large genome like human genome would not take several months/years but weeks/days. By using “shotgun” Sanger sequencing or chip-based pyrosequencing to get(mostly) unbiased samples of all genes from all membersof sampled communities, we can start to under the genetic material recovered directly from environmental samples. Such kind of work can’t be done in traditional microbiology and microbial genome sequencing relied upon cultivated clonal cultures. Several shotgun sequencing projects of various communities have been completed and started. Following the flood of massive sequence data, there are several interesting computational problems that arise from WGS sequencing of communities. Those issues related with how to compare communities, how to separate sequence from different organisms in silico, and how to model population structures using WGS assembly statistics, will be new challenges in the field of bioinformatics. Our approach here is to integrate various databases, gene expression analysis, proteomic results and phylogenetic reconstruction to achieve a comprehensive view of microbial communities.