Research Fellow/Professor  |  Shih, Arthur Chun-Chieh  
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Research Descriptions

        My major research topics focus on bioinformatics and biological problem study. What I have been doing is to develop useful bioinformatics tools and novel methodologies not only for service to a wide range of biologists but also for ourselves to study important biological problems as well as to answer interesting biological questions. Although I am a computer scientist by training, I firmly believe that studying biological problems and questions through collaboration with biologists can definitely enhance our understanding of what problems and questions are important and interesting to the biology community and what kinds of new bioinformatics tools are urgently needed for biologists.

        In the bioinformatics tool development in 2006 and 2007, we have developed two visualization tools, SinicView and Phylo-mLogo , for the usage of comparative genomics and influenza virus evolution. Because Phylo-mLogo can assistusers to compare and visualize the changes of polymorphisms and indel events across different clades or subtypes in the alignment of a large number of sequences, this tool has become one of the major tools for the CDC (Center for Disease Control, Taiwan) specialists to examine whether the recommended vaccine strains currently in Taiwan and worldwide circulation will continue to dominate in the next epidemic season in maintaining its effectiveness.

        In the study of biological problems, the major topics I am interested not only in molecular evolution, including influenza virus evolution and plant mitochondria and chloroplast evolution, but also in functional genetics and genomics, including microRNAs and their target genes prediction, largescale small RNA sequencing analysis, and biofuel.

        In the study of influenza virus evolution, we have introduced a new approach to analyze the HA1 sequences, the HA1 domain of hemagglutinin (HA) of influenza A viruses, and identified many substitutions, to resolve controversies on whether only a few or many residue sites of HA1 have undergone positive selection, whether positive selection at HA1 is continual or punctuated, and whether antigenic change is punctuated. Our results suggest that positive selection has been ongoing most of the time, not sporadic, and antigenic change is less punctuated than recently proposed. Moreover, whether the majority or minority of these parallel substitutions were hitchhiking is still controversial. Thus, we have also developed another novel method without reconstructing the phylogeny that can estimate the yearly ratio of synonymous and nonsynonymous substitution changes for each site in influenza A virus H3HA1 genes. Based on the result, we find that the simultaneous amino acid substitutions occurred in the population is because of positive selection rather than hitchhiking.

        MicroRNAs (miRNAs) play an important role in posttranscriptional regulation of genes. We developed a method to predict human miRNAs without requiring cross-species conservation. We first identified lowly/moderately expressed tissue-selective genes using EST data and then identified overrepresented motifs in the 3' UTRs of these genes. Using these motifs as potential target sites of miRNAs, we recovered more than two thirds of the known human miRNAs. We then used those motifs that did not match any known human miRNA seed region to infer novel miRNAs. We predicted dozens of new human miRNA genes when a stringent criterion was used and many more novel miRNAs when a less stringent criterion was used. We tested the expression of 11 predicted miRNAs in three human cell lines and found five of them expressed in all three cell lines and one expressed in one cell line. We selected two of them to do functional validation, using their mimics and inhibitors and using both luciferase assay and western blotting. These experiments provided strong evidence that both are novel miRNAs. The result has been published in Proceedings of the National Academy of Sciences 2008.