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Research Project

Arthur Chun-Chieh Shih , PhD
Associate Research Fellow

Research interest

Computational Biology, Molecular Evolution, and Multimedia Signal Processing

Contact

Institute of Information Science Academia Sinica, Nankang 115 Taipei, Taiwan

E-mail: arthur@iis.sinica.edu.tw Tel: +886-2-2788-3799 ext. 1719 Fax: +886-2-2782-4814

Research Description

My major research interests focus on bioinformatics and the study of biological problems. I have developed a number useful bioinformatics tools and novel methodologies for use by biologists as well as for our own use in the study of important biological problems and for answering interesting biological questions. Although I am a computer scientist by training, I firmly believe that studying biological problems and questions in collaboration with biologists will enhance our understanding of the problems and questions that are important and interesting to the biology community. It will also help us design new bioinformatics tools that are urgently needed by biologists.

We have developed several bioinformatics visualization tools, GS-Aligner, SinicView and Phylo-mLogo, for use in comparative genomics and influenza virus evolution, respectively. Phylo-mLogo helps users compare and visualize changes in polymorphisms and indel events across different clades or subtypes in the alignment of a large number of sequences. As a result, it has become one of the major tools used by CDC (Center for Disease Control, Taiwan) specialists to assess whether the recommended vaccine strains currently used in Taiwan and worldwide will continue to be effective in the next influenza season.

With regard to the study of biological problems, I am interested in two key areas: 1) molecular evolution, including influenza virus evolution, and plant mitochondria and chloroplast evolution; and 2) functional genetics and genomics, including prediction and functional analysis of microRNA regulation pathway, large-scale small RNA sequencing analysis, and evolutionary analysis of biofuel strains.

Selected Publication Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur Chun-Chieh Shih*, "GR-Aligner: an algorithm for aligning pairwise genomic se-quences containing rearrangement events," to appear in Bioinformatics. (*: corresponding author) Yao-Ming Chang, Hsueh-Fen Juan, Tzu-Ying Lee, Ya-Ya Chang, Yao-Ming Yeh, Wen-Hsiung Li*, and Arthur Chun-Chieh Shih*, "Prediction of human miRNAs using tissue-selective motifs in 3' UTRs," Proceedings of the National Academy of Sciences, vol. 105, no. 44, pp. 17061¡V17066, 2008. (abstract) (pdf)(*: corresponding authors) Arthur Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho, and Wen-Hsiung Li, "Simultaneous Amino Acid Substitutions at Antigenic Sites Drive Influenza A Hemagglutinin Evolution," Proceedings of the National Academy of Sciences, vol. 104, no. 15, pp. 6283-6288, 2007. (pdf) Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng , and Yu-Wei Wu,¡§Phylo-mLogo: An interactive multiple-logo visualization tool for large-number sequence alignments¡¨, BMC Bioinformatics 2007, 8:63. (pdf) Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng , Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao, and Mu-Fen Hsieh, "SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools," BMC Bioinformatics 2006, 7:103. (pdf) Arthur Chun-Chieh Shih and Wen-Hsiung Li, ¡§GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations,¡¨ Molecular Biology and Evolution, vol. 20, pp.1299-1309, 2003. (pdf) Arthur Chun-Chieh Shih, Hong-Yaun Mark Liao, and Chun-Shieh Lu, ¡§Dyadic Wavelet-based Nonlinear Conduction Equation: Theory and Applications,¡¨ IEEE Trans. on Image Processing, vol. 12, no.4, p.466-476, 2003. (pdf) (MATLAB source code) More ...

Ongoing Research Topic

¡P	Functional analysis of microRNA regulation pathway
	Collaborators: Dr. Wen-Hsiung Li, Genomics Research Center and Biodiversity Research Center, Academia Sinica, and Dr. Hsueh-Fen Juan, Department of Life Science, National Taiwan University, Taiwan Ph.D. student: Yao-Ming Chang (National Taiwan Normal Univ., Taiwan)

¡P	Influenza virus evolution analysis
	Collaborators: Dr. Mei-Shang Ho, Institute of Biomedical Sciences and Dr. Wen-Hsiung Li, Genomics Research Center and Biodiversity Research Center, Academia Sinica, Taiwan Postdoc: Li-Ching Hsieh Ph.D. student: Yi-Chiao Fang (National Chiao Tung Univ., Taiwan)
¡P	Human genome rearrangement analysis
	Collaborators: Dr. D.T. Lee, IIS, Academia Sinica, Taiwan Ph.D. student: Te-Ching Chu (National Taiwan Normal Univ., Taiwan)
¡P	Distance-based spectral clustering and its applications Collaborators: Dr. Chi-Fang Chin (CSIE, Yuanpei Univ., Taiwan)
¡P	Others
	> Mesh object decomposition > Multimedia Signal Processing Collaborator: Dr. Mark Liao, IIS, Academia Sinica, Taiwan
		Available Bioinformatics Tool
	Phylo-mLogo: An interactive multiple-logo visualization tool for large-number sequence alignments
	SinicView:A visualization environment for comparisons of multiple nucleotide sequence alignment tools

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Last modified: 5/31/2009

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