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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 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.

Currently, we work on developing a systemic approach which can integrate high-throughput next generation sequencing and other experimental data to uncover microRNA regulatory pathways in breast cancer metastasis, B-cell differentiation, and T-type Ca2+ channels involved in cardiac hypertrophy. Moreover, we have joined a C4 rice project, leaded by Academician Dr. Wen-Hsiung Li, from 2010. We focus on identifying important factors involved in C3 and C4 plant photosynthesis pathways. In the study of microRNA evolution, we have been developing a computational method to search and identify homologous miRNAs in distant genomes. We expect that the new generated data can provide us more details on how the role of miRNAs in gene regulation has been expanded in evolution, especially in the lineage leading to human.

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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 sequences containing rearrangement events," Bioinformatics, vol. 25, no. 17, p. 2188-2193, 2009. (abstract) (pdf) (*: 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. (abstract) (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)

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 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: 8/21/2010

 

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