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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.
More...
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. 17061–17066,
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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