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研究員
施純傑 Arthur Chun-Chieh Shih

Research Fellow
Ph.D., Computer Science and Information Engineering, National Central University
Tel: +886-2-2788-3799 ext. 1719 Fax: +886-2-2782-4814
Email: arthur@iis.sinica.edu.tw
http://www.iis.sinica.edu.tw/~arthur

● Research Fellow, IIS, Academia Research Description
Sinica (2014 - )
● Associate Research Fellow, IIS, My research interests focus on the development of bioinformatic tools and the study of
Academia Sinica (2008 - 2014) issues related to molecular evolution. Bioinformatics is an interdisciplinary research dis-
● Assistant Research Fellow, IIS, cipline that integrates computational sciences and biology to process and analyze large
Academia Sinica (2002 - 2008) data for exploring biological unknowns. The major computational challenge is to design a

useful method that can be executed e ciently and e ectively solve biological problems.

● Postdoctoral Fellow, Department
of Ecology and Evolution, Univer- On the other hand, the challenge for biology is to identify meaningful patterns from large

sity of Chicago (2001 - 2002) data before forming a hypothesis. My recent research ndings and achievements can be
divided into three categories: tool development, interdisciplinary collaboration, and study
● Postdoctoral Fellow, IIS, Aca-
demia Sinica (1998 - 2001) of evolution subjects. As regards tool development, we have developed GR-Aligner and
JR-Assembler, which can identify the breakpoints of rearrangement events, and assemble
● Ph.D. Computer Science and In-
formation Engineering, National a giga-base-pair genome using lllumina short reads, respectively. Our interdisciplinary
Center University (1998) collaborations have been with biologists from various institutes and research centers in
Academia Sinica; through these collaborations, we study gene regulation in C4 plant leaf
● Academia Sinica Career Develop-

ment Award (2010) development, and miRNA regulatory networks in B cell di erentiation and cardiac hyper-
trophy. Finally, we have used computational approaches to study gene duplication in C4
plant photosynthesis evolution and the origin of human miRNA evolution.
Publications
1. Te-Chin Chu, Chen-Hua Lu, Tsunglin Liu, Greg C. Lee, Wen- Evolution,” Proceedings of the National Academy of Sciences
Hsiung Li* and Arthur Chun-Chieh Shih*, “Assembler for de 104(15): 6283-6288, 2007.
novo assembly of large genomes.” Proceedings of the Nation-
7. Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng, and Yu-
al Academy of Sciences 110(36): E3417-3424, 2013.
Wei Wu, “Phylo-mLogo: An interactive multiple-logo visu-
2. Yao-Ming Chang, Chia-Lin Chang, Wen-Hsiung Li, Arthur alization tool for large-number sequence alignments”, BMC

Chun-Chieh Shih*, “Historical Profiling of Maize Duplicate Bioinformatics 8:63, 2007.
Genes Sheds Light on the Evolution of C4 Photosynthesis in
Grasses,” Molecular Phylogenetics and Evolution 66(2): 453- 8. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin
462, 2013. Peng , Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong,
Meng-Yuan Chou, Tze-Chang Shiao, and Mu-Fen Hsieh,
3. Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Ar- “SinicView: A visualization environment for comparisons of
thur Chun-Chieh Shih*, “GR-Aligner: an algorithm for align- multiple nucleotide sequence alignment tools,” BMC Bioin-
ing pairwise genomic sequences containing rearrangement formatics 7:103, 2006.
events,” Bioinformatics 25(17): 2188-2193, 2009.
9. Arthur Chun-Chieh Shih and Wen-Hsiung Li, “GS-Aligner: A
4. Yao-Ming Chang, Hsueh-Fen Juan, Tzu-Ying Lee, Ya-Ya Novel Tool for Aligning Genomic Sequences Using Bit-Level
Chang, Yao-Ming Yeh, Wen-Hsiung Li*, and Arthur Chun- Operations,” Molecular Biology and Evolution 20(8): 1299-
Chieh Shih*, “Prediction of human miRNAs using tissue- 1309, 2003.
selective motifs in 3’ UTRs,” Proceedings of the National
10. Arthur Chun-Chieh Shih, Hong-Yaun Mark Liao, and Chun-
Academy of Sciences 105(44): 17061–17066, 2008.
Shieh Lu, “A New Iterated Two-Band Diffusion Equation:
5. Shu-Miaw Chaw, Arthur Chun-Chieh Shih, Daryi Wang, Theory and Its Application,” IEEE Trans. on Image Process-
Yu-Wei Wu, Shu-Mei Liu, and The-Yuan Chou, “The Mito- ing 12(4): 466-476, 2003.
chondrial Genome of the Gymnosperm Cycas taitungensis
Contains a Novel Family of Short Interspersed Elements, Bpu
sequences, and Abundant RNA Editing Sites,” Molecular Bi-
ology and Evolution 25(3): 603-615, 2008.
6. Arthur Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho,
and Wen-Hsiung Li, “Simultaneous Amino Acid Substitu-
tions at Antigenic Sites Drive Influenza A Hemagglutinin

72 研究人員 Research Faculty