Page 70 - 2017 Brochure
P. 70
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/pages/arthur
• Research Fellow, Institute of Information Science, Academia Sinica (2014-present)
• Associate Research Fellow, Institute of Information Science, Academia Sinica (2008-2014)
• Assistant Research Fellow, Institute of Information Science, Academia Sinica (2002-2008)
• Postdoctoral Fellow, Ecology and Evolution, University of Chicago (2001-2002)
• Postdoctoral Fellow, Institute of Information Science, Academia Sinica (1998-2001)
• Ph.D. Computer Science and Information Engineering, National Central University (1998)
• Academia Sinica Career Development Award (2010)
Research Description In collaboration with biologists from various institutes and research
centers in Academia Sinica, we have used computational
My research interests focus on the development of computational approaches and made significant discoveries related to gene
tools for processing biological big data and the study of biological regulation in C4 plant leaf development, gene duplication in C4
issues related to molecular evolution and genetic regulatory plant photosynthesis evolution, miRNA regulatory networks in B
networks. The major computational challenge that we face is to cell differentiation, and genetic regulatory networks in cardiac
design methods that can be executed efficiently and effectively hypertrophy.
to solve important biological problems. On the other hand, the
main challenges for our biological studies include analyzing and
extracting meaning patterns from large data sets, while at the
same time, proposing testable hypotheses to explain natural
mechanisms. With regard to the tool development, in the past
decade we have created powerful tools for genomic sequence
alignment (GS-Aligner), visualization of sequence alignment
results (SinicView and Phylo-mLogo), identifying the breakpoints of
rearrangement events (GR-Aligner), and assembly of a giga-base-
pair genome from lllumina short reads (JR-Assembler). Recently,
we have developed a new method for assembling short sequences
from RNA-seq (JR-Trans), which will be released soon.
Publications 6. Arthur Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho, and Wen-
Hsiung Li, “Simultaneous Amino Acid Substitutions at Antigenic
1. Tong-Yen Tsai, Shih-Ying Wu, Cheng-Han Chung, Pang-Yen Yang, Sites Drive Influenza A Hemagglutinin Evolution,” Proceedings of the
Shin-Tang Su, Yu-Hsuan Tseng, Tong-Cheng Wang, Wen-Hsiung Li, National Academy of Sciences 104(15): 6283-6288, 2007.
Arthur Chun-Chieh Shih*, and Kuo-I Lin*, “Uncovering MicroRNA
Regulatory Hubs that Modulate Plasma Cell Differentiation,” Scientific 7. Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng, and Yu-Wei Wu,
Reports 5: 17957, 2015. “Phylo-mLogo: An interactive multiple-logo visualization tool for
large-number sequence alignments”, BMC Bioinformatics 8:63, 2007.
2. Te-Chin Chu, Chen-Hua Lu, Tsunglin Liu, Greg C. Lee, Wen-Hsiung
Li* and Arthur Chun-Chieh Shih*, “Assembler for de novo assembly 8. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng,
of large genomes.” Proceedings of the National Academy of Sciences Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou,
110(36): E3417-3424, 2013. Tze-Chang Shiao, and Mu-Fen Hsieh, “SinicView: A visualization
environment for comparisons of multiple nucleotide sequence
3. Yao-Ming Chang, Chia-Lin Chang, Wen-Hsiung Li, Arthur Chun- alignment tools,” BMC Bioinformatics 7:103, 2006.
Chieh Shih*, “Historical Profiling of Maize Duplicate Genes Sheds
Light on the Evolution of C4 Photosynthesis in Grasses,” Molecular 9. Arthur Chun-Chieh Shih and Wen-Hsiung Li, “GS-Aligner: A Novel
Phylogenetics and Evolution 66(2): 453-462, 2013. Tool for Aligning Genomic Sequences Using Bit-Level Operations,”
Molecular Biology and Evolution 20(8): 1299-1309, 2003.
4. Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur
Chun-Chieh Shih*, “GR-Aligner: an algorithm for aligning pairwise 10. Arthur Chun-Chieh Shih, Hong-Yaun Mark Liao, and Chun-Shieh
genomic sequences containing rearrangement events,” Bioinformatics Lu, “A New Iterated Two-Band Diffusion Equation: Theory and Its
25(17): 2188-2193, 2009. Application,” IEEE Trans. on Image Processing 12(4): 466-476, 2003.
5. 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 105(44):
17061–17066, 2008.
68 研究人員 Research Faculty
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/pages/arthur
• Research Fellow, Institute of Information Science, Academia Sinica (2014-present)
• Associate Research Fellow, Institute of Information Science, Academia Sinica (2008-2014)
• Assistant Research Fellow, Institute of Information Science, Academia Sinica (2002-2008)
• Postdoctoral Fellow, Ecology and Evolution, University of Chicago (2001-2002)
• Postdoctoral Fellow, Institute of Information Science, Academia Sinica (1998-2001)
• Ph.D. Computer Science and Information Engineering, National Central University (1998)
• Academia Sinica Career Development Award (2010)
Research Description In collaboration with biologists from various institutes and research
centers in Academia Sinica, we have used computational
My research interests focus on the development of computational approaches and made significant discoveries related to gene
tools for processing biological big data and the study of biological regulation in C4 plant leaf development, gene duplication in C4
issues related to molecular evolution and genetic regulatory plant photosynthesis evolution, miRNA regulatory networks in B
networks. The major computational challenge that we face is to cell differentiation, and genetic regulatory networks in cardiac
design methods that can be executed efficiently and effectively hypertrophy.
to solve important biological problems. On the other hand, the
main challenges for our biological studies include analyzing and
extracting meaning patterns from large data sets, while at the
same time, proposing testable hypotheses to explain natural
mechanisms. With regard to the tool development, in the past
decade we have created powerful tools for genomic sequence
alignment (GS-Aligner), visualization of sequence alignment
results (SinicView and Phylo-mLogo), identifying the breakpoints of
rearrangement events (GR-Aligner), and assembly of a giga-base-
pair genome from lllumina short reads (JR-Assembler). Recently,
we have developed a new method for assembling short sequences
from RNA-seq (JR-Trans), which will be released soon.
Publications 6. Arthur Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho, and Wen-
Hsiung Li, “Simultaneous Amino Acid Substitutions at Antigenic
1. Tong-Yen Tsai, Shih-Ying Wu, Cheng-Han Chung, Pang-Yen Yang, Sites Drive Influenza A Hemagglutinin Evolution,” Proceedings of the
Shin-Tang Su, Yu-Hsuan Tseng, Tong-Cheng Wang, Wen-Hsiung Li, National Academy of Sciences 104(15): 6283-6288, 2007.
Arthur Chun-Chieh Shih*, and Kuo-I Lin*, “Uncovering MicroRNA
Regulatory Hubs that Modulate Plasma Cell Differentiation,” Scientific 7. Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng, and Yu-Wei Wu,
Reports 5: 17957, 2015. “Phylo-mLogo: An interactive multiple-logo visualization tool for
large-number sequence alignments”, BMC Bioinformatics 8:63, 2007.
2. Te-Chin Chu, Chen-Hua Lu, Tsunglin Liu, Greg C. Lee, Wen-Hsiung
Li* and Arthur Chun-Chieh Shih*, “Assembler for de novo assembly 8. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng,
of large genomes.” Proceedings of the National Academy of Sciences Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou,
110(36): E3417-3424, 2013. Tze-Chang Shiao, and Mu-Fen Hsieh, “SinicView: A visualization
environment for comparisons of multiple nucleotide sequence
3. Yao-Ming Chang, Chia-Lin Chang, Wen-Hsiung Li, Arthur Chun- alignment tools,” BMC Bioinformatics 7:103, 2006.
Chieh Shih*, “Historical Profiling of Maize Duplicate Genes Sheds
Light on the Evolution of C4 Photosynthesis in Grasses,” Molecular 9. Arthur Chun-Chieh Shih and Wen-Hsiung Li, “GS-Aligner: A Novel
Phylogenetics and Evolution 66(2): 453-462, 2013. Tool for Aligning Genomic Sequences Using Bit-Level Operations,”
Molecular Biology and Evolution 20(8): 1299-1309, 2003.
4. Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur
Chun-Chieh Shih*, “GR-Aligner: an algorithm for aligning pairwise 10. Arthur Chun-Chieh Shih, Hong-Yaun Mark Liao, and Chun-Shieh
genomic sequences containing rearrangement events,” Bioinformatics Lu, “A New Iterated Two-Band Diffusion Equation: Theory and Its
25(17): 2188-2193, 2009. Application,” IEEE Trans. on Image Processing 12(4): 466-476, 2003.
5. 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 105(44):
17061–17066, 2008.
68 研究人員 Research Faculty
