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Research Fellow 施純傑 研
究
Arthur Chun-Chieh Shih 人
員
Ph.D., Computer Science and Information Engineering, Faculty
National Central University, Taiwan
T +886-2-2788-3799 ext. 2470 E arthur@iis.sinica.edu.tw
F +886-2-2782-4814 W www.iis.sinica.edu.tw/pages/arthur
・ Research Fellow, IIS, Academia Sinica (2014-present)
・ Associate Research Fellow, IIS, Academia Sinica (2008-2014)
・ Assistant Research Fellow, IIS, Academia Sinica (2002-2008)
・ Postdoctoral Fellow, Department of Ecology and Evolution, University of Chicago
(2001-2002)
・ Postdoctoral Fellow, IIS, Academia Sinica (1998-2001)
・ Ph.D. Computer Science and Information Engineering, National Central University
(1998)
・ Academia Sinica Career Development Award (2010)
Research Description
In the past decade, my research interests focused on the development of computational tools for processing biological big data and the study
of biological issues related to molecular evolution and genetic regulatory networks. The major computational challenge that we face was to
design methods that can be executed e ciently and e ectively solve important biological problems. On the other hand, the main challenges
for our biological studies included analyzing and extracting meaning from patterns within large data sets, while at the same time, proposing
testable hypotheses to explain natural mechanisms. With regard to the tool development, 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). In addition, a new
method for assembling short sequences from RNA-seq (JR-Trans) has been also developed recently. In the collaboration with biologists from
various institutes and research centers in Academia Sinica, we have used computational approaches and made signi cant discoveries related
to gene regulation in C4 plant leaf development, gene duplication in C4 plant photosynthesis evolution, miRNA regulatory networks in B cell
di erentiation, and genetic regulatory networks in cardiac hypertrophy.
Currently, my research interests have been changed to the eld of optogenetics in observing neural activities in nervous systems. We are
going to develop a low-cost uorescent mouse head-mounted miniature microscope and related image processing techniques that can be
applied to observe neuron activity in brain in a freely moving mouse, especially in chronic pain study.
1. Yao-Ming Chang, Li Ling, Ya-Ting Chang, Yu-Wang Chang, Publications Brochure 2020
Wen-Hsiung Li, Arthur Chun-Chieh Shih*, and Chien-Chang
Chen*, "Three TF Co-expression Modules Regulate Pressure- 6. Yao-Ming Chang, Hsueh-Fen Juan, Tzu-Ying Lee, Ya-Ya Chang,
Overload Cardiac Hypertrophy in Male Mice," Scientific Reports Yao-Ming Yeh, Wen-Hsiung Li*, and Arthur Chun-Chieh Shih*,
7: 7560, 2017. "Prediction of human miRNAs using tissue-selective motifs in
3' UTRs," Proceedings of the National Academy of Sciences
2. Tong-Yen Tsai, Shih-Ying Wu, Cheng-Han Chung, Pang-Yen 105(44): 17061-17066, 2008.
Yang, Shin-Tang Su, Yu-Hsuan Tseng, Tong-Cheng Wang,
Wen-Hsiung Li, Arthur Chun-Chieh Shih*, and Kuo-I Lin*, 7. Arthur Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho, and
"Uncovering MicroRNA Regulatory Hubs that Modulate Plasma Wen-Hsiung Li, "Simultaneous Amino Acid Substitutions at
Cell Differentiation," Scientific Reports 5: 17957, 2015. Antigenic Sites Drive Influenza A Hemagglutinin Evolution,"
Proceedings of the National Academy of Sciences 104(15): 6283-
3. Te-Chin Chu, Chen-Hua Lu, Tsunglin Liu, Greg C. Lee, Wen- 6288, 2007.
Hsiung Li* and Arthur Chun-Chieh Shih*, "Assembler for de
novo assembly of large genomes." Proceedings of the National 8. Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng, and Yu-Wei
Academy of Sciences 110(36): E3417-3424, 2013. Wu, "Phylo-mLogo: An interactive multiple-logo visualization
tool for large-number sequence alignments", BMC Bioinformatics
4. Yao-Ming Chang, Chia-Lin Chang, Wen-Hsiung Li, Arthur Chun- 8:63, 2007.
Chieh Shih*, "Historical Profiling of Maize Duplicate Genes
Sheds Light on the Evolution of C4 Photosynthesis in Grasses," 9. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng,
Molecular Phylogenetics and Evolution 66(2): 453-462, 2013. Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan
Chou, Tze-Chang Shiao, and Mu-Fen Hsieh, "SinicView: A
5. Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur visualization environment for comparisons of multiple nucleotide
Chun-Chieh Shih*, "GR-Aligner: an algorithm for aligning sequence alignment tools," BMC Bioinformatics 7:103, 2006.
pairwise genomic sequences containing rearrangement events,"
Bioinformatics 25(17): 2188-2193, 2009. 10. 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 20(8): 1299-1309,
2003.
163
究
Arthur Chun-Chieh Shih 人
員
Ph.D., Computer Science and Information Engineering, Faculty
National Central University, Taiwan
T +886-2-2788-3799 ext. 2470 E arthur@iis.sinica.edu.tw
F +886-2-2782-4814 W www.iis.sinica.edu.tw/pages/arthur
・ Research Fellow, IIS, Academia Sinica (2014-present)
・ Associate Research Fellow, IIS, Academia Sinica (2008-2014)
・ Assistant Research Fellow, IIS, Academia Sinica (2002-2008)
・ Postdoctoral Fellow, Department of Ecology and Evolution, University of Chicago
(2001-2002)
・ Postdoctoral Fellow, IIS, Academia Sinica (1998-2001)
・ Ph.D. Computer Science and Information Engineering, National Central University
(1998)
・ Academia Sinica Career Development Award (2010)
Research Description
In the past decade, my research interests focused on the development of computational tools for processing biological big data and the study
of biological issues related to molecular evolution and genetic regulatory networks. The major computational challenge that we face was to
design methods that can be executed e ciently and e ectively solve important biological problems. On the other hand, the main challenges
for our biological studies included analyzing and extracting meaning from patterns within large data sets, while at the same time, proposing
testable hypotheses to explain natural mechanisms. With regard to the tool development, 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). In addition, a new
method for assembling short sequences from RNA-seq (JR-Trans) has been also developed recently. In the collaboration with biologists from
various institutes and research centers in Academia Sinica, we have used computational approaches and made signi cant discoveries related
to gene regulation in C4 plant leaf development, gene duplication in C4 plant photosynthesis evolution, miRNA regulatory networks in B cell
di erentiation, and genetic regulatory networks in cardiac hypertrophy.
Currently, my research interests have been changed to the eld of optogenetics in observing neural activities in nervous systems. We are
going to develop a low-cost uorescent mouse head-mounted miniature microscope and related image processing techniques that can be
applied to observe neuron activity in brain in a freely moving mouse, especially in chronic pain study.
1. Yao-Ming Chang, Li Ling, Ya-Ting Chang, Yu-Wang Chang, Publications Brochure 2020
Wen-Hsiung Li, Arthur Chun-Chieh Shih*, and Chien-Chang
Chen*, "Three TF Co-expression Modules Regulate Pressure- 6. Yao-Ming Chang, Hsueh-Fen Juan, Tzu-Ying Lee, Ya-Ya Chang,
Overload Cardiac Hypertrophy in Male Mice," Scientific Reports Yao-Ming Yeh, Wen-Hsiung Li*, and Arthur Chun-Chieh Shih*,
7: 7560, 2017. "Prediction of human miRNAs using tissue-selective motifs in
3' UTRs," Proceedings of the National Academy of Sciences
2. Tong-Yen Tsai, Shih-Ying Wu, Cheng-Han Chung, Pang-Yen 105(44): 17061-17066, 2008.
Yang, Shin-Tang Su, Yu-Hsuan Tseng, Tong-Cheng Wang,
Wen-Hsiung Li, Arthur Chun-Chieh Shih*, and Kuo-I Lin*, 7. Arthur Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho, and
"Uncovering MicroRNA Regulatory Hubs that Modulate Plasma Wen-Hsiung Li, "Simultaneous Amino Acid Substitutions at
Cell Differentiation," Scientific Reports 5: 17957, 2015. Antigenic Sites Drive Influenza A Hemagglutinin Evolution,"
Proceedings of the National Academy of Sciences 104(15): 6283-
3. Te-Chin Chu, Chen-Hua Lu, Tsunglin Liu, Greg C. Lee, Wen- 6288, 2007.
Hsiung Li* and Arthur Chun-Chieh Shih*, "Assembler for de
novo assembly of large genomes." Proceedings of the National 8. Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng, and Yu-Wei
Academy of Sciences 110(36): E3417-3424, 2013. Wu, "Phylo-mLogo: An interactive multiple-logo visualization
tool for large-number sequence alignments", BMC Bioinformatics
4. Yao-Ming Chang, Chia-Lin Chang, Wen-Hsiung Li, Arthur Chun- 8:63, 2007.
Chieh Shih*, "Historical Profiling of Maize Duplicate Genes
Sheds Light on the Evolution of C4 Photosynthesis in Grasses," 9. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng,
Molecular Phylogenetics and Evolution 66(2): 453-462, 2013. Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan
Chou, Tze-Chang Shiao, and Mu-Fen Hsieh, "SinicView: A
5. Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur visualization environment for comparisons of multiple nucleotide
Chun-Chieh Shih*, "GR-Aligner: an algorithm for aligning sequence alignment tools," BMC Bioinformatics 7:103, 2006.
pairwise genomic sequences containing rearrangement events,"
Bioinformatics 25(17): 2188-2193, 2009. 10. 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 20(8): 1299-1309,
2003.
163
