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Research Faculty 研究人員

副研究員 副研究員
林仲彥 Chung-Yen Lin 施純傑 Arthur Chun-Chieh Shih

Associate Research Fellow Associate Research Fellow
Ph.D., Zoology, National Taiwan University Ph.D., Computer Science and Information Engineering, National Central
University
Tel: +886-2-2788-3799 ext. 1704 Fax: +886-2-2782-4814 Tel: +886-2-2788-3799 ext. 1719 Fax: +886-2-2782-4814
Email: cylin@iis.sinica.edu.tw Email: arthur@iis.sinica.edu.tw
http://www.iis.sinica.edu.tw/pages/cylin http://www.iis.sinica.edu.tw/~arthur

Laboratory URL: http://eln.iis.sinica.edu.tw

● Visiting Scholar , Institute of Molecular & Medical Phamacol- ● Joint-appointed Assistant Professor , National Taiwan University, ● Academia Sincia Career Development Award, 2010. ● Ph.D., CSIE, National Central University, Taiwan, 1998.
ogy , David Geffen School of Medicine at UCLA, United States College of Life Science, Taiwan (2005/2–present) ● Assistant Research Fellow, IIS, Academia Sinica (2002-2008) ● MS. EE, National Chung Cheng University, Taiwan, 1996.
(2010/8–2011/7) ● Assistant Investigator, National Health Research Institutes, Divi- ● Postdoctoral Fellow, IIS, Academia Sinica (1998-2001 and 2002) ● BS., EE, Chinese Culture University, Taiwan, 1994.
● Joint-appointed Associate Principle Investigator, National Health sion of Biostatistics and Bioinformatics, Taiwan (2004/1–2005/10) ● Postdoctoral Fellow, Ecology and Evolution, The University of
Research Institutes, Division of Biostatistics and Bioinformatics, Chicago (2001-2002)
Taiwan (2005/11–present)
Research Description Publications

Research Description Publications
My major research focuses on using the next-generation 1. Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Ar-
sequencing technology to study the genomics and tran- thur Chun-Chieh Shih*, “GR-Aligner: an algorithm for align-
As a research fellow starting the carrier from biology, I am 1. Wang, Y.B., Chen, S. H., Lin, C.Y. and Yu, J.K. EST and tran- scriptomics issues including: (a) gene regulation and ing pairwise genomic sequences containing rearrangement
interesting in drilling down to the secret of life via IT inno- scriptome analysis of cephalochordate amphioxus - past, pre- evolution of C4 plant photosynthesis development, (b) events,” Bioinformatics, vol. 25, no. 17, p. 2188-2193, 2009.
vations. Most of our works are also constructed into web sent, and future. Brief in Functional Genomics. 2012. Feb 4. microRNAs in diseases and cell di erentiation, (c) genome (*: corresponding author).

[Epub ahead of print] PMID: 22308056
applications and public databases to make further bene- structural variations of autism spectrum disorder, and (d) 2. Li-Ching Hsieh, Shu-I Lin, Arthur Chun-Chieh Shih, June-Wei
Chen, Wei-Yi Lin, Ching-Ying Tseng, Su-Fen Chiang, Wen-

ts to the research community worldwide. In the past few 2. Leu, J. H., Chen, S. H., Wang, Y. B., Chen, Y. C., Su, S. Y., development of short read sequence assembler and re- Hsiung Li, and Tzyy-Jen Chiou, “Uncovering small RNA-
Lin, C. Y*., Ho, J. M*., Lo, C. F*., “A review of the major

years, we have published over 20 SCI papers with 4 web penaeid shrimp EST studies and the construction of a shrimp lated analysis tools. The collaborators are from BRC, GRC, mediated responses to phosphate-deficiency in Arabidopsis by
deep sequencing,” Plant Physiology, 151:2120-2132, 2009.
databases, 6 web applications, 2 patents and 2 technology transcriptome database based on the ESTs from four penaeid and IBMS, Academia Sinica, National Taiwan University 3. Shu-Miaw Chaw, Arthur Chun-Chieh Shih, Daryi Wang, Yu-
transfers. My recent research topics are focused on the fol- shrimp” Marine Biotechnology, 13(4): 608-621, April 2011, Hospital (NTHU), and National Health Research Institute Wei Wu, Shu-Mei Liu, and The-Yuan Chou, “The Mitochon-
ref website: http://sysbio.iis.sinica.edu.tw/page (SCI/ 2.58)
lowing important issues: drial Genome of the GymnospermCycas taitungensis Contains

3. Chen, S. H., Lo, C. Z., Su, S. Y., Kuo, B. H., Hsiung, A. C., Lin, (NHRI). In the rst topic, we study gene regulations of C3 a Novel Family of Short Interspersed Elements, Bpu sequenc-
C. Y.*, “UPS 2.0: Unique Probe Selector for Probe Design and and C4 photosynthesis pathways during the early leaf de- es, and Abundant RNA Editing Sites,” Molecular Biology and
Oligonucleotide Microarrays in Pangenomic/ Genomic Level” velopment. We will predict key regulators of C4 photosyn- Evolution, vol. 25, no. 3, p. 603-615, 2008.
(1) Network analysis of human protein interactions for BMC Genomics, 11(8): S6, December 2010, http://array.iis.si- 4. Yao-Ming Chang, Hsueh-Fen Juan, Tzu-Ying Lee, Ya-Ya
Tumorigenesis and infectious diseases in systems biol- nica.edu.tw/ups (SCI/ 4.3) thesis pathway, predict key regulators to Kranz anatomy Chang, Yao-Ming Yeh, Wen-Hsiung Li*, and Arthur Chun-
ogy: 4. Chen, S.H., Su, S. Y., Lo, C. Z., Huang, T. J., Kuo, B. H., formation, and construct their gene regulatory networks. Chieh Shih*, “Prediction of human miRNAs using tissue-
Lin, C. Y.*, “Phylogenetic reconstruction by Automatic Like- The subjects on the second topic include breast cancer selective motifs in 3’ UTRs,” Proceedings of the National
We reconstruct protein-protein interaction networks lihood Model Selector (PALM) : A Framework for Phyloge- metastasis, B cell di erentiation, and cardiac hypertrophy. Academy of Sciences, vol. 105, no. 44, p.17061–17066, 2008.

based on experimental outputs with predicted interac- netic Analysis with the Best Substitution Model” PLoS ONE, We have sequenced small RNA samples collected from (*: corresponding authors)
tions by novel statistical models. Meanwhile, several al- 4(12): e8116, December 2009, http://palm.iis.sinica.edu.tw our collaborators’ laboratories by Next-Generation Se- 5. Arthur Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho,
and Wen-Hsiung Li, “Simultaneous Amino Acid Substitutions
(SCI/ 4.3)
gorithms to identify those essential components/ sub- quencing (NGS). We will analyze the sequenced raw read at Antigenic Sites Drive Influenza A Hemagglutinin Evolu-

network with various topological features are developed. 5. Lin, C. Y.*, Chin, C. H., Wu, H. H., Chen, S. H., Ho, C. W.,* data, predict potential co-targeting pathways, and nally tion,” Proceedings of the National Academy of Sciences, vol.

Ko, M. T.*, “Hubba: Hub Objects Analyzer : A Framework of
Objectives of our work are to improve understanding of Interactome Hubs Identification for Network Biology” Nucle- validate by experiment. We expect that our results can 104, no. 15, p. 6283-6288, 2007.

the puzzle during development stage, carcinogenesis, in- ic Acids Research, 36: W438-W443, July 2008, Nucleic Acids increase the knowledge of miRNA regulation on diseases 6. Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng , and Yu-
Wei Wu,“Phylo-mLogo: An interactive multiple-logo visu-
fectious mechanism and co-infection. Research (http://hub.iis.sinica.edu.tw) (SCI/ 7.69) and cell di erentiation. In the autism project, we will use alization tool for large-number sequence alignments”, BMC

6. Lin, C. Y.*, Lin, F.K., Lin, C.H., Lai, L.W., Hsu, S.J., Chen, NGS technology to sequence autism family’s genomes Bioinformatics 2007, 8:63.
S.H., Hsiung, C. A., “POWER: PhylOgenetic WEb Repeater and then identify genomic and genetic variations be- 7. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin
- An integrated and user-optimized framework for bio-molec- Peng , Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong,
(2) Personalized medicine and Metagenomics: ular phylogenetic analysis.” Nucleic Acids Research, 33: 553- tween autism children and their parents. We will analyze Meng-Yuan Chou, Tze-Chang Shiao, and Mu-Fen Hsieh,
We are engaged on two major projects using high 556, July 2005, (SCI/ 7.69) (Access URL : http://power.nhri. how these variations cause genetic changes on neuron “SinicView: A visualization environment for comparisons of
org.tw)
throughput sequence-based approach recently: 1) identi- and brain functions. In the last topic, we focus on devel- multiple nucleotide sequence alignment tools,” BMC Bioin-
formatics 2006, 7:103.
fying individual genome abnormality (Gene fusion/ Trans- 7. Li, L.H., Li, J. C., Lin, Y. F., Lin, C. Y., Chen, C.Y., Tsai, S. F., oping a novel de novo assembly algorithm to assemble 8. Arthur Chun-Chieh Shih and Wen-Hsiung Li, “GS-Aligner:
“Genomic Shotgun Array: A Procedure Linking Large-Scale
location) from clinical cancer biopsy by new algorithms for DNA Sequencing with Regional Transcript Mapping.,” Nucle- a genome using Illumina short reads alone and an e ec- A Novel Tool for Aligning Genomic Sequences Using Bit-

speedy high accurate mapping performance, 2) decipher- ic Acids Research, 32(3): 27-35, February 2004, (SCI/ 7.69) tive and e cient algorithms to identify genome structural Level Operations,” Molecular Biology and Evolution, vol. 20,
p.1299-1309, 2003.
ing the metabolic uniqueness of coral and the symbionts 8. Lin, C. Y.*, Chen, S. H, Lo, C.Z., Cho, C.S., Hsiung, C. A., variations and breakpoints. 9. Arthur Chun-Chieh Shih, Hong-Yaun Mark Liao, and Chun-
under the global climate changes scheme. “Primer Design Assistant (PDA): a Web-based Primer Design Shieh Lu, “A New Iterated Two-Band Diffusion Equation:
Tool.” Nucleic Acids Research, 31: 3751-3754, July 2003, Theory and Its Application,” IEEE Trans. on Image Process-
(SCI/ 7.69) (Access URL : http://dbb.nhri.org.tw/primer/)
ing, vol. 12, no.4, p.466-476, 2003.
10. Chwen-Jye Sze, Hong-Yaun Mark Liao, and Kuo-Chin Fan,
“A New Image Flux Conduction Model and It’s Application to
Selective Image Smoothing,” IEEE Trans. on Image Process-
ing, vol.10, no.2, p.296-306, 2001. (Arthur Chun-Chieh Shih
研究人員 is also known as Chwen-Jye Sze)
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