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研究人員 ｜ Research Faculty

● Assistant Research Fellow, IIS, Academia Sinica (July 2002 - March
施純傑 Arthur Chun-Chieh Shih 2008)
● Postdoctoral Fellow, IIS, Academia Sinica (Oct. 1998- Mar. 2001 and
Mar. 2002 - July 2002)
● Postdoctoral Fellow, Ecology and Evolution, The University of Chi-
副研究員 Associate Research Fellow cago (Apr. 2001 - Feb. 2002)
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

李文雄院士主持的 C4 稻米改造計畫，專注於尋找在 C3 和 C4 植物光合作用調 experiment and provided strong evidence that our predicted microRNA cardiac hypertrophy. Moreover, we have joined a C4 rice project, hosted
控路徑中的重要因子。另外在研究微型核糖核酸的演化部分，我們剛發展一個 and their targets are indeed the direct targets. The paper has been pub- by Academician Dr. Wen-Hsiung Li, in 2010 and focus on identifying im-
具有生物意義的計算方法來尋找在演化距離甚遠的基因組中的同源微型核糖核 lished in PNAS 2008 and highlighted by Nature Biotechnology and Na- portant factors involved in C3 and C4 plant photosynthesis pathways. In
酸。我們預期新的成果將會增加我們對於微RNA演化的瞭解。特別是在人類、 ture SciBX as well. the study of microRNA evolution, we have been developing a compu-
果蠅和線蟲間，微 RNA 擴增在基因調控演化中所扮演的角色。 tational method to search and identify homologous miRNAs in distant
Currently, we work on developing a systemic approach which can inte- genomes. We expect that the new generated data can provide us more
grate high-throughput next generation sequencing and other experi- details on how the role of miRNAs in gene regulation has been expanded
研究簡介 Research Description mental data to uncover microRNA regulatory pathways in breast cancer in evolution, especially in the lineage leading to human.
metastasis, B-cell differentiation, and T-type Ca channels involved in
2+
我的研究主題包含生物資訊和生物問題的探討兩部分。 My major research topics focus on bioinformatics and biological problem study.
目前的研究工作，不僅是在發展生物資訊的工具和方法 What I have been doing is to develop useful bioinformatics tools and novel meth-
論，提供生物學家使用，同時也參與研究生物方面的 odologies not only for service to a wide range of biologists but also for ourselves
重要議題。在生物資訊工具的開發，在2006、2007和 to study important biological problems as well as to answer interesting biological 代表著作 Publications
2009我們分別已經發展兩個視覺化的工具 (SinicView 和 questions. Although I am a computer scientist by training, I firmly believe that stud-
Phylo-mLogo)，提供比較基因體學和流感病毒演化等相 ying biological problems and questions through collaboration with biologists can Bioinformatics or biological journals 10. Arthur Chun-Chieh Shih and Wen-Hsiung Li (2003). GS-Aligner: a
關研究使用和一個可以用來排整重組過的基因序列演算 definitely enhance our understanding of what problems and questions are impor- novel tool for aligning genomic sequences using bit-level operations.
法及工具 (GR-Aligner)。因為 Phylo-mLogo 可以協助使用 tant and interesting to the biology community and what kinds of new bioinformat- 1. Te-Chin Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur Chun- Molecular Biology and Evolution 20, 1299-1309.
者比較和分析大數量序列間單點突變在不同的子集間的 ics tools are urgently needed for biologists. Chieh Shih* (2009). GR-Aligner: an algorithm for aligning pairwise
genomic sequences containing rearrangement events. Bioinformatics
差異，這個工具已經成為在台灣疾病管制局的專家，用 25, 2188-2193. Computer Science Journals
來檢驗 WHO 所推薦的流感疫苗株在台灣及世界各地流 In the bioinformatics tool development in 2006, 2007, and 2009, we have developed
行的病毒株是否有差異，對於下一個流感流行季節的流 two visualization tools, SinicView and Phylo-mLogo, for the usage of comparative 2. Li-Ching Hsieh1, Shu-I Lin, Arthur Chun-Chieh Shih, June-Wei 11. Jung-Shiong Chang, Arthur Chun-Chieh Shih, Hsiao-Rong Tyan and
Chen, Wei-Yi Lin, Ching-Ying Tseng, Su-Fen Chiang, Wen-Hsiung
行病毒群是否會繼續有效等問題。 genomics and influenza virus evolution and an alignment tool, GR-Aligner, for align- Li, and Tzyy-Jen Chiou (2009). Uncovering small RNA-mediated re- Wen-Hsien Fang (2009). Principal Component Analysis-based Mesh
Decomposition. Journal of Information Science and Engineering 25,
ing pairwise genomic sequences containing rearrangement events. Because Phylo- sponses to phosphate deficiency in Arabidopsis by deep sequencing. 971-987.
在研究生物問題方面，我主要有興趣的課題不只在分子 Plant Physiology 151, 2120-2132.
演化相關議題，包含流感病毒的演化、植物粒腺體及葉 mLogo can assist users to compare and visualize the changes of polymorphisms and 12. Yu-Ming Liang, Sheng-Wen Shih, Arthur Chun-Chieh Shih, Hong-
綠素演化、和微型核糖核酸 (microRNAs) 演化問題，而 indel events across different clades or subtypes in the alignment of a large number 3. Yao-Ming Chang, Hsueh-Fen Juan, Tzu-Ying Lee, Ya-Ya Chang, Yao- Yuan Mark Liao, and Cheng-Chung Lin (2009). Learning Atomic
Ming Yeh, Wen-Hsiung Li*, and Arthur Chun-Chieh Shih* (2008).
且也在功能基因學和基因體學的相關議題，這部分包 of sequences, this tool has become one of the major tools for the CDC (Center for Prediction of human miRNAs using tissue-selective motifs in 3’ Human Actions Using Variable-length Markov Model. IEEE Trans-
含：微型核糖核酸和其目標基因在癌症和心臟調控路徑 Disease Control, Taiwan) specialists to examine whether the recommended vaccine UTRs. Proceedings of the National Academy of Sciences U S A 105, actions on Systems, Man, and Cybernetics, Part B: Cybernetics 39,
268-280.
的預測、新一代短 RNA 定序分析和生質能及植物光合 strains currently in Taiwan and worldwide circulation will continue to dominate in 17061-17066.
作用路徑的預測。與我們合作的學者來自中研院基因體 the next epidemic season in maintaining its effectiveness. 4. Shu-Miaw Chaw, Arthur Chun-Chieh Shih, Daryi Wang, Yu-Wei Wu, 13. Arthur Chun-Chieh Shih, Hong-Yaun Mark Liao, and Chun-Shieh
Lu (2003). Dyadic Wavelet-based Nonlinear Conduction Equation:
中心、生物多樣性中心及生醫所和國內其他大學。我們 In the study of biological problems, the major topics I am interested not only in Shu-Mei Liu, and The-Yuan Chou (2008). The mitochondrial genome Theory and Applications. IEEE Transactions on Image Processing
已經發表一些生物方面的國際期刊。下述兩個重要的發 molecular evolution, including influenza virus evolution, plant mitochondria and of the gymnosperm Cycas taitungensis contains a novel family of 12, 466-476.
現結果： short interspersed elements, Bpu sequences, and abundant RNA edit-
chloroplast evolution, and microRNA evolution, but also in functional genetics and ing sites. Molecular Biology and Evolution 25, 603-615.
在流感病毒演化的問題，我們利用群體基因學的概念發 genomics, including microRNAs and their regulatory pathway prediction in cancer (Arthur Chun-Chieh Shih is as known as Chun-Chieh Shih and Chwen-Jye
展一個新的計算的方法，分析許多 H3N2 HA1 的序列， and cardiac diseases, next-generation small RNA sequencing analysis, and plant 5. Chi-Fang Chin, Arthur Chun-Chieh Shih, and Kuo-Chin Fan (2007). Sze)
Influence of mRNA decay rates on the computational prediction of
發現正向天擇的影響是一直持續不斷的，而非分散的； photosynthesis regulatory pathway prediction. The collaborators are from different transcription rate profiles from gene expression profiles. Journal of 14. Lian-Hua Chen, Chih-Wen Su, Hong-Yuan Liao, and Chun-Chieh
在抗原位點的正向多重突變的累積增強抗原的飄移顯 institutes of life science division in Academia Sinica, including Genomics Research Biosciences 32, 1251-1262. Shih (2003). On the Preview of Digital Movies. Journal of Visual
示，抗原的變化並不像來其他文獻提到是間斷式的變 Center, Biodiversity Research Center, and Institute of Biomedical Science, and other 6. Arthur Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho, and Wen- Communication and Image Representation 14, 358-368.
化。我們已經將研究成果發表在2007年的美國國家科學 domestic universities. We have published several journal papers in biology. Two ma- Hsiung Li (2007). Simultaneous amino acid substitutions at antigenic 15. C. H. Wang, H. C. Lin, C. C. Shih, H. R. Tyan, C. F. Lin, and H. Y.
院期刊 (PNAS)。另外微型核糖核酸在基因後轉譯調控及 jor biological discoveries are described below. sites drive influenza A hemagglutinin evolution. Proceedings of the Mark Liao (2003). Querying Image Database by Video Content. Jour-
疾病上扮演相當重要的角色。我們利用先尋找可能的目 National Academy of Sciences U S A 104, 6283-6288. nal of Information Science and Engineering 19, 967-987.
標基因，然後來預測人類微型核糖核酸基因的概念，發 Antigenic drift in circulating influenza viruses is a major process of accumulating 7. Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng , and Yu-Wei Wu 16. Chwen-Jye Sze, Hong-Yaun Mark Liao, and Kuo-Chin Fan (2001). A
展一套「逆向尋找」的計算方法。在人類基因組中，我 mutations at the antibody binding sites in hemagglutinin (HA) that evade recog- (2007). Phylo-mLogo: an interactive and hierarchical multiple-logo New Image Flux Conduction Model and It’s Application to Selective
們找到許多已知和未知的微型核糖核酸。而且利用實驗 nition by host’s antibodies. In 2007, we have introduced a new approach to ana- visualization tool for alignment of many sequences. BMC Bioinfor- Image Smoothing. IEEE Transactions on Image Processing 10, 296-
的方式，證明我們一些預測的新微型核糖核酸真的會在 lyze the HA sequences and identified many substitutions under positive selection. matics 8, 63. 306.
細胞株表現，而且目標基因也和我們預測一致。這篇論 Our results suggest that positive selection has been ongoing most of the time, not 8. Daryi Wang, Yu-Wei Wu, Arthur Chun-Chieh Shih, Chung-Shien Wu, 17. Chwen-Jye Sze, Hong-Yaun Mark Liao, Hai-Lung Hung, Kuo-Chin
文發表在 PNAS 2008 而且 Nature Biotechnology 和 Nature sporadic, and antigenic change is less punctuated than recently proposed. We have Ya-Nan Wang, Shu-Miaw Chaw (2007). Transfer of chloroplast ge- Fan, and Jun-Wei Hsieh (1998). Multiscale Edge Detection on Range
SciBX 也報導過我們發表的成果。 published these results in Proceedings of the National Academy of Sciences (PNAS) nomic DNA to mitochondrial genome occurred at least 300 MYA. Images via Normal Changes. IEEE Transactions on Circuits and Sys-
Molecular Biology and Evolution 24, 2040-2048.
tems II, Special issue on Multirate Systems, Filter Banks, Wavelets,
目前，我們正在發展一套系統化的方式，藉由整合新一 2007. 9. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng , and Applications 45, 1087-1092.
代高速定序短序和其他實驗資料，來尋找微型核糖核酸 MicroRNAs play an important role in posttranscriptional regulation of genes and Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, 18. Chwen-Jye Sze, Hong-Yaun Mark Liao, Kuo-Chin Fan, Ming-Yang
在乳癌轉移、B 細胞的分化和T型態鈣離子通道在心室肥 diseases. In 2008, we developed a novel method and predicted dozens of new hu- Tze-Chang Shiao, and Mu-Fen Hsieh (2006). SinicView: a visuali- Chern, and Chen-Kuo Tsao (1996). Fractal image coding system
大的調控路徑。除此之外在2010年，我們也開始參與由 zation environment for comparisons of multiple nucleotide sequence based on an adaptive side-coupling quadtree structure. Image and Vi-
man miRNA genes. Some of them and their target genes have been validated by
alignment tools. BMC Bioinformatics 7, 103. sion Computing 14, 401-415.
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