Journal papers
1.
Te-Chin Chu, Chen-Hua Lu, Tsunglin Liu, Greg C.
Lee, Wen-Hsiung Li* and Arthur Chun-Chieh Shih*, "Assembler for de novo
assembly of large genomes." Proceedings
of the National Academy of Sciences 110 (36): E3417-3424, 2013. (abstract)(pdf)
2.
Wen-Yu
Liu, Yao-Ming Chang, Sean C.-C. Chen, Chen-Hua Lu, Yeh-Hwa Wu, Mei-Yeh Jade Lu, Di-Rong Chen, Arthur Chun-Chieh Shih, Chiou-Rong Sheue, Hsuan-Cheng
Huang, Chun-Ping Yug, Hsin-Hung Lin, Shin-Han Shiu,
Maurice S. B. Ku, and Wen-Hsiung Li, "Anatomical and
transcriptional dynamics of maize embryonic leaves during seed
germination," Proceedings
of the National Academy of Sciences 110 (10): 3979–3984, 2013. (abstract)(pdf)
3.
Yao-Ming
Chang, Chia-Lin Chang, Wen-Hsiung Li, Arthur Chun-Chieh Shih*, "Historical Profiling of
Maize Duplicate Genes Sheds Light on the Evolution of C4 Photosynthesis in
Grasses," Molecular Phylogenetics and
Evolution 66(2): 453-462, 2013.
(abstract)(pdf)
4.
Yu-Ming
Liang, Sheng-Wen Shih, and Arthur
Chun-Chieh Shih, "Human action segmentation and classification
based on the Isomap algorithm,"
Multimedia Tools and Applications
62(3): 561–580, 2013. )(pdf)
5.
Yao-Ming
Chang, Wen-Yu Liu, Arthur
Chun-Chieh Shih, Meng-Ni Shen, Chen-Hua Lu, Mei-Yeh Jade Lu, Hui-Wen
Yang, Tzi-Yuan
Wang, Sean C.-C. Chen, Stella Maris Chen, Wen-Hsiung Li
and Maurice S. B. Ku, "Characterizing Regulatory and Functional
Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis," Plant
Physiology 160(1): 165-177,
2012. (abstract)(pdf)
6.
Chien-wei Tseng, Hsuan-cheng Huang, Arthur Chun-chieh Shih, Ya-ya Chang, Chung Cheng Hsu, Jen-yun Chang, Hsueh-fen Juan , Wen-hsiung Li, "Revealing the Anti-tumor
Effect of ArtificialmiRNA p-27-5p on Human Breast Carcinoma
Cell Line T-47D," International
Journal of Molecular Sciences 13(5):
6352-6369, 2012. (abstract)(pdf)
7.
Tzi-Yuan Wang, Hsin-Liang
Chen, Mei-Yeh Jade Lu, Yo-Chia
Chen, Huang-Mo Sung, Chi-Tang Mao, Hsing-Yi Cho, Huei-Mien Ke, Teh-Yang Hwa, Sz-Kai Ruan, Kuo-Yen Hung, Chih-Kuan Chen,
Jeng-Yi Li, Yueh-Chin
Wu, Yu-Hsiang Chen, Shao-Pei Chou, Ya-Wen Tsai, Te-Chin Chu, Arthur
Chun-Chieh Shih, Wen-Hsiung Li, Ming-Che Shih, "Functional Characterization of Cellulases Identified from the Cow Rumen Fungus Neocallimastix patriciarum W5
by Transcriptome and Secretome
Analyses," Biotechnology
for Biofuels 4:24, 2011. (abstract)(pdf)
8.
Chi-Fang Chin, Arthur
Chun-Chieh Shih and Kuo-Chin Fan, "A Novel Spectral Clustering Method
based on Pairwise Distance Matrix," Journal of Information
Science and Engineering 26: 649-658, 2010. (pdf)
9.
Michael Lee Salmans, Shu-Miaw Chaw, Ching-Ping
Lin, Arthur Chun-Chieh
Shih, Yu-Wei Wu and R. Michael Mulliga,
"Editing site analysis in a gymnosperm mitochondrial genome reveals
similarities with angiosperm mitochondrial genomes," Current
Genetics 56(5):439-46, 2010. (abstract)(pdf)
10. Li-Ching Hsieh, Shu-I Lin, Arthur
Chun-Chieh Shih, June-Wei Chen, Wei-Yi Lin, Ching-Ying
Tseng, Su-Fen Chiang, Wen-Hsiung Li, and Tzyy-Jen Chiou, ÒUncovering
small RNA-mediated responses to phosphate-deficiency in Arabidopsis by deep
sequencing,Ó Plant Physiology, 151(4): 2120-2132, 2009. (abstract)(pdf)
11.
Te-Chin
Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur Chun-Chieh Shih*,
"GR-Aligner: an algorithm for aligning pairwise genomic sequences
containing rearrangement events," Bioinformatics
25(17): 2188-2193, 2009. (abstract)(pdf)
12.
Jung-Shiong Chang, Arthur Chun-Chieh Shih,
Hsiao-Rong Tyan and
Wen-Hsien Fang, ÒPrincipal Component
Analysis-based Mesh Decomposition,Ó Journal
of Information Science and Engineering 25(4): 971-987, 2009. (pdf)
13.
Yu-Ming Liang, Sheng-Wen Shih, Arthur Chun-Chieh Shih,
Hong-Yuan Mark Liao, and Cheng-Chung Lin, "Learning Atomic Human
Actions Using Variable-length Markov Model," IEEE Transactions on Systems,
Man, and Cybernetics, Part B: Cybernetics
39(1): 268-280, 2009. (pdf)
14.
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. (abstract)(pdf)
15. Shu-Miaw
Chaw, Arthur Chun-Chieh Shih, Daryi
Wang, Yu-Wei Wu, Shu-Mei Liu, and The-Yuan
Chou, "The Mitochondrial Genome of the GymnospermCycas
taitungensis Contains a Novel Family of
Short Interspersed Elements, Bpu sequences, and
Abundant RNA Editing Sites," Molecular Biology and Evolution
25(3): 603-615, 2008. (abstract)(pdf)
16. Arthur
Chun-Chieh Shih, Tze-Chang Shiao, Mei-Shang Ho, and Wen-Hsiung
Li, "Simultaneous Amino Acid Substitutions at Antigenic Sites Drive
Influenza A Hemagglutinin Evolution," Proceedings
of the National Academy of Sciences 104(15): 6283-6288, 2007. (abstract)(pdf)
17.
Arthur
Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng,
and Yu-Wei Wu, ÒPhylo-mLogo: An
interactive multiple-logo visualization tool for large-number sequence
alignmentsÓ, BMC
Bioinformatics 8:63, 2007. (abstract)(pdf)
18.
Chi-Fang Chin, Arthur
Chun-Chieh Shih, Kuo-Chin Fan,
ÒInfluences of mRNA decay rates on the computational prediction of transcription
rate profiles from gene expression profilesÓ, Journal of Biosciences, 32(7), 1251-1261, 2007. (abstract)(pdf)
19.
Daryi
Wang, Yu-Wei Wu, Arthur
Chun-Chieh Shih, Chung-Shien Wu, Ya-Nan Wang, Shu-Miaw Chaw,
"Transfer of chloroplast genomic DNA to mitochondrial genome occurred
at least 300 million years ago," Molecular
Biology and Evolution, 24(9):
2040-2048, 2007. (abstract)(pdf)
20.
Arthur Chun-Chieh Shih,
D.T. Lee, Laurent Lin, Chin-Lin Peng , Shiang-Heng Chen, Yu-Wei
Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao, and Mu-Fen
Hsieh, "SinicView: A visualization
environment for comparisons of multiple nucleotide sequence alignment
tools," BMC Bioinformatics 7:103, 2006. (abstract)(pdf)
21.
Arthur Chun-Chieh Shih and Wen-Hsiung
Li, ÒGS-Aligner: A Novel Tool for Aligning Genomic Sequences Using
Bit-Level Operations,Ó Molecular
Biology and Evolution 20(8):
1299-1309, 2003. (abstract)(pdf)
22.
Arthur Chun-Chieh Shih,
Hong-Yaun Mark Liao, and Chun-Shieh
Lu, ÒA New Iterated Two-Band Diffusion Equation: Theory and Its Application,Ó IEEE Trans. on Image Processing
12(4): 466-476, 2003. (abstract)(pdf)
(Arthur
Chun-Chieh Shih is also known
as Chun-Chieh Shih and Chwen-Jye Sze)
23.
Lian-Hua
Chen, Chih-Wen Su, Hong-Yuan Liao, and Chun-Chieh Shih,
"On the Preview of Digital Movies," Journal of Visual Communication
and Image Representation 14:
358-368, 2003. (pdf)
24.
C. H. Wang, H. C. Lin, C. C. Shih, H. R. Tyan, C. F. Lin, and H. Y. Mark Liao, " Querying
Image Database by Video Content," Journal
of Information Science and Engineering 19(6): 967-987, 2003.
25.
Chwen-Jye Sze, Hong-Yaun
Mark Liao, and Kuo-Chin Fan, "A New Image
Flux Conduction Model and ItÕs Application to Selective Image Smoothing,Ó IEEE Trans. on Image Processing,
10(2): 296-306, 2001.
26.
Chwen-Jye Sze, Hsiao-Rong
Tyan, Hong-Yuan Mark Liao, Chun-Shieh Lu and Shih-Kun Huang, ÒShape-based Retrieval on
a Fish Database of Taiwan,Ó Tamkang Journal of Science and Engineering 2(3):
p.163-173, 2000.
27.
Chun-Shieh Lu, Hong-Yuan
Mark Liao, Shih-Kun Huang, and Chwen-Jye Sze,
ÒCocktail watermarking for digital image protection,Ó IEEE Trans. on Multimedia
2(4): 209-224, December 2000.
28.
Chun-Shieh Lu, Shih-Kun
Huang, Chwen-Jye
Sze, and Hong-Yuan Mark Liao, ÒA new
watermarking technique for multimedia protection, in Multimedia Image and Video
Processing, eds. Ling Guan, Jan Larsen, and S. Y. Kung, CRC Press Inc.,
Chapter 18, p.507-530, 2000.
29.
Chwen-Jye Sze, Hong-Yaun
Mark Liao, Hai-Lung Hung, Kuo-Chin
Fan, and Jun-Wei Hsieh, "Multiscale Edge
Detection on Range Images via Normal Changes", IEEE Trans. on Circuits and
Systems II, Special issue on Multirate Systems,
Filter Banks, Wavelets, and Applications, vol. 45, no. 8, p.1087-1092,
1998. (pdf)
30.
Chwen-Jye Sze, Hong-Yaun
Mark Liao, Kuo-Chin Fan, Ming-Yang Chern, and Chen-Kuo Tsao, " Fractal image coding system based on an
adaptive side-coupling quadtree structure," Image and Vision Computing,
vol.14, p. 401-415, 1996. (pdf)
Book Chapter
1. Arthur Chun-Chieh Shih and Tsunglin Liu,
"Predicting MicroRNAs," Hsueh Fen
Juan and Hsuan Cheng Huang, editor, Systems Biology: Applications
in Cancer-related Research, 10, World Scientific Publishing Company, January
2012. (link)
Conference papers
1.
Yao-Ming Chang, Wen-Hsiung Li, and Arthur Chun-Chieh Shih,
ÒCell-type Preference Change of Duplicate Genes Contributed to the
Evolution of C4 Photosynthesis,Ó 2013 Annual Meeting of Society for Molecular Biology and
Evolution (SMBE 2013), Chicago, 2013,
poster.
2.
Te-Chin Chu, Tsunglin Liu, Chen-Hua Lu, Greg C. Lee, Wen-Hsiung
Li and Arthur Chun-Chieh Shih,
ÒJR-Assembler: a large-scale de novo assembly of short read sequences by
jumping extension and read remapping,Ó 11th
European Conference on Computational Biology, Basel, Switzerland, 2012, poster.
3.
L.-C. Hsieh, Y.-C.
Fang, W.-H. Li and A. C. Shih,"Not Genetic
Hitchhiking but Positive Selection Plays a Major Role in Influenza A Hemagglutinin Evolution," 2012 Annual Meeting of Society for
Molecular Biology and Evolution (SMBE 2012), Dublin,
Ireland, 2012, poster.
4.
Arthur Chun-Cheih Shih, Yu-Shan Hsiao, Ling Li, and Chien-Chang
Chen, " MicroRNA Co-targeting Regulation in Mouse Cardiac Hypertrophy,
" Regulatory RNAs at
Chicago, 2011, poster.
5.
Yao-Ming Chang, Wen-Hsiung Li, and Arthur Chun-Chieh Shih,
"Using Gene Duplication Patterns to Profile Evolution of C4
Photosynthesis," SMBE 2011 – Annual Meeting of the
Society for Molecular Biology and Evolution, 2011, oral.
6.
Yao-Ming Chang, Yu-Ting
Chuang, Wen-Hsiung Li, and Arthur Chun-Chieh Shih, "Hundreds of human miRNAs have homologs in worms or flies," SMBE
2010 - Annual Meeting of the Society for Molecular Biology and Evolution,
2010, poster.
7.
Te-Chin
Chu, Tsunglin Liu, D.T. Lee, Greg C. Lee, and Arthur Chun-Chieh Shih,
ÒAnalyzing the breakpoint regions of genomic rearrangement events at
nucleotide level by sequence alignment,Ó in
2009 International
Conference on Systems Biology (poster).
8.
Jung-Shiong Chang,
Arthur C-C Shih, H-Y Lin, H-F Kao, H-Y Mark Liao, and W-H Fang, Ò3-D Mesh
Representation and Retrieval Using Isomap Manifold,Ó in 2008International Workshop
on Multimedia Signal Processing.
9.
Jung-Shiong Chang, Arthur Chun-Chieh Shih,
Hong-Yuan Mark Liao, and Wen-Hsien Fang,
"Principal Component Analysis-based Mesh Decomposition," in 2007International
Workshop on Multimedia Signal Processing.
10.
Yu-Ming Liang, Sheng-Wen Shih, Arthur Chun-Chieh Shih,
Hong-Yuan Mark Liao, Cheng-Chung Lin, "A Language Modeling Approach to
Atomic Human Action Recognition," in
2007 International
Workshop on Multimedia Signal Processing.
11.
Chi-Fang Chin, Arthur
Chun-Chieh Shih, Kuo-Chin Fan, " A
Distance-based spectral clustering by automatic cluster extraction,"
in 2007 20th IPPR Conference on Computer
Vision, Graphics, and Image Processing.
12.
Chi-Fang Chin, Feng-Yang
Hsieh, Kuo-Chin Fan, and Arthur Chun-Chieh Shih,
"Distance-based Spectral Clustering Applied to Image
Segmentation," in 2007 20th IPPR Conference on Computer
Vision, Graphics, and Image Processing.
13.
Arthur Chun-Chieh Shih,
D.T. Lee, Chin-Lin Peng, and Yu-Wei Wu, "Phylo-mLogo: An interactive multiple-logo visualization
tool for large-number sequence alignments," in 2006 IEEE Computational Systems
Bioinformatics Conference (poster).
14.
Chi-Fang Chin, Arthur
Chun-Chieh Shih, and Kuo-Chin Fan,
"Clustering and extraction of co-transcription profiles from
time-course gene expression data," in the 11th Conference on Artificial
Intelligent and Applications, December 2006.
15.
Yu-Ming Liang, Sheng-Wen Shih, Arthur Chun-Chieh Shih,
and Hong-Yuan Mark Liao, "Understanding
Human Behavior Using a Language Modeling Approach", IEEE International Conference
on Intelligent Information Hiding and Multimedia Signal Processing, pp. 331-334, December 2006.
16.
Arthur Chun-Chieh Shih,
D.T. Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Chun-Yi Wong, Meng-Yuan
Chou, and Tze-Chang Shiao,
"SinicView: An Interactive Visualization
Tool for Comparison of Multiple Sequence Alignment Results," in the 2005 IEEE Computational
Systems Bioinformatics Conference (poster).
17.
Jung-Shiong Chang, Arthur Chun-Chieh Shih,
Hong-Yuan Mark Liao, and Wen-Hsien Fang,
"Using Normal Vectors for Stereo Correspondence Construction," in the 2005 Ninth International
Conference on Knowledge-Based Intelligent Information & Engineering
Systems.
18.
Yu-Ming Liang, Arthur
Chun-Chieh Shih, Hsiao-Rong Tyan, Hong-Yuan Mark Liao:
Background Modeling Using Phase Space for Day and Night Video Surveillance
Systems. PCM (1): 206-213, 2004.
19.
Chun-Chieh Shih,
Hsiao-Rong Tyan and
Hong-Yaun Mark Liao, ÒShot Change Detection based
on the Reynolds Transport TheoremÓ, Proc.
Second IEEE Pacific Rim Conference on Multimedia, Oct.24-26, Beijing, China, LNCS 2195, pp.819-824,
2001.
20.
Chwen-Jye Sze, Hong-Yaun
Mark Liao, Chun-Shieh Lu, and Simon C. Li,
``Shape-based Retrieval on A Fish Database of Taiwan, in Ó Fourth Asian Conference on
Computer Vision, vol.I,
pp.370-375, 2000. (invited paper).
21.
Chwen-Jye Sze, Hong-Yaun Mark Liao, and Kuo-Chin
Fan, ÒSelective Image Smoothing Based on An Image Flux Conduction ModelÓ, in Fourth Asian Conference on
Computer Vision, vol.I,
pp.553-558, 2000.
22.
Chwen-Jye Sze, Hong-Yaun
Mark Liao, Chun-Shieh Lu, and Shih-Kun Huang,
ÒDyadic Wavelet-based Nonlinear Conduction Equation: Theory and
Applications,Ó 2000
International Conference on Image Processing, vol. I, pp. 880-883,
2000.
23.
Chwen-Jye Sze, Hong-Yaun
Mark Liao, Shih-Kun Huang and Chun-Shieh Lu,
ÒSelective Image Smoothing via Dyadic Wavelet-based Conduction Equation,Ó
in IEEE Workshop on Neural
Network for Signal Processing, pp.400-408, 1999.
24.
Chwen-Jye Sze, Hong-Yaun
Mark Liao, and Kuo-Chin Fan, "Selective
Image Smoothing Based on An Image Flux Conduction Model," in IPPR
Conference on Computer Vision, Graphics and Image Processing, pp. 537-546,
1998. ( paper award ).
25.
Chwen-Jye Sze, Hong-Yaun
Mark Liao, Hai-Lung Hung, Kuo-Chin
Fan and Jun-Wei Hsieh, " Multiscale Edge
Detection via Normal Changes," in 9th International Conference on
Image Analysis and Processing 1997, Florence, Italy, pp.22-29, 1997.
26.
Chwen-Jye Sze, Hong-Yaun
Liao, and , Kuo-Chin
Fan, "Thermal Boundary Detection Based on Normal Changes," in Proceedings of
National Computer Symposium 1997, vol. I, pp.B141-B145,
1997.
27.
Hai-Lung
Hung, Hong-Yaun Mark Liao, Chwen-Jye
Sze, Shing-Jong
Lin, Wei-Chung Lin, and Kuo-Chin Fan, " CFART : A Multi-Resolutional
Adaptive Resonance System," in Proc. International Conference on
Neural Network, pp.1312-1317, 1996.
28.
Shing-Jong
Lin, Hong-Yaun Mark Liao, Hai-Lung
Hung, Chwen-Jye
Sze, Kuo-Chin
Fan, and Wei-Chung Lin, " CFART and Its Application to Color Image
Segmentation," in IPPR Conference on Computer Vision, Graphics and
Image Processing, pp. 501-507, 1996. ( paper award
).
29.
Chwen-Jye Sze, Hong-Yaun
Liao, Chen-Kuo Tsao,
and Ming-Yang Chern, " A Fractal Image
Coding System Based on An Adaptive Side-Coupling Quadtree
Structure," in Proc. SPIE International Conference on Visual
Communications and Image Processing, pp. 455-466, 1994.
Technical report
1. Arthur Chun-Chieh Shih, D. T. Lee, Chi-Fang Chin,
Hong-Yuan Mark Liao, and Wen-Hsiung Li, "Palindrome-like Patterns
in Genomes," Technical Report No. TR-IIS-04-019, Institute of Information
Science, Academia Sinica, Taiwan, 2004. (pdf)
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