Publication

Citation distribution of our published papers until June, 2014 by Google Scholar:

(Screenshot taken from Google Scholar Citation)

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, “Uncovering small RNA-mediated responses to phosphate-deficiency in Arabidopsis by deep sequencing,” 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, “Principal Component Analysis-based Mesh Decomposition,” 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, “Phylo-mLogo: An interactive multiple-logo visualization tool for large-number sequence alignments”, BMC Bioinformatics 8:63, 2007. (abstract)(pdf)

18. Chi-Fang Chin, Arthur Chun-Chieh Shih, Kuo-Chin Fan, “Influences of mRNA decay rates on the computational prediction of transcription rate profiles from gene expression profiles”, 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, “GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations,” Molecular Biology and Evolution 20(8): 1299-1309, 2003. (abstract)(pdf)

22. Arthur Chun-Chieh Shih, Hong-Yaun Mark Liao, and Chun-Shieh Lu, “A New Iterated Two-Band Diffusion Equation: Theory and Its Application,” 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 It’s Application to Selective Image Smoothing,” 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, “Shape-based Retrieval on a Fish Database of Taiwan,” 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, “Cocktail watermarking for digital image protection,” 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, “A 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, “Cell-type Preference Change of Duplicate Genes Contributed to the Evolution of C4 Photosynthesis,” 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, “JR-Assembler: a large-scale de novo assembly of short read sequences by jumping extension and read remapping,” 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, “Analyzing the breakpoint regions of genomic rearrangement events at nucleotide level by sequence alignment,” 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, “3-D Mesh Representation and Retrieval Using Isomap Manifold,” 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 20^th 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 20^th 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, “Shot Change Detection based on the Reynolds Transport Theorem”, 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 ” 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, “Selective Image Smoothing Based on An Image Flux Conduction Model”, 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, “Dyadic Wavelet-based Nonlinear Conduction Equation: Theory and Applications,” 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, “Selective Image Smoothing via Dyadic Wavelet-based Conduction Equation,” 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)