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Research Fellow  |  Shih, Arthur Chun-Chieh  
 
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Publications
 
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, Submitted.
2. Tong-Yen Tsai, Shih-Ying Wu, Cheng-Han Chung, Pang-Yen Yang, Shin-Tang Su, Yu-Hsuan Tseng, Tong-Cheng Wang, Wen-Hsiung Li, Arthur Chun-Chieh Shih and Kuo-I Lin, "miRNAome analysis profiles miRNA hubs synergistically regulate key transcription factors in directing human plasma cell differentiation," Submitted, under preparation
3. 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," to appear in 2013 Annual Meeting of Society for Molecular Biology and Evolution (SMBE 2013),.
4. 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, volume 110, number 10, pages 3979–3984, March 2013.
5. 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, volume 62, number 3, pages 561–580, February 2013.
6. 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, volume 66, number 2, pages 453-462, February 2013.
7. 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, volume 160, number 1, pages 165-177, September 2012.
8. 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," ECCB'12 (11th European Conference on Computational Biology), September 2012.
9. 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. June 23-26, June 2012.
10. 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 Artificial miRNA p-27-5p on Human Breast Carcinoma Cell Line T-47D," International Journal of Molecular Sciences, volume 13, number 5, pages 6352-6369, May 2012. :::icon
11. Arthur Chun-Chieh Shih and Tsunglin Liu,, chapter "10," Predicting MicroRNAs, Hsueh Fen Juan and Hsuan Cheng Huang, editor, pages 189-207, World Scientific Publishing Company, January 2012.
12. Yao-Ming Chang, Wen-Hsiung Li, and Arthur Chun-Chieh Shih, "Using Gene Duplication Patterns to Profile Evolution of C4 Photosynthesis," SMBE – Annual Meeting of the Society for Molecular Biology and Evolution, November 2011.
13. 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, volume 4:24, August 2011.
14. Arthur Chun-Cheih Shih, Yu-Shan Hsiao, Ling Li, and Chien-Chang Chen, "MicroRNA Co-targeting Regulation in Mouse Cardiac Hypertrophy," Cell Symposia: Regulatory RNA, 2011. :::icon
15. 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, volume 26, pages 649-658, 2010. :::icon
16. 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.
17. 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, 2010, DOI 10.1007/s00294-010-0312-4
18. Li-Ching Hsieh, Shu-I. Lin, Arthur Chun-Chieh Shih, June-Wei Chen, Wei-Yi Lin, Ching-Ying Tseng, Wen-Hsiung Li and Tzyy-Jen Chiou, "Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencin," Plant Physiology, volume 151, pages 2120–2132, December 2009.
19. Y.-M Liang, S-W Shih, A. C-C. Shih, H.-Y. Mark Liao, and C.-C. Lin, "Learning Atomic Human Actions Using Variable-length Markov Model," IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics, volume 39, number 1, pages 268-80, February 2009.
20. Yao-Ming Chang, Yao-Ming Yeh, and Arthur Chun-Chieh Shih, "Atypical miRNA Target Site Prediction Using Tissue-Selective Profiles," The Seventh Symposium of Bioinformatics and Systems Biology, 2009, poster.
21. 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," The 10th International Conference on Systems Biology, 2009, poster
22. 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, volume 25, number 17, pages 2188-2193, 2009.
23. 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, volume 25, number 4, pages 971-987, 2009. :::icon
24. 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," 2008 International Workshop on Multimedia Signal Processing, 2008.
25. Shu-Miaw Chaw, Arthur Chun-Chieh Shih, Daryi Wang, Yu-Wei Wu, Shu-Mei Liu, The-Yuan Chou, "The Mitochondrial Genome of the Gymnosperm Cycas taitungensis Contains a Novel Family of Short Interspersed Elements, Bpu sequences, and Abundant RNA Editing Sites," Molecular Biology and Evolution, volume 25, number 3, pages 603-15, 2008. :::icon
26. 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, volume 105, number 44, pages 17061–17066, 2008, (*: corresponding authors) :::icon
27. 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, volume 8:63, February 2007. :::icon
28. Chi-Fang Chin, Arthur Chun-Chieh Shih, Kuo-Chin Fan, "A Distance-based spectral clustering by automatic cluster extraction," 20th IPPR Conference on Computer Vision, Graphics, and Image Processing, 2007.
29. 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," International Workshop on Multimedia Signal Processing, 2007.
30. 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, volume 32, number 7, pages 1251-1261, 2007. :::icon
31. 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, volume 24, number 9, pages 2040-48, 2007.
32. Chi-Fang Chin, Feng-Yang Hsieh, Kuo-Chin Fan, and Arthur Chun-Chieh Shih, "Distance-based Spectral Clustering Applied to Image Segmentation," 20th IPPR Conference on Computer Vision, Graphics, and Image Processing, 2007.
33. 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, volume 104, number 15, pages 6283-6288, 2007. :::icon
34. 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, volume 7:103, pages 1471-2105, March 2006. :::icon
35. Chi-Fang Chin, Arthur Chun-Chieh Shih, and Kuo-Chin Fan, "Clustering and extraction of co-transcription profiles from time-course gene expression data," the 11th Conference on Artificial Intelligent and Applications, 2006.
36. 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, pages 331-334, 2006.
37. Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Chun-Yi Wong, Meng-Yuan Chou, and Tze-Chan, "SinicView: An Interactive Visualization Tool for Comparison of Multiple Sequence Alignment Results," IEEE Computational Systems Bioinformatics Conference, pages 269-270, Stanford University, California, August 2005.
38. Jung-Shiong Chang, Arthur Chun-Chieh Shih, Hong-Yuan Mark Liao, Wen-Hsien Fang, "Using Normal Vectors for Stereo Correspondence Construction," KES (1), pages 582-588, 2005.
39. Yu-Ming Liang, Arthur Chun-Chieh Shih, Hsiao-Rong Tyan, and Hong-Yuan Mark Liao, "Background Modeling Using Phase Space for Day and Night Video Surveillance Systems," PCM (1), pages 206-213, 2004.
40. 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, volume 12, number 4, pages 466-476, January 2003. :::icon
41. 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, volume 20, pages 1299-1309, January 2003. :::icon
42. 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, volume 14, pages 358-368, 2003.
43. 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, volume 19, number 6, pages 967-987, 2003.
44. Ming-Shing Su, Chun-Yen Chen, Chun-Chieh Shih and K. Y. Cheng, "Smoothing of 3D Polygon Meshes Using Non-Linear Diffusion Equations," Computer Graphics Workshop, 2002.
45. Chwen-Jye Sze, Hong-Yuan 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, volume 10, number 2, pages 296-306, January 2001.
46. Chun-Chieh Shih, Hsiao-Rong Tyan and Hong-Yaun Mark Liao, "Shot Change Detection based on the Reynolds Transport Theorem," Proc. Second Pacific Rim Conference on Multimedia, pages 819-824, Beijing, China, January 2001, LNCS 2195
47. Chun-Shieh Lu, Hong-Yuan Mark Liao, Shih-Kun Huang, and Chwen-Jye Sze, "Cocktail Watermarking for Digital Image Protection," IEEE Transactions on Multimedia, volume 2, number 4, December 2000.
48. Chwen-Jye Sze, Hong-Yuan Mark Liao, and Kuo-Chin Fan, "Selective Image Smoothing Based on an Image Flux Conduction Model," Asian Conference on Computer Vision, volume 1, pages 553-558, January 2000.
49. Arthur Chun-Chieh Shih, Hong-Yuan Mark Liao, Chun-Shieh Lu, and Shih-Kun Huang, "Dyadic Wavelet-based Nonlinear Conduction Equation: Theory and Applications," International Conference on Image Processing, volume 1, pages 880-883, January 2000.
50. 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, volume 2, number 3, pages 163-173, January 2000.
51. Chwen-Jye Sze, Hong-Yuan Mark Liao, Chun-Shieh Lu, and Simon C. Li, "Shape-based Retrieval on a Fish Database of Taiwan," Asian Conference on Computer Vision, volume 1, pages 370-375, January 2000.
52. Chun-Shieh Lu, Shih-Kun Huang, Chwen-Jye Sze, and Hong-Yuan Mark Liao, "A New Watermarking Technique for Multimedia Protection," Multimedia Image and Video Processing, number 507-530, 2000.
53. Chwen-Jye Sze, Hong-Yaun Mark Liao, Shih-Kun Huang and Chun-Shieh Lu, "Selective Image Smoothing via Dyadic Wavelet-based Conduction Equation," IEEE Workshop on Neural Network for Signal Processing, pages 400-408, 1999.
54. Chwen-Jye Sze, Hong-Yuan 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, volume 45, number 8, pages 1087-1092, January 1998.
55. Chwen-Jye Sze, Hong-Yaun Mark Liao, and Kuo-Chin Fan, "Selective Image Smoothing Based on an Image Flux Conduction Model," IPPR Conference on Computer Vision, Graphics and Image Processing, number 537-546, 1998, paper award
56. Chwen-Jye Sze, Hong-Yuan Liao, and , Kuo-Chin Fan, "Thermal Boundary Detection Based on Normal Changes," National Computer Syposium, volume 1, pages B141-B145, January 1997.
57. Chwen-Jye Sze, Hong-Yuan Mark Liao, Hai-Lung Hung, Kuo-Chin Fan and Jun-Wei Hsieh, "Multiscale Edge Detection via Normal Changes," Proc. 9th International Conference on Image Analysis and Processing, pages 22-29, Florence, Italy, January 1997, Florence, Italy
58. Chwen-Jye Sze, Hong-Yuan 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, volume 14, pages 401-415, January 1996.
59. Hai-Lung Hung, Hong-Yuan Mark Liao, Chwen-Jye Sze, Shing-Jong Lin, Wei-Chung Lin, and Kuo-Chin Fan, "CFART : A Multi-Resolutional Adaptive Resonance System," Proc. International Conference on Neural Network, number 1312-1317, 1996.
60. 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," IPPR Conference on Computer Vision, Graphics and Image Processing, pages 501-507, 1996, paper award
61. Chwen-Jye Sze, Hong-Yuan Liao, Chen-Kuo Tsao, and Ming-Yang Chern, "A Fractal Image Coding System Based on an Adaptive Side-Coupling Quadtree Structure," Proc. SPIE International Conference on Visual Communications and Image Processing, pages 455-466, 1994.
 
 
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