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Journal Papers
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J.1.
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, vol.
105, no. 44, pp. 17061–17066, 2008. (abstract)
(pdf)
J.2.
Shu-Miaw
Chaw, Arthur Chun-Chieh Shih, Daryi
Wang, Yu-Wei Wu, Shu-Mei
Liu, and 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, vol. 25, no. 3, pp. 603-615, 2008. (full text)
J.3.
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, vol. 104, no. 15, pp. 6283-6288, 2007. (pdf)
J.4.
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, vol. 24, no.9, pp.2040-2048,
2007. (pdf)
J.5.
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
2007, 8:63. (pdf)
J.6.
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. (pdf)
J.7.
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
2006, 7:103. (pdf)
J.8.
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,
vol. 20, pp.1299-1309, 2003. (pdf)
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