Publication List of Dr. Tree-Juen Chuang (莊樹諄)

(Last update: October 28, 2010; Homepage maintained by Ms. Min_Chin Hsu徐銘璟)

Research field:

(1) Bioinformatics (current interest)
    Bioinformatics and Computational Biology, Evolutionary Genomics, Genome Annotation, Comparative Analysis, Human Genetics,Chimpanzee-human divergence analysis, System Biology。 基因體註解，跨物種分析，演化暨比較基因體學，黑猩猩及靈長類動物相關研究，系統生物學。

(2) Computer science
      影像處理 (Image Processing)、圖樣識別 (Pattern Recognition)、影像壓縮 (Image Compression)、影像加密 (Image  Encryption)、漸進式傳輸 (Progressive Transmission)、隱像術 (Image hiding)、 浮水印 (water marking)、分群法 (Clustering)。

　

(A)   Journal papers (*correspondence author)

(A.1) Bioinformatics or Computing Biology 

1.      Feng-Chi Chen, Chueng-Jong Chen, Wen-Hsiung Li, and Trees-Juen Chuang* (2010) Gene family size conservation is a good indicator of evolutionary rates. Molecular Biology and Evolution, 27(8), 1750-8. (SCI: 9.872)

2.      Kong-Bung Choo, Trees-Juen Chuang, Wan-Yi Lin, Che-Ming Chang, Yao-Hui Tsai and Chiu-Jung Huang* (2010) Evolutionary expansion of SPOP and associated TD/POZ gene family: Impact of evolutionary route on gene expression pattern. Gene, 460(1-2), 39-47. (SCI: 2.416)

3.      Chun-Hsi Chen#, Trees-Juen Chuang#, Ben-Yang Liao, and Feng-Chi Chen (2009) Scanning for the signatures of positive selection for human-specific insertions and deletions. Genome Biology and Evolution. Vol. 2009:415. # Equal contribution.

4.      Fan-Kai Lin, Chia-Lin Pan, Jinn-Moon Yang, Trees-Juen Chuang* and Feng-Chi Chen* (2009) CAPIH: A Web interface for comparative analyses and visualization of host-HIV protein-protein interactions. BMC Microbiology 2009, 9:164. (SCI: 2.89)

5.      Feng-Chi Chen, Yen-Zho Chen, and Trees-Juen Chuang* (2009) CNVVdb: a database of copy number variations across vertebrate genomes. Bioinformatics 25(11), 1419-1421. (SCI: 4.926)

6.      Yao-Ting Huang, Feng-Chi Chen*, Chiuan-Jung Chen, Hsin-Liang Chen and Trees-Juen Chuang* (2008). Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons. Genome Research 18(7), 1163-1170. (SCI: 11.342)

7.      Feng-Chi Chen and Trees-Juen Chuang* (March 2008). Nucleotide Sequence Divergence between Humans and Chimpanzees. In: ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [DOI: 10.1002/ 9780470015902.a0020751], Invited review article.

8.      Feng-Chi Chen and Trees-Juen Chuang* (2007). Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation. BMC Evolutionary Biology, 7(1):179. (SCI: 4.294)

9.      Feng-Chi Chen, Shu-Miaw Chaw, Yun-Huei Tzeng, Sheng-Shun Wang, and Trees-Juen Chuang* (2007). Opposite Evolutionary Effects between Different Alternative Splicing Patterns. Molecular Biology and Evolution, 24(7):1443-6. (SCI: 9.872)

10. Feng-Chi Chen, Chueng-Jong Chen, and Trees-Juen Chuang* (2007). INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events, Nucleic Acids Research, 35 (Web Server issue):W633-8. (SCI: 7.479)

11. Feng-Chi Chen, Chueng-Jong Chen, Wen-Hsiung Li*, and Trees-Juen Chuang* (2007). Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Research, 17(1), 16-22. (SCI: 11.342)

12. Feng-Chi Chen, Sheng-Shun Wang, Shu-Miaw Chaw, Yao-Ting Huang, and Trees-Juen Chuang* (2007). Plant Gene and Alternatively Spliced Variant Annotator. A Plant Genome Annotation Pipeline for Rice Gene and Alternatively Spliced Variant Identification with Cross-Species Expressed Sequence Tag Conservation from Seven Plant Species. Plant Physiology, 143(3), 1086-1095. (SCI: 6.235)

13. Lin YC, Diccianni MB, Kim Y, Lin HH, Lee CH, Lin RJ, Joo SH, Li J, Chuang TJ, Yang AS, Kuo HH, Tsai MD, Yu AL (2007). Human p16bold italic gamma, a novel transcriptional variant of p16INK4A, coexpresses with p16INK4A in cancer cells and inhibits cell-cycle progression. Oncogene, 26(49):7017-27. (SCI: 7.135)

14. Yun-Huei Tzeng, Wen-Hsiung Li, Trees-Juen Chuang* (2007). Mathematical Properties of Some Measures of Evolutionary Distance. Journal of Theoretical Biology, 245(4), 790-792. (SCI: 2.454 )

15. Feng-Chi Chen and Trees-Juen Chuang* (2006). The effects of multiple features of alternatively spliced exons on the Ka/Ks ratio test. BMC Bioinformatics, 7:259. (SCI: 3.428)

16. Feng-Chi Chen, Sheng-Shun Wang, Chuang-Jong Chen, Wen-Hsiung Li and Trees-Juen Chuang* (2006). Alternatively and Constitutively Spliced Exons are Subject to Different Evolutionary Forces. Molecular Biology and Evolution, 23(3), 675–682. (SCI: 9.872) (collected in 65 significant publications of Academia Sinica, 2005~2006)

17. Feng-Chi Chen, Chuang-Jong Chen, Jar-Yi Ho, and Trees-Juen Chuang* (2006). Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. BMC Bioinformatics, 7:136. (SCI: 3.428)

18. Feng-Chi Chen, and Trees-Juen Chuang* (2005). ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants. Bioinformatics 21, 2510-2513. (SCI: 4.926)

19. Trees-Juen Chuang*, Feng-Chi Chen, and Meng-Yuan Chou (2004). A comparative method for identification of gene structures and alternatively spliced variants. Bioinformatics 20, 3064-3079. (SCI: 4.926) (collected in 30 significant publications of Academia Sinica, 2004~2005)

20. Trees-Juen Chuang, Wen-Chang Lin, Hurng-Chun Lee, Chi-Wei Wang, Keh-Lin Hsiao, Zi-Hao Wang, Danny Shieh, Simon C. Lin, and Lan-Yang Ch’ang (2003) “A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences,” Genome Research, 13(2), 313-322. (SCI: 11.342)

(A.2) Computer Image & Vision

  1. T.J. Chuang and J.C. Lin, “Lossy Compression by Base Switching (BS),” Pattern Recognition and Image Analysis, Vol. 7, No. 4, pp. 423-430, 1997.

  2. T.J. Chuang and J.C. Lin, “A New Approach to Image Encryption,” Journal of Electronic Imaging, Vol. 7, No. 2, pp. 350-356, 1998. (SCI)

  3. T.J. Chuang and J.C. Lin, “A New Algorithm for Lossless Still Image Compression,” Pattern Recognition, Vol. 31, No. 9, pp.1343-1352, 1998. (SCI)

  4.  T.J. Chuang and J.C. Lin, “On the Multiresolution Encryption of Still Image,” Pattern Recognition and Image Analysis. Vol.9, No.3, pp. 431-436, 1999.

  5.  T.J. Chuang, J.C. Lin, and W.H. Tsai, “A New Efficient Approach to Image Hiding by Digit Number Transformation,” Pattern Recognition and Image Analysis, Vol. 10, No. 3, pp.309-314, 2000.

(B)   Conference papers

(B.1) Bioinformatics or Computing Biology

1.       Feng-Chi and Trees-Juen Chuang*. “Different Alternative Splicing Patterns Are Subject to Opposite Evolutionary Effects,” Annual Meeting of the Society of Molecular Biology and Evolution (SMBE 2008), June 2008, Barcelona, Span (poster).

2.       Feng-Chi Chen, Chuang-Jong Chen, Sheng-Shun Wang, Jar-Yi Ho, Wen-Hsiung Li, and Trees-Juen Chuang*. “Identification and evolutionary analysis of alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat,” 2006 Computer Society Bioinformatics Conference (CSB2006), August 2006, Stanford University, California, USA. (Poster)

3.       T.J. Chuang, W.C. Lin, and L.Y. Chang, " Framework Annotation of the Human Genome by CRASA," The fifth annual international conference on computational molecular biology (RECOMB2001), Montrèal, Canada (Currents in computational molecular biology pp.253-255), 2001. (Poster)

4.       T.J. Chuang, W.C. Lin, and L.Y. Chang, "A New Algorithm for Global Alignment of DNA Sequence," Proc. of the second Taiwan Biochemistry and Molecular Biology Symposium, Nantou, Taiwan, Nov. 2000.

(B.2) Computer Image & Vision

1.     T.J. Chuang, J.C. Lin, and W.H. Tsai, "Image Hiding Using Digit Number Transformation," Proc. of IPPR Conf. on CVGIP, Taipei, Taiwan, Aug. 1998.

2.     T.J. Chuang and J.C. Lin, “On the Lossless Compression of Still Images,” Proc. of the 12th Intern. Computer Symposium on Image Processing and Character Recognition, Kaohsiung, Taiwan, pp.230-237, Dec. 1996.

3.     R.F. Su, T.J. Chuang, and J.C. Lin, “A Contour-based Color Image Compression Method,” Proc. of IPPR Conf. on CVGIP, Taichung, Taiwan, pp. 313-320, Aug. 1996.

 (C)   Patent:

              1. T.J. Chuang and L.Y. Chang, A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences (Patent no: TW238854)