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

(Last update: May 12, 2020)

Research field:

(1) Bioinformatics (current interest)
    Bioinformatics and computational biology, Big data (NGS) analysis, Evolutionary & comparative Genomics, cis-/trans-splcing, RNA editing, Imprinting, Systems biology。

生物資訊，大數據(NGS)分析，演化暨比較基因體學，轉錄體研究(cis-/trans-splicing, RNA editing)，基因印記，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)。

　

Publication List: (*corresponding author)

 PART 1. Publications at GRC

1. Yen-Ju Chen, Chia-Ying Chen, Te-Lun Mai, Chih-Fan Chuang, Yu-Chen Chen, Sachin Kumar Gupta, Laising Yen, Yi-Da Wang, and Trees-Juen Chuang* (2020) Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism. Genome Research, 30(3):375-391. (Corresponding author; SCI impact factor: 11.093; Rank (Biotechnology& Applied Microbiology): 4/156; Q1) è highlighted in (1) Asia-Pacific Biotech News, Vol. 24, No. 6, Page 52-53, June 2020 and (2) Academia Sinica newsletter, May 21, 2020.

2.      Te-Lun Mai and Trees-Juen Chuang* (2019) A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations. Genome Research, 29(11):1766-1776. (Corresponding author; SCI impact factor: 11.093; Rank (Biotechnology& Applied Microbiology): 4/156; Q1) è highlighted in Academia Sinica newsletter, Nov. 28, 2019.

3.      Chia-Ying Chen and Trees-Juen Chuang* (2019) Comment on “A comprehensive overview and evaluation of circular RNA detection tools”. PLoS Comput Biol., 15: e1006158. (Corresponding author; SCI impact factor: 4.7; Rank (MATHEMATICAL & COMPUTATIONAL BIOLOGY): 6/59; Q1)

4.      Lien-Szu Wu, Wei-Cheng Cheng, Chia-Ying Chen, Ming-Che Wu, Yi-Chi Wang, Yu-Hsiang Tseng, Trees-Juen Chuang*, C-K James Shen* (2019) Transcriptomopathies of Pre- and Post-Symptomatic Frontotemporal Dementia-like Mice with TDP-43 Depletion in Forebrain Neurons. Acta Neuropathologica Communications, 7:50. (Corresponding author; SCI impact factor: 6.27; Rank (NEUROSCIENCES): 27/271; Q1)

5.      Chia-Ying Chen and Trees-Juen Chuang* (2019) NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors. BMC Bioinformatics, 20:3. (Corresponding author; SCI impact factor: 3.242; Rank (MATHEMATICAL & COMPUTATIONAL BIOLOGY): 9/59; Q1)

6.      Trees-Juen Chuang*, Yen-Ju Chen, Chia-Ying Chen, Te-Lun Mai, Yi-Da Wang, Chung-Shu Yeh, Min-Yu Yang, Yu-Ting Hsiao, Tien-Hsien Chang, Tzu-Chien Kuo, Hsin-Hua Cho, Chia-Ning Shen, Hung-Chih Kuo, Mei-Yeh Lu, Yi-Hua Chen, Shan-Chi Hsieh, and Tai-Wei Chiang (2018) Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells. Nucleic Acids Research, 46(7): 3671-3691. (Corresponding & first author; SCI impact factor: 11.501; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 15/297; Q1)

7.      Li-Yuan Hung, Yen-Ju Chen, Te-Lun Mai, Chia-Ying Chen, Min-Yu Yang, Tai-Wei Chiang, Yi-Da Wang, and Trees-Juen Chuang* (2018) An evolutionary landscape of A-to-I RNA editome across metazoan species. Genome Biology and Evolution, 10(2):521-537. (Corresponding author; SCI impact factor: 3.462; Rank (EVOLUTIONARY BIOLOGY): 17/50)

8.      Trees-Juen Chuang*, Yu-Hsiang Tseng, Chia-Ying Chen, Yi-Da Wang (2017) “Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios”, Scientific Reports, 7:7038. (Corresponding & first author; SCI impact factor: 3.998; Rank (MULTIDISCIPLINARY SCIENCES): 17/71; Q1)

9.      Chia-Ying Chen, Li-Yuan Hung, Chan-Shuo Wu, and Trees-Juen Chuang* (2016) Purifying selection shapes the coincident SNP distribution of primate coding sequences. Scientific Reports, 6:27272. (Corresponding author; SCI impact factor: 3.998; Rank (MULTIDISCIPLINARY SCIENCES): 17/71; Q1)

10.   Trees-Juen Chuang*, Chan-Shuo Wu, Chia-Ying Chen, Li-Yang Hung, Tai-Wei Chiang, and Min-Yu Yang (2016) NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing, and circular RNA) with a good balance between sensitivity and precision. Nucleic Acids Research, 44(3), e29. (Corresponding & first author; SCI impact factor: 11.501; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 15/297; Q1) è collected in 2016 significant publications of Academia Sinica.

11.   Iju Chen, Chia-Ying Chen and Trees-Juen Chuang* (2015) Biogenesis, identification, and function of exonic circular RNAs. WIREs RNA, 6(5):563-79. (Corresponding author; SCI impact factor: 6.913; Rank (CELL BIOLOGY): 35/195; Q1) è the top 5 most cited articles over the past two years in WIREs RNA.

12.   Trees-Juen Chuang*, Min-Yu Yang, Chuang-Chieh Lin, Ping-Hom Hsieh and Li-Yuan Hung (2015) Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants. BMC Plant Biology, 2015, 15:39. (Corresponding & first author; SCI impact factor: 3.497; Rank (PLANT SCIENCES): 38/234; Q1)

13.   Chun-Ying Yu, Hsiao-Jung Liu, Li-Yuan Hung, Hung-Chih Kuo* and Trees-Juen Chuang* (2014) Is an Observed Non-co-linear RNA Product Spliced in trans, in cis, or just in vitro? Nucleic Acids Research, 42(14), 9410-9423. (Corresponding author; SCI impact factor: 11.501; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 15/297; Q1)

14.   Feng-Chi Chen*, Trees-Juen Chuang*, Hsuan-Yu Lin and Min-Kung Hsu (2014) The evolution of the coding exome of the Arabidopsis species - the influences of DNA methylation, relative exon position, and exon length. BMC Evolutionary Biology, 2014, 14:145. (Corresponding author; SCI impact factor: 3.058; Rank (EVOLUTIONARY BIOLOGY): 19/50; Q2)

15.   Trees-Juen Chuang* and Tai-Wei Chiang (2014) Impacts of Pre-transcriptional DNA Methylation, Transcriptional Transcription Factor and Post-transcriptional microRNA Regulations on Protein Evolutionary Rate. Genome Biology and Evolution, 6(6), 1530-1541. (Corresponding & first author; SCI impact factor: 3.462; Rank (EVOLUTIONARY BIOLOGY): 17/50)

16.   Chan-Shuo Wu, Chun-Ying Yu, Ching-Yu Chuang, Michael Hsiao, Cheng-Fu Kao, Hung-Chih Kuo* and Trees-Juen Chuang* (2014) Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. Genome Research. 24(1), 25-36. (Corresponding author; SCI impact factor: 11.093; Rank (Biotechnology& Applied Microbiology): 4/156; Q1) è highlighted in Nature Reviews Genetics 14, 822, 2013.

17.   Trees-Juen Chuang* and Feng-Chi Chen* (2014) DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals. Molecular Biology and Evolution. 31(2), 387-396. (Corresponding & first author; SCI impact factor: 11.062; Rank (GENETICS & HEREDITY): 7/177; Q1)

18.   Trees-Juen Chuang, Shian-Zu Wu and Yao-Ting Huang* (2013) A Novel Framework for the Identification and Analysis of Duplicons between Human and Chimpanzee. BioMed Research International (formerly titled Journal of Biomedicine and Biotechnology), 2013 (2013). (First author; SCI impact factor: 2.276; Rank (BIOTECHNOLOGY & APPLIED MICROBIOLOGY): 92/156)

19.   Yi-Ching Chen, Jen-Hao Cheng, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai* and Trees-Juen Chuang* (2013) The Impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins. Nucleic Acids Research, 13 (41), 6371-6380. (Corresponding author; SCI impact factor: 11.501; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 15/297; Q1)

20.   Trees-Juen Chuang*, Feng-Chi Chen*, Yen-Zho Chen (2012) Position-dependent correlations between the level of DNA methylation and the evolutionary rates of mammalian coding exons. P Natl Acad Sci USA, 109(39), 15841-15846. (Corresponding & first author; SCI impact factor: 9.412; Rank (MULTIDISCIPLINARY SCIENCES): 8/71; Q1) è highlighted in A-IMBN (Asia-Pacific International Molecular Biology Network) Research

21.   Jean-Christophe Gelly, Hsuan-Yu Lin, Alexandre G. de Brevern*, Trees-Juen Chuang*, and Feng-Chi Chen* (2012) Selective Constraint on Human Pre-mRNA Splicing by Protein Structural Properties. Genome Biology and Evolution, 4(9): 842–851. (Corresponding author; SCI impact factor: 3.462; Rank (EVOLUTIONARY BIOLOGY): 17/50)

22.   Ming-Chih Wang, Feng-Chi Chen*, Yen-Zho Chen, Yao-Ting Huang and Trees-Juen Chuang* (2012) LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. BMC Research Note 2012, 5:212. (Corresponding author)

23.   Sean Chun-Chang Chen, Trees-Juen Chuang, Wen-Hsiung Li* (2011) The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate. Molecular Biology and Evolution, 28(9), 2513-20. (Co-author; SCI impact factor: 11.062; Rank (GENETICS & HEREDITY): 7/177; Q1)

24.   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. (Co-author; SCI impact factor: 3.759; Rank (GENETICS & HEREDITY): 53/177)

25.   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. (Corresponding author; SCI impact factor: 11.062; Rank (GENETICS & HEREDITY): 7/177; Q1) è collected in 2010 significant publications of Academia Sinica.

26.   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. (Corresponding author; SCI impact factor: 2.989; Rank (MICROBIOLOGY): 67/134; Q2)

27.   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. (Co-first author; SCI impact factor: 3.462; Rank (EVOLUTIONARY BIOLOGY): 17/50)

28.   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. (Corresponding author; SCI impact factor: 5.61; Rank (MATHEMATICAL & COMPUTATIONAL BIOLOGY): 3/59; Q1)

29.   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. (Corresponding author; SCI impact factor: 11.093; Rank (Biotechnology& Applied Microbiology): 4/156; Q1)

30.   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. (Corresponding author)

31.   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. (Corresponding author; SCI impact factor: 3.058; Rank (EVOLUTIONARY BIOLOGY): 19/50; Q2)

32.   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. (Corresponding author; SCI impact factor: 11.062; Rank (GENETICS & HEREDITY): 7/177; Q1)

33.   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. (Corresponding author; SCI impact factor: 11.501; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 15/297; Q1)

34.   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. (Corresponding author; SCI impact factor: 11.093; Rank (Biotechnology& Applied Microbiology): 4/156; Q1)

35.   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. (Corresponding author; SCI impact factor: 6.902; Rank (PLANT SCIENCES): 10/234; Q1)

36.   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 p16 bold italic gamma , a novel transcriptional variant of p16INK4A, coexpresses with p16INK4A in cancer cells and inhibits cell-cycle progression. Oncogene, 26(49):7017-27. (Co-author; SCI impact factor: 7.971; Rank (GENETICS & HEREDITY): 14/177; Q1)

37.   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. (Corresponding author; SCI impact factor: 2.327; Rank (MATHEMATICAL & COMPUTATIONAL BIOLOGY): 17/59)

38.   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. (Corresponding author; SCI impact factor: 3.242; Rank (MATHEMATICAL & COMPUTATIONAL BIOLOGY): 9/59; Q1)

39.   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. (Corresponding author; SCI impact factor: 11.062; Rank (GENETICS & HEREDITY): 7/177; Q1) è collected in 65 significant publications of Academia Sinica, 2005~2006.

40.   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. (Corresponding author; SCI impact factor: 3.242; Rank (MATHEMATICAL & COMPUTATIONAL BIOLOGY): 9/59; Q1)

41.   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. (Corresponding author; SCI impact factor: 5.61; Rank (MATHEMATICAL & COMPUTATIONAL BIOLOGY): 3/59; Q1)

42.   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. (Corresponding & first author; SCI impact factor: 5.61; Rank (MATHEMATICAL & COMPUTATIONAL BIOLOGY): 3/59; Q1) è collected in 30 significant publications of Academia Sinica, 2004~2005.

 

PART 2. Publications before joining GRC (before Oct. 2003)

 

(A) Bioinformatics or Computing Biology

 

1.      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. (First author; SCI impact factor: 11.093; Rank (Biotechnology& Applied Microbiology): 4/156; Q1)

2.      Patent: T.J. Chuang and L.Y. Ch’ang (2003) “A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences” (Patent no: TW238854).

 

(B) Computer Image & Vision

 

3.      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.

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 and J.C. Lin, “A New Algorithm for Lossless Still Image Compression,” Pattern Recognition, Vol. 31, No. 9, pp.1343-1352, 1998. (First author; SCI impact factor: 5.898; Rank (ENGINEERING, ELECTRICAL & ELECTRONIC): 25/265; Q1)

6.      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. (First author; SCI impact factor: 0.924; Rank (ENGINEERING, ELECTRICAL & ELECTRONIC): 220/265)

7.      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.