NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision
EDUCATION AND POSITIONS HELD:
- B.S., Department of Computer Science, Soochow University, Taiwan, 1988-1992.
- Ph.D., Institute of Computer and Information Science, National Chiao Tung University, Taiwan, 1992-1998.
- Postdoctoral Fellow, Institute of Biomedical Sciences, Academia Sinica, Taiwan (military service), 1998-2003.
- Assistant Research Fellow, Genomics Research Center, Academia Sinica, Taiwan, 2003-2007.
- Associate Research Fellow, Genomics Research Center, Academia Sinica, Taiwan, 2007-2014.
- Research Fellow, Genomics Research Center, Academia Sinica, Taiwan, 2014-present.
- Project for Excellent Junior Research Investigators Award, Ministry of Science and Technology, 2014-2018.
- Pius XI Medal, the Pontifical Academy of Sciences, Vatican, 2012.
- Academia Sinica Research Award for Junior Research Investigators, 2007.
- Wu Ta-Yuo Memorial Award, National Science Council, 2007.
- Post-doctoral Research Award of National Health Research Institutes (NHRI, Taiwan), 2000.
- Academia Sinica Post-doctoral Fellowship, 1999-2000.
- Academic Paper Awards from the Image Processing and Pattern Recognition (IPPR) Society, 1998.
- Bioinformatics and Big Data Analysis
- Comparative & Evolutionary Genomics/Transcriptomics
- Post-transcriptional Regulation
- Genomic imprinting
- Primate Evolution
- Systems Biology
The goal of our studies is to comprehensively probe transcriptome complexity across species (especially for human vs. other non-human primates). It has been recognized that several post-transcriptional events such as alternative splicing (including cis- and trans-splicing) and RNA editing can generate many different transcript isoforms from the same genes, increasing the complexity of transcriptome/proteome. Despite the small genetic differences, human and other primates exhibit fairly different phenotypes. Some diseases attracting attention extensively such as Alzheimer's and Parkinson's disease, autism spectrum disorders, hepatitis B/C, AIDS, and cancers either are specific to human or have different symptoms/severity in non-human primates. Therefore, comparative genomics/transcriptomics analyses between human and non-human primates may not only increase our understanding of human (or primate) evolution but also radiate some light on the molecular mechanisms underlying such differences between primates in disease susceptibility. Recently, the next-generation sequencing technologies have been demonstrated to have the tremendous power of both profiling coverage and quantitative accuracy in genomics and transcriptomics studies. Based on such technologies, we analyze transcriptome variations (diversity/divergence) at both the DNA and RNA levels and try to shed light on decryption of different “RNA codes” in primates. Our research directions include:
- identification of gene structures and post-transcriptionally co-linear/non-co-linear events (including trans-spiced and circular RNAs);
- functional and evolutionary analysis of post-transcriptional events;
- investigation of dynamic transcriptomes during neural differentiation of human/non-human primate embryonic stem cells;
- identification and analysis of genetic variations between human and non-human primates;
- analysis of impacts of varied biological factors on evolutionary rates; and
- annotation of crop genomes.
- Chia-Ying Chen and Chuang Trees-Juen*, accepted, “Comment on “A comprehensive overview and evaluation of circular RNA detection tools””, PLOS COMPUTATIONAL BIOLOGY. (SCI)
- 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. (SCI)
- Chuang Trees-Juen*; Chen, Yen-Ju; Chen, Chia-Ying; Mai, Te-Lun; Wang, Yi-Da; Yeh, Chung-Shu; Yang, Min-Yu; Hsiao, Yu-Ting; Chang, Tien-Hsien; Kuo, Tzu-Chien; Cho, Hsin-Hua; Shen, Chia-Ning; Kuo, Hung-Chih; Lu, Mei-Yeh; Chen, Yi-Hua; Hsieh, Shan-Chi; Chiang, Tai-Wei, 2018, “Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells”, NUCLEIC ACIDS RESEARCH, 46(7), 3671-3691. (SCI)
- 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(1), 7038. (SCI)
- 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, e29. (SCI)
- Chen CY, Hung LY, Wu CS, Chuang TJ*, 2016, “Purifying selection shapes the coincident SNP distribution of primate coding sequences.”, Scientific reports, 6, 27272. (SCI)
- Iju Chen, Chia-Ying Chen and Tree-Juen Chuang*, 2015, “Biogenesis, identification, and function of exonic circular RNAs”, WIREs RNA, 6(5), 563-79 (SCI impact factor: 6.019; Rank (CELL BIOLOGY): 38/185; Q1). (SCI)
- 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, 15, 39 (impact factor: 3.942; Ranking: 22/199 (PLANT SCIENCES)). (SCI)
- Trees-Juen Chuang*, 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 (impact factor: 4.759; ranking: 33/164: GENETICS & HEREDITY). (SCI)
- 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 (impact factor: 10.353; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCI)
- 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 (impact factor: 14.397; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY). (SCI)
- 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 (SCI: 8.278; ranking=27/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCI)
- Yi-Ching Chen, Jen-Hao Cheng, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai*, Trees-Juen Chuang*, 2013, “The Impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins”, NUCLEIC ACIDS RESEARCH, 41(13), 6371-6380 (impact factor: 8.278; ranking: 27/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCI)
- Jean-Christophe Gelly, Hsuan-Yu Lin, Alexandre G. de Brevern*, Trees-Juen Chuang*, Feng-Chi Chen*, 2012, “Selective Constraint on Human Pre-mRNA Splicing by Protein Structural Properties”, Genome Biology and Evolution, 4(9), 842-851. (SCI)
- 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”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(39), 15841-15846 (impact factor: 9.737; ranking: 4/54: MULTIDISCIPLINARY SCIENCES). (SCI)
- Chen SC, Chuang TJ, Li WH, 2011, “The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate.”, MOLECULAR BIOLOGY AND EVOLUTION, 28(9), 2513-2520 (impact factor: 10.353; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCI)
- 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), 1750-1758 (impact factor: 10.353; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCI)
- Chun-Hsi Chen; Trees-Juen Chuang; Ben-Yang Liao; Feng-Chi Chen, 2009, “Scanning for the signatures of positive selection for human-specific insertions and deletions”, Genome Biology and Evolution, 2009, 415-419. (SCI)
- Feng-Chi Chen, Yen-Zho Chen, and Trees-Juen Chuang*, 2009, “CNVVdb: a database of copy number variations across vertebrate genomes”, Bioinformatics, 25, 1419-1421. (SCI)
- 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 (impact factor: 14.397; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY). (SCI)
- Feng-Chi Chen and Trees-Juen Chuang*, 2008, “Nucleotide Sequence Divergence between Humans and Chimpanzees”, ENCYCLOPEDIA OF LIFE SCIENCES, DOI:10.1002/9780470015902.a0020751.
- 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)
- 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, 1443-1446 (impact factor: 10.353; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCI)
- Feng-Chi Chen, Sheng-Shun Wang, Shu-Miaw Chaw, Yao-Ting Huang and Trees-Juen Chuang*, 2007, “PGAA: a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species EST conservationfrom seven plant species”, Plant Physiology, 143(3), 1086-1095 (impact factor: 6.555; ranking: 8/195: PLANT SCIENCES). (SCI)
- 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 (impact factor: 14.397; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY). (SCI)
- Feng-Chi, Chen; Chueng-Jong, Chen; 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 (impact factor: 8.278; ranking: 27/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCI)
- F. C. Chen, S. S. Wang, C. J. Chen, W. H. Li and T. J. Chuang*, 2006, “Alternatively and Constitutively Spliced Exons Are Subject to Different Evolutionary Forces”, Mol Biol Evol, 23, 675-682 (impact factor: 10.353; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCI)
- F. C. Chen, C. J. Chen, J. Y. Ho and T. J. 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)
- F. C. Chen and T. J. Chuang*, 2006, “The effects of multiple features of alternatively spliced exons on the Ka/Ks ratio test”, BMC Bioinformatics, 7, 259. (SCI)
- Chen, F. C. and Chuang, T. J., 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(10), 2510-2513. (SCI)
- T. J. Chuang*, F. C. Chen and M. Y. Chou, 2004, “A comparative method for identification of gene structures and alternatively spliced variants”, Bioinformatics, 20, 3064-3079. (SCI)
- T. J. Chuang, W. C. Lin, H. C. Lee, C. W. Wang, K. L. Hsiao, Z. H. Wang, D. Shieh, S. C. Lin and L. Y. Ch'ang, 2003, “A complexity reduction algorithm for analysis and annotation of large genomic sequences”, Genome Res, 13(2), 313-322 (impact factor: 14.397; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY). (SCI)
- T. J. Chuang, J. C. Lin and W. H. Tsai, 2000, “A New Efficient Approach to Image Hiding by Digit Number Transformation”, Pattern Recognition and Image Analysis, 10, 309-314.
- T. J. Chaung, J.C. Lin, 1998, “A NEW ALGORITHM FOR LOSSLESS STILL IMAGE COMPRESSION”, Pattern recognition, 31, 1343-1352. (SCI, EI)
- T. J. Chuang, J. C. Lin, 1998, “New approach to image encryption”, Journal of Electronic Imaging, 7, 350-356. (SCI, EI)