Professor

trees
02-27871244
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 Professor, Genomics Research Center, Academia Sinica, Taiwan, 2003-2007.
• Associate Professor, Genomics Research Center, Academia Sinica, Taiwan, 2007-2014.
• Professor, Genomics Research Center, Academia Sinica, Taiwan, 2014-present.
• Division director of the Physical and Computational Genomics division, Genomics Research Center, Academia Sinica, 2022-2023

HONORS:

• 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.

RESEARCH INTERESTS:

• 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.

SELECTED PUBLICATIONS:

• Tai-Wei Chiang, Song-En Jhong, Yu-Chen Chen, Chia-Ying Chen, Wei-Sheng Wu*, Trees-Juen Chuang*, 2024, “FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing”, NUCLEIC ACIDS RESEARCH, 52, D115-D123 (impact factor: 14.9; Rank: 10/285). (SCIE)
• Yu-Chen Chen, Chia-Ying Chen, Tai-Wei Chiang, Ming-Hsien Chan, Michael Hsiao, Huei-Mien Ke, Isheng Jason Tsai, and Trees-Juen Chuang*, 2023, “Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing”, NUCLEIC ACIDS RESEARCH, 51(15), 7777-7797 (impact factor: 14.9; Rank: 10/285). (SCIE)
• Marieke Vromman, Jasper Anckaert, Stefania Bortoluzzi, Alessia Buratin, Chia-Ying Chen, Qinjie Chu, Trees-Juen Chuang, Roozbeh Dehghannasiri, Christoph Dieterich, Xin Dong, Paul Flicek, Enrico Gaffo, Wanjun Gu, Chunjiang He, Steve Hoffmann, Osagie Izuogu, Michael S. Jackson, Tobias Jakobi, Eric C. Lai, Justine Nuytens, Julia Salzman, Mauro Santibanez-Koref, Peter Stadler, Olivier Thas, Eveline Vanden Eynde, Kimberly Verniers, Guoxia Wen, Jakub Westholm, Li Yang, Chu-Yu Ye, Nurten Yigit, Guo-Hua Yuan, Jinyang Zhang, Fangqing Zhao, Jo Vandesompele, Pieter-Jan Volders, 2023, “Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.”, NATURE METHODS, 20, 1159-1169 (impact factor: 48.0; Rank: 1/77). (SCIE)
• Trees-Juen Chuang*, Tai-Wei Chiang, and Chia-Ying Chen, 2023, “Assessing the impacts of various factors on circular RNA reliability”, LIFE SCIENCE ALLIANCE, 6(5), e202201793. (SCIE)
• Te-Lun Mai, Chia-Ying Chen, Yu-Chen Chen, Tai-Wei Chiang, and Trees-Juen Chuang*, 2022, “Trans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism”, MOLECULAR PSYCHIATRY, 27, 4695-4706. (SCIE)
• 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. (SCIE)
• Te-Lun Mai, 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. (SCIE)
• Chia-Ying Chen and Chuang Trees-Juen*, 2019, “Comment on “A comprehensive overview and evaluation of circular RNA detection tools””, PLOS COMPUTATIONAL BIOLOGY, 15, e1006158. (SCIE)
• 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. (SCIE)
• 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. (SCIE)
• 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. (Corresponding & first author; SCI impact factor: 10.162; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 14/286; Q1). (SCIE)
• Iju Chen, Chia-Ying Chen and Tree-Juen Chuang*, 2015, “Biogenesis, identification, and function of exonic circular RNAs”, WIREs RNA, 6(5), 563-79 (Corresponding author; SCI impact factor: 4.838; Rank (CELL BIOLOGY): 53/189; Q2)  the top 5 most cited articles over the past two years in WIREs RNA.. (SCIE)
• 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: 10.217; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCIE)
• 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: 10.101; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY). (SCIE)
• 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 & first author; SCI impact factor: 10.162; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 14/286; Q1). (SCIE)
• 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). (SCIE)
• 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). (SCIE)
• 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: 10.217; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY). (SCIE)
• 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). (SCIE)
• 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. (SCIE)
• 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). (SCIE)
• 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). (SCIE)
• 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). (SCIE)
• 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). (SCIE)
• 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). (SCIE)
• 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). (SCIE)
• 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. (SCIE)
• 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. (SCIE)
• 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). (SCIE)