Trees-Juen Chuang, Ph.D.
Name Trees-Juen Chuang, Ph.D.
Incumbent Professor
所屬單位

Ph.D., Institute of Computer and Information Science, National Chiao Tung University, Taiwan, 1992-1998.
B.S., Department of Computer Science, Soochow University, Taiwan, 1988-1992.
 
NCLscan:
研究方向/領域

RESEARCH INTERESTS

This is a Bioinformatics & Bio-Causality (BBC) Lab. We investigate the causal relationships between genetic variants and molecular phenotype changes in human complex diseases such as neuropsychiatric disorders (e.g., autism spectrum disorder (ASD), schizophrenia (SCZ), and Alzheimer's disease (AD)) and cancer (e.g., glioma and breast cancer).

  • Subject: Comparative & Evolutionary Genomics/Transcriptomics, Causative Biology, Systems Biology, Molecular Biology
  • Topic: Cis-/Trans-splicing, Circular RNA, RNA Editing, Post-transcriptional Regulation, Causal Inference
  • Strategy: Computer Science, Statistics, Evolution, Experimental Validation
  • Research flow: raw data → information → validation → knowledge → new data
  • Disease: Neuropsychiatric Disorders, Glioma, Breast Cancer

Developed tools/databases:

NCLscan: a high-accuracy package for detecting non-co-linear RNAs (circRNAs, trans-spliced RNAs, or gene fusion events)

NCLcomparator: a comprehensive tool for analyzing non-co-linear RNAs (circRNAs, trans-spliced RNAs, or gene fusion events)

CircMiMi: a stand-alone software for constructing circRNA-miRNA-mRNA interactions across species

FL-circAS: a database for full-length alternatively spliced circRNA isoforms
 
EDUCATION AND POSITIONS HELD
  • 2022-2023 Division director of the Physical and Computational Genomics division, Genomics Research Center, Academia Sinica
  • 2014-present Professor, Genomics Research Center, Academia Sinica, Taiwan
  • 2007-2014 Associate Professor, Genomics Research Center, Academia Sinica, Taiwan
  • 2003-2007 Assistant Professor, Genomics Research Center, Academia Sinica, Taiwan
  • 1998-2003 Postdoctoral Fellow, Institute of Biomedical Sciences, Academia Sinica, Taiwan (military service)
HONORS
  • 2014-2018 Project for Excellent Junior Research Investigators Award, Ministry of Science and Technology
  • 2012 Pius XI Medal, the Pontifical Academy of Sciences, Vatican
  • 2007 Academia Sinica Research Award for Junior Research Investigators
  • 2007 Wu Ta-Yuo Memorial Award, National Science Council
  • 2000 Post-doctoral Research Award of National Health Research Institutes (NHRI, Taiwan)
  • 1999-2000 Academia Sinica Post-doctoral Fellowship
  • 1998 Academic Paper Awards from the Image Processing and Pattern Recognition (IPPR) Society
Year Paper Title
2025 Bagheri N, Margvelani G, Chiang TW, Nelson PT, (Chuang TJ, Stamm S*, Circular RNAs from the MAPT and TARDBP genes: Novel players in neurodegeneration?, Neurochemistry international, vol. 189, 106019, 2025任職中研院著作;
2024 Tai-Wei Chiang, Song-En Jhong, Yu-Chen Chen, Chia-Ying Chen, Wei-Sheng Wu*, (Trees-Juen Chuang*, FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing, NUCLEIC ACIDS RESEARCH, vol. 52, D115-D123 (SCI impact factor: 16.6; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 6/313), 2024具代表性; 任職中研院著作;
2024 Wei-Min Ho, Chia-Ying Chen, Tai-Wei Chiang, Trees-Juen Chuang*, A longer time to relapse is associated with a larger increase in differences between paired primary and recurrent IDH wild-type glioblastomas at both the transcriptomic and genomic levels, ACTA NEUROPATHOLOGICA COMMUNICATIONS, vol. 12, 77 (SCI impact factor: 6.2; Rank (NEUROSCIENCES): 32/310), 2024具代表性; 任職中研院著作;
2024 Wei-Min Ho, Chia-Ying Chen, Tai-Wei Chiang, Trees-Juen Chuang*, Correction: A longer time to relapse is associated with a larger increase in differences between paired primary and recurrent IDH wild-type glioblastomas at both the transcriptomic and genomic levels, ACTA NEUROPATHOLOGICA COMMUNICATIONS, vol. 12, 119, 2024任職中研院著作;
2023 Jing-Ping Wang, Chun-Hao Hung, Yao-Huei Liou, Ching-Chen Liu, Kun-Hai Yeh, Keh-Yang Wang, Zheng-Sheng Lai, Tzu-Chi Hsu, Tung-Liang Lee, Yu-Chiau Shyu, Pei-Wen Hsiao, Liuh-Yow Chen, (Trees-Juen Chuang, Chen-Hsin Albert Yu, Nah-Shih Liao, Che-Kun James Shen*, Long-term hematopoietic transfer of the anti-cancer and lifespan-extending capabilities of a genetically engineered blood system by transplantation of bone marrow mononuclear cells, eLife, vol. 12, RP88275, 2023任職中研院著作;
2023 Trees-Juen Chuang*, Tai-Wei Chiang, Chia-Ying Chen, Assessing the impacts of various factors on circular RNA reliability, LIFE SCIENCE ALLIANCE, vol. 6(5), e202201793, 2023具代表性; 任職中研院著作;
2023 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, Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision., NATURE METHODS, vol. 20, 1159-1169 (impact factor: 48.0; Rank: 1/77), 2023具代表性; 任職中研院著作;
2023 Yu-Chen Chen, Chia-Ying Chen, Tai-Wei Chiang, Ming-Hsien Chan, Michael Hsiao, Huei-Mien Ke, Isheng Jason Tsai, Trees-Juen Chuang*, Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing, NUCLEIC ACIDS RESEARCH, vol. 51(15), 7777-7797 (SCI impact factor: 16.6; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 6/313), 2023具代表性; 任職中研院著作;
2022 Tai‑Wei Chiang, Te‑Lun Mai, Trees‑Juen Chuang*, CircMiMi: a stand‑alone software for constructing circular RNA‑microRNA‑mRNA interactions across species, BMC Bioinformatics, vol. 23, 164, 2022任職中研院著作;
2022 Te-Lun Mai, Chia-Ying Chen, Yu-Chen Chen, Tai-Wei Chiang, Trees-Juen Chuang*, Trans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism, MOLECULAR PSYCHIATRY, vol. 27, 4695-4706 (SCI impact factor: 9.6; Rank (PSYCHIATRY): 6/276), 2022具代表性; 任職中研院著作;
2021 Lin Po-Yu, Yang Denny, Chuang Chi-Hsuan, Lin Hsuan, Chen Wei-Ju, Chen Chia-Ying, (Chuang Trees-Juen, Lai Chien-Ying, Li Long-Yuan, Schuyler Scott C., Lu Frank Leigh, Liu Yu-Chuan, Lu Jean, Comparative Analyses of Single-Cell Transcriptomic Profiles between In Vitro Totipotent Blastomere-like Cells and In Vivo Early Mouse Embryonic Cells, Cells, vol. 10(11), 3111, 2021任職中研院著作;
2020 Yen-Ju Chen, Chia-Ying Chen, Te-Lun Mai, Chih-Fan Chuang, Yu-Chen Chen, Sachin Kumar Gupta, Laising Yen, Yi-Da Wang, Trees-Juen Chuang*, Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism, GENOME RESEARCH, vol. 30(3), 375-391, 2020具代表性; 任職中研院著作;
2019 Chia-Ying Chen, (Trees-Juen Chuang*, NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors, BMC BIOINFORMATICS, vol. 20(1), 3, 2019任職中研院著作;
2019 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*, Transcriptomopathies of Pre- and Post-Symptomatic Frontotemporal Dementia-like Mice with TDP-43 Depletion in Forebrain Neurons, Acta Neuropathologica Communications, vol. 7:50, 2019具代表性; 任職中研院著作;
2019 Chia-Ying Chen, Chuang Trees-Juen*, Comment on “A comprehensive overview and evaluation of circular RNA detection tools”, PLOS COMPUTATIONAL BIOLOGY, vol. 15, e1006158, 2019具代表性; 任職中研院著作;
2019 Te-Lun Mai, (Trees-Juen Chuang*, A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations, GENOME RESEARCH, vol. 29(11), 1766-1776, 2019具代表性; 任職中研院著作;
2018 Li-Yuan Hung, Yen-Ju Chen, Te-Lun Mai, Chia-Ying Chen, Min-Yu Yang, Tai-Wei Chiang, Yi-Da Wang, Trees-Juen Chuang*, An evolutionary landscape of A-to-I RNA editome across metazoan species, Genome Biology and Evolution, vol. 10(2), 521-537, 2018任職中研院著作;
2018 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, Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells, NUCLEIC ACIDS RESEARCH, vol. 46(7), 3671-3691, 2018具代表性; 任職中研院著作;
2017 Trees-Juen Chuang*, Yu-Hsiang Tseng, Chia-Ying Chen, Yi-Da Wang, Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios, SCIENTIFIC REPORTS, vol. 7(1), 7038, 2017任職中研院著作;
2016 Chen CY, Hung LY, Wu CS, (Chuang TJ*, Purifying selection shapes the coincident SNP distribution of primate coding sequences., Scientific reports, vol. 6, 27272, 2016任職中研院著作;
2016 Trees-Juen Chuang*, Chan-Shuo Wu, Chia-Ying Chen, Li-Yang Hung, Tai-Wei Chiang, Min-Yu Yang, 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, vol. 44, e29. (Corresponding & first author; SCI impact factor: 10.162; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 14/286; Q1), 2016具代表性; 任職中研院著作;
2015 Trees-Juen Chuang)*, Min-Yu Yang, Chuang-Chieh Lin, Ping-Hom Hsieh, Li-Yuan Hung, Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants, BMC PLANT BIOLOGY, vol. 15, 39 (impact factor: 3.942; Ranking: 22/199 (PLANT SCIENCES)), 2015任職中研院著作;
2015 Iju Chen, Chia-Ying Chen, Tree-Juen Chuang)*, Biogenesis, identification, and function of exonic circular RNAs, WIREs RNA, vol. 6(5), 563-579, 2015具代表性; 任職中研院著作;
2014 Feng-Chi Chen*, (Trees-Juen Chuang)*, Hsuan-Yu Lin, Min-Kung Hsu, The evolution of the coding exome of the Arabidopsis species - the influences of DNA methylation, relative exon position, and exon length, BMC EVOLUTIONARY BIOLOGY, vol. 14, 145, 2014任職中研院著作;
2014 Chun-Ying Yu, Hsiao-Jung Liu, Li-Yuan Hung, Hung-Chih Kuo*, Trees-Juen Chuang)*, Is an Observed Non-co-linear RNA Product Spliced in trans, in cis, or just in vitro?, NUCLEIC ACIDS RESEARCH, vol. 42(14), 9410-9423 (Corresponding & first author; SCI impact factor: 10.162; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 14/286; Q1), 2014具代表性; 任職中研院著作;
2014 Chan-Shuo Wu, Chun-Ying Yu, Ching-Yu Chuang, Michael Hsiao, Cheng-Fu Kao, Hung-Chih Kuo*, Trees-Juen Chuang)*, Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency, Genome Research, vol. 24(1), 25-36 (impact factor: 10.101; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY), 2014具代表性; 任職中研院著作;
2014 Trees-Juen Chuang)*, Feng-Chi Chen*, DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals, Molecular Biology and Evolution, vol. 31(2), 387-396 (impact factor: 10.217; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY), 2014具代表性; 任職中研院著作;
2014 Trees-Juen Chuang)*, Tai-Wei Chiang, Impacts of Pre-transcriptional DNA Methylation, Transcriptional Transcription Factor and Post-transcriptional microRNA Regulations on Protein Evolutionary Rate, Genome Biology and Evolution, vol. 6(6), 1530-1541, 2014任職中研院著作;
2013 Yi-Ching Chen, Jen-Hao Cheng, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai*, (Trees-Juen Chuang)*, The Impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins, NUCLEIC ACIDS RESEARCH, vol. 41(13), 6371-6380 (impact factor: 8.278; ranking: 27/290: BIOCHEMISTRY & MOLECULAR BIOLOGY), 2013具代表性; 任職中研院著作;
2013 Trees-Juen Chuang, Shian-Zu Wu, Yao-Ting Huang*, A Novel Framework for the Identification and Analysis of Duplicons between Human and Chimpanzee, BioMed Research International, vol. 264532, 2013任職中研院著作;
2012 Trees-Juen Chuang)*, Feng-Chi Chen*, Yen-Zho Chen, 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, vol. 109(39), 15841-15846 (impact factor: 9.737; ranking: 4/54: MULTIDISCIPLINARY SCIENCES), 2012具代表性; 任職中研院著作;
2012 Ming-Chih Wang, Feng-Chi Chen*, Yen-Zho Chen, Yao-Ting Huang, Trees-Juen Chuang*, LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs., BMC Research Note, vol. 5, 212, 2012任職中研院著作;
2012 Jean-Christophe Gelly, Hsuan-Yu Lin, Alexandre G. de Brevern*, (Trees-Juen Chuang)*, Feng-Chi Chen*, Selective Constraint on Human Pre-mRNA Splicing by Protein Structural Properties, Genome Biology and Evolution, vol. 4(9), 842-851, 2012任職中研院著作;
2011 Chen SC, Chuang TJ, Li WH, The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate., MOLECULAR BIOLOGY AND EVOLUTION, vol. 28(9), 2513-2520 (impact factor: 10.217; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY), 2011具代表性; 任職中研院著作;
2010 Choo KB, Chuang TJ, Lin WY, Chang CM, Tsai YH, Huang CJ, Evolutionary expansion of SPOP and associated TD/POZ gene family: impact of evolutionary route on gene expression pattern., Gene, vol. 460(1-2), 39-47, 2010任職中研院著作;
2010 Feng-Chi Chen, Chueng-Jong Chen, Wen-Hsiung Li, Trees-Juen Chuang*, Gene family size conservation is a good indicator of evolutionary rates, Molecular Biology and Evolution, vol. 27(8), 1750-1758 (impact factor: 10.353; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY), 2010具代表性; 任職中研院著作;
2009 Feng-Chi Chen, Yen-Zho Chen, Trees-Juen Chuang*, CNVVdb: a database of copy number variations across vertebrate genomes, Bioinformatics, vol. 25, 1419-1421, 2009具代表性; 任職中研院著作;
2009 Fan-Kai Lin, Chia-Lin Pan, Jinn-Moon Yang, Trees-Juen Chuang*, Feng-Chi Chen*, CAPIH: A Web interface for comparative analyses and visualization of host-HIV protein-protein interactions, BMC Microbiology, vol. 9, 164, 2009任職中研院著作;
2009 Chun-Hsi Chen; Trees-Juen Chuang; Ben-Yang Liao; Feng-Chi Chen, Scanning for the signatures of positive selection for human-specific insertions and deletions, Genome Biology and Evolution, vol. 2009, 415-419, 2009任職中研院著作;
2008 Feng-Chi Chen, Trees-Juen Chuang*, Nucleotide Sequence Divergence between Humans and Chimpanzees, ENCYCLOPEDIA OF LIFE SCIENCES, vol. DOI:10.1002/9780470015902.a0020751, 2008任職中研院著作;
2008 Yao-Ting Huang, Feng-Chi Chen*, Chiuan-Jung Chen, Hsin-Liang Chen, Trees-Juen Chuang*, Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons, Genome Research, vol. 18(7), 1163-1170 (impact factor: 14.397; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY), 2008具代表性; 任職中研院著作;
2007 Feng-Chi, Chen; Chueng-Jong, Chen; (Trees-Juen, Chuang)*, INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events, Nucleic Acids Research, vol. 35(Web Server issue), W633-8 (impact factor: 8.278; ranking: 27/290: BIOCHEMISTRY & MOLECULAR BIOLOGY), 2007具代表性; 任職中研院著作;
2007 Feng-Chi Chen, Chueng-Jong Chen, Wen-Hsiung Li*, Trees-Juen Chuang*, Human-specific insertions and deletions inferred from mammalian genome sequences, Genome Research, vol. 17(1), 16-22 (impact factor: 14.397; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY), 2007具代表性; 任職中研院著作;
2007 Feng-Chi Chen, Sheng-Shun Wang, Shu-Miaw Chaw, Yao-Ting Huang, Trees-Juen Chuang)*, PGAA: a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species EST conservationfrom seven plant species, Plant Physiology, vol. 143(3), 1086-1095 (impact factor: 6.555; ranking: 8/195: PLANT SCIENCES), 2007具代表性; 任職中研院著作;
2007 Yun-Huei Tzeng, Wen-Hsiung Li, Trees-Juen Chuang*, Mathematical Properties of Some Measures of Evolutionary Distance, Journal of Theoretical Biology, vol. 245(4), 790-792, 2007任職中研院著作;
2007 Feng-Chi Chen, Shu-Miaw Chaw, Yun-Huei Tzeng, Sheng-Shun Wang, Trees-Juen Chuang*, Opposite Evolutionary Effects between Different Alternative Splicing Patterns, Molecular Biology and Evolution, vol. 24, 1443-1446 (impact factor: 10.353; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY), 2007具代表性; 任職中研院著作;
2007 Feng-Chi Chen, Trees-Juen Chuang*, Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation., BMC Evolutionary Biology, vol. 7(1):179, 2007任職中研院著作;
2007 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, Human p16 , a novel transcriptional variant of p16INK4A, coexpresses with p16INK4A in cancer cells and inhibits cell-cycle progression, Oncogene, vol. 26(49), 7017-7027, 2007任職中研院著作;
2006 F. C. Chen, T. J. Chuang*, The effects of multiple features of alternatively spliced exons on the Ka/Ks ratio test, BMC Bioinformatics, vol. 7, 259, 2006具代表性; 任職中研院著作;
2006 F. C. Chen, C. J. Chen, J. Y. Ho, T. J. Chuang*, 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, vol. 7, 136, 2006任職中研院著作;
2006 F. C. Chen, S. S. Wang, C. J. Chen, W. H. Li, T. J. Chuang*, Alternatively and Constitutively Spliced Exons Are Subject to Different Evolutionary Forces, Mol Biol Evol, vol. 23, 675-682 (impact factor: 10.353; ranking: 14/290: BIOCHEMISTRY & MOLECULAR BIOLOGY), 2006具代表性; 任職中研院著作;
2005 Chen, F. C., Chuang, T. J.*, ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants., Bioinformatics, vol. 21(10), 2510-2513, 2005任職中研院著作;
2004 T. J. Chuang*, F. C. Chen, M. Y. Chou, A comparative method for identification of gene structures and alternatively spliced variants, Bioinformatics, vol. 20, 3064-3079, 2004具代表性; 任職中研院著作;
2003 T. J. Chuang, W. C. Lin, H. C. Lee, C. W. Wang, K. L. Hsiao, Z. H. Wang, D. Shieh, S. C. Lin, L. Y. Ch'ang, A complexity reduction algorithm for analysis and annotation of large genomic sequences, Genome Res, vol. 13(2), 313-322 (impact factor: 14.397; ranking: 3/160: BIOTECHNOLOGY & APPLIED MICROBIOLOGY), 2003具代表性; 任職中研院著作;
1997 T. J. Chuang, J. C. Lin, Lossy Compression by Base Switching (BS), Pattern Recognition and Image Analysis, vol. 7, 423-430, 1997