研究員

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:

生物資訊與因果生物學 (Bioinformatics & Bio-Causality; BBC) 實驗室

我們致力於探討人類複雜疾病，基因型(genotype – DNA level)和表現型(phenotype – molecular level)變化間的因果關係。

• 方向: 比較與演化基因體/轉錄體、因果生物學、系統生物學、分子生物學
• 主題: 分子內/分子間選擇性剪接、環狀RNA、RNA編輯、後轉錄調控、因果推論
• 策略: 資訊演算法、統計模型、演化推演、分生實驗
• 流程: raw data → information → validation → knowledge → new data
• 疾病: 神經發育/退化疾病、腦膠質瘤、乳癌

我們以生命科學為出發點，資訊人的邏輯思維，回答複雜的生物因果關係。歡迎有志於學術研究的同學加入我們，組成堅強的台灣團隊，共同『挑戰未知、超越自我、台灣發光、放射國際』。

歡迎具備以下背景同學(二擇一即可)加入我們：

1. 熟悉任何一種程式語言；
2. 熟悉 cell-based 相關分生實驗 or 電生理學；

本團隊開發的軟體或資料庫：

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

RESEARCH HIGHLIGHTS:

• 入選中央研究院年重要成果選輯2004, 2006, 2010, 2016, 2020, and 2023.
• 次世代定序打造癌症預測器--從非編碼RNA、NGS 大數據分析到精準醫療的關聯. 科學人 Issue 1, No.269, Jul. 1, 2024.
• 大腦中的環狀 RNA：解開自閉症基因調控網路的黑盒子. 中央研究院 研之有物 Aug. 30, 2023.
• 被圈住的心靈Part II: 探討基因型、環狀RNA與自閉症間的因果關係網路. Academia Sinica Newsletter, No. 1782, Jan. 12, 2023.
• 自然 RNA 修飾，基因檢測的新興潛力股！專訪中研院莊樹諄研究員 GeneOnline Sep. 17, 2021.
• Autism-Associated Circular RNA Regulatory Networks (自閉症相關的環狀RNA調控網路). Asia-Pacific Biotech News, Vol. 24, No. 6, Page 52-53, June 2020.
• 「被圈住的心靈！」首度建構自閉症腦組織的環狀 RNA 與基因間調控網路圖譜Academia Sinica Newsletter, No. 1715, May 21, 2020.
• 大數據看出端倪 基因突變的豬隊友也可能是神救援. Academia Sinica Newsletter, No. 1704, Nov. 28, 2019.
• Controls and roles of trans-splicing (分子間剪接事件的調控與角色) Nature Reviews Genetics, 14, 822, Dec. 2013.
• 生物資訊演算法，找出對全能性幹細胞功能性具關鍵力的分子間剪接RNA. 中研院週報, Dec. 2013.
• Methylation and Mutation (甲基化與突變). Asia-Pacific International Molecular Biology Network (A-IMBN), AR724, 2012.
• 增減序列 化猿為人. 科學人, Jun. 2006.
• 解基因序列之謎 助釐清病因 【聯合報╱記者李名揚／台北報導】 Jun. 6, 2007.
• 人為什麼是人？簡介人和黑猩猩基因體序列之間的插入和刪除事件 Academia Sinica Newsletter, No. 1155, Jan. 17, 2006.
• 大海撈針 -- 尋找基因的方法. 科學發展月刊, 396期, Dec. 05, 2005.

SELECTED PUBLICATIONS:

• Wei-Min Ho, Chia-Ying Chen, Tai-Wei Chiang, and Trees-Juen Chuang*, 2024, “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, 12, 77 (SCI impact factor: 6.2; Rank (NEUROSCIENCES): 32/310). (SCIE)
• 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 (SCI impact factor: 16.6; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 6/313). (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 (SCI impact factor: 16.6; Rank (BIOCHEMISTRY & MOLECULAR BIOLOGY): 6/313). (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 (SCI impact factor: 9.6; Rank (PSYCHIATRY): 6/276). (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), 563-579. (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)