| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 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 | Wei-Min Ho; Chia-Ying Chen; Tai-Wei Chiang; Trees-Juen Chuang | ACTA NEUROPATHOLOGICA COMMUNICATIONS 12, 77 | | | |
| 2019 | A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations | Te-Lun Mai; Trees-Juen Chuang | GENOME RESEARCH 29(11), 1766-1776 | | | |
| 2023 | Assessing the impacts of various factors on circular RNA reliability | Trees-Juen Chuang ; Tai-Wei Chiang; Chia-Ying Chen | LIFE SCIENCE ALLIANCE 6(5), e202201793 | | | |
| 2017 | Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios | Trees-Juen Chuang ; Yu-Hsiang Tseng; Chia-Ying Chen; Yi-Da Wang | SCIENTIFIC REPORTS 7, 7038 | | | |
| 2022 | CircMiMi: a stand‑alone software for constructing circular RNA‑microRNA‑mRNA interactions across species | Tai-Wei Chiang; Te-Lun Mai; Trees-Juen Chuang | BMC Bioinformatics 23, 164 | | | |
| 2021 | Comparative analyses of single-cell transcriptomic profiles between In vitro totipotent blastomere-like cells and In vivo early mouse embryonic cells | 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 | Cells 10(11), 3111 | | | |
| 2023 | Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing | Yu-Chen Chen; Chia-Ying Chen; Tai-Wei Chiang; Ming-Hsien Chan; Michael Hsiao ; Huei-Mien Ke; Isheng Jason Tsai ; Trees-Juen Chuang | Nucleic Acids Research 51(15), 7777-7797 | | | |
| 2014 | DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals | Trees-Juen Chuang ; Feng-Chi Chen | Molecular Biology and Evolution 31(2), 387-396 | | | |
| 2024 | FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing | Tai-Wei Chiang; Song-En Jhong; Yu-Chen Chen; Chia-Ying Chen; Wei-Sheng Wu; Trees-Juen Chuang | NUCLEIC ACIDS RESEARCH 52(D1), D115-D123 | | | |
| 2010 | Gene family size conservation is a good indicator of evolutionary rates | Chen, Feng-Chi; Chen, Chueng-Jong; Li, Wen-Hsiung ; Chuang, Trees-Juen | Molecular Biology and Evolution 27(8), 1750-1758 | | | |
| 2020 | Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism | 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 RESEARCH 30(3), 375-391 | | | |
| 2007 | Human-specific insertions and deletions inferred from mammalian genome sequences | Chen, F. C.; Chen, C. J.; Li, W. H. ; Chuang, T. J. | Genome Research 17(1), 16-22 | | | |
| 2014 | Impacts of Pretranscriptional DNA Methylation, Transcriptional Transcription Factor, and Posttranscriptional microRNA Regulations on Protein Evolutionary Rate | Trees-Juen Chuang ; Tai-Wei Chiang | Genome Biology and Evolution 6(6), 1530-1541 | | | |
| 2014 | Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency | Chan-Shuo Wu; Chun-Ying Yu; Ching-Yu Chuang; Michael Hsiao; Cheng-Fu Kao; Hung-Chih Kuo; Trees-Juen Chuang | Genome Research 24(1), 25-36 | | | |
| 2018 | Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells | Chuang, Trees-Juen ; Chen, Yen-Ju; Chen, Chia-Ying; Mai, Te-Lun; Wang, Yi-Da; Yeh, ChungShu; 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 | NUCLEIC ACIDS RESEARCH 46(7), 3671-3691 | | | |
| 2014 | Is an Observed Non-co-linear RNA Product Spliced in trans, in cis or just in vitro? | Chun-Ying Yu; Hsiao-Jung Liu; Li-Yuan Hung; Hung-Chih Kuo; Trees-Juen Chuang | NUCLEIC ACIDS RESEARCH 42(14), 9410-9423 | | | |
| 2023 | Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision | 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 | NATURE METHODS 20, 1159-1169 | | | |
| 2024 | 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 | 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 | eLife 12, RP88275 | | | |
| 2007 | Mathematical Properties of Some Measures of Evolutionary Distance | Tzeng, Yun-Huei; Li, Wen-Hsiung ; Chuang, Trees-Juen | Journal of Theoretical Biology 245(4), 790-792 | | | |
| 2019 | NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors | Chia-Ying Chen; Trees-Juen Chuang | BMC BIOINFORMATICS 20, 3 | | | |
