Publications by authors named "Trees-Juen Chuang"

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Circular RNAs from the MAPT and TARDBP genes: Novel players in neurodegeneration?
Naghme Bagheri, Giorgi Margvelani, Tai-Wei Chiang, Peter T Nelson, Trees-Juen Chuang

Neurochem Int· October 2025

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Author Correction: 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, Trees-Juen Chuang

Nat Methods· February 2025

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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.
Wei-Min Ho, Chia-Ying Chen, Tai-Wei Chiang, Trees-Juen Chuang

Acta Neuropathol Commun· July 2024

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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, Yae-Huei Liou, Ching-Chen Liu, Kun-Hai Yeh, Trees-Juen Chuang

Elife· May 2024

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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 Neuropathol Commun· May 2024

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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 Res· January 2024

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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, Trees-Juen Chuang

Nat Methods· August 2023

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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, Trees-Juen Chuang

Nucleic Acids Res· August 2023

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Assessing the impacts of various factors on circular RNA reliability.
Trees-Juen Chuang, Tai-Wei Chiang, Chia-Ying Chen

Life Sci Alliance· May 2023

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Trans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism.
Te-Lun Mai, Chia-Ying Chen, Yu-Chen Chen, Tai-Wei Chiang, Trees-Juen Chuang

Mol Psychiatry· November 2022

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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· May 2022

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Comparative Analyses of Single-Cell Transcriptomic Profiles between In Vitro Totipotent Blastomere-like Cells and In Vivo Early Mouse Embryonic Cells.
Po-Yu Lin, Denny Yang, Chi-Hsuan Chuang, Hsuan Lin, Wei-Ju Chen, Trees-Juen Chuang

Cells· November 2021

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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, Trees-Juen Chuang

Genome Res· March 2020

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A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations.
Te-Lun Mai, Trees-Juen Chuang

Genome Res· November 2019

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Comment on "A comprehensive overview and evaluation of circular RNA detection tools".
Chia-Ying Chen, Trees-Juen Chuang

PLoS Comput Biol· May 2019

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Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons.
Lien-Szu Wu, Wei-Cheng Cheng, Chia-Ying Chen, Ming-Che Wu, Yi-Chi Wang, Trees-Juen Chuang

Acta Neuropathol Commun· March 2019

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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· January 2019

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Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells.
Trees-Juen Chuang, Yen-Ju Chen, Chia-Ying Chen, Te-Lun Mai, Yi-Da Wang

Nucleic Acids Res· April 2018

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An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species.
Li-Yuan Hung, Yen-Ju Chen, Te-Lun Mai, Chia-Ying Chen, Min-Yu Yang, Trees-Juen Chuang

Genome Biol Evol· February 2018

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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

Sci Rep· August 2017

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Purifying selection shapes the coincident SNP distribution of primate coding sequences.
Chia-Ying Chen, Li-Yuan Hung, Chan-Shuo Wu, Trees-Juen Chuang

Sci Rep· June 2016

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Biogenesis, identification, and function of exonic circular RNAs.
Iju Chen, Chia-Ying Chen, Trees-Juen Chuang

Wiley Interdiscip Rev RNA· May 2016

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NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.
Trees-Juen Chuang, Chan-Shuo Wu, Chia-Ying Chen, Li-Yuan Hung, Tai-Wei Chiang

Nucleic Acids Res· February 2016

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Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants.
Trees-Juen Chuang, Min-Yu Yang, Chuang-Chieh Lin, Ping-Hung Hsieh, Li-Yuan Hung

BMC Plant Biol· February 2015

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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 Res· August 2014

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