Trees-Juen Chuang

发表

Scanning for the Signatures of Positive Selection for Human-Specific Insertions and Deletions

Feng-Chi Chen, Chun-Hsi Chen, Trees-Juen Chuang, 2009, Genome biology and evolution.

Human-specific insertions and deletions inferred from mammalian genome sequences.

Feng-Chi Chen, Wen-Hsiung Li, Trees-Juen Chuang, 2006, Genome research.

Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism

Trees-Juen Chuang, Laising Yen, Yen-Ju Chen, 2020, Genome research.

Genome-wide, integrative analysis implicates circular RNA dysregulation in autism and the corresponding circular RNA-microRNA-mRNA regulatory axes

Trees-Juen Chuang, Laising Yen, Yen-Ju Chen, 2019, bioRxiv.

The Impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins

Trees-Juen Chuang, Z. Tsai, Huai-Kuang Tsai, 2013, Nucleic acids research.

A Novel Framework for the Identification and Analysis of Duplicons between Human and Chimpanzee

Trees-Juen Chuang, Shian-Zu Wu, Yao-Ting Huang, 2013, BioMed research international.

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency

Trees-Juen Chuang, M. Hsiao, Chan-Shuo Wu, 2014, Genome research.

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, Chia-Ying Chen, Chan-Shuo Wu, 2015, Nucleic acids research.

Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons

Feng-Chi Chen, Trees-Juen Chuang, Yen-Zho Chen, 2012, Proceedings of the National Academy of Sciences.

Impacts of Pretranscriptional DNA Methylation, Transcriptional Transcription Factor, and Posttranscriptional microRNA Regulations on Protein Evolutionary Rate

Trees-Juen Chuang, Tai-Wei Chiang, 2014, Genome biology and evolution.

Plant Gene and Alternatively Spliced Variant Annotator. A Plant Genome Annotation Pipeline for Rice Gene and Alternatively Spliced Variant Identification with Cross-Species Expressed Sequence Tag Conservation from Seven Plant Species1[W][OA]

Feng-Chi Chen, Trees-Juen Chuang, S. Chaw, 2007, Plant Physiology.

Detecting intragenic trans-splicing events with hybrid transcriptome sequencing in cancer cells

Trees-Juen Chuang, Isheng. J. Tsai, Chia-Ying Chen, 2022, bioRxiv.

Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells

Trees-Juen Chuang, Yu-Ting Hsiao, Yen-Ju Chen, 2018, Nucleic acids research.

Biogenesis, identification, and function of exonic circular RNAs

Trees-Juen Chuang, Chia-Ying Chen, I. Chen, 2015, Wiley interdisciplinary reviews. RNA.

Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Trees-Juen Chuang, Chia-Ying Chen, Wei-Cheng Cheng, 2019, Acta Neuropathologica Communications.

Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?

Trees-Juen Chuang, Hung-Chih Kuo, Chun-Ying Yu, 2014, Nucleic acids research.

A complexity reduction algorithm for analysis and annotation of large genomic sequences.

Trees-Juen Chuang, Lan-Yang Ch'ang, Simon C. Lin, 2003, Genome research.

Purifying selection shapes the coincident SNP distribution of primate coding sequences

Trees-Juen Chuang, Chia-Ying Chen, Chan-Shuo Wu, 2016, Scientific Reports.

An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species

Trees-Juen Chuang, Yen-Ju Chen, Chia-Ying Chen, 2017, Genome biology and evolution.

Selective Constraint on Human Pre-mRNA Splicing by Protein Structural Properties

Feng-Chi Chen, Trees-Juen Chuang, A. D. de Brevern, 2012, Genome biology and evolution.

CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species

Trees-Juen Chuang, Te-Lun Mai, Tai-Wei Chiang, 2022, BMC Bioinform..

DNA Methylation is Associated with an Increased Level of Conservation at Nondegenerate Nucleotides in Mammals

Feng-Chi Chen, Trees-Juen Chuang, 2013, Molecular biology and evolution.

A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations

Trees-Juen Chuang, Te-Lun Mai, 2019, Genome Research.

Nonsynonymous A-to-I RNA editing contributes to burden of deleterious missense variants in healthy individuals

Trees-Juen Chuang, Te-Lun Mai, 2018 .

Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios

Trees-Juen Chuang, Chia-Ying Chen, Yi-Da Wang, 2017, Scientific Reports.

Alternatively and constitutively spliced exons are subject to different evolutionary forces.

Feng-Chi Chen, Wen-Hsiung Li, Trees-Juen Chuang, 2006, Molecular biology and evolution.

comparisons inferred from cross-species transcript and processed pseudogene Identification and analysis of ancestral hominoid transcriptome Material

Feng-Chi Chen, Trees-Juen Chuang, Yao-Ting Huang, 2008 .

Trans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism

Trees-Juen Chuang, Chia-Ying Chen, Te-Lun Mai, 2021, Molecular Psychiatry.

Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants

Trees-Juen Chuang, Min-Yu Yang, P. Hsieh, 2015, BMC Plant Biology.

Gene Family Size Conservation Is a Good Indicator of Evolutionary Rates

Feng-Chi Chen, Wen-Hsiung Li, Trees-Juen Chuang, 2010, Molecular biology and evolution.

PGAA: a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species EST conservation from seven plant species

Feng-Chi Chen, Trees-Juen Chuang, S. Chaw, 2007 .

Human p16γ, a novel transcriptional variant of p16INK4A, coexpresses with p16INK4A in cancer cells and inhibits cell-cycle progression

Trees-Juen Chuang, A. Yang, M. Tsai, 2007, Oncogene.

Human p16gamma, a novel transcriptional variant of p16(INK4A), coexpresses with p16(INK4A) in cancer cells and inhibits cell-cycle progression.

Trees-Juen Chuang, A. Yang, M. Tsai, 2007, Oncogene.

Evolutionary expansion of SPOP and associated TD/POZ gene family: impact of evolutionary route on gene expression pattern.

Trees-Juen Chuang, K. Choo, Chiu-Jung Huang, 2010, Gene.

The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate.

Wen-Hsiung Li, Trees-Juen Chuang, Sean Chun-Chang Chen, 2011, Molecular biology and evolution.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat

Trees-Juen Chuang, Feng-Chi Chen, Chuang-Jong Chen, 2006, BMC Bioinformatics.

LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs

Feng-Chi Chen, Trees-Juen Chuang, Yao-Ting Huang, 2012, BMC Research Notes.

NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors

Trees-Juen Chuang, Chia-Ying Chen, Trees-Juen Chuang, 2019, BMC Bioinformatics.

Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons.

Trees-Juen Chuang, Feng-Chi Chen, Feng-Chi Chen, 2008, Genome research.

Nucleotide Sequence Divergence between Humans and Chimpanzees

Feng-Chi Chen, Trees-Juen Chuang, 2008 .

Assessing the impacts of various factors on circular RNA reliability

Trees-Juen Chuang, Chia-Ying Chen, Tai-Wei Chiang, 2023, Life Science Alliance.

Assessing the impacts of various factors related to identification, conservation, biogenesis, and function on circular RNA reliability

Trees-Juen Chuang, Chia-Ying Chen, Tai-Wei Chiang, 2022, bioRxiv.

Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Trees-Juen Chuang, Chia-Ying Chen, Lien-Szu Wu, 2019, Acta neuropathologica communications.

The evolution of the coding exome of the Arabidopsis species - the influences of DNA methylation, relative exon position, and exon length

Feng-Chi Chen, Trees-Juen Chuang, Min-Kung Hsu, 2014, BMC Evolutionary Biology.

The effects of multiple features of alternatively spliced exons on the KA/KS ratio test

Trees-Juen Chuang, Feng-Chi Chen, Feng-Chi Chen, 2006, BMC Bioinformatics.

Comparative Analyses of Single-Cell Transcriptomic Profiles between In Vitro Totipotent Blastomere-like Cells and In Vivo Early Mouse Embryonic Cells

Trees-Juen Chuang, Chia-Ying Chen, S. C. Schuyler, 2021, Cells.

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

Osagie G. Izuogu, P. Flicek, P. Stadler, 2022, bioRxiv.

Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation

Feng-Chi Chen, Trees-Juen Chuang, 2007, BMC Evolutionary Biology.

Opposite evolutionary effects between different alternative splicing patterns.

Trees-Juen Chuang, Feng-Chi Chen, Sheng-Shun Wang, 2007, Molecular biology and evolution.

CNVVdb: a database of copy number variations across vertebrate genomes

Trees-Juen Chuang, Feng-Chi Chen, Yen-Zho Chen, 2009, Bioinform..

Hematopoietic Transfer of the Anti-Cancer and Lifespan-Extending Capabilities of A Genetically Engineered Blood System

Trees-Juen Chuang, Jing-Ping Wang, Liuh-Yow Chen, 2023, bioRxiv.

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

Osagie G. Izuogu, P. Flicek, P. Stadler, 2023, bioRxiv.

CAPIH: A Web interface for comparative analyses and visualization of host-HIV protein-protein interactions

Trees-Juen Chuang, Fan-Kai Lin, Feng-Chi Chen, 2009, BMC Microbiology.

Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing

Trees-Juen Chuang, Isheng. J. Tsai, Chia-Ying Chen, 2023, Nucleic acids research.

NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors

Trees-Juen Chuang, Chia-Ying Chen, 2019, BMC Bioinformatics.

Comment on "A comprehensive overview and evaluation of circular RNA detection tools"

Trees-Juen Chuang, Chia-Ying Chen, Trees-Juen Chuang, 2019, PLoS Comput. Biol..

FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing

Trees-Juen Chuang, Chia-Ying Chen, Tai-Wei Chiang, 2023, Nucleic acids research.

Bioinformatics Applications Note Estviewer: a Web Interface for Visualizing Mouse, Rat, Cattle, Pig and Chicken Conserved Ests in Human Genes and Human Alternatively Spliced Variants

Feng-Chi Chen, Trees-Juen Chuang, 2022 .

A comparative method for identification of gene structures and alternatively spliced variants

Trees-Juen Chuang, Feng-Chi Chen, Meng-Yuan Chou, 2004, Bioinform..

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

Trees-Juen Chuang, Chia-Ying Chen, Tai-Wei Chiang, 2024, Acta neuropathologica communications.

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

Trees-Juen Chuang, Jing-Ping Wang, Liuh-Yow Chen, 2024, bioRxiv.