Trees Juen Chuang

Summary

Affiliation: Academia Sinica
Country: Taiwan

Publications

  1. pmc The impact of trans-regulation on the evolutionary rates of metazoan proteins
    Yi Ching Chen
    Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
    Nucleic Acids Res 41:6371-80. 2013
  2. ncbi request reprint Impacts of Pretranscriptional DNA Methylation, Transcriptional Transcription Factor, and Posttranscriptional microRNA Regulations on Protein Evolutionary Rate
    Trees Juen Chuang
    Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Genome Biol Evol 6:1530-41. 2014
  3. doi request reprint DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals
    Trees Juen Chuang
    Physical and Computational Genomics Division, Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Mol Biol Evol 31:387-96. 2014
  4. pmc INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, National Health Research Institute, Miaoli County 350, Taiwan
    Nucleic Acids Res 35:W633-8. 2007
  5. pmc CNVVdb: a database of copy number variations across vertebrate genomes
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taipei, Taiwan
    Bioinformatics 25:1419-21. 2009
  6. pmc Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons
    Trees Juen Chuang
    Physical and Computational Genomics Division, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
    Proc Natl Acad Sci U S A 109:15841-6. 2012
  7. ncbi request reprint 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
    Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
    Bioinformatics 21:2510-3. 2005
  8. pmc Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat
    Feng Chi Chen
    Genomics Research Center, Academia Sinica, Academia Road, Nankang, Taipei 11529, Taiwan
    BMC Bioinformatics 7:136. 2006
  9. ncbi request reprint A comparative method for identification of gene structures and alternatively spliced variants
    Trees Juen Chuang
    Genomics Research Center, Academia, Sinica, Taipei, Taiwan
    Bioinformatics 20:3064-79. 2004
  10. pmc Gene family size conservation is a good indicator of evolutionary rates
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
    Mol Biol Evol 27:1750-8. 2010

Collaborators

Detail Information

Publications24

  1. pmc The impact of trans-regulation on the evolutionary rates of metazoan proteins
    Yi Ching Chen
    Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
    Nucleic Acids Res 41:6371-80. 2013
    ....
  2. ncbi request reprint Impacts of Pretranscriptional DNA Methylation, Transcriptional Transcription Factor, and Posttranscriptional microRNA Regulations on Protein Evolutionary Rate
    Trees Juen Chuang
    Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Genome Biol Evol 6:1530-41. 2014
    ....
  3. doi request reprint DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals
    Trees Juen Chuang
    Physical and Computational Genomics Division, Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Mol Biol Evol 31:387-96. 2014
    ..In addition, the positive correlation between CpG methylation and the level of conservation at zero-fold degenerate nucleotides implies that CpG methylation may serve as an "indicator" of functional importance of these nucleotides. ..
  4. pmc INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, National Health Research Institute, Miaoli County 350, Taiwan
    Nucleic Acids Res 35:W633-8. 2007
    ..The server also provides analytic figures and supports indel identification from user-uploaded alignments/annotations. INDELSCAN is freely accessible at http://indelscan.genomics.sinica.edu.tw/IndelScan/...
  5. pmc CNVVdb: a database of copy number variations across vertebrate genomes
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taipei, Taiwan
    Bioinformatics 25:1419-21. 2009
    ..With the combination of CNV, SNP, pseudogene and functional information, CNVVdb can be very useful for comparative and functional studies in vertebrates...
  6. pmc Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons
    Trees Juen Chuang
    Physical and Computational Genomics Division, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
    Proc Natl Acad Sci U S A 109:15841-6. 2012
    ..The first exons appear more prone to the mutagenic effects, whereas the other exons are more influenced by the regulatory effects of DNA methylation...
  7. ncbi request reprint 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
    Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
    Bioinformatics 21:2510-3. 2005
    ..The percentages of the UCSC, Vega and PSEP annotated exons covered by ESTs of the six studied species are also displayed in the interface...
  8. pmc Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat
    Feng Chi Chen
    Genomics Research Center, Academia Sinica, Academia Road, Nankang, Taipei 11529, Taiwan
    BMC Bioinformatics 7:136. 2006
    ..However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult to study AS evolution in mammals and its biomedical implications...
  9. ncbi request reprint A comparative method for identification of gene structures and alternatively spliced variants
    Trees Juen Chuang
    Genomics Research Center, Academia, Sinica, Taipei, Taiwan
    Bioinformatics 20:3064-79. 2004
    ..Increasing evidence indicates that a large portion of genes have AS forms. Hence AS variants should be considered while analyzing gene structures...
  10. pmc Gene family size conservation is a good indicator of evolutionary rates
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
    Mol Biol Evol 27:1750-8. 2010
    ..Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes...
  11. pmc A complexity reduction algorithm for analysis and annotation of large genomic sequences
    Trees Juen Chuang
    Bioinformatics Research Center, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
    Genome Res 13:313-22. 2003
    ..With its large-scale processing capability, CRASA can be used as a robust tool for genome annotation with high accuracy by matching the EST sequences precisely to the genomic sequences...
  12. pmc The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test
    Feng Chi Chen
    Genomics Research Center, Academia Sinica, Academia Road, Nankang, Taipei 11529, Taiwan
    BMC Bioinformatics 7:259. 2006
    ..Furthermore, which exon feature dominates the results of the KA/KS ratio test and whether multiple exon features have additive effects have remained unexplored...
  13. pmc 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 species
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, National Health Research Institute, Miaoli County 350, Taiwan
    Plant Physiol 143:1086-95. 2007
    ..The data and the Web-based interface, RiceViewer, are available for public access at http://RiceViewer.genomics.sinica.edu.tw/...
  14. ncbi request reprint Alternatively and constitutively spliced exons are subject to different evolutionary forces
    Feng Chi Chen
    Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Mol Biol Evol 23:675-82. 2006
    ..The overall trends of higher KA and lower KS in ASEs than in CSEs are also observed in human-rat and mouse-rat comparisons. Therefore, our observations hold for mammals of different molecular clocks...
  15. pmc Human-specific insertions and deletions inferred from mammalian genome sequences
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, National Health Research Institute, Miaoli County 350, Taiwan
    Genome Res 17:16-22. 2007
    ..This functional bias suggests that human-specific indels might have contributed to human unique traits by causing changes at the RNA and protein level...
  16. pmc LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs
    Ming Chih Wang
    Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
    BMC Res Notes 5:212. 2012
    ..A user-friendly web resource that integrates information about non-physical SNP linkages, gene annotations, SNP information, and SNP-disease associations may thus be a good reference for biomedical research...
  17. pmc The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate
    Sean Chun Chang Chen
    Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan
    Mol Biol Evol 28:2513-20. 2011
    ..Our study reveals the relative strength of each rate indicator and increases our understanding of protein evolution...
  18. pmc A novel framework for the identification and analysis of duplicons between human and chimpanzee
    Trees Juen Chuang
    Genomics Research Center, Academia Sinica, Taipei, Taiwan
    Biomed Res Int 2013:264532. 2013
    ..Phylogenetic analyses using duplicons suggested that most CNVs/SDs share common duplication ancestry. Many human/chimpanzee duplicons flank both ends of CNVs, which may be hotspots of nonallelic homologous recombination. ..
  19. pmc Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, National Health Research Institutes, Miaoli County 350, Taiwan
    BMC Evol Biol 7:179. 2007
    ..Therefore, it is necessary to re-evaluate the evolutionary effects of such splicing patterns on frame preservation...
  20. pmc Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
    Yao Ting Huang
    Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
    Genome Res 18:1163-70. 2008
    ....
  21. ncbi request reprint Evolutionary expansion of SPOP and associated TD/POZ gene family: impact of evolutionary route on gene expression pattern
    Kong Bung Choo
    Department of Medical Research and Education, Taipei Veterans General Hospital, Shipai, Taipei, Taiwan
    Gene 460:39-47. 2010
    ....
  22. pmc CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions
    Fan Kai Lin
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350 Taiwan, Republic of China
    BMC Microbiol 9:164. 2009
    ..However, the differences in host-HIV-1 interactions between human and these model organisms have remained unexplored...
  23. ncbi request reprint The evolution of the coding exome of the Arabidopsis species--the influences of DNA methylation, relative exon position, and exon length
    Feng Chi Chen
    Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
    BMC Evol Biol 14:145. 2014
    ..Importantly, the evolutionary effects of these intrinsic/extrinsic features may differ significantly between animals and plants. Such inter-lineage differences, however, have not been systematically examined...
  24. pmc Scanning for the signatures of positive selection for human-specific insertions and deletions
    Chun Hsi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
    Genome Biol Evol 2009:415-9. 2009
    ..Our results suggest that HS indels may have been associated with human adaptive changes at both the species level and the subpopulation level...