Feng Chi Chen

Summary

Affiliation: National Health Research Institutes
Country: Taiwan

Publications

  1. 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
  2. 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
  3. pmc Selective constraint on the upstream open reading frames that overlap with coding sequences in animals
    Ming Kung Hsu
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
    PLoS ONE 7:e48413. 2012
  4. pmc Determinants of exon-level evolutionary rates in Arabidopsis species
    Gideon C T Wu
    Graduate Institute of Life Sciences, National Defense Medical Center, 114 Taiwan
    Evol Bioinform Online 8:389-415. 2012
  5. ncbi request reprint Assessing determinants of exonic evolutionary rates in mammals
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan, Republic of China
    Mol Biol Evol 29:3121-9. 2012
  6. 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
  7. doi request reprint Independent effects of alternative splicing and structural constraint on the evolution of mammalian coding exons
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan, Republic of China
    Mol Biol Evol 29:187-93. 2012
  8. pmc A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    BMC Syst Biol 5:8. 2011
  9. 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
  10. pmc The plausible reason why the length of 5' untranslated region is unrelated to organismal complexity
    Chun Hsi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, 350 Taiwan
    BMC Res Notes 4:312. 2011

Collaborators

Detail Information

Publications33

  1. 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...
  2. 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...
  3. pmc Selective constraint on the upstream open reading frames that overlap with coding sequences in animals
    Ming Kung Hsu
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
    PLoS ONE 7:e48413. 2012
    ..Nevertheless, once the functions of VuORFs were established, they became subject to negative selection...
  4. pmc Determinants of exon-level evolutionary rates in Arabidopsis species
    Gideon C T Wu
    Graduate Institute of Life Sciences, National Defense Medical Center, 114 Taiwan
    Evol Bioinform Online 8:389-415. 2012
    ..Furthermore, the relative importance of different exon features also differs between plants and animals. Our study thus may shed a new light on the evolution of plant genes...
  5. ncbi request reprint Assessing determinants of exonic evolutionary rates in mammals
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan, Republic of China
    Mol Biol Evol 29:3121-9. 2012
    ....
  6. 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...
  7. doi request reprint Independent effects of alternative splicing and structural constraint on the evolution of mammalian coding exons
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan, Republic of China
    Mol Biol Evol 29:187-93. 2012
    ..Our results imply that nature can select for different biological features with regard to ASEs and IDRs, even though the two biological features tend to be localized in the same protein regions...
  8. pmc A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
    Ines Thiele
    Center for Systems Biology, University of Iceland, Reykjavik, Iceland
    BMC Syst Biol 5:8. 2011
    ..Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem...
  9. 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...
  10. pmc The plausible reason why the length of 5' untranslated region is unrelated to organismal complexity
    Chun Hsi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, 350 Taiwan
    BMC Res Notes 4:312. 2011
    ..abstract:..
  11. 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...
  12. 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...
  13. 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...
  14. 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
    ....
  15. 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/...
  16. pmc The genomic features that affect the lengths of 5' untranslated regions in multicellular eukaryotes
    Chun Hsi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, 350 Taiwan, Republic of China
    BMC Bioinformatics 12:S3. 2011
    ..Furthermore, different selective constraints between vertebrates and invertebrates may lead to differences in the determinants of 5'UTR length, which have not been systematically analyzed...
  17. doi request reprint GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization
    Yu Chieh Liao
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan, R O C
    Bioinformatics 28:1752-8. 2012
    ..Although some of the required functions have been served separately by existing tools, a free software resource that simultaneously serves the needs of the three major components is not yet available...
  18. 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...
  19. 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/...
  20. 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...
  21. doi request reprint MrBac: a web server for draft metabolic network reconstructions for bacteria
    Yu Chieh Liao
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan
    Bioeng Bugs 2:284-7. 2011
    ..The high efficiency and accuracy of MrBac may accelerate the advances of systems biology studies on microbiology. MrBac is freely available at http://sb.nhri.org.tw/MrBac...
  22. pmc An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228
    Yu Chieh Liao
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan
    J Bacteriol 193:1710-7. 2011
    ..The genome-scale metabolic reconstruction for K. pneumoniae presented here thus provides an experimentally validated in silico platform for further studies of this important industrial and biomedical organism...
  23. 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...
  24. ncbi request reprint Pros and cons of the tuberculosis drugome approach - an empirical analysis
    Feng Chi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan Department of Life Sciences, National Chiao Tung University, Hsinchu, Taiwan Department of Dentistry, China Medical University, Taichung, Taiwan
    PLoS ONE 9:e100829. 2014
    ..Our findings can also be extended to other structure-based drug repositioning methods. ..
  25. pmc Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals
    Sean Chun Chang Chen
    Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan
    Mol Biol Evol 27:2548-54. 2010
    ..We also find that the human lineage has gained more phosphorylated T residues and lost fewer phosphorylated Y residues than the mouse lineage. The cause of the gain/loss imbalance remains a mystery but should be worth exploring...
  26. pmc Exploring the selective constraint on the sizes of insertions and deletions in 5' untranslated regions in mammals
    Chun Hsi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, 350 Taiwan
    BMC Evol Biol 11:192. 2011
    ..The presence of non-3n indels in uORFs can potentially disrupt the functions of these regulatory elements. We thus hypothesize that natural selection disfavors non-3n indels in 5'UTRs when these regulatory elements are present...
  27. 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...
  28. pmc Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes
    Chieh Hua Lin
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35 Keyen Road, Zhunan Town, Miaoli County, Taiwan, Republic of China
    BMC Bioinformatics 12:S19. 2011
    ..Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes...
  29. doi request reprint The evolutionary landscape of the Mycobacterium tuberculosis genome
    Tai Chun Wang
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35 Keyen Road, Zhunan, Miaoli County, 350 Taiwan
    Gene 518:187-93. 2013
    ..Importantly, our results indicate that selection on synonymous substitutions is common in the M. tuberculosis genome. Therefore, the dN/dS ratio test must be applied carefully for measuring selection pressure on M. tuberculosis genes...
  30. ncbi request reprint Opposite evolutionary effects between different alternative splicing patterns
    Feng Chi Chen
    Mol Biol Evol 24:1443-6. 2007
    ..Therefore, the previous view that ASEs accelerate evolution of protein subsequences needs to be modified...
  31. 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...
  32. 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...