Feng Chi Chen

Summary

Affiliation: National Health Research Institutes
Country: Taiwan

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi 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
  10. ncbi 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

Collaborators

  • Trees Juen Chuang
  • Ben Yang Liao
  • Yao Ting Huang
  • Wen Hsiung Li
  • Jinn Moon Yang
  • Fan Kai Lin
  • Shu Miaw Chaw
  • Chun Hsi Chen
  • Yu Chieh Liao
  • Chao A Hsiung
  • Ming Chih Wang
  • Chieh Hua Lin
  • Ines Thiele
  • Chia Lin Pan
  • Bernhard O Palsson
  • Hsuan Yu Lin
  • Pep Charusanti
  • Sean Chun Chang Chen
  • Yen Zho Chen
  • Ming Hsin Tsai
  • Inge M Thijs
  • Chun Yi Lian
  • Tzu Wen Huang
  • Yueh Hsia Tang
  • Anu Raghunathan
  • Sook Il Shin
  • Monica L Mo
  • Daniel R Hyduke
  • Benjamin Steeb
  • Neil Swainston
  • Susanna Bazzani
  • Jay S J Hong
  • Kathleen Marchal
  • Suresh Sudarsan
  • Hwan You Chang
  • Jennifer L Reed
  • Sigrid C J De Keersmaecker
  • Min Hsin Tsai
  • Douglas K Allen
  • Jonas Steinmann
  • Karsten Zengler
  • Chao Agnes Hsiung
  • Emre Ozdemir
  • Ronan M T Fleming
  • Julie Chih Yu Chen
  • Dirk Bumann
  • Sara Sigurbjörnsdóttir
  • Guy Fankam
  • Shih Feng Tsai
  • Joshua N Adkins

Detail Information

Publications27

  1. ncbi 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
    ....
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi 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...
  5. ncbi 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...
  6. ncbi 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:..
  7. ncbi 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...
  8. ncbi 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...
  9. ncbi 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...
  10. ncbi 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
    ....
  11. ncbi 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/...
  12. ncbi 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/...
  13. ncbi 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...
  14. ncbi 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...
  15. ncbi 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...
  16. ncbi 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...
  17. ncbi 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...
  18. ncbi 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...
  19. ncbi 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...
  20. ncbi 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
    ..AVAILABILITY: CNVVdb is freely accessible at (http://CNVVdb.genomics.sinica.edu.tw)...
  21. ncbi 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...
  22. ncbi 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...
  23. ncbi 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...
  24. ncbi 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...
  25. ncbi 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...
  26. ncbi 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...
  27. ncbi 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
    ..With its dual functions in cross-species conserved sequence analysis and AS analysis, PSEP is highly suitable for studying the evolution of AS patterns and for finding unidentified gene expression features...