Jung Kyoon Choi

Summary

Publications

  1. pmc Genome-wide reorganization of histone H2AX toward particular fragile sites on cell activation
    Jungmin Seo
    Research Institute of Bioinformatics, Omicsis, Inc, Daejeon 305 333, Korea, Department of Bio and Brain Engineering, KAIST, Daejeon 305 701, Korea, Graduate School of Medical Science and Engineering, KAIST, Daejeon 305 701, Korea, Medical Genomics Research Center, KRIBB, Daejeon 305 333, Korea and Department of Life Science, Ewha Womans University, Seoul 120 750, Korea
    Nucleic Acids Res 42:1016-25. 2014
  2. pmc Nucleosome deposition and DNA methylation at coding region boundaries
    Jung Kyoon Choi
    Department of Biochemistry, College of Life Science and Technology, Yonsei University, 134 Sinchon dong, Seodaemun gu, Seoul, Korea
    Genome Biol 10:R89. 2009
  3. doi request reprint Systems biology and epigenetic gene regulation
    J K Choi
    KAIST, Department of Bio and Brain Engineering, Daejeon, Republic of Korea
    IET Syst Biol 4:289-95. 2010
  4. pmc Contrasting chromatin organization of CpG islands and exons in the human genome
    Jung Kyoon Choi
    Department of Biology and Brain Engineering, KAIST, 335 Gwahak ro, Daejeon 305 701, Republic of Korea
    Genome Biol 11:R70. 2010
  5. pmc Environmental effects on gene expression phenotype have regional biases in the human genome
    Jung Kyoon Choi
    Korean BioInformation Center, KRIBB, Yooseong goo, Daejeon, 305 806, Korea
    Genetics 175:1607-13. 2007
  6. pmc Genetic landscape of open chromatin in yeast
    Kibaick Lee
    Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
    PLoS Genet 9:e1003229. 2013
  7. ncbi request reprint Differential coexpression analysis using microarray data and its application to human cancer
    Jung Kyoon Choi
    National Genome Information Center, Korea Research Institute of Bioscience and Biotechnology, 52 Ueun dong, Yuseong Gu, Daejeon, Korea
    Bioinformatics 21:4348-55. 2005
  8. doi request reprint Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development
    Yu Mi Woo
    Department of Biological Science, Sookmyung Women s University, Seoul, 140 742, Korea
    Hum Genet 133:281-97. 2014
  9. doi request reprint Epigenetic regulation and the variability of gene expression
    Jung Kyoon Choi
    Genome Regulation Center, Yonsei University, 134 Sinchon dong, Seodaemun gu, Seoul 120 749, Korea
    Nat Genet 40:141-7. 2008
  10. ncbi request reprint Microarray analysis of the gene expression profiles of SL2 cells stimulated by LPS/PGN and curdlan
    Li Hua Jin
    Department of Biochemistry, Yonsei University, Seoul 120 749, Korea
    Mol Cells 25:553-8. 2008

Collaborators

Detail Information

Publications22

  1. pmc Genome-wide reorganization of histone H2AX toward particular fragile sites on cell activation
    Jungmin Seo
    Research Institute of Bioinformatics, Omicsis, Inc, Daejeon 305 333, Korea, Department of Bio and Brain Engineering, KAIST, Daejeon 305 701, Korea, Graduate School of Medical Science and Engineering, KAIST, Daejeon 305 701, Korea, Medical Genomics Research Center, KRIBB, Daejeon 305 333, Korea and Department of Life Science, Ewha Womans University, Seoul 120 750, Korea
    Nucleic Acids Res 42:1016-25. 2014
    ..Our findings suggest that active DNA replication is accompanied with the specific localization of H2AX and INO80 for efficient damage repair or replication-fork stabilization in actively transcribed regions. ..
  2. pmc Nucleosome deposition and DNA methylation at coding region boundaries
    Jung Kyoon Choi
    Department of Biochemistry, College of Life Science and Technology, Yonsei University, 134 Sinchon dong, Seodaemun gu, Seoul, Korea
    Genome Biol 10:R89. 2009
    ..Nucleosome deposition downstream of transcription initiation and DNA methylation in the gene body suggest that control of transcription elongation is a key aspect of epigenetic regulation...
  3. doi request reprint Systems biology and epigenetic gene regulation
    J K Choi
    KAIST, Department of Bio and Brain Engineering, Daejeon, Republic of Korea
    IET Syst Biol 4:289-95. 2010
    ....
  4. pmc Contrasting chromatin organization of CpG islands and exons in the human genome
    Jung Kyoon Choi
    Department of Biology and Brain Engineering, KAIST, 335 Gwahak ro, Daejeon 305 701, Republic of Korea
    Genome Biol 11:R70. 2010
    ..Intragenic nucleosomes and their modifications have been recently associated with RNA splicing. Because the function of intragenic DNA methylation remains unclear, I explored the possibility of its involvement in splicing regulation...
  5. pmc Environmental effects on gene expression phenotype have regional biases in the human genome
    Jung Kyoon Choi
    Korean BioInformation Center, KRIBB, Yooseong goo, Daejeon, 305 806, Korea
    Genetics 175:1607-13. 2007
    ....
  6. pmc Genetic landscape of open chromatin in yeast
    Kibaick Lee
    Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
    PLoS Genet 9:e1003229. 2013
    ..Our findings provide a global quantitative picture of the genetic architecture of chromatin regulation...
  7. ncbi request reprint Differential coexpression analysis using microarray data and its application to human cancer
    Jung Kyoon Choi
    National Genome Information Center, Korea Research Institute of Bioscience and Biotechnology, 52 Ueun dong, Yuseong Gu, Daejeon, Korea
    Bioinformatics 21:4348-55. 2005
    ..However, alteration in coexpression relationships has not been studied. Here we introduce a model for finding differential coexpression from microarrays and test its biological validity with respect to cancer...
  8. doi request reprint Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development
    Yu Mi Woo
    Department of Biological Science, Sookmyung Women s University, Seoul, 140 742, Korea
    Hum Genet 133:281-97. 2014
    ..Therefore, our results reveal a critical role for hypermethylation of PKD1 and cystogenesis-related regulatory genes in cyst development, suggesting epigenetic therapy as a potential treatment for ADPKD. ..
  9. doi request reprint Epigenetic regulation and the variability of gene expression
    Jung Kyoon Choi
    Genome Regulation Center, Yonsei University, 134 Sinchon dong, Seodaemun gu, Seoul 120 749, Korea
    Nat Genet 40:141-7. 2008
    ..The lack of activating histone modifications may subject TATA-containing promoters to chromatin regulation processes. Our results propose that epigenetic regulation has a central role in the variation and evolution of gene expression...
  10. ncbi request reprint Microarray analysis of the gene expression profiles of SL2 cells stimulated by LPS/PGN and curdlan
    Li Hua Jin
    Department of Biochemistry, Yonsei University, Seoul 120 749, Korea
    Mol Cells 25:553-8. 2008
    ....
  11. pmc Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes
    Jung Kyoon Choi
    Department of Biochemistry, Yonsei University, Seoul, Republic of Korea
    PLoS ONE 3:e3002. 2008
    ..These results propose modulation of chromatin stability as an important determinant of environmental adaptation and cellular differentiation...
  12. doi request reprint Controlling transcriptional programs for cellular adaptation by chromatin regulation
    Sang Cheol Kim
    Korean BioInformation Center, KRIBB, Daejeon 305 701, Korea
    Mol Biosyst 7:1713-9. 2011
    ..These regulatory mechanisms can also contribute to evolutionary adaptation...
  13. pmc Identification of DNA methylation changes associated with human gastric cancer
    Jung Hoon Park
    Department of Biochemistry, College of Life Science and Technology, Yonsei University, Seoul, Korea
    BMC Med Genomics 4:82. 2011
    ..Epigenetic alteration of gene expression is a common event in human cancer. DNA methylation is a well-known epigenetic process, but verifying the exact nature of epigenetic changes associated with cancer remains difficult...
  14. pmc Impact of transcriptional properties on essentiality and evolutionary rate
    Jung Kyoon Choi
    Korean BioInformation Center, KRIBB, Daejeon 305 806, Korea
    Genetics 175:199-206. 2007
    ..Transcriptional variability, rather than transcriptional activity, might be a common indicator of essentiality and evolutionary rate, contributing to the correlation between the two variables...
  15. ncbi request reprint Integrative analysis of multiple gene expression profiles applied to liver cancer study
    Jung Kyoon Choi
    National Genome Information Center, Korea Research Institute of Biosciences and Biotechnology, Daejeon, Republic of Korea
    FEBS Lett 565:93-100. 2004
    ..Our findings support the use of meta-analysis for a variety of microarray data beyond the scope of this specific application...
  16. doi request reprint Intrinsic variability of gene expression encoded in nucleosome positioning sequences
    Jung Kyoon Choi
    Department of Biochemistry, Yonsei University, Seodaemun gu, Seoul, Korea
    Nat Genet 41:498-503. 2009
    ..This is a unique example of how promoter sequences intrinsically encode regulatory flexibility, which is vital for biological processes such as adaptation, development and evolution...
  17. ncbi request reprint Implications of the nucleosome code in regulatory variation, adaptation and evolution
    Jung Kyoon Choi
    Department of Biochemistry, Yonsei University, Seoul, Korea
    Epigenetics 4:291-5. 2009
    ..This is supported by the observation that the relevant nucleosome codes in the genomes of yeast species reflect their phylogenetic relationships...
  18. ncbi request reprint TO-GO: a Java-based Gene Ontology navigation environment
    Ungsik Yu
    National Genome Information Center, KRIBB, Oun 52, Yusong, Daejeon 305 333, Korea
    Bioinformatics 21:3580-1. 2005
    ..A copy/paste function is also implemented in order to facilitate data exchange between applications...
  19. ncbi request reprint HBx induces hypomethylation of distal intragenic CpG islands required for active expression of developmental regulators
    Sun Min Lee
    Department of Biochemistry, College of Life Science and Technology, Yonsei University, Seoul 120 749, Korea
    Proc Natl Acad Sci U S A 111:9555-60. 2014
    ..Here we provide an intriguing epigenetic regulation mediated by mCGI that is required for cell differentiation and describe a previously unidentified epigenetic role for HBx in promoting HCC development. ..
  20. pmc Genome-wide profiles of H2AX and γ-H2AX differentiate endogenous and exogenous DNA damage hotspots in human cells
    Jungmin Seo
    Research Institute of Bioinformatics, Omicsis, Inc, BVC, KRIBB, Daejeon 305 333, Korea
    Nucleic Acids Res 40:5965-74. 2012
    ..Sub-telomeres were less responsive to external DNA damage than to endogenous stress. Our findings provide insight into DNA repair programs of cancer and may have implications for cancer therapy...
  21. pmc Requirement of Split ends for epigenetic regulation of Notch signal-dependent genes during infection-induced hemocyte differentiation
    Li Hua Jin
    Department of Biochemistry, Yonsei University, Seoul, Republic of Korea
    Mol Cell Biol 29:1515-25. 2009
    ..Our observations reveal a novel connection between the Notch and Toll/IMD signaling pathways and demonstrate a coactivating role for Spen in activating Notch-dependent genes in differentiating cells...
  22. ncbi request reprint Combining multiple microarray studies and modeling interstudy variation
    Jung Kyoon Choi
    Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 371 1 Guseong dong Yuseong gu, Daejeon 305 701, Korea
    Bioinformatics 19:i84-90. 2003
    ..We also developed an alternative modeling procedure based on a Bayesian approach, which would offer flexibility and robustness compared to the classical procedure...