Seon Young Kim

Summary

Affiliation: Korea Research Institute of Bioscience and Biotechnology
Country: Korea

Publications

  1. pmc Effects of sample size on robustness and prediction accuracy of a prognostic gene signature
    Seon Young Kim
    Medical Genomics Research Center, KRIBB, Yuseong Gu, Daejeon, Republic of Korea
    BMC Bioinformatics 10:147. 2009
  2. pmc A known expressed sequence tag, BM742401, is a potent lincRNA inhibiting cancer metastasis
    Seong Min Park
    Medical Genomics Research Center, KRIBB, Daejeon, Republic of Korea
    Exp Mol Med 45:e31. 2013
  3. ncbi request reprint REGNET: mining context-specific human transcription networks using composite genomic information
    Sang Mun Chi
    School of Life Sciences, UNIST, Ulsan, Republic of Korea
    BMC Genomics 15:450. 2014
  4. pmc GENT: Gene Expression Database of Normal and Tumor Tissues
    Gwangsik Shin
    Department of Bio and Information Technology, Graduate School, Chungbuk National University, 410 Seongbong ro, Heungdeok Gu, Cheongju, Chungbuk, 361 763
    Cancer Inform 10:149-57. 2011
  5. pmc MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering
    Eun Youn Kim
    National Institute for Mathematical Sciences NIMS, Yuseong, Daejeon 305 340, Republic of Korea
    BMC Bioinformatics 10:260. 2009
  6. pmc PAGE: parametric analysis of gene set enrichment
    Seon Young Kim
    Molecular Virology Division, St Luke s Roosevelt Hospital Center, Columbia University, New York, NY 10019, USA
    BMC Bioinformatics 6:144. 2005
  7. pmc Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data
    Seon Young Kim
    Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun dong, Yuseong Gu, Daejeon 305 333, Korea
    BMC Bioinformatics 7:330. 2006
  8. pmc A gene sets approach for identifying prognostic gene signatures for outcome prediction
    Seon Young Kim
    Human Genomics Laboratory, Functional Genomics Research Center, KRIBB, Daejeon 305 806, Korea
    BMC Genomics 9:177. 2008
  9. doi request reprint Epigenetic down-regulation and suppressive role of DCBLD2 in gastric cancer cell proliferation and invasion
    Mirang Kim
    Functional Genomics Research Center, KRIBB, Yuseong Gu, Daejeon, Korea
    Mol Cancer Res 6:222-30. 2008
  10. doi request reprint Frequent silencing of popeye domain-containing genes, BVES and POPDC3, is associated with promoter hypermethylation in gastric cancer
    Mirang Kim
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea 305 806
    Carcinogenesis 31:1685-93. 2010

Collaborators

Detail Information

Publications48

  1. pmc Effects of sample size on robustness and prediction accuracy of a prognostic gene signature
    Seon Young Kim
    Medical Genomics Research Center, KRIBB, Yuseong Gu, Daejeon, Republic of Korea
    BMC Bioinformatics 10:147. 2009
    ..One recent study suggested that thousands of samples are needed to generate a robust prognostic gene signature...
  2. pmc A known expressed sequence tag, BM742401, is a potent lincRNA inhibiting cancer metastasis
    Seong Min Park
    Medical Genomics Research Center, KRIBB, Daejeon, Republic of Korea
    Exp Mol Med 45:e31. 2013
    ..Ectopic overexpression of BM742401 inhibited metastasis-related phenotypes and decreased the concentration of extracellular MMP9. These results suggest that BM742401 is a potential lincRNA marker and therapeutic target. ..
  3. ncbi request reprint REGNET: mining context-specific human transcription networks using composite genomic information
    Sang Mun Chi
    School of Life Sciences, UNIST, Ulsan, Republic of Korea
    BMC Genomics 15:450. 2014
    ..We propose an approach for mining context-specific transcription networks from a large collection of gene expression fold-change profiles and composite gene-set information...
  4. pmc GENT: Gene Expression Database of Normal and Tumor Tissues
    Gwangsik Shin
    Department of Bio and Information Technology, Graduate School, Chungbuk National University, 410 Seongbong ro, Heungdeok Gu, Cheongju, Chungbuk, 361 763
    Cancer Inform 10:149-57. 2011
    ..A database with a large sample size would be a great advantage when searching for genes over-expressed in only a subset of patients...
  5. pmc MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering
    Eun Youn Kim
    National Institute for Mathematical Sciences NIMS, Yuseong, Daejeon 305 340, Republic of Korea
    BMC Bioinformatics 10:260. 2009
    ..However, most existing methods focus on clusters with compact shapes and do not reflect the geometric complexity of the high dimensional microarray clusters, which limits their performance...
  6. pmc PAGE: parametric analysis of gene set enrichment
    Seon Young Kim
    Molecular Virology Division, St Luke s Roosevelt Hospital Center, Columbia University, New York, NY 10019, USA
    BMC Bioinformatics 6:144. 2005
    ..GSEA is especially useful when gene expression changes in a given microarray data set is minimal or moderate...
  7. pmc Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data
    Seon Young Kim
    Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun dong, Yuseong Gu, Daejeon 305 333, Korea
    BMC Bioinformatics 7:330. 2006
    ..Studies of genome wide transcriptional networks of human genomes currently lag behind those of yeast...
  8. pmc A gene sets approach for identifying prognostic gene signatures for outcome prediction
    Seon Young Kim
    Human Genomics Laboratory, Functional Genomics Research Center, KRIBB, Daejeon 305 806, Korea
    BMC Genomics 9:177. 2008
    ....
  9. doi request reprint Epigenetic down-regulation and suppressive role of DCBLD2 in gastric cancer cell proliferation and invasion
    Mirang Kim
    Functional Genomics Research Center, KRIBB, Yuseong Gu, Daejeon, Korea
    Mol Cancer Res 6:222-30. 2008
    ..These data suggest that down-regulation of DCBLD2, often associated with promoter hypermethylation, is a frequent event that may be related to the development of gastric cancer...
  10. doi request reprint Frequent silencing of popeye domain-containing genes, BVES and POPDC3, is associated with promoter hypermethylation in gastric cancer
    Mirang Kim
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea 305 806
    Carcinogenesis 31:1685-93. 2010
    ..Knockdown of POPDC3 in SNU-216 cells caused increased cell migration and invasion. Thus, epigenetic inactivation of BVES and POPDC3 occurs frequently in gastric tumors and may promote gastric cancer cell migration and invasion...
  11. ncbi request reprint Integrative genomics analysis reveals the multilevel dysregulation and oncogenic characteristics of TEAD4 in gastric cancer
    Byungho Lim
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon 305 806, Republic of Korea
    Carcinogenesis 35:1020-7. 2014
    ..In conclusion, the multilevel perturbations of TEAD4 at epigenetic, transcriptional and posttranslational levels may contribute to GC development. ..
  12. ncbi request reprint Meta- and gene set analysis of stomach cancer gene expression data
    Seon Young Kim
    Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305 806, Korea
    Mol Cells 24:200-9. 2007
    ..We have incorporated the results of our meta- and gene set analyses into a web accessible database (http://human-genome.kribb.re.kr/stomach/)...
  13. doi request reprint Epigenetic inactivation of protein kinase D1 in gastric cancer and its role in gastric cancer cell migration and invasion
    Mirang Kim
    Medical Genomics Research Center, KRIBB, Daejeon 305 806, Korea
    Carcinogenesis 29:629-37. 2008
    ..Based on these results, we propose that PKD1 is frequently silenced by epigenetic regulation, which plays a role in cell migration and metastasis in gastric cancer...
  14. doi request reprint Aberrant up-regulation of LAMB3 and LAMC2 by promoter demethylation in gastric cancer
    Oh Hyung Kwon
    Medical Genomics Research Center, University of Science and Technology, KRIBB, and Daejeon 305 806, Republic of Korea
    Biochem Biophys Res Commun 406:539-45. 2011
    ..The expression level of LAMB3 affected multiple malignant phenotypes in gastric cancer cell lines. These results suggest that epigenetic activation of LAMB3 and LAMC2 may play an important role in gastric carcinogenesis...
  15. ncbi request reprint Microarray analysis of changes in cellular gene expression induced by productive infection of primary human astrocytes: implications for HAD
    Seon Young Kim
    Molecular Virology Division, St Luke s Roosevelt Hospital Center, 432 West 58th Street, Antenucci Building, Room 709, New York, NY 10019, USA
    J Neuroimmunol 157:17-26. 2004
    ..Our data suggest that HIV-1 expression in astrocytes profoundly alters host cell biology, with potential consequences for the physiological function of astrocytes during HIV-1 infection in the brain...
  16. doi request reprint Overexpression and clinical significance of carcinoembryonic antigen-related cell adhesion molecule 6 in colorectal cancer
    Kwang Soo Kim
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305 806, Republic of Korea
    Clin Chim Acta 415:12-9. 2013
    ..In this study, we analyzed CEACAM6 as a gene that is highly upregulated in colon cancer tissues, and examined the assertion that CEACAM6 might be a suitable candidate tumor marker for the diagnosis of colon cancer...
  17. doi request reprint Epigenetic alteration of CCDC67 and its tumor suppressor function in gastric cancer
    Sung Joon Park
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305 806, Korea
    Carcinogenesis 33:1494-501. 2012
    ..We suggest that CCDC67 is a putative tumor suppressor gene that is silenced in gastric cancers by promoter CpG methylation and that it may play an important role in cell signaling and migration related to tumorigenesis...
  18. doi request reprint Pyruvate kinase M2 promotes the growth of gastric cancer cells via regulation of Bcl-xL expression at transcriptional level
    Oh Hyung Kwon
    Medical Genomics Research Center, KRIBB, Daejeon 305 806, Republic of Korea
    Biochem Biophys Res Commun 423:38-44. 2012
    ..Therefore, PKM2 may function as an upstream molecule that regulates p65 function and thus enhances the growth of tumor cells...
  19. doi request reprint Elevated fibroblast growth factor-inducible 14 expression promotes gastric cancer growth via nuclear factor-κB and is associated with poor patient outcome
    Oh Hyung Kwon
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
    Cancer Lett 314:73-81. 2012
    ..These results suggest that Fn14 may play an important role in gastric tumor growth by regulating NF-κB-mediated anti-apoptosis and that Fn14 may be a useful prognostic marker for gastric cancer...
  20. ncbi request reprint Hepatocellular carcinoma model cell lines with two distinct migration modes
    In Jeong Lee
    Functional Genomics Research Center, Division of Molecular Therapeutics, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305 333, South Korea
    Biochem Biophys Res Commun 346:1217-27. 2006
    ..Thus, HCM1 and HCM4 cells have distinct migration and gene expression patterns, and together with HC9 cells, they can serve as model cell lines for understanding how migration is acquired and controlled in hepatocellular carcinoma...
  21. ncbi request reprint ADGO: analysis of differentially expressed gene sets using composite GO annotation
    Dougu Nam
    Korean BioInformation Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoun Dong Yuseong Gu, Daejeon 305 333, Korea
    Bioinformatics 22:2249-53. 2006
    ..However, current annotations have limited analytical power, because they are classified by single categories providing only unary information for the gene sets...
  22. doi request reprint Identification of potential serum biomarkers for gastric cancer by a novel computational method, multiple normal tissues corrected differential analysis
    Mirang Kim
    Medical Genomics Research Center, KRIBB, Daejeon, Republic of Korea
    Clin Chim Acta 413:428-33. 2012
    ..Genes specifically expressed in one or a few tissues and upregulated in tumors are potentially good serum biomarkers...
  23. ncbi request reprint Epigenetic regulation of microRNA-10b and targeting of oncogenic MAPRE1 in gastric cancer
    Kwoneel Kim
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon, Korea
    Epigenetics 6:740-51. 2011
    ..miR-10b methylation may be a useful molecular biomarker for assessing the risk of gastric cancer development, and modulation of miR-10b may represent a therapeutic approach for treating gastric cancer...
  24. ncbi request reprint Transcriptional regulation of human excitatory amino acid transporter 1 (EAAT1): cloning of the EAAT1 promoter and characterization of its basal and inducible activity in human astrocytes
    Seon Young Kim
    Molecular Virology Division, St Luke s Roosevelt Hospital Center and Columbia University, New York, USA
    J Neurochem 87:1485-98. 2003
    ..Conversely, tumor necrosis factor-alpha reduced both EAAT promoter activity and cellular EAAT1 mRNA expression. These results enable studies of transcriptional regulation of EAAT1 gene at the promoter level...
  25. ncbi request reprint Cloning and characterization of the 3'-untranslated region of the human excitatory amino acid transporter 2 transcript
    Seon Young Kim
    Molecular Virology Division, St Luke s Roosevelt Hospital Center, New York, New York, USA
    J Neurochem 86:1458-67. 2003
    ..The individual fragments varied in their effects on reporter gene expression in human astrocytes by a factor of eight to ten suggesting a complex role of the 3'-UTR in post-transcriptional regulation of EAAT2 gene expression...
  26. ncbi request reprint Productive infection of primary murine astrocytes, lymphocytes, and macrophages by human immunodeficiency virus type 1 in culture
    Jadwiga Nitkiewicz
    Molecular Virology Division, St Luke s Roosevelt Hospital Center, New York, New York 10019, USA
    J Neurovirol 10:400-8. 2004
    ..Susceptibility mapped neither to the Fv locus nor to a possible polymorphism in cyclin T1. This study indicates that there are no intrinsic intracellular barriers to HIV-1 replication in primary mouse cells when virus entry is efficient...
  27. doi request reprint MENT: methylation and expression database of normal and tumor tissues
    Su Jin Baek
    Medical Genomics Research Center, KRIBB, Gwahangno, Yuseong Gu, Daejeon 305 806, Republic of Korea
    Gene 518:194-200. 2013
    ..Its user-friendly interface allows users to easily search and view both DNA methylation and gene expression patterns. MENT is freely available at http://mgrc.kribb.re.kr:8080/MENT/...
  28. doi request reprint Aberrant upregulation of ASCL2 by promoter demethylation promotes the growth and resistance to 5-fluorouracil of gastric cancer cells
    Oh Hyung Kwon
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
    Cancer Sci 104:391-7. 2013
    ..These results suggest that ASCL2 might play an important role in gastric tumor growth and chemoresistance, and could be a useful prognostic marker for GC patients...
  29. ncbi request reprint GAzer: gene set analyzer
    Sang Bae Kim
    Korean BioInformation Center, KRIBB, Daejeon 305 806, Korea
    Bioinformatics 23:1697-9. 2007
    ..Moreover, GAzer offers extensive annotation for each gene...
  30. ncbi request reprint OIP5 is a highly expressed potential therapeutic target for colorectal and gastric cancers
    Ho Kyung Chun
    Medical Genomics Research Center, KRIBB, Daejeon, Korea
    BMB Rep 43:349-54. 2010
    ..Therefore, we suggest that OIP5 might be a potential cancer therapeutic target, although the mechanisms of OIP5-induced carcinogenesis should be elucidated...
  31. doi request reprint Genome-wide mRNA profiling and multiplex quantitative RT-PCR for forensic body fluid identification
    Seong Min Park
    Medical Genomics Research Center, KRIBB, Department of Functional Genomics, Republic of Korea
    Forensic Sci Int Genet 7:143-50. 2013
    ..This study will provide a thorough examination of body-fluid-specifically expressed mRNAs, which will enlarge the possibility of practical use of RNA for forensic purpose...
  32. doi request reprint Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage
    Mirang Kim
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon 305 806, Korea
    Hum Mol Genet 23:657-67. 2014
    ..Our findings will help elucidate the molecular mechanisms underlying lineage-specific differentiation of pluripotent stem cells during human embryonic development. ..
  33. pmc CpG methylation in exon 1 of transcription factor 4 increases with age in normal gastric mucosa and is associated with gene silencing in intestinal-type gastric cancers
    Seung Kyoon Kim
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Department of Functional Genomics, University of Science and Technology, 52 Eoeun dong, Yuseong Gu, Daejeon 305 806, Republic of Korea
    Carcinogenesis 29:1623-31. 2008
    ..Based on these results, we propose that the observed frequent epigenetic-mediated TCF4 silencing plays a role in tumor formation and progression...
  34. pmc Significant effects of antiretroviral therapy on global gene expression in brain tissues of patients with HIV-1-associated neurocognitive disorders
    Alejandra Borjabad
    Molecular Virology Division, St Luke s Roosevelt Hospital Center and Columbia University, New York, New York, United States of America
    PLoS Pathog 7:e1002213. 2011
    ..Aberrantly expressed transcripts common to untreated and treated HAND may contribute to neurocognitive changes defying ART...
  35. ncbi request reprint STMN2 is a novel target of beta-catenin/TCF-mediated transcription in human hepatoma cells
    Heun Sik Lee
    Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305 600, Republic of Korea
    Biochem Biophys Res Commun 345:1059-67. 2006
    ..Our results suggest that STMN2 might be a novel player of beta-catenin/TCF-mediated carcinogenesis in the liver...
  36. pmc Genome-wide association of serum bilirubin levels in Korean population
    Tae Wook Kang
    Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong Gu, Daejeon, Republic of Korea
    Hum Mol Genet 19:3672-8. 2010
    ..Our result supports the idea that there are considerable ethnic differences in genetic association of bilirubin levels between Koreans and European-derived populations...
  37. doi request reprint Gene-set approach for expression pattern analysis
    Dougu Nam
    Functional Genomics Research Center, KRIBB, 111 Gwahangno, Yuseong Gu, Daejeon 305 806, Korea
    Brief Bioinform 9:189-97. 2008
    ..We review those methods and currently available tools, classify them according to the statistical methods employed, and discuss their pros and cons. We also discuss several interesting extensions to the methods...
  38. pmc Copy number variations (CNVs) identified in Korean individuals
    Tae Wook Kang
    Medical Genomics Research Center, KRIBB, 52 Eoeun dong, Yuseong Gu, Daejeon 305 806, Republic of Korea
    BMC Genomics 9:492. 2008
    ..However, the identification of new CNVs has not yet reached saturation, and more CNVs from diverse populations remain to be discovered...
  39. pmc GSA-SNP: a general approach for gene set analysis of polymorphisms
    Dougu Nam
    School of Nano Biotech and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 689 798, Seoul, Korea
    Nucleic Acids Res 38:W749-54. 2010
    ..GSA-SNP provides a fast computation and an easy-to-use interface. The software and test datasets are freely available at http://gsa.muldas.org. We provide an exemplary analysis on adult heights in a Korean population...
  40. doi request reprint Serum cancer biomarker discovery through analysis of gene expression data sets across multiple tumor and normal tissues
    Hoon Jin
    Medical Genomics Research Center, KRIBB, Daejeon 305 806, Republic of Korea
    J Biomed Inform 44:1076-85. 2011
    ..We discussed a few important points that should be considered during biomarker discovery from omics data...
  41. doi request reprint Identification of DNA methylation markers for lineage commitment of in vitro hepatogenesis
    Mirang Kim
    1Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
    Hum Mol Genet 20:2722-33. 2011
    ..This study provides valuable methylation markers for the lineage commitment of in vitro hepatogenesis and should help elucidate the molecular mechanisms underlying stem cell differentiation and liver development...
  42. pmc CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics
    Young Kyu Park
    Medical Genomics Research Center, KRIBB, Daejeon 305 806, Korea Department of Bio and Brain Engineering, KAIST, Daejeon 305 701, Korea
    Genomics Inform 10:33-9. 2012
    ..We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study...
  43. doi request reprint TWEAK/Fn14 signaling mediates gastric cancer cell resistance to 5-fluorouracil via NF-κB activation
    Oh Hyung Kwon
    Medical Genomics Research Center, KRIBB, Daejeon 305 806, Republic of Korea
    Int J Oncol 44:583-90. 2014
    ..Taken together, our results suggest that Fn14 is a novel therapeutic target and that inhibition of Fn14 combined with 5-FU treatment may be an effective molecular therapeutic strategy to treat 5-FU-resistant gastric cancers. ..
  44. doi request reprint XAGE-1a and XAGE-1d are potential biomarkers of lung squamous cell carcinoma
    Jong Seong Ha
    Aging Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon, Korea
    Clin Chim Acta 413:1226-31. 2012
    ..Lung cancer is the leading cause of cancer deaths worldwide. We evaluated the diagnostic potential of sera XAGE-1a and XAGE-1d in lung cancer, both of which are variants of the X antigen family, member 1...
  45. doi request reprint Upregulation of the cysteine protease inhibitor, cystatin SN, contributes to cell proliferation and cathepsin inhibition in gastric cancer
    Eun Hwa Choi
    Medical Genomic Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
    Clin Chim Acta 406:45-51. 2009
    ..CST1 was identified as an upregulated gene in gastric cancer tissues compared to noncancerous regions using our Affymetrix GeneChip microarray...
  46. doi request reprint Role of TMPRSS4 during cancer progression
    So Young Choi
    Therapeutic Antibody Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon, Korea
    Drug News Perspect 21:417-23. 2008
    ..The target molecule for TMPRSS4 that initiates the EMT stimulatory pathway is still not defined. Regulation of the EMT by proteases such as TMPRSS4 may provide novel therapeutic targets for a cancer metastasis inhibitor...
  47. ncbi request reprint Effects of human immunodeficiency virus type 1 on astrocyte gene expression and function: potential role in neuropathogenesis
    Zhuying Wang
    Molecular Virology Division, St Luke s Roosevelt Hospital Center and College of Physicians and Surgeons, Columbia University, New York, New York 10019, USA
    J Neurovirol 10:25-32. 2004
    ..These findings define new pathways through which HIV-1 may contribute to neuropathogenesis under conditions of limited virus replication in the brain...
  48. ncbi request reprint Shifts of soil enzyme activities in wetlands exposed to elevated CO(2)
    Hojeong Kang
    Department of Environmental Science and Engineering, Ewha Womans University, Seoul 120 750, South Korea
    Sci Total Environ 337:207-12. 2005
    ..Such changes were absent from the fen and marsh where inorganic nutrients were abundant, suggesting that enzyme activities involved in N or P mineralisation only increase under elevated CO(2) when nutrient limitation is strongly exerted...