Jihyun F Kim

Summary

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

Publications

  1. pmc Complete genome sequence of Leuconostoc citreum KM20
    Jihyun F Kim
    Systems Microbiology Research Center, KRIBB, 111 Gwahangno, Yuseong Gu, Daejeon 305 806, South Korea
    J Bacteriol 190:3093-4. 2008
  2. doi request reprint Recent progress of microbial genome projects in Korea
    Haeyoung Jeong
    Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
    Biotechnol J 3:601-11. 2008
  3. pmc Evolution of ribosomal DNA-derived satellite repeat in tomato genome
    Sung Hwan Jo
    Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
    BMC Plant Biol 9:42. 2009
  4. pmc PR genes of apple: identification and expression in response to elicitors and inoculation with Erwinia amylovora
    Jean M Bonasera
    Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA
    BMC Plant Biol 6:23. 2006
  5. pmc The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli
    Colin T Archer
    Australian Institute for Bioengineering and Nanotechnology, Cnr Cooper and College Rds, The University of Queensland, St Lucia, Queensland 4072 Australia
    BMC Genomics 12:9. 2011
  6. pmc Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011
    Jihyun F Kim
    Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong, Daejeon 305 806, Korea
    J Bacteriol 191:678-9. 2009
  7. pmc Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681
    Jihyun F Kim
    Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Yuseong Gu, Daejeon, South Korea
    J Bacteriol 192:6103-4. 2010
  8. ncbi request reprint Two bacterial entophytes eliciting both plant growth promotion and plant defense on pepper (Capsicum annuum L.)
    Seung Hoon Kang
    Laboratory of Microbial Genomics, Systems Microbiology Research Center KRIBB, Daejeon 305 806, Korea
    J Microbiol Biotechnol 17:96-103. 2007
  9. pmc Comparative multi-omics systems analysis of Escherichia coli strains B and K-12
    Sung Ho Yoon
    Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305 806, Korea
    Genome Biol 13:R37. 2012
  10. pmc Towards pathogenomics: a web-based resource for pathogenicity islands
    Sung Ho Yoon
    Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, 52 Oun Dong, Yuseong, Daejeon 305 806, Republic of Korea
    Nucleic Acids Res 35:D395-400. 2007

Collaborators

Detail Information

Publications25

  1. pmc Complete genome sequence of Leuconostoc citreum KM20
    Jihyun F Kim
    Systems Microbiology Research Center, KRIBB, 111 Gwahangno, Yuseong Gu, Daejeon 305 806, South Korea
    J Bacteriol 190:3093-4. 2008
    ..We have determined the complete genome sequence of L. citreum KM20. It consists of a 1.80-Mb chromosome and four circular plasmids and reveals genes likely involved in kimchi fermentation and its probiotic effects...
  2. doi request reprint Recent progress of microbial genome projects in Korea
    Haeyoung Jeong
    Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
    Biotechnol J 3:601-11. 2008
  3. pmc Evolution of ribosomal DNA-derived satellite repeat in tomato genome
    Sung Hwan Jo
    Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
    BMC Plant Biol 9:42. 2009
    ..Satellite repeats can expand and contract dramatically, which may cause genome size variation among genetically-related species. However, the origin and expansion mechanism are not clear yet and needed to be elucidated...
  4. pmc PR genes of apple: identification and expression in response to elicitors and inoculation with Erwinia amylovora
    Jean M Bonasera
    Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA
    BMC Plant Biol 6:23. 2006
    ..However within the range of species examined, components of the pathway seem to be highly conserved. In this study, we attempted to identify downstream components of the SAR pathway in apple to serve as markers for its activation...
  5. pmc The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli
    Colin T Archer
    Australian Institute for Bioengineering and Nanotechnology, Cnr Cooper and College Rds, The University of Queensland, St Lucia, Queensland 4072 Australia
    BMC Genomics 12:9. 2011
    ..E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses...
  6. pmc Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011
    Jihyun F Kim
    Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong, Daejeon 305 806, Korea
    J Bacteriol 191:678-9. 2009
    ....
  7. pmc Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681
    Jihyun F Kim
    Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Yuseong Gu, Daejeon, South Korea
    J Bacteriol 192:6103-4. 2010
    ..polymyxa E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes...
  8. ncbi request reprint Two bacterial entophytes eliciting both plant growth promotion and plant defense on pepper (Capsicum annuum L.)
    Seung Hoon Kang
    Laboratory of Microbial Genomics, Systems Microbiology Research Center KRIBB, Daejeon 305 806, Korea
    J Microbiol Biotechnol 17:96-103. 2007
    ..9% and 41.5%, respectively. The two strains also elicited induced systemic resistance of plants against Xanthomonas axonopodis pv. vesicatoria...
  9. pmc Comparative multi-omics systems analysis of Escherichia coli strains B and K-12
    Sung Ho Yoon
    Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305 806, Korea
    Genome Biol 13:R37. 2012
    ..Here, we demonstrate that comparative analyses of multi-omics data combined with a computational modeling approach provide a framework for elucidating the phenotypic characteristics of organisms whose genomes are sequenced...
  10. pmc Towards pathogenomics: a web-based resource for pathogenicity islands
    Sung Ho Yoon
    Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, 52 Oun Dong, Yuseong, Daejeon 305 806, Republic of Korea
    Nucleic Acids Res 35:D395-400. 2007
    ..PAIDB is freely accessible at http://www.gem.re.kr/paidb...
  11. doi request reprint Genome sequences of Escherichia coli B strains REL606 and BL21(DE3)
    Haeyoung Jeong
    Korea Research Institute of Bioscience and Biotechnology KRIBB, 111 Gwahangno, Yuseong, Daejeon 305 806, Korea
    J Mol Biol 394:644-52. 2009
    ..coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome...
  12. pmc Identification of a polymyxin synthetase gene cluster of Paenibacillus polymyxa and heterologous expression of the gene in Bacillus subtilis
    Soo Keun Choi
    Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong Gu, Daejeon 305 806, Republic of Korea
    J Bacteriol 191:3350-8. 2009
    ..Taken together, our findings demonstrate that the pmx gene cluster is responsible for polymyxin biosynthesis...
  13. pmc Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins
    Soon Kyeong Kwon
    Systems and Synthetic Biology Research Center, Division of Biosystems Research, Korea Research Institute of Bioscience and Biotechnology, Yuseong Gu, Daejeon, Korea
    Genome Biol Evol 5:187-99. 2013
    ....
  14. pmc Genome-wide screening and identification of factors affecting the biosynthesis of prodigiosin by Hahella chejuensis, using Escherichia coli as a surrogate host
    Soon Kyeong Kwon
    Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, 111 Gwahangno, Yuseong Gu, Daejeon 305 806, South Korea
    Appl Environ Microbiol 76:1661-8. 2010
    ..coli, or in the natural producer, H. chejuensis...
  15. ncbi request reprint MELDB: a database for microbial esterases and lipases
    Ho Young Kang
    Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, P O Box 115, Yuseong, Daejeon 305 600, Republic of Korea
    FEBS Lett 580:2736-40. 2006
    ..HMM profiles of each cluster were generated to classify unknown sequences. Contents of the database can be keyword-searched and query sequences can be aligned to sequence profiles and sequences themselves...
  16. pmc Genome sequence of the thermotolerant yeast Kluyveromyces marxianus var. marxianus KCTC 17555
    Haeyoung Jeong
    Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong Gu, Daejeon, Republic of Korea
    Eukaryot Cell 11:1584-5. 2012
    ..Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548)...
  17. pmc Draft genome sequence of the Paenibacillus polymyxa type strain (ATCC 842T), a plant growth-promoting bacterium
    Haeyoung Jeong
    Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, 125 Gwahak ro, Yuseong Gu, Daejeon 305 806, Republic of Korea
    J Bacteriol 193:5026-7. 2011
    ..The P. polymyxa genome contains a repertoire of biosynthetic genes for antibiotics and hydrolytic enzymes that account for its beneficial effects in the rhizosphere to the host plants it associates with...
  18. ncbi request reprint Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches
    Dong Su Yu
    Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak ro, Yuseong Gu, Daejeon 305 806, Korea
    J Microbiol Biotechnol 22:1054-8. 2012
    ....
  19. ncbi request reprint Identification and functional analysis of the fusaricidin biosynthetic gene of Paenibacillus polymyxa E681
    Soo Keun Choi
    Systems Microbiology Research Center, KRIBB, 111 Gwahangno, Yuseong Gu, Daejeon 305 806, Republic of Korea
    Biochem Biophys Res Commun 365:89-95. 2008
    ..Our findings suggested that FusA can produce more than one kind of fusaricidin, as various forms of fusaricidins were identified from P. polymyxa E681...
  20. pmc Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1
    Byung Kwon Kim
    Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, 125 Gwahak ro, Yuseong Gu, Daejeon 305 806, Republic of Korea
    J Bacteriol 193:5539-40. 2011
    ..Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite...
  21. ncbi request reprint Interference of quorum sensing and virulence of the rice pathogen Burkholderia glumae by an engineered endophytic bacterium
    Hyun Soo Cho
    Laboratory of Microbial Genomics, Systems Microbiology Research Center, KRIBB, Daejeon 305 806, Korea
    FEMS Microbiol Ecol 60:14-23. 2007
    ..Our results indicate the possibility that a bacterial endophyte transformed with the aiiA gene can be used as a novel biological control agent against pathogenic Burkholderia glumae that are known to occupy the same ecological niche...
  22. pmc Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent
    Haeyoung Jeong
    Genome Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, PO Box 115, Yuseong, Daejeon 305 600, Republic of Korea
    Nucleic Acids Res 33:7066-73. 2005
    ..In conclusion, our work provides new insights into mitigating algal blooms in addition to genetic make-up, physiology, biotic interactions and biological roles in the community of a marine bacterium...
  23. pmc A computational approach for identifying pathogenicity islands in prokaryotic genomes
    Sung Ho Yoon
    Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Oun Dong, Yuseong, Daejeon 305 333, Korea
    BMC Bioinformatics 6:184. 2005
    ..These approaches often lead to the identification of genomic islands, rather than PAIs...
  24. pmc CFGP: a web-based, comparative fungal genomics platform
    Jongsun Park
    Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Center for Fungal Genetic Resource, Seoul National University, San 56 1, Sillim 9 Dong, Seoul 151 921, Korea
    Nucleic Acids Res 36:D562-71. 2008
    ..A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI...
  25. ncbi request reprint The Erwinia chrysanthemi EC16 hrp/hrc gene cluster encodes an active Hrp type III secretion system that is flanked by virulence genes functionally unrelated to the Hrp system
    Clemencia M Rojas
    Department of Plant Pathology, Cornell University, Ithaca, NY 14853 4203, USA
    Mol Plant Microbe Interact 17:644-53. 2004
    ..chrysanthemi Hrp regulator genes hrpL and hrpS. Thus, the 44-kb region of the E. chrysanthemi EC16 genome that is centered on the hrplhrc cluster encodes a potpourri of virulence factors, but none of these appear to be a TTSS effector...