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 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. pmc Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4
    Dong Su Yu
    Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon, Republic of Korea
    J Bacteriol 194:4757-8. 2012
  10. pmc Complete genome sequence of the endophytic bacterium Burkholderia sp. strain KJ006
    Min Jung Kwak
    Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
    J Bacteriol 194:4432-3. 2012

Collaborators

Detail Information

Publications34

  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 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. 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
    ....
  9. pmc Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4
    Dong Su Yu
    Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon, Republic of Korea
    J Bacteriol 194:4757-8. 2012
    ..We completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that had been isolated from the fecal sample of a healthy breast-fed infant, and annotated 1,835 coding sequences...
  10. pmc Complete genome sequence of the endophytic bacterium Burkholderia sp. strain KJ006
    Min Jung Kwak
    Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
    J Bacteriol 194:4432-3. 2012
    ..strain KJ006, an endophytic bacterium of rice with antifungal activity. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds...
  11. 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...
  12. 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...
  13. 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...
  14. pmc Draft genome sequence of Streptomyces clavuligerus NRRL 3585, a producer of diverse secondary metabolites
    Ju Yeon Song
    Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon, Republic of Korea
    J Bacteriol 192:6317-8. 2010
    ..Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics...
  15. 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
    ....
  16. 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...
  17. 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...
  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. doi request reprint Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods
    Mee Jung Han
    Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering BK21 Program, BioProcess Engineering Research Center, and Institute for the BioCentury, KAIST, Yuseong Gu, Daejeon, Republic of Korea
    Proteomics 11:1213-27. 2011
    ..coli B, and will be useful as a reference for proteome profiling studies under various conditions. The complete proteome data are available online (http://ecolib.kaist.ac.kr)...
  20. 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...
  21. 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...
  22. pmc Genome sequence of the agar-degrading marine bacterium Alteromonadaceae sp. strain G7
    Min Jung Kwak
    Biosystems and Bioengineering Program, University of Science and Technology, Yuseong Gu, Daejeon, Republic of Korea
    J Bacteriol 194:6961-2. 2012
    ..The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases...
  23. 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...
  24. pmc Genome sequence of the hemolytic-uremic syndrome-causing strain Escherichia coli NCCP15647
    Haeyoung Jeong
    Systems and Synthetic Biology Research Center, Yuseong Gu, Daejeon, Republic of Korea
    J Bacteriol 194:3747-8. 2012
    ..Here we present the draft genome sequence of NCCP15647, an EHEC isolate from an HUS patient. Its genome exhibits features of EHEC, such as genes for verotoxins, a type III secretion system, and prophages...
  25. doi request reprint Characterization of an adenylate cyclase gene (cyaB) deletion mutant of Corynebacterium glutamicum ATCC 13032
    Pu Hyeon Cha
    Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon, Korea
    Appl Microbiol Biotechnol 85:1061-8. 2010
    ..The observation that glyoxylate bypass enzymes are derepressed in cyaB mutant indicates the involvement of cAMP in the repression of aceB and aceA...
  26. 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)...
  27. 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...
  28. 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...
  29. 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...
  30. 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...
  31. ncbi request reprint Ensemble learning of genetic networks from time-series expression data
    Dougu Nam
    Korea Research Institute of Bioscience and Biotechnology KRIBB, PO Box 115, Yuseong, Daejeon 305 600, Republic of Korea
    Bioinformatics 23:3225-31. 2007
    ..Previous approaches assign the single most likely combination of regulators to each target gene, which often causes over-fitting of the small number of data...
  32. ncbi request reprint Secretory production of recombinant proteins in Escherichia coli
    Sung Ho Yoon
    Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology KRIBB, Yuseong, Daejeon, Republic of Korea
    Recent Pat Biotechnol 4:23-9. 2010
    ..Here, we review recent patents on the secretory production of recombinant proteins in E. coli...
  33. 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...
  34. 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...