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Research Output 1996 2019

Article
47 Citations (Scopus)

A computational approach for identifying pathogenicity islands in prokaryotic genomes

Yoon, S. H., Hur, C. G., Kang, H. Y., Kim, Y. H., Oh, T. K. & Kim, J. F., 2005 Jul 21, In : BMC bioinformatics. 6, 184.

Research output: Contribution to journalArticle

Genomic Islands
Genomics
Genome
Genes
Gene
6 Citations (Scopus)

A direct approach for finding functional lipolytic enzymes from the Paenibacillus polymyxa genome

Jung, Y. J., Kim, H. K., Kim, J. F., Park, S. H., Oh, T. K. & Lee, J. K., 2005 Feb 1, In : Journal of microbiology and biotechnology. 15, 1, p. 155-160 6 p.

Research output: Contribution to journalArticle

Lipase
Genome
Enzymes
Escherichia coli
Genes
4 Citations (Scopus)

Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches

Yu, D. S., Lee, D. H., Kim, S. K., Lee, C. H., Song, J. Y., Kong, E. B. & Kim, J. F., 2012 Aug 1, In : Journal of microbiology and biotechnology. 22, 8, p. 1054-1058 5 p.

Research output: Contribution to journalArticle

Proteins
Polytetrafluoroethylene
Sequence Homology
Protein Databases
Computational Biology
20 Citations (Scopus)

Analysis of a prodigiosin biosynthetic gene cluster from the marine bacterium Hahella chejuensis KCTC 2396

Kim, D., Park, Y. K., Lee, J. S., Kim, J. F., Jeong, H., Kim, B. S. & Lee, C. H., 2006 Dec 1, In : Journal of microbiology and biotechnology. 16, 12, p. 1912-1918 7 p.

Research output: Contribution to journalArticle

Prodigiosin
Multigene Family
Bacteria
Genes
Swine
16 Citations (Scopus)

An expansin from the marine bacterium Hahella chejuensis acts synergistically with xylanase and enhances xylan hydrolysis

Lee, H. J., Kim, I. J., Kim, J. F., Choi, I. G. & Kim, K. H., 2013 Jan 1, In : Bioresource Technology. 149, 1 p.

Research output: Contribution to journalArticle

Xylans
Cellulose
hydrolysis
Hydrolysis
Bacteria
49 Citations (Scopus)

Apple proteins that interact with DspA/E, a pathogenicity effector of Erwinia amylovora, the fire blight pathogen

Meng, X., Bonasera, J. M., Kim, J. F., Nissinen, R. M. & Beer, S. V., 2006 Jan 1, In : Molecular Plant-Microbe Interactions. 19, 1, p. 53-61 9 p.

Research output: Contribution to journalArticle

Erwinia amylovora
Malus
Virulence
pathogenicity
apples
49 Citations (Scopus)

Biosynthesis of antibiotic prodiginines in the marine bacterium Hahella chejuensis KCTC 2396

Kim, D., Lee, J. S., Park, Y. K., Kim, J. F., Jeong, H., Oh, T. K., Kim, B. S. & Lee, C. H., 2007 Apr 1, In : Journal of Applied Microbiology. 102, 4, p. 937-944 8 p.

Research output: Contribution to journalArticle

Prodigiosin
Anti-Bacterial Agents
Bacteria
prodiginine
Tandem Mass Spectrometry
67 Citations (Scopus)

CFGP: A web-based, comparative fungal genomics platform

Park, J., Park, B., Jung, K., Jang, S., Yu, K., Choi, J., Kong, S., Park, J., Kim, S., Kim, H., Kim, S., Kim, J. F., Blair, J. E., Lee, K., Kang, S. & Lee, Y. H., 2008 Jan 1, In : Nucleic acids research. 36, SUPPL. 1, p. D562-D571

Research output: Contribution to journalArticle

Genomics
Genome
Informatics
Computational Biology
Saccharomyces cerevisiae
16 Citations (Scopus)

Characterization of an adenylate cyclase gene (cyaB) deletion mutant of Corynebacterium glutamicum ATCC 13032

Cha, P. H., Park, S. Y., Moon, M. W., Subhadra, B., Oh, T. K., Kim, E., Kim, J. F. & Lee, J. K., 2010 Jan, In : Applied Microbiology and Biotechnology. 85, 4, p. 1061-1068 8 p.

Research output: Contribution to journalArticle

Corynebacterium glutamicum
Gene Deletion
Adenylyl Cyclases
Acetates
Glucose
33 Citations (Scopus)

Characterization of bacteria that cause "bacterial shoot blight of pear" in Japan

Beer, S. V., Kim, J. H., Zumoff, C. H., Bogdanove, A. J., Laby, R. J., Gustafson, H. L., Momol, T., Aldwinckle, H. S., Tanii, A. & Tamura, O., 1996 Dec 1, In : Acta Horticulturae. 411, 1, p. 179-181 3 p.

Research output: Contribution to journalArticle

blight
pears
Japan
shoots
bacteria
23 Citations (Scopus)

Characterization of erwinia amylovora strains from different hosts and geographical areas

Kim, J. H., Beer, S. V., Zumoff, C. H., Laby, R. J., Gustafson, H. L., Aldwinckle, H. S. & Tanii, A., 1996 Dec 1, In : Acta Horticulturae. 411, 1, p. 183-185 3 p.

Research output: Contribution to journalArticle

Erwinia amylovora
31 Citations (Scopus)

Charting microbial phenotypes in multiplex nanoliter batch bioreactors

Dai, J., Yoon, S. H., Sim, H. Y., Yang, Y. S., Oh, T. K., Kim, J. F. & Hong, J. W., 2013 Jun 18, In : Analytical Chemistry. 85, 12, p. 5892-5899 8 p.

Research output: Contribution to journalArticle

Bioreactors
Cell culture
Microfluidics
Evaporation
Throughput
24 Citations (Scopus)
Genomics
Membrane Proteins
Escherichia coli
Lac Operon
Lac Repressors
81 Citations (Scopus)

Comparative multi-omics systems analysis of Escherichia coli strains B and K-12

Yoon, S. H., Han, M. J., Jeong, H., Lee, C. H., Xia, X. X., Lee, D. H., Shim, J. H., Lee, S. Y., Oh, T. K. & Kim, J. F., 2012 May 25, In : Genome biology. 13, 5, R37.

Research output: Contribution to journalArticle

Escherichia coli B
systems analysis
Systems Analysis
genome
Escherichia coli
6 Citations (Scopus)

Complete genome sequence of Bifidobacterium longum KCTC 12200BP, a probiotic strain promoting the intestinal health

Kwon, S. K., Kwak, M. J., Seo, J. G., Chung, M. J. & Kim, J. F., 2015 Nov 20, In : Journal of Biotechnology. 214, p. 169-170 2 p.

Research output: Contribution to journalArticle

Probiotics
Bacteria
Genes
Health
Genome
50 Citations (Scopus)

Complete genome sequence of Leuconostoc citreum KM20

Kim, J. F., Jeong, H., Lee, J. S., Choi, S. H., Ha, M., Hur, C. G., Kim, J. S., Lee, S., Park, H. S., Park, Y. H. & Tae, K. O., 2008 Apr 1, In : Journal of Bacteriology. 190, 8, p. 3093-3094 2 p.

Research output: Contribution to journalArticle

Leuconostoc
Probiotics
Fermentation
Lactic Acid
Plasmids
9 Citations (Scopus)

Complete genome sequence of Streptomyces venezuelae ATCC 15439, a promising cell factory for production of secondary metabolites

Song, J. Y., Yoo, Y. J., Lim, S. K., Cha, S. H., Kim, J. E., Roe, J. H., Kim, J. F. & Yoon, Y. J., 2016 Feb 10, In : Journal of Biotechnology. 219, p. 57-58 2 p.

Research output: Contribution to journalArticle

Macrolides
Streptomyces
Metabolites
Industrial plants
Genes
3 Citations (Scopus)

Complete genome sequence of the probiotic bacterium Bifidobacterium breve KCTC 12201BP isolated from a healthy infant

Kwak, M. J., Yoon, J. K., Kwon, S. K., Chung, M. J., Seo, J. G. & Kim, J. F., 2015 Nov 20, In : Journal of Biotechnology. 214, p. 156-157 2 p.

Research output: Contribution to journalArticle

Probiotics
Bacteria
Genes
Genome
Health Promotion
2 Citations (Scopus)
Microbial Rhodopsins
Photobiology
Flavobacterium
Seawater
Korea

Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T

Kwak, M. J., Kwon, S. K. & Kim, J. F., 2017 Jul 25, In : Standards in Genomic Sciences. 12, 1, 44.

Research output: Contribution to journalArticle

Actinobacteria
Genome
Steroids
Multigene Family
Genes
155 Citations (Scopus)

Construction and manipulation of a new Kaposi's sarcoma-associated herpesvirus bacterial artificial chromosome clone

Brulois, K. F., Chang, H., Lee, A. S. Y., Ensser, A., Wong, L. Y., Toth, Z., Lee, S. H., Lee, H. R., Myoung, J., Ganem, D., Oh, T. K., Kim, J. F., Gao, S. J. & Jung, J. U., 2012 Sep 1, In : Journal of Virology. 86, 18, p. 9708-9720 13 p.

Research output: Contribution to journalArticle

Human herpesvirus 8
Bacterial Artificial Chromosomes
Human Herpesvirus 8
bacterial artificial chromosomes
Clone Cells
15 Citations (Scopus)

Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif

Kim, K., Kwon, S. K., Jun, S. H., Cha, J. S., Kim, H., Lee, W., Kim, J. F. & Cho, H. S., 2016 Aug 24, In : Nature communications. 7, 12677.

Research output: Contribution to journalArticle

Chlorides
Rhodopsin
Crystal structure
chlorides
Pumps
79 Citations (Scopus)

Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods

Eun, C. S., Kim, B. K., Han, D. S., Kim, S. Y., Kim, K. M., Choi, B. Y., Song, K. S., Kim, Y. S. & Kim, J. F., 2014 Dec 1, In : Helicobacter. 19, 6, p. 407-416 10 p.

Research output: Contribution to journalArticle

Intestinal Neoplasms
Microbiota
Metaplasia
Gastritis
Stomach Neoplasms
26 Citations (Scopus)

Diversity of root-associated Paenibacillus spp. in winter crops from the southern part of Korea

Cheong, H., Park, S. Y., Ryu, C. M., Kim, J. F., Park, S. H. & Park, C. S., 2005 Dec 1, In : Journal of microbiology and biotechnology. 15, 6, p. 1286-1298 13 p.

Research output: Contribution to journalArticle

Paenibacillus
Korea
Bacillus
Cucumis sativus
Onions
8 Citations (Scopus)

Does the intestinal microbial community of Korean Crohn's disease patients differ from that of western patients?

Eun, C. S., Kwak, M. J., Han, D. S., Lee, A. R., Park, D. I., Yang, S. K., Kim, Y. S. & Kim, J. F., 2016 Feb 29, In : BMC Gastroenterology. 16, 1, 28.

Research output: Contribution to journalArticle

Crohn Disease
Mucous Membrane
Fusobacteria
Tumor Necrosis Factor-alpha
Dysbiosis
38 Citations (Scopus)

Draft genome sequence of Streptomyces clavuligerus NRRL 3585, a producer of diverse secondary metabolites

Song, J. Y., Jeong, H., Yu, D. S., Fischbach, M. A., Park, H. S., Kim, J. J., Seo, J. S., Jensen, S. E., Oh, T. K., Lee, K. J. & Kim, J. F., 2010 Dec 1, In : Journal of Bacteriology. 192, 23, p. 6317-6318 2 p.

Research output: Contribution to journalArticle

Streptomyces
Genome
Anti-Bacterial Agents
Clavulanic Acid
Replicon
14 Citations (Scopus)

Ensemble learning of genetic networks from time-series expression data

Nam, D., Yoon, S. H. & Kim, J. F., 2007 Dec 1, In : Bioinformatics. 23, 23, p. 3225-3231 7 p.

Research output: Contribution to journalArticle

Ensemble Learning
Genetic Network
Linear systems
Time series
Genes
18 Citations (Scopus)

Eop1 from a rubus strain of erwinia amylovora functions as a host-range limiting factor

Asselin, J. E., Bonasera, J. M., Kim, J. F., Oh, C. S. & Beer, S. V., 2011 Aug 1, In : Phytopathology. 101, 8, p. 935-944 10 p.

Research output: Contribution to journalArticle

Rubus
Erwinia amylovora
host range
host specificity
pears
10 Citations (Scopus)

Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function

Kwak, M. J., Kwon, S. K., Yoon, J. K., Song, J. Y., Seo, J. G., Chung, M. J. & Kim, J. F., 2016 Oct 1, In : Systematic and Applied Microbiology. 39, 7, p. 429-439 11 p.

Research output: Contribution to journalArticle

Bifidobacterium
probiotics
Probiotics
phylogeny
metabolism
28 Citations (Scopus)

Evolution of ribosomal DNA-derived satellite repeat in tomato genome

Jo, S. H., Koo, D. H., Kim, J. F., Hur, C. G., Lee, S., Yang, T. J., Kwon, S. Y. & Choi, D., 2009 May 20, In : BMC Plant Biology. 9, 42.

Research output: Contribution to journalArticle

ribosomal DNA
tomatoes
genome
intergenic DNA
ribosomal RNA
2 Citations (Scopus)

Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5

Yoon, K., Song, J. Y., Kwak, M. J., Kwon, S. K. & Kim, J. F., 2017 Jul 1, In : Journal of Microbiology. 55, 7, p. 561-567 7 p.

Research output: Contribution to journalArticle

Flavobacterium
Genome
Flavobacteriaceae
Bacteria
Tenacibaculum
706 Citations (Scopus)

Genome evolution and adaptation in a long-term experiment with Escherichia coli

Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., Lenski, R. E. & Kim, J. F., 2009 Oct 29, In : Nature. 461, 7268, p. 1243-1247 5 p.

Research output: Contribution to journalArticle

Genome
Escherichia coli
Population
Genetic Drift
Mutation
1 Citation (Scopus)

Genome information of maribacter dokdonensis DSW-8 and comparative analysis with other maribacter genomes

Kwak, M. J., Lee, J., Kwon, S. K. & Kim, J. F., 2017 Mar 1, In : Journal of Microbiology and Biotechnology. 27, 3, p. 591-597 7 p.

Research output: Contribution to journalArticle

Seawater
Genome
Eutrophication
Genes
Flavobacterium
24 Citations (Scopus)

Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere

Kwak, M. J., Jeong, H., Madhaiyan, M., Lee, Y., Sa, T. M., Oh, T. K. & Kim, J. F., 2014 Sep 11, In : PloS one. 9, 9, e106704.

Research output: Contribution to journalArticle

Methylobacterium
phyllosphere
Oryza
Probiotics
probiotics
1 Citation (Scopus)

Genome sequence of Escherichia coli NCCP15653, a group D strain isolated from a diarrhea patient

Kwak, M. J., Kim, M. S., Kwon, S. K., Cho, S. H. & Kim, J. F., 2016 Feb 23, In : Gut Pathogens. 8, 1, 84.

Research output: Contribution to journalArticle

Uropathogenic Escherichia coli
Diarrhea
Genome
Escherichia coli
Escherichia coli Meningitis
2 Citations (Scopus)

Genome sequence of Lysobacter dokdonensis DS-58T, a gliding bacterium isolated from soil in Dokdo, Korea

Kwak, M. J., Kwon, S. K., Yoon, J. H. & Kim, J. F., 2015 Dec 9, In : Standards in Genomic Sciences. 10, 1, 123.

Research output: Contribution to journalArticle

Lysobacter
Korea
Soil
Genome
Bacteria
1 Citation (Scopus)

Genome sequence of Porphyrobacter dokdonensis DSW-74T, isolated from seawater offDokdo in the East Sea (Sea of Korea)

Song, J. Y., Hong, J., Kwak, M. J., Kwon, S. K. & Kim, J. F., 2016 Jan 1, In : Genome Announcements. 4, 5, e00903-16.

Research output: Contribution to journalArticle

Seawater
Korea
Oceans and Seas
Genome
Republic of Korea
6 Citations (Scopus)

Genome sequence of the agar-degrading marine bacterium alteromonadaceae sp. Strain G7

Kwak, M. J., Song, J. Y., Kim, B. K., Chi, W. J., Kwon, S. K., Choi, S., Chang, Y. K., Hong, S. K. & Kim, J. F., 2012 Oct 1, In : Journal of Bacteriology. 194, 24, p. 6961-6962 2 p.

Research output: Contribution to journalArticle

Alteromonadaceae
Agar
Genome
Sulfatases
Bacteria
3 Citations (Scopus)

Genome sequence of the marine flavobacterium Croceitalea dokdonensis DOKDO 023 that contains proton- and sodium-pumping rhodopsins

Kwon, S. K., Lee, H. G., Kwak, M. J. & Kim, J. F., 2016 Apr 1, In : Marine Genomics. 26, p. 1-3 3 p.

Research output: Contribution to journalArticle

Flavobacterium
rhodopsin
Rhodopsin
protons
Protons
62 Citations (Scopus)

Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937

Glasner, J. D., Yang, C. H., Reverchon, S., Hugouvieux-Cotte-Pattat, N., Condemine, G., Bohin, J. P., van Gijsegem, F., Yang, S., Franza, T., Expert, D., Plunkett, G., Francisco, M. J. S., Charkowski, A. O., Py, B., Bell, K., Rauscher, L., Rodriguez-Palenzuela, P., Toussaint, A., Holeva, M. C., He, S. Y. & 27 others, Douet, V., Boccara, M., Blanco, C., Toth, I., Anderson, B. D., Biehl, B. S., Mau, B., Flynn, S. M., Barras, F., Lindeberg, M., Birch, P. R. J., Tsuyumu, S., Shi, X., Hibbing, M., Yap, M. N., Carpentier, M., Dassa, E., Umehara, M., Kim, J. F., Rusch, M., Soni, P., Mayhew, G. F., Fouts, D. E., Gill, S. R., Blattner, F. R., Keen, N. T. & Perna, N. T., 2011 Apr, In : Journal of Bacteriology. 193, 8, p. 2076-2077 2 p.

Research output: Contribution to journalArticle

Plant Genome
Plant Diseases
Enterobacteriaceae
Virulence
Molecular Biology
59 Citations (Scopus)

Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681

Kim, J. F., Jeong, H., Park, S. Y., Kim, S. B., Park, Y. K., Choi, S. K., Ryu, C. M., Hur, C. G., Ghim, S. Y., Oh, T. K., Kim, J. J., Park, C. S. & Park, S. H., 2010 Nov 1, In : Journal of Bacteriology. 192, 22, p. 6103-6104 2 p.

Research output: Contribution to journalArticle

Polymyxins
Probiotics
Genome
Plant Diseases
Republic of Korea
56 Citations (Scopus)

Genome sequence of the probiotic bacterium bifidobacterium animalis subsp. lactis AD011

Kim, J. F., Jeong, H., Yu, D. S., Choi, S. H., Hur, C. G., Park, M. S., Yoon, S. H., Kim, D. W., Ji, G. E., Park, H. S. & Oh, T. K., 2009 Jan 1, In : Journal of Bacteriology. 191, 2, p. 678-679 2 p.

Research output: Contribution to journalArticle

Probiotics
Genome
Bacteria
Chromosomes, Human, Pair 1
Polysaccharides
35 Citations (Scopus)

Genome sequence of the thermotolerant yeast Kluyveromyces marxianus var. marxianus KCTC 17555

Jeong, H., Lee, D. H., Kim, S. H., Kim, H. J., Lee, K., Song, J. Y., Kim, B. K., Sung, B. H., Park, J. C., Sohn, J. H., Koo, H. M. & Kim, J. F., 2012 Dec 1, In : Eukaryotic Cell. 11, 12, p. 1584-1585 2 p.

Research output: Contribution to journalArticle

Bioelectric Energy Sources
Kluyveromyces
Yeasts
Genome
Enzymes
189 Citations (Scopus)

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

Jeong, H., Barbe, V., Lee, C. H., Vallenet, D., Yu, D. S., Choi, S. H., Couloux, A., Lee, S. W., Yoon, S. H., Cattolico, L., Hur, C. G., Park, H. S., Ségurens, B., Kim, S. C., Oh, T. K., Lenski, R. E., Studier, F. W., Daegelen, P. & Kim, J. F., 2009 Dec 11, In : Journal of Molecular Biology. 394, 4, p. 644-652 9 p.

Research output: Contribution to journalArticle

Genome
Escherichia coli
Multigene Family
Molecular Biology
Lysogeny

Genome sequences of the Shiga-like toxin-producing Escherichia coli nccp15655 and nccp15656

Kwak, M. J., Kwon, S. K., Cho, S. H. & Kim, J. F., 2015 May 12, In : Gut Pathogens. 7, 13.

Research output: Contribution to journalArticle

Shiga Toxins
Shiga-Toxigenic Escherichia coli
Genome
Virulence
Escherichia coli
14 Citations (Scopus)

Genome snapshot of paenibacillus polymyxa ATCC 842T

Jeong, H., Kim, J. F., Park, Y. K., Kim, S. B., Kim, C. & Park, S. H., 2006 Oct 1, In : Journal of microbiology and biotechnology. 16, 10, p. 1650-1655 6 p.

Research output: Contribution to journalArticle

Genome
Paenibacillus
Nitrogen Fixation
Sequence Analysis
Electrophoresis
12 Citations (Scopus)

Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods

Han, M. J., Yun, H., Lee, J. W., Lee, Y. H., Lee, S. Y., Yoo, J. S., Kim, J. Y., Kim, J. F. & Hur, C. G., 2011 Apr 1, In : Proteomics. 11, 7, p. 1213-1227 15 p.

Research output: Contribution to journalArticle

Proteome
Computational methods
Escherichia coli
Genes
Genome
13 Citations (Scopus)
Hahella chejuensis
Prodigiosin
pigment
genome
pigments
12 Citations (Scopus)

Genomic and transcriptomic landscape of Escherichia coli BL21(DE3)

Kim, S., Jeong, H., Kim, E. Y., Kim, J. F., Lee, S. Y. & Yoon, S. H., 2017 May 19, In : Nucleic acids research. 45, 9, p. 5285-5293 9 p.

Research output: Contribution to journalArticle

Escherichia coli
Transcriptome
Genome
Untranslated RNA
Biotechnology
117 Citations (Scopus)

Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent

Jeong, H., Yim, J. H., Lee, C., Choi, S. H., Park, Y. K., Yoon, S. H., Hur, C. G., Kang, H. Y., Kim, D., Lee, H. H., Park, K. H., Park, S. H., Park, H. S., Lee, H. K., Oh, T. K. & Kim, J. F., 2005 Dec 1, In : Nucleic acids research. 33, 22, p. 7066-7073 8 p.

Research output: Contribution to journalArticle

Harmful Algal Bloom
Genes
Sequence Analysis
Prodigiosin
Molecular Motor Proteins