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Research Output 1996 2019

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
21 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

Analysis of three bacterial strains isolated from symptomatic plants in Australia

Kim, J. F., Garr, E. R., Bauer, D. W., Beer, S. V., Gustafson, H. L., Momol, E. A., Momol, M. T., Aldwinckle, H. S. & Vanneste, J. L., 1999 Dec 1, VIII International Workshop on Fire Blight. Momol, M. T. & Saygili, H. (eds.). p. 149-154 6 p. (Acta Horticulturae; vol. 489).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

pears
apples
Erwinia amylovora
polymerase chain reaction
Middle East
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
6 Citations (Scopus)

Author correction: Rhizosphere microbiome structure alters to enable wilt resistance in tomato (Nat. Biotechnol., (2018) 36, 11, (1100-1116), 10.1038/nbt.4232)

Kwak, M. J., Kong, H. G., Choi, K., Kwon, S. K., Song, J. Y., Lee, J., Lee, P. A., Choi, S. Y., Seo, M., Lee, H. J., Jung, E. J., Park, H., Roy, N., Kim, H., Lee, M. M., Rubin, E. M., Lee, S. W. & Kim, J. F., 2018 Nov 9, In : Nature Biotechnology. 36, 11, 1 p.

Research output: Contribution to journalComment/debate

Rhizosphere
HTML
Disease Resistance
Microbiota
Lycopersicon esculentum

Batch cultivation of bacterial cells in nanoliter reactor array

Dai, J., Yoon, S. H., Sim, H. Y., Oh, T. K., Kim, J. F. & Hong, J. W., 2011 Dec 1, 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011. p. 1710-1712 3 p. (15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011; vol. 3).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Antibiotics
Microfluidics
Escherichia coli
Carbon
Experiments
50 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
25 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
51 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
17 Citations (Scopus)

Complete genome sequence of the endophytic Bacterium burkholderia sp. strain KJ006

Kwak, M. J., Song, J. Y., Kim, S. Y., Jeong, H., Kang, S. G., Kim, B. K., Kwon, S. K., Lee, C. H., Yu, D. S., Park, S. H. & Kima, J. F., 2012 Aug 1, In : Journal of Bacteriology. 194, 16, p. 4432-4433 2 p.

Research output: Contribution to journalComment/debate

Burkholderia
Genome
Bacteria
Endophytes
Plasmids
26 Citations (Scopus)

Complete genome sequence of the polycyclic aromatic hydrocarbon-degrading bacterium Alteromonas sp. strain SN2

Jin, H. M., Jeong, H., Moon, E. J., Math, R. K., Lee, K., Kim, H. J., Jeon, C. O., Oh, T. K. & Kim, J. F., 2011 Aug 1, In : Journal of Bacteriology. 193, 16, p. 4292-4293 2 p.

Research output: Contribution to journalComment/debate

Alteromonas
Polycyclic Aromatic Hydrocarbons
Oceans and Seas
Genome
Bacteria
16 Citations (Scopus)

Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4

Yu, D. S., Jeong, H., Lee, D. H., Kwon, S. K., Song, J. Y., Kim, B. K., Park, M. S., Ji, G. E., Oh, T. K. & Kim, J. F., 2012 Sep 1, In : Journal of Bacteriology. 194, 17, p. 4757-4758 2 p.

Research output: Contribution to journalComment/debate

Probiotics
Genome
Bacteria
Breast
Health
4 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
156 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
16 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
8 Citations (Scopus)

Draft genome sequence of the antifungal-producing plant-benefiting bacterium Burkholderia pyrrocinia CH-67

Song, J. Y., Kwak, M. J., Lee, K. Y., Kong, H. G., Kim, B. K., Kwon, S. K., Lee, S. W. & Kim, J. F., 2012 Dec 1, In : Journal of Bacteriology. 194, 23, p. 6649-6650 2 p.

Research output: Contribution to journalComment/debate

Burkholderia
Genome
Bacteria
Probiotics
Agriculture
20 Citations (Scopus)

Draft genome sequence of the Paenibacillus polymyxa type strain (ATCC 842 T), a plant growth-promoting bacterium

Jeong, H., Park, S. Y., Chung, W. H., Kim, S. H., Kim, N., Park, S. H. & Kim, J. F., 2011 Sep 1, In : Journal of Bacteriology. 193, 18, p. 5026-5027 2 p.

Research output: Contribution to journalComment/debate

Genome
Bacteria
Growth
Gram-Positive Endospore-Forming Bacteria
Rhizosphere
9 Citations (Scopus)

DspE of Erwinia amylovora interacts with receptor kinases of apple

Meng, X., Bonasera, J. M., Kim, J. F., Nissinen, R. M. & Beer, S. V., 2002 Jan 1, IX International Workshop on Fire Blight. International Society for Horticultural Science, p. 463-466 4 p. (Acta Horticulturae; vol. 590).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Erwinia amylovora
phosphotransferases (kinases)
apples
clones
receptors
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

Erratum: Genome sequence of the probiotic bacterium bifidobacterium animalis subsp. lactis AD011 (Journal of Bacteriology (2009) 191:2 (678-679))

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 Mar 1, In : Journal of Bacteriology. 191, 6, 1 p.

Research output: Contribution to journalComment/debate

Bacteriology
Probiotics
Genome
Bacteria
Bifidobacterium animalis

Erratum: Characterization of an adenylate cyclase gene (cyaB) deletion mutant of Corynebacterium glutamicum ATCC 13032 (Applied Microbiology and Biotechnology DOI: 10.1007/s00253-009-2066-9)

Cha, P. H., Park, S. Y., Moon, M. W., Subhadra, B., Oh, T. K., Kim, E., Kim, J. F. & Lee, J. K., 2010 Mar 1, In : Applied Microbiology and Biotechnology. 86, 1, 1 p.

Research output: Contribution to journalComment/debate

Corynebacterium glutamicum
Gene Deletion
Biotechnology
Microbiology
Adenylyl Cyclases
1 Citation (Scopus)
Erwinia amylovora
Pathogens
Fires
pathogenicity
apples
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
707 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
66 Citations (Scopus)

Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1

Kim, B. K., Jung, M. Y., Yu, D. S., Park, S. J., Oh, T. K., Rhee, S. K. & Kim, J. F., 2011 Oct 1, In : Journal of Bacteriology. 193, 19, p. 5539-5540 2 p.

Research output: Contribution to journalComment/debate

Carbon Cycle
Rhizosphere
Archaea
Ammonia
Soil
4 Citations (Scopus)

Genome sequence of an oligohaline hyperthermophilic archaeon, Thermococcus zilligii AN1, isolated from a terrestrial geothermal freshwater spring

Kim, B. K., Lee, S. H., Kim, S. Y., Jeong, H., Kwon, S. K., Lee, C. H., Song, J. Y., Yu, D. S., Kang, S. G. & Kim, J. F., 2012 Jul 1, In : Journal of Bacteriology. 194, 14, p. 3765-3766 2 p.

Research output: Contribution to journalComment/debate

Thermococcus
Hot Springs
Archaea
Fresh Water
Genome
5 Citations (Scopus)

Genome sequence of enterohemorrhagic Escherichia coli NCCP15658

Song, J. Y., Yoo, R. H., Jang, S. Y., Seong, W. K., Kim, S. Y., Jeong, H., Kang, S. G., Kim, B. K., Kwon, S. K., Lee, C. H., Yu, D. S., Park, M. S., Cho, S. H. & Kim, J. F., 2012 Jul 1, In : Journal of Bacteriology. 194, 14, p. 3749-3750 2 p.

Research output: Contribution to journalComment/debate

Enterohemorrhagic Escherichia coli
Genome Size
Republic of Korea
Foodborne Diseases
Virulence Factors
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