Google Scholar (https://scholar.google.com/citations?user=vnyseUoAAAAJ&hl=en)
Huang, Y., Liu, Y.,Pandey, N., Shah, S., Simon-Soro, A., Hsu, J., Ren, Z., Xiang Z., Kim, D., Ito, T., Oh, M. J., Buckley, C., Alawi, F., Li, Y., Smeets, P., Boyer, S., Zhao, X., Joester, D., Zero, D., Cormode, D., Koo, H. Iron oxide nanozymes stabilize stannous fluoride for targeted biofilm killing and synergistic oral disease prevention. Nat. Commun. 14, 6087 (2023)
Kim, D.#, Kim, S. W.#, Charchoghlyan, H., Jeong, H. Han, G. D. Combinatorial herbal extracts alleviate alcohol-induced hepatic disorders. Plant Foods Hum. Nutr. 78, 432-438 (2023)
Cai, J.-N., Kim, D.* Biofilm ecology associated with dental caries: understanding of microbial interactions in oral communities leads to development of therapeutic strategies targeting cariogenic biofilms. Adv. Appl. Microbiol. 122, 27-75 (2023)
Xiang, Z., Wakade, R. S.,Ribeiro, A. A., Hu, W., Bittinger, K., Simon-Soro, A., Kim, D., Li, J., Krysan, D. J., Liu, Y., Koo, H. Human tooth as a fungal niche: Candida albicans traits in dental plaque isolates. mBio 14, e02769-22 (2023)
Kim, D.* , Ito, T., Hara, A., Li, Y., Kreth, J., Koo, H. Antagonistic interactions by a high H2O2-producing commensal streptococcus modulate caries development by Streptococcus mutans. Mol. Oral Microbiol. 37, 244-255 (2022) (Special Issue on Functional Oral Microbiome)
Negrini, T. C., Ren, Z., Miao, Y., Kim, D., Simon-Soro, A., Liu, Y., Koo, H., Arthur, R. A. Dietary sugar modulate bacteria-fungal interactions in saliva and inter-kingdom biofilm formation on apatitic surface. Front. Microbiol. 12, 993640 (2022)
Jung, H.-Y., Cai, J.-N., Yoo, S. C., Kim, S.-H., Jeon, J.-G., Kim, D.* Collagen peptide in a combinatorial treatment ith Lactobacillus rhamnosus inhibits the cariogenic properties of Streptococcus mutans: An in vitro study. Int. J. Mol. Sci. 23, 1860 (2022) (*Corresponding author)
Liu, Y., Huang, Y., Kim, D., Ren, Z., Oh, M. J., Cormode, D. P., Hara, A. T., Zero, D. T., Koo, H. Ferumoxytol Nanoparticles target biofilms causing tooth decay in the human mouth. Nano Lett. 21, 9442-9449 (2021) (Cover image)
Hashidoko, Y., Kim, D.* Bidirectional cell-cell communication via indole and cyclo(Pro-Tyr) modulates interspecies biofilm formation. Appl. Environ. Microbiol. 87, e01277-21 (2021) (*Corresponding author)
Simon-Soro, A., Kim, D., Li, Y., Liu, Y., Ito, T., Sims, K. R., Benoit, D. S. W., Bittinger, K., Koo, H. Impact of the repurposed drug thonzonium bromide on host oral-gut microbiomes. NPJ Biofilms Microbiomes 7, 7 (2021)
Huang, Y., Liu, Y., Shah, S., Kim, D., Simon-Soro, A., Ito, T., Hajfathalian, M., Li, Y., Hsu, J. C., Nieves, L. M., Alawi, F., Naha, P. C., Cormode, D. P., Koo, H. Precison targeting of bacterial pathogen via bi-functional nanozyme activated by biofilm microenviroment. Biomaterials 268, 120581 (2021)
Kim, D., Barraza, J. P., Rodrigo, A., Hara, A., Lewis, K., Liu, Y., Scisci, E. L., Hajishengallis, E., Whiteley, M., Koo, H. Spatial mapping of polymicrobial communities reveals a precise biogeography associated with human dental caries. Proc. Natl. Acad. Sci. U.S.A 117, 12375‒12386 (2020) *Selected as recommended articles by faculty of 1000 [F1000Prime]
Kim, D., Koo, H. Spatial design of oral polymicrobial communities in its native state. J. Dent. Res. 99, 597‒603. (2020) (Special Issue on the Oral Microbiome, cover image) *Selected as recommended articles by faculty of 1000 [F1000Prime]
Parry-Nweye, E., Onukwugha, N. -E., Balmuri, S, Shane, J., Kim, D., Koo, H., Niepa. T. Electrochemical Strategy for Eradicating Fluconazole-Tolerant Candida albicans on Implantable Titanium. ACS Appl. Mater. Interfaces 11, 40997‒41008. (2019)
Naha, P. C., Liu, Y., Hwang, G., Huang, Y., Gubara, S., Jonnakuti, V., Simon-Soro, A., Kim, D., Gao, L., Koo, H., Cormode, D. P. Dextran coated iron oxide nanoparticles as biomimetic catalysts for localized and pH-activated biofilm disruption. ACS Nano 13, 4960‒4971. (2019)
Ren, Z., Kim, D., Paula, A. J., Hwang, G., Liu, Y., Li, J., Daniell, H., Koo, H. Dual-targeting approach degrades biofilm matrix and enhances bacterial killing. J. Dent. Res. 98, 322‒330. (2019)
Jeong, H. #, Kim, D. #, Song, H. J., Lee, S., Kim, M., Kim, K.-J., Han, G. D. Beta-glucan enriched fermented barley bran (Sigumjang meju) extracts attenuate gastric mucosal injury induced by acute alcohol intake in vivo. Food Biosci. 28, 20‒26. (2019) (#contributed equally as co-first author)
Liu, Y., Naha, P. C., Hwang, G., Kim, D., Huang, Y., Simon-Soro, A., Jung, H. -I., Ren, Z., Li, Gubara, S., Alawi, F., Zero, D., Hara, A. T., Cormode, D. P., Koo, H. Topical ferumoxytol nanoparticles disrupt biofilms and prevent tooth decay in vivo via intrinsic catalytic activity. Nat. Commun. 9, 2920. (2018)
Kim, D., Liu, Y., Benhamou R. I., Sanchez, H., Simon-Soro, A., Li, Y., Hwang, G., Fridman, M., Andes, D. R., Koo, H. Bacterial-derived exopolysaccharides enhance antifungal drug tolerance in a cross-kingdom oral biofilm. ISME J. 12, 1427‒1442. (2018).
Bukhari, S., Kim, D., Liu, Y., Karabucak, B., Koo, H. Novel endodontic disinfection approach using catalytic nanoparticles. J. Endod. 44, 806‒812. (2018).
Lee, S.-H., Kim, K. M., Kim, D., Han, G. D. Changes in ginsenoside patterns of red ginseng extracts according to manufacturing and storage conditions. Food Sci. Biotechnol. 26, 1735‒1741. (2017)
Glazier V. E., Murante, T., Murante, D., Koselny, K., Liu, Y., Kim, D., Koo, H., Krysan, D. J. Genetic analysis of the Candida albicans biofilm transcription factor network using simple and complex haploinsufficiency. PLoS Genet. 13, e1006948. (2017)
Xiao, J., Hara, A., Kim, D., Zero, D., Koo, H., Hwang, G. Biofilm 3D architecture influences in situ pH distribution pattern on the enamel surface. Int. J. Oral Sci. 9, 74‒79. (2017)
Hwang, G., Liu, Y., Kim, D., Li, Y., Krysan D. J., Koo, H. Candida albicans mannans mediate Streptococcus mutans exoenzyme GtfB binding to modulate cross-kingdom biofilm development in vivo. PLoS Pathog. 13, e1006407. (2017) *Selected as recommended articles by faculty of 1000 [F1000Prime] and featured research in PLoS Pathogens
He, J. #, Kim, D. #, Zhou, X., Ahn, S. J., Burne, R. A, Richards, V. P., Koo, H. RNA-Seq reveals enhanced sugar metabolism in Streptococcus mutans co-cultured with Candida albicans within mixed-species biofilms. Front. Microbiol. 8, 1036. (2017) (# contributed equally as co-first author)
Ikeda, A., Kim, D., Hashidoko Y. Identification of diacetonamine form soybean curd residue as a sporulation-inducing factor toward Bacillus spp. AMB Express 7, 101. (2017)
Kim, D., Sengupta, A., Niepa, T. H. R., Lee, B. H., Weljie, A., Freitas-Blanco, V. S., Murata, R. M., Stebe, K. J., Lee, D., Koo, H. Candida albicans stimulates Streptococcus mutans microcolony development via cross-kingdom biofilm-derived metabolites. Sci. Rep. 7, 41332. (2017) *Selected as recommended articles by faculty of 1000 [F1000Prime]
Jeong, H., Lee, S., Kim, S. W., Kim, D., Han, G. D. Inhibitory effects of Sigumjang extract on adipogenesis and lipogenesis during 3T3-L1 differentiation. Food Sci. Biotechnol. 25, 1727‒1735. (2016)
Wei, P., Liu, Y., Li, W., Qian, Y., Nie, Y., Kim, D., Wang, M. Metabolic and dynamic profiling for risk assessment of fluopyram, a typical phenylamide fungicide widely applied in vegetable ecosystem. Sci. Rep. 6, 33898. (2016)
Hwang, G., Liu, Y., Kim, D., Sun, V., Aviles-Reyes, A., Kajfasz, J. K., Lemos, J. A., Koo, H. Simultaneous spatiotemporal mapping of in situ pH and bacterial activity within an intact 3D microcolony structure. Sci. Rep. 6, 32841. (2016)
Gao, L., Liu, Y., Kim, D., Li, Y., Hwang, G., Naha, P. C., Cormode, D. P., Koo, H. Nanocatalysts promote Streptococcus mutans biofilm matrix degradation and enhance bacterial killing to suppress dental caries in vivo. Biomaterials 101, 272‒284. (2016) *Selected as recommended articles by faculty of 1000 [F1000Prime]
Kim, D., Kim, G. W., Lee, S. H., Han, G. D. Ligularia fischeri extract attenuates liver damage induced by chronic alcohol intake. Pharm. Biol. 54, 1465‒1473. (2016)
Kim D., Hwang, G., Liu, Y., Wang, Y., Singh, A. P., Vorsa, N., Koo, H. Cranberry flavonoids modulate cariogenic properties of mixed-species biofilm through exopolysaccharides-matrix disruption. PLoS One 10, e0145844. (2015)
Kim, D., Ko, Y. H., Chung, H. C., Han, G. D. Straightforward bacteria-fungal fermentation between Lactobacillus plantarum and Pleurotus eryngii for synergistic improvement of bioactivity. Food Sci. Biotechnol. 24, 607‒610. (2015)
Horev, B., Klein, M. I., Hwang, G., Li, Y., Kim, D., Koo, H., Benoit, D. S. W. pH-Activated nanoparticles for controlled topical delivery of farnesol to disrupt oral biofilm virulence. ACS Nano 9, 2390‒2404. (2015)
Wang, M., Takayama, T., Kim, D., Sakihama, Y., Tahara, S., Hashidoko, Y. Effect of different classes of attractants, cochliophilin A and N-(E)-feruloyl-4-o-methyldopamine, on the response of Aphanomyces cochlioides zoospores in their chemoattraction and activation of motility linked with intracellular cAMP. J. Pestic. Sci. 38, 181‒187. (2013)
Wang, L., Hisano, W., Murai, Y., Sakurai, M., Ikemoto, H., Okamoto, M., Murotani, T., Isoda, R., Kim, D., Sakihama, Y., Sitepu, I. R., Hashidoko, Y., Hatanaka, Y., Hashimoto, M. Distinct metabolites for photoreactive L-phenylalanine derivatives in Klebsiella sp. CK6 isolated from rhizosphere of a wild dipterocarp sapling. Molecules 18, 8393‒8401. (2013)
Kim, D., Sitepu, I. R., Hashidoko, Y. Induction of biofilm formation in the betaproteobacterium Burkholderia unamae CK43B exposed to exogenous indole and gallic acid. Appl. Environ. Microbiol. 79, 4845‒4852. (2013)
Kim, D., Rahman, A., Sitepu, I. R., Hashidoko, Y. Accelerated degradation of exogenous indole by Burkholderia unamae strain CK43B exposed to pyrogallol-type polyphenols. Biosci. Biotechnol. Biochem. 77, 1722‒1727. (2013)
Kim, D.*, Park, J. –H.*, Kweon, D. –J., Han, G. D. Bioavailability of nanoemulsified conjugated linoleic acid for an antiobesity effect. Int. J. Nanomed. 8, 451‒459. (2013) (* contributed equally as co-first author)
Kim, D., Han, G. D. High hydrostatic pressure treatment combined with enzymes increases the extractability and bioactivity of fermented rice bran. Innovat. Food. Sci. Emerg. Tech. 16, 191‒197. (2012)
Kim, D., Han, G. D. Ameliorating effects of fermented rice bran extract on oxidative stress induced by high glucose and hydrogen peroxide in 3T3-L1 adipocytes. Plant Foods Hum. Nutr. 66, 285‒290. (2011)
Fan, J. P., Kim, D., Kawachi, H., Ha T. –S., Han, G. D. Ameliorating effects of L-carnitine on diabetic podocyte injury. J. Med. Food 13, 1324‒1330. (2010)
Kim, D., Fan, J. P., Chung, H. C., Han, G. D. Changes in extractability and antioxidant activity of Jerusalem artichoke (Helianthus tuberosus L.) tubers by various high hydrostatic pressure treatments. Food Sci. Biotechnol. 19, 1365‒1371. (2010)
Kim, D., Han, G. D. Effect of pegmatite, precious stone and grape pomace extracts supplement for meat quality improvement of pigs. Korean J. Food Sci. Ani. Resour. 30, 252‒260. (2010)
Jeong, B. –Y., Kim, D., Fan, J. P., Chung, H. C., Han, G. D. Studies on prevalence of meat allergy and potential beef allergens. Korean J. Food Sci. Ani. Resour. 29, 151‒156. (2009)
Fan, J. P., Kim, D., Han, G. D. Correlation between meat color and L-carnitine content in livestock meats. Food Sci. Biotechnol. 18, 257‒261. (2009)
Kim, D., Kim, B. D., Baek, S. G., Jeong, H. J., Kim, D. G., Han, G. D. Correlation between shear force and grade decision factors on Hanwoo cow carcass. Korean J. Food Sci. Ani. Resour. 28, 344‒348. (2008)
Kim, D., Fan, J. P., Choi, D., Park, H., Han, G. D. Effects of fermented rice bran addition on the quality improvement of pork. Korean J. Food Sci. Technol. 39, 608‒613. (2007)
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Chapter in Book
Kim, D., Han, G. D. Fermented rice bran attenuates oxidative stress. In Wheat and Rice in Disease Prevention and Health: Benefits, risks and mechanisms of whole grains in health promotion (Eds, Watson, R. R., Preedy, V., Zibadi, S), Elsevier, pp. 467‒480 (2014)
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Design of scientific diagrams
Bowen, W. H., Burne, R. A., Wu, H., Koo, H. Oral biofilms: Pathogens, matrix, and polymicrobial interactions in microenvironments. Trend Microbiol. 26, 229‒242 (2018)
Koo, H., Andes, D. R., Krysan, D. J. Candida-streptococcal interactions in biofilm-associated oral diseases. PLoS Pathog. 14, e1007342 (2018)
Lamont, R., Koo, H., Hajishengallis, G. The oral microbiota: dynamic communities and host interactions. Nat. Rev. Microbiol. 16, 745‒759 (2018)