한림대학교 HALLYM UNIVERSITY

■ 논문
- Fisetin-rich extracts of Rhus verniciflua stokes improve blood flow rates in mice fed both normal and high-Fat diets. 2016. J Med Food. 19(2):120-6.
- IL32γ activates natural killer receptor-expressing innate immune cells to produce IFNγ via dendritic cell-derived IL12. 2015. Biochem Biophys Res Commun.461(1):86-94.
- The HIF-1/glial TIM-3 axis controls inflammation associated brain damage under hypoxia. 2015. Nat Commun.6:6340. doi: 10.1038/ncomms7340.
- Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins. 2015. Sci Rep.5:14269.
- Application of in utero electroporation of G-protein coupled receptor (GPCR) genes, for subcellular localization of hardly identifiable GPCR in mouse cerebral cortex. 2014. Mol cells.37(7):554-561.
- nc886, a non-coding RNA of anti-proliferative role, is suppressed by CpG DNA methylation in human gastric cancer. 2014. Oncotarget5(11):3944-3955.
- TopBP1 deficiency impairs V(D)J recombination during lymphocyte development. 2014. EMBO J. 33(3):217-228.
- Cell death/proliferation roles for nc886, a non-coding RNA, in the protein kinase R pathway in cholangiocarcinoma. 2013. Oncogene32(32):3722-31.
- Compartmentalized, functional role of angiogenin during spotted fever group rickettsia-induced endothelial barrier dysfunction: evidence of possible mediation by host tRNA-derived small noncoding RNAs. 2013. BMC Infect Dis.23;13:285.
- Involvement of the cAMP response element binding protein, CREB, and Cyclin D1 in LPA-induced proliferation of P19 embryonic carcinoma cells. 2012. Mol cells.34(3):323-328.
- A tumor surveillance model: A non-coding RNA senses neoplastic cells and its protein partner signals cell death. 2012. Int. J. Mol. Sci.13(10):13134-13139.
- Characterization of the direct physical interaction of nc886, a cellular non-coding RNA, and PKR. 2012. FEBS Lett.586(19):3477-3484.
- DNA Aptamers against the Receptor Binding Region of Hemagglutinin Prevent Avian Influenza Viral Infection. 2011. Mol. cells32(6):527-533.
- Activation of natural killer T cells inhibits the development of induced regulatory T cells via IFNγ. 2011. Biochem. Biophys. Res. Commun..411(3):599-606.
- Gold nanoparticle-based colorimetric detection of kanamycin using a DNA aptamer. 2011. Anal. Biochem.415(2):175-81.
- Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity. 2011. RNA 17(6):1076-89.
- Galectin-3 exerts cytokine-like regulatory actions through the JAK-STAT pathway. 2010. J Immunol.185(11):7037-46.
- Twist2 regulates CD7 expression and galectin-1-induced apoptosis in mature T-cells. 2009. Mol Cells.28(6):553-558.
- The Effect of CD28 Stimulation on in vitro Generation of Regulatory T Cells with IL2 and TGFβ. 2008. GENES &GENOMICS. 30(6): 555-561.
- Down-Regulation of the SWI/SNF Chromatin Remodeling Activity by TCR Signaling Is Required for Proper ThymocyteMaturation. 2007. J Immunol.178(11):7088-96.
- SRG3 interacts directly with the major components of the SWI/SNF chromatin remodeling complex and protects them from proteasomal degradation. 2007. J Biol Chem.282(14):10614-24.
- Notch1 Confers Thymocytes a Resistance to GC-induced Apoptosis via Deltex1 by Blocking the Recruitment of p300 to E2A/HEB and Regulating the SRG3 Expression. 2006. Cell death differ.13:1495-1505.
- Expression of SRG3, a Core Component of Mouse SWI/SNF Chromatin Remodeling Complex, Is Regulated by Cooperative Interactions between Sp1/Sp3 and Ets Transcription Factors. 2005. Biochem. Biophys. Res. Commun. 338:1435-1446.
- Ecto-and exo-protein kinases in Schistosoma mansoni: regulation of surface phosphorylation by acetylcholine and identification of the alpha subunit of CKII as a major secreted protein kinase. 2005. J. Parasitol. 91:756-63.
- Modulation of androgen receptortransactivation by the SWI3-related gene product (SRG3) in multiple ways. 2005. Mol. Cell Biol. 25(12) 4841-4852.
- A DNA aptamer prevents influenza infection by blocking the receptor binding region of the viral haemagglutinin. 2004. J. Biol.Chem.279(46): 48410-48419.
- Nitric oxide inhibits glucocorticoid-induced apoptosis oft hymocytes by down-regulating the SRG3 expression. 2004. J. Biol.Chem. 279(33): 34373-34379.
- E2A/HEB and Id3 proteins control the sensitivity to glucocorticoid-induced apoptosis in thymocytes by regulating the SRG3 expression. 2004. J. Biol. Chem. 279(21): 21916-23.
- T-cell receptor signaling inhibits glucocorticoid-induced apoptosis by repressing the SRG3 expression via Ras activation. 2004. J. Biol. Chem. 279(21): 21903-15.
- Twist2, a novel ADD1/SREBP1c interacting protein, represses the transcriptional activity of ADD1/SREBP1c. 2003. Nucleic Acids Res.31(24):7165-74.
- Overexpression of SRG3/SWI3 protein disrupts the cell cycle progression in mature T cells and yeast. 2002. Korean J. Biol.Sci. 6:335-339.
- Intranasal immunization with synthetic recombinant vaccine containing multiple epitopes of influenza virus. 2002. Vaccine20: 2772-2780.
- Immunization with Influenza Virus Hemagglutinin Globular Region Containing the Receptor-Binding Pocket. 2002. Viral Immunol. 15: 165-176.
- Notch1 confers developing thymocytes a resistance to glucocorticoid induced apoptosis by down-regulating SRG3 expression. 2001. Proc. Natl.Acad. Sci. U.S.A. 98:10267-72.
- Two species of mRNAs for the fyn proto-oncogene are produced by an alternative polyadenylation. 1998. Mol. &Cells8:746-749.
- Down-regulation of Tcf-1 expression by activation-induced apoptosis of T cell hybridoma. 1998. Korean J. Biol.Sci. 2:403-410.
- Expression of Tcf-1 mRNA and surface TCR/CD3 complexes are reduced during apoptosis of T-cells. 1998. Int. Immunol. 10:1519-1527.
- A new mouse gene, SRG3, related to the SWI3of Saccharomyces cerevisiae, is required for apoptosis induced by glucocorticoids in thymoma cell line. 1997. J. Exp. Med. 185:1827-1836.
- Overexpressed RAD4 protein required for excision repair of Saccharomyces cerevisiaeis toxic to the host Escherichia coli. 1994. In Vitro Toxicol. 7:269-275.
- Expression of RAD4gene of Saccharomyces cerevisiae that can be propagated in Escherichia coli without inactivation. 1993. Biochem. Biophys. Res. Commun. 193:191-197.
- The isolated RAD4gene required for nucleotide excision repair in Saccharomyces cerevisiaedose not contain a suppressor gene. 1990. Korean J. Genetics. 12:147-155.
 

■ 저서
- 세균과 세균바이러스의 유전학. 2015. 필수 유전학 6판. by D.L. Hartl (ed. 양재섭 외). chap. 7, pp 226-259. 바이오사이언스 출판
- 번역, 조절 RNA, 2014. 왓슨 분자생물학 7판 by J. Watson (ed. 양재섭 외). chap. 15, pp. 509-571; chap. 20, pp. 701-732 바이오사이언스 출판
- 세포생물학, 2014. by G. Plopper 범문 에듀케이션
- 전이. 2013. 분자생물학 5판 by R.F. Weaver, (ed. 최준호 외). chap. 23, pp. 677-701. 라이프사이언스
- 필수세포생물학 2판. 2003. by B.Alberts (ed. 박상대 외) 교보문고
- Apoptosis in immune system. 1998. 유전. 2: 129-146.
 

■ 특허
- DNA aptamers and their mixture for the prevention of infection and detection of avian influenza virus, H9N2. 2008. Korea 10-2008-0039199.
- Nucleic acid molecules, polypeptides, antibodies and compositions for treating and detecting influenza virus infection. 2010. US 7786279 B2
- DNA aptamer binding to kanamycin with specificity. 2010. Korea 10-1263450
- DNA aptamer binding to ampicillin with specificity. 2010. Korea 10-1258600
- DNA aptamer binding to sulfadimethoxine with specificity. 2010. Korea 10-1263449
- Functional health food composition using color food for anti-oxidative and anti-inflammatory effect and method for manufacturing the same. 2015. Korea 10-2015-0024442

■ 학회활동
- 한국세포분자생물학회 재무위원
- 대한면역학회 정회원
- 한국유전학회 정회원

■ 주요 연구주제
- non-coding RNA에 의한 면역세포의 분화 및 암 조절 기전 연구: 단백질을 암호화하지 않는 비번역 RNA가 면역기능을 담당하는 대식세포의 분화와 활성 조절에 관여하는 신호전달과 유전자 발현에 중요한 조절자로서 기능할 가능성에 대한 연구. 이 RNA는 세포의 증식과 암세포의 발병과정에서도 중요한 역할을 한다는 것을 밝힘으로써, 항암 또는 면역질환의 치료제 발굴에 관한 단서를 제공함.
- 항-바이러스 치료제 및 백신 개발: 인플루엔자 바이러스 감염을 억제하는 치료제 및 백신 후보물질의 발굴과 관련된 연구
- 기능성 천연소재의 면역활성 효능평가 및 조절기전 분석: 국내외 다양한 식물에서 유래한 면역조절 후보물질의 효능평가를 통한 기능성 식품, 화장품, 면역조절 치료제 발굴과 관련된 연구

■ 연구 및 저서

- Won J-I, Lee JB, Lee HW, Shin JM, Yoon JH, Jeong D-H. (2019) WebPORD: a web-based pipeline of RNA degradome. Int, J. Data Mining and Bioinformatics. 22: 216-230

- Franke KR, Schmidt SA, Park S, Jeong D-H, Accerbi M, Green PJ. (2018) Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops. BMC Genomics. 19: 547

- Chung PJ, Jung H, JeongD-H,Ha SH, Choi YD, Kim JK. (2016) Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice. BMC Genomics.17: 563

-  Jeong D-H(2016) Functional diversity of microRNA variants in plants J. Plant Biol.59: 303-310

- Kim C-Y, Vo KTX, Nguyen CD, JeongD-H, Lee S-K, Kumar M, Kim S-R, Park S-H, Kim J-K, Jeon J-S. (2016) Functional analysis of a cold-responsive rice WRKY gene, OsWRKY71. Plant Biotechnology Reports.10:13-23

- Schmidt SA, Foley PL, JeongD-H, Rymarquis LA, Doyle F, Tenenbaum SA, Belasco JG,, and Green PJ. (2015) Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells. Nucleic Acids Res. 43: 309-323

-  Jeong D-H, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, De Paoli E, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, and Green PJ. (2013) Parallel analysis of RNA ends enhances global investigation of miRNAs and target RNAs of Brachypodium distachyon.Genome Biology 14:R145

-  Jeong D-H, and Green PJ. (2013) The role of rice microRNAs in abiotic stress responses. J. Plant Biol.56: 187-197 (review)

-  Jeong D-H*, Thatcher SR*, Brown RSH, Zhai J, Park S, Rymarquis LA, Meyers BC, and Green PJ. (2013)Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading and target cleavage. Plant Physiol.162:1225-1245 (*co-first authors)

-  Jeong D-H, and Green PJ. (2012) Methods for validation of miRNA sequence variants and the cleavage of their targets. Methods 58:135-143

- Song X, Li P, Zhai J, Zhou M, Liu B, Ma L, JeongD-H, Nakata M, Cao S, Liu C, Chu C, Wang X-J, Green PJ, Meyers BC, and Cao X.(2012) Role of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J. 69:462-474

-  Jeong D-H, Park S, Zhai J, Gurazada SGR, De Paoli E, Meyers BC, and Green PJ. (2011) Massive analysis of rice small RNAs: Mechanistic implication of regulated miRNAs and variants for differential target RNA cleavage. Plant Cell23: 4185-4207

- Zhai J, JeongD-H,De Paoli E,Park S,Rosen BD, Li Y, González AJ,Yan Z, Kitto SL, Grusak MA, Jackson SA, Stacey G, Cook DR, Green PJ, Sherrier DJ, Meyers BC. (2011) microRNAs as Master Regulators of the Plant NB-LRR Defense Gene Family via the Production of Phased, Trans-acting siRNAs. Genes and Development25:1540

- Young ND, Debellé F, Oldroyd G, Geurts R, Cannon SB, Mayer KFX, Gouzy J, Van de Peer Y, Schoof H, Udvardi MK, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Proost S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Benedito VA, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Doyle JJ, Dudez A-M, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray S, JeongD-H,Jing Y, Jöcker A, Kenton SM, Kim D-J, Kathrin Klee, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun J-H, Najar FZ, Nicholson C, Noirot C, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Saurat O, Scarpelli C, Schiex T, Segurens B, Seigfried M, Severin A, Sherrier DJ, Shi R, Sims S, Sinharoy S, Sterck L, Vasylenko I, Viollet A, Wang K, Wang B-B, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA. (2011) The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses. Nature480:520-524

- Lee Y-S, JeongD-H, Lee D-Y, Yi J, Ryu C-H, Kim SL, Jeong HJ, Choi SC, Jin P, Yang J, Choi L-H, Choi H, and An G (2010) OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB. Plant J. 63:1830.

- Joshi T, Yan Z, Libault M, JeongD-H, Park S, Green PJ, Sherrier Dj, Farmer A, May G, Meyers BC, Xu D, Stacey G (2010) Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics11 (Suppl 1):S14.

■ 주요 연구주제

- RNA Genomics: 차세대염기서열분석기술(Next Generation Sequencing technology)를 이용하여small RNA 및mRNA와 같은 다양한 전사체(transcriptome)를 유전체 수준에서 연구함

- Crop Functional Genomics: 벼의 꽃발달 관여 유전자 및 환경스트레스 관련 유용유전자의 발굴과 형질전환식물체 개발을 통한 기능유전체 연구를 수행하고 있음.

- Post-transcriptional Gene Regulation: microRNA를포함한small RNA가 전사후단계에서 유전자발현을 조절하는 기작을 연구하며, RNA degradome 분석을 통한RNA 분해기작을 주로 연구함.

- Epigenetics and Epitranscriptomics: DNA 및 RNA의 변형이 유전자 발현 및 mRNA 안정화에 미치는 영향을 연구함.

■ 학회활동

- 한국식물학회

- 한국유전학회

■ 수상

- 한국식물학회JPB 논문상(2016)

연구실 홈페이지

■ 논문

<자세한 내용은 연구실 홈페이지 링크 참조>

• Ji-Ung Park, Bumjo Oh, Jung Pyo Lee, Min-Ha Choi, Min-Jung Lee, Bong-Soo Kim*. (2019) Influence of microbiota on diabetic foot wound in comparison with adjacent normal skin based on the clinical features. BioMed Research International. 2019. 7459236.

• Hyo-Eun Kim, Jin-Jae Lee, Min-Jung Lee, Bong-Soo Kim*. (2019) Analysis of microbiome in raw chicken meat from butcher shops and packaged products in South Korea to detect the potential risk of foodborne illness. Food Research International. 122, 517-527.

• Jin-Jae Lee, Sae-Hoon Kim, Min-Jung Lee, Byung-Keun Kim, Woo-Jung Song, Heung-Woo Park, Sang-Heon Cho, Soo-Jong Hong, Yoon-Seok Chang, Bong-Soo Kim*. (2019) Different upper airway microbiome and their functional genes associated with asthma in young adults and elderly individuals. Allergy. 74(4), 709-719.

• Bong-Soo Kim, Chong Won Choi, Hyoseung Shin, Seon-Pil Jin, Jung-Soo Bae, Mira Han, Eun Young Seo, Jongsik Chun, Jin Ho Chung. (2019) Comparison of the gut microbiota of centenarians in longevity villages of South Korea with those of other age groups. Journal of Microbiology and Biotechnology. 29(3), 429-440.

• Han Young Chung, Byungho Lee, Eun Jung Na, Kyu-Ho Lee, Sangryeol Ryu, Hyunjin Yoon, Ju-Hoon Lee, Hyeun Bum Kim, Heebal Kim, Hee Gon Jeong, Bong-Soo Kim*, Sang Ho Choi. (2018) Potential survival and pathogenesis of a novel strain, Vibrio parahaemolyticus FORC_022, isolated from a soy sauce marinated crab by genome and transcriptome analyses. Frontiers in Microbiology. 9, 1504.

• Min-Jung Lee, Mi-Jin Kang, So-Yeon Lee, Eun Lee, Kangjin Kim, Sungho Won, Dong In Suh, Kyung Won Kim, Young Ho Sheen, Kangmo Ahn, Bong-Soo Kim*, Soo-Jong Hong. (2018) Perturbation of the gut microbiome genes in infants with atopic dermatitis according to feeding type. Journal of Allergy and Clinical Immunology. 141(4), 1310-1319

<Editors’ choice of Issue>

<Selected latest research in AAAAI (American Academy of Allergy Asthma & Immunology>

• Bong-Soo Kim, Eun Lee, Min-Jung Lee, Mi-Jin Kang, Jisun Yoon, Hyun-Ju Cho, Jaehyun Park, Sungho Won, So Yeon Lee, Soo-Jong Hong. (2018) Different functional genes of upper airway microbiome associated with natural course of childhood asthma. Allergy. 73(3), 644-652.

• Bong-Soo Kim, Dong-Hun Han, Ho Lee, Bumjo Oh. (2018) Association of salivary microbiota with dental caries incidence with dentine involvement after 4 years. Journal of Microbiology and Biotechnology. 28(3), 454-464.

• Jin Hee Park, Bong-Soo Kim*, Chul-Min Chon. (2018) Characterization of iron and manganese minerals and their associated microbiota in different mine sites to reveal the potential interactions of microbiota with mineral formation. Chemosphere. 191, 245-252.

• Jung-Soo Lim, Seung Hak Yang, Bong-Soo Kim, Eun Young Lee. (2018) Comparison of microbial communities in swine manure at various temperatures and storage times. Asian-Australasian Journal of Animal Sciences. 31(8), 1373-1380.

• Jin-Jae Lee, Tae-Yoon Kim, Sang Ho Choi, Bong-Soo Kim*. (2017) Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management. Food Research International. 102, 51-60.

• Tae-Yoon Kim, Jin-Jae Lee, Bong-Soo Kim*, Sang Ho Choi. (2017) Whole-body microbiota of sea cucumber (Apostichopus japonicas) from South Korea for improved seafood management. Journal of Microbiology and Biotechnology. 27(10), 1753-1762.

• Seung-Hak Yang, Hee Kwon Ahn, Bong-Soo Kim, Sun Sik Chang, Ki Yong Chung, Eun Mi Lee, Kwang Seok Ki, Eung Gi Kwon. (2017) Comparison of bacterial communities in leachate from decomposing bovine carcasses. Asian-Australasian Journal of Animal Sciences. 30(11), 1660-1666.

• Suyeon Kim, Min-Jung Lee, Jin-Jae Lee, Sang Ho Choi, Bong-Soo Kim*. (2017) Analysis of microbiota of the swimming crab (Portunus trituberculatus) in South Korea to identify risk markers for foodborne illness. LWT –Food Science and Technology. 86, 483-491.

• Jing-Hua Wang, Bong-Soo Kim, Kyungsun Han, Hojun Kim. (2017) Ephedra-treated donor-derived gut microbiota transplantation ameliorates high fat diet-induced obesity in rats. International Journal of Environmental Research and Public health. 14 (6), 555.

• Yiseul Yeom, Bong-Soo Kim, Se-Jae Kim, Yuri Kim. (2016) Sasa quelpaertensis leaf extract regulates microbial dysbiosis by modulating the composition and diversity of the microbiota in dextran sulfate sodium-induced colitis mice. BMC Complementary and Alternative Medicine. 16:481

• Han Young Chung, Kyu-Ho Lee, Sangryeol Ryu, Hyunjin Yoon, Ju-Hoon Lee, Hyeun Bum Kim, Heebal Kim, Hee Gon Jeong, Sang Ho Choi, Bong-Soo Kim*. (2016) Genome sequence of Bacillus cereus FORC_021, a food-borne pathogen isolated from a knife at a sashimi restaurant. Journal of Microbiology and Biotechnology. 26(12), 2030-2035.

• Woo-Jun Sul, In-Soo Kim, Kalu I. Ekpeghere, Bongkeun Song, Bong-Soo Kim, Hong-Gi Kim, Jong-Tae Kim, Sung-Cheol Koh. (2016) Metagenomic insight of nitrogen metabolism in a tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1. Journal of Environmental Science and Health, Part A.51(13), 1164-1172.

• Min-Jung Lee, Jin-Jae Lee, Han Young Chung, Sang Ho Choi, Bong-Soo Kim*. (2016) Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management. International Journal of Food Microbiology. 234, 45-52.

• Eun Lee, So-Yeon Lee, Mi-Jin Kang, Kangjin Kim, Sungho Won, Byoung-Ju Kim, Kil Yong Choi, Bong-Soo Kim, Hyun-Ju Cho, Yeongho Kim, Song I. Yang, Soo-Jong Hong. (2016) Clostridia in the gut and onset of atopic dermatitis via eosinophilic inflammation. Annals of Allergy, Asthma & Immunology. 117(1), 91-92.e1.

• Bumjo Oh, Jong Seung Kim, Meera Kweon, Bong-Soo Kim, In Sil Huh. (2016) Six-week diet correction for body weight reduction and its subsequent changes of gut microbiota: a case report. Clinical Nutrition Research. 5, 137-140.

• Han Young Chung, Eun Jung Na, Kyu-Ho Lee, Sangryeol Ryu, Hyunjin Yoon, Ju-Hoon Lee, Hyeun Bum Kim, Heebal Kim, Sang Ho Choi, Bong-Soo Kim*. (2016) Complete genome sequence of Vibrio parahaemolyticus FORC_023 isolated from raw fish storage water. Pathogens and Diseases. 74(4).

• Bumjo Oh, Ji Won Kim, Bong-Soo Kim*. (2016) Changes in the functional potential of the gut microbiome following probiotic supplementation during Helicobacter pylori treatment. Helicobacter. 21(6), 493-503.

• Bumjo Oh†, Bong-Soo Kim†, Ji Won Kim, Jong Seung Kim, Seong-Joon Koh, Byeong Gwan Kim, Kook Lae Lee, Jongsik Chun. (2016) The effect of probiotics on gut microbiota during the Helicobacter pylori eradication: randomized controlled trial. Helicobacter. 21(3), 165-174.

• SeungHak Yang, Joung Soo Lim, Modabber Ahmed Khan, Bong-Soo Kim, Dong Yoon Choi, Eun Young Lee, HeeKwon Ahn. (2015) High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses. Genetics and Molecular Biology. 38(3), 373-380.

• Kyungsun Han, Shambhunath Bose, Young-Mi Kim, Young-Won Chin, Bong-Soo Kim, Jing-hua Wang, Jung-Ho Lee, Hojun Kim. (2015) Rehmannia glutinosa reduced waist circumferences of Korean obese women possibly through modulation of gut microbiota. Food & Function. 6(8):2684-2692.

• Hea Young Oh†, Bong-Soo Kim†, Sang-Soo Seo, Ji-Sook Kong, Jae-Kwan Lee, Sang-Yoon Park, Kyeong-Man Hong, Hyun-Kyoung Kim, Mi Kyung Kim. (2015) The association of uterine cervical microbiota with an increased risk for cervical intraepithelial neoplasia in Korea. Clinical Microbiology and Infection 21(7): 674.e1-9.

• Sang A Lee, Ji Ye Lim, Bong-Soo Kim, Su Jin Cho, Nak Yon Kim, Ok Bin Kim, Yuri Kim. (2015) Comparison of the gut microbiota profile in breast- and formula- fed Korean infants using pyrosequencing. Nutrition Research and Practice. 9(3):242-248.

• Kyungsun Han, Shambhunath Bose, Jing-hua Wang, Bong-Soo Kim, Mi Jeong Kim, Eun-Jung Kim, Hojun Kim. (2015) Contrasting effects of fresh and fermented kimchi consumption on gut microbiota composition and gene expression related to metabolic syndrome in obese Korean women. Molecular Nutrition & Food Research. 59(5), 1004-1008.

• SangJoon Mo†, Bong-Soo Kim†, Sung-Jo Yun, Jung-Ju Lee, Suk-Hyun Yoon, Chung-Hun Oh. (2015) Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces. Gut Pathogens.7:8.

• Ohgew Kweon, Seong-Jae Kim, Jochen Blom, Sung-Kwan Kim, Bong-Soo Kim, Dong-Heon Baek, Su Park, John B. Sutherland, Carl E. Cerniglia. (2015) Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium. BMC Evolutionary Biology. 15:21.

• Yoon-Seong Jeon, Sang-Cheol Park, Jeongmin Lim, Jongsik Chun, Bong-Soo Kim*. (2015) Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform. Journal of Microbiology. 53 (1), 60-69.

• Yu-jin Lee, Bong-Soo Kim, Min-jeong Kim, Sehee Nam, Sung-Ae Oh, Yun S. Kim, Ilhwan Choi, Jong-Geun Park, Gyu-Cheol Lee. (2014) Molecular characterization of Actinomycetes isolated from terrestrial environment and their synthesis of Geosmin and 2-MIB. Journal of Pure and Applied Microbiology. 8. 103-113.

• Sunhyun Park, Kyung-Mo Song, Hyo-Jin Kim, Bong-Soo Kim, Young Kyung Rhee, Myung-Ki Lee. (2014) Characterization and use of microbial communities in Doenjang to control the unpleasant odor of Ginkgo epicarp. Food Science and Biotechnology. 23(6), 1959-1964.

• Hoy Jin Kim, Min-Jeong Kim, Timothy Lee Turner, Bong-Soo Kim, Kyung-Mo Song, Sung Hun Yi and Myung-Ki Lee. (2014) Pyrosequencing analysis of microbiota reveals that lactic acid bacteria are dominant in Korean flat fish fermented food, Gajami-sikhae. Bioscience Biotechnology and Biochemistry. 78(9), 1611-1618.

• Yangsoon Lee†, Bong-Soo Kim†, Jongsik Chun, Ji Hyun Yong, Yeong Seon Lee, Jung Sik Yoo, Dongeun Yong, Seong Geun Hong, Roshan D’Souza, Kenneth S. Thomson, Kyungwon Lee, Yunsop Chong. (2014) Clonality and resistome analysis of KPC-producing Klebsiella pneumonia strain isolated in Korea using whole genome sequencing. Biomed Research International. 2014:352862.

• Mi-young Song, Bong-Soo Kim, Hojun Kim. (2014) Influence of Panax ginseng on obesity and gut microbiota in obese middle-aged Korean women. Journal of Ginseng Research. 38(2), 106-115.

• Bong-Soo Kim, Hana Yi, Jongsik Chun, Chang-Jun Cha. (2014) Genome sequence of type strain Staphylococcus aureus subsp. aureus. Gut Pathogens. 6:6.

• Bong-Soo Kim, Mi-young Song, Hojun Kim. (2014) The anti-obesity effect of Ephedra sinica through modulation of gut microbiota in obese Korean women. Journal of Ethnopharmacology. 152 (3), 532-539.

• Yoon-Seong Jeon, Kihyun Lee, Sang-Cheol Park, Bong-Soo Kim, Yong-Joon Cho, Sung-Min Ha, Jongsik Chun. (2014) EzEditor: A versatile sequence alignment editor for both ribosomal RNA and protein coding genes. International Journal of Systematic and Evolutionary Microbiology. 64(2), 689-691.

• Bong-Soo Kim, Hyo Sang Bae, Chi-yeon Lim, Mi Jeong Kim, Jae-gu Seo, Jong Yeol Kim, Jae-eun Kim, Hojun Kim. (2013) Comparison of gut microbiota between Sasang constitutions. Evidence-Based Complementary and Alternative Medicine. Volume 2013, article ID 171643, doi:10.1155./2013/171643.

• In-Soo Kim, Kalu I. Ekpeghere, Shin-Young Ha, Bong-Soo Kim, Bongkeun Song, Jong-Tae Kim, Hong-Gi Kim, Sung-Cheol Koh. (2013) Full-scale biological treatment of tannery wastewater using the novel microbial consortium BM-S-1. Journal of Environmental Science and Health, Part A. 49(3), 355-364

• Moonsuk Hur, Injung Lee, Bo-Mi Tak, Hae Jin Lee, Jae Jeong Yu, Se Uk Cheon, Bong-Soo Kim*. (2013) Temporal shifts in cyanobacterial communities at different sites on the Nakdong River in Korea. Water Research. 47(19), 6973-6982.

• Mincheol Kim, Ki-Hyun Lee, Seok-Whan Yoon, Bong-Soo Kim, Jongsik Chun and Hana Yi. (2013) Analytical tools and databases for metagenomics in Next-Generation Sequencing era. Genomics & Informatics. 11(3), 102-113.

• Bong-Soo Kim*, Yoon-Seong Jeon and Jongsik Chun. (2013) Current status and future promise of the human microbiome. Pediatric Gastroenterology, Hepatology & Nutrition. 16 (2), 71-79.

• In-Soo Kim, Kalu Ibe Ekpeghere, Shin-Young Ha, Soo-Hyeon Kim, Bong-Soo Kim, Bongkeun Song, Jongsik Chun, Jae-Soo Chang, Hong-Gi Kim and Sung-Cheol Koh. (2013) An eco-friendly treatment of tannery wastewater by bioaugmentation of a novel microbial consortium. Journal of Environmental Science and Health, Part A. 48(13), 1732-1739.

• Yoon-Seong Jeon, Jongsik Chun and Bong-Soo Kim*. (2013) Identification of household bacterial community and analysis of species shared with human microbiome. Current Microbiology. 67(5):557-563.

• Kwang Ho Ahn, Kwang Baik Ko, Baek Woo Sung, June Seok Choi, Bong-Soo Kim, Kwang Soo Kim. (2013) Settling and dewatering characteristics of mixed microorganisms according to changes in the SRT. Desalination and Water Treatment. 51:6201-6209.

• Mariya Khodakovskaya, Bong-Soo Kim, Jong Nam Kim, Mohammad Alimohammadi, Enkeleda Dervishi, Thikra Mustafa, and Carl E. Cernigla. (2013) Carbon nanotubes as plant growth regulators: effects on tomato growth, reproductive system and soil microbial community. Small. 9(1):115-123.

• Chong-Tai Kim, Bong-Soo Kim, Min-Ji Kim, Bang Heon Park, Sujin Kwon, Hack Young Maeng, Jangyul Kwak, Jongsik Chun, Yong-Jin Cho, Namsoo Kim, Chul-Jin Kim, and Jin-Soo Maeng. (2012) Draft genome sequencing of Bacillus sp. M2-6, Isolated from the roots of a Korean Ginseng, Panax ginseng C. A. Meyer, after high hydrostatic pressure processing. Journal of Bacteriology. 194 (24):7003-7004.

• Jong Nam Kim†, Bong-Soo Kim†, Seong-Jae Kim, and Carl E. Cerniglia. (2012) Effects of Crude oil, Dispersant, and Oil-dispersant mixtures on Human fecal microbiota in an in vitro culture system. mBio. 3(5): doi:10.1128/mBio.00376-12.

• Bong-Soo Kim, Chong-Tai Kim, Bang Heon Park, Sujin Kwon, Yong-Jin Cho, Namsoo Kim, Chul-Jin Kim, Jongsik Chun, Jangyul Kwak and Jin-Soo Maeng. (2012) Draft genome sequencing of Staphylococcus saprophyticus subsp. saprophyticus M1-1, isolated from the Gills of a Korean Rockfish, Sebastes schlegili Hilgendorf, after high hydrostatic pressure processing. Journal of Bacteriology. 194(16):4441-4442.

• Bong-Soo Kim, Jong Nam Kim, Suk-Hwan Yoon, Jongsik Chun and Carl E. Cerniglia. (2012) Impact of enrofloxacin on the human intestinal microbiota revealed by comparative molecular analysis. Anaerobe. 18 (3), 310-320.

• Dae-Wi Kim, Thomas M. Heinze, Bong-Soo Kim, Laura K. Schnackenberg, Kellie A. Woodling and John B. Sutherland. (2011) Modification of Norfloxacin by a Microbacterium sp. Strain Isolated from a Wastewater Treatment Plant. Applied and Environmental Microbiology. 77(17), 6100-6108.

• Bong-Soo Kim, Jong Nam Kim and Carl E. Cerniglia. (2011) In vitro culture conditions for maintaining a complex population of human gastrointestinal tract microbiota. Journal of Biomedicine and Biotechnology. Vol 2011, 838040. doi:10.1155/2011/838040.

• Young Woon Lim, Byung Kwon Kim, Changmu Kim, Hack Sung Jung, Bong-Soo Kim, Jae-Hak Lee, Jongsik Chun. (2010) Assessment of soil fungal communities using pyrosequencing. Journal of Microbiology. 48(3), 284-289.

• Bong-Soo Kim, Ok Sun Kim, Eun Young Moon and Jongsik Chun. (2010) Vitellibacter aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Vitellibacter. Int J Syst Evol Microbiol. 60(9), 1989-1992.

• Bong-Soo Kim, Young Woon Lim and Jongsik Chun. (2008) Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater. Int J Syst Evol Microbiol. 58(10), 2415-2419.

• Bong-Soo Kim, Byung Kwon Kim, Jae-Hak Lee, Myungjin Kim, Young Woon Lim and Jongsik Chun. (2008) Rapid Phylogenetic Dissection of Prokaryotic Community Structure in Tidal flat using pyrosequencing. Journal of Microbiology.46(4), 357-363.

• Ju-Hyoung Kim, Ki-Youn Kim, Young-Tae Hahm, Bong-Soo Kim, Jongsik Chun and Chang-Jun Cha. (2008) Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. Int J Syst Evol Microbiol. 58, 139-143.

• Bong-Soo Kim, Huyn-Myung Oh, Hojeong Kang and Jongsik Chun. (2005) Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. Journal of Microbiology. 43(2), 144-151.

• Bong-Soo Kim, Huyn-Myung Oh, Hojeong Kang, Seok-Soon Park and Jongsik Chun. (2004) Remarkable bacterial diversity in the tidal flat sediment as revealed by 16S rDNA analysis. Journal of Microbiology and.Biotechnology. 14 (1), 205-211.

■ 학회할동 
• 한국미생물학회 
• 한국미생물생명공학회 

■ 주요 연구주제 
• 인간미생물체 연구 (Human Microbiome)인간의 몸에는 인간 세포와 유전자수보다 훨씬 많고 다양한 미생물들이 존재하고 있습니다. 이 다양한 미생물들의 구성과 역할을 대용량 염기서열 분석 장비인 Next-Generation Sequencer를 활용한 연구 수행을 통해 밝히고자 합니다. 이를 통해 여러 질병과 미생물 군집의 상관성 연구 및 건강 유지를 위한 응용 방안들을 연구합니다. 밝혀낸 다양한 결과를 산업, 보건학 분야에서 활용 가능하도록 합니다. 

• 미생물 메타지노믹스 연구 (Metagenomics)우리 인간을 포함한 지구상의 모든 환경에는 미생물들이 복잡한 구성을 이루며 공존하고 있습니다. 하지만, 대부분의 미생물들은 실험실에서 배양할 수 없는 종들이 대부분입니다. 환경에 실제 존재하는 미생물들의 구성과 생태적 역할을 메타지노믹스를 활용하여 연구를 합니다. 실제 우리가 생활하고 있는 환경의 미생물 군집의 연구 (Household microbiome) 와 여러 환경의 미생물 군집 연구 (Ecosystem microbiome) 결과를 통해 다양한 환경의 관리 방안에 도움을 주고자 합니다. 

• 미생물 유전체 연구 (Genomics)유익한 미생물 종들과 유해한 미생물 종들의 전유전체 (Whole genome) 분석을 통해 이들의 역할과 진화생태적인 상관성을 연구합니다. 연구를 통해 다양한 유전자 검출법과 유전자 활용 기법을 고안하고자 합니다. 

연구실 홈페이지

■ 논문

• Malinow RA, Ying P, Koorman T, Boxem M, Jin Y#, Kim KW#. Functional Dissection of C. elegans bZip-Protein CEBP-1 Reveals Novel Structural Motifs Required for Axon Regeneration and Nuclear Import. Frontiers in Cellular Neuroscience (2019) 13:348

• Kim KW#, Tang NH, Andrusiak MG, Wu Z, Chisholm AD, and Jin Y#. A neuronal piRNA pathway inhibits axon regeneration in C. elegans. Neuron (2018) 97(3):511-519

• Sharifnia P, Kim KW*, Wu Z, and Jin Y. Distinct cis elements in the 3' UTR of the C. elegans cebp-1 mRNA mediate its regulation in neuronal development. Developmental Biology (2017) 429(1):240-248.

• Kim KW*, Thakur N, Piggott CA, Omi S, Polanowska J, Jin Y, and Pujol N. Coordinated inhibition of C/EBP by Tribbles in multiple tissues is essential for C. elegans development. BMC biology (2016) 14(1):104-118.

• Xu S, Wang Z, Kim KW*, Jin Y, and Chisholm AD. Targeted mutagenesis of duplicated genes in Caenorhabditis elegans. Journal of Genetics and Genomics. (2016) 43(2):103-106.

• Noble DC, Aoki ST, Ortiz MA, Kim KW*, Verheyden JM, and Kimble J. Genomic Analyses of Sperm Fate Regulator Targets Reveal a Common Set of Oogenic mRNAs in Caenorhabditis elegans. Genetics (2016) 202:221-234.

• Kim KW# and Jin Y#. Neuronal responses to stress and injury in C. elegans. FEBS Letters (2015) 589(14):1644-1652.

• Lee M-H*, Kim KW*, Morgan CT, Morgan DE and Kimble J. Phosphorylation state of a TOB/BTG protein, FOG-3, regulates initiation and maintenance of the Caenorhabditis elegans sperm fate program. PNAS (2011) 108: 9125-9130. *equally contributed.

• Kim KW*, Wilson TL, and Kimble J. GLD-2/RNP-8 cytoplasmic poly(A) polymerase is a broad-spectrum regulator of the oogenesis program. PNAS (2010) 107:17445-17450.

• Kim KW*, Nykamp K, Suh N, Bachorik JL, Wang L and Kimble J. Antagonism between GLD-2 binding partners controls gamete sex. Developmental Cell (2009) 16: 723-733. 

• Hesselson D, Newman C, Kim KW and Kimble J. GON-1 and fibulin have antagonistic roles in control of organ shape. Current Biology (2004) 14: 2005-2010 

• Kim KW*, Shin JH, Moon J, Kim M, Lee J, Park MC and Lee I. The function of the flowering time gene AGL20 is conserved in Crucifers. Molecules and Cells (2003) 16: 136-141.

■ 주요연구주제

• 신경 재생 및 퇴행
• 신경 독성
• 동물 발달 및 노화
• small RNA 연구

■ 학회활동

• 미국유전학회(GSA) 정회원
• 한국분자·세포생물학회(KSMCB) 회원운영위원
• 한국뇌신경과학회(KSBNS) 정회원

■ 연구비 수상
• 한국연구재단 개인연구사업 중견연구, 2019-2021년
• 한국연구재단 뇌과학원천기술개발사업, 2019-2021년
• 미국심장학회(AHA), 2013 – 2014년

"Diversion of locomotor activity rhythm and neural control Azadirachtin in Leucophaea maderae", 동물학회지, 1988.10

"저준위 방사능이 Neurospora crassa의 리듬에 미치는 영향", 발암원학회지, 1991.3

"LiCl이 Goldhamster의 빛민감성과 활동주기에 미치는 영향", 동물학회지, 1992.10

"방사선물질 Li+, Rb+, Cs+이 Neurospora crassa의 성장 일주기에 미치는 영향", 한국독성학회지, 1993.4

"Neurospora crassa의 포자형성주기에 미치는 빛-파장과 중금속이온의 영향관계 조사", 한국환경독성학회지, 11, 1995.

"Melatonin and other Methoxyindoles in Yeast, Saccharomyces cereviside", Journal of Uni Goettingen, 1996.

"Circardian Locomotor Activity of Musca Flies: Effects of 50 and 100Hz Squarewave Electric Fields", Bioelectromagnetics, 18, 1997.

저 작

바이오 리듬의 규명과 응용, 아카데미서적, 1993.8.

연구분야

동물생리학, 생체주기학, 생태학