한림대학교 HALLYM UNIVERSITY

■ 논문 (최근 5년)
- Development of an enzymatic encapsulation process for a cycloamylose inclusion complex with resveratrol. (2021) Food Chemistry. 345:128777.
- Ubiquitous Overexpression of Chromatin Remodeling Factor SRG3 Exacerbates Atopic Dermatitis in NC/Nga Mice by Enhancing Th2 Immune Responses. (2021) International Journal of Molecular Sciences. 22:3043.
- nc886, a novel suppressor of the type I interferon response upon pathogen intrusion. (2021) International Journal of Molecular Sciences.22:2003.
- Chromatin Regulator SRG3 Overexpression Protects against LPS/D-GalN-induced Sepsis by Increasing IL10-producing Macrophages and Decreasing IFNγ-producing NK cells in the Liver. (2021) International Journal of Molecular Sciences.22: 1553.
- Design and Synthesis of π-Extended Resveratrol Analogues and In Vitro Antioxidant and Anti-Inflammatory Activity Evaluation. (2021) Molecules 26:646.
- Growth and drug reaction monitoring of NIH 3T3 cells using impedance biosensor. (2020) New Physics: Sae Mulli 70:1015-1020.
- Twist2 promotes CD8+ T-cell differentiation by repressing ThPOK expression. (2020) Cell Death and Differentiation. 27:3053-3064.
- A Regulatory Noncoding RNA, nc886, Suppresses Esophageal Cancer by Inhibiting the AKT Pathway and Cell Cycle Progression. (2020) Cells 9:801.
- Discovery of Epinastine-NSAID Hybrids as Potential Anti-inflammatory Agents: Synthesis and In Vitro Nitric Oxide Production Inhibitory Activity Study. (2020) Journal of the Korean Chemical Society 64:79-83.
- Novel Hybrid Molecules of Epinastine and Mefenamic Acid for Bioactive Assessment as Potential Anti-inflammatory Agents. (2020) Bull. Korean Chem. Soc. 41:444-449
- Effects of Corn-Derived Arabinoxylan-Containing Polysaccharides on Innate Immune Activity. (2020) J Korean Soc Food Sci Nutr. 49:119-126.
- Synthesis and Biological Assay of Hybrids Between Epinastine and Salicylic Acid as Promising Nitric Oxide Production Inhibitors. (2019) B. Korean Chem. Soc. 40: 735-740.
- TLR4-dependent effects of ISAg treatment on conventional T cell polarization in vivo. (2019) Anim Cells Syst. 23(3): 184-191.
- nc886, a non-coding RNA, inhibits UVB-induced MMP-9 and COX-2 expression via the PKR pathway in human keratinocytes. (2019) Biochem Biophys Res Commun. 512(4):647-652.
nc886 is induced by TGF-β and suppresses the microRNA pathway in ovarian cancer. (2018) Nat Commun. 9(1):1166
- Anti-cancer activity of Angelica gigas by increasing immune response and stimulating natural killer and natural killer T cells. (2018) BMC Complement Altern Med. 18(1):218.
- Enzymatic Synthesis of a Novel Kaempferol-3‑O‑β‑D‑glucopyranosyl-(1→4)‑O‑α‑D‑glucopyranoside Using Cyclodextrin Glucanotransferase and Its Inhibitory Effects on Aldose Reductase, Inflammation, and Oxidative Stress. (2017) J. Agric. Food Chem. 2017, 65, 2760−2767

■ 저서
- 전이. 2021. 분자생물학 5판 by R.F. Weaver.. chap. 23, 교문사
- 세균과 세균바이러스의 유전학. 2020. 필수 유전학 7판 월드사이언스 
- 번역, 조절 RNA, 2014. 왓슨 분자생물학 7판 by J. Watson. chap. 15, 20, 바이오사이언스
- 세포생물학, 2014. by G. Plopper 범문 에듀케이션
- 필수세포생물학 2판. 2003. by B.Alberts 교보문고

■ 특허 등록 (최근 5년)
- 코르너스 오블롱가 추출물을 이용한 궤양성 대장염 개선용 조성물 2021. 10-2226448
- 코르너스 오블롱가 추출물을 이용한 항염증용 조성물 2021. 10-2226439
- 큰만병초 추출물을 포함하는 항바이러스 조성물 2021. 10-2215336
- 레스베라트롤 유사 화합물을 포함하는 항산화 조성물 2019. 10-1985005
- 레스베라트롤 유사 화합물을 포함하는 항산화제 및 항염증제 2018. 10-1854829
- Nucleic acid molecules, polypeptides, antibodies and compositions for treating and detecting influenza virus infection. 2010. US 7786279 B2
- 카나마이신에 특이적으로 결합하는 ＤＮＡ 앱타머 2010. 10-1263450
- 암피실린에 특이적으로 결합하는 ＤＮＡ 앱타머 2010. 10-1258600
- 설파디메톡신에 특이적으로 결합하는 ＤＮＡ 앱타머 2010. 10-1263449

■ 학회 및 산학협의체 활동
- (재)강원지역사업평가단 이사
- (재)홍천메디칼허브연구소 운영위원
- 한국세포분자생물학회 강원분회장
- 한국통합생물학회 정보위원장
- 대한면역학회 정회원
- 한국유전학회 정회원
 

■ 주요 연구주제
- non-coding RNA에 의한 면역세포의 분화 및 암 조절 기전 연구 
- 항-바이러스 치료제 및 백신 개발: 인플루엔자 바이러스 감염을 억제하는 치료제 및 백신 후보물질의 발굴기능성 천연소재의 면역활성 효능평가 및 조절기전 분석

■ 논문
구글스칼라 페이지

1. Won J-I, Shin JM, Park SY, Yoon JH, Jeong D-H. (2020) Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts. Int. J. Mol. Sci. 21: 6452 

2. Park SY, Choi JH, Oh DH, Johnson JC, Dassanayake M, Jeong D-H, Oh MH. (2020) Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana. Genes Genomics. 42: 957-969. 

3. 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

4. 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

5. Chung PJ, Jung H, Jeong D-H, Ha SH, Choi YD, Kim JK. (2016) Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice. BMC Genomics. 17: 56 

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

7. Kim C-Y, Vo KTX, Nguyen CD, Jeong D-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 

8. Schmidt SA,  Foley PL, Jeong D-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

9. 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

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

11. 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)

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

13. Song X, Li P, Zhai J, Zhou M, Liu B, Ma L, Jeong D-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

14. 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 Cell 23: 4185-4207

15. Zhai J, Jeong D-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 Development 25:1540

16. 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, Jeong D-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. Nature 480:520-524

17. Lee Y-S, Jeong D-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.

18. Joshi T, Yan Z, Libault M, Jeong D-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 Bioinformatics 11 (Suppl 1):S14. 

19. De Paoli E, Dorantes A, Zhai J, Accerbi M, Jeong D-H, Park S, Meyers BC, Jorgensen RA, Green PJ (2009). Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA 15:1965-1970.

20. Haas BJ, Kamoun S, Zody MC, Jiang RHY, HandsakerRE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AMV, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JIB, Broad Institute Genome Sequencing Platform, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R,Fahlgren N,Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grünwald NJ, Horn K, Horner NR, Hu C-H, Huitema E, Jeong D-H, Jones AME, Jones JDJ, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma LJ, MacLean D, Marcus C, McDonald H, McWalters J, Meijer HJG, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzón A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJI, Vipaporn P, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PRJ, Whisson SC, Judelson HS, Nusbaum C (2009). Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393-398.

21. Moon S, Giglione C, Lee D-Y, An S, Jeong D-H, Meinnel T, An G (2008) Rice peptide deformylase PDF1B is crucial for development of chloroplasts. Plant and Cell Physiology 49: 1535-1546.

22. Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vasquez M, Sidorenko L, Jeong D-H, Yen Y, Chandler V, Green PJ, Meyers BC (2008) A novel size distribution of endogenous siRNAs in maize: evidence from sequencing in the mop1-1 mutant. P.N.A.S. 105:14958-14963.

23. German MA, Pillay M, Jeong D-H, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol. 26:941-946.

24. Lee S, Jeong D-H, An G (2008) A possible working mechanism for rice SVP group MADS-box proteins as negative regulators of brassinosteroid responses. Plant signaling & behavior 3: 471-474.

25. Lu C, Jeong D-H, Kulkarni K, Pillay M, Nobuta K,  German R, Thatcher SR, Maher C,  Zhang L, Ware D, Liu B, Cao X, Meyers BC, Green PJ (2008) Genome-wide analysis for discovery of unique rice miRNAs reveals natural antisense miRNAs (nat-miRNAs). P.N.A.S. 105:4951-4956.

26. Jeong D-H, Lee S, Kim SL, Hwang I, An G, (2007) Regulation of brassinosteroid responses by phytochrome B in rice. Plant Cell Environ. 30: 590-599.

27. Jeong D-H*, An S*, Park S, Kang H-G, Park G-G, Kim S-R, Sim J, Kim Y-O, Kim M-K, Kim S-R, Kim J, Shin M, Jung M, An G. (2006) Generation of flanking sequence tag database for activation tagging lines in japonica rice, Plant J. 45:123-132. (*co-first authors)

28. Kim SJ, Jeong DH, An G, Kim S-R (2005) Characterization of a drought-responsive gene, OsTPS1, identified by the T-DNA gene-trap system in rice, J. Plant Biol. 48:371-379. 

29. Shin J-H, Jeong D-H, Park MC, An G. (2005) Characterization and transcriptional expression of the α-expansin gene family in rice, Mol. Cells, 20:210-218.

30. An G, Jeong D-H, Jung K-H, Lee S. (2005) Reverse genetic approaches for functional genomics of rice. Plant Mol. Biol. 59:111-123. (review) 

31. Lee S-C, Kim J-Y, Kim S-H, Kim S-J, Lee K, Han S-K, Choi H-S, Jeong D-H, An G, Kim S-R, (2004) Trapping and characterization of cold-responsive genes from T-DNA tagging lines in rice, Plant Science,166: 69-79.

32. Lee S, Kim J, Son J-S, Nam J, Jeong D-H, Lee K, Jang S, Yoo J, Lee J, Lee D-Y, Kang H-G, An G, (2003) Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case. Plant Cell Physiol, 44: 1403-1411.

33. An S, Park S, Jeong D-H, Lee D-Y, Kang H-G, Yu J-H, Hur J, Kim S-R, Kim Y-H, Lee M, Han S, Kim S-J, Yang J, Kim E, Wi SJ, Chung HS, Hong J-P, Choe V, Lee H-K, Choi J-H, Nam J, Kim S-R, Park P-B, Park KY, Kim WT, Choe S, Lee C-B, An G. (2003) Generation and analysis of end-sequence database for T-DNA tagging lines in rice. Plant Physiol 133: 2040-2047.

34. Sasaki A, Itoh H, Gomi K, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Jeong D-H, An G, Kitano H, Ashikari M, Matsuoka M. (2003) Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science 299: 1896-1898.

35. Jeong D-H, An S, Kang H-G, Moon S, Han J-J, Park S, Lee H S, An K, An G. (2002) T-DNA insertional mutagenesis for activation tagging in rice. Plant Physiol. 130:1636-1644. 

36. Yang K, Jeong D-H, Jang S, An G. (2001) Molecular cloning and characterization of a rice PP2C, OsPP2C4. J. Plant Biol. 44: 1-6. 

37. Sung S-K, Yu G-H, Nam J, Jeong D-H, An G. (2000) Developmentally regulated expression of two MADS-box genes, MdMADS3 and MdMADS4, in the morphogenesis of flower buds and fruits in apple. Planta 210: 519-528. 

38. Jeon J-S, Lee S, Jung K-H, Jun S-H, Jeong D-H, Lee J, Kim C, Jang S, Lee S-Y, Yang K, Nam J-M, An K, Han M-J, Sung R-J, Choi H-S, Yu J-W, Choi J-H, Cho S-Y, Cha S-S, An G. (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J. 22: 561-570. 

39. Kim C, Jeong D-H, An G. (2000) Molecular cloning and characterization of OsLRK1 encoding a putative receptor-like protein kinase from Oryza sativa. Plant Sci. 152: 17-26. 

40. Jeong D-H, Sung S-K, An G. (1999) Molecular cloning and characterization of CONSTANS-like cDNA clones of the Fuji apple. J. Plant Biol. 42: 23-31. 

41. Sung S-K, Jeong D-H, Nam J, Kim S-H, Kim S.-R, An G. (1998) Expressed sequence tags of fruits, peels, and carpels and analysis of mRNAs expression levels of the tagged cDNAs of fruits from the Fuji apple. Mol. Cells 8: 565-577.

■  특허

- 전종성, 이상규, 심수현, 고희종, 김백기, 정동훈, 박소영 (2021) 벼의 폐화수정 유도를 위한 MicroRNA172b 유전자 및 이의 돌연변이에 의한 폐화수정 벼의 제조방법. 국내특허출원번호 10-2021-0084572

- 전종성, 김치열, 키우 티 수안 보, 얀 콩 뉴엔, 정동훈, 김성룡, 김주곤, 이상규 (2016) OsWRKY71 유전자의 발현이 증진된 저온 내성 형질전환 식물체. 출원번호: 10-2016-0048355

- An G, Lee S, Jeong D-H, Yoo JH, Ryu C-H, Jeon J-S, Kim S-R, Kim Y-O, Kim J, An S, (2014) Regulator for flowering time, transgenic plant transformed with the same, and method for regulating flowering time. US Patent No. 8785724B2

- An G, Jeong D-H, Kang H-G, An S, An K, S-O Moon. The method for preparing transformed monocotyledon with T-DNA tagging vector comprising an enhancer element for activation tagging and a reporter gene trapping and the transformants prepared by this method. Republic of Korea, Patent No. 0464677 (2004.12.22). 

■ 주요 연구주제
- RNA Genomics: 차세대염기서열분석기술(Next Generation Sequencing technology)를이용하여 small RNA 및 mRNA와 같은 다양한 전사체(transcriptome)를 유전체 수준에서 연구함
- Crop Functional Genomics: 벼의 꽃발달 관여 유전자 및 환경스트레스 관련 유전자의 발굴과 형질전환식물체 개발을 통한 기능유전체 연구를 수행하고 있음
- Post-transcriptional Gene Regulation: microRNA를 포함한 small RNA가 전사후단계에서 유전자 발현을 조절하는 기작을 연구하며, RNA degradome 분석을 통한 RNA 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 링크

■ 논문

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- Jaehyun Park, Sharon M. Lutz, Seungil Choi, Sanghun Lee, Sangcheol Park, Kangjin Kim, Hosik Choi, Hansoo Park, So-Yeon Lee, Scott T. Weiss, Soo-Jong Hong, Bong-Soo Kim*, Sungho Won*. (2021) Multi-omics analyses implicate EARS2 in the pathogenesis of atopic dermatitis. Allergy. 76(8); 2602-2604.
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- Ji Eun Kim, Hyo-Eun Kim, Hyunjeong Cho, Ji In Park, Min-Jung Kwak, Byung-Yong Kim, Seung Hee Yang, Jung Pyo Lee, Dong Ki Kim, Kwon Wook Joo, Yon Su Kim, Bong-Soo Kim, Hajeong Lee. (2020) Effect of the similarity of gut microbiota composition between donor and recipient on graft function after living donor kidney transplantation. Scientific Reports. 10, 18881.
- Ji In Park, Tae-Yoon Kim, Bumjo Oh, Hyunjeong Cho, Ji Eun Kim, Seong Ho Yoo, Jung Pyo Lee, Yon Su, Kim, Jongsik Chun, Bong-Soo Kim*, Hajeong Lee*. (2020) Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases. Scientific Reports. 10, 16206.
- Bo Kyoung Hwang, HeyLim Choi, Sang Ho Choi*, Bong-Soo Kim*. (2020) Analysis of microbiota structure and potential functions influencing spoilage of fresh beef meat. Frontiers in Microbiology. 11, 1657.
- Ji Eun Kim, Hyo-Eun Kim, Ji In Park, Hyunjeong Cho, Min-Jung Kwak, Byung-Yong Kim, Seung Gee Yang, Jung Pyo Lee, Dong Ki Kim, Kwon Wook Joo, Yon Su Kim, Bong-Soo Kim*, Hajeong Lee*. (2020) The association between gut microbiota and uremia of chronic kidney disease. Microorganisms. 8, 907.
- HyeLim Choi, Bo Kyoung Hwang, Bong-Soo Kim*, Sang Ho Choi*. (2020) Influence of pathogen contamination on beef microbiota under different storage temperature. Food Research International. 132, 109-118.
- Yoon Mee Park, So-Yeon Lee, Mi-Jin Kang, Bong-Soo Kim, Min-Jung Lee, Sung Su Jung, Ji Sun Yoon, Hyun-Ju Cho, Eun Lee, Song-I Yang, Ju-Hee Seo, Hyo-Bin Kim, Dong In Suh, Youn Ho Shin, Kyung Won Kim, Kangmo Ahn, Soo-Jong Hong. (2020) Imbalance of gut Streptococcus, Clostridium, and Akkermansia determines the natural course of atopic dermatitis in infant. Allergy Asthma & Immunology Research. 12(2); 322-337.
- 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.
- 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.
- 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.
- Han Young Chung, Byungho Lee, Eun Jung Na, Kyu-Ho Lee, Sangryeol Ryu, Hyungjin 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.
- Joung-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.
- 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.
- 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, Huyn-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.
- 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.
- 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.
- 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.
- 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.
- 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.

■ 학회활동 
• 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 [https://sites.google.com/view/hallym-rn]

■ 논문

# : corresponding author 

- Jeong, H*, Park KH*, Lee, Y, Jeong A, Choi S, Kim KW#. The Regulation and Role of piRNAs and PIWI Proteins in Cancer. Processes 2021;9(7):1208. *equally contributed. https://doi.org/10.3390/pr9071208.
- Lee Y, Jeong H, Park KH, Kim KW#. Effects of NAD+ in Caenorhabditis elegans Models of Neuronal Damage. Biomolecules. 2020;10(7):E993. Published 2020 Jul 2. https://doi.org/10.3390/biom10070993.
- Tang NH, Kim KW, Xu S, et al. The mRNA Decay Factor CAR- 1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics. Curr Biol. 2020;30(5):865- 876.e7. https://doi.org/10.1016/j.cub.2019.12.061.
- Kim KW#. PIWI Proteins and piRNAs in the Nervous System. Mol Cells. 2019;42(12):828- 835. https://doi.org/10.14348/molcells.2019.0241.
- 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. Front Cell Neurosci. 2019;13:348. https://doi.org/10.3389/fncel.2019.00348.
- Kim KW#, Tang NH, Piggott CA, et al. Expanded genetic screening in Caenorhabditis elegans identifies new regulators and an inhibitory role for NAD+ in axon regeneration. Elife. 2018;7:e39756. https://doi.org/10.7554/eLife.39756.
- Kim KW, Tang NH, Andrusiak MG, Wu Z, Chisholm AD, Jin Y. A Neuronal piRNA Pathway Inhibits Axon Regeneration in C. elegans. Neuron. 2018;97(3):511- 519.e6. https://doi.org/10.1016/j.neuron.2018.01.014.
- Sharifnia P, Kim KW, Wu Z, Jin Y. Distinct cis elements in the 3' UTR of the C. elegans cebp- 1 mRNA mediate its regulation in neuronal development. Dev Biol. 2017;429(1):240- 248. https://doi.org/10.1016/j.ydbio.2017.06.022.
- Kim KW#, Thakur N, Piggott CA, et al. Coordinated inhibition of C/EBP by Tribbles in multiple tissues is essential for Caenorhabditis elegans development. BMC Biol. 2016;14(1):104. https://doi.org/10.1186/s12915- 016- 0320- z.
- Xu S, Wang Z, Kim KW, Jin Y, Chisholm AD. Targeted Mutagenesis of Duplicated Genes in Caenorhabditis elegans Using CRISPR- Cas9. J Genet Genomics. 2016;43(2):103- 106. https://doi.org/10.1016/j.jgg.2015.11.004.
- Kim KW#, Jin Y. Neuronal responses to stress and injury in C. elegans. FEBS Lett. 2015;589(14):1644- 1652. https://doi.org/10.1016/j.febslet.2015.05.005.
- Lee MH*, Kim KW*, Morgan CT, Morgan DE, Kimble J. Phosphorylation state of a Tob/BTG protein, FOG- 3, regulates initiation and maintenance of the Caenorhabditis elegans sperm fate program. Proc Natl Acad Sci U S A. 2011;108(22):9125- 9130. *equally contributed. https://doi.org/10.1073/pnas.1106027108.
- Kim KW, Nykamp K, Suh N, Bachorik JL, Wang L, Kimble J. Antagonism between GLD- 2 binding partners controls gamete sex. Dev Cell. 2009;16(5):723- 733. https://doi.org/10.1016/j.devcel.2009.04.002.
- Hesselson D, Newman C, Kim KW, Kimble J. GON- 1 and fibulin have antagonistic roles in control of organ shape. Curr Biol. 2004;14(22):2005- 2010. https://doi.org/10.1016/j.cub.2004.11.006.
- Kim KW, Shin JH, Moon J, et al. The function of the flowering time gene AGL20 is conserved in Crucifers. Mol Cells. 2003;16(1):136- 141. https://www.ncbi.nlm.nih.gov/pubmed/14503858.

■ 주요연구주제

- 신경 재생 및 퇴행 기전 
- 유해환경물질에 의한 신경 독성
- small RNA (piRNA) 연구
- 동물 발달 및 노화

■ 학회 및 대외활동

- 2021~현재 한국뇌신경과학회(KSBNS) 선거관리위원
- 2020년 한국분자·세포생물학회(KSMCB) 선거관리위원회, 분회운영위원회 위원
- 2019~2020 한국분자·세포생물학회(KSMCB) 강원분회 총무, 간사
- 2019년 한국분자·세포생물학회(KSMCB) 회원운영위원회 위원
- 한국분자·세포생물학회(KSMCB) 정회원
- 한국뇌신경과학회(KSBNS) 정회원
- 미국유전학회(GSA) 정회원

■ 연구비 수상

- 2020~ 4단계 BK21 사업
- 2019~2022 한국연구재단 개인연구사업 중견연구
- 2019~2022 한국연구재단 뇌과학원천기술개발사업
- 2013~2014 미국심장학회(AHA) fellowship

1. Lee SY, Kim JJ*, Miller KM*. Bromodomain proteins: protectors againstendogenous DNA damage and facilitators of genome integrity. Accepted in Experimental & Molecular Medicine (2021) (* Co-correspondence)

2. Ren W#, Fan H#, Grimm SA, Kim JJ, Li L, Petell CJ, Tan XF, Zhang ZM, Coan JP, Yin J, Guo Y, Gao L, Cai L, Detrick B, Çetin B, Patel DJ, Wang Y, Cui Q, Strahl BD, Gozani O, Miller KM, O'Leary SE, Wade PA, Wang GG*, Song J*. DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNAmethylation. Nature Communications (2021) May 3;12(1):2490 (# Co-first author, * Co-correspondence)

3. Lee SY*, Kim JJ*, Miller KM. Emerging Roles ofRNA Modifications in Genome Integrity. Briefings in Functional Genomics (2020) Dec; elaa022. (* Co-first author)

4. Kim JJ*, Lee SY*,ChoiJH, Woo HG, Xhemalce B, Miller KM. PCAF-mediated histone acetylationpromotes replication fork degradation by MRE11 and EXO1 in BRCA-deficientcells. Molecular Cell (2020) Oct 15;80(2):327-344.e8. (* Co-first author)

5. Ren W*, Fan H*, Grimm SA, Guo Y, Kim JJ, Li L, Petell CJ, Tan XF, Zhang ZM, Coan JP, Yin J, Gao L, Cai L,Detrick B, Cetin B, Wang Y, Cui Q, Strahl BD, Gozani O, Miller KM, O’LearySE, Wade PA, Patel DJ, Wang GG, Song J. Direct readout of heterochromaticH3K9me3 regulates DNMT1-mediated maintenance DNA methylation. Proc. Natl. Acad. Sci. USA (2020) Aug 4;117(31):18439-18447. (* Co-first author)

6. Kim JJ*, Lee SY*, Gong F,Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, PaullTT, Brodbelt JS, Marcotte EM, Miller KM.Systematic bromodomain protein screens identify homologous recombinationand R-loop suppression pathways involved in genome integrity. Genes & Development (2019) Dec 1;33(23-24):1751-1774. (* Co-first author)

7. Kim JJ*, LeeSY*,Miller KM. Preserving Genome Integrity and Function: The DNA Damage Responseand Histone Modifications. Crit. Rev. Biochem. Mol. Biol. (2019) Jun 4;54(3):208-241. (* Co-first author)

8. Kim JJ, Kumbhar R, Gong F, Miller KM. InTime and Space: Laser Microirradiation and the DNA Damage Response. Methods Mol. Biol. (2019);1999:61-74.

9. Kim JJ*, Lee SY*, Kim S, Chung JM, KwonM, Yoon JH, Park S, Hwang Y, Park D, Lee JS, Kang HC. A Novel Reciprocal Crosstalk between RNF168 and PARP1 to Regulate DNA Repair Processes. Molelcules and Cells (2018) Aug 31;41(8):799-807. (* Co-first author)

10. Kim JH, Moon SH, No M, Kim JJ, Choi EJ, Cho BJ, Kim JS, Kim IH, Kim IA. Isotype-specific Inhibition of Histone Deacetylases: Identification of Optimal Targets for Radiosensitization. Cancer Res. Treat. (2016) Jul;48(3):1130-40.

11. Kim YP*, Park D*, Kim JJ*, Chi WJ, Lee SH, Lee SY, Kim S, Chung JM, Jeon J, Lee BD,Shin JH, Lee YI, Cho H, Lee JM, Kang HC. Effective therapeutic approach forhead and neck cancer by an engineered minibody targeting the EGFR receptor. PLoS ONE (2014) 1;9(12):e113442. (* Co-first author)

12. Nguyen TT, Kim YM, Kim TD, Le OT, Kim JJ, Kang HC, Hasegawa H, Kanaho Y, Jou I, Lee SY. Phosphatidylinositol4-phosphate 5-kinase α facilitates Toll-like receptor 4-mediated microglial inflammation through regulation of the Toll/interleukin-1 receptor domain-containing adaptor protein (TIRAP) location. J. Biol. Chem. (2013) Feb 22;288(8):5645-59.

13. Yang H, Ko HJ, Yang JY, Kim JJ, Seo SU, Park SG, Choi SS, Seong JK, Kweon MN.  Interleukin-1 promotes coagulation, which is necessary for protective immunity in the lung against Streptococcus pneumoniae infection. J. Infect. Dis. (2013) Jan 1;207(1):50-60.

14. Jiang J, Kim JJ, Kim DY, Kim MK, Oh NH, Koppula S, Park PJ, Choi DK, Shin YK, KimIH, Kang TB, Lee KH. Acorus gramineus inhibits microglia mediated neuroinflammation and prevents neurotoxicity in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model of Parkinson's disease. J. Ethnopharmacol. (2012) Dec 18;144(3):506-13.

15. Seo SU, Kim JJ, Yang H, Kwon HJ, Yang JY, Curtiss Iii R, Kweon MN. Effective protection against secondary pneumococcal pneumonia by oral vaccination with attenuated Salmonella delivering PspA antigen in mice. Vaccine (2012) Nov 6;30(48):6816-23.

16. Kim JJ*,Jiang J*, Shim DW, Kwon SC, Kim TJ, Ye SK, Kim MK, Shin YK, Koppula S, Kang TB, Choi DK, Lee KH. Anti-inflammatory and anti-allergic effects of Agrimonia pilosa Ledeb extract on murine cell lines and OVA-induced airway inflammation. J. Ethnopharmacol. (2012) Mar 27; 140(2):213-21. (* Co-first author)

17. Ma JS, Kim WJ, Kim JJ, Kim TJ, Ye SK, Song MD, Kang H, Kim DW, Moon WK, Lee KH. Gold nanoparticles attenuate LPS-induced NO production through the inhibition of NF-kappaB and IFN-beta/STAT1 pathways in RAW264.7 cells. Nitric Oxide (2010) Nov 1;23(3):214-9.

18. Oh JS*, Kim JJ*, Byun JY*, KimIA. Lin28-let7 modulates radiosensitivity of human cancer cells with activation of K-Ras. Int. J. Radiat. Oncol. Biol. Phys. (2010) Jan 1;76(1):5-8. (* Co-first author)

-한국분자세포생물학회 정회원

-주요 연구 주제

유전체 불안정성은 세포 내/외부적인 요인에 의해 축적되는 DNA 손상에 의해 생성되며 암, 신경퇴행성 뇌질환, 노화와 같은 다양한 질병에 원인으로 밝혀지고 있습니다. 저희 연구실은 다양한 스크리닝 기법과 단백체학 기법들을 활용해 새로운 DNA 손상 복구 기전을 규명하고 이와 관련된 질병을 예방-치료하기 위한 새로운 치료제를 개발하는 것을 목표로 하고 있습니다.

저희 연구실의 세부 연구 주제는 다음과 같습니다.

1) DNA 전사 과정에 발생되는 R-loop를 조절할 수 있는 단백질 네트워크 규명

2) DNA 복제 스트레스 조절 단백질 네트워크 규명

3) DNA 손상 복구 단백질 조절을 통한 면역 항암 보조제 개발

4) Poly(ADP-ribose) 결합 단백질 네트워크 규명을 통한 신경퇴행성 뇌질환 기전 연구

5) 합성치사 기반 신규 표적 항암제 개발 연구  

"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