서울대학교 생물정보연구소와 생물정보학 협동과정 공동 주최로 세미나를 아래와 같이 열고자 하오니, 많은 참여 바랍니다.

일시: 2017년 4월 19일 수요일 오전 11시

연사: 이재형 (경희대학교 나노의약생명과학과)

장소: 서울대학교 25동 411호

Title : Bioinformatic Analysis of Next Generation Sequencing Data in Dental Research

Abstract : Lately, the massive increase of the biological data for the system-wide measurement of biological variables change the paradigm of the biological and medical science. Particularly, the development in the next generation sequencing (NGS) technology is allowing us to study medical problems in the system level. In this presentation, I will introduce how various NGS techniques can beused for the dental research,1) genomics (DNA genome sequencing); whole genome characterization and comparative genomics ofPrevotella intermedia that cause periodontal diseases, 2) metagenomics (microbial community profiling); characterization of subgingival bacterial communities from the plaque samples of smokers and non-smokers, and 3) transcriptomics (RNA sequencing, RNA-Seq); analysis of transcriptome of gingival tissues to understand gene regulations in periodontitis disease. Ultimately, the present studies will provide a global picture of the complicated molecular mechanisms in various host-pathogen interactions, which could have important implications for the development of novel therapies to the periodontal disease.

Education

2002 - 2007 Ph.D., Bioinformatics and Computational Biology, Iowa State University

• Co-major professors: Drena Dobbs (GDCB) and Kai-Ming Ho (Physics)

• Dissertation: Analysis of protein-RNA and protein-peptide interactions in equine infectious anemia virus (EIAV) infection

2001 Intensive training in Bioinformatics, Korea National Institute of Health (KNIH)

2001 B.S., Biochemistry, Yonsei University, Seoul, Korea　

Professional experience

3/2013 - pres. Assistant Professor, Kyung Hee University

• Department of Maxillofacial Biomedical Engineering, School of Dentistry

• Department of Life and Nanopharmaceutical Sciences

6/2009 – 2/2013 Postdoctoral Research Associate, University of California, Los Angeles

• Department of Integrative Biology and Physiology

• Mentor: Xinshu (Grace) Xiao

1/2008 – 6/2009 Postdoctoral Research Associate, Iowa State University

• Center for Computational Intelligence, Learning and Discovery (CCILD)

• Mentors: Vasant Honavar (ComS) and Drena Dobbs (GDCB)

2001 - 2002 Researcher, Bioinformatics, Center for Genome Sciences, Korean NIH (KNIH)

• Constructing bioinformatics infrastructure for KNIH

• Managing database servers for KNIH

2001 Samsung Data System (SDS) Training Course

Selected Publications

1. Song, M., Lee, J.-H., Bae, J., Bu, Y., Kim, E.C. (2017) Human dental pulp stem cells are more effective than human bone marrow-derived mesenchymal stem cells in cerebral ischemic injury, Cell Transplant. [Epub ahead of print]

2. Kim, B.C., Jun, S.M., Kim, S.Y., Kwon, Y.D., Choe, S.C., Kim, E.C., Lee, J.-H., Kim, J., Suh, J.F., Hwang, Y.S. (2017) Engineering three dimensional micro nerve tissue using postnatal stem cells from human dental apical papilla, Biotechnol Bioeng. 114(4): 903-914

3. Yun, K. H., Lee, H.-S., Nam, O. H., Moon, C. Y., Lee, J.-H., Choi, S. C. (2017) Analysis of bacterial community profiles of endodontically infected primary teeth using pyrosequencing, Int J Paediatr Dent. 27(1): 56-65

4. Lim, C.S., Kim, H., Yu, N.K., Kang, S.J., Kim, T., Ko, H.G., Lee, J., Yang, J.E., Ryu, H.H., Park, T., Gim, J., Nam, H.J., Baek, S.H., Wegener, S., Schmitz, D., Boeckers, T.M., Lee, M.G., Kim, E., Lee, J.H. +, Lee, Y.S., Kaang, B.K. (2017) Enhancing inhibitory synaptic function reverses spatial memory deficits in Shank2 mutant mice, Neuropharmacology. 112: 104-112 +Cocorresponding authors

5. Moon, J.-H., Kim, M., Lee, J.-H. (2017) Genome sequence of Prevotella intermedia SUNY aB G8-9K- 3, a biofilm forming strain with drug-resistance, Braz J Microbiol. 48(1): 5-6

6. Moon, J.-H., Lee, J.-H. (2016) Probing the diversity of healthy oral microbiome with bioinformatics approaches. BMB Rep. 49(12): 662-670

7. Kim, Y.G., Kim, M., Kang, J.H., Kim, H.J., Park, J.W., Lee, J.M., Suh, J.Y., Kim, J.Y., Lee, J.H. +, Lee, Y. (2016) Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns. Hum Genomics. 10:28 +Cocorresponding authors

8. Hwang, S.-K.+, Lee, J.-H.+, Yang, J.-E.+, Lim, C.-S.+, Lee, J.-A., Lee, Y.-S., Lee, K., Kaang, B.-K. (2016) Everolimus improves neuropsychiatric symptoms in a patient with tuberous sclerosis carrying a novel TSC2 mutation, Mol Brain. 9:56 +These authors contributed equally to this work.

9. Cass, A. A., Bahn, J. H., Lee, J.-H., Greer, C., Lin, X., Kim, Y., Hsiao, Y.-H. E., Xiao, X. (2016) Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets, Nucleic Acids Res. 44(7): 3253-3263

10. Fuxjager, M. J.+, Lee, J.-H.+, Chan, T.-M., Bahn, J. H., Chew, J. G., Xiao, X., Schlinger, B. A. (2016) Research resource: Hormones, genes, and athleticism: Effect of androgens on the avian muscular transcriptome, Mol Endocrinol. 30(2): 254-271 +These authors contributed equally to this work.

11. Gao,C., Ren, S., Lee, J.-H., Qiu, J., Chapski, D. J., Rau, C. D., Zhou, Y., Abdellatif, M., Nakano, A., Vondriska, T. M., Xiao, X., Fu, X.-D., Chen, J.-N., Wang, Y. (2016) RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure, J Clin Invest. 126(1): 195-206

12. Bhate, A., Parker, D. J., Bebee, T. W., Ahn, J., Arif, W., Rashan. E. H., Chorghade, S., Chau, A., Lee, J.-H., Anakk, S., Carstens, R. P., Xiao, X., Kalsotra, A. (2015) ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation, Nat Commun. 6, Article

13. Sohn, W.-J., Gwon, G.-J., Kim, H.-S., Neupane, S, Cho, S.-J., Lee, J.-H., Yamamoto, H, Choi, J.Y., An, C.-H., Lee, Y, Shin, H.-I., Lee, S, Kim, J.-Y. (2015) Mesenchymal signaling in dorsoventral differentiation of palatal epithelium, Cell Tissue Res., 28 June 2015

14. Bahn, J., Ahn, J., Lin, X., Zhang, Q., Lee, J.-H., Civelek, M., Xiao, X. (2015) Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways, Nat Commun. 6, Article number: 6355

15. Nahm, K-Y., Heo, J., Lee, J.-H., Lee, D.-Y., Chung, K.-R., Ahn, H.-W., Kim, S.-H. (2015) Gene profiling of bone around orthodontic mini-implants by RNA-sequencing analysis, Biomed Res Int. Volume 2015, Article ID 538080

16. Moon, J.-H., Lee, J.-H., Lee, J.-Y. (2014) Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients, Mol Oral Microbiol. 30(3): 227-241

17. Kim, J.H., Song, P., Lim, H., Lee, J.-H., Lee, J.H., Park, S.A. (2014) Gene-Based Rare Allele Analysis Identified a Risk Gene of Alzheimer’s Disease, PLoS ONE 9(10): e107983

18. Moon, J.-H., Lee, J.-H., Lee, J.-Y. (2014) Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate, BMC Microbiol. 14:218

19. Xu, Y., Gao, X. D., Lee, J.-H., Huang, H., Tan, H., Ahn, J., Reinke, L. M., Peter, M. E., Feng, Y., Gius, D., Siziopikou, K. P., Peng, J., Xiao, X., Cheng, C. (2014) Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing, Genes Dev. 28(11):1191

20. Lee, J.-H., Ang, J, Xiao, X. (2013) Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants, RNA 19(6):725-732

21. Li, G., Bahn, J., Lee, J.-H., Peng, G., Chen, Z., Nelson., S., Xiao, X. (2012) Identification of allelespecific alternative mRNA processing via transcriptome sequencing, Nucleic Acids Res. 40(13): e104

22. Gomez, G., Lee, J.-H., Veldman, M, Lu, J., Xiao, X., Lin, S. (2012) Identification of vascular and Hematopoietic genes downstream of etsrp by deep sequencing in Zebrafish, PLoS ONE 7(3): e31658

23. Bahn, J.+, Lee, J.-H.+, Li, G., Greer, C., Peng, G., Xiao, X. (2012) Accurate identification of A-to-I RNA editing in human by transcriptome sequencing, Genome Res. 22: 142-150, +These authors contributed equally to this work.

24. Lee, J.-H., Gao, C., Peng, G., Greer, C., Ren, S., Wang, Y., Xiao, X. (2011) Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts, Circ. Res. 109(12): 1332-1341

25. Xiao, X., Lee, J.-H. (2010) Systems analysis of alternative splicing and its regulation, Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2:550-565

26. Ihm, Y., Sparks, W. O., Lee J.-H., Cao, H., Carpenter, S., Wang, C.-Z., Ho, K.-M., and Dobbs, D. (2009) Structural Model of the Rev Regulatory Protein from Equine Infectious Anemia Virus. PLoS ONE 4(1): e4178

27. Lee, J.-H., Culver, G., Carpenter, S., and Dobbs, D. (2008) Analysis of the EIAV Rev-responsive element (RRE) reveals a conserved RNA motif required for high affinity Rev binding in both HIV-1 and EIAV. PLoS ONE 3(6): e2272

28. Lee, J.-H., Hamilton, M., Gleeson, C., Caragea, C., Zaback, P., Sander, J.D., Li, X., Wu, F., Terribilini, M., Honavar, V., and Dobbs, D. (2008) Striking similarities in structure and nucleic acid binding sites of diverse telomerase proteins revealed by combining structure prediction and machine learning approaches. Pac Symp Biocomput. (PSB08) 13:501-512

29. Terribilini, M., Sander, J., Lee, J.-H., Zaback, P., Jernigan, R., Honavar, V., and Dobbs, D. (2007) RNABindR: A server for analyzing and predicting RNA binding sites in proteins, Nucleic Acids Res. (Web Server issue) 35:W578-584

30. Terribilini, M., Lee, J.-H., Yan, C., Jernigan, R., Honavar, V., and Dobbs, D. (2006) Prediction of RNA binding sites in proteins from amino acid sequence, RNA 12(8):1450-1462

31. Terribilini, M., Lee, J.-H., Yan, C., Jernigan, R., Carpenter, S., Honavar, V., and Dobbs, D. (2006) Identifying interaction sites in "recalcitrant" proteins: Predicted protein and RNA binding sites in Rev proteins of HIV-1 and EIAV agree with experimental data, Pac Symp Biocomput. (PSB06) 11:415-426

32. Mealey, R., Lee, J.-H., Leib, S., Littke, M., and McGuire, T. (2006) A single amino acid difference within the α-2 domain of two naturally occurring equine MHC class I molecules alters the recognition of Gag and Rev epitopes by EIAV-specific CTL, J. Immunol. 177(10):7377-7390 33. Lee, J.-H., Murphy S., Belshan, M., Sparks, W., Wannemuehler, Y., Liu, S., Hope, T., Dobbs, D., and Carpenter, S. (2006) Characterization of functional domains of equine infectious anemia virus Rev suggests a bipartite RNA-binding domain, J Virol. 80(8):3844-3852

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