About Professor Nam, Jin-Wu

After receiving his bachelor degree from Dept. of Biology of Yonsei Univ., Prof. Nam studied bioinformatics in the interdisciplinary program in bioinformatics of Seoul National Univ. (SNU). During his PhD in the lab of Prof. Byoung-Tak Zhang at SNU, he developed probabilistic graphical methods for human microRNA (miRNA) identification and target prediction (Nam et al., NAR, 2005; Nam et al., NAR, 2006; Kim*, Nam* et al., BMC Bioinformatics, 2006) and identified structural principles for miRNA biogenesis (Han et al., Cell, 2006; Kim and Nam, Trends in Genetics, 2006) with collaborating with Prof. V. Narry Kim at SNU.

During his postdoctoral work in the lab of Prof. David Bartel at the Whitehead Institute/MIT, he studied a novel form of gene regulation by miRNAs that is mediated by a new type of target site (centered site) (Shin*, Nam* et al, 2010, Mol Cell). Related to this work, he studied how miRNA targeting varies between cell types due to alternative polyadenylation (APA), which was assayed using poly(A) position profile-sequencing (3P-seq) (Nam et al., 2014. Mol Cell). In separate work, he used ab initio transcriptome reconstruction to identify hundreds of long intervening non-coding RNAs (lincRNAs) that are temporally and spatially regulated during C. elegans development (Nam and Bartel, Genome Res., 2012).

In Sept 2012, he moved to a faculty position of the Graduate School in Biomedical Science and Engineering at Hanyang Univ, Seoul, and then joined a faculty in Dept. of Life Science, College of Natural Sciences at the same univ. He has been developing machine-learning-based methods to identify non-coding transcripts (Choi and Nam, 2018, BMC Bioinfo.; Choi et al., 2018, Briefings in Bioinfo.) and to predict the 3'-end of transcript (Kim et al., Methods, 2015), and he has been also focusing on reconstructing coding and non-coding transcriptome maps in human (You et al., Genome Res. 2017) and vertebrates (Hong et al., IJMS, 2018). To further understand the interaction between coding and non-coding elements and the regulatory roles in the relationship, we have been developing an efficient CRISPR/Cas system (Kim et al., 2017, Nature Methods), which was applied to the human XIST study, leading to finding of functional elements of Human XIST (Lee et al., Nucleic Acids Res. 2019), identifying a novel lncRNA gene that regulates Wnt signaling pathways in development of squamous cell-tpye carcinoma (You et al., 2019 PNAS), and uncovering a novel UPF1-dependent miRNA-mediated mRNA decay pathway (Park et al., Nature Comm.). Recently, he has been expanding his interests to genome assembly (Sohn et al., 2018, GigaScience; Sohn et al., 2018, Briefings in Bioinfo.), its related algorithms to efficiently detect genomic variations (in preparation) and  single-cell transcriptome studies (in preparation). 

Education

  • Sep, 2004. ~ Aug, 2007. Ph. D. in Bioinformatics of Seoul National University.

  • Sep, 2002 ~ Aug, 2004. ME in Bioinformatics of Seoul National University.

  • Mar, 1994 ~ Feb, 2001. BS in Biology of Yonsei University.

Professional Experiences

  • 2019.1~2020.2        Visiting Professor, Dept of Biochemistry, Univ. of Washington

  • 2016.9~                   Associate Professor, Dept. of Life Science, Hanyang University.

  • 2014.3~2016.8        Assistant Professor, Dept. of Life Science, Hanyang University.

  • 2012.9~2014.2        Assistant Professor, Grad. School in Biomedical Science and Eng., Hanyang University.

  • 2008-2012                Postdoctoral fellow, MIT, HHMI, Whitehead Institute for Biomedical Research

  • 2007-2008                Postdoctoral fellow, Seoul National University, MicroRNA Research Center

  • 2002-2008                Researcher, Center for Bioinformation Technology (CBIT), Seoul National University.

  • 2003                         Visiting Researcher, Sakakibara Lab, Keio University, Japan. 

  • 2001~2002               Research Assistant, Genome Sequencing and SNP Analysis, Corporation Pangenomics

Projects

  • 교육부, 연구재단 BK+   ~2020

  • 과기정통부, 연구재단 중견연구 “암특이 lncRNA 이소체 연구“  ~2020

  • 과기정통부, 연구재단 바이오의료기술개발 “차세대유세포기술개발“ ~2022

  • 보건복지부, 보건산업진흥원, 다부처유전체 암유전체플랫폼연구 ~2021

  • 과기정통부, 연구재단, 다부처유전체 생물정보기술개발 ~2021

  • LG 연암재단, 국제학술교류지원사업 2019

Honors

  • 2020,1                      한국분자세포생물학회 BlueRibbon Award

  • 2018.11                    OnBIT Award, 한국생명정보학회 학술상

  • 2018.11                    LG연암재단 국제학술교류지원 사업 선정

  • 2018.06                    RNA meeting 2018 Poster Award (UC Berkely)

  • 2016                         한양대 자연과학연구소 학술상

  • 2012                         Whitehead postdoctoral travel award

  • 2008                         KOSEF, Postdoctoral fellowship

  • 2005-2006                Seoul Science Fellowship, Seoul City.

  • 2005                         Excellent Student Scholarship, Seoul National University

  • 2004                         Lotte Fellowship, Lotte Corporation.

  • 2003                         Excellent Paper Awards, Korean Society for Bioinformatics

  • 2003                         Excellent Paper Awards, Korean Information Science Society

  • 2000                         The President Award, Yonsei University

Academic Activities

  • 2020,2                       APBC2020 Program Chair

  • 2019, 9                      The 28th KOGO International Conference, Session Chair & Organizer

  • 2018,11                     TBC/BIOINFO 2018 Program Chair

  • 2018,11                     K-Genome Competition 심사위원

  • 2018,9                      한국분자세포생물학회 심포지움 Chair & Organizer

  • 2018.7~                    Genes and Genomics, Associate Editor

  • 2018.1~                    Animal cells and systems, Editorial board member

  • 2017~                       한국창의재단 교과서검정심의위원

  • 2017~                       한국창의재단 디지털교과서연구위원

  • 2017~                       ACCR Active Member

  • 2015.1~                    한국유전학회 전산운영위원/운영위원장

  • 2013.9~현재             한국생물정보시스템생물학회 학술이사

  • 2017                         GIW/BIOINFO 2017 Program Chair & BMC Guest editor

  • 2016.1~2017            한국분자세포생물학회 리보핵산분과 총무간사

  • 2013.9~2015.12       한국분자세포생물학회 리보핵산분과 이사

  • 2014.10~2016.12     한국분자세포생물학회 교육위원

  • 2013~2016               CSBio Committee member

  • 2013~2016               TBC Committee member

  • 2014.3~2014.10       소프트웨어정책연구소 자문위원

  • 2014.3~2015.12       EMM 저널 운영위원

Academic Services

  • 2019,9                       한양대학교 의과대학 초청세미나 (서울)

  • 2019, 2                      Keystone Symposia: Long noncoding RNAs, Speaker (Whislter)

  • 2018,11                      IBS RNA Symposium 주제강연

  • 2018,6                       한국분자세포생물학회 리보핵산분과 주제발표 (경주)

  • 2018,6                       한국분자세포생물학회 섬모세포소기관 분과 발표 (양평)

  • 2018,6                       대한역학회 주제발표(서울대의대)

  • 2018,3                       Ewha-Jax Joint Symposium (이화여대)

  • 2018,2                       동계유전체학회 주제강연 (홍천)

  • 2017,12                     동아시아 유전체 국제 심포지움 주제강연 (전주)

  • 2017,12                     한국분자세포생물학회 에피유전체분과 주제강연 (홍천)

  • 2017,11                     실험혈액학회 주제강연 (서울대의대)

  • 2017,10                     KAIST 의과학대학원 세미나 (대전)

  • 2017,10                     고려대 생명과학부 세미나 (고려대)

  • 2017,09                     한국유전체학회 국제심포지움 주제강연 (건국대)

  • 2017,09                     삼성의료원 유전체 교육 2회 주제강연

  • 2017,07                     UofBern 초청 세미나

  • 2017,06                     한중일 Tri-Bioinformatics 심포지움 주제강연 (코레아나호텔)

  • 2017,04                     삼성의료원 유전체 교육 1회 주제강연

  • 2016,12                     대한역학회 주제강연 (서울대의대)

  • 2016,11                     대한간학회 주제강연 (서울)

  • 2016,9                       국제의료정보학회 주제강연

  • 2016,3                       IBS-CNRS Join Symposium on RNA Biology 주제강연 (서울대)

  • 2016,3                       연세대학교 생명공학과 정기 세미나

  • 2016,2                       유전체학회 주제강연 (홍천)

  • 2015,12                     서울시립대 세미나

  • 2015,11                     고려대학교 의과대학 세미나

  • 2015,10                     유전학회 마이크로심포지움 (고려대)

  • 2015,6                       RNA summer symposium (부여)

  • 2014,12                     분자세포생물학회 에피유전체분과 동계 심포지움 주제강연

  • 2014,11                     한국생물정보시스템생물학회 주제강연

  • 2014,11                     암학회 주제강연

  • 2014,10                     서울대학교 생명과학부 세미나

  • 2014,8                       소프트웨어 정책연구소강연 (판교)

  • 2014,7                       RNA summer symposium (문경STX)

  • 2014,4                       춘계바이오칩학회 초청강연

  • 2014,4                       카톨릭의대 ncRNA 워크샵 주제강연

  • 2014,3                       농촌진흥청 초청 세미나

  • 2014,2                       국립암연구소 초청 세미나

  • 2014,2                       분자세포생물학회 이동성분과 심포지움 초청강연

  • 2014,2                       동계유전체학회 심포지움 주제강연: Cancer genomic studies using NGS

  • 2013, 12                    Session speaker, Epigenomics Winter Symposium (Hongcheon)

  • 2013, 10                    Session speaker, KSMCB (Seoul).

  • 2013, 11                    PAGGI Conference speaker (Kwanggyu)

  • 2013, 9                      Conference speaker, KOGO conference (Seoul)

  • 2013, 6                      Session speaker, RNA meeting, Busan.

  • 2013, 5                      Invited talk, 'Analysis of next-generation sequencing data', DGIST, (Daegu).

  • 2013, 5                      Invited talk, 'Cancer genomics', Samsung Genome Insititute (SGI), (Seoul).

  • 2013, 5                      Invited talk,  Samsung Advanced Institute for Health Sciences & Technology. (Seoul).

  • 2013, 3                      Invited talk, Korea Center for Disease Control and Prevention. (Osong).

  • 2013, 3                      Invited talk, RNA section, Round Table Meeting. (Seoul).

  • 2013                          Invited talk, Keystone meeting (Vancouver).

  • 2012                          Invited talk, BMS/Illumina Symposium, Intercontinental Hotel at Coex.

  • 2012                          Vice Chairman, International Cancer Genome Conference 2012, Lotte Hotel.

  • 2012                          Invited talk, ‘Noncoding RNA’ Keystone meeting (Utan, Snowbird)

  • 2011                          Invited talk, Yonsei University “Endogenous siRNAs in C. elegans”

  • 2010                          Invited talk, New England Biological Society / Harvard.

  • 2010                          Invited referee, Molecules and Cells,

  • 2008                          Invited talk, Seoul National University “Regulatory non-coding RNAs”

  • 2007                          Invited referee, Pattern Recognition in Bioinformatics (PRIB), 2007.

  • 2007                          Invited referee, Nucleic Acids Research, 2007, Web Sever Issue.

  • 2007                          Invited referee, Nucleic Acids Research, 2007, Database Issue.

  • 2007                          Program committee, 2007 IEEE symposium on CIBCB.

  • 2006                          Invited referee, 2006 IEEE symposium on CIBCB.

  • 2006                          Assistant Instructor, Seoul Science School (S cube).

  • 2005                          Invited referee of Bioinformatics

Selected publications

[Peer-reviewed Papers]

  • ​Bo-Hyun You*, Jung-Ho Yoon*, Hoin Kang, Eun Kyung Lee, Sang Kil Lee#, and Jin-Wu Nam#, HERES, a lncRNA that Regulates Canonical and Noncanonical Wnt Signaling Pathways via Interaction with EZH2, PNAS116 (49) 24620-24629

  • Jeongyoon Park*, Jwa-Won Seo*, Narae Ahn, Seokju Park, Jungwook Hwang#, and Jin-Wu Nam#. UPF1/SMG7-dependent MicroRNA-mediated Gene Regulation, Nature Communications, 10:4181, 2019.

  • Hyeon Lee*,  Ramu Gopalappa*, Hongjae Sunwoo*, Seowon Choi, Suresh Ramakrishna, Jeannie Lee,  Hyongbum (Henry) Kim#,  Jin-Wu Nam#, En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements, Nucleic Acids Res., 47:8, 3875–3887, 2019.

  • Jang-il Sohn*, Kyoungwoo Nam*, Hyosun Hong*, Jun-Mo Kim*, Dajeong Lim, Kyung-Tai Lee, Yoon Jung Do, Chang Yeon Cho, Namshin Kim, Han-Ha Chai# and Jin-Wu Nam# Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye, GigaScience,  giy086,  https://doi.org/10.1093/gigascience/giy086, 2018.

  • Seo-Won Choi*, Hyunwoo Kim*, and Jin-Wu Nam, The small peptide world in long non-coding RNAs, Briefings in Bioinformatics, bby055, https://doi.org/10.1093/bib/bby055, 2018

  • Seo-Won Choi and Jin-Wu Nam, TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA binding protein association. BMC Bioinformatics, 19(Suppl 1):41, 2018.

  • Jang-il Sohn and Jin-Wu Nam, The Present and Future of De Novo Whole Genome Assembly, Briefings in Bioinformatics, 19(1):23-40. doi: 10.1093/bib/bbw096. 2018.

  • Bo-Hyun You, Sang-Ho Yoon, and Jin-Wu Nam. High-Confidence Coding and Noncoding Transcriptome Maps. Genome Res. 27:1050-1062, 2017.

  • Kyung-Tae Lee and Jin-Wu Nam. Post-transcriptional and translational regulation of mRNA-like long non-coding RNAs by microRNAs in early developmental stages of zebrafish embryos. BMB Rep. pii: 3769, 2017 Mar 21.

  • Hui Kwon Kim, Myungjae Song, Jinu Lee, Adrussery. Vipin Menon, Soobin Jung, Young-Mook Kang, Euijeon Woo, Jin-Wu Nam, and Hyongbum (Henry) Kim. In vivo high-throughput profiling of CRISPR-Cpf1 activity based on target sequence composition. Nature Methods. 14:153-197, 2017.

  • Jin-Wu Nam, Seo-Won Choi, and Bo-Hyun You, Incredible RNA: Dual Functions of Coding and Noncoding. Mol. Cells. 39(5):367-374. 2016.

  • MinHyeok Kim, Bo-Hyun You, and Jin-Wu Nam. Global Estimation of the 3' Untranslated Region Landscape Using RNA Sequencing. Methods, 83:111-117, 2015.

  • J.-W. Nam, O. Rissland, D. Kopstein, V. Agarwal, C. Jan, M. Yildrim and D. Bartel, Global analyses of the effect of different cellular contexts on microRNA targeting. , Mol Cell, 53(6), 1031–1043, 2014.

  • June Hyun Park, Soungyub Ahn, Soyoung Kim, Junho Lee, Jin-Wu Nam*, Chanseok Shin* Degradome sequencing reveals an endogenous microRNA target in C. elegans, FEBS Letters 587(2013) 964-969, 2013.

  • J.-W. Nam and D. Bartel, Long non-coding RNAs in C.elegans. Genome Research. 22: 2529-2540, 2012. Media: Nature Method.

[Before 2012]

  • C.Shin*, J.-W. Nam*, K.Farh*, R.Chiang, A.Shkumatava, and D.Bartel. Expanding the MicroRNA Targeting Code: A Novel Type of Site with Centered Pairing., Mol Cell, 38(6):789-802, 2010. Highlight paper

  • S. Hyun*, J.H. Lee*, H. J*. J.-W. Nam, B.J. Namkoong, G. Lee, J. Chung, V.N. Kim, Conserved MicroRNA miR-8/miR-200 and Its Target USH/FOG2 Control Growth by Regulating PI3K, Cell, 139(6):1096-1108, 2009.

  • S. Y. Park*, J. H. Lee*, M. Ha, J.-W. Nam and V. N. Kim. "miR-29 miRNAs activate p53 by targeting p85a and CDC42" Nature Structural and Molecular Biology 16(1):23-9, 2009.

  • J.-W. Nam, I.-H. Lee, K.-B. Hwang, S.-B. Park, and B.-T. Zhang, Dinucleotide step parameterization of pre-miRNAs using multi-objective evolutionary algorithms. EvoBio, 2007.

  • J. Han, Y.T. Kim, K.-H Yeom, J.-W. Nam, I.H. Hur, Je-keun Rhee, B.-T. Zhang and V.N. Kim. Molecular basis for the recognition and processing of primary microRNA by Drosha.  Cell, 125:887-901, 2006.

  • J.-W. Nam*, J.H.Kim*, S.K.Kim, B.-T. Zhang. ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.  Nucleic Acids Research 34:W455-W458, 2006

  • J.-W. Nam*, S.K. Kim* Je-Keun Rhee, W.J. Lee, B.-T. Zhang. miTarget: microRNA target-gene prediction using a Support Vector Machine. BMC Bioinformatics 7(1):411, 2006. Highlight paper.

  • V.N. Kim and J.-W. Nam, Genomics of microRNA.  Trends in Genetics, 22(3):165-173, 2006. Most downloaded paper

  • J.-W. Nam, K.R. Shin, J.J. Han, Y.T. Lee, V.N. Kim and B.T.Zhang. Human miRNA prediction through probabilistic co-learning of sequence and structure. Nucleic Acids Research, 33(11):3570-3581, 2005. Hot paper

  • J.-W. Nam, Joung, J.-G., Ahn, Y.S. and Zhang, B.-T. Two-Step Genetic Programming for Optimization of RNA Common-Structure.  Lecture Notes in Computer Science, vol. 3005, pp. 73-83, 2004 .

© 2014 by BIG Lab. All copyrights reserved. Editor: JWNAM

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