Members

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, he has 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), uncovering a novel UPF1-dependent miRNA-mediated mRNA decay pathway (Park et al., 2019 Nature Comm.), identifying novel oncogenic isomir of miR-21 in HCCs (Park et al., 2022, EMM), and constructing interactome maps of human and fly α-arrestins(Lee et al., eLife, 2024). 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 (Sohn et al., 2022, Nature Biomedical Engineering; Lee et al., Briefings in Bioinfo., 2023) and single-cell transcriptome studies (Cho et al., 2020, Nature Comm; Yoon et al., npj Precision Onco. 2021; Park et al., Briefings in Bioinfo,2021; Yoon et al., Briefings in Bioinfo. 2023; Yoon et al., PLos Genetics 2023). In addition, his group has been developing AI-aided RNA design algorithms to design augmented/aritificial mRNA vaccines, shRNAs, and RNA drugs (Park et al., BioRxiv, 2024).

In Dec 2023, he also started to serve a Director, Division of Next-Generation Biotechnology, Directorate for National Strategic R&D Programs, National Research Foundation(NRF), Korea, for two years.

Education&Training

Mar, 2008 ~ Jul, 2012, Postdoc. MIT/Whitehead Institute
Sep, 2007 ~ Feb. 2008 Postdoc, SNU
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

2024. 1~ 과학기술정통부 첨단바이오 규제로드맵 실무위원회
2024. 1~ 과학기술정통부 디지털바이오육성(범부처 보스톤-코리아 공동연구사업) 추진위원회 위원
2023. 12~ 한국연구재단 국책본부 차세대바이오단 단장, Director, Division of Next-Generation Biotechnology, Directorate for National Strategic R&D Programs, National Research Foundation(NRF)
2023. 12~ 과학기술정통부 데이터발전위원회 위원
2023. 12~ 과학기술정통부 기초원천소재위원회 위원
2023. 12~ 과학기술정통부 K-BDS 자문위원회 위원
2023. 12~ 국가통합바이오빅데이터 사업 유전체, 오믹스 자문위원
2023. 1~ 한국연구재단 생명과학단 기획-자문위원회 위원
2022. 10~ STEPI 바이오데이터 규제혁신 위원회 위원
2022. 7~ 식품의약안전처 체외진단의료기기 전문가위원
2022. 2~ 한국연구재단 국책사업단 차세대바이오 기획위원(RP)
2021.12~ 한양생명과학기술원 부원장 Deputy Director, HY Institute of Bioscience and Biotechnology (HY-IBB)
2021.12~ 한양생명과학기술원 바이오빅데이터센터장 Director, Bio-Bigdata Center, HY-IBB
2021.9~ Professor, Dept. of Life Science, Hanyang University.
2020.7~ Directer, BRL Tumor-Immune Microenvironment-regulating lncRNAs
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

2022.12 과학기술정보통신부 장관 표창
2020.11 한국생명정보학회 테라젠 올해의 생명정보인상
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

2023- 한국분자세포생물학회 동계학술운영위원, 정책위원
2023- 한국생화학생물학회 산학운영위원
2023 한국유전학회 기획위원장
2022-2023 한국생명정보학회 총무위원장
2022 한국분자세포생물학회 전산운영위원
2021-2022 한국유전학회 홍보위원장
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]

Jang-il Sohn*, Min-Hak Choi*, Dohun Yi*, A Vipin Menon, Yeon Jeong Kim, Junehawk Lee, Jung Woo Park, Sungkyu Kyung, Seung-Ho Shin, Byunggook Na, Je-Gun Joung, Sungroh Yoon, Young Seok Ju, Min Sun Yeom, Youngil Koh, Sung-Soo Yoon, Daehyun Baek, Tae-Min Kim, and Jin-Wu Nam, Ultra-fast Prediction of Somatic Structural Variations by Reduced Read Mapping via Pan-Genome k-mer Sets, Nature Biomed. Eng. 10.1038/s41551-022-00980-5 , Dec. 19, 2022.
Eun-Gyeong Park, Sung-Jin Pyo, Youixi Cui, Sang-Ho Yoon, and Jin-Wu Nam. Tumor Immune Microenvironment lncRNAs, Briefings in Bioinfo. 23(1):bbab504, 2022
Sang-Ho Yoon , Seo-Won Choi , Suk Woo Nam , Kyoung Bun Lee#, and Jin-Wu Nam#. Preoperative immune landscape predisposes adverse outcomes in hepatocellular carcinoma patients with liver transplantation, npj Precision Oncology 5:27, 2021.
Bumsik Cho*, Sang-Ho Yoon*, Daewon Lee, Ferdinand Koranteng, Sudhir Gopal Tattikota, Nuri Cha, Mingyu Shin, Hobin Do, Yanhui Hu, Sue Young Oh, Seok Joon Moon, Norbert Perrimon, Jin-Wu Nam#, Jiwon Shim#. Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila, Nature Comm., 11:4483, 2020.
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, PNAS, 116 (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 .

BIOINFORMATICS & GENOMICS

Bioinformatics & Genomics