Jin-Wu Nam

Biointelligence Lab (BI)
School of Computer Sci. and Eng.
Seoul National University
Seoul 151-742, Korea

Office: 138-409
Phone: +82-2-880-5890
Fax: +82-2-883-9120
jwnam at wi.mit.edu
Personal home page: http://bi.snu.ac.kr/~jwnam
Research interests: MicroRNA prediction and Target Prediction using Machine Learning Approaches, Systems Biology, SNP analysis, DNA computing.


  • KSBI2003 (Korean Society for Bioinformatics) Excellent Paper Award : Computational Method for Searching Human miRNA precursors
  • KISS2003  Fall, Excellent Poster Award : Theorem Proving in Horn-Clause Logic Using DNA Computing
  • Lotte Fellowship: 2004. 9.~2005. 2.
  • Seoul Science Fellowship: 2005. 9.~

Domestic patents

  • Computerized method for identifying ncRNA sequences, J.W. NAM, J.G. JOUNG AND B.T. ZHANG 2005. 7. 19. 제0504039호
  • Mature microRNA Prediction Method Using Bidirectional Hidden Markov Model And Media Recording The Program To Perform This Method.   B.T. ZHANG, J.W. NAM, K.R. SHIN 2004. 5. 6. (제10-0614827호)

International patents

  • Mature microRNA Prediction Method Using Bidirectional Hidden Markov Model And Media Recording The Program To Perform This Method.  B.T. ZHANG, J.W. NAM, K.R. SHIN 2005. 5. 3. (pending in USA)


  • Research assistant, 2001. 3. ~ 2002. 8. Pangenomics (Biotechology Venture).
  • Visiting Research, 2004. 1. ~ 2004. 2. Sakakibara Lab in Bioinformatics Depart. on Keio Univ.
  • Researcher 2002.9~ present. Center for Bioinformation Technology.
  • Invited reviewer Bioinformatics, 2005.12.
  • Assistant Instructor, Seoul Science School (S cube) 2006.1.
  • Invited reviewer, 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
  • Program Committee, 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
  • Invited reviewer, 2007, Nucleic acids research, Database Issue.
  • Invited reviewer, 2007, Nucleic acids research, Web server Issue.

Book Chapter

  • Supervised learning approach for microRNA studies, Machine Learning in Bioinformatics, 2007. B.-T. Zhang and J.-W. Nam

International papers

  • 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
  • J.-W. Nam, W.J. Lee, B.T. ZHANG. Computational Methods for Identification of Human microRNA Precursors.  Lecture Notes in Artificial Intelligence, vol. 3157, pp. 732-741, 2004. (Cited number: 2)
  • Park, E.-J., Nam, J.-W., Lee, I.-H., and Zhang, B.-T. Solving the monkey and banana problem using DNA computing, Preliminary Proceedings of the Tenth International Meeting on DNA Computing (DNA10), p.452, 2004.
  • W.J. Lee, J.-W. Nam, S.K. Kim, B.T. Zhang. Identification of C.elegans MicroRNA Targets Using a Kernel Method.  Genomics and Informatics vol. 3(1):15-23, 2005.
  • SA Lee, KM Lee, WY Park, B Kim, J.-W. Nam, KY Yoo,  DY Noh, SH Ahn, A Hironen, D Kang. Obesity and genetic polymorphism of ERCC2 and ERCC2 as modifiers of risk of breast cancer  Exp. Mol. Med. 37(2):86-90, 2005.
  •  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  (Cited number: 16)
  • S.K. Kim, J.-W. Nam, W.J. Lee, B.T. Zhang. A Kernel Method for MicroRNA Target Prediction Using Sensible Data and Position-Based Features. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005), pp. 46-52, 2005.
  • V.N. Kim and J.-W. Nam, Genomics of microRNA.  Trends in Genetics, 22(3):165-173, 2006. Most downlaoded paper (Cited number: 17)
  • 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. (Cited number: 11)
  • J.-W. Nam*, J.H.Kim*, S.K.Kim, B.-T. Zhang. ProMiR II: a web server for clutered, nonclustered, conserved, nonconserved miRNA prediction. Nucleic Acids Research, 34:W455-W458, 2006
  • S.K. Kim*, J.-W. Nam*, 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 (Cited number: 1).
  • 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., EvoBio2007 (accepted).
  • J.-G. Joung, K.-B.Hwang, J.-W. Nam, S.-J. Kim, B.-T. Zhang. Discovery of microRNA-mRNA modules via population-based probabilistic learning., Bioinformatics (in press).
  • J.-W. Nam, B.-H. Kim, J.J. Han, V.N. Kim, B.-T. Zhang, Predicting microRNAs and designing artificial primary miRNAs using a Bayesian network model of position-based features. (submitted)
  • J.-W. Nam, B.-T. Zhang, Inferring genome-wide correlation networks of miRNAs to indentify expression pattern families (In preparation).
  • J.-W. Nam*, J.-K. Rhee*, S.-J. Kim, and J.-H. Lee, and B.-T Zhang, MirNet: Comprehensive analysis of microRNA regulation over disease-related pathways (In preparation).
  • J.-W. Nam and B.-T. Zhang, Identification of Drosha/DGCR8 substrate using evolutioanry algorithms. (In preparation).

*: Equally contributing authors


Domestic papers

  • Evolutionary Algorithm to Construct Regulatory Genetic Network , J.G. JOUNG, S.J. O, J.W. NAM, B.T. ZHANG, KISS Spring, 30 1 pp. 431-433, 2003.
  • Learning of RNA Structural Grammar using Genetic Programming, J.W. NAM, J.G. JOUNG, B.T. ZHANG, KISS Spring, 30 1 pp. 425-427, 2003.
  • DNA Computing for In Vitro Regulatory Machinery Modeling, J.W. NAM, J.G. JOUNG, B.T. ZHANG, KISS Fall 30-2 pp. 67-69, 2003
  • Theorem Proving in Horn-Clause Logic Using DNA Computing, E.J. PARK, J.W. NAM, I.H. LEE, B.T. ZHANG, KISS Fall 30-2  pp. 58-60, 2003 .
  • Computational Method for Searching Human miRNA Precursors , J.W. NAM, W.J. LEE, J.G. JOUNG, B.T. ZHANG, KSBI2003, 2 pp. 288-297, 2003 (Excellent Paper Award)             
  • PromSearch: a core-promoter prediction program using neural networks, 김병희, 김윤희, 남진우, 임명은, 심정섭, 박선희, 장병탁, 한국정보과학회 추계학술대회, 30 2 pp. 769-771, 2003                                                                     
  • Learning miRNA Scoring Model Using Base IUPAC Code W.J. LEE, J.W. NAM, B.T. ZHANG, KISS Fall  30-2 pp. 775-777, 2003
  • 유전알고리즘을 이용한 MicroRNA 이중나선 구조의 Dinucleotide Step 파라미터 추정, 남진우, 장병탁 KCC2005, 제32권 1(B), pp. 262-264.
  • RNA 공통 구조 기술자 Committee machine을 이용한 ncRNA 예측 성능 향상 기법, 남진우, 김성규, 장병탁, KISS Fall, 2005.
  • 동역학 시스템의 진화적 학습에 의한 초파리 발생과정 모델링, 이제근, 남진우, 정제균, 장병탁, KISS Fall, 2005.
  • 유전알고리즘을 이용한 Pre-miRNA 3차 구조 파라미터 추정, 남진우, 장병탁, 제 2회 컴퓨테이셔널 인텔리젼스 합동학술대회, 제2권, pp. 181-185, 2006.01
  • microRNA 발현데이터의 상관관계 분석을 통한 microRNA functional family 탐색, 남진우, 장병탁 KCC2006, pp.13-15, 2006.
  • Mature microRNA 위치 예측 모델의 진화적 최적화. 김진한, 남진우, 장병탁, KCC2006, pp.67-69, 2006.
  • 베이지안 네트웍을 이용한 microRNA 예측과 특질 의존성 분석, 남진우, 박종선, 장병탁, KCC2006 fall.

Usable Techniques

  • Experimental Techniques
  • DNA sequencing  (by ABI sequencer)

  • Genotyping, SNP analysis, Haplotype analysis

  • Quantitative Real Time PCR

  • Other DNA works (cloning, ligation, gel electrophoresis,...)

  • Machine Learning Algorithms
  • Hidden Markov Models

  • Evolutionary algorithm (Genetic programming, Genetic algorithm)

  • Decision Tree

  • Neural Networks

  • SVM, Kernel machine

  • Bioinformatics
  • Genome analysis and Comparative analysis

  • MicroRNA prediction and target prediction

  • Microarray data analysis

  • Systems Biology (S-system for Dynamic modeling, Network construction & inference)

  • DNA Computing (Molecular Design)
  • Java, Matlab, R, mySql

Activities & Experiences

  • 연세대학교 생물학과 학생회장 1996.
  • 만기 군복무(1997~1999, 공군 무기정비특기, 41610)
  • (주) Pangenomics 연구원 (2001.3. ~ 2002.8.)