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
E-mail: 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.

Awards

  • 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)

Career

  • 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, 제30권 1호 pp. 431-433, 2003.
  • Learning of RNA Structural Grammar using Genetic Programming, J.W. NAM, J.G. JOUNG, B.T. ZHANG, KISS Spring, 제30권 1호 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, 제2차 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, 제30권 2호 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.)