Sun Kim

Postdoctoral Fellow
Computational Biology Branch
National Center for Biotechnology Information (NCBI)
National Institutes of Health (NIH)
Bethesda, MD 20894, USA
Phone: +1-301-496-2484

NCBI page: click here

Research Interests
  • Machine learning (kernel methods, evolutionary algorithms)
  • Text mining for web documents and biomedical lierature
  • Bioinformatics (microarray data analysis, protein-protein interaction extraction)
  • Evolutionary hypernetworks for biomedical applications and online data filtering
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Academic Services
  • Reviewer: PLoS Computational Biology, Bioinformatics, Journal of the American Medical Informatics Association, Advances in Bioinformatics, PSB 2010
  • PC Member: ICMLA 2010, ICMLA 2011
Journal Publications
  • PIE the search: Searching PubMed Literature for Protein Interaction Information, S. Kim, D. Kwon, S.-Y. Shin, and W. J. Wilbur, Bioinformatics, 2012 (in press).
  • Classifying Protein-Protein Interaction Articles Using Word and Syntactic Features, S. Kim and W. J. Wilbur, BMC Bioinformatics, 12(Suppl 8), S9, 2011.
  • The Protein-Protein Interaction Tasks of BioCreative III: Classification/Ranking of Articles and Linking Bio-Ontology Concepts to Full Text, M. Krallinger, M. Vazquez, F. Leitner, D. Salgado, A. Chatr-Aryamontri, A. Winter, L. Perfetto, L. Briganti, L. Licata, M. Iannuccelli, L. Castagnoli, G. Cesareni, M. Tyers, G. Schneider, F. Rinaldi, R. Leaman, G. Gonzalez, S. Matos, S. Kim, W. J. Wilbur, L. Rocha, H. Shatkay, A. V. Tendulkar, S. Agarwal, F. Liu, X. Wang, R. Rak, K. Noto, C. Elkan, Z. Lu, R. I. Dogan, J.-F. Fontaine, M. A. Andrade-Navarro, and A. Valencia, BMC Bioinformatics, 12(Suppl 8), S3, 2011.
  • Ensembled Support Vector Machines for Human Papillomavirus Risk Type Prediction from Protein Secondary Structures, S. Kim, J. Kim, and B.-T. Zhang, Computers in Biology and Medicine, 39(2), pp. 187-193, 2009.
  • Introducing Meta-Services for Biomedical Information Extraction, F. Leitner, M. Krallinger, C. Rodriguez-Penagos, J. Hakenberg, C. Plake, C.-J. Kuo, C.-N. Hsu, R. T. Tasi, H.-C. Hung, W. W. lau, C. A. Johnson, R. Satre, K. Yoshida, Y. H. Chen, S. Kim, S.-Y. Shin, B.-T. Zhang, W. A. Baumgartner, Jr., L. Hunter, B. Haddow, M. Matthews, X. Wang, P. Ruch, F. Ehrler, A. Ozgur, G. Erkan, D. R. Radev, M. Krauthammer, T. Luong, R. Hoffmann, C. Sander, and A. Valencia, Genome Biology, 9(Suppl 2), S6, 2008.
  • PIE: an online prediction system for protein-protein interactions from text, S. Kim*, S.-Y. Shin*, I.-H. Lee, S.-J. Kim, R. Sriram, and B.-T. Zhang, Nucleic Acids Research, 36, W411-W415, 2008.
  • Human Papillomavirus Risk Type Classification from Protein Sequences Using Support Vector Machines, S. Kim and B.-T. Zhang, Lecture Notes in Computer Science (EVOBIO 2006), 3907, pp. 57-66, 2006.
  • Multi-objective Evolutionary Probe Design Based on Thermodynamic Criteria for HPV Detection, I.-H. Lee, S. Kim, and B.-T. Zhang, Lecture Notes in Artificial Intelligence (PRICAI 2004), 3157, pp. 742-750, 2004.
  • Genetic Mining of HTML Structures for Effective Web-Document Retrieval, S. Kim and B.-T. Zhang, Applied Intelligence, 18(3), pp. 243-256, 2003.
Conference Publications (Full Papers, not Abstracts)
  • An EM Clustering Algorithm which Produces a Dual Representation, S. Kim and W. J. Wilbur, International Conference on Machine Learning and Applications (ICMLA 2011), pp. 90-95, 2011.
  • Improving Protein-Protein Interaction Article Classification Performance by Utilizing Grammatical Relations, S. Kim and W. J. Wilbur, Third BioCreative Challenge Workshop, pp. 83-88, 2010 (ranked first).
  • Evolutionary Hypernetwork Classifiers for Protein-Protein Interaction Sentence Filtering, J. Bootkrajang, S. Kim, and B.-T. Zhang, Genetic and Evolutionary Computation Conference (GECCO 2009), pp. 185-192, 2009.
  • Evolving Hypernetwork Models of Binary Time Series for Forecasting Price Movements on Stock Markets, E. Bautu, S. Kim, A. Bautu, H. Luchian, and B.-T. Zhang, IEEE Congress on Evolutionary Computation (CEC 2009), pp. 166-173, 2009.
  • Finding Cancer-Related Gene Combinations Using a Molecular Evolutionary Algorithm, C.-H. Park*, S.-J. Kim*, S. Kim, D.-Y. Cho, and B.-T. Zhang, IEEE International Symposium on Bioinformatics and Biomedical Engineering (BIBE 2007), pp. 158-163, 2007.
  • Evolving Hypernetwork Classifiers for microRNA Expression Profile Analysis, S. Kim*, S.-J. Kim*, and B.-T. Zhang, IEEE Congress on Evolutionary Computation (CEC 2007), pp. 313-319, 2007.
  • Use of Evolutionary Hypernetworks for Mining Prostate Cancer Data, C.-H. Park*, S.-J. Kim*, S. Kim, D.-Y. Cho, and B.-T. Zhang, International Symposium on Advanced Intelligent Systems, pp. 702-706, 2007.
  • Identifying Protein-Protein Interaction Sentences Using Boosting and Kernel Methods, S.-Y. Shin*, S. Kim*, J.-H. Eom, B.-T. Zhang, and R. Sriram, Second BioCreative Challenge Workshop, pp. 187-192, 2007.
  • Text Classifiers Evolved on a Simulated DNA Computer, S. Kim, M.-O. Heo, and B.-T. Zhang, IEEE Congress on Evolutionary Computation (CEC 2006), pp. 9196-9202, 2006.
  • A Tree Kernel-Based Method for Protein-Protein Interaction Mining from Biomedical Literature, J.-H. Eom, S. Kim, S.-H. Kim, and B.-T. Zhang, Lecture Notes in Bioinformatics (KDLL 2006), 3886, pp. 42-52, 2006.
  • Evolutionary Learning of Web-Document Structure for Information Retrieval, S. Kim and B.-T. Zhang, IEEE Congress on Evolutionary Computation (CEC 2001), pp. 1253-1260, 2001.
  • SCAI Experiments on TREC-9, Y.-H. Kim, S. Kim, J.-H. Eom, and B.-T. Zhang, Text Retrieval Conference (TREC-9), pp. 392-399, 2000.
  • Web-Document Retrieval by Genetic Learning of Importance Factors for HTML Tags, S. Kim and B.-T. Zhang, PRICAI 2000 Workshop on Text and Web Mining, pp. 13-23, 2000.
  • SCAI TREC-8 Experiments, D.-H. Shin, Y.-H. Kim, S. Kim, J.-H. Eom, H.-J. Shin, and B.-T. Zhang, Text Retrieval Conference (TREC-8), pp. 511-518, 1999.
Book Chapters
  • Natural Language Processing, Y.-T. Kim et al., 2001. (in Korean)
Korean Publications
  • 클러스터 기반 가중치 부여를 통해 희소성을 제거한 협력적 여과, 신원진, 김선, 장병탁, 한국컴퓨터종합학술대회 논문집, 36(1), pp. 451-456, 2009.
  • 하이퍼네트워크 모델을 이용한 텍스트 문장 분류, 작가멧, 김선, 장병탁, 대한전자공학회 추계학술대회 논문집, 31(2), pp. 987-988, 2008.
  • 기계번역문장 품질 평가를 위한 하이퍼네트워크 기반 언어 모델링, 고영길, 장하영, 김선, 장병탁, 정보통신분야학회 합동학술대회 논문집, pp. 277-280, 2008.
  • 마이크로어레이 기반 miRNA 모듈 분석을 위한 하이퍼망 분류 기법, 김선, 김수진, 장병탁, 정보과학회논문지 : 소프트웨어 및 응용, 35(6), pp. 347-356, 2008.
  • DNA Chip Informatics 기술, 장병탁, 황규백, 정제균, 김선, 엄재홍, 바이오웹진, 2003.
  • 다수의 목표 유전자에서 진화연산을 이용한 Oligonucleotide Probe 선택, 신기루, 김선, 장병탁, 한국정보과학회 봄 학술발표 논문집, 30(1), pp. 455-457, 2003.
  • Oligonucleotide Microarray의 Probe 선택을 위한 진화적인 접근 방법, 김선, 장병탁, 한국데이터마이닝학회 추계학술대회 논문집, pp. 140-147, 2002.
  • 유전 알고리즘을 이용한 DNA Microarray의 Probe 선택, 김선, 장병탁, 한국퍼지 및 지능시스템학회 춘계 학술발표 논문집, pp. 183-186, 2002.
  • 진화연산을 이용한 웹 문서의 특성 학습, 김선, 장병탁, 한국퍼지 및 지능시스템학회 춘계 학술발표 논문집, pp. 43-46, 2000.
Talks
  • DNAChipBench: Integrated DNA-Chip Informatics Platform, ICT-Asia Seminar, French Ministry of Foreign and European Affairs, Taipei, Nov. 20, 2007.
  • 진화연산 기반의 웹 문서 검색방법, 서울디지털산업단지 기술장터, Seoul Industry Academia Forum and Seoul National University Industry Foundation, Seoul, Jun. 14, 2007.
Patents
  • Evolutionary Computation-Based Method for Web-Document Retrieval, S. Kim and B.-T. Zhang (Korea Patent No. 10-0416156)
Publications in Google Scholar


Revised: Jan 25, 2012