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Sun Kim
Postdoctoral Fellow
Computational Biology Branch
National Center for Biotechnology Information (NCBI)
National Institutes of Health (NIH)
Bethesda, MD 20894

Tel: 301-496-2484
E-mail: sun.kim at nih.gov, skim at bi.snu.ac.kr
More details at http://echosf.net
Short Bio
Sun Kim is a Postdoctoral Fellow at the National Center for Biotechnology Information (NCBI), where he joined right after receiving his PhD degree in Computer Science and Engineering from Seoul National University in 2009. His research interests include:
  • Machine learning
  • Text mining
  • Bioinformatics
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, 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)
  • 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).
Publications in Google Scholar


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