Publications

  • Aoki, K. F., Ueda, N., Yamaguchi, A., Kanehisa M., Akutsu, T. and Mamitsuka, H., Application of a New Probabilistic Model for Recognizing Complex Patterns in Glycans, Proceedings of the Twelvth International Conference on Intelligent Systems for Molecular Biology (Supplement of Bioinformatics), Glasgow, Scotland, UK, August, 2004, Oxford University Press.

  • Aoki, K. F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S., and Kanehisa, M., KCaM (KEGG Carbohydrate Matcher): A Software Tool for Analyzing the Structures of Carbohydrate Sugar Chains, ACM SIGMOD Record, 33 (2), 2004.

  • Aoki, K. F., Ueda, N., Yamaguchi, A., Akutsu, T., Kanehisa, M. and Mamitsuka, H., Managing and Analyzing Carbohydrate Data, ACM SIGMOD Record, 33 (2), 2004.

  • Ueda, N., Aoki, K. F. and Mamitsuka, H., A General Probabilistic Framework for Mining Labeled Ordered Trees, Proceedings of the Fourth SIAM International Conference on Data Mining, pp. 357-368, Orlando, FL, April, 2004, SIAM, Philadelphia, USA.

  • Aoki, K. F., Yamaguchi, A., Okuno, Y., Akutsu, T., Ueda, N., Kanehisa, M. and Mamitsuka, H., Efficient Tree-Matching Methods for Accurate Carbohydrate Database Queries, Proceedings of the Fourteenth International Conference on Genome Informatics ( Genome Informatics, 14), pp. 134-143, Yokohama, Japan, December, 2003, Universal Academy Press.

  • Chen, J.Y., Hoff, B., Yu, K, Salonga, F, Aoki, K.F., Sun, Q., Wang, C., Yu, A., "Enterprise-wide Data Management and Analysis for Microarrays," Cambridge Healthtech Institute's Second Annual Microarray Data Analysis Conference, Sept. 2002.

  • Lin, L.H., Lee, D.T. Aoki, K.F., DAViD: A distributed algorithm visualization and debugging system for geometric computing, In Proc. 3rd Int'l Conf. Human and Computer 2000, Univ. of Aizu and Waseda Univ., Japan, Sept. 6-9, 2000.

  • Aoki, K.F., Lee, D.T., A Web-Based Distributed Programming Environment, the 8th International Conference on High-Performance Computing and Networking Europe 2000, 237-246, Amsterdam, The Netherlands, May 8-10, Springer-Verlag, LNCS, 2000.

  • Aoki, K.F., Lee, D.T., Towards Web-Based Computing, International Journal of Computational Geometry and Applications, 11(1), 71-104, 1999.

  • Singh, L., Chen, B., Haight, R., Scheuermann, P., Aoki, K.F., A Robust System Architecture for Mining Semi-structured Data, Proceedings of the International Conference on Knowledge Discovery and Data Mining (KDD), 329-333, New York City, New York, USA, August 27-31, 1998, The AAAI Press.

    Book Chapter

  • Aoki, K., Petrov, A., A Comprehensive Microarray Data Management Approach, a book chapter in "Microarray Methods and Applications: Nuts and Bolts," (Gary Hardiman, ed.), pp. 171-192, ISBN: 0-96640-276-6, June, 2003.

    Theses

  • Aoki, K.F., A Web-Based Distributed Programming Environment, Doctoral thesis, July, 1999.

  • Aoki, K.F., GeoManager, a dynamic geometric algorithm visualization system, Master's project, December, 1995.

    Patents

  • Aoki, K.F., Hoff, B., Apparatus, method, and computer program product for plotting proteomic and genomic data, patent application submitted Dec. 2001.

    Hoff, B., Shams, S., Draghici, S., Aoki, K.F., System and Method for Specifying and Applying Microarray Data Preparation, patent application submitted in Oct. 2001.

    Presentations

  • Glycan Alignment And Scoring, Twelvth International Conference on Intelligent Systems for Molecular Biology, Glasgow, Scotland, UK, August, 2004.

  • Statistical Significance of Tree Similarity Scores, The 14th International Conference on Genome Informatics, Yokohama, Japan, Dec. 14-17, 2003.

  • Efficient Tree-Matching Methods for Accurate Carbohydrate Database Queries, International Workshop on Bioinformatics and Systems Biology, Dresden, Germany, Aug. 16-19, 2003.

  • A Comprehensive Tool for Normalization and Data Preparation Using GeneSight, MGED IV, Boston, MA, Feb. 2002.

  • GeneDirector: The Complete Data Management Solution for MicroArrays, MGED IV, Boston, MA, Feb. 2002.

  • Introduction to the GeoJAVA System, National Taiwan University, Dec. 1999.

  • Towards Web-Based Computing, Academia Sinica, Taiwan, Dec. 1998.

  • A Web-Based Distributed Programming Environment, Mathematics and Computer Science Division, Argonne National Laboratory, Aug. 1999.