Ueda, N., Aoki-Kinoshita, K. F., Yamaguchi, A., Akutsu, T., and Mamitsuka, H., A probabilistic model for mining labeled ordered trees: capturing patterns in carbohydrate sugar chains, IEEE Transactions on Knowledge and Data Engineering, 17(8), 1051-1064, Aug 2005.

Hashimoto, K., Kawano, S., Goto, S., Aoki-Kinoshita, K., Kawashima, M., and Kanehisa, M.; A global representation of the carbohydrate structures: a tool for the analysis of glycan. Genome Informatics, 16(1), 214-222, 2005.

Aoki, K.F., Kanehisa, M., Using the KEGG database resource, chapter 1.12 in "Current Protocols in Bioinformatics," Current Protocols, (series ed. Liz Miranker), John Wiley & Sons, Ltd., August, 2005.

Aoki, K. F., Mamitsuka, H., Akutsu, T., and Kanehisa, M., A score matrix to reveal the hidden links in glycans, Bioinformatics, 21(8), 1457-1463, Apr 2005. PMID: 15585530

Wan, R., Mamitsuka, H. and Aoki, K. F. Cleaning Microarray Expression Data Using Markov Random Fields based on Profile Similarity. Proceedings of the Twentieth ACM Symposium on Applied Computing (SAC 2005), 206-207, Santa Fe, NM, March, 2005

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Yamaguchi, A., Aoki, K. F., and Mamitsuka, H., Finding the Maximum Common Subgraph of a Partial k-Tree and a Graph with a Polynomially Bounded Number of Spanning Trees, Information Processing Letters, 92(2), 57-63, 2004.

Igarashi, Y., Aoki, K. F., Mamitsuka, H., Kuma, k., and Kanehisa, M., The Evolutionary Repertoires of the Eukaryotic-Type ABC Transporters in Terms of the Phylogeny of ATP-binding Domains in Eukaryotes and Prokaryotes, Molecular Biology and Evolution, 21(11), 2149-2160, 2004.

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, Nucleic Acids Research, 32, W267-W272, July 2004. PMID: 15215393

Aoki, K. F., Ueda, N., Yamaguchi, A., Akutsu, T., Kanehisa, M. and Mamitsuka, H., Managing and Analyzing Carbohydrate Data, ACM SIGMOD Record, 33 (2), 33-38, June 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 (SDM 2004), 357-368, Orlando, FL, April, 2004, SIAM.

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. Bioinformatics, 20, i6-i14, 2004. PMID: 15262775

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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.

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, Genome Informatics, 14, pp. 134-143, 2003.

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Chen, J.Y., Hoff, B., Yu, K., Salonga, F., Aoki, K., 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.

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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.

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

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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.

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