KINOSHITA Flora Kiyoko(Professor)


Specialized field Computer system network
Biological/living body informatics
Applied genome science
Living organism molecular science
Classes GCP Tutorial A1
GCP Tutorial A2
GCP Tutorial B1
GCP Tutorial B2
GCP Tutorial B3
GCP Tutorial B4
Bioinformatics Seminar 3
Bioinformatics Seminar 4
Algorithms for Bioinformatics
Japan Studies Program Enginieering and Natural Sciences
Data Structures
General Topics in Science and Engineering
Project Studies A
Project Studies B
Practical Bioinformatics
Genome Informatics
Computer Programming in Bioinformatics
Design and Analysis of Algorithms I
Current Topics in Biological Information Systems
Advanced Study of Biological Information Systems
Preparation for Scientific Papers in English
Advanced Course of Bioengineering
Advanced Laboratory Course of Bioengineering
Laboratory in Bioinformatics 1
Laboratory in Bioinformatics 2
Research theme Development of a glycome informatics resource to reveal glycan function

Application for coverage

Detail of researcher information

Bioinformatics of Graduate school of engineering

  • Academic experience Feb., 1973 - Born in Kansas City, Missouri, USA
    June, 1996 - Both BS and MS degrees in Computer Science from Northwestern University, USA
    Dec., 1999 - PhD in Computer Engineering from Northwestern University, USA
    Jan., 2000 - Postdoctoral fellow at Institute for Information Science, Academia Sinica, Taiwan
    May, 2000 - Senior software engineer at BioDiscovery, Inc., in Los Angeles, California, USA
    Apr., 2003 - Postdoctoral fellow at Bioinformatics Center, Institute for Chemical Research, Kyoto University
    Apr., 2004 - Research Associate/Assistant Professor at Bioinformatics Center, Institute for Chemical Research, Kyoto University
    Apr., 2006 - Lecturer in Department of Bioinformatics, Faculty of Engineering, Soka University
    Apr., 2008 - Associate Professor in Department of Bioinformatics, Faculty of Engineering, Soka University
    Apr., 2014 - Professor in Department of Bioinformatics, Faculty of Engineering, Soka University
    Research Theme Knowledge discovery
    Glycome informatics
    Distributed systems (agents)
    Publications Aoki-Kinoshita, K.F. and Kanehisa, M. Bioinformatics analysis of glycan structures from a genomic perspective. In "Bioinformatics for Glycobiology and Glycomics: an Introduction" (von der Lieth, C.-W., Luetteke, T., Frank, M., eds.), pp. 125-141, 2010.

    Li L, Ching WK, Yamaguchi T, Aoki-Kinoshita KF. A weighted q-gram method for glycan structure classification. BMC Bioinformatics. 11 Suppl 1:S33, 2010.

    Akune Y, Hosoda M, Kaiya S, Shinmachi D, Aoki-Kinoshita KF. The RINGS resource for glycome informatics analysis and data mining on the Web. OMICS. 14(4):475-86, 2010.

    Katayama T, Arakawa K, Nakao M, Ono, K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernandez JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T. J Biomed Semantics. 1(1):8, 2010.

    Aoki-Kinoshita, K.F. and Kanehisa, M.; Using KEGG in the transition from genomics to chemical genomics. In "Bioinformatics for Systems Biology" (Krawetz, S., ed.), pp.429-445, Humana Press (2009).

    Kinoshita, K. Overview of glycome informatics. Biochemistry Journal (Japanese), 80(11), 1038-1041, 2008.

    Aoki-Kinoshita, K.F. Using glycome databases for drug discovery. Expert Opinion on Drug Discovery, 3(8), 877-890, 2008.

    Aoki-Kinoshita, K.F. and Kanehisa, M., Systems approach to metabolism. In "Wiley Encyclopedia of Chemical Biology" (Begley, T.P., ed.) wecb589 (2008).

    Kuboyama, T., Hirata, K., Aoki-Kinoshita, K.F. An Efficient Unordered Tree Kernel and Its Application to Glycan Classification. Proc. 12th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD2008). Lecture Notes in Artificial Intelligence 5012, 184-195, 2008

    Aoki-Kinoshita, K.F. An Introduction to Bioinformatics for Glycomics Research. PLoS Computational Biology 4(5): e1000075, 2008. doi:10.1371/journal.pcbi.1000075

    Hashimoto, K., Aoki-Kinoshita, K.F., Ueda, N., Kanehisa, M., Mamitsuka, H. A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology, ACM Trans. on Knowledge Discovery from Data (TKDD), 2(1), Article No. 6, 2008.

    Packer, N.H., von der Lieth, C.W., Aoki-Kinoshita, K.F., Lebrilla, C.B., Paulson, J.C., Raman, R., Rudd, P., Sasisekharan, R., Taniguchi, N., York, W.S., Frontiers in glycomics: Bioinformatics and biomarkers in disease An NIH White Paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13, 2006). Proteomics. Jan;8(1), 8-20, 2008.

    Aoki-Kinoshita, K.F. and Kanehisa, M.; Gene annotation and pathway mapping in KEGG. In "Comparative Genomics Volume 2" (Bergman, N.H., ed.), Humana Press, Methods Mol. Biol. 396, 71-92, 2007.

    Aoki-Kinoshita, K.F. and Kanehisa, M., Bioinformatics approaches in glycomics and drug discovery, Current Opinion in Molecular Therapeutics, 8(6), 514-520, 2006.

    Kuboyama, T., Hirata, K., Aoki-Kinoshita, K.F., Kashima, H., and Yasuda, H., A Gram Distribution Kernel Applied to Glycan Classification and Motif Extraction, Genome Informatics, 17(2), 25-34, 2006.

    Aoki-Kinoshita, K.F., Kanehisa, M., Kao, M.-L., Li, X.-Y., and Wang, W., A 6-Approximation Algorithm for Computing the Least Common AoN-supertree with Application to the Reconstruction of Glycan Trees, In T. Asano, editor, Lecture Notes in Computer Science 4288: Proc. of 17th Annual International Symposium on Algorithms and Computation (ISAAC), pp. 100-110. Springer-Verlag, New York, NY, 2006.

    Kuboyama, T., Kashima, H., Aoki-Kinoshita, K.F., Hirata, K. and Yasuda, H., A Spectrum Tree Kernel, In Proc. The International Workshop on Data-Mining and Statistical Science (DMSS2006), 106-119, 2006.

    Aoki-Kinoshita, K.F., (Special Topic: Commentary) Overview of KEGG applications to omics-related research, J. Pestic. Sci., 31(3), 296-299, 2006.

    Hashimoto, K., Aoki-Kinoshita, K.F., Ueda, N., Kanehisa, M., and Mamitsuka, H., A New Efficient Probabilistic Model for Mining Labeled Ordered Trees, Proc. KDD, 177-186, 2006.

    Aoki-Kinoshita, K.F., Ueda, N., Mamitsuka, H., and Kanehisa, M., ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains, Bioinformatics, 22, e25-e34, 2006.

    Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., and Kanehisa, M., KEGG as a glycome informatics resource, Glycobiology, 16, 63R-70R, May 2006.

    Zhu, S., Udaka, K., Sidney, J., Sette, A., Aoki-Kinoshita, K.F., and Mamitsuka, H., Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules, Bioinformatics, 22 (13), 1648-1655, 2006.

    Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M., From genomics to chemical genomics: new developments in KEGG, Nucleic Acids Research, 34, D354-7, 2006.

    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.

    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

    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.

    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.

    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., Lee, D.T., Towards Web-Based Computing, International Journal of Computational Geometry and Applications, 11(1), 71-104, 1999.
    Membership of Academic Societies JSBi: Japanese Society for Bioinformatics
    JSCR: Japanese Society for Carbohydrate Research
    Japanese Biochemical Society
    Information Processing Society of Japan
    FCCA Forum: Carbohydrates Coming of Age
    IEEE: Institute of Electrical and Electronics Engineers, Inc.
    ISCB: International Society for Computational Biology
    Society for Glycobiology