Professor

Kinoshita  Flora Kiyoko

Profile

Specialized field

Computer Systems and Networks, Bioinformatics, Applied Genomics, Biomolecular Science

Research theme

Development of glycoinformatics resources for elucidating the functions of glycans

Subjects in charge

Data Structure, Bioinformatics Seminar, Genome Information Science, Bioprogramming, General Theory of Science and Engineering, Project Studies A & B, Seminar I & II, Japan Studies Program Engineering and Natural Sciences

Specialized field

Knowledge discovery, glycoinformatics, algorithms, distributed systems and mobile agents, networks

Research theme

In the field of bioinformatics, glycan information has been amplified, but compared to DNA and proteins, glycan structures are complex and pose various problems in their analysis. First, glycan structures are in the form of a "tree" rather than a sequence, so the methods that have been used for sequences up until now cannot be easily applied. Therefore, we analyze glycan structures using methods such as computational theory and data mining. In addition, to make these methods available on the web, we are developing glycoinformatics resources in a project called RINGS. We aim to elucidate the complex functions of glycans through RINGS.

Subjects in charge

Specialized bioinformatics courses, English paper writing exercises, cutting-edge research, data analysis exercises, etc.

Main career, work history, and academic background

February 1973 Born in Kansas City, Missouri, USA
June 1996: Received bachelor's and master's degrees in computer science from Northwestern University in the United States.
December 1999: Ph.D. in Computer Engineering from Northwestern University, USA
2000.1 Postdoctoral Fellow, Taiwan Central Research Institute
May 2000: Senior Software Development Engineer at BioDiscovery, USA
2003.4 Postdoctoral Fellow, Institute for Chemical Research, Kyoto University
2004.4 Research Assistant, Institute for Chemical Research, Kyoto University
2006.4 Lecturer Department of Bioinformatics, Faculty of Engineering, Soka University
2008.4 Associate Professor, Department of Bioinformatics, Faculty of Engineering, Soka University
2014.4 Professor, Department of Bioinformatics, Faculty of Engineering, Soka University
2023.4 Professor, Department of Information Systems Engineering Faculty of Science and Engineering

Affiliated academic societies and organizations

Japanese Society for Bioinformatics
Japanese Society of 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

Main Papers and Publications

The latest information can be found at this link.
Aoki-Kinoshita, KF 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, KF 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).
Kiyoshi Kinoshita. Overview of Glycoinformatics. Journal of Biochemistry, Vol. 80, No. 11, 1038-1041, 2008.
Aoki-Kinoshita, KF Using glycome databases for drug discovery. Expert Opinion on Drug Discovery, 3(8), 877-890, 2008.
Aoki-Kinoshita, KF and Kanehisa, M., Systems approach to metabolism. In "Wiley Encyclopedia of Chemical Biology" (Begley, TP, ed.) wecb589 (2008).
Kuboyama, T., Hirata, K., Aoki-Kinoshita, KF 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, KF An Introduction to Bioinformatics for Glycomics Research. PLoS Computational Biology 4(5): e1000075, 2008. doi:10.1371/journal.pcbi.1000075
Hashimoto, K., Aoki-Kinoshita, KF, Ueda, N., Kanehisa, M., Mamitsuka, H. A new probabilistic model for mining efficient labeled ordered trees applied to glycobiology, ACM Trans. on Knowledge Discovery from Data (TKDD), 2(1), Article No. 6, 2008.
Packer, NH, von der Lieth, CW, Aoki-Kinoshita, KF, Lebrilla, CB, Paulson, JC, Raman, R., Rudd, P., Sasisekharan, R., Taniguchi, N., York, WS, 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, KF and Kanehisa, M., Gene annotation and pathway mapping in KEGG. In "Comparative Genomics Volume 2" (Bergman, NH, ed.), Humana Press, Methods Mol. Biol. 396, 71-92, 2007.
Aoki-Kinoshita, KF 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, KF, 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, KF, 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, KF, 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, KF, (Special Topic: Commentary) Overview of KEGG applications to omics-related research, J. Pestic. Sci., 31(3), 296-299, 2006.
Hashimoto, K., Aoki-Kinoshita, KF, Ueda, N., Kanehisa, M., and Mamitsuka, H., A New Efficient Probabilistic Model for Mining Labeled Ordered Trees, Proc. KDD, 177-186, 2006.
Aoki-Kinoshita, KF, 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, KF, 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, KF, 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, KF, 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, KF, 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, KF, 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, KF, 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, KF 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, KF, 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, KF, 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, KF, 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, KF, 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, KF 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, KF, 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, KF, Lee, DT, Towards Web-Based Computing, International Journal of Computational Geometry and Applications, 11(1), 71-104, 1999.

Specialized field

Computer Systems and Networks, Bioinformatics, Applied Genomics, Biomolecular Science

Research theme

Development of glycoinformatics resources for elucidating the functions of glycans

Specialized field

Computer Systems and Networks, Bioinformatics, Applied Genomics, Biomolecular Science

Research theme

Development of glycoinformatics resources for elucidating the functions of glycans