The RINGS resource for glycome informatics analysis and data mining on the web

OMICS A Journal of Integrative Biology

Volumn 14, Issue 4, 2010, Pages 475-486

  Akune, Yukie ^a   Hosoda, Masae ^a   Kaiya, Sakiko ^a   Shinmachi, Daisuke ^a   Aoki Kinoshita, Kiyoko F ^a  

^a SOKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCAN; MONOSACCHARIDE;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; GLYCOBIOLOGY; GLYCOME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS;

ALGORITHMS; CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; DATA MINING; DATABASES, FACTUAL; GLYCOMICS; INFORMATICS; INTERNET; MOLECULAR SEQUENCE DATA; SOFTWARE;

EID: 77956030977     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2009.0129     Document Type: Article

References (24)

1. Aoki-Kinoshita, K.F. (2008). An introduction to bioinformatics for glycomics research. PLoS Comput Biol 4, e1000075.
2. Aoki, K.F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S., et al. (2004). KCaM (KEGG carbohydrate matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res 32, W267-W272.
3. Aoki, K.F., Mamitsuka, H., Akutsu, T., and Kanehisa, M. (2005). A score matrix to reveal the hidden links in glycans. Bioinformatics 21, 1457-1463.
4. Aoki-Kinoshita, K.F., Ueda, N., Mamitsuka, H., and Kanehisa, M. (2006). ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. Bioinformatics 22, e25-e34.
5. Attrill, H., Takazawa, H, Witt, S., Kelm, S., Isecke, R., Brossmer, R., et al. (2006). The structure of siglec-7 in complex with sialosides: leads for rational structure-based inhibitor design. Biochem J 397(Pt 2), 271-278.
6. Banin, E., Neuberger, Y., Altshuler, Y., Halevi, A., Inbar,O., Dotan, N., et al. (2002). A novel linear code nomenclature for complex carbohydrates. Trends Glycosci Glycotechnol 14, 127-137.
7. Bohne-Lang, A., Lang, E., Forster, T., Von Der Lieth, C.W. (2001). LINUCS: linear notation for unique description of carbohydrate sequences. Carbohydr Res 336, 1-11.
8. Diligenti, M., Frasconi, P., and Gori, M. (2003). Hidden tree Markov models for document image classification. IEEE Trans on PAMI 25, 519-523.
9. Durbin, R., Eddy, S.R., Krogh, A., and Mitchison, G. (1999). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (Cambridge University Press, Cambridge, UK).
10. Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., et al. (2006). KEGG as a glycome informatics resource. Glycobiology 16, 63R-70R.
11. Hashimoto, K., Aoki-Kinoshita, K.F., Ueda, N., Kanehisa, M., and Mamitsuka, H. (2008a). A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology. ACM Trans Knowl Discov Data (TKDD) 2(1), Article No. 6.
12. Hashimoto, K., Takigawa, I., Shiga, M., Kanehisa, M., and Mamitsuka, H. (2008b). Mining significant tree patterns in carbohydrate sugar chains. Bioinformatics. 24, i167-i173.
13. Hashimoto, K., Tokimatsu, T., Kawano, S., Yoshizawa, A.C., Okuda, S., Goto, S., et al. (2009). Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydrate Res 344, 881-887.
14. Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M. (2003). Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc 125, 11853-11865.
15. Henikoff, S., and Henikoff, J.G. (1992). Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89, 10915-10919.
16. Herget, S., Ranzinger, R., Maass, K., and Von Der Lieth, C.W. (2008). GlycoCT-a unifying sequence format for carbohydrates. Carbohydr Res 343, 2162-2171.
17. Hizukuri, Y., Yamanishi, Y., Nakamura, O., Yagi, F., Goto, S., and Kanehisa, M. (2005). Extraction of leukemia specific glycan motifs in humans by computational glycomics. Carbohydr Res 340, 2270-2278.
18. Kikuchi, N., and Narimatsu, H. (2006). Bioinformatics for comprehensive finding and analysis of glycosyltransferases. Biochim Biophys Acta 1760, 578-583.
19. Krambeck, F.J., and Betenbaugh, M.J. (2005). A mathematical model of N-linked glycosylation. Biotechnol Bioeng 92, 711-728.
20. Lutteke, T., Bohne-Lang, A., Loss, A., Goetz, T., Frank, M., and Von Der Lieth, C.W. (2006). GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 16, 71R-81R.
21. Packer, N.H., Von Der Lieth, C.W., Aoki-Kinoshita, K.F., Lebrilla, C.B., Paulson, J.C., Raman, R., et al. (2008). 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 8, 8-20.
22. Raman, R., Venkataraman, M., Ramakrishnan, S., Lang, W., Raguram, S., and Sasisekharan, R. (2006). Advancing glycomics: implementation strategies at the Consortium for Functional Glycomics. Glycobiology 16, 82R-90R.
23. Ranzinger, R., Herget, S., Wetter, T., and Von Der Lieth, C.W. (2008). GlycomeDB-integration of open-access carbohydrate structure databases. BMC Bioinformatics 9, 384.
24. Ueda, N., Aoki-Kinoshita, K.F., Yamaguchi, A., Akutsu, T., and Mamitsuka, H. (2005). A probabilistic model for mining labeled ordered trees: capturing patterns in carbohydrate sugar chains. IEEE Trans Knowl Data Eng 17, 1051-1064.