Publications

2017

Tsuchiya S, Aoki NP, Shinmachi D, Matsubara M, Yamada I, Aoki-Kinoshita KF, Narimatsu H. Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans. Carbohydr Res. 445:104-116, 2017. (doi: 10.1016/j.carres.2017.04.015.) (PMID: 28525772)

Matsubara M, Aoki-Kinoshita KF, Aoki NP, Yamada I, Narimatsu H. WURCS 2.0 update to encapuslate ambiguous carbohydrate structures. J. Chem. Inf. Model, 57(4):632-637, 2017. (doi: 10.1021/acs.jcim/6b00650) (PMID: 28263066)

Hosoda M, Akune Y, Aoki-Kinoshita KF. Development and application of an algorithm to compute weighted multiple glycan alignments. Bioinformatics, 33(9):1317-1323, 2017. (doi: 10.1093/bioinformatics/btw827) (PMID: 28093404)

2016

Aoki-Kinoshita KF, Aoki NP, Fujita A, Fujita N, Kawasaki T, Matsubara M, Okuda S, Shikanai T, Shinmachi D, Solovieva E, Suzuki Y, Tsuchiya S, Yamada I, Narimatsu H. Latest developments in Semantic Web technologies applied to the Glycosciences. Perspectives in Science, 11:18-23, 2016. (doi: 10.1016/j.pisc.2016.05.012)

Barnett CB, Aoki-Kinoshita KF, Naidoo KJ. The Glycome Analytics Platform: an integrative framework for glycobioinformatics. Bioinformatics. 32(19):3005-3011, 2016. (doi: 10.1093/bioinformatics/btw341) (PMID: 27288496)

Struwe WB, Agravat S, Aoki-Kinoshita KF, Campbell MP, Costello CE, Dell A, Ten Feizi, Haslam SM, Karlsson NG, Khoo KH, Kolarich D, Liu Y, McBride R, Novotny MV, Packer NH, Paulson JC, Rapp E, Ranzinger R, Rudd PM, Smith DF, Tiemeyer M, Wells L, York WS, Zaia J, Kettner C. The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets. Glycobiology. 26(9):907-910, 2016. (PMID: 27654115)

Hou W, Qiu Y, Hashimoto N, Ching WK and Aoki-Kinoshita KF. A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks. BMC Bioinformatics, 17(Suppl 7):240, 2016. (doi: 10.1186/s12859-016-1094-6) (PMID: 27454116)

Akune Y, Lin CH, Abrahams JL, Zhang J, Packer NH, Aoki-Kinoshita KF, Campbell MP. Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database. Carbohydr Res. 431:56-63, 2016. (doi: 10.1016/j.carres.2016.05.012) (PMID: 27318307)

Aoki-Kinoshita K, Agravat S, Aoki NP, Arpinar S, Cummings RD, Fujita A, Fujita N, Hart GM, Haslam SM, Kawasaki T, Matsubara M, Moreman KW, Okuda S, Pierce M, Ranzinger R, Shikanai T, Shinmachi D, Solovieva E, Suzuki Y, Tsuchiya S, Yamada I, York WS, Zaia J, Narimatsu H. GlyTouCan 1.0 - The international glycan structure repository. Nucleic Acids Res. 44(D1):D1237-D1242, 2016. (doi: 10.1093/nar/gkv1041) (PMID: 26476458)

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2015

Varki A, Cummings RD, Aebi M, Packer NH, Seeberger PH, Esko JD, Stanley P, Hart G, Darvill A, Kinoshita T, Prestegard JJ, Schnaar RL, Freeze HH, Marth JD, Bertozzi CR, Etzler ME, Frank M, Vliegenthart JF, Lütteke T, Perez S, Bolton E, Rudd P, Paulson J, Kanehisa M, Toukach P, Aoki-Kinoshita KF, Dell A, Narimatsu H, York W, Taniguchi N, Kornfeld S. Symbol Nomenclature for Graphical Representations of Glycans. Glycobiology. 25(12):1323-4, 2015. (doi: 10.1093/glycob/cwv091) (PMID: 26543186)

Yamamoto-Hino M, Yoshida H, Ichimiya T, Sakamura S, Maeda M, Kimura Y, Sasaki N, Aoki-Kinoshita KF, Kinoshita-Toyoda A, Toyoda H, Ueda R, Nishihara S, Goto S. Phenotype-based clustering of glycosylation-related genes by RNAi-mediated gene silencing. Genes Cells. 20(6):521-42, 2015. (doi: 10.1111/gtc.12246) (PMID: 25940448)

Aoki-Kinoshita, KF, Kinjo, AR, Morita, M, Igarashi, Y, Chen, Y, Shigemoto, Y, Fujisawa, T, Akune, Y, Katoda, T, Kokubu, A, Mori, T, Nakao, M, Kawashima, S, Okamoto, S, Katayama, T and Ogishima, S. Implementation of linked data in the life sciences at BioHackathon 2011. Journal of Biomedical Semantics 6:3, 2015. (doi:10.1186/2041-1480-6-3)

Yamaguchi, A. and Aoki-Kinoshita, K.F. "Chemical Compound Complexity in Biological Pathways" in Quantitative graph theory : mathematical foundations and applications (ed. Matthias Dehmer, Frank Emmert-Streib), CRC Press, Taylor & Francis Group, Boca Raton, FL, USA. 2015.

Aoki-Kinoshita, KF. Analyzing Glycan-Binding Patterns with the ProfilePSTMM Tool. Methods Mol Biol. 1273:193-202, 2015. (doi: 10.1007/978-1-4939-2343-4_14.) (PMID: 25753712)

Aoki-Kinoshita, KF. Analyzing Glycan Structure Synthesis with the Glycan Pathway Predictor (GPP) Tool. Methods Mol Biol. 1273:139-47, 2015. (doi: 10.1007/978-1-4939-2343-4_10.) (PMID: 25753708)

Aoki-Kinoshita KF, Kanehisa M. Glycomic Analysis Using KEGG GLYCAN. Methods Mol Biol. 1273:97-107, 2015. (doi: 10.1007/978-1-4939-2343-4_7.) (PMID: 25753705)

Hirabayashi J, Tateno H, Shikanai T, Aoki-Kinoshita KF, Narimatsu H. The Lectin Frontier Database (LfDB), and Data Generation Based on Frontal Affinity Chromatography. Molecules. 8;20(1):951-973, 2015. (PMID: 25580689)

Ranzinger R, Aoki-Kinoshita KF, Campbell MP, Kawano S, Lütteke T, Okuda S, Shinmachi D, Shikanai T, Sawaki H, Toukach P, Matsubara M, Yamada I, Narimatsu H. GlycoRDF: an ontology to standardize glycomics data in RDF. Bioinformatics. 31(6):919-925, 2015. (doi: 10.1093/bioinformatics/btu732.) (PMID: 25388145)

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2014

Fujita A, Hosoda M, Tsuchiya S, Akune Y, Aoki-Kinoshita KF. Trends and Future Perspectives for Glycoinformatics. Trends in Glycoscience and Glycotechnology (TIGG), 28(150):89-97, 2014. (doi: 10.4052/tigg.26.89)

Qiu Y, Shimada K, Hiraoka N, Maeshiro K, Ching WK, Aoki-Kinoshita KF, Furuta K. Knowledge discovery for pancreatic cancer using inductive logic programming. IET Syst Biol., 8(4):162-8, 2014. (doi: 10.1049/iet-syb.2013.0044.) (PMID: 25075529)

Tanaka K, Aoki-Kinoshita KF, Kotera M, Sawaki H, Tsuchiya S, Fujita N, Shikanai T, Kato M, Kawano S, Yamada I, Narimatsu H. WURCS: The Web3 Unique Representation of Carbohydrate Structures. J. Chem. Inf. Model., 54(6):1558–1566, 2014. (doi: 10.1021/ci400571e) (PMID: 24897372)

York WS, Agravat S, Aoki-Kinoshita KF, McBride R, Campbell MP, Costello CE, Dell A, Feizi T, Haslam SM, Karlsson N, Khoo KH, Kolarich D, Liu Y, Novotny M, Packer NH, Paulson JC, Rapp E, Ranzinger R, Rudd PM, Smith DF, Struwe WB, Tiemeyer M, Wells L, Zaia J, Kettner C. MIRAGE - The minimum information required for a glycomics experiment. Glycobiology, 24(5):402-406, 2014. (doi: 10.1093/glycob/cwu018) (PMID: 24653214)

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics. 5(1):5, 2014.

Campbell, M.P., Ranzinger, R., Luetteke, T., Mariethoz, J., Hayes, C.A., Zhang, J., Akune, Y., Aoki-Kinoshita, K.F., Damerell, D., Carta, G., York, W.S., Haslam, S.M., Narimatsu, H., Rudd, P.M., Karlsson, N.G., Packer, N.H. and Lisacek, F. Toolboxes for a standardised and systematic study of glycans. BMC Bioinformatics. 15(Suppl 1):S9, 2014.

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2013

Aoki-Kinoshita, K.F., Bolleman, J., Campbell, M., Kawano, S., Kim, J.D., Luetteke, T., Matsubara, M., Okuda, S., Ranzinger, R., Sawaki, H., Shikanai, T., Shinmachi, D., Suzuki, Y., Toukach, P., Yamada, I., Packer, N.H., and Narimatsu, H. Introducing glycomics data into the Semantic Web, J. Biomed. Semantics. 4(1):39, 2013.

Campbell, M.P., Peterson, R., Mariethoz, J., Gasteiger, E., Akune, Y., Aoki-Kinoshita, K.F., Lisacek, F. and Packer, N.H. UniCarbKB: building a knowledge platform for glycoproteomics. Nucleic Acids Res. 42(1):D215-D221, 2013.

Aoki-Kinoshita, K.F., Sawaki, H., An, H.J., Campbell, M., Cao, Q., Cummings, R., Hsu, D., Kato, M., Kawasaki, T., Khoo, K.-H., Kim, J., Kolarich, D., Li, X., Matsubara, M., Okuda, S., Packer, N.H., Ranzinger, R., Shen, H., Shikanai, T., Shinmachi, D., Toukach, P., Yamada, I., Yamaguchi, Y., Yang, P., Ying, W., Yoo, J.S., Zhang, Y., Zhang, Y. and Narimatsu, H. The Fifth ACGG-DB Meeting Report: Towards an International Glycan Structure Repository. Glycobiology. 23(12):1422-1424, 2013.

Ichimiya, T., Nishihara, S., Takase-Yoden, S., Kida, H., Aoki-Kinoshita, K.F. Frequent glycan structure mining of influenza virus data revealed a sulfated glycan motif that increased viral infection. Bioinformatics. 30(5):706-711, 2013.

Aoki-Kinoshita, K.F. Introduction to informatics in glycoprotein analysis. in "Mass Spectrometry of Glycoproteins : Methods and Protocols", 951:257-67, 2013.

Aoki-Kinoshita, K.F., Sawaki, H., An, H.J., Cho, J.W., Hsu, D., Kato, M., Kawano, S., Kawasaki, T., Khoo, K.-H., Kim, J., Kim, J.-D., Li, X., Lütteke, L., Okuda, S., Packer, N.H., Paulson, J.C., Raman, R., Ranzinger, R., Shen, H., Shikanai, T., Yamada, I., Yang, P., Yamaguchi, Y., Ying, W., Yoo, J.S., Zhang, Y., and Narimatsu, H. The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics. Glycobiology. 23(2):144-146, 2013.

Aoki-Kinoshita, K.F. Mining frequent subtrees in glycan data using the RINGS glycan miner tool. Methods Mol. Biol. 939:87-95, 2013.

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2012

Yano, H., Yamamoto-Hino, M., Awano, W., Aoki-Kinoshita, K.F., Tsuda-Sakurai, K., Okano, H., Goto, S. Identification of proteasome components required for apical localization of Chaoptin using functional genomics. J Neurogenet. 26(1):53-63, 2012.

Konishi, Y. and Aoki-Kinoshita, K.F. The GlycomeAtlas tool for visualizing and querying glycome data. Bioinformatics. 28(21):2849-2850, 2012.

Hosoda, M., Akune, Y., Aoki-Kinoshita, K.F. Multiple Tree Alignment with Weights Applied to Carbohydrates to Extract Binding Recognition Patterns. Lecture Notes in Computer Science (PRIB 2012), Volume 7632, 49-58, 2012.

Jiang, H., Ching, W.-K., Aoki-Kinoshita, K.F., Guo, D. Modeling Genetic Regulatory Networks: A Delay Discrete Dynamical Model Approach, Journal of Systems Science & Complexity, 25(6):1052-1067, 2012.

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2011

Campbell, M. P., Hayes, C. A., Struwe, W. B., Wilkins, M. R., Aoki-Kinoshita, K. F., Harvey, D. J., Rudd, P. M., Kolarich, D., Lisacek, F., Karlsson, N. G. and Packer, N. H., UniCarbKB: Putting the pieces together for glycomics research. Proteomics, 11: 4117–4121, 2011.

Jiang, H., Aoki-Kinoshita, K.F. and Ching, W. Extracting Glycan Motifs using a Biochemically-Weighted Kernel, Bioinformation, 7(8):405-412, 2011.

Aoki-Kinoshita, K.F. Informatics for Glycobiology and Glycomics. In "Carbohydrate Recognition: Biological Problems, Methods, and Applications" (eds. B. Wang, G.-J. Boons), pp. 409-426, 2011.

Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernandez JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T. The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics. 2:4, 2011.

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2010

Yamamoto-Hino, M., Kanie, Y., Awano, W., Aoki-Kinoshita, K.F., Yano, H., Nishihara, S., Okano, H., Ueda, R., Kanie, O., Goto, S. Identification of genes required for neural-specific glycosylation using functional genomics. PLoS Genet. 6(12):e1001254, 2010.

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.), Wiley, 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.

Jiang H, Ching WK, Aoki-Kinoshita KF, Guo DJ. Delay Discrete Dynamical Models for Genetic Regulatory Networks. Systems Biology. 93-100, 2010.

Chen X, Ching, WK, Aoki-Kinoshita KF, Furuta K. Support Vector Machine methods for the prediction of cancer growth. 3rd International Joint Conference on Computational Sciences and Optimization, CSO 2010: Theoretical Development and Engineering Practice. Volume 1, Article number 5533163, 229-232, 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. PMID: 20726803

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. The DBCSL BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium. J Biomed Semantics. 1(1):8, 2010.

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2009

Aoki-Kinoshita, K.F. Glycome Informatics: Methods and Applications, CRC Press (2009). ISBN: 9781420083347, ISBN 10: 1420083341.

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).

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2008

Aoki-Kinoshita, K.F. An introduction to glycome informatics, J. Biochemistry, Vol. 80, 1038-1041, 2008.(in Japanese)

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

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2007

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.

2006

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. PMID: 16873479

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.

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