Glycoinformatics Project

スタッフ紹介

研究室長
山田 一作 https://orcid.org/0000-0001-9504-189X
メンバー
小野 多美子
北風 春湖
塩田 正明
土屋 伸一郎
平野 清子
松原 正陽
(五十音順)


研究概要

  糖鎖情報科学研究室は2021年4月に発足した「糖鎖インフォマティクスプロジェクト」を改組して2022年4月に発足しました。糖鎖科学とインフォマティクスを融合した糖鎖インフォマティクスの研究を実施しています。これまで蓄積してきた糖鎖構造のデータ化や他のライフサイエンス分野とのデータ連携など各種融合分野の研究について、糖鎖構造を軸として研究しています。


《研究内容の紹介》
〇糖鎖構造の線形文字列化
〇糖鎖関連情報のLinked Open Data(LOD)構築
〇糖鎖立体構造の解析
〇糖鎖関連情報を活用した研究




業績リスト

Yagi H, Amagasa E, Shiota M, Yamada I, Aoki-Kinoshita KF, Kato K. GALAXY ver3: updated web application for glycosylation profiling based on 3D HPLC map. Glycobiology. 2022 Jul 13;32(8):646-650. doi: 10.1093/glycob/cwac025. PMID: 35452093.

Tsuchiya S, Matsubara M, Aoki-Kinoshita KF, Yamada I. SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures. Molecules. 2021 Nov25;26(23):7149. doi: 10.3390/molecules26237149. PMID: 34885724; PMCID: PMC8659005.

Yamada I, Campbell MP, Edwards N, Castro LJ, Lisacek F, Mariethoz J, Ono T, Ranzinger R, Shinmachi D, Aoki-Kinoshita KF. The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. Glycobiology. 2021 Aug 7;31(7):741-750. doi: 10.1093/glycob/cwab013. Erratum in: Glycobiology. 2021 Aug 10;: PMID: 33677548; PMCID: PMC8351504.

Feng Z, Westbrook JD, Sala R, Smart OS, Bricogne G, Matsubara M, Yamada I, Tsuchiya S, Aoki-Kinoshita KF, Hoch JC, Kurisu G, Velankar S, Burley SK, Young JY. Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank. Structure. 2021 Apr 1;29(4):393-400.e1. doi: 10.1016/j.str.2021.02.004. Epub 2021 Mar 2. PMID: 33657417; PMCID: PMC8026741.

Fujita A, Aoki NP, Shinmachi D, Matsubara M, Tsuchiya S, Shiota M, Ono T, Yamada I, Aoki-Kinoshita KF. The international glycan repository GlyTouCan version 3.0. Nucleic Acids Res. 2021 Jan 8;49(D1):D1529-D1533. doi: 10.1093/nar/gkaa947. PMID: 33125071; PMCID: PMC7779025.

Yamada I, Shiota M, Shinmachi D, Ono T, Tsuchiya S, Hosoda M, Fujita A, Aoki NP, Watanabe Y, Fujita N, Angata K, Kaji H, Narimatsu H, Okuda S, Aoki-Kinoshita KF. The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences. Nat Methods. 2020 Jul;17(7):649-650. doi: 10.1038/s41592-020-0879-8. PMID: 32572234.

Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Res. 2020 Feb 24;9:136. doi: 10.12688/f1000research.18236.1. PMID: 32308977; PMCID: PMC7141167.

Neelamegham S, Aoki-Kinoshita K, Bolton E, Frank M, Lisacek F, Lütteke T, O'Boyle N, Packer NH, Stanley P, Toukach P, Varki A, Woods RJ; SNFG Discussion Group. Updates to the Symbol Nomenclature for Glycans guidelines. Glycobiology. 2019 Aug 20;29(9):620-624. doi: 10.1093/glycob/cwz045. PMID: 31184695; PMCID: PMC7335484.

Tsuchiya S, Yamada I, Aoki-Kinoshita KF. GlycanFormatConverter: a conversion tool for translating the complexities of glycans. Bioinformatics. 2019 Jul 15;35(14):2434-2440. doi: 10.1093/bioinformatics/bty990. PMID: 30535258; PMCID: PMC6612873.

Tiemeyer M, Aoki K, Paulson J, Cummings RD, York WS, Karlsson NG, Lisacek F, Packer NH, Campbell MP, Aoki NP, Fujita A, Matsubara M, Shinmachi D, Tsuchiya S, Yamada I, Pierce M, Ranzinger R, Narimatsu H, Aoki-Kinoshita KF. GlyTouCan: an accessible glycan structure repository. Glycobiology. 2017 Oct 1;27(10):915-919. doi: 10.1093/glycob/cwx066. PMID: 28922742; PMCID: PMC5881658.

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. 2017 Jun 5;445:104-116. doi: 10.1016/j.carres.2017.04.015. Epub 2017 Apr 19. PMID: 28525772.

Matsubara M, Aoki-Kinoshita KF, Aoki NP, Yamada I, Narimatsu H. WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures. J Chem Inf Model. 2017 Apr 24;57(4):632-637. doi: 10.1021/acs.jcim.6b00650. Epub 2017 Mar 22. PMID: 28263066.

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. 2016 Jan 4;44(D1):D1237-42. doi: 10.1093/nar/gkv1041. Epub 2015 Oct 17. PMID: 26476458; PMCID: PMC4702779.

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. 2015 Mar 15;31(6):919-25. doi: 10.1093/bioinformatics/btu732. Epub 2014 Nov 11. PMID: 25388145; PMCID: PMC4380026.

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. 2014 Jun 23;54(6):1558-66. doi: 10.1021/ci400571e. Epub 2014 Jun 4. PMID: 24897372.

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, Kalaš 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. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5. PMID: 24495517; PMCID: PMC3978116.

Aoki-Kinoshita KF, Bolleman J, Campbell MP, Kawano S, Kim JD, Lütteke T, Matsubara M, Okuda S, Ranzinger R, Sawaki H, Shikanai T, Shinmachi D, Suzuki Y, Toukach P, Yamada I, Packer NH, Narimatsu H. Introducing glycomics data into the Semantic Web. J Biomed Semantics. 2013 Nov 26;4(1):39. doi: 10.1186/2041-1480-4-39. PMID: 24280648; PMCID: PMC4177142.

Aoki-Kinoshita KF, Sawaki H, An HJ, Cho JW, Hsu D, Kato M, Kawano S, Kawasaki T, Khoo KH, Kim J, Kim JD, Li X, Lütteke T, Okuda S, Packer NH, Paulson JC, Raman R, Ranzinger R, Shen H, Shikanai T, Yamada I, Yang P, Yamaguchi Y, Ying W, Yoo JS, Zhang Y, Narimatsu H. The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics. Glycobiology. 2013 Feb;23(2):144-6. doi: 10.1093/glycob/cws167. PMID: 23271684; PMCID: PMC3988462.



野口遵賞応募 野口遵研究助成金 野口遵賞 GlycoNAVI フルオラス科学研究会
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