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Towards a standardized bioinformatics infrastructure for N- and O-glycomics.
Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP, Shinmachi D, Ashwood C, Madunic K, Zhang T, Miller RL, Horlacher O, Struwe WB, Watanabe Y, Okuda S, Levander F, Kolarich D, Rudd PM, Wuhrer M, Kettner C, Packer NH, Aoki-Kinoshita KF, Lisacek F, Karlsson NG. Rojas-Macias MA, et al. Among authors: aoki np. Nat Commun. 2019 Jul 22;10(1):3275. doi: 10.1038/s41467-019-11131-x. Nat Commun. 2019. PMID: 31332201 Free PMC article. Review.
The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences.
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. Yamada I, et al. Among authors: aoki np. Nat Methods. 2020 Jul;17(7):649-650. doi: 10.1038/s41592-020-0879-8. Nat Methods. 2020. PMID: 32572234 No abstract available.
Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans.
Tsuchiya S, Aoki NP, Shinmachi D, Matsubara M, Yamada I, Aoki-Kinoshita KF, Narimatsu H. Tsuchiya S, et al. Among authors: aoki np. Carbohydr Res. 2017 Jun 5;445:104-116. doi: 10.1016/j.carres.2017.04.015. Epub 2017 Apr 19. Carbohydr Res. 2017. PMID: 28525772 Free article.
GlyTouCan: an accessible glycan structure repository.
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. Tiemeyer M, et al. Among authors: aoki np. Glycobiology. 2017 Oct 1;27(10):915-919. doi: 10.1093/glycob/cwx066. Glycobiology. 2017. PMID: 28922742 Free PMC article.
The international glycan repository GlyTouCan version 3.0.
Fujita A, Aoki NP, Shinmachi D, Matsubara M, Tsuchiya S, Shiota M, Ono T, Yamada I, Aoki-Kinoshita KF. Fujita A, et al. Among authors: aoki np. Nucleic Acids Res. 2021 Jan 8;49(D1):D1529-D1533. doi: 10.1093/nar/gkaa947. Nucleic Acids Res. 2021. PMID: 33125071 Free PMC article.
WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures.
Matsubara M, Aoki-Kinoshita KF, Aoki NP, Yamada I, Narimatsu H. Matsubara M, et al. Among authors: aoki np. J Chem Inf Model. 2017 Apr 24;57(4):632-637. doi: 10.1021/acs.jcim.6b00650. Epub 2017 Mar 22. J Chem Inf Model. 2017. PMID: 28263066 Free article.
GlyTouCan 1.0--The international glycan structure repository.
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. Aoki-Kinoshita K, et al. Among authors: aoki np. Nucleic Acids Res. 2016 Jan 4;44(D1):D1237-42. doi: 10.1093/nar/gkv1041. Epub 2015 Oct 17. Nucleic Acids Res. 2016. PMID: 26476458 Free PMC article.
BioHackathon 2015: Semantics of data for life sciences and reproducible research.
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. Vos RA, et al. Among authors: aoki np. F1000Res. 2020 Feb 24;9:136. doi: 10.12688/f1000research.18236.1. eCollection 2020. F1000Res. 2020. PMID: 32308977 Free PMC article.