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GlyGen data model and processing workflow.
Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman BC, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Garcia L, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R. Kahsay R, et al. Bioinformatics. 2020 Jun 1;36(12):3941-3943. doi: 10.1093/bioinformatics/btaa238. Bioinformatics. 2020. PMID: 32324859 Free PMC article.
UniCarbKB: putting the pieces together for glycomics research.
Campbell MP, Hayes CA, Struwe WB, Wilkins MR, Aoki-Kinoshita KF, Harvey DJ, Rudd PM, Kolarich D, Lisacek F, Karlsson NG, Packer NH. Campbell MP, et al. Proteomics. 2011 Nov;11(21):4117-21. doi: 10.1002/pmic.201100302. Epub 2011 Sep 19. Proteomics. 2011. PMID: 21898825
UniCarbKB: building a knowledge platform for glycoproteomics.
Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH. Campbell MP, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D215-21. doi: 10.1093/nar/gkt1128. Epub 2013 Nov 13. Nucleic Acids Res. 2014. PMID: 24234447 Free PMC article.
Introducing glycomics data into the Semantic Web.
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. Aoki-Kinoshita KF, et al. J Biomed Semantics. 2013 Nov 26;4(1):39. doi: 10.1186/2041-1480-4-39. J Biomed Semantics. 2013. PMID: 24280648 Free PMC article.
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
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. Katayama T, et al. J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5. J Biomed Semantics. 2014. PMID: 24495517 Free PMC article.
Toolboxes for a standardised and systematic study of glycans.
Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F. Campbell MP, et al. BMC Bioinformatics. 2014;15 Suppl 1(Suppl 1):S9. doi: 10.1186/1471-2105-15-S1-S9. Epub 2014 Jan 10. BMC Bioinformatics. 2014. PMID: 24564482 Free PMC article.
MIRAGE: the minimum information required for a glycomics experiment.
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. York WS, et al. Glycobiology. 2014 May;24(5):402-6. doi: 10.1093/glycob/cwu018. Epub 2014 Mar 20. Glycobiology. 2014. PMID: 24653214 Free PMC article.
GlycoRDF: an ontology to standardize glycomics data in RDF.
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. Ranzinger R, et al. Bioinformatics. 2015 Mar 15;31(6):919-25. doi: 10.1093/bioinformatics/btu732. Epub 2014 Nov 11. Bioinformatics. 2015. PMID: 25388145 Free PMC 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. 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.
92 results