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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: rudd pm. Nat Commun. 2019 Jul 22;10(1):3275. doi: 10.1038/s41467-019-11131-x. Nat Commun. 2019. PMID: 31332201 Free PMC article. Review.
UniCarb-DB: a database resource for glycomic discovery.
Hayes CA, Karlsson NG, Struwe WB, Lisacek F, Rudd PM, Packer NH, Campbell MP. Hayes CA, et al. Among authors: rudd pm. Bioinformatics. 2011 May 1;27(9):1343-4. doi: 10.1093/bioinformatics/btr137. Epub 2011 Mar 12. Bioinformatics. 2011. PMID: 21398669
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. Among authors: rudd pm. Proteomics. 2011 Nov;11(21):4117-21. doi: 10.1002/pmic.201100302. Epub 2011 Sep 19. Proteomics. 2011. PMID: 21898825
The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets.
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. Struwe WB, et al. Among authors: rudd pm. Glycobiology. 2016 Sep;26(9):907-910. doi: 10.1093/glycob/cww082. Epub 2016 Sep 21. Glycobiology. 2016. PMID: 27654115 Free PMC article.
Databases and Associated Tools for Glycomics and Glycoproteomics.
Lisacek F, Mariethoz J, Alocci D, Rudd PM, Abrahams JL, Campbell MP, Packer NH, Ståhle J, Widmalm G, Mullen E, Adamczyk B, Rojas-Macias MA, Jin C, Karlsson NG. Lisacek F, et al. Among authors: rudd pm. Methods Mol Biol. 2017;1503:235-264. doi: 10.1007/978-1-4939-6493-2_18. Methods Mol Biol. 2017. PMID: 27743371
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. Among authors: rudd pm. Glycobiology. 2014 May;24(5):402-6. doi: 10.1093/glycob/cwu018. Epub 2014 Mar 20. Glycobiology. 2014. PMID: 24653214 Free PMC article.
Comparison of analytical methods for profiling N- and O-linked glycans from cultured cell lines : HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study.
Ito H, Kaji H, Togayachi A, Azadi P, Ishihara M, Geyer R, Galuska C, Geyer H, Kakehi K, Kinoshita M, Karlsson NG, Jin C, Kato K, Yagi H, Kondo S, Kawasaki N, Hashii N, Kolarich D, Stavenhagen K, Packer NH, Thaysen-Andersen M, Nakano M, Taniguchi N, Kurimoto A, Wada Y, Tajiri M, Yang P, Cao W, Li H, Rudd PM, Narimatsu H. Ito H, et al. Among authors: rudd pm. Glycoconj J. 2016 Jun;33(3):405-415. doi: 10.1007/s10719-015-9625-3. Epub 2015 Oct 28. Glycoconj J. 2016. PMID: 26511985 Free PMC article.
The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data.
Liu Y, McBride R, Stoll M, Palma AS, Silva L, Agravat S, Aoki-Kinoshita KF, Campbell MP, Costello CE, Dell A, Haslam SM, Karlsson NG, Khoo KH, Kolarich D, Novotny MV, Packer NH, Ranzinger R, Rapp E, Rudd PM, Struwe WB, Tiemeyer M, Wells L, York WS, Zaia J, Kettner C, Paulson JC, Feizi T, Smith DF. Liu Y, et al. Among authors: rudd pm. Glycobiology. 2017 Apr;27(4):280-284. doi: 10.1093/glycob/cww118. Epub 2016 Nov 22. Glycobiology. 2017. PMID: 27993942 Free PMC article.
GlycoStore: a database of retention properties for glycan analysis.
Zhao S, Walsh I, Abrahams JL, Royle L, Nguyen-Khuong T, Spencer D, Fernandes DL, Packer NH, Rudd PM, Campbell MP. Zhao S, et al. Among authors: rudd pm. Bioinformatics. 2018 Sep 15;34(18):3231-3232. doi: 10.1093/bioinformatics/bty319. Bioinformatics. 2018. PMID: 29897488
379 results