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Items: 31

1.

GlyGen: Computational and Informatics Resources for Glycoscience.

York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M, Natale DA, Packer NH, Woods RJ, Agarwal G, Arpinar S, Bhat S, Blake J, Castro LJG, Fochtman B, Gildersleeve J, Goldman R, Holmes X, Jain V, Kulkarni S, Mahadik R, Mehta A, Mousavi R, Nakarakommula S, Navelkar R, Pattabiraman N, Pierce MJ, Ross K, Vasudev P, Vora J, Williamson T, Zhang W.

Glycobiology. 2020 Jan 28;30(2):72-73. doi: 10.1093/glycob/cwz080. No abstract available.

PMID:
31616925
2.

GRITS Toolbox-a freely available software for processing, annotating and archiving glycomics mass spectrometry data.

Weatherly DB, Arpinar FS, Porterfield M, Tiemeyer M, York WS, Ranzinger R.

Glycobiology. 2019 Jun 1;29(6):452-460. doi: 10.1093/glycob/cwz023.

PMID:
30913289
3.

The minimum information required for a glycomics experiment (MIRAGE) project: LC guidelines.

Campbell MP, Abrahams JL, Rapp E, Struwe WB, Costello CE, Novotny M, Ranzinger R, York WS, Kolarich D, Rudd PM, Kettner C.

Glycobiology. 2019 May 1;29(5):349-354. doi: 10.1093/glycob/cwz009.

PMID:
30778580
4.

GLYDE-II: The GLYcan data exchange format.

Ranzinger R, Kochut KJ, Miller JA, Eavenson M, Lütteke T, York WS.

Perspect Sci (Neth). 2017 Jan;11:24-30. doi: 10.1016/j.pisc.2016.05.013. Epub 2016 Oct 20.

5.

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.

Glycobiology. 2017 Oct 1;27(10):915-919. doi: 10.1093/glycob/cwx066.

6.

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.

Glycobiology. 2017 Apr;27(4):280-284. Epub 2016 Nov 22.

7.

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.

Glycobiology. 2016 Sep;26(9):907-910. Epub 2016 Sep 21.

8.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1237-42. doi: 10.1093/nar/gkv1041. Epub 2015 Oct 17.

9.

GlycomeDB.

Ranzinger R, York WS.

Methods Mol Biol. 2015;1273:109-24. doi: 10.1007/978-1-4939-2343-4_8.

PMID:
25753706
10.

Annotation of glycomics MS and MS/MS spectra using the GlycoWorkbench software tool.

Damerell D, Ceroni A, Maass K, Ranzinger R, Dell A, Haslam SM.

Methods Mol Biol. 2015;1273:3-15. doi: 10.1007/978-1-4939-2343-4_1.

PMID:
25753699
11.

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.

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

12.

EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard data.

Al Jadda K, Porterfield MP, Bridger R, Heiss C, Tiemeyer M, Wells L, Miller JA, York WS, Ranzinger R.

Bioinformatics. 2015 Jan 15;31(2):242-5. doi: 10.1093/bioinformatics/btu609. Epub 2014 Sep 12.

13.

Qrator: a web-based curation tool for glycan structures.

Eavenson M, Kochut KJ, Miller JA, Ranzinger R, Tiemeyer M, Aoki K, York WS.

Glycobiology. 2015 Jan;25(1):66-73. doi: 10.1093/glycob/cwu090. Epub 2014 Aug 27.

14.

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.

Glycobiology. 2014 May;24(5):402-6. doi: 10.1093/glycob/cwu018. Epub 2014 Mar 20.

15.

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.

BMC Bioinformatics. 2014;15 Suppl 1:S9. doi: 10.1186/1471-2105-15-S1-S9. Epub 2014 Jan 10.

16.

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.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

17.

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.

J Biomed Semantics. 2013 Nov 26;4(1):39. doi: 10.1186/2041-1480-4-39.

18.

The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting mass-spectrometry-based glycoanalytic data.

Kolarich D, Rapp E, Struwe WB, Haslam SM, Zaia J, McBride R, Agravat S, Campbell MP, Kato M, Ranzinger R, Kettner C, York WS.

Mol Cell Proteomics. 2013 Apr;12(4):991-5. doi: 10.1074/mcp.O112.026492. Epub 2013 Feb 1.

19.

The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics.

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.

Glycobiology. 2013 Feb;23(2):144-6. doi: 10.1093/glycob/cws167. No abstract available.

20.

The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments.

Damerell D, Ceroni A, Maass K, Ranzinger R, Dell A, Haslam SM.

Biol Chem. 2012 Nov;393(11):1357-62. doi: 10.1515/hsz-2012-0135.

PMID:
23109548
21.

EUROCarbDB: An open-access platform for glycoinformatics.

von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K, Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lütteke T, Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, Schloissnig S, Stenutz R, Vranken WF, Widmalm G, Haslam SM.

Glycobiology. 2011 Apr;21(4):493-502. doi: 10.1093/glycob/cwq188. Epub 2010 Nov 23.

22.

GlycomeDB--a unified database for carbohydrate structures.

Ranzinger R, Herget S, von der Lieth CW, Frank M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D373-6. doi: 10.1093/nar/gkq1014. Epub 2010 Nov 2.

23.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

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, Fernández 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.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.

24.

Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences.

Ranzinger R, Frank M, von der Lieth CW, Herget S.

Glycobiology. 2009 Dec;19(12):1563-7. doi: 10.1093/glycob/cwp137. Epub 2009 Sep 16.

PMID:
19759275
25.

GlycomeDB - integration of open-access carbohydrate structure databases.

Ranzinger R, Herget S, Wetter T, von der Lieth CW.

BMC Bioinformatics. 2008 Sep 19;9:384. doi: 10.1186/1471-2105-9-384.

26.

Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans.

Herget S, Toukach PV, Ranzinger R, Hull WE, Knirel YA, von der Lieth CW.

BMC Struct Biol. 2008 Aug 11;8:35. doi: 10.1186/1472-6807-8-35.

27.

GlycoCT-a unifying sequence format for carbohydrates.

Herget S, Ranzinger R, Maass K, Lieth CW.

Carbohydr Res. 2008 Aug 11;343(12):2162-71. doi: 10.1016/j.carres.2008.03.011. Epub 2008 Mar 13.

PMID:
18436199
28.

"Glyco-peakfinder"--de novo composition analysis of glycoconjugates.

Maass K, Ranzinger R, Geyer H, von der Lieth CW, Geyer R.

Proteomics. 2007 Dec;7(24):4435-44.

PMID:
18072204
29.

Exploring the structural diversity of mammalian carbohydrates ("glycospace") by statistical databank analysis.

Werz DB, Ranzinger R, Herget S, Adibekian A, von der Lieth CW, Seeberger PH.

ACS Chem Biol. 2007 Oct 19;2(10):685-91.

PMID:
18041818
30.

Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de.

Toukach P, Joshi HJ, Ranzinger R, Knirel Y, von der Lieth CW.

Nucleic Acids Res. 2007 Jan;35(Database issue):D280-6.

31.

AISMIG--an interactive server-side molecule image generator.

Bohne-Lang A, Groch WD, Ranzinger R.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W705-9.

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