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Items: 1 to 50 of 98

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. 2019 Oct 16. pii: cwz080. doi: 10.1093/glycob/cwz080. [Epub ahead of print] No abstract available.

PMID:
31616925
2.

The GlySpace Alliance: towards a collaborative global glycoinformatics community.

Aoki-Kinoshita KF, Lisacek F, Mazumder R, York WS, Packer NH.

Glycobiology. 2019 Oct 1. pii: cwz078. doi: 10.1093/glycob/cwz078. [Epub ahead of print] No abstract available.

PMID:
31573039
3.

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
4.

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
5.

Corrigendum: Complex pectin metabolism by gut bacteria reveals novel catalytic functions.

Ndeh D, Rogowski A, Cartmell A, Luis AS, Baslé A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O'Neill MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, Gilbert HJ.

Nature. 2017 Aug 31;548(7669):612. doi: 10.1038/nature23659. Epub 2017 Aug 23.

PMID:
29411780
6.

Designer biomass for next-generation biorefineries: leveraging recent insights into xylan structure and biosynthesis.

Smith PJ, Wang HT, York WS, Peña MJ, Urbanowicz BR.

Biotechnol Biofuels. 2017 Nov 30;10:286. doi: 10.1186/s13068-017-0973-z. eCollection 2017. Review.

7.

RElative QUantitation Inferred by Evaluating Mixtures (REQUIEM).

Tuomivaara ST, Schliekelman P, Nairn AV, Moremen KW, York WS.

Anal Chim Acta. 2017 Nov 15;993:22-37. doi: 10.1016/j.aca.2017.09.023. Epub 2017 Oct 4.

8.

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.

9.

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.

10.

Glycoinformatics.

Campbell MP, Aoki-Kinoshita KF, Lisacek F, York WS, Packer NH.

In: Varki A, Cummings RD, Esko JD, Stanley P, Hart GW, Aebi M, Darvill AG, Kinoshita T, Packer NH, Prestegard JH, Schnaar RL, Seeberger PH, editors. Essentials of Glycobiology [Internet]. 3rd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2015-2017. Chapter 52.
2017.

11.

Glycans in Bioenergy and Materials Science.

O'Neill MA, Moon RJ, York WS, Darvill AG.

In: Varki A, Cummings RD, Esko JD, Stanley P, Hart GW, Aebi M, Darvill AG, Kinoshita T, Packer NH, Prestegard JH, Schnaar RL, Seeberger PH, editors. Essentials of Glycobiology [Internet]. 3rd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2015-2017. Chapter 59.
2017.

12.

Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism.

Urbanowicz BR, Bharadwaj VS, Alahuhta M, Peña MJ, Lunin VV, Bomble YJ, Wang S, Yang JY, Tuomivaara ST, Himmel ME, Moremen KW, York WS, Crowley MF.

Plant J. 2017 Sep;91(6):931-949. doi: 10.1111/tpj.13628. Epub 2017 Aug 28.

13.

Complex pectin metabolism by gut bacteria reveals novel catalytic functions.

Ndeh D, Rogowski A, Cartmell A, Luis AS, Baslé A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O'Neil MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, Gilbert HJ.

Nature. 2017 Apr 6;544(7648):65-70. doi: 10.1038/nature21725. Epub 2017 Mar 22. Erratum in: Nature. 2017 Aug 31;548(7669):612.

14.

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. 2016 Nov 22. [Epub ahead of print]

15.

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.

16.

Structural diversity of xylans in the cell walls of monocots.

Peña MJ, Kulkarni AR, Backe J, Boyd M, O'Neill MA, York WS.

Planta. 2016 Sep;244(3):589-606. doi: 10.1007/s00425-016-2527-1. Epub 2016 Apr 22.

PMID:
27105886
17.

Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis.

Srivastava AC, Chen F, Ray T, Pattathil S, Peña MJ, Avci U, Li H, Huhman DV, Backe J, Urbanowicz B, Miller JS, Bedair M, Wyman CE, Sumner LW, York WS, Hahn MG, Dixon RA, Blancaflor EB, Tang Y.

Biotechnol Biofuels. 2015 Dec 21;8:224. doi: 10.1186/s13068-015-0403-z. eCollection 2015.

18.

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.

19.

Xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I do not have identical structures in soybean root and root hair cell walls.

Muszyński A, O'Neill MA, Ramasamy E, Pattathil S, Avci U, Peña MJ, Libault M, Hossain MS, Brechenmacher L, York WS, Barbosa RM, Hahn MG, Stacey G, Carlson RW.

Planta. 2015 Nov;242(5):1123-38. doi: 10.1007/s00425-015-2344-y. Epub 2015 Jun 12.

PMID:
26067758
20.

GlycomeDB.

Ranzinger R, York WS.

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

PMID:
25753706
21.

Galactose-depleted xyloglucan is dysfunctional and leads to dwarfism in Arabidopsis.

Kong Y, Peña MJ, Renna L, Avci U, Pattathil S, Tuomivaara ST, Li X, Reiter WD, Brandizzi F, Hahn MG, Darvill AG, York WS, O'Neill MA.

Plant Physiol. 2015 Apr;167(4):1296-306. doi: 10.1104/pp.114.255943. Epub 2015 Feb 11.

22.

Generation and structural validation of a library of diverse xyloglucan-derived oligosaccharides, including an update on xyloglucan nomenclature.

Tuomivaara ST, Yaoi K, O'Neill MA, York WS.

Carbohydr Res. 2015 Jan 30;402:56-66. doi: 10.1016/j.carres.2014.06.031. Epub 2014 Jul 9.

PMID:
25497333
23.

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.

24.

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.

25.

Two Arabidopsis proteins synthesize acetylated xylan in vitro.

Urbanowicz BR, Peña MJ, Moniz HA, Moremen KW, York WS.

Plant J. 2014 Oct;80(2):197-206. doi: 10.1111/tpj.12643. Epub 2014 Sep 20.

26.

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.

27.

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.

28.

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.

29.

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.

30.

A galacturonic acid-containing xyloglucan is involved in Arabidopsis root hair tip growth.

Peña MJ, Kong Y, York WS, O'Neill MA.

Plant Cell. 2012 Nov;24(11):4511-24. doi: 10.1105/tpc.112.103390. Epub 2012 Nov 21.

31.

DeMO: An Ontology for Discrete-event Modeling and Simulation.

Silver GA, Miller JA, Hybinette M, Baramidze G, York WS.

Simulation. 2011 Sep;87(9):747-773.

32.

4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein.

Urbanowicz BR, Peña MJ, Ratnaparkhe S, Avci U, Backe J, Steet HF, Foston M, Li H, O'Neill MA, Ragauskas AJ, Darvill AG, Wyman C, Gilbert HJ, York WS.

Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):14253-8. doi: 10.1073/pnas.1208097109. Epub 2012 Aug 14.

33.

Structural characterization of the heteroxylans from poplar and switchgrass.

Mazumder K, Peña MJ, O'Neill MA, York WS.

Methods Mol Biol. 2012;908:215-28. doi: 10.1007/978-1-61779-956-3_19.

PMID:
22843402
34.

Methods for structural characterization of the products of cellulose- and xyloglucan-hydrolyzing enzymes.

Peña MJ, Tuomivaara ST, Urbanowicz BR, O'Neill MA, York WS.

Methods Enzymol. 2012;510:121-39. doi: 10.1016/B978-0-12-415931-0.00007-0.

PMID:
22608724
35.

Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains.

McKee LS, Peña MJ, Rogowski A, Jackson A, Lewis RJ, York WS, Krogh KB, Viksø-Nielsen A, Skjøt M, Gilbert HJ, Marles-Wright J.

Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6537-42. doi: 10.1073/pnas.1117686109. Epub 2012 Apr 6.

36.

AXY8 encodes an α-fucosidase, underscoring the importance of apoplastic metabolism on the fine structure of Arabidopsis cell wall polysaccharides.

Günl M, Neumetzler L, Kraemer F, de Souza A, Schultink A, Pena M, York WS, Pauly M.

Plant Cell. 2011 Nov;23(11):4025-40. doi: 10.1105/tpc.111.089193. Epub 2011 Nov 11.

37.

The ability of land plants to synthesize glucuronoxylans predates the evolution of tracheophytes.

Kulkarni AR, Peña MJ, Avci U, Mazumder K, Urbanowicz BR, Pattathil S, Yin Y, O'Neill MA, Roberts AW, Hahn MG, Xu Y, Darvill AG, York WS.

Glycobiology. 2012 Mar;22(3):439-51. doi: 10.1093/glycob/cwr117. Epub 2011 Nov 2.

PMID:
22048859
38.

Structure and function of an arabinoxylan-specific xylanase.

Correia MA, Mazumder K, Brás JL, Firbank SJ, Zhu Y, Lewis RJ, York WS, Fontes CM, Gilbert HJ.

J Biol Chem. 2011 Jun 24;286(25):22510-20. doi: 10.1074/jbc.M110.217315. Epub 2011 Mar 4.

39.

Interaction of Nectarin 4 with a fungal protein triggers a microbial surveillance and defense mechanism in nectar.

Harper AD, Stalnaker SH, Wells L, Darvill A, Thornburg R, York WS.

Phytochemistry. 2010 Dec;71(17-18):1963-9. doi: 10.1016/j.phytochem.2010.09.009. Epub 2010 Oct 21.

PMID:
20970816
40.

Structural analysis of arabinoxylans isolated from ball-milled switchgrass biomass.

Mazumder K, York WS.

Carbohydr Res. 2010 Oct 13;345(15):2183-93. doi: 10.1016/j.carres.2010.07.034. Epub 2010 Jul 30.

PMID:
20797699
41.

A comprehensive toolkit of plant cell wall glycan-directed monoclonal antibodies.

Pattathil S, Avci U, Baldwin D, Swennes AG, McGill JA, Popper Z, Bootten T, Albert A, Davis RH, Chennareddy C, Dong R, O'Shea B, Rossi R, Leoff C, Freshour G, Narra R, O'Neil M, York WS, Hahn MG.

Plant Physiol. 2010 Jun;153(2):514-25. doi: 10.1104/pp.109.151985. Epub 2010 Apr 2.

42.

IDAWG: Metabolic incorporation of stable isotope labels for quantitative glycomics of cultured cells.

Orlando R, Lim JM, Atwood JA 3rd, Angel PM, Fang M, Aoki K, Alvarez-Manilla G, Moremen KW, York WS, Tiemeyer M, Pierce M, Dalton S, Wells L.

J Proteome Res. 2009 Aug;8(8):3816-23. doi: 10.1021/pr8010028.

43.

Improved procedures for the selective chemical fragmentation of rhamnogalacturonans.

Deng C, O'Neill MA, Hahn MG, York WS.

Carbohydr Res. 2009 Sep 28;344(14):1852-7. doi: 10.1016/j.carres.2008.11.011. Epub 2008 Dec 3.

PMID:
19162261
44.

Moss and liverwort xyloglucans contain galacturonic acid and are structurally distinct from the xyloglucans synthesized by hornworts and vascular plants.

Peña MJ, Darvill AG, Eberhard S, York WS, O'Neill MA.

Glycobiology. 2008 Nov;18(11):891-904. doi: 10.1093/glycob/cwn078. Epub 2008 Aug 14.

PMID:
18703646
45.

Regulation of glycan structures in animal tissues: transcript profiling of glycan-related genes.

Nairn AV, York WS, Harris K, Hall EM, Pierce JM, Moremen KW.

J Biol Chem. 2008 Jun 20;283(25):17298-313. doi: 10.1074/jbc.M801964200. Epub 2008 Apr 14.

46.

Biochemical control of xylan biosynthesis - which end is up?

York WS, O'Neill MA.

Curr Opin Plant Biol. 2008 Jun;11(3):258-65. doi: 10.1016/j.pbi.2008.02.007. Epub 2008 Apr 18. Review.

PMID:
18374624
47.

Frontiers in glycomics: bioinformatics and biomarkers in disease. An NIH white paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13, 2006).

Packer NH, von der Lieth CW, Aoki-Kinoshita KF, Lebrilla CB, Paulson JC, Raman R, Rudd P, Sasisekharan R, Taniguchi N, York WS.

Proteomics. 2008 Jan;8(1):8-20.

PMID:
18095367
48.

Quantitation by isobaric labeling: applications to glycomics.

Atwood JA 3rd, Cheng L, Alvarez-Manilla G, Warren NL, York WS, Orlando R.

J Proteome Res. 2008 Jan;7(1):367-74. Epub 2007 Nov 30.

PMID:
18047270
49.

Tools for glycomics: relative quantitation of glycans by isotopic permethylation using 13CH3I.

Alvarez-Manilla G, Warren NL, Abney T, Atwood J 3rd, Azadi P, York WS, Pierce M, Orlando R.

Glycobiology. 2007 Jul;17(7):677-87. Epub 2007 Mar 23.

PMID:
17384119
50.

Arabidopsis irregular xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis.

Peña MJ, Zhong R, Zhou GK, Richardson EA, O'Neill MA, Darvill AG, York WS, Ye ZH.

Plant Cell. 2007 Feb;19(2):549-63. Epub 2007 Feb 23.

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