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William York
Professor of Biochemistry and Molecular Biology, Adjunct Professor of Computer Science and Plant Biology

Structure, assembly, and morphogenesis of primary cell walls of plants; Bioinformatics for Glycobiology and Glycomics

Telephone: 706-542-4628
Fax: 706-542-4412

Short Biography
Research Interests

Short Biography:
Dr. York received his B.A. in molecular, cellular, and developmental biology in 1978 from the University of Colorado and his Ph.D. in biochemistry and molecular biology in 1996 from the University of Georgia. He was senior research chemist at the CCRC from 1985-96. Full publications: 96.

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Research Interests:
Dr. York's diverse research interests include the development and application of spectroscopic and computational methods for the structural and conformational analysis of complex carbohydrates, the development of bioinformatics tools to study the roles of carbohydrates in living systems, and the use of these tools to develop realistic models describing the assembly and morphogenesis of the "primary cell walls" that surround the growing cells of higher plants.

His early research focused on the analysis of plant cell walls using a multidisciplinary approach. Extensive spectroscopic analysis of xyloglucan, a load-bearing polysaccharide involved in controlling the rate and orientation of cell wall growth, have been performed in Dr. York's laboratory. The results of these spectroscopic studies have been summarized in the form of a database that provides chemical shift information taken from the NMR spectra of over 50 xyloglucan oligosaccharides that have been characterized in Dr. York's laboratory. The organization and user interface of this database facilitates the retrieval of information regarding specific correlations between structural featurres of the oligosaccharides and the chemical shifts of diagnostic resonances in the NMR spectra. The availability of this information makes it possibly to rapidly and accurately identify oligosaccharides that are present in the database and to identify structural features of related oligosaccharides that have not yet been characterized. As a result of Dr. York's interest in database development and data mining methodology, he has recently initiated a bioinformatics project as part of the Integrated Technology Resource for Biomedical Glycomics funded by the National Center for Research Resources of the NIH.

The Plant Cell Wall. Expansion of the primary cell wall determines the final size and shape of each plant cell, thereby defining the morphology of the entire plant. It is generally accepted that, with the exception of cellulose, the macromolecular components of the primary cell wall are synthesized within the Golgi and exported to the apoplasm. Cellulose, which is synthesized at the plasmalemma, combines with these components to form a cross-linked matrix (the primary cell wall) that expands at a controlled rate in a defined direction. The process of cell wall assembly thus depends on the incorporation and subsequent reorganization of polysaccharides. In order to develop a coherent picture of this complex process, it is necessary to combine information regarding the biosynthetic mechanisms and chemical structures of cell wall polysaccharides, the physical bases for their assembly (i.e., their molecular conformations and dynamics), the nature of their covalent and non-covalent interconnections, the specificity and regulation of enzymes that catalyze the formation and/or cleavage of these interconnections, the overall topology of interconnected polysaccharide networks, and the rheological consequences of these interacting factors. This is a formidable problem demanding a multidisciplinary approach.

York is addressing this problem by examining the structural details of the cell walls of various plants, thereby determining how their primary, secondary, and higher-order structures vary from tissue to tissue and from plant to plant. Conserved features are likely to confer essential functions upon the cell wall. For example, features that are consistently associated with a specific developmental stage or morphogenetic process (e.g., cell elongation) probably play important roles in plant cell differentiation. The abundance of individual oligosaccharide subunits of the polysaccharide may vary, or novel, chemically modified subunits may be produced at specific developmental stages. For further information regarding the mulitdisciplinary study of plant cell walls see the CCRC's Plant Cell Walls Web Site.

Spectroscopic methods to analyze complex glycans. Although much less sensitive than chromatographic and mass spectral methods, NMR spectroscopy can often provide all of the information necessary to completely define the primary structure of a complex glycan. York and his colleagues have used NMR (along with other techniques) to determine the primary structures of more than 50 oligosaccharides derived from XGs isolated from the cell walls of various plants. These analyses make it possible to identify previously characterized XG oligosaccharides by their NMR spectra and have revealed many correlations between the structural features of XG oligosaccharides and characteristic resonances in their NMR spectra, facilitating the structural analysis of novel XG oligosaccharides. Continued development of this approach will provide crucial information necessary for studying cell wall structure and metabolism, and is a prerequisite for the comprehensive application of chromatographic methods that rely on well characterized standards.

Recently, York and colleagues have developed methods for the selective fragmentaion of pectic polysaccharides based on β-elimination reactions. Effective utilization of this class of reactions to break pectic polysaccharides into well-defined fragments has been a long-standing goal in the plant cell wall research community. The new methods developed in York's lab have the potential to greatly simplify the characterization of pectic polysaccharides that are modified as plant cells develop.

In collaboration with other scientists at the CCRC (notably the Orlando Laboratory) York has developed new methods using isobaric labeling and multiple mass spectrometry (MSn) techniques to simultaneously identify and quantitate glycans at high sensitivity. The new method, called Quantitation by Isobaric Labeling (QUIBL) can even be used to quantitate mixtures of isomeric glycans, which is extremely difficult using more traditional methods.

The molecular conformations and dynamics of complex glycans. The assembly and expansion of the primary plant cell wall is directed by the conformation and dynamics of the cell wall polysaccharides that must interact during this process. York and co-workers have developed models, based on conformational energy calculations, for the incorporation of XGs into the primary cell wall. These calculations suggest that the XG can adopt specific, low energy conformations that allow all of the side chains to fold onto one face of the XG chain, freeing the other face to interact with cellulose. Rigorous evaluation of this model will require further experimental and computational analyses, and will depend on improvements in the accuracy of molecular force fields.

Polysaccharides and other glycans often exhibit complex dynamic behavior in solution because they can adopt many different low energy conformations, making them difficult to study by crystallographic and spectroscopic techniques. Their flexibility, compared to globular proteins, may paradoxically arise from the rigidity of the glycosyl residues from which they are constructed. Rigid glycosyl residues may not fold into a neatly packed, low energy structure the way the flexible amino acid side chains of a typical protein do. Therefore, it is often proper to define the conformation of a complex glycan in terms of an ensemble of interconverting states. NMR spectroscopy is the most frequently used technique to study these dynamic ensembles, but it rarely provides sufficient information to describe them in detail. Therefore, conformational models must rely on the agreement of computational methods with experimental methods such as NMR. Although these rapidly evolving techniques currently provide a limited picture of the conformational dynamics of complex glycans, they are indispensable tools for elaborating a dynamic structural model of the primary cell wall.

Informatics for glycobiology and glycomics. Dr. York has a long-standing interest in informatics technology that can be applied to complex glycan structures. He was actively involved in the creation of CARBBANK, which was the first worldwide, comprehensive database of glycan structures. More recently, York has been developing methods for the exchange of glycan structural data over the Internet. His most important contribution in this area is GLYDE-II, an XML standard for structural data exchange that has been accepted as the standard protocol by the leading carbohydrate databases in the United States, Germany, and Japan.

Dr. York's work is supported by the United States Department of Agriculture, the Department of Energy, the National Science Foundation, The National Institutes of Health, and the University of Georgia Research Foundation.

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Publications: Author's Last Name: York

Journal Articles
Book Chapters are listed at the bottom of this page.

PS Smith, MJ Pena, WS York, BR Urbanowicz. 2020. Analytical Techniques for Determining the Role of Domain of Unknown Function 579 Proteins in the Synthesis of O-Methylated Plant Polysaccharides. Slas Technol Aug;25(4): 345-355. PMID:32204644

V Lunin, HT Wang, VS Bharadwaj, P Alahuhta, MJ Pena, JY Yang, SA Archer-Hartmann, PA Azadi, ME Himmel, KW Moremen, WS York, YJ Bomble, BR Urbanowicz. 2020. Molecular mechanism of polysaccharide acetylation by the AtXOAT1 xylan O-acetyltransferase. Plant Cell Jul;32(7): 2367-2382. PMID:32354790

V Lunin, HT Wang, V Bharadwaj, PM Alahuhta, MJ Pena, JY Yang, SA Archer-Hartmann, P Azadi, M Himmel, KW Moremen, WS York, YJ Bomble, B Urbanowicz. 2020. Molecular mechanism of polysaccharide acetylation by the Arabidopsis xylan O-acetyltransferase XOAT1. Plant Cell 32(7): 2367-2382. PMID:32354790

S Neelamegham, K Aoki-Kinoshita, E Bolton, M Frank, F Lisacek, T Lutteke, N O'Boyle, NH Packer, P Stanley, P Toukach, A Varki, RJ Woods, A Darvill, A Dell, B Henrissat, C Bertozzi, G Hart, H Narimatsu, H Freeze, I Yamada, J Paulson, J Prestegard, J Marth, JFG Vliegenthart, M Etzler, M Aebi, M Kanehisa, N Taniguchi, N Edwards, P Rudd, P Seeberger, R Mazumder, R Ranzinger, R Cummings, R Schnaar, S Perez, S Kornfeld, T Kinoshita, W York, Y Knirel, SD Grp. 2019. Updates to the Symbol Nomenclature for Glycans guidelines. Glycobiology Aug 20; 29(9): 620-624. PMID:31184695

S.T. Tuomivaara, P. Schliekelman, A.V. Nairn, K.W. Moremen, W.S. York. 2017. RElative QUantitation Inferred by Evaluating Mixtures (REQUIEM). Anal. Chim. Acta 993: 22-37. PMID:29078952

M. Tiemeyer, K. Aoki, J. Paulson, R.D. Cummings, W.S. York, N.G. Karlsson, F. Lisacek, N.H. Packer, M.P. Campbell, N.P. Aoki, A. Fujita, M. Matsubara, D. Shinmachi, S. Tsuchiya, I. Yamada, M. Pierce, R. Ranzinger, H. Narimatsu, K.F. Aoki-Kinoshita. 2017. GlyTouCan: An accessible glycan structure repository. Glycobiology 27: 915-919. PMID:28922742

B.R. Urbanowicz, V.S. Bharadwaj, M. Alahuhta, M.J. Pena, V.V. Lunin, Y.J. Bomble, S. Wang, J.Y. Yang, S.T. Tuomivaara, M.E. Himmel, K.W. Moremen, W.S. York, M.F. Crowley. 2017. Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism. Plant J. 91: 931-949. PMID:28670741

D. Ndeh, A. Rogowski, A. Cartmell, A.S. Luis, A. Basle, J. Gray, I. Venditto, J. Briggs, X. Zhang, A. Labourel, N. Terrapon, F. Buffetto, S. Nepogodiev, Y. Xiao, R.A. Field, Y. Zhu, M.A. O'Neill, B.R. Urbanowicz, W.S. York, G.J. Davies, D.W. Abbott, M.C. Ralet, E.C. Martens, B. Henrissat, H.J. Gilbert. 2017. Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature 544: 65-70. PMID:28329766

P.J. Smith, H.T. Wang, W.S. York, M.J. Pena, B.R. Urbanowicz. 2017. Designer biomass for next-generation biorefineries: Leveraging recent insights into xylan structure and biosynthesis. Biotechnol. Biofuels 10: 286-286. PMID:29213325

M.J. Pena, A.R. Kulkarni, J. Backe, M. Boyd, M.A. O'Neill, W.S. York. 2016. Structural diversity of xylans in the cell walls of monocots. Planta 244: 589-606. PMID:27105886

WB Struwe, S. Agravat, KF Aoki-Kinoshita, MP Campbell, CE Costello, A. Dell, T Feizi, SM Haslam, NG Karlsson, KH Khoo, D. Kolarich, Y. Liu, R. McBride, MV Novotny, NH Packer, JC Paulson, E. Rapp, R. Ranzinger, PM Rudd, DF Smith, M. Tiemeyer, L. Wells, WS York, J. Zaia, C Kettner. 2016. The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets. Glycbiology Sept 26(9): 907-910. PMID:27654115

K Aoki-Kinoshita, S Agravat, NP Aoki, S Arpinar, RD Cummings, A Fujita, N Fujita, GM Hart, SM Haslam, T Kawasaki, M Matsubara, KW Moremen, S Okuda, M Pierce, R Ranzinger, T Shikanai, D Shinmachi, E Solovieva, Y Suzuki, S Tsuchiya, I Yamada, WS York, J Zaia, H Narimatsu. 2016. GlyTouCan 1.0--The international glycan structure repository. Nucleic Acids Res 44: D1237-D1242. PMID:26476458

Al Jadda, MP Porterfield, R. Bridger, C. Heiss, M. Tiemeyer, L. Wells, JA Miller, WS York, R. Ranzinger. 2015. EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard date. Bioinformatics Jan 15;31(2): 242-245. PMID:25217575

AC Muszynski, MA O'Neill, E Ramasamy, S Pattathil, U Avci, MJ Pena, M Libault, MS Hossain, L Brechenmacher, WS York, RM Barbosa, MG Hahn, G Stacey, RW Carlson. 2015. Xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan, I do not have identical structures in soybean root and root hair cell walls. Planta 242(5): 1123-1138. PMID:26067758

A.C. Srivastava, F. Chen, T. Ray, S. Pattathil, M.J. Pena, U. Avci, H. Li, D.V. Huhman, J. Backe, B. Urbanowicz, J.S. Miller, M. Bedair, C.E. Wyman, L.W. Sumner, W.S. York, M.G. Hahn, R.A. Dixon, E.B. Blancaflor, Y. Tang. 2015. Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis. Biotechnol. Biofuels 8: 224-. PMID:26697113

Y. Kong, M.J. Pena, L. Renna, U. Avci, S. Pattathil, S.T. Tuomivaara, X. Li, W.-D. Reiter, F. Brandizzi, M.G. Hahn, A.G. Darvill, W.S. York, M.A. O'Neill. 2015. Galactose-depleted xyloglucan is dysfunctional and leads to dwarfism in Arabidopsis. Plant Physiol. 167: 1296-1306. PMID:25673778

A Varki, RD Cummings, M Aebi, NH Packer, PH Seeberger, JD Esko, P Stanley, GJ Hart, A Darvill, T Kinoshita, JH Prestegard, RL Schnaar, HH Freeze, JD Marth, CR Bertozzi, ME Etzler, M Frank, JF Vliegenthart, T Lutteke, S Perez, E Bolton, P Rudd, J Paulson, M Kanehisa, P Toukach, KF Aoki-Kinoshita, A Dell, H Narimatsu, W York, N Taniguchi, S Kornfeld. 2015. Symbol Nomenclature for Graphical Representations of Glycans. Glycobiology 25: 1323-1324. PMID:26543186

WS York, S. Agravat, KF Aoki-Kinoshita, R. McBride, MP Campbell, CE Costello, A. Dell, T Feizi, SM Haslam, N.G. Karlsson, KH Khoo, D. Kolarich, Y. Liu, M.V. Novotny, NH Packer, JC Paulson, E. Rapp, R Razinger, PM Rudd, DF Smith, WB Struwe, M. Tiemeyer, L. Wells, J. Zaia, C Kettner. 2014. MIRAGE: the minimum information required for a glycomics experiment. Glycobiology 24(5): 402-406. PMID:24653214

MP Campbell, R Ranzinger, T Lutteke, J Mariethoz, CA Hayes, J Zhang, Y Akune, KF Aoki-Kinoshita, D Damerell, G Carta, WS York, SM Haslam, H Narimatsu, PM Rudd, NG Karlsson, NH Packer, F Lisacek. 2014. Toolboxes for a standardized and systematic study of glycans.. BMC Bioinformatics Suppl 1: -S9. PMID:24564482

T Katayama, MD Wilkinson, KF Aoki-Kinoshita, S Kawashima, Y Yamamoto, A Yamaguchi, S Okamoto, S Kawano, JD Kim, Y Wang, H Wu, Y Kano, H Ono, H Bono, S Kocbek, J Aerts, Y Akune, E Antezana, K Arakawa, B Aranda, J Baran, J Bolleman, RJ Bonnal, PL Buttigieg, MP Campbell, YA Chen, H Chiba, PJ Cock, KB Cohen, A Constantin, G Duck, M Dumontier, T Fujisawa, T Fujiwara, N Goto, R Hoehndorf, Y Igarashi, H Itaya, M Ito, W Iwasaki, M Kalas, T Katoda, T Kim, A Kokubu, Y Komiyama, M Kotera, C Laibe, H Lapp, T Lutteke, MS Marshall, T Mori, H Mori, M Morita, K Murakami, M Nakao, H Narimatsu, H Nishide, Y Nishimura, J Nystrom-Persson, S Ogishima, Y Okamura, S Okuda, K Oshita, NH Packer, P Prins, R Ranzinger, P Rocca-Serra, S Sansone, H Sawaki, SH Shin, A Splendiani, F Strozzi, S Tadaka, P Toukach, I Uchiyama, M Umezaki, R Vos, PL Whetzel, I Yamada, C Yamasaki, R Yamashita, WS York, CM Zmasek, S Kawamoto, T Takagi. 2014. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics 5(1): -5. PMID:24495517

B.R. Urbanowicz, M.J. Pena, H.A. Moniz, K.W. Moremen, W.S. York. 2014. Two Arabidopsis proteins synthesize acetylated xylan in vitro. Plant J. 80: 197-206. PMID:25141999

D. Kolarich, E. Rapp, W.B. Struwe, S.M. Haslam, J. Zaia, R. McBride, S. Agravat, M.P. Campbell, M. Kato, R. Ranzinger, C. Kettner, W.S. York. 2013. The minimum information required for a glycomics experiment (MIRAGE) project: Improving the standards for reporting mass-spectrometry-based glycoanalytic data. Mol. Cell Proteomics 12: 991-995. PMID:23378518

A. Kulkarni, M.J. Pena, U. Avci, K. Mazumder, B. Urbanowicz, S. Pattathil, Y. Yin, M.A. ONeill, A.W. Roberts, M.G. Hahn, Y. Xu, A.G. Darvill, W.A. York. 2012. The ability of land plants to synthesize glucoronoxylans predates the evolution of tracheophytes. Glycobiology 22: 439-451. PMID:22048859

L.S. McKee, M.J. Pena, A. Rogowski, K.A. Jackson, R.J. Lewis, W.S. York, K.B.R.M. Krogh, A. Vikso-Nielsen, M. Skjot, H.J. Gilbert, J. Marles-Wright. 2012. Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains. Proc. Natl. Acad. Sci. USA 109: 6537-6542. PMID:22492980

A.R. Kulkarni, S. Pattathil, M.G. Hahn, W.S. York, M.A. ONeill. 2012. Comparison of arabinoxylan structure in bioenergy and model grasses. Industrial Biotechnol. 8: 222-229.

M.J. Pena, Y. Kong, W.S. York, M ONeill. 2012. A galacturonic acid-containing xyloglucan is involved in Arabidopsis root hair tip growth. Plant Cell 24: 4511-4524. PMID:23175743

M.J. Pena, S.T. Tuomivaara, B.R. Urbanowicz, M.A. ONeill, W.S. York. 2012. Methods for structural characterization of the products of cellulose- and xyloglucan-hydrolyzing enzymes. Methods Enzymol. 510: 121-139. PMID:22608724

B.R. Urbanowicz, M.J. Pena, S. Ratnaparkhe, U. Avci, J. Backe, H.F. Steet, M. Foston, H. Li, M.A. O'Neill, A.J. Ragauskas, A.G. Darvill, C. Wyman, H.J. Gilbert, W.S. York. 2012. 4-O-Methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein. Proc. Natl. Acad. Sci. USA 109: 14253-14258. PMID:22893684

K. Mazumder, M.J. Pena, M.A. O'Neill, W.S. York. 2012. Structural characterization of the heteroxylans from poplar and switchgrass. Methods Mol. Biol. 908: 215-228. PMID:22843402

M.A.S. Correia, K. Mazumder, J.L.A. Bras, S.J. Firbank, Y. Zhu, R.J. Lewis, W.S. York, C.M.G.A. Fontes, H.J. Gilbert. 2011. The structure and function of arabionoxylan-specific xylanase. J. Biol. Chem. 286: 22510-22520. PMID:21378160

M. Gunl, L. Neumetzier, F. Kraemer, A. de, A. Schultink, M.J. Pena, W.S. York, M. Pauly. 2011. AZY8 encodes an alpha-fucosidase, underscoring the importance of apoplastic metabolism on the fine structure of Arabidopsis cell wall polysaccharides. Plant Cell 23: 4025-4040. PMID:22080600

G.A. Silver, J.A. Miller, M. Hybinette, G. Baramidze, W.S. York. 2011. DeMO: An ontology for discrete-event modeling and simultion. Simulation 87: 747-773. PMID:22919114

S. Pattathil, U. Avci, D. Baldwin, A.G. Swennes, J.A. McGill, Z. Popper, T. Bootten, A. Albert, R.H. Davis, C. Chenareddy, R. Dong, E. O, R. Rossi, C. Leoff, G. Freshour, R. Narra, M. O, W.S. York, M.G. Hahn. 2010. A comprehensive toolkit of plant cell wall glycan-directed monoclonal antibodies. Plant Physiol. 153: 514-525. PMID:20363856

A.D. Harper, S.H. Stalnaker, L. Wells, A. Darvill, R. Thornburg, W.S. York. 2010. Interaction of Nectarin 4 with a fungal protein triggers a microbial surveillance and defense mechanism in nectar. Phytochemistry 71: 1963-1969. PMID:20970816

K. Mazumder, W.S. York. 2010. Structural analysis of arabinoxylans isolated from ball milled switchgrass biomass. Carbohydr. Res. 345: 2183-2193. PMID:20797699

R. Orlando, J.M. Lim, J.A. Atwood, P.M. Angel, M. Feng, G. Alvarez-Manilla, K.W. Moremen, W.S. York, M. Tiemeyer, J.M. Pierce, S. Dalton, R.L. Wells. 2009. IDAWG: Metabolic incorporation of stable isotope labels for quantitative glycomics of cultured cells. J. Proteome Res. 8: 3816-3823. PMID:19449840

C. Deng, M.A. O'Neill, M.G. Hahn, W.S. York. 2009. Improved procedures for the selective chemical fragmentation of rhamnogalacturonans. Carbohydr. Res. 344: 1852-1857. PMID:19162261

J.A. Atwood III, L. Cheng, G. Alvarez-Manilla, N.L. Warren, W.S. York, R. Orlando. 2008. Quantitation by isobaric labeling: applications to glycomics. J Proteome Res 7: 367-374. PMID:18047270

A.V. Nairn, W.S. York, K. Harris, E.M. Hall, J.M. Pierce, K.W. Moremen. 2008. Regulation of glycan structures in animal tissues: transcript profiling of glycan-related genes. J. Biol. Chem. 283: 17298-17313. PMID:18411279

N.H. Packer, C.W. Von der Lieth, K.F. Aoki-Kinoshita, C.B. Lebrilla, J.C. Paulson, R. Ramon, P. Rudd, R. Sasisekharan, N. Taniguchi, W.S. York. 2008. Frontiers in glycomics: Bioinformatics and biomarkers in disease. Proteomics 8: 8-20. PMID:18095367

J.C. Botelho, J.A. Atwodd, L. Cheng, G. Alvarez-Manilla, W.S. York, R. Orlando. 2008. Quantification by isobaric labeling (QUIBL)for the comparative glycomic study of O-linked glycans. Intl. J. Mass Spectrom 278: 137-142.

W.S. York, M.A. O'Neill. 2008. Biochemical control of xylan biosynthesis - which end is up?. Curr. Opin. Plant Biol. 11: 258-265. PMID:18374624

M.J. Pena, A.G. Darvill, S. Eberhard, W.S. York, M.A. ONeill. 2008. Moss and liverwort xyloglucans contain galacturonic acid and are structurally distinct from the xyloglucans synthesized by horn. Glycobiology 18: 891-904. PMID:18703646

G. Alvarez-Manilla, N.L. Warren, T. Abney, J.A. Atwood, P. Azadi, W.S. York, M. Pierce, R. Orlando. 2007. Tools for glycomics: relative quantitation of glycans by isotopic permethylation using 13CH3I. Glycobiology 17: 677-6787. PMID:17384119

J.A. Atwood III, L. Cheng, G. Alvarez-Manilla, N.L. Warren, W.S. York, R. Orlando. 2007. Quantitation by isobaric labelling: applications to glycomics. J. Proteome Res. 7: 367-374. PMID:18047270

M.J. Pena, R. Zhong, G.K. Zhou, E.A. Richardson, M.A. ONeill, A.G. Darvill, W.S. York, Z.H. Ye. 2007. Arabidopsis irregulat xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis. Plant Cell 19: 549-563. PMID:17322407

C. Deng, M.A. O`Neill, W.S. York. 2006. Selective chemical depolymerization of rhamnogalacturonans. Carbohydr. Res. 341: 474-484. PMID:16414034

Z-H. Ye, W.S. York, A.G. Darvill. 2006. Important new players in secondary wall synthesis. Trends Plant Sci. 11: 162-164. PMID:16537114

M. Hoffman, Z. Jia, M.J. Pena, M. Cash, A. Harper, A.R. Blackburn, A. Darvill, W.S. York. 2005. Structural analysis of xyloglucans in the primary cell walls of plants in the subclass Asteridae. Carbohydr. Res. 340: 1826-1840. PMID:15975566

Z. Jia, M. Cash, A.G. Darvill, W.S. York. 2005. NMR characterization of endogenously O-acetylated oligosaccharides isolated from tomato (Lycopersicon esculentum) xyloglucan. Carbohydr. Res. 340: 1818-1825. PMID:15927168

J.A.. Atwood, S.S. Sahoo, G.A. Manilla, D.B. Weatherly, K.V.S. Kolli, R. Orlando, W.S. York. 2005. Simple modification of a protein database for mass spectral identification of N-linked glycopeptides. Rapid Commun. Mass Spectrom. 19: 3002-3006. PMID:16196021

S.S. Sahoo, C.A. Thomas, A. Sheth, C. Henson, W.S. York. 2005. GLYDE- An expressive XML standard for the representation of glycan structure. Carbohydr. Res. 340: 2802-2807. PMID:16242678

S.M.S. Naqvi, A. Harper, C. Carter, G. Adelt, A. Guirgis, W.S. York, R.W. Thornburg. 2005. Nectarin IV, a potent endogluconase inhibitor secreted into the nectar of ornamental tobacco plants; Isolation, cloning, and characterization. Plant Physiol. 139: 1389-1400. PMID:16244157

R. Zhong, M.J. Peña, G-K. Zhou, C.J. Nairn, A. Wood-Jones, E.A. Richardson, W.H. Morrison, A.G. Darvill, W.S. York, Z-H. Ye. 2005. Arabidopsis Fragile Fiber8, which encodes a putative glucuronyltransferase, is essential for normal seccondary wall synthesis. Plant Cell 17: 3390-3408. PMID:16272433

W.S. York, Q. Qin, J.K.C. Rose. 2004. Proteinaceous inhibitors of endo-b-glucanases. Biochemica et Biophysica Acta 1696: 223-233. PMID:14871663

X. Yi, W.S. York. 2004. CONDORR -- CONstrained Dynamics Of Rigid Residues: A molecular dynamics program for constrained molecules. J. Mol. Modeling 10: 271-289. PMID:15322949

J.N. Glushka, M. Terrell, W.S. York, M.A. O'Neill, A. Gucwa, A.G. Darvill, P. Albersheim, J.H. Prestegard. 2003. Primary structure of the 2-O-methyl-a-L-fucose-containing side chain of the pectic polysaccharide, rhamnogalacturonan II. Carbohydr. Res. 338: 341-352. PMID:12559732

Z. Jia, Q. Qin, A.G. Darvill, W.S. York. 2003. Structure of the xyloglucan produced by suspension-cultured tomato cells. Carbohydr. Res. 338: 1197-1208. PMID:12747862

R.M. Perrin, Z. Jia, T.A. Wagner, M.A. O'Neill, R. Sarria, W.S. York, N.V. Raikhel, K. Keegstra. 2003. Analysis of xyloglucan fucosylation in Arabidopsis. Plant Physiol. 132: 768-778. PMID:12805606

Q. Qin, C.W. Bergmann, J.K.C. Rose, M. Saladie, V.S. Kumar, P. Albersheim, A.G. Darvill, W.S. York. 2003. Characterization of a tomato protein that inhibits a xyloglucan-specific endoglucanase. Plant J. 34: 327-338. PMID:12713539

M. Marry, D.M. Cavalier, J.K. Schnurr, J. Netland, Z. Yang, V. Pezeshk, W.S. York, M. Pauly, A.R. White. 2002. Structural characterization of chemically and enzymatically derived standard oligosaccharides isolated from partially purified tamarind xyloglucan. Carohydr. Polymers 51: 347-356.

J. Loh, R.W. Carlson, W.S. York, G. Stacey. 2002. Bradyoxetin, a unique chemical signal involved in symbolic gene regulation. Proc. Natl. Acad. Sci. USA 99: 14446-14451. PMID:12393811

M. Pauly, Q. Qin, H. Greene, P. Albersheim, A. Darvill, W.S. York. 2001. Changes in the structure of xyloglucan during cell elongation. Planta 212: 842-850. PMID:11346960

E. Vierhuis, W.S. York, J.-P. Vincken, H.A. Schols, G.-J.W.M. Van, A.G.J. Voragen. 2001. Structural analyses of two arabinose containing oligosaccharides derived from olive fruit xyloglucan: XXSG and XLSG. Carbohydr. Res. 332: 285-297. PMID:11376608

M. Pauly, S. Eberhard, P. Albersheim, A. Darvill, W.S. York. 2001. Effects of the mur1 mutation on xyloglucans produced by suspension-cultured Arabidopsis thaliana cells. Planta 214: 67-74. PMID:11762172

C. Catala, J.K.C. Rose, W.S. York, P. Albersheim, A.G. Darvill, A.B. Bennett. 2001. Characterization of a tomato xyloglucan endotransglycosylase gene that is down-regulated by auxin in etiolated hypocotyls. Plant Physiol. 127: 1180-1192. PMID:11706197

W.S. York, R. Hawkins. 2000. Preparation of oligomeric b-glycosides from cellulose and hemicellulosic polysaccharides via the glycosyl transferase activity of a Trichoderma reesei cellulase. Glycobiology 10: 193-201. PMID:10642611

S. Vidal, T. Doco, P. Williams, P. Pellerin, W.S. York, M.A. O'Neill, J. Glushka, A.G. Darvill, P. Albersheim. 2000. Structural characterization of the pectic polysaccharide rhamnogalacturonan II: Evidence for the location of the aceric acid-containing oligoglycosyl side chain. Carbohydr. Res. 326: 277-294. PMID:10890275

M. Pauly, L.N. Andersen, S. Kaupinen, L.V. Kofod, W.S. York, P. Albersheim, A.G. Darvill. 1999. A xyloglucan-specific endo-b-1,4-glucanase from Aspergillus aculeatus: expression cloning in yeast, purification, and characterization of the recombinant enzyme. Glycobiology 9: 93-100. PMID:9884411

M. Pauly, P. Albersheim, A. Darvill, W.S. York. 1999. Molecular domains of the cellulose-xyloglucan network in the cell walls of higher plants. The Plant J. 20: 629-639. PMID:10652135

V.S.K. Kolli, W.S. York, R. Orlando. 1998. Fast atom bombardment-mass spectrometry of carbohydrates contaminated with inorganic salts using crown ethers. J. Mass Spectrom. 33: 680-682. PMID:9692250

T. Mishima, M. Hisamatsu, W.S. York, K. Teranishi, T. Yamada. 1998. Adhesion of beta-glucans to cellulose. Carbohydr. Res. 308: 389-395.

M. Pauly, W.S. York. 1998. Isolation of complex carbohydrates by reversed-phase chromatography with evaporative light scattering detection. Am. Biotech. Lab. 1998: 14-.

S. Hantus, M. Pauly, A.G. Darvill, P. Albersheim, W.S. York. 1997. Structural characterization of novel l-galactose-containing oligosaccharide subunits of jojoba seed xyloglucans. Carbohydr. Res. 304: 11-20. PMID:9403992

J.-P. Vincken, W.S. York, G. Beldman, A.G.J. Voragen. 1997. Two general branching patterns of xyloglucan: XXXG and XXGG. Plant Physiol. 114: 9-13. PMID:9159939

W.S. York, S. Hantus, P. Albersheim, A.G. Darvill. 1997. Determination of the absolute configuration of monosaccharides by 1H NMR spectroscopy of their per-O-(S)-2-methylbutyrate derivatives. Carbohydr. Res. 300: 199-206.

M. Pauly, W.S. York, R. Guillen, P. Albersheim, A.G. Darvill. 1996. Improved protocol for the formation of N-(p-nitrobenzyloxy)-aminoalditol derivatives of oligosaccharides. Carbohydr. Res. 282: 1-12. PMID:8721734

W.S. York, V.S.K. Kolli, R. Orlando, P. Albersheim, A.G. Darvill. 1996. The structures of arabinoxyloglucans produced by solanaceous plants. Carbohydr. Res. 285: 99-128. PMID:9011379

E. Zablackis, W.S. York, M. Pauly, W.-D. Reiter, C.C.S. Chapple, C.R. Somerville, P. Albersheim, A. Darvill. 1996. Substitution of L-fucose by L-galactose in cell walls of Arabidopsis mur1. Science 272: 1808-1810. PMID:8650583

A. Darvill, C. Bergmann, F. Cervone, G. De, K.-S. Ham, M.D. Spiro, W.S. York, P. Albersheim. 1995. Oligosaccharins involved in plant growth and host-pathogen interactions. Biochem. Soc. Symp. 60: 89-94. PMID:7639795

R. Guillen, W.S. York, M. Pauly, J. An, G. Impallomeni, P. Albersheim, A.G. Darvill. 1995. Metabolism of xyloglucan generates xylose-deficient oligosaccharide subunits of this polysaccharide in etiolated peas. Carbohydr. Res. 277: 291-311. PMID:8556737

W.S. York. 1995. A conformational model for cyclic b-(12)-linked glucans based on NMR analysis of the b-glucans produced by Xanthomonas campestris. Carbohydr. Res. 278: 205-225. PMID:8590443

W.S. York, G. Impallomeni, M. Hisamatsu, P. Albersheim, A.G. Darvill. 1995. Eleven newly characterized xyloglucan oligoglycosyl alditols: the specific effects of sidechain structure and location on 1H NMR chemical shifts. Carbohydr. Res. 267: 79-104. PMID:7697670

P. Albersheim, J. An, G. Freshour, M.S. Fuller, R. Guillen, K.-S. Ham, M.G. Hahn, J. Huang, M. O'Neill, A. Whitcombe, M.V. Williams, W.S. York, A.G. Darvill. 1994. Structure and function studies of plant cell wall polysaccharides. Biochem. Soc. Trans. 22: 374-378.

S.C. Fry, W.S. York, P. Albersheim, A. Darvill, T. Hayashi, J.-P. Joseleau, Y. Kato, E.P. Lorences, G.A. Maclachlan, M. McNeil, A.J. Mort, J.S.G. Reid, H.-U. Seitz, R.R. Selvendran, A.G.J. Voragen, A.R. White. 1993. An unambiguous nomenclature for xyloglucan-derived oligosaccharides. Physiol. Plant. 89: 1-3.

L. Poppe, W.S. York, H. Van Halbeek. 1993. Measurement of inter-glycosidic 13C-1H coupling constants in a cyclic b(1->2)-glucan by 13C-filtered 2D {1H,1H} ROESY. J. Biomol. NMR 3: 81-89.

W.S. York, J.U. Thomsen, B. Meyer. 1993. The conformations of cyclic (1->2)-b-D-glucans: application of multidimensional clustering analysis to conformational data sets obtained by Metropolis Monte Carlo calculations. Carbohydr. Res. 248: 55-80.

W.S. York, L.K. Harvey, R. Guillen, P. Albersheim, A.G. Darvill. 1993. Structural analysis of tamarind seed xyloglucan oligosaccharides using b-galactosidase digestion and spectroscopic methods. Carbohydr. Res. 248: 285-301.

P. Albersheim, C. Augur, J.-J. Cheong, S. Eberhard, M.G. Hahn, V. Marfa, D. Mohnen, M.A. O'Neill, M.D. Spiro, W.S. York, A. Darvill. 1992. Oligosaccharins -- oligosaccharide regulatory molecules. Accts. Chem. Res. 25: 77-83.

A. Darvill, C. Augur, C. Bergmann, R.W. Carlson, J.-J. Cheong, S. Eberhard, M.G. Hahn, V.-M. Lo, V. Marfa, B. Meyer, D. Mohnen, M.A. O'Neill, M.D. Spiro, H. van Halbeek, W.S. York, P. Albersheim. 1992. Oligosaccharins - oligosaccharides that regulate growth, development and defense reponses in plants. Glycobiology 2: 181-198.

M. Hisamatsu, W.S. York, A.G. Darvill, P. Albersheim. 1992. Structure of Plant Cell Walls XXXIV. Characterization of seven xyloglucan oligosaccharides containing from seventeen to twenty glycosyl residues. Carbohydr. Res. 227: 45-71.

M. Hisamatsu, G. Impallomeni, W.S. York, P. Albersheim, A.G. Darvill. 1991. A new undecasaccharide subunit of xyloglucans with two a-fucosyl residues. Carbohydr. Res. 211: 117-129.

S. Levy, W.S. York, R. Stuike-Prill, B. Meyer, L.A. Staehelin. 1991. Simulations of the static and dynamic molecular conformations of xyloglucan. The role of the fucosylated sidechain in surface specific sidechain folding. Plant J. 1: 195-215.

B. Meyer, T. Hansen, D. Nute, P. Albersheim, A. Darvill, W. York, J. Sellers. 1991. Identification of the 1H-NMR spectra of complex oligosaccharides with artificial neural networks. Science 251: 542-544.

H.P. Spaink, D.M. Sheeley, A.A.N. van Brussel, J. Glushka, W.S. York, T. Tak, O. Geiger, E.P. Kennedy, V.N. Reinhold, B.J.J. Lugtenberg. 1991. A novel, highly unsaturated, fatty acid moiety of lipo-oligosaccharide signals determines host specitifity of Rhizobium. Nature 354: 125-130.

L.L. Kiefer, W.S. York, P. Albersheim, A.G. Darvill. 1990. The Structure of Plant Cell Walls XXX. Structural characterization of an arabinose-containing heptadecasaccharide enzymatically isolated from sycamore extracellular xyloglucan. Carbohydr. Res. 197: 139-158.

D.A. Powell, W.S. York, H. Van Halbeek, J.T. Etse, A.I. Gray, P.G. Waterman. 1990. Structural characterization, by two-dimensional NMR spectroscopy and fast-atom-bombardment mass spectrometry, of a highly acylated trirhamnoside from Mezzettia leptopoda (Annonaceae). Can J. Chem. 68: 1044-1050.

J. Sellers, W. York, P. Albersheim, A. Darvill, B. Meyer. 1990. Identification of the mass spectra of partially methylated alditol acetates by artificial neural networks. Carbohydr. Res. 207: C1-C5.

W. Von Deyn, W.S. York, P. Albersheim, A. Darvill. 1990. 1-alkoxyamino-1-deoxy alditols, useful u.v.-absorbing derivatives of neutral and acidic oligosaccharides. Carbohydr. Res. 201: 135-144.

W.S. York, L.L. Kiefer, A.G. Darvill, P. Albersheim. 1990. Oxidation of oligoglycosyl alditols during methylation catalyzed by sodium hydroxide and iodomethane in methyl sulfoxide. Carbohydr. Res. 208: 175-182.

W.S. York, H. Van, A.G. Darvill, P. Albersheim. 1990. Structural analysis of xyloglucan oligosaccharides by 1H-n.m.r. spectroscopy and fast-atom-bombardment mass spectrometry. Carbohydr. Res. 200: 9-31.

L. Kiefer, W. York, A. Darvill, P. Albersheim. 1989. The Structure of Plant Cell Walls XXVII. Xyloglucan isolated from suspension-cultured sycamore cell walls is O-acetylated. Phytochemistry 28: 2105-2107.

R.A. O'Neill, A.R. White, W.S. York, A.G. Darvill, P. Albersheim. 1988. A gas chromatographic-mass spectrometric assay for glycosylases. Phytochemistry 27: 329-333.

W.S. York, J.E. Oates, H. Van Halbeek, A.G. Darvill, P. Albersheim, P.R. Tiller, A. Dell. 1988. Structure of Plant Cell Walls XXI. Location of the O-acetyl substituents on a nonasaccharide repeating unit of sycamore extracellular xyloglucan. Carbohydr. Res. 173: 113-132.

A.G. Darvill, P. Albersheim, M. McNeil, J.M. Lau, W.S. York, T.T. Stevenson, J. Thomas, S. Doares, D.J. Gollin, P. Chelf, K. Davis. 1985. Structure and function of plant cell wall polysaccharides. J. Cell Sci. Suppl. 2: 203-217.

W.S. York, A.G. Darvill, M. McNeil, P. Albersheim. 1985. 3-deoxy-D-manno-2-octulosonic acid (KDO) is a component of rhamnogalacturonan II, a pectic polysaccharide in the primary cell walls of plants. Carbohydr. Res. 138: 109-126.

W.S. York, A.G. Darvill, M. McNeil, T.T. Stevenson, P. Albersheim. 1985. Isolation and characterization of plant cell walls and cell-wall components. Methods Enzymol. 118: 3-40.

Book Chapters

W.S. York, R. Ranzinger. 2012. MIRAGE: Minimum Information Required for a Glycomics Experiment . In: In: Proceedings of the 2nd Beilstein Symposium on Glyco-Bioinformatics - Cracking the Sugar Code by Navigating the Glycospace, Postdam, Germany .

R. Ranzinger, W.S. York. 2012. Glyco-Bioinformatics today (August 2011) - Solutions and problems. In: In: Proceedings of the 2nd Beilstein Symposium on Glyco-Bioinformatics - Cracking the Sugar Code by Navigating the Glycospace. Potsdam Germany .

W.S. York, K.J. Kochut, J.A. Miller. 2009. Integration of glycomics knowledge and data. In: Handbook of Glycomics (R.D. Cummings and J.M. Pierce, eds.), pp. 179-195. Academic Press.

M. Eavenson, M. Janik, S. Nimmagadda, J.A. Miller, K.J. Kochut, W.S. York. 2008. GlycoBrowser: A tool for contextual visualization of biological data and pathways using ontologies. In: Bioinformatics Research and Applications, pp. 305-316. Springer.

S. Nimmagadda, A. Basu, M. Eavenson, W.J. Zhang, M. Janik, R. Narra, K. Nimmagadda, A. Sharma, K.J. Kochut, J.A. Miller, W.S. York. 2008. GlycoVault: A bioinformatics infrastructure for glycan pathway visualization, analysis, and modeling. In: Fifth International Conference on Information Technology: New Generation, pp. 692-697.

W.S. York, M.A. O'Neill. 2003. Structure, topology, and function of plant wall polysaccharides. In: Dietary Fiber: Vahouny 2000 (D. Kritchevsky, C.T. Bonfield, C.A. Edwards, eds.). ISBN #0-97445390-0-0 . Kluwer Academic-Plenum Publishers, New York.

M.A. O'Neill, W.S. York. 2003. The composition and structures of primary cell walls . In: The Plant Cell Wall, Annual Plant Reviews (J.K.C. Rose, ed.), Vol.8:1-54. CRC Press, Boca Raton, FL.

W.S. York, M. Pauly, Q. Qin, Z. Jia, R.L. Doong, J.P. Simon, P. Albersheim, A.G. Darvill. 2002. The xyloglucan-cellulose network of plant cell walls: A prototype for the chemoenzymatic preparation of novel polysaccharide composites. In: Carbohydrate Bioengineering Interdisplinary Approaches (T. Teeri, B. Svensson, H.J. Gilbert, and T. Feizi, eds.), pp. 143-150. Royal Society of Chemistry, Stockholm.

W.S. York, M. Pauly, Q. Qin, Z. Jia, R.L. Doong, J.P. Simon, P. Albersheim, A.G. Darvill. 2001. The xyloglucan-cellulose network of plant cell walls: A prototype for the chemoenzymatic preparation of novel polysaccharide composites. In: Conference Proceedings of the 4th Carbohydrate Bioengineering Meeting, pp. In press. Royal Society of Chemistry.

A.G. Darvill, P. Albersheim, P. Bucheli, S. Doares, N. Doubrava, S. Eberhard, D.J. Gollin, M.G. Hahn, V. Marfa-Riera, W.S. York, D. Mohnen. 1989. Oligosaccharins - plant regulatory molecules. In: Molecular Signals in Microbe-Plant Symbiotic and Pathogenic Systems, NATO/ASI Series, Vol. H36 (B.J.J. Lugtenberg, ed.), pp. 41-48. Spring-Verlag, Berlin-Heidelberg.

P. Albersheim, A.G. Darvill, K.R. Davis, S.H. Doares, D.J. Gollin, R.A. O'Neill, P.R. Toubart, W.S. York. 1987. Oligosaccharins--complex carbohydrate regulatory molecules. In: The Cell Surface in Signal Transduction (E. Wagner et al., eds.), pp. 147-149. Springer-Verlag, Berlin-Heidelberg.

A.G. Darvill, K.R. Davis, S.H. Doares, D.J. Gollin, R.A. O'Neill, P.R. Toubart, W.S. York, P. Albersheim. 1987. Oligosaccharins - molecules that can regulate plant morphogenesis and defense against disease. In: Molecular Mechanisms in the Regulation of Cell Behavior, pp. 283-284. Alan R. Liss, Inc., New York.

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