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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.


O-glycosylation on cerebrospinal fluid and plasma Apolipoprotein E differs in the lipid binding domain.

Flowers SA, Grant OC, Woods RJ, Rebeck GW.

Glycobiology. 2019 Oct 16. pii: cwz084. doi: 10.1093/glycob/cwz084. [Epub ahead of print]


Development and implementation of a sustainable research curriculum for general surgery residents: A foundation for developing a research culture.

Harrison LM, Woods RJ, McCarthy MC, Parikh PP.

Am J Surg. 2019 Sep 26. pii: S0002-9610(19)30244-2. doi: 10.1016/j.amjsurg.2019.09.028. [Epub ahead of print]


Bystander Selection for Antimicrobial Resistance: Implications for Patient Health.

Morley VJ, Woods RJ, Read AF.

Trends Microbiol. 2019 Oct;27(10):864-877. doi: 10.1016/j.tim.2019.06.004. Epub 2019 Jul 6. Review.


Updates to the Symbol Nomenclature for Glycans guidelines.

Neelamegham S, Aoki-Kinoshita K, Bolton E, Frank M, Lisacek F, Lütteke T, O'Boyle N, Packer NH, Stanley P, Toukach P, Varki A, Woods RJ; SNFG Discussion Group.

Glycobiology. 2019 Aug 20;29(9):620-624. doi: 10.1093/glycob/cwz045.


NMR Resonance Assignment Methodology: Characterizing Large Sparsely Labeled Glycoproteins.

Chalmers GR, Eletsky A, Morris LC, Yang JY, Tian F, Woods RJ, Moremen KW, Prestegard JH.

J Mol Biol. 2019 May 31;431(12):2369-2382. doi: 10.1016/j.jmb.2019.04.029. Epub 2019 Apr 26.


GAG Builder: a web-tool for modeling 3D structures of glycosaminoglycans.

Singh A, Montgomery D, Xue X, Foley BL, Woods RJ.

Glycobiology. 2019 Jul 1;29(7):515-518. doi: 10.1093/glycob/cwz027.


Vancomycin-Resistant Enterococcus Acquisition in a Tertiary Care Hospital: Testing the Roles of Antibiotic Use, Proton Pump Inhibitor Use, and Colonization Pressure.

Chanderraj R, Millar JA, Patel TS, Read AF, Washer L, Kaye KS, Woods RJ.

Open Forum Infect Dis. 2019 Mar 15;6(4):ofz139. doi: 10.1093/ofid/ofz139. eCollection 2019 Apr.


Corrigendum: Induction of Antibodies Directed Against Branched Core O-Mannosyl Glycopeptides-Selectivity Complimentary to the ConA Lectin.

Yu J, Grant OC, Pett C, Stahl S, Woods RJ, Westerlind U.

Chemistry. 2019 Mar 12;25(15):3963. doi: 10.1002/chem.201900093. Epub 2019 Feb 21. No abstract available.


Impact of an Antimicrobial Stewardship Intervention on Within- and Between-Patient Daptomycin Resistance Evolution in Vancomycin-Resistant Enterococcus faecium.

Kinnear CL, Patel TS, Young CL, Marshall V, Newton DW, Read AF, Woods RJ.

Antimicrob Agents Chemother. 2019 Mar 27;63(4). pii: e01800-18. doi: 10.1128/AAC.01800-18. Print 2019 Apr.


Synthesis and O-Glycosidic Linkage Conformational Analysis of 13C-Labeled Oligosaccharide Fragments of an Antifreeze Glycolipid.

Zhang W, Meredith R, Yoon MK, Wang X, Woods RJ, Carmichael I, Serianni AS.

J Org Chem. 2019 Feb 15;84(4):1706-1724. doi: 10.1021/acs.joc.8b01411. Epub 2019 Jan 29.


Use of Circular Statistics To Model αMan-(1→2)-αMan and αMan-(1→3)-α/βMan O-Glycosidic Linkage Conformation in 13C-Labeled Disaccharides and High-Mannose Oligosaccharides.

Zhang W, Meredith R, Pan Q, Wang X, Woods RJ, Carmichael I, Serianni AS.

Biochemistry. 2019 Feb 12;58(6):546-560. doi: 10.1021/acs.biochem.8b01050. Epub 2019 Jan 24.


Fluorescent Trimeric Hemagglutinins Reveal Multivalent Receptor Binding Properties.

Nemanichvili N, Tomris I, Turner HL, McBride R, Grant OC, van der Woude R, Aldosari MH, Pieters RJ, Woods RJ, Paulson JC, Boons GJ, Ward AB, Verheije MH, de Vries RP.

J Mol Biol. 2019 Feb 15;431(4):842-856. doi: 10.1016/j.jmb.2018.12.014. Epub 2018 Dec 29.


Cross-Ring Fragmentation Patterns in the Tandem Mass Spectra of Underivatized Sialylated Oligosaccharides and Their Special Suitability for Spectrum Library Searching.

De Leoz MLA, Simón-Manso Y, Woods RJ, Stein SE.

J Am Soc Mass Spectrom. 2019 Mar;30(3):426-438. doi: 10.1007/s13361-018-2106-8. Epub 2018 Dec 18.


Galectin binding to cells and glycoproteins with genetically modified glycosylation reveals galectin-glycan specificities in a natural context.

Nielsen MI, Stegmayr J, Grant OC, Yang Z, Nilsson UJ, Boos I, Carlsson MC, Woods RJ, Unverzagt C, Leffler H, Wandall HH.

J Biol Chem. 2018 Dec 28;293(52):20249-20262. doi: 10.1074/jbc.RA118.004636. Epub 2018 Nov 1.


Structural Rearrangements Maintain the Glycan Shield of an HIV-1 Envelope Trimer After the Loss of a Glycan.

Ferreira RC, Grant OC, Moyo T, Dorfman JR, Woods RJ, Travers SA, Wood NT.

Sci Rep. 2018 Oct 9;8(1):15031. doi: 10.1038/s41598-018-33390-2.


Predicting the Structures of Glycans, Glycoproteins, and Their Complexes.

Woods RJ.

Chem Rev. 2018 Sep 12;118(17):8005-8024. doi: 10.1021/acs.chemrev.8b00032. Epub 2018 Aug 9. Review.


Downstream Products are Potent Inhibitors of the Heparan Sulfate 2-O-Sulfotransferase.

Thieker DF, Xu Y, Chapla D, Nora C, Qiu H, Felix T, Wang L, Moremen KW, Liu J, Esko JD, Woods RJ.

Sci Rep. 2018 Aug 7;8(1):11832. doi: 10.1038/s41598-018-29602-4.


Defining the Specificity of Carbohydrate-Protein Interactions by Quantifying Functional Group Contributions.

Sood A, Gerlits OO, Ji Y, Bovin NV, Coates L, Woods RJ.

J Chem Inf Model. 2018 Sep 24;58(9):1889-1901. doi: 10.1021/acs.jcim.8b00120. Epub 2018 Aug 22.


A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen.

Amon R, Grant OC, Leviatan Ben-Arye S, Makeneni S, Nivedha AK, Marshanski T, Norn C, Yu H, Glushka JN, Fleishman SJ, Chen X, Woods RJ, Padler-Karavani V.

Sci Rep. 2018 Jul 17;8(1):10786. doi: 10.1038/s41598-018-29209-9.


A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus.

Fitzsimmons WJ, Woods RJ, McCrone JT, Woodman A, Arnold JJ, Yennawar M, Evans R, Cameron CE, Lauring AS.

PLoS Biol. 2018 Jun 28;16(6):e2006459. doi: 10.1371/journal.pbio.2006459. eCollection 2018 Jun.


Stochastic processes constrain the within and between host evolution of influenza virus.

McCrone JT, Woods RJ, Martin ET, Malosh RE, Monto AS, Lauring AS.

Elife. 2018 May 3;7. pii: e35962. doi: 10.7554/eLife.35962.


Oligosaccharide model of the vascular endothelial glycocalyx in physiological flow.

Pikoula M, Tessier MB, Woods RJ, Ventikos Y.

Microfluid Nanofluidics. 2018;22(2):21. doi: 10.1007/s10404-018-2037-5. Epub 2018 Jan 29.


A Traveling Wave Ion Mobility Spectrometry (TWIMS) Study of the Robo1-Heparan Sulfate Interaction.

Zhao Y, Yang JY, Thieker DF, Xu Y, Zong C, Boons GJ, Liu J, Woods RJ, Moremen KW, Amster IJ.

J Am Soc Mass Spectrom. 2018 Jun;29(6):1153-1165. doi: 10.1007/s13361-018-1903-4. Epub 2018 Mar 8.


Enhanced Human-Type Receptor Binding by Ferret-Transmissible H5N1 with a K193T Mutation.

Peng W, Bouwman KM, McBride R, Grant OC, Woods RJ, Verheije MH, Paulson JC, de Vries RP.

J Virol. 2018 Apr 27;92(10). pii: e02016-17. doi: 10.1128/JVI.02016-17. Print 2018 May 15.


Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking.

Makeneni S, Thieker DF, Woods RJ.

J Chem Inf Model. 2018 Mar 26;58(3):605-614. doi: 10.1021/acs.jcim.7b00588. Epub 2018 Mar 9.


Histoplasma Tenosynovitis Revealed by Fungal Culture in a Patient Treated with Infliximab.

Woods RJ, Reyes EJ, Knight JS.

J Rheumatol. 2018 Feb;45(2):284-285. doi: 10.3899/jrheum.170505. No abstract available.


Institution-wide and Within-Patient Evolution of Daptomycin Susceptibility in Vancomycin-Resistant Enterococcus faecium Bloodstream Infections.

Woods RJ, Patel TS, Nagel JL, Newton DW, Read AF.

Infect Control Hosp Epidemiol. 2018 Feb;39(2):226-228. doi: 10.1017/ice.2017.279. Epub 2018 Jan 14.


The promise and problems of non-physician practitioners in general surgery education: Results of a multi-center, mixed-methods study of faculty.

Coverdill JE, Shelton JS, Alseidi A, Borgstrom DC, Dent DL, Dumire R, Fryer J, Hartranft TH, Holsten SB, Nelson MT, Shabahang MM, Sherman SR, Termuhlen PM, Woods RJ, Mellinger JD.

Am J Surg. 2018 Feb;215(2):222-226. doi: 10.1016/j.amjsurg.2017.10.040. Epub 2017 Nov 5.


Assessing the 16 hour intern shift limit: Results of a multi-center, mixed-methods study of residents and faculty in general surgery.

Coverdill JE, Alseidi A, Borgstrom DC, Dent DL, Dumire R, Fryer J, Hartranft TH, Holsten SB, Nelson MT, Shabahang MM, Sherman SR, Termuhlen PM, Woods RJ, Mellinger JD.

Am J Surg. 2018 Feb;215(2):326-330. doi: 10.1016/j.amjsurg.2017.08.053. Epub 2017 Nov 4.


Evolution-informed forecasting of seasonal influenza A (H3N2).

Du X, King AA, Woods RJ, Pascual M.

Sci Transl Med. 2017 Oct 25;9(413). pii: eaan5325. doi: 10.1126/scitranslmed.aan5325.


O2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases.

Sheikh MO, Thieker D, Chalmers G, Schafer CM, Ishihara M, Azadi P, Woods RJ, Glushka JN, Bendiak B, Prestegard JH, West CM.

J Biol Chem. 2017 Nov 17;292(46):18897-18915. doi: 10.1074/jbc.M117.809160. Epub 2017 Sep 19.


Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed by Neutron Crystallography.

Gerlits OO, Coates L, Woods RJ, Kovalevsky A.

Biochemistry. 2017 Sep 12;56(36):4747-4750. doi: 10.1021/acs.biochem.7b00654. Epub 2017 Aug 30.


Knee osteoarthritis has doubled in prevalence since the mid-20th century.

Wallace IJ, Worthington S, Felson DT, Jurmain RD, Wren KT, Maijanen H, Woods RJ, Lieberman DE.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):9332-9336. doi: 10.1073/pnas.1703856114. Epub 2017 Aug 14.


New insights into influenza A specificity: an evolution of paradigms.

Ji Y, White YJ, Hadden JA, Grant OC, Woods RJ.

Curr Opin Struct Biol. 2017 Jun;44:219-231. doi: 10.1016/ Epub 2017 Jul 1. Review.


Three mutations switch H7N9 influenza to human-type receptor specificity.

de Vries RP, Peng W, Grant OC, Thompson AJ, Zhu X, Bouwman KM, de la Pena ATT, van Breemen MJ, Ambepitiya Wickramasinghe IN, de Haan CAM, Yu W, McBride R, Sanders RW, Woods RJ, Verheije MH, Wilson IA, Paulson JC.

PLoS Pathog. 2017 Jun 15;13(6):e1006390. doi: 10.1371/journal.ppat.1006390. eCollection 2017 Jun.


Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans.

Singh A, Tessier MB, Pederson K, Wang X, Venot AP, Boons GJ, Prestegard JH, Woods RJ.

Can J Chem. 2016 Nov;94(11):927-935. doi: 10.1139/cjc-2015-0606. Epub 2016 Feb 9.


The Tetrameric Plant Lectin BanLec Neutralizes HIV through Bidentate Binding to Specific Viral Glycans.

Hopper JTS, Ambrose S, Grant OC, Krumm SA, Allison TM, Degiacomi MT, Tully MD, Pritchard LK, Ozorowski G, Ward AB, Crispin M, Doores KJ, Woods RJ, Benesch JLP, Robinson CV, Struwe WB.

Structure. 2017 May 2;25(5):773-782.e5. doi: 10.1016/j.str.2017.03.015. Epub 2017 Apr 20.


Synthesis of 3-O-Sulfated Oligosaccharides to Understand the Relationship between Structures and Functions of Heparan Sulfate.

Wang Z, Hsieh PH, Xu Y, Thieker D, Chai EJE, Xie S, Cooley B, Woods RJ, Chi L, Liu J.

J Am Chem Soc. 2017 Apr 12;139(14):5249-5256. doi: 10.1021/jacs.7b01923. Epub 2017 Apr 3.


Conformational Populations of β-(1→4) O-Glycosidic Linkages Using Redundant NMR J-Couplings and Circular Statistics.

Zhang W, Turney T, Meredith R, Pan Q, Sernau L, Wang X, Hu X, Woods RJ, Carmichael I, Serianni AS.

J Phys Chem B. 2017 Apr 13;121(14):3042-3058. doi: 10.1021/acs.jpcb.7b02252. Epub 2017 Mar 30.


How to Use a Chemotherapeutic Agent When Resistance to It Threatens the Patient.

Hansen E, Woods RJ, Read AF.

PLoS Biol. 2017 Feb 9;15(2):e2001110. doi: 10.1371/journal.pbio.2001110. eCollection 2017 Feb.


Gly-Spec: a webtool for predicting glycan specificity by integrating glycan array screening data and 3D structure.

Grant OC, Xue X, Ra D, Khatamian A, Foley BL, Woods RJ.

Glycobiology. 2016 Oct;26(10):1027-1028. doi: 10.1093/glycob/cww094. No abstract available.


Structural Analysis of the Glycosylated Intact HIV-1 gp120-b12 Antibody Complex Using Hydroxyl Radical Protein Footprinting.

Li X, Grant OC, Ito K, Wallace A, Wang S, Zhao P, Wells L, Lu S, Woods RJ, Sharp JS.

Biochemistry. 2017 Feb 21;56(7):957-970. doi: 10.1021/acs.biochem.6b00888. Epub 2017 Feb 6.


Give Me a Hand: Adult Involvement During Object Exploration Affects Object Individuation in Infancy.

Johnson KM, Woods RJ.

Infant Child Dev. 2016 Sep-Oct;25(5):406-425. doi: 10.1002/icd.1942. Epub 2015 Oct 16.


Induction of Antibodies Directed Against Branched Core O-Mannosyl Glycopeptides-Selectivity Complimentary to the ConA Lectin.

Yu J, Grant OC, Pett C, Strahl S, Stahl S, Woods RJ, Westerlind U.

Chemistry. 2017 Mar 8;23(14):3466-3473. doi: 10.1002/chem.201605627. Epub 2017 Feb 16. Erratum in: Chemistry. 2019 Mar 12;25(15):3963. Stahl S [corrected to Strahl S].


Recent H3N2 Viruses Have Evolved Specificity for Extended, Branched Human-type Receptors, Conferring Potential for Increased Avidity.

Peng W, de Vries RP, Grant OC, Thompson AJ, McBride R, Tsogtbaatar B, Lee PS, Razi N, Wilson IA, Woods RJ, Paulson JC.

Cell Host Microbe. 2017 Jan 11;21(1):23-34. doi: 10.1016/j.chom.2016.11.004. Epub 2016 Dec 22.


O-Acetyl Side-Chains in Monosaccharides: Redundant NMR Spin-Couplings and Statistical Models for Acetate Ester Conformational Analysis.

Turney T, Pan Q, Sernau L, Carmichael I, Zhang W, Wang X, Woods RJ, Serianni AS.

J Phys Chem B. 2017 Jan 12;121(1):66-77. doi: 10.1021/acs.jpcb.6b10028. Epub 2016 Dec 21.


Professionalism in the Twilight Zone: A Multicenter, Mixed-Methods Study of Shift Transition Dynamics in Surgical Residencies.

Coverdill JE, Alseidi A, Borgstrom DC, Dent DL, Dumire RD, Fryer J, Hartranft TH, Holsten SB, Nelson MT, Shabahang M, Sherman S, Termuhlen PM, Woods RJ, Mellinger JD.

Acad Med. 2016 Nov;91(11 Association of American Medical Colleges Learn Serve Lead: Proceedings of the 55th Annual Research in Medical Education Sessions):S31-S36.


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