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Proteomics, glycomics, and glycoproteomics of matrisome molecules.

Raghunathan R, Sethi MK, Klein JA, Zaia J.

Mol Cell Proteomics. 2019 Aug 30. pii: mcp.R119.001543. doi: 10.1074/mcp.R119.001543. [Epub ahead of print] Review.


Sequencing Heparan Sulfate Using HILIC LC-NETD-MS/MS.

Wu J, Wei J, Chopra P, Boons GJ, Lin C, Zaia J.

Anal Chem. 2019 Sep 17;91(18):11738-11746. doi: 10.1021/acs.analchem.9b02313. Epub 2019 Aug 29.


Structural studies of serum clusterin in ATTRwt amyloidosis.

Torres-Arancivia C, Chang D, Zaia J, Connors LH.

Amyloid. 2019;26(sup1):51-52. doi: 10.1080/13506129.2019.1582516. No abstract available.


glypy: An Open Source Glycoinformatics Library.

Klein J, Zaia J.

J Proteome Res. 2019 Sep 6;18(9):3532-3537. doi: 10.1021/acs.jproteome.9b00367. Epub 2019 Jul 30.


Characterization and Quantification of Highly Sulfated Glycosaminoglycan Isomers by Gated-Trapped Ion Mobility Spectrometry Negative Electron Transfer Dissociation MS/MS.

Wei J, Wu J, Tang Y, Ridgeway ME, Park MA, Costello CE, Zaia J, Lin C.

Anal Chem. 2019 Feb 19;91(4):2994-3001. doi: 10.1021/acs.analchem.8b05283. Epub 2019 Jan 31.


psims - A Declarative Writer for mzML and mzIdentML for Python.

Klein J, Zaia J.

Mol Cell Proteomics. 2019 Mar;18(3):571-575. doi: 10.1074/mcp.RP118.001070. Epub 2018 Dec 18.


A fifty-year odyssey: prospects for a cytomegalovirus vaccine in transplant and congenital infection.

Diamond DJ, La Rosa C, Chiuppesi F, Contreras H, Dadwal S, Wussow F, Bautista S, Nakamura R, Zaia JA.

Expert Rev Vaccines. 2018 Oct;17(10):889-911. doi: 10.1080/14760584.2018.1526085. Epub 2018 Oct 3. Review.


Glycomic and Proteomic Changes in Aging Brain Nigrostriatal Pathway.

Raghunathan R, Polinski NK, Klein JA, Hogan JD, Shao C, Khatri K, Leon D, McComb ME, Manfredsson FP, Sortwell CE, Zaia J.

Mol Cell Proteomics. 2018 Sep;17(9):1778-1787. doi: 10.1074/mcp.RA118.000680. Epub 2018 Jun 18.


CIRM Alpha Stem Cell Clinics: Collaboratively Addressing Regenerative Medicine Challenges.

Jamieson CHM, Millan MT, Creasey AA, Lomax G, Donohoe ME, Walters MC, Abedi M, Bota DA, Zaia JA, Adams JS.

Cell Stem Cell. 2018 Jun 1;22(6):801-805. doi: 10.1016/j.stem.2018.05.007.


Focus on Mass Spectrometry in Glycobiology and Related Fields, Honoring Catherine E. Costello, Recipient of the 2017 ASMS Award for a Distinguished Contribution in Mass Spectrometry.

Zaia J, Bierbaum VM.

J Am Soc Mass Spectrom. 2018 Jun;29(6):1061-1064. doi: 10.1007/s13361-018-1957-3. No abstract available.


Application of network smoothing to glycan LC-MS profiling.

Klein J, Carvalho L, Zaia J.

Bioinformatics. 2018 Oct 15;34(20):3511-3518. doi: 10.1093/bioinformatics/bty397.


Deep Sequencing of Complex Proteoglycans: A Novel Strategy for High Coverage and Site-specific Identification of Glycosaminoglycan-linked Peptides.

Klein JA, Meng L, Zaia J.

Mol Cell Proteomics. 2018 Aug;17(8):1578-1590. doi: 10.1074/mcp.RA118.000766. Epub 2018 May 17.


Lectin-mediated binding and sialoglycans of porcine surfactant protein D synergistically neutralize influenza A virus.

van Eijk M, Rynkiewicz MJ, Khatri K, Leymarie N, Zaia J, White MR, Hartshorn KL, Cafarella TR, van Die I, Hessing M, Seaton BA, Haagsman HP.

J Biol Chem. 2018 Jul 6;293(27):10646-10662. doi: 10.1074/jbc.RA117.001430. Epub 2018 May 16.


Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides.

Khatri K, Pu Y, Klein JA, Wei J, Costello CE, Lin C, Zaia J.

J Am Soc Mass Spectrom. 2018 Jun;29(6):1075-1085. doi: 10.1007/s13361-018-1909-y. Epub 2018 Apr 16.


Software for Peak Finding and Elemental Composition Assignment for Glycosaminoglycan Tandem Mass Spectra.

Hogan JD, Klein JA, Wu J, Chopra P, Boons GJ, Carvalho L, Lin C, Zaia J.

Mol Cell Proteomics. 2018 Jul;17(7):1448-1456. doi: 10.1074/mcp.RA118.000590. Epub 2018 Apr 3.


Negative Electron Transfer Dissociation Sequencing of 3-O-Sulfation-Containing Heparan Sulfate Oligosaccharides.

Wu J, Wei J, Hogan JD, Chopra P, Joshi A, Lu W, Klein J, Boons GJ, Lin C, Zaia J.

J Am Soc Mass Spectrom. 2018 Jun;29(6):1262-1272. doi: 10.1007/s13361-018-1907-0. Epub 2018 Mar 21.


Sensitive method for glycosaminoglycan analysis of tissue sections.

Turiák L, Tóth G, Ozohanics O, Révész Á, Ács A, Vékey K, Zaia J, Drahos L.

J Chromatogr A. 2018 Apr 6;1544:41-48. doi: 10.1016/j.chroma.2018.02.034. Epub 2018 Feb 25.


CD19 CAR-T therapy and sepsis: dancing with the devil.

Budde LE, Zaia JA.

Blood. 2018 Jan 4;131(1):7-8. doi: 10.1182/blood-2017-11-812982. No abstract available.


Imaging specific cellular glycan structures using glycosyltransferases via click chemistry.

Wu ZL, Person AD, Anderson M, Burroughs B, Tatge T, Khatri K, Zou Y, Wang L, Geders T, Zaia J, Sackstein R.

Glycobiology. 2018 Feb 1;28(2):69-79. doi: 10.1093/glycob/cwx095.


Role of Nursing Competencies for Accelerating Clinical Trials in Stem Cell Clinics.

Perrin M, Kim T, Stan R, Giesie P, Tabor J, Le Verche V, Johnson S, Lomax GP, Zaia JA.

Stem Cells Transl Med. 2018 Jan;7(1):6-10. doi: 10.1002/sctm.17-0165. Epub 2017 Nov 3.


Heparan sulfate: Resilience factor and therapeutic target for cocaine abuse.

Chen J, Kawamura T, Sethi MK, Zaia J, Repunte-Canonigo V, Sanna PP.

Sci Rep. 2017 Oct 24;7(1):13931. doi: 10.1038/s41598-017-13960-6.


How I treat patients with HIV-related hematological malignancies using hematopoietic cell transplantation.

Alvarnas JC, Zaia JA, Forman SJ.

Blood. 2017 Nov 2;130(18):1976-1984. doi: 10.1182/blood-2017-04-551606. Epub 2017 Sep 7. Review.


Microfluidic Capillary Electrophoresis-Mass Spectrometry for Analysis of Monosaccharides, Oligosaccharides, and Glycopeptides.

Khatri K, Klein JA, Haserick JR, Leon DR, Costello CE, McComb ME, Zaia J.

Anal Chem. 2017 Jun 20;89(12):6645-6655. doi: 10.1021/acs.analchem.7b00875. Epub 2017 Jun 6.


[Health literacy: translation and validation of a research instrument on health promotion in Brazil].

Quemelo PR, Milani D, Bento VF, Vieira ER, Zaia JE.

Cad Saude Publica. 2017 Mar 30;33(2):e00179715. doi: 10.1590/0102-311X00179715. Portuguese.


Construction of a Database of Collision Cross Section Values for Glycopeptides, Glycans, and Peptides Determined by IM-MS.

Glaskin RS, Khatri K, Wang Q, Zaia J, Costello CE.

Anal Chem. 2017 Apr 18;89(8):4452-4460. doi: 10.1021/acs.analchem.6b04146. Epub 2017 Mar 30.


Musculoskeletal disorders and stress among footwear industry workers.

de Almeida LB, Vieira ER, Zaia JE, de Oliveira Santos BM, Lourenço AR, Quemelo PR.

Work. 2017;56(1):67-73. doi: 10.3233/WOR-162463.


Non-reducing end labeling of heparan sulfate via click chemistry and a high throughput ELISA assay for heparanase.

Wu ZL, Huang X, Ethen CM, Tatge T, Pasek M, Zaia J.

Glycobiology. 2017 Jun 1;27(6):518-524. doi: 10.1093/glycob/cww130.


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]


A New Agent in the Strategy to Cure AIDS.

Zaia JA.

Mol Ther. 2016 Nov;24(11):1894-1896. doi: 10.1038/mt.2016.194. No abstract available.


Preclinical development and qualification of ZFN-mediated CCR5 disruption in human hematopoietic stem/progenitor cells.

DiGiusto DL, Cannon PM, Holmes MC, Li L, Rao A, Wang J, Lee G, Gregory PD, Kim KA, Hayward SB, Meyer K, Exline C, Lopez E, Henley J, Gonzalez N, Bedell V, Stan R, Zaia JA.

Mol Ther Methods Clin Dev. 2016 Nov 9;3:16067. eCollection 2016.


Complete Molecular Weight Profiling of Low-Molecular Weight Heparins Using Size Exclusion Chromatography-Ion Suppressor-High-Resolution Mass Spectrometry.

Zaia J, Khatri K, Klein J, Shao C, Sheng Y, Viner R.

Anal Chem. 2016 Nov 1;88(21):10654-10660. Epub 2016 Oct 17.


MVA vaccine encoding CMV antigens safely induces durable expansion of CMV-specific T cells in healthy adults.

La Rosa C, Longmate J, Martinez J, Zhou Q, Kaltcheva TI, Tsai W, Drake J, Carroll M, Wussow F, Chiuppesi F, Hardwick N, Dadwal S, Aldoss I, Nakamura R, Zaia JA, Diamond DJ.

Blood. 2017 Jan 5;129(1):114-125. doi: 10.1182/blood-2016-07-729756. Epub 2016 Oct 19.


Use of an informed search space maximizes confidence of site-specific assignment of glycoprotein glycosylation.

Khatri K, Klein JA, Zaia J.

Anal Bioanal Chem. 2017 Jan;409(2):607-618. doi: 10.1007/s00216-016-9970-5. Epub 2016 Oct 12.


Nematodes join the family of chondroitin sulfate-synthesizing organisms: Identification of an active chondroitin sulfotransferase in Caenorhabditis elegans.

Dierker T, Shao C, Haitina T, Zaia J, Hinas A, Kjellén L.

Sci Rep. 2016 Oct 5;6:34662. doi: 10.1038/srep34662.


Effects of physical exercise on musculoskeletal disorders, stress and quality of life in workers.

Serra MVGB, Camargo PR, Zaia JE, Tonello MGM, Quemelo PRV.

Int J Occup Saf Ergon. 2018 Mar;24(1):62-67. doi: 10.1080/10803548.2016.1234132. Epub 2016 Oct 6.


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.


Extracellular matrix proteomics in schizophrenia and Alzheimer's disease.

Sethi MK, Zaia J.

Anal Bioanal Chem. 2017 Jan;409(2):379-394. doi: 10.1007/s00216-016-9900-6. Epub 2016 Sep 6. Review.


Phosphatidylethanolamine binding protein 4 (PEBP4) is a secreted protein and has multiple functions.

He H, Liu D, Lin H, Jiang S, Ying Y, Chun S, Deng H, Zaia J, Wen R, Luo Z.

Biochim Biophys Acta. 2016 Jul;1863(7 Pt A):1682-9. doi: 10.1016/j.bbamcr.2016.03.022. Epub 2016 Mar 28.


Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions.

Khatri K, Klein JA, White MR, Grant OC, Leymarie N, Woods RJ, Hartshorn KL, Zaia J.

Mol Cell Proteomics. 2016 Jun;15(6):1895-912. doi: 10.1074/mcp.M116.058016. Epub 2016 Mar 16.


Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen-Deuterium Exchange Mass Spectrometry.

Tykesson E, Mao Y, Maccarana M, Pu Y, Gao J, Lin C, Zaia J, Westergren-Thorsson G, Ellervik U, Malmström L, Malmström A.

Chem Sci. 2016 Feb 1;7(2):1447-1456. Epub 2015 Nov 30.


Viraemia, immunogenicity, and survival outcomes of cytomegalovirus chimeric epitope vaccine supplemented with PF03512676 (CMVPepVax) in allogeneic haemopoietic stem-cell transplantation: randomised phase 1b trial.

Nakamura R, La Rosa C, Longmate J, Drake J, Slape C, Zhou Q, Lampa MG, O'Donnell M, Cai JL, Farol L, Salhotra A, Snyder DS, Aldoss I, Forman SJ, Miller JS, Zaia JA, Diamond DJ.

Lancet Haematol. 2016 Feb;3(2):e87-98. doi: 10.1016/S2352-3026(15)00246-X. Epub 2015 Dec 24.


Evaluation of postural balance in mild cognitive impairment through a three-dimensional electromagnetic system.

Borges AP, Carneiro JA, Zaia JE, Carneiro AA, Takayanagui OM.

Braz J Otorhinolaryngol. 2016 Jul-Aug;82(4):433-41. doi: 10.1016/j.bjorl.2015.08.023. Epub 2015 Dec 23.


Algorithms and design strategies towards automated glycoproteomics analysis.

Hu H, Khatri K, Zaia J.

Mass Spectrom Rev. 2017 Jul;36(4):475-498. doi: 10.1002/mas.21487. Epub 2016 Jan 4. Review.


A Novel Class of HIV-1 Antiviral Agents Targeting HIV via a SUMOylation-Dependent Mechanism.

Madu IG, Li S, Li B, Li H, Chang T, Li YJ, Vega R, Rossi J, Yee JK, Zaia J, Chen Y.

Sci Rep. 2015 Dec 8;5:17808. doi: 10.1038/srep17808.


A review of methods for interpretation of glycopeptide tandem mass spectral data.

Hu H, Khatri K, Klein J, Leymarie N, Zaia J.

Glycoconj J. 2016 Jun;33(3):285-96. doi: 10.1007/s10719-015-9633-3. Epub 2015 Nov 26. Review.


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.


Targeting Human Cancer by a Glycosaminoglycan Binding Malaria Protein.

Salanti A, Clausen TM, Agerbæk MØ, Al Nakouzi N, Dahlbäck M, Oo HZ, Lee S, Gustavsson T, Rich JR, Hedberg BJ, Mao Y, Barington L, Pereira MA, LoBello J, Endo M, Fazli L, Soden J, Wang CK, Sander AF, Dagil R, Thrane S, Holst PJ, Meng L, Favero F, Weiss GJ, Nielsen MA, Freeth J, Nielsen TO, Zaia J, Tran NL, Trent J, Babcook JS, Theander TG, Sorensen PH, Daugaard M.

Cancer Cell. 2015 Oct 12;28(4):500-514. doi: 10.1016/j.ccell.2015.09.003.


Response of Preterm Infants to 2 Noninvasive Ventilatory Support Systems: Nasal CPAP and Nasal Intermittent Positive-Pressure Ventilation.

Silveira CS, Leonardi KM, Melo AP, Zaia JE, Brunherotti MA.

Respir Care. 2015 Dec;60(12):1772-6. doi: 10.4187/respcare.03565. Epub 2015 Sep 15.


CMVpp65 Vaccine Enhances the Antitumor Efficacy of Adoptively Transferred CD19-Redirected CMV-Specific T Cells.

Wang X, Wong CW, Urak R, Mardiros A, Budde LE, Chang WC, Thomas SH, Brown CE, La Rosa C, Diamond DJ, Jensen MC, Nakamura R, Zaia JA, Forman SJ.

Clin Cancer Res. 2015 Jul 1;21(13):2993-3002. doi: 10.1158/1078-0432.CCR-14-2920. Epub 2015 Apr 2.


HIV-associated non-Hodgkin lymphoma: viral origins and therapeutic options.

Krishnan A, Zaia JA.

Hematology Am Soc Hematol Educ Program. 2014 Dec 5;2014(1):584-9. doi: 10.1182/asheducation-2014.1.584. Epub 2014 Nov 18. Review.


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