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Alterations in the Salivary Proteome and N-Glycome of Sjögren's Syndrome Patients.

Hall SC, Hassis ME, Williams KE, Albertolle ME, Prakobphol A, Dykstra AB, Laurance M, Ona K, Niles RK, Prasad N, Gormley M, Shiboski C, Criswell LA, Witkowska HE, Fisher SJ.

J Proteome Res. 2017 Apr 7;16(4):1693-1705. doi: 10.1021/acs.jproteome.6b01051. Epub 2017 Mar 24.


Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions.

Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin MD.

Mol Cell Proteomics. 2016 Jun;15(6):2186-202. doi: 10.1074/mcp.M115.057117. Epub 2016 Apr 20.


Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.

Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G.

Mol Cell Proteomics. 2016 May;15(5):1539-55. doi: 10.1074/mcp.M115.054692. Epub 2016 Feb 12.


Urine, peritoneal fluid and omental fat proteomes of reproductive age women: Endometriosis-related changes and associations with endocrine disrupting chemicals.

Williams KE, Miroshnychenko O, Johansen EB, Niles RK, Sundaram R, Kannan K, Albertolle M, Zhou Y, Prasad N, Drake PM, Giudice LC, Hall SC, Witkowska HE, Buck Louis GM, Fisher SJ.

J Proteomics. 2015 Jan 15;113:194-205. doi: 10.1016/j.jprot.2014.09.015. Epub 2014 Oct 13.


The lethal cargo of Myxococcus xanthus outer membrane vesicles.

Berleman JE, Allen S, Danielewicz MA, Remis JP, Gorur A, Cunha J, Hadi MZ, Zusman DR, Northen TR, Witkowska HE, Auer M.

Front Microbiol. 2014 Sep 9;5:474. doi: 10.3389/fmicb.2014.00474. eCollection 2014.


Aberrant hetero-disulfide bond formation by the hypertriglyceridemia-associated p.Gly185Cys APOA5 variant (rs2075291).

Sharma V, Witkowski A, Witkowska HE, Dykstra A, Simonsen JB, Nelbach L, Beckstead JA, Pullinger CR, Kane JP, Malloy MJ, Watson G, Forte TM, Ryan RO.

Arterioscler Thromb Vasc Biol. 2014 Oct;34(10):2254-60. doi: 10.1161/ATVBAHA.114.304027. Epub 2014 Aug 14.


Preferential and selective degradation and removal of amelogenin adsorbed on hydroxyapatites by MMP20 and KLK4 in vitro.

Zhu L, Liu H, Witkowska HE, Huang Y, Tanimoto K, Li W.

Front Physiol. 2014 Jul 24;5:268. doi: 10.3389/fphys.2014.00268. eCollection 2014.


Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection.

Roan NR, Liu H, Usmani SM, Neidleman J, Müller JA, Avila-Herrera A, Gawanbacht A, Zirafi O, Chu S, Dong M, Kumar ST, Smith JF, Pollard KS, Fändrich M, Kirchhoff F, Münch J, Witkowska HE, Greene WC.

J Virol. 2014 Jul;88(13):7221-34. doi: 10.1128/JVI.00269-14. Epub 2014 Apr 16.


Interaction of fibronectin with semen amyloids synergistically enhances HIV infection.

Roan NR, Chu S, Liu H, Neidleman J, Witkowska HE, Greene WC.

J Infect Dis. 2014 Oct 1;210(7):1062-6. doi: 10.1093/infdis/jiu220. Epub 2014 Apr 8.


In multiple sclerosis, oligoclonal bands connect to peripheral B-cell responses.

Bankoti J, Apeltsin L, Hauser SL, Allen S, Albertolle ME, Witkowska HE, von Büdingen HC.

Ann Neurol. 2014 Feb;75(2):266-76. doi: 10.1002/ana.24088. Epub 2014 Feb 20.


Quantitatively and kinetically identifying binding motifs of amelogenin proteins to mineral crystals through biochemical and spectroscopic assays.

Zhu L, Hwang P, Witkowska HE, Liu H, Li W.

Methods Enzymol. 2013;532:327-41. doi: 10.1016/B978-0-12-416617-2.00015-1.


Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains.

Remis JP, Wei D, Gorur A, Zemla M, Haraga J, Allen S, Witkowska HE, Costerton JW, Berleman JE, Auer M.

Environ Microbiol. 2014 Feb;16(2):598-610. doi: 10.1111/1462-2920.12187. Epub 2013 Jul 15.


Architectural insights into a ciliary partition.

Ounjai P, Kim KD, Liu H, Dong M, Tauscher AN, Witkowska HE, Downing KH.

Curr Biol. 2013 Feb 18;23(4):339-44. doi: 10.1016/j.cub.2013.01.029. Epub 2013 Jan 31.


The proteolytic processing of amelogenin by enamel matrix metalloproteinase (MMP-20) is controlled by mineral ions.

Khan F, Liu H, Reyes A, Witkowska HE, Martinez-Avila O, Zhu L, Li W, Habelitz S.

Biochim Biophys Acta. 2013 Mar;1830(3):2600-7.


High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.

Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, Biggin MD, Jap BK.

J Proteome Res. 2012 Dec 7;11(12):5720-35. doi: 10.1021/pr300548d. Epub 2012 Oct 25.


Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers.

Drake PM, Schilling B, Niles RK, Prakobphol A, Li B, Jung K, Cho W, Braten M, Inerowicz HD, Williams K, Albertolle M, Held JM, Iacovides D, Sorensen DJ, Griffith OL, Johansen E, Zawadzka AM, Cusack MP, Allen S, Gormley M, Hall SC, Witkowska HE, Gray JW, Regnier F, Gibson BW, Fisher SJ.

J Proteome Res. 2012 Apr 6;11(4):2508-20. doi: 10.1021/pr201206w. Epub 2012 Mar 13.


Amelogenin exons 8 and 9 encoded peptide enhances leucine rich amelogenin peptide mediated dental pulp repair.

Huang Y, Goldberg M, Le T, Qiang R, Warner D, Witkowska HE, Liu H, Zhu L, Denbesten P, Li W.

Cells Tissues Organs. 2012;196(2):151-60. doi: 10.1159/000331248. Epub 2012 Feb 1.


Fluoride incorporation into apatite crystals delays amelogenin hydrolysis.

DenBesten PK, Zhu L, Li W, Tanimoto K, Liu H, Witkowska HE.

Eur J Oral Sci. 2011 Dec;119 Suppl 1:3-7. doi: 10.1111/j.1600-0722.2011.00903.x.


Peptides released by physiological cleavage of semen coagulum proteins form amyloids that enhance HIV infection.

Roan NR, Müller JA, Liu H, Chu S, Arnold F, Stürzel CM, Walther P, Dong M, Witkowska HE, Kirchhoff F, Münch J, Greene WC.

Cell Host Microbe. 2011 Dec 15;10(6):541-50. doi: 10.1016/j.chom.2011.10.010.


Breaking the bottleneck in the protein biomarker pipeline.

Witkowska HE, Hall SC, Fisher SJ.

Clin Chem. 2012 Feb;58(2):321-3. doi: 10.1373/clinchem.2011.175034. Epub 2011 Dec 2. No abstract available.


Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.

Chhabra SR, Butland G, Elias DA, Chandonia JM, Fok OY, Juba TR, Gorur A, Allen S, Leung CM, Keller KL, Reveco S, Zane GM, Semkiw E, Prathapam R, Gold B, Singer M, Ouellet M, Szakal ED, Jorgens D, Price MN, Witkowska HE, Beller HR, Arkin AP, Hazen TC, Biggin MD, Auer M, Wall JD, Keasling JD.

Appl Environ Microbiol. 2011 Nov;77(21):7595-604. doi: 10.1128/AEM.05495-11. Epub 2011 Sep 9.


Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Price MN, Deutschbauer AM, Kuehl JV, Liu H, Witkowska HE, Arkin AP.

J Bacteriol. 2011 Oct;193(20):5716-27. doi: 10.1128/JB.05563-11. Epub 2011 Aug 12.


Hydrolysis of amelogenin by matrix metalloprotease-20 accelerates mineralization in vitro.

Uskoković V, Khan F, Liu H, Witkowska HE, Zhu L, Li W, Habelitz S.

Arch Oral Biol. 2011 Dec;56(12):1548-59. doi: 10.1016/j.archoralbio.2011.06.016. Epub 2011 Jul 20.


Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow.

Liu H, Yang L, Khainovski N, Dong M, Hall SC, Fisher SJ, Biggin MD, Jin J, Witkowska HE.

Anal Chem. 2011 Aug 15;83(16):6286-93. doi: 10.1021/ac200911v. Epub 2011 Jul 15. Erratum in: Anal Chem. 2011 Aug 15;83(16):6293.


ABRF-PRG07: advanced quantitative proteomics study.

Falick AM, Lane WS, Lilley KS, MacCoss MJ, Phinney BS, Sherman NE, Weintraub ST, Witkowska HE, Yates NA.

J Biomol Tech. 2011 Apr;22(1):21-6.


The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses.

Friedman DB, Andacht TM, Bunger MK, Chien AS, Hawke DH, Krijgsveld J, Lane WS, Lilley KS, MacCoss MJ, Moritz RL, Settlage RE, Sherman NE, Weintraub ST, Witkowska HE, Yates NA, Turck CW.

Proteomics. 2011 Apr;11(8):1371-81. doi: 10.1002/pmic.201000736. Epub 2011 Mar 11.


A lectin affinity workflow targeting glycosite-specific, cancer-related carbohydrate structures in trypsin-digested human plasma.

Drake PM, Schilling B, Niles RK, Braten M, Johansen E, Liu H, Lerch M, Sorensen DJ, Li B, Allen S, Hall SC, Witkowska HE, Regnier FE, Gibson BW, Fisher SJ.

Anal Biochem. 2011 Jan 1;408(1):71-85. doi: 10.1016/j.ab.2010.08.010. Epub 2010 Aug 10.


Survey of large protein complexes in D. vulgaris reveals great structural diversity.

Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, Biggin MD, Glaeser RM.

Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16580-5. doi: 10.1073/pnas.0813068106. Epub 2009 Sep 11.


A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples.

Johansen E, Schilling B, Lerch M, Niles RK, Liu H, Li B, Allen S, Hall SC, Witkowska HE, Regnier FE, Gibson BW, Fisher SJ, Drake PM.

J Vis Exp. 2009 Oct 1;(32). pii: 1398. doi: 10.3791/1398.


The sodium-hydrogen exchanger NHE1 is an Akt substrate necessary for actin filament reorganization by growth factors.

Meima ME, Webb BA, Witkowska HE, Barber DL.

J Biol Chem. 2009 Sep 25;284(39):26666-75. doi: 10.1074/jbc.M109.019448. Epub 2009 Jul 21.


Acid-catalyzed oxygen-18 labeling of peptides.

Niles R, Witkowska HE, Allen S, Hall SC, Fisher SJ, Hardt M.

Anal Chem. 2009 Apr 1;81(7):2804-9. doi: 10.1021/ac802484d.


Rapid alterations in cortical protein profiles underlie spontaneous sleep and wake bouts.

Vazquez J, Hall SC, Witkowska HE, Greco MA.

J Cell Biochem. 2008 Dec 15;105(6):1472-84. doi: 10.1002/jcb.21970.


Reduced amelogenin-MMP20 interactions in amelogenesis imperfecta.

Tanimoto K, Le T, Zhu L, Witkowska HE, Robinson S, Hall S, Hwang P, Denbesten P, Li W.

J Dent Res. 2008 May;87(5):451-5.


The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions.

Denny P, Hagen FK, Hardt M, Liao L, Yan W, Arellanno M, Bassilian S, Bedi GS, Boontheung P, Cociorva D, Delahunty CM, Denny T, Dunsmore J, Faull KF, Gilligan J, Gonzalez-Begne M, Halgand F, Hall SC, Han X, Henson B, Hewel J, Hu S, Jeffrey S, Jiang J, Loo JA, Ogorzalek Loo RR, Malamud D, Melvin JE, Miroshnychenko O, Navazesh M, Niles R, Park SK, Prakobphol A, Ramachandran P, Richert M, Robinson S, Sondej M, Souda P, Sullivan MA, Takashima J, Than S, Wang J, Whitelegge JP, Witkowska HE, Wolinsky L, Xie Y, Xu T, Yu W, Ytterberg J, Wong DT, Yates JR 3rd, Fisher SJ.

J Proteome Res. 2008 May;7(5):1994-2006. doi: 10.1021/pr700764j. Epub 2008 Mar 25.


A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking.

Dong M, Yang LL, Williams K, Fisher SJ, Hall SC, Biggin MD, Jin J, Witkowska HE.

J Proteome Res. 2008 May;7(5):1836-49. doi: 10.1021/pr700624e. Epub 2008 Mar 13.


A mass spectrometry-based strategy for detecting and characterizing endogenous proteinase activities in complex biological samples.

Robinson S, Niles RK, Witkowska HE, Rittenbach KJ, Nichols RJ, Sargent JA, Dixon SE, Prakobphol A, Hall SC, Fisher SJ, Hardt M.

Proteomics. 2008 Feb;8(3):435-45. doi: 10.1002/pmic.200700680.


The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation.

Turck CW, Falick AM, Kowalak JA, Lane WS, Lilley KS, Phinney BS, Weintraub ST, Witkowska HE, Yates NA; Association of Biomolecula Resource Facilities Proteomics Research Group.

Mol Cell Proteomics. 2007 Aug;6(8):1291-8. Epub 2007 May 18.


Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris.

Garczarek F, Dong M, Typke D, Witkowska HE, Hazen TC, Nogales E, Biggin MD, Glaeser RM.

J Struct Biol. 2007 Jul;159(1):9-18. Epub 2007 Feb 17.


Apolipoprotein E*dipalmitoylphosphatidylcholine particles are ellipsoidal in solution.

Peters-Libeu CA, Newhouse Y, Hall SC, Witkowska HE, Weisgraber KH.

J Lipid Res. 2007 May;48(5):1035-44. Epub 2007 Feb 17.


High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition.

Chiu YL, Witkowska HE, Hall SC, Santiago M, Soros VB, Esnault C, Heidmann T, Greene WC.

Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15588-93. Epub 2006 Oct 9.


Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents.

Hardt M, Witkowska HE, Webb S, Thomas LR, Dixon SE, Hall SC, Fisher SJ.

Anal Chem. 2005 Aug 1;77(15):4947-54.


Toward defining the human parotid gland salivary proteome and peptidome: identification and characterization using 2D SDS-PAGE, ultrafiltration, HPLC, and mass spectrometry.

Hardt M, Thomas LR, Dixon SE, Newport G, Agabian N, Prakobphol A, Hall SC, Witkowska HE, Fisher SJ.

Biochemistry. 2005 Mar 1;44(8):2885-99.


Head-to-head coiled arrangement of the subunits of the animal fatty acid synthase.

Witkowski A, Ghosal A, Joshi AK, Witkowska HE, Asturias FJ, Smith S.

Chem Biol. 2004 Dec;11(12):1667-76.


Desorption/ionization on silicon time-of-flight/time-of-flight mass spectrometry.

Go EP, Prenni JE, Wei J, Jones A, Hall SC, Witkowska HE, Shen Z, Siuzdak G.

Anal Chem. 2003 May 15;75(10):2504-6.


Characterization of embryonic globin genes of the zebrafish.

Brownlie A, Hersey C, Oates AC, Paw BH, Falick AM, Witkowska HE, Flint J, Higgs D, Jessen J, Bahary N, Zhu H, Lin S, Zon L.

Dev Biol. 2003 Mar 1;255(1):48-61.


Hb H hydrops foetalis syndrome: a case report and review of literature.

Lorey F, Charoenkwan P, Witkowska HE, Lafferty J, Patterson M, Eng B, Waye JS, Finklestein JZ, Chui DH.

Br J Haematol. 2001 Oct;115(1):72-8. Review.


Universal newborn screening for Hb H disease in California.

Lorey F, Cunningham G, Vichinsky EP, Lubin BH, Witkowska HE, Matsunaga A, Azimi M, Sherwin J, Eastman J, Farina F, Waye JS, Chui DH.

Genet Test. 2001 Summer;5(2):93-100.


Characterization of glycated hemoglobin in diabetic patients: usefulness of electrospray mass spectrometry in monitoring the extent and distribution of glycation.

Zhang X, Medzihradszky KF, Cunningham J, Lee PD, Rognerud CL, Ou CN, Harmatz P, Witkowska HE.

J Chromatogr B Biomed Sci Appl. 2001 Aug 5;759(1):1-15.


Fetal expression of a human Agamma globin transgene rescues globin chain imbalance but not hemolysis in EKLF null mouse embryos.

Perkins AC, Peterson KR, Stamatoyannopoulos G, Witkowska HE, Orkin SH.

Blood. 2000 Mar 1;95(5):1827-33.


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