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Activity-based Protein Profiling Approaches for Transplantation.

Navarrete M, Wilkins JA, Lao Y, Rush DN, Nickerson PW, Ho J.

Transplantation. 2019 Sep;103(9):1790-1798. doi: 10.1097/TP.0000000000002752.


Activity-Based Protein Profiling of Intraoperative Serine Hydrolase Activities during Cardiac Surgery.

Navarrete M, Ho J, Dwivedi RC, Choi N, Ezzati P, Spicer V, Arora RC, Rigatto C, Wilkins JA.

J Proteome Res. 2018 Oct 5;17(10):3547-3556. doi: 10.1021/acs.jproteome.8b00500. Epub 2018 Sep 19.


Interferon γ induced compositional changes in human bone marrow derived mesenchymal stem/stromal cells.

Guan Q, Ezzati P, Spicer V, Krokhin O, Wall D, Wilkins JA.

Clin Proteomics. 2017 Jul 6;14:26. doi: 10.1186/s12014-017-9161-1. eCollection 2017.


New developments in transplant proteomics.

Ho J, Hirt-Minkowski P, Wilkins JA.

Curr Opin Nephrol Hypertens. 2017 May;26(3):229-234. doi: 10.1097/MNH.0000000000000319. Review.


The integrin PSI domain has an endogenous thiol isomerase function and is a novel target for antiplatelet therapy.

Zhu G, Zhang Q, Reddy EC, Carrim N, Chen Y, Xu XR, Xu M, Wang Y, Hou Y, Ma L, Li Y, Rui M, Petruzziello-Pellegrini TN, Lavalle C, Stratton TW, Lei X, Adili R, Chen P, Zhu C, Wilkins JA, Hynes RO, Freedman J, Ni H.

Blood. 2017 Mar 30;129(13):1840-1854. doi: 10.1182/blood-2016-07-729400. Epub 2017 Jan 25.


A proteomic evaluation of urinary changes associated with cardiopulmonary bypass.

Dwivedi RC, Navarrete M, Choi N, Spicer V, Rigatto C, Arora RC, Krokhin O, Ho J, Wilkins JA.

Clin Proteomics. 2016 Aug 15;13:17. doi: 10.1186/s12014-016-9118-9. eCollection 2016.


Elevated Urinary Matrix Metalloproteinase-7 Detects Underlying Renal Allograft Inflammation and Injury.

Ho J, Rush DN, Krokhin O, Antonovici M, Gao A, Bestland J, Wiebe C, Hiebert B, Rigatto C, Gibson IW, Wilkins JA, Nickerson PW.

Transplantation. 2016 Mar;100(3):648-54. doi: 10.1097/TP.0000000000000867.


3D HPLC-MS with Reversed-Phase Separation Functionality in All Three Dimensions for Large-Scale Bottom-Up Proteomics and Peptide Retention Data Collection.

Spicer V, Ezzati P, Neustaeter H, Beavis RC, Wilkins JA, Krokhin OV.

Anal Chem. 2016 Mar 1;88(5):2847-55. doi: 10.1021/acs.analchem.5b04567. Epub 2016 Feb 18.


Phosphatidylinositol-3,4-Bisphosphate and Its Binding Protein Lamellipodin Regulate Chemotaxis of Malignant B Lymphocytes.

Li H, Wu X, Hou S, Malek M, Kielkowska A, Noh E, Makondo KJ, Du Q, Wilkins JA, Johnston JB, Gibson SB, Lin F, Marshall AJ.

J Immunol. 2016 Jan 15;196(2):586-95. doi: 10.4049/jimmunol.1500630. Epub 2015 Dec 22.


Development of an SRM method for absolute quantitation of MYDGF/C19orf10 protein.

Dwivedi RC, Krokhin OV, El-Gabalawy HS, Wilkins JA.

Proteomics Clin Appl. 2016 Jun;10(6):663-70. doi: 10.1002/prca.201500057. Epub 2015 Dec 15.


Identification of broadly conserved cross-species protective Leishmania antigen and its responding CD4+ T cells.

Mou Z, Li J, Boussoffara T, Kishi H, Hamana H, Ezzati P, Hu C, Yi W, Liu D, Khadem F, Okwor I, Jia P, Shitaoka K, Wang S, Ndao M, Petersen C, Chen J, Rafati S, Louzir H, Muraguchi A, Wilkins JA, Uzonna JE.

Sci Transl Med. 2015 Oct 21;7(310):310ra167. doi: 10.1126/scitranslmed.aac5477.


Effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in Pseudomonas putida LS46.

Fu J, Sharma P, Spicer V, Krokhin OV, Zhang X, Fristensky B, Wilkins JA, Cicek N, Sparling R, Levin DB.

Appl Microbiol Biotechnol. 2015 Jul;99(13):5583-92. doi: 10.1007/s00253-015-6685-z. Epub 2015 May 23.


Podocalyxin enhances breast tumor growth and metastasis and is a target for monoclonal antibody therapy.

Snyder KA, Hughes MR, Hedberg B, Brandon J, Hernaez DC, Bergqvist P, Cruz F, Po K, Graves ML, Turvey ME, Nielsen JS, Wilkins JA, McColl SR, Babcook JS, Roskelley CD, McNagny KM.

Breast Cancer Res. 2015 Mar 27;17:46. doi: 10.1186/s13058-015-0562-7.


Towards further defining the proteome of mouse saliva.

Blanchard AA, Ezzati P, Shamshurin D, Nistor AC, Leygue E, Wilkins JA, Myal Y.

Proteome Sci. 2015 Feb 25;13:10. doi: 10.1186/s12953-015-0068-3. eCollection 2015.


N-capping motifs promote interaction of amphipathic helical peptides with hydrophobic surfaces and drastically alter hydrophobicity values of individual amino acids.

Spicer V, Lao YW, Shamshurin D, Ezzati P, Wilkins JA, Krokhin OV.

Anal Chem. 2014 Dec 2;86(23):11498-502. doi: 10.1021/ac503352h. Epub 2014 Nov 10.


Whole cell, label free protein quantitation with data independent acquisition: quantitation at the MS2 level.

McQueen P, Spicer V, Schellenberg J, Krokhin O, Sparling R, Levin D, Wilkins JA.

Proteomics. 2015 Jan;15(1):16-24. doi: 10.1002/pmic.201400188. Epub 2014 Dec 10.


Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca.

Vanee N, Brooks JP, Spicer V, Shamshurin D, Krokhin O, Wilkins JA, Deng Y, Fong SS.

BMC Syst Biol. 2014 Aug 13;8:86. doi: 10.1186/s12918-014-0086-2.


Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics.

Schellenberg JJ, Verbeke TJ, McQueen P, Krokhin OV, Zhang X, Alvare G, Fristensky B, Thallinger GG, Henrissat B, Wilkins JA, Levin DB, Sparling R.

BMC Genomics. 2014 Jul 7;15:567. doi: 10.1186/1471-2164-15-567.


Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum.

Rydzak T, Grigoryan M, Cunningham ZJ, Krokhin OV, Ezzati P, Cicek N, Levin DB, Wilkins JA, Sparling R.

Appl Microbiol Biotechnol. 2014;98(14):6497-510. doi: 10.1007/s00253-014-5798-0. Epub 2014 May 20.


Thermoanaerobacter thermohydrosulfuricus WC1 shows protein complement stability during fermentation of key lignocellulose-derived substrates.

Verbeke TJ, Spicer V, Krokhin OV, Zhang X, Schellenberg JJ, Fristensky B, Wilkins JA, Levin DB, Sparling R.

Appl Environ Microbiol. 2014 Mar;80(5):1602-15. doi: 10.1128/AEM.03555-13. Epub 2013 Dec 20.


Proteomic characterization of serine hydrolase activity and composition in normal urine.

Navarrete M, Ho J, Krokhin O, Ezzati P, Rigatto C, Reslerova M, Rush DN, Nickerson P, Wilkins JA.

Clin Proteomics. 2013 Nov 15;10(1):17. doi: 10.1186/1559-0275-10-17.


Knockdown of specific host factors protects against influenza virus-induced cell death.

Tran AT, Rahim MN, Ranadheera C, Kroeker A, Cortens JP, Opanubi KJ, Wilkins JA, Coombs KM.

Cell Death Dis. 2013 Aug 15;4:e769. doi: 10.1038/cddis.2013.296.


Quantification of the host response proteome after mammalian reovirus T1L infection.

Berard AR, Cortens JP, Krokhin O, Wilkins JA, Severini A, Coombs KM.

PLoS One. 2012;7(12):e51939. doi: 10.1371/journal.pone.0051939. Epub 2012 Dec 11.


Influenza virus induces apoptosis via BAD-mediated mitochondrial dysregulation.

Tran AT, Cortens JP, Du Q, Wilkins JA, Coombs KM.

J Virol. 2013 Jan;87(2):1049-60. doi: 10.1128/JVI.02017-12. Epub 2012 Nov 7.


Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression.

Rydzak T, McQueen PD, Krokhin OV, Spicer V, Ezzati P, Dwivedi RC, Shamshurin D, Levin DB, Wilkins JA, Sparling R.

BMC Microbiol. 2012 Sep 21;12:214. doi: 10.1186/1471-2180-12-214.


Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: case study using a whole cell digest of Clostridium thermocellum.

McQueen P, Spicer V, Rydzak T, Sparling R, Levin D, Wilkins JA, Krokhin O.

Proteomics. 2012 Apr;12(8):1160-9. doi: 10.1002/pmic.201100425.


Functional interaction of CD154 protein with α5β1 integrin is totally independent from its binding to αIIbβ3 integrin and CD40 molecules.

El Fakhry Y, Alturaihi H, Yacoub D, Liu L, Guo W, Leveillé C, Jung D, Khzam LB, Merhi Y, Wilkins JA, Li H, Mourad W.

J Biol Chem. 2012 May 25;287(22):18055-66. doi: 10.1074/jbc.M111.333989. Epub 2012 Mar 29.


Granzyme B inhibits vaccinia virus production through proteolytic cleavage of eukaryotic initiation factor 4 gamma 3.

Marcet-Palacios M, Duggan BL, Shostak I, Barry M, Geskes T, Wilkins JA, Yanagiya A, Sonenberg N, Bleackley RC.

PLoS Pathog. 2011 Dec;7(12):e1002447. doi: 10.1371/journal.ppat.1002447. Epub 2011 Dec 15.


Mitochondrial dysfunction resulting from the absence of mitochondrial porin in Neurospora crassa.

Summers WA, Wilkins JA, Dwivedi RC, Ezzati P, Court DA.

Mitochondrion. 2012 Mar;12(2):220-9. doi: 10.1016/j.mito.2011.09.002. Epub 2011 Sep 18.


IQGAP1 involvement in MTOC and granule polarization in NK-cell cytotoxicity.

Kanwar N, Wilkins JA.

Eur J Immunol. 2011 Sep;41(9):2763-73. doi: 10.1002/eji.201040444. Epub 2011 Aug 3.


Requirement of podocalyxin in TGF-beta induced epithelial mesenchymal transition.

Meng X, Ezzati P, Wilkins JA.

PLoS One. 2011 Apr 12;6(4):e18715. doi: 10.1371/journal.pone.0018715.


Relaxin enhances the collagenolytic activity and in vitro invasiveness by upregulating matrix metalloproteinases in human thyroid carcinoma cells.

Bialek J, Kunanuvat U, Hombach-Klonisch S, Spens A, Stetefeld J, Sunley K, Lippert D, Wilkins JA, Hoang-Vu C, Klonisch T.

Mol Cancer Res. 2011 Jun;9(6):673-87. doi: 10.1158/1541-7786.MCR-10-0411. Epub 2011 Apr 14.


Focal adhesion kinase is required for intestinal regeneration and tumorigenesis downstream of Wnt/c-Myc signaling.

Ashton GH, Morton JP, Myant K, Phesse TJ, Ridgway RA, Marsh V, Wilkins JA, Athineos D, Muncan V, Kemp R, Neufeld K, Clevers H, Brunton V, Winton DJ, Wang X, Sears RC, Clarke AR, Frame MC, Sansom OJ.

Dev Cell. 2010 Aug 17;19(2):259-69. doi: 10.1016/j.devcel.2010.07.015.


p53 mutation and loss have different effects on tumourigenesis in a novel mouse model of pleomorphic rhabdomyosarcoma.

Doyle B, Morton JP, Delaney DW, Ridgway RA, Wilkins JA, Sansom OJ.

J Pathol. 2010 Oct;222(2):129-37. doi: 10.1002/path.2748.


Dynamics of plasma proteome during leptin-replacement therapy in genetically based leptin deficiency.

Andreev VP, Dwivedi RC, Paz-Filho G, Krokhin OV, Wong ML, Wilkins JA, Licinio J.

Pharmacogenomics J. 2011 Jun;11(3):174-90. doi: 10.1038/tpj.2010.30. Epub 2010 May 11.


Investigating the role of P311 in the hypertrophic scar.

Tan J, Peng X, Luo G, Ma B, Cao C, He W, Yuan S, Li S, Wilkins JA, Wu J.

PLoS One. 2010 Apr 9;5(4):e9995. doi: 10.1371/journal.pone.0009995.


Assessment of the reproducibility of random hexapeptide peptide library-based protein normalization.

Dwivedi RC, Krokhin OV, Cortens JP, Wilkins JA.

J Proteome Res. 2010 Feb 5;9(2):1144-9. doi: 10.1021/pr900608z.


Defining the membrane proteome of NK cells.

Ghosh D, Lippert D, Krokhin O, Cortens JP, Wilkins JA.

J Mass Spectrom. 2010 Jan;45(1):1-25. doi: 10.1002/jms.1696.


Prenatal alcohol exposure alters phosphorylation and glycosylation of proteins in rat offspring liver.

Fofana B, Yao XH, Rampitsch C, Cloutier S, Wilkins JA, Nyomba BL.

Proteomics. 2010 Feb;10(3):417-34. doi: 10.1002/pmic.200800969.


Rab5 mediates caspase-8-promoted cell motility and metastasis.

Torres VA, Mielgo A, Barbero S, Hsiao R, Wilkins JA, Stupack DG.

Mol Biol Cell. 2010 Jan 15;21(2):369-76. doi: 10.1091/mbc.E09-09-0769. Epub 2009 Nov 18.


TAPP2 links phosphoinositide 3-kinase signaling to B-cell adhesion through interaction with the cytoskeletal protein utrophin: expression of a novel cell adhesion-promoting complex in B-cell leukemia.

Costantini JL, Cheung SM, Hou S, Li H, Kung SK, Johnston JB, Wilkins JA, Gibson SB, Marshall AJ.

Blood. 2009 Nov 19;114(21):4703-12. doi: 10.1182/blood-2009-03-213058. Epub 2009 Sep 28.


The effects of infliximab therapy on the serum proteome of rheumatoid arthritis patients.

Dwivedi RC, Dhindsa N, Krokhin OV, Cortens J, Wilkins JA, El-Gabalawy HS.

Arthritis Res Ther. 2009;11(2):R32. doi: 10.1186/ar2637. Epub 2009 Mar 6.


PPP1R9B (Neurabin 2): involvement and dynamics in the NK immunological synapse.

Meng X, Kanwar N, Du Q, Goping IS, Bleackley RC, Wilkins JA.

Eur J Immunol. 2009 Feb;39(2):552-60. doi: 10.1002/eji.200838474.


B-catenin deficiency, but not Myc deletion, suppresses the immediate phenotypes of APC loss in the liver.

Reed KR, Athineos D, Meniel VS, Wilkins JA, Ridgway RA, Burke ZD, Muncan V, Clarke AR, Sansom OJ.

Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18919-23. doi: 10.1073/pnas.0805778105. Epub 2008 Nov 24. Erratum in: Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1168.


Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics.

Dwivedi RC, Spicer V, Harder M, Antonovici M, Ens W, Standing KG, Wilkins JA, Krokhin OV.

Anal Chem. 2008 Sep 15;80(18):7036-42. doi: 10.1021/ac800984n. Epub 2008 Aug 8.


C-Myc is a critical mediator of the phenotypes of Apc loss in the intestine.

Wilkins JA, Sansom OJ.

Cancer Res. 2008 Jul 1;68(13):4963-6. doi: 10.1158/0008-5472.CAN-07-5558. Review.


Proteomics and renal transplantation: searching for novel biomarkers and therapeutic targets.

Schaub S, Wilkins JA, Nickerson P.

Contrib Nephrol. 2008;160:65-75. doi: 10.1159/000125934. Review.


The identification and characterization of membranome components.

Ghosh D, Beavis RC, Wilkins JA.

J Proteome Res. 2008 Apr;7(4):1572-83. doi: 10.1021/pr070509u. Epub 2008 Feb 22.


Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns.

Spicer V, Yamchuk A, Cortens J, Sousa S, Ens W, Standing KG, Wilkins JA, Krokhin OV.

Anal Chem. 2007 Nov 15;79(22):8762-8. Epub 2007 Oct 16.


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