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Items: 41

1.

A Highly Versatile Expression System for the Production of Multiply Phosphorylated Proteins.

Zhu P, Gafken PR, Mehl RA, Cooley RB.

ACS Chem Biol. 2019 Jul 19;14(7):1564-1572. doi: 10.1021/acschembio.9b00307. Epub 2019 Jun 17.

PMID:
31243963
2.

Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of facioscapulohumeral muscular dystrophy.

Jagannathan S, Ogata Y, Gafken PR, Tapscott SJ, Bradley RK.

Elife. 2019 Jan 15;8. pii: e41740. doi: 10.7554/eLife.41740.

3.

The Helicobacter pylori cell shape promoting protein Csd5 interacts with the cell wall, MurF, and the bacterial cytoskeleton.

Blair KM, Mears KS, Taylor JA, Fero J, Jones LA, Gafken PR, Whitney JC, Salama NR.

Mol Microbiol. 2018 Oct;110(1):114-127. doi: 10.1111/mmi.14087. Epub 2018 Sep 28.

4.

Murine chronic graft-versus-host disease proteome profiling discovers CCL15 as a novel biomarker in patients.

Du J, Flynn R, Paz K, Ren HG, Ogata Y, Zhang Q, Gafken PR, Storer BE, Roy NH, Burkhardt JK, Mathews W, Tolar J, Lee SJ, Blazar BR, Paczesny S.

Blood. 2018 Apr 12;131(15):1743-1754. doi: 10.1182/blood-2017-08-800623. Epub 2018 Jan 18.

5.

Ubiquitination-Linked Phosphorylation of the FANCI S/TQ Cluster Contributes to Activation of the Fanconi Anemia I/D2 Complex.

Cheung RS, Castella M, Abeyta A, Gafken PR, Tucker N, Taniguchi T.

Cell Rep. 2017 Jun 20;19(12):2432-2440. doi: 10.1016/j.celrep.2017.05.081.

6.

DGCR8 Mediates Repair of UV-Induced DNA Damage Independently of RNA Processing.

Calses PC, Dhillon KK, Tucker N, Chi Y, Huang JW, Kawasumi M, Nghiem P, Wang Y, Clurman BE, Jacquemont C, Gafken PR, Sugasawa K, Saijo M, Taniguchi T.

Cell Rep. 2017 Apr 4;19(1):162-174. doi: 10.1016/j.celrep.2017.03.021.

7.

Biomarker Panel for Chronic Graft-Versus-Host Disease.

Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S.

J Clin Oncol. 2016 Aug 1;34(22):2583-90. doi: 10.1200/JCO.2015.65.9615. Epub 2016 May 23.

8.

Proteomics-driven Antigen Discovery for Development of Vaccines Against Gonorrhea.

Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE.

Mol Cell Proteomics. 2016 Jul;15(7):2338-55. doi: 10.1074/mcp.M116.058800. Epub 2016 May 2.

9.

Translation Control of Swarming Proficiency in Bacillus subtilis by 5-Amino-pentanolylated Elongation Factor P.

Rajkovic A, Hummels KR, Witzky A, Erickson S, Gafken PR, Whitelegge JP, Faull KF, Kearns DB, Ibba M.

J Biol Chem. 2016 May 20;291(21):10976-85. doi: 10.1074/jbc.M115.712091. Epub 2016 Mar 21.

10.

Proteomic Characterization Reveals That MMP-3 Correlates With Bronchiolitis Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung Transplantation.

Liu X, Yue Z, Yu J, Daguindau E, Kushekhar K, Zhang Q, Ogata Y, Gafken PR, Inamoto Y, Gracon A, Wilkes DS, Hansen JA, Lee SJ, Chen JY, Paczesny S.

Am J Transplant. 2016 Aug;16(8):2342-51. doi: 10.1111/ajt.13750. Epub 2016 Mar 14.

11.

13C- and 15N-Labeling Strategies Combined with Mass Spectrometry Comprehensively Quantify Phospholipid Dynamics in C. elegans.

Dancy BC, Chen SW, Drechsler R, Gafken PR, Olsen CP.

PLoS One. 2015 Nov 3;10(11):e0141850. doi: 10.1371/journal.pone.0141850. eCollection 2015.

12.

Cyclic Rhamnosylated Elongation Factor P Establishes Antibiotic Resistance in Pseudomonas aeruginosa.

Rajkovic A, Erickson S, Witzky A, Branson OE, Seo J, Gafken PR, Frietas MA, Whitelegge JP, Faull KF, Navarre W, Darwin AJ, Ibba M.

MBio. 2015 Jun 9;6(3):e00823. doi: 10.1128/mBio.00823-15.

13.

Kinetic analysis of BCL11B multisite phosphorylation-dephosphorylation and coupled sumoylation in primary thymocytes by multiple reaction monitoring mass spectroscopy.

Vogel WK, Gafken PR, Leid M, Filtz TM.

J Proteome Res. 2014 Dec 5;13(12):5860-8. doi: 10.1021/pr5007697. Epub 2014 Nov 25.

14.

Identification of long-lived proteins retained in cells undergoing repeated asymmetric divisions.

Thayer NH, Leverich CK, Fitzgibbon MP, Nelson ZW, Henderson KA, Gafken PR, Hsu JJ, Gottschling DE.

Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):14019-26. doi: 10.1073/pnas.1416079111. Epub 2014 Sep 16.

15.

Quantitative proteomic analysis of the cell envelopes and native membrane vesicles derived from gram-negative bacteria.

Zielke RA, Gafken PR, Sikora AE.

Curr Protoc Microbiol. 2014 Aug 1;34:1F.3.1-16. doi: 10.1002/9780471729259.mc01f03s34.

PMID:
25082006
16.

Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets.

Zielke RA, Wierzbicki IH, Weber JV, Gafken PR, Sikora AE.

Mol Cell Proteomics. 2014 May;13(5):1299-317. doi: 10.1074/mcp.M113.029538. Epub 2014 Mar 8.

17.

Identification of an atypical calcium-dependent calmodulin binding site on the C-terminal domain of GluN2A.

Bajaj G, Hau AM, Hsu P, Gafken PR, Schimerlik MI, Ishmael JE.

Biochem Biophys Res Commun. 2014 Feb 21;444(4):588-94. doi: 10.1016/j.bbrc.2014.01.111. Epub 2014 Jan 31.

18.

Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers.

Jones KA, Kim PD, Patel BB, Kelsen SG, Braverman A, Swinton DJ, Gafken PR, Jones LA, Lane WS, Neveu JM, Leung HE, Shaffer SA, Leszyk JD, Stanley BA, Fox TE, Stanley A, Hall MJ, Hampel H, South CD, de la Chapelle A, Burt RW, Jones DA, Kopelovich L, Yeung AT.

J Proteome Res. 2013 Oct 4;12(10):4351-65. doi: 10.1021/pr400307u. Epub 2013 Sep 19.

19.

Aberrant glycosylation of plasma proteins in severe preeclampsia promotes monocyte adhesion.

Flood-Nichols SK, Kazanjian AA, Tinnemore D, Gafken PR, Ogata Y, Napolitano PG, Stallings JD, Ippolito DL.

Reprod Sci. 2014 Feb;21(2):204-14. doi: 10.1177/1933719113492210. Epub 2013 Jun 11.

20.

Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study.

Pan S, Chen R, Brand RE, Hawley S, Tamura Y, Gafken PR, Milless BP, Goodlett DR, Rush J, Brentnall TA.

J Proteome Res. 2012 Mar 2;11(3):1937-48. doi: 10.1021/pr201117w. Epub 2012 Feb 8.

21.

A targeted proteomics-based pipeline for verification of biomarkers in plasma.

Whiteaker JR, Lin C, Kennedy J, Hou L, Trute M, Sokal I, Yan P, Schoenherr RM, Zhao L, Voytovich UJ, Kelly-Spratt KS, Krasnoselsky A, Gafken PR, Hogan JM, Jones LA, Wang P, Amon L, Chodosh LA, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG.

Nat Biotechnol. 2011 Jun 19;29(7):625-34. doi: 10.1038/nbt.1900.

22.

Collision energy optimization of b- and y-ions for multiple reaction monitoring mass spectrometry.

Holstein Sherwood CA, Gafken PR, Martin DB.

J Proteome Res. 2011 Jan 7;10(1):231-40. doi: 10.1021/pr1004289. Epub 2010 Nov 22.

PMID:
20968307
23.

Myc-dependent mitochondrial generation of acetyl-CoA contributes to fatty acid biosynthesis and histone acetylation during cell cycle entry.

Morrish F, Noonan J, Perez-Olsen C, Gafken PR, Fitzgibbon M, Kelleher J, VanGilst M, Hockenbery D.

J Biol Chem. 2010 Nov 19;285(47):36267-74. doi: 10.1074/jbc.M110.141606. Epub 2010 Sep 2. Erratum in: J Biol Chem. 2011 Mar 11;286(10):8708.

24.

Dynamic changes in histone acetylation regulate origins of DNA replication.

Unnikrishnan A, Gafken PR, Tsukiyama T.

Nat Struct Mol Biol. 2010 Apr;17(4):430-7. doi: 10.1038/nsmb.1780. Epub 2010 Mar 14.

25.

An overview of the qualitative analysis of phosphoproteins by mass spectrometry.

Gafken PR.

Methods Mol Biol. 2009;527:159-72, ix. doi: 10.1007/978-1-60327-834-8_12. Review.

PMID:
19241012
26.

A chicken ovalbumin upstream promoter transcription factor I (COUP-TFI) complex represses expression of the gene encoding tumor necrosis factor alpha-induced protein 8 (TNFAIP8).

Zhang LJ, Liu X, Gafken PR, Kioussi C, Leid M.

J Biol Chem. 2009 Mar 6;284(10):6156-68. doi: 10.1074/jbc.M807713200. Epub 2008 Dec 26.

27.

Ubiquitin proteasome-mediated synaptic reorganization: a novel mechanism underlying rapid ischemic tolerance.

Meller R, Thompson SJ, Lusardi TA, Ordonez AN, Ashley MD, Jessick V, Wang W, Torrey DJ, Henshall DC, Gafken PR, Saugstad JA, Xiong ZG, Simon RP.

J Neurosci. 2008 Jan 2;28(1):50-9. doi: 10.1523/JNEUROSCI.3474-07.2008.

28.

Phosphorylation at S365 is a gatekeeper event that changes the structure of Cx43 and prevents down-regulation by PKC.

Solan JL, Marquez-Rosado L, Sorgen PL, Thornton PJ, Gafken PR, Lampe PD.

J Cell Biol. 2007 Dec 17;179(6):1301-9.

29.

Comparison of ESI-MS interfaces for the analysis of UV-crosslinked peptide-nucleic acid complexes.

Gafken PR, Doneanu CE, Bennett SE, Barofsky DF.

J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Dec 15;860(2):145-52. Epub 2007 Sep 29.

30.

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.

Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB.

J Proteome Res. 2008 Jan;7(1):96-103. Epub 2007 Aug 21.

31.

NFX1-123 and poly(A) binding proteins synergistically augment activation of telomerase in human papillomavirus type 16 E6-expressing cells.

Katzenellenbogen RA, Egelkrout EM, Vliet-Gregg P, Gewin LC, Gafken PR, Galloway DA.

J Virol. 2007 Apr;81(8):3786-96. Epub 2007 Jan 31.

32.

Methodologies for characterizing phosphoproteins by mass spectrometry.

Gafken PR, Lampe PD.

Cell Commun Adhes. 2006 Sep-Dec;13(5-6):249-62. Review.

33.

Ultrasensitive detection and characterization of posttranslational modifications using surface-enhanced Raman spectroscopy.

Sundararajan N, Mao D, Chan S, Koo TW, Su X, Sun L, Zhang J, Sung KB, Yamakawa M, Gafken PR, Randolph T, McLerran D, Feng Z, Berlin AA, Roth MB.

Anal Chem. 2006 Jun 1;78(11):3543-50.

PMID:
16737206
34.

Myc influences global chromatin structure.

Knoepfler PS, Zhang XY, Cheng PF, Gafken PR, McMahon SB, Eisenman RN.

EMBO J. 2006 Jun 21;25(12):2723-34. Epub 2006 May 25.

37.

Proteomic analysis of native metabotropic glutamate receptor 5 protein complexes reveals novel molecular constituents.

Farr CD, Gafken PR, Norbeck AD, Doneanu CE, Stapels MD, Barofsky DF, Minami M, Saugstad JA.

J Neurochem. 2004 Oct;91(2):438-50.

38.

Histone H3.3 is enriched in covalent modifications associated with active chromatin.

McKittrick E, Gafken PR, Ahmad K, Henikoff S.

Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1525-30. Epub 2004 Jan 19.

39.

Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4.

Smith CM, Gafken PR, Zhang Z, Gottschling DE, Smith JB, Smith DL.

Anal Biochem. 2003 May 1;316(1):23-33.

PMID:
12694723
40.

Heritable chromatin structure: mapping "memory" in histones H3 and H4.

Smith CM, Haimberger ZW, Johnson CO, Wolf AJ, Gafken PR, Zhang Z, Parthun MR, Gottschling DE.

Proc Natl Acad Sci U S A. 2002 Dec 10;99 Suppl 4:16454-61. Epub 2002 Aug 26.

41.

Dot1p modulates silencing in yeast by methylation of the nucleosome core.

van Leeuwen F, Gafken PR, Gottschling DE.

Cell. 2002 Jun 14;109(6):745-56.

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