Philip R. Gafken, Ph.D. - Publications

2000 Oregon State University, Corvallis, OR 
Biochemistry, Analytical Chemistry

36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.


Year Citation  Score
2016 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, et al. Biomarker Panel for Chronic Graft-Versus-Host Disease. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. PMID 27217465 DOI: 10.1200/JCO.2015.65.9615  1
2016 Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE. Proteomics-driven antigen discovery for development of vaccines against gonorrhea. Molecular & Cellular Proteomics : McP. PMID 27141096 DOI: 10.1074/mcp.M116.058800  1
2016 Rajkovic A, Hummels KR, Witzky A, Erickson S, Gafken PR, Whitelegge JP, Faull KF, Kearns DB, Ibba M. Translation control of swarming proficiency in Bacillus subtilis by 5-amino-pentanolylated elongation factor P. The Journal of Biological Chemistry. PMID 27002156 DOI: 10.1074/jbc.M115.712091  1
2016 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. Proteomic characterization reveals that MMP-3 correlates with bronchiolitis obliterans syndrome following allogeneic hematopoietic cell and lung transplantation. American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons. PMID 26887344 DOI: 10.1111/ajt.13750  1
2015 Dancy BC, Chen SW, Drechsler R, Gafken PR, Olsen CP. 13C- and 15N-Labeling Strategies Combined with Mass Spectrometry Comprehensively Quantify Phospholipid Dynamics in C. elegans. Plos One. 10: e0141850. PMID 26528916 DOI: 10.1371/journal.pone.0141850  1
2015 Rajkovic A, Erickson S, Witzky A, Branson OE, Seo J, Gafken PR, Frietas MA, Whitelegge JP, Faull KF, Navarre W, Darwin AJ, Ibba M. Cyclic Rhamnosylated Elongation Factor P Establishes Antibiotic Resistance in Pseudomonas aeruginosa. Mbio. 6: e00823. PMID 26060278 DOI: 10.1128/mBio.00823-15  1
2014 Vogel WK, Gafken PR, Leid M, Filtz TM. Kinetic analysis of BCL11B multisite phosphorylation-dephosphorylation and coupled sumoylation in primary thymocytes by multiple reaction monitoring mass spectroscopy. Journal of Proteome Research. 13: 5860-8. PMID 25423098 DOI: 10.1021/pr5007697  1
2014 Thayer NH, Leverich CK, Fitzgibbon MP, Nelson ZW, Henderson KA, Gafken PR, Hsu JJ, Gottschling DE. Identification of long-lived proteins retained in cells undergoing repeated asymmetric divisions. Proceedings of the National Academy of Sciences of the United States of America. 111: 14019-26. PMID 25228775 DOI: 10.1073/pnas.1416079111  1
2014 Zielke RA, Gafken PR, Sikora AE. Quantitative proteomic analysis of the cell envelopes and native membrane vesicles derived from gram-negative bacteria. Current Protocols in Microbiology. 34: 1F.3.1-16. PMID 25082006 DOI: 10.1002/9780471729259.mc01f03s34  1
2014 Zielke RA, Wierzbicki IH, Weber JV, Gafken PR, Sikora AE. Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets. Molecular & Cellular Proteomics : McP. 13: 1299-317. PMID 24607996 DOI: 10.1074/mcp.M113.029538  1
2014 Bajaj G, Hau AM, Hsu P, Gafken PR, Schimerlik MI, Ishmael JE. Identification of an atypical calcium-dependent calmodulin binding site on the C-terminal domain of GluN2A. Biochemical and Biophysical Research Communications. 444: 588-94. PMID 24491550 DOI: 10.1016/j.bbrc.2014.01.111  1
2014 Flood-Nichols SK, Kazanjian AA, Tinnemore D, Gafken PR, Ogata Y, Napolitano PG, Stallings JD, Ippolito DL. Aberrant glycosylation of plasma proteins in severe preeclampsia promotes monocyte adhesion. Reproductive Sciences (Thousand Oaks, Calif.). 21: 204-14. PMID 23757314 DOI: 10.1177/1933719113492210  1
2013 Jones KA, Kim PD, Patel BB, Kelsen SG, Braverman A, Swinton DJ, Gafken PR, Jones LA, Lane WS, Neveu JM, Leung HC, Shaffer SA, Leszyk JD, Stanley BA, Fox TE, et al. Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers. Journal of Proteome Research. 12: 4351-65. PMID 24004147 DOI: 10.1021/pr400307u  1
2012 Pan S, Chen R, Brand RE, Hawley S, Tamura Y, Gafken PR, Milless BP, Goodlett DR, Rush J, Brentnall TA. Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. Journal of Proteome Research. 11: 1937-48. PMID 22316387 DOI: 10.1021/pr201117w  1
2011 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, et al. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nature Biotechnology. 29: 625-34. PMID 21685906 DOI: 10.1038/nbt.1900  1
2011 Thompson S, Pearson AN, Ashley MD, Jessick V, Murphy BM, Gafken P, Henshall DC, Morris KT, Simon RP, Meller R. Identification of a novel Bcl-2-interacting mediator of cell death (Bim) E3 ligase, tripartite motif-containing protein 2 (TRIM2), and its role in rapid ischemic tolerance-induced neuroprotection Journal of Biological Chemistry. 286: 19331-19339. PMID 21478148 DOI: 10.1074/jbc.M110.197707  1
2011 Sherwood CAH, Gafken PR, Martin DB. Collision energy optimization of b- and y-ions for multiple reaction Monitoring mass spectrometry Journal of Proteome Research. 10: 231-240. PMID 20968307 DOI: 10.1021/pr1004289  1
2010 Morrish F, Noonan J, Perez-Olsen C, Gafken PR, Fitzgibbon M, Kelleher J, VanGilst M, Hockenbery D. Myc-dependent mitochondrial generation of acetyl-CoA contributes to fatty acid biosynthesis and histone acetylation during cell cycle entry. The Journal of Biological Chemistry. 285: 36267-74. PMID 20813845 DOI: 10.1074/jbc.M110.141606  1
2010 Unnikrishnan A, Gafken PR, Tsukiyama T. Dynamic changes in histone acetylation regulate origins of DNA replication. Nature Structural & Molecular Biology. 17: 430-7. PMID 20228802 DOI: 10.1038/nsmb.1780  1
2009 Gafken PR. An overview of the qualitative analysis of phosphoproteins by mass spectrometry. Methods in Molecular Biology (Clifton, N.J.). 527: 159-72, ix. PMID 19241012 DOI: 10.1007/978-1-60327-834-8_12  1
2009 Zhang LJ, Liu X, Gafken PR, Kioussi C, Leid M. 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). The Journal of Biological Chemistry. 284: 6156-68. PMID 19112178 DOI: 10.1074/jbc.M807713200  1
2008 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. Ubiquitin proteasome-mediated synaptic reorganization: a novel mechanism underlying rapid ischemic tolerance. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 28: 50-9. PMID 18171922 DOI: 10.1523/JNEUROSCI.3474-07.2008  1
2008 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. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. Journal of Proteome Research. 7: 96-103. PMID 17711323 DOI: 10.1021/pr070244j  1
2007 Solan JL, Marquez-Rosado L, Sorgen PL, Thornton PJ, Gafken PR, Lampe PD. Phosphorylation at S365 is a gatekeeper event that changes the structure of Cx43 and prevents down-regulation by PKC. The Journal of Cell Biology. 179: 1301-9. PMID 18086922 DOI: 10.1083/jcb.200707060  1
2007 Gafken PR, Doneanu CE, Bennett SE, Barofsky DF. Comparison of ESI-MS interfaces for the analysis of UV-crosslinked peptide-nucleic acid complexes. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 860: 145-52. PMID 18042442 DOI: 10.1016/j.jchromb.2007.09.029  1
2007 Katzenellenbogen RA, Egelkrout EM, Vliet-Gregg P, Gewin LC, Gafken PR, Galloway DA. NFX1-123 and poly(A) binding proteins synergistically augment activation of telomerase in human papillomavirus type 16 E6-expressing cells. Journal of Virology. 81: 3786-96. PMID 17267499 DOI: 10.1128/JVI.02007-06  1
2006 Gafken PR, Lampe PD. Methodologies for characterizing phosphoproteins by mass spectrometry. Cell Communication & Adhesion. 13: 249-62. PMID 17162667 DOI: 10.1080/15419060601077917  1
2006 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. Ultrasensitive detection and characterization of posttranslational modifications using surface-enhanced Raman spectroscopy. Analytical Chemistry. 78: 3543-50. PMID 16737206 DOI: 10.1021/ac051525i  1
2006 Knoepfler PS, Zhang XY, Cheng PF, Gafken PR, McMahon SB, Eisenman RN. Myc influences global chromatin structure. The Embo Journal. 25: 2723-34. PMID 16724113 DOI: 10.1038/sj.emboj.7601152  1
2005 Mitchell BL, Yasui Y, Lampe JW, Gafken PR, Lampe PD. Evaluation of matrix-assisted laser desorption/ionization-time of flight mass spectrometry proteomic profiling: identification of alpha 2-HS glycoprotein B-chain as a biomarker of diet. Proteomics. 5: 2238-46. PMID 15841498 DOI: 10.1002/pmic.200401099  1
2004 Doneanu CE, Gafken PR, Bennett SE, Barofsky DF. Mass spectrometry of UV-cross-linked protein-nucleic acid complexes: identification of amino acid residues in the single-stranded DNA-binding domain of human replication protein A. Analytical Chemistry. 76: 5667-76. PMID 15456284 DOI: 10.1021/ac049547c  1
2004 Farr CD, Gafken PR, Norbeck AD, Doneanu CE, Stapels MD, Barofsky DF, Minami M, Saugstad JA. Proteomic analysis of native metabotropic glutamate receptor 5 protein complexes reveals novel molecular constituents. Journal of Neurochemistry. 91: 438-50. PMID 15447677 DOI: 10.1111/j.1471-4159.2004.02735.x  1
2004 McKittrick E, Gafken PR, Ahmad K, Henikoff S. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proceedings of the National Academy of Sciences of the United States of America. 101: 1525-30. PMID 14732680 DOI: 10.1073/pnas.0308092100  1
2003 Smith CM, Gafken PR, Zhang Z, Gottschling DE, Smith JB, Smith DL. Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4. Analytical Biochemistry. 316: 23-33. PMID 12694723 DOI: 10.1016/S0003-2697(03)00032-0  1
2002 van Leeuwen F, Gafken PR, Gottschling DE. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell. 109: 745-56. PMID 12086673 DOI: 10.1016/S0092-8674(02)00759-6  1
2002 Doneanu CE, Gafken PR, Barofsky DF. Mass spectrometric analysis of UV-crosslinked protein-nucleic acid complexes: Identification of amino acid residues in the single-stranded dna binding domain of human replication protein a Proceedings 50th Asms Conference On Mass Spectrometry and Allied Topics. 467-468.  1
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