Philip R Gafken

Philip R Gafken

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Philip R Gafken

Philip R Gafken

Publications by authors named "Philip R Gafken"

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40Publications

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

ACS Chem Biol 2019 07 17;14(7):1564-1572. Epub 2019 Jun 17.

Oregon State University , Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences , Corvallis , Oregon 97331 , United States.

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http://dx.doi.org/10.1021/acschembio.9b00307DOI Listing
July 2019

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

Elife 2019 01 15;8. Epub 2019 Jan 15.

Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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http://dx.doi.org/10.7554/eLife.41740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349399PMC
January 2019

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

Mol Microbiol 2018 10 28;110(1):114-127. Epub 2018 Sep 28.

Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA.

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http://dx.doi.org/10.1111/mmi.14087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195823PMC
October 2018

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

Cell Rep 2017 06;19(12):2432-2440

Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.05.081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538132PMC
June 2017

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

Cell Rep 2017 04;19(1):162-174

Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.03.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423785PMC
April 2017

Biomarker Panel for Chronic Graft-Versus-Host Disease.

J Clin Oncol 2016 08 23;34(22):2583-90. Epub 2016 May 23.

Jeffrey Yu, Kushi Kushekhar, Mohammad Abu Zaid, and Sophie Paczesny, Indiana University School of Medicine, Indianapolis, IN; Barry E. Storer, Paul J. Martin, Mary E. Flowers, John A. Hansen, Stephanie J. Lee, Qing Zhang, Philip R. Gafken, and Yuko Ogata, Fred Hutchinson Cancer Research Center; Barry E. Storer, University of Washington School of Medicine, Seattle, WA; Mukta Arora, University of Minnesota, Minneapolis, MN; Corey Cutler, Dana-Farber Cancer Institute, Boston, MA; Madan Jagasia, Vanderbilt University, Nashville, TN; Joseph Pidala, H. Lee Moffitt Cancer Center, Tampa, FL; Betty K. Hamilton, Cleveland Clinic Foundation, Cleveland, OH; George L. Chen, Roswell Park Cancer Institute, Buffalo, NY; and Iskra Pusic, Washington University School of Medicine, St Louis, MO.

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http://dx.doi.org/10.1200/JCO.2015.65.9615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012688PMC
August 2016

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

Mol Cell Proteomics 2016 07 2;15(7):2338-55. Epub 2016 May 2.

From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon;

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http://dx.doi.org/10.1074/mcp.M116.058800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937508PMC
July 2016

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

PLoS One 2015 3;10(11):e0141850. Epub 2015 Nov 3.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141850PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631354PMC
June 2016

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

J Biol Chem 2016 May 21;291(21):10976-85. Epub 2016 Mar 21.

From the Molecular, Cellular, and Developmental Biology Program and Center for RNA Biology and Microbiology, Ohio State University, Columbus, Ohio 43210,

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http://dx.doi.org/10.1074/jbc.M115.712091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4900249PMC
May 2016

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

J Proteome Res 2014 Dec 25;13(12):5860-8. Epub 2014 Nov 25.

Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University , Corvallis, Oregon 97331, United States.

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http://pubs.acs.org/doi/10.1021/pr5007697
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http://dx.doi.org/10.1021/pr5007697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4261940PMC
December 2014

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

Proc Natl Acad Sci U S A 2014 Sep 16;111(39):14019-26. Epub 2014 Sep 16.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and

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http://dx.doi.org/10.1073/pnas.1416079111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191815PMC
September 2014

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

Curr Protoc Microbiol 2014 Aug 1;34:1F.3.1-16. Epub 2014 Aug 1.

Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon.

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http://dx.doi.org/10.1002/9780471729259.mc01f03s34DOI Listing
August 2014

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

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

1Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Madigan Army Medical Center, Tacoma, WA, USA.

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http://dx.doi.org/10.1177/1933719113492210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879990PMC
February 2014

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

Biochem Biophys Res Commun 2014 Feb 31;444(4):588-94. Epub 2014 Jan 31.

Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2014.01.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385326PMC
February 2014

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

J Proteome Res 2012 Mar 8;11(3):1937-48. Epub 2012 Feb 8.

Department of Medicine, University of Washington , Seattle, Washington 98195, United States.

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http://dx.doi.org/10.1021/pr201117wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3292708PMC
March 2012

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

J Proteome Res 2011 Jan 22;10(1):231-40. Epub 2010 Nov 22.

Institute for Systems Biology, Seattle, Washington 98103, USA.

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http://dx.doi.org/10.1021/pr1004289DOI Listing
January 2011

Dynamic changes in histone acetylation regulate origins of DNA replication.

Nat Struct Mol Biol 2010 Apr 14;17(4):430-7. Epub 2010 Mar 14.

Divison of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nsmb.1780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060656PMC
April 2010

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

Authors:
Philip R Gafken

Methods Mol Biol 2009 ;527:159-72, ix

Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-60327-834-8_12DOI Listing
May 2009

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

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

Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States.

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http://dx.doi.org/10.1016/j.jchromb.2007.09.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238692PMC
December 2007

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

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

Molecular Diagnostics Program and 2Proteomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://www.jcb.org/lookup/doi/10.1083/jcb.200707060
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http://dx.doi.org/10.1083/jcb.200707060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2140020PMC
December 2007

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

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

Fred Hutchinson Cancer Research Center, and Department of Pediatrics, University of Washington, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1128/JVI.02007-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866132PMC
April 2007

Methodologies for characterizing phosphoproteins by mass spectrometry.

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

Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1080/15419060601077917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2185548PMC
March 2007

Myc influences global chromatin structure.

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

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-4417, USA.

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http://dx.doi.org/10.1038/sj.emboj.7601152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500848PMC
June 2006

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.

Anal Chem 2004 Oct;76(19):5667-76

Department of Chemistry, Department of Environmental & Molecular Toxicology, and Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331 USA.

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http://dx.doi.org/10.1021/ac049547cDOI Listing
October 2004

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

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

Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1073/pnas.0308092100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC341768PMC
February 2004

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

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

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1016/s0003-2697(03)00032-0DOI Listing
May 2003

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

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

Division of Basic Sciences and Proteomics Facility, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1073/pnas.182424999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC139908PMC
December 2002

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

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

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1016/s0092-8674(02)00759-6DOI Listing
June 2002