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Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB.

Kim J, Flood JJ, Kristofich MR, Gidfar C, Morgenthaler AB, Fuhrer T, Sauer U, Snyder D, Cooper VS, Ebmeier CC, Old WM, Copley SD.

Proc Natl Acad Sci U S A. 2019 Nov 11. pii: 201915569. doi: 10.1073/pnas.1915569116. [Epub ahead of print]


Changes to the TDP-43 and FUS Interactomes Induced by DNA Damage.

Kawaguchi T, Rollins MG, Moinpour M, Morera AA, Ebmeier CC, Old WM, Schwartz JC.

J Proteome Res. 2019 Nov 6. doi: 10.1021/acs.jproteome.9b00575. [Epub ahead of print]


Temporal Metabolite, Ion, and Enzyme Activity Profiling Using Fluorescence Microscopy and Genetically Encoded Biosensors.

Chapnick DA, Bunker E, Liu X, Old WM.

Methods Mol Biol. 2019;1978:343-353. doi: 10.1007/978-1-4939-9236-2_21.


The nuclear interactome of DYRK1A reveals a functional role in DNA damage repair.

Guard SE, Poss ZC, Ebmeier CC, Pagratis M, Simpson H, Taatjes DJ, Old WM.

Sci Rep. 2019 Apr 25;9(1):6539. doi: 10.1038/s41598-019-42990-5.


Ubiquitin-dependent switch during assembly of the proteasomal ATPases mediated by Not4 ubiquitin ligase.

Fu X, Sokolova V, Webb KJ, Old W, Park S.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):13246-13251. doi: 10.1073/pnas.1805353115. Epub 2018 Dec 10.


A Novel Class of ER Membrane Proteins Regulates ER-Associated Endosome Fission.

Hoyer MJ, Chitwood PJ, Ebmeier CC, Striepen JF, Qi RZ, Old WM, Voeltz GK.

Cell. 2018 Sep 20;175(1):254-265.e14. doi: 10.1016/j.cell.2018.08.030. Epub 2018 Sep 13.


Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme.

Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD.

PLoS Genet. 2018 Aug 27;14(8):e1007615. doi: 10.1371/journal.pgen.1007615. eCollection 2018 Aug.


Smoking abstinence 1 year after acute coronary syndrome: follow-up from a randomized controlled trial of varenicline in patients admitted to hospital.

Windle SB, Dehghani P, Roy N, Old W, Grondin FR, Bata I, Iskander A, Lauzon C, Srivastava N, Clarke A, Cassavar D, Dion D, Haught H, Mehta SR, Baril JF, Lambert C, Madan M, Abramson BL, Eisenberg MJ; EVITA Investigators.

CMAJ. 2018 Mar 26;190(12):E347-E354. doi: 10.1503/cmaj.170377.


Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir.

Stabell AC, Meyerson NR, Gullberg RC, Gilchrist AR, Webb KJ, Old WM, Perera R, Sawyer SL.

Elife. 2018 Mar 20;7. pii: e31919. doi: 10.7554/eLife.31919.


Specificity of Phosphorylation Responses to Mitogen Activated Protein (MAP) Kinase Pathway Inhibitors in Melanoma Cells.

Basken J, Stuart SA, Kavran AJ, Lee T, Ebmeier CC, Old WM, Ahn NG.

Mol Cell Proteomics. 2018 Apr;17(4):550-564. doi: 10.1074/mcp.RA117.000335. Epub 2017 Dec 18.


Identification of the primary peptide contaminant that inhibits fibrillation and toxicity in synthetic amyloid-β42.

Adams DJ, Nemkov TG, Mayer JP, Old WM, Stowell MHB.

PLoS One. 2017 Aug 9;12(8):e0182804. doi: 10.1371/journal.pone.0182804. eCollection 2017.


Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications.

Ebmeier CC, Erickson B, Allen BL, Allen MA, Kim H, Fong N, Jacobsen JR, Liang K, Shilatifard A, Dowell RD, Old WM, Bentley DL, Taatjes DJ.

Cell Rep. 2017 Aug 1;20(5):1173-1186. doi: 10.1016/j.celrep.2017.07.021.


Smokers and Postcessation Weight Gain After Acute Coronary Syndrome.

Dehghani P, Habib B, Windle SB, Roy N, Old W, Grondin FR, Bata I, Iskander A, Lauzon C, Srivastava N, Clarke A, Cassavar D, Dion D, Haught H, Mehta SR, Baril JF, Lambert C, Madan M, Abramson BL, Eisenberg MJ.

J Am Heart Assoc. 2017 Apr 18;6(4). pii: e004785. doi: 10.1161/JAHA.116.004785.


A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate.

Kershner JP, Yu McLoughlin S, Kim J, Morgenthaler A, Ebmeier CC, Old WM, Copley SD.

J Bacteriol. 2016 Sep 22;198(20):2853-63. doi: 10.1128/JB.00262-16. Print 2016 Oct 15.


Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics.

Poss ZC, Ebmeier CC, Odell AT, Tangpeerachaikul A, Lee T, Pelish HE, Shair MD, Dowell RD, Old WM, Taatjes DJ.

Cell Rep. 2016 Apr 12;15(2):436-50. doi: 10.1016/j.celrep.2016.03.030. Epub 2016 Mar 31.


Varenicline for Smoking Cessation in Hospitalized Patients With Acute Coronary Syndrome.

Eisenberg MJ, Windle SB, Roy N, Old W, Grondin FR, Bata I, Iskander A, Lauzon C, Srivastava N, Clarke A, Cassavar D, Dion D, Haught H, Mehta SR, Baril JF, Lambert C, Madan M, Abramson BL, Dehghani P; EVITA Investigators.

Circulation. 2016 Jan 5;133(1):21-30. doi: 10.1161/CIRCULATIONAHA.115.019634. Epub 2015 Nov 9.


Erratum to: Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss During Collision Induced Dissociation.

Brown R, Stuart SA, Houel S, Ahn NG, Old WM.

J Am Soc Mass Spectrom. 2015 Oct;26(10):1796. doi: 10.1007/s13361-015-1222-y. No abstract available.


Centromere protein F includes two sites that couple efficiently to depolymerizing microtubules.

Volkov VA, Grissom PM, Arzhanik VK, Zaytsev AV, Renganathan K, McClure-Begley T, Old WM, Ahn N, McIntosh JR.

J Cell Biol. 2015 Jun 22;209(6):813-28. doi: 10.1083/jcb.201408083.


Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation.

Brown R, Stuart SA, Houel S, Ahn NG, Old WM.

J Am Soc Mass Spectrom. 2015 Jul;26(7):1128-42. doi: 10.1007/s13361-015-1109-y. Epub 2015 Apr 8. Erratum in: J Am Soc Mass Spectrom. 2015 Oct;26(10):1796. Stuart, Scott S [corrected to Stuart, Scott A].


A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells.

Stuart SA, Houel S, Lee T, Wang N, Old WM, Ahn NG.

Mol Cell Proteomics. 2015 Jun;14(6):1599-615. doi: 10.1074/mcp.M114.047233. Epub 2015 Apr 7.


Identification of a family of fatty-acid-speciated sonic hedgehog proteins, whose members display differential biological properties.

Long J, Tokhunts R, Old WM, Houel S, Rodgriguez-Blanco J, Singh S, Schilling N, J Capobianco A, Ahn NG, Robbins DJ.

Cell Rep. 2015 Mar 3;10(8):1280-1287. doi: 10.1016/j.celrep.2015.01.058. Epub 2015 Feb 26.


Gas-phase acidities of nitrated azoles as determined by the extended kinetic method and computations.

Nichols CM, Old WM, Lineberger WC, Bierbaum VM.

J Phys Chem A. 2015 Jan 15;119(2):395-402. doi: 10.1021/jp5110533. Epub 2014 Dec 31.


Dosage and temporal thresholds in microRNA proteomics.

Lee T, Wang N, Houel S, Couts K, Old W, Ahn N.

Mol Cell Proteomics. 2015 Feb;14(2):289-302. doi: 10.1074/mcp.M114.043851. Epub 2014 Dec 2.


Licensing of yeast centrosome duplication requires phosphoregulation of sfi1.

Avena JS, Burns S, Yu Z, Ebmeier CC, Old WM, Jaspersen SL, Winey M.

PLoS Genet. 2014 Oct 23;10(10):e1004666. doi: 10.1371/journal.pgen.1004666. eCollection 2014 Oct.


Development of substrate-selective probes for affinity pulldown of histone demethylases.

Marholz LJ, Chang L, Old WM, Wang X.

ACS Chem Biol. 2015 Jan 16;10(1):129-37. doi: 10.1021/cb5006867. Epub 2014 Oct 29.


Profiling Chlamydomonas metabolism under dark, anoxic H2-producing conditions using a combined proteomic, transcriptomic, and metabolomic approach.

Subramanian V, Dubini A, Astling DP, Laurens LM, Old WM, Grossman AR, Posewitz MC, Seibert M.

J Proteome Res. 2014 Dec 5;13(12):5431-51. doi: 10.1021/pr500342j. Epub 2014 Oct 21.


Identification of global ferredoxin interaction networks in Chlamydomonas reinhardtii.

Peden EA, Boehm M, Mulder DW, Davis R, Old WM, King PW, Ghirardi ML, Dubini A.

J Biol Chem. 2013 Dec 6;288(49):35192-209. doi: 10.1074/jbc.M113.483727. Epub 2013 Oct 7.


The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II.

Ponicsan SL, Houel S, Old WM, Ahn NG, Goodrich JA, Kugel JF.

J Mol Biol. 2013 Oct 9;425(19):3625-38. doi: 10.1016/j.jmb.2013.01.035. Epub 2013 Feb 8.


IsoformResolver: A peptide-centric algorithm for protein inference.

Meyer-Arendt K, Old WM, Houel S, Renganathan K, Eichelberger B, Resing KA, Ahn NG.

J Proteome Res. 2011 Jul 1;10(7):3060-75. doi: 10.1021/pr200039p. Epub 2011 Jun 7.


Spectrum-to-spectrum searching using a proteome-wide spectral library.

Yen CY, Houel S, Ahn NG, Old WM.

Mol Cell Proteomics. 2011 Jul;10(7):M111.007666. doi: 10.1074/mcp.M111.007666. Epub 2011 Apr 30.


Optimization of filaggrin expression and processing in cultured rat keratinocytes.

Chatterjea SM, Resing KA, Old W, Nirunsuksiri W, Fleckman P.

J Dermatol Sci. 2011 Jan;61(1):51-9. doi: 10.1016/j.jdermsci.2010.11.003. Epub 2010 Nov 13.


Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies.

Houel S, Abernathy R, Renganathan K, Meyer-Arendt K, Ahn NG, Old WM.

J Proteome Res. 2010 Aug 6;9(8):4152-60. doi: 10.1021/pr1003856.


Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma.

Old WM, Shabb JB, Houel S, Wang H, Couts KL, Yen CY, Litman ES, Croy CH, Meyer-Arendt K, Miranda JG, Brown RA, Witze ES, Schweppe RE, Resing KA, Ahn NG.

Mol Cell. 2009 Apr 10;34(1):115-31. doi: 10.1016/j.molcel.2009.03.007.


Budding yeast centrosome duplication requires stabilization of Spc29 via Mps1-mediated phosphorylation.

Holinger EP, Old WM, Giddings TH Jr, Wong C, Yates JR 3rd, Winey M.

J Biol Chem. 2009 May 8;284(19):12949-55. doi: 10.1074/jbc.M900088200. Epub 2009 Mar 5.


Structural and mechanistic insights into Mps1 kinase activation.

Wang W, Yang Y, Gao Y, Xu Q, Wang F, Zhu S, Old W, Resing K, Ahn N, Lei M, Liu X.

J Cell Mol Med. 2009 Aug;13(8B):1679-94. doi: 10.1111/j.1582-4934.2008.00605.x.


A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins.

Yen CY, Meyer-Arendt K, Eichelberger B, Sun S, Houel S, Old WM, Knight R, Ahn NG, Hunter LE, Resing KA.

Mol Cell Proteomics. 2009 Apr;8(4):857-69. doi: 10.1074/mcp.M800384-MCP200. Epub 2008 Dec 22.


Regulation of kinetochore recruitment of two essential mitotic spindle checkpoint proteins by Mps1 phosphorylation.

Xu Q, Zhu S, Wang W, Zhang X, Old W, Ahn N, Liu X.

Mol Biol Cell. 2009 Jan;20(1):10-20. doi: 10.1091/mbc.E08-03-0324. Epub 2008 Oct 15.


Mapping protein post-translational modifications with mass spectrometry.

Witze ES, Old WM, Resing KA, Ahn NG.

Nat Methods. 2007 Oct;4(10):798-806. Review.


Mps1 activation loop autophosphorylation enhances kinase activity.

Mattison CP, Old WM, Steiner E, Huneycutt BJ, Resing KA, Ahn NG, Winey M.

J Biol Chem. 2007 Oct 19;282(42):30553-61. Epub 2007 Aug 28.


Achieving in-depth proteomics profiling by mass spectrometry.

Ahn NG, Shabb JB, Old WM, Resing KA.

ACS Chem Biol. 2007 Jan 23;2(1):39-52. Review.


Improved validation of peptide MS/MS assignments using spectral intensity prediction.

Sun S, Meyer-Arendt K, Eichelberger B, Brown R, Yen CY, Old WM, Pierce K, Cios KJ, Ahn NG, Resing KA.

Mol Cell Proteomics. 2007 Jan;6(1):1-17. Epub 2006 Oct 2.


Analysis of membrane proteins from human chronic myelogenous leukemia cells: comparison of extraction methods for multidimensional LC-MS/MS.

Ruth MC, Old WM, Emrick MA, Meyer-Arendt K, Aveline-Wolf LD, Pierce KG, Mendoza AM, Sevinsky JR, Hamady M, Knight RD, Resing KA, Ahn NG.

J Proteome Res. 2006 Mar;5(3):709-19.


Comparison of label-free methods for quantifying human proteins by shotgun proteomics.

Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG.

Mol Cell Proteomics. 2005 Oct;4(10):1487-502. Epub 2005 Jun 23.


Proteomic informatics.

Russell SA, Old W, Resing KA, Hunter L.

Int Rev Neurobiol. 2004;61:127-57. Review. No abstract available.


Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics.

Resing KA, Meyer-Arendt K, Mendoza AM, Aveline-Wolf LD, Jonscher KR, Pierce KG, Old WM, Cheung HT, Russell S, Wattawa JL, Goehle GR, Knight RD, Ahn NG.

Anal Chem. 2004 Jul 1;76(13):3556-68.


Exclusion of candidate genes and loci for multiple lentigines syndrome.

Pacheco TR, Bellus GA, Oreskovich NM, Talbert J, Old W, Fain PR.

J Invest Dermatol. 2002 Aug;119(2):535-8. No abstract available.


Risk-directed immunosuppression in heart transplant recipients: maintenance prednisone can be avoided in selected patients.

Arnold AN, Huffman M, Eich DM, Bernstein RC, Old WD, Mooney M, Szentpetery S, Hagberg R, McGrath M, Rich J, Herre JM, Barnhart GR.

Transplant Proc. 2002 Aug;34(5):1830-3. No abstract available.


Mapping of an autoimmunity susceptibility locus (AIS1) to chromosome 1p31.3-p32.2.

Alkhateeb A, Stetler GL, Old W, Talbert J, Uhlhorn C, Taylor M, Fox A, Miller C, Dills DG, Ridgway EC, Bennett DC, Fain PR, Spritz RA.

Hum Mol Genet. 2002 Mar 15;11(6):661-7.


Modulation of the G protein regulator phosducin by Ca2+/calmodulin-dependent protein kinase II phosphorylation and 14-3-3 protein binding.

Thulin CD, Savage JR, McLaughlin JN, Truscott SM, Old WM, Ahn NG, Resing KA, Hamm HE, Bitensky MW, Willardson BM.

J Biol Chem. 2001 Jun 29;276(26):23805-15. Epub 2001 Apr 30.


Job compensation in the biotechnology core laboratory.

McMillen DA, Old WM, Bleibaum JL, Nicolet CM, Resing KR, Sarath G, Yadav SP.

Nat Biotechnol. 2000 Jun;18(6):686-9. No abstract available.


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