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William Old

TitleAsst Professor
InstitutionUniversity of Colorado Boulder
DepartmentBiology-MCD Instruction
ORCID ORCID Icon0000-0002-9499-8478 Additional info

    Collapse Research 
    Collapse research activities and funding
    R01CA126240     (OLD, WILLIAM MARLAND)Sep 28, 2006 - Jul 31, 2012
    NIH/NCI
    COMPUTATIONAL TOOLS FOR CANCER PROTEOMICS
    Role: Principal Investigator
    R01CA155453     (OLD, WILLIAM MARLAND)Sep 1, 2011 - Jul 31, 2016
    NIH/NCI
    A New Model of Peptide Fragmentation for Improved Protein Identification and Targ
    Role: Principal Investigator
    R21CA175448     (OLD, WILLIAM MARLAND)Jan 1, 2014 - Dec 31, 2015
    NIH/NCI
    Comprehensive Identification of CDK8 Kinase Targets Using SILAC Phosphoproteomics
    Role: Principal Investigator
    R21CA205912     (TAATJES, DYLAN J)Apr 1, 2016 - Mar 31, 2018
    NIH/NCI
    Mediator Kinases and AML Cell Proliferation
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Ball KA, Webb KJ, Coleman SJ, Cozzolino KA, Jacobsen J, Jones KR, Stowell MHB, Old WM. An isothermal shift assay for proteome scale drug-target identification. Commun Biol. 2020 Feb 14; 3(1):75. PMID: 32060372.
      View in: PubMed
    2. Park JD, Moon K, Miller C, Rose J, Xu F, Ebmeier CC, Jacobsen JR, Mao D, Old WM, DeShazer D, Seyedsayamdost MR. Thailandenes, Cryptic Polyene Natural Products Isolated from Burkholderia thailandensis Using Phenotype-Guided Transposon Mutagenesis. ACS Chem Biol. 2020 Jan 02. PMID: 31816232.
      View in: PubMed
    3. Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD. Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome. Elife. 2019 12 09; 8. PMID: 31815667.
      View in: PubMed
    4. Kawaguchi T, Rollins MG, Moinpour M, Morera AA, Ebmeier CC, Old WM, Schwartz JC. Changes to the TDP-43 and FUS Interactomes Induced by DNA Damage. J Proteome Res. 2020 Jan 03; 19(1):360-370. PMID: 31693373.
      View in: PubMed
    5. Miles M, Bhattacharjee B, Sridhar N, Fajrial AK, Ball K, Lee YC, Stowell MHB, Old WM, Ding X. Flattening of Diluted Species Profile via Passive Geometry in a Microfluidic Device. Micromachines (Basel). 2019 Nov 30; 10(12). PMID: 31801276.
      View in: PubMed
    6. Guard SE, Ebmeier CC, Old WM. Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling. J Vis Exp. 2019 Nov 17; (153). PMID: 31789314.
      View in: PubMed
    7. Kim J, Flood JJ, Kristofich MR, Gidfar C, Morgenthaler AB, Fuhrer T, Sauer U, Snyder D, Cooper VS, Ebmeier CC, Old WM, Copley SD. Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB. Proc Natl Acad Sci U S A. 2019 11 26; 116(48):24164-24173. PMID: 31712440.
      View in: PubMed
    8. Guard SE, Poss ZC, Ebmeier CC, Pagratis M, Simpson H, Taatjes DJ, Old WM. The nuclear interactome of DYRK1A reveals a functional role in DNA damage repair. Sci Rep. 2019 Apr 25; 9(1):6539. PMID: 31024071.
      View in: PubMed
    9. Chapnick DA, Bunker E, Liu X, Old WM. Temporal Metabolite, Ion, and Enzyme Activity Profiling Using Fluorescence Microscopy and Genetically Encoded Biosensors. Methods Mol Biol. 2019; 1978:343-353. PMID: 31119673.
      View in: PubMed
    10. Fu X, Sokolova V, Webb KJ, Old W, Park S. Ubiquitin-dependent switch during assembly of the proteasomal ATPases mediated by Not4 ubiquitin ligase. Proc Natl Acad Sci U S A. 2018 12 26; 115(52):13246-13251. PMID: 30530678.
      View in: PubMed
    11. Hoyer MJ, Chitwood PJ, Ebmeier CC, Striepen JF, Qi RZ, Old WM, Voeltz GK. A Novel Class of ER Membrane Proteins Regulates ER-Associated Endosome Fission. Cell. 2018 09 20; 175(1):254-265.e14. PMID: 30220460.
      View in: PubMed
    12. Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genet. 2018 08; 14(8):e1007615. PMID: 30148850.
      View in: PubMed
    13. Stabell AC, Meyerson NR, Gullberg RC, Gilchrist AR, Webb KJ, Old WM, Perera R, Sawyer SL. Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir. Elife. 2018 03 20; 7. PMID: 29557779.
      View in: PubMed
    14. Basken J, Stuart SA, Kavran AJ, Lee T, Ebmeier CC, Old WM, Ahn NG. Specificity of Phosphorylation Responses to Mitogen Activated Protein (MAP) Kinase Pathway Inhibitors in Melanoma Cells. Mol Cell Proteomics. 2018 04; 17(4):550-564. PMID: 29255136.
      View in: PubMed
    15. Adams DJ, Nemkov TG, Mayer JP, Old WM, Stowell MHB. Identification of the primary peptide contaminant that inhibits fibrillation and toxicity in synthetic amyloid-ß42. PLoS One. 2017; 12(8):e0182804. PMID: 28792968.
      View in: PubMed
    16. 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. Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications. Cell Rep. 2017 08 01; 20(5):1173-1186. PMID: 28768201.
      View in: PubMed
    17. Kershner JP, Yu McLoughlin S, Kim J, Morgenthaler A, Ebmeier CC, Old WM, Copley SD. A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate. J Bacteriol. 2016 10 15; 198(20):2853-63. PMID: 27501982.
      View in: PubMed
    18. Poss ZC, Ebmeier CC, Odell AT, Tangpeerachaikul A, Lee T, Pelish HE, Shair MD, Dowell RD, Old WM, Taatjes DJ. Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics. Cell Rep. 2016 Apr 12; 15(2):436-50. PMID: 27050516.
      View in: PubMed
    19. Brown R, Stuart SA, Houel S, Ahn NG, Old WM. Erratum to: Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss During Collision Induced Dissociation. J Am Soc Mass Spectrom. 2015 Oct; 26(10):1796. PMID: 26169511.
      View in: PubMed
    20. Volkov VA, Grissom PM, Arzhanik VK, Zaytsev AV, Renganathan K, McClure-Begley T, Old WM, Ahn N, McIntosh JR. Centromere protein F includes two sites that couple efficiently to depolymerizing microtubules. J Cell Biol. 2015 Jun 22; 209(6):813-28. PMID: 26101217.
      View in: PubMed
    21. Brown R, Stuart SA, Stuart SS, Houel S, Ahn NG, Old WM. Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation. J Am Soc Mass Spectrom. 2015 Jul; 26(7):1128-42. PMID: 25851653.
      View in: PubMed
    22. Stuart SA, Houel S, Lee T, Wang N, Old WM, Ahn NG. A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells. Mol Cell Proteomics. 2015 Jun; 14(6):1599-615. PMID: 25850435.
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    23. Long J, Tokhunts R, Old WM, Houel S, Rodgriguez-Blanco J, Singh S, Schilling N, J Capobianco A, Ahn NG, Robbins DJ. Identification of a family of fatty-acid-speciated sonic hedgehog proteins, whose members display differential biological properties. Cell Rep. 2015 Mar 03; 10(8):1280-1287. PMID: 25732819.
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    24. Nichols CM, Old WM, Lineberger WC, Bierbaum VM. Gas-phase acidities of nitrated azoles as determined by the extended kinetic method and computations. J Phys Chem A. 2015 Jan 15; 119(2):395-402. PMID: 25521708.
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    25. Lee T, Wang N, Houel S, Couts K, Old W, Ahn N. Dosage and temporal thresholds in microRNA proteomics. Mol Cell Proteomics. 2015 Feb; 14(2):289-302. PMID: 25467838.
      View in: PubMed
    26. Marholz LJ, Chang L, Old WM, Wang X. Development of substrate-selective probes for affinity pulldown of histone demethylases. ACS Chem Biol. 2015 Jan 16; 10(1):129-37. PMID: 25335116.
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    27. Avena JS, Burns S, Yu Z, Ebmeier CC, Old WM, Jaspersen SL, Winey M. Licensing of yeast centrosome duplication requires phosphoregulation of sfi1. PLoS Genet. 2014 Oct; 10(10):e1004666. PMID: 25340401.
      View in: PubMed
    28. Subramanian V, Dubini A, Astling DP, Laurens LM, Old WM, Grossman AR, Posewitz MC, Seibert M. Profiling Chlamydomonas metabolism under dark, anoxic H2-producing conditions using a combined proteomic, transcriptomic, and metabolomic approach. J Proteome Res. 2014 Dec 05; 13(12):5431-51. PMID: 25333711.
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    29. Ponicsan SL, Houel S, Old WM, Ahn NG, Goodrich JA, Kugel JF. The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II. J Mol Biol. 2013 Oct 09; 425(19):3625-38. PMID: 23416138.
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    30. Meyer-Arendt K, Old WM, Houel S, Renganathan K, Eichelberger B, Resing KA, Ahn NG. IsoformResolver: A peptide-centric algorithm for protein inference. J Proteome Res. 2011 Jul 01; 10(7):3060-75. PMID: 21599010.
      View in: PubMed
    31. Yen CY, Houel S, Ahn NG, Old WM. Spectrum-to-spectrum searching using a proteome-wide spectral library. Mol Cell Proteomics. 2011 Jul; 10(7):M111.007666. PMID: 21532008.
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    32. Chatterjea SM, Resing KA, Old W, Nirunsuksiri W, Fleckman P. Optimization of filaggrin expression and processing in cultured rat keratinocytes. J Dermatol Sci. 2011 Jan; 61(1):51-9. PMID: 21146962.
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    33. Houel S, Abernathy R, Renganathan K, Meyer-Arendt K, Ahn NG, Old WM. Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. J Proteome Res. 2010 Aug 06; 9(8):4152-60. PMID: 20578722.
      View in: PubMed
    34. Wang W, Yang Y, Gao Y, Xu Q, Wang F, Zhu S, Old W, Resing K, Ahn N, Lei M, Liu X. Structural and mechanistic insights into Mps1 kinase activation. J Cell Mol Med. 2009 Aug; 13(8B):1679-94. PMID: 19120698.
      View in: PubMed
    35. 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. Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma. Mol Cell. 2009 Apr 10; 34(1):115-31. PMID: 19362540.
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    36. Holinger EP, Old WM, Giddings TH, Wong C, Yates JR, Winey M. Budding yeast centrosome duplication requires stabilization of Spc29 via Mps1-mediated phosphorylation. J Biol Chem. 2009 May 08; 284(19):12949-55. PMID: 19269975.
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    37. Yen CY, Meyer-Arendt K, Eichelberger B, Sun S, Houel S, Old WM, Knight R, Ahn NG, Hunter LE, Resing KA. A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins. Mol Cell Proteomics. 2009 Apr; 8(4):857-69. PMID: 19106086.
      View in: PubMed
    38. Xu Q, Zhu S, Wang W, Zhang X, Old W, Ahn N, Liu X. Regulation of kinetochore recruitment of two essential mitotic spindle checkpoint proteins by Mps1 phosphorylation. Mol Biol Cell. 2009 Jan; 20(1):10-20. PMID: 18923149.
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    39. Witze ES, Old WM, Resing KA, Ahn NG. Mapping protein post-translational modifications with mass spectrometry. Nat Methods. 2007 Oct; 4(10):798-806. PMID: 17901869.
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    40. Mattison CP, Old WM, Steiner E, Huneycutt BJ, Resing KA, Ahn NG, Winey M. Mps1 activation loop autophosphorylation enhances kinase activity. J Biol Chem. 2007 Oct 19; 282(42):30553-61. PMID: 17728254.
      View in: PubMed
    41. Ahn NG, Shabb JB, Old WM, Resing KA. Achieving in-depth proteomics profiling by mass spectrometry. ACS Chem Biol. 2007 Jan 23; 2(1):39-52. PMID: 17243782.
      View in: PubMed
    42. Sun S, Meyer-Arendt K, Eichelberger B, Brown R, Yen CY, Old WM, Pierce K, Cios KJ, Ahn NG, Resing KA. Improved validation of peptide MS/MS assignments using spectral intensity prediction. Mol Cell Proteomics. 2007 Jan; 6(1):1-17. PMID: 17018520.
      View in: PubMed
    43. 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. Analysis of membrane proteins from human chronic myelogenous leukemia cells: comparison of extraction methods for multidimensional LC-MS/MS. J Proteome Res. 2006 Mar; 5(3):709-19. PMID: 16512687.
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    44. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics. 2005 Oct; 4(10):1487-502. PMID: 15979981.
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    45. 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. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem. 2004 Jul 01; 76(13):3556-68. PMID: 15228325.
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    46. Russell SA, Old W, Resing KA, Hunter L. Proteomic informatics. Int Rev Neurobiol. 2004; 61:127-57. PMID: 15482814.
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    47. Pacheco TR, Bellus GA, Oreskovich NM, Talbert J, Old W, Fain PR. Exclusion of candidate genes and loci for multiple lentigines syndrome. J Invest Dermatol. 2002 Aug; 119(2):535-8. PMID: 12190883.
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    48. 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. Mapping of an autoimmunity susceptibility locus (AIS1) to chromosome 1p31.3-p32.2. Hum Mol Genet. 2002 Mar 15; 11(6):661-7. PMID: 11912181.
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    49. Thulin CD, Savage JR, McLaughlin JN, Truscott SM, Old WM, Ahn NG, Resing KA, Hamm HE, Bitensky MW, Willardson BM. Modulation of the G protein regulator phosducin by Ca2+/calmodulin-dependent protein kinase II phosphorylation and 14-3-3 protein binding. J Biol Chem. 2001 Jun 29; 276(26):23805-15. PMID: 11331285.
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    50. McMillen DA, Old WM, Bleibaum JL, Nicolet CM, Resing KR, Sarath G, Yadav SP. Job compensation in the biotechnology core laboratory. Nat Biotechnol. 2000 Jun; 18(6):686-9. PMID: 10835613.
      View in: PubMed
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