W. McDonald
Faculty Member
Last active: 1/26/2016

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Publications

The following timeline graph is generated from all co-authored publications.

Featured publications are shown below:

  1. Antagonistic roles for the ubiquitin ligase Asr1 and the ubiquitin-specific protease Ubp3 in subtelomeric gene silencing. McCann TS, Guo Y, McDonald WH, Tansey WP (2016) Proc Natl Acad Sci U S A 113(5): 1309-14
    › Primary publication · 26787877 (PubMed) · PMC4747757 (PubMed Central)
  2. Molecular and Structural Analysis of the Helicobacter pylori cag Type IV Secretion System Core Complex. Frick-Cheng AE, Pyburn TM, Voss BJ, McDonald WH, Ohi MD, Cover TL (2016) MBio 7(1): e02001-15
    › Primary publication · 26758182 (PubMed) · PMC4725015 (PubMed Central)
  3. Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II. Maklashina E, Rajagukguk S, Starbird CA, McDonald WH, Koganitsky A, Eisenbach M, Iverson TM, Cecchini G (2016) J Biol Chem 291(6): 2904-16
    › Primary publication · 26644464 (PubMed) · PMC4742753 (PubMed Central)
  4. LMO2 Oncoprotein Stability in T-Cell Leukemia Requires Direct LDB1 Binding. Layer JH, Alford CE, McDonald WH, Davé UP (2015) Mol Cell Biol 36(3): 488-506
    › Primary publication · 26598604 (PubMed) · PMC4719424 (PubMed Central)
  5. Growth phase-dependent composition of the Helicobacter pylori exoproteome. Snider CA, Voss BJ, McDonald WH, Cover TL (2016) J Proteomics : 94-107
    › Primary publication · 26363098 (PubMed) · PMC4640983 (PubMed Central)
  6. Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration. Voss BJ, Loh JT, Hill S, Rose KL, McDonald WH, Cover TL (2015) Proteomics Clin Appl 9(11-12): 1021-34
    › Primary publication · 26109032 (PubMed) · PMC4690801 (PubMed Central)
  7. Iron Toxicity in the Retina Requires Alu RNA and the NLRP3 Inflammasome. Gelfand BD, Wright CB, Kim Y, Yasuma T, Yasuma R, Li S, Fowler BJ, Bastos-Carvalho A, Kerur N, Uittenbogaard A, Han YS, Lou D, Kleinman ME, McDonald WH, Núñez G, Georgel P, Dunaief JL, Ambati J (2015) Cell Rep 11(11): 1686-93
    › Primary publication · 26074074 (PubMed) · PMC4481133 (PubMed Central)
  8. P-REX1 creates a positive feedback loop to activate growth factor receptor, PI3K/AKT and MEK/ERK signaling in breast cancer. Dillon LM, Bean JR, Yang W, Shee K, Symonds LK, Balko JM, McDonald WH, Liu S, Gonzalez-Angulo AM, Mills GB, Arteaga CL, Miller TW (2015) Oncogene 34(30): 3968-76
    › Primary publication · 25284585 (PubMed) · PMC4387124 (PubMed Central)
  9. Short forms of Ste20-related proline/alanine-rich kinase (SPAK) in the kidney are created by aspartyl aminopeptidase (Dnpep)-mediated proteolytic cleavage. Markadieu N, Rios K, Spiller BW, McDonald WH, Welling PA, Delpire E (2014) J Biol Chem 289(42): 29273-84
    › Primary publication · 25164821 (PubMed) · PMC4200278 (PubMed Central)
  10. Shotgun proteomics: identification of unique protein profiles of apoptotic bodies from biliary epithelial cells. Lleo A, Zhang W, McDonald WH, Seeley EH, Leung PS, Coppel RL, Ansari AA, Adams DH, Afford S, Invernizzi P, Gershwin ME (2014) Hepatology 60(4): 1314-23
    › Primary publication · 24841946 (PubMed) · PMC4175017 (PubMed Central)
  11. Analysis of surface-exposed outer membrane proteins in Helicobacter pylori. Voss BJ, Gaddy JA, McDonald WH, Cover TL (2014) J Bacteriol 196(13): 2455-71
    › Primary publication · 24769695 (PubMed) · PMC4054173 (PubMed Central)
  12. Sepp1(UF) forms are N-terminal selenoprotein P truncations that have peroxidase activity when coupled with thioredoxin reductase-1. Kurokawa S, Eriksson S, Rose KL, Wu S, Motley AK, Hill S, Winfrey VP, McDonald WH, Capecchi MR, Atkins JF, Arnér ES, Hill KE, Burk RF (2014) Free Radic Biol Med : 67-76
    › Primary publication · 24434121 (PubMed) · PMC3960317 (PubMed Central)
  13. A unique covalent bond in basement membrane is a primordial innovation for tissue evolution. Fidler AL, Vanacore RM, Chetyrkin SV, Pedchenko VK, Bhave G, Yin VP, Stothers CL, Rose KL, McDonald WH, Clark TA, Borza DB, Steele RE, Ivy MT, Aspirnauts, Hudson JK, Hudson BG (2014) Proc Natl Acad Sci U S A 111(1): 331-6
    › Primary publication · 24344311 (PubMed) · PMC3890831 (PubMed Central)
  14. Global phosphotyrosine proteomics identifies PKCδ as a marker of responsiveness to Src inhibition in colorectal cancer. McKinley ET, Liu H, McDonald WH, Luo W, Zhao P, Coffey RJ, Hanks SK, Manning HC (2013) PLoS One 8(11): e80207
    › Primary publication · 24260357 (PubMed) · PMC3832668 (PubMed Central)
  15. Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture. Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX (2014) Mol Cell Proteomics 13(1): 360-71
    › Primary publication · 24187338 (PubMed) · PMC3879627 (PubMed Central)
  16. Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry. Sirbu BM, McDonald WH, Dungrawala H, Badu-Nkansah A, Kavanaugh GM, Chen Y, Tabb DL, Cortez D (2013) J Biol Chem 288(44): 31458-67
    › Primary publication · 24047897 (PubMed) · PMC3814742 (PubMed Central)
  17. Staphylococcus aureus LukAB cytotoxin kills human neutrophils by targeting the CD11b subunit of the integrin Mac-1. DuMont AL, Yoong P, Day CJ, Alonzo F, McDonald WH, Jennings MP, Torres VJ (2013) Proc Natl Acad Sci U S A 110(26): 10794-9
    › Primary publication · 23754403 (PubMed) · PMC3696772 (PubMed Central)
  18. Electrophilic adduction of ubiquitin activating enzyme E1 by N,N-diethyldithiocarbamate inhibits ubiquitin activation and is accompanied by striatal injury in the rat. Viquez OM, Caito SW, McDonald WH, Friedman DB, Valentine WM (2012) Chem Res Toxicol 25(11): 2310-21
    › Primary publication · 22874009 (PubMed) · PMC3502677 (PubMed Central)
  19. Dnt1 acts as a mitotic inhibitor of the spindle checkpoint protein dma1 in fission yeast. Wang Y, Li WZ, Johnson AE, Luo ZQ, Sun XL, Feoktistova A, McDonald WH, McLeod I, Yates JR, Gould KL, McCollum D, Jin QW (2012) Mol Biol Cell 23(17): 3348-56
    › Primary publication · 22809626 (PubMed) · PMC3431938 (PubMed Central)
  20. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A (2012) Curr Biol 22(15): 1403-9
    › Primary publication · 22795693 (PubMed) · PMC3416971 (PubMed Central)
  21. Long isoform mouse selenoprotein P (Sepp1) supplies rat myoblast L8 cells with selenium via endocytosis mediated by heparin binding properties and apolipoprotein E receptor-2 (ApoER2). Kurokawa S, Hill KE, McDonald WH, Burk RF (2012) J Biol Chem 287(34): 28717-26
    › Primary publication · 22761431 (PubMed) · PMC3436540 (PubMed Central)
  22. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, González V, Mavingui P, Zhulin IB (2011) PLoS Genet 7(12): e1002430
    › Primary publication · 22216014 (PubMed) · PMC3245306 (PubMed Central)
  23. Obesity and altered glucose metabolism impact HDL composition in CETP transgenic mice: a role for ovarian hormones. Martinez MN, Emfinger CH, Overton M, Hill S, Ramaswamy TS, Cappel DA, Wu K, Fazio S, McDonald WH, Hachey DL, Tabb DL, Stafford JM (2012) J Lipid Res 53(3): 379-89
    › Primary publication · 22215797 (PubMed) · PMC3276461 (PubMed Central)
  24. Helicobacter pylori exploits a unique repertoire of type IV secretion system components for pilus assembly at the bacteria-host cell interface. Shaffer CL, Gaddy JA, Loh JT, Johnson EM, Hill S, Hennig EE, McClain MS, McDonald WH, Cover TL (2011) PLoS Pathog 7(9): e1002237
    › Primary publication · 21909278 (PubMed) · PMC3164655 (PubMed Central)
  25. Characterization of the MDSC proteome associated with metastatic murine mammary tumors using label-free mass spectrometry and shotgun proteomics. Boutté AM, McDonald WH, Shyr Y, Yang L, Lin PC (2011) PLoS One 6(8): e22446
    › Primary publication · 21853032 (PubMed) · PMC3154190 (PubMed Central)
  26. Glucose autoxidation induces functional damage to proteins via modification of critical arginine residues. Chetyrkin S, Mathis M, Pedchenko V, Sanchez OA, McDonald WH, Hachey DL, Madu H, Stec D, Hudson B, Voziyan P (2011) Biochemistry 50(27): 6102-12
    › Primary publication · 21661747 (PubMed) · PMC3140462 (PubMed Central)
  27. Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle. Panosian TD, Nannemann DP, Watkins GR, Phelan VV, McDonald WH, Wadzinski BE, Bachmann BO, Iverson TM (2011) J Biol Chem 286(10): 8043-54
    › Primary publication · 21193409 (PubMed) · PMC3048691 (PubMed Central)
  28. Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase. Tomasiak TM, Archuleta TL, Andréll J, Luna-Chávez C, Davis TA, Sarwar M, Ham AJ, McDonald WH, Yankovskaya V, Stern HA, Johnston JN, Maklashina E, Cecchini G, Iverson TM (2011) J Biol Chem 286(4): 3047-56
    › Primary publication · 21098488 (PubMed) · PMC3024798 (PubMed Central)
  29. Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site. Roberts-Galbraith RH, Ohi MD, Ballif BA, Chen JS, McLeod I, McDonald WH, Gygi SP, Yates JR, Gould KL (2010) Mol Cell 39(1): 86-99
    › Primary publication · 20603077 (PubMed) · PMC2916701 (PubMed Central)
  30. A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. Pan C, Park BH, McDonald WH, Carey PA, Banfield JF, VerBerkmoes NC, Hettich RL, Samatova NF (2010) BMC Bioinformatics : 118
    › Primary publication · 20205730 (PubMed) · PMC2838866 (PubMed Central)
  31. Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia. Torres VJ, Attia AS, Mason WJ, Hood MI, Corbin BD, Beasley FC, Anderson KL, Stauff DL, McDonald WH, Zimmerman LJ, Friedman DB, Heinrichs DE, Dunman PM, Skaar EP (2010) Infect Immun 78(4): 1618-28
    › Primary publication · 20100857 (PubMed) · PMC2849423 (PubMed Central)
  32. An analysis pipeline for the inference of protein-protein interaction networks. Taylor RC, Singhal M, Daly DS, Gilmore J, Cannon WR, Domico K, White AM, Auberry DL, Auberry KJ, Hooker BS, Hurst G, McDermott JE, McDonald WH, Pelletier DA, Schmoyer D, Wiley HS (2009) Int J Data Min Bioinform 3(4): 409-30
    › Primary publication · 20052905 (PubMed)
  33. Evaluation of affinity-tagged protein expression strategies using local and global isotope ratio measurements. Hervey WJ, Khalsa-Moyers G, Lankford PK, Owens ET, McKeown CK, Lu TY, Foote LJ, Asano KG, Morrell-Falvey JL, McDonald WH, Pelletier DA, Hurst GB (2009) J Proteome Res 8(7): 3675-88
    › Primary publication · 19459691 (PubMed)
  34. Modulation of the structure, catalytic activity, and fidelity of African swine fever virus DNA polymerase X by a reversible disulfide switch. Voehler MW, Eoff RL, McDonald WH, Guengerich FP, Stone MP (2009) J Biol Chem 284(27): 18434-44
    › Primary publication · 19419958 (PubMed) · PMC2709365 (PubMed Central)
  35. A general system for studying protein-protein interactions in Gram-negative bacteria. Pelletier DA, Hurst GB, Foote LJ, Lankford PK, McKeown CK, Lu TY, Schmoyer DD, Shah MB, Hervey WJ, McDonald WH, Hooker BS, Cannon WR, Daly DS, Gilmore JM, Wiley HS, Auberry DL, Wang Y, Larimer FW, Kennel SJ, Doktycz MJ, Morrell-Falvey JL, Owens ET, Buchanan MV (2008) J Proteome Res 7(8): 3319-28
    › Primary publication · 18590317 (PubMed)
  36. The Clp1/Cdc14 phosphatase contributes to the robustness of cytokinesis by association with anillin-related Mid1. Clifford DM, Wolfe BA, Roberts-Galbraith RH, McDonald WH, Yates JR, Gould KL (2008) J Cell Biol 181(1): 79-88
    › Primary publication · 18378776 (PubMed) · PMC2287289 (PubMed Central)
  37. Cross-species global proteomics reveals conserved and unique processes in Phytophthora sojae and Phytophthora ramorum. Savidor A, Donahoo RS, Hurtado-Gonzales O, Land ML, Shah MB, Lamour KH, McDonald WH (2008) Mol Cell Proteomics 7(8): 1501-16
    › Primary publication · 18316789 (PubMed) · PMC2500229 (PubMed Central)
  38. The SBF- and MBF-associated protein Msa1 is required for proper timing of G1-specific transcription in Saccharomyces cerevisiae. Ashe M, de Bruin RA, Kalashnikova T, McDonald WH, Yates JR, Wittenberg C (2008) J Biol Chem 283(10): 6040-9
    › Primary publication · 18160399 (PubMed)
  39. Dual-tagging system for the affinity purification of mammalian protein complexes. Giannone RJ, McDonald WH, Hurst GB, Huang Y, Wu J, Liu Y, Wang Y (2007) Biotechniques 43(3): 296, 298, 300 passim
    › Primary publication · 17907572 (PubMed)
  40. Statistically inferring protein-protein associations with affinity isolation LC-MS/MS assays. Sharp JL, Anderson KK, Hurst GB, Daly DS, Pelletier DA, Cannon WR, Auberry DL, Schmoyer DD, McDonald WH, White AM, Hooker BS, Victry KD, Buchanan MV, Kery V, Wiley HS (2007) J Proteome Res 6(9): 3788-95
    › Primary publication · 17691832 (PubMed)
  41. Expressed peptide tags: an additional layer of data for genome annotation. Savidor A, Donahoo RS, Hurtado-Gonzales O, Verberkmoes NC, Shah MB, Lamour KH, McDonald WH (2006) J Proteome Res 5(11): 3048-58
    › Primary publication · 17081056 (PubMed)
  42. ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. Pan C, Kora G, McDonald WH, Tabb DL, VerBerkmoes NC, Hurst GB, Pelletier DA, Samatova NF, Hettich RL (2006) Anal Chem 78(20): 7121-31
    › Primary publication · 17037911 (PubMed)
  43. Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics. Pan C, Kora G, Tabb DL, Pelletier DA, McDonald WH, Hurst GB, Hettich RL, Samatova NF (2006) Anal Chem 78(20): 7110-20
    › Primary publication · 17037910 (PubMed)
  44. Phosphorylation of Rad55 on serines 2, 8, and 14 is required for efficient homologous recombination in the recovery of stalled replication forks. Herzberg K, Bashkirov VI, Rolfsmeier M, Haghnazari E, McDonald WH, Anderson S, Bashkirova EV, Yates JR, Heyer WD (2006) Mol Cell Biol 26(22): 8396-409
    › Primary publication · 16966380 (PubMed) · PMC1636779 (PubMed Central)
  45. Phospho-regulation of the Cdc14/Clp1 phosphatase delays late mitotic events in S. pombe. Wolfe BA, McDonald WH, Yates JR, Gould KL (2006) Dev Cell 11(3): 423-30
    › Primary publication · 16950131 (PubMed)
  46. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL (2006) Science 313(5791): 1261-6
    › Primary publication · 16946064 (PubMed)
  47. Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback. de Bruin RA, Kalashnikova TI, Chahwan C, McDonald WH, Wohlschlegel J, Yates J, Russell P, Wittenberg C (2006) Mol Cell 23(4): 483-96
    › Primary publication · 16916637 (PubMed)
  48. Ppc89 links multiple proteins, including the septation initiation network, to the core of the fission yeast spindle-pole body. Rosenberg JA, Tomlin GC, McDonald WH, Snydsman BE, Muller EG, Yates JR, Gould KL (2006) Mol Biol Cell 17(9): 3793-805
    › Primary publication · 16775007 (PubMed) · PMC1593159 (PubMed Central)
  49. Developments in mass spectrometry for the analysis of complex protein mixtures. Khalsa-Moyers G, McDonald WH (2006) Brief Funct Genomic Proteomic 5(2): 98-111
    › Primary publication · 16772276 (PubMed)
  50. Protein disulfide isomerase serves as a molecular chaperone to maintain estrogen receptor alpha structure and function. Schultz-Norton JR, McDonald WH, Yates JR, Nardulli AM (2006) Mol Endocrinol 20(9): 1982-95
    › Primary publication · 16690750 (PubMed)
  51. The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex. Pebernard S, Wohlschlegel J, McDonald WH, Yates JR, Boddy MN (2006) Mol Cell Biol 26(5): 1617-30
    › Primary publication · 16478984 (PubMed) · PMC1430260 (PubMed Central)
  52. Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. VerBerkmoes NC, Shah MB, Lankford PK, Pelletier DA, Strader MB, Tabb DL, McDonald WH, Barton JW, Hurst GB, Hauser L, Davison BH, Beatty JT, Harwood CS, Tabita FR, Hettich RL, Larimer FW (2006) J Proteome Res 5(2): 287-98
    › Primary publication · 16457594 (PubMed)
  53. Cip1 and Cip2 are novel RNA-recognition-motif proteins that counteract Csx1 function during oxidative stress. Martín V, Rodríguez-Gabriel MA, McDonald WH, Watt S, Yates JR, Bähler J, Russell P (2006) Mol Biol Cell 17(3): 1176-83
    › Primary publication · 16407405 (PubMed) · PMC1382307 (PubMed Central)
  54. Dynamics of the peroxisomal import cycle of PpPex20p: ubiquitin-dependent localization and regulation. Léon S, Zhang L, McDonald WH, Yates J, Cregg JM, Subramani S (2006) J Cell Biol 172(1): 67-78
    › Primary publication · 16390998 (PubMed) · PMC2063535 (PubMed Central)
  55. MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra. Tabb DL, Thompson MR, Khalsa-Moyers G, VerBerkmoes NC, McDonald WH (2005) J Am Soc Mass Spectrom 16(8): 1250-61
    › Primary publication · 15979332 (PubMed)
  56. Tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity. Martin SG, McDonald WH, Yates JR, Chang F (2005) Dev Cell 8(4): 479-91
    › Primary publication · 15809031 (PubMed)
  57. Analysis of the role of phosphorylation in fission yeast Cdc13p/cyclinB function. Ren L, Feoktistova A, McDonald WH, Haese GD, Morrell JL, Gould KL (2005) J Biol Chem 280(15): 14591-6
    › Primary publication · 15705571 (PubMed)
  58. Swi1 and Swi3 are components of a replication fork protection complex in fission yeast. Noguchi E, Noguchi C, McDonald WH, Yates JR, Russell P (2004) Mol Cell Biol 24(19): 8342-55
    › Primary publication · 15367656 (PubMed) · PMC516732 (PubMed Central)
  59. Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo. Jessani N, Humphrey M, McDonald WH, Niessen S, Masuda K, Gangadharan B, Yates JR, Mueller BM, Cravatt BF (2004) Proc Natl Acad Sci U S A 101(38): 13756-61
    › Primary publication · 15356343 (PubMed) · PMC518829 (PubMed Central)
  60. Nse1, Nse2, and a novel subunit of the Smc5-Smc6 complex, Nse3, play a crucial role in meiosis. Pebernard S, McDonald WH, Pavlova Y, Yates JR, Boddy MN (2004) Mol Biol Cell 15(11): 4866-76
    › Primary publication · 15331764 (PubMed) · PMC524734 (PubMed Central)
  61. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR (2004) Rapid Commun Mass Spectrom 18(18): 2162-8
    › Primary publication · 15317041 (PubMed)
  62. Automatic quality assessment of peptide tandem mass spectra. Bern M, Goldberg D, McDonald WH, Yates JR (2004) Bioinformatics : i49-54
    › Primary publication · 15262780 (PubMed)
  63. Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5. de Bruin RA, McDonald WH, Kalashnikova TI, Yates J, Wittenberg C (2004) Cell 117(7): 887-98
    › Primary publication · 15210110 (PubMed)
  64. Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain. Flick K, Ouni I, Wohlschlegel JA, Capati C, McDonald WH, Yates JR, Kaiser P (2004) Nat Cell Biol 6(7): 634-41
    › Primary publication · 15208638 (PubMed)
  65. Cell cycle-dependent phosphorylation of the DNA polymerase epsilon subunit, Dpb2, by the Cdc28 cyclin-dependent protein kinase. Kesti T, McDonald WH, Yates JR, Wittenberg C (2004) J Biol Chem 279(14): 14245-55
    › Primary publication · 14747467 (PubMed)
  66. Assigning function to yeast proteins by integration of technologies. Hazbun TR, Malmström L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, Yates JR, Davis TN (2003) Mol Cell 12(6): 1353-65
    › Primary publication · 14690591 (PubMed)
  67. Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast. Graumann J, Dunipace LA, Seol JH, McDonald WH, Yates JR, Wold BJ, Deshaies RJ (2004) Mol Cell Proteomics 3(3): 226-37
    › Primary publication · 14660704 (PubMed)
  68. RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress. Rodríguez-Gabriel MA, Burns G, McDonald WH, Martín V, Yates JR, Bähler J, Russell P (2003) EMBO J 22(23): 6256-66
    › Primary publication · 14633985 (PubMed) · PMC291838 (PubMed Central)
  69. Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Coulon S, Gaillard PH, Chahwan C, McDonald WH, Yates JR, Russell P (2004) Mol Biol Cell 15(1): 71-80
    › Primary publication · 14528010 (PubMed) · PMC307528 (PubMed Central)
  70. Novel essential DNA repair proteins Nse1 and Nse2 are subunits of the fission yeast Smc5-Smc6 complex. McDonald WH, Pavlova Y, Yates JR, Boddy MN (2003) J Biol Chem 278(46): 45460-7
    › Primary publication · 12966087 (PubMed)
  71. Replication checkpoint kinase Cds1 regulates recombinational repair protein Rad60. Boddy MN, Shanahan P, McDonald WH, Lopez-Girona A, Noguchi E, Yates III JR, Russell P (2003) Mol Cell Biol 23(16): 5939-46
    › Primary publication · 12897162 (PubMed) · PMC166335 (PubMed Central)
  72. Shotgun proteomics: integrating technologies to answer biological questions. McDonald WH, Yates JR (2003) Curr Opin Mol Ther 5(3): 302-9
    › Primary publication · 12870441 (PubMed)
  73. Proteomic characterization of the Chlamydomonas reinhardtii chloroplast ribosome. Identification of proteins unique to th e70 S ribosome. Yamaguchi K, Beligni MV, Prieto S, Haynes PA, McDonald WH, Yates JR, Mayfield SP (2003) J Biol Chem 278(36): 33774-85
    › Primary publication · 12826678 (PubMed)
  74. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. Tabb DL, McDonald WH, Yates JR (2002) J Proteome Res 1(1): 21-6
    › Primary publication · 12643522 (PubMed) · PMC2811961 (PubMed Central)
  75. Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: identification of a novel S1 domain-containing protein and unusually large orthologs of bacterial S2, S3, and S5. Yamaguchi K, Prieto S, Beligni MV, Haynes PA, McDonald WH, Yates JR, Mayfield SP (2002) Plant Cell 14(11): 2957-74
    › Primary publication · 12417713 (PubMed) · PMC152739 (PubMed Central)
  76. Shotgun proteomics and biomarker discovery. McDonald WH, Yates JR (2002) Dis Markers 18(2): 99-105
    › Primary publication · 12364816 (PubMed) · PMC3851423 (PubMed Central)
  77. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Verma R, Aravind L, Oania R, McDonald WH, Yates JR, Koonin EV, Deshaies RJ (2002) Science 298(5593): 611-5
    › Primary publication · 12183636 (PubMed)
  78. Charting the protein complexome in yeast by mass spectrometry. Deshaies RJ, Seol JH, McDonald WH, Cope G, Lyapina S, Shevchenko A, Shevchenko A, Verma R, Yates JR (2002) Mol Cell Proteomics 1(1): 3-10
    › Primary publication · 12096135 (PubMed)
  79. Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA. Saitoh S, Chabes A, McDonald WH, Thelander L, Yates JR, Russell P (2002) Cell 109(5): 563-73
    › Primary publication · 12062100 (PubMed)
  80. Shotgun identification of protein modifications from protein complexes and lens tissue. MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI, Yates JR (2002) Proc Natl Acad Sci U S A 99(12): 7900-5
    › Primary publication · 12060738 (PubMed) · PMC122992 (PubMed Central)
  81. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Gould KL (2002) Mol Cell Biol 22(7): 2011-24
    › Primary publication · 11884590 (PubMed) · PMC133674 (PubMed Central)
  82. Mus81-Eme1 are essential components of a Holliday junction resolvase. Boddy MN, Gaillard PH, McDonald WH, Shanahan P, Yates JR, Russell P (2001) Cell 107(4): 537-48
    › Primary publication · 11719193 (PubMed)
  83. Vectors and gene targeting modules for tandem affinity purification in Schizosaccharomyces pombe. Tasto JJ, Carnahan RH, McDonald WH, Gould KL (2001) Yeast 18(7): 657-62
    › Primary publication · 11329175 (PubMed)
  84. Proteomic tools for cell biology. McDonald WH, Yates JR (2000) Traffic 1(10): 747-54
    › Primary publication · 11208064 (PubMed)
  85. Use of high specific activity StarFire oligonucleotide probes to visualize low-abundance pre-mRNA splicing intermediates in S. pombe. Behlke MA, Dames SA, McDonald WH, Gould KL, Devor EJ, Walder JA (2000) Biotechniques 29(4): 892-7
    › Primary publication · 11056821 (PubMed)
  86. Isolation of an essential Schizosaccharomyces pombe gene, prp31(+), that links splicing and meiosis. Bishop DT, McDonald WH, Gould KL, Forsburg SL (2000) Nucleic Acids Res 28(11): 2214-20
    › Primary publication · 10871341 (PubMed) · PMC102626 (PubMed Central)
  87. Myb-related fission yeast cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing. McDonald WH, Ohi R, Smelkova N, Frendewey D, Gould KL (1999) Mol Cell Biol 19(8): 5352-62
    › Primary publication · 10409726 (PubMed) · PMC84378 (PubMed Central)