|DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics|
DL Tabb, WH McDonald, JR Yates
Journal of proteome research 1 (1), 21-26, 2002
|Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome|
R Verma, L Aravind, R Oania, WH McDonald, JR Yates, EV Koonin, ...
Science 298 (5593), 611-615, 2002
|Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis|
BM Tyler, S Tripathy, X Zhang, P Dehal, RHY Jiang, A Aerts, ...
Science 313 (5791), 1261-1266, 2006
|Shotgun identification of protein modifications from protein complexes and lens tissue|
MJ MacCoss, WH McDonald, A Saraf, R Sadygov, JM Clark, JJ Tasto, ...
Proceedings of the National Academy of Sciences 99 (12), 7900-7905, 2002
|Sirt3-mediated deacetylation of evolutionarily conserved lysine 122 regulates MnSOD activity in response to stress|
R Tao, MC Coleman, JD Pennington, O Ozden, SH Park, H Jiang, HS Kim, ...
Molecular cell 40 (6), 893-904, 2010
|Mus81-Eme1 are essential components of a Holliday junction resolvase|
MN Boddy, PHL Gaillard, WH McDonald, P Shanahan, JR Yates 3rd, ...
Cell 107 (4), 537-548, 2001
|Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5|
RAM De Bruin, WH McDonald, TI Kalashnikova, J Yates III, C Wittenberg
Cell 117 (7), 887-898, 2004
|Shotgun proteomics and biomarker discovery|
WH McDonald, JR Yates
Disease markers 18 (2), 99-105, 2002
|Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimension LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT|
WH McDonald, R Ohi, DT Miyamoto, TJ Mitchison, JR Yates III
International Journal of Mass Spectrometry 219 (1), 245-251, 2002
|MS1, MS2, and SQT—three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications|
WH McDonald, DL Tabb, RG Sadygov, MJ MacCoss, J Venable, ...
Rapid Communications in Mass Spectrometry 18 (18), 2162-2168, 2004
|Assigning function to yeast proteins by integration of technologies|
TR Hazbun, L Malmström, S Anderson, BJ Graczyk, B Fox, M Riffle, ...
Molecular cell 12 (6), 1353-1365, 2003
|Automatic quality assessment of peptide tandem mass spectra|
M Bern, D Goldberg, WH Mcdonald, JR Yates III
Bioinformatics 20 (suppl_1), i49-i54, 2004
|Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs|
MD Ohi, AJ Link, L Ren, JL Jennings, WH McDonald, KL Gould
Molecular and cellular biology 22 (7), 2011-2024, 2002
|Tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity|
SG Martin, WH McDonald, JR Yates III, F Chang
Developmental cell 8 (4), 479-491, 2005
|Swi1 and Swi3 are components of a replication fork protection complex in fission yeast|
E Noguchi, C Noguchi, WH McDonald, JR Yates, P Russell
Molecular and Cellular Biology 24 (19), 8342-8355, 2004
|Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo|
N Jessani, M Humphrey, WH McDonald, S Niessen, K Masuda, ...
Proceedings of the National Academy of Sciences 101 (38), 13756-13761, 2004
|Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast|
J Graumann, LA Dunipace, JH Seol, WH McDonald, JR Yates, BJ Wold, ...
Molecular & Cellular Proteomics 3 (3), 226-237, 2004
|Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain|
K Flick, I Ouni, JA Wohlschlegel, C Capati, WH McDonald, JR Yates 3rd, ...
Nature Cell Biology 6 (7), 634, 2004
|Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments|
F Wisniewski-Dye, K Borziak, G Khalsa-Moyers, G Alexandre, ...
PLoS genetics 7 (12), e1002430, 2011
|Cid13 is a cytoplasmic poly (A) polymerase that regulates ribonucleotide reductase mRNA|
S Saitoh, A Chabes, WH McDonald, L Thelander, JR Yates III, P Russell
Cell 109 (5), 563-573, 2002