Username:
Password:

For new collaborations:
Register with the YRC



Search for proteins:


Search: Descriptions Names
Advanced Search

Visit the YRC PDR

Click here to send feedback.


  Publications

Jump to: Mass Spectrometry, Yeast Two-Hybrid, Fluorescence Microscopy, Protein Structure Prediction, Informatics

  • Integrated Technologies
    1. Klammer AA, Reynolds SM, Bilmes JA, MacCoss MJ, Noble WS. Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics. 2008 Jul 1;24(13):i348-56. PMID: 18586734
    2. Park CY, Klammer AA, Käll L, MacCoss MJ, Noble WS. Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res. 2008 Jul;7(7):3022-7. Epub 2008 May 28. PMID: 18505281
    3. Qiu J, Sheffler W, Baker D, Noble WS. Ranking predicted protein structures with support vector regression. Proteins. 2008 May 15;71(3):1175-82. PMID: 18004754
    4. Käll L, Storey JD, MacCoss MJ, Noble WS. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res. 2008 Jan;7(1):29-34.
    5. Käll L, Storey JD, MacCoss MJ, Noble WS. Posterior error probabilities and false discovery rates: two sides of the same coin. J Proteome Res. 2008 Jan;7(1):40-4.
    6. Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods. 2007 Nov;4(11):923-5. Epub 2007 Oct 21. PMID: 17952086
    7. Klammer AA, Yi X, MacCoss MJ, Noble WS. Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions. Anal Chem. 2007 Aug 15;79(16):6111-8.
    8. Malmstrom L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D. Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology. PLoS Biol 2007;5(4):e76.
    9. Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem 2006;78(16):5678-84.
    10. Rosenberg JA, Tomlin GC, McDonald WH, Snydsman BE, Muller EG, Yates JR 3rd, Gould KL. Ppc89 links multiple proteins, including the septation initiation network, to the core of the fission yeast spindle-pole body. Mol Biol Cell 2006;17(9):3793-805.
    11. Shimogawa MM, Graczyk B, Gardner MK, Francis SE, White EA, Ess M, Molk JN, Ruse C, Niessen S, Yates JR 3rd, Muller EG, Bloom K, Odde DJ, Davis TN. Mps1 phosphorylation of Dam1 couples kinetochores to microtubule plus ends at metaphase. Curr Biol 2006;16(15):1489-501.
    12. Miller JP, Lo RS, Ben-Hur A, Desmarais C, Stagljar I, Noble WS, Fields S. Large-scale identification of yeast intergral membrane protein interactions. Proc Natl Acad Sci USA 2005;102(34):12123-8.
    13. Hazbun TR, Malmstrom 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 3rd, Davis TN. Assigning function to yeast proteins by integration of technologies. Mol Cell 2003;12:1353-65.
    14. Pot I, Measday V, Snydsman B, Cagney G, Fields S, Davis TN, Muller EG, Hieter P. Chl3p and iml3p are two new members of the budding yeast outer kinetochore. Mol Biol Cell 2003;14:460-76.
    15. Measday V, Hailey DW, Pot I, Givan SA, Hyland KM, Cagney G, Fields S, Davis TN, Hieter P. Ctf3p, the Mis6 budding yeast homolog, interacts with Mcm22p and Mcm16p at the yeast outer kinetochore. Genes Dev 2002;16:101-113.
  • Mass Spectrometry
    1. Findlay GD, Yi X, Maccoss MJ, Swanson WJ. Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating. PLoS Biol. 2008 Jul 29;6(7):e178. PMID: 18666829
    2. Carvalho PC, Fischer JS, Chen EI, Yates JR 3rd, Barbosa VC. PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics. 2008 Jul 21;9:316. PMID: 18644148
    3. Scorah J, Dong MQ, Yates JR 3rd, Scott M, Gillespie D, McGowan CH. A conserved proliferating cell nuclear antigen-interacting protein sequence in Chk1 is required for checkpoint function. J Biol Chem. 2008 Jun 20;283(25):17250-9. Epub 2008 Apr 30. PMID: 18448427
    4. Xu S, Wong CC, Tong EH, Chung SS, Yates JR 3rd, Yin Y, Ko BC. Phosphorylation by casein kinase 1 regulates tonicity-induced osmotic response element-binding protein/tonicity enhancer-binding protein nucleocytoplasmic trafficking. J Biol Chem. 2008 Jun 20;283(25):17624-34. Epub 2008 Apr 14. PMID: 18411282
    5. Seki A, Coppinger JA, Jang CY, Yates JR, Fang G. Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry. Science. 2008 Jun 20;320(5883):1655-8. PMID: 18566290
    6. Neuman BW, Joseph JS, Saikatendu KS, Serrano P, Chatterjee A, Johnson MA, Liao L, Klaus JP, Yates JR 3rd, Wüthrich K, Stevens RC, Buchmeier MJ, Kuhn P. Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3. J Virol. 2008 Jun;82(11):5279-94. Epub 2008 Mar 26. PMID: 18367524
    7. Patra KP, Johnson JR, Cantin GT, Yates JR 3rd, Vinetz JM. Proteomic analysis of zygote and ookinete stages of the avian malaria parasite Plasmodium gallinaceum delineates the homologous proteomes of the lethal human malaria parasite Plasmodium falciparum. Proteomics. 2008 Jun;8(12):2492-9. PMID: 18563747
    8. Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd. Motif-specific sampling of phosphoproteomes. J Proteome Res. 2008 May;7(5):2140-50. PMID: 18452278
    9. Rao AK, Ziegler YS, McLeod IX, Yates JR, Nardulli AM. Effects of Cu/Zn superoxide dismutase on estrogen responsiveness and oxidative stress in human breast cancer cells. Mol Endocrinol. 2008 May;22(5):1113-24. Epub 2008 Feb 7. PMID: 18258688
    10. Jang CY, Wong J, Coppinger JA, Seki A, Yates JR 3rd, Fang G. DDA3 recruits microtubule depolymerase Kif2a to spindle poles and controls spindle dynamics and mitotic chromosome movement. J Cell Biol. 2008 Apr 21;181(2):255-67. Epub 2008 Apr 14. PMID: 18411309
    11. Clifford DM, Wolfe BA, Roberts-Galbraith RH, McDonald WH, Yates JR 3rd, Gould KL. The Clp1/Cdc14 phosphatase contributes to the robustness of cytokinesis by association with anillin-related Mid1. J Cell Biol. 2008 Apr 7;181(1):79-88. Epub 2008 Mar 31. PMID: 18378776
    12. Seki A, Coppinger JA, Du H, Jang CY, Yates JR 3rd, Fang G. Plk1- and beta-TrCP-dependent degradation of Bora controls mitotic progression. J Cell Biol. 2008 Apr 7;181(1):65-78. Epub 2008 Mar 31. PMID: 18378770
    13. Park SK, Venable JD, Xu T, Yates JR 3rd. A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods. 2008 Apr;5(4):319-22. Epub 2008 Mar 16. PMID: 18345006
    14. Sanderson SJ, Xia D, Prieto H, Yates J, Heiges M, Kissinger JC, Bromley E, Lal K, Sinden RE, Tomley F, Wastling JM. Determining the protein repertoire of Cryptosporidium parvum sporozoites. Proteomics. 2008 Apr;8(7):1398-414. PMID: 18306179
    15. Ashe M, de Bruin RA, Kalashnikova T, McDonald WH, Yates JR 3rd, Wittenberg C. The SBF- and MBF-associated protein Msa1 is required for proper timing of G1-specific transcription in Saccharomyces cerevisiae. J Biol Chem. 2008 Mar 7;283(10):6040-9. Epub 2007 Dec 26. PMID: 18160399
    16. Lu B, Motoyama A, Ruse C, Venable J, Yates JR 3rd. Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data. Anal Chem. 2008 Mar 15;80(6):2018-25. Epub 2008 Feb 15. PMID: 18275164
    17. Diop SB, Bertaux K, Vasanthi D, Sarkeshik A, Goirand B, Aragnol D, Tolwinski NS, Cole MD, Pradel J, Yates JR 3rd, Mishra RK, Graba Y, Saurin AJ. Reptin and Pontin function antagonistically with PcG and TrxG complexes to mediate Hox gene control. EMBO Rep. 2008 Mar;9(3):260-6. Epub 2008 Feb 8. PMID: 18259215
    18. Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd. Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. J Proteome Res. 2008 Mar;7(3):1346-51. Epub 2008 Jan 26. PMID: 18220336
    19. Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ. Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data. Anal Chem. 2008 Feb 15;80(4):961-71. Epub 2008 Jan 12. PMID: 18189369
    20. Usaite R, Wohlschlegel J, Venable JD, Park SK, Nielsen J, Olsson L, Yates III JR. Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression Saccharomyces cerevisiae strains: the comparison of two quantitative methods. J Proteome Res. 2008 Jan;7(1):266-75. PMID: 18173223
    21. Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, Sewell AK, Liu X, Yates JR 3rd, Han M. Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell. 2007 Nov 30;28(4):598-613. PMID: 18042455
    22. Curtis CD, Likhite VS, McLeod IX, Yates JR, Nardulli AM.  Interaction of the tumor metastasis suppressor nonmetastatic protein 23 homologue H1 and estrogen receptor alpha alters estrogen-responsive gene expression. Cancer Res. 2007 Nov 1;67(21):10600-7. PMID: 17975005 
    23. El Marzouk S, Schultz-Norton JR, Likhite VS, McLeod IX, Yates JR, Nardulli AM.  Rho GDP dissociation inhibitor alpha interacts with estrogen receptor alpha and influences estrogen responsiveness. J Mol Endocrinol. 2007 Oct;39(4):249-59. PMID: 17909265 
    24. Wong CC, Xu T, Rai R, Bailey AO, Yates JR 3rd, Wolf YI, Zebroski H, Kashina A.  Global analysis of posttranslational protein arginylation. PLoS Biol. 2007 Oct;5(10):e258. PMID: 17896865 
    25. Kilburn CL, Pearson CG, Romijn EP, Meehl JB, Giddings TH Jr, Culver BP, Yates  JR 3rd, Winey M.  New Tetrahymena basal body protein components identify basal body domain structure. J Cell Biol. 2007 Sep 10;178(6):905-12. Erratum in: J Cell Biol. 2007 Oct 8;179(1):167. PMID: 17785518 
    26. McClatchy DB, Liao L, Park SK, Venable JD, Yates JR.  Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res. 2007 Sep;17(9):1378-88. Aug 3. PMID: 17675365 
    27. Chen EI, Yates JR. Cancer Proteomics by Quantitative Shotgun Proteomics. Mol Oncol. 2007 Sep;1(2):144-159. PMID: 18443658
    28. Dong MQ, Venable JD, Au N, Xu T, Park SK, Cociorva D, Johnson JR, Dillin A, Yates JR 3rd.  Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science. 2007 Aug 3;317(5838):660-3.  PMID: 17673661 
    29. Schultz-Norton JR, Gabisi VA, Ziegler YS, McLeod IX, Yates JR, Nardulli AM.  Interaction of estrogen receptor alpha with proliferating cell nuclear antigen. Nucleic Acids Res. 2007;35(15):5028-38.  PMID: 17636311 
    30. Xiao K, McClatchy DB, Shukla AK, Zhao Y, Chen M, Shenoy SK, Yates JR 3rd, Lefkowitz RJ.  Functional specialization of beta-arrestin interactions revealed by proteomic analysis. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12011-6.   PMID: 17620599 
    31. Bailey AO, Miller TM, Dong MQ, Vande Velde C, Cleveland DW, Yates JR.  RCADiA: simple automation platform for comparative multidimensional protein identification technology. Anal Chem. 2007 Aug 15;79(16):6410-8. PMID: 17616168 
    32. Wan J, Roth AF, Bailey AO, Davis NG.  Palmitoylated proteins: purification and identification. Nat Protoc. 2007;2(7):1573-84.  PMID: 17585299 
    33. Cantin GT, Shock TR, Park SK, Madhani HD, Yates JR 3rd.  Optimizing TiO2-based phosphopeptide enrichment for automated multidimensional liquid chromatography coupled to tandem mass spectrometry. Anal Chem. 2007 Jun 15;79(12):4666-73.  PMID: 17523591
    34. Audhya A, McLeod IX, Yates JR, Oegema K. MVB-12, a fourth subunit of metazoan ESCRT-I, functions in receptor downregulation. PLoS ONE. 2007 Sep 26;2(9):e956. PMID: 17895996
    35. Schultz-Norton JR, Walt KA, Ziegler YS, McLeod IX, Yates JR, Raetzman LT, Nardulli AM.  The deoxyribonucleic acid repair protein flap endonuclease-1 modulates estrogen-responsive gene expression. Mol Endocrinol. 2007 Jul;21(7):1569-80.  PMID: 17488975 
    36. Ranish JA, Brand M, Aebersold R.  Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition. Methods Mol Biol. 2007;359:17-35.  PMID: 17484108 
    37. McClatchy DB, Dong MQ, Wu CC, Venable JD, Yates JR 3rd.  15N metabolic labeling of mammalian tissue with slow protein turnover. J Proteome Res. 2007 May;6(5):2005-10. PMID: 17375949 
    38. Chen EI, Hewel J, Krueger JS, Tiraby C, Weber MR, Kralli A, Becker K, Yates JR 3rd, Felding-Habermann B. Adaptation of energy metabolism in breast cancer brain metastases. Cancer Res. 2007;67(4):1472-86.
    39. Eakin CM, Maccoss MJ, Finney GL, Klevit RE. Estrogen receptor alpha is a putative substrate for the BRCA1 ubiquitin ligase. Proc Natl Acad Sci U S A. 2007;104(14):5794-9.
    40. Koch HB, Zhang R, Verdoodt B, Bailey A, Zhang CD, Yates JR 3rd, Menssen A, Hermeking H. Large-scale identification of c-MYC-associated proteins using a combined TAP/MudPIT approach. Cell Cycle. 2007;6(2):205-17.
    41. Liao L, Pilotte J, Xu T, Wong CC, Edelman GM, Vanderklish P, Yates JR 3rd. BDNF induces widespread changes in synaptic protein content and up-regulates components of the translation machinery: an analysis using high-throughput proteomics. J Proteome Res. 2007;6(3):1059-71.
    42. Lu B, Ruse C, Xu T, Park SK, Yates J 3rd. Automatic validation of phosphopeptide identifications from tandem mass spectra. Anal Chem. 2007;79(4):1301-10.
    43. Min J, Kyung Kim Y, Cipriani PG, Kang M, Khersonsky SM, Walsh DP, Lee JY, Niessen S, Yates JR 3rd, Gunsalus K, Piano F, Chang YT. Forward chemical genetic approach identifies new role for GAPDH in insulin signaling. Nat Chem Biol. 2007;3(1):55-9.
    44. Aagaard JE, Yi X, MacCoss MJ, Swanson WJ. Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs. Proc Natl Acad Sci U S A. 2006;103(46):17302-7.
    45. Angers S, Li T, Yi X, MacCoss MJ, Moon RT, Zheng N. Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature. 2006;443(7111):590-3.
    46. Angers S, Thorpe CJ, Biechele TL, Goldenberg SJ, Zheng N, MacCoss MJ, Moon RT. The KLHL12-Cullin-3 ubiquitin ligase negatively regulates the Wnt-beta-catenin pathway by targeting Dishevelled for degradation. Nat Cell Biol. 2006;8(4):348-57.
    47. Azarian SM, McLeod I, Lillo C, Gibbs D, Yates JR, Williams DS. Proteomic analysis of mature melanosomes from the retinal pigmented epithelium. J Proteome Res. 2006;5(3):521-9
    48. Blackler AR, Klammer AA, MacCoss MJ, Wu CC. Quantitative comparison of proteomic data quality between a 2D and 3D quadrupole ion trap. Anal Chem. 2006;78(4):1337-44.
    49. Cantin GT, Venable JD, Cociorva D, Yates JR 3rd. Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J Proteome Res. 2006;5(1):127-34.
    50. Cao H, Deterding LJ, Venable JD, Kennington EA, Yates JR 3rd, Tomer KB, Blackshear PJ. Identification of the anti-inflammatory protein tristetraprolin as a hyperphosphorylated protein by mass spectrometry and site-directed mutagenesis. Biochem J. 2006;394(Pt 1):285-97.
    51. Chu DS, Liu H, Nix P, Wu TF, Ralston EJ, Yates JR 3rd, Meyer BJ. Sperm chromatin proteomics identifies evolutionarily conserved fertility factors. Nature. 2006;443(7107):101-5.
    52. De Craene JO, Coleman J, Estrada de Martin P, Pypaert M, Anderson S, Yates JR 3rd, Ferro-Novick S, Novick P. Rtn1p Is Involved in Structuring the Cortical ER. Mol Biol Cell. 2006 Apr 19; [Epub ahead of print].
    53. Duchaine TF, Wohlschlegel JA, Kennedy S, Bei Y, Conte D Jr, Pang K, Brownell DR, Harding S, Mitani S, Ruvkun G, Yates JR 3rd, Mello CC. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell. 2006;124(2):343-54.
    54. Foltz DR, Jansen LE, Black BE, Bailey AO, Yates JR, Cleveland DW. The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol. 2006;8(5):458-69.
    55. Grosshans BL, Andreeva A, Gangar A, Niessen S, Yates JR 3rd, Brennwald P, Novick P. The yeast lgl family member Sro7p is an effector of the secretory Rab GTPase Sec4p. J Cell Biol. 2006;172(1):55-66.
    56. Guelman S, Suganuma T, Florens L, Swanson SK, Kiesecker CL, Kusch T, Anderson S, Yates JR 3rd, Washburn MP, Abmayr SM, Workman JL. Host cell factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila. Mol Cell Biol. 2006;26(3):871-82.
    57. Harashima T, Anderson S, Yates JR 3rd, Heitman J. The kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with th yeast RasGAP neurofibromin homologs Ira1 and Ira2. Mol Cell. 2006;22(6):819-30.
    58. Herzberg K, Bashkirov VI, Rolfsmeier M, Haghnazari E, McDonald WH, Anderson S, Bashkirova EV, Yates JR 3rd, Heyer WD. Phosphorylation of Rad55 on serines 2, 8, and 14 is required for efficient homologous recombination in the recovery of stalled replication forks. Mol Cell Biol. 2006;26(22):8396-409.
    59. Karakozova M, Kozak M, Wong CC, Bailey AO, Yates JR 3rd, Mogilner A, Zebroski H, Kashina A. Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science. 2006;313(5784):192-6.
    60. Klammer AA, MacCoss MJ. Effects of modified digestion schemes on the identification of proteins from complex mixtures. J Proteome Res. 2006;5(3):695-700.
    61. Martin V, Chahwan C, Gao H, Blais V, Wohlschlegel J, Yates JR 3rd, McGowan CH, Russell P. Sws1 is a conserved regulator of homologous recombination in eukaryotic cells. EMBO J. 2006;25(11):2564-74.
    62. Martin V, Rodriguez-Gabriel MA, McDonald WH, Watt S, Yates JR 3rd, Bahler J, Russell P. Cip1 and Cip2 are novel RNA-recognition-motif proteins that counteract Csx1 function during oxidative stress. Mol Biol Cell. 2006;17(3):1176-83.
    63. Okada M, Cheeseman IM, Hori T, Okawa K, McLeod IX, Yates JR 3rd, Desai A, Fukagawa T. The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat Cell Biol. 2006;8(5):446-57.
    64. Olson SK, Bishop JR, Yates JR, Oegema K, Esko JD. Identification of novel chondroitin proteoglycans in Caenorhabditis elegans: embryonic cell division depends on CPG-1 and CPG-2. J Cell Biol. 2006;173(6):985-94.
    65. Pebernard S, Wohlschlegel J, McDonald WH, Yates JR 3rd, Boddy MN. The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex. Mol Cell Biol. 2006;26(5):1617-30. Erratum in: Mol Cell Biol. 2006 Apr;26(8):3336.
    66. Raffa GD, Wohlschlegel J, Yates JR 3rd, Boddy MN. SUMO-binding motifs mediate the Rad60-dependent response to replicative stress and self-association. J Biol Chem. 2006;281(38):27973-81.
    67. Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN, Phinney BS, Yates JR 3rd, Davis NG. Global analysis of protein palmitoylation in yeast. Cell. 2006;125(5):1003-13.
    68. Sadygov R, Wohlschlegel J, Park SK, Xu T, Yates JR 3rd. Central limit theorem as an approximation for intensity-based scoring function. Anal Chem. 2006;78(1):89-95.
    69. Sandall S, Severin F, McLeod IX, Yates JR 3rd, Oegema K, Hyman A, Desai A. A Bir1-Sli15 complex connects centromeres to microtubules and is required to sense kinetochore tension. Cell. 2006;127(6):1179-91.
    70. Schneider DA, French SL, Osheim YN, Bailey AO, Vu L, Dodd J, Yates JR, Beyer AL, Nomura M. RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci U S A. 2006;103(34):12707-12.
    71. Schultz-Norton JR, McDonald WH, Yates JR, Nardulli AM. Protein disulfide isomerase serves as a molecular chaperone to maintain estrogen receptor alpha structure and function. Mol Endocrinol. 2006;20(9):1982-95.
    72. Venable JD, Xu T, Cociorva D, Yates JR 3rd. Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra. Anal Chem. 2006;78(6):1921-9.
    73. Wang X, Venable J, LaPointe P, Hutt DM, Koulov AV, Coppinger J, Gurkan C, Kellner W, Matteson J, Plutner H, Riordan JR, Kelly JW, Yates JR 3rd, Balch WE. Hsp90 cochaperone Aha1 downregulation rescues misfolding of CFTR in cystic fibrosis. Cell. 2006;127(4):803-15.
    74. Widlund PO, Lyssand JS, Anderson S, Niessen S, Yates JR 3rd, Davis TN. Phosphorylation of the chromosomal passenger protein Bir1 is required for localization of Ndc10 to the spindle during anaphase and full spindle elongation. Mol Biol Cell. 2006;17(3):1065-74.
    75. Wohlschlegel JA, Johnson ES, Reed SI, Yates JR 3rd. Improved identification of SUMO attachment sites using C-terminal SUMO mutants and tailored protease digestion strategies. J Proteome Res. 2006;5(4):761-70.
    76. Wolfe BA, McDonald WH, Yates JR 3rd, Gould KL. Phospho-regulation of the Cdc14/Clp1 phosphatase delays late mitotic events in S. pombe. Dev Cell. 2006;11(3):423-30.
    77. Xiong Y, Wiltsie J, Woods A, Guo J, Pivnichny JV, Tang W, Bansal A, Cummings RT, Cunningham BR, Friedlander AM, Douglas CM, Salowe SP, Zaller DM, Scolnick EM, Schmatz DM, Bartizal K, Hermes JD, MacCoss M, Chapman KT. The discovery of a potent and selective lethal factor inhibitor for adjunct therapy of anthrax infection. Bioorg Med Chem Lett. 2006;16(4):964-8.
    78. Yates JR, Cociorva D, Liao L, Zabrouskov V. Performance of a linear ion trap-Orbitrap hybrid for peptide analysis. Anal Chem. 2006;78(2):493-500.

    • Click here for 139 mass spec publications before 2006

  • Two-hybrid Analysis
    1. Khoury CM, Yang Z, Li XY, Vignali M, Fields S, Greenwood MT. A TSC22-like motif defines a novel antiapoptotic protein family. FEMS Yeast Res. 2008 Jun;8(4):540-63. Epub 2008 Mar 18. PMID: 18355271
    2. Wong J, Nakajima Y, Westermann S, Shang C, Kang JS, Goodner C, Houshmand P, Fields S, Chan CS, Drubin D, Barnes G, Hazbun T. A protein interaction map of the mitotic spindle. Mol Biol Cell. 2007 Oct;18(10):3800-9.
    3. Zhang Z, Hesselberth JR, Fields S. Genome-wide identification of spliced introns using a tiling microarray. Genome Res. 2007;17(4):503-9.
    4. Montpetit B, Hazbun TR, Fields S, Hieter P. Sumoylation of the budding yeast kinetochore protein Ndc10 is required for Ndc10 spindle localization and regulation of anaphase spindle elongation. J Cell Biol. 2006;147(5):653-63.
    5. Gingras AC, Caballero M, Zarske M, Sanchez A, Hazbun TR, Fields S, Sonenberg N, Hafen E, Raught B, Aebersold R. A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity. Mol Cell Proteomics. 2005.
    6. Antoniacci LM, Kenna MA, Uetz P, Fields S, Skibbens RV. The spindle pole body assembly component mps3p/nep98p functions in sister chromatid cohesion. J Biol Chem. 2004 Nov 19;279(47) :49542-50. Epub 2004 Sep 07.
    7. Guo M, Hazbun TR, Xu X-J, Fields S, Kuo M-H. A tethered catalysis two-hybrid system to identify protein-protein interactions requiring post-translational modifications. Nature Biotechnology. 2004 Jul;22(7) :888-92. Epub 2004 Jun 20.
    8. Tucker CL, Fields S. Quantitative genome-wide analysis of yeast deletion strain sensitivities to oxidative and chemical stress. Comparative and Functional Genomics 2004;5:216-24.
    9. Guo M, Aston C, Burchett SA, Dyke C, Fields S, Rajarao SJ, Utez P, Wang Y, Young K, Dohlman HG. The yeast G protein alpha subunit Gpa1 transmits a signal through an RNA binding effector protein Scp160.Mol Cell 2003;12:517-24.
    10. Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale. Nature 2003;422:208-15.
    11. Shang C, Hazbun TR, Cheeseman IM, Aranda J, Fields S, Drubin DG, Barnes G. Kinetochore protein interactions and their regulation by the Aurora kinase Ipl1p. Mol Biol Cell 2003;14:3342-55.
    12. Burchett SA, Flanary P, Aston C, Jiang L, Young KH, Uetz P, Fields S, Dohlman HG. Regulation of stress response signaling by the N-terminal dishevelled/EGL-10/pleckstrin domain of Sst2, a regulator of G protein signaling in Saccharomyces cerevisiae. J Biol Chem 2002;277:22156-67.
    13. Gera JF, Hazbun TR, Fields S. Array-based methods for identifying protein-protein and protein-nucleic acid interactions. Methods Enzymol 2002;350:499-512.
    14. Hazbun TR, Fields S. A genome-wide screen for site-specific DNA-binding proteins. Mol Cell Proteomics 2002;1:538-43.
    15. Phizicky EM, Martzen MR, McCraith SM, Spinelli SL, Xing F, Shull NP, Van Slyke C, Montagne RK, Torres FM, Fields S, Grayhack EJ. Biochemical genomics approach to map activities to genes. Methods Enzymol 2002;350:546-59.
    16. Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 2002;295:321-324.
    17. Cagney G, Uetz P, Fields S. Two-hybrid analysis of the Saccharomyces cerevisiae 26S proteasome. Physiol Genomics 2001;7:27-34.
    18. Fields S. The interplay of biology and technology. Proc Natl Acad Sci U S A 2001;98:10051-10054.
  • Microscopy
    1. Kollman JM, Zelter A, Muller EG, Fox B, Rice LM, Davis TN, Agard DA.The structure of the gamma-tubulin small complex: implications of its architecture and fexibility for microtubule nucleation.Mol Biol Cell. 2008 Jan;19(1):207-215.
    2. Mc Intyre J., Muller EGD, Weltzer S, Snydsman BE, Davis TN, Uhlmann F. In vivo analysis of cohesin architecture using FRET in the budding yeast Saccharomyces cerevisiae. EMBO J. 2007 Aug 22;26(16):3783-93.
    3. Davis TN, Muller EGD. Measuring the proximity of proteins in living cells by fluorescence resonance energy transfer between CFP and YFP.  Meth. Microbiol. 2007;36:269-280.
    4. Muller EGD, Davis TN. Protein localization by cell imaging. pp. 137-155. In T. D. Veenstra and J. R. Yates, III, (eds) Proteomics for Biological Discovery. 2006. Wiley-Liss, Inc., Hoboken, New Jersey.
    5. Muller EG, Snydsman BE, Novik I, Hailey DW, Gestaut DR, Niemann CA, O'Toole ET, Giddings TH Jr, Sundin BA, Davis, TN. The organization of the core proteins of the yeast spindle pole body. Mol Biol Cell. 2005;16(7):3341-52.
    6. Yoder TJ, McElwain MA, Francis SE, Bagley J, Muller EG, Pak B, O'Toole ET, Winey M, Davis, TN. Analysis of a spindle pole body mutant reveals a defect in biorientation and illuminates spindle forces. Mol Biol Cell. 2005 Jan;16(1) :141-52. Epub 2004 Nov 3.
    7. Flory MR, Carson AR, Muller EG, Aebersold R. An SMC-domain protein in fission yeast links telomeres to the meiotic centrosome. Mol Cell. 2004 Nov 19;16(4) :619-30.
    8. Sundin BA, Chiu C, Riffle M, Davis TN, Muller EGD. Localization of proteins that are coordinately expressed with Cln2 during the cell cycle. Yeast 2004 Jul 15;21(9) :793-800.
    9. Davis TN. Protein localization in proteomics. Curr Opin Chem Biol 2004;8(1):49-53.
    10. Hailey DW, Davis TN, Muller GD. Fluorescence resonance energy transfer using color variants of green fluorescent protein. Methods Enzymol 2002;351:34-49.
  • Protein Structure Prediction
    1. Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science. 2005;309:1868-71.
    2. Kim DE, Chivian D, Baker D. Protein Structure prediction and analysis using the Robetta server. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue) :W526-31.
    3. Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. Automated prediction of CASP-5 structures using the robetta server. Proteins 2003;53 suppl-6:524-33.
    4. Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. J Mol Biol 2002;322:65-78.
  • Informatics
    1. Käll L, Storey JD, Noble WS. Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics. 2008 Aug 15;24(16):i42-8. PMID: 18689838
    2. Qiu J, Noble WS. Predicting co-complexed protein pairs from heterogeneous data. PLoS Comput Biol. 2008 Apr 18;4(4):e1000054. PMID: 18421371
    3. Vert JP, Qiu J, Noble WS. A new pairwise kernel for biological network inference with support vector machines. BMC Bioinformatics. 2007;8 Suppl 10:S8. PMID: 18269702
    4. Qiu J, Hue M, Ben-Hur A, Vert JP, Noble WS. A structural alignment kernel for protein structures. Bioinformatics. 2007 May 1;23(9):1090-8. Epub 2007 Jan 18. PMID: 17234638
    5. Ben-Hur A and Noble WS. Choosing negative examples for the prediction of protein-protein interactions. Bioinformatics 2006;Suppl 1:S2, doi:10.
    6. Ben-Hur A and Noble WS. Kernel methods for predicting protein-protein interactions. Bioinformatics2005;Suppl 1:i38-i46.
    7. Riffle M, Malmstrom L, Davis TN. The Yeast Resource Center Public Data Repository. Nucleic Acids Res. 2005 Jan 1;33 Database Issue: D378-82.