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  Publications

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

  • Integrated Technologies
    1. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 2009 Apr;6(4):283-9. PMCID: 2668528
    2. 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.
    3. 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.
    4. 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
    5. Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res. 2008 Oct;18(10):1660-9. Epub 2008 Jul 24. PMID: 18653799
    6. 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
    7. 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
    8. 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
    9. 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.
    10. 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.
    11. 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.
    12. 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.
    13. 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.
    14. 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.
    15. 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.
    16. 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.
    17. 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. Hou H, Wang Y, Kallgren SP, Thompson J, Yates JR, Jia S. Histone variant H2A.Z regulates centromere silencing and chromosome segregation in fission yeast. J Biol Chem. Epub 2009 Nov 12. PMCID:
    2. Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT. Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl. 2009 Jan 1;3(1):116-13. PMCID: 2773554
    3. Usaite R, Jewett MC, Oliveira AP, Yates JR, 3rd, Olsson L, Nielsen J. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Mol Syst Biol. 2009;5:319. PMCID:
    4. Ambatipudi KS, Lu B, Hagen FK, Melvin JE, Yates JR. Quantitative analysis of age specific variation in the abundance of human female parotid salivary proteins. J Proteome Res. 2009 Nov;8(11):5093-102. PMCID:
    5. Liu GH, Guan T, Datta K, Coppinger J, Yates J, 3rd, Gerace L. Regulation of myoblast differentiation by the nuclear envelope protein NET39. Mol Cell Biol. 2009 Nov;29(21):5800-12. PMCID: 2772732
    6. Nishimura N, Sarkeshik A, Nito K, Park SY, Wang A, Carvalho PC, Lee S, Caddell DF, Cutler SR, Chory J, Yates JR, Schroeder JI. PYR/PYL/RCAR family members are major in-vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis. Plant J. Epub 2009 Oct 26. PMCID:
    7. Lal K, Bromley E, Oakes R, Prieto JH, Sanderson SJ, Kurian D, Hunt L, Yates JR, 3rd, Wastling JM, Sinden RE, Tomley FM. Proteomic comparison of four Eimeria tenella life-cycle stages: unsporulated oocyst, sporulated oocyst, sporozoite and second-generation merozoite. Proteomics. 2009 Oct;9(19):4566-76. PMCID:
    8. Cornillez-Ty CT, Liao L, Yates JR, 3rd, Kuhn P, Buchmeier MJ. Severe acute respiratory syndrome coronavirus nonstructural protein 2 interacts with a host protein complex involved in mitochondrial biogenesis and intracellular signaling. J Virol. 2009 Oct;83(19):10314-8. PMCID: 2748024
    9. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, Chen CY, Shyu AB, Yates JR, 3rd, Hannon GJ, Filipowicz W, Duchaine TF, Sonenberg N. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell. 2009 Sep 24;35(6):868-80. PMCID:
    10. Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V. Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem. 2009 Sep 15;81(18):7757-65. PMCID:
    11. Amako Y, Sarkeshik A, Hotta H, Yates J, 3rd, Siddiqui A. Role of oxysterol binding protein in hepatitis C virus infection. J Virol. 2009 Sep;83(18):9237-46. PMCID: 2738263
    12. Curtis CD, Thorngren DL, Ziegler YS, Sarkeshik A, Yates JR, Nardulli AM. Apurinic/apyrimidinic endonuclease 1 alters estrogen receptor activity and estrogen-responsive gene expression. Mol Endocrinol. 2009 Sep;23(9):1346-59. PMCID: 2737565
    13. Dammermann A, Pemble H, Mitchell BJ, McLeod I, Yates JR, 3rd, Kintner C, Desai AB, Oegema K. The hydrolethalus syndrome protein HYLS-1 links core centriole structure to cilia formation. Genes Dev. 2009 Sep 1;23(17):2046-59. PMCID: 2751977
    14. Dean MD, Clark NL, Findlay GD, Karn RC, Yi X, Swanson WJ, MacCoss MJ, Nachman MW. Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). Mol Biol Evol. 2009 Aug;26(8):1733-43. PMCID: 2734151
    15. Chuang LC, Teixeira LK, Wohlschlegel JA, Henze M, Yates JR, Mendez J, Reed SI. Phosphorylation of Mcm2 by Cdc7 promotes pre-replication complex assembly during cell-cycle re-entry. Mol Cell. 2009 Jul 31;35(2):206-16. PMCID: 2725784
    16. Rao A, Ziegler Y, McLeod I, Yates J, Nardulli A. Thioredoxin and thioredoxin reductase influence estrogen receptor {alpha} mediated gene expression in human breast cancer cells. J Mol Endocrinol. 2009 Jul 20. [Epub ahead of print]. PMCID:
    17. Liao L, McClatchy DB, Yates JR. Shotgun proteomics in neuroscience. Neuron. 2009 Jul 16;63(1):12-26. PMCID: 2746002
    18. Fekairi S, Scaglione S, Chahwan C, Taylor ER, Tissier A, Coulon S, Dong MQ, Ruse C, Yates JR, 3rd, Russell P, Fuchs RP, McGowan CH, Gaillard PH. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell. 2009 Jul 10;138(1):78-89. PMCID:
    19. Choi SH, Peli-Gulli MP, McLeod I, Sarkeshik A, Yates JR, 3rd, Simanis V, McCollum D. Phosphorylation state defines discrete roles for monopolin in chromosome attachment and spindle elongation. Curr Biol. 2009 Jun 23;19(12):985-95. PMCID: 2726783
    20. Prakash A, Tomazela DM, Frewen B, Maclean B, Merrihew G, Peterman S, Maccoss MJ. Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J Proteome Res. 2009 Jun;8(6):2733-9. PMCID: 2743471
    21. Jourdain I, Spielewoy N, Thompson J, Dhut S, Yates JR, Toda T. Identification of a conserved F-box protein 6 interactor essential for endocytosis and cytokinesis in fission yeast. Biochem J. 2009 May 13;420(2):169-77. PMID: 19243310
    22. Hoopmann MR, Merrihew GE, von Haller PD, MacCoss MJ. Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures. J Proteome Res. 2009 Apr;8(4):1870-5. PMCID: 2671646
    23. Holinger EP, Old WM, Giddings TH Jr, Wong C, Yates JR 3rd, Winey M. Budding Yeast Centrosome Duplication Requires Stabilization of Spc29 via Mps1-mediated Phosphorylation. J Biol Chem. 2009 May 8;284(19):12949-55. Epub 2009 Mar 5. PMID: 19269975
    24. Foltz DR, Jansen LE, Bailey AO, Yates JR 3rd, Bassett EA, Wood S, Black BE, Cleveland DW. Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell. 2009 May 1;137(3):472-84. PMID: 19410544
    25. Wong CC, Cociorva D, Venable JD, Xu T, Yates JR 3rd. Comparison of Different Signal Thresholds on Data Dependent Sampling in Orbitrap and LTQ Mass Spectrometry for the Identification of Peptides and Proteins in Complex Mixtures. J Am Soc Mass Spectrom. 2009 Aug;20(8):1405-14. PMCID:
    26. Jang CY, Coppinger JA, Seki A, Yates JR, 3rd, Fang G. Plk1 and Aurora A regulate the depolymerase activity and the cellular localization of Kif2a. J Cell Sci. 2009 May 1;122(Pt 9):1334-41. PMCID: 2671931
    27. Klammer AA, Park CY, Noble WS. Statistical calibration of the SEQUEST XCorr function. J Proteome Res. 2009 Apr;8(4):2106-13. PMCID:
    28. Shock TR, Thompson J, Yates JR 3rd, Madhani HD. Hog1 mitogen-activated protein kinase (MAPK) interrupts signal transduction between the Kss1 MAPK and the Tec1 transcription factor to maintain pathway specificity. Eukaryot Cell. 2009 Apr;8(4):606-16. Epub 2009 Feb 13. PMID: 19218425
    29. Park SK, Liao L, Kim JY, Yates JR, 3rd. A computational approach to correct arginine-to-proline conversion in quantitative proteomics. Nat Methods. 2009 Mar;6(3):184-5. PMCID:
    30. Welburn JP, Grishchuk EL, Backer CB, Wilson-Kubalek EM, Yates JR, 3rd, Cheeseman IM. The human kinetochore Ska1 complex facilitates microtubule depolymerization-coupled motility. Dev Cell. 2009 Mar;16(3):374-85. PMCID: 2746561
    31. Gonzalez-Begne M, Lu B, Han X, Hagen FK, Hand AR, Melvin JE, Yates JR. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). J Proteome Res. 2009 Mar;8(3):1304-14. PMCID: 2693447
    32. Ma L, Tsai MY, Wang S, Lu B, Chen R, Iii JR, Zhu X, Zheng Y. Requirement for Nudel and dynein for assembly of the lamin B spindle matrix. Nat Cell Biol. 2009 Mar;11(3):247-56. Epub 2009 Feb 8. PMID: 19198602
    33. Nakajima Y, Tyers RG, Wong CC, Yates JR 3rd, Drubin DG, Barnes G. Nbl1p: a Borealin/Dasra/CSC-1-like protein essential for Aurora/Ipl1 complex function and integrity in Saccharomyces cerevisiae. Mol Biol Cell. 2009 Mar;20(6):1772-84. Epub 2009 Jan 21. PMID: 19158380
    34. Cui Z, Chen X, Lu B, Park SK, Xu T, Xie Z, Xue P, Hou J, Hang H, Yates JR 3rd, Yang F. Preliminary quantitative profile of differential protein expression between rat L6 myoblasts and myotubes by stable isotope labeling with amino acids in cell culture. Proteomics. 2009 Mar;9(5):1274-92. PMID: 19253283
    35. Lal K, Prieto JH, Bromley E, Sanderson SJ, Yates JR 3rd, Wastling JM, Tomley FM, Sinden RE. Characterisation of Plasmodium invasive organelles; an ookinete microneme proteome. Proteomics. 2009 Mar;9(5):1142-51. PMID: 19206106
    36. Wang Y, Reddy B, Thompson J, Wang H, Noma K, Yates JR 3rd, Jia S. Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein. Mol Cell. 2009 Feb 27;33(4):428-37. PMID: 19250904
    37. Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates JR 3rd, Frank J, Manley JL. Molecular architecture of the human pre-mRNA 3' processing complex. Mol Cell. 2009 Feb 13;33(3):365-76. PMID: 19217410
    38. Carvalho PC, Cociorva D, Wong CC, Carvalho MD, Barbosa VC, Yates JR. Charge Prediction Machine: Tool for Inferring Precursor Charge States of Electron Transfer Dissociation Tandem Mass Spectra. Anal Chem. 2009 Feb 9. PMID: 19203245
    39. Csankovszki G, Collette K, Spahl K, Carey J, Snyder M, Petty E, Patel U, Tabuchi T, Liu H, McLeod I, Thompson J, Sarkesik A, Yates J, Meyer BJ, Hagstrom K. Three distinct condensin complexes control C. elegans chromosome dynamics. Curr Biol. 2009 Jan 13;19(1):9-19. PMID: 19119011
    40. Xu T, Wong CC, Kashina A, Yates JR 3rd. Identification of N-terminally arginylated proteins and peptides by mass spectrometry. Nat Protoc. 2009;4(3):325-32. PMID: 19229197
    41. 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
    42. Canterbury JD, Yi X, Hoopmann MR, MacCoss MJ. Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics. Anal Chem. 2008 Sep 15;80(18):6888-97. Epub 2008 Aug 12. PMID: 18693747
    43. 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
    44. Carvalho PC, Hewel J, Barbosa VC, Yates JR 3rd. Identifying differences in protein expression levels by spectral counting and feature selection. Genet Mol Res. 2008 Apr 15;7(2):342-56. PMID: 18551400
    45. 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
    46. Chen EI, McClatchy D, Park SK, Yates JR 3rd. Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome. Anal Chem. 2008 Nov 15;80(22):8694-701. Epub 2008 Oct 21. PMID: 18937422
    47. Chiranand W, McLeod I, Zhou H, Lynn JJ, Vega LA, Myers H, Yates JR 3rd, Lorenz MC, Gustin MC. CTA4 transcription factor mediates induction of nitrosative stress response in Candida albicans. Eukaryot Cell. 2008 Feb;7(2):268-78. Epub 2007 Dec 14.
    48. 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
    49. Creekmore AL, Walt KA, Schultz-Norton JR, Ziegler YS, McLeod IX, Yates JR, Nardulli AM. The role of retinoblastoma-associated proteins 46 and 48 in estrogen receptor alpha mediated gene expression. Mol Cell Endocrinol. 2008 Sep 10;291(1-2):79-86. Epub 2008 Jun 5. PMID: 18577416
    50. Dentin R, Hedrick S, Xie J, Yates J 3rd, Montminy M. Hepatic glucose sensing via the CREB coactivator CRTC2. Science. 2008 Mar 7;319(5868):1402-5. PMID: 18323454
    51. DiMaggio PA Jr, Floudas CA, Lu B, Yates JR 3rd. A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry. J Proteome Res. 2008 Apr;7(4):1584-93. Epub 2008 Mar 7. PMID: 18324765
    52. 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
    53. Ducat D, Kawaguchi S, Liu H, Yates JR 3rd, Zheng Y. Regulation of microtubule assembly and organization in mitosis by the AAA+ ATPase Pontin. Mol Biol Cell. 2008 Jul;19(7):3097-110. Epub 2008 May 7. PMID: 18463163
    54. 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
    55. 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
    56. Gassmann R, Essex A, Hu JS, Maddox PS, Motegi F, Sugimoto A, O'Rourke SM, Bowerman B, McLeod I, Yates JR 3rd, Oegema K, Cheeseman IM, Desai A. A new mechanism controlling kinetochore-microtubule interactions revealed by comparison of two dynein-targeting components: SPDL-1 and the Rod/Zwilch/Zw10 complex. Genes Dev. 2008 Sep 1;22(17):2385-99. PMID: 18765790
    57. Han X, Aslanian A, Yates JR 3rd. Mass spectrometry for proteomics. Curr Opin Chem Biol. 2008 Oct;12(5):483-90. Review. PMID: 18718552
    58. 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
    59. Jelluma N, Brenkman AB, McLeod I, Yates JR 3rd, Cleveland DW, Medema RH, Kops GJ. Chromosomal instability by inefficient Mps1 auto-activation due to a weakened mitotic checkpoint and lagging chromosomes. PLoS ONE. 2008 Jun 11;3(6):e2415.
    60. Kang R, Wan J, Arstikaitis P, Takahashi H, Huang K, Bailey AO, Thompson JX, Roth AF, Drisdel RC, Mastro R, Green WN, Yates JR 3rd, Davis NG, El-Husseini A. Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature. 2008 Dec 18;456(7224):904-9. PMID: 19092927
    61. Kline KG, Frewen B, Bristow MR, Maccoss MJ, Wu CC. High quality catalog of proteotypic peptides from human heart. J Proteome Res. 2008 Nov;7(11):5055-61. Epub 2008 Sep 20. PMID: 18803417
    62. Liao L, Park SK, Xu T, Vanderklish P, Yates JR 3rd. Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15281-6. Epub 2008 Sep 30. PMID: 18829439
    63. 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
    64. Lu B, Ruse CI, Yates JR 3rd. Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search. J Proteome Res. 2008 Aug;7(8):3628-34. Epub 2008 Jun 19. PMID: 18563924
    65. 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
    66. 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
    67. 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
    68. Prieto JH, Koncarevic S, Park SK, Yates J 3rd, Becker K. Large-scale differential proteome analysis in Plasmodium falciparum under drug treatment. PLoS ONE. 2008;3(12):e4098. Epub 2008 Dec 31. PMID: 19116658
    69. Rai R, Wong CC, Xu T, Leu NA, Dong DW, Guo C, McLaughlin KJ, Yates JR 3rd, Kashina A. Arginyltransferase regulates alpha cardiac actin function, myofibril formation and contractility during heart development. Development. 2008 Dec;135(23):3881-9. Epub 2008 Oct 23. Erratum in: Development. 2008 Dec;135(23):3971. PMID: 18948421
    70. 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
    71. Romijn EP, Yates JR 3rd. Analysis of organelles by on-line two-dimensional liquid chromatography-tandem mass spectrometry. Methods Mol Biol. 2008;432:1-16. PMID: 18370007
    72. 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
    73. 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
    74. Schultz-Norton JR, Ziegler YS, Likhite VS, Yates JR, Nardulli AM. Isolation of novel coregulatory protein networks associated with DNA-bound estrogen receptor alpha. BMC Mol Biol. 2008 Oct 30;9:97. PMID: 18973695
    75. 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
    76. 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
    77. 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
    78. Steiniger SC, Coppinger JA, Krüger JA, Yates J 3rd, Janda KD. Quantitative mass spectrometry identifies drug targets in cancer stem cell-containing side population. Stem Cells. 2008 Dec;26(12):3037-46. Epub 2008 Sep 18. PMID: 18802034
    79. 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
    80. Xia D, Sanderson SJ, Jones AR, Prieto JH, Yates JR, Bromley E, Tomley FM, Lal K, Sinden RE, Brunk BP, Roos DS, Wastling JM. The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. Genome Biol. 2008;9(7):R116. Epub 2008 Jul 21. PMID: 18644147
    81. 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
    82. Zhu H, Coppinger JA, Jang CY, Yates JR 3rd, Fang G. FAM29A promotes microtubule amplification via recruitment of the NEDD1-gamma-tubulin complex to the mitotic spindle. J Cell Biol. 2008 Dec 1;183(5):835-48. Epub 2008 Nov 24. PMID: 19029337
    83. 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
    84. 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 
    85. 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
    86. 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.
    87. Chen EI, Yates JR. Cancer Proteomics by Quantitative Shotgun Proteomics. Mol Oncol. 2007 Sep;1(2):144-159. PMID: 18443658
    88. 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 
    89. 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 
    90. 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.
    91. 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 
    92. 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 
    93. 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.
    94. 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.
    95. 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.
    96. 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 
    97. 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 
    98. 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.
    99. 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 
    100. 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 
    101. 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 
    102. Wan J, Roth AF, Bailey AO, Davis NG.  Palmitoylated proteins: purification and identification. Nat Protoc. 2007;2(7):1573-84.  PMID: 17585299 
    103. 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 
    104. 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 
    105. 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

    • Click here for 174 mass spec publications before 2007

  • Two-hybrid Analysis
    1. Brett CL, Plemel RL, Lobinger BT, Vignali M, Fields S, Merz AJ. Efficient termination of vacuolar Rab GTPase signaling requires coordinated action by a GAP and a protein kinase. J Cell Biol. 2008 Sep 22;182(6):1141-51. PMID: 18809726
    2. 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
    3. 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.
    4. Zhang Z, Hesselberth JR, Fields S. Genome-wide identification of spliced introns using a tiling microarray. Genome Res. 2007;17(4):503-9.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    11. Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale. Nature 2003;422:208-15.
    12. 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.
    13. 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.
    14. Gera JF, Hazbun TR, Fields S. Array-based methods for identifying protein-protein and protein-nucleic acid interactions. Methods Enzymol 2002;350:499-512.
    15. Hazbun TR, Fields S. A genome-wide screen for site-specific DNA-binding proteins. Mol Cell Proteomics 2002;1:538-43.
    16. 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.
    17. 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.
    18. Cagney G, Uetz P, Fields S. Two-hybrid analysis of the Saccharomyces cerevisiae 26S proteasome. Physiol Genomics 2001;7:27-34.
    19. Fields S. The interplay of biology and technology. Proc Natl Acad Sci U S A 2001;98:10051-10054.

  • Microscopy
    1. Choy RM, Kollman JM, Zelter A, Davis TN, Agard DA. Localization and orientation of the gamma-tubulin small complex components using protein tags as labels for single particle EM. J Struct Biol. 2009 Dec;168(3):571-4. PMCID:
    2. 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.
    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. 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.
    5. 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.
    6. 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.
    7. 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.
    8. Davis TN. Protein localization in proteomics. Curr Opin Chem Biol 2004;8(1):49-53.
    9. 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.
    10. 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.
    11. 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. Spreter T, Yip CK, Sanowar S, André I, Kimbrough TG, Vuckovic M, Pfuetzner RA, Deng W, Yu AC, Finlay BB, Baker D, Miller SI, Strynadka NC. A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nat Struct Mol Biol. 2009 May;16(5):468-76. Epub 2009 Apr 26. PMID: 19396170
    2. Zhu J, Luo BH, Barth P, Schonbrun J, Baker D, Springer TA. The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3. Mol Cell. 2009 Apr 24;34(2):234-49. PMID: 19394300
    3. Shen Y, Vernon R, Baker D, Bax A. De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR. 2009 Feb;43(2):63-78. Epub 2008 Nov 26. PMID: 19034676
    4. Luo BH, Karanicolas J, Harmacek LD, Baker D, Springer TA. Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. J Biol Chem. 2009 Feb 6;284(6):3917-24. Epub 2008 Nov 19. PMID: 19019827
    5. Barth P, Wallner B, Baker D. Prediction of membrane protein structures with complex topologies using limited constraints. Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1409-14. PMID: 19190187
    6. Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4144-9. Epub 2008 Mar 5. PMID: 18322008
    7. Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL. A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms. Cell. 2008 Sep 19;134(6):1007-18. PMID: 18805093
    8. Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science. 2005;309:1868-71.
    9. 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.
    10. 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.
    11. 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. QVALITY: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics. 2009 Apr 1;25(7):964-6. Epub 2009 Feb 4. PMID: 19193729
    2. Shimogawa MM, Widlund PO, Riffle M, Ess M, Davis TN. Bir1 is required for the tension checkpoint. Mol Biol Cell. 2009 Feb;20(3):915-23. Epub 2008 Dec 3. PMID: 19056681
    3. 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
    4. Qiu J, Noble WS. Predicting co-complexed protein pairs from heterogeneous data. PLoS Comput Biol. 2008 Apr 18;4(4):e1000054. PMID: 18421371
    5. Reynolds SM, Käll L, Riffle ME, Bilmes JA, Noble WS. Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol. 2008 Nov;4(11):e1000213. Epub 2008 Nov 7. PMID: 18989393
    6. 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
    7. 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
    8. Ben-Hur A and Noble WS. Choosing negative examples for the prediction of protein-protein interactions. Bioinformatics 2006;Suppl 1:S2, doi:10.
    9. Ben-Hur A and Noble WS. Kernel methods for predicting protein-protein interactions. Bioinformatics2005;Suppl 1:i38-i46.
    10. Riffle M, Malmstrom L, Davis TN. The Yeast Resource Center Public Data Repository. Nucleic Acids Res. 2005 Jan 1;33 Database Issue: D378-82.