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  • Urresti, J., Zhang, P., Moran-Losada, P., Yu, N. K., Negraes, P. D., Trujillo, C. A., Antaki, D., Amar, M., Chau, K., Pramod, A. B., Diedrich, J., Tejwani, L., et al. Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism Molecular Psychiatry  2021  DOI:10.1038/s41380-021-01243-6  PMID:34433918
  • Robinson, K. E., Holding, M. L., Whitford, M. D., Saviola, A. J., Yates III, J. R., Clark, R. W. Phenotypic and functional variation in venom and venom resistance of two sympatric rattlesnakes and their prey Journal of Evolutionary Biology  2021 34:1447-1465  DOI:10.1111/jeb.13907  PMID:34322920
  • Hancock, W., Tabb, D. L., McDonald, H., Yates III, J. R., Brown, K., Yao, X. D., Fenselau, C., Lo, L. C., Kuo, C. H., Griffin, T., Aebersold, R., Korenberg, M., et al. Where Are They Now...? Journal of Proteome Research  2021 20:3775-3781  DOI:10.1021/acs.jproteome.1c00582  PMID:34353030
  • Arslanhan, M. D., Rauniyar, N., Yates III, J. R., Firat-Karalar, E. N. Aurora Kinase A proximity map reveals centriolar satellites as regulators of its ciliary function EMBO Reports  2021 22  DOI:10.15252/embr.202051902  PMID:34169630  PMCID:PMC8339716
  • Mohieldin, A. M., Pala, R., Beuttler, R., Moresco, J. J., Yates III, J. R., Nauli, S. M. Ciliary extracellular vesicles are distinct from the cytosolic extracellular vesicles Journal of Extracellular Vesicles  2021 10  DOI:10.1002/jev2.12086  PMID:33936569  PMCID:PMC8077156
  • Negraes, P. D., Trujillo, C. A., Yu, N. K., Wu, W., Yao, H., Liang, N., Lautz, J. D., Kwok, E., McClatchy, D., Diedrich, J., de Bartolome, S. M., Truong, J., et al. Altered network and rescue of human neurons derived from individuals with early-onset genetic epilepsy Molecular Psychiatry  2021  DOI:10.1038/s41380-021-01104-2  PMID:33888873
  • Bamberger, C., Pankow, S., Martinez-Bartolome, S., Ma, M., Diedrich, J., Rissman, R. A., Yates III, J. R. Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer's Disease Journal of Proteome Research  2021 20:2762-2771  DOI:10.1021/acs.jproteome.0c00912  PMID:33872013  PMCID:PMC8477671
  • Cui, H. S., Kapur, M., Diedrich, J. K., Yates III, J. R., Ackerman, S. L., Schimmel, P. Regulation of ex-translational activities is the primary function of the multi-tRNA synthetase complex Nucleic Acids Research  2021 49:3603-3616  DOI:10.1093/nar/gkaa1183  PMID:33341895  PMCID:PMC8053116
  • Coutinho-Rodrigues, C. J. B., da Rosa, R. L., de Freitas, M. C., Berger, M., Santi, L., Beys-da-Silva, W. O., Yates III, J. R. Exposure to a sublethal menadione concentration modifies the mycelial secretome and conidial enzyme activities of Metarhizium anisopliae sensu lato and increases its virulence against Rhipicephalus microplus Microbiological Research  2021 248  DOI:10.1016/j.micres.2021.126753  PMID:33882376
  • Bagdonaite, I., Thompson, A. J., Wang, X. N., Sogaard, M., Fougeroux, C., Frank, M., Diedrich, J. K., Yates III, J. R., Salanti, A., Vakhrushev, S. Y., Paulson, J. C., Wandall, H. H. Site-Specific O-Glycosylation Analysis of SARS-CoV-2 Spike Protein Produced in Insect and Human Cells Viruses-Basel  2021 13  DOI:10.3390/v13040551  PMID:33806155  PMCID:PMC8064498
  • Amar, M., Pramod, A. B., Yu, N. K., Herrera, V. M., Qiu, L. R., Moran-Losada, P., Zhang, P., Trujillo, C. A., Ellegood, J., Urresti, J., Chau, K., Diedrich, J., et al. Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling Molecular Psychiatry  2021  DOI:10.1038/s41380-021-01052-x  PMID:33727673
  • Pirie, E., Oh, C. K., Zhang, X., Han, X. M., Cieplak, P., Scott, H. R., Deal, A. K., Ghatak, S., Martinez, F. J., Yeo, G. W., Yates III, J. R., Nakamura, T., et al. S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD Proceedings of the National Academy of Sciences of the United States of America  2021 118  DOI:10.1073/pnas.2021368118  PMID:33692125  PMCID:PMC7980404
  • Kim, T. K., Tirloni, L., Bencosme-Cuevas, E., Kim, T. H., Diedrich, J. K., Yates III, J. R., Mulenga, A. Borrelia burgdorferi infection modifies protein content in saliva of Ixodes scapularis nymphs BMC Genomics  2021 22  DOI:10.1186/s12864-021-07429-0  PMID:33663385  PMCID:PMC7930271
  • Choi, C. P., Tay, R. J., Starostik, M. R., Feng, S. H., Moresco, J. J., Montgomery, B. E., Xu, E., Hammonds, M. A., Schatz, M. C., Montgomery, T. A., Yates III, J. R., Jacobsen, S. E., et al. SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans eLife  2021 10  DOI:10.7554/eLife.60681  PMID:33587037  PMCID:PMC7884074
  • Lu, S., Ye, Q. Z., Singh, D., Cao, Y., Diedrich, J. K., Yates III, J. R., Villa, E., Cleveland, D. W., Corbett, K. D. The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein Nature Communications  2021 12  DOI:10.1038/s41467-020-20768-y  PMID:33479198  PMCID:PMC7820290
  • Zanon, P., Pizzato, S. B., da Rosa, R. L., Terraciano, P. B., Moraes, J. A., Beys-da-Silva, W. O., Santi, L., Yates III, J. R., Passos, E. P., Barja-Fidalgo, C., Guimaraes, J. A., Berger, M. Urine proteomic analysis reveals alterations in heme/hemoglobin and aminopeptidase metabolism during Lonomia obliqua venom-induced acute kidney injury Toxicology Letters  2021 341:11-22  DOI:10.1016/j.toxlet.2021.01.012  PMID:33472085
  • Tran, J. R., Paulson, D. I., Moresco, J. J., Adam, S. A., Yates III, J. R., Goldman, R. D., Zheng, Y. X. An APEX2 proximity ligation method for mapping interactions with the nuclear lamina Journal of Cell Biology  2021 220  DOI:10.1083/jcb.202002129  PMID:33306092  PMCID:PMC7737704
  • Shan, C. M., Bao, K. H., Diedrich, J., Chen, X., Lu, C., Yates III, J. R., Jia, S. T. The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin Cell Reports  2020 33  DOI:10.1016/j.celrep.2020.108561  PMID:33378674  PMCID:PMC7896557
  • Chaves, D. A., Dai, H., Li, L. C., Moresco, J. J., Oh, M. E., Conte, D., Yates III, J. R., Mello, C. C., Gu, W. F. The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans Molecular Cell  2020 81  DOI:10.1016/j.molcel.2020.12.004  PMID:33378643
  • Yu, H. Y., Lu, S., Gasior, K., Singh, D., Vazquez-Sanchez, S., Tapia, O., Toprani, D., Beccari, M. S., Yates III, J. R., Cruz, S., Newby, J. M., Lafarga, M., et al. HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells Science  2020 371  DOI:10.1126/science.abb4309  PMID:33335017  PMCID:PMC8286096
  • Hong, S. L., Yu, C. H., Wang, P., Shi, Y., Cao, W. Q., Cheng, B., Chapla, D. G., Ma, Y. H., Li, J., Rodrigues, E., Narimatsu, Y., Yates III, J. R., et al. Glycoengineering of NK Cells with Glycan Ligands of CD22 and Selectins for B-Cell Lymphoma Therapy Angewandte Chemie-International Edition  2020 60:3603-3610  DOI:10.1002/anie.202005934  PMID:33314603
  • Nakamura, T., Oh, C. K., Liao, L. J., Zhang, X., Lopez, K. M., Gibbs, D., Deal, A. K., Scott, H. R., Spencer, B., Masliah, E., Rissman, R. A., Yates III, J. R., et al. Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease Science  2020 371  DOI:10.1126/science.aaw0843  PMID:33273062  PMCID:PMC8091809
  • Ma, Y. H., McClatchy, D. B., Martinez-Bartolome, S., Bamberger, C., Yates III, J. R. Temporal Quantitative Profiling of Newly Synthesized Proteins during A beta Accumulation Journal of Proteome Research  2020 20:763-775  DOI:10.1021/acs.jproteome.0c00645  PMID:33147027  PMCID:PMC7775911
  • Alves, A., Diel, L., Ramos, G., Pinto, A., Bernardi, L., Yates III, J. R., Lamers, M. Tumor microenvironment and Oral Squamous Cell Carcinoma: A crosstalk between the inflammatory state and tumor cell migration Oral Oncology  2020 112  DOI:10.1016/j.oraloncology.2020.105038  PMID:33129055
  • Berndsen, Z. T., Chakraborty, S., Wang, X. N., Cottrell, C. A., Torres, J. L., Diedrich, J. K., Lopez, C. A., Yates III, J. R., van Gils, M. J., Paulson, J. C., Gnanakaran, S., Ward, A. B. Visualization of the HIV-1 Env glycan shield across scales Proceedings of the National Academy of Sciences of the United States of America  2020 117:28014-28025  DOI:10.1073/pnas.2000260117  PMID:33093196  PMCID:PMC7668054
  • Mun, D. G., Renuse, S., Saraswat, M., Madugundu, A., Udainiya, S., Kim, H., Park, S. K. R., Zhao, H., Nirujogi, R. S., Na, C. H., Kannan, N., Yates III, J. R., et al. PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies Analytical Chemistry  2020 92:14466-14475  DOI:10.1021/acs.analchem.0c02513  PMID:33079518
  • Bangaru, S., Ozorowski, G., Turner, H. L., Antanasijevic, A., Huang, D. L., Wang, X. N., Torres, J. L., Diedrich, J. K., Tian, J. H., Portnoff, A. D., Patel, N., Massare, M. J., et al. Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate Science  2020 370:1089-1094  DOI:10.1126/science.abe1502  PMID:33082295  PMCID:PMC7857404
  • Huang, L., McClatchy, D. B., Maher, P., Liang, Z. B., Diedrich, J. K., Soriano-Castell, D., Goldberg, J., Shokhirev, M., Yates III, J. R., Schubert, D., Currais, A. Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death Cell Death & Disease  2020 11  DOI:10.1038/s41419-020-03020-9  PMID:33024077  PMCID:PMC7538552
  • McClatchy, D. B., Martinez-Bartolome, S., Gao, Y., Lavallee-Adam, M., Yates III, J. R. Quantitative analysis of global protein stability rates in tissues Scientific Reports  2020 10  DOI:10.1038/s41598-020-72410-y  PMID:32994440  PMCID:PMC7524747
  • Gomes, F. P., Park, R., Viana, A. G., Fernandez-Costa, C., Topper, E., Kaya, A., Memili, E., Yates III, J. R., Moura, A. A. Protein signatures of seminal plasma from bulls with contrasting frozen-thawed sperm viability Scientific Reports  2020 10  DOI:10.1038/s41598-020-71015-9  PMID:32887897  PMCID:PMC7474054
  • Chen, H., Victor, A. K., Klein, J., Tacer, K. F., Tai, D. J. C., de Esch, C., Nuttle, A., Temirov, J., Burnett, L. C., Rosenbaum, M., Zhang, Y. Y., Ding, L., et al. Loss of MAGEL2 in Prader-Willi syndrome leads to decreased secretory granule and neuropeptide production JCI Insight  2020 5  DOI:10.1172/jci.insight.138576  PMID:32879135  PMCID:PMC7526459
  • Souza, A. P. B., Lopes, T. N., da Silva, A. F. T., Santi, L., Beys-da-Silva, W. O., Yates III, J. R., Bustamante, I. C. Changes in porcine cauda epididymal fluid proteome by disrupting the HPT axis: Unveiling potential mechanisms of male infertility Molecular Reproduction and Development  2020  DOI:10.1002/mrd.23408  PMID:32749760
  • Srzentic, K., Fornelli, L., Tsybin, Y. O., Loo, J. A., Seckler, H., Agar, J. N., Anderson, L. C., Bai, D. N. L., Beck, A., Brodbelt, J. S., van der Burgt, Y. E. M., Chamot-Rooke, J., et al. Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry Journal of the American Society for Mass Spectrometry  2020 31:1783-1802  DOI:10.1021/jasms.0c00036  PMID:32812765  PMCID:PMC7539639
  • Santi, L., Beys-da-Silva, W. O., Berger, M., Yates III, J. R., Brandelli, A., Vainstein, M. H. Penicillium oxalicum secretomic analysis identify plant cell wall degrading enzymes important for fruit juice extraction Journal of Food Science and Technology-Mysore  2020  DOI:10.1007/s13197-020-04688-9
  • Souza, A. P. B., Lopes, T. N., Silva, A. F. T., Santi, L., Beys-da-Silva, W. O., Yates III, J. R., Bustamante, I. C. How does secondary hypogonadism affect the spermatozoa proteome? Lessons from a porcine animal model Reproduction Fertility and Development  2020  DOI:10.1071/rd20017
  • Yates III, J. R. Amblyomma americanum serpin 41 (AAS41) inhibits inflammation by targeting chymase and chymotrypsin International Journal of Biological Macromolecules  2020 156:1007-1021  DOI:10.1016/j.ijbiomac.2020.04.088  PMID:32320803
  • Mohieldin, A. M., Pala, R., Sherpa, R. T., Alanazi, M., Alanazi, A., Shamloo, K., Ahsan, A., AbouAlaiwi, W. A., Moresco, J. J., Yates III, J. R., Nauli, S. M. Proteomic Identification Reveals the Role of Ciliary Extracellular-Like Vesicle in Cardiovascular Function Advanced Science  2020  DOI:10.1002/advs.201903140  PMID:32832346  PMCID:PMC7435257
  • Giadone, R. M., Liberti, D. C., Matte, T. M., Rosarda, J. D., Torres-Arancivia, C., Ghosh, S., Diedrich, J. K., Pankow, S., Skvir, N., Jean, J. C., Yates III, J. R., Wilson, A. A., et al. Expression of Amyloidogenic Transthyretin Drives Hepatic Proteostasis Remodeling in an Induced Pluripotent Stem Cell Model of Systemic Amyloid Disease Stem Cell Reports  2020 15:515-528  DOI:10.1016/j.stemcr.2020.07.003  PMID:32735824  PMCID:PMC7419739
  • Chen, M. R., Kuhle, B., Diedrich, J., Liu, Z., Moresco, J. J., Yates III, J. R., Pan, T., Yang, X. L. Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation Nucleic Acids Research  2020 48:6445-6457  DOI:10.1093/nar/gkaa469  PMID:32484512  PMCID:PMC7337962
  • Yates III, J. R. The Journey Is the Reward, a Taoist Proverb: John B. Fenn Award for Distinguished Contribution in Mass Spectrometry Lecture Journal of the American Society for Mass Spectrometry  2020 31:1327-1336  DOI:10.1021/jasms.0c00073  PMID:32338000
  • Fernandez-Costa, C., Martinez-Bartolome, S., McClatchy, D. B., Saviola, A. J., Yu, N. K., Yates III, J. R. Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results Journal of Proteome Research  2020 19:3153-3161  DOI:10.1021/acs.jproteome.0c00153  PMID:32510229
  • Alghanem, B., Ali, R., Nehdi, A., Al Zahrani, H., Altolayyan, A., Shaibah, H., Baz, O., Alhallaj, A., Moresco, J. J., Diedrich, J. K., Yates III, J. R., Boudjelal, M. Proteomics Profiling of KAIMRC1 in Comparison to MDA-MB231 and MCF-7 International Journal of Molecular Sciences  2020 21  DOI:10.3390/ijms21124328  PMID:32570693  PMCID:PMC7352455
  • Freund, E. C., Sapiro, A. L., Li, Q., Linder, S., Moresco, J. J., Yates III, J. R., Li, J. B. Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing Cell Reports  2020 31  DOI:10.1016/j.celrep.2020.107656  PMID:32433965  PMCID:PMC7306178
  • Thompson, A. J., Cao, L., Ma, Y., Wang, X., Diedrich, J. K., Kikuchi, C., Willis, S., Worth, C., McBride, R., Yates III, J. R., Paulson, J. C. Human Influenza Virus Hemagglutinins Contain Conserved Oligomannose N-Linked Glycans Allowing Potent Neutralization by Lectins Cell Host & Microbe  2020 27:725-735  DOI:10.1016/j.chom.2020.03.009  PMID:32298658  PMCID:PMC7158820
  • Kagan, J., Moritz, R. L., Mazurchuk, R., Lee, J. H., Kharchenko, P. V., Rozenblatt-Rosen, O., Ruppin, E., Edfors, F., Ginty, F., Goltsev, Y., Wells, J. A., LaCava, J., et al. National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions Journal of Proteome Research  2020 19:1900-1912  DOI:10.1021/acs.jproteome.0c00021  PMID:32163288
  • Rantalainen, K., Berndsen, Z. T., Antanasijevic, A., Schiffner, T., Zhang, X., Lee, W. H., Torres, J. L., Zhang, L., Irimia, A., Copps, J., Zhou, K. H., Kwon, Y. D., et al. HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies Cell Reports  2020 31  DOI:10.1016/j.celrep.2020.107583  PMID:32348769  PMCID:PMC7196886
  • Fuller, G. G., Han, T., Freeberg, M. A., Moresco, J. J., Niaki, A. G., Roach, N. P., Yates III, J. R., Myong, S., Kim, J. K. RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia Elife  2020 9  DOI:10.7554/eLife.48480  PMID:32298230  PMCID:PMC7162659
  • Yang, S., Svensson, M. N. D., Harder, N. H. O., Hsieh, W. C., Santelli, E., Kiosses, W. B., Moresco, J. J., Yates III, J. R., King, C. C., Liu, L., Stanford, S. M., Bottini, N. PTPN22 phosphorylation acts as a molecular rheostat for the inhibition of TCR signaling Science Signaling  2020 13  DOI:10.1126/scisignal.aaw8130  PMID:32184287
  • Saviola, A. J., Negrao, F., Yates III, J. R. Proteomics of Select Neglected Tropical Diseases Annual Review of Analytical Chemistry  2020 13:315-336  DOI:10.1146/annurev-anchem-091619-093003  PMID:32109150
  • Gomes, F. P., Diedrich, J. K., Saviola, A. J., Memili, E., Moura, A. A., Yates III, J. R. EThcD and 213 nm UVPD for top-down analysis of bovine seminal plasma proteoforms on electrophoretic and chromatographic time frames Analytical Chemistry  2020 92:2979-2987  DOI:10.1021/acs.analchem.9b03856  PMID:31962043
  • Weber, A., Argenti, L. E., de Souza, A. P. B., Santi, L., Beys-da-Silva, W. O., Yates III, J. R., Bustamante, I. C. Ready for the journey: a comparative proteome profiling of porcine cauda epididymal fluid and spermatozoa Cell and Tissue Research  2020 379:389-405  DOI:10.1007/s00441-019-03080-0  PMID:31444576
  • Kim, T. K., Tirloni, L., Pinto, A. F. M., Diedrich, J. K., Moresco, J. J., Yates III, J. R., Vaz, I. D., Mulenga, A. Time-resolved proteomic profile of Amblyomma americanum tick saliva during feeding Plos Neglected Tropical Diseases  2020 14  DOI:10.1371/journal.pntd.0007758  PMID:32049966  PMCID:PMC7041860
  • Catania, S., Dumesic, P. A., Pimentel, H., Nasif, A., Stoddard, C. I., Burke, J. E., Diedrich, J. K., Cook, S., Shea, T., Geinger, E., Lintner, R., Yates III, J., et al. Evolutionary persistence of DNA methylation for millions of years after ancient loss of a de novo methyltransferase Cell  2020 180:263-277  DOI:10.1016/j.cell.2019.12.012  PMID:31955845
  • Fernandez-Costa, C., Martinez-Bartolome, S., McClatchy, D., Yates III, J. R. Improving proteomics data reproducibility with a dual-search strategy Analytical Chemistry  2020 92:1697-1701  DOI:10.1021/acs.analchem.9b04955  PMID:31880919
  • Jaiswal, D., Turniansky, R., Moresco, J. J., Ikram, S., Ramaprasad, G., Akinwole, A., Wolf, J., Yates III, J. R., Green, E. M. Function of the MYND domain and C-terminal region in regulating the subcellular localization and catalytic activity of the SMYD family lysine methyltransferase Set5 Molecular and Cellular Biology  2020 40:e00341-19  DOI:10.1128/mcb.00341-19
  • Singh, J. P., Qian, K., Lee, J. S., Zhou, J., Han, X., Zhang, B., Ong, Q., Ni, W., Jiang, M., Ruan, H. B., Li, M. D., Zhang, K., et al. O-GlcNAcase targets pyruvate kinase M2 to regulate tumor growth Oncogene  2020 39:560-573  DOI:10.1038/s41388-019-0975-3  PMID:31501520
  • Stein, B. D., Calzolari, D., Hellberg, K., Hu, Y. S., He, L., Hung, C. M., Toyama, E. Q., Ross, D. S., Lillemeier, B. F., Cantley, L. C., Yates III, J. R., Shaw, R. J. Quantitative in vivo proteomics of metformin response in liver reveals AMPK-dependent and -independent signaling networks Cell Reports  2019 29:3331-3348  DOI:10.1016/j.celrep.2019.10.117  PMID:31801093
  • Sonntag, T., Moresco, J. J., Yates III, J. R., Montminy, M. The KLDpT activation loop motif is critical for MARK kinase activity PLoS One  2019 14  DOI:10.1371/journal.pone.0225727  PMID:31794565  PMCID:PMC6890249
  • Negrao, F., Diedrich, J. K., Giorgio, S., Eberlin, M. N., Yates III, J. R. Tandem mass tag proteomic analysis of in vitro and in vivo models of cutaneous leishmaniasis reveals parasite-specific and nonspecific modulation of proteins in the host Acs Infectious Diseases  2019 5:2136-2147  DOI:10.1021/acsinfecdis.9b00275  PMID:31600437
  • Rosa, R. L., Berger, M., Santi, L., Driemeier, D., Terraciano, P. B., Campos, A. R., Guimaraes, J. A., Vainstein, M. H., Yates III, J. R., Beys-da-Silva, W. O. Proteomics of rat lungs infected by cryptococcus gattii reveals a potential Warburg-like effect Journal of Proteome Research  2019 18:3885-3895  DOI:10.1021/acs.jproteome.9b00326  PMID:31502459
  • Gomes, F. P., Yates III, J. R. Recent trends of capillary electrophoresis-mass spectrometry in proteomics research Mass Spectrometry Reviews  2019  DOI:10.1002/mas.21599  PMID:31407381
  • Stein, B. D., Herzig, S., Martinez-Bartolome, S., Lavallee-Adam, M., Shaw, R. J., Yates III, J. R. Comparison of CRISPR genomic tagging for affinity purification and endogenous immunoprecipitation coupled with quantitative mass spectrometry to identify the dynamic AMPKα2 interactome Journal of Proteome Research  2019 18:3703-3714  DOI:10.1021/acs.jproteome.9b00378  PMID:31398040
  • Brandstaedter, C., Delahunty, C., Schipper, S., Rahlfs, S., Yates III, J. R., Becker, K. The interactome of 2-Cys peroxiredoxins in Plasmodium falciparum Scientific Reports  2019 9  DOI:10.1038/s41598-019-49841-3  PMID:31537845  PMCID:PMC6753162
  • Schiapparelli, L. M., Shah, S. H., Ma, Y., McClatchy, D. B., Sharma, P., Li, J., Yates III, J. R., Goldberg, J. L., Cline, H. T. The retinal ganglion cell transportome identifies proteins transported to axons and presynaptic compartments in the visual system in vivo Cell Reports  2019 28:1935-1947  DOI:10.1016/j.celrep.2019.07.037  PMID:31412257  PMCID:PMC6707540
  • Sharma, P., Mesci, P., Carromeu, C., McClatchy, D. R., Schiapparelli, L., Yates III, J. R., Muotri, A. R., Cline, H. T. Exosomes regulate neurogenesis and circuit assembly Proceedings of the National Academy of Sciences of the United States of America  2019 116:16086-16094  DOI:10.1073/pnas.1902513116  PMID:31320591  PMCID:PMC6689941
  • Xavier, M. A., Tirloni, L., Torquato, R., Tanaka, A., Pinto, A. F. M., Diedrich, J. K., Yates III, J. R., Vaz, I. D., Seixas, A., Termignoni, C. Blood anticlotting activity of a Rhipicephalus microplus cathepsin L-like enzyme Biochimie  2019 163:12-20  DOI:10.1016/j.biochi.2019.04.025  PMID:31059753
  • Negrao, F., Giorgio, S., Eberlin, M. N., Yates III, J. R. Comparative proteomic analysis of murine cutaneous lesions induced by leishmania amazonensis or leishmania major ACS Infectious Diseases  2019 5:1295-1305  DOI:10.1021/acsinfecdis.8b00370  PMID:31094195
  • Di Maggio, L. S., Tirloni, L., Pinto, A. F. M., Diedrich, J. K., Yates III, J. R., Carmona, C., Berasain, P., Vaz, I. D. Dataset supporting the proteomic differences found between excretion/secretion products from two isolates of Fasciola hepatica newly excysted juveniles (NEJ) derived from different snail hosts Data in Brief  2019 25  DOI:10.1016/j.dib.2019.104272  PMID:31384652  PMCID:PMC6661421
  • Alonso, A. M., Turowski, V. R., Ruiz, D. M., Orelo, B. D., Moresco, J. J., Yates III, J. R., Corvi, M. M. Exploring protein myristoylation in Toxoplasma gondii Experimental Parasitology  2019 203:8-18  DOI:10.1016/j.exppara.2019.05.007  PMID:31150653
  • Martinez-Bartolome, S., Bamberger, T. C., Lavallee-Adam, M., McClatchy, D. B., Yates III, J. R. Proteomics INTegrator (PINT): an online tool to store, query, and visualize large proteomics experiment results Journal of Proteome Research  2019 18:2999-3008  DOI:10.1021/acs.jproteome.8b00711  PMID:31260318
  • Burke, J. E., Longhurst, A. D., Natarajan, P., Rao, B. D., Liu, J., Sales-Lee, J., Mortensen, Y., Moresco, J. J., Diedrich, J. K., Yates III, J. R., Madhani, H. D. A non-dicer RNase III and four other novel factors required for RNAi-mediated transposon suppression in the human pathogenic yeast Cryptococcus neoformans G3-Genes Genomes Genetics  2019 9:2235-2244  DOI:10.1534/g3.119.400330  PMID:31092606  PMCID:PMC6643885
  • Yates III, J. R. Innovation: risk-takers and visionaries Journal of Proteome Research  2019 18:2693-2694  DOI:10.1021/acs.jproteome.8b00460  PMID:31120765
  • Di Maggio, L. S., Tirloni, L., Pinto, A. F. M., Diedrich, J. K., Yates III, J. R., Carmona, C., Berasain, P., da Silva Vaz Jr., I. A proteomic comparison of excretion/secretion products in Fasciola hepatica newly excysted juveniles (NEJ) derived from Lymnaea viatrix or Pseudosuccinea columella Experimental Parasitology  2019 201:11-20  DOI:10.1016/j.exppara.2019.04.004  PMID:31022392
  • Xavier, M. A., Tirloni, L., Pinto, A. F. M., Diedrich, J. K., Yates III, J. R., Gonzales, S., Farber, M., Vaz, I. D., Termignoni, C. Tick Gene's organ engagement in lipid metabolism revealed by a combined transcriptomic and proteomic approach Ticks and Tick-Borne Diseases  2019 10:787-797  DOI:10.1016/j.ttbdis.2019.03.013  PMID:30904537
  • Kachaev, Z. M., Lebedeva, L. A., Shaposhnikov, A. V., Moresco, J. J., Yates III, J. R., Schedl, P., Shidlovskii, Y. V. Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila FEBS Letters  2019 593:1102-1112  DOI:10.1002/1873-3468.13391  PMID:31001806  PMCID:PMC6538421
  • Cho, Y., Tachibana, S., Hazen, B. C., Moresco, J. J., Yates III, J. R., Kok, B., Saez, E., Ross, R. S., Russell, A. P., Kralli, A. Perm1 regulates CaMKII activation and shapes skeletal muscle responses to endurance exercise training Molecular Metabolism  2019 23:88-97  DOI:10.1016/j.molmet.2019.02.009  PMID:30862473  PMCID:PMC6480336
  • Santi, L., Coutinho-Rodrigues, C. J. B., Berger, M., Klein, L. A. S., De Souza, E. M., Rosa, R. L., Guimaraes, J. A., Yates III, J. R., Perinotto, W. M. S., Bittencourt, Vrep, Beys-da-Silva, W. O. Secretomic analysis of Beauveria bassiana related to cattle tick, Rhipicephalus microplus, infection Folia Microbiologica  2019 64:361-372  DOI:10.1007/s12223-018-0659-3  PMID:30361880
  • Jones, B. K., Saviola, A. J., Reilly, S. B., Stubbs, A. L., Arida, E., Iskandar, D. T., McGuire, J. A., Yates III, J. R., Mackessy, S. P. Venom composition in a phenotypically variable Pit Viper (Trimeresurus insularis) across the Lesser Sunda archipelago Journal of Proteome Research  2019 18:2206-2220  DOI:10.1021/acs.jproteome.9b00077  PMID:30958009
  • Xie, J., Han, X., Zhao, C., Canonigo-Balancio, A. J., Yates III, J. R., Li, Y., Lillemeier, B. F., Altman, A. Phosphotyrosine-dependent interaction between the kinases PKCθ and Zap70 promotes proximal TCR signaling Science Signaling  2019 12  DOI:10.1126/scisignal.aar3349  PMID:30992398
  • Bernardi, L., Pinto, A. F. M., Mendes, E., Yates III, J. R., Lamers, M. L. Lonomia obliqua bristle extract modulates Rac1 activation, membrane dynamics and cell adhesion properties Toxicon  2019 162:32-39  DOI:10.1016/j.toxicon.2019.02.019  PMID:30849455
  • Fontoura, R., Daroit, D. J., Correa, A. P. F., Moresco, K. S., Santi, L., Beys-da-Silva, W. O., Yates III, J. R., Moreira, J. C. F., Brandelli, A. Characterization of a novel antioxidant peptide from feather keratin hydrolysates New Biotechnology  2019 49:71-76  DOI:10.1016/j.nbt.2018.09.003  PMID:30223040
  • Shimojo, M., Madara, J., Pankow, S., Liu, X., Yates III, J., Sudhof, T. C., Maximov, A. Synaptotagmin-11 mediates a vesicle trafficking pathway that is essential for development and synaptic plasticity Genes & Development  2019 33:365-376  DOI:10.1101/gad.320077.118  PMID:30808661  PMCID:PMC6411015
  • Kim, J. J., Savas, J. N., Miller, M. T., Hu, X. D., Carromeu, C., Lavallee-Adam, M., Freitas, B. C. G., Muotri, A. R., Yates III, J. R., Ghosh, A. Proteomic analyses reveal misregulation of LIN28 expression and delayed timing of glial differentiation in human iPS cells with MECP2 loss-of-function PLoS One  2019 14  DOI:10.1371/journal.pone.0212553  PMID:30789962
  • Park, S. K. R., Jung, T., Thuy-Boun, P. S., Wang, A. Y., Yates III, J. R., Wolan, D. W. ComPIL 2.0: An updated comprehensive metaproteomics database Journal of Proteome Research  2019 18:616-622  DOI:10.1021/acs.jproteome.8b00722  PMID:30525664
  • Antonucci, L., Di Magno, L., D'Amico, D., Manni, S., Serrao, S. M., Di Pastena, F., Bordone, R., Yurtsever, Z. N., Caimano, M., Petroni, M., Giorgi, A., Schinina, M. E., et al. Mitogen-activated kinase kinase kinase 1 inhibits hedgehog signaling and medulloblastoma growth through GLI1 phosphorylation International Journal of Oncology  2019 54:505-514  DOI:10.3892/ijo.2018.4638  PMID:30483764  PMCID:PMC6317670
  • Pankow, S., Martinez-Bartolome, S., Bamberger, C., Yates III, J. R. Understanding molecular mechanisms of disease through spatial proteomics Current Opinion in Chemical Biology  2019 48:19-25  DOI:10.1016/j.cbpa.2018.09.016  PMID:30308467  PMCID:PMC6435883
  • Correia, S. P.*, Chan, A. B.*, Vaughan, M., Zolboot, N., Perea, V., Huber, A. L., Kriebs, A., Moresco, J. J., Yates III, J. R., Lamia, K. A. The circadian E3 ligase complex SCFFBXL3+CRY targets TLK2 Scientific Reports  2019 9  DOI:10.1038/s41598-018-36618-3  PMID:30655559  PMCID:PMC6336870 (* = equal contribution)
  • Pankow, S., Bamberger, C., Yates III, J. R. A posttranslational modification code for CFTR maturation is altered in cystic fibrosis Science Signaling  2019 12  DOI:10.1126/scisignal.aan7984  PMID:30600261
  • Bao, K., Shan, C. M., Moresco, J., Yates III, J., Jia, S. Anti-silencing factor Epe1 associates with SAGA to regulate transcription within heterochromatin Genes & Development  2019 33:116-126  DOI:10.1101/gad.318030.118  PMID:30573453
  • Wang, J., Yates III, J. R., Kashina, A. Biochemical analysis of protein arginylation Methods in Enzymology  2019 626:89-113  DOI:10.1016/bs.mie.2019.07.028
  • Cheng, L. C., Baboo, S., Lindsay, C., Brusman, L., Martinez-Bartolome, S., Tapia, O., Zhang, X., Yates III, J. R., Gerace, L. Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells Nucleus  2019 10:126-143  DOI:10.1080/19491034.2019.1618175  PMID:31142202  PMCID:PMC6550788
  • Wortham, M., Benthuysen, J. R., Wallace, M., Savas, J. N., Mulas, F., Divakaruni, A. S., Liu, F., Albert, V., Taylor, B. L., Sui, Y., Saez, E., Murphy, A. N., et al. Integrated in vivo quantitative proteomics and nutrient tracing reveals age-related metabolic rewiring of pancreatic β cell function Cell Reports  2018 25:2904-2918  DOI:10.1016/j.celrep.2018.11.031  PMID:30517875  PMCID:PMC6317899
  • Ritter, A. C., Santi, L., Vannini, L., Beys-da-Silva, W. O., Gozzi, G., Yates III, J., Ragni, L., Brandelli, A. Comparative proteomic analysis of foodborne Salmonella Enteritidis SE86 subjected to cold plasma treatment Food Microbiology  2018 76:310-318  DOI:10.1016/j.fm.2018.06.012  PMID:30166156
  • Louka, P., Vasudevan, K. K., Guha, M., Joachimiak, E., Wloga, D., Tomasi, R. F. X., Baroud, C. N., Dupuis-Williams, P., Galati, D. F., Pearson, C. G., Rice, L. M., Moresco, J. J., et al. Proteins that control the geometry of microtubules at the ends of cilia Journal of Cell Biology  2018 217:4298-4313  DOI:10.1083/jcb.201804141  PMID:30217954  PMCID:PMC6279374
  • McClatchy, D. B., Yu, N. K., Martinez-Bartolome, S., Patel, R., Pelletier, A. R., Lavalle-Adam, M., Powell, S. B., Roberto, M., Yates III, J. R. Structural analysis of hippocampal kinase signal transduction ACS Chemical Neuroscience  2018 9:3072-3085  DOI:10.1021/acschemneuro.8b00284  PMID:30053369
  • Lin, X. X., Sen, I., Janssens, G. E., Zhou, X., Fonslow, B. R., Edgar, D., Stroustrup, N., Swobodv, P., Yates III, J. R., Ruvkun, G., Riedel, C. G. DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity Nature Communications  2018 9  DOI:10.1038/s41467-018-06624-0  PMID:30353013  PMCID:PMC6199276
  • Gonzalez, D. P., Lamb, H. V., Partida, D., Wilson, Z. T., Harrison, M. C., Prieto, J. A., Moresco, J. J., Diedrich, J. K., Yates III, J. R., Olson, S. K. CBD-1 organizes two independent complexes required for eggshell vitelline layer formation and egg activation in C. elegans Developmental Biology  2018 442:288-300  DOI:10.1016/j.ydbio.2018.08.005  PMID:30120927  PMCID:PMC6143425
  • Rathore, A., Chu, C., Tan, D., Martinez, T. F., Donaldson, C. J., Diedrich, J. K., Yates III, J. R., Saghatelian, A. MIEF1 microprotein regulates mitochondrial translation Biochemistry  2018 57:5564-5575  DOI:10.1021/acs.biochem.8b00726  PMID:30215512
  • Ziegler, Y. S., Moresco, J. J., Tu, P. G., Yates III, J. R., Nardulli, A. M. Proteomic analysis identifies highly expressed plasma membrane proteins for detection and therapeutic targeting of specific breast cancer subtypes Clinical Proteomics  2018 15  DOI:10.1186/s12014-018-9206-0  PMID:30250408  PMCID:PMC6145347
  • Cao, L. W., Pauthner, M., Andrabi, R., Rantalainen, K., Berndsen, Z., Diedrich, J. K., Menis, S., Sok, D., Bastidas, R., Park, S. K. R., Delahunty, C. M., He, L., et al. Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer Nature Communications  2018 9  DOI:10.1038/s41467-018-06121-4  PMID:30209313  PMCID:PMC6135743
  • Wang, Z., Wu, C., Aslanian, A., Yates III, J. R., Hunter, T. Defective RNA polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 pathway Elife  2018 7  DOI:10.7554/eLife.35447  PMID:30192228  PMCID:PMC6128692
  • Diniz, M. R. V., Paiva, A. L. B., Guerra-Duarte, C., Nishiyama, M. Y., Mudadu, M. A., de Oliveira, U., Borges, M. H., Yates III, J. R., Junqueira-de-Azevedo, I. D. An overview of Phoneutria nigriventer spider venom using combined transcriptomic and proteomic approaches PLoS One  2018 13  DOI:10.1371/journal.pone.0200628  PMID:30067761  PMCID:PMC6070231
  • Ma, Y., McClatchy, D. B., Barkallah, S., Wood, W. W., Yates III, J. R. Quantitative analysis of newly synthesized proteins Nature Protocols  2018 13:1744-1762  DOI:10.1038/s41596-018-0012-y  PMID:30038347
  • McClatchy, D. B., Ma, Y., Liem, D. A., Ng, D. C. M., Ping, P., Yates III, J. R. Quantitative temporal analysis of protein dynamics in cardiac remodeling Journal of Molecular and Cellular Cardiology  2018 121:163-172  DOI:10.1016/j.yjmcc.2018.07.126  PMID:30009778
  • Mutlu, B., Chen, H. M., Moresco, J. J., Orelo, B. D., Yang, B., Gaspar, J. M., Keppler-Ross, S., Yates III, J. R., Hall, D. H., Maine, E. M., Mango, S. E. Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos Science Advances  2018 4  DOI:10.1126/sciadv.aat6224  PMID:30140741  PMCID:PMC6105299
  • Havenar-Daughton, C., Sarkar, A., Kulp, D. W., Toy, L., Hu, X., Deresa, I., Kalyuzhniy, O., Kaushik, K., Upadhyay, A. A., Menis, S., Landais, E., Cao, L., et al. The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen Science Translational Medicine  2018 10  DOI:10.1126/scitranslmed.aat0381  PMID:29973404
  • Bamberger, C., Martinez-Bartolome, S., Montgomery, M., Pankow, S., Hulleman, J. D., Kelly, J. W., Yates III, J. R. Deducing the presence of proteins and proteoforms in quantitative proteomics Nature Communications  2018 9  DOI:10.1038/s41467-018-04411-5  PMID:29899466  PMCID:PMC5998138
  • Zhu, Q., Hoong, N., Aslanian, A., Hara, T., Benner, C., Heinz, S., Miga, K. H., Ke, E., Verma, S., Soroczynski, J., Yates III, J. R., Hunter, T., et al. Heterochromatin-encoded satellite RNAs induce breast cancer Molecular Cell  2018 70:842-853  DOI:10.1016/j.molcel.2018.04.023  PMID:29861157
  • Nishimura, N., Tsuchiya, W., Moresco, J. J., Hayashi, Y., Satoh, K., Kaiwa, N., Irisa, T., Kinoshita, T., Schroeder, J. I., Yates III, J. R., Hirayama, T., Yamazaki, T. Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme Nature Communications  2018 9  DOI:10.1038/s41467-018-04437-9  PMID:29875377  PMCID:PMC5989226
  • Cao, L., Diedrich, J. K., Ma, Y., Wang, N., Pauthner, M., Park, S. K. R., Delahunty, C. M., McLellan, J. S., Burton, D. R., Yates III, J. R., Paulson, J. C. Global site-specific analysis of glycoprotein N-glycan processing Nature Protocols  2018 13:1196-1212  DOI:10.1038/nprot.2018.024  PMID:29725121  PMCID:PMC5941933
  • Vo, M. N., Terrey, M., Lee, J. W., Roy, B., Moresco, J. J., Sun, L. T., Fu, H. J., Liu, Q., Weber, T. G., Yates III, J. R., Fredrick, K., Schimmel, P., et al. ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase Nature  2018 557:510-515  DOI:10.1038/s41586-018-0137-8  PMID:29769718  PMCID:PMC5973781
  • Song, C., Wang, L., Wu, X., Wang, K., Xie, D., Xiao, Q., Li, S., Jiang, K., Liao, L., Yates III, J. R., Lee, J. D., Yang, Q. PML Recruits TET2 to Regulate DNA Modification and Cell Proliferation in Response to Chemotherapeutic Agent Cancer Research  2018 78:2475-2489  DOI:10.1158/0008-5472.can-17-3091  PMID:29735542
  • Burke, J. E., Longhurst, A. D., Merkurjev, D., Sales-Lee, J., Rao, B., Moresco, J. J., Yates III, J. R., Li, J. J., Madhani, H. D. Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution Cell  2018 173:1014-1030  DOI:10.1016/j.cell.2018.03.020  PMID:29727661  PMCID:PMC5940017
  • Xu, M., Moresco, J. J., Chang, M., Mukim, A., Smith, D., Diedrich, J. K., Yates III, J. R., Jones, K. A. SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy PLoS Pathogens  2018 14  DOI:10.1371/journal.ppat.1007071  PMID:29791506  PMCID:PMC5988312
  • Martinez-Bartolome, S., Medina-Aunon, J. A., Lopez-Garcia, M. A., Gonzalez-Tejedo, C., Prieto, G., Navajas, R., Salazar-Donate, E., Fernandez-Costa, C., Yates III, J. R., Albar, J. P. PACOM: a versatile tool for integrating, filtering, visualizing, and comparing multiple large mass spectrometry proteomics data sets Journal of Proteome Research  2018 17:1547-1558  DOI:10.1021/acs.jproteome.7b00858  PMID:29558135
  • Xavier, M. A., Tirloni, L., Pinto, A. F. M., Diedrich, J. K., Yates III, J. R., Mulenga, A., Logullo, C., Vaz, I. D., Seixas, A., Termignoni, C. A proteomic insight into vitellogenesis during tick ovary maturation Scientific Reports  2018 8  DOI:10.1038/s41598-018-23090-2  PMID:29549327  PMCID:PMC5856802
  • Hollmann, T., Kim, T. K., Tirloni, L., Radulovic, Z. M., Pinto, A. F. M., Diedrich, J. K., Yates III, J. R., da Silva Vaz, Jr., I., Mulenga, A. Identification and characterization of proteins in the Amblyomma americanum tick cement cone International Journal for Parasitology  2018 48:211-224  DOI:10.1016/j.ijpara.2017.08.018  PMID:29258831  PMCID:PMC5844823
  • Bamberger, C., Martinez-Bartolome, S., Montgomery, M., Lavallee-Adam, M., Yates III, J. R. Increased proteomic complexity in Drosophila hybrids during development Science Advances  2018 4  DOI:10.1126/sciadv.aao3424  PMID:29441361  PMCID:PMC5810618
  • Iwasaki, M., Minder, P., Cai, Y., Kuhn, J. H., Yates III, J. R., Torbett, B. E., de la Torre, J. C. Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na+/K+ transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses PLoS Pathogens  2018 14  DOI:10.1371/journal.ppat.1006892
  • Liu, H. H., McClatchy, D. B., Schiapparelli, L., Shen, W. H., Yates III, J. R., Cline, H. T. Role of the visual experience-dependent nascent proteome in neuronal plasticity Elife  2018 7  DOI:10.7554/eLife.33420  PMID:29412139  PMCID:PMC5815848
  • Seixas, A., Alzugaray, M. F., Tirloni, L., Parizi, L. F., Pinto, A. F. M., Githaka, N. W., Konnai, S., Ohashi, K., Yates III, J. R., Termignoni, C., Vaz, I. D. Expression profile of Rhipicephalus microplus vitellogenin receptor during oogenesis Ticks and Tick-Borne Diseases  2018 9:72-81  DOI:10.1016/j.ttbdis.2017.10.006  PMID:29054547
  • Richard, P., Ogami, K., Chen, Y., Feng, S., Moresco, J. J., Yates III, J. R., Manley, J. L. NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells RNA Biology  2018 15:868-876  DOI:10.1080/15476286.2018.1467180  PMID:29902117  PMCID:PMC6161687
  • Ma, Y., Yates III, J. R. Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications? Expert Review of Proteomics  2018 15:545-554  DOI:10.1080/14789450.2018.1500902  PMID:30005169  PMCID:PMC6329588
  • Song, Y., Zhou, H., Vo, M. N., Shi, Y., Nawaz, M. H., Vargas-Rodriguez, O., Diedrich, J. K., Yates III, J. R., Kishi, S., Musier-Forsyth, K., Schimmel, P. Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid Nature Communications  2017 8  DOI:10.1038/s41467-017-02201-z  PMID:29273753  PMCID:PMC5741666
  • Tirloni, L., Kim, T. K., Pinto, A. F. M., Yates III, J. R., Vaz, I. D., Mulenga, A. Tick-host range adaptation: changes in protein profiles in unfed adult Ixodes scapularis and amblyomma americanum saliva stimulated to feed on different hosts Frontiers in Cellular and Infection Microbiology  2017 7  DOI:10.3389/fcimb.2017.00517
  • Blasi, E. A. R., Buffon, G., Rativa, A. G. S., Lopes, M. C. B., Berger, M., Santi, L., Lavallee-Adame, M., Yates III, J. R., Schwambach, J., Beys-da-Silva, W. O., Sperotto, R. A. High infestation levels of Schizotetranychus oryzae severely affects rice metabolism Journal of Plant Physiology  2017 219:100-111  DOI:10.1016/j.jplph.2017.10.005  PMID:29096082
  • Hwang, H., Park, G. W., Park, J. Y., Lee, H. K., Lee, J. Y., Jeong, J. E., Park, S. K. R., Yates III, J. R., Kwon, K. N., Park, Y. M., Lee, H. J., Paik, Y. K., et al. Next generation proteomic pipeline for chromosome-based proteomic research using neXtProt and GENCODE databases Journal of Proteome Research  2017 16:4425-4434  DOI:10.1021/acs.jproteome.7b00223  PMID:28965411
  • Aguilar, A. L., Gao, Y., Hou, X., Lauvau, G., Yates III, J. R., Wu, P. Profiling of protein O-GIcNAcylation in murine CD8(+) effector- and memory-like T cells ACS Chemical Biology  2017 12:3031-3038  DOI:10.1021/acschembio.7b00869  PMID:29125738
  • Savas, J. N., Wang, Y. Z., DeNardo, L. A., Martinez-Bartolome, S., McClatchy, D. B., Hark, T. J., Shanks, N. F., Cozzolino, K. A., Lavallee-Adam, M., Smukowski, S. N., Park, S. K., Kelly, J. W., et al. Amyloid accumulation drives proteome-wide alterations in mouse models of Alzheimer's disease-like pathology Cell Reports  2017 21:2614-2627  DOI:10.1016/j.celrep.2017.11.009  PMID:29186695  PMCID:PMC5726791
  • Oh, C. K., Sultan, A., Platzer, J., Dolatabadi, N., Soldner, F., McClatchy, D. B., Diedrich, J. K., Yates III, J. R., Ambasudhan, R., Nakamura, T., Jaenisch, R., Lipton, S. A. S-nitrosylation of PINK1 attenuates PINK1/Parkin-dependent mitophagy in hiPSC-based Parkinson's disease models Cell Reports  2017 21:2171-2182  DOI:10.1016/j.celrep.2017.10.068  PMID:29166608  PMCID:PMC5705204
  • Frankel, E. B., Shankar, R., Moresco, J. J., Yates III, J. R., Volkmann, N., Audhya, A. Ist1 regulates ESCRT-III assembly and function during multivesicular endosome biogenesis in Caenorhabditis elegans embryos Nature Communications  2017 8  DOI:10.1038/s41467-017-01636-8  PMID:29129923  PMCID:PMC5682282
  • Chaves, D. F. S., Carvalho, P. C., Brasili, E., Rogero, M. M., Hassimotto, N. A., Diedrich, J. K., Moresco, J. J., Yates III, J. R., Lajolo, F. M. Proteomic analysis of peripheral blood mononuclear cells after a high-fat, high-carbohydrate meal with orange juice Journal of Proteome Research  2017 16:4086-4092  DOI:10.1021/acs.jproteome.7b00476  PMID:28927270
  • Subramanian, K., Rauniyar, N., Lavallee-Adam, M., Yates III, J. R., Balch, W. E. Quantitative analysis of the proteome response to the histone deacetylase inhibitor (HDACi) Vorinostat in Niemann-Pick type C1 disease Molecular & Cellular Proteomics  2017 16:1938-1957  DOI:10.1074/mcp.M116.064949  PMID:28860124  PMCID:PMC5672001
  • Widjaja, C. E., Olvera, J. G., Metz, P. J., Phan, A. T., Savas, J. N., de Bruin, G., Leestemaker, Y., Berkers, C. R., de Jong, A., Florea, B. I., Fisch, K., Lopez, J., et al. Proteasome activity regulates CD8(+) T lymphocyte metabolism and fate specification Journal of Clinical Investigation  2017 127:3609-3623  DOI:10.1172/jci90895  PMID:28846070  PMCID:PMC5617668
  • Mu, R., Tat, J., Zamudio, R., Zhang, Y., Yates III, J. R., Kumagai, A., Dunphy, W. G., Reed, S. I. CKS proteins promote checkpoint recovery by stimulating phosphorylation of treslin Molecular and Cellular Biology  2017 37:e00344-17  DOI:10.1128/mcb.00344-17  PMID:28739856  PMCID:PMC5615187
  • Wang, J., Han, X., Leu, N. A., Sterling, S., Kurosaka, S., Fina, M., Lee, V. M., Dong, D. W., Yates III, J. R., Kashina, A. Protein arginylation targets alpha synuclein, facilitates normal brain health, and prevents neurodegeneration Scientific Reports  2017 7  DOI:10.1038/s41598-017-11713-z  PMID:28900170  PMCID:PMC5595787
  • Jin, M., Fuller, G. G., Han, T., Yao, Y., Alessi, A. F., Freeberg, M. A., Roach, N. P., Moresco, J. J., Karnovsky, A., Baba, M., Yates III, J. R., Gitler, A. D., et al. Glycolytic enzymes coalesce in G bodies under hypoxic stress Cell Reports  2017 20:895-908  DOI:10.1016/j.celrep.2017.06.082  PMID:28746874
  • Chu, Q., Rathore, A., Diedrich, J. K., Donaldson, C. J., Yates III, J. R., Saghatelian, A. Identification of microprotein-protein interactions via APEX tagging Biochemistry  2017 56:3299-3306  DOI:10.1021/acs.biochem.7b00265  PMID:28589727  PMCID:PMC5499098
  • French, M. E., Klosowiak, J. L., Aslanian, A., Reed, S. I., Yates III, J. R., Hunter, T. Mechanism of ubiquitin chain synthesis employed by a HECT domain ubiquitin ligase Journal of Biological Chemistry  2017 292:10398-10413  DOI:10.1074/jbc.M117.789479  PMID:28461335
  • Ogami, K., Richard, P., Chen, Y., Hoque, M., Li, W., Moresco, J. J., Yates III, J. R., Tian, B., Manley, J. L. An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression Genes & Development  2017 31:1257-1271  DOI:10.1101/gad.302604.117  PMID:28733371
  • Ma, Y., McClatchy, D. B., Barkallah, S., Wood, W. W., Yates III, J. R. HILAQ: A novel strategy for newly synthesized protein quantification Journal of Proteome Research  2017 16:2213-2220  DOI:10.1021/acs.jproteome.7b00005  PMID:28437088
  • Nagar, S., Noveral, S. M., Trudler, D., Lopez, K. M., McKercher, S. R., Han, X., Yates III, J. R., Pina-Crespo, J. C., Nakanishi, N., Satoh, T., Okamoto, S., Lipton, S. A. MEF2D haploinsufficiency downregulates the NRF2 pathway and renders photoreceptors susceptible to light-induced oxidative stress Proceedings of the National Academy of Sciences of the United States of America  2017 114:E4048-E4056  DOI:10.1073/pnas.1613067114  PMID:28461502  PMCID:PMC5441815
  • Mack, H. I. D., Zhang, P. C., Fonslow, B. R., Yates III, J. R. The protein kinase MBK-1 contributes to lifespan extension in daf-2 mutant and germline-deficient Caenorhabditis elegans Aging  2017 9:1414-1432  DOI:10.18632/aging.101244  PMID:28562327  PMCID:PMC5472741
  • Conkar, D., Culfa, E., Odabasi, E., Rauniyar, N., Yates III, J. R., Firat-Karalar, E. N. The centriolar satellite protein CCDC66 interacts with CEP290 and functions in cilium formation and trafficking Journal of Cell Science  2017 130:1450-1462  DOI:10.1242/jcs.196832  PMID:28235840  PMCID:PMC5399785
  • Koizumi, H., Fujioka, H., Togashi, K., Thompson, J., Yates III, J. R., Gleeson, J. G., Emoto, K. DCLK1 phosphorylates the microtubule-associated protein MAP7D1 to promote axon elongation in cortical neurons Developmental Neurobiology  2017 77:493-510  DOI:10.1002/dneu.22428  PMID:27503845
  • Cao, L., Diedrich, J. K., Kulp, D. W., Pauthner, M., He, L., Park, S. K. R., Sok, D., Su, C. Y., Delahunty, C. M., Menis, S., Andrabi, R., Guenaga, J., et al. Global site-specific N-glycosylation analysis of HIV envelope glycoprotein Nature Communications  2017 8  DOI:10.1038/ncomms14954  PMID:28348411
  • Rehain-Bell, K., Love, A., Werner, M. E., MacLeod, I., Yates III, J. R., Maddox, A. S. A sterile 20 family kinase and its co-factor CCM-3 regulate contractile ring proteins on germline intercellular bridges Current Biology  2017 27:860-867  DOI:10.1016/j.cub.2017.01.058  PMID:28285996  PMCID:PMC5367925
  • Lomaev, D., Mikhailova, A., Erokhin, M., Shaposhnikov, A. V., Moresco, J. J., Blokhina, T., Wolle, D., Aoki, T., Ryabykh, V., Yates III, J. R., Shidlovskii, Y. V., Georgiev, P., et al. The GAGA factor regulatory network: Identification of GAGA factor associated proteins PLoS One  2017 12  DOI:10.1371/journal.pone.0173602  PMID:28296955
  • Matthews, M. L., He, L., Horning, B. D., Olson, E. J., Correia, B. E., Yates III, J. R., Dawson, P. E., Cravatt, B. F. Chemoproteomic profiling and discovery of protein electrophiles in human cells Nature Chemistry  2017 9:234-243  DOI:10.1038/nchem.2645  PMID:28221344  PMCID:PMC5325178
  • Sonntag, T., Moresco, J. J., Vaughan, J. M., Matsumura, S., Yates III, J. R., Montminy, M. Analysis of a cAMP regulated coactivator family reveals an alternative phosphorylation motif for AMPK family members PLoS One  2017 12  DOI:10.1371/journal.pone.0173013  PMID:28235073  PMCID:PMC5325614
  • Hickox, A. E., Wong, A. C. Y., Pak, K., Strojny, C., Ramirez, M., Yates III, J. R., Ryan, A. F., Savas, J. N. Global analysis of protein expression of inner ear hair cells Journal of Neuroscience  2017 37:1320-1339  DOI:10.1523/jneurosci.2267-16.2016  PMID:28039372  PMCID:PMC5296798
  • Thakar, S., Wang, L., Yu, T., Ye, M., Onishi, K., Scott, J., Qi, J., Fernandes, C., Han, X., Yates III, J. R., Berg, D. K., Zou, Y. Evidence for opposing roles of Celsr3 and Vangl2 in glutamatergic synapse formation Proceedings of the National Academy of Sciences of the United States of America  2017 114:E610-E618  DOI:10.1073/pnas.1612062114  PMID:28057866  PMCID:PMC5278468
  • Luhtala, N., Aslanian, A., Yates III, J. R., Hunter, T. Secreted glioblastoma nanovesicles contain intracellular signaling proteins and active Ras incorporated in a farnesylation-dependent manner Journal of Biological Chemistry  2017 292:611-628  DOI:10.1074/jbc.M116.747618  PMID:27909058  PMCID:PMC5241736
  • Ju Lee, H., Bartsch, D., Xiao, C., Guerrero, S., Ahuja, G., Schindler, C., Moresco, J. J., Yates III, J. R., Gebauer, F., Bazzi, H., Dieterich, C., Kurian, L., et al. A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells Nature Communications  2017 8  DOI:10.1038/s41467-017-01744-5  PMID:29129916  PMCID:PMC5682285
  • Chao, L. F., Singh, M., Thompson, J., Yates III, J. R., Hagstrom, K. A. An SMC-like protein binds and regulates Caenorhabditis elegans condensins PLoS Genetics  2017 13  DOI:10.1371/journal.pgen.1006614  PMID:28301465  PMCID:PMC5373644
  • Yates III, J. R. Matchmaking in proteomics Clinical Chemistry  2017 63:1297-1298  DOI:10.1373/clinchem.2016.267856  PMID:28483788
  • Hanna IV, M. G., Block, S., Frankel, E. B., Hou, F., Johnson, A., Yuan, L., Knight, G., Moresco, J. J., Yates III, J. R., Ashton, R., Schekman, R., Tong, Y., et al. TFG facilitates outer coat disassembly on COPII transport carriers to promote tethering and fusion with ER-Golgi intermediate compartments Proceedings of the National Academy of Sciences of the United States of America  2017 114:E7707-E7716  DOI:10.1073/pnas.1709120114  PMID:28851831  PMCID:PMC5604033
  • Song, C., Wang, L., Xu, Q., Wang, K., Xie, D., Yu, Z., Jiang, K., Liao, L., Yates III, J. R., Lee, J. D., Yang, Q. Targeting BMK1 impairs the drug resistance to combined inhibition of BRAF and MEK1/2 in melanoma Scientific Reports  2017 7  DOI:10.1038/srep46244  PMID:28387310  PMCID:PMC5384194
  • Jarvas, G., Fonslow, B., Yates III, J. R., Foret, F., Guttman, A. Characterization of a porous nano-electrospray capillary emitter at ultra-low flow rates Journal of Chromatographic Science  2017 55:47-51  DOI:10.1093/chromsci/bmw148  PMID:27993863
  • Mita, P., Savas, J. N., Briggs, E. M., Ha, S., Gnanakkan, V., Yates III, J. R., Robins, D. M., David, G., Boeke, J. D., Garabedian, M. J., Logan, S. K. URI regulates KAP1 phosphorylation and transcriptional repression via PP2A phosphatase in prostate cancer cells Journal of Biological Chemistry  2016 291:25516-25528  DOI:10.1074/jbc.M116.741660  PMID:27780869  PMCID:PMC5207251
  • Pankow, S., Bamberger, C., Calzolari, D., Bamberger, A., Yates III, J. R. Deep interactome profiling of membrane proteins by co-interacting protein identification technology Nature Protocols  2016 11:2515-2528  DOI:10.1038/nprot.2016.140  PMID:27854364  PMCID:PMC5444904
  • Sunico, C. R., Sultan, A., Nakamura, T., Dolatabadi, N., Parker, J., Shan, B., Han, X., Yates III, J. R., Masliah, E., Ambasudhan, R., Nakanishi, N., Lipton, S. A. Role of sulfiredoxin as a peroxiredoxin-2 denitrosylase in human iPSC-derived dopaminergic neurons Proceedings of the National Academy of Sciences of the United States of America  2016 113:E7564-E7571  DOI:10.1073/pnas.1608784113  PMID:27821734  PMCID:PMC5127299
  • Park, G. W., Hwang, H., Kim, K. H., Lee, J. Y., Lee, H. K., Park, J. Y., Ji, E. S., Park, S. K. R., Yates III, J. R., Kwon, K. H., Park, Y. M., Lee, H. J., et al. Integrated proteomic pipeline using multiple search engines for a proteogenomic study with a controlled protein false discovery rate Journal of Proteome Research  2016 15:4082-4090  DOI:10.1021/acs.jproteome.6b00376  PMID:27537616
  • Liang, Z., Zhan, Y., Shen, Y., Wong, C. C. L., Yates III, J. R., Plattner, F., Lai, K. O., Ip, N. Y. The pseudokinase CaMKv is required for the activity-dependent maintenance of dendritic spines Nature Communications  2016 7  DOI:10.1038/ncomms13282  PMID:27796283  PMCID:PMC5095516
  • Shan, C. M., Wang, J., Xu, K., Chen, H., Yue, J. X., Andrews, S., Moresco, J. J., Yates III, J. R., Nagy, P. L., Tong, L., Jia, S. A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading Elife  2016 5  DOI:10.7554/eLife.17903  PMID:27648579  PMCID:PMC5030085
  • Di Maggio, L. S., Tirloni, L., Pinto, A. F. M., Diedrich, J. K., Yates III, J. R., Benavides, U., Carmona, C., Vaz, I. D., Berasain, P. Across intra-mammalian stages of the liver fluke Fasciola hepatica: a proteomic study Scientific Reports  2016 6  DOI:10.1038/srep32796  PMID:27600774  PMCID:PMC5013449
  • Chatterjee, S., Stupp, G. S., Park, S. K. R., Ducom, J. C., Yates III, J. R., Su, A. I., Wolan, D. W. A comprehensive and scalable database search system for metaproteomics BMC Genomics  2016 17  DOI:10.1186/s12864-016-2855-3  PMID:27528457  PMCID:PMC4986259
  • Ziegler, Y. S., Moresco, J. J., Yates III, J. R., Nardulli, A. M. Integration of breast cancer secretomes with clinical data elucidates potential serum markers for disease detection, diagnosis, and prognosis PLoS One  2016 11  DOI:10.1371/journal.pone.0158296  PMID:27355404  PMCID:PMC4927101
  • Janke, R., Kong, J., Braberg, H., Cantin, G., Yates III, J. R., Krogan, N. J., Heyer, W. D. Nonsense-mediated decay regulates key components of homologous recombination Nucleic Acids Research  2016 44:5218-5230  DOI:10.1093/nar/gkw182  PMID:27001511  PMCID:PMC4914092
  • Zhao, X., Hirota, T., Han, X., Cho, H., Chong, L. W., Lamia, K., Liu, S., Atkins, A. R., Banayo, E., Liddle, C., Yu, R. T., Yates III, J. R., et al. Circadian amplitude regulation via FBXW7-targeted REV-ERBα degradation Cell  2016 165:1644-1657  DOI:10.1016/j.cell.2016.05.012  PMID:27238018  PMCID:PMC4912445
  • Homer, C. M., Summers, D. K., Goranov, A. I., Clarke, S. C., Wiesner, D. L., Diedrich, J. K., Moresco, J. J., Toffaletti, D., Upadhya, R., Caradonna, I., Petnic, S., Pessino, V., et al. Intracellular action of a secreted peptide required for fungal virulence Cell Host & Microbe  2016 19:849-864  DOI:10.1016/j.chom.2016.05.001  PMID:27212659
  • Shrestha, E., Hussein, M. A., Savas, J. N., Ouimet, M., Barrett, T. J., Leone, S., Yates III, J. R., Moore, K. J., Fisher, E. A., Garabedian, M. J. Poly(ADP-ribose) polymerase 1 represses liver X receptor-mediated ABCA1 expression and cholesterol efflux in macrophages Journal of Biological Chemistry  2016 291:11172-11184  DOI:10.1074/jbc.M116.726729  PMID:27026705  PMCID:PMC4900266
  • Borges, M. H., Figueiredo, S. G., Leprevost, F. V., De Lima, M. E., do N. Cordeiro, M., Diniz, M. R. V., Moresco, J., Carvalho, P. C., Yates III, J. R. Venomous extract protein profile of Brazilian tarantula Grammostola iheringi: searching for potential biotechnological applications Journal of Proteomics  2016 136:35-47  DOI:10.1016/j.jprot.2016.01.013  PMID:26828374
  • Gonzalez, N., Moresco, J. J., Cabezas, F., de la Vega, E., Bustos, F., Yates III, J. R., Olguin, H. C. Ck2-dependent phosphorylation is required to maintain Pax7 protein levels in proliferating muscle progenitors PLoS One  2016 11  DOI:10.1371/journal.pone.0154919  PMID:27144531  PMCID:PMC4856311
  • Andress, A., Bei, Y., Fonslow, B. R., Giri, R., Wu, Y., Yates III, J. R., Carthew, R. W. Spindle-E cycling between nuage and cytoplasm is controlled by Qin and PIWI proteins Journal of Cell Biology  2016 213:201-211  DOI:10.1083/jcb.201411076  PMID:27091448
  • Ma, J., Diedrich, J. K., Jungreis, I., Donaldson, C., Vaughan, J., Kellis, M., Yates III, J. R., Saghatelian, A. Improved identification and analysis of small open reading frame encoded polypeptides Analytical Chemistry  2016 88:3967-3975  DOI:10.1021/acs.analchem.6b00191  PMID:27010111  PMCID:PMC4939623
  • Miao, Y., Han, X., Zheng, L., Xie, Y., Mu, Y., Yates III, J. R., Drubin, D. G. Fimbrin phosphorylation by metaphase Cdk1 regulates actin cable dynamics in budding yeast Nature Communications  2016 7  DOI:10.1038/ncomms11265  PMID:27068241  PMCID:PMC4832064
  • Wang, J., Cohen, A. L., Letian, A., Tadeo, X., Moresco, J. J., Liu, J., Yates III, J. R., Qiao, F., Jia, S. The proper connection between shelterin components is required for telomeric heterochromatin assembly Genes & Development  2016 30:827-839  DOI:10.1101/gad.266718.115  PMID:26988418  PMCID:PMC4826398
  • Yonashiro, R., Tahara, E. B., Bengtson, M. H., Khokhrina, M., Lorenz, H., Chen, K. C., Kigoshi-Tansho, Y., Savas, J. N., Yates III, J. R., Craig, E. A., Mogk, A., Bukau, B. The Rqc2/Tae2 subunit of the ribosome-associated quality control (RQC) complex marks ribosome-stalled nascent polypeptide chains for aggregation Elife  2016 5  DOI:10.7554/eLife.11794  PMID:26943317  PMCID:PMC4805532
  • McClatchy, D. B., Savas, J. N., Martinez-Bartolome, S., Park, S. K., Maher, P., Powell, S. B., Yates III, J. R. Global quantitative analysis of phosphorylation underlying phencyclidine signaling and sensorimotor gating in the prefrontal cortex Molecular Psychiatry  2016 21:205-215  DOI:10.1038/mp.2015.41  PMID:25869802  PMCID:PMC4605830
  • Buffon, G., Blasi, E. A. R., Adamski, J. M., Ferla, N. J., Berger, M., Santi, L., Lavallee-Adam, M., Yates III, J. R., Beys-da-Silva, W. O., Sperotto, R. A. Physiological and molecular alterations promoted by Schizotetranychus oryzae mite infestation in rice leaves Journal of Proteome Research  2016 15:431-446  DOI:10.1021/acs.jproteome.5b00729  PMID:26667653  PMCID:PMC4861152
  • Leite, F. S., Minozzo, F. C., Kalganov, A., Cornachione, A. S., Cheng, Y. S., Leu, N. A., Han, X., Saripalli, C., Granzier, H., Kashina, A. S., Rassier, D. E. Reduced passive force in skeletal muscles lacking protein arginylation American Journal of Physiology-Cell Physiology  2016 310:C127-C135  DOI:10.1152/ajpcell.00269.2015  PMID:26511365  PMCID:PMC4719035
  • Pedros, C., Zhang, Y., Hu, J. K., Choi, Y. S., Canonigo-Balancio, A. J., Yates III, J. R., Altman, A., Crotty, S., Kong, K. F. A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center T-FH cells via the kinase TBK1 Nature Immunology  2016 17:825-833  DOI:10.1038/ni.3463  PMID:27135603  PMCID:PMC4915981
  • Kim, T. K., Tirloni, L., Pinto, A. F. M., Moresco, J., Yates III, J. R., da Silva Vaz Jr., I., Mulenga, A. Ixodes scapularis tick saliva proteins sequentially secreted every 24 h during blood feeding PLoS Neglected Tropical Diseases  2016 10  DOI:10.1371/journal.pntd.0004323  PMID:26751078  PMCID:PMC4709002
  • Zich, J., May, K., Paraskevopoulos, K., Sen, O., Syred, H. M., van der Sar, S., Patel, H., Moresco, J. J., Sarkeshik, A., Yates III, J. R., Rappsilber, J., Hardwick, K. G. Mps1Mph1 kinase phosphorylates Mad3 to inhibit Cdc20Slp1-APC/C and maintain spindle checkpoint arrests PLoS Genetics  2016 12  DOI:10.1371/journal.pgen.1005834  PMID:26882497  PMCID:PMC4755545
  • Yates III, J. Trends in separation science: tackling protein analysis LC-GC North America  2016 34:422-423
  • Magdeldin, S., Hirao, Y., Elguoshy, A., Xu, B., Zhang, Y., Fujinaka, H., Yamamoto, K., Yates III, J. R., Yamamoto, T. A proteomic glimpse into human ureter proteome Proteomics  2016 16:80-84  DOI:10.1002/pmic.201500214  PMID:26442468  PMCID:PMC4737284
  • Silva, E., Betleja, E., John, E., Spear, P., Moresco, J. J., Zhang, S. W., Yates III, J. R., Mitchell, B. J., Mahjoub, M. R. Ccdc11 is a novel centriolar satellite protein essential for ciliogenesis and establishment of left-right asymmetry Molecular Biology of the Cell  2016 27:48-63  DOI:10.1091/mbc.E15-07-0474  PMID:26538025  PMCID:PMC4694761
  • Carvalho, P. C., Lima, D. B., Leprevost, F. V., Santos, M. D. M., Fischer, J. S. G., Aquino, P. F., Moresco, J. J., Yates III, J. R., Barbosa, V. C. Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0 Nature Protocols  2016 11:102-117  DOI:10.1038/nprot.2015.133  PMID:26658470
  • Alessi, A. F., Khivansara, V., Han, T., Freeberg, M. A., Moresco, J. J., Tu, P. G., Montoye, E., Yates III, J. R., Karp, X., Kim, J. K. Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1 Proceedings of the National Academy of Sciences of the United States of America  2015 112:E7213-E7222  DOI:10.1073/pnas.1509499112  PMID:26669440  PMCID:PMC4702986
  • Pankow, S., Bamberger, C., Calzolari, D., Martinez-Bartolome, S., Lavallee-Adam, M., Balch, W. E., Yates III, J. R. ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis Nature  2015 528:510-516  DOI:10.1038/nature15729  PMID:26618866  PMCID:PMC4826614
  • Callaci, S., Morrison, K., Shao, X., Schuh, A. L., Wang, Y., Hardin, J., Audhya, A. Phosphoregulation of the C. elegans cadherin-catenin complex Biochemical Journal  2015 472:339-352  DOI:10.1042/bj20150410  PMID:26443865  PMCID:PMC4663164
  • Wang, L., Delahunty, C., Fritz-Wolf, K., Rahlfs, S., Prieto, J. H., Yates III, J. R., Becker, K. Characterization of the 26S proteasome network in Plasmodium falciparum Scientific Reports  2015 5:17818  DOI:10.1038/srep17818  PMID:26639022  PMCID:PMC4671066
  • Hwang, H., Park, G. W., Kim, K. H., Lee, J. Y., Lee, H. K., Ji, E. S., Park, S. K. R., Yates III, J. R., Kwon, K. H., Park, Y. M., Lee, H. J., Paik, Y. K., et al. Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases Journal of Proteome Research  2015 14:5028-5037  DOI:10.1021/acs.jproteome.5b00472  PMID:26549206
  • Sun, S., Shi, G., Sha, H., Ji, Y., Han, X., Shu, X., Ma, H., Inoue, T., Gao, B., Kim, H., Bu, P., Guber, R. D., et al. IRE1α is an endogenous substrate of endoplasmic-reticulum-associated degradation Nature Cell Biology  2015 17:1546-1555  DOI:10.1038/ncb3266  PMID:26551274  PMCID:PMC4670240
  • He, L., Diedrich, J., Chu, Y. Y., Yates III, J. R. Extracting accurate precursor information for tandem mass spectra by raw converter Analytical Chemistry  2015 87:11361-11367  DOI:10.1021/acs.analchem.5b02721  PMID:26499134  PMCID:PMC4777630
  • Xu, T., Park, S. K., Venable, J. D., Wohlschlegel, J. A., Diedrich, J. K., Cociorva, D., Lu, B., Liao, L., Hewel, J., Han, X., Wong, C. C. L., Fonslow, B., et al. ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity Journal of Proteomics  2015 129:16-24  DOI:10.1016/j.jprot.2015.07.001  PMID:26171723  PMCID:PMC4630125
  • Zhang, Y., Xu, T., Shan, B., Hart, J., Aslanian, A., Han, X., Zong, N., Li, H., Choi, H., Wang, D., Acharya, L., Du, L., et al. ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects Journal of Proteomics  2015 129:25-32  DOI:10.1016/j.jprot.2015.07.006  PMID:26196237  PMCID:PMC4630118
  • Lavallee-Adam, M., Park, S. K. R., Martinez-Bartolome, S., He, L., Yates III, J. R. From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics Journal of the American Society for Mass Spectrometry  2015 26:1820-1826  DOI:10.1007/s13361-015-1161-7  PMID:26002791  PMCID:PMC4607643
  • Kersten, R. D., Diedrich, J. K., Yates III, J. R., Noel, J. P. Mechanism-based post-translational modification and inactivation in terpene synthases ACS Chemical Biology  2015 10:2501-2511  DOI:10.1021/acschembio.5b00539  PMID:26378620  PMCID:PMC4655415
  • McClatchy, D. B., Ma, Y., Liu, C., Stein, B. D., Martinez-Bartolome, S., Vasquez, D., Hellberg, K., Shaw, R. J., Yates III, J. R. Pulsed azidohomoalanine labeling in mammals (PALM) detects changes in liver-specific LKB1 knockout mice Journal of Proteome Research  2015 14:4815-4822  DOI:10.1021/acs.jproteome.5b00653  PMID:26445171  PMCID:PMC4642245
  • Dumesic, P. A., Rosenblad, M. A., Samuelsson, T., Nguyen, T., Moresco, J. J., Yates III, J. R., Madhani, H. D. Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans Nucleic Acids Research  2015 43:9017-9027  DOI:10.1093/nar/gkv819  PMID:26275773  PMCID:PMC4605306
  • D'Amico, D., Antonucci, L., Di Magno, L., Coni, S., Sdruscia, G., Macone, A., Miele, E., Infante, P., Di Marcotullio, L., De Smaele, E., Ferretti, E., Ciapponi, L., et al. Non-canonical Hedgehog/AMPK-mediated control of polyamine metabolism supports neuronal and medulloblastoma cell growth Developmental Cell  2015 35:21-35  DOI:10.1016/j.devcel.2015.09.008  PMID:26460945  PMCID:PMC4607931
  • Bustos, F., de la Vega, E., Cabezas, F., Thompson, J., Cornelison, D. D. W., Olwin, B. B., Yates III, J. R., Olguin, H. C. NEDD4 regulates PAX7 levels promoting activation of the differentiation program in skeletal muscle precursors Stem Cells  2015 33:3138-3151  DOI:10.1002/stem.2125  PMID:26304770  PMCID:PMC4579044
  • Das, M., Nunez, I., Rodriguez, M., Wiley, D. J., Rodriguez, J., Sarkeshik, A., Yates III, J. R., Buchwald, P., Verde, F. Phosphorylation-dependent inhibition of Cdc42 GEF Gef1 by 14-3-3 protein Rad24 spatially regulates Cdc42 GTPase activity and oscillatory dynamics during cell morphogenesis Molecular Biology of the Cell  2015 26:3520-3534  DOI:10.1091/mbc.E15-02-0095  PMID:26246599  PMCID:PMC4591695
  • Waadt, R., Manalansan, B., Rauniyar, N., Munemasa, S., Booker, M. A., Brandt, B., Waadt, C., Nusinow, D. A., Kay, S. A., Kunz, H. H., Schumacher, K., DeLong, A., et al. Identification of open stomatal-interacting proteins reveals interactions with sucrose non-fermenting1-related protein kinases2 and with type 2A protein phosphatases that function in abscisic acid responses Plant Physiology  2015 169:760-779  DOI:10.1104/pp.15.00575  PMID:26175513  PMCID:PMC4577397
  • Xia, H. G., Najafov, A., Geng, J., Galan-Acosta, L., Han, X., Guo, Y., Shan, B., Zhang, Y., Norberg, E., Zhang, T., Pan, L., Liu, J., et al. Degradation of HK2 by chaperone-mediated autophagy promotes metabolic catastrophe and cell death Journal of Cell Biology  2015 210:705-716  DOI:10.1083/jcb.201503044  PMID:26323688  PMCID:PMC4555813
  • Tang, B., Wang, T., Wan, H., Han, L., Qin, X., Zhang, Y., Wang, J., Yu, C., Berton, F., Francesconi, W., Yates III, J. R., Vanderklish, P. W., et al. Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome Proceedings of the National Academy of Sciences of the United States of America  2015 112:E4697-E4706  DOI:10.1073/pnas.1502258112  PMID:26307763  PMCID:PMC4553823
  • Savas, J. N., Ribeiro, L. F., Wierda, K. D., Wright, R., DeNardo-Wilke, L. A., Rice, H. C., Chamma, I., Wang, Y. Z., Zemla, R., Lavallee-Adam, M., Vennekens, K. M., O'Sullivan, M. L., et al. The sorting receptor SorCS1 regulates trafficking of neurexin and AMPA receptors Neuron  2015 87:764-780  DOI:10.1016/j.neuron.2015.08.007  PMID:26291160  PMCID:PMC4692362
  • Sanders, S. S., Martin, D. D. O., Butland, S. L., Lavallee-Adam, M., Calzolari, D., Kay, C., Yates III, J. R., Hayden, M. R. Curation of the mammalian palmitoylome indicates a pivotal role for palmitoylation in diseases and disorders of the nervous system and cancers PLoS Computational Biology  2015 11:e1004405  DOI:10.1371/journal.pcbi.1004405  PMID:26275289  PMCID:PMC4537140
  • Cajigas, I., Leib, D. E., Cochrane, J., Luo, H., Swyter, K. R., Chen, S., Clark, B. S., Thompson, J., Yates III, J. R., Kingston, R. E., Kohtz, J. D. Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling Development  2015 142:2641-U207  DOI:10.1242/dev.126318  PMID:26138476  PMCID:PMC4529037
  • Heimbucher, T., Liu, Z., Bossard, C., McCloskey, R., Carrano, A. C., Riedel, C. G., Tanasa, B., Klammt, C., Fonslow, B. R., Riera, C. E., Lillemeier, B. F., Kemphues, K., et al. The deubiquitylase MATH-33 Controls DAF-16 stability and function in metabolism and longevity Cell Metabolism  2015 22:151-163  DOI:10.1016/j.cmet.2015.06.002  PMID:26154057  PMCID:PMC4502596
  • Fuhs, S. R., Meisenhelder, J., Aslanian, A., Ma, L., Zagorska, A., Stankova, M., Binnie, A., Al-Obeidi, F., Mauger, J., Lemke, G., Yates III, J. R., Hunter, T. Monoclonal 1-and 3-phosphohistidine antibodies: New tools to study histidine phosphorylation Cell  2015 162:198-210  DOI:10.1016/j.cell.2015.05.046  PMID:26140597  PMCID:PMC4491144
  • Peng, Y., Moritz, M., Han, X., Giddings, T. H., Lyon, A., Kollman, J., Winey, M., Yates III, J., Agar, D. A., Drubin, D. G., Barnes, G. Interaction of CK1δ with γTuSC ensures proper microtubule assembly and spindle positioning Molecular Biology of the Cell  2015 26:2505-2518  DOI:10.1091/mbc.E14-12-1627  PMID:25971801  PMCID:PMC4571304
  • Rauniyar, N., Subramanian, K., Lavallee-Adam, M., Martinez-Bartolome, S., Balch, W. E., Yates III, J. R. Quantitative proteomics of human fibroblasts with I1061T mutation in Niemann-Pick C1 (NPC1) protein provides insights into the disease pathogenesis Molecular & Cellular Proteomics  2015 14:1734-1749  DOI:10.1074/mcp.M114.045609  PMID:25873482  PMCID:PMC4587331
  • Thiffault, I., Wolf, N. I., Forget, D., Guerrero, K., Tran, L. T., Choquet, K., Lavalleee-Adam, M., Poitras, C., Brais, B., Yoon, G., Sztriha, L., Webster, R. I., et al. Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III Nature Communications  2015 6:7623  DOI:10.1038/ncomms8623  PMID:26151409  PMCID:PMC4506509
  • Tirloni, L., Islam, M. S., Kim, T. K., Diedrich, J. K., Yates III, J. R., Pinto, A. F. M., Mulenga, A., You, M. J., Da Silva Vaz Jr., I. Saliva from nymph and adult females of Haemaphysalis longicornis: a proteomic study Parasites & Vectors  2015 8:338  DOI:10.1186/s13071-015-0918-y  PMID:26104117  PMCID:PMC4484640
  • Scruggs, S. B., Watson, K., Su, A. I., Hermjakob, H., Yates III, J. R., Lindsey, M. L., Ping, P. Harnessing the heart of big data Circulation Research  2015 116:1115-1119  DOI:10.1161/circresaha.115.306013  PMID:25814682
  • Schuh, A. L., Hanna, M., Quinney, K., Wang, L., Sarkeshik, A., Yates III, J. R., Audhya, A. The VPS-20 subunit of the endosomal sorting complex ESCRT-III exhibits an open conformation in the absence of upstream activation Biochemical Journal  2015 466:625-637  DOI:10.1042/bj20141202  PMID:25588614  PMCID:PMC4384658
  • Papp, S. J., Huber, A. L., Jordan, S. D., Kriebs, A., Nguyen, M., Moresco, J. J., Yates III, J. R., Lamia, K. A. DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization Elife  2015 4  DOI:10.7554/eLife.04883  PMID:25756610  PMCID:PMC4352707
  • Berger, M., Santi, L., Beys-da-Silva, W. O., Oliveira, F. M. S., Caliari, M. V., Yates III, J. R., Vieira, M. A. R., Guimares, J. A. Mechanisms of acute kidney injury induced by experimental Lonomia obliqua envenomation Archives of Toxicology  2015 89:459-483  DOI:10.1007/s00204-014-1264-0  PMID:24798088  PMCID:PMC4401067
  • Brennand, K., Savas, J. N., Kim, Y., Tran, N., Simone, A., Hashimoto-Torii, K., Beaumont, K. G., Kim, H. J., Topol, A., Ladran, I., Abdelrahim, M., Matikainen-Ankney, B., et al. Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia Molecular Psychiatry  2015 20:361-368  DOI:10.1038/mp.2014.22  PMID:24686136  PMCID:PMC4182344
  • Magdeldin, S., Blaser, R. E., Yamamoto, T., Yates III, J. R. Behavioral and proteomic analysis of stress response in zebrafish (Danio rerio) Journal of Proteome Research  2015 14:943-952  DOI:10.1021/pr500998e  PMID:25398274  PMCID:PMC4324451
  • Tsai, H. Y., Chen, C. C. G., Conte Jr., D., Moresco, J. J., Chaves, D. A., Mitani, S., Yates III, J. R., Tsai, M. D., Mello, C. C. A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi Cell  2015 160:407-419  DOI:10.1016/j.cell.2015.01.010  PMID:25635455  PMCID:PMC4318647
  • Hart, J. R., Zhang, Y., Liao, L., Ueno, L., Du, L., Jonkers, M., Yates III, J. R., Vogt, P. K. The butterfly effect in cancer: A single base mutation can remodel the cell Proceedings of the National Academy of Sciences of the United States of America  2015 112:1131-1136  DOI:10.1073/pnas.1424012112  PMID:25583473  PMCID:PMC4313835
  • Peng, Y., Grassart, A., Lu, R., Wong, C. C. L., Yates III, J., Barnes, G., Drubin, D. G. Casein kinase 1 promotes initiation of clathrin-mediated endocytosis Developmental Cell  2015 32:231-240  DOI:10.1016/j.devcel.2014.11.014  PMID:25625208  PMCID:PMC4308670
  • Dumesic, P. A., Homer, C. M., Moresco, J. J., Pack, L. R., Shanle, E. K., Coyle, S. M., Strahl, B. D., Fujimori, D. G., Yates III, J. R., Madhani, H. D. Product binding enforces the genomic specificity of a yeast polycomb repressive complex Cell  2015 160:204-218  DOI:10.1016/j.cell.2014.11.039  PMID:25533783  PMCID:PMC4303595
  • Xiao, H., Wang, H., Silva, E. A., Thompson, J., Guillou, A., Yates III, J. R., Buchon, N., Franc, N. C. The Pallbearer E3 ligase promotes actin remodeling via RAC in efferocytosis by degrading the ribosomal protein S6 Developmental Cell  2015 32:19-30  DOI:10.1016/j.devcel.2014.11.015  PMID:25533207  PMCID:PMC4293263
  • Yates III, J. R. Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching Journal of the American Society for Mass Spectrometry  2015 26:1804-1813  DOI:10.1007/s13361-015-1220-0  PMID:26286455  PMCID:PMC4625908
  • Pasillas, M. P., Shields, S., Reilly, R., Strnadel, J., Behl, C., Park, R., Yates III, J. R., Klemke, R., Gonias, S. L., Coppinger, J. A. Proteomic analysis reveals a role for Bcl2-associated athanogene 3 and major vault protein in resistance to apoptosis in senescent cells by regulating ERK1/2 activation Molecular & Cellular Proteomics  2015 14:1-14  DOI:10.1074/mcp.M114.037697  PMID:24997994  PMCID:PMC4288246
  • Hassler, J. R., Scheuner, D. L., Wang, S., Han, J., Kodali, V. K., Li, P., Nguyen, J., George, J. S., Davis, C., Wu, S. P., Bai, Y., Sartor, M., et al. The IRE1 α/XBP1s pathway is essential for the glucose response and protection of β cells PLoS Biology  2015 13:e1002277  DOI:10.1371/journal.pbio.1002277  PMID:26469762  PMCID:PMC4607427
  • Han, X., Wang, Y., Aslanian, A., Fonslow, B., Graczyk, B., Davis, T. N., Yates III, J. R. In-line separation by capillary electrophoresis prior to analysis by top-down mass spectrometry enables sensitive characterization of protein complexes Journal of Proteome Research  2014 13:6078-6086  DOI:10.1021/pr500971h  PMID:25382489  PMCID:PMC4262260
  • Rauniyar, N., Yates III, J. R. Isobaric labeling-based relative quantification in shotgun proteomics Journal of Proteome Research  2014 13:5293-5309  DOI:10.1021/pr500880b  PMID:25337643  PMCID:PMC4261935
  • Tien, J. F., Umbreit, N. T., Zelter, A., Riffle, M., Hoopmann, M. R., Johnson, R. S., Fonslow, B. R., Yates III, J. R., MacCoss, M. J., Moritz, R. L., Asbury, C. L., Davis, T. N. Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex Genetics  2014 198:1483-1493  DOI:10.1534/genetics.114.167775  PMID:25230952  PMCID:PMC4256767
  • Lavallee-Adam, M., Rauniyar, N., McClatchy, D. B., Yates III, J. R. PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data Journal of Proteome Research  2014 13:5496-5509  DOI:10.1021/pr500473n  PMID:25177766  PMCID:PMC4258137
  • Han, X., Wang, Y., Aslanian, A., Bern, M., Lavallee-Adam, M., Yates III, J. R. Sheathless capillary electrophoresis-tandem mass spectrometry for top-down characterization of Pyrococcus furiosus proteins on a proteome scale Analytical Chemistry  2014 86:11006-11012  DOI:10.1021/ac503439n  PMID:25346219  PMCID:PMC4238646
  • Choi, M. S., Nakamura, T., Cho, S. J., Han, X., Holland, E. A., Qu, J., Petsko, G. A., Yates III, J. R., Liddington, R. C., Lipton, S. A. Transnitrosylation from DJ-1 to PTEN attenuates neuronal cell death in parkinson's disease models Journal of Neuroscience  2014 34:15123-15131  DOI:10.1523/jneurosci.4751-13.2014  PMID:25378175  PMCID:PMC4220036
  • Chan, S. L., Huppertz, I., Yao, C., Weng, L., Moresco, J. J., Yates III, J. R., Ule, J., Manley, J. L., Shi, Y. CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3 ' processing Genes & Development  2014 28:2370-2380  DOI:10.1101/gad.250993.114  PMID:25301780  PMCID:PMC4215182
  • Shan, B., Xu, C., Zhang, Y., Xu, T., Gottesfeld, J. M., Yates III, J. R. Quantitative proteomic analysis identifies targets and pathways of a 2-aminobenzamide HDAC inhibitor in Friedreich's ataxia patient iPSC-derived neural stem cells Journal of Proteome Research  2014 13:4558-4566  DOI:10.1021/pr500514r  PMID:24933366  PMCID:PMC4227551
  • Rauniyar, N., Gupta, V., Balch, W. E., Yates III, J. R. Quantitative proteomic profiling reveals differentially regulated proteins in cystic fibrosis cells Journal of Proteome Research  2014 13:4668-4675  DOI:10.1021/pr500370g  PMID:24818864  PMCID:PMC4224989
  • Baird, N. A., Douglas, P. M., Simic, M. S., Grant, A. R., Moresco, J. J., Wolff, S. C., Yates III, J. R., Manning, G., Dillin, A. HSF-1-mediated cytoskeletal integrity determines thermotolerance and life span Science  2014 346:360-363  DOI:10.1126/science.1253168  PMID:25324391  PMCID:PMC4403873
  • Chen, Y., Zhang, L., Estaras, C., Choi, S. H., Moreno Jr., L., Karn, J., Moresco, J. J., Yates III, J. R., Jones, K. A. A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation Genes & Development  2014 28:2261-2275  DOI:10.1101/gad.250449.114  PMID:25319827  PMCID:PMC4201287
  • Wang, J., Tadeo, X., Hou, H., Andrews, S., Moresco, J. J., Yates III, J. R., Nagy, P. L., Jia, S. Tls1 regulates splicing of shelterin components to control telomeric heterochromatin assembly and telomere length Nucleic Acids Research  2014 42:11419-11432  DOI:10.1093/nar/gku842  PMID:25245948  PMCID:PMC4191416
  • Kedmi, A., Zehavi, Y., Glick, Y., Orenstein, Y., Ideses, D., Wachtel, C., Doniger, T., Ben-Asher, H. W., Muster, N., Thompson, J., Anderson, S., Avrahami, D., et al. Drosophila TRF2 is a preferential core promoter regulator Genes & Development  2014 28:2163-2174  DOI:10.1101/gad.245670.114  PMID:25223897  PMCID:PMC4180977
  • Samson, M., Jow, M. M., Wong, C. C. L., Fitzpatrick, C., Aslanian, A., Saucedo, I., Estrada, R., Ito, T., Park, S. K. R., Yates III, J. R., Chu, D. S. The specification and global reprogramming of histone epigenetic marks during gamete formation and early embryo development in C. elegans PLoS Genetics  2014 10  DOI:10.1371/journal.pgen.1004588  PMID:25299455  PMCID:PMC4191889
  • McGann, J., Oyer, J. A., Garg, S., Yao, H., Liu, J., Feng, X., Liao, L., Yates III, J. R., Mandel, G. Polycomb and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype Elife  2014 3:e04235  DOI:10.7554/eLife.04235  PMID:25250711  PMCID:PMC4371837
  • Castaneda, J., Genzor, P., van der Heijden, G. W., Sarkeshik, A., Yates III, J. R., Ingolia, N. T., Bortvin, A. Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice EMBO Journal  2014 33:1999-2019  DOI:10.15252/embj.201386855  PMID:25063675  PMCID:PMC4195769
  • Smith, C. L., Matheson, T. D., Trombly, D. J., Sun, X., Campeau, E., Han, X., Yates III, J. R., Kaufman, P. D. A separable domain of the p150 subunit of human chromatin assembly factor-1 promotes protein and chromosome associations with nucleoli Molecular Biology of the Cell  2014 25:2866-2881  DOI:10.1091/mbc.E14-05-1029  PMID:25057015  PMCID:PMC4161520
  • Shanks, N. F., Cais, O., Maruo, T., Savas, J. N., Zaika, E. I., Azumaya, C. M., Yates III, J. R., Greger, I., Nakagawa, T. Molecular dissection of the interaction between the AMPA receptor and cornichon homolog-3 Journal of Neuroscience  2014 34:12104-12120  DOI:10.1523/jneurosci.0595-14.2014  PMID:25186755  PMCID:PMC4152608
  • Schiapparelli, L. M., McClatchy, D. B., Liu, H. H., Sharma, P., Yates III, J. R., Cline, H. T. Direct detection of biotinylated proteins by mass spectrometry Journal of Proteome Research  2014 13:3966-3978  DOI:10.1021/pr5002862  PMID:25117199  PMCID:PMC4156236
  • Savas, J. N., De Wit, J., Comoletti, D., Zemla, R., Ghosh, A., Yates III, J. R. Ecto-Fc MS identifies ligand-receptor interactions through extracellular domain Fc fusion protein baits and shotgun proteomic analysis Nature Protocols  2014 9:2061-2074  DOI:10.1038/nprot.2014.140  PMID:25101821  PMCID:PMC4384169
  • Leprevost, F. V., Valente, R. H., Lima, D. B., Perales, J., Melani, R., Yates III, J. R., Barbosa, V. C., Junqueira, M., Carvalho, P. C. PepExplorer: a similarity-driven tool for analyzing de novo sequencing results Molecular & Cellular Proteomics  2014 13:2480-2489  DOI:10.1074/mcp.M113.037002  PMID:24878498  PMCID:PMC4159663
  • Tan, Y. L., Genereux, J. C., Pankow, S., Aerts, J. M. F. G., Yates III, J. R., Kelly, J. W. ERdj3 Is an endoplasmic reticulum degradation factor for mutant glucocerebrosidase variants linked to Gaucher's disease Chemistry & Biology  2014 21:967-976  DOI:10.1016/j.chembiol.2014.06.008  PMID:25126989  PMCID:PMC4136546
  • Talman, A. M., Prieto, J. H., Marques, S., Ubaida-Mohien, C., Lawniczak, M., Wass, M. N., Xu, T., Frank, R., Ecker, A., Stanway, R. S., Krishna, S., Sternberg, M. J. E., et al. Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility Malaria Journal  2014 13:315  DOI:10.1186/1475-2875-13-315  PMID:25124718  PMCID:PMC4150949
  • Zong, N., Ping, P., Lau, E., Choi, H. J. H., Ng, D. C. M., Meyer, D., Fang, C., Li, H., Wang, D., Zelaya, I. M., Yates III, J. R., Lam, M. P. Y. Lysine ubiquitination and acetylation of human cardiac 20S proteasomes Proteomics Clinical Applications  2014 8:590-594  DOI:10.1002/prca.201400029  PMID:24957502
  • Comachione, A. S., Leite, F. S., Wang, J., Leu, N. A., Kalganov, A., Volgin, D., Han, X., Xu, T., Cheng, Y. S., Yates III, J. R., Rassier, D. E., Kashina, A. Arginylation of myosin heavy chain regulates skeletal muscle strength Cell Reports  2014 8:469-475  DOI:10.1016/j.celrep.2014.06.019  PMID:25017061  PMCID:PMC4126752
  • Lee, G. H., Chhangawala, Z., von Daake, S., Savas, J. N., Yates III, J. R., Comoletti, D., D'Arcangelo, G. Reelin induces Erk1/2 signaling in cortical neurons through a non-canonical pathway Journal of Biological Chemistry  2014 289:20307-20317  DOI:10.1074/jbc.M114.576249  PMID:24876378  PMCID:PMC4106344
  • Ziegler, Y. S., Moresco, J. J., Tu, P. G., Yates III, J. R., Nardulli, A. M. Plasma membrane proteomics of human breast cancer cell lines identifies potential targets for breast cancer diagnosis and treatment PLoS One  2014 9:e102341  DOI:10.1371/journal.pone.0102341  PMID:25029196  PMCID:PMC4100819
  • Okamoto, S., Nakamura, T., Cieplak, P., Chan, S. F., Kalashnikova, E., Liao, L., Saleem, S., Han, X., Clemente, A., Nutter, A., Sances, S., Brechtel, C., et al. S-nitrosylation-mediated redox transcriptional switch modulates neurogenesis and neuronal cell death Cell Reports  2014 8:217-228  DOI:10.1016/j.celrep.2014.06.005  PMID:25001280  PMCID:PMC4114155
  • Karttunen, H., Savas, J. N., McKinney, C., Chen, Y. H., Yates III, J. R., Hukkanen, V., Huang, T. T., Mohr, I. Co-opting the Fanconi anemia genomic stability pathway enables herpesvirus DNA synthesis and productive growth Molecular Cell  2014 55:111-122  DOI:10.1016/j.molcel.2014.05.020  PMID:24954902  PMCID:PMC4376326
  • Gammon, D. B., Duraffour, S., Rozelle, D. K., Hehnly, H., Sharma, R., Sparks, M. E., West, C. C., Chen, Y., Moresco, J. J., Andrei, G., Connor, J. H., Conte, D., et al. A single vertebrate DNA virus protein disarms invertebrate immunity to RNA virus infection Elife  2014 3:e02910  DOI:10.7554/eLife.02910  PMID:24966209  PMCID:PMC4112549
  • Wang, L., Delahunty, C., Prieto, J. H., Rahlfs, S., Jortzik, E., Yates III, J. R., Becker, K. Protein S-nitrosylation in Plasmodium falciparum Antioxidants & Redox Signaling  2014 20:2923-2935  DOI:10.1089/ars.2013.5553  PMID:24256207  PMCID:PMC4039001
  • Voog, J., Sandall, S. L., Hime, G. R., Resende, L. P. F., Loza-Coll, M., Aslanian, A., Yates III, J. R., Hunter, T., Fuller, M. T., Jones, L. Escargot restricts niche cell to stem cell conversion in the Drosophila testis Cell Reports  2014 7:722-734  DOI:10.1016/j.celrep.2014.04.025  PMID:24794442  PMCID:PMC4128242
  • Bartocci, C., Diedrich, J. K., Ouzounov, I., Li, J., Piunti, A., Pasini, D., Yates III, J. R., Denchi, E. L. Isolation of chromatin from dysfunctional telomeres reveals an important role for Ring1b in NHEJ-mediated chromosome fusions Cell Reports  2014 7:1320-1332  DOI:10.1016/j.celrep.2014.04.002  PMID:24813883  PMCID:PMC4054697
  • Kong, K. F., Fu, G., Zhang, Y., Yokosuka, T., Casas, J., Canonigo-Balancio, A. J., Becart, S., Kim, G., Yates III, J. R., Kronenberg, M., Saito, T., Gascoigne, N. R. J., et al. Protein kinase C-eta controls CTLA-4-mediated regulatory T cell function Nature Immunology  2014 15:465-472  DOI:10.1038/ni.2866  PMID:24705298  PMCID:PMC4040250
  • Beys-da-Silva, W. O., Santi, L., Berger, M., Calzolari, D., Passos, D. O., Guimaraes, J. A., Moresco, J. J., Yates, J. R. Secretome of the biocontrol agent Metarhizium anisopliae induced by the cuticle of the cotton pest Dysdercus peruvianus reveals new insights into infection Journal of Proteome Research  2014 13:2282-2296  DOI:10.1021/pr401204y  PMID:24702058  PMCID:PMC4012838
  • Kallgren, S. P., Andrews, S., Tadeo, X., Hou, H., Moresco, J. J., Tu, P. G., Yates III, J. R., Nagy, P. L., Jia, S. T. The proper splicing of RNAi factors is critical for pericentric heterochromatin assembly in fission yeast PLoS Genetics  2014 10:e1004334  DOI:10.1371/journal.pgen.1004334  PMID:24874881  PMCID:PMC4038458
  • Tirloni, L., Reck, J., Terra, R. M. S., Martins, J. R., Mulenga, A., Sherman, N. E., Fox, J. W., Yates III, J. R., Termignoni, C., Pinto, A. F. M., da Silva Vaz Jr., I. Proteomic analysis of cattle tick Rhipicephalus (Boophilus) microplus saliva: a comparison between partially and fully engorged females PLoS One  2014 9:e94831  DOI:10.1371/journal.pone.0094831  PMID:24762651  PMCID:PMC3998978
  • Wang, J., Han, X., Wong, C. C., Cheng, H., Aslanian, A., Xu, T., Leavis, P., Roder, H., Hedstrom, L., Yates III, J. R., Kashina, A. Arginyltransferase ATE1 catalyzes midchain arginylation of proteins at side chain carboxylates in vivo Chemistry & Biology  2014 21:331-337  DOI:10.1016/j.chembiol.2013.12.017  PMID:24529990  PMCID:PMC4010198
  • Firat-Karalar, E. N., Rauniyar, N., Yates III, J. R., Stearns, T. Proximity interactions among centrosome components identify regulators of centriole duplication Current Biology  2014 24:664-670  DOI:10.1016/j.cub.2014.01.067  PMID:24613305  PMCID:PMC4004176
  • Magdeldin, S., Yamamoto, K., Yoshida, Y., Xu, B., Zhang, Y., Fujinaka, H., Yaoita, E., Yates III, J. R., Yamamoto, T. Deep proteome mapping of mouse kidney based on OFFGel prefractionation reveals remarkable protein post- translational modifications Journal of Proteome Research  2014 13:1636-1646  DOI:10.1021/pr401122m  PMID:24495006  PMCID:PMC3993965
  • Bamberger, C., Pankow, S., Park, S. K. R., Yates III, J. R. Interference-free proteome quantification with MS/MS-based isobaric isotopologue detection Journal of Proteome Research  2014 13:1494-1501  DOI:10.1021/pr401035z  PMID:24417624  PMCID:PMC3993960
  • Lian, L., Suzuki, A., Hayes, V., Saha, S., Han, X., Xu, T., Yates III, J. R., Poncz, M., Kashina, A., Abrams, C. S. Loss of ATE1-mediated arginylation leads to impaired platelet myosin phosphorylation, clot retraction, and in vivo thrombosis formation Haematologica  2014 99:554-560  DOI:10.3324/haematol.2013.093047  PMID:24293517  PMCID:PMC3943321
  • Aslanian, A., Yates III, J. R., Hunter, T. Mass spectrometry-based quantification of the cellular response to methyl methanesulfonate treatment in human cells DNA Repair  2014 15:29-38  DOI:10.1016/j.dnarep.2013.12.007  PMID:24461736  PMCID:PMC4046014
  • Santi, L., Beys-da-Silva, W. O., Berger, M., Calzolari, D., Guimaraes, J. A., Moresco, J. J., Yates III, J. R. Proteomic profile of Cryptococcus neoformans biofilm reveals changes in metabolic processes Journal of Proteome Research  2014 13:1545-1559  DOI:10.1021/pr401075f  PMID:24467693  PMCID:PMC3993910
  • Jiang, H., He, X., Wang, S., Jia, J., Wan, Y., Wang, Y., Zeng, R., Yates III, J., Zhu, X., Zheng, Y. A microtubule-associated zinc finger protein, BuGZ, regulates mitotic chromosome alignment by ensuring Bub3 stability and kinetochore targeting Developmental Cell  2014 28:268-281  DOI:10.1016/j.devcel.2013.12.013  PMID:24462186  PMCID:PMC3927447
  • Shen, W., Liu, H. H., Schiapparelli, L., McClatchy, D., He, H. Y., Yates III, J. R., Cline, H. T. Acute synthesis of CPEB is required for plasticity of visual avoidance behavior in Xenopus Cell Reports  2014 6:737-747  DOI:10.1016/j.celrep.2014.01.024  PMID:24529705  PMCID:PMC3962200
  • Lotz, C., Lin, A. J., Black, C. M., Zhang, J., Lau, E., Deng, N., Wang, Y., Zong, N. C., Choi, J. H., Xu, T., Liem, D. A., Korge, P., et al. Characterization, design, and function of the mitochondrial proteome: from organs to organisms Journal of Proteome Research  2014 13:433-446  DOI:10.1021/pr400539j  PMID:24070373  PMCID:PMC4076470
  • Ma, H., Han, B. K., Guaderrama, M., Aslanian, A., Yates III, J. R., Hunter, T., Wittenberg, C. Psy2 targets the PP4 family phosphatase Pph3 to dephosphorylate Mth1 and repress glucose transporter gene expression Molecular and Cellular Biology  2014 34:452-463  DOI:10.1128/mcb.00279-13  PMID:24277933  PMCID:PMC3911506
  • Aguirre, A., Montserrat, N., Zacchigna, S., Nivet, E., Hishida, T., Krause, M. N., Kurian, L., Ocampo, A., Vazquez-Ferrer, E., Rodriguez-Esteban, C., Kumar, S., Moresco, J. J., et al. In vivo activation of a conserved microRNA program induces mammalian heart regeneration Cell Stem Cell  2014 15:589-604  DOI:10.1016/j.stem.2014.10.003  PMID:25517466  PMCID:PMC4270016
  • Yates III, J. R., Mohammed, S., Heck, A. J. R. Phosphoproteomics Analytical Chemistry  2014 86:1313  DOI:10.1021/ac404019p  PMID:24422449
  • Qin, X., Zheng, C., Yates III, J. R., Liao, L. Quantitative phosphoproteomic profiling of PINK1-deficient cells identifies phosphorylation changes in nuclear proteins Molecular Biosystems  2014 10:1719-1729  DOI:10.1039/c3mb70565j  PMID:24626860  PMCID:PMC4343256
  • Sun, S., Shi, G., Han, X., Francisco, A. B., Ji, Y., Mendonca, N., Liu, X., Locasale, J. W., Simpson, K. W., Duhamel, G. E., Kersten, S., Yates III, J. R., et al. Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival Proceedings of the National Academy of Sciences of the United States of America  2014 111:E582-E591  DOI:10.1073/pnas.1318114111  PMID:24453213  PMCID:PMC3918815
  • Conine, C. C., Moresco, J. J., Gu, W., Shirayama, M., Conte, D., Yates, J. R., Mello, C. C. Argonautes promote male fertility and provide a paternal memory of germline gene expression in C. elegans Cell  2013 155:1532-1544  DOI:10.1016/j.cell.2013.11.032  PMID:24360276  PMCID:PMC3924572
  • Parkhurst, C. N., Yang, G., Ninan, I., Savas, J. N., Yates, J. R., Lafaille, J. J., Hempstead, B. L., Littman, D. R., Gan, W. B. Microglia promote learning-dependent synapse formation through brain-derived neurotrophic factor Cell  2013 155:1596-1609  DOI:10.1016/j.cell.2013.11.030  PMID:24360280  PMCID:PMC4033691
  • Wang, Y. J., Han, D. Y., Tabib, T., Yates, J. R., Mu, T. W. Identification of GABA(c) receptor protein homeostasis network components from three tandem mass spectrometry proteomics approaches Journal of Proteome Research  2013 12:5570-5586  DOI:10.1021/pr400535z  PMID:24079818  PMCID:PMC3864119
  • Yao, C., Choi, E. A., Weng, L., Xie, X., Wan, J., Xing, Y., Moresco, J. J., Tu, P. G., Yates, J. R., Shi, Y. Overlapping and distinct functions of CstF64 and CstF64 tau in mammalian mRNA 3' processing RNA-a Publication of the RNA Society  2013 19:1781-1790  DOI:10.1261/rna.042317.113  PMID:24149845  PMCID:PMC3884657
  • Wan, J., Savas, J. N., Roth, A. F., Sanders, S. S., Singaraja, R. R., Hayden, M. R., Yates, J. R., Davis, N. G. Tracking brain palmitoylation change: predominance of glial change in a mouse model of Huntington's disease Chemistry & Biology  2013 20:1421-1434  DOI:10.1016/j.chembiol.2013.09.018  PMID:24211138  PMCID:PMC3880188
  • Miao, Y., Wong, C. C. L., Mennella, V., Michelot, A., Agard, D. A., Holt, L. J., Yates, J. R., Drubin, D. G. Cell-cycle regulation of formin-mediated actin cable assembly Proceedings of the National Academy of Sciences of the United States of America  2013 110:E4446-E4455  DOI:10.1073/pnas.1314000110  PMID:24133141  PMCID:PMC3839727
  • Wang, S., Ketcham, S. A., Schon, A., Goodman, B., Wang, Y., Yates, J., Freire, E., Schroer, T. A., Zheng, Y. Nudel/NudE and Lis1 promote dynein and dynactin interaction in the context of spindle morphogenesis Molecular Biology of the Cell  2013 24:3522-3533  DOI:10.1091/mbc.E13-05-0283  PMID:24025714  PMCID:PMC3826990
  • Choi, S. H., Estaras, C., Moresco, J. J., Yates, J. R., Jones, K. A. alpha-Catenin interacts with APC to regulate beta-catenin proteolysis and transcriptional repression of Wnt target genes Genes & Development  2013 27:2473-2488  DOI:10.1101/gad.229062.113  PMID:24240237  PMCID:PMC3841736
  • Klaus, J. P., Eisenhauer, P., Russo, J., Mason, A. B., Do, D., King, B., Taatjes, D., Cornillez-Ty, C., Boyson, J. E., Thali, M., Zheng, C., Liao, L., et al. The intracellular cargo receptor ERGIC-53 is required for the production of infectious arenavirus, coronavirus, and filovirus particles Cell Host & Microbe  2013 14:522-534  DOI:10.1016/j.chom.2013.10.010  PMID:24237698  PMCID:PMC3999090
  • Diedrich, J. K., Pinto, A. F. M., Yates, J. R. Energy dependence of HCD on peptide fragmentation: stepped collisional energy finds the sweet spot Journal of the American Society for Mass Spectrometry  2013 24:1690-1699  DOI:10.1007/s13361-013-0709-7  PMID:23963813  PMCID:PMC3815594
  • Zong, N. C., Li, H., Li, H., Lam, M. P. Y., Jimenez, R. C., Kim, C. S., Deng, N., Kim, A. K., Choi, J. H., Zelaya, I., Liem, D., Meyer, D., et al. Integration of cardiac proteome biology and medicine by a specialized knowledgebase Circulation Research  2013 113:1043-1053  DOI:10.1161/circresaha.113.301151  PMID:23965338
  • Chaves, D. F. S., Carvalho, P. C., Lima, D. B., Nicastro, H., Lorenzeti, F. M., Siqueira-Filho, M., Hirabara, S. M., Alves, P. H. M., Moresco, J. J., Yates, J. R., Lancha, A. H. Comparative proteomic analysis of the aging soleus and extensor digitorum longus rat muscles using TMT labeling and mass spectrometry Journal of Proteome Research  2013 12:4532-4546  DOI:10.1021/pr400644x  PMID:24001182  PMCID:PMC3845496
  • Yates, J. R., Washburn, M. P. Quantitative proteomics Analytical Chemistry  2013 85:8881  DOI:10.1021/ac402745w  PMID:24079386
  • Costa, A., Pazman, C., Sinsimer, K. S., Wong, L. C., McLeod, I., Yates, J., Haynes, S., Schedl, P. Rasputin functions as a positive regulator of orb in Drosophila oogenesis PLoS One  2013 8:e72864  DOI:10.1371/journal.pone.0072864  PMID:24069162  PMCID:PMC3771913
  • Faust, A. M. E., Wong, C. C. L., Yates, J. R., Drubin, D. G., Barnes, G. The FEAR protein Slk19 restricts Cdc14 phosphatase to the nucleus until the end of anaphase, regulating its participation in mitotic exit in Saccharomyces cerevisiae PLoS One  2013 8:e73194  DOI:10.1371/journal.pone.0073194  PMID:24039885  PMCID:PMC3769316
  • Wang, J. Y., Tadeo, X., Hou, H. T., Tu, P. G., Thompson, J., Yates, J. R., Jia, S. T. Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries Genes & Development  2013 27:1886-1902  DOI:10.1101/gad.221010.113  PMID:24013502  PMCID:PMC3778242
  • Pottekat, A., Becker, S., Spencer, K. R., Yates, J. R., Manning, G., Itkin-Ansari, P., Balch, W. E. Insulin biosynthetic interaction network component, TMEM24, facilitates insulin reserve pool release Cell Reports  2013 4:921-930  DOI:10.1016/j.celrep.2013.07.050  PMID:24012759  PMCID:PMC3839581
  • Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., Hetzer, M. W. Identification of long-lived proteins reveals exceptional stability of essential cellular structures Cell  2013 154:971-982  DOI:10.1016/j.cell.2013.07.037  PMID:23993091  PMCID:PMC3788602
  • de Wit, J., O'Sullivan, M. L., Savas, J. N., Condomitti, G., Caccese, M. C., Vennekens, K. M., Yates, J. R., Ghosh, A. Unbiased discovery of glypican as a receptor for LRRTM4 in regulating excitatory synapse development Neuron  2013 79:696-711  DOI:10.1016/j.neuron.2013.06.049  PMID:23911103  PMCID:PMC4003527
  • Pratt-Hyatt, M., Pai, D. A., Haeusler, R. A., Wozniak, G. G., Good, P. D., Miller, E. L., McLeod, I. X., Yates, J. R., Hopper, A. K., Engelke, D. R. Mod5 protein binds to tRNA gene complexes and affects local transcriptional silencing Proceedings of the National Academy of Sciences of the United States of America  2013 110:E3081-E3089  DOI:10.1073/pnas.1219946110  PMID:23898186  PMCID:PMC3746885
  • Schlaitz, A. L., Thompson, J., Wong, C. C. L., Yates, J. R., Heald, R. REEP3/4 ensure endoplasmic reticulum clearance from metaphase chromatin and proper nuclear envelope architecture Developmental Cell  2013 26:315-323  DOI:10.1016/j.devcel.2013.06.016  PMID:23911198  PMCID:PMC3745822
  • Mayers, J. R., Wang, L., Pramanik, J., Johnson, A., Sarkeshik, A., Wang, Y., Saengsawang, W., Yates, J. R., Audhya, A. Regulation of ubiquitin-dependent cargo sorting by multiple endocytic adaptors at the plasma membrane Proceedings of the National Academy of Sciences of the United States of America  2013 110:11857-11862  DOI:10.1073/pnas.1302918110  PMID:23818590  PMCID:PMC3718112
  • Yang, Q., Liao, L., Deng, X., Chen, R., Gray, N. S., Yates, J. R., Lee, J. D. BMK1 is involved in the regulation of p53 through disrupting the PML-MDM2 interaction Oncogene  2013 32:3156-3164  DOI:10.1038/onc.2012.332  PMID:22869143  PMCID:PMC3493705
  • Rauniyar, N., McClatchy, D. B., Yates, J. R. Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis Methods  2013 61:260-268  DOI:10.1016/j.ymeth.2013.03.008  PMID:23523555
  • Zheng, H., Seit-Nebi, A., Han, X., Aslanian, A., Tat, J., Liao, R., Yates, J. R., 3rd, Sun, P. A posttranslational modification cascade involving p38, Tip60, and PRAK mediates oncogene-induced senescence Molecular Cell  2013 50:699-710  DOI:10.1016/j.molcel.2013.04.013  PMID:23685072  PMCID:PMC3679363
  • Nito, K., Wong, C. C. L., Yates, J. R., Chory, J. Tyrosine phosphorylation regulates the activity of phytochrome photoreceptors Cell Reports  2013 3:1970-1979  DOI:10.1016/j.celrep.2013.05.006  PMID:23746445  PMCID:PMC4023694
  • Tsai, W. W., Niessen, S., Goebel, N., Yates, J. R., Guccione, E., Montminy, M. PRMT5 modulates the metabolic response to fasting signals Proceedings of the National Academy of Sciences of the United States of America  2013 110:8870-8875  DOI:10.1073/pnas.1304602110  PMID:23671120  PMCID:PMC3670393
  • Rock, J. M., Lim, D., Stach, L., Ogrodowicz, R. W., Keck, J. M., Jones, M. H., Wong, C. C. L., Yates, J. R., Winey, M., Smerdon, S. J., Yaffe, M. B., Amon, A. Activation of the yeast Hippo pathway by phosphorylation-dependent assembly of signaling complexes Science  2013 340:871-875  DOI:10.1126/science.1235822  PMID:23579499  PMCID:PMC3884217
  • Mita, P., Savas, J. N., Ha, S., Djouder, N., Yates, J. R., Logan, S. K. Analysis of URI nuclear interaction with RPB5 and components of the R2TP/prefoldin-like complex PLoS One  2013 8:e63879  DOI:10.1371/journal.pone.0063879  PMID:23667685  PMCID:PMC3648552
  • Webb, K. J., Xu, T., Park, S. K., Yates, J. R. Modified MuDPIT separation identified 4488 proteins in a system-wide analysis of quiescence in yeast Journal of Proteome Research  2013 12:2177-2184  DOI:10.1021/pr400027m  PMID:23540446  PMCID:PMC3815592
  • Dehe, P. M., Coulon, S., Scaglione, S., Shanahan, P., Takedachi, A., Wohlschlegel, J. A., Yates, J. R., Llorente, B., Russell, P., Gaillard, P. H. L. Regulation of Mus81-Eme1 Holliday junction resolvase in response to DNA damage Nature Structural & Molecular Biology  2013 20:598-603  DOI:10.1038/nsmb.2550  PMID:23584455  PMCID:PMC3978046
  • Zhang, Y., Fonslow, B. R., Shan, B., Baek, M. C., Yates, J. R., 3rd Protein analysis by shotgun/bottom-up proteomics Chemical Reviews  2013  DOI:10.1021/cr3003533  PMID:23438204  PMCID:PMC3751594
  • Shoulders, M. D., Ryno, L. M., Genereux, J. C., Moresco, J. J., Tu, P. G., Wu, C., Yates, J. R., 3rd, Su, A. I., Kelly, J. W., Wiseman, R. L. Stress-independent activation of XBP1s and/or ATF6 reveals three functionally diverse ER proteostasis environments Cell Reports  2013 3:1279-1292  DOI:10.1016/j.celrep.2013.03.024  PMID:23583182  PMCID:PMC3754422
  • Ong, D. S. T., Wang, Y. J., Tan, Y. L., Yates, J. R., Mu, T. W., Kelly, J. W. FKBP10 depletion enhances glucocerebrosidase proteostasis in Gaucher disease fibroblasts Chemistry & Biology  2013 20:403-415  DOI:10.1016/j.chembiol.2012.11.014  PMID:23434032  PMCID:PMC3624024
  • Kropinski, A. M., Waddell, T., Meng, J. C., Franklin, K., Ackermann, H. W., Ahmed, R., Mazzocco, A., Yates, J., Lingohr, E. J., Johnson, R. P. The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5 Virology Journal  2013 10:76  DOI:10.1186/1743-422x-10-76  PMID:23497209  PMCID:PMC3606486
  • Okamoto, K., Bartocci, C., Ouzounov, I., Diedrich, J. K., Yates, J. R., Denchi, E. L. A two-step mechanism for TRF2-mediated chromosome-end protection Nature  2013 494:502-505  DOI:10.1038/nature11873  PMID:23389450  PMCID:PMC3733551
  • Dumesic, P. A., Natarajan, P., Chen, C. B., Drinnenberg, I. A., Schiller, B. J., Thompson, J., Moresco, J. J., Yates, J. R., Bartel, D. P., Madhani, H. D. Stalled spliceosomes are a signal for RNAi-mediated genome defense Cell  2013 152:957-968  DOI:10.1016/j.cell.2013.01.046  PMID:23415457  PMCID:PMC3645481
  • Butko, M. T., Savas, J. N., Friedman, B., Delahunty, C., Ebner, F., Yates, J. R., Tsien, R. Y. In vivo quantitative proteomics of somatosensory cortical synapses shows which protein levels are modulated by sensory deprivation Proceedings of the National Academy of Sciences of the United States of America  2013 110:E726-E735  DOI:10.1073/pnas.1300424110  PMID:23382246  PMCID:PMC3581967
  • Yates, J. R. The revolution and evolution of shotgun proteomics for large-scale proteome analysis Journal of the American Chemical Society  2013 135:1629-1640  DOI:10.1021/ja3094313  PMID:23294060  PMCID:PMC3751590
  • Huang, T. Y., Michael, S., Xu, T., Sarkeshik, A., Moresco, J. J., Yates, J. R., 3rd, Masliah, E., Bokoch, G. M., DerMardirossian, C. A novel Rac1 GAP splice variant relays poly-Ub accumulation signals to mediate Rac1 inactivation Molecular Biology of the Cell  2013 24:194-209  DOI:10.1091/mbc.E12-07-0565  PMID:23223568  PMCID:PMC3564530
  • Rauniyar, N., Gao, B. B., McClatchy, D. B., Yates, J. R. Comparison of protein expression ratios observed by sixplex and duplex TMT labeling method Journal of Proteome Research  2013 12:1031-1039  DOI:10.1021/pr3008896  PMID:23214967  PMCID:PMC3751587
  • Zhang, S. F., Zhou, Y. J., Sarkeshik, A., Yates, J. R., Thomson, T. M., Zhang, Z. T., Lee, E. Y. C., Lee, Mywt Identification of RNF8 as a ubiquitin ligase involved in targeting the p12 subunit of DNA polymerase δ for degradation in response to DNA damage Journal of Biological Chemistry  2013 288:2941-2950  DOI:10.1074/jbc.M112.423392  PMID:23233665  PMCID:PMC3561517
  • Wong, C. C. L., Cociorva, D., Miller, C. A., Schmidt, A., Monell, C., Aebersold, K., Yates, J. R. Proteomics of Pyrococcus furiosus (Pfu): identification of extracted proteins by three independent methods Journal of Proteome Research  2013 12:763-770  DOI:10.1021/pr300840j  PMID:23298259  PMCID:PMC3751585
  • Lyons, N. A., Fonslow, B. R., Diedrich, J. K., Yates, J. R., Morgan, D. O. Sequential primed kinases create a damage-responsive phosphodegron on Eco1 Nature Structural & Molecular Biology  2013 20:194-201  DOI:10.1038/nsmb.2478  PMID:23314252  PMCID:PMC3565030
  • Ma, C. H., Cui, H., Hajra, S., Rowley, P. A., Fekete, C., Sarkeshik, A., Ghosh, S. K., Yates, J. R., Jayaram, M. Temporal sequence and cell cycle cues in the assembly of host factors at the yeast 2 micron plasmid partitioning locus Nucleic Acids Research  2013 41:2340-2353  DOI:10.1093/nar/gks1338  PMID:23275556  PMCID:PMC3575823
  • Fonslow, B. R., Stein, B. D., Webb, K. J., Xu, T., Choi, J., Park, S. K., Yates III, J. R. Digestion and depletion of abundant proteins improves proteomic coverage Nature Methods  2013 10:54-56  DOI:10.1038/nmeth.2250  PMID:23160281  PMCID:PMC3531578
  • Ryan, S. D., Dolatabadi, N., Chan, S. F., Zhang, X., Akhtar, M. W., Parker, J., Soldner, F., Sunico, C. R., Nagar, S., Talantova, M., Lee, B., Lopez, K., et al. Isogenic human iPSC Parkinson's model shows nitrosative stress-induced dysfunction in MEF2-PGC1 alpha transcription Cell  2013 155:1351-1364  DOI:10.1016/j.cell.2013.11.009  PMID:24290359  PMCID:PMC4028128
  • Freeberg, M. A., Han, T., Moresco, J. J., Kong, A., Yang, Y. C., Lu, Z. J., Yates, J. R., Kim, J. K. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae Genome Biology  2013 14:R13  DOI:10.1186/gb-2013-14-2-r13  PMID:23409723  PMCID:PMC4053964
  • Wang, H. L., Shi, L. Z., Wong, C. C. L., Han, X. M., Hwang, P. Y. H., Truong, L. N., Zhu, Q. Y., Shao, Z. P., Chen, D. J., Berns, M. W., Yates, J. R., Chen, L. C., et al. The interaction of CtIP and Nbs1 connects CDK and ATM to regulate HR-mediated double-strand break repair PLoS Genetics  2013 9:e1003277  DOI:10.1371/journal.pgen.1003277  PMID:23468639  PMCID:PMC3585124
  • Yates III, J. R., Kelleher, N. L. Top down proteomics Analytical Chemistry  2013 85:6151  DOI:10.1021/ac401484r  PMID:23705843  PMCID:PMC4418644
  • Li, K., Zhou, T., Liao, L., Yang, Z., Wong, C., Henn, F., Malinow, R., Yates, J. R., Hu, H. L. betaCaMKII in lateral habenula mediates core symptoms of depression Science  2013 341:1016-1020  DOI:10.1126/science.1240729  PMID:23990563  PMCID:PMC3932364
  • Lu, C. S., Truong, L. N., Aslanian, A., Shi, L. Z., Li, Y., Hwang, P. Y. H., Koh, K. H., Hunter, T., Yates, J. R., Berns, M. W., Wu, X. The RING finger protein RNF8 ubiquitinates Nbs1 to promote DNA double-strand break repair by homologous recombination Journal of Biological Chemistry  2012 287:43984-43994  DOI:10.1074/jbc.M112.421545  PMID:23115235  PMCID:PMC3527981
  • Aoki, T., Sarkeshik, A., Yates, J., Schedl, P. Elba, a novel developmentally regulated chromatin boundary factor is a hetero-tripartite DNA binding complex Elife  2012 1:e00171  DOI:10.7554/eLife.00171  PMID:23240086  PMCID:PMC3510454
  • He, Y., Beatty, A., Han, X. M., Ji, Y. W., Ma, X. F., Adelstein, R. S., Yates, J. R., Kemphues, K., Qi, L. Nonmuscle myosin IIB links cytoskeleton to IRE1 alpha signaling during ER stress Developmental Cell  2012 23:1141-1152  DOI:10.1016/j.devcel.2012.11.006  PMID:23237951  PMCID:PMC3547290
  • Liu, G. H., Qu, J., Suzuki, K., Nivet, E., Li, M., Montserrat, N., Yi, F., Xu, X. L., Ruiz, S., Zhang, W. Q., Wagner, U., Kim, A., et al. Progressive degeneration of human neural stem cells caused by pathogenic LRRK2 Nature  2012 491:603-607  DOI:10.1038/nature11557  PMID:23075850  PMCID:PMC3504651
  • Sando, R., Gounko, N., Pieraut, S., Liao, L. J., Yates, J., Maximov, A. HDAC4 governs a transcriptional program essential for synaptic plasticity and memory Cell  2012 151:821-834  DOI:10.1016/j.cell.2012.09.037  PMID:23141539  PMCID:PMC3496186
  • Jia, J. L., Zheng, X. B., Hu, G. Q., Cui, K. R., Zhang, J. Q., Zhang, A. Y., Jiang, H., Lu, B. W., Yates, J., Liu, C. Y., Zhao, K. J., Zheng, Y. X. Regulation of pluripotency and self- renewal of ESCs through epigenetic-threshold modulation and mRNA pruning Cell  2012 151:576-589  DOI:10.1016/j.cell.2012.09.023  PMID:23101626  PMCID:PMC3575637
  • Wang, Y., Fonslow, B. R., Wong, C. C. L., Nakorchevsky, A., Yates, J. R. Improving the comprehensiveness and sensitivity of sheath less capillary electrophoresis-tandem mass spectrometry for proteomic analysis Analytical Chemistry  2012 84:8505-8513  DOI:10.1021/ac301091m  PMID:23004022  PMCID:PMC3498465
  • Ambatipudi, K. S., Swatkoski, S., Moresco, J. J., Tu, P. G., Coca, A., Anolik, J. H., Gucek, M., Sanz, I., Yates, J. R., Melvin, J. E. Quantitative proteomics of parotid saliva in primary Sjögren's syndrome Proteomics  2012 12:3113-3120  DOI:10.1002/pmic.201200208  PMID:22888089  PMCID:PMC3806318
  • Klein, M. I., Xiao, J., Lu, B. W., Delahunty, C. M., Yates, J. R., Koo, H. Streptococcus mutans protein synthesis during mixed-species biofilm development by high-throughput quantitative proteomics PLoS One  2012 7:e45795  DOI:10.1371/journal.pone.0045795  PMID:23049864  PMCID:PMC3458072
  • Kurosaka, S., Leu, N. A., Pavlov, I., Han, X. M., Ribeiro, P. A. B., Xu, T., Bunte, R., Saha, S., Wang, J. L., Cornachione, A., Mai, W., Yates, J. R., et al. Arginylation regulates myofibrils to maintain heart function and prevent dilated cardiomyopathy Journal of Molecular and Cellular Cardiology  2012 53:333-341  DOI:10.1016/j.yjmcc.2012.05.007  PMID:22626847  PMCID:PMC3418387
  • Wang, Y. M., Li, W. Z., Johnson, A. E., Luo, Z. Q., Sun, X. L., Feoktistova, A., McDonald, W. H., McLeod, I., Yates, J. R., Gould, K. L., McCollum, D., Jin, Q. W. Dnt1 acts as a mitotic inhibitor of the spindle checkpoint protein dma1 in fission yeast Molecular Biology of the Cell  2012 23:3348-3356  DOI:10.1091/mbc.E11-12-1020  PMID:22809626  PMCID:PMC3431938
  • Wasik, A. A., Polianskyte-Prause, Z., Dong, M. Q., Shaw, A. S., Yates, J. R., Farquhar, M. G., Lehtonen, S. Septin 7 forms a complex with CD2AP and nephrin and regulates glucose transporter trafficking Molecular Biology of the Cell  2012 23:3370-3379  DOI:10.1091/mbc.E11-12-1010  PMID:22809625  PMCID:PMC3431928
  • Bargaje, R., Gupta, S., Sarkeshik, A., Park, R., Xu, T., Sarkar, M., Halimani, M., Roy, S. S., Yates, J., Pillai, B. Identification of novel targets for miR-29a using miRNA proteomics PLoS One  2012 7:e43243  DOI:10.1371/journal.pone.0043243  PMID:22952654  PMCID:PMC3428309
  • Nie, M. H., Aslanian, A., Prudden, J., Heideker, J., Vashisht, A. A., Wohlschlegel, J. A., Yates, J. R., Boddy, M. N. Dual recruitment of Cdc48 (p97)-Ufd1-Npl4 ubiquitin-selective segregase by small ubiquitin-like modifier protein (SUMO) and ubiquitin in SUMO-targeted ubiquitin ligase-mediated genome stability functions Journal of Biological Chemistry  2012 287:29610-29619  DOI:10.1074/jbc.M112.379768  PMID:22730331  PMCID:PMC3436128
  • Gawlowski, T., Suarez, J., Scott, B., Torres-Gonzalez, M., Wang, H., Schwappacher, R., Han, X. M., Yates, J. R., Hoshijima, M., Dillmann, W. Modulation of dynamin-related protein 1 (DRP1) function by increased O-linked-beta-N-acetylglucosamine modification (O-GlcNAc) in cardiac myocytes Journal of Biological Chemistry  2012 287:30024-30034  DOI:10.1074/jbc.M112.390682  PMID:22745122  PMCID:PMC3436129
  • Ruan, H. B., Han, X. M., Li, M. D., Singh, J. P., Qian, K., Azarhoush, S., Zhao, L., Bennett, A. M., Samuel, V. T., Wu, J., Yates, J. R., Yang, X. O-GlcNAc transferase/host cell factor C1 complex regulates gluconeogenesis by modulating PGC-1α stability Cell Metabolism  2012 16:226-237  DOI:10.1016/j.cmet.2012.07.006  PMID:22883232  PMCID:PMC3480732
  • Banerjee, S., Liao, L. J., Russo, R., Nakamura, T., McKercher, S. R., Okamoto, S., Haun, F., Nikzad, R., Zaidi, R., Holland, E., Eroshkin, A., Yates, J. R., et al. Isobaric tagging-based quantification by mass spectrometry of differentially regulated proteins in synaptosomes of HIV/gp120 transgenic mice: implications for HIV-associated neurodegeneration Experimental Neurology  2012 236:298-306  DOI:10.1016/j.expneurol.2012.04.013  PMID:22575597  PMCID:PMC3392539
  • Wass, M. N., Stanway, R., Blagborough, A. M., Lal, K., Prieto, J. H., Raine, D., Sternberg, M. J. E., Talman, A. M., Tomley, F., Yates, J., Sinden, R. E. Proteomic analysis of plasmodium in the mosquito: progress and pitfalls Parasitology  2012 139:1131-1145  DOI:10.1017/s0031182012000133  PMID:22336136  PMCID:PMC3417538
  • Culver, B. P., Savas, J. N., Park, S. K., Choi, J. H., Zheng, S. Q., Zeitlin, S. O., Yates, J. R., Tanese, N. Proteomic analysis of wild-type and mutant huntingtin-associated proteins in mouse brains identifies unique interactions and involvement in protein synthesis Journal of Biological Chemistry  2012 287:21599-21614  DOI:10.1074/jbc.M112.359307  PMID:22556411  PMCID:PMC3381125
  • Carvalho, P. C., Yates, J. R., Barbosa, V. C. Improving the TFold test for differential shotgun proteomics Bioinformatics  2012 28:1652-1654  DOI:10.1093/bioinformatics/bts247  PMID:22539673  PMCID:PMC3371870
  • Raso, C., Cosentino, C., Gaspari, M., Malara, N., Han, X. M., McClatchy, D., Park, S. K., Renne, M., Vadala, N., Prati, U., Cuda, G., Mollace, V., et al. Characterization of breast cancer interstitial fluids by TmT labeling, LTQ-Orbitrap Velos mass spectrometry, and pathway analysis Journal of Proteome Research  2012 11:3199-3210  DOI:10.1021/pr2012347  PMID:22563702  PMCID:PMC3562392
  • Shanks, N. F., Savas, J. N., Maruo, T., Cais, O., Hirao, A., Oe, S., Ghosh, A., Noda, Y., Greger, I. H., Yates, J. R., Nakagawa, T. Differences in AMPA and kainate receptor interactomes facilitate identification of AMPA receptor auxiliary subunit GSG1L Cell Reports  2012 1:590-598  DOI:10.1016/j.celrep.2012.05.004  PMID:22813734  PMCID:PMC3401968
  • Coppinger, J. A., Hutt, D. M., Razvi, A., Koulov, A. V., Pankow, S., Yates, J. R., Balch, W. E. A chaperone trap contributes to the onset of cystic fibrosis PLoS One  2012 7:e37682  DOI:10.1371/journal.pone.0037682  PMID:22701530  PMCID:PMC3365120
  • Shia, W. J., Okumura, A. J., Yan, M., Sarkeshik, A., Lo, M. C., Matsuura, S., Komeno, Y., Zhao, X., Nimer, S. D., Yates III, J. R., Zhang, D. E. PRMT1 interacts with AML1-ETO to promote its transcriptional activation and progenitor cell proliferative potential Blood  2012 119:4953-4962  DOI:10.1182/blood-2011-04-347476  PMID:22498736  PMCID:PMC3367897
  • Ozcan, L., Wong, C. C. L., Li, G., Xu, T., Pajvani, U., Park, S. K. R., Wronska, A., Chen, B. X., Marks, A. R., Fukamizu, A., Backs, J., Singer, H. A., et al. Calcium signaling through CaMKII regulates hepatic glucose production in fasting and obesity Cell Metabolism  2012 15:739-751  DOI:10.1016/j.cmet.2012.03.002  PMID:22503562  PMCID:PMC3348356
  • Fonslow, B. R., Niessen, S. M., Singh, M., Wong, C. C. L., Xu, T., Carvalho, P. C., Choi, J., Park, S. K., Yates, J. R. Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT Journal of Proteome Research  2012 11:2697-2709  DOI:10.1021/pr300200x  PMID:22509746  PMCID:PMC3365658
  • Yates, J. R., Robin Park, S. K., Delahunty, C. M., Xu, T., Savas, J. N., Cociorva, D., Carvalho, P. C. Toward objective evaluation of proteomic algorithms Nature Methods  2012 9:455-456  DOI:10.1038/nmeth.1983  PMID:22543378  PMCID:PMC3509209
  • Chaurushiya, M. S., Lilley, C. E., Aslanian, A., Meisenhelder, J., Scott, D. C., Landry, S., Ticau, S., Boutell, C., Yates III, J. R., Schulman, B. A., Hunter, T., Weitzman, M. D. Viral E3 ubiquitin ligase-mediated degradation of a cellular E3: viral mimicry of a cellular phosphorylation mark targets the RNF8 FHA domain Molecular Cell  2012 46:79-90  DOI:10.1016/j.molcel.2012.02.004  PMID:22405594  PMCID:PMC3648639
  • Travesa, A., Kuo, D., de Bruin, R. A. M., Kalashnikova, T. I., Guaderrama, M., Thai, K., Aslanian, A., Smolka, M. B., Yates, J. R., Ideker, T., Wittenberg, C. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1 EMBO Journal  2012 31:1811-1822  DOI:10.1038/emboj.2012.28  PMID:22333915  PMCID:PMC3321207
  • McClatchy, D. B., Liao, L., Lee, J. H., Park, S. K., Yates III, J. R. Dynamics of subcellular proteomes during brain development Journal of Proteome Research  2012 11:2467-2479  DOI:10.1021/pr201176v  PMID:22397461  PMCID:PMC3334332
  • Naji, S., Ambrus, G., Cimermancic, P., Reyes, J. R., Filbrandt, R., Huber, M. D., Vesely, P., Krogan, N. J., Yates, J. R., Saphire, A. C., Gerace, L., Johnson, J. R. Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production Molecular & Cellular Proteomics  2012 11:M111.015313  DOI:10.1074/mcp.M111.015313  PMID:22174317  PMCID:PMC3322577
  • Carvalho, P. C., Fischer, J. S. G., Xu, T., Cociorva, D., Balbuena, T. S., Valente, R. H., Perales, J., Yates III, J. R., Barbosa, V. C. Search engine processor: filtering and organizing peptide spectrum matches Proteomics  2012 12:944-949  DOI:10.1002/pmic.201100529  PMID:22311825  PMCID:PMC3334471
  • O'Sullivan, M. L., de Wit, J., Savas, J. N., Comoletti, D., Otto-Hitt, S., Yates III, J. R., Ghosh, A. FLRT proteins are endogenous latrophilin ligands and regulate excitatory synapse development Neuron  2012 73:903-910  DOI:10.1016/j.neuron.2012.01.018  PMID:22405201  PMCID:PMC3326387
  • Ishikawa, H., Thompson, J., Yates III, J. R., Marshall, W. F. Proteomic analysis of mammalian primary cilia Current Biology  2012 22:414-419  DOI:10.1016/j.cub.2012.01.031  PMID:22326026  PMCID:PMC3298568
  • Hernandez, L. G., Lu, B., da Cruz, G. C. N., Calabria, L. K., Martins, N. F., Togawa, R., Espindola, F. S., Yates III, J. R., Cunha, R. B., de Sousa, M. V. Worker honeybee brain proteome Journal of Proteome Research  2012 11:1485-1493  DOI:10.1021/pr2007818  PMID:22181811  PMCID:PMC3321609
  • Savas, J. N., Toyama, B. H., Xu, T., Yates III, J. R., Hetzer, M. W. Extremely long-lived nuclear pore proteins in the rat brain Science  2012 335:942  DOI:10.1126/science.1217421  PMID:22300851  PMCID:PMC3296478
  • Wang, Y., Kallgren, S. P., Reddy, B. D., Kuntz, K., Lopez-Maury, L., Thompson, J., Watt, S., Ma, C., Hou, H., Shi, Y., Yates III, J. R., Bahler, J., et al. Histone H3 lysine 14 acetylation is required for activation of a DNA damage checkpoint in fission yeast Journal of Biological Chemistry  2012 287:4386-4393  DOI:10.1074/jbc.M111.329417  PMID:22184112  PMCID:PMC3281674
  • Liao, L. J., Sando, R. C., Farnum, J. B., Vanderklish, P. W., Maximov, A., Yates, J. R. 15N-labeled brain enables quantification of proteome and phosphoproteome in cultured primary neurons Journal of Proteome Research  2012 11:1341-1353  DOI:10.1021/pr200987h  PMID:22070516  PMCID:PMC3279198
  • Kuo, J. C., Han, X., Yates, J. R., 3rd, Waterman, C. M. Isolation of focal adhesion proteins for biochemical and proteomic analysis Methods in Molecular Biology  2012 757:297-323  DOI:10.1007/978-1-61779-166-6_19  PMID:21909920  PMCID:PMC4158431
  • Carvalho, P. C., Fischer, J. S., Xu, T., Yates III, J. R., Barbosa, V. C. PatternLab: from mass spectra to label-free differential shotgun proteomics Current Protocols in Bioinformatics  2012 40:13.19.1-13.19.18  DOI:10.1002/0471250953.bi1319s40  PMID:23255152
  • Qu, M., Yang, B., Tao, L., Yates, J. R., Russell, P., Dong, M. Q., Du, L. L. Phosphorylation-dependent interactions between Crb2 and Chk1 are essential for DNA damage checkpoint PLoS Genetics  2012 8:e1002817  DOI:10.1371/journal.pgen.1002817  PMID:22792081  PMCID:PMC3390401
  • Crestani, J., Carvalho, P. C., Han, X. M., Seixas, A., Broetto, L., Fischer, J. D. D., Staats, C. C., Schrank, A., Yates, J. R., Vainstein, M. H. Proteomic profiling of the influence of iron availability on Cryptococcus gattii Journal of Proteome Research  2012 11:189-205  DOI:10.1021/pr2005296  PMID:21970549  PMCID:PMC3253262
  • Kinsinger, C. R., Apffel, J., Baker, M., Bian, X. P., Borchers, C. H., Bradshaw, R., Brusniak, M. Y., Chan, D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles) Proteomics  2012 12:11-20  DOI:10.1002/pmic.201100562  PMID:22069307
  • Jeong, H., Cohen, D. E., Cui, L. B., Supinski, A., Savas, J. N., Mazzulli, J. R., Yates, J. R., Bordone, L., Guarente, L., Krainc, D. Sirt1 mediates neuroprotection from mutant huntingtin by activation of the TORC1 and CREB transcriptional pathway Nature Medicine  2012 18:159-165  DOI:10.1038/nm.2559  PMID:22179316  PMCID:PMC3509213
  • Xiao, J., Klein, M. I., Falsetta, M. L., Lu, B., Delahunty, C. M., Yates III, J. R., Heydorn, A., Koo, H. The exopolysaccharide matrix modulates the interaction between 3D architecture and virulence of a mixed-species oral biofilm PLoS Pathogens  2012 8:e1002623  DOI:10.1371/journal.ppat.1002623  PMID:22496649  PMCID:PMC3320608
  • Miles, L. A., Lighvani, S., Baik, N., Andronicos, N. M., Chen, E. I., Parmer, C. M., Khaldoyanidi, S., Diggs, J. E., Kiosses, W. B., Kamps, M. P., Yates, J. R., 3rd, Parmer, R. J. The plasminogen receptor, Plg-R(KT), and macrophage function Journal of Biomedicine & Biotechnology  2012 2012:250464  DOI:10.1155/2012/250464  PMID:23125524  PMCID:PMC3484331
  • Sim, S., Yao, J., Weinberg, D. E., Niessen, S., Yates, J. R., Wolin, S. L. The zipcode-binding protein ZBP1 influences the subcellular location of the Ro 60-kDa autoantigen and the noncoding Y3 RNA RNA-a Publication of the RNA Society  2012 18:100-110  DOI:10.1261/rna.029207.111  PMID:22114317  PMCID:PMC3261732
  • Kehr, S., Jortzik, E., Delahunty, C., Yates, J. R., Rahlfs, S., Becker, K. Protein S-glutathionylation in malaria parasites Antioxidants & Redox Signaling  2011 15:2855-2865  DOI:10.1089/ars.2011.4029  PMID:21595565  PMCID:PMC4932784
  • Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C. H., Bradshaw, R., Brusniak, M. Y., Chan, D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles) Molecular & Cellular Proteomics  2011 10:O111.015446  DOI:10.1074/mcp.O111.015446  PMID:22052993  PMCID:PMC3237091
  • Kinsinger, C. R., Apffel, J., Baker, M., Bian, X. P., Borchers, C. H., Bradshaw, R., Brusniak, M. Y., Chan, D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles) Proteomics Clinical Applications  2011 5:580-589  DOI:10.1002/prca.201100097  PMID:22213554
  • Chun, H. B., Scott, M., Niessen, S., Hoover, H., Baird, A., Yates, J., Torbett, B. E., Eliceiri, B. P. The proteome of mouse brain microvessel membranes and basal lamina Journal of Cerebral Blood Flow and Metabolism  2011 31:2267-2281  DOI:10.1038/jcbfm.2011.104  PMID:21792245  PMCID:PMC3323187
  • Saha, S., Wong, C. C. L., Xu, T., Namgoong, S., Zebroski, H., Yates, J. R., Kashina, A. Arginylation and methylation double up to regulate nuclear proteins and nuclear architecture in vivo Chemistry & Biology  2011 18:1369-1378  DOI:10.1016/j.chembiol.2011.08.019  PMID:22118671  PMCID:PMC3227866
  • Talukdar, I., Sen, S., Urbano, R., Thompson, J., Yates, J. R., Webster, N. J. G. hnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene PLoS One  2011 6:e27869  DOI:10.1371/journal.pone.0027869  PMID:22132154  PMCID:PMC3223206
  • Gonzalez-Begne, M., Lu, B. W., Liao, L. J., Xu, T., Bedi, G., Melvin, J. E., Yates, J. R. Characterization of the human submandibular/sublingual saliva glycoproteome using lectin affinity chromatography coupled to multidimensional protein identification technology Journal of Proteome Research  2011 10:5031-5046  DOI:10.1021/pr200505t  PMID:21936497  PMCID:PMC3279195
  • Jones, M. H., Keck, J. M., Wong, C. C. L., Xu, T., Yates, J. R., Winey, M. Cell cycle phosphorylation of mitotic exit network (MEN) proteins Cell Cycle  2011 10:3435-3440  DOI:10.4161/cc.10.20.17790  PMID:22031224  PMCID:PMC3266174
  • Paramasivam, M., Sarkeshik, A., Yates, J. R., Fernandes, M. J. G., McCollum, D. Angiomotin family proteins are novel activators of the LATS2 kinase tumor suppressor Molecular Biology of the Cell  2011 22:3725-3733  DOI:10.1091/mbc.E11-04-0300  PMID:21832154  PMCID:PMC3183025
  • Barboza, R., Cociorva, D., Xu, T., Barbosa, V. C., Perales, J., Valente, R. H., Franca, F. M. G., Yates, J. R., Carvalho, P. C. Can the false-discovery rate be misleading? Proteomics  2011 11:4105-4108  DOI:10.1002/pmic.201100297  PMID:21834134  PMCID:PMC3313620
  • Wong, L. C., Costa, A., McLeod, I., Sarkeshik, A., Yates, J., Kyin, S., Perlman, D., Schedl, P. The functioning of the Drosophila CPEB protein Orb is regulated by phosphorylation and requires casein kinase 2 activity PLoS One  2011 6:e24355  DOI:10.1371/journal.pone.0024355  PMID:21949709  PMCID:PMC3176278
  • Grigoryev, Y. A., Kurian, S. M., Hart, T., Nakorchevsky, A. A., Chen, C. F., Campbell, D., Head, S. R., Yates, J. R., Salomon, D. R. MicroRNA regulation of molecular networks mapped by global microRNA, mRNA, and protein expression in activated T lymphocytes Journal of Immunology  2011 187:2233-2243  DOI:10.4049/jimmunol.1101233  PMID:21788445  PMCID:PMC3159804
  • Nebl, T., Prieto, J. H., Kapp, E., Smith, B. J., Williams, M. J., Yates, J. R., Cowman, A. F., Tonkin, C. J. Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex PLoS Pathogens  2011 7:e1002222  DOI:10.1371/journal.ppat.1002222  PMID:21980283  PMCID:PMC3182922
  • Mita, P., Savas, J. N., Djouder, N., Yates, J. R., Ha, S., Ruoff, R., Schafler, E. D., Nwachukwu, J. C., Tanese, N., Cowan, N. J., Zavadil, J., Garabedian, M. J., et al. Regulation of androgen receptor-mediated transcription by RPB5 binding protein URI/RMP Molecular and Cellular Biology  2011 31:3639-3652  DOI:10.1128/mcb.05429-11  PMID:21730289  PMCID:PMC3165545
  • Lauwaet, T., Smith, A. J., Reiner, D. S., Romijn, E. P., Wong, C. C. L., Davids, B. J., Shah, S. A., Yates, J. R., Gillin, F. D. Mining the Giardia genome and proteome for conserved and unique basal body proteins International Journal for Parasitology  2011 41:1079-1092  DOI:10.1016/j.ijpara.2011.06.001  PMID:21723868  PMCID:PMC4521607
  • Hart, J. R., Liao, L. J., Yates, J. R., Vogt, P. K. Essential role of Stat3 in PI3K-induced oncogenic transformation Proceedings of the National Academy of Sciences of the United States of America  2011 108:13247-13252  DOI:10.1073/pnas.1110486108  PMID:21788516  PMCID:PMC3156164
  • Yates, J. R. A century of mass spectrometry: from atoms to proteomes Nature Methods  2011 8:633-637  DOI:10.1038/nmeth.1659
  • Marvin, M. C., Clauder-Munster, S., Walker, S. C., Sarkeshik, A., Yates, J. R., Steinmetz, L. M., Engelke, D. R. Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae RNA-a Publication of the RNA Society  2011 17:1441-1450  DOI:10.1261/rna.2737511  PMID:21665995  PMCID:PMC3153969
  • Fonslow, B. R., Carvalho, P. C., Academia, K., Freeby, S., Xu, T., Nakorchevsky, A., Paulus, A., Yates, J. R. Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT Journal of Proteome Research  2011 10:3690-3700  DOI:10.1021/pr200304u  PMID:21702434  PMCID:PMC3161494
  • Peng, Y. T., Wong, C. C. L., Nakajima, Y., Tyers, R. G., Sarkeshik, A. S., Yates, J., Drubin, D. G., Barnes, G. Overlapping kinetochore targets of CK2 and Aurora B kinases in mitotic regulation Molecular Biology of the Cell  2011 22:2680-2689  DOI:10.1091/mbc.E10-11-0915  PMID:21633108  PMCID:PMC3145544
  • Snaith, H. A., Thompson, J., Yates, J. R., Sawin, K. E. Characterization of Mug33 reveals complementary roles for actin cable-dependent transport and exocyst regulators in fission yeast exocytosis Journal of Cell Science  2011 124:2187-2199  DOI:10.1242/jcs.084038  PMID:21652630  PMCID:PMC3113670
  • Savas, J. N., Stein, B. D., Wu, C. C., Yates, J. R. Mass spectrometry accelerates membrane protein analysis Trends in Biochemical Sciences  2011 36:388-396  DOI:10.1016/j.tibs.2011.04.005  PMID:21616670  PMCID:PMC3222592
  • Keck, J. M., Jones, M. H., Wong, C. C. L., Binkley, J., Chen, D. C., Jaspersen, S. L., Holinger, E. P., Xu, T., Niepel, M., Rout, M. P., Vogel, J., Sidow, A., et al. A cell cycle phosphoproteome of the yeast centrosome Science  2011 332:1557-1561  DOI:10.1126/science.1205193  PMID:21700874  PMCID:PMC3825980
  • Bonner, M. K., Poole, D. S., Xu, T., Sarkeshik, A., Yates, J. R., Skop, A. R. Mitotic spindle proteomics in Chinese hamster ovary cells PLoS One  2011 6:e20489  DOI:10.1371/journal.pone.0020489  PMID:21647379  PMCID:PMC3103581
  • Jones, A. C., Monroe, E. A., Podell, S., Hess, W. R., Klages, S., Esquenazi, E., Niessen, S., Hoover, H., Rothmann, M., Lasken, R. S., Yates, J. R., Reinhardt, R., et al. Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula Proceedings of the National Academy of Sciences of the United States of America  2011 108:8815-8820  DOI:10.1073/pnas.1101137108  PMID:21555588  PMCID:PMC3102346
  • Wang, B., Moya, N., Niessen, S., Hoover, H., Mihaylova, M. M., Shaw, R. J., Yates, J. R., Fischer, W. H., Thomas, J. B., Montminy, M. A hormone-dependent module regulating energy balance Cell  2011 145:596-606  DOI:10.1016/j.cell.2011.04.013  PMID:21565616  PMCID:PMC3129781
  • Jang, C. Y., Coppinger, J. A., Yates, J. R., Fang, G. W. Mitotic kinases regulate MT-polymerizing/MT-bundling activity of DDA3 Biochemical and Biophysical Research Communications  2011 408:174-179  DOI:10.1016/j.bbrc.2011.04.004  PMID:21473853
  • Liu, G. H., Barkho, B. Z., Ruiz, S., Diep, D., Qu, J., Yang, S. L., Panopoulos, A. D., Suzuki, K., Kurian, L., Walsh, C., Thompson, J., Boue, S., et al. Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome Nature  2011 472:221-225  DOI:10.1038/nature09879  PMID:21346760  PMCID:PMC3088088
  • Kuo, J. C., Han, X. M., Hsiao, C. T., Yates, J. R., Waterman, C. M. Analysis of the myosin-II-responsive focal adhesion proteome reveals a role for beta-Pix in negative regulation of focal adhesion maturation Nature Cell Biology  2011 13:383-393  DOI:10.1038/ncb2216  PMID:21423176  PMCID:PMC3279191
  • Hart, J. R., Liao, L. J., Ueno, L., Yates, J. R., Vogt, P. K. Protein expression profiles of C3H 10T1/2 murine fibroblasts and of isogenic cells transformed by the H1047R mutant of phosphoinositide 3-kinase (PI3K) Cell Cycle  2011 10:971-976  DOI:10.4161/cc.10.6.15077  PMID:21350335  PMCID:PMC3100876
  • Sansing, H. A., Sarkeshik, A., Yates, J. R., Patel, V., Gutkind, J. S., Yamada, K. M., Berrier, A. L. Integrin alpha beta 1, alpha(v)beta, alpha(6)beta effectors p130Cas, Src and talin regulate carcinoma invasion and chemoresistance Biochemical and Biophysical Research Communications  2011 406:171-176  DOI:10.1016/j.bbrc.2011.01.109  PMID:21291860  PMCID:PMC3102534
  • Wang, J. L., Han, X. M., Saha, S., Xu, T., Rai, R., Zhang, F. L., Wolf, Y. I., Wolfson, A., Yates, J. R., Kashina, A. Arginyltransferase is an ATP-independent self-regulating enzyme that forms distinct functional complexes in vivo Chemistry & Biology  2011 18:121-130  DOI:10.1016/j.chembiol.2010.10.016  PMID:21276945  PMCID:PMC3031169
  • Englert, M., Sheppard, K., Aslanian, A., Yates, J. R., Soll, D. Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation Proceedings of the National Academy of Sciences of the United States of America  2011 108:1290-1295  DOI:10.1073/pnas.1018307108  PMID:21209330  PMCID:PMC3029724
  • McClatchy, D. B., Liao, L. J., Park, S. K., Xu, T., Lu, B. W., Yates, J. R. Differential proteomic analysis of mammalian tissues using SILAM PLoS One  2011 6:e16039  DOI:10.1371/journal.pone.0016039  PMID:21283754  PMCID:PMC3024400
  • Carvalho, P. C., Fischer, J. S. G., Perales, J., Yates, J. R., Barbosa, V. C., Bareinboim, E. Analyzing marginal cases in differential shotgun proteomics Bioinformatics  2011 27:275-276  DOI:10.1093/bioinformatics/btq632  PMID:21075743  PMCID:PMC3018820
  • Zanin, E., Dumont, J., Gassmann, R., Cheeseman, I., Maddox, P., Bahmanyar, S., Carvalho, A., Niessen, S., Yates, J. R., Oegema, K., Desai, A. Affinity purification of protein complexes in C. elegans Methods in Cell Biology  2011 106:289-322  DOI:10.1016/b978-0-12-544172-8.00011-6  PMID:22118282  PMCID:PMC3319706
  • Petsko, G. A., Yates III, J. R. Analyzing molecular interactions Current Protocols in Bioinformatics  2011 36:8.1.1-8.1.4  DOI:10.1002/0471250953.bi0801s36  PMID:22161570  PMCID:PMC3486783
  • Balch, W. E., Yates, J. R., 3rd Application of mass spectrometry to study proteomics and interactomics in cystic fibrosis Methods in Molecular Biology  2011 742:227-247  DOI:10.1007/978-1-61779-120-8_14  PMID:21547736
  • Fischer, J. D. D., Carvalho, P. C., da Fonseca, C. O., Liao, L. J., Degrave, W. M., Carvalho, M. D. D., Yates, J. R., Domont, G. B. Chemo-resistant protein expression pattern of glioblastoma cells (A172) to perillyl alcohol Journal of Proteome Research  2011 10:153-160  DOI:10.1021/pr100677g  PMID:20806975  PMCID:PMC3017632
  • Baum, B. J., Yates III, J. R., Srivastava, S., Wong, D. T., Melvin, J. E. Scientific frontiers: emerging technologies for salivary diagnostics Advances in Dental Research  2011 23:360-368  DOI:10.1177/0022034511420433  PMID:21917746  PMCID:PMC3172997
  • Schuh, A. L., Hegermann, J., Sarkeshik, A., Mayers, J. R., Schwarze, K., Yates, J. R., Eimer, S., Audhya, A., Witte, K. TFG-1 function in protein secretion and oncogenesis Nature Cell Biology  2011 13:550-558  DOI:10.1038/ncb2225  PMID:21478858  PMCID:PMC3311221
  • Wicky, S., Tjandra, H., Schieltz, D., Yates, J., Kellogg, D. R. The Zds proteins control entry into mitosis and target protein phosphatase 2A to the Cdc25 phosphatase Molecular Biology of the Cell  2011 22:20-32  DOI:10.1091/mbc.E10-06-0487  PMID:21119008  PMCID:PMC3016974
  • Papoulas, O., Monzo, K. F., Cantin, G. T., Ruse, C., Yates, J. R., Ryu, Y. H., Sisson, J. C. dFMRP and Caprin, translational regulators of synaptic plasticity, control the cell cycle at the Drosophila mid-blastula transition Development  2010 137:4201-4209  DOI:10.1242/dev.055046  PMID:21068064  PMCID:PMC2990211
  • Li, Q. A., Vande Velde, C., Israelson, A., Xie, J., Bailey, A. O., Dong, M. Q., Chun, S. J., Roy, T., Winer, L., Yates, J. R., Capaldi, R. A., Cleveland, D. W., et al. ALS-linked mutant superoxide dismutase 1 (SOD1) alters mitochondrial protein composition and decreases protein import Proceedings of the National Academy of Sciences of the United States of America  2010 107:21146-21151  DOI:10.1073/pnas.1014862107  PMID:21078990  PMCID:PMC3000256
  • Diao, Y. R., Liu, W., Wong, C. C. L., Wang, X., Lee, K., Cheung, P. Y., Pan, L. F., Xu, T., Han, J. H., Yates, J. R., Zhang, M. J., Wu, Z. G. Oxidation-induced intramolecular disulfide bond inactivates mitogen-activated protein kinase kinase 6 by inhibiting ATP binding Proceedings of the National Academy of Sciences of the United States of America  2010 107:20974-20979  DOI:10.1073/pnas.1007225107  PMID:21078955  PMCID:PMC3000308
  • Ambatipudi, K. S., Hagen, F. K., Delahunty, C. M., Han, X. M., Shafi, R., Hryhorenko, J., Gregoire, S., Marquis, R. E., Melvin, J. E., Koo, H., Yates, J. R. Human common salivary protein 1 (CSP-1) promotes binding of Streptococcus mutans to experimental salivary pellicle and glucans formed on hydroxyapatite surface Journal of Proteome Research  2010 9:6605-6614  DOI:10.1021/pr100786y  PMID:20858015  PMCID:PMC2997150
  • Saddic, L. A., West, L. E., Aslanian, A., Yates, J. R., Rubin, S. M., Gozani, O., Sage, J. Methylation of the retinoblastoma tumor suppressor by SMYD2 Journal of Biological Chemistry  2010 285:37733-37740  DOI:10.1074/jbc.M110.137612  PMID:20870719  PMCID:PMC2988378
  • Hutson, S. L., Mui, E., Kinsley, K., Witola, W. H., Behnke, M. S., El Bissati, K., Muench, S. P., Rohrman, B., Liu, S. R., Wollmann, R., Ogata, Y., Sarkeshik, A., et al. T. gondii RP promoters & knockdown reveal molecular pathways associated with proliferation and cell-cycle arrest PLoS One  2010 5:e14057  DOI:10.1371/journal.pone.0014057  PMID:21124925  PMCID:PMC2989910
  • Michelot, A., Costanzo, M., Sarkeshik, A., Boone, C., Yates, J. R., Drubin, D. G. Reconstitution and protein composition analysis of endocytic actin patches Current Biology  2010 20:1890-1899  DOI:10.1016/j.cub.2010.10.016  PMID:21035341  PMCID:PMC2998891
  • Moresco, J. J., Carvalho, P. C., Yates, J. R. Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry Journal of Proteomics  2010 73:2198-2204  DOI:10.1016/j.jprot.2010.05.008  PMID:20546956  PMCID:PMC3279190
  • Rosenfeld, R. J., Bonaventura, J., Szymczyna, B. R., MacCoss, M. J., Arvai, A. S., Yates, J. R., Tainer, J. A., Getzoff, E. D. Nitric-oxide synthase forms N-NO-pterin and S-NO-cys: implications for activity, allostery, and regulation Journal of Biological Chemistry  2010 285:31581-31589  DOI:10.1074/jbc.M109.072496  PMID:20659888  PMCID:PMC2951232
  • Xu, Z. M., Fulop, Z., Wu, G. K., Pone, E. J., Zhang, J. S., Mai, T., Thomas, L. M., Al-Qahtani, A., White, C. A., Park, S. R., Steinacker, P., Li, Z. G., et al. 14-3-3 adaptor proteins recruit AID to 5'-AGCT-3'-rich switch regions for class switch recombination Nature Structural & Molecular Biology  2010 17:1124-1135  DOI:10.1038/nsmb.1884  PMID:20729863  PMCID:PMC3645988
  • Nilsson, T., Mann, M., Aebersold, R., Yates, J. R., Bairoch, A., Bergeron, J. J. M. Mass spectrometry in high-throughput proteomics: ready for the big time Nature Methods  2010 7:681-685  DOI:10.1038/nmeth0910-681  PMID:20805795
  • Fonslow, B. R., Kang, S. A., Gestaut, D. R., Graczyk, B., Davis, T. N., Sabatini, D. M., Yates, J. R. Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes Analytical Chemistry  2010 82:6643-6651  DOI:10.1021/ac101235k  PMID:20614870  PMCID:PMC2920374
  • Nakamura, T., Wang, L., Wong, C. C. L., Scott, F. L., Eckelman, B. P., Han, X. M., Tzitzilonis, C., Meng, F. J., Gu, Z. Z., Holland, E. A., Clemente, A. T., Okamoto, S., et al. Transnitrosylation of XIAP regulates caspase-dependent neuronal cell death Molecular Cell  2010 39:184-195  DOI:10.1016/j.molcel.2010.07.002  PMID:20670888  PMCID:PMC2924818
  • Roberts-Galbraith, R. H., Ohi, M. D., Ballif, B. A., McLeod, I., McDonald, W. H., Gygi, S. P., Yates, J. R., Gould, K. L. Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site Molecular Cell  2010 39:86-99  DOI:10.1016/j.molcel.2010.06.012  PMID:20603077  PMCID:PMC2916701
  • Pham, E., Crews, L., Ubhi, K., Hansen, L., Adame, A., Cartier, A., Salmon, D., Galasko, D., Michael, S., Savas, J. N., Yates, J. R., Glabe, C. Progressive accumulation of amyloid-beta oligomers in Alzheimer's disease and in amyloid precursor protein transgenic mice is accompanied by selective alterations in synaptic scaffold proteins FEBS Journal  2010 277:3051-3067  DOI:10.1111/j.1742-4658.2010.07719.x  PMID:20573181  PMCID:PMC2933033
  • Xu, H., Jun, Y., Thompson, J., Yates, J., Wickner, W. HOPS prevents the disassembly of trans-SNARE complexes by Sec17p/Sec18p during membrane fusion EMBO Journal  2010 29:1948-1960  DOI:10.1038/emboj.2010.97  PMID:20473271  PMCID:PMC2892374
  • Lee, J. H., Kim, B. G., Ahn, J. M., Park, H. J., Park, S. K., Yoo, J. S., Yates, J. R., Cho, J. Y. Role of PI3K on the regulation of BMP2-induced beta-Catenin activation in human bone marrow stem cells Bone  2010 46:1522-1532  DOI:10.1016/j.bone.2010.02.013  PMID:20167300
  • West, G. M., Tucker, C. L., Xu, T., Park, S. K., Han, X. M., Yates, J. R., Fitzgerald, M. C. Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements Proceedings of the National Academy of Sciences of the United States of America  2010 107:9078-9082  DOI:10.1073/pnas.1000148107  PMID:20439767  PMCID:PMC2889096
  • Kops, G. J. P. L, van der Voet, M., Manak, M. S., van Osch, M. H. J., Naini, S. M., Brear, A., McLeod, I. X., Hentschel, D. M., Yates, J. R., van den Heuvel, S., Shah, J. V. APC16 is a conserved subunit of the anaphase-promoting complex/cyclosome Journal of Cell Science  2010 123:1623-1633  DOI:10.1242/jcs.061549  PMID:20392738  PMCID:PMC2864710
  • Welburn, J. P. I., Vleugel, M., Liu, D., Yates, J. R., Lampson, M. A., Fukagawa, T., Cheeseman, I. M. Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface Molecular Cell  2010 38:383-392  DOI:10.1016/j.molcel.2010.02.034  PMID:20471944  PMCID:PMC2873218
  • Tayo, L. L., Lu, B. W., Cruz, L. J., Yates, J. R. Proteomic analysis provides insights on venom processing in Conus textile Journal of Proteome Research  2010 9:2292-2301  DOI:10.1021/pr901032r  PMID:20334424  PMCID:PMC2909976
  • Janke, R., Herzberg, K., Rolfsmeier, M., Mar, J., Bashkirov, V. I., Haghnazari, E., Cantin, G., Yates, J. R., Heyer, W. D. A truncated DNA-damage-signaling response is activated after DSB formation in the G1 phase of Saccharomyces cerevisiae Nucleic Acids Research  2010 38:2302-2313  DOI:10.1093/nar/gkp1222  PMID:20061370  PMCID:PMC2853130
  • Spielewoy, N., Guaderrama, M., Wohlschlegel, J. A., Ashe, M., Yates, J. R., Wittenberg, C. Npr2, yeast homolog of the human tumor suppressor NPRL2, is a target of Grr1 required for adaptation to growth on diverse nitrogen sources Eukaryotic Cell  2010 9:592-601  DOI:10.1128/ec.00192-09  PMID:20154027  PMCID:PMC2863403
  • Koulov, A. V., LaPointe, P., Lu, B. W., Razvi, A., Coppinger, J., Dong, M. Q., Matteson, J., Laister, R., Arrowsmith, C., Yates, J. R., Balch, W. E. Biological and structural basis for Aha1 regulation of Hsp90 ATPase activity in maintaining proteostasis in the human disease cystic fibrosis Molecular Biology of the Cell  2010 21:871-884  DOI:10.1091/mbc.E09-12-1017  PMID:20089831  PMCID:PMC2836968
  • Carvalho, P. C., Han, X. M., Xu, T., Cociorva, D., Carvalho, M. D., Barbosa, V. C., Yates, J. R. XDIA: improving on the label-free data-independent analysis Bioinformatics  2010 26:847-848  DOI:10.1093/bioinformatics/btq031  PMID:20106817  PMCID:PMC2832823
  • Fischer, J. D. D., Liao, L., Carvalho, P. C., Barbosa, V. C., Domont, G. B., Carvalho, M. D. D., Yates, J. R. Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol Journal of Proteomics  2010 73:1018-1027  DOI:10.1016/j.jprot.2010.01.003  PMID:20083244  PMCID:PMC2834810
  • Jang, C. Y., Coppinger, J. A., Yates, J. R., Fang, G. W. Phospho-regulation of DDA3 function in mitosis Biochemical and Biophysical Research Communications  2010 393:259-263  DOI:10.1016/j.bbrc.2010.01.115  PMID:20117088  PMCID:PMC2950654
  • Baker, S. P., Phillips, J., Anderson, S., Qiu, Q. F., Shabanowitz, J., Smith, M. M., Yates, J. R., Hunt, D. F., Grant, P. A. Histone H3 Thr 45 phosphorylation is a replication-associated post-translational modification in S. cerevisiae Nature Cell Biology  2010 12:294-298  DOI:10.1038/ncb2030  PMID:20139971  PMCID:PMC2856316
  • Lardelli, R. M., Thompson, J. X., Yates, J. R., Stevens, S. W. Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing RNA-a Publication of the RNA Society  2010 16:516-528  DOI:10.1261/rna.2030510  PMID:20089683  PMCID:PMC2822917
  • Minamide, L. S., Maiti, S., Boyle, J. A., Davis, R. C., Coppinger, J. A., Bao, Y., Huang, T. Y., Yates, J., Bokoch, G. M., Bamburg, J. R. Isolation and characterization of cytoplasmic cofilin-actin rods Journal of Biological Chemistry  2010 285:5450-5460  DOI:10.1074/jbc.M109.063768  PMID:20022956  PMCID:PMC2820773
  • Andronicos, N. M., Chen, E. I., Baik, N., Bai, H., Parmer, C. M., Kiosses, W. B., Kamps, M. P., Yates, J. R., Parmer, R. J., Miles, L. A. Proteomics-based discovery of a novel, structurally unique, and developmentally regulated plasminogen receptor, Plg-RKT, a major regulator of cell surface plasminogen activation Blood  2010 115:1319-1330  DOI:10.1182/blood-2008-11-188938  PMID:19897580  PMCID:PMC2826757
  • Nakorchevsky, A., Hewel, J. A., Kurian, S. M., Mondala, T. S., Campbell, D., Head, S. R., Marsh, C. L., Yates, J. R., Salomon, D. R. Molecular mechanisms of chronic kidney transplant rejection via large-scale proteogenomic analysis of tissue biopsies Journal of the American Society of Nephrology  2010 21:362-373  DOI:10.1681/asn.2009060628  PMID:20093355  PMCID:PMC2834542
  • Hou, H. T., Wang, Y., Kallgren, S. P., Thompson, J., Yates, J. R., Jia, S. T. Histone variant H2A.Z regulates centromere silencing and chromosome segregation in fission yeast Journal of Biological Chemistry  2010 285:1909-1918  DOI:10.1074/jbc.M109.058487  PMID:19910462  PMCID:PMC2804349
  • Park, S. K., Yates III, J. R. Census for proteome quantification Current Protocols in Bioinformatics  2010 29:13.12.1-13.12.  DOI:10.1002/0471250953.bi1312s29  PMID:20205189
  • Ramya, T. N., Weerapana, E., Liao, L., Zeng, Y., Tateno, H., Yates, J. R., 3rd, Cravatt, B. F., Paulson, J. C. In situ trans ligands of CD22 identified by glycan-protein photocross-linking-enabled proteomics Molecular & Cellular Proteomics  2010 9:1339-1351  DOI:10.1074/mcp.M900461-MCP200  PMID:20172905  PMCID:PMC2877991
  • Huang, H. N., Jeon, M. S., Liao, L. J., Yang, C., Elly, C., Yates, J. R., Liu, Y. C. K33-linked polyubiquitination of T cell receptor-zeta regulates proteolysis-independent T cell signaling Immunity  2010 33:60-70  DOI:10.1016/j.immuni.2010.07.002  PMID:20637659  PMCID:PMC2927827
  • Nishimura, N., Sarkeshik, A., Nito, K., Park, S. Y., Wang, A., Carvalho, P. C., Lee, S., Caddell, D. F., Cutler, S. R., Chory, J., Yates, J. R., Schroeder, J. I. PYR/PYL/RCAR family members are major in vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis Plant Journal  2010 61:290-299  DOI:10.1111/j.1365-313X.2009.04054.x  PMID:19874541  PMCID:PMC2807913
  • Yang, Q. K., Deng, X. M., Lu, B. W., Cameron, M., Fearns, C., Patricelli, M. P., Yates, J. R., Gray, N. S., Lee, J. D. Pharmacological inhibition of BMK1 suppresses tumor growth through promyelocytic leukemia protein Cancer Cell  2010 18:258-267  DOI:10.1016/j.ccr.2010.08.008  PMID:20832753  PMCID:PMC2939729
  • Wang, Y. C., Kelber, J. A., Cao, H. S. T., Cantin, G. T., Lin, R., Wang, W., Kaushal, S., Bristow, J. M., Edgington, T. S., Hoffman, R. M., Bouvet, M., Yates, J. R., et al. Pseudopodium-enriched atypical kinase 1 regulates the cytoskeleton and cancer progession Proceedings of the National Academy of Sciences of the United States of America  2010 107:10920-10925  DOI:10.1073/pnas.0914776107  PMID:20534451  PMCID:PMC2890752
  • Hutt, D. M., Herman, D., Rodrigues, A. P. C., Noel, S., Pilewski, J. M., Matteson, J., Hoch, B., Kellner, W., Kelly, J. W., Schmidt, A., Thomas, P. J., Matsumura, Y., et al. Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis Nature Chemical Biology  2010 6:25-33  DOI:10.1038/nchembio.275  PMID:19966789  PMCID:PMC2901172
  • de Wit, J., Sylwestrak, E., O'Sullivan, M. L., Otto, S., Tiglio, K., Savas, J. N., Yates, J. R., Comoletti, D., Taylor, P., Ghosh, A. LRRTM2 interacts with Neurexin1 and regulates excitatory synapse formation Neuron  2009 64:799-806  DOI:10.1016/j.neuron.2009.12.019  PMID:20064388  PMCID:PMC2829666
  • Dovey, C. L., Aslanian, A., Sofueva, S., Yates, J. R., Russell, P. Mms1-Mms22 complex protects genome integrity in Schizosaccharomyces pombe DNA Repair  2009 8:1390-1399  DOI:10.1016/j.dnarep.2009.09.008  PMID:19819763  PMCID:PMC2787726
  • Grigoryev, Y. A., Kurian, S. M., Nakorchevskiy, A. A., Burke, J. P., Campbell, D., Head, S. R., Deng, J., Kantor, A. B., Yates, J. R., Salomon, D. R. Genome-wide analysis of immune activation in human T and B cells reveals distinct classes of alternatively spliced genes PLoS One  2009 4:e7906  DOI:10.1371/journal.pone.0007906  PMID:19936255  PMCID:PMC2775942
  • Ambatipudi, K. S., Lu, B. W., Hagen, F. K., Melvin, J. E., Yates, J. R. Quantitative analysis of age specific variation in the abundance of human female parotid salivary proteins Journal of Proteome Research  2009 8:5093-5102  DOI:10.1021/pr900478h  PMID:19764810  PMCID:PMC2834885
  • Usaite, R., Jewett, M. C., Oliveira, A. P., Yates, J. R., Olsson, L., Nielsen, J. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator Molecular Systems Biology  2009 5:319  DOI:10.1038/msb.2009.67  PMID:19888214  PMCID:PMC2795470
  • Liu, G. H., Guan, T., Datta, K., Coppinger, J., Yates, J., Gerace, L. Regulation of myoblast differentiation by the nuclear envelope protein NET39 Molecular and Cellular Biology  2009 29:5800-5812  DOI:10.1128/mcb.00684-09  PMID:19704009  PMCID:PMC2772732
  • Rao, A. K., Ziegler, Y. S., McLeod, I. X., Yates, J. R., Nardulli, A. M. Thioredoxin and thioredoxin reductase influence estrogen receptor alpha-mediated gene expression in human breast cancer cells Journal of Molecular Endocrinology  2009 43:251-261  DOI:10.1677/jme-09-0053  PMID:19620238  PMCID:PMC2994277
  • Gu, W. F., Shirayama, M., Conte, D., Vasale, J., Batista, P. J., Claycomb, J. M., Moresco, J. J., Youngman, E. M., Keys, J., Stoltz, M. J., Chen, C. C. G., Chaves, D. A., et al. Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline Molecular Cell  2009 36:231-244  DOI:10.1016/j.molcel.2009.09.020  PMID:19800275  PMCID:PMC2776052
  • Carvalho, P. C., Xu, T., Han, X. M., Cociorva, D., Barbosa, V. C., Yates, J. R. YADA: a tool for taking the most out of high-resolution spectra Bioinformatics  2009 25:2734-2736  DOI:10.1093/bioinformatics/btp489  PMID:19684088  PMCID:PMC3140806
  • Kim, B. G., Lee, J. H., Ahn, J. M., Park, S. K., Cho, J. H., Hwang, D., Yoo, J. S., Yates, J. R., Ryoo, H. M., Cho, J. Y. 'Two-stage double-technique hybrid (TSDTH)' identification strategy for the analysis of BMP2-induced transdifferentiation of premyoblast C2C12 cells to osteoblast Journal of Proteome Research  2009 8:4441-4454  DOI:10.1021/pr900231a  PMID:19655815
  • Li, J., Cai, T. X., Wu, P., Cui, Z. Y., Chen, X. L., Hou, J. J., Xie, Z. S., Xue, P., Shi, L. A., Liu, P. S., Yates, J. R., Yang, F. Q. Proteomic analysis of mitochondria from Caenorhabditis elegans Proteomics  2009 9:4539-4553  DOI:10.1002/pmic.200900101  PMID:19670372
  • Lal, K., Bromley, E., Oakes, R., Prieto, J. H., Sanderson, S. J., Kurian, D., Hunt, L., Yates, J. R., Wastling, J. M., Sinden, R. E., Tomley, F. M. Proteomic comparison of four Eimeria tenella life-cycle stages: unsporulated oocyst, sporulated oocyst, sporozoite and second-generation merozoite Proteomics  2009 9:4566-4576  DOI:10.1002/pmic.200900305  PMID:19795439  PMCID:PMC2947549
  • Cornillez-Ty, C. T., Liao, L. J., Yates, J. R., Kuhn, P., Buchmeier, M. J. Severe acute respiratory syndrome coronavirus nonstructural protein 2 interacts with a host protein complex involved in mitochondrial biogenesis and intracellular signaling Journal of Virology  2009 83:10314-10318  DOI:10.1128/jvi.00842-09  PMID:19640993  PMCID:PMC2748024
  • Maffini, S., Maia, A. R. R., Manning, A. L., Maliga, Z., Pereira, A. L., Junqueira, M., Shevchenko, A., Hyman, A., Yates, J. R., Galjart, N., Compton, D. A., Maiato, H. Motor-independent targeting of CLASPs to kinetochores by CENP-E promotes microtubule turnover and poleward flux Current Biology  2009 19:1566-1572  DOI:10.1016/j.cub.2009.07.059  PMID:19733075  PMCID:PMC2766669
  • Fabian, M. R., Mathonnet, G., Sundermeier, T., Mathys, H., Zipprich, J. T., Svitkin, Y. V., Rivas, F., Jinek, M., Wohischlegel, J., Doudna, J. A., Chen, C. Y. A., Shyu, A. B., et al. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation Molecular Cell  2009 35:868-880  DOI:10.1016/j.molcel.2009.08.004  PMID:19716330  PMCID:PMC2803087
  • Amako, Y., Sarkeshik, A., Hotta, H., Yates, J., Siddiqui, A. Role of oxysterol binding protein in hepatitis C virus infection Journal of Virology  2009 83:9237-9246  DOI:10.1128/jvi.00958-09  PMID:19570870  PMCID:PMC2738263
  • Curtis, C. D., Thorngren, D. L., Ziegler, Y. S., Sarkeshik, A., Yates, J. R., Nardulli, A. M. Apurinic/apyrimidinic endonuclease 1 alters estrogen receptor activity and estrogen-responsive gene expression Molecular Endocrinology  2009 23:1346-1359  DOI:10.1210/me.2009-0093  PMID:19460860  PMCID:PMC2737565
  • Dammermann, A., Pemble, H., Mitchell, B. J., McLeod, I., Yates, J. R., Kintner, C., Desai, A. B., Oegema, K. The hydrolethalus syndrome protein HYLS-1 links core centriole structure to cilia formation Genes & Development  2009 23:2046-2059  DOI:10.1101/gad.1810409  PMID:19656802  PMCID:PMC2751977
  • Koncarevic, S., Rohrbach, P., Deponte, M., Krohne, G., Prieto, J. H., Yates, J., Rahlfs, S., Becker, K. The malarial parasite Plasmodium falciparum imports the human protein peroxiredoxin 2 for peroxide detoxification Proceedings of the National Academy of Sciences of the United States of America  2009 106:13323-13328  DOI:10.1073/pnas.0905387106  PMID:19666612  PMCID:PMC2726359
  • Wong, C. C. L., Cociorva, D., Venable, J. D., Xu, T., Yates, J. R. 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 Journal of the American Society for Mass Spectrometry  2009 20:1405-1414  DOI:10.1016/j.jasms.2009.04.007  PMID:19467883  PMCID:PMC2946190
  • Chuang, L. C., Teixeira, L. K., Wohlschlegel, J. A., Henze, M., Yates, J. R., Mendez, J., Reed, S. I. Phosphorylation of Mcm2 by Cdc7 promotes pre-replication complex assembly during cell-cycle re-entry Molecular Cell  2009 35:206-216  DOI:10.1016/j.molcel.2009.06.014  PMID:19647517  PMCID:PMC2725784
  • Liao, L. J., McClatchy, D. B., Yates, J. R. Shotgun proteomics in neuroscience Neuron  2009 63:12-26  DOI:10.1016/j.neuron.2009.06.011  PMID:19607789  PMCID:PMC2746002
  • Kurian, S. M., Heilman, R., Mondala, T. S., Nakorchevsky, A., Hewel, J. A., Campbell, D., Robison, E. H., Wang, L., Lin, W., Gaber, L., Solez, K., Shidban, H., et al. Biomarkers for early and late stage chronic allograft nephropathy by proteogenomic profiling of peripheral blood PLoS One  2009 4:e6212  DOI:10.1371/journal.pone.0006212  PMID:19593431  PMCID:PMC2703807
  • Fekairi, S., Scaglione, S., Chahwan, C., Taylor, E. R., Tissier, A., Coulon, S., Dong, M. Q., Ruse, C., Yates, J. R., Russell, P., Fuchs, R. P., McGowan, C. H., et al. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases Cell  2009 138:78-89  DOI:10.1016/j.cell.2009.06.029  PMID:19596236  PMCID:PMC2861413
  • Webby, C. J., Wolf, A., Gromak, N., Dreger, M., Kramer, H., Kessler, B., Nielsen, M. L., Schmitz, C., Butler, D. S., Yates, J. R., Delahunty, C. M., Hahn, P., et al. Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing Science  2009 325:90-93  DOI:10.1126/science.1175865  PMID:19574390
  • Rodriguez, H., Snyder, M., Uhlen, M., Andrews, P., Beavis, R., Borchers, C., Chalkley, R. J., Cho, S. Y., Cottingham, K., Dunn, M., Dylag, T., Edgar, R., et al. Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles Journal of Proteome Research  2009 8:3689-3692  DOI:10.1021/pr900023z  PMID:19344107  PMCID:PMC2742685
  • Choi, S. H., Peli-Gulli, M. P., McLeod, I., Sarkeshik, A., Yates, J. R., Simanis, V., McCollum, D. Phosphorylation state defines discrete roles for monopolin in chromosome attachment and spindle elongation Current Biology  2009 19:985-995  DOI:10.1016/j.cub.2009.05.042  PMID:19523829  PMCID:PMC2726783
  • Jourdain, I., Spielewoy, N., Thompson, J., Dhut, S., Yates, J. R., Toda, T. Identification of a conserved F-box protein 6 interactor essential for endocytosis and cytokinesis in fission yeast Biochemical Journal  2009 420:169-177  DOI:10.1042/bj20081659  PMID:19243310  PMCID:PMC2950653
  • Holinger, E. P., Old, W. M., Giddings, T. H., Wong, C., Yates, J. R., Winey, M. Budding yeast centrosome duplication requires stabilization of Spc29 via Mps1-mediated phosphorylation Journal of Biological Chemistry  2009 284:12949-12955  DOI:10.1074/jbc.M900088200  PMID:19269975  PMCID:PMC2676026
  • Foltz, D. R., Jansen, L. E. T., Bailey, A. O., Yates, J. R., Bassett, E. A., Wood, S., Black, B. E., Cleveland, D. W. Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP Cell  2009 137:472-484  DOI:10.1016/j.cell.2009.02.039  PMID:19410544  PMCID:PMC2747366
  • Jang, C. Y., Coppinger, J. A., Seki, A., Yates, J. R., Fang, G. W. Plk1 and Aurora A regulate the depolymerase activity and the cellular localization of Kif2a Journal of Cell Science  2009 122:1334-1341  DOI:10.1242/jcs.044321  PMID:19351716  PMCID:PMC2671931
  • Chen, Y. L., Lu, B. W., Yang, Q. K., Fearns, C., Yates, J. R., Lee, J. D. Combined integrin phosphoproteomic analyses and small interfering RNA-based functional screening identify key regulators for cancer cell adhesion and migration Cancer Research  2009 69:3713-3720  DOI:10.1158/0008-5472.can-08-2515  PMID:19351860  PMCID:PMC2669841
  • Fonslow, B. R., Yates, J. R. Capillary electrophoresis applied to proteomic analysis Journal of Separation Science  2009 32:1175-1188  DOI:10.1002/jssc.200800592  PMID:19360788  PMCID:PMC3509210
  • Shock, T. R., Thompson, J., Yates, J. R., Madhani, H. D. Hog1 mitogen-activated protein kinase (MAPK) interrupts signal transduction between the Kss1 MAPK and the Tec1 transcription factor to maintain pathway specificity Eukaryotic Cell  2009 8:606-616  DOI:10.1128/ec.00005-09  PMID:19218425  PMCID:PMC2669196
  • Welburn, J. P. I., Grishchuk, E. L., Backer, C. B., Wilson-Kubalek, E. M., Yates, J. R., Cheeseman, I. M. The human kinetochore Ska1 complex facilitates microtubule depolymerization-coupled motility Developmental Cell  2009 16:374-385  DOI:10.1016/j.devcel.2009.01.011  PMID:19289083  PMCID:PMC2746561
  • Chen, R. Q., Yang, Q. K., Lu, B. W., Yi, W., Cantin, G., Chen, Y. L., Fearns, C., Yates, J. R., Lee, J. D. CDC25B mediates rapamycin-induced oncogenic responses in cancer cells Cancer Research  2009 69:2663-2668  DOI:10.1158/0008-5472.can-08-3222  PMID:19276368  PMCID:PMC2697620
  • Nakajima, Y., Tyers, R. G., Wong, C. C. L., Yates, J. R., Drubin, D. G., Barnes, G. Nbl1p: a Borealin/Dasra/CSC-1-like protein essential for Aurora/Ipl1 complex function and integrity in Saccharomyces cerevisiae Molecular Biology of the Cell  2009 20:1772-1784  DOI:10.1091/mbc.E08-10-1011  PMID:19158380  PMCID:PMC2655253
  • Park, S. K., Liao, L., Kim, J. Y., Yates, J. R. A computational approach to correct arginine-to-proline conversion in quantitative proteomics Nature Methods  2009 6:184-185  DOI:10.1038/nmeth0309-184  PMID:19247291  PMCID:PMC2946183
  • Lal, K., Prieto, J. H., Bromley, E., Sanderson, S. J., Yates, J. R., Wastling, J. M., Tomley, F. M., Sinden, R. E. Characterisation of Plasmodium invasive organelles: an ookinete microneme proteome Proteomics  2009 9:1142-1151  DOI:10.1002/pmic.200800404  PMID:19206106  PMCID:PMC2706521
  • Carvalho, P. C., Cociorva, D., Wong, C. C. L., Carvalho, M. D. D., Barbosa, V. C., Yates, J. R. Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra Analytical Chemistry  2009 81:1996-2003  DOI:10.1021/ac8025288  PMID:19203245  PMCID:PMC2865572
  • Cui, Z. Y., Chen, X. L., Lu, B. W., Park, S. K., Xu, T., Xie, Z. S., Xue, P., Hou, J. J., Hang, H. Y., Yates, J. R., Yang, F. Q. 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 9:1274-1292  DOI:10.1002/pmic.200800354  PMID:19253283  PMCID:PMC2946197
  • Gonzalez-Begne, M., Lu, B. W., Han, X. M., Hagen, F. K., Hand, A. R., Melvin, J. E., Yates, J. R. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT) Journal of Proteome Research  2009 8:1304-1314  DOI:10.1021/pr800658c  PMID:19199708  PMCID:PMC2693447
  • Ma, L., Tsai, M. Y., Wang, S. S., Lu, B. W., Chen, R., Yates, J. R., Zhu, X. L., Zheng, Y. X. Requirement for Nudel and dynein for assembly of the lamin B spindle matrix Nature Cell Biology  2009 11:246-256  DOI:10.1038/ncb1832  PMID:19198602  PMCID:PMC2699591
  • Wang, Y., Reddy, B., Thompson, J., Wang, H. B., Noma, K., Yates, J. R., Jia, S. T. Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein Molecular Cell  2009 33:428-437  DOI:10.1016/j.molcel.2009.02.002  PMID:19250904  PMCID:PMC2673476
  • Carvalho, P. C., Fischer, J. S. G., Chen, E. I., Domont, G. B., Carvalho, M. G. C., Degrave, W. M., Yates, J. R., Barbosa, V. C. GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data Proteome Science  2009 7:6  DOI:10.1186/1477-5956-7-6  PMID:19239707  PMCID:PMC2652440
  • Shi, Y. S., Di Giammartino, D. C., Taylor, D., Sarkeshik, A., Rice, W. J., Yates, J. R., Frank, J., Manley, J. L. Molecular architecture of the human pre-mRNA 3' processing complex Molecular Cell  2009 33:365-376  DOI:10.1016/j.molcel.2008.12.028  PMID:19217410  PMCID:PMC2946185
  • Wang, J., Farr, G. W., Zeiss, C. J., Rodriguez-Gil, D. J., Wilson, J. H., Furtak, K., Rutkowski, D. T., Kaufman, R. J., Ruse, C. I., Yates, J. R., Perrin, S., Feany, M. B., et al. Progressive aggregation despite chaperone associations of a mutant SOD1-YFP in transgenic mice that develop ALS Proceedings of the National Academy of Sciences of the United States of America  2009 106:1392-1397  DOI:10.1073/pnas.0813045106  PMID:19171884  PMCID:PMC2631083
  • Keller, L. C., Geimer, S., Romijn, E., Yates, J., Zamora, I., Marshall, W. F. Molecular architecture of the centriole proteome: the conserved WD40 domain protein POC1 is required for centriole duplication and length control Molecular Biology of the Cell  2009 20:1150-1166  DOI:10.1091/mbc.E08-06-0619  PMID:19109428  PMCID:PMC2642750
  • Dinglasan, R. R., Devenport, M., Florens, L., Johnson, J. R., McHugh, C. A., Donnelly-Doman, M., Carucci, D. J., Yates, J. R., Jacobs-Lorena, M. The Anopheles gambiae adult midgut peritrophic matrix proteome Insect Biochemistry and Molecular Biology  2009 39:125-134  DOI:10.1016/j.ibmb.2008.10.010  PMID:19038338  PMCID:PMC2684889
  • Xu, T., Wong, C. C. L., Kashina, A., Yates, J. R. Identification of N-terminally arginylated proteins and peptides by mass spectrometry Nature Protocols  2009 4:325-332  DOI:10.1038/nprot.2008.248  PMID:19229197  PMCID:PMC2683362
  • Yates, J. R., Ruse, C. I., Nakorchevsky, A. Proteomics by mass spectrometry: approaches, advances, and applications Annual Review of Biomedical Engineering  2009 11:49-79  DOI:10.1146/annurev-bioeng-061008-124934  PMID:19400705
  • Lu, B., Xu, T., Park, S. K., Yates, J. R., 3rd Shotgun protein identification and quantification by mass spectrometry Methods in Molecular Biology  2009 564:261-288  DOI:10.1007/978-1-60761-157-8_15  PMID:19544028
  • Lu, B., Xu, T., Park, S. K., McClatchy, D. B., Liao, L., Yates, J. R., 3rd Shotgun protein identification and quantification by mass spectrometry in neuroproteomics Methods in Molecular Biology  2009 566:229-259  DOI:10.1007/978-1-59745-562-6_16  PMID:20058176
  • Yan, W. H., Apweiler, R., Balgley, B. M., Boontheung, P., Bundy, J. L., Cargile, B. J., Cole, S., Fang, X. P., Gonzalez-Begne, M., Griffin, T. J., Hagen, F., Hu, S., et al. Systematic comparison of the human saliva and plasma proteomes Proteomics Clinical Applications  2009 3:116-134  DOI:10.1002/prca.200800140  PMID:19898684  PMCID:PMC2773554
  • Csankovszki, G., Collette, K., Spahl, K., Carey, J., Snyder, M., Petty, E., Patel, U., Tabuchi, T., Liu, H., McLeod, I., Thompson, J., Sarkesik, A., et al. Three distinct condensin complexes control C. elegans chromosome dynamics Current Biology  2009 19:9-19  DOI:10.1016/j.cub.2008.12.006  PMID:19119011  PMCID:PMC2682549
  • Prieto, J. H., Koncarevic, S., Park, S. K., Yates, J., Becker, K. Large-scale differential proteome analysis in Plasmodium falciparum under drug treatment PLoS One  2008 3:e4098  DOI:10.1371/journal.pone.0004098  PMID:19116658  PMCID:PMC2605551
  • Kang, R. J., Wan, J. M., Arstikaitis, P., Takahashi, H., Huang, K., Bailey, A. O., Thompson, J. X., Roth, A. F., Drisdel, R. C., Mastro, R., Green, W. N., Yates, J. R., et al. Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation Nature  2008 456:904-909  DOI:10.1038/nature07605  PMID:19092927  PMCID:PMC2610860
  • Zhu, H., Coppinger, J. A., Jang, C. Y., Yates, J. R., Fang, G. W. FAM29A promotes microtubule amplification via recruitment of the NEDD1-gamma-tubulin complex to the mitotic spindle Journal of Cell Biology  2008 183:835-848  DOI:10.1083/jcb.200807046  PMID:19029337  PMCID:PMC2592839
  • Kaeser, M. D., Aslanian, A., Dong, M. Q., Yates, J. R., Emerson, B. M. BRD7, a novel PBAF-specific SWI/SNF subunit, is required for target gene activation and repression in embryonic stem cells Journal of Biological Chemistry  2008 283:32254-32263  DOI:10.1074/jbc.M806061200  PMID:18809673  PMCID:PMC2583284
  • Chen, E. I., McClatchy, D., Park, S. K., Yates, J. R. Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome Analytical Chemistry  2008 80:8694-8701  DOI:10.1021/ac800606w  PMID:18937422  PMCID:PMC2975600
  • Liu, Y., Dentin, R., Chen, D., Hedrick, S., Ravnskjaer, K., Schenk, S., Milne, J., Meyers, D. J., Cole, P., Yates, J., Olefsky, J., Guarente, L., et al. A fasting inducible switch modulates gluconeogenesis via activator/coactivator exchange Nature  2008 456:269-273  DOI:10.1038/nature07349  PMID:18849969  PMCID:PMC2597669
  • Liao, L. J., McClatchy, D. B., Park, S. K., Xu, T., Lu, B. W., Yates, J. R. Quantitative analysis of brain nuclear phosphoproteins identifies developmentally regulated phosphorylation events Journal of Proteome Research  2008 7:4743-4755  DOI:10.1021/pr8003198  PMID:18823140  PMCID:PMC2659596
  • Le Roch, K. G., Johnson, J. R., Ahiboh, H., Chung, D. W. D., Prudhomme, J., Plouffe, D., Henson, K., Zhou, Y. Y., Witola, W., Yates, J. R., Ben Mamoun, C., Winzeler, E. A., et al. A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum BMC Genomics  2008 9:513  DOI:10.1186/1471-2164-9-513  PMID:18973684  PMCID:PMC2596145
  • Schultz-Norton, J. R., Ziegler, Y. S., Likhite, V. S., Yates, J. R., Nardulli, A. M. Isolation of novel coregulatory protein networks associated with DNA-bound estrogen receptor alpha BMC Molecular Biology  2008 9:97  DOI:10.1186/1471-2199-9-97  PMID:18973695  PMCID:PMC2585101
  • Liao, L. J., Park, S. K., Xu, T., Vanderklish, P., Yates, J. R. Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice Proceedings of the National Academy of Sciences of the United States of America  2008 105:15281-15286  DOI:10.1073/pnas.0804678105  PMID:18829439  PMCID:PMC2563066
  • Han, X. M., Aslanian, A., Yates, J. R. Mass spectrometry for proteomics Current Opinion in Chemical Biology  2008 12:483-490  DOI:10.1016/j.cbpa.2008.07.024  PMID:18718552  PMCID:PMC2642903
  • Motoyama, A., Yates, J. R. Multidimensional lc separations in shotgun proteomics Analytical Chemistry  2008 80:7187-7193  DOI:10.1021/ac8013669  PMID:18826178
  • Lu, B. W., McClatchy, D. B., Kim, J. Y., Yates, J. R. Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry Proteomics  2008 8:3947-3955  DOI:10.1002/pmic.200800120  PMID:18780349
  • Creekmore, A. L., Walt, K. A., Schultz-Norton, J. R., Ziegler, Y. S., McLeod, I. X., Yates, J. R., Nardulli, A. M. The role of retinoblastoma-associated proteins 46 and 48 in estrogen receptor alpha mediated gene expression Molecular and Cellular Endocrinology  2008 291:79-86  DOI:10.1016/j.mce.2008.05.016  PMID:18577416  PMCID:PMC2642675
  • Zhao, W. M., Coppinger, J. A., Seki, A., Cheng, X. L., Yates, J. R., Fang, G. W. RCS1, a substrate of APC/C, controls the metaphase to anaphase transition Proceedings of the National Academy of Sciences of the United States of America  2008 105:13415-13420  DOI:10.1073/pnas.0709227105  PMID:18757745  PMCID:PMC2533204
  • Mu, T. W., Ong, D. S. T., Wang, Y. J., Balch, W. E., Yates, J. R., Segatori, L., Kelly, J. W. Chemical and biological approaches synergize to ameliorate protein-folding diseases Cell  2008 134:769-781  DOI:10.1016/j.cell.2008.06.037  PMID:18775310  PMCID:PMC2650088
  • Gassmann, R., Essex, A., Hu, J. S., Maddox, P. S., Motegi, F., Sugimoto, A., O'Rourke, S. M., Bowerman, B., McLeod, I., Yates, J. R., Oegema, K., Cheeseman, I. M., et al. A new mechanism controlling kinetochore-microtubule interactions revealed by comparison of two dynein-targeting components: SPDL-1 and the Rod/Zwilch/Zw10 complex Genes & Development  2008 22:2385-2399  DOI:10.1101/gad.1687508  PMID:18765790  PMCID:PMC2532926
  • Moresco, J. J., Dong, M. Q., Yates, J. R. Quantitative mass spectrometry as a tool for nutritional proteomics American Journal of Clinical Nutrition  2008 88:597-604  PMID:18779273
  • de Bruin, R. A. M., Kalashnikova, T. I., Aslanian, A., Wohischlegel, J., Chahwan, C., Yates, J. R., Russell, P., Wittenberg, C. DNA replication checkpoint promotes G1-S transcription by inactivating the MBF repressor Nrm1 Proceedings of the National Academy of Sciences of the United States of America  2008 105:11230-11235  DOI:10.1073/pnas.0801106105  PMID:18682565  PMCID:PMC2516226
  • Lu, B. W., Ruse, C. I., Yates, J. R. Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search Journal of Proteome Research  2008 7:3628-3634  DOI:10.1021/pr8001194  PMID:18563924  PMCID:PMC2587238
  • Carvalho, P. C., Fischer, J. S., Chen, E. I., Yates, J. R., Barbosa, V. C. PatternLab for proteomics: a tool for differential shotgun proteomics BMC Bioinformatics  2008 9:316  DOI:10.1186/1471-2105-9-316  PMID:18644148  PMCID:PMC2488363
  • Ducat, D., Kawaguchi, S., Liu, H. B., Yates, J. R., Zheng, Y. X. Regulation of microtubule assembly and organization in mitosis by the AAA plus ATPase pontin Molecular Biology of the Cell  2008 19:3097-3110  DOI:10.1091/mbc.E07-11-1202  PMID:18463163  PMCID:PMC2441676
  • Scorah, J., Dong, M. Q., Yates, J. R., Scott, M., Gillespie, D., McGowan, C. H. A conserved proliferating cell nuclear antigen-interacting protein sequence in Chk1 is required for checkpoint function Journal of Biological Chemistry  2008 283:17250-17259  DOI:10.1074/jbc.M800369200  PMID:18448427  PMCID:PMC2427339
  • Seki, A., Coppinger, J. A., Jang, C. Y., Yates, J. R., Fang, G. W. Bora and the kinase Aurora A cooperatively activate the kinase Plk1 and control mitotic entry Science  2008 320:1655-1658  DOI:10.1126/science.1157425  PMID:18566290  PMCID:PMC2834883
  • Xu, S. X., Wong, C. C. L., Tong, E. H. Y., Chung, S. S. M., Yates, J. R., Yin, Y. B., Ko, B. C. B. Phosphorylation by casein kinase 1 regulates tonicity-induced osmotic response element-binding protein/tonicity enhancer-binding protein nucleocytoplasmic trafficking Journal of Biological Chemistry  2008 283:17624-17634  DOI:10.1074/jbc.M800281200  PMID:18411282  PMCID:PMC2427355
  • Jelluma, N., Brenkman, A. B., McLeod, I., Yates, J. R., Cleveland, D. W., Medema, R. H., Kops, G. J. P. L Chromosomal instability by inefficient Mps1 auto-activation due to a weakened mitotic checkpoint and lagging chromosomes PLoS One  2008 3:e2415  DOI:10.1371/journal.pone.0002415  PMID:18545697  PMCID:PMC2408436
  • Patra, K. P., Johnson, J. R., Cantin, G. T., Yates, J. R., Vinetz, J. M. 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 8:2492-2499  DOI:10.1002/pmic.200700727  PMID:18563747  PMCID:PMC2637033
  • Neuman, B. W., Joseph, J. S., Saikatendu, K. S., Serrano-Navarro, P., Chatterjee, A., Johnson, M. A., Liao, L., Klaus, J. P., Yates, J. R., Wuethrich, K., Stevens, R. C., Buchmeier, M. J., et al. Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3 Journal of Virology  2008 82:5279-5294  DOI:10.1128/jvi.02631-07  PMID:18367524  PMCID:PMC2395186
  • Duran, J. M., Kinseth, M., Bossard, C., Rose, D. W., Polishchuk, R., Wu, C. C., Yates, J., Zimmerman, T., Malhotra, V. The role of GRASP55 in Golgi fragmentation and entry of cells into mitosis Molecular Biology of the Cell  2008 19:2579-2587  DOI:10.1091/mbc.E07-10-0998  PMID:18385516  PMCID:PMC2397314
  • Rao, A. K., Ziegler, Y. S., McLeod, I. X., Yates, J. R., Nardulli, A. M. Effects of Cu/Zn superoxide dismutase on estrogen responsiveness and oxidative stress in human breast cancer cells Molecular Endocrinology  2008 22:1113-1124  DOI:10.1210/me.2007-0381  PMID:18258688  PMCID:PMC2366184
  • Ruse, C. I., McClatchy, D. B., Lu, B. W., Cociorva, D., Motoyama, A., Park, S. K., Yates, J. R. Motif-specific sampling of phosphoproteomes Journal of Proteome Research  2008 7:2140-2150  DOI:10.1021/pr800147u  PMID:18452278  PMCID:PMC2703005
  • Denny, P., Hagen, F. K., Hardt, M., Liao, L. J., Yan, W. H., Arellanno, M., Bassilian, S., Bedi, G. S., Boontheung, P., Cociorva, D., Delahunty, C. M., Denny, T., et al. The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions Journal of Proteome Research  2008 7:1994-2006  DOI:10.1021/pr700764j  PMID:18361515  PMCID:PMC2839126
  • Jang, C. Y., Wong, J., Coppinger, J. A., Seki, A., Yates, J. R., Fang, G. W. DDA3 recruits microtubule depolymerase Kif2a to spindle poles and controls spindle dynamics and mitotic chromosome movement Journal of Cell Biology  2008 181:255-267  DOI:10.1083/jcb.200711032  PMID:18411309  PMCID:PMC2315673
  • Seki, A., Coppinger, J. A., Du, H., Jang, C. Y., Yates, J. R., Fang, G. Plk1- and beta-TrCP-dependent degradation of Bora controls mitotic progression Journal of Cell Biology  2008 181:65-78  DOI:10.1083/jcb.200712027  PMID:18378770  PMCID:PMC2287288
  • Clifford, D. M., Wolfe, B. A., Roberts-Galbraith, R. H., McDonald, W. H., Yates, J. R., Gould, K. L. The Clp1/Cdc14 phosphatase contributes to the robustness of cytokinesis by association with anillin-related Mid1 Journal of Cell Biology  2008 181:79-88  DOI:10.1083/jcb.200709060  PMID:18378776  PMCID:PMC2287289
  • DiMaggio, P. A., Floudas, C. A., Lu, B. W., Yates, J. R. A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry Journal of Proteome Research  2008 7:1584-1593  DOI:10.1021/pr700577z  PMID:18324765
  • Park, S. K., Venable, J. D., Xu, T., Yates, J. R. A quantitative analysis software tool for mass spectrometry-based proteomics Nature Methods  2008 5:319-322  DOI:10.1038/nmeth.1195  PMID:18345006  PMCID:PMC3509211
  • Sanderson, S. J., Xia, D., Prieto, H., Yates, J., Heiges, M., Kissinger, J. C., Bromley, E., Lal, K., Sinden, R. E., Tomley, F., Wastling, J. M. Determining the protein repertoire of Cryptosporidium parvum sporozoites Proteomics  2008 8:1398-1414  DOI:10.1002/pmic.200700804  PMID:18306179  PMCID:PMC2770187
  • Zhu, J. H., Chen, R., Yi, W., Cantin, G. T., Fearns, C., Yang, Y., Yates, J. R., Lee, J. D. Protein tyrosine phosphatase PTPN13 negatively regulates Her2/ErbB2 malignant signaling Oncogene  2008 27:2525-2531  DOI:10.1038/sj.onc.1210922  PMID:17982484
  • Lu, B. W., Motoyama, A., Ruse, C., Venable, J., Yates, J. R. Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data Analytical Chemistry  2008 80:2018-2025  DOI:10.1021/ac701697w  PMID:18275164  PMCID:PMC3509208
  • Dentin, R., Hedrick, S., Xie, J. X., Yates, J., Montminy, M. Hepatic glucose sensing via the CREB coactivator CRTC2 Science  2008 319:1402-1405  DOI:10.1126/science.1151363  PMID:18323454
  • Ashe, M., de Bruin, R. A. M., Kalashnikova, T., McDonald, W. H., Yates, J. R., Wittenberg, C. The SBF- and MBF-associated protein Msa1 is required for proper timing of G(1)-specific transcription in Saccharomyces cerevisiae Journal of Biological Chemistry  2008 283:6040-6049  DOI:10.1074/jbc.M708248200  PMID:18160399
  • Cantin, G. T., Yi, W., Lu, B. W., Park, S. K., Xu, T., Lee, J. D., Yates, J. R. Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis Journal of Proteome Research  2008 7:1346-1351  DOI:10.1021/pr0705441  PMID:18220336
  • Diop, S. B., Bertaux, K., Vasanthi, D., Sarkeshik, A., Goirand, B., Aragnol, D., Tolwinski, N. S., Cole, M. D., Pradel, J., Yates, J. R., Mishra, R. K., Graba, Y., et al. Reptin and Pontin function antagonistically with PcG and TrxG complexes to mediate Hox gene control EMBO Reports  2008 9:260-266  DOI:10.1038/embor.2008.8  PMID:18259215  PMCID:PMC2267392
  • Chiranand, W., McLeod, I., Zhou, H. J., Lynn, J. J., Vega, L. A., Myers, H., Yates, J. R., Lorenz, M. C., Gustin, M. C. CTA4 transcription factor mediates induction of nitrosative stress response in Candida albicans Eukaryotic Cell  2008 7:268-278  DOI:10.1128/ec.00240-07  PMID:18083829  PMCID:PMC2238162
  • Mathivanan, S., Ahmed, M., Ahn, N. G., Hainard, A., Amanchy, R., Andrews, P. C., Bader, J. S., Balgley, B. M., Bantscheff, M., Bennett, K. L., Bjorling, E., Blagoev, B., et al. Human Proteinpedia enables sharing of human protein data Nature Biotechnology  2008 26:164-167  DOI:10.1038/nbt0208-164  PMID:18259167
  • Romijn, E. P., Yates, J. R., 3rd Analysis of organelles by on-line two-dimensional liquid chromatography-tandem mass spectrometry Methods in Molecular Biology  2008 432:1-16  DOI:10.1007/978-1-59745-028-7_1  PMID:18370007
  • Rai, R., Wong, C. C. L., Xu, T., Leu, N. A., Dong, D. W. W., Guo, C. Y., McLaughlin, K. J., Yates, J. R., Kashina, A. Arginyltransferase regulates alpha cardiac actin function, myofibril formation and contractility during heart development Development  2008 135:3881-3889  DOI:10.1242/dev.022723  PMID:18948421  PMCID:PMC2582055
  • Usaite, R., Wohlschlegel, J., Venable, J. D., Park, S. K., Nielsen, J., Olsson, L., Yates, J. R. Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression Saccharomyces cerevisiae strains: the comparison of two quantitative methods Journal of Proteome Research  2008 7:266-275  DOI:10.1021/pr700580m  PMID:18173223  PMCID:PMC2538956
  • Carvalho, P. C., Hewel, J., Barbosa, V. C., Yates, J. R. Identifying differences in protein expression levels by spectral counting and feature selection Genetics and Molecular Research  2008 7:342-356  PMID:18551400  PMCID:PMC2703009
  • Steiniger, S. C. J., Coppinger, J. A., Kruger, J. A., Yates, J., Janda, K. D. Quantitative mass spectrometry identifies drug targets in cancer stem cell-containing side population Stem Cells  2008 26:3037-3046  DOI:10.1634/stemcells.2008-0397  PMID:18802034  PMCID:PMC2745975
  • McClatchy, D. B., Yates III, J. R. Stable Isotope Labeling of Mammals (SILAM) CSH Protocols  2008 2008  DOI:10.1101/pdb.prot4940  PMID:21356771
  • Xia, D., Sanderson, S. J., Jones, A. R., Prieto, J. H., Yates, J. R., Bromley, E., Tomley, F. M., Lal, K., Sinden, R. E., Brunk, B. P., Roos, D. S., Wastling, J. M. The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation Genome Biology  2008 9:R116  DOI:10.1186/gb-2008-9-7-r116  PMID:18644147  PMCID:PMC2530874
  • Cravatt, B. F., Simon, G. M., Yates III, J. R. The biological impact of mass-spectrometry-based proteomics Nature  2007 450:991-1000  DOI:10.1038/nature06525  PMID:18075578
  • Zhang, L., Ding, L., Cheung, T. H., Dong, M. Q., Chen, J., Sewell, A. K., Liu, X., Yates, J. R., Han, M. Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2 Molecular Cell  2007 28:598-613  DOI:10.1016/j.molcel.2007.09.014  PMID:18042455  PMCID:PMC2186060
  • Curtis, C. D., Likhite, V. S., McLeod, I. X., Yates, J. R., Nardulli, A. M. Interaction of the tumor metastasis suppressor nonmetastatic protein 23 homologue H1 and estrogen receptor alpha alters estrogen-responsive gene expression Cancer Research  2007 67:10600-10607  DOI:10.1158/0008-5472.can-07-0055  PMID:17975005
  • Delahunty, C. M., Yates, J. R. MudPIT: multidimensional protein identification technology Biotechniques  2007 43:563
    -567  PMID:18072585
  • Ahrendt, A. J., Tollaksen, S. L., Lindberg, C., Zhu, W. H., Yates, J. R., Nevin, K. P., Babnigg, G., Lovley, D. R., Giometti, C. S. Steady state protein levels in Geobacter metallireducens grown with iron (III) citrate or nitrate as terminal electron acceptor Proteomics  2007 7:4148-4157  DOI:10.1002/pmic.200600955  PMID:17994620
  • Lunn, M. L., Nassirpour, R., Arrabit, C., Tan, J., McLeod, I., Arias, C. M., Sawchenko, P. E., Yates, J. R., Slesinger, P. A. A unique sorting nexin regulates trafficking of potassium channels via a PDZ domain interaction Nature Neuroscience  2007 10:1249-1259  DOI:10.1038/nn1953  PMID:17828261
  • Wong, C. C. L., Xu, T., Rai, R., Bailey, A. O., Yates, J. R., Wolf, Y. I., Zebroski, H., Kashina, A. Global analysis of posttranslational protein arginylation PLoS Biology  2007 5:2231-2242  DOI:10.1371/journal.pbio.0050258  PMID:17896865  PMCID:PMC1988855
  • Cass, C. L., Johnson, J. R., Califf, L. L., Xu, T., Hernandez, H. J., Stadecker, M. J., Yates, J. R., Williams, D. L. Proteomic analysis of Schistosoma mansoni egg secretions Molecular and Biochemical Parasitology  2007 155:84-93  DOI:10.1016/j.molbiopara.2007.06.002  PMID:17644200  PMCID:PMC2077830
  • Audhya, A., McLeod, I. X., Yates, J. R., Oegema, K. MVB-12, a fourth subunit of metazoan ESCRT-I, functions in receptor downregulation PLoS One  2007 2:e956  DOI:10.1371/journal.pone.0000956  PMID:17895996  PMCID:PMC1978536
  • Rexroth, S., Wong, C. C. L., Park, J. H., Yates, J. R., Barry, B. A. An activated glutamate residue identified in photosystern II at the interface between the manganese-stabilizing subunit and the D2 polypeptide Journal of Biological Chemistry  2007 282:27802-27809  DOI:10.1074/jbc.M704394200  PMID:17666402
  • Dentin, R., Liu, Y., Koo, S. H., Hedrick, S., Vargas, T., Heredia, J., Yates, J., Montminy, M. Insulin modulates gluconeogenesis by inhibition of the coactivator TORC2 Nature  2007 449:366-369  DOI:10.1038/nature06128  PMID:17805301
  • Kilburn, C. L., Pearsorl, C. G., Romiin, E. P., Meehl, J. B., Giddings, T. H., Culver, B. P., Yates, J. R., Winey, M. New Tetrohymena basal body protein components identify basal body domain structure Journal of Cell Biology  2007 178:905-912  DOI:10.1083/jcb.200703109  PMID:17785518  PMCID:PMC2064616
  • Chen, E. I., Yates, J. R. Cancer proteomics by quantitative shotgun proteomics Molecular Oncology  2007 1:144-159  DOI:10.1016/j.molonc.2007.05.001  PMID:18443658  PMCID:PMC2352161
  • McClatchy, D. B., Liao, L. J., Park, S. K., Venable, J. D., Yates, J. R. Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development Genome Research  2007 17:1378-1388  DOI:10.1101/gr.6375007  PMID:17675365  PMCID:PMC1950906
  • El Marzouk, S., Schultz-Norton, J. R., Likhite, V. S., McLeod, I. X., Yates, J. R., Nardulli, A. M. Rho GDP dissociation inhibitor alpha interacts with estrogen receptor alpha and influences estrogen responsiveness Journal of Molecular Endocrinology  2007 39:249-259  DOI:10.1677/jme-07-0055  PMID:17909265
  • Bailey, A. O., Miller, T. M., Dong, M. Q., Velde, C. V., Cleveland, D. W., Yates, J. R. RCADiA: simple automation platform for comparative multidimensional protein identification technology Analytical Chemistry  2007 79:6410-6418  DOI:10.1021/ac070585g  PMID:17616168  PMCID:PMC2528021
  • Dong, M. Q., Venable, J. D., Au, N., Xu, T., Park, S. K., Cociorva, D., Johnson, J. R., Dillin, A., Yates, J. R. Quantitative mass spectrometry identifies insulin signaling targets in C. elegans Science  2007 317:660-663  DOI:10.1126/science.1139952  PMID:17673661
  • Sanders, P. R., Cantin, G. T., Greenbaum, D. C., Gilson, P. R., Nebl, T., Moritz, R. L., Yates, J. R., Hodder, A. N., Crabb, B. S. Identification of protein complexes in detergent-resistant membranes of Plasmodium falciparum schizonts Molecular and Biochemical Parasitology  2007 154:148-157  DOI:10.1016/j.molbiopara.2007.04.013  PMID:17553576
  • Schultz-Norton, J. R., Gabisi, V. A., Ziegler, Y. S., McLeod, I. X., Yates, J. R., Nardulli, A. M. Interaction of estrogen receptor alpha with proliferating cell nuclear antigen Nucleic Acids Research  2007 35:5028-5038  DOI:10.1093/nar/gkm533  PMID:17636311  PMCID:PMC1976446
  • Aronova, S., Wedaman, K., Anderson, S., Yates, J., Powers, T. Probing the membrane environment of the TOR kinases reveals functional interactions between TORC1, actin, and membrane trafficking in Saccharomyces cerevisiae Molecular Biology of the Cell  2007 18:2779-2794  DOI:10.1091/mbc.E07-03-0274  PMID:17507646  PMCID:PMC1949386
  • Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P. A., Julian, R. K., Jones, A. R., Zhu, W. M., Apweiler, R., Aebersold, R., Deutsch, E. W., Dunn, M. J., Heck, A. J. R. The minimum information about a proteomics experiment (MIAPE) Nature Biotechnology  2007 25:887-893  DOI:10.1038/nbt1329  PMID:17687369
  • Xiao, K., McClatchy, D. B., Shukla, A. K., Zhao, Y., Chen, M., Shenoy, S. K., Yates, J. R., Lefkowitz, R. J. Functional specialization of beta-arrestin interactions revealed by proteomic analysis Proceedings of the National Academy of Sciences of the United States of America  2007 104:12011-12016  DOI:10.1073/pnas.0704849104  PMID:17620599  PMCID:PMC1913545
  • Jung, P., Verdoodt, B., Bailey, A., Yates, J. R., Menssen, A., Hermeking, H. Induction of Cullin 7 by DNA damage attenuates p53 function Proceedings of the National Academy of Sciences of the United States of America  2007 104:11388-11393  DOI:10.1073/pnas.0609467104  PMID:17586686  PMCID:PMC2040908
  • Schultz-Norton, J. R., Walt, K. A., Ziegler, Y. S., McLeod, I. X., Yates, J. R., Raetzman, L. T., Nardulli, A. M. The deoxyribonucleic acid repair protein flap endonuclease-1 modulates estrogen-responsive gene expression Molecular Endocrinology  2007 21:1569-1580  DOI:10.1210/me.2006-0519  PMID:17488975
  • Kiselev, A. O., Stamm, W. E., Yates, J. R., Lampe, M. F. Expression, processing, and localization of PmpD of Chlamydia trachomatis Serovar L2 during the chlamydial developmental cycle PLoS One  2007 2:e568  DOI:10.1371/journal.pone.0000568  PMID:17593967  PMCID:PMC1892801
  • Ravnskjaer, K., Kester, H., Liu, Y., Zhang, X., Lee, D., Yates, J. R., Montminy, M. Cooperative interactions between CBP and TORC2 confer selectivity to CREB target gene expression EMBO Journal  2007 26:2880-2889  DOI:10.1038/sj.emboj.7601715  PMID:17476304  PMCID:PMC1894761
  • Cantin, G. T., Shock, T. R., Park, S. K., Madhani, H. D., Yates, J. R. Optimizing TiO2-based phosphopeptide enrichment for automated multidimensional liquid chromatography coupled to tandem mass spectrometry Analytical Chemistry  2007 79:4666-4673  DOI:10.1021/ac0618730  PMID:17523591  PMCID:PMC2535607
  • Efimov, A., Kharitonov, A., Efimova, N., Loncarek, J., Miller, P. M., Andreyeva, N., Gleeson, P., Galjart, N., Maia, A. R. R., McLeod, I. X., Yates, J. R., Maiato, H., et al. Asymmetric CLASP-dependent nucleation of noncentrosomal microtubules at the trans-Golgi network Developmental Cell  2007 12:917-930  DOI:10.1016/j.devcel.2007.04.002  PMID:17543864  PMCID:PMC2705290
  • O'Neill, B. M., Szyjka, S. J., Lis, E. T., Bailey, A. O., Yates, J. R., Aparicio, O. M., Romesberg, F. E. Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage Proceedings of the National Academy of Sciences of the United States of America  2007 104:9290-9295  DOI:10.1073/pnas.0703252104  PMID:17517611  PMCID:PMC1890487
  • Motoyama, A., Xu, T., Ruse, C. I., Wohlschlegel, J. A., Yates, J. R. Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides Analytical Chemistry  2007 79:3623-3634  DOI:10.1021/ac062292d  PMID:17411013  PMCID:PMC2538959
  • McCusker, D., Denison, C., Anderson, S., Egelhofer, T. A., Yates, J. R., Gygi, S. P., Kellogg, D. R. Cdk1 coordinates cell-surface growth with the cell cycle Nature Cell Biology  2007 9:506-515  DOI:10.1038/ncb1568  PMID:17417630
  • Venable, J. D., Wohlschlegel, J., McClatchy, D. B., Park, S. K., Yates, J. R. Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer Analytical Chemistry  2007 79:3056-3064  DOI:10.1021/ac062054i  PMID:17367114  PMCID:PMC3586273
  • Liao, L., Pilotte, J., Xu, T., Wong, C. C. L., Edelman, G. M., Vanderklish, P., Yates, J. R. BDNF induces widespread changes in synaptic protein content and up-regulates components of the translation machinery: an analysis using high-throughput proteomics Journal of Proteome Research  2007 6:1059-1071  DOI:10.1021/pr060358f  PMID:17330943
  • Chen, E. I., Hewel, J., Krueger, J. S., Tiraby, C., Weber, M. R., Kralli, A., Becker, K., Yates, J. R., Felding-Habermann, B. Adaptation of energy metabolism in breast cancer brain metastases Cancer Research  2007 67:1472-1486  DOI:10.1158/0008-5472.can-06-3137  PMID:17308085
  • Lu, B. W., Ruse, C., Xu, T., Park, S. K., Yates, J. Automatic validation of phosphopeptide identifications from tandem mass spectra Analytical Chemistry  2007 79:1301-1310  DOI:10.1021/ac061334v  PMID:17297928  PMCID:PMC2527591
  • Toshima, J., Toshima, J. Y., Duncan, M. C., Cope, Mjtv, Sun, Y. D., Martin, A. C., Anderson, S., Yates, J. R., Mizuno, K., Drubin, D. G. Negative regulation of yeast Eps15-like Arp2/3 complex activator, Pan1p, by the Hip1R-related protein, Sla2p, during endocytosis Molecular Biology of the Cell  2007 18:658-668  DOI:10.1091/mbc.E06-09-0788  PMID:17151356  PMCID:PMC1783767
  • Sun, P. Q., Yoshizuka, N., New, L., Moser, B. A., Li, Y. L., Liao, R., Xie, C. C., Chen, J. M., Deng, Q. D., Yamout, M., Dong, M. Q., Frangou, C. G., et al. PRAK is essential for ras-induced senescence and tumor suppression Cell  2007 128:295-308  DOI:10.1016/j.cell.2006.11.050  PMID:17254968
  • Koch, H. B., Zhang, R., Verdoodt, B., Bailey, A., Zhang, C. D., Yates, J. R., Menssen, A., Hermeking, H. Large-scale identification of c-MYC-associated proteins using a combined TAP/MudPIT approach Cell Cycle  2007 6:205-217  DOI:10.4161/cc.6.2.3742  PMID:17314511
  • Schlaitz, A. L., Srayko, M., Dammermann, A., Quintin, S., Wielsch, N., MacLeod, I., de Robillard, Q., Zinke, A., Yates, J. R., Muller-Reichert, T., Shevchenko, A., Oegema, K., et al. The C. elegans RSA complex localizes protein phosphatase 2A to centrosomes and regulates mitotic spindle assembly Cell  2007 128:115-127  DOI:10.1016/j.cell.2006.10.050  PMID:17218259  PMCID:PMC2987564
  • Yates III, J. R., Stafford, G. C., Shabanowitz, J. Foreword: Donald F. Hunt International Journal of Mass Spectrometry  2007 259:vii-xi  DOI:10.1016/s1387-3806(06)00507-0
  • McClatchy, D. B., Dong, M. Q., Wu, C. C., Venable, J. D., Yates, J. R. 15N metabolic labeling of mammalian tissue with slow protein turnover Journal of Proteome Research  2007 6:2005-2010  DOI:10.1021/pr060599n  PMID:17375949  PMCID:PMC2527585
  • Park, Z. Y., Sadygov, R., Clark, J. M., Clark, J. I., Yates, J. R. Assigning in vivo carbamylation and acetylation in human lens proteins using tandem mass spectrometry and database searching International Journal of Mass Spectrometry  2007 259:161-173  DOI:10.1016/j.ijms.2006.08.013
  • Min, J., Kim, Y. K., Cipriani, P. G., Kang, M., Khersonsky, S. M., Walsh, D. P., Lee, J. Y., Niessen, S., Yates, J. R., Gunsalus, K., Piano, F., Chang, Y. T. Forward chemical genetic approach identifies new role for GAPDH in insulin signaling Nature Chemical Biology  2007 3:55-59  DOI:10.1038/nchembio833  PMID:17115034
  • Yates III, J. R., Osterman, A. L. Introduction: Advances in genomics and proteomics Chemical Reviews  2007 107:3363-3366  DOI:10.1021/cr068201u
  • Chen, E. I., Cociorva, D., Norris, J. L., Yates, J. R. Optimization of mass spectrometry-compatible surfactants for shotgun proteomics Journal of Proteome Research  2007 6:2529-2538  DOI:10.1021/pr060682a  PMID:17530876  PMCID:PMC2570269
  • Krishnamurthy, T., Deshpande, S., Hewel, J., Liu, H. B., Wick, C. H., Yates, J. R. Specific identification of Bacillus anthracis strains International Journal of Mass Spectrometry  2007 259:140-146  DOI:10.1016/j.ijms.2006.09.013
  • Cociorva, D., Tabb, D. L., Yates, J. R. Validation of tandem mass spectrometry database search results using DTASelect Current Protocols in Bioinformatics  2007 16:13.4.1-13.4.14  DOI:10.1002/0471250953.bi1304s16  PMID:18428785
  • Sandall, S., Severin, F., McLeod, I. X., Yates, J. R., Oegema, K., Hyman, A., Desai, A. A Bir1-Sli15 complex connects centromeres to microtubules and is required to sense kinetochore tension Cell  2006 127:1179-1191  DOI:10.1016/j.cell.2006.09.049  PMID:17174893  PMCID:PMC2265205
  • Varsano, T., Dong, M. Q., Niesman, I., Gacula, H., Lou, X., Ma, T., Testa, J. R., Yates, J. R., Farquhar, M. G. GIPC is recruited by APPL to peripheral TrkA endosomes and regulates TrkA trafficking and signaling Molecular and Cellular Biology  2006 26:8942-8952  DOI:10.1128/mcb.00305-06  PMID:17015470  PMCID:PMC1636811
  • Monzo, K., Papoulas, O., Cantin, G. T., Wang, Y., Yates, J. R., Sisson, J. C. Fragile X mental retardation protein controls trailer hitch expression and cleavage furrow formation in Drosophila embryos Proceedings of the National Academy of Sciences of the United States of America  2006 103:18160-18165  DOI:10.1073/pnas.0606508103  PMID:17110444  PMCID:PMC1838723
  • Wang, X. D., Venable, J., LaPointe, P., Hutt, D. M., Koulov, A. V., Coppinger, J., Gurkan, C., Kellner, W., Matteson, J., Plutner, H., Riordan, J. R., Kelly, J. W., et al. Hsp90 cochaperone Aha1 downregulation rescues misfolding of CFTR in cystic fibrosis Cell  2006 127:803-815  DOI:10.1016/j.cell.2006.09.043  PMID:17110338
  • Herzberg, K., Bashkirov, V. I., Rolfsmeier, M., Haghnazari, E., McDonald, W. H., Anderson, S., Bashkirova, E. V., Yates, J. R., Heyer, W. D. Phosphorylation of Rad55 on serines 2, 8, and 14 is required for efficient homologous recombination in the recovery of stalled replication forks Molecular and Cellular Biology  2006 26:8396-8409  DOI:10.1128/mcb.01317-06  PMID:16966380  PMCID:PMC1636779
  • Chapman, E., Farr, G. W., Usaite, R., Furtak, K., Fenton, W. A., Chaudhuri, T. K., Hondorp, E. R., Matthews, R. G., Wolf, S. G., Yates, J. R., Pypaert, M., Horwich, A. L. Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL Proceedings of the National Academy of Sciences of the United States of America  2006 103:15800-15805  DOI:10.1073/pnas.0607534103  PMID:17043235  PMCID:PMC1613232
  • Roth, A. F., Wan, J. M., Green, W. N., Yates, J. R., Davis, N. G. Proteomic identification of palmitoylated proteins Methods  2006 40:135-142  DOI:10.1016/j.ymeth.2006.05.026  PMID:17012025  PMCID:PMC2806795
  • Sedgwick, C., Rawluk, M., Decesare, J., Raithatha, S., Wohlschlegel, J., Semchuk, P., Ellison, M., Yates, J., Stuart, D. Saccharomyces cerevisiae lme2 phosphorylates Sic1 at multiple PXS/T sites but is insufficient to trigger Sic1 degradation Biochemical Journal  2006 399:151-160  DOI:10.1042/bj20060363  PMID:16776651  PMCID:PMC1570159
  • Raffa, G. D., Wohlschlegel, J., Yates, J. R., Boddy, M. N. SUMO-binding motifs mediate the Rad60-dependent response to replicative stress and self-association Journal of Biological Chemistry  2006 281:27973-27981  DOI:10.1074/jbc.M601943200  PMID:16880212
  • Chu, D. S., Liu, H. B., Nix, P., Wu, T. F., Ralston, E. J., Yates, J. R., Meyer, B. J. Sperm chromatin proteomics identifies evolutionarily conserved fertility factors Nature  2006 443:101-105  DOI:10.1038/nature05050  PMID:16943775  PMCID:PMC2731558
  • Wolfe, B. A., McDonald, W. H., Yates, J. R., Gould, K. L. Phospho-regulation of the Cdc14/Clp1 phosphatase delays late mitotic events in S. pombe Developmental Cell  2006 11:423-430  DOI:10.1016/j.devcel.2006.07.018  PMID:16950131
  • Rosenberg, J. A., Tomlin, G. C., McDonald, W. H., Snydsman, B. E., Mullert, E. G., Yates, J. R., Gould, K. L. Ppc89 links multiple proteins, including the septation initiation network, to the core of the fission yeast spindle-pole body Molecular Biology of the Cell  2006 17:3793-3805  DOI:10.1091/mbc.E06-01-0039  PMID:16775007  PMCID:PMC1593159
  • Schultz-Norton, J. R., McDonald, W. H., Yates, J. R., Nardulli, A. M. Protein disulfide isomerase serves as a molecular chaperone to maintain estrogen receptor alpha structure and function Molecular Endocrinology  2006 20:1982-1995  DOI:10.1210/me.2006-0006  PMID:16690750
  • Schneider, D. A., French, S. L., Osheim, Y. N., Bailey, A. O., Vu, L., Dodd, J., Yates, J. R., Beyer, A. L., Nomura, M. RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing Proceedings of the National Academy of Sciences of the United States of America  2006 103:12707-12712  DOI:10.1073/pnas.0605686103  PMID:16908835  PMCID:PMC1568913
  • de Bruin, R. A. M., Kalashnikova, T. I., Chahwan, C., McDonald, W. H., Wohlschlegel, J., Yates, J., Russell, P., Wittenberg, C. Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback Molecular Cell  2006 23:483-496  DOI:10.1016/j.molcel.2006.06.025  PMID:16916637
  • Shimogawa, M. M., Graczyk, B., Gardner, M. K., Francis, S. E., White, E. A., Ess, M., Molk, J. N., Ruse, C., Niessen, S., Yates, J. R., Muller, E. G. D., Bloom, K., et al. Mps1 phosphorylation of Dam1 couples kinetochores to microtubule plus ends at metaphase Current Biology  2006 16:1489-1501  DOI:10.1016/j.cub.2006.06.063  PMID:16890524  PMCID:PMC1762913
  • Motoyama, A., Venable, J. D., Ruse, C. I., Yates, J. R. Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples Analytical Chemistry  2006 78:5109-5118  DOI:10.1021/ac060354u  PMID:16841936
  • Karakozova, M., Kozak, M., Wong, C. C. L., Bailey, A. O., Yates, J. R., Mogilner, A., Zebroski, H., Kashina, A. Arginylation of beta-actin regulates actin cytoskeleton and cell motility Science  2006 313:192-196  DOI:10.1126/science.1129344  PMID:16794040
  • De Craene, J. O., Coleman, J., de Martin, P. E., Pypaert, M., Anderson, S., Yates, J. R., Ferro-Novick, S., Novick, P. Rtn1p is involved in structuring the cortical endoplasmic reticulum Molecular Biology of the Cell  2006 17:3009-3020  DOI:10.1091/mbc.E06-01-0080  PMID:16624861  PMCID:PMC1483037
  • Qi, L., Heredia, J. E., Altarejos, J. Y., Screaton, R., Goebel, N., Niessen, S., MacLeod, I. X., Liew, C. W., Kulkarni, R. N., Bain, J., Newgard, C., Nelson, M., et al. TRB3 links the E3 ubiquitin ligase COP1 to lipid metabolism Science  2006 312:1763-1766  DOI:10.1126/science.1123374  PMID:16794074
  • Harashima, T., Anderson, S., Yates, J. R., Heitman, J. The Kelch proteins Gpb1 and Gpb2 inhibit Ras activitv via association with the yeast RasGAP neurofibromin hornologs Ira1 and Ira2 Molecular Cell  2006 22:819-830  DOI:10.1016/j.molcel.2006.05.011  PMID:16793550
  • Olson, S. K., Bishop, J. R., Yates, J. R., Oegema, K., Esko, J. D. Identification of novel chondroitin proteoglycans in Caenorhabditis elegans: embryonic cell division depends on CPG-1 and CPG-2 Journal of Cell Biology  2006 173:985-994  DOI:10.1083/jcb.200603003  PMID:16785326  PMCID:PMC2063922
  • Martin, V., Chahwan, C., Gao, H., Blais, V., Wohlschlegel, J., Yates, J. R., McGowan, C. H., Russell, P. Sws1 is a conserved regulator of homologous recombination in eukaryotic cells EMBO Journal  2006 25:2564-2574  DOI:10.1038/sj.emboj.7601141  PMID:16710300  PMCID:PMC1478202
  • Roth, A. F., Wan, J. M., Bailey, A. O., Sun, B. M., Kuchar, J. A., Green, W. N., Phinney, B. S., Yates, J. R., Davis, N. G. Global analysis of protein palmitoylation in yeast Cell  2006 125:1003-1013  DOI:10.1016/j.cell.2006.03.042  PMID:16751107  PMCID:PMC2246083
  • Yates, J. R. The power of mass spectrometry in biological discovery Biotechniques  2006 40:779  DOI:10.2144/000112199
  • Okada, M., Cheeseman, I. M., Hori, T., Okawa, K., McLeod, I. X., Yates, J. R., Desai, A., Fukagawa, T. The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres Nature Cell Biology  2006 8:446-457  DOI:10.1038/ncb1396  PMID:16622420
  • Foltz, D. R., Jansen, L. E. T., Black, B. E., Bailey, A. O., Yates, J. R., Cleveland, D. W. The human CENP-A centromeric nucleosome-associated complex Nature Cell Biology  2006 8:458-469  DOI:10.1038/ncb1397  PMID:16622419
  • Wohlschlegel, J. A., Johnson, E. S., Reed, S. I., Yates, J. R. Improved identification of SUMO attachment sites using C-terminal SUMO mutants and tailored protease digestion strategies Journal of Proteome Research  2006 5:761-770  DOI:10.1021/pr050451o  PMID:16602682  PMCID:PMC2535609
  • Venable, J. D., Xu, T., Cociorva, D., Yates, J. R. Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra Analytical Chemistry  2006 78:1921-1929  DOI:10.1021/ac051636h  PMID:16536429
  • Martin, V., Rodriguez-Gabriel, M. A., McDonald, W. H., Watt, S., Yates, J. R., Bahler, J., Russell, P. Cip1 and Cip2 are novel RNA-recognition-motif proteins that counteract Csx1 function during oxidative stress Molecular Biology of the Cell  2006 17:1176-1183  DOI:10.1091/mbc.E05-09-0847  PMID:16407405  PMCID:PMC1382307
  • Widlund, P. O., Lyssand, J. S., Anderson, S., Niessen, S., Yates, J. R., Davis, T. N. Phosphorylation of the chromosomal passenger protein Bir1 is required for localization of Ndc10 to the spindle during anaphase and full spindle elongation Molecular Biology of the Cell  2006 17:1065-1074  DOI:10.1091/mbc.E05-07-0640  PMID:16381814  PMCID:PMC1382298
  • Azarian, S. M., McLeod, I., Lillo, C., Gibbs, D., Yates, J. R., Williams, D. S. Proteomic analysis of mature melanosomes from the retinal pigmented epithelium Journal of Proteome Research  2006 5:521-529  DOI:10.1021/pr0502323  PMID:16512666
  • Cao, H. P., Deterding, L. J., Venable, J. D., Kennington, E. A., Yates, J. R., Tomer, K. B., Blackshear, P. J. Identification of the anti-inflammatory protein tristetraprolin as a hyperphosphorylated protein by mass spectrometry and site-directed mutagenesis Biochemical Journal  2006 394:285-297  DOI:10.1042/bj20051316  PMID:16262601  PMCID:PMC1386027
  • Hu, K., Johnson, J., Florens, L., Fraunholz, M., Suravajjala, S., DiLullo, C., Yates, J., Roos, D. S., Murray, J. M. Cytoskeletal components of an invasion machine: the apical complex of Toxoplasma gondii PLoS Pathogens  2006 2:121-138  DOI:10.1371/journal.ppat.0020013  PMID:16518471  PMCID:PMC1383488
  • Guelman, S., Suganuma, T., Florens, L., Swanson, S. K., Kiesecker, C. L., Kusch, T., Anderson, S., Yates, J. R., Washburn, M. P., Abmayr, S. M., Workman, J. L. Host cell factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila Molecular and Cellular Biology  2006 26:871-882  DOI:10.1128/mcb.26.3.871-882.2006  PMID:16428443  PMCID:PMC1347012
  • Duchaine, T. F., Wohlschlegel, J. A., Kennedy, S., Bei, Y. X., Conte, D., Pang, K. M., Brownell, D. R., Harding, S., Mitani, S., Ruvkun, G., Yates, J. R., Mello, C. C. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways Cell  2006 124:343-354  DOI:10.1016/j.cell.2005.11.036  PMID:16439208
  • Yates, J. R., Cociorva, D., Liao, L. J., Zabrouskov, V. Performance of a linear ion trap-Orbitrap hybrid for peptide analysis Analytical Chemistry  2006 78:493-500  DOI:10.1021/ac0514624  PMID:16408932
  • Leon, S., Zhang, L., McDonald, W. H., Yates, J., Cregg, J. M., Subramani, S. Dynamics of the peroxisomal import cycle of PpPex20p: ubiquitin-dependent localization and regulation Journal of Cell Biology  2006 172:67-78  DOI:10.1083/jcb.200508096  PMID:16390998  PMCID:PMC2063535
  • Grosshans, B. L., Andreeva, A., Gangar, A., Niessen, S., Yates, J. R., Brennwald, P., Novick, P. The yeast IgI family member Sro7p is an effector of the secretory Rab GTPase Sec4p Journal of Cell Biology  2006 172:55-66  DOI:10.1083/jcb.200510016  PMID:16390997  PMCID:PMC2063532
  • Roman, E., Yates III, J. R., Veithen, M., Vanderbilt, D., Souza, I. Ab initio study of the nonlinear optics of III-V semiconductors in the terahertz regime Physical Review B  2006 74  DOI:10.1103/PhysRevB.74.245204
  • Wohlschlegel, J., Park, S. K., Xu, T., Yates, J. R. Central limit theorem as an approximation for intensity-based scoring function Analytical Chemistry  2006 78:89-95  DOI:10.1021/ac051206r  PMID:16383314
  • Khare, T., Esteve-Nunez, A., Nevin, K. P., Zhu, W. H., Yates, J. R., Lovley, D., Giometti, C. S. Differential protein expression in the metal-reducing bacterium Geobacter sulfurreducens strain PCA grown with fumarate or ferric citrate Proteomics  2006 6:632-640  DOI:10.1002/pmic.200500137  PMID:16342140
  • Niessen, S., McLeod, I., Yates III, J. R. Direct enzymatic digestion of protein complexes for MS analysis CSH Protocols  2006 2006  DOI:10.1101/pdb.prot4662  PMID:22484679
  • Niessen, S., McLeod, I., Yates III, J. R. HPLC separation of digested proteins and preparation for matrix-assisted laser desorption/ionization analysis CSH Protocols  2006 2006  DOI:10.1101/pdb.prot4663  PMID:22484680
  • Cherqui, S., Kurian, S. M., Schussler, O., Hewel, J. A., Yates, J. R., Salomon, D. R. Isolation and angiogenesis by endothelial progenitors in the fetal liver Stem Cells  2006 24:44-54  DOI:10.1634/stemcells.2005-0070  PMID:16099996
  • Chen, E. I., Hewel, J., Felding-Habermann, B., Yates, J. R. Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT) Molecular & Cellular Proteomics  2006 5:53-56  DOI:10.1074/mcp.T500013-MCP200  PMID:16272560
  • Chen, E. I., Yates, J. R. Maspin and tumor metastasis IUBMB Life  2006 58:25-29  DOI:10.1080/15216540500531721  PMID:16540429
  • Niessen, S., McLeod, I., Yates III, J. R. Overview of affinity purification in combination with mass spectrometry CSH Protocols  2006 2006  DOI:10.1101/pdb.top3  PMID:22484688
  • Cantin, G. T., Venable, J. D., Cociorva, D., Yates, J. R. Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway Journal of Proteome Research  2006 5:127-134  DOI:10.1021/pr050270m  PMID:16396503  PMCID:PMC2570265
  • Niessen, S., McLeod, I., Yates III, J. R. Silver staining, digestion, and extraction of peptides from an acrylamide gel for MS analysis CSH Protocols  2006 2006  DOI:10.1101/pdb.prot4661  PMID:22484678
  • Krishnamurthy, T., Hewel, J., Bonzagni, N. J., Dabbs, J., Bull, R. L., Yates, J. R. Simultaneous identification and verification of Bacillus anthracis Rapid Communications in Mass Spectrometry  2006 20:2053-2056  DOI:10.1002/rcm.2564  PMID:16755617
  • Pebernard, S., Wohschlegel, J., McDonald, W. H., Yates, J. R., Boddy, M. N. The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex Molecular and Cellular Biology  2006 26:1617-1630  DOI:10.1128/mcb.26.5.1617-1630.2006  PMID:16478984  PMCID:PMC1430260
  • Huang, J. K., Phillips, G. R., Roth, A. D., Pedraza, L., Shan, W. S., Belkaid, W., Mi, S., Fex-Svenningsen, A., Florens, L., Yates, J. R., Colman, D. R. Glial membranes at the node of Ranvier prevent neurite outgrowth Science  2005 310:1813-1817  DOI:10.1126/science.1118313  PMID:16293723
  • Page, L. J., Suk, J. Y., Huff, M. E., Lim, H. J., Venable, J., Yates, J., Kelly, J. W., Balch, W. E. Metalloendoprotease cleavage triggers gelsolin amyloidogenesis EMBO Journal  2005 24:4124-4132  DOI:10.1038/sj.emboj.7600872  PMID:16281052  PMCID:PMC1356312
  • Sanders, P. R., Gilson, P. R., Cantin, G. T., Greenbaum, D. C., Nebl, T., Carucci, D. J., McConville, M. J., Schofield, L., Hodder, A. N., Yates, J. R., Crabb, B. S. Distinct protein classes including novel merozoite surface antigens in Raft-like membranes of Plasmodium falciparum Journal of Biological Chemistry  2005 280:40169-40176  DOI:10.1074/jbc.M509631200  PMID:16203726
  • Liu, J. D., Rivas, F. V., Wohlschlegel, J., Yates, J. R., Parker, R., Hannon, G. J. A role for the P-body component GW182 in microRNA function Nature Cell Biology  2005 7:1261-1266  DOI:10.1038/ncb1333  PMID:16284623  PMCID:PMC1804202
  • Zhu, W. H., Venable, J., Giometti, C. S., Khare, T., Tollaksen, S., Ahrendt, A. J., Yates, J. R. Large-scale mu LC-MS/MS for silver- and Coomassie blue-stained polyacrylamide gels Electrophoresis  2005 26:4495-4507  DOI:10.1002/elps.200500093  PMID:16315175
  • MacCoss, M. J., Wu, C. C., Matthews, D. E., Yates, J. R. Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides Analytical Chemistry  2005 77:7646-7653  DOI:10.1021/ac0508393  PMID:16316172
  • Green, E. M., Antczak, A. J., Bailey, A. O., Franco, A. A., Wu, K. J., Yates, J. R., Kaufman, P. D. Replication-independent histone deposition by the HIR complex and Asf1 Current Biology  2005 15:2044-2049  DOI:10.1016/j.cub.2005.10.053  PMID:16303565  PMCID:PMC2819815
  • Carrozza, M. J., Florens, L., Swanson, S. K., Shia, W. J., Anderson, S., Yates, J., Washburn, M. P., Workman, J. L. Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex Biochimica et Biophysica Acta-Gene Structure and Expression  2005 1731:77-87  DOI:10.1016/j.bbaexp.2005.09.005  PMID:16314178
  • Carrozza, M. J., Li, B., Florens, L., Suganuma, T., Swanson, S. K., Lee, K. K., Shia, W. J., Anderson, S., Yates, J., Washburn, M. P., Workman, J. L. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription Cell  2005 123:581-592  DOI:10.1016/j.cell.2005.10.023  PMID:16286007
  • Wilson, A. C., Wu, C. C., Yates, J. R., Tan, M. Chlaraydial GroEL autoregulates its own expression through direct interactions with the HrcA repressor protein Journal of Bacteriology  2005 187:7535-7542  DOI:10.1128/jb.187.21.7535-7542.2005  PMID:16237037  PMCID:PMC1272993
  • Audhya, A., Hyndman, F., McLeod, I. X., Maddox, A. S., Yates, J. R., Desai, A., Oegema, K. A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans Journal of Cell Biology  2005 171:267-279  DOI:10.1082/jcb.200506124  PMID:16247027  PMCID:PMC2171198
  • Lee, S., Comer, F. I., Sasaki, A., McLeod, I. X., Duong, Y., Okumura, K., Yates, J. R., Parent, C. A., Firtel, R. A. TOR complex 2 integrates cell movement during chemotaxis and signal relay in Dictyostelium Molecular Biology of the Cell  2005 16:4572-4583  DOI:10.1091/mbc.E05-04-0342  PMID:16079174  PMCID:PMC1237065
  • Phillips, G. R., Florens, L., Tanaka, H., Khaing, Z. Z., Fidler, L., Yates, J. R., Colman, D. R. Proteomic comparison of two fractions derived from the transsynaptic scaffold Journal of Neuroscience Research  2005 81:762-775  DOI:10.1002/jnr.20614  PMID:16047384
  • Jessani, N., Niessen, S., Wei, B. Q., Nicolau, M., Humphrey, M., Ji, Y., Han, W., Noh, D. Y., Yates, J. R., 3rd, Jeffrey, S. S., Cravatt, B. F. A streamlined platform for high-content functional proteomics of primary human specimens Nature Methods  2005 2:691-697  DOI:10.1038/nmeth778  PMID:16118640
  • Yates, J. R., Gilchrist, A., Howell, K. E., Bergeron, J. J. M. Proteomics of organelles and large cellular structures Nature Reviews Molecular Cell Biology  2005 6:702-714  DOI:10.1038/nrm1711  PMID:16231421
  • Liu, X. K., McLeod, I., Anderson, S., Yates, J. R., He, X. W. Molecular analysis of kinetochore architecture in fission yeast EMBO Journal  2005 24:2919-2930  DOI:10.1038/sj.emboj.7600762  PMID:16079914  PMCID:PMC1187945
  • Gottschalk, A., Almedom, R. B., Schedletzky, T., Anderson, S. D., Yates, J. R., Schafer, W. R. Identification and characterization of novel nicotinic receptor-associated proteins in Caenorhabditis elegans EMBO Journal  2005 24:2566-2578  DOI:10.1038/sj.emboj.7600741  PMID:15990870  PMCID:PMC1176467
  • Liu, H. Q., Du, X., Wang, M., Huang, Q. L., Ding, L. L., McDonald, H. W., Yates, J. R., Beutler, B., Horwitz, J., Gong, X. H. Crystallin gamma B-I4F mutant protein binds to alpha-crystallin and affects lens transparency Journal of Biological Chemistry  2005 280:25071-25078  DOI:10.1074/jbc.M502490200  PMID:15878859
  • Keller, L. C., Romijn, E. P., Zamora, I., Yates, J. R., Marshall, W. F. Proteomic analysis of isolated Chlamydomonas centrioles reveals orthologs of ciliary-disease genes Current Biology  2005 15:1090-1098  DOI:10.1016/j.cub.2005.05.024  PMID:15964273
  • McMahon, S. J., Pray-Grant, M. G., Schieltz, D., Yates, J. R., Grant, P. A. Polyglutamine-expanded spinocerebellar ataxia-7 protein disrupts normal SAGA and SLIK histone acetyltransferase activity Proceedings of the National Academy of Sciences of the United States of America  2005 102:8478-8482  DOI:10.1073/pnas.0503493102  PMID:15932941  PMCID:PMC1150861
  • Benzinger, A., Muster, N., Koch, H. B., Yates, J. R., Hermeking, H. Targeted proteomic analysis of 14-3-3 sigma, a p53 effector commonly silenced in cancer Molecular & Cellular Proteomics  2005 4:785-795  DOI:10.1074/mcp.M500021-MCP200  PMID:15778465
  • Kops, G. J. P. L, Kim, Y., Weaver, B. A. A., Mao, Y. H., McLeod, I., Yates, J. R., Tagaya, M., Cleveland, D. W. ZW10 links mitotic checkpoint signaling to the structural kinetochore Journal of Cell Biology  2005 169:49-60  DOI:10.1083/jcb.200411118  PMID:15824131  PMCID:PMC1351127
  • Chen, E. I., Florens, L., Axelrod, F. T., Monosov, E., Barbas, C. F., Yates, J. R., Felding-Habermann, B., Smith, J. W. Maspin alters the carcinoma proteome FASEB Journal  2005 19:1123-1124  DOI:10.1096/fj.04-2970fje  PMID:15857880
  • Martin, S. G., McDonald, W. H., Yates, J. R., Chang, F. tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity Developmental Cell  2005 8:479-491  DOI:10.1016/j.devcel.2005.02.008  PMID:15809031
  • Sauerwald, A., Zhu, W., Major, T. A., Roy, H., Palioura, S., Jahn, D., Whitman, W. B., Yates III, J. R., Ibba, M., Soll, D. RNA-Dependent cysteine biosynthesis in archaea Science  2005 307:1969-1972  DOI:10.1126/science.1108329  PMID:15790858
  • Sauerwald, A., Zhu, W. H., Major, T. A., Roy, H., Palioura, S., Jahn, D., Whitman, W. B., Yates, J. R., Ibba, M., Soll, D. RNA-dependent cysteine biosynthesis in archaea Science  2005 307:1969-1972  DOI:10.1126/science.1108329  PMID:15790858
  • Carnahan, R. H., Feoktistova, A., Ren, L., Niessen, S., Yates, J. R., Gould, K. L. Dim1p is required for efficient splicing and export of mRNA encoding Lid1p, a component of the fission yeast anaphase-promoting complex Eukaryotic Cell  2005 4:577-587  DOI:10.1128/ec.4.3.577-587.2005  PMID:15755920  PMCID:PMC1087801
  • Delahunty, C., Yates, J. R. Protein identification using 2D-LC-MS/MS Methods  2005 35:248-255  DOI:10.1016/j.ymeth.2004.08.016  PMID:15722221
  • Kolker, E., Picone, A. F., Galperin, M. Y., Romine, M. F., Higdon, R., Makarova, K. S., Kolker, N., Anderson, G. A., Qiu, X. Y., Auberry, K. J., Babnigg, G., Beliaev, A. S., et al. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations Proceedings of the National Academy of Sciences of the United States of America  2005 102:2099-2104  DOI:10.1073/pnas.0409111102  PMID:15684069  PMCID:PMC548307
  • Yates, J. Proteomics power to the people! Scientist  2005 19:30-31
  • Pray-Grant, M. G., Daniel, J. A., Schieltz, D., Yates, J. R., Grant, P. A. Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation Nature  2005 433:434-438  DOI:10.1038/nature03242  PMID:15647753
  • Kashyap, A. K., Schieltz, D., Yates, J., Kellogg, D. R. Biochemical and genetic characterization of Yra1p in budding yeast Yeast  2005 22:43-56  DOI:10.1002/yea.1185  PMID:15584090
  • Hall, N., Karras, M., Raine, J. D., Carlton, J. M., Kooij, T. W. A., Berriman, M., Florens, L., Janssen, C. S., Pain, A., Christophides, G. K., James, K., Rutherford, K., et al. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses Science  2005 307:82-86  DOI:10.1126/science.1103717  PMID:15637271
  • Schirmer, E. C., Florens, L., Guan, T., Yates III, J. R., Gerace, L. Identification of novel integral membrane proteins of the nuclear envelope with potential disease links using subtractive proteomics Novartis Foundation Symposium  2005 264:63-80  PMID:15773748
  • Cheeseman, I. M., MacLeod, I., Yates, J. R., Oegema, K., Desai, A. The CENP-F-like proteins HCP-1 and HCP-2 target CLASP to kinetochores to mediate chromosome segregation Current Biology  2005 15:771-777  DOI:10.1016/j.cub.2005.03.018  PMID:15854912
  • Bao, M. Z., Schwartz, M. A., Cantin, G. T., Yates, J. R., Madhani, H. D. Pheromone-dependent destruction of the Tec1 transcription factor is required for MAP kinase signaling specificity in yeast Cell  2004 119:991-1000  DOI:10.1016/j.cell.2004.11.052  PMID:15620357
  • Kadrmas, J. L., Smith, M. A., Clark, K. A., Pronovost, S. M., Muster, N., Yates, J. R., Beckerle, M. C. The integrin effector PINCH regulates JNK activity and epithelial migration in concert with Ras suppressor 1 Journal of Cell Biology  2004 167:1019-1024  DOI:10.1083/jcb.200408090  PMID:15596544  PMCID:PMC2034365
  • Kusch, T., Florens, L., MacDonald, W. H., Swanson, S. K., Glaser, R. L., Yates, J. R., Abmayr, S. M., Washburn, M. P., Workman, J. L. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions Science  2004 306:2084-2087  DOI:10.1126/science.1103455  PMID:15528408
  • Sadygov, R. G., Cociorva, D., Yates, J. R. Large-scate database searching using tandem mass spectra: looking up the answer in the back of the book Nature Methods  2004 1:195-202  DOI:10.1038/nmeth725  PMID:15789030
  • Loven, M. A., Davis, R. E., Curtis, C. D., Muster, N., Yates, J. R., Nardulli, A. M. A novel estrogen receptor α-associated protein alters receptor-deoxyribonucleic acid interactions and represses receptor-mediated transcription Molecular Endocrinology  2004 18:2649-2659  DOI:10.1210/me.2003-0195  PMID:15308690
  • Le Roch, K. G., Johnson, J. R., Florens, L., Zhou, Y. Y., Santrosyan, A., Grainger, M., Yan, S. F., Williamson, K. C., Holder, A. A., Carucci, D. J., Yates, J. R., Winzeler, E. A. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle Genome Research  2004 14:2308-2318  DOI:10.1101/gr.2523904  PMID:15520293  PMCID:PMC525690
  • Pebernard, S., McDonald, W. H., Pavlova, Y., Yates, J. R., Boddy, M. N. Nse1, Nse2, and a novel subunit of the Smc5-Smc6 complex, Nse3, play a crucial role in meiosis Molecular Biology of the Cell  2004 15:4866-4876  DOI:10.1091/mbc.E04-05-0436  PMID:15331764  PMCID:PMC524734
  • Wohlschlegel, J. A., Johnson, E. S., Reed, S. I., Yates, J. R. Global analysis of protein sumoylation in Saccharomyces cerevisiae Journal of Biological Chemistry  2004 279:45662-45668  DOI:10.1074/jbc.M409203200  PMID:15326169
  • Cantin, G. T., Yates, J. R. Strategies for shotgun identification of post-translational modifications by mass spectrometry Journal of Chromatography A  2004 1053:7-14  DOI:10.1016/j.chroma.2004.06.046  PMID:15543967
  • Phillips, G. R., Anderson, T. R., Florens, L., Gudas, C., Magda, G., Yates, J. R., Colman, D. R. Actin-binding proteins in a postsynaptic preparation: Lasp-1 is a component of central nervous system synapses and dendritic spines Journal of Neuroscience Research  2004 78:38-48  DOI:10.1002/jnr.20224  PMID:15372503
  • Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A., Yates, J. R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra Nature Methods  2004 1:39-45  DOI:10.1038/nmeth705  PMID:15782151
  • Trueman, H. E., Raine, J. D., Florens, L., Dessens, J. T., Mendoza, J., Johnson, J., Waller, C. C., Delrieu, I., Holder, A. A., Langhorne, J., Carucci, D. J., Yates III, J. R., et al. Functional characterization of an LCCL-lectin domain containing protein family in Plasmodium berghei Journal of Parasitology  2004 90:1062-1071  DOI:10.1645/ge-3368  PMID:15562607
  • Noguchi, E., Noguchi, C., McDonald, W. H., Yates, J. R., Russell, P. Swi1 and Swi3 are components of a replication fork protection complex in fission yeast Molecular and Cellular Biology  2004 24:8342-8355  DOI:10.1128/mcb.24.19.8342-8355.2004  PMID:15367656  PMCID:PMC516732
  • Screaton, R. A., Conkright, M. D., Katoh, Y., Best, J. L., Canettieri, G., Jeffries, S., Guzman, E., Niessen, S., Yates, J. R., Takemori, H., Okamoto, M., Montminy, M. The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector Cell  2004 119:61-74  DOI:10.1016/j.cell.2004.09.015  PMID:15454081
  • Jessani, N., Humphrey, M., McDonald, W. H., Niessen, S., Masuda, K., Gangadharan, B., Yates, J. R., 3rd, Mueller, B. M., Cravatt, B. F. Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo Proceedings of the National Academy of Sciences of the United States of America  2004 101:13756-13761  DOI:10.1073/pnas.0404727101  PMID:15356343  PMCID:PMC518829
  • Cheeseman, I. M., Niessen, S., Anderson, S., Hyndman, F., Yates, J. R., Oegema, K., Desai, A. A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension Genes & Development  2004 18:2255-2268  DOI:10.1101/gad.1234104  PMID:15371340  PMCID:PMC517519
  • Xirasagar, S., Gustafson, S., Merrick, B. A., Tomer, K. B., Stasiewicz, S., Chan, D. D., Yost, K. J., Yates, J. R., Sumner, S., Xiao, N. Q., Waters, M. D. CEBS object model for systems biology data, SysBio-OM Bioinformatics  2004 20:2004-2015  DOI:10.1093/bioinformatics/bth189  PMID:15044233
  • Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E., Yates, J. R. Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis Analytical Chemistry  2004 76:4951-4959  DOI:10.1021/ac049208j  PMID:15373428
  • Sam-Yellowe, T. Y., Florens, L., Wang, T. M., Raine, J. D., Carucci, D. J., Sinden, R., Yates, J. R. Proteome analysis of rhoptry-enriched fractions isolated from Plasmodium merozoites Journal of Proteome Research  2004 3:995-1001  DOI:10.1021/pr049926m  PMID:15473688
  • Bern, M., Goldberg, D., McDonald, W. H., Yates, J. R. Automatic quality assessment of peptide tandem mass spectra Bioinformatics  2004 20:49-54  DOI:10.1093/bioinformatics/bth947  PMID:15262780
  • Durr, E., Yu, J. Y., Krasinska, K. M., Carver, L. A., Yates, J. R., Testa, J. E., Oh, P., Schnitzer, J. E. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture Nature Biotechnology  2004 22:985-992  DOI:10.1038/nbt993  PMID:15258593
  • Liu, H. B., Sadygov, R. G., Yates, J. R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics Analytical Chemistry  2004 76:4193-4201  DOI:10.1021/ac0498563  PMID:15253663
  • Anderson, L. B., Ouellette, A. J. A., Eaton-Rye, J., Maderia, M., MacCoss, M. J., Yates, J. R., Barry, B. A. Evidence for a post-translational modification, aspartyl aldehyde, in a photosynthetic membrane protein Journal of the American Chemical Society  2004 126:8399-8405  DOI:10.1021/ja0478781  PMID:15237995
  • Skop, A. R., Liu, H. B., Yates, J., Meyer, B. J., Heald, R. Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms Science  2004 305:61-66  DOI:10.1126/science.1097931  PMID:15166316  PMCID:PMC3679889
  • Flick, K., Ouni, I., Wohlschlegel, J. A., Capati, C., McDonald, W. H., Yates, J. R., Kaiser, P. Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain Nature Cell Biology  2004 6:634-641  DOI:10.1038/ncb1143  PMID:15208638
  • de Bruin, R. A. M., McDonald, W. H., Kalashnikova, T. I., Yates, J., Wittenberg, C. Cln3 activates G1-specific transcription via phosphorylation of the SBF transcription bound repressor Whi5 Cell  2004 117:887-898  DOI:10.1016/j.cell.2004.05.025  PMID:15210110
  • Sam-Yellowe, T. Y., Florens, L., Johnson, J. R., Wang, T. M., Drazba, J. A., Le Roch, K. G., Zhou, Y. Y., Batalov, S., Carucci, D. J., Winzeler, E. A., Yates, J. R. A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling Genome Research  2004 14:1052-1059  DOI:10.1101/gr.2126104  PMID:15140830  PMCID:PMC419783
  • Yates, J. R. Mass spectrometry as an emerging tool for systems biology Biotechniques  2004 36:917-919  DOI:10.2144/3606A0917  PMID:15211739
  • Leonoudakis, D., Conti, L. R., Anderson, S., Radeke, C. M., McGuire, L. M. M., Adams, M. E., Froehner, S. C., Yates, J. R., Vandenberg, C. A. Protein trafficking and anchoring complexes revealed by proteomic analysis of inward rectifier potassium channel (Kir2.x)-associated proteins Journal of Biological Chemistry  2004 279:22331-22346  DOI:10.1074/jbc.M400285200  PMID:15024025
  • Venable, J. D., Yates, J. R. Impact of ion trap tandem mass spectra variability on the identification of peptides Analytical Chemistry  2004 76:2928-2937  DOI:10.1021/ac0348219  PMID:15144207
  • Lin, Y. H., Park, Z. Y., Lin, D., Brahmbhatt, A. A., Rio, M. C., Yates, J. R., Klemke, R. L. Regulation of cell migration and survival by focal adhesion targeting of Lasp-1 Journal of Cell Biology  2004 165:421-432  DOI:10.1083/jcb.200311045  PMID:15138294  PMCID:PMC2172195
  • Florens, L., Liu, X., Wang, Y. F., Yang, S. G., Schwartz, O., Peglar, M., Carucci, D. J., Yates, J. R., Wu, Y. M. Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes Molecular and Biochemical Parasitology  2004 135:1-11  DOI:10.1016/j.molbiopara.2003.12.007  PMID:15287581
  • Zhu, W. H., Reich, C. I., Olsen, G. J., Giometti, C. S., Yates, J. R. Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis Journal of Proteome Research  2004 3:538-548  DOI:10.1021/pr034109s  PMID:15253435
  • Likhite, V. S., Cass, E. I., Anderson, S. D., Yates, J. R., Nardulli, A. M. Interaction of estrogen receptor alpha with 3-methyladenine DNA glycosylase modulates transcription and DNA repair Journal of Biological Chemistry  2004 279:16875-16882  DOI:10.1074/jbc.M313155200  PMID:14761960
  • Reinke, A., Anderson, S., McCaffery, J. M., Yates, J., Aronova, S., Chu, S., Fairclough, S., Iverson, C., Wedaman, K. P., Powers, T. TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae Journal of Biological Chemistry  2004 279:14752-14762  DOI:10.1074/jbc.M313062200  PMID:14736892
  • Kesti, T., McDonald, W. H., Yates, J. R., Wittenberg, C. Cell cycle-dependent phosphorylation of the DNA polymerase epsilon subunit, Dpb2, by the Cdc28 cyclin-dependent protein kinase Journal of Biological Chemistry  2004 279:14245-14255  DOI:10.1074/jbc.M313289200  PMID:14747467
  • Ling, I. T., Florens, L., Dluzewski, A. R., Kaneko, O., Grainger, M., Lim, Bysy, Tsuboi, T., Hopkins, J. M., Johnson, J. R., Torii, M., Bannister, L. H., Yates, J. R., et al. The Plasmodium falciparum clag9 gene encodes a rhoptry protein that is transferred to the host erythrocyte upon invasion Molecular Microbiology  2004 52:107-118  DOI:10.1111/j.1365-2958.2003.03969.x  PMID:15049814
  • Sadygov, R. G., Liu, H. B., Yates, J. R. Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases Analytical Chemistry  2004 76:1664-1671  DOI:10.1021/ac035112y  PMID:15018565
  • Graumann, J., Dunipace, L. A., Seol, J. H., McDonald, W. H., Yates, J. R., Wold, B. J., Deshaies, R. J. Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast Molecular & Cellular Proteomics  2004 3:226-237  DOI:10.1074/mcp.M300099-MCP200  PMID:14660704
  • Tabb, D. L., Huang, Y. Y., Wysocki, V. H., Yates, J. R. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides Analytical Chemistry  2004 76:1243-1248  DOI:10.1021/ac0351163  PMID:14987077  PMCID:PMC2813199
  • Johnson, J. R., Florens, L., Carucci, D. J., Yates, J. R. Proteomics in malaria Journal of Proteome Research  2004 3:296-306  DOI:10.1021/pr0340781  PMID:15113107
  • Daniel, J. A., Torok, M. S., Sun, Z. W., Schieltz, D., Allis, C. D., Yates, J. R., Grant, P. A. Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription Journal of Biological Chemistry  2004 279:1867-1871  DOI:10.1074/jbc.C300494200  PMID:14660634
  • Xu, W., Cho, H., Kadam, S., Banayo, E. M., Anderson, S., Yates, J. R., Emerson, B. M., Evans, R. M. A methylation-mediator complex in hormone signaling Genes & Development  2004 18:144-156  DOI:10.1101/gad.1141704  PMID:14729568  PMCID:PMC324421
  • Yates III, J., Snyder, M. Proteomics and genomics. Editorial overview Current Opinion in Chemical Biology  2004 8:1-2  DOI:10.1016/j.cbpa.2003.12.011
  • Liu, H. B., Bergman, N. H., Thomason, B., Shallom, S., Hazen, A., Crossno, J., Rasko, D. A., Ravel, J., Read, T. D., Peterson, S. N., Yates, J., Hanna, P. C. Formation and composition of the Bacillus anthracis endospore Journal of Bacteriology  2004 186:164-178  DOI:10.1128/jb.186.1.164-178.2004  PMID:14679236  PMCID:PMC303457
  • McDonald, W. H., Tabb, D. L., Sadygov, R. G., MacCoss, M. J., Venable, J., Graumann, J., Johnson, J. R., Cociorva, D., Yates, J. R. MS1, MS2, and SQT: three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications Rapid Communications in Mass Spectrometry  2004 18:2162-2168  DOI:10.1002/rcm.1603  PMID:15317041
  • Yates, J. R. Mass spectral analysis in proteomics Annual Review of Biophysics and Biomolecular Structure  2004 33:297-316  DOI:10.1146/annurev.biophys.33.111502.082538  PMID:15139815
  • Wu, C. C., MacCoss, M. J., Mardones, G., Finnigan, C., Mogelsvang, S., Yates, J. R., Howell, K. E. Organellar proteomics reveals Golgi arginine dimethylation Molecular Biology of the Cell  2004 15:2907-2919  DOI:10.1091/mbc.E04-02-0101  PMID:15047867  PMCID:PMC420113
  • Coulon, S., Gaillard, P. H. L., Chahwan, C., McDonald, W. H., Yates, J. R., Russell, P. Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast Molecular Biology of the Cell  2004 15:71-80  DOI:10.1091/mbc.E03-08-0586  PMID:14528010  PMCID:PMC307528
  • MacCoss, M. J., Wu, C. C., Liu, H. B., Sadygov, R., Yates, J. R. A correlation algorithm for the automated quantitative analysis of shotgun proteomics data Analytical Chemistry  2003 75:6912-6921  DOI:10.1021/ac034790h  PMID:14670053
  • Hazbun, T. R., Malmstrom, L., Anderson, S., Graczyk, B. J., Fox, B., Riffle, M., Sundin, B. A., Aranda, J. D., McDonald, W. H., Chiu, C. H., Snydsman, B. E., Bradley, P., et al. Assigning function to yeast proteins by integration of technologies Molecular Cell  2003 12:1353-1365  DOI:10.1016/s1097-2765(03)00476-3  PMID:14690591
  • Tabb, D. L., Saraf, A., Yates, J. R. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model Analytical Chemistry  2003 75:6415-6421  DOI:10.1021/ac0347462  PMID:14640709  PMCID:PMC2915448
  • Rodriguez-Gabriel, M. A., Burns, G., McDonald, W. H., Martin, V., Yates, J. R., Bahler, J., Russell, P. RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress EMBO Journal  2003 22:6256-6266  DOI:10.1093/emboj/cdg597  PMID:14633985  PMCID:PMC291838
  • McDonald, W. H., Pavlova, Y., Yates, J. R., Boddy, M. N. Novel essential DNA repair proteins Nse1 and Nse2 are subunits of the fission yeast Smc5-Smc6 complex Journal of Biological Chemistry  2003 278:45460-45467  DOI:10.1074/jbc.M308828200  PMID:12966087
  • Doolan, D. L., Aguiar, J. C., Weiss, W. R., Sette, A., Felgner, P. L., Regis, D. P., Quinones-Casas, P., Yates, J. R., Blair, P. L., Ritchie, T. L., Hoffman, S. L., Carucci, D. J. Utilization of genomic sequence information to develop malaria vaccines Journal of Experimental Biology  2003 206:3789-3802  DOI:10.1242/jeb.00615  PMID:14506214
  • Westermann, S., Cheeseman, I. M., Anderson, S., Yates, J. R., Drubin, D. G., Barnes, G. Architecture of the budding yeast kinetochore reveals a conserved molecular core Journal of Cell Biology  2003 163:215-222  DOI:10.1083/jcb.200305100  PMID:14581449  PMCID:PMC2173538
  • Wohlschlegel, J. A., Yates, J. R. Proteomics: where's Waldo in yeast? Nature  2003 425:671-672  DOI:10.1038/425671a  PMID:14562083
  • Washburn, M. P., Ulaszek, R. R., Yates III, J. R. Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology Analytical Chemistry  2003 75:5054-5061  DOI:10.1021/ac034120b  PMID:14708778
  • Schirmer, E. C., Florens, L., Guan, T. L., Yates, J. R., Gerace, L. Nuclear membrane proteins with potential disease links found by subtractive proteomics Science  2003 301:1380-1382  DOI:10.1126/science.1088176  PMID:12958361
  • Geyer, R., Wee, S., Anderson, S., Yates, J., Wolf, D. A. BTB/POZ domain proteins are putative substrate adaptors for cullin 3 ubiquitin ligases Molecular Cell  2003 12:783-790  DOI:10.1016/s1097-2765(03)00341-1  PMID:14527422
  • Zhong, J., Haynes, P. A., Zhang, S., Yang, X., Andon, N. L., Eckert, D., Yates III, J. R., Wang, X., Budworth, P. Development of a system for the study of protein-protein interactions in planta: characterization of a TATA-box binding protein complex in Oryza sativa Journal of Proteome Research  2003 2:514-522  DOI:10.1021/pr034023z  PMID:14582648
  • Lim, H., Eng, J., Yates, J. R., Tollaksen, S. L., Giometti, C. S., Holden, J. F., Adams, M. W. W., Reich, C. I., Olsen, G. J., Hays, L. G. Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry Journal of the American Society for Mass Spectrometry  2003 14:957-970  DOI:10.1016/s1044-0305(03)00144-2  PMID:12954164
  • Doolan, D. L., Southwood, S., Freilich, D. A., Sidney, J., Graber, N. L., Shatney, L., Bebris, L., Florens, L., Dobano, C., Witney, A. A., Appella, E., Hoffman, S. L., et al. Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data Proceedings of the National Academy of Sciences of the United States of America  2003 100:9952-9957  DOI:10.1073/pnas.1633254100  PMID:12886016  PMCID:PMC187898
  • Sadygov, R. G., Yates, J. R. A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases Analytical Chemistry  2003 75:3792-3798  DOI:10.1021/ac034157w  PMID:14572045
  • Boddy, M. N., Shanahan, P., McDonald, W. H., Lopez-Girona, A., Noguchi, E., Yates, J. R., Russell, P. Replication checkpoint kinase Cds1 regulates recombinational repair protein Rad60 Molecular and Cellular Biology  2003 23:5939-5946  DOI:10.1128/mcb.23.16.5939-5946.2003  PMID:12897162  PMCID:PMC166335
  • Andon, N. L., Eckert, D., Yates III, J. R., Haynes, P. A. High-throughput functional affinity purification of mannose binding proteins from Oryza sativa Proteomics  2003 3:1270-1278  DOI:10.1002/pmic.200300447  PMID:12872227
  • Cooper, B., Eckert, D., Andon, N. L., Yates, J. R., Haynes, P. A. Investigative proteomics: identification of an unknown plant virus from infected plants using mass spectrometry Journal of the American Society for Mass Spectrometry  2003 14:736-741  DOI:10.1016/s1044-0305(03)00125-9  PMID:12837595
  • McDonald, W. H., Yates, J. R. Shotgun proteomics: integrating technologies to answer biological questions Current Opinion in Molecular Therapeutics  2003 5:302-309  PMID:12870441
  • Willert, K., Brown, J. D., Danenberg, E., Duncan, A. W., Weissman, I. L., Reya, T., Yates, J. R., Nusse, R. Wnt proteins are lipid-modified and can act as stem cell growth factors Nature  2003 423:448-452  DOI:10.1038/nature01611  PMID:12717451
  • Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., Yates, J. R. Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility Analytical Chemistry  2003 75:2470-2477  DOI:10.1021/ac026424o  PMID:12918992
  • Wu, C. C., MacCoss, M. J., Howell, K. E., Yates, J. R. A method for the comprehensive proteomic analysis of membrane proteins Nature Biotechnology  2003 21:532-538  DOI:10.1038/nbt819  PMID:12692561
  • Giometti, C. S., Khare, T., Tollaksen, S. L., Tsapin, A., Zhu, W. H., Yates, J. R., Nealson, K. H. Analysis of the Shewanella oneidensis proteome by two-dimensional gel electrophoresis under nondenaturing conditions Proteomics  2003 3:777-785  DOI:10.1002/pmic.200300406  PMID:12748955
  • Breci, L. A., Tabb, D. L., Yates, J. R., Wysocki, V. H. Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra Analytical Chemistry  2003 75:1963-1971  DOI:10.1021/ac026359i  PMID:12720328
  • Lin, D., Tabb, D. L., Yates, J. R. Large-scale protein identification using mass spectrometry Biochimica et Biophysica Acta-Proteins and Proteomics  2003 1646:1-10  DOI:10.1016/s1570-9639(02)00546-0  PMID:12637006
  • Washburn, M. P., Koller, A., Oshiro, G., Ulaszek, R. R., Plouffe, D., Deciu, C., Winzeler, E., Yates, J. R. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae Proceedings of the National Academy of Sciences of the United States of America  2003 100:3107-3112  DOI:10.1073/pnas.0634629100  PMID:12626741  PMCID:PMC152254
  • Li, B., Howe, L., Anderson, S., Yates, J. R., Workman, J. L. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II Journal of Biological Chemistry  2003 278:8897-8903  DOI:10.1074/jbc.M212134200  PMID:12511561
  • Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D., Stead, D. A., Yin, Z. K., Deutsch, E. W., Selway, L., Walker, J., Riba-Garcia, I., Mohammed, S., Deery, M. J., et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data Nature Biotechnology  2003 21:247-254  DOI:10.1038/nbt0303-247  PMID:12610571
  • Canettieri, G., Morantte, I., Guzman, E., Asahara, H., Herzig, S., Anderson, S. D., Yates, J. R., Montminy, M. Attenuation of a phosphorylation-dependent activator by an HDAC-PP1 complex Nature Structural Biology  2003 10:175-181  DOI:10.1038/nsb895  PMID:12567184
  • Tabb, D. L., Smith, L. L., Breci, L. A., Wysocki, V. H., Lin, D., Yates, J. R. Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides Analytical Chemistry  2003 75:1155-1163  DOI:10.1021/ac026122m  PMID:12641236  PMCID:PMC2819022
  • Wu, C. C., Yates, J. R. The application of mass spectrometry to membrane proteomics Nature Biotechnology  2003 21:262-267  DOI:10.1038/nbt0303-262  PMID:12610573
  • Wedaman, K. P., Reinke, A., Anderson, S., Yates, J., McCaffery, J. M., Powers, T. Tor kinases are in distinct membrane-associated protein complexes in Saccharomyces cerevisiae Molecular Biology of the Cell  2003 14:1204-1220  DOI:10.1091/mbc.E02-09-0609  PMID:12631735  PMCID:PMC151591
  • Lindstrom, D. L., Squazzo, S. L., Muster, N., Burckin, T. A., Wachter, K. C., Emigh, C. A., McCleery, J. A., Yates, J. R., Hartzog, G. A. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins Molecular and Cellular Biology  2003 23:1368-1378  DOI:10.1128/mcb.23.4.1368-1378.2003  PMID:12556496  PMCID:PMC141151
  • Sellers, T. A., Yates, J. R. Review of proteomics with applications to genetic epidemiology Genetic Epidemiology  2003 24:83-98  DOI:10.1002/gepi.10226  PMID:12548670
  • Loven, M. A., Muster, N., Yates, J. R., Nardulli, A. M. A novel estrogen receptor alpha-associated protein, template-activating factor I beta, inhibits acetylation and transactivation Molecular Endocrinology  2003 17:67-78  DOI:10.1210/me.2002-0280  PMID:12511607
  • Schieltz, D. M., Yates, J. R., 3rd Direct identification of proteins in ultracomplex mixtures. Applications to proteome analysis Methods in Molecular Biology  2003 211:235-245  PMID:12489435
  • Delahunty, C., Yates III, J. R. Identification of proteins in complex mixtures using liquid chromatography and mass spectrometry Current Protocols in Cell Biology  2003 Unit 5:17:5.6.1–17:5.6.17  DOI:10.1002/0471143030.cb0505s17  PMID:18228436
  • Schirmer, E. C., Yates, J. R., Gerace, L. MudPIT: a powerful proteomics tool for discovery Discovery Medicine  2003 3:38-39  PMID:20704860
  • Yamaguchi, K., Beligni, M. V., Prieto, S., Haynes, P. A., McDonald, W. H., Yates, J. R., Mayfield, S. P. Proteomic characterization of the Chlamydomonas reinhardtii chloroplast ribosome. Identification of proteins unique to th e70 S ribosome Journal of Biological Chemistry  2003 278:33774-33785  DOI:10.1074/jbc.M301934200  PMID:12826678
  • Giometti, C. S., Reich, C., Tollaksen, S., Babnigg, G., Lim, H. J., Zhu, W. H., Yates, J., Olsen, G. Global analysis of a "simple" proteome: Methanococcus jannaschii Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences  2002 782:227-243  DOI:10.1016/s1570-0232(02)00568-8  PMID:12458009
  • Hunter, T. C., Andon, N. L., Koller, A., Yates III, J. R., Haynes, P. A. The functional proteomics toolbox: methods and applications Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences  2002 782:165-181  DOI:10.1016/s1570-0232(02)00570-6  PMID:12458005
  • Carucci, D. J., Yates, J. R., Florens, L. Exploring the proteome of Plasmodium International Journal for Parasitology  2002 32:1539-1542  DOI:10.1016/s0020-7519(02)00181-9  PMID:12435437
  • Shim, J., Lim, H., Yates, J. R., Karin, M. Nuclear export of NF90 is required for interleukin-2 mRNA stabilization Molecular Cell  2002 10:1331-1344  DOI:10.1016/s1097-2765(02)00730-x  PMID:12504009
  • Pray-Grant, M. G., Schieltz, D., McMahon, S. J., Wood, J. M., Kennedy, E. L., Cook, R. G., Workman, J. L., Yates, J. R., Grant, P. A. The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway Molecular and Cellular Biology  2002 22:8774-8786  DOI:10.1128/mcb.22.24.8774-8786.2002  PMID:12446794  PMCID:PMC139885
  • Anderson, L. B., Maderia, M., Ouellette, A. J., Putnam-Evans, C., Higgins, L., Krick, T., MacCoss, M. J., Lim, H., Yates, J. R., 3rd, Barry, B. A. Posttranslational modifications in the CP43 subunit of photosystem II Proceedings of the National Academy of Sciences of the United States of America  2002 99:14676-14681  DOI:10.1073/pnas.232591599  PMID:12417747  PMCID:PMC137478
  • MacCoss, M. J., Wu, C. C., Yates, J. R. Probability-based validation of protein identifications using a modified SEQUEST algorithm Analytical Chemistry  2002 74:5593-5599  DOI:10.1021/ac025826t  PMID:12433093
  • Yamaguchi, K., Prieto, S., Beligni, M. V., Haynes, P. A., McDonald, W. H., Yates, J. R., Mayfield, S. P. 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 Plant Cell  2002 14:2957-2974  DOI:10.1105/tpc.004341  PMID:12417713  PMCID:PMC152739
  • Cheeseman, L. M., Anderson, S., Jwa, M., Green, E. M., Kang, J. S., Yates, J. R., Chan, C. S. M., Drubin, D. G., Barnes, G. Phospho-regulation of kinetochore-microtubule attachments by the aurora kinase Ipl1p Cell  2002 111:163-172  PMID:12408861
  • Verma, R., Aravind, L., Oania, R., McDonald, W. H., Yates, J. R., Koonin, E. V., Deshaies, R. J. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome Science  2002 298:611-615  DOI:10.1126/science.1075898  PMID:12183636
  • Florens, L., Washburn, M. P., Raine, J. D., Anthony, R. M., Grainger, M., Haynes, J. D., Moch, J. K., Muster, N., Sacci, J. B., Tabb, D. L., Witney, A. A., Wolters, D., et al. A proteomic view of the Plasmodium falciparum life cycle Nature  2002 419:520-526  DOI:10.1038/nature01107  PMID:12368866
  • Carlton, J. M., Angiuoli, S. V., Suh, B. B., Kooij, T. W., Pertea, M., Silva, J. C., Ermolaeva, M. D., Allen, J. E., Selengut, J. D., Koo, H. L., Peterson, J. D., Pop, M., et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii Nature  2002 419:512-519  DOI:10.1038/nature01099  PMID:12368865
  • Koller, A., Washburn, M. P., Lange, B. M., Andon, N. L., Deciu, C., Haynes, P. A., Hays, L., Schieltz, D., Ulaszek, R., Wei, J., Wolters, D., Yates III, J. R. Proteomic survey of metabolic pathways in rice Proceedings of the National Academy of Sciences of the United States of America  2002 99:11969-11974  DOI:10.1073/pnas.172183199  PMID:12163647  PMCID:PMC129378
  • Andon, N. L., Hollingworth, S., Koller, A., Greenland, A. J., Yates III, J. R., Haynes, P. A. Proteomic characterization of wheat amyloplasts using identification of proteins by tandem mass spectrometry Proteomics  2002 2:1156-1168  DOI:10.1002/1615-9861(200209)2:9<1156::aid-prot1156>3.0.co;2-4  PMID:12362334
  • McDonald, W. H., Ohi, R., Miyamoto, D. T., Mitchison, T. J., Yates, J. R. 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 International Journal of Mass Spectrometry  2002 219:245-251  DOI:10.1016/s1387-3806(02)00563-8
  • Oshiro, G., Wodicka, L. M., Washburn, M. P., Yates, J. R., Lockhart, D. J., Winzeler, E. A. Parallel identification of new genes in Saccharomyces cerevisiae Genome Research  2002 12:1210-1220  DOI:10.1101/gr.226802  PMID:12176929  PMCID:PMC186640
  • Huang, Y. Y., Wysocki, V. H., Tabb, D. L., Yates, J. R. The influence of histidine on cleavage C-terminal to acidic residues in doubly protonated tryptic peptides International Journal of Mass Spectrometry  2002 219:233-244  DOI:10.1016/s1387-3806(02)00660-7
  • Inada, T., Winstall, E., Tarun, S. Z., Yates, J. R., Schieltz, D., Sachs, A. B. One-step affinity purification of the yeast ribosome and its associated proteins and mRNAs RNA-a Publication of the RNA Society  2002 8:948-958  DOI:10.1017/s1355838202026018  PMID:12166649  PMCID:PMC1370311
  • Howe, L., Kusch, T., Muster, N., Chaterji, R., Yates, J. R., Workman, J. L. Yng1p modulates the activity of Sas3p as a component of the yeast NuA3 histone acetyltransferase complex Molecular and Cellular Biology  2002 22:5047-5053  DOI:10.1128/mcb.22.14.5047-5053.2002  PMID:12077334  PMCID:PMC139787
  • MacCoss, M. J., McDonald, W. H., Saraf, A., Sadygov, R., Clark, J. M., Tasto, J. J., Gould, K. L., Wolters, D., Washburn, M., Weiss, A., Clark, J. I., Yates, J. R. Shotgun identification of protein modifications from protein complexes and lens tissue Proceedings of the National Academy of Sciences of the United States of America  2002 99:7900-7905  DOI:10.1073/pnas.122231399  PMID:12060738  PMCID:PMC122992
  • Mortensen, E. M., McDonald, H., Yates III, J., Kellogg, D. R. Cell cycle-dependent assembly of a Gin4-septin complex Molecular Biology of the Cell  2002 13:2091-2105  DOI:10.1091/mbc.01-10-0500  PMID:12058072  PMCID:PMC117627
  • Saitoh, S., Chabes, A., McDonald, W. H., Thelander, L., Yates, J. R., Russell, P. Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA Cell  2002 109:563-573  DOI:10.1016/s0092-8674(02)00753-5  PMID:12062100
  • Sadygov, R. G., Eng, J., Durr, E., Saraf, A., McDonald, H., MacCoss, M. J., Yates, J. R. Code developments to improve the efficiency of automated MS/MS spectra interpretation Journal of Proteome Research  2002 1:211-215  DOI:10.1021/pr015514r  PMID:12645897
  • Washburn, M. P., Ulaszek, R., Deciu, C., Schieltz, D. M., Yates, J. R. Analysis of quantitative proteomic data generated via multidimensional protein identification technology Analytical Chemistry  2002 74:1650-1657  DOI:10.1021/ac015704l  PMID:12043600
  • Liu, H. B., Lin, D. Y., Yates, J. R. Multidimensional separations for protein/peptide analysis in the post-genomic era Biotechniques  2002 32:898, 900, 902 passim  PMID:11962611
  • Thompson, D. K., Beliaev, A. S., Giometti, C. S., Tollaksen, S. L., Khare, T., Lies, D. P., Nealson, K. H., Lim, J., Yates, J., Brandt, C. C., Tiedje, J. M., Zhou, J. Z. Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress Applied and Environmental Microbiology  2002 68:881-892  DOI:10.1128/aem.68.2.881-892.2002  PMID:11823232  PMCID:PMC126683
  • Deshaies, R. J., Seol, J. H., McDonald, W. H., Cope, G., Lyapina, S., Shevchenko, A., Verma, R., Yates, J. R. Charting the protein complexome in yeast by mass spectrometry Molecular & Cellular Proteomics  2002 1:3-10  DOI:10.1074/mcp.R100001-MCP200  PMID:12096135
  • Tabb, D. L., McDonald, W. H., Yates, J. R. DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics Journal of Proteome Research  2002 1:21-26  DOI:10.1021/pr015504q  PMID:12643522  PMCID:PMC2811961
  • Beliaev, A. S., Thompson, D. K., Khare, T., Lim, H., Brandt, C. C., Li, G., Murray, A. E., Heidelberg, J. F., Giometti, C. S., Yates III, J. R., Nealson, K. H., Tiedje, J. M., et al. Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors OMICS: A Journal of Integrative Biology  2002 6:39-60  PMID:11881834
  • Zhu, W., Yates III, J. R. Proteome analysis of microbes: to gel or not to gel Applied Genomics and Proteomics  2002 1:3-12
  • McDonald, W. H., Yates, J. R. Shotgun proteomics and biomarker discovery Disease Markers  2002 18:99-105  DOI:10.1155/2002/505397  PMID:12364816  PMCID:PMC3851423
  • Cheeseman, I. M., Brew, C., Wolyniak, M., Desai, A., Anderson, S., Muster, N., Yates, J. R., Huffaker, T. C., Drubin, D. G., Barnes, G. Implication of a novel multiprotein Dam1p complex in outer kinetochore function Journal of Cell Biology  2001 155:1137-1145  DOI:10.1083/jcb.200109063  PMID:11756468  PMCID:PMC2199314
  • Wolters, D. A., Washburn, M. P., Yates, J. R. An automated multidimensional protein identification technology for shotgun proteomics Analytical Chemistry  2001 73:5683-5690  DOI:10.1021/ac010617e  PMID:11774908
  • Osada, S., Sutton, A., Muster, N., Brown, C. E., Yates, J. R., Sternglanz, R., Workman, J. L. The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1 Genes & Development  2001 15:3155-3168  DOI:10.1101/gad.907201  PMID:11731479  PMCID:PMC312835
  • Boddy, M. N., Gaillard, P. H. L., McDonald, W. H., Shanahan, P., Yates, J. R., Russell, P. Mus81-Eme1 are essential components of a Holliday junction resolvase Cell  2001 107:537-548  DOI:10.1016/s0092-8674(01)00536-0  PMID:11719193
  • Segarini, P. R., Nesbitt, J. E., Li, D. X., Hays, L. G., Yates, J. R., Carmichael, D. F. The low density lipoprotein receptor-related protein/alpha(2)-macroglobulin receptor is a receptor for connective tissue growth factor Journal of Biological Chemistry  2001 276:40659-40667  DOI:10.1074/jbc.M105180200  PMID:11518710
  • Holden, J. F., Poole, F. L., Tollaksen, S. L., Giometti, C. S., Lim, H., Yates, J. R., Adams, M. W. W. Identification of membrane proteins in the hyperthermophilic archaeon Pyrococcus furiosus using proteomics and prediction programs Comparative and Functional Genomics  2001 2:275-288  DOI:10.1002/cfg.110  PMID:18629240  PMCID:PMC2448401
  • MacCoss, M. J., Yates, J. R. Proteomics: analytical tools and techniques Current Opinion in Clinical Nutrition and Metabolic Care  2001 4:369-375  DOI:10.1097/00075197-200109000-00006  PMID:11568497
  • Verma, R., McDonald, H., Yates III, J. R., Deshaies, R. J. Selective degradation of ubiquitinated Sic1 by purified 26S proteasome yields active S phase cyclin-Cdk Molecular Cell  2001 8:439-448  DOI:10.1016/s1097-2765(01)00308-2  PMID:11545745
  • Giometti, C. S., Reich, C. I., Tollaksen, S. L., Babnigg, G., Lim, H., Yates, J. R., Olsen, G. J. Structural modifications of Methanococcus jannaschii flagellin proteins revealed by proteome analysis Proteomics  2001 1:1033-1042  DOI:10.1002/1615-9861(200108)1:8<1033::aid-prot1033>3.0.co;2-#  PMID:11683504
  • Friedman, D. B., Kern, J. W., Huneycutt, B. J., Vinh, D. B. N., Crawford, D. K., Steiner, E., Scheiltz, D., Yates III, J., Resing, K. A., Ahn, N. G., Winey, M., Davis, T. N. Yeast Mps1p phosphorylates the spindle pole component Spc110p in the N-terminal domain Journal of Biological Chemistry  2001 276:17958-17967  DOI:10.1074/jbc.M010461200  PMID:11278681  PMCID:PMC4013285
  • Dongre, A. R., Kovats, S., deRoos, P., McCormack, A. L., Nakagawa, T., Paharkova-Vatchkova, V., Eng, J., Caldwell, H., Yates, J. R., Rudensky, A. Y. In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses European Journal of Immunology  2001 31:1485-1494  DOI:10.1002/1521-4141(200105)31:5<1485::aid-immu1485>3.0.co;2-a  PMID:11465105
  • Kleemann-Fischer, D., Kleemann, G. R., Engel, D., Yates, J. R., Wu, J. J., Eyre, D. R. Molecular properties of matrilin-3 isolated from human growth cartilage Archives of Biochemistry and Biophysics  2001 387:209-215  DOI:10.1006/abbi.2000.2256  PMID:11370843
  • Boldogh, I. R., Yang, H. C., Nowakowski, W. D., Karmon, S. L., Hays, L. G., Yates, J. R., Pon, L. A. Arp2/3 complex and actin dynamics are required for actin-based mitochondrial motility in yeast Proceedings of the National Academy of Sciences of the United States of America  2001 98:3162-3167  DOI:10.1073/pnas.051494698  PMID:11248049  PMCID:PMC30624
  • Washburn, M. P., Wolters, D., Yates, J. R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nature Biotechnology  2001 19:242-247  DOI:10.1038/85686  PMID:11231557
  • Bark, S. J., Muster, N., Yates, J. R., Siuzdak, G. High-temperature protein mass mapping using a thermophilic protease Journal of the American Chemical Society  2001 123:1774-1775  DOI:10.1021/ja002909n  PMID:11456785
  • Honey, S., Schneider, B. L., Schieltz, D. M., Yates, J. R., Futcher, B. A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin-CDK complex Nucleic Acids Research  2001 29:e24  DOI:10.1093/nar/29.4.e24  PMID:11160944  PMCID:PMC29631
  • Emili, A., Schieltz, D. W., Yates, J. R., Hartwell, L. H. Dynamic interaction of DNA damage checkpoint protein Rad53 with chromatin assembly factor Asf1 Molecular Cell  2001 7:13-20  DOI:10.1016/s1097-2765(01)00150-2  PMID:11172707
  • Chen, W. B., Laidig, K. E., Park, Y., Park, K., Yates, J. R., Lamont, R. J., Hackett, M. Searching the Porphyromonas gingivalis genome with peptide fragmentation mass spectra Analyst  2001 126:52-57  DOI:10.1039/b008012h  PMID:11205512
  • Tong, W., Yates, J. R. Sensitive and high resolution CE/MS/MS for protein identification in complex mixtures Chromatographia  2001 53:90-99  DOI:10.1007/978-3-322-83021-0_10
  • Giometti, C. S., Tollaksen, S. L., Babnigg, G., Reich, C. I., Olsen, G. J., Lim, H., Yates, J. R. Structural modifications of Methanococcus jannaschii flagellin proteins revealed by proteome analysis European Journal of Mass Spectrometry  2001 7:207-217  DOI:10.1255/ejms.404
  • Todorow, Z., Spang, A., Carmack, E., Yates, J., Schekman, R. Active recycling of yeast Golgi mannosyltransferase complexes through the endoplasmic reticulum Proceedings of the National Academy of Sciences of the United States of America  2000 97:13643-13648  DOI:10.1073/pnas.250472397  PMID:11095735  PMCID:PMC17629
  • Hefner, Y., Borsch-Haubold, A. G., Murakami, M., Wilde, J. I., Pasquet, S., Schieltz, D., Ghomashchi, F., Yates, J. R., Armstrong, C. G., Paterson, A., Cohen, P., Fukunaga, R., et al. Serine 727 phosphorylation and activation of cytosolic phospholipase A(2) by MNK1-related protein kinases Journal of Biological Chemistry  2000 275:37542-37551  DOI:10.1074/jbc.M003395200  PMID:10978317
  • Verma, R., Chen, S., Feldman, R., Schieltz, D., Yates, J., Dohmen, T., Deshaies, R. J. Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes Molecular Biology of the Cell  2000 11:3425-3439  PMID:11029046  PMCID:PMC15004
  • Wu, C. C., Yates, J. R., Neville, M. C., Howell, K. E. Proteomic analysis of two functional states of the Golgi complex in mammary epithelial cells Traffic  2000 1:769-782  DOI:10.1034/j.1600-0854.2000.011004.x  PMID:11208067
  • McDonald, W. H., Yates, J. R. Proteomic tools for cell biology Traffic  2000 1:747-754  DOI:10.1034/j.1600-0854.2000.011001.x  PMID:11208064
  • Taylor, R. S., Wu, C. C., Hays, L. G., Eng, J. K., Yates, J. R., Howell, K. E. Proteomics of rat liver Golgi complex: minor proteins are identified through sequential fractionation Electrophoresis  2000 21:3441-3459  DOI:10.1002/1522-2683(20001001)21:16<3441::aid-elps3441>3.0.co;2-g  PMID:11079564
  • Wu, C. C., Howell, K. E., Neville, M. C., Yates, J. R., McManaman, J. L. Proteomics reveal a link between the endoplasmic reticulum and lipid secretory mechanisms in mammary epithelial cells Electrophoresis  2000 21:3470-3482  DOI:10.1002/1522-2683(20001001)21:16<3470::aid-elps3470>3.3.co;2-7  PMID:11079566
  • Krahmer, M. T., Walters, J. J., Fox, K. F., Fox, A., Creek, K. E., Pirisi, L., Wunschel, D. S., Smith, R. D., Tabb, D. L., Yates, J. R. MS for identification of single nucleotide polymorphisms and MS/MS for discrimination of isomeric PCR products Analytical Chemistry  2000 72:4033-4040  DOI:10.1021/ac000142b  PMID:10994962
  • Haynes, P. A., Yates III, J. R. Proteome profiling: pitfalls and progress Yeast  2000 17:81-87  DOI:10.1002/1097-0061(20000630)17:2<81::aid-yea22>3.3.co;2-q  PMID:10900454  PMCID:PMC2448324
  • Washburn, M. P., Yates, J. R. Analysis of the microbial proteome Current Opinion in Microbiology  2000 3:292-297  DOI:10.1016/s1369-5274(00)00092-8  PMID:10851159
  • Gatlin, C. L., Eng, J. K., Cross, S. T., Detter, J. C., Yates, J. R. Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry Analytical Chemistry  2000 72:757-763  DOI:10.1021/ac991025n  PMID:10701260
  • Yates III, J. R. Foreword: Biological mass spectrometry Analyst  2000 125
  • Yates, J. R., 3rd, Link, A. J., Schieltz, D. Direct analysis of proteins in mixtures. Application to protein complexes Methods in Molecular Biology  2000 146:17-26  DOI:10.1385/1-59259-045-4:17  PMID:10948494
  • Sacher, M., Barrowman, J., Schieltz, D., Yates, J. R., Ferro-Novick, S. Identification and characterization of five new subunits of TRAPP European Journal of Cell Biology  2000 79:71-80  DOI:10.1078/s0171-9335(04)70009-6  PMID:10727015
  • Krishnamurthy, T., Rajamani, U., Ross, P. L., Jabhour, R., Nair, H., Eng, J., Yates, J., Davis, M. T., Stahl, D. C., Lee, T. D. Mass spectral investigations on microorganisms Journal of Toxicology-Toxin Reviews  2000 19:95-117
  • Yates, J. R. Mass spectrometry: from genomics to proteomics Trends in Genetics  2000 16:5-8  DOI:10.1016/s0168-9525(99)01879-x  PMID:10637622
  • Whitten, M. E., Yokoyama, K., Schieltz, D., Ghomashchi, F., Lam, D., Yates, J. R., Palczewski, K., Gelb, M. H. Structural analysis of protein prenyl groups and associated C-terminal modifications Methods in Enzymology  2000 316:436-451  DOI:10.1016/S0076-6879(00)16741-2  PMID:10800693  PMCID:PMC1435690
  • Muchowski, P. J., Hays, L. G., Yates, J. R., Clark, J. I. ATP and the core "alpha-crystallin" domain of the small heat-shock protein alpha B-crystallin Journal of Biological Chemistry  1999 274:30190-30195  DOI:10.1074/jbc.274.42.30190  PMID:10514509
  • Eberharter, A., Sterner, D. E., Schieltz, D., Hassan, A., Yates, J. R., Berger, S. L., Workman, J. L. The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae Molecular and Cellular Biology  1999 19:6621-6631  PMID:10490601  PMCID:PMC84637
  • Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., Yates, J. R. Direct analysis of protein complexes using mass spectrometry Nature Biotechnology  1999 17:676-682  PMID:10404161
  • Tong, W., Link, A., Eng, J. K., Yates, J. R. Identification of proteins in complexes by solid phase microextraction multistep elution capillary electrophoresis tandem mass spectrometry Analytical Chemistry  1999 71:2270-2278  DOI:10.1021/ac9901182  PMID:10405597
  • Meeusen, S., Tieu, Q. T., Wong, E., Weiss, E., Schieltz, D., Yates, J. R., Nunnari, J. Mgm101p is a novel component of the mitochondrial nucleoid that binds DNA and is required for the repair of oxidatively damaged mitochondrial DNA Journal of Cell Biology  1999 145:291-304  DOI:10.1083/jcb.145.2.291  PMID:10209025  PMCID:PMC2133103
  • Aird, S. D., Womble, G. C., Yates, J. R., Griffin, P. R. Primary structure of gamma-bungarotoxin, a new postsynaptic neurotoxin from venom of Bungarus multicinctus Toxicon  1999 37:609-625  DOI:10.1016/s0041-0101(98)00199-8  PMID:10082161
  • Lawrence, J. B., Oxvig, C., Overgaard, M. T., Sottrup-Jensen, L., Gleich, G. J., Hays, L. G., Yates, J. R., Conover, C. A. The insulin-like growth factor (IGF)-dependent IGF binding protein-4 protease secreted by human fibroblasts is pregnancy-associated plasma protein-A Proceedings of the National Academy of Sciences of the United States of America  1999 96:3149-3153  DOI:10.1073/pnas.96.6.3149  PMID:10077652  PMCID:PMC15910
  • Kerwin, J. L., Turecek, F., Xu, R. D., Kramer, K. J., Hopkins, T. L., Gatlin, C. L., Yates, J. R. Mass spectrometric analysis of catechol-histidine adducts from insect cuticle Analytical Biochemistry  1999 268:229-237  DOI:10.1006/abio.1998.3069  PMID:10075812
  • Goode, B. L., Wong, J. J., Butty, A. C., Peter, M., McCormack, A. L., Yates, J. R., Drubin, D. G., Barnes, G. Coronin promotes the rapid assembly and cross-linking of actin filaments and may link the actin and microtubule cytoskeletons in yeast Journal of Cell Biology  1999 144:83-98  DOI:10.1083/jcb.144.1.83  PMID:9885246  PMCID:PMC2148128
  • Yates, J. R., 3rd, Carmack, E., Hays, L., Link, A. J., Eng, J. K. Automated protein identification using microcolumn liquid chromatography-tandem mass spectrometry Methods in Molecular Biology  1999 112:553-569  PMID:10027276
  • Grant, P. A., Schieltz, D., Pray-Grant, M. G., Yates, J. R., Workman, J. L. The ATM-related cofactor Tra1 is a component of the purified SAGA complex Molecular Cell  1998 2:863-867  DOI:10.1016/s1097-2765(00)80300-7  PMID:9885573
  • Carroll, C. W., Altman, R., Schieltz, D., Yates, J. R., Kellogg, D. The septins are required for the mitosis-specific activation of the Gin4 kinase Journal of Cell Biology  1998 143:709-717  DOI:10.1083/jcb.143.3.709  PMID:9813092  PMCID:PMC2148151
  • Saleh, A., Schieltz, D., Ting, N., McMahon, S. B., Litchfield, D. W., Yates, J. R., Lees-Miller, S. P., Cole, M. D., Brandl, C. J. Tra1p is a component of the yeast Ada.Spt transcriptional regulatory complexes Journal of Biological Chemistry  1998 273:26559-26565  DOI:10.1074/jbc.273.41.26559  PMID:9756893
  • Gatlin, C. L., Kleemann, G. R., Hays, L. G., Link, A. J., Yates, J. R. Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography microspray and nanospray mass spectrometry Analytical Biochemistry  1998 263:93-101  DOI:10.1006/abio.1998.2809  PMID:9750149
  • Yates, J. R., Morgan, S. F., Gatlin, C. L., Griffin, P. R., Eng, J. K. Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis Analytical Chemistry  1998 70:3557-3565  DOI:10.1021/ac980122y  PMID:9737207
  • Dongre, A. R., Eng, J. K., Yates III, J. R. Tandem mass spectrometry Biofutur  1998
  • Grant, P. A., Schieltz, D., Pray-Grant, M. G., Steger, D. J., Reese, J. C., Yates, J. R., Workman, J. L. A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation Cell  1998 94:45-53  DOI:10.1016/s0092-8674(00)81220-9  PMID:9674426
  • Yates, J. R. Database searching using mass spectrometry data Electrophoresis  1998 19:893-900  DOI:10.1002/elps.1150190604  PMID:9638935
  • Gray, P. C., Johnson, B. D., Westenbroek, R. E., Hays, L. G., Yates, J. R., Scheuer, T., Catterall, W. A., Murphy, B. J. Primary structure and function of an A kinase anchoring protein associated with calcium channels Neuron  1998 20:1017-1026  DOI:10.1016/s0896-6273(00)80482-1  PMID:9620705
  • Sacher, M., Jiang, Y., Barrowman, J., Scarpa, A., Burston, J., Zhang, L., Schieltz, D., Yates, J. R., Abeliovich, H., Ferro-Novick, S. TRAPP, a highly conserved novel complex on the cis-Golgi that mediates vesicle docking and fusion EMBO Journal  1998 17:2494-2503  DOI:10.1093/emboj/17.9.2494  PMID:9564032  PMCID:PMC1170591
  • Carney, J. P., Maser, R. S., Olivares, H., Davis, E. M., Le Beau, M., Yates, J. R., Hays, L., Morgan, W. F., Petrini, J. H. J. The hMre11/hRad50 protein complex and Nijmegen breakage syndrome: linkage of double-strand break repair to the cellular DNA damage response Cell  1998 93:477-486  DOI:10.1016/s0092-8674(00)81175-7  PMID:9590181
  • Ducret, A., Van Oostveen, I., Eng, J. K., Yates, J. R., Aebersold, R. High throughput protein characterization by automated reverse-phase chromatography electrospray tandem mass spectrometry Protein Science  1998 7:706-719  DOI:10.1002/pro.5560070320  PMID:9541403  PMCID:PMC2143958
  • Yates, J. R. Mass spectrometry and the age of the proteome Journal of Mass Spectrometry  1998 33:1-19  DOI:10.1002/(SICI)1096-9888(199801)33:1<1::AID-JMS624>3.0.CO;2-9  PMID:9449829
  • Dongre, A. R., Eng, J. K., Yates, J. R. Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins Trends in Biotechnology  1997 15:418-425  DOI:10.1016/s0167-7799(97)01110-4  PMID:9351286
  • Link, A. J., Hays, L. G., Carmack, E. B., Yates, J. R. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143 Electrophoresis  1997 18:1314-1334  DOI:10.1002/elps.1150180808  PMID:9298647
  • Yates, J. R., McCormack, A. L., Schieltz, D., Carmack, E., Link, A. Direct analysis of protein mixtures by tandem mass spectrometry Journal of Protein Chemistry  1997 16:495-497  DOI:10.1023/A:1026365528484  PMID:9246634
  • Scalley, M. L., Yi, Q., Gu, H. D., McCormack, A., Yates, J. R., Baker, D. Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L Biochemistry  1997 36:3373-3382  DOI:10.1021/bi9625758  PMID:9116017
  • McCormack, A. L., Schieltz, D. M., Goode, B., Yang, S., Barnes, G., Drubin, D., Yates, J. R. Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level Analytical Chemistry  1997 69:767-776  DOI:10.1021/ac960799q  PMID:9043199
  • Jonscher, K. R., Yates, J. R. Matrix-assisted laser desorption ionization/quadrupole ion trap mass spectrometry of peptides. Application to the localization of phosphorylation sites on the P protein from Sendai virus Journal of Biological Chemistry  1997 272:1735-1741  PMID:8999854
  • Link, A. J., Carmack, E., Yates, J. R. A strategy for the identification of proteins localized to subcellular spaces: application to E. coli periplasmic proteins International Journal of Mass Spectrometry and Ion Processes  1997 160:303-316  DOI:10.1016/s0168-1176(96)04489-8
  • Jonscher, K. R., Yates, J. R. The quadrupole ion trap mass spectrometer: a small solution to a big challenge Analytical Biochemistry  1997 244:1-15  DOI:10.1006/abio.1996.9877  PMID:9025900
  • Figeys, D., Ducret, A., Yates, J. R., Aebersold, R. Protein identification by solid phase microextraction-capillary zone electrophoresis-microelectrospray-tandem mass spectrometry Nature Biotechnology  1996 14:1579-1583  DOI:10.1038/nbt1196-1579  PMID:9634825
  • Yates, J. R., Eng, J. K., Clauser, K. R., Burlingame, A. L. Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides Journal of the American Society for Mass Spectrometry  1996 7:1089-1098  DOI:10.1016/s1044-0305(96)00079-7  PMID:24203070
  • Hayden, J. B., McCormack, A. L., Yates, J. R., Davey, M. P. Analysis of naturally processed peptides eluted from HLA DRB1*0402 and *0404 Journal of Neuroscience Research  1996 45:795-802  DOI:10.1002/(sici)1097-4547(19960915)45:6<795::aid-jnr16>3.0.co;2-v  PMID:8892091
  • Yates, J. R., McCormack, A. L., Eng, J. Mining genomes with MS Analytical Chemistry  1996 68:534A-540A  DOI:10.1021/ac962050l  PMID:8794913
  • Link, A. J., Eng, J., Yates, J. R. Analyzing complex biological systems using micro-LC-ESI-MS-MS American Laboratory  1996 28:27-30
  • Yates, J. R., McCormack, A. L., Link, A. J., Schieltz, D., Eng, J., Hays, L. Future prospects for the analysis of complex biological systems using micro-column liquid chromatography-electrospray tandem mass spectrometry Analyst  1996 121:65R-76R  DOI:10.1039/an996210065r  PMID:8757920
  • deCarvalho, M. G. S., McCormack, A. L., Olson, E., Ghomashchi, F., Gelb, M. H., Yates, J. R., Leslie, C. C. Identification of phosphorylation sites of human 85-kDa cytosolic phospholipase A(2) expressed in insect cells and present in human monocytes Journal of Biological Chemistry  1996 271:6987-6997  PMID:8636128
  • Jonscher, K. R., Yates, J. R. Mixture analysis using a quadrupole mass filter quadrupole ion trap mass spectrometer Analytical Chemistry  1996 68:659-667  DOI:10.1021/ac950978s  PMID:8999740
  • McCormack, A. L., Eng, J. K., DeRoos, P. C., Rudensky, A. Y., Yates III, J. R. Microcolumn liquid chromatography electrospray ionization tandem mass spectrometry. Analysis of immunological samples ACS Symposium Series  1996 619:207-225  DOI:10.1021/bk-1995-0619.ch010
  • Eng, J. K., Yates III, J. R. Protein database searching with MS(n) spectra of polypeptides Proceedings of the Society of Photo-Optical Instrumentation Engineers  1996 2680:378-382  DOI:10.1117/12.237626
  • Yates, J. R. Protein structure analysis by mass spectrometry Methods in Enzymology  1996 271:351-377  DOI:10.1016/S0076-6879(96)71017-0  PMID:8782561
  • Yates, J. R., Eng, J. K., McCormack, A. L. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases Analytical Chemistry  1995 67:3202-3210  DOI:10.1021/ac00114a016  PMID:8686885
  • Yates, J. R., Eng, J. K., McCormack, A. L., Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database Analytical Chemistry  1995 67:1426-1436  DOI:10.1021/ac00104a020  PMID:7741214
  • McCormack, A. L., Mononen, I., Kaartinen, V., Yates, J. R. Localization of the disulfide bond involved in post-translational processing of glycosylasparaginase and disrupted by a mutation in the Finnish-type aspartylglycosaminuria Journal of Biological Chemistry  1995 270:3212-3215  PMID:7852406
  • Griffin, P. R., MacCoss, M. J., Eng, J. K., Blevins, R. A., Aaronson, J. S., Yates, J. R. Direct database searching with MALDI-PSD spectra of peptides Rapid Communications in Mass Spectrometry  1995 9:1546-1551  DOI:10.1002/rcm.1290091515  PMID:8652878
  • Monji, T., McCormack, A. L., Yates, J. R., Pious, D. Invariant-cognate peptide exchange restores class II dimer stability in HLA-DM mutants Journal of Immunology  1994 153:4468-4477  PMID:7525705
  • Eng, J. K., McCormack, A. L., Yates, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database Journal of the American Society for Mass Spectrometry  1994 5:976-989  DOI:10.1016/1044-0305(94)80016-2  PMID:24226387
  • McCormack, A. L., Eng, J. K., Yates, J. R. Peptide sequence analysis on quadrupole mass spectrometers Methods-A Companion to Methods in Enzymology  1994 6:274-283  DOI:10.1006/meth.1994.1029
  • Currie, G. J., Yates, J. R. Analysis of oligodeoxynucleotides by negative-ion matrix-assisted laser-desorption mass spectrometry Journal of the American Society for Mass Spectrometry  1993 4:955-963  DOI:10.1016/1044-0305(93)80022-q  PMID:24227604
  • Yates, J. R., Speicher, S., Griffin, P. R., Hunkapiller, T. Peptide mass maps: a highly informative approach to protein identification Analytical Biochemistry  1993 214:397-408  DOI:10.1006/abio.1993.1514  PMID:8109726
  • Jonscher, K., Currie, G., McCormack, A. L., Yates, J. R. Matrix-assisted laser desorption of peptides and proteins on a quadrupole ion trap mass spectrometer Rapid Communications in Mass Spectrometry  1993 7:20-26  DOI:10.1002/rcm.1290070106  PMID:8428025
  • Petra, P. H., Griffin, P. R., Yates, J. R., Moore, K., Zhang, W. Complete enzymatic deglycosylation of native sex steroid-binding protein (SBP or SHBG) of human and rabbit plasma: effect on the steroid-binding activity Protein Science  1992 1:902-909  DOI:10.1002/pro.5560010708  PMID:1304375  PMCID:PMC2142156
  • Burdick, D., Soreghan, B., Kwon, M., Kosmoski, J., Knauer, M., Henschen, A., Yates, J., Cotman, C., Glabe, C. Assembly and aggregation properties of synthetic Alzheimer's A4/beta amyloid peptide analogs Journal of Biological Chemistry  1992 267:546-554  PMID:1730616
  • Griffin, P. R., Coffman, J. A., Hood, L. E., Yates, J. R. Structural analysis of proteins by capillary HPLC electrospray tandem mass spectrometry International Journal of Mass Spectrometry and Ion Processes  1991 111:131-149  DOI:10.1016/0168-1176(91)85052-n
  • Mononen, I., Heisterkamp, N., Kaartinen, V., Williams, J. C., Yates, J. R., Griffin, P. R., Hood, L. E., Groffen, J. Aspartylglycosaminuria in the Finnish population: identification of two point mutations in the heavy chain of glycoasparaginase Proceedings of the National Academy of Sciences of the United States of America  1991 88:2941-2945  DOI:10.1073/pnas.88.7.2941  PMID:2011603
  • Kaartinen, V., Williams, J. C., Tomich, J., Yates III, J. R., Hood, L. E., Mononen, I. Glycosaparaginase from human leukocytes. Inactivation and covalent modification with diazo-oxonorvaline Journal of Biological Chemistry  1991 266:5860-5869  PMID:2005122
  • Aird, S. D., Yates, J. R., Martino, P. A., Shabanowitz, J., Hunt, D. F., Kaiser, II The amino acid sequence of the acidic subunit B-chain of crotoxin Biochimica et Biophysica Acta  1990 1040:217-224  DOI:10.1016/0167-4838(90)90079-u  PMID:2400773
  • Osawa, Y., Martin, B. M., Griffin, P. R., Yates, J. R., Shabanowitz, J., Hunt, D. F., Murphy, A. C., Chen, L., Cotter, R. J., Pohl, L. R. Metabolism-based covalent bonding of the heme prosthetic group to its apoprotein during the reductive debromination of BrCCl3 by myoglobin Journal of Biological Chemistry  1990 265:10340-10346  PMID:2355004
  • Bieber, A. L., Becker, R. R., McParland, R., Hunt, D. F., Shabanowitz, J., Yates, J. R., Martino, P. A., Johnson, G. R. The complete sequence of the acidic subunit from Mojave toxin determined by Edman degradation and mass spectrometry Biochimica et Biophysica Acta  1990 1037:413-421  DOI:10.1016/0167-4838(90)90045-h  PMID:2310754
  • Hung, D. F., Shabanowitz, J., Yates, J. R., Griffin, P. R., Zhu, N. Z. Protein sequence analysis by tandem mass spectrometry Practical Spectroscopy  1990 8:169-195
  • Moore, C. R., Yates, J. R., Griffin, P. R., Shabanowitz, J., Martino, P. A., Hunt, D. F., Cafiso, D. S. Proteolytic fragments of the nicotinic acetylcholine receptor identified by mass spectrometry: implications for receptor topography Biochemistry  1989 28:9184-9191  DOI:10.1021/bi00449a034  PMID:2605252
  • Hunt, D. F., Shabanowitz, J., Yates, J. R., Griffin, P. R., Zhu, N. Z. Tandem quadrupole Fourier transform mass spectrometry Analytica Chimica Acta  1989 225:1-10  DOI:10.1016/s0003-2670(00)84589-4
  • Krishnamurthy, T., Szafraniec, L., Hunt, D. F., Shabanowitz, J., Yates, J. R., Hauer, C. R., Carmichael, W. W., Skulberg, O., Codd, G. A., Missler, S. Structural characterization of toxic cyclic peptides from blue-green algae by tandem mass spectrometry Proceedings of the National Academy of Sciences of the United States of America  1989 86:770-774  DOI:10.1073/pnas.86.3.770  PMID:2492662  PMCID:PMC286558
  • Hunt, D. F., Yates, J. R., Shabanowitz, J., Bruns, M. E., Bruns, D. E. Amino acid sequence analysis of two mouse calbindin-D9k isoforms by tandem mass spectrometry. Protein modification by internal insertion of a single amino acid Journal of Biological Chemistry  1989 264:6580-6586  PMID:2703505
  • Cooper, H. M., Jemmerson, R., Hunt, D. F., Griffin, P. R., Yates, J. R., Shabanowitz, J., Zhu, N. Z., Paterson, Y. Site-directed chemical modification of horse cytochrome c results in changes in antigenicity due to local and long-range conformational perturbations Journal of Biological Chemistry  1987 262:11591-11597  PMID:2442150
  • Hunt, D. F., Yates, J. R., Shabanowitz, J., Zhu, N. Z., Zirino, T., Averill, B. A., Dauratlarroque, S. T., Roberts, R. M., Shewale, J. G., Brew, K. Sequence homology in the metalloproteins: purple acid phosphatase from beef spleen and uteroferrin from porcine uterus Biochemical and Biophysical Research Communications  1987 144:1154-1160  DOI:10.1016/0006-291x(87)91432-x  PMID:3579955