- Academic article
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- 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
- 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
- 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
- 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
- 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
- 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 polypeptidesAnalytical Chemistry 2016 88:3967-3975 DOI:10.1021/acs.analchem.6b00191 PMID:27010111 PMCID:PMC4939623
- 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
- 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
- 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
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- 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 201615:431-446 DOI:10.1021/acs.jproteome.5b00729 PMID:26667653 PMCID:PMC4861152
- 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
- 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
- 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 2016213:201-211 DOI:10.1083/jcb.201411076 PMID:27091448
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- 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
- Yates III, J. Trends in separation science: tackling protein analysis LC-GC North America 201634:422-423
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- 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
- 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
- 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 2015160:407-419 DOI:10.1016/j.cell.2015.01.010 PMID:25635455 PMCID:PMC4318647
- 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
- 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
- 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
- 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
- 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
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- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Fonslow, B. R., Stein, B. D., Webb, K. J., Xu, T., Choi, J., Park, S. K., Yates III, J. R. Addendum: Digestion and depletion of abundant proteins improves proteomic coverage Nature Methods 2014 11:347-348 DOI:10.1038/nmeth0314-347 PMID:24724171
- 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., et al. 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
- 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
- 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 201428:2370-2380 DOI:10.1101/gad.250993.114 PMID:25301780 PMCID:PMC4215182
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 2014346:360-363 DOI:10.1126/science.1253168 PMID:25324391 PMCID:PMC4403873
- 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
- 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
- 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
- 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
- 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
- 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., et al. Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex Genetics 2014198:1483-1493 DOI:10.1534/genetics.114.167775 PMID:25230952 PMCID:PMC4256767
- 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
- 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., et al. Lysine ubiquitination and acetylation of human cardiac 20S proteasomes Proteomics Clinical Applications 2014 8:590-594 DOI:10.1002/prca.201400029 PMID:24957502
- 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
- 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
- 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 201413:5496-5509 DOI:10.1021/pr500473n PMID:25177766 PMCID:PMC4258137
- 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
- Yates III, J. R., Mohammed, S., Heck, A. J. R. Phosphoproteomics Analytical Chemistry 2014 86:1313 DOI:10.1021/ac404019p PMID:24422449
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., et al. 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
- 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 2013155:1532-1544 DOI:10.1016/j.cell.2013.11.032 PMID:24360276 PMCID:PMC3924572
- 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
- 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
- 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
- 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
- Fonslow, B. R., Stein, B. D., Webb, K. J., Xu, T., Choi, J., Park, S. K., Yates, 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
- 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 201324:1690-1699 DOI:10.1007/s13361-013-0709-7 PMID:23963813 PMCID:PMC3815594
- 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 201327:1886-1902 DOI:10.1101/gad.221010.113 PMID:24013502 PMCID:PMC3778242
- 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
- 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
- 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
- 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
- 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 2013110:E726-E735 DOI:10.1073/pnas.1300424110 PMID:23382246 PMCID:PMC3581967
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Yates, J. R., Washburn, M. P. Quantitative proteomics Analytical Chemistry 2013 85:8881 DOI:10.1021/ac402745w PMID:24079386
- 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 201326:315-323 DOI:10.1016/j.devcel.2013.06.016 PMID:23911198 PMCID:PMC3745822
- 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
- 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
- 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 2013110:11857-11862 DOI:10.1073/pnas.1302918110 PMID:23818590 PMCID:PMC3718112
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Yates III, J. R., Kelleher, N. L. Top down proteomics Analytical Chemistry 2013 85:6151 DOI:10.1021/ac401484r PMID:23705843 PMCID:PMC4418644
- 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
- 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
- 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
- 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 201327:2473-2488 DOI:10.1101/gad.229062.113 PMID:24240237 PMCID:PMC3841736
- 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
- 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
- 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
- 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
- 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
- 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 201211:3199-3210 DOI:10.1021/pr2012347 PMID:22563702 PMCID:PMC3562392
- 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
- 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
- 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., et al. 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., et al. Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production Molecular & Cellular Proteomics 201211:M111.015313 DOI:10.1074/mcp.M111.015313 PMID:22174317 PMCID:PMC3322577
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., et al. 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
- 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
- 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 20128:e1002817 DOI:10.1371/journal.pgen.1002817 PMID:22792081 PMCID:PMC3390401
- 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
- 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
- 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 2012287:21599-21614 DOI:10.1074/jbc.M112.359307 PMID:22556411 PMCID:PMC3381125
- 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
- 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 201212:3113-3120 DOI:10.1002/pmic.201200208 PMID:22888089 PMCID:PMC3806318
- 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
- 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., et al. 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
- 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
- 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
- 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. (127834) Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT Journal of Proteome Research 201211:2697-2709 DOI:10.1021/pr300200x PMID:22509746 PMCID:PMC3365658
- 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
- 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
- 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
- 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. (122384), 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 (127834), Parmer, R. J., et al. 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
- Yates, J. R. (127834), 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., et al. 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
- 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
- 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
- Yates, J. R. A century of mass spectrometry: from atoms to proteomes Nature Methods 2011 8:633-637 DOI:10.1038/nmeth.1659
- 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 2011145:596-606 DOI:10.1016/j.cell.2011.04.013 PMID:21565616 PMCID:PMC3129781
- 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
- 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
- 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
- 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
- Petsko, G. A., Yates III, J. R. Analyzing molecular interactions Current Protocols in Bioinformatics 201136:8.1.1-8.1.4 DOI:10.1002/0471250953.bi0801s36 PMID:22161570 PMCID:PMC3486783
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 2011108:13247-13252 DOI:10.1073/pnas.1110486108 PMID:21788516 PMCID:PMC3156164
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Witte, K., Schuh, A. L., Hegermann, J., Sarkeshik, A., Mayers, J. R., Schwarze, K., Yates, J. R., Eimer, S., Audhya, A. 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Park, S. K., Yates III, J. R. Census for proteome quantification Current Protocols in Bioinformatics 201029:13.12.1-13.12. DOI:10.1002/0471250953.bi1312s29 PMID:20205189
- Roberts-Galbraith, R. H., Ohi, M. D., Ballif, B. A., Chen, J. S., 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
- 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
- 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
- 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
- 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 2010285:1909-1918 DOI:10.1074/jbc.M109.058487 PMID:19910462 PMCID:PMC2804349
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., et al. 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
- 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., et al. 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
- 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
- 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., et al. 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
- 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
- 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
- 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
- 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 2010107:9078-9082 DOI:10.1073/pnas.1000148107 PMID:20439767 PMCID:PMC2889096
- 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
- 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
- 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
- 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 201046:1522-1532 DOI:10.1016/j.bone.2010.02.013 PMID:20167300
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 20099:1142-1151 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
- 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
- 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
- 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., 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
- 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
- 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
- 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
- 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
- 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 2009420:169-177 DOI:10.1042/bj20081659 PMID:19243310 PMCID:PMC2950653
- 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
- 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 200964:799-806 DOI:10.1016/j.neuron.2009.12.019 PMID:20064388 PMCID:PMC2829666
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- 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
- 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
- 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
- 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., et al. Motor-independent targeting of CLASPs to kinetochores by CENP-E promotes microtubule turnover and poleward flux Current Biology 200919:1566-1572 DOI:10.1016/j.cub.2009.07.059 PMID:19733075 PMCID:PMC2766669
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., et al. Proteomic analysis of mitochondria from Caenorhabditis elegans Proteomics 20099:4539-4553 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
- 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
- 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 20098:5093-5102 DOI:10.1021/pr900478h PMID:19764810 PMCID:PMC2834885
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- 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 20095:319 DOI:10.1038/msb.2009.67 PMID:19888214 PMCID:PMC2795470
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 2009106:13323-13328 DOI:10.1073/pnas.0905387106 PMID:19666612 PMCID:PMC2726359
- 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
- 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
- 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
- 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
- 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
- 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
- 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
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- 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
- 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
- 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
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- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 2008183:835-848 DOI:10.1083/jcb.200807046 PMID:19029337 PMCID:PMC2592839
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Motoyama, A., Yates, J. R. Multidimensional lc separations in shotgun proteomics Analytical Chemistry 2008 80:7187-7193 DOI:10.1021/ac8013669 PMID:18826178
- 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
- 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
- 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
- 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
- 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
- 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, 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- McClatchy, D. B., Yates III, J. R. Stable Isotope Labeling of Mammals (SILAM) CSH Protocols 2008 2008 DOI:10.1101/pdb.prot4940 PMID:21356771
- 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
- 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
- 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
- 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., et al. 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 200779:3623-3634 DOI:10.1021/ac062292d PMID:17411013 PMCID:PMC2538959
- 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
- 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
- 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
- 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., Yates, J. R. Cancer proteomics by quantitative shotgun proteomics Molecular Oncology 20071:144-159 DOI:10.1016/j.molonc.2007.05.001 PMID:18443658 PMCID:PMC2352161
- 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
- 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
- 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
- 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., et al. 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Yates III, J. R., Osterman, A. L. Introduction: Advances in genomics and proteomics Chemical Reviews 2007 107:3363-3366 DOI:10.1021/cr068201u
- 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
- 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
- Delahunty, C. M., Yates, J. R. MudPIT: multidimensional protein identification technology Biotechniques 2007 43:563
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- 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
- 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., 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
- 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
- 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
- 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
- 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
- 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 2007155:84-93 DOI:10.1016/j.molbiopara.2007.06.002 PMID:17644200 PMCID:PMC2077830
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 2007128:115-127 DOI:10.1016/j.cell.2006.10.050 PMID:17218259 PMCID:PMC2987564
- Cravatt, B. F., Simon, G. M., Yates, J. R. The biological impact of mass-spectrometry-based proteomics Nature 2007 450:991-1000 DOI:10.1038/nature06525 PMID:18075578
- 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
- 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., et al. The minimum information about a proteomics experiment (MIAPE) Nature Biotechnology 2007 25:887-893 DOI:10.1038/nbt1329 PMID:17687369
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 2006172:67-78 DOI:10.1083/jcb.200508096 PMID:16390998 PMCID:PMC2063535
- 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
- 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., et al. 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
- 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
- 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., et al. 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., 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 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
- 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 2006281:27973-27981 DOI:10.1074/jbc.M601943200 PMID:16880212
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Yates, J. R. The power of mass spectrometry in biological discovery Biotechniques 2006 40:779 DOI:10.2144/000112199
- 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 2006172:55-66 DOI:10.1083/jcb.200510016 PMID:16390997 PMCID:PMC2063532
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 2005280:40169-40176 DOI:10.1074/jbc.M509631200 PMID:16203726
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 200577:7646-7653 DOI:10.1021/ac0508393 PMID:16316172
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Yates, J. Proteomics power to the people! Scientist 2005 19:30-31
- 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
- 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
- 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
- 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
- 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
- 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 2005169:49-60 DOI:10.1083/jcb.200411118 PMID:15824131 PMCID:PMC1351127
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 2004101:13756-13761 DOI:10.1073/pnas.0404727101 PMID:15356343 PMCID:PMC518829
- 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
- 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
- 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
- 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
- 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
- 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
- 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., et al. 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
- 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
- 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
- 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., et al. 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
- 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
- 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
- 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
- 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
- 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
- Yates, J. R. Mass spectrometry as an emerging tool for systems biology Biotechniques 2004 36:917-919 DOI:10.2144/3606A0917 PMID:15211739
- 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
- 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
- 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
- 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
- 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 2004279:22331-22346 DOI:10.1074/jbc.M400285200 PMID:15024025
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., et al. 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
- 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 200452:107-118 DOI:10.1111/j.1365-2958.2003.03969.x PMID:15049814
- 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
- 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
- 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
- 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
- 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 200317:67-78 DOI:10.1210/me.2002-0280 PMID:12511607
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Schirmer, E. C., Yates, J. R., Gerace, L. MudPIT: a powerful proteomics tool for discovery Discovery Medicine 2003 3:38-39 PMID:20704860
- 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
- 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
- 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 2003100:3107-3112 DOI:10.1073/pnas.0634629100 PMID:12626741 PMCID:PMC152254
- 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
- Wohlschlegel, J. A., Yates, J. R. Proteomics: where’s Waldo in yeast? Nature 2003 425:671-672 DOI:10.1038/425671a PMID:14562083
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 200314:1204-1220 DOI:10.1091/mbc.E02-09-0609 PMID:12631735 PMCID:PMC151591
- 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., et al. Utilization of genomic sequence information to develop malaria vaccines Journal of Experimental Biology 2003 206:3789-3802 DOI:10.1242/jeb.00615 PMID:14506214
- 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
- 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
- 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
- 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
- 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 20021:3-10 DOI:10.1074/mcp.R100001-MCP200 PMID:12096135
- 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 20021:211-215 DOI:10.1021/pr015514r PMID:12645897
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Zhu, W., Yates III, J. R. Proteome analysis of microbes: to gel or not to gel Applied Genomics and Proteomics 2002 1:3-12
- 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
- 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
- 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., et al. 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
- 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
- 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., et al. 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
- 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
- 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
- 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 2002219:233-244 DOI:10.1016/s1387-3806(02)00660-7
- 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
- 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., et al. 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., 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
- 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
- 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
- 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
- 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., et al. 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
- 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
- Washburn, M. P., Yates, J. R. Analysis of the microbial proteome Current Opinion in Microbiology 20003:292-297 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, 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
- 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
- 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 200019:95-117
- 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
- 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
- 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
- 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 200021:3470-3482 DOI:10.1002/1522-2683(20001001)21:16<3470::aid-elps3470>3.3.co;2-7 PMID:11079566
- 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
- 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
- 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 1999112:553-569 PMID:10027276
- 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
- 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
- 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 1999268:229-237 DOI:10.1006/abio.1998.3069 PMID:10075812
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Dongre, A. R., Eng, J. K., Yates, J. R. Tandem mass spectrometry Biofutur 1998
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Yates, J. R., McCormack, A. L., Eng, J. Mining genomes with MS Analytical Chemistry 1996 68:534A-540A DOI:10.1021/ac962050l PMID:8794913
- 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
- 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
- Figeys, D., Ducret, A., Yates, J. R., Aebersold, R. Protein identification by solid phase microextraction-capillary zone electrophoresis-microelectrospray-tandem mass spectrometry Nature Biotechnology 199614:1579-1583 DOI:10.1038/nbt1196-1579 PMID:9634825
- 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., 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 19937:20-26 DOI:10.1002/rcm.1290070106 PMID:8428025
- 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
- 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
- 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 PMID:1304375 PMCID:PMC2142156
- 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:1737774
- 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
- 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
- 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 1990265:10340-10346 PMID:2355004
- 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
- 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
- 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
- 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
- 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
- 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., 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
- Hunt, D. F., Shabanowitz, J., Yates, J. R. Peptide sequence analysis by laser photodissociation Fourier-transform mass spectrometry Journal of the Chemical Society-Chemical Communications 1987 548-550 DOI:10.1039/c39870000548
- Hunt, D. F., Yates III, J. R., Shabanowitz, J. Protein sequencing by tandem mass spectrometry Experimental Biology and Medicine 1987 14:149-153 DOI:10.1007/978-1-59259-480-1_10
- 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
- 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., Shabanowitz, J., Yates, J. R., Zhu, N. Z., Russell, D. H., Castro, M. E. Tandem quadrupole Fourier-transform mass spectrometry of oligopeptides and small proteins Proceedings of the National Academy of Sciences of the United States of America 1987 84:620-623 DOI:10.1073/pnas.84.3.620 PMID:3468502 PMCID:PMC304265
- Hunt, D. F., Yates, J. R., Shabanowitz, J., Winston, S., Hauer, C. R. Protein sequencing by tandem mass spectrometry Proceedings of the National Academy of Sciences of the United States of America 198683:6233-6237 DOI:10.1073/pnas.83.17.6233 PMID:3462691 PMCID:PMC386476
- Yates, J. R., Anderegg, R. J. Mixed gas chemical ionization mass spectrometry of peptide derivatives Biomedical Mass Spectrometry 1983 10:567-571 DOI:10.1002/bms.1200101007
- Thesis
