{"id":1225,"date":"2023-10-10T15:10:23","date_gmt":"2023-10-10T22:10:23","guid":{"rendered":"https:\/\/villenlab.gs.washington.edu\/wordpress\/?page_id=1225"},"modified":"2023-11-26T20:39:24","modified_gmt":"2023-11-27T04:39:24","slug":"publications","status":"publish","type":"page","link":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n
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Publications<\/p>\n<\/div><\/div>\n<\/div><\/div><\/div>\n<\/div><\/div>\n\n\n\n

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Our Lab<\/a><\/div>\n<\/div>\n<\/div><\/div>\n\n\n\n
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Our Lab<\/h2>\n<\/div><\/div>\n<\/div><\/div><\/div>\n\n\n\n
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Mario\u00a0Leutert,\u00a0Anthony S.\u00a0Barente,\u00a0Noelle K.\u00a0Fukuda,\u00a0Ricard A.\u00a0Rodriguez-Mias, Judit\u00a0Vill\u00e9n<\/strong>. The regulatory landscape of the yeast phosphoproteome. Nat Struct Mol Biol 2023 30(11):1761-1773<\/strong>; \u00a0doi:\u00a010.1038\/s41594-023-01115-3<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Ecaterina Cozma, Megha Rao, Madison Dusick, Julie Genereaux, Ricard A. Rodriguez-Mias, Judit Vill\u00e9n,<\/strong> Christopher J. Brandl, Matthew D. Berg<\/strong>. Anticodon sequence determines the impact of mistranslating tRNAAla variants. bioRxiv 2022.11.23.517754<\/strong>; doi: 10.1101\/2022.11.23.517754<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Alexis Chang, Mario Leutert, Ricard A. Rodriguez-Mias,\u00a0 Judit Vill\u00e9n. <\/strong>Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. Journal of Proteome Research 2023 22<\/em> (6)<\/strong>, 1868-1880. doi: 10.1021\/acs.jproteome.2c00850<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Ricard A. Rodriguez-Mias, Kyle N. Hess, Bianca Y. Ruiz, Ian R. Smith, Anthony S. Barente<\/strong>, Stephanie M. Zimmerman, Yang Y. Lu, William S. Noble, Stanley Fields, Judit Vill\u00e9n<\/strong>. Proteome-wide identification of amino acid substitutions deleterious for protein function. bioRxiv 2022.04.06.487405<\/strong>; doi: 10.1101\/2022.04.06.487405<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Smith IR, Eng JK, Barente AS, Hogrebe A, Llovet A, Rodriguez-Mias RA, Vill\u00e9n J.<\/strong> Coisolation of Peptide Pairs for Peptide Identification and MS\/MS-Based Quantification. Anal Chem. 2022 <\/strong>Nov 8;94(44):15198-15206. doi: 10.1021\/acs.analchem.2c01711<\/a>.<\/p>\n<\/div><\/div>\n\n\n\n

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Smith IR, Hess KN, Bakhtina AA, Valente AS, Rodr\u00edguez-Mias RA, Vill\u00e9n J. <\/strong>Identification of phosphosites that alter protein thermal stability. Nat Methods. 2021<\/strong> Jul;18(7):760-762. doi: 10.1038\/s41592-021-01178-4<\/a>.<\/p>\n<\/div><\/div>\n\n\n\n

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Hogrebe A, Hess KN, Llovet A, Ramos YJ, Barente AS, Hernandez-Portugues D, Smith IR, Rodr\u00edguez-Mias RA, Vill\u00e9n J. <\/strong>IsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides. Proteomics. 2022<\/strong>\u00a0Oct;22(19-20):e2100253. doi: 10.1002\/pmic.202100253<\/a>.\u00a0<\/p>\n<\/div><\/div>\n\n\n\n

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Leutert M, Entwisle SW, Vill\u00e9n J.<\/strong> Decoding Post-Translational Modification Crosstalk With Proteomics. Mol Cell Proteomics. 2021<\/strong>;20:100129. doi: 10.1016\/j.mcpro.2021.100129. <\/a> <\/p>\n<\/div><\/div>\n\n\n\n

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Martin-Perez M<\/strong>, <\/strong>Grillo AS, Ito TK, Valente AS<\/strong>, Han J, Entwisle SW<\/strong>, Huang HZ, Kim D, Yajima M, Kaeberlein M, Vill\u00e9n J.<\/strong> PKC downregulation upon rapamycin treatment attenuates mitochondrial disease. Nat Metab. 2020<\/strong> Dec;2(12):1472-1481. doi: 10.1038\/s42255-020-00319-x. <\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Leutert M, Rodr\u00edguez-Mias RA, Fukuda NK, Vill\u00e9n J.<\/strong> R2-P2 rapid-robotic phosphoproteomics enables multidimensional cell signaling studies. Mol Syst Biol. 2019<\/strong> Dec;15(12):e9021. doi: 10.15252\/msb.20199021.<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Entwisle SW<\/strong>, Martinez Calejman C, Valente AS<\/strong>, Lawrence RT<\/strong>, Hung CM, Guertin DA, Vill\u00e9n J<\/strong>. Proteome and Phosphoproteome Analysis of Brown Adipocytes Reveals That RICTOR Loss Dampens Global Insulin\/AKT Signaling. Mol Cell Proteomics. 2020 Jul;19(7):1104-1119. doi: 10.1074\/mcp.RA120.001946<\/a>.<\/p>\n<\/div><\/div>\n\n\n\n

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Entwisle SW<\/strong>, Sanchez-Gurmaches J, Lawrence RT<\/strong>, Pedersen DJ, Jung SM, Martin-Perez M<\/strong>, Guilherme A, Czech MP , Guertin DA, Villen J<\/strong>. Cold-Induced Thermogenesis Increases Acetylation on the Brown Fat Proteome and Metabolome. bioRxiv<\/strong> 445718; doi: 10.1101\/445718<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Searle BC, Lawrence RT<\/strong>, MacCoss MJ, Vill\u00e9n J<\/strong>. (2019) Thesaurus: quantifying phosphopeptide positional isomers. Nat Methods<\/strong>. 16(8):703-706. doi: 10.1038\/s41592-019-0498-4<\/a>. <\/p>\n<\/div><\/div>\n\n\n\n

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Martin-Perez M<\/strong> and\u00a0Vill\u00e9n J.\u00a0<\/strong>(2017) Determinants and Regulation of Protein Turnover in Yeast.\u00a0Cell Systems<\/strong>. Cell Systems 5, 283\u2013294. doi:\u00a010.1016\/j.cels.2017.08.008<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Lawrence RT, Searle BC, Llovet A and Vill\u00e9n J. <\/strong>Plug and play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry. Nature Methods<\/strong> (2016) Mar 28. doi: 0.1038\/nmeth.3811.<\/p>\n<\/div><\/div>\n\n\n\n

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Swaney DL, Rodr\u00edguez-Mias RA, Vill\u00e9n J.<\/strong> (2015). Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. EMBO Rep.<\/strong> 16,1131\u20131144.<\/p>\n<\/div><\/div>\n\n\n\n

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Martin-Perez, M., and Villen, J.<\/strong> (2015). Feasibility of protein turnover studies in prototroph S. cerevisiae strains. Anal. Chem.<\/strong> 87, 4008\u20134014.<\/p>\n<\/div><\/div>\n\n\n\n

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Lawrence RT, Perez EM, Hern\u00e1ndez D<\/strong>, Miller CP, Haas KM<\/strong>, Irie HY, Lee SI, Blau CA, Vill\u00e9n J.<\/strong> (2015). The proteomic landscape of triple-negative breast cancer. Cell Rep.<\/strong> 11, 630\u2013644.<\/p>\n<\/div><\/div>\n\n\n\n

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Edelman, W.C., Haas, K.M., Hsu, J.I., Lawrence, R.T., and Villen, J.<\/strong> (2014). A practical recipe to survey phosphoproteomes. Methods Mol. Biol.<\/strong> 1156, 389\u2013405.<\/p>\n<\/div><\/div>\n\n\n\n

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Lawrence, R.T., and Villen, J.<\/strong> (2014). Drafts of the human proteome. Nat. Biotechnol. <\/strong>32, 752\u2013753.<\/p>\n<\/div><\/div>\n\n\n\n

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Swaney, D.L.<\/strong>, Beltrao, P., Starita, L., Guo, A., Rush, J., Fields, S., Krogan, N.J., and Villen, J.<\/strong> (2013). Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nature Methods<\/strong> 10, 676\u2013682. PDF Supplementary_info RAW data<\/a><\/p>\n<\/div><\/div>\n<\/div><\/div>\n\n\n\n

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Collaborations<\/h2>\n\n\n\n
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Berg MD<\/strong>, Zhu Y, Loll-Krippleber R, San Luis BJ, Genereaux J, Boone C, Vill\u00e9n J<\/strong>, Brown GW, Brandl CJ. Genetic background and mistranslation frequency determine the impact of mistranslating tRNASerUGG. G3 (Bethesda). 2022<\/strong> Jul 6;12(7):jkac125. doi: 10.1093\/g3journal\/jkac125. <\/p>\n<\/div><\/div>\n\n\n\n

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Isaacson JR, Berg MD<\/strong>, Charles B, Jagiello J, Vill\u00e9n J<\/strong>, Brandl CJ, Moehring AJ. A novel mistranslating tRNA model in Drosophila melanogaster has diverse, sexually dimorphic effects. G3 (Bethesda). 2022 <\/strong>May 6;12(5):jkac035. doi: 10.1093\/g3journal\/jkac035.<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Berg MD<\/strong>, Isaacson JR, Cozma E, Genereaux J, Lajoie P, Vill\u00e9n J<\/strong>, Brandl CJ. Regulating Expression of Mistranslating tRNAs by Readthrough RNA Polymerase II Transcription. ACS Synth Biol. 2021<\/strong> Nov 19;10(11):3177-3189. doi: 10.1021\/acssynbio.1c00461<\/a>.<\/p>\n<\/div><\/div>\n\n\n\n

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Berg MD<\/strong>, Zhu Y, Ruiz BY, Loll-Krippleber R, Isaacson J, San Luis BJ, Genereaux J, Boone C, Vill\u00e9n J<\/strong>, Brown GW, Brandl CJ. The amino acid substitution affects cellular response to mistranslation. G3 (Bethesda). 2021 <\/strong>Sep 27;11(10):jkab218. doi: 10.1093\/g3journal\/jkab218.<\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Vidal-Dom\u00e8nech F, Riquelme G, Pinacho R, Rodriguez-Mias R<\/strong>, Vera A, Monje A, Ferrer I, Callado LF, Meana JJ, Vill\u00e9n J<\/strong>, Ramos B. Calcium-binding proteins are altered in the cerebellum in schizophrenia. PLoS One. 2020 Jul 8;15(7):e0230400. doi: 10.1371\/journal.pone.0230400<\/a>.<\/p>\n<\/div><\/div>\n\n\n\n

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Martinez Calejman C, Trefely S, Entwisle SW<\/strong>, Luciano A, Jung SM, Hsiao W, Torres A, Hung CM, Li H, Snyder NW, Vill\u00e9n J<\/strong>, Wellen KE, Guertin DA. mTORC2-AKT signaling to ATP-citrate lyase drives brown adipogenesis and de novo lipogenesis. Nat Commun. 2020<\/strong> Jan 29;11(1):575. doi: 10.1038\/s41467-020-14430-w. <\/a><\/p>\n<\/div><\/div>\n\n\n\n

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Berg MD, Zhu Y, Genereaux J, Ruiz BY<\/strong>, Rodriguez-Mias RA<\/strong>, Allan T, Bahcheli A, Vill\u00e9n J<\/strong>, Brandl CJ. (2019). Modulating mistranslation potential of tRNASer<\/sup> in Saccharomyces cerevisiae. <\/em>GENETICS<\/strong> 213(3):849-863.<\/p>\n<\/div><\/div>\n\n\n\n

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Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT<\/strong>, MacLean BX, Vill\u00e9n J<\/strong>, MacCoss MJ. Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nat Commun. 2018<\/strong> Dec 3;9(1):5128. doi: 10.1038\/s41467-018-07454-w.<\/a> <\/p>\n<\/div><\/div>\n\n\n\n

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Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI<\/strong>, Vi\u00e9itez C, Sol\u00e9 C, Swaney DL, Stanford LB<\/strong>, Liachko I, B\u00f6ttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Vill\u00e9n J<\/strong>. Evolution of protein phosphorylation across 18 fungal species. Science<\/strong> 2016 Oct 14;354(6309):229-232.<\/p>\n<\/div><\/div>\n\n\n\n

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Pruneda, J.N., Smith, F.D., Daurie, A., Swaney, D.L., Villen, J<\/strong>., Scott, J.D., Stadnyk, A.W., Le Trong, I., Stenkamp, R.E., Klevit, R.E., et al. (2014). E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis. EMBO J<\/strong>. 33, 437\u2013449.<\/p>\n<\/div><\/div>\n\n\n\n

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Eaton, J.M., Takkellapati, S., Lawrence, R.T<\/strong>., McQueeney, K.E., Boroda, S., Mullins, G.R., Sherwood, S.G., Finck, B.N., Villen, J.<\/strong>, and Harris, T.E. (2014). Lipin 2 binds phosphatidic acid by the electrostatic-hydrogen bond switch mechanism independent of phosphorylation. J. Biol. Chem. <\/strong>289, 18055-66<\/p>\n<\/div><\/div>\n\n\n\n

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Chow, J.D.Y., Lawrence, R.T.*<\/strong>, Healy, M.E., Dominy, J.E., Liao, J.A., Breen, D.S., Byrne, F.L., Kenwood, B.M., Lackner, C., Okutsu, S., Mas, V.R., Caldwell, S.H., Tomsig, J.L., Cooney, G.J., Puigserver, P.B., Turner, N., James, D.E., Vill\u00e9n, J.#<\/strong>, and Hoehn, K.L.# (2014). Genetic inhibition of hepatic acetyl-CoA carboxylase activity increases liver fat and alters global protein acetylation. Mol. Metab.<\/strong> 3, 419\u2013431. (*equal contribution; #co-corresponding)<\/p>\n<\/div><\/div>\n\n\n\n

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Eichhorn, S.W., Guo, H., McGeary, S.E., Rodr\u00edguez-Mias, R.A.<\/strong>, Shin, C., Baek, D., Hsu, S.-H., Ghoshal, K., Villen, J<\/strong>., and Bartel, D.P. (2014). mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol. Cell<\/strong> 56, 104\u2013115.<\/p>\n<\/div><\/div>\n\n\n\n

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Beltrao, P., Alban\u00e8se, V., Kenner, L.R., Swaney, D.L.<\/strong>, Burlingame, A., Villen, J.<\/strong>, Lim, W.A., Fraser, J.S., Frydman, J., and Krogan, N.J. (2012). Systematic functional prioritization of protein posttranslational modifications. Cell<\/strong> 150, 413\u2013425.<\/p>\n<\/div><\/div>\n\n\n\n

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Ranjitkar, P., Perera, B.G.K., Swaney, D.L.<\/strong>, Hari, S.B., Larson, E.T., Krishnamurty, R., Merritt, E.A., Villen, J.<\/strong>, and Maly, D.J. (2012). Affinity-based probes based on type II kinase inhibitors. J. Am. Chem. Soc.<\/strong> 134, 19017\u201319025.<\/p>\n<\/div><\/div>\n\n\n\n

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Helmlinger, D., Marguerat, S., Villen, J., Swaney, D.L.<\/strong>, Gygi, S.P., B\u00e4hler, J., and Winston, F. (2011). Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex. EMBO J<\/strong>. 30, 2843\u20132852<\/p>\n<\/div><\/div>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"

Mario\u00a0Leutert,\u00a0Anthony S.\u00a0Barente,\u00a0Noelle K.\u00a0Fukuda,\u00a0Ricard A.\u00a0Rodriguez-Mias, Judit\u00a0Vill\u00e9n. The regulatory landscape of the yeast phosphoproteome. Nat Struct Mol Biol 2023 30(11):1761-1773; \u00a0doi:\u00a010.1038\/s41594-023-01115-3 Ecaterina Cozma, Megha Rao, Madison Dusick, Julie Genereaux, Ricard A. Rodriguez-Mias, Judit Vill\u00e9n, Christopher J. Brandl, Matthew D. Berg. Anticodon sequence determines the impact of mistranslating tRNAAla variants. bioRxiv 2022.11.23.517754; doi: 10.1101\/2022.11.23.517754 Alexis Chang, Mario Leutert,… Read More »Publications<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"on","footnotes":""},"class_list":["post-1225","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/pages\/1225","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/comments?post=1225"}],"version-history":[{"count":32,"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/pages\/1225\/revisions"}],"predecessor-version":[{"id":1594,"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/pages\/1225\/revisions\/1594"}],"wp:attachment":[{"href":"https:\/\/villenlab.gs.washington.edu\/wordpress\/index.php\/wp-json\/wp\/v2\/media?parent=1225"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}