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Items: 44

1.

Quantitative proteomics of MDCK cells identify unrecognized roles of clathrin adaptor AP-1 in polarized distribution of surface proteins.

Caceres PS, Gravotta D, Zager PJ, Dephoure N, Rodriguez-Boulan E.

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11796-11805. doi: 10.1073/pnas.1821076116. Epub 2019 May 29.

2.

CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis.

Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE.

Cancer Cell. 2019 May 13;35(5):817-819. doi: 10.1016/j.ccell.2019.04.012. No abstract available.

PMID:
31085180
3.

Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program.

Kikani CK, Wu X, Fogarty S, Kang SAW, Dephoure N, Gygi SP, Sabatini DM, Rutter J.

Proc Natl Acad Sci U S A. 2019 May 21;116(21):10382-10391. doi: 10.1073/pnas.1804013116. Epub 2019 May 9.

PMID:
31072927
4.

CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis.

Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE.

Cancer Cell. 2019 Apr 15;35(4):603-617.e8. doi: 10.1016/j.ccell.2019.03.001. Epub 2019 Mar 28. Erratum in: Cancer Cell. 2019 May 13;35(5):817-819.

PMID:
30930119
5.

Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome.

Boehm KM, Bhinder B, Raja VJ, Dephoure N, Elemento O.

BMC Bioinformatics. 2019 Jan 5;20(1):7. doi: 10.1186/s12859-018-2561-z.

6.

Robust, Reproducible, and Economical Phosphopeptide Enrichment Using Calcium Titanate.

Ahmed A, Raja VJ, Cavaliere P, Dephoure N.

J Proteome Res. 2019 Mar 1;18(3):1411-1417. doi: 10.1021/acs.jproteome.8b00883. Epub 2019 Jan 3.

PMID:
30576142
7.

Serine-Dependent Sphingolipid Synthesis Is a Metabolic Liability of Aneuploid Cells.

Hwang S, Gustafsson HT, O'Sullivan C, Bisceglia G, Huang X, Klose C, Schevchenko A, Dickson RC, Cavaliere P, Dephoure N, Torres EM.

Cell Rep. 2017 Dec 26;21(13):3807-3818. doi: 10.1016/j.celrep.2017.11.103.

8.

Post-transcriptional Regulation of De Novo Lipogenesis by mTORC1-S6K1-SRPK2 Signaling.

Lee G, Zheng Y, Cho S, Jang C, England C, Dempsey JM, Yu Y, Liu X, He L, Cavaliere PM, Chavez A, Zhang E, Isik M, Couvillon A, Dephoure NE, Blackwell TK, Yu JJ, Rabinowitz JD, Cantley LC, Blenis J.

Cell. 2017 Dec 14;171(7):1545-1558.e18. doi: 10.1016/j.cell.2017.10.037. Epub 2017 Nov 16.

9.

A conserved signaling network monitors delivery of sphingolipids to the plasma membrane in budding yeast.

Clarke J, Dephoure N, Horecka I, Gygi S, Kellogg D.

Mol Biol Cell. 2017 Oct 1;28(20):2589-2599. doi: 10.1091/mbc.E17-01-0081. Epub 2017 Aug 9.

10.

Focal Adhesion- and IGF1R-Dependent Survival and Migratory Pathways Mediate Tumor Resistance to mTORC1/2 Inhibition.

Yoon SO, Shin S, Karreth FA, Buel GR, Jedrychowski MP, Plas DR, Dedhar S, Gygi SP, Roux PP, Dephoure N, Blenis J.

Mol Cell. 2017 Aug 3;67(3):512-527.e4. doi: 10.1016/j.molcel.2017.06.033. Epub 2017 Jul 27.

11.

Deep Coverage of Global Protein Expression and Phosphorylation in Breast Tumor Cell Lines Using TMT 10-plex Isobaric Labeling.

Huang FK, Zhang G, Lawlor K, Nazarian A, Philip J, Tempst P, Dephoure N, Neubert TA.

J Proteome Res. 2017 Mar 3;16(3):1121-1132. doi: 10.1021/acs.jproteome.6b00374. Epub 2017 Feb 3.

12.

Protein Kinase C Controls Binding of Igo/ENSA Proteins to Protein Phosphatase 2A in Budding Yeast.

Thai V, Dephoure N, Weiss A, Ferguson J, Leitao R, Gygi SP, Kellogg DR.

J Biol Chem. 2017 Mar 24;292(12):4925-4941. doi: 10.1074/jbc.M116.753004. Epub 2017 Jan 18.

13.

Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation.

Ron-Harel N, Santos D, Ghergurovich JM, Sage PT, Reddy A, Lovitch SB, Dephoure N, Satterstrom FK, Sheffer M, Spinelli JB, Gygi S, Rabinowitz JD, Sharpe AH, Haigis MC.

Cell Metab. 2016 Jul 12;24(1):104-17. doi: 10.1016/j.cmet.2016.06.007.

14.

Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks.

Zhou C, Elia AE, Naylor ML, Dephoure N, Ballif BA, Goel G, Xu Q, Ng A, Chou DM, Xavier RJ, Gygi SP, Elledge SJ.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):E3667-75. doi: 10.1073/pnas.1602827113. Epub 2016 Jun 13.

15.

Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response.

Elia AE, Boardman AP, Wang DC, Huttlin EL, Everley RA, Dephoure N, Zhou C, Koren I, Gygi SP, Elledge SJ.

Mol Cell. 2015 Sep 3;59(5):867-81. doi: 10.1016/j.molcel.2015.05.006. Epub 2015 Jun 4.

16.

Nucleocytoplasmic transport in the midzone membrane domain controls yeast mitotic spindle disassembly.

Lucena R, Dephoure N, Gygi SP, Kellogg DR, Tallada VA, Daga RR, Jimenez J.

J Cell Biol. 2015 May 11;209(3):387-402. doi: 10.1083/jcb.201412144.

17.

Proteomic Profiling of Paclitaxel Treated Cells Identifies a Novel Mechanism of Drug Resistance Mediated by PDCD4.

Xu H, Dephoure N, Sun H, Zhang H, Fan F, Liu J, Ning X, Dai S, Liu B, Gao M, Fu S, Gygi SP, Zhou C.

J Proteome Res. 2015 Jun 5;14(6):2480-91. doi: 10.1021/acs.jproteome.5b00004. Epub 2015 May 14.

PMID:
25928036
18.

Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast.

Dephoure N, Hwang S, O'Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM.

Elife. 2014 Jul 29;3:e03023. doi: 10.7554/eLife.03023.

19.

SDHAF4 promotes mitochondrial succinate dehydrogenase activity and prevents neurodegeneration.

Van Vranken JG, Bricker DK, Dephoure N, Gygi SP, Cox JE, Thummel CS, Rutter J.

Cell Metab. 2014 Aug 5;20(2):241-52. doi: 10.1016/j.cmet.2014.05.012. Epub 2014 Jun 19.

20.

Msp1/ATAD1 maintains mitochondrial function by facilitating the degradation of mislocalized tail-anchored proteins.

Chen YC, Umanah GK, Dephoure N, Andrabi SA, Gygi SP, Dawson TM, Dawson VL, Rutter J.

EMBO J. 2014 Jul 17;33(14):1548-64. doi: 10.15252/embj.201487943. Epub 2014 May 19.

21.

PP2ARts1 is a master regulator of pathways that control cell size.

Zapata J, Dephoure N, Macdonough T, Yu Y, Parnell EJ, Mooring M, Gygi SP, Stillman DJ, Kellogg DR.

J Cell Biol. 2014 Feb 3;204(3):359-76. doi: 10.1083/jcb.201309119.

22.

The Hippo signaling pathway interactome.

Kwon Y, Vinayagam A, Sun X, Dephoure N, Gygi SP, Hong P, Perrimon N.

Science. 2013 Nov 8;342(6159):737-40. doi: 10.1126/science.1243971. Epub 2013 Oct 10.

23.

Changes in cell morphology are coordinated with cell growth through the TORC1 pathway.

Goranov AI, Gulati A, Dephoure N, Takahara T, Maeda T, Gygi SP, Manalis S, Amon A.

Curr Biol. 2013 Jul 22;23(14):1269-79. doi: 10.1016/j.cub.2013.05.035. Epub 2013 Jun 27.

24.

SIRT4 coordinates the balance between lipid synthesis and catabolism by repressing malonyl CoA decarboxylase.

Laurent G, German NJ, Saha AK, de Boer VC, Davies M, Koves TR, Dephoure N, Fischer F, Boanca G, Vaitheesvaran B, Lovitch SB, Sharpe AH, Kurland IJ, Steegborn C, Gygi SP, Muoio DM, Ruderman NB, Haigis MC.

Mol Cell. 2013 Jun 6;50(5):686-98. doi: 10.1016/j.molcel.2013.05.012.

25.

Intramolecular interactions control Vms1 translocation to damaged mitochondria.

Heo JM, Nielson JR, Dephoure N, Gygi SP, Rutter J.

Mol Biol Cell. 2013 May;24(9):1263-73. doi: 10.1091/mbc.E13-02-0072. Epub 2013 Mar 6.

26.

Mapping and analysis of phosphorylation sites: a quick guide for cell biologists.

Dephoure N, Gould KL, Gygi SP, Kellogg DR.

Mol Biol Cell. 2013 Mar;24(5):535-42. doi: 10.1091/mbc.E12-09-0677. Review.

27.

A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans.

Bricker DK, Taylor EB, Schell JC, Orsak T, Boutron A, Chen YC, Cox JE, Cardon CM, Van Vranken JG, Dephoure N, Redin C, Boudina S, Gygi SP, Brivet M, Thummel CS, Rutter J.

Science. 2012 Jul 6;337(6090):96-100. doi: 10.1126/science.1218099. Epub 2012 May 24.

28.
29.

Identification of a protein mediating respiratory supercomplex stability.

Chen YC, Taylor EB, Dephoure N, Heo JM, Tonhato A, Papandreou I, Nath N, Denko NC, Gygi SP, Rutter J.

Cell Metab. 2012 Mar 7;15(3):348-60. doi: 10.1016/j.cmet.2012.02.006.

30.

A phosphatase threshold sets the level of Cdk1 activity in early mitosis in budding yeast.

Harvey SL, Enciso G, Dephoure N, Gygi SP, Gunawardena J, Kellogg DR.

Mol Biol Cell. 2011 Oct;22(19):3595-608. doi: 10.1091/mbc.E11-04-0340. Epub 2011 Aug 17.

31.

A large-scale method to measure absolute protein phosphorylation stoichiometries.

Wu R, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME, Gygi SP.

Nat Methods. 2011 Jul 3;8(8):677-83. doi: 10.1038/nmeth.1636.

32.

Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes.

Wu R, Dephoure N, Haas W, Huttlin EL, Zhai B, Sowa ME, Gygi SP.

Mol Cell Proteomics. 2011 Aug;10(8):M111.009654. doi: 10.1074/mcp.M111.009654. Epub 2011 May 7.

33.

A solid phase extraction-based platform for rapid phosphoproteomic analysis.

Dephoure N, Gygi SP.

Methods. 2011 Aug;54(4):379-86. doi: 10.1016/j.ymeth.2011.03.008. Epub 2011 Apr 1.

34.

Activation of multiple proto-oncogenic tyrosine kinases in breast cancer via loss of the PTPN12 phosphatase.

Sun T, Aceto N, Meerbrey KL, Kessler JD, Zhou C, Migliaccio I, Nguyen DX, Pavlova NN, Botero M, Huang J, Bernardi RJ, Schmitt E, Hu G, Li MZ, Dephoure N, Gygi SP, Rao M, Creighton CJ, Hilsenbeck SG, Shaw CA, Muzny D, Gibbs RA, Wheeler DA, Osborne CK, Schiff R, Bentires-Alj M, Elledge SJ, Westbrook TF.

Cell. 2011 Mar 4;144(5):703-18. doi: 10.1016/j.cell.2011.02.003.

35.

Constitutive activated Cdc42-associated kinase (Ack) phosphorylation at arrested endocytic clathrin-coated pits of cells that lack dynamin.

Shen H, Ferguson SM, Dephoure N, Park R, Yang Y, Volpicelli-Daley L, Gygi S, Schlessinger J, De Camilli P.

Mol Biol Cell. 2011 Feb 15;22(4):493-502. doi: 10.1091/mbc.E10-07-0637. Epub 2010 Dec 17.

36.

A stress-responsive system for mitochondrial protein degradation.

Heo JM, Livnat-Levanon N, Taylor EB, Jones KT, Dephoure N, Ring J, Xie J, Brodsky JL, Madeo F, Gygi SP, Ashrafi K, Glickman MH, Rutter J.

Mol Cell. 2010 Nov 12;40(3):465-80. doi: 10.1016/j.molcel.2010.10.021.

37.

A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage.

Chou DM, Adamson B, Dephoure NE, Tan X, Nottke AC, Hurov KE, Gygi SP, Colaiácovo MP, Elledge SJ.

Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18475-80. doi: 10.1073/pnas.1012946107. Epub 2010 Oct 11.

38.

Identification of aneuploidy-tolerating mutations.

Torres EM, Dephoure N, Panneerselvam A, Tucker CM, Whittaker CA, Gygi SP, Dunham MJ, Amon A.

Cell. 2010 Oct 1;143(1):71-83. doi: 10.1016/j.cell.2010.08.038. Epub 2010 Sep 16.

39.

SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma.

Hao HX, Khalimonchuk O, Schraders M, Dephoure N, Bayley JP, Kunst H, Devilee P, Cremers CW, Schiffman JD, Bentz BG, Gygi SP, Winge DR, Kremer H, Rutter J.

Science. 2009 Aug 28;325(5944):1139-42. doi: 10.1126/science.1175689. Epub 2009 Jul 23.

40.

A quantitative atlas of mitotic phosphorylation.

Dephoure N, Zhou C, Villén J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP.

Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi: 10.1073/pnas.0805139105. Epub 2008 Jul 31.

41.

Construction, verification and experimental use of two epitope-tagged collections of budding yeast strains.

Howson R, Huh WK, Ghaemmaghami S, Falvo JV, Bower K, Belle A, Dephoure N, Wykoff DD, Weissman JS, O'Shea EK.

Comp Funct Genomics. 2005;6(1-2):2-16. doi: 10.1002/cfg.449.

42.

The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics.

Bakalarski CE, Haas W, Dephoure NE, Gygi SP.

Anal Bioanal Chem. 2007 Nov;389(5):1409-19. Epub 2007 Sep 14.

PMID:
17874083
43.

Combining chemical genetics and proteomics to identify protein kinase substrates.

Dephoure N, Howson RW, Blethrow JD, Shokat KM, O'Shea EK.

Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):17940-5. Epub 2005 Dec 5.

44.

Global analysis of protein expression in yeast.

Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS.

Nature. 2003 Oct 16;425(6959):737-41.

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