Publications by Cell Signaling Technology Scientists
2013
2012
- Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(1), D261–70.
- Katayama R, Shaw AT, Khan TM, Mino-Kenudson M, Solomon BJ, Halmos B, Jessop NA, Wain JC, Yeo AT, Benes C, Drew L, Saeh JC, Crosby K, Sequist LV, Iafrate AJ, Engelman JA (2012) Mechanisms of acquired crizotinib resistance in ALK-rearranged lung Cancers. Sci Transl Med 4(120), 120ra17.
- Cheung WC, Beausoleil SA, Zhang X, Sato S, Schieferl SM, Wieler JS, Beaudet JG, Ramenani RK, Popova L, Comb MJ, Rush J, Polakiewicz RD (2012) A proteomics approach for the identification and cloning of monoclonal antibodies from serum. Nat. Biotechnol. 30(5), 447–52.
- Stokes MP, Farnsworth CL, Moritz A, Silva JC, Jia X, Lee KA, Guo A, Polakiewicz RD, Comb MJ (2012) PTMScan direct: identification and quantification of peptides from critical signaling proteins by immunoaffinity enrichment coupled with LC-MS/MS. Mol. Cell Proteomics 11(5), 187–201.
- Ren H, Tan ZP, Zhu X, Crosby K, Haack H, Ren JM, Beausoleil S, Moritz A, Innocenti G, Rush J, Zhang Y, Zhou XM, Gu TL, Yang YF, Comb MJ (2012) Identification of anaplastic lymphoma kinase as a potential therapeutic target in ovarian cancer. Cancer Res. 72(13), 3312–23.
- Rimkunas VM, Crosby KE, Li D, Hu Y, Kelly ME, Gu TL, Mack JS, Silver MR, Zhou X, Haack H (2012) Analysis of Receptor Tyrosine Kinase ROS1-Positive Tumors in Non-Small Cell Lung Cancer: Identification of a FIG-ROS1 Fusion. Clin. Cancer Res. 18(16), 4449–57.
- Xu W, Mollapour M, Prodromou C, Wang S, Scroggins BT, Palchick Z, Beebe K, Siderius M, Lee MJ, Couvillon A, Trepel JB, Miyata Y, Matts R, Neckers L (2012) Dynamic tyrosine phosphorylation modulates cycling of the HSP90-P50(CDC37)-AHA1 chaperone machine. Mol. Cell 47(3), 434–43.
- Hitosugi T, Zhou L, Elf S, Fan J, Kang HB, Seo JH, Shan C, Dai Q, Zhang L, Xie J, Gu TL, Jin P, Alečković M, Leroy G, Kang Y, Sudderth JA, Deberardinis RJ, Luan CH, Chen GZ, Muller S, Shin DM, Owonikoko TK, Lonial S, Arellano ML, Khoury HJ, Khuri FR, Lee BH, Ye K, Boggon TJ, Kang S, He C, Chen J (2012) Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth. Cancer Cell 22(5), 585–600.
- Sato S, Beausoleil SA, Popova L, Beaudet JG, Ramenani RK, Zhang X, Wieler JS, Schieferl SM, Cheung WC, Polakiewicz RD (2012) Proteomics-directed cloning of circulating antiviral human monoclonal antibodies. Nat. Biotechnol. 30(11), 1039–43.
- Buckley SM, Aranda-Orgilles B, Strikoudis A, Apostolou E, Loizou E, Moran-Crusio K, Farnsworth CL, Koller AA, Dasgupta R, Silva JC, Stadtfeld M, Hochedlinger K, Chen EI, Aifantis I (2012) Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell 11(6), 783-98
- Stokes MP, Silva JC, Jia X, Lee KA, Polakiewicz RD, Comb MJ (2012) Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct. Int J Mol Sci 14(1), 286–307.
- Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA (2012) Cooperative Effects of Drug-Resistance Mutations in the Flap Region of HIV-1 Protease. ACS Chem. Biol. [Epub ahead of print].
2011
- Gu TL, Deng X, Huang F, Tucker M, Crosby K, Rimkunas V, Wang Y, Deng G, Zhu L, Tan Z, Hu Y, Wu C, Nardone J, MacNeill J, Ren J, Reeves C, Innocenti G, Norris B, Yuan J, Yu J, Haack H, Shen B, Peng C, Li H, Zhou X, Liu X, Rush J, Comb MJ (2011) Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma. PLoS ONE 6(1), e15640.
- Kettenbach AN, Rush J, Gerber SA (2011) Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat Protoc 6(2), 175–86.
- Dammer EB, Na CH, Xu P, Seyfried NT, Duong DM, Cheng D, Gearing M, Rees H, Lah JJ, Levey AI, Rush J, Peng J (2011) Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease. J. Biol. Chem. 286(12), 10457–65.
- Brave SR, Ratcliffe K, Wilson Z, James NH, Ashton S, Wainwright A, Kendrew J, Dudley P, Broadbent N, Sproat G, Taylor S, Barnes C, Silva JC, Farnsworth CL, Hennequin L, Ogilvie DJ, Jürgensmeier JM, Shibuya M, Wedge SR, Barry ST (2011) Assessing the activity of cediranib, a VEGFR-2/3 tyrosine kinase inhibitor, against VEGFR-1 and members of the structurally related PDGFR family. Mol. Cancer Ther. 10(5), 861–73.
- Pighi C, Gu TL, Dalai I, Barbi S, Parolini C, Bertolaso A, Pedron S, Parisi A, Ren J, Cecconi D, Chilosi M, Menestrina F, Zamò A (2011) Phospho-proteomic analysis of mantle cell lymphoma cells suggests a pro-survival role of B-cell receptor signaling. Cell Oncol (Dordr) 34(2), 141–53.
- Gu TL, Nardone J, Wang Y, Loriaux M, Villén J, Beausoleil S, Tucker M, Kornhauser J, Ren J, MacNeill J, Gygi SP, Druker BJ, Heinrich MC, Rush J, Polakiewicz RD (2011) Survey of activated FLT3 signaling in leukemia. PLoS ONE 6(4), e19169.
- Kremer KN, Clift IC, Miamen AG, Bamidele AO, Qian NX, Humphreys TD, Hedin KE (2011) Stromal Cell-Derived Factor-1 Signaling via the CXCR4-TCR Heterodimer Requires Phospholipase C-{beta}3 and Phospholipase C-{gamma}1 for Distinct Cellular Responses. J. Immunol. 187(3), 1440–7.
- Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP (2011) Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell 44(2), 325-40
- Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ (2011) Global Identification of Modular Cullin-RING Ligase Substrates. Cell 147(2), 459–74.
- Feng H, Hu B, Liu KW, Li Y, Lu X, Cheng T, Yiin JJ, Lu S, Keezer S, Fenton T, Furnari FB, Hamilton RL, Vuori K, Sarkaria JN, Nagane M, Nishikawa R, Cavenee WK, Cheng SY (2011) Activation of Rac1 by Src-dependent phosphorylation of Dock180Y1811 mediates PDGFRα-stimulated glioma tumorigenesis in mice and humans. J. Clin. Invest. 121(12), 4670–84.
- Fan J, Hitosugi T, Chung TW, Xie J, Ge Q, Gu TL, Polakiewicz RD, Chen GZ, Boggon TJ, Lonial S, Khuri FR, Kang S, Chen J (2011) Tyrosine Phosphorylation of Lactate Dehydrogenase A Is Important for NADH/NAD+ Redox Homeostasis in Cancer Cells. Mol. Cell. Biol. 31(24), 4938-50
- Hitosugi T, Fan J, Chung TW, Lythgoe K, Wang X, Xie J, Ge Q, Gu TL, Polakiewicz RD, Roesel JL, Chen GZ, Boggon TJ, Lonial S, Fu H, Khuri FR, Kang S, Chen J (2011) Tyrosine phosphorylation of mitochondrial pyruvate dehydrogenase kinase 1 is important for cancer metabolism. Mol. Cell 44(6), 864-77
- Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR (2011) Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. J. Biol. Chem. 286(48), 41530–8.
2010
- Moritz A, Li Y, Guo A, Villén J, Wang Y, MacNeill J, Kornhauser J, Sprott K, Zhou J, Possemato A, Ren JM, Hornbeck P, Cantley LC, Gygi SP, Rush J, Comb MJ (2010) Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases. Sci Signal 3(136), ra64. More Information.
- van Vugt MA, Gardino AK, Linding R, Ostheimer GJ, Reinhardt HC, Ong SE, Tan CS, Miao H, Keezer SM, Li J, Pawson T, Lewis TA, Carr SA, Smerdon SJ, Brummelkamp TR, Yaffe MB (2010) A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PLoS Biol. 8(1), e1000287.
- Gu TL, Cherry J, Tucker M, Wu J, Reeves C, Polakiewicz RD (2010) Identification of activated Tnk1 kinase in Hodgkin's lymphoma. Leukemia 24(4), 861-5.
- Pecquet C, Staerk J, Chaligné R, Goss V, Lee KA, Zhang X, Rush J, Van Hees J, Poirel HA, Scheiff JM, Vainchenker W, Giraudier S, Polakiewicz RD, Constantinescu SN (2010) Induction of myeloproliferative disorder and myelofibrosis by thrombopoietin receptor W515 mutants is mediated by cytosolic tyrosine 112 of the receptor. Blood 115(5), 1037-48.
- Hudon V, Sabourin S, Dydensborg AB, Kottis V, Ghazi A, Paquet M, Crosby K, Pomerleau V, Uetani N, Pause A (2010) Renal tumour suppressor function of the Birt-Hogg-Dubé syndrome gene product folliculin. J. Med. Genet. 47(3), 182-9.
- Hirschey MD, Shimazu T, Goetzman E, Jing E, Schwer B, Lombard DB, Grueter CA, Harris C, Biddinger S, Ilkayeva OR, Stevens RD, Li Y, Saha AK, Ruderman NB, Bain JR, Newgard CB, Farese RV, Alt FW, Kahn CR, Verdin E (2010) SIRT3 regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation. Nature 464(7285), 121-5.
- Schoeberl B, Faber AC, Li D, Liang MC, Crosby K, Onsum M, Burenkova O, Pace E, Walton Z, Nie L, Fulgham A, Song Y, Nielsen UB, Engelman JA, Wong KK (2010) An ErbB3 antibody, MM-121, is active in cancers with ligand-dependent activation. Cancer Res. 70(6), 2485-94.
- Ghosh R, Graham H, Rivas P, Tan XJ, Crosby K, Bhaskaran S, Schoolfield J, Banu J, Fernandes G, Yeh IT, Kumar AP (2010) Phellodendron amurense bark extract prevents progression of prostate tumors in transgenic adenocarcinoma of mouse prostate: potential for prostate cancer management. Anticancer Res. 30(3), 857-65.
- Kang S, Elf S, Lythgoe K, Hitosugi T, Taunton J, Zhou W, Xiong L, Wang D, Muller S, Fan S, Sun SY, Marcus AI, Gu TL, Polakiewicz RD, Chen ZG, Khuri FR, Shin DM, Chen J (2010) p90 ribosomal S6 kinase 2 promotes invasion and metastasis of human head and neck squamous cell carcinoma cells. J. Clin. Invest. 120(4), 1165-77.
- Bonnette PC, Robinson BS, Silva JC, Stokes MP, Brosius AD, Baumann A, Buckbinder L (2010) Phosphoproteomic characterization of PYK2 signaling pathways involved in osteogenesis. J Proteomics 73(7), 1306-20.
- Aguiar M, Haas W, Beausoleil SA, Rush J, Gygi SP (2010) Gas-Phase Rearrangements Do Not Affect Site Localization Reliability in Phosphoproteomics Data Sets. J Proteome Res.
- Carretero J, Shimamura T, Rikova K, Jackson AL, Wilkerson MD, Borgman CL, Buttarazzi MS, Sanofsky BA, McNamara KL, Brandstetter KA, Walton ZE, Gu TL, Silva JC, Crosby K, Shapiro GI, Maira SM, Ji H, Castrillon DH, Kim CF, García-Echeverría C, Bardeesy N, Sharpless NE, Hayes ND, Kim WY, Engelman JA, Wong KK (2010) Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell 17(6), 547-59.
- Andersen JN, Sathyanarayanan S, Di Bacco A, Chi A, Zhang T, Chen AH, Dolinski B, Kraus M, Roberts B, Arthur W, Klinghoffer RA, Gargano D, Li L, Feldman I, Lynch B, Rush J, Hendrickson RC, Blume-Jensen P, Paweletz CP (2010) Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med 2(43), 43ra55.
- Buel GR, Rush J, Ballif BA (2010) Fyn promotes phosphorylation of collapsin response mediator protein 1 at tyrosine 504, a novel, isoform-specific regulatory site. J Cell Biochem.
- Knowlton ML, Selfors LM, Wrobel CN, Gu TL, Ballif BA, Gygi SP, Polakiewicz R, Brugge JS (2010) Profiling Y561-dependent and -independent substrates of CSF-1R in epithelial cells. PLoS ONE 5(10), e13587.
- 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 (2010) A stress-responsive system for mitochondrial protein degradation. Mol. Cell 40(3), 465-80
- Emek Demir, Michael P Cary, Sasha Tkachev, Peter Hornbeck, Chris Sander, Gary D Bader, & 82 others. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnology 28, 935-942.
- Bennett EJ, Rush J, Gygi SP, Harper JW (2010) Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell 143(6), 951–65.
2009
- Gordus A, Krall JA, Beyer EM, Kaushansky A, Wolf-Yadlin A, Sevecka M, Chang BH, Rush J, MacBeath G (2009) Linear combinations of docking affinities explain quantitative differences in RTK signaling. Mol. Syst. Biol. 5, 235.
- Hitosugi T, Kang S, Vander Heiden MG, Chung TW, Elf S, Lythgoe K, Dong S, Lonial S, Wang X, Chen GZ, Xie J, Gu TL, Polakiewicz RD, Roesel JL, Boggon TJ, Khuri FR, Gilliland DG, Cantley LC, Kaufman J, Chen J (2009) Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth. Sci Signal 2(97), ra73.
- Harrington MG, Fonteh AN, Oborina E, Liao P, Cowan RP, McComb G, Chavez JN, Rush J, Biringer RG, Hühmer AF (2009) The morphology and biochemistry of nanostructures provide evidence for synthesis and signaling functions in human cerebrospinal fluid. Cerebrospinal Fluid Res 6, 10.
- Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, Zhang J, Brentnall TA (2009) Mass spectrometry based targeted protein quantification: methods and applications. J. Proteome Res. 8(2), 787-97.
- Boccalatte FE, Voena C, Riganti C, Bosia A, D'Amico L, Riera L, Cheng M, Ruggeri B, Jensen ON, Goss VL, Lee K, Nardone J, Rush J, Polakiewicz RD, Comb MJ, Chiarle R, Inghirami G (2009) The enzymatic activity of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase is enhanced by NPM-ALK: new insights in ALK-mediated pathogenesis and the treatment of ALCL. Blood 113(12), 2776-90.
- Kang S, Elf S, Dong S, Hitosugi T, Lythgoe K, Guo A, Ruan H, Lonial S, Khoury HJ, Williams IR, Lee BH, Roesel JL, Karsenty G, Hanauer A, Taunton J, Boggon TJ, Gu TL, Chen J (2009) Fibroblast growth factor receptor 3 associates with and tyrosine phosphorylates p90 RSK2, leading to RSK2 activation that mediates hematopoietic transformation. Mol. Cell. Biol. 29(8), 2105-17.
- ten Klooster JP, Jansen M, Yuan J, Oorschot V, Begthel H, Di Giacomo V, Colland F, de Koning J, Maurice MM, Hornbeck P, Clevers H (2009) Mst4 and Ezrin induce brush borders downstream of the Lkb1/Strad/Mo25 polarization complex. Dev. Cell 16(4), 551–62.
- Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, Robert J, Rush J, Hochstrasser M, Finley D, Peng J (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137(1), 133-45.
- Yu J, Kane S, Wu J, Benedettini E, Li D, Reeves C, Innocenti G, Wetzel R, Crosby K, Becker A, Ferrante M, Cheung WC, Hong X, Chirieac LR, Sholl LM, Haack H, Smith BL, Polakiewicz RD, Tan Y, Gu TL, Loda M, Zhou X, Comb MJ (2009) Mutation-specific antibodies for the detection of EGFR mutations in non-small-cell lung cancer. Clin. Cancer Res. 15(9), 3023-8.
- Haack H, Johnson LA, Fry CJ, Crosby K, Polakiewicz RD, Stelow EB, Hong SM, Schwartz BE, Cameron MJ, Rubin MA, Chang MC, Aster JC, French CA (2009) Diagnosis of NUT midline carcinoma using a NUT-specific monoclonal antibody. Am. J. Surg. Pathol. 33(7), 984-91.
- Yu Y, Anjum R, Kubota K, Rush J, Villen J, Gygi SP (2009) A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 106(28), 11606-11.
- Kasyapa C, Gu TL, Nagarajan L, Natarajan L, Polakiewicz R, Cowell JK (2009) Phosphorylation of the SSBP2 and ABL proteins by the ZNF198-FGFR1 fusion kinase seen in atypical myeloproliferative disorders as revealed by phosphopeptide-specific MS. Proteomics 9(16), 3979-88.
- Schwer B, Eckersdorff M, Li Y, Silva JC, Fermin D, Kurtev MV, Giallourakis C, Comb MJ, Alt FW, Lombard DB (2009) Calorie restriction alters mitochondrial protein acetylation. Aging Cell 8(5), 604-6.
- Kubota K, Anjum R, Yu Y, Kunz RC, Andersen JN, Kraus M, Keilhack H, Nagashima K, Krauss S, Paweletz C, Hendrickson RC, Feldman AS, Wu CL, Rush J, Villén J, Gygi SP (2009) Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nat. Biotechnol. 27(10), 933-40.
- Ji H, Wang J, Nika H, Hawke D, Keezer S, Ge Q, Fang B, Fang X, Fang D, Litchfield DW, Aldape K, Lu Z (2009) EGF-induced ERK activation promotes CK2-mediated disassociation of alpha-Catenin from beta-Catenin and transactivation of beta-Catenin. Mol. Cell 36(4), 547-59.
- Lechtreck KF, Johnson EC, Sakai T, Cochran D, Ballif BA, Rush J, Pazour GJ, Ikebe M, Witman GB (2009) The Chlamydomonas reinhardtii BBSome is an IFT cargo required for export of specific signaling proteins from flagella. J. Cell Biol. 187(7), 1117-32.
2008
- Guo A, Villén J, Kornhauser J, Lee KA, Stokes MP, Rikova K, Possemato A, Nardone J, Innocenti G, Wetzel R, Wang Y, MacNeill J, Mitchell J, Gygi SP, Rush J, Polakiewicz RD, Comb MJ (2008) Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci. U.S.A. 105(2), 692-7.
- Pan S, Rush J, Peskind ER, Galasko D, Chung K, Quinn J, Jankovic J, Leverenz JB, Zabetian C, Pan C, Wang Y, Oh JH, Gao J, Zhang J, Montine T, Zhang J (2008) Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform. J. Proteome Res. 7(2), 720-30.
- Kang S, Dong S, Guo A, Ruan H, Lonial S, Khoury HJ, Gu TL, Chen J (2008) Epidermal growth factor stimulates RSK2 activation through activation of the MEK/ERK pathway and src-dependent tyrosine phosphorylation of RSK2 at Tyr-529. J. Biol. Chem. 283(8), 4652-7.
- Li K, Casta A, Wang R, Lozada E, Fan W, Kane S, Ge Q, Gu W, Orren D, Luo J (2008) Regulation of WRN protein cellular localization and enzymatic activities by SIRT1-mediated deacetylation. J. Biol. Chem. 283(12), 7590-8.
- Dentin R, Hedrick S, Xie J, Yates J, Montminy M (2008) Hepatic glucose sensing via the CREB coactivator CRTC2. Science 319(5868), 1402-5.
- Taylor EB, An D, Kramer HF, Yu H, Fujii NL, Roeckl KS, Bowles N, Hirshman MF, Xie J, Feener EP, Goodyear LJ (2008) Discovery of TBC1D1 as an insulin-, AICAR-, and contraction-stimulated signaling nexus in mouse skeletal muscle. J. Biol. Chem. 283(15), 9787-96.
- Miyake Z, Takekawa M, Ge Q, Saito H (2007) Activation of MTK1/MEKK4 by GADD45 through induced N-C dissociation and dimerization-mediated trans autophosphorylation of the MTK1 kinase domain. Mol. Cell. Biol. 27(7), 2765-76.
- Li Y, Zhang X, Polakiewicz RD, Yao TP, Comb MJ (2008) HDAC6 is required for epidermal growth factor-induced beta-catenin nuclear localization. J. Biol. Chem. 283(19), 12686-90.
- Kaushansky A, Gordus A, Chang B, Rush J, MacBeath G (2008) A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R. Mol Biosyst 4(6), 643-53.
- Kaushansky A, Gordus A, Budnik BA, Lane WS, Rush J, MacBeath G (2008) System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties. Chem. Biol. 15(8), 808-17.
- Pan W, Choi SC, Wang H, Qin Y, Volpicelli-Daley L, Swan L, Lucast L, Khoo C, Zhang X, Li L, Abrams CS, Sokol SY, Wu D (2008) Wnt3a-mediated formation of phosphatidylinositol 4,5-bisphosphate regulates LRP6 phosphorylation. Science 321(5894), 1350-3.
- Altarejos JY, Goebel N, Conkright MD, Inoue H, Xie J, Arias CM, Sawchenko PE, Montminy M (2008) The Creb1 coactivator Crtc1 is required for energy balance and fertility. Nat. Med. 14(10), 1112-7.
- Stratford AL, Fry CJ, Desilets C, Davies AH, Cho YY, Li Y, Dong Z, Berquin IM, Roux PP, Dunn SE (2008) Y-box binding protein-1 serine 102 is a downstream target of p90 ribosomal S6 kinase in basal-like breast cancer cells. Breast Cancer Res. 10(6), R99.
- Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ (2007) Profiling of UV-induced ATM/ATR signaling pathways. Proc. Natl. Acad. Sci. U.S.A. 104(50), 19855-60.
- Engelman JA, Chen L, Tan X, Crosby K, Guimaraes AR, Upadhyay R, Maira M, McNamara K, Perera SA, Song Y, Chirieac LR, Kaur R, Lightbown A, Simendinger J, Li T, Padera RF, García-Echeverría C, Weissleder R, Mahmood U, Cantley LC, Wong KK (2008) Effective use of PI3K and MEK inhibitors to treat mutant Kras G12D and PIK3CA H1047R murine lung cancers. Nat. Med. 14(12), 1351-6.
2007
- Gerber SA, Kettenbach AN, Rush J, Gygi SP (2007) The absolute quantification strategy: application to phosphorylation profiling of human separase serine 1126. Methods Mol. Biol. 359, 71-86.
- Gu TL, Popova L, Reeves C, Nardone J, Macneill J, Rush J, Nimer SD, Polakiewicz RD (2007) Phosphoproteomic analysis identifies the M0-91 cell line as a cellular model for the study of TEL-TRKC fusion-associated leukemia. Leukemia 21(3), 563-6.
- Li X, Monks B, Ge Q, Birnbaum MJ (2007) Akt/PKB regulates hepatic metabolism by directly inhibiting PGC-1alpha transcription coactivator. Nature 447(7147), 1012-6.
- Dong S, Kang S, Gu TL, Kardar S, Fu H, Lonial S, Khoury HJ, Khuri F, Chen J (2007) 14-3-3 Integrates prosurvival signals mediated by the AKT and MAPK pathways in ZNF198-FGFR1-transformed hematopoietic cells. Blood 110(1), 360-9.
- Gu TL, Mercher T, Tyner JW, Goss VL, Walters DK, Cornejo MG, Reeves C, Popova L, Lee K, Heinrich MC, Rush J, Daibata M, Miyoshi I, Gilliland DG, Druker BJ, Polakiewicz RD (2007) A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia. Blood 110(1), 323-33.
- Kang S, Dong S, Gu TL, Guo A, Cohen MS, Lonial S, Khoury HJ, Fabbro D, Gilliland DG, Bergsagel PL, Taunton J, Polakiewicz RD, Chen J (2007) FGFR3 activates RSK2 to mediate hematopoietic transformation through tyrosine phosphorylation of RSK2 and activation of the MEK/ERK pathway. Cancer Cell 12(3), 201-14.
- Kass EM, Ahn J, Tanaka T, Freed-Pastor WA, Keezer S, Prives C (2007) Stability of checkpoint kinase 2 is regulated via phosphorylation at serine 456. J. Biol. Chem. 282(41), 30311-21.
- Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131(6), 1190-203.
2006
- Steen H, Jebanathirajah JA, Rush J, Morrice N, Kirschner MW (2006) Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements. Mol. Cell Proteomics 5(1), 172-81.
- Shalizi A, Gaudillière B, Yuan Z, Stegmüller J, Shirogane T, Ge Q, Tan Y, Schulman B, Harper JW, Bonni A (2006) A calcium-regulated MEF2 sumoylation switch controls postsynaptic differentiation. Science 311(5763), 1012-7.
- Kling DE, Brandon KL, Sollinger CA, Cavicchio AJ, Ge Q, Kinane TB, Donahoe PK, Schnitzer JJ (2006) Distribution of ERK1/2 and ERK3 during normal rat fetal lung development. Anat. Embryol. 211(2), 139-53.
- Goss VL, Lee KA, Moritz A, Nardone J, Spek EJ, MacNeill J, Rush J, Comb MJ, Polakiewicz RD (2006) A common phosphotyrosine signature for the Bcr-Abl kinase. Blood 107(12), 4888-97.
- Cheng D, Hoogenraad CC, Rush J, Ramm E, Schlager MA, Duong DM, Xu P, Wijayawardana SR, Hanfelt J, Nakagawa T, Sheng M, Peng J (2006) Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol. Cell Proteomics 5(6), 1158-70.
- Kirkpatrick DS, Hathaway NA, Hanna J, Elsasser S, Rush J, Finley D, King RW, Gygi SP (2006) Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat. Cell Biol. 8(7), 700-10.
- Walters DK, Mercher T, Gu TL, O'Hare T, Tyner JW, Loriaux M, Goss VL, Lee KA, Eide CA, Wong MJ, Stoffregen EP, McGreevey L, Nardone J, Moore SA, Crispino J, Boggon TJ, Heinrich MC, Deininger MW, Polakiewicz RD, Gilliland DG, Druker BJ (2006) Activating alleles of JAK3 in acute megakaryoblastic leukemia. Cancer Cell 10(1), 65-75.
- Griswold IJ, MacPartlin M, Bumm T, Goss VL, O'Hare T, Lee KA, Corbin AS, Stoffregen EP, Smith C, Johnson K, Moseson EM, Wood LJ, Polakiewicz RD, Druker BJ, Deininger MW (2006) Kinase domain mutants of Bcr-Abl exhibit altered transformation potency, kinase activity, and substrate utilization, irrespective of sensitivity to imatinib. Mol. Cell. Biol. 26(16), 6082-93.
- Walters DK, Goss VL, Stoffregen EP, Gu TL, Lee K, Nardone J, McGreevey L, Heinrich MC, Deininger MW, Polakiewicz R, Druker BJ (2006) Phosphoproteomic analysis of AML cell lines identifies leukemic oncogenes. Leuk. Res. 30(9), 1097-104.
- Mercher T, Wernig G, Moore SA, Levine RL, Gu TL, Fröhling S, Cullen D, Polakiewicz RD, Bernard OA, Boggon TJ, Lee BH, Gilliland DG (2006) JAK2T875N is a novel activating mutation that results in myeloproliferative disease with features of megakaryoblastic leukemia in a murine bone marrow transplantation model. Blood 108(8), 2770-9.
- Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24(10), 1285-92.
- Gu TL, Goss VL, Reeves C, Popova L, Nardone J, Macneill J, Walters DK, Wang Y, Rush J, Comb MJ, Druker BJ, Polakiewicz RD (2006) Phosphotyrosine profiling identifies the KG-1 cell line as a model for the study of FGFR1 fusions in acute myeloid leukemia. Blood 108(13), 4202-4.
2005
- Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD, Comb MJ (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 23(1), 94-101.
- Faure S, Cau J, de Santa Barbara P, Bigou S, Ge Q, Delsert C, Morin N (2005) Xenopus p21-activated kinase 5 regulates blastomeres' adhesive properties during convergent extension movements. Dev. Biol. 277(2), 472-92.
- Pan S, Zhang H, Rush J, Eng J, Zhang N, Patterson D, Comb MJ, Aebersold R (2005) High throughput proteome screening for biomarker detection. Mol. Cell Proteomics 4(2), 182-90.
- Koon HB, Bubley GJ, Pantanowitz L, Masiello D, Smith B, Crosby K, Proper J, Weeden W, Miller TE, Chatis P, Egorin MJ, Tahan SR, Dezube BJ (2005) Imatinib-induced regression of AIDS-related Kaposi's sarcoma. J. Clin. Oncol. 23(5), 982-9.
- Park SS, Kim JS, Tessarollo L, Owens JD, Peng L, Han SS, Tae Chung S, Torrey TA, Cheung WC, Polakiewicz RD, McNeil N, Ried T, Mushinski JF, Morse HC, Janz S (2005) Insertion of c-Myc into Igh induces B-cell and plasma-cell neoplasms in mice. Cancer Res. 65(4), 1306-15.
- Morrison MD, Reiley W, Zhang M, Sun SC (2005) An atypical tumor necrosis factor (TNF) receptor-associated factor-binding motif of B cell-activating factor belonging to the TNF family (BAFF) receptor mediates induction of the noncanonical NF-kappaB signaling pathway. J. Biol. Chem. 280(11), 10018-24.
- Westfall MD, Joyner AS, Barbieri CE, Livingstone M, Pietenpol JA (2005) Ultraviolet radiation induces phosphorylation and ubiquitin-mediated degradation of DeltaNp63alpha. Cell Cycle 4(5), 710-6.
- Zhang R, Luo D, Miao R, Bai L, Ge Q, Sessa WC, Min W (2005) Hsp90-Akt phosphorylates ASK1 and inhibits ASK1-mediated apoptosis. Oncogene 24(24), 3954-63.
- Zhang Y, Wolf-Yadlin A, Ross PL, Pappin DJ, Rush J, Lauffenburger DA, White FM (2005) Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell Proteomics 4(9), 1240-50.
- Wetzel R, Goss VL, Norris B, Popova L, Melnick M, Smith BL (2005) Evaluation of CML model cell lines and imatinib mesylate response: determinants of signaling profiles. J. Immunol. Methods 305(1), 59-66.
2004
- Scholl D, Kieleczawa J, Kemp P, Rush J, Richardson CC, Merril C, Adhya S, Molineux IJ (2004) Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup. J. Mol. Biol. 335(5), 1151-71.
- Schrantz N, da Silva Correia J, Fowler B, Ge Q, Sun Z, Bokoch GM (2004) Mechanism of p21-activated kinase 6-mediated inhibition of androgen receptor signaling. J. Biol. Chem. 279(3), 1922-31.
- Papa S, Zazzeroni F, Bubici C, Jayawardena S, Alvarez K, Matsuda S, Nguyen DU, Pham CG, Nelsbach AH, Melis T, De Smaele E, Tang WJ, D'Adamio L, Franzoso G (2004) Gadd45 beta mediates the NF-kappa B suppression of JNK signalling by targeting MKK7/JNKK2. Nat. Cell Biol. 6(2), 146-53.
- Clark LB, Viswanathan P, Quigley G, Chiang YC, McMahon JS, Yao G, Chen J, Nelsbach A, Denis CL (2004) Systematic mutagenesis of the leucine-rich repeat (LRR) domain of CCR4 reveals specific sites for binding to CAF1 and a separate critical role for the LRR in CCR4 deadenylase activity. J. Biol. Chem. 279(14), 13616-23.
- Thompson PR, Wang D, Wang L, Fulco M, Pediconi N, Zhang D, An W, Ge Q, Roeder RG, Wong J, Levrero M, Sartorelli V, Cotter RJ, Cole PA (2004) Regulation of the p300 HAT domain via a novel activation loop. Nat. Struct. Mol. Biol. 11(4), 308-15.
- Pende M, Um SH, Mieulet V, Sticker M, Goss VL, Mestan J, Mueller M, Fumagalli S, Kozma SC, Thomas G (2004) S6K1(-/-)/S6K2(-/-) mice exhibit perinatal lethality and rapamycin-sensitive 5'-terminal oligopyrimidine mRNA translation and reveal a mitogen-activated protein kinase-dependent S6 kinase pathway. Mol. Cell. Biol. 24(8), 3112-24.
- Raught B, Peiretti F, Gingras AC, Livingstone M, Shahbazian D, Mayeur GL, Polakiewicz RD, Sonenberg N, Hershey JW (2004) Phosphorylation of eucaryotic translation initiation factor 4B Ser422 is modulated by S6 kinases. EMBO J. 23(8), 1761-9.
- Russello SV (2004) Assessing cellular protein phosphorylation: high throughput drug discovery technologies. Assay Drug Dev Technol 2(2), 225-35.
- Cheung WC, Kim JS, Linden M, Peng L, Van Ness B, Polakiewicz RD, Janz S (2004) Novel targeted deregulation of c-Myc cooperates with Bcl-X(L) to cause plasma cell neoplasms in mice. J. Clin. Invest. 113(12), 1763-73.
- Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B (2004) PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4(6), 1551-61.
- Ohira T, Bannenberg G, Arita M, Takahashi M, Ge Q, Van Dyke TE, Stahl GL, Serhan CN, Badwey JA (2004) A stable aspirin-triggered lipoxin A4 analog blocks phosphorylation of leukocyte-specific protein 1 in human neutrophils. J. Immunol. 173(3), 2091-8.
- Smith BL, Chin D, Maltzman W, Crosby K, Hortobagyi GN, Bacus SS (2004) The efficacy of Herceptin therapies is influenced by the expression of other erbB receptors, their ligands and the activation of downstream signalling proteins. Br. J. Cancer 91(6), 1190-4.
- Sun L, Rush J, Ghosh I, Maunus JR, Xu MQ (2004) Producing peptide arrays for epitope mapping by intein-mediated protein ligation. BioTechniques 37(3), 430-6, 438, 440 passim.
- Li Y, Soos TJ, Li X, Wu J, Degennaro M, Sun X, Littman DR, Birnbaum MJ, Polakiewicz RD (2004) Protein kinase C Theta inhibits insulin signaling by phosphorylating IRS1 at Ser(1101). J. Biol. Chem. 279(44), 45304-7.
- Maleri S, Ge Q, Hackett EA, Wang Y, Dohlman HG, Errede B (2004) Persistent activation by constitutive Ste7 promotes Kss1-mediated invasive growth but fails to support Fus3-dependent mating in yeast. Mol. Cell. Biol. 24(20), 9221-38.
- Mattioli I, Dittrich-Breiholz O, Livingstone M, Kracht M, Schmitz ML (2004) Comparative analysis of T-cell costimulation and CD43 activation reveals novel signaling pathways and target genes. Blood 104(10), 3302-4.
- Pasqualucci L, Guglielmino R, Houldsworth J, Mohr J, Aoufouchi S, Polakiewicz R, Chaganti RS, Dalla-Favera R (2004) Expression of the AID protein in normal and neoplastic B cells. Blood 104(10), 3318-25.
- Buss H, Dörrie A, Schmitz ML, Frank R, Livingstone M, Resch K, Kracht M (2004) Phosphorylation of serine 468 by GSK-3beta negatively regulates basal p65 NF-kappaB activity. J. Biol. Chem. 279(48), 49571-4.
- Thomas GV, Horvath S, Smith BL, Crosby K, Lebel LA, Schrage M, Said J, De Kernion J, Reiter RE, Sawyers CL (2004) Antibody-based profiling of the phosphoinositide 3-kinase pathway in clinical prostate cancer. Clin. Cancer Res. 10(24), 8351-6.
2003
- Dolled-Filhart M, Camp RL, Kowalski DP, Smith BL, Rimm DL (2003) Tissue microarray analysis of signal transducers and activators of transcription 3 (Stat3) and phospho-Stat3 (Tyr705) in node-negative breast cancer shows nuclear localization is associated with a better prognosis. Clin. Cancer Res. 9(2), 594-600.
- Kielhorn E, Provost E, Olsen D, D'Aquila TG, Smith BL, Camp RL, Rimm DL (2003) Tissue microarray-based analysis shows phospho-beta-catenin expression in malignant melanoma is associated with poor outcome. Int. J. Cancer 103(5), 652-6.
- Yang H, Cooley D, Legakis JE, Ge Q, Andrade R, Mattingly RR (2003) Phosphorylation of the Ras-GRF1 exchange factor at Ser916/898 reveals activation of Ras signaling in the cerebral cortex. J. Biol. Chem. 278(15), 13278-85.
- Kovarova H, Hajduch M, Livingstone M, Dzubak P, Lefkovits I (2003) Analysis of state-specific phosphorylation of proteins by two-dimensional gel electrophoresis approach. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 787(1), 53-61.
- Wang Y, Ge Q, Houston D, Thorner J, Errede B, Dohlman HG (2003) Regulation of Ste7 ubiquitination by Ste11 phosphorylation and the Skp1-Cullin-F-box complex. J. Biol. Chem. 278(25), 22284-9.
- Solan JL, Fry MD, TenBroek EM, Lampe PD (2003) Connexin43 phosphorylation at S368 is acute during S and G2/M and in response to protein kinase C activation. J. Cell. Sci. 116(Pt 11), 2203-11.
- Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 100(12), 6940-5.
- Choe G, Horvath S, Cloughesy TF, Crosby K, Seligson D, Palotie A, Inge L, Smith BL, Sawyers CL, Mischel PS (2003) Analysis of the phosphatidylinositol 3'-kinase signaling pathway in glioblastoma patients in vivo. Cancer Res. 63(11), 2742-6.
- Jacobberger JW, Sramkoski RM, Frisa PS, Ye PP, Gottlieb MA, Hedley DW, Shankey TV, Smith BL, Paniagua M, Goolsby CL (2003) Immunoreactivity of Stat5 phosphorylated on tyrosine as a cell-based measure of Bcr/Abl kinase activity. Cytometry A 54(2), 75-88.
- Li Y, Eitan S, Wu J, Evans CJ, Kieffer B, Sun X, Polakiewicz RD (2003) Morphine induces desensitization of insulin receptor signaling. Mol. Cell. Biol. 23(17), 6255-66.
- Eitan S, Bryant CD, Saliminejad N, Yang YC, Vojdani E, Keith D, Polakiewicz R, Evans CJ (2003) Brain region-specific mechanisms for acute morphine-induced mitogen-activated protein kinase modulation and distinct patterns of activation during analgesic tolerance and locomotor sensitization. J. Neurosci. 23(23), 8360-9.
- Zhan Q, Ge Q, Ohira T, Van Dyke T, Badwey JA (2003) p21-activated kinase 2 in neutrophils can be regulated by phosphorylation at multiple sites and by a variety of protein phosphatases. J. Immunol. 171(7), 3785-93.
- Ohira T, Zhan Q, Ge Q, VanDyke T, Badwey JA (2003) Protein phosphorylation in neutrophils monitored with phosphospecific antibodies. J. Immunol. Methods 281(1-2), 79-94.
2002
- Zhande R, Mitchell JJ, Wu J, Sun XJ (2002) Molecular mechanism of insulin-induced degradation of insulin receptor substrate 1. Mol. Cell. Biol. 22(4), 1016-26.
- Kohn EA, Ruth ND, Brown MK, Livingstone M, Eastman A (2002) Abrogation of the S phase DNA damage checkpoint results in S phase progression or premature mitosis depending on the concentration of 7-hydroxystaurosporine and the kinetics of Cdc25C activation. J. Biol. Chem. 277(29), 26553-64.
- Kim GD, Ni J, Kelesoglu N, Roberts RJ, Pradhan S (2002) Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases. EMBO J. 21(15), 4183-95.
- Zhang H, Zha X, Tan Y, Hornbeck PV, Mastrangelo AJ, Alessi DR, Polakiewicz RD, Comb MJ (2002) Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. J. Biol. Chem. 277(42), 39379-87.
- Eastman A, Kohn EA, Brown MK, Rathman J, Livingstone M, Blank DH, Gribble GW (2002) A novel indolocarbazole, ICP-1, abrogates DNA damage-induced cell cycle arrest and enhances cytotoxicity: similarities and differences to the cell cycle checkpoint abrogator UCN-01. Mol. Cancer Ther. 1(12), 1067-78.
- Kue PF, Taub JS, Harrington LB, Polakiewicz RD, Ullrich A, Daaka Y (2002) Lysophosphatidic acid-regulated mitogenic ERK signaling in androgen-insensitive prostate cancer PC-3 cells. Int. J. Cancer 102(6), 572-9.
2001
- Hornbeck P (2001) Enzyme-linked immunosorbent assays. Curr Protoc Immunol Chapter 2, Unit 2.1.
- Hornbeck P, Fleisher TA, Papadopoulos NM (2001) Isotype determination of antibodies. Curr Protoc Immunol Chapter 2, Unit 2.2.
- Kansra V, Groves C, Gutierrez-Ramos JC, Polakiewicz RD (2001) Phosphatidylinositol 3-kinase-dependent extracellular calcium influx is essential for CX(3)CR1-mediated activation of the mitogen-activated protein kinase cascade. J. Biol. Chem. 276(34), 31831-8.
- Davids MS, Crawford E, Weremowicz S, Morton CC, Copeland NG, Gilbert DJ, Jenkins NA, Phelan MC, Comb MJ, Melnick MB (2001) STK25 is a candidate gene for pseudopseudohypoparathyroidism. Genomics 77(1-2), 2-4.
- Gingras AC, Raught B, Gygi SP, Niedzwiecka A, Miron M, Burley SK, Polakiewicz RD, Wyslouch-Cieszynska A, Aebersold R, Sonenberg N (2001) Hierarchical phosphorylation of the translation inhibitor 4E-BP1. Genes Dev. 15(21), 2852-64.
- Tang H, Hornstein E, Stolovich M, Levy G, Livingstone M, Templeton D, Avruch J, Meyuhas O (2001) Amino acid-induced translation of TOP mRNAs is fully dependent on phosphatidylinositol 3-kinase-mediated signaling, is partially inhibited by rapamycin, and is independent of S6K1 and rpS6 phosphorylation. Mol. Cell. Biol. 21(24), 8671-83.
- Rao N, Ghosh AK, Ota S, Zhou P, Reddi AL, Hakezi K, Druker BK, Wu J, Band H (2001) The non-receptor tyrosine kinase Syk is a target of Cbl-mediated ubiquitylation upon B-cell receptor stimulation. EMBO J. 20(24), 7085-95.
- Chung GG, Provost E, Kielhorn EP, Charette LA, Smith BL, Rimm DL (2001) Tissue microarray analysis of beta-catenin in colorectal cancer shows nuclear phospho-beta-catenin is associated with a better prognosis. Clin. Cancer Res. 7(12), 4013-20.
1999
- Gingras AC, Gygi SP, Raught B, Polakiewicz RD, Abraham RT, Hoekstra MF, Aebersold R, Sonenberg N (1999) Regulation of 4E-BP1 phosphorylation: a novel two-step mechanism. Genes Dev. 13(11), 1422-37.
- Carroll RS, Zhang J, Bello L, Melnick MB, Maruyama T, McL Black P (1999) KDR activation in astrocytic neoplasms. Cancer 86(7), 1335-41.