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2021年 文献
Khbouz B, Rowart P, Poma L, Dahlke E, Bottner M, Stokes M , Bolen G, Rahmouni S, Theilig F, Jouret F. The genetic deletion of the Dual Specificity Phosphatase 3 (DUSP3) attenuates kidney damage and inflammation following ischemia/reperfusion injury in mouse Acta Physiol (Oxf). 2021;e13735
Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J , Croteau J, Small EC, Sood A, Caprioli RM, Angelo MR, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging Nature Methods. 2021
Simpson CM , Zhang B , Hornbeck PV , Gnad F . Systematic analysis of the intersection of disease mutations with protein modifications. BMC Med Genomics. 2019;12(Suppl 6):109Tan HK, Wu CS, Li J, Hoffman JR , Fry CJ , et al. DNMT3B shapes the mCA landscape and regulates mCG for promoter bivalency in human embryonic stem cells. Nucleic Acids Res. 2019.
Castillo J, Wu E, Lowe C, Stokes MP , et al. CBP/p300 drives the differentiation of Regulatory T cells through transcriptional and non-transcriptional mechanisms. Cancer Res. 2019.
Doll S, Gnad F , Mann M. The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine. Proteomics Clin Appl. 2019;13(2):e1800113.
Guo J, Dai X, Laurent B, Zheng N, Gan W, Zhang J, Guo A , Yuan M, Liu P, Asara JM, Toker A, Shi Y, Pier Pandolfi PP, Wei W. AKT methylation by SETDB1 promotes AKT kinase activity and oncogenic functions. Nat Cell Biol. 2019;21(2):226-237.
Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F , Beltrao P, Perrimon N. iProteinDB: An Integrative Database of Post-translational Modifications. G3 (Bethesda). 2019;9(1):1-11.
Axel Weber, Sharmistha Dam, Vera V. Saul, Irina Kuznetsova, Christin Müller, Karin Fritz-Wolf, Katja Becker, Uwe Linne, Hongbo Gu , Matthew P. Stokes , Stephan Pleschka, Michael Kracht, M. Lienhard Schmitz. Phosphoproteome analysis of cells infected with adapted and non-adapted influenza A virus reveals novel pro- and antiviral signaling networks. J Virol. 2019.
Kumar S, Gu Y, Abudu YP, Bruun JA, Jain A, Farzam F, Mudd M, Anonsen JH, Rusten TE, Kasof G , Ktistakis N, Lidke KA, Johansen T, Deretic V. Phosphorylation of Syntaxin 17 by TBK1 Controls Autophagy Initiation. Dev Cell. 2019 2月27日 [Epub ahead of print].
Doll S, Gnad F , Mann M. The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine. Proteomics Clin Appl. 2019.
Guo J, Dai X, Laurent B, Zheng N, Gan W, Zhang J , Guo A , Yuan M, Liu P, Asara JM, Toker A, Shi Y, Pandolfi PP, Wei W. AKT methylation by SETDB1 promotes AKT kinase activity and oncogenic functions. Nat Cell Biol. 2019.
Del Rosario BC, Kriz AJ, Del Rosario AM, Anselmo A, Fry CJ , White FM, Sadreyev RI, Lee JT. Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition. Elife. 2019.
Bansal M, He J, Peyton M, Kustagi M, Iyer A, Comb M , White M, Minna JD, Califano A. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis. PLoS One. 2019.
Krug K, Mertins P, Zhang B , Hornbeck P , Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, Carr SA, Mani DR. A Curated Resource for Phosphosite-specific Signature Analysis. Mol Cell Proteomics. 2019.
Hornbeck PV, Kornhauser JM, Latham V, Murray B, Nandhikonda V, Nord A, Skrzypek E, Wheeler T, Zhang B, Gnad F. 15 years of PhosphoSitePlus® : integrating post-translationally modified sites, disease variants and isoforms. Nucleic Acids Res. 2019.Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F , Beltrao P, Perrimon N. iProteinDB: An Integrative Database of Drosophila Post-translational Modifications. G3 (Bethesda). 2019.
Nord A, Carey K, Hornbeck P , Wheeler T. Splice-Aware Multiple Sequence Alignment of Protein Isoforms. ACM BCB. 2018:200-210.
Paulo JA, Navarrete-perea J, Erickson AR, Knott J , Gygi SP. An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies. J Am Soc Mass Spectrom. 2018;29(7):1505-1511.
Menk AV, Scharping NE, Moreci RS, Xie J , et al. Early TCR Signaling Induces Rapid Aerobic Glycolysis Enabling Distinct Acute T Cell Effector Functions. Cell Rep. 2018;22(6):1509-1521.
Cheng D, Vemulapalli V, Lu Y, Shen J, Aoyagi S , Fry CJ , Yang Y, Foulds CE, Stossi F, Treviño LS, Mancini MA, O'Malley BW, Walker CL, Boyer TG, Bedford MT. CARM1 methylates MED12 to regulate its RNA-binding ability. Life Sci Alliance. 2018.
Hamidi T, Singh AK, Veland N, Vemulapalli V, Chen J, Hardikar S, Bao J, Fry CJ , Yang V , Lee KA , Guo A , Arrowsmith CH, Bedford MT, Chen T. Identification of Rpl29 as a major substrate of the lysine methyltransferase Set7/9. J Biol Chem. 2018.
Thompson SM, Jondal DE, Butters KA, Knudsen BE, Anderson JL, Stokes MP , Jia X , Grande JP, Roberts LR, Callstrom MR, Woodrum DA. Heat stress induced, ligand-independent MET and EGFR signalling in hepatocellular carcinoma. Int J Hyperthermia. 2018.
Paulo JA, Navarrete-Perea J, Erickson AR, Knott J , Gygi SP. An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies. J Am Soc Mass Spectrom. 2018.
Grimes M, Hall B , Foltz L, Levy T , Rikova K , Gaiser J, Cook W, Smirnova E, Wheeler T, Clark NR, Lachmann A, Zhang B , Hornbeck P , Ma'ayan A, Comb M . Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. Sci Signal. 2018.
Ying L, Yan F, Meng Q, Yu L, Yuan X, Gantier MP, Williams BRG, Chan DW, Shi L, Tu Y , Ni P, Wang X, Chen W, Zang X, Xu D, Hu Y. PD-L1 expression is a prognostic factor in subgroups of gastric cancer patients stratified according to their levels of CD8 and FOXP3 immune markers. Oncoimmunology. 2018.
Menk AV, Scharping NE, Moreci RS, Zeng X, Guy C, Salvatore S, Bae H, Xie J , Young HA, Wendell SG, Delgoffe GM. Early TCR Signaling Induces Rapid Aerobic Glycolysis Enabling Distinct Acute T Cell Effector Functions. Cell Rep. 2018.
Wan L, Xu K, Wei Y, Zhang J, Han T, Fry C , Zhang Z, Wang YV, Huang L, Yuan M, Xia W, Chang WC, Huang WC, Liu CL, Chang YC, Liu J, Wu Y, Jin VX, Dai X, Guo J, Liu J, Jiang S, et al. Phosphorylation of EZH2 by AMPK Suppresses PRC2 Methyltransferase Activity and Oncogenic Function. Mol Cell. 2018.
Stokes MP, Zhu Y, Farnsworth CL. Mass spectrometry-based proteomic analysis of the DNA damage response. Front Biosci (Landmark Ed). 2018.Kumar S, Lu B, Davra V, Hornbeck P , Machida K, Birge RB. Crk Tyrosine Phosphorylation Regulates PDGF-BB-inducible Src Activation and Breast Tumorigenicity and Metastasis. Mol Cancer Res. 2018.
Gu H , Ren J , Jia X , Stokes MP (2017) Identification of Post-Translational Modifications from Serum/Plasma by Immunoaffinity Enrichment and LC-MS/MS Analysis Without Depletion of Abundant Proteins. Methods Mol. Biol. 1619, 119–125.Dogan T, Gnad F , Chan J, Phu L, Young A, Chen MJ, Doll S, Stokes MP , Belvin M, Friedman LS, Kirkpatrick DS, Hoeflich KP, Hatzivassiliou G (2017) Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling to the cell cycle. J. Biol. Chem. [Epub ahead of print].
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. Post-transcriptional Regulation of De Novo Lipogenesis by mTORC1-S6K1-SRPK2 Signaling. Cell. 2017.
Hershberger KA, Abraham DM, Martin AS, Mao L, Liu J, Gu H , Locasale JW, Hirschey MD. Sirtuin 5 is required for mouse survival in response to cardiac pressure overload. J Biol Chem. 2017.
Lumpkin RJ, Gu H , Zhu Y, Leonard M, Ahmad AS, Clauser KR, Meyer JG, Bennett EJ, Komives EA. Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. Nat Commun. 2017.
Ying L, Yan F, Meng Q, Yuan X, Yu L, Williams BRG, Chan DW, Shi L, Tu Y , Ni P, Wang X, Xu D, Hu Y. Understanding immune phenotypes in human gastric disease tissues by multiplexed immunohistochemistry. J Transl Med. 2017.
Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K , Hornbeck P , Ma'ayan A. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. Sci Data. 2017.
Takada M, Zhang W, Suzuki A, Kuroda TS, Yu Z, Inuzuka H, Gao D, Wan L, Zhuang M, Hu L, Zhai B, Fry CJ , Bloom K, Li G, Karpen GH, Wei W, Zhang Q. FBW7 Loss Promotes Chromosomal Instability and Tumorigenesis via Cyclin E1/CDK2-Mediated Phosphorylation of CENP-A. Cancer Res. 2017.
Dogan T, Gnad F , Chan J, Phu L, Young A, Chen MJ, Doll S, Stokes MP , Belvin M, Friedman LS, Kirkpatrick DS, Hoeflich KP, Hatzivassiliou G. Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling pathways to the cell cycle. J Biol Chem. 2017.
Chen R, Lai LA, Sullivan Y, Wong M, Wang L, Riddell J , Jung L, Pillarisetty VG, Brentnall TA, Pan S. Disrupting glutamine metabolic pathways to sensitize gemcitabine-resistant pancreatic cancer. Sci Rep. 2017.
Everley RA, Huttlin EL, Erickson AR, Beausoleil SA , Gygi SP. Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags. J Proteome Res. 2017.
Shimizu K, Fukushima H, Ogura K, Lien EC, Nihira NT, Zhang J, North BJ, Guo A , Nagashima K, Nakagawa T, Hoshikawa S, Watahiki A, Okabe K, Yamada A, Toker A, Asara JM, Fukumoto S, Nakayama KI, Nakayama K, Inuzuka H, Wei W. The SCFΒ-TRCP E3 ubiquitin ligase complex targets Lipin1 for ubiquitination and degradation to promote hepatic lipogenesis. Sci Signal. 2017.
Gu H, Ren J, Jia X, Stokes MP. Identification of Post-Translational Modifications from Serum/Plasma by Immunoaffinity Enrichment and LC-MS/MS Analysis Without Depletion of Abundant Proteins. Methods Mol Biol. 2017.Tsanov KM, Pearson DS, Wu Z, Han A, Triboulet R, Seligson MT, Powers JT, Osborne JK, Kane S , Gygi SP, Gregory RI, Daley GQ. LIN28 phosphorylation by MAPK/ERK couples signalling to the post-transcriptional control of pluripotency. Nat Cell Biol. 2017.
Lohmueller JJ, Sato S , Popova L , Chu IM , Tucker MA , Barberena R , Innocenti GM , Cudic M, Ham JD, Cheung WC, Polakiewicz RD , Finn OJ (2016) Antibodies elicited by the first non-viral prophylactic cancer vaccine show tumor-specificity and immunotherapeutic potential. Sci Rep 6, 31740.
Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP , Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M (2016) Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network. Proteomics 16(14), 1992-7.
Gnad F, Doll S, Song K, Stokes MP , Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M (2016) Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms. Proteomics 16(14), 1998-2004.
Li MO , Rudensky AY (2016) T cell receptor signalling in the control of regulatory T cell differentiation and function. Nat. Rev. Immunol. 16(4), 220–33.Gu H, Ren JM, Jia X, Levy T, Rikova K, Yang V, Lee KA, Stokes MP, Silva JC (2016) Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion. Mol. Cell Proteomics 15(2), 692–702.Stokes M. , et al. Antibody-Based Proteomic Analysis of Apoptosis Signaling. In: Perpetua M. (Ed.) Apoptosis Methods in Toxicology. New York, NY: Humana Press; 2016: 163-178.Gu H, Stokes MP , Silva JC. Proteomic Analysis of Post-Translational Modifications in Neurobiology. In: Grant J, Hong L (Eds.) Analysis of Post-Translation Modifications and Proteolysis in Neuroscience. Vol. 114. New York, NY: Humana Press; 2016: TBD.Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA , Jedrychowski MP, Finley DJ, Harper JW, Gygi SP. Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes. Cell Syst. 2016.
Beckerman R, Yoh K, Mattia-Sansobrino M, Zupnick A, Laptenko O, Karni-Schmidt O, Ahn J, Byeon IJ, Keezer S , Prives C. Lysines in the tetramerization domain of p53 selectively modulate G1 arrest. Cell Cycle. 2016.
Massey KJ, Li Q, Rossi NF, Keezer SM , Mattingly RR, Yingst DR. Phosphorylation of rat kidney Na-K pump at Ser938 is required for rapid angiotensin II-dependent stimulation of activity and trafficking in proximal tubule cells. Am J Physiol Cell Physiol. 2016.
Morvan MG , Lanier LL (2015) NK cells and cancer: you can teach innate cells new tricks. Nat Rev Cancer 16(1), 7-19.Childs RW , Carlsten M (2015) Therapeutic approaches to enhance natural killer cell cytotoxicity against cancer: the force awakens. Nat Rev Drug Discov 14(7), 487-98.Kumar S, Lu B, Dixit U, Hossain S, Liu Y, Li J, Hornbeck P , Zheng W, Sowalsky AG, Kotula L, Birge RB (2015) Reciprocal regulation of Abl kinase by Crk Y251 and Abi1 controls invasive phenotypes in glioblastoma. Oncotarget 6(35), 37792–807.
Sriram G, Jankowski W, Kasikara C, Reichman C, Saleh T, Nguyen KQ, Li J, Hornbeck P , Machida K, Liu T, Li H, Kalodimos CG, Birge RB (2015) Iterative tyrosine phosphorylation controls non-canonical domain utilization in Crk. Oncogene 34(32), 4260–9.
Hornbeck PV (2015) Enzyme-Linked Immunosorbent Assays. Curr Protoc Immunol 110, 2.1.1–23.Gray LR, Sultana MR, Rauckhorst AJ, Oonthonpan L, Tompkins SC, Sharma A, Fu X, Miao R, Pewa AD, Brown KS, Lane EE, Dohlman A, Zepeda-Orozco D, Xie J , Rutter J, Norris AW, Cox JE, Burgess SC, Potthoff MJ, Taylor EB (2015) Hepatic Mitochondrial Pyruvate Carrier 1 Is Required for Efficient Regulation of Gluconeogenesis and Whole-Body Glucose Homeostasis. Cell Metab. 22(4), 669–81.
Wimberly H, Brown JR, Schalper K, Haack H, Silver MR , Nixon C, Bossuyt V, Pusztai L, Lannin DR, Rimm DL (2015) PD-L1 Expression Correlates with Tumor-Infiltrating Lymphocytes and Response to Neoadjuvant Chemotherapy in Breast Cancer. Cancer Immunol Res 3(4), 326–32.
Kee JM, Oslund RC, Couvillon AD , Muir TW (2015) A second-generation phosphohistidine analog for production of phosphohistidine antibodies. Org. Lett. 17(2), 187–9.
Honda T, Obara Y, Yamauchi A, Couvillon AD , Mason JJ , Ishii K, Nakahata N (2015) Phosphorylation of ERK5 on Thr732 is associated with ERK5 nuclear localization and ERK5-dependent transcription. PLoS ONE 10(2), e0117914.
Werner S, Brors B, Eick J, Marques E, Pogenberg V, Parret A, Kemming D, Wood AW , Edgren H, Neubauer H, Streichert T, Riethdorf S, Bedi U, Baccelli I, Jucker M, Eils R, Fehm T, Trumpp A, Johnsen SA, Klefstrom J, Wilmanns M, Muller V, Pantel K, Wikman H (2015) Suppression of early hematogenous dissemination of human breast cancer cells to bone marrow by retinoic acid induced 2. Cancer Discov [Epub ahead of print].
Lawan A, Zhang L, Gatzke F, Min K, Jurczak MJ, Al-Mutairi M, Richter P, Camporez JP, Couvillon A , Pesta D, Roth Flach RJ, Shulman GI, Bennett AM (2015) Hepatic mitogen-activated protein kinase phosphatase 1 selectively regulates glucose metabolism and energy homeostasis. Mol. Cell. Biol. 35(1), 26–40.
Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E (2015) PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 43(Database issue), D512–20.Paulo JA, McAllister FE, Everley RA, Beausoleil SA , Banks AS, Gygi SP (2015) Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics. Proteomics 15(2-3), 462–73.
Lin R, Elf S, Shan C, Kang HB, Ji Q, Zhou L, Hitosugi T, Zhang L, Zhang S, Seo JH, Xie J , Tucker M , Gu TL , Sudderth J, Jiang L, Mitsche M, DeBerardinis RJ, Wu S, Li Y, Mao H, Chen PR, Wang D, Chen GZ, Hurwitz SJ, Lonial S, Arellano ML, Khoury HJ, Khuri FR, Lee BH, Lei Q, Brat DJ, Ye K, Boggon TJ, He C, Kang S, Fan J, Chen J (2015) 6-Phosphogluconate dehydrogenase links oxidative PPP, lipogenesis and tumour growth by inhibiting LKB1-AMPK signalling. Nat. Cell Biol. 17(11), 1484–96.
Patterson HC, Gerbeth C, Thiru P, Vögtle NF, Knoll M, Shahsafaei A, Samocha KE, Huang CX, Harden MM, Song R, Chen C, Kao J, Shi J, Salmon W, Shaul YD, Stokes MP , Silva JC, Bell GW, MacArthur DG, Ruland J, Meisinger C, Lodish HF (2015) A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling. Proc. Natl. Acad. Sci. U.S.A. 112(42), E5679–88.
Barrows D, Schoenfeld SM, Hodakoski C, Silkov A, Honig B, Couvillon A , Shymanets A, Nuernberg B, Asara JM, Parsons R (2015) PAK kinases mediate the phosphorylation of PREX2 to initiate feedback inhibition of Rac1. J. Biol. Chem. [Epub ahead of print].
Lawan A, Zhang L, Gatzke F, Min K, Jurczak MJ, Al-Mutairi M, Richter P, Camporez JP, Couvillon A , Pesta D, Roth Flach RJ, Shulman GI, Bennett AM (2015) Hepatic mitogen-activated protein kinase phosphatase 1 selectively regulates glucose metabolism and energy homeostasis. Mol. Cell. Biol. 35(1), 26–40.
Zhang L, Tran NT, Su H, Wang R, Lu Y, Tang H, Aoyagi S , Guo A , Khodadadi-Jamayran A, Zhou D, Qian K, Hricik T, Côté J, Han X, Zhou W, Laha S, Abdel-Wahab O, Levine RL, Raffel G, Liu Y, Chen D, Li H, et al. Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing. Elife 2015.
Shan C, Elf S, Ji Q, Kang HB, Zhou L, Hitosugi T, Jin L, Lin R, Zhang L, Seo JH, Xie J , Tucker M , Gu TL , Sudderth J, Jiang L, DeBerardinis RJ, Wu S, Li Y, Mao H, Chen PR, Wang D, Chen GZ, Lonial S, Arellano ML, Khoury HJ, Khuri FR, Lee BH, Brat DJ, Ye K, Boggon TJ, He C, Kang S, Fan J, Chen J (2014) Lysine acetylation activates 6-phosphogluconate dehydrogenase to promote tumor growth. Mol. Cell 55(4), 552–65.
Mulherkar S, Uddin MD, Couvillon AD , Sillitoe RV, Tolias KF (2014) The small GTPases RhoA and Rac1 regulate cerebellar development by controlling cell morphogenesis, migration and foliation. Dev. Biol. 394(1), 39–53.
Oslund RC, Kee JM, Couvillon AD , Bhatia VN, Perlman DH, Muir TW (2014) A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism. J. Am. Chem. Soc. 136(37), 12899–911.
Lauriol J, Keith K, Jaffré F, Couvillon A , Saci A, Goonasekera SA, McCarthy JR, Kessinger CW, Wang J, Ke Q, Kang PM, Molkentin JD, Carpenter C, Kontaridis MI (2014) RhoA signaling in cardiomyocytes protects against stress-induced heart failure but facilitates cardiac fibrosis. Sci Signal 7(348), ra100.
Fan J, Kang HB, Shan C, Elf S, Lin R, Xie J , Gu TL, Aguiar M , Lonning S, Chung TW, Arellano M, Khoury HJ, Shin DM, Khuri FR, Boggon TJ, Kang S, Chen J (2014) Tyr-301 phosphorylation inhibits pyruvate dehydrogenase by blocking substrate binding and promotes the Warburg effect. J. Biol. Chem. 289(38), 26533–41.
Fan J, Shan C, Kang HB, Elf S, Xie J , Tucker M, Gu TL, Aguiar M , Lonning S, Chen H, Mohammadi M, Britton LM, Garcia BA, Alečković M, Kang Y, Kaluz S, Devi N, Van Meir EG, Hitosugi T, Seo JH, Lonial S, Gaddh M, Arellano M, Khoury HJ, Khuri FR, Boggon TJ, Kang S, Chen J (2014) Tyr phosphorylation of PDP1 toggles recruitment between ACAT1 and SIRT3 to regulate the pyruvate dehydrogenase complex. Mol. Cell 53(4), 534–48.
Guo A, Gu H, Zhou J, Mulhern D, Wang Y, Lee KA, Yang V, Aguiar M , Kornhauser J, Jia X, Ren J, Beausoleil SA, Silva JC , Vemulapalli V, Bedford MT, Comb MJ (2014) Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol. Cell Proteomics 13(1), 372–87.Wang L, Zhao Z, Meyer MB, Saha S, Yu M, Guo A , Wisinski KB, Huang W, Cai W, Pike JW, Yuan M, Ahlquist P, Xu W (2014) CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis. Cancer Cell 25(1), 21–36.
Sanidas I, Polytarchou C, Hatziapostolou M, Ezell SA, Kottakis F, Hu L, Guo A, Xie J, Comb MJ , Iliopoulos D, Tsichlis PN (2014) Phosphoproteomics screen reveals akt isoform-specific signals linking RNA processing to lung cancer. Mol. Cell 53(4), 577–90.
Schell JC, Olson KA, Jiang L, Hawkins AJ, Van Vranken JG, Xie J , Egnatchik RA, Earl EG, DeBerardinis RJ, Rutter J (2014) A role for the mitochondrial pyruvate carrier as a repressor of the warburg effect and colon cancer cell growth. Mol. Cell 56(3), 400–13.
Paardekooper Overman J, Yi JS, Bonetti M, Soulsby M, Preisinger C, Stokes MP, Hui L, Silva JC, Overvoorde J, Giansanti P, Heck AJ, Kontaridis MI, den Hertog J, Bennett AM (2014) PZR coordinates Shp2 Noonan and LEOPARD syndrome signaling in zebrafish and mice. Mol. Cell. Biol. 34(15), 2874–89.
Li N, Fassl A, Chick J, Inuzuka H, Li X, Mansour MR, Liu L, Wang H, King B, Shaik S, Gutierrez A, Ordureau A, Otto T, Kreslavsky T, Baitsch L, Bury L, Meyer CA, Ke N, Mulry KA, Kluk MJ, Roy M, Kim S, Zhang X , Geng Y, Zagozdzon A, Jenkinson S, Gale RE, Linch DC, Zhao JJ, Mullighan CG, Harper JW, Aster JC, Aifantis I, von Boehmer H, Gygi SP, Wei W, Look AT, Sicinski P (2014) Cyclin C is a haploinsufficient tumour suppressor. Nat. Cell Biol. 16(11), 1080–91.
Nifoussi SK, Ratcliffe NR, Ornstein DL, Kasof G , Strack S, Craig RW (2014) Inhibition of protein phosphatase 2A (PP2A) prevents Mcl-1 protein dephosphorylation at the Thr-163/Ser-159 phosphodegron, dramatically reducing expression in Mcl-1-amplified lymphoma cells. J. Biol. Chem. 289(32), 21950–9.
Gerhardt DM, Pajcini KV, D'altri T, Tu L, Jain R, Xu L, Chen MJ, Rentschler S, Shestova O, Wertheim GB, Tobias JW, Kluk M, Wood AW , Aster JC, Gimotty PA, Epstein JA, Speck N, Bigas A, Pear WS (2014) The Notch1 transcriptional activation domain is required for development and reveals a novel role for Notch1 signaling in fetal hematopoietic stem cells. Genes Dev. 28(6), 576–93.
Semenova I, Ikeda K, Resaul K, Kraikivski P, Aguiar M , Gygi S, Zaliapin I, Cowan A, Rodionov V (2014) Regulation of microtubule-based transport by MAP4. Mol. Biol. Cell 25(20), 3119–32.
Liew GM, Ye F, Nager AR, Murphy JP, Lee JS, Aguiar M , Breslow DK, Gygi SP, Nachury MV (2014) The Intraflagellar Transport Protein IFT27 Promotes BBSome Exit from Cilia through the GTPase ARL6/BBS3. Dev. Cell 31(3), 265–78.
Verma R, Su S, McCrann DJ, Green JM, Leu K, Young PR, Schatz PJ, Silva JC , Stokes MP, Wojchowski DM (2014) RHEX, a novel regulator of human erythroid progenitor cell expansion and erythroblast development. J. Exp. Med. 211(9), 1715–22.
Shan C, Kang HB, Elf S, Xie J, Gu TL, Aguiar M, Lonning S, Hitosugi T, Chung TW, Arellano M, Khoury HJ, Shin DM, Khuri FR, Boggon TJ, Fan J (2014) Tyr-94 phosphorylation inhibits pyruvate dehydrogenase phosphatase 1 and promotes tumor growth. J. Biol. Chem. 289(31), 21413–22.
Ordureau A, Sarraf SA, Duda DM, Heo JM, Jedrychowski MP, Sviderskiy VO, Olszewski JL, Koerber JT, Xie T, Beausoleil SA , Wells JA, Gygi SP, Schulman BA, Harper JW (2014) Quantitative Proteomics Reveal a Feedforward Mechanism for Mitochondrial PARKIN Translocation and Ubiquitin Chain Synthesis. Mol. Cell 56(3), 360–75.
Gray VE, Liu L, Nirankari R, Hornbeck PV , Kumar S (2014) Signatures of natural selection on mutations of residues with multiple posttranslational modifications. Mol. Biol. Evol. 31(7), 1641–5.
Sriram G, Jankowski W, Kasikara C, Reichman C, Saleh T, Nguyen KQ, Li J, Hornbeck P , Machida K, Liu T, Li H, Kalodimos CG, Birge RB (2014) Iterative tyrosine phosphorylation controls non-canonical domain utilization in Crk. Oncogene [Epub ahead of print].
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Aguiar M , Masse R, Gibbs BF (2006) Mass spectrometric quantitation of C-reactive protein using labeled tryptic peptides. Anal. Biochem. 354(2), 175–81.Schmelzle K, Kane S, Gridley S, Lienhard GE, White FM (2006) Temporal dynamics of tyrosine phosphorylation in insulin signaling. Diabetes 55(8), 2171–9.
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