Publications

T Schild, MR McReynolds, C Shea, V Low, BE Schaffer, JM Asara, . . . J Blenis, "NADK is activated by oncogenic signaling to sustain pancreatic ductal adenocarcinoma." Cell Rep. 2021.

C Lhuillier, NP Rudqvist, T Yamazaki, T Zhang, M Charpentier, L Galluzzi, . . . S Demaria, "Radiotherapy-exposed CD8+ and CD4+ neoantigens enhance tumor control." J Clin Invest. PMC7919731. 2021.

S Hwang, P Cavaliere, R Li, LJ Zhu, N Dephoure, EM Torres, "Consequences of aneuploidy in human fibroblasts with trisomy 21." Proc Natl Acad Sci U S A. PMC8017964. 2021.

CE Egan, D Stefanova, A Ahmed, VJ Raja, JW Thiesmeyer, KJ Chen, . . . IM Min, "CSPG4 Is a Potential Therapeutic Target in Anaplastic Thyroid Cancer." Thyroid. 2021.

LW Hii, FF Chung, CW Mai, ZY Yee, HH Chan, VJ Raja, . . . CO Leong, "Sphingosine Kinase 1 Regulates the Survival of Breast Cancer Stem Cells and Non-stem Breast Cancer Cells by Suppression of STAT1." Cells. PMC7226795. 2020.

AP Gomes, D Ilter, V Low, JE Endress, J Fernandez-Garcia, A Rosenzweig, . . . J Blenis, "Age-induced accumulation of methylmalonic acid promotes tumour progression." Nature. PMC7785256. 2020.

J Cyrta, A Augspach, MR De Filippo, D Prandi, P Thienger, M Benelli, . . . MA Rubin, "Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity." Nat Commun. PMC7642293. 2020.

CK Kikani, X Wu, S Fogarty, SAW Kang, N Dephoure, SP Gygi, . . . J Rutter, "Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program." Proc Natl Acad Sci U S A. PMC6534978. 2019.

N Gomez-Banoy, JS Guseh, G Li, A Rubio-Navarro, T Chen, B Poirier, . . . JC Lo, "Adipsin preserves beta cells in diabetic mice and associates with protection from type 2 diabetes in humans." Nat Med. PMC7256970. 2019.

AP Gomes, D Ilter, V Low, A Rosenzweig, ZJ Shen, T Schild, . . . J Blenis, "Dynamic Incorporation of Histone H3 Variants into Chromatin Is Essential for Acquisition of Aggressive Traits and Metastatic Colonization." Cancer Cell. PMC6801101. 2019.

DC Di Giammartino, A Kloetgen, A Polyzos, Y Liu, D Kim, D Murphy, . . . E Apostolou, "KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks." Nat Cell Biol. PMC7339746. 2019.

PS Caceres, D Gravotta, PJ Zager, N Dephoure, E Rodriguez-Boulan, "Quantitative proteomics of MDCK cells identify unrecognized roles of clathrin adaptor AP-1 in polarized distribution of surface proteins." Proc Natl Acad Sci U S A. PMC6575629. 2019.

KM Boehm, B Bhinder, VJ Raja, N Dephoure, O Elemento, "Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome." BMC Bioinformatics. PMC6321722. 2019.

A Berger, NJ Brady, R Bareja, BD Robinson, V Conteduca, MA Augello, . . . DS Rickman, "N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer." J Clin Invest. 2019.

MA Augello, D Liu, LD Deonarine, BD Robinson, D Huang, S Stelloo, . . . CE Barbieri, "CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis." Cancer Cell. 2019.

A Ahmed, VJ Raja, P Cavaliere, N Dephoure, "Robust, Reproducible, and Economical Phosphopeptide Enrichment Using Calcium Titanate." J Proteome Res. 2019.

SO Yoon, S Shin, FA Karreth, GR Buel, MP Jedrychowski, DR Plas, . . . J Blenis, "Focal Adhesion- and IGF1R-Dependent Survival and Migratory Pathways Mediate Tumor Resistance to mTORC1/2 Inhibition." Mol Cell. 2017.

V Thai, N Dephoure, A Weiss, J Ferguson, R Leitao, SP Gygi, DR Kellogg, "Protein Kinase C Controls Binding of Igo/ENSA Proteins to Protein Phosphatase 2A in Budding Yeast." J Biol Chem. PMC5377806. 2017.

G Lee, Y Zheng, S Cho, C Jang, C England, JM Dempsey, . . . J Blenis, "Post-transcriptional Regulation of De Novo Lipogenesis by mTORC1-S6K1-SRPK2 Signaling." Cell. 2017.

S Hwang, HT Gustafsson, C O'Sullivan, G Bisceglia, X Huang, C Klose, . . . EM Torres, "Serine-Dependent Sphingolipid Synthesis Is a Metabolic Liability of Aneuploid Cells." Cell Rep. PMC5747309. 2017.

FK Huang, G Zhang, K Lawlor, A Nazarian, J Philip, P Tempst, . . . TA Neubert, "Deep Coverage of Global Protein Expression and Phosphorylation in Breast Tumor Cell Lines Using TMT 10-plex Isobaric Labeling." J Proteome Res. PMC5336479. 2017.

J Clarke, N Dephoure, I Horecka, S Gygi, D Kellogg, "A conserved signaling network monitors delivery of sphingolipids to the plasma membrane in budding yeast." Mol Biol Cell. PMC5620368. 2017.

C Zhou, AE Elia, ML Naylor, N Dephoure, BA Ballif, G Goel, . . . SJ Elledge, "Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks." Proc Natl Acad Sci U S A. PMC4932963. 2016.

N Ron-Harel, D Santos, JM Ghergurovich, PT Sage, A Reddy, SB Lovitch, . . . MC Haigis, "Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation." Cell Metab. PMC5330619. 2016.

H Xu, N Dephoure, H Sun, H Zhang, F Fan, J Liu, . . . C Zhou, "Proteomic Profiling of Paclitaxel Treated Cells Identifies a Novel Mechanism of Drug Resistance Mediated by PDCD4." Journal of Proteome Research. 2015.

R Lucena, N Dephoure, S Gygi, D Kellogg, V Tallada, R Daga, J Jimenez, "Nucleocytoplasmic transport in the midzone membrane domain controls yeast mitotic spindle disassembly." Journal of Cell Biology. 2015.

A Elia, A Boardman, D Wang, E Huttlin, R Everley, N Dephoure, . . . S Elledge, "Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response." Molecular Cell. 2015.

J Zapata, N Dephoure, T MacDonough, Y Yu, E Parnell, M Mooring, . . . D Kellogg, "PP2A(Rts1) is a master regulator of pathways that control cell size." Journal of Cell Biology. 2014.

J Van Vranken, D Bricker, N Dephoure, S Gygi, J Cox, C Thummel, J Rutter, "SDHAF4 Promotes Mitochondrial Succinate Dehydrogenase Activity and Prevents Neurodegeneration." Cell Metabolism. 2014.

N Dephoure, S Hwang, C O'Sullivan, S Dodgson, S Gygi, A Amon, E Torres, "Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast." Elife. 2014.

Y Chen, G Umanah, N Dephoure, S Andrabi, S Gygi, T Dawson, . . . J Rutter, "Msp1/ATAD1 maintains mitochondrial function by facilitating the degradation of mislocalized tail-anchored proteins." Embo Journal. 2014.

G Laurent, N German, A Saha, V de Boer, M Davies, T Koves, . . . M Haigis, "SIRT4 Coordinates the Balance between Lipid Synthesis and Catabolism by Repressing Malonyl CoA Decarboxylase." Molecular Cell. 2013.

Y Kwon, A Vinayagam, X Sun, N Dephoure, S Gygi, P Hong, N Perrimon, "The Hippo Signaling Pathway Interactome." Science. 2013.

J Heo, J Nielson, N Dephoure, S Gygi, J Rutter, "Intramolecular interactions control Vms1 translocation to damaged mitochondria." Molecular Biology of the Cell. 2013.

A Goranov, A Gulati, N Dephoure, T Takahara, T Maeda, S Gygi, . . . A Amon, "Changes in Cell Morphology Are Coordinated with Cell Growth through the TORC1 Pathway." Current Biology. 2013.

N Dephoure, K Gould, S Gygi, D Kellogg, "Mapping and analysis of phosphorylation sites: a quick guide for cell biologists." Molecular Biology of the Cell. 2013.

N Dephoure, S Gygi, "Hyperplexing: A Method for Higher-Order Multiplexed Quantitative Proteomics Provides a Map of the Dynamic Response to Rapamycin in Yeast." Science Signaling. 2012.

Y Chen, E Taylor, N Dephoure, J Heo, A Tonhato, I Papandreou, . . . J Rutter, "Identification of a Protein Mediating Respiratory Supercomplex Stability." Cell Metabolism. 2012.

D Bricker, E Taylor, J Schell, T Orsak, A Boutron, Y Chen, . . . J Rutter, "A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila, and Humans." Science. 2012.

R Wu, W Haas, N Dephoure, E Huttlin, B Zhai, M Sowa, S Gygi, "A large-scale method to measure absolute protein phosphorylation stoichiometries." Nature Methods. 2011.

R Wu, N Dephoure, W Haas, E Huttlin, B Zhai, M Sowa, S Gygi, "Correct Interpretation of Comprehensive Phosphorylation Dynamics Requires Normalization by Protein Expression Changes." Molecular & Cellular Proteomics. 2011.

T Sun, N Aceto, K Meerbrey, J Kessler, C Zhou, I Migliaccio, . . . T Westbrook, "Activation of Multiple Proto-oncogenic Tyrosine Kinases in Breast Cancer via Loss of the PTPN12 Phosphatase." Cell. 2011.

H Shen, S Ferguson, N Dephoure, R Park, Y Yang, L Volpicelli-Daley, . . . P De Camilli, "Constitutive activated Cdc42-associated kinase (Ack) phosphorylation at arrested endocytic clathrin-coated pits of cells that lack dynamin." Molecular Biology of the Cell. 2011.

S Harvey, G Enciso, N Dephoure, S Gygi, J Gunawardena, D Kellogg, "A phosphatase threshold sets the level of Cdk1 activity in early mitosis in budding yeast." Molecular Biology of the Cell. 2011.

N Dephoure, S Gygi, "A solid phase extraction-based platform for rapid phosphoproteomic analysis." Methods. 2011.

E Torres, N Dephoure, A Panneerselvam, C Tucker, C Whittaker, S Gygi, . . . A Amon, "Identification of Aneuploidy-Tolerating Mutations." Cell. 2010.

J Heo, N Livnat-Levanon, E Taylor, K Jones, N Dephoure, J Ring, . . . J Rutter, "A Stress-Responsive System for Mitochondrial Protein Degradation." Molecular Cell. 2010.

D Chou, B Adamson, N Dephoure, X Tan, A Nottke, K Hurov, . . . S Elledge, "A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage." Proceedings of the National Academy of Sciences of the United States of America. 2010.

H Hao, O Khalimonchuk, M Schraders, N Dephoure, J Bayley, H Kunst, . . . J Rutter, "SDH5, a Gene Required for Flavination of Succinate Dehydrogenase, Is Mutated in Paraganglioma." Science. 2009.

N Dephoure, C Zhou, J Villen, S Beausoleil, C Bakalarski, S Elledge, S Gygi, "A quantitative atlas of mitotic phosphorylation." Proceedings of the National Academy of Sciences of the United States of America. 2008.

C Bakalarski, W Haas, N Dephoure, S Gygi, "The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics." Analytical and Bioanalytical Chemistry. 2007.

R Howson, W Huh, S Ghaemmaghami, J Falvo, K Bower, A Belle, . . . E O'Shea, "Construction, verification and experimental use of two epitope-tagged collections budding yeast strains." Comparative and Functional Genomics. 2005.

N Dephoure, R Howson, J Blethrow, K Shokat, E O'Shea, "Combining chemical genetics and proteomics to identify protein kinase substrates." Proceedings of the National Academy of Sciences of the United States of America. 2005.

S Ghaemmaghami, W Huh, K Bower, R Howson, A Belle, N Dephoure, . . . J Weissman, "Global analysis of protein expression in yeast." Nature. 2003.