Publications Content

A Cell-Line-Specific Atlas of PARP-Mediated Protein Asp/Glu-ADP-Ribosylation in Breast Cancer.

Zhen Y, Zhang Y, Yu Y Cell Rep 2017 Nov 21 8 2326-2337

Global Phosphoproteomic Analysis of Insulin/Akt/mTORC1/S6K Signaling in Rat Hepatocytes.

Zhang Y, Zhang Y, Yu Y J. Proteome Res. 2017 Jul

Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation.

 Gibson BA, Zhang Y, Jiang H, Hussey KM, Shrimp JH, Lin H, Schwede F, Yu Y, Kraus WL Science 2016 Jun

Secreted IGFBP5 mediates mTORC1-dependent feedback inhibition of IGF-1 signalling.

 Ding M, Bruick RK, Yu Y Nat. Cell Biol. 2016 Feb

The LC Domain of hnRNPA2 Adopts Similar Conformations in Hydrogel Polymers, Liquid-like Droplets, and Nuclei.

 Xiang S, Kato M, Wu LC, Lin Y, Ding M, Zhang Y, Yu Y, McKnight SL Cell 2015 Nov 163 4 829-39

Crescendo: A Protein Sequence Database Search Engine for Tandem Mass Spectra.

 Wang J, Zhang Y, Yu Y J. Am. Soc. Mass Spectrom. 2015 Apr

Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome.

 Zhang Y, Wang J, Ding M, Yu Y Nat. Methods 2013 Aug

Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling.

 Yu Y, Yoon SO, Poulogiannis G, Yang Q, Ma XM, Villén J, Kubica N, Hoffman GR, Cantley LC, Gygi SP, Blenis J Science 2011 Jun 332 6035 1322-6

A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry.

 Yu Y, Anjum R, Kubota K, Rush J, Villen J, Gygi SP Proc. Natl. Acad. Sci. U.S.A. 2009 Jul 106 28 11606-11

Determination of the sites of tyrosine O-sulfation in peptides and proteins.

 Yu Y, Hoffhines AJ, Moore KL, Leary JA Nat. Methods 2007 Jul 4 7 583-8

Demethylation of the Protein Phosphatase PP2A Promotes Demethylation of Histones to Enable Their Function as a Methyl Group Sink.

 Ye C, Sutter BM, Wang Y, Kuang Z, Zhao X, Yu Y, Tu BP Mol. Cell 2019 Feb

Mapping the molecular signatures of diet-induced NASH and its regulation by the hepatokine Tsukushi.

 Xiong X, Wang Q, Wang S, Zhang J, Liu T, Guo L, Yu Y, Lin JD Mol Metab 2018 Dec

Quantitative phosphoproteomic analysis of the molecular substrates of sleep need.

 Wang Z, Ma J, Miyoshi C, Li Y, Sato M, Ogawa Y, Lou T, Ma C, Gao X, Lee C, Fujiyama T, Yang X, Zhou S, Hotta-Hirashima N, Klewe-Nebenius D, Ikkyu A, Kakizaki M, Kanno S, Cao L, Takahashi S, Peng J, Yu Y, Funato H, Yanagisawa M, Liu Q Nature 2018 Jun

Loss of a Negative Regulator of mTORC1 Induces Aerobic Glycolysis and Altered Fiber Composition in Skeletal Muscle.

 Dutchak PA, Estill-Terpack SJ, Plec AA, Zhao X, Yang C, Chen J, Ko B, Deberardinis RJ, Yu Y, Tu BP Cell Rep 2018 May 23 7 1907-1914

mTORC1 Promotes Metabolic Reprogramming by the Suppression of GSK3-Dependent Foxk1 Phosphorylation.

 He L, Gomes AP, Wang X, Yoon SO, Lee G, Nagiec MJ, Cho S, Chavez A, Islam T, Yu Y, Asara JM, Kim BY, Blenis J Mol. Cell 2018 May

Proteomic analysis of the downstream signaling network of PARP1.

 Zhen Y, Yu Y Biochemistry 2018 Jan

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 Nov

Genome-wide identification and differential analysis of translational initiation.

 Zhang P, He D, Xu Y, Hou J, Pan BF, Wang Y, Liu T, Davis CM, Ehli EA, Tan L, Zhou F, Hu J, Yu Y, Chen X, Nguyen TM, Rosen JM, Hawke DH, Ji Z, Chen Y Nat Commun 2017 Nov 8 1 1749

EZH2 contributes to the response to PARP inhibitors through its PARP-mediated poly-ADP ribosylation in breast cancer.

 Yamaguchi H, Du Y, Nakai K, Ding M, Chang SS, Hsu JL, Yao J, Wei Y, Nie L, Jiao S, Chang WC, Chen CH, Yu Y, Hortobagyi GN, Hung MC Oncogene 2017 Sep

Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer.

 Zhao X, Huffman KE, Fujimoto J, Canales JR, Girard L, Nie G, Heymach JV, Wistuba II, Minna JD, Yu Y J. Am. Soc. Mass Spectrom. 2017 Jul

Biomarker Accessible and Chemically Addressable Mechanistic Subtypes of BRAF Melanoma.

 Eskiocak B, McMillan E, Mendiratta S, Kollipara R, Zhang H, Humphries C, Wang C, Garcia-Rodriguez J, Ding M, Zaman A, Rosales T, Eskiocak U, Smith MP, Sudderth J, Komurov K, DeBerardinis RJ, Wellbrock C, Davies MA, Wargo JA, Yu Y, De Brabander JK, Williams NS, Chin L, Rizos H, Long GV, Kittler R, White M Cancer Discov 2017 Apr

Toxic PRn poly-dipeptides encoded by the C9orf72 repeat expansion block nuclear import and export.

 Shi KY, Mori E, Nizami ZF, Lin Y, Kato M, Xiang S, Wu LC, Ding M, Yu Y, Gall JG, McKnight SL Proc. Natl. Acad. Sci. U.S.A. 2017 Jan

PARP-1 Controls the Adipogenic Transcriptional Program by PARylating C/EBPß and Modulating Its Transcriptional Activity.

 Luo X, Ryu KW, Kim DS, Nandu T, Medina CJ, Gupte R, Gibson BA, Soccio RE, Yu Y, Gupta RK, Kraus WL Mol. Cell 2017 Jan 65 2 260-271

The Emerging Function and Mechanism of ceRNAs in Cancer.

 Wang Y, Hou J, He D, Sun M, Zhang P, Yu Y, Chen Y Trends Genet. 2016 Feb

Quantitative Secretomic Analysis Identifies Extracellular Protein Factors That Modulate the Metastatic Phenotype of Non-Small Cell Lung Cancer.

 Hu R, Huffman KE, Chu M, Zhang Y, Minna JD, Yu Y J. Proteome Res. 2016 Jan

Poly-ADP ribosylation of PTEN by tankyrases promotes PTEN degradation and tumor growth.

 Li N, Zhang Y, Han X, Liang K, Wang J, Feng L, Wang W, Songyang Z, Lin C, Yang L, Yu Y, Chen J Genes Dev. 2015 Jan 29 2 157-70

Orexin/Hypocretin Activates mTOR Complex 1 (mTORC1) via an Erk/Akt-independent and Calcium-stimulated Lysosome v-ATPase Pathway.

 Wang Z, Liu S, Kakizaki M, Hirose Y, Ishikawa Y, Funato H, Yanagisawa M, Yu Y, Liu Q J. Biol. Chem. 2014 Oct

Quantitative phosphoproteomic analysis reveals system-wide signaling pathways downstream of SDF-1/CXCR4 in breast cancer stem cells.

 Yi T, Zhai B, Yu Y, Kiyotsugu Y, Raschle T, Etzkorn M, Seo HC, Nagiec M, Luna RE, Reinherz EL, Blenis J, Gygi SP, Wagner G Proc. Natl. Acad. Sci. U.S.A. 2014 Apr

Grb10 Promotes Lipolysis and Thermogenesis by Phosphorylation-Dependent Feedback Inhibition of mTORC1.

 Liu M, Bai J, He S, Villarreal R, Hu D, Zhang C, Yang X, Liang H, Slaga TJ, Yu Y, Zhou Z, Blenis J, Scherer PE, Dong LQ, Liu F Cell Metab. 2014 Apr

Sin1 phosphorylation impairs mTORC2 complex integrity and inhibits downstream Akt signalling to suppress tumorigenesis.

 Liu P, Gan W, Inuzuka H, Lazorchak AS, Gao D, Arojo O, Liu D, Wan L, Zhai B, Yu Y, Yuan M, Kim BM, Shaik S, Menon S, Gygi SP, Lee TH, Asara JM, Manning BD, Blenis J, Su B, Wei W Nat. Cell Biol. 2013 Oct

Glycogen synthase kinase-3ß positively regulates protein synthesis and cell proliferation through the regulation of translation initiation factor 4E-binding protein 1.

 Shin S, Wolgamott L, Tcherkezian J, Vallabhapurapu S, Yu Y, Roux PP, Yoon SO Oncogene 2013 Apr

Glycogen synthase kinase (GSK)-3 promotes p70 ribosomal protein S6 kinase (p70S6K) activity and cell proliferation.

 Shin S, Wolgamott L, Yu Y, Blenis J, Yoon SO Proc. Natl. Acad. Sci. U.S.A. 2011 Nov 108 47 E1204-13

Sensitive multiplexed analysis of kinase activities and activity-based kinase identification.

 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 Nat. Biotechnol. 2009 Oct 27 10 933-40

CCR2 chemokines bind selectively to acetylated heparan sulfate octasaccharides.

 Schenauer MR, Yu Y, Sweeney MD, Leary JA J. Biol. Chem. 2007 Aug 282 35 25182-8

Heterodimerization of CCR2 chemokines and regulation by glycosaminoglycan binding.

 Crown SE, Yu Y, Sweeney MD, Leary JA, Handel TM J. Biol. Chem. 2006 Sep 281 35 25438-46

Effects of sulfate position on heparin octasaccharide binding to CCL2 examined by tandem mass spectrometry.

 Sweeney MD, Yu Y, Leary JA J. Am. Soc. Mass Spectrom. 2006 Aug 17 8 1114-9

Potential inhibitors of chemokine function: analysis of noncovalent complexes of CC chemokine and small polyanionic molecules by ESI FT-ICR mass spectrometry.

 Yu Y, Sweeney MD, Saad OM, Leary JA J. Am. Soc. Mass Spectrom. 2006 Apr 17 4 524-35

Chemokine-glycosaminoglycan binding: specificity for CCR2 ligand binding to highly sulfated oligosaccharides using FTICR mass spectrometry.

 Yu Y, Sweeney MD, Saad OM, Crown SE, Hsu AR, Handel TM, Leary JA J. Biol. Chem. 2005 Sep 280 37 32200-8

Mechanism and kinetics of metalloenzyme phosphomannose isomerase: measurement of dissociation constants and effect of zinc binding using ESI-FTICR mass spectrometry.

 Gao H, Yu Y, Leary JA Anal. Chem. 2005 Sep 77 17 5596-603

Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes.

 Yu Y, Ji H, Doudna JA, Leary JA Protein Sci. 2005 Jun 14 6 1438-46

Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA.

 Ji H, Fraser CS, Yu Y, Leary J, Doudna JA Proc. Natl. Acad. Sci. U.S.A. 2004 Dec 101 49 16990-5

Characterization of noncovalent protein-ligand complexes and associated enzyme intermediates of GlcNAc-6-O-sulfotransferase by electrospray ionization FT-ICR mass spectrometry.

 Yu Y, Kirkup CE, Pi N, Leary JA J. Am. Soc. Mass Spectrom. 2004 Oct 15 10 1400-7

Observation of a hybrid random ping-pong mechanism of catalysis for NodST: a mass spectrometry approach.

 Pi N, Yu Y, Mougous JD, Leary JA Protein Sci. 2004 Apr 13 4 903-12