Steven P. Gygi - Publications

2011-2016 Cell Biology Harvard Medical School, Boston, MA, United States 

260 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Sendinc E, Valle-Garcia D, Dhall A, Chen H, Henriques T, Navarrete-Perea J, Sheng W, Gygi SP, Adelman K, Shi Y. PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression. Molecular Cell. PMID 31279659 DOI: 10.1016/j.molcel.2019.05.030  0.56
2019 Wang LW, Shen H, Nobre L, Ersing I, Paulo JA, Trudeau S, Wang Z, Smith NA, Ma Y, Reinstadler B, Nomburg J, Sommermann T, Cahir-McFarland E, Gygi SP, Mootha VK, et al. Epstein-Barr-Virus-Induced One-Carbon Metabolism Drives B Cell Transformation. Cell Metabolism. PMID 31257153 DOI: 10.1016/j.cmet.2019.06.003  0.56
2019 Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanović S, Gygi SP, Gujar S. Therapy-induced MHC I ligands shape neo antitumor CD8 T cell responses during oncolytic virus-based cancer immunotherapy. Journal of Proteome Research. PMID 31095916 DOI: 10.1021/acs.jproteome.9b00173  0.56
2019 Hwang JY, Mannowetz N, Zhang Y, Everley RA, Gygi SP, Bewersdorf J, Lishko PV, Chung JJ. Dual Sensing of Physiologic pH and Calcium by EFCAB9 Regulates Sperm Motility. Cell. PMID 31056283 DOI: 10.1016/j.cell.2019.03.047  0.48
2019 Poulin EJ, Bera AK, Lu J, Lin YJ, Strasser SD, Paulo JA, Huang TQ, Morales C, Yan W, Cook J, Nowak JA, Brubaker DK, Joughin BA, Johnson CW, DeStefanis RA, ... ... Gygi SP, et al. Tissue-specific oncogenic activity of K-RasA146T. Cancer Discovery. PMID 30952657 DOI: 10.1158/2159-8290.CD-18-1220  0.56
2019 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, et al. Author Correction: Sin1 phosphorylation impairs mTORC2 complex integrity and inhibits downstream Akt signalling to suppress tumorigenesis. Nature Cell Biology. PMID 30783264 DOI: 10.1038/s41556-019-0280-y  0.56
2019 Murphy JP, Yu Q, Konda P, Paulo JA, Jedrychowski MP, Kowalewski DJ, Schuster H, Kim Y, Clements DR, Jain A, Stevanović S, Gygi SP, Mancias JD, Gujar S. Multiplexed relative quantitation with isobaric tagging mass spectrometry reveals MHC-I ligand dynamics in response to doxorubicin. Analytical Chemistry. PMID 30779550 DOI: 10.1021/acs.analchem.8b05616  0.56
2019 Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey D, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Woulters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP. Characterization and optimization of multiplexed quantitative analyses using high-field asymmetric-waveform ion mobility mass spectrometry. Analytical Chemistry. PMID 30672687 DOI: 10.1021/acs.analchem.8b05399  0.68
2019 Erickson BK, Mintseris J, Schweppe DK, Navarrete-Perea J, Erickson AR, Nusinow DP, Paulo JA, Gygi SP. Active instrument engagement combined with a real-time database search for improved performance of sample multiplexing workflows. Journal of Proteome Research. PMID 30658528 DOI: 10.1021/acs.jproteome.8b00899  0.68
2019 Byrum AK, Carvajal-Maldonado D, Mudge MC, Valle-Garcia D, Majid MC, Patel R, Sowa ME, Gygi SP, Harper JW, Shi Y, Vindigni A, Mosammaparast N. Mitotic regulators TPX2 and Aurora A protect DNA forks during replication stress by counteracting 53BP1 function. The Journal of Cell Biology. PMID 30602538 DOI: 10.1083/jcb.201803003  0.68
2018 Ron-Harel N, Notarangelo G, Ghergurovich JM, Paulo JA, Sage PT, Santos D, Satterstrom FK, Gygi SP, Rabinowitz JD, Sharpe AH, Haigis MC. Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice. Proceedings of the National Academy of Sciences of the United States of America. 115: 13347-13352. PMID 30530686 DOI: 10.1073/pnas.1804149115  0.56
2018 Rose CM, Erickson BK, Schweppe DK, Viner R, Choi J, Rogers J, Bomgarden R, Gygi SP, Kirkpatrick DS. TomahaqCompanion: A tool for the creation and analysis of isobaric label based multiplexed targeted assays. Journal of Proteome Research. PMID 30501201 DOI: 10.1021/acs.jproteome.8b00767  0.68
2018 Paulo JA, Navarrete-Perea J, Guha Thakurta S, Gygi SP. TKO6: A Peptide Standard to Assess Interference for Unit-Resolved Isobaric Labeling Platforms. Journal of Proteome Research. PMID 30481031 DOI: 10.1021/acs.jproteome.8b00902  0.56
2018 O'Brien JJ, Gunawardena HP, Paulo JA, Chen X, Ibrahim JG, Gygi SP, Qaqish BF. The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments. The Annals of Applied Statistics. 12: 2075-2095. PMID 30473739 DOI: 10.1214/18-AOAS1144  0.56
2018 Gygi JP, Yu Q, Navarrete-Perea J, Rad R, Gygi SP, Paulo JA. A web-based search tool for visualizing instrument performance using the Triple Knockout (TKO) proteome standard. Journal of Proteome Research. PMID 30451507 DOI: 10.1021/acs.jproteome.8b00737  0.56
2018 Motnenko A, Liang CC, Yang D, Lopez-Martinez D, Yoshikawa Y, Zhan B, Ward KE, Tian J, Haas W, Spingardi P, Kessler BM, Kriaucionis S, Gygi SP, Cohn MA. Identification of UHRF2 as a novel DNA interstrand crosslink sensor protein. Plos Genetics. 14: e1007643. PMID 30335751 DOI: 10.1371/journal.pgen.1007643  0.48
2018 Mahmoud AI, Galdos FX, Dinan KA, Jedrychowski MP, Davis JC, Vujic A, Rachmin I, Shigley C, Pancoast JR, Lee S, Hollister-Lock J, MacGillivray CM, Gygi SP, Melton DA, Weir GC, et al. Apolipoprotein E is a pancreatic extracellular factor that maintains mature β-cell gene expression. Plos One. 13: e0204595. PMID 30303984 DOI: 10.1371/journal.pone.0204595  0.48
2018 Martin SES, Tan ZW, Itkonen HM, Duveau DY, Paulo JA, Janetzko J, Boutz PL, Törk L, Moss FA, Thomas CJ, Gygi SP, Lazarus MB, Walker S. Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors. Journal of the American Chemical Society. PMID 30285435 DOI: 10.1021/jacs.8b07328  0.56
2018 Bretones G, Álvarez MG, Arango JR, Rodríguez D, Nadeu F, Prado MA, Valdés-Mas R, Puente DA, Paulo JA, Delgado J, Villamor N, López-Guillermo A, Finley DJ, Gygi SP, Campo E, et al. Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia. Blood. PMID 30181176 DOI: 10.1182/blood-2017-09-804401  0.56
2018 Murphy JP, Giacomantonio MA, Paulo JA, Everley RA, Kennedy BE, Pathak GP, Clements DR, Kim Y, Dai C, Sharif T, Gygi SP, Gujar S. The NAD Salvage Pathway Supports PHGDH-Driven Serine Biosynthesis. Cell Reports. 24: 2381-2391.e5. PMID 30157431 DOI: 10.1016/j.celrep.2018.07.086  0.56
2018 Di Stefano B, Ueda M, Sabri S, Brumbaugh J, Huebner AJ, Sahakyan A, Clement K, Clowers KJ, Erickson AR, Shioda K, Gygi SP, Gu H, Shioda T, Meissner A, Takashima Y, et al. Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells. Nature Methods. PMID 30127506 DOI: 10.1038/s41592-018-0104-1  0.56
2018 Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D. Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability. Nature. PMID 30051891 DOI: 10.1038/s41586-018-0398-2  0.56
2018 Mills EL, Pierce KA, Jedrychowski MP, Garrity R, Winther S, Vidoni S, Yoneshiro T, Spinelli JB, Lu GZ, Kazak L, Banks AS, Haigis MC, Kajimura S, Murphy MP, Gygi SP, et al. Accumulation of succinate controls activation of adipose tissue thermogenesis. Nature. PMID 30022159 DOI: 10.1038/s41586-018-0353-2  0.48
2018 Sustarsic EG, Ma T, Lynes MD, Larsen M, Karavaeva I, Havelund JF, Nielsen CH, Jedrychowski MP, Moreno-Torres M, Lundh M, Plucinska K, Jespersen NZ, Grevengoed TJ, Kramar B, Peics J, ... ... Gygi SP, et al. Cardiolipin Synthesis in Brown and Beige Fat Mitochondria Is Essential for Systemic Energy Homeostasis. Cell Metabolism. PMID 29861389 DOI: 10.1016/j.cmet.2018.05.003  0.48
2018 Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA. SL-TMT: A Streamlined Protocol for Quantitative (Phospho)proteome Profiling using TMT-SPS-MS3. Journal of Proteome Research. PMID 29734811 DOI: 10.1021/acs.jproteome.8b00217  0.56
2018 Yim SH, Everley RA, Schildberg FA, Lee SG, Orsi A, Barbati ZR, Karatepe K, Fomenko DE, Tsuji PA, Luo HR, Gygi SP, Sitia R, Sharpe AH, Hatfield DL, Gladyshev VN. Role of Selenof as a Gatekeeper of Secreted Disulfide-Rich Glycoproteins. Cell Reports. 23: 1387-1398. PMID 29719252 DOI: 10.1016/j.celrep.2018.04.009  0.48
2018 Pease BN, Huttlin EL, Jedrychowski MP, Dorin-Semblat D, Sebastiani D, Segarra DT, Roberts BF, Chakrabarti R, Doerig C, Gygi SP, Chakrabarti D. Characterization of Plasmodium falciparum Atypical Kinase PfPK7-Dependent Phosphoproteome. Journal of Proteome Research. PMID 29678115 DOI: 10.1021/acs.jproteome.8b00062  0.68
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. Journal of the American Society For Mass Spectrometry. PMID 29671274 DOI: 10.1007/s13361-018-1946-6  0.56
2018 Paulo JA, Gygi SP. Isobaric Tag-Based Protein Profiling of a Nicotine-Treated Alpha7 Nicotinic Receptor-Null Human Haploid Cell Line. Proteomics. e1700475. PMID 29663646 DOI: 10.1002/pmic.201700475  0.56
2018 Hong S, Song W, Zushin PH, Liu B, Jedrychowski MP, Mina AI, Deng Z, Cabarkapa D, Hall JA, Palmer CJ, Aliakbarian H, Szpyt J, Gygi SP, Tavakkoli A, Lynch L, et al. Phosphorylation of Beta-3 adrenergic receptor at serine 247 by ERK MAP kinase drives lipolysis in obese adipocytes. Molecular Metabolism. PMID 29661693 DOI: 10.1016/j.molmet.2018.03.012  0.48
2018 Paulo JA, Jedrychowski MP, Chouchani ET, Kazak L, Gygi SP. Multiplexed isobaric tag-based profiling of seven murine tissues following in vivo nicotine treatment using a minimalistic proteomics strategy. Proteomics. e1700326. PMID 29660237 DOI: 10.1002/pmic.201700326  0.56
2018 Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, Hou Z, Heo JM, Rubin LL, Sidhu SS, Gygi SP, Harper JW. Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Molecular Cell. PMID 29656925 DOI: 10.1016/j.molcel.2018.03.012  0.68
2018 O'Connell JD, Paulo JA, O'Brien JJ, Gygi SP. Proteome-Wide Evaluation of Two Common Protein Quantification Methods. Journal of Proteome Research. PMID 29635916 DOI: 10.1021/acs.jproteome.8b00016  0.56
2018 Stepanova E, Gygi SP, Paulo JA. Filter-based Protein Digestion (FPD): A Detergent-free and Scaffold-based Strategy for TMT workflows. Journal of Proteome Research. PMID 29402085 DOI: 10.1021/acs.jproteome.7b00840  0.56
2018 Geng Y, Michowski W, Chick JM, Wang YE, Jecrois ME, Sweeney KE, Liu L, Han RC, Ke N, Zagozdzon A, Sicinska E, Bronson RT, Gygi SP, Sicinski P. Kinase-independent function of E-type cyclins in liver cancer. Proceedings of the National Academy of Sciences of the United States of America. PMID 29339491 DOI: 10.1073/pnas.1711477115  0.56
2017 Fraile JM, Campos-Iglesias D, Rodríguez F, Astudillo A, Vilarrasa-Blasi R, Verdaguer-Dot N, Prado MA, Paulo JA, Gygi SP, Martín-Subero JI, Freije JMP, López-Otín C. Loss of the Deubiquitinase USP36 Destabilizes the RNA Helicase DHX33 and Causes Preimplantation Lethality in Mice. The Journal of Biological Chemistry. PMID 29273634 DOI: 10.1074/jbc.M117.788430  0.56
2017 O'Brien JJ, O'Connell JD, Paulo JA, Thakurta S, Rose CM, Weekes MP, Huttlin EL, Gygi SP. Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags. Journal of Proteome Research. PMID 29195270 DOI: 10.1021/acs.jproteome.7b00699  0.68
2017 Presler M, Van Itallie E, Klein AM, Kunz R, Coughlin ML, Peshkin L, Gygi SP, Wühr M, Kirschner MW. Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg. Proceedings of the National Academy of Sciences of the United States of America. 114: E10838-E10847. PMID 29183978 DOI: 10.1073/pnas.1709207114  0.72
2017 Bird IM, Kim SH, Schweppe DK, Caetano-Lopes J, Robling AG, Charles JF, Gygi SP, Warman ML, Smits PJ. The skeletal phenotype of Achondrogenesis type 1A is caused exclusively by cartilage defects. Development (Cambridge, England). PMID 29180569 DOI: 10.1242/dev.156588  0.68
2017 Gu X, Orozco JM, Saxton RA, Condon KJ, Liu GY, Krawczyk PA, Scaria SM, Harper JW, Gygi SP, Sabatini DM. SAMTOR is an S-adenosylmethionine sensor for the mTORC1 pathway. Science (New York, N.Y.). 358: 813-818. PMID 29123071 DOI: 10.1126/science.aao3265  0.68
2017 Schweppe DK, Huttlin EL, Harper JW, Gygi SP. BioPlex Display: An interactive suite for large-scale, AP-MS protein-protein interaction data. Journal of Proteome Research. PMID 29054129 DOI: 10.1021/acs.jproteome.7b00572  0.68
2017 Palmer CJ, Bruckner RJ, Paulo JA, Kazak L, Long JZ, Mina AI, Deng Z, LeClair KB, Hall JA, Hong S, Zushin PH, Smith KL, Gygi SP, Hagen S, Cohen DE, et al. Cdkal1, a type 2 diabetes susceptibility gene, regulates mitochondrial function in adipose tissue. Molecular Metabolism. 6: 1212-1225. PMID 29031721 DOI: 10.1016/j.molmet.2017.07.013  0.56
2017 Lim MY, O'Brien J, Paulo JA, Gygi SP. An Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling. Journal of Proteome Research. PMID 28985074 DOI: 10.1021/acs.jproteome.7b00571  0.56
2017 Mirzaei M, Gupta VB, Chick JM, Greco TM, Wu Y, Chitranshi N, Wall RV, Hone E, Deng L, Dheer Y, Abbasi M, Rezaeian M, Braidy N, You Y, Salekdeh GH, ... ... Gygi SP, et al. Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes. Scientific Reports. 7: 12685. PMID 28978942 DOI: 10.1038/s41598-017-12858-7  0.56
2017 Navarrete-Perea J, Isasa M, Paulo JA, Corral-Corral R, Flores-Bautista J, Hernández-Téllez B, Bobes RJ, Fragoso G, Sciutto E, Soberón X, Gygi SP, Laclette JP. Quantitative multiplexed proteomics of Taenia solium cysts obtained from the skeletal muscle and central nervous system of pigs. Plos Neglected Tropical Diseases. 11: e0005962. PMID 28945737 DOI: 10.1371/journal.pntd.0005962  0.56
2017 Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, et al. Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins. Elife. 6. PMID 28933694 DOI: 10.7554/eLife.26435  0.56
2017 Susman MW, Karuna EP, Kunz RC, Gujral TS, Cantú AV, Choi SS, Jong BY, Okada K, Scales MK, Hum J, Hu LS, Kirschner MW, Nishinakamura R, Yamada S, Laird DJ, ... ... Gygi SP, et al. Kinesin superfamily protein Kif26b links Wnt5a-Ror signaling to the control of cell and tissue behaviors in vertebrates. Elife. 6. PMID 28885975 DOI: 10.7554/eLife.26509  0.72
2017 Nguyen AT, Prado MA, Schmidt PJ, Sendamarai AK, Wilson-Grady JT, Min M, Campagna DR, Tian G, Shi Y, Dederer V, Kawan M, Kuehnle N, Paulo JA, Yao Y, Weiss MJ, ... ... Gygi SP, et al. UBE2O remodels the proteome during terminal erythroid differentiation. Science (New York, N.Y.). 357. PMID 28774900 DOI: 10.1126/science.aan0218  0.56
2017 Clements DR, Murphy JP, Sterea A, Kennedy BE, Kim Y, Helson E, Almasi S, Holay N, Konda P, Paulo JA, Sharif T, Lee PW, Weekes MP, Gygi SP, Gujar S. Quantitative temporal in vivo proteomics (QTiPs) deciphers the transition of virus-driven myeloid cells into M2 macrophages. Journal of Proteome Research. PMID 28768414 DOI: 10.1021/acs.jproteome.7b00425  0.56
2017 Yoon SO, Shin S, Karreth FA, Buel GR, Jedrychowski MP, Plas DR, Dedhar S, Gygi SP, Roux PP, Dephoure N, Blenis J. Focal Adhesion- and IGF1R-Dependent Survival and Migratory Pathways Mediate Tumor Resistance to mTORC1/2 Inhibition. Molecular Cell. PMID 28757207 DOI: 10.1016/j.molcel.2017.06.033  0.48
2017 Lee HJ, Jedrychowski MP, Vinayagam A, Wu N, Shyh-Chang N, Hu Y, Min-Wen C, Moore JK, Asara JM, Lyssiotis CA, Perrimon N, Gygi SP, Cantley LC, Kirschner MW. Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation. Cell Reports. 20: 721-736. PMID 28723573 DOI: 10.1016/j.celrep.2017.06.074  0.72
2017 Vethe H, Bjørlykke Y, Ghila LM, Paulo JA, Scholz H, Gygi SP, Chera S, Ræder H. Probing the missing mature β-cell proteomic landscape in differentiating patient iPSC-derived cells. Scientific Reports. 7: 4780. PMID 28684784 DOI: 10.1038/s41598-017-04979-w  0.56
2017 Jih G, Iglesias N, Currie MA, Bhanu NV, Paulo JA, Gygi SP, Garcia BA, Moazed D. Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription. Nature. PMID 28682306 DOI: 10.1038/nature23267  0.56
2017 Biancur DE, Paulo JA, Małachowska B, Del Rey MQ, Sousa CM, Wang X, Sohn ASW, Chu GC, Gygi SP, Harper JW, Fendler W, Mancias JD, Kimmelman AC. Compensatory metabolic networks in pancreatic cancers upon perturbation of glutamine metabolism. Nature Communications. 8: 15965. PMID 28671190 DOI: 10.1038/ncomms15965  0.68
2017 Renko K, Martitz J, Hybsier S, Heynisch B, Voss L, Everley RA, Gygi SP, Stoedter M, Wisniewska M, Köhrle J, Gladyshev VN, Schomburg L. Aminoglycoside-driven biosynthesis of selenium-deficient Selenoprotein P. Scientific Reports. 7: 4391. PMID 28663583 DOI: 10.1038/s41598-017-04586-9  0.48
2017 Kazak L, Chouchani ET, Stavrovskaya IG, Lu GZ, Jedrychowski MP, Egan DF, Kumari M, Kong X, Erickson BK, Szpyt J, Rosen ED, Murphy MP, Kristal BS, Gygi SP, Spiegelman BM. UCP1 deficiency causes brown fat respiratory chain depletion and sensitizes mitochondria to calcium overload-induced dysfunction. Proceedings of the National Academy of Sciences of the United States of America. PMID 28630339 DOI: 10.1073/pnas.1705406114  0.56
2017 Wang H, Nicolay BN, Chick JM, Gao X, Geng Y, Ren H, Gao H, Yang G, Williams JA, Suski JM, Keibler MA, Sicinska E, Gerdemann U, Haining WN, Roberts TM, ... ... Gygi SP, et al. The metabolic function of cyclin D3-CDK6 kinase in cancer cell survival. Nature. PMID 28607489 DOI: 10.1038/nature22797  0.56
2017 Ersing I, Nobre L, Wang LW, Soday L, Ma Y, Paulo JA, Narita Y, Ashbaugh CW, Jiang C, Grayson NE, Kieff E, Gygi SP, Weekes MP, Gewurz BE. A Temporal Proteomic Map of Epstein-Barr Virus Lytic Replication in B Cells. Cell Reports. 19: 1479-1493. PMID 28514666 DOI: 10.1016/j.celrep.2017.04.062  0.56
2017 Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H, Szpyt J, Tam S, Zarraga G, Pontano-Vaites L, Swarup S, ... ... Gygi SP, et al. Architecture of the human interactome defines protein communities and disease networks. Nature. PMID 28514442 DOI: 10.1038/nature22366  0.68
2017 Paek J, Kalocsay M, Staus DP, Wingler L, Pascolutti R, Paulo JA, Gygi SP, Kruse AC. Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. Cell. 169: 338-349.e11. PMID 28388415 DOI: 10.1016/j.cell.2017.03.028  0.56
2017 Paulo JA, Mancias JD, Gygi SP. Proteome-Wide Protein Expression Profiling Across Five Pancreatic Cell Lines. Pancreas. PMID 28375945 DOI: 10.1097/MPA.0000000000000800  0.56
2017 Li J, Haas W, Jackson K, Kuru E, Jewett MC, Fan ZH, Gygi SP, Church GM. Co-generating synthetic parts toward a self-replicating system. Acs Synthetic Biology. PMID 28330337 DOI: 10.1021/acssynbio.6b00342  0.48
2017 Ganter M, Goldberg JM, Dvorin JD, Paulo JA, King JG, Tripathi AK, Paul AS, Yang J, Coppens I, Jiang RH, Elsworth B, Baker DA, Dinglasan RR, Gygi SP, Duraisingh MT. Erratum: Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nature Microbiology. 2: 17038. PMID 28263306 DOI: 10.1038/nmicrobiol.2017.38  0.56
2017 Ganter M, Goldberg JM, Dvorin JD, Paulo JA, King JG, Tripathi AK, Paul AS, Yang J, Coppens I, Jiang RH, Elsworth B, Baker DA, Dinglasan RR, Gygi SP, Duraisingh MT. Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nature Microbiology. 2: 17017. PMID 28211852 DOI: 10.1038/nmicrobiol.2017.17  0.56
2017 Bai L, Jastrab JB, Isasa M, Hu K, Yu H, Gygi SP, Darwin KH, Li H. Structural analysis of Mycobacterium tuberculosis homologues of the eukaryotic proteasome assembly chaperone 2 (PAC2). Journal of Bacteriology. PMID 28193903 DOI: 10.1128/JB.00846-16  0.44
2017 Liu L, Michowski W, Inuzuka H, Shimizu K, Nihira NT, Chick JM, Li N, Geng Y, Meng AY, Ordureau A, Kołodziejczyk A, Ligon KL, Bronson RT, Polyak K, Harper JW, ... Gygi SP, et al. G1 cyclins link proliferation, pluripotency and differentiation of embryonic stem cells. Nature Cell Biology. PMID 28192421 DOI: 10.1038/ncb3474  0.68
2017 Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, ... ... Gygi SP, et al. Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation. Elife. 6. PMID 28186488 DOI: 10.7554/eLife.22206  0.56
2017 Possemato AP, Paulo JA, Mulhern D, Guo A, Gygi SP, Beausoleil SA. Multiplexed phosphoproteomic profiling using titanium dioxide and immuno-affinity enrichments reveals complementary phosphorylation events. Journal of Proteome Research. PMID 28171727 DOI: 10.1021/acs.jproteome.6b00905  0.6
2016 Erickson BK, Rose CM, Braun CR, Erickson AR, Knott J, McAlister GC, Wühr M, Paulo JA, Everley RA, Gygi SP. A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization. Molecular Cell. PMID 28065596 DOI: 10.1016/j.molcel.2016.12.005  0.56
2016 Wu L, Zhou B, Oshiro-Rapley N, Li M, Paulo JA, Webster CM, Mou F, Kacergis MC, Talkowski ME, Carr CE, Gygi SP, Zheng B, Soukas AA. An Ancient, Unified Mechanism for Metformin Growth Inhibition in C. elegans and Cancer. Cell. 167: 1705-1718.e13. PMID 27984722 DOI: 10.1016/j.cell.2016.11.055  0.56
2016 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. Journal of Proteome Research. PMID 27978624 DOI: 10.1021/acs.jproteome.6b00487  0.68
2016 Yang W, Nagasawa K, Münch C, Xu Y, Satterstrom K, Jeong S, Hayes SD, Jedrychowski MP, Vyas FS, Zaganjor E, Guarani V, Ringel AE, Gygi SP, Harper JW, Haigis MC. Mitochondrial Sirtuin Network Reveals Dynamic SIRT3-Dependent Deacetylation in Response to Membrane Depolarization. Cell. 167: 985-1000.e21. PMID 27881304 DOI: 10.1016/j.cell.2016.10.016  0.68
2016 Paulo JA, Gygi SP. Nicotine-induced protein expression profiling reveals mutually altered proteins across four human cell lines. Proteomics. PMID 27862958 DOI: 10.1002/pmic.201600319  0.56
2016 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 Systems. PMID 27667366 DOI: 10.1016/j.cels.2016.08.009  0.68
2016 German NJ, Yoon H, Yusuf RZ, Murphy JP, Finley LW, Laurent G, Haas W, Satterstrom FK, Guarnerio J, Zaganjor E, Santos D, Pandolfi PP, Beck AH, Gygi SP, Scadden DT, et al. PHD3 Loss in Cancer Enables Metabolic Reliance on Fatty Acid Oxidation via Deactivation of ACC2. Molecular Cell. 63: 1006-1020. PMID 27635760 DOI: 10.1016/j.molcel.2016.08.014  0.72
2016 Van Vranken JG, Jeong MY, Wei P, Chen YC, Gygi SP, Winge DR, Rutter J. The mitochondrial acyl carrier protein (ACP) coordinates mitochondrial fatty acid synthesis with iron sulfur cluster biogenesis. Elife. 5. PMID 27540631 DOI: 10.7554/eLife.17828  0.72
2016 Turnbull ML, Wise HM, Nicol MQ, Smith N, Dunfee RL, Beard PM, Jagger BW, Ligertwood Y, Hardisty GR, Xiao H, Benton DJ, Coburn AM, Paulo JA, Gygi SP, McCauley JW, et al. The Role of the B-Allele of the Influenza A Virus Segment 8 in Setting Mammalian Host Range and Pathogenicity. Journal of Virology. PMID 27489273 DOI: 10.1128/JVI.01205-16  0.56
2016 Boke E, Ruer M, Wühr M, Coughlin M, Lemaitre R, Gygi SP, Alberti S, Drechsel D, Hyman AA, Mitchison TJ. Amyloid-like Self-Assembly of a Cellular Compartment. Cell. 166: 637-650. PMID 27471966 DOI: 10.1016/j.cell.2016.06.051  0.68
2016 Paulo JA, O'Connell JD, Everley RA, O'Brien J, Gygi MA, Gygi SP. Quantitative mass spectrometry-based multiplexing compares the abundance of 5000S. cerevisiae proteins across 10 carbon sources. Journal of Proteomics. PMID 27432472 DOI: 10.1016/j.jprot.2016.07.005  0.72
2016 Paulo JA, O'Connell JD, Gygi SP. A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments. Journal of the American Society For Mass Spectrometry. PMID 27400695 DOI: 10.1007/s13361-016-1434-9  0.72
2016 Long JZ, Svensson KJ, Bateman LA, Lin H, Kamenecka T, Lokurkar IA, Lou J, Rao RR, Chang MR, Jedrychowski MP, Paulo JA, Gygi SP, Griffin PR, Nomura DK, Spiegelman BM. The Secreted Enzyme PM20D1 Regulates Lipidated Amino Acid Uncouplers of Mitochondria. Cell. PMID 27374330 DOI: 10.1016/j.cell.2016.05.071  0.72
2016 Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP. Defining the consequences of genetic variation on a proteome-wide scale. Nature. PMID 27309819 DOI: 10.1038/nature18270  0.68
2016 Zhou C, Elia AE, Naylor ML, Dephoure N, Ballif BA, Goel G, Xu Q, Ng A, Chou DM, Xavier RJ, Gygi SP, Elledge SJ. Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks. Proceedings of the National Academy of Sciences of the United States of America. PMID 27298372 DOI: 10.1073/pnas.1602827113  0.72
2016 Primo V, Graham M, Bigger-Allen AA, Chick JM, Ospina C, Quiroz YT, Manent J, Gygi SP, Lopera F, D'Amore PA, Arboleda-Velasquez JF. Blood Biomarkers in a Mouse Model of CADASIL. Brain Research. PMID 27174004 DOI: 10.1016/j.brainres.2016.05.008  0.72
2016 Coloff JL, Murphy JP, Braun CR, Harris IS, Shelton LM, Kami K, Gygi SP, Selfors LM, Brugge JS. Differential Glutamate Metabolism in Proliferating and Quiescent Mammary Epithelial Cells. Cell Metabolism. PMID 27133130 DOI: 10.1016/j.cmet.2016.03.016  0.72
2016 Lee BH, Lu Y, Prado MA, Shi Y, Tian G, Sun S, Elsasser S, Gygi SP, King RW, Finley D. USP14 deubiquitinates proteasome-bound substrates that are ubiquitinated at multiple sites. Nature. PMID 27074503 DOI: 10.1038/nature17433  0.72
2016 Chouchani ET, Kazak L, Jedrychowski MP, Lu GZ, Erickson BK, Szpyt J, Pierce KA, Laznik-Bogoslavski D, Vetrivelan R, Clish CB, Robinson AJ, Gygi SP, Spiegelman BM. Mitochondrial ROS regulate thermogenic energy expenditure and sulfenylation of UCP1. Nature. PMID 27027295 DOI: 10.1038/nature17399  0.72
2016 Tavares CD, Sharabi K, Dominy JE, Lee Y, Isasa M, Orozco JM, Jedrychowski MP, Kamenecka TM, Griffin PR, Gygi SP, Puigserver P. The Methionine Transamination Pathway Controls Hepatic Glucose Metabolism through Regulation of the GCN5 Acetyl Transferase and the PGC-1α Transcriptional Coactivator. The Journal of Biological Chemistry. PMID 27022023 DOI: 10.1074/jbc.M115.706200  0.48
2016 Chantranupong L, Scaria SM, Saxton RA, Gygi MP, Shen K, Wyant GA, Wang T, Harper JW, Gygi SP, Sabatini DM. The CASTOR Proteins Are Arginine Sensors for the mTORC1 Pathway. Cell. PMID 26972053 DOI: 10.1016/j.cell.2016.02.035  0.72
2016 Greenblatt MB, Shin DY, Oh H, Lee KY, Zhai B, Gygi SP, Lotinun S, Baron R, Liu D, Su B, Glimcher LH, Shim JH. MEKK2 mediates an alternative β-catenin pathway that promotes bone formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26884171 DOI: 10.1073/pnas.1600813113  0.72
2016 Svensson KJ, Long JZ, Jedrychowski MP, Cohen P, Lo JC, Serag S, Kir S, Shinoda K, Tartaglia JA, Rao RR, Chédotal A, Kajimura S, Gygi SP, Spiegelman BM. A Secreted Slit2 Fragment Regulates Adipose Tissue Thermogenesis and Metabolic Function. Cell Metabolism. PMID 26876562 DOI: 10.1016/j.cmet.2016.01.008  0.72
2015 Butovsky O, Jedrychowski MP, Cialic R, Murugaiyan G, Wu PM, Doykan CE, Fanek Z, Greco DJ, Kiner O, Lawson RJ, Frosch MP, Pochet N, Krichevsky AM, Gygi SP, Berry J, et al. REMOVED: Targeting miR-155 restores dysfunctional microglia and ameliorates disease in the SOD1 model of ALS. International Journal of Developmental Neuroscience : the Official Journal of the International Society For Developmental Neuroscience. 47: 5. PMID 29887088 DOI: 10.1016/j.ijdevneu.2015.04.023  0.48
2015 Butovsky O, Jedrychowski MP, Moore CS, Cialic R, Lanser AJ, Gabriely G, Koeglsperger T, Dake B, Wu PM, Doykan CE, Fanek Z, Liu L, Chen Z, Rothstein JD, Ransohoff RM, ... Gygi SP, et al. REMOVED: Identification of a unique molecular and functional microglia signature in health and disease. International Journal of Developmental Neuroscience : the Official Journal of the International Society For Developmental Neuroscience. 47: 5. PMID 29887087 DOI: 10.1016/j.ijdevneu.2015.04.022  0.48
2015 Zhao J, Zhai B, Gygi SP, Goldberg AL. mTOR inhibition activates overall protein degradation by the ubiquitin proteasome system as well as by autophagy. Proceedings of the National Academy of Sciences of the United States of America. PMID 26669439 DOI: 10.1073/pnas.1521919112  0.72
2015 Jedrychowski MP, Liu L, Laflamme CJ, Karastergiou K, Meshulam T, Ding SY, Wu Y, Lee MJ, Gygi SP, Fried SK, Pilch PF. Adiporedoxin, an upstream regulator of ER oxidative folding and protein secretion in adipocytes. Molecular Metabolism. 4: 758-770. PMID 26629401 DOI: 10.1016/j.molmet.2015.09.002  0.72
2015 Isasa M, Suñer C, Díaz M, Puig-Sàrries P, Zuin A, Bichmann A, Gygi SP, Rebollo E, Crosas B. Cold Temperature Induces the Reprogramming of Proteolytic Pathways in Yeast. The Journal of Biological Chemistry. PMID 26601941 DOI: 10.1074/jbc.M115.698662  0.72
2015 Mick DU, Rodrigues RB, Leib RD, Adams CM, Chien AS, Gygi SP, Nachury MV. Proteomics of Primary Cilia by Proximity Labeling. Developmental Cell. PMID 26585297 DOI: 10.1016/j.devcel.2015.10.015  0.72
2015 Peshkin L, Wühr M, Pearl E, Haas W, Freeman RM, Gerhart JC, Klein AM, Horb M, Gygi SP, Kirschner MW. On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development. Developmental Cell. 35: 383-94. PMID 26555057 DOI: 10.1016/j.devcel.2015.10.010  0.72
2015 Isasa M, Rose CM, Elsasser S, Navarrete-Perea J, Paulo JA, Finley DJ, Gygi SP. Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains. Journal of Proteome Research. PMID 26503604 DOI: 10.1021/acs.jproteome.5b00802  0.72
2015 Guerra-Moreno A, Isasa M, Bhanu MK, Waterman DP, Eapen VV, Gygi SP, Hanna J. Proteomic Analysis Identifies Ribosome Reduction as an Effective Proteotoxic Stress Response. The Journal of Biological Chemistry. PMID 26491016 DOI: 10.1074/jbc.M115.684969  0.72
2015 Elia AE, Wang DC, Willis NA, Boardman AP, Hajdu I, Adeyemi RO, Lowry E, Gygi SP, Scully R, Elledge SJ. RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks. Molecular Cell. 60: 280-93. PMID 26474068 DOI: 10.1016/j.molcel.2015.09.011  0.72
2015 Turanov AA, Everley RA, Hybsier S, Renko K, Schomburg L, Gygi SP, Hatfield DL, Gladyshev VN. Regulation of Selenocysteine Content of Human Selenoprotein P by Dietary Selenium and Insertion of Cysteine in Place of Selenocysteine. Plos One. 10: e0140353. PMID 26452064 DOI: 10.1371/journal.pone.0140353  0.72
2015 Wühr M, Güttler T, Peshkin L, McAlister GC, Sonnett M, Ishihara K, Groen AC, Presler M, Erickson BK, Mitchison TJ, Kirschner MW, Gygi SP. The Nuclear Proteome of a Vertebrate. Current Biology : Cb. 25: 2663-71. PMID 26441354 DOI: 10.1016/j.cub.2015.08.047  0.72
2015 Paulo JA, O'Connell JD, Gaun A, Gygi SP. Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. Molecular Biology of the Cell. 26: 4063-74. PMID 26399295 DOI: 10.1091/mbc.E15-07-0499  0.72
2015 Braun CR, Bird GH, Wühr M, Erickson BK, Rad R, Walensky LD, Gygi SP, Haas W. Generation of Multiple Reporter Ions from a Single Isobaric Reagent Increases Multiplexing Capacity for Quantitative Proteomics. Analytical Chemistry. 87: 9855-63. PMID 26308379 DOI: 10.1021/acs.analchem.5b02307  0.72
2015 Jedrychowski MP, Wrann CD, Paulo JA, Gerber KK, Szpyt J, Robinson MM, Nair KS, Gygi SP, Spiegelman BM. Detection and Quantitation of Circulating Human Irisin by Tandem Mass Spectrometry. Cell Metabolism. 22: 734-40. PMID 26278051 DOI: 10.1016/j.cmet.2015.08.001  0.56
2015 Paulo JA, Gaun A, Gygi SP. Global Analysis of Protein Expression and Phosphorylation Levels in Nicotine-Treated Pancreatic Stellate Cells. Journal of Proteome Research. 14: 4246-56. PMID 26265067 DOI: 10.1021/acs.jproteome.5b00398  0.72
2015 Chick JM, Kolippakkam D, Nusinow DP, Zhai B, Rad R, Huttlin EL, Gygi SP. Erratum: A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides. Nature Biotechnology. 33: 882. PMID 26252148 DOI: 10.1038/nbt0815-882d  0.68
2015 Fortian A, Dionne LK, Hong SH, Kim W, Gygi SP, Watkins S, Sorkin A. Endocytosis of ubiquitylation-deficient EGF receptor mutants via clathrin coated pits is mediated by ubiquitylation. Traffic (Copenhagen, Denmark). PMID 26251007 DOI: 10.1111/tra.12314  0.72
2015 Yang L, Calay ES, Fan J, Arduini A, Kunz RC, Gygi SP, Yalcin A, Fu S, Hotamisligil GS. METABOLISM. S-Nitrosylation links obesity-associated inflammation to endoplasmic reticulum dysfunction. Science (New York, N.Y.). 349: 500-6. PMID 26228140 DOI: 10.1126/science.aaa0079  0.72
2015 Grice GL, Lobb IT, Weekes MP, Gygi SP, Antrobus R, Nathan JA. The Proteasome Distinguishes between Heterotypic and Homotypic Lysine-11-Linked Polyubiquitin Chains. Cell Reports. 12: 545-53. PMID 26190103 DOI: 10.1016/j.celrep.2015.06.061  0.72
2015 Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, ... ... Gygi SP, et al. The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell. 162: 425-40. PMID 26186194 DOI: 10.1016/j.cell.2015.06.043  0.68
2015 Murphy JP, Stepanova E, Everley RA, Paulo JA, Gygi SP. Comprehensive temporal protein dynamics during the diauxic shift in Saccharomyces cerevisiae. Molecular & Cellular Proteomics : McP. PMID 26077900 DOI: 10.1074/mcp.M114.045849  0.72
2015 Chick JM, Kolippakkam D, Nusinow DP, Zhai B, Rad R, Huttlin EL, Gygi SP. A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides. Nature Biotechnology. 33: 743-9. PMID 26076430 DOI: 10.1038/nbt.3267  0.72
2015 Elia AE, Boardman AP, Wang DC, Huttlin EL, Everley RA, Dephoure N, Zhou C, Koren I, Gygi SP, Elledge SJ. Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response. Molecular Cell. PMID 26051181 DOI: 10.1016/j.molcel.2015.05.006  0.72
2015 Yi T, Arthanari H, Akabayov B, Song H, Papadopoulos E, Qi HH, Jedrychowski M, Güttler T, Guo C, Luna RE, Gygi SP, Huang SA, Wagner G. eIF1A augments Ago2-mediated Dicer-independent miRNA biogenesis and RNA interference. Nature Communications. 6: 7194. PMID 26018492 DOI: 10.1038/ncomms8194  0.72
2015 Guarani V, McNeill EM, Paulo JA, Huttlin EL, Fröhlich F, Gygi SP, Van Vactor D, Harper JW. QIL1 is a novel mitochondrial protein required for MICOS complex stability and cristae morphology. Elife. 4. PMID 25997101 DOI: 10.7554/eLife.06265  0.72
2015 Lucena R, Dephoure N, Gygi SP, Kellogg DR, Tallada VA, Daga RR, Jimenez J. Nucleocytoplasmic transport in the midzone membrane domain controls yeast mitotic spindle disassembly. The Journal of Cell Biology. 209: 387-402. PMID 25963819 DOI: 10.1083/jcb.201412144  0.72
2015 Egan ES, Jiang RH, Moechtar MA, Barteneva NS, Weekes MP, Nobre LV, Gygi SP, Paulo JA, Frantzreb C, Tani Y, Takahashi J, Watanabe S, Goldberg J, Paul AS, Brugnara C, et al. Malaria. A forward genetic screen identifies erythrocyte CD55 as essential for Plasmodium falciparum invasion. Science (New York, N.Y.). 348: 711-4. PMID 25954012 DOI: 10.1126/science.aaa3526  0.72
2015 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. Proteomic Profiling of Paclitaxel Treated Cells Identifies a Novel Mechanism of Drug Resistance Mediated by PDCD4. Journal of Proteome Research. 14: 2480-91. PMID 25928036 DOI: 10.1021/acs.jproteome.5b00004  0.72
2015 Nakamura T, Kunz RC, Zhang C, Kimura T, Yuan CL, Baccaro B, Namiki Y, Gygi SP, Hotamisligil GS. A critical role for PKR complexes with TRBP in Immunometabolic regulation and eIF2α phosphorylation in obesity. Cell Reports. 11: 295-307. PMID 25843719 DOI: 10.1016/j.celrep.2015.03.021  0.72
2015 Jastrab JB, Wang T, Murphy JP, Bai L, Hu K, Merkx R, Huang J, Chatterjee C, Ovaa H, Gygi SP, Li H, Darwin KH. An adenosine triphosphate-independent proteasome activator contributes to the virulence of Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. 112: E1763-72. PMID 25831519 DOI: 10.1073/pnas.1423319112  0.72
2015 Liang CC, Zhan B, Yoshikawa Y, Haas W, Gygi SP, Cohn MA. UHRF1 is a sensor for DNA interstrand crosslinks and recruits FANCD2 to initiate the Fanconi anemia pathway. Cell Reports. 10: 1947-56. PMID 25801034 DOI: 10.1016/j.celrep.2015.02.053  0.48
2015 Samanovic MI, Tu S, Novák O, Iyer LM, McAllister FE, Aravind L, Gygi SP, Hubbard SR, Strnad M, Darwin KH. Proteasomal control of cytokinin synthesis protects Mycobacterium tuberculosis against nitric oxide. Molecular Cell. 57: 984-94. PMID 25728768 DOI: 10.1016/j.molcel.2015.01.024  0.72
2015 Nakao LS, Everley RA, Marino SM, Lo SM, de Souza LE, Gygi SP, Gladyshev VN. Mechanism-based proteomic screening identifies targets of thioredoxin-like proteins. The Journal of Biological Chemistry. 290: 5685-95. PMID 25561728 DOI: 10.1074/jbc.M114.597245  0.72
2015 Erickson BK, Jedrychowski MP, McAlister GC, Everley RA, Kunz R, Gygi SP. Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer. Analytical Chemistry. 87: 1241-9. PMID 25521595 DOI: 10.1021/ac503934f  0.72
2015 Banks AS, McAllister FE, Camporez JP, Zushin PJ, Jurczak MJ, Laznik-Bogoslavski D, Shulman GI, Gygi SP, Spiegelman BM. An ERK/Cdk5 axis controls the diabetogenic actions of PPARγ. Nature. 517: 391-5. PMID 25409143 DOI: 10.1038/nature13887  0.72
2015 Butovsky O, Jedrychowski MP, Cialic R, Krasemann S, Murugaiyan G, Fanek Z, Greco DJ, Wu PM, Doykan CE, Kiner O, Lawson RJ, Frosch MP, Pochet N, Fatimy RE, Krichevsky AM, ... Gygi SP, et al. Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice. Annals of Neurology. 77: 75-99. PMID 25381879 DOI: 10.1002/ana.24304  0.72
2015 Paulo JA, Gygi SP. A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14-3-3 orthologs and associated effects of rapamycin. Proteomics. 15: 474-86. PMID 25315811 DOI: 10.1002/pmic.201400155  0.72
2015 Paulo JA, McAllister FE, Everley RA, Beausoleil SA, Banks AS, Gygi SP. Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics. Proteomics. 15: 462-73. PMID 25195567 DOI: 10.1002/pmic.201400154  0.72
2015 Jedrychowski MP, Wrann CD, Paulo JA, Gerber KK, Szpyt J, Robinson MM, Nair KS, Gygi SP, Spiegelman BM. Detection and Quantitation of Circulating Human Irisin by Tandem Mass Spectrometry Cell Metabolism. DOI: 10.1016/j.cmet.2015.08.001  0.72
2015 Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, ... ... Gygi SP, et al. The BioPlex Network: A Systematic Exploration of the Human Interactome Cell. 162: 425-440. DOI: 10.1016/j.cell.2015.06.043  0.72
2014 Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski P. The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis. Cell Cycle (Georgetown, Tex.). 13: 2889-900. PMID 25486477 DOI: 10.4161/15384101.2014.946850  0.72
2014 Liew GM, Ye F, Nager AR, Murphy JP, Lee JS, Aguiar M, Breslow DK, Gygi SP, Nachury MV. The intraflagellar transport protein IFT27 promotes BBSome exit from cilia through the GTPase ARL6/BBS3. Developmental Cell. 31: 265-78. PMID 25443296 DOI: 10.1016/j.devcel.2014.09.004  0.72
2014 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, ... ... Gygi SP, et al. Cyclin C is a haploinsufficient tumour suppressor. Nature Cell Biology. 16: 1080-91. PMID 25344755 DOI: 10.1038/ncb3046  0.72
2014 White JP, Wrann CD, Rao RR, Nair SK, Jedrychowski MP, You JS, Martínez-Redondo V, Gygi SP, Ruas JL, Hornberger TA, Wu Z, Glass DJ, Piao X, Spiegelman BM. G protein-coupled receptor 56 regulates mechanical overload-induced muscle hypertrophy. Proceedings of the National Academy of Sciences of the United States of America. 111: 15756-61. PMID 25336758 DOI: 10.1073/pnas.1417898111  0.72
2014 Qendro V, Lundgren DH, Rezaul K, Mahony F, Ferrell N, Bi A, Latifi A, Chowdhury D, Gygi S, Haas W, Wilson L, Murphy M, Han DK. Large-scale proteomic characterization of melanoma expressed proteins reveals nestin and vimentin as biomarkers that can potentially distinguish melanoma subtypes. Journal of Proteome Research. 13: 5031-40. PMID 25322343 DOI: 10.1021/pr5006789  0.72
2014 Choi JH, Choi SS, Kim ES, Jedrychowski MP, Yang YR, Jang HJ, Suh PG, Banks AS, Gygi SP, Spiegelman BM. Thrap3 docks on phosphoserine 273 of PPARγ and controls diabetic gene programming. Genes & Development. 28: 2361-9. PMID 25316675 DOI: 10.1101/gad.249367.114  0.72
2014 Sopko R, Foos M, Vinayagam A, Zhai B, Binari R, Hu Y, Randklev S, Perkins LA, Gygi SP, Perrimon N. Combining genetic perturbations and proteomics to examine kinase-phosphatase networks in Drosophila embryos. Developmental Cell. 31: 114-27. PMID 25284370 DOI: 10.1016/j.devcel.2014.07.027  0.72
2014 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. Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis. Molecular Cell. 56: 360-75. PMID 25284222 DOI: 10.1016/j.molcel.2014.09.007  0.72
2014 Chantranupong L, Wolfson RL, Orozco JM, Saxton RA, Scaria SM, Bar-Peled L, Spooner E, Isasa M, Gygi SP, Sabatini DM. The Sestrins interact with GATOR2 to negatively regulate the amino-acid-sensing pathway upstream of mTORC1. Cell Reports. 9: 1-8. PMID 25263562 DOI: 10.1016/j.celrep.2014.09.014  0.72
2014 Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S. Transcription factor networks in Drosophila melanogaster. Cell Reports. 8: 2031-43. PMID 25242320 DOI: 10.1016/j.celrep.2014.08.038  0.72
2014 Semenova I, Ikeda K, Resaul K, Kraikivski P, Aguiar M, Gygi S, Zaliapin I, Cowan A, Rodionov V. Regulation of microtubule-based transport by MAP4. Molecular Biology of the Cell. 25: 3119-32. PMID 25143402 DOI: 10.1091/mbc.E14-01-0022  0.72
2014 Lu G, Zhang Q, Huang Y, Song J, Tomaino R, Ehrenberger T, Lim E, Liu W, Bronson RT, Bowden M, Brock J, Krop IE, Dillon DA, Gygi SP, Mills GB, et al. Phosphorylation of ETS1 by Src family kinases prevents its recognition by the COP1 tumor suppressor. Cancer Cell. 26: 222-34. PMID 25117710 DOI: 10.1016/j.ccr.2014.06.026  0.72
2014 Dephoure N, Hwang S, O'Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM. Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast. Elife. 3: e03023. PMID 25073701 DOI: 10.7554/eLife.03023  0.72
2014 Krutauz D, Reis N, Nakasone MA, Siman P, Zhang D, Kirkpatrick DS, Gygi SP, Brik A, Fushman D, Glickman MH. Extended ubiquitin species are protein-based DUB inhibitors. Nature Chemical Biology. 10: 664-70. PMID 24997605 DOI: 10.1038/nchembio.1574  0.72
2014 Yamada T, Yang Y, Hemberg M, Yoshida T, Cho HY, Murphy JP, Fioravante D, Regehr WG, Gygi SP, Georgopoulos K, Bonni A. Promoter decommissioning by the NuRD chromatin remodeling complex triggers synaptic connectivity in the mammalian brain. Neuron. 83: 122-34. PMID 24991957 DOI: 10.1016/j.neuron.2014.05.039  0.72
2014 Zheng X, Zhai B, Koivunen P, Shin SJ, Lu G, Liu J, Geisen C, Chakraborty AA, Moslehi JJ, Smalley DM, Wei X, Chen X, Chen Z, Beres JM, Zhang J, ... ... Gygi SP, et al. Prolyl hydroxylation by EglN2 destabilizes FOXO3a by blocking its interaction with the USP9x deubiquitinase. Genes & Development. 28: 1429-44. PMID 24990963 DOI: 10.1101/gad.242131.114  0.72
2014 Van Vranken JG, Bricker DK, Dephoure N, Gygi SP, Cox JE, Thummel CS, Rutter J. SDHAF4 promotes mitochondrial succinate dehydrogenase activity and prevents neurodegeneration. Cell Metabolism. 20: 241-52. PMID 24954416 DOI: 10.1016/j.cmet.2014.05.012  0.72
2014 Wühr M, Freeman RM, Presler M, Horb ME, Peshkin L, Gygi SP, Kirschner MW. Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Current Biology : Cb. 24: 1467-75. PMID 24954049 DOI: 10.1016/j.cub.2014.05.044  0.72
2014 McAlister GC, Nusinow DP, Jedrychowski MP, Wühr M, Huttlin EL, Erickson BK, Rad R, Haas W, Gygi SP. MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Analytical Chemistry. 86: 7150-8. PMID 24927332 DOI: 10.1021/ac502040v  0.72
2014 Ryu H, Gygi SP, Azuma Y, Arnaoutov A, Dasso M. SUMOylation of Psmd1 controls Adrm1 interaction with the proteasome. Cell Reports. 7: 1842-8. PMID 24910440 DOI: 10.1016/j.celrep.2014.05.009  0.72
2014 Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, Wang EC, Aicheler R, Murrell I, Wilkinson GW, Lehner PJ, Gygi SP. Quantitative temporal viromics: an approach to investigate host-pathogen interaction. Cell. 157: 1460-72. PMID 24906157 DOI: 10.1016/j.cell.2014.04.028  0.72
2014 Rao RR, Long JZ, White JP, Svensson KJ, Lou J, Lokurkar I, Jedrychowski MP, Ruas JL, Wrann CD, Lo JC, Camera DM, Lachey J, Gygi S, Seehra J, Hawley JA, et al. Meteorin-like is a hormone that regulates immune-adipose interactions to increase beige fat thermogenesis. Cell. 157: 1279-91. PMID 24906147 DOI: 10.1016/j.cell.2014.03.065  0.72
2014 Schöndorf DC, Aureli M, McAllister FE, Hindley CJ, Mayer F, Schmid B, Sardi SP, Valsecchi M, Hoffmann S, Schwarz LK, Hedrich U, Berg D, Shihabuddin LS, Hu J, Pruszak J, ... Gygi SP, et al. iPSC-derived neurons from GBA1-associated Parkinson's disease patients show autophagic defects and impaired calcium homeostasis. Nature Communications. 5: 4028. PMID 24905578 DOI: 10.1038/ncomms5028  0.72
2014 Turanov AA, Shchedrina VA, Everley RA, Lobanov AV, Yim SH, Marino SM, Gygi SP, Hatfield DL, Gladyshev VN. Selenoprotein S is involved in maintenance and transport of multiprotein complexes. The Biochemical Journal. 462: 555-65. PMID 24897171 DOI: 10.1042/BJ20140076  0.72
2014 Chen YC, Umanah GK, Dephoure N, Andrabi SA, Gygi SP, Dawson TM, Dawson VL, Rutter J. Msp1/ATAD1 maintains mitochondrial function by facilitating the degradation of mislocalized tail-anchored proteins. The Embo Journal. 33: 1548-64. PMID 24843043 DOI: 10.15252/embj.201487943  0.72
2014 Chung JJ, Shim SH, Everley RA, Gygi SP, Zhuang X, Clapham DE. Structurally distinct Ca(2+) signaling domains of sperm flagella orchestrate tyrosine phosphorylation and motility. Cell. 157: 808-22. PMID 24813608 DOI: 10.1016/j.cell.2014.02.056  0.72
2014 Besche HC, Sha Z, Kukushkin NV, Peth A, Hock EM, Kim W, Gygi S, Gutierrez JA, Liao H, Dick L, Goldberg AL. Autoubiquitination of the 26S proteasome on Rpn13 regulates breakdown of ubiquitin conjugates. The Embo Journal. 33: 1159-76. PMID 24811749 DOI: 10.1002/embj.201386906  0.72
2014 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. Quantitative phosphoproteomic analysis reveals system-wide signaling pathways downstream of SDF-1/CXCR4 in breast cancer stem cells. Proceedings of the National Academy of Sciences of the United States of America. 111: E2182-90. PMID 24782546 DOI: 10.1073/pnas.1404943111  0.72
2014 Egan ED, Braun CR, Gygi SP, Moazed D. Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex. Rna (New York, N.Y.). 20: 867-81. PMID 24713849 DOI: 10.1261/rna.044479.114  0.72
2014 Mancias JD, Wang X, Gygi SP, Harper JW, Kimmelman AC. Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy. Nature. 509: 105-9. PMID 24695223 DOI: 10.1038/nature13148  0.72
2014 Liu P, Begley M, Michowski W, Inuzuka H, Ginzberg M, Gao D, Tsou P, Gan W, Papa A, Kim BM, Wan L, Singh A, Zhai B, Yuan M, Wang Z, ... Gygi SP, et al. Cell-cycle-regulated activation of Akt kinase by phosphorylation at its carboxyl terminus. Nature. 508: 541-5. PMID 24670654 DOI: 10.1038/nature13079  0.72
2014 Murphy JP, Everley RA, Coloff JL, Gygi SP. Combining amine metabolomics and quantitative proteomics of cancer cells using derivatization with isobaric tags. Analytical Chemistry. 86: 3585-93. PMID 24611633 DOI: 10.1021/ac500153a  0.72
2014 Raju RM, Jedrychowski MP, Wei JR, Pinkham JT, Park AS, O'Brien K, Rehren G, Schnappinger D, Gygi SP, Rubin EJ. Post-translational regulation via Clp protease is critical for survival of Mycobacterium tuberculosis. Plos Pathogens. 10: e1003994. PMID 24603869 DOI: 10.1371/journal.ppat.1003994  0.72
2014 Cohen S, Lee D, Zhai B, Gygi SP, Goldberg AL. Trim32 reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. The Journal of Cell Biology. 204: 747-58. PMID 24567360 DOI: 10.1083/jcb.201304167  0.72
2014 Tcherkezian J, Cargnello M, Romeo Y, Huttlin EL, Lavoie G, Gygi SP, Roux PP. Proteomic analysis of cap-dependent translation identifies LARP1 as a key regulator of 5'TOP mRNA translation. Genes & Development. 28: 357-71. PMID 24532714 DOI: 10.1101/gad.231407.113  0.72
2014 Engel U, Zhan Y, Long JB, Boyle SN, Ballif BA, Dorey K, Gygi SP, Koleske AJ, Vanvactor D. Abelson phosphorylation of CLASP2 modulates its association with microtubules and actin. Cytoskeleton (Hoboken, N.J.). 71: 195-209. PMID 24520051 DOI: 10.1002/cm.21164  0.72
2014 Zapata J, Dephoure N, Macdonough T, Yu Y, Parnell EJ, Mooring M, Gygi SP, Stillman DJ, Kellogg DR. PP2ARts1 is a master regulator of pathways that control cell size. The Journal of Cell Biology. 204: 359-76. PMID 24493588 DOI: 10.1083/jcb.201309119  0.72
2014 Tabata M, Rodgers JT, Hall JA, Lee Y, Jedrychowski MP, Gygi SP, Puigserver P. Cdc2-like kinase 2 suppresses hepatic fatty acid oxidation and ketogenesis through disruption of the PGC-1α and MED1 complex. Diabetes. 63: 1519-32. PMID 24458359 DOI: 10.2337/db13-1304  0.72
2014 Lee JG, Kim W, Gygi S, Ye Y. Characterization of the deubiquitinating activity of USP19 and its role in endoplasmic reticulum-associated degradation. The Journal of Biological Chemistry. 289: 3510-7. PMID 24356957 DOI: 10.1074/jbc.M113.538934  0.72
2014 Guarani V, Paulo J, Zhai B, Huttlin EL, Gygi SP, Harper JW. TIMMDC1/C3orf1 functions as a membrane-embedded mitochondrial complex I assembly factor through association with the MCIA complex. Molecular and Cellular Biology. 34: 847-61. PMID 24344204 DOI: 10.1128/MCB.01551-13  0.72
2014 Butovsky O, Jedrychowski MP, Moore CS, Cialic R, Lanser AJ, Gabriely G, Koeglsperger T, Dake B, Wu PM, Doykan CE, Fanek Z, Liu L, Chen Z, Rothstein JD, Ransohoff RM, ... Gygi SP, et al. Identification of a unique TGF-β-dependent molecular and functional signature in microglia. Nature Neuroscience. 17: 131-43. PMID 24316888 DOI: 10.1038/nn.3599  0.72
2014 Hanna J, Waterman D, Isasa M, Elsasser S, Shi Y, Gygi S, Finley D. Cuz1/Ynl155w, a zinc-dependent ubiquitin-binding protein, protects cells from metalloid-induced proteotoxicity. The Journal of Biological Chemistry. 289: 1876-85. PMID 24297164 DOI: 10.1074/jbc.M113.534032  0.72
2014 Ræder H, McAllister FE, Tjora E, Bhatt S, Haldorsen I, Hu J, Willems SM, Vesterhus M, El Ouaamari A, Liu M, Ræder MB, Immervoll H, Hoem D, Dimcevski G, Njølstad PR, ... ... Gygi SP, et al. Carboxyl-ester lipase maturity-onset diabetes of the young is associated with development of pancreatic cysts and upregulated MAPK signaling in secretin-stimulated duodenal fluid. Diabetes. 63: 259-69. PMID 24062244 DOI: 10.2337/db13-1012  0.72
2014 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. Quantitative phosphoproteomic analysis reveals system-wide signaling pathways downstream of SDF-1/CXCR4 in breast cancer stem cells (Proceedings of the National Academy of Sciences of the United States of America (2014) 111 (E2182-E2190) DOI: 10.1073/pnas.1404943111) Proceedings of the National Academy of Sciences of the United States of America. 111: 11223. DOI: 10.1073/pnas.1411381111  0.72
2013 Mosammaparast N, Kim H, Laurent B, Zhao Y, Lim HJ, Majid MC, Dango S, Luo Y, Hempel K, Sowa ME, Gygi SP, Steen H, Harper JW, Yankner B, Shi Y. The histone demethylase LSD1/KDM1A promotes the DNA damage response. The Journal of Cell Biology. 203: 457-70. PMID 24217620 DOI: 10.1083/jcb.201302092  0.72
2013 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, et al. Sin1 phosphorylation impairs mTORC2 complex integrity and inhibits downstream Akt signalling to suppress tumorigenesis. Nature Cell Biology. 15: 1340-50. PMID 24161930 DOI: 10.1038/ncb2860  0.72
2013 Kwon Y, Vinayagam A, Sun X, Dephoure N, Gygi SP, Hong P, Perrimon N. The Hippo signaling pathway interactome. Science (New York, N.Y.). 342: 737-40. PMID 24114784 DOI: 10.1126/science.1243971  0.72
2013 Garbe DS, Fang Y, Zheng X, Sowcik M, Anjum R, Gygi SP, Sehgal A. Cooperative interaction between phosphorylation sites on PERIOD maintains circadian period in Drosophila. Plos Genetics. 9: e1003749. PMID 24086144 DOI: 10.1371/journal.pgen.1003749  0.72
2013 Huang F, Zeng X, Kim W, Balasubramani M, Fortian A, Gygi SP, Yates NA, Sorkin A. Lysine 63-linked polyubiquitination is required for EGF receptor degradation. Proceedings of the National Academy of Sciences of the United States of America. 110: 15722-7. PMID 24019463 DOI: 10.1073/pnas.1308014110  0.72
2013 Shim JH, Greenblatt MB, Zou W, Huang Z, Wein MN, Brady N, Hu D, Charron J, Brodkin HR, Petsko GA, Zaller D, Zhai B, Gygi S, Glimcher LH, Jones DC. Schnurri-3 regulates ERK downstream of WNT signaling in osteoblasts. The Journal of Clinical Investigation. 123: 4010-22. PMID 23945236 DOI: 10.1172/JCI69443  0.72
2013 Johnson A, Wu R, Peetz M, Gygi SP, Moazed D. Heterochromatic gene silencing by activator interference and a transcription elongation barrier. The Journal of Biological Chemistry. 288: 28771-82. PMID 23940036 DOI: 10.1074/jbc.M113.460071  0.72
2013 Zou W, Greenblatt MB, Brady N, Lotinun S, Zhai B, de Rivera H, Singh A, Sun J, Gygi SP, Baron R, Glimcher LH, Jones DC. The microtubule-associated protein DCAMKL1 regulates osteoblast function via repression of Runx2. The Journal of Experimental Medicine. 210: 1793-806. PMID 23918955 DOI: 10.1084/jem.20111790  0.72
2013 Pease BN, Huttlin EL, Jedrychowski MP, Talevich E, Harmon J, Dillman T, Kannan N, Doerig C, Chakrabarti R, Gygi SP, Chakrabarti D. Global analysis of protein expression and phosphorylation of three stages of Plasmodium falciparum intraerythrocytic development. Journal of Proteome Research. 12: 4028-45. PMID 23914800 DOI: 10.1021/pr400394g  0.72
2013 Ye L, Wu J, Cohen P, Kazak L, Khandekar MJ, Jedrychowski MP, Zeng X, Gygi SP, Spiegelman BM. Fat cells directly sense temperature to activate thermogenesis. Proceedings of the National Academy of Sciences of the United States of America. 110: 12480-5. PMID 23818608 DOI: 10.1073/pnas.1310261110  0.72
2013 Goranov AI, Gulati A, Dephoure N, Takahara T, Maeda T, Gygi SP, Manalis S, Amon A. Changes in cell morphology are coordinated with cell growth through the TORC1 pathway Current Biology. 23: 1269-1279. PMID 23810534 DOI: 10.1016/j.cub.2013.05.035  0.72
2013 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, et al. SIRT4 coordinates the balance between lipid synthesis and catabolism by repressing malonyl CoA decarboxylase. Molecular Cell. 50: 686-98. PMID 23746352 DOI: 10.1016/j.molcel.2013.05.012  0.72
2013 Everley RA, Kunz RC, McAllister FE, Gygi SP. Increasing throughput in targeted proteomics assays: 54-plex quantitation in a single mass spectrometry run. Analytical Chemistry. 85: 5340-6. PMID 23662842 DOI: 10.1021/ac400845e  0.72
2013 Tobe R, Naranjo-Suarez S, Everley RA, Carlson BA, Turanov AA, Tsuji PA, Yoo MH, Gygi SP, Gladyshev VN, Hatfield DL. High error rates in selenocysteine insertion in mammalian cells treated with the antibiotic doxycycline, chloramphenicol, or geneticin. The Journal of Biological Chemistry. 288: 14709-15. PMID 23589299 DOI: 10.1074/jbc.M112.446666  0.72
2013 Neilson KA, Scafaro AP, Chick JM, George IS, Van Sluyter SC, Gygi SP, Atwell BJ, Haynes PA. The influence of signals from chilled roots on the proteome of shoot tissues in rice seedlings. Proteomics. 13: 1922-33. PMID 23580440 DOI: 10.1002/pmic.201200475  0.72
2013 Wilson-Grady JT, Haas W, Gygi SP. Quantitative comparison of the fasted and re-fed mouse liver phosphoproteomes using lower pH reductive dimethylation. Methods (San Diego, Calif.). 61: 277-86. PMID 23567750 DOI: 10.1016/j.ymeth.2013.03.031  0.48
2013 Ræder H, Vesterhus M, El Ouaamari A, Paulo JA, McAllister FE, Liew CW, Hu J, Kawamori D, Molven A, Gygi SP, Njølstad PR, Kahn CR, Kulkarni RN. Absence of diabetes and pancreatic exocrine dysfunction in a transgenic model of carboxyl-ester lipase-MODY (maturity-onset diabetes of the young). Plos One. 8: e60229. PMID 23565203 DOI: 10.1371/journal.pone.0060229  0.72
2013 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW. Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. Nature. 496: 372-6. PMID 23503661 DOI: 10.1038/nature12043  0.72
2013 Zhang X, Lavoie G, Fort L, Huttlin EL, Tcherkezian J, Galan JA, Gu H, Gygi SP, Carreno S, Roux PP. Gab2 phosphorylation by RSK inhibits Shp2 recruitment and cell motility. Molecular and Cellular Biology. 33: 1657-70. PMID 23401857 DOI: 10.1128/MCB.01353-12  0.72
2013 Aukrust I, Bjørkhaug L, Negahdar M, Molnes J, Johansson BB, Müller Y, Haas W, Gygi SP, Søvik O, Flatmark T, Kulkarni RN, Njølstad PR. SUMOylation of pancreatic glucokinase regulates its cellular stability and activity. The Journal of Biological Chemistry. 288: 5951-62. PMID 23297408 DOI: 10.1074/jbc.M112.393769  0.48
2013 Arbab M, Mahony S, Cho H, Chick JM, Rolfe PA, van Hoff JP, Morris VW, Gygi SP, Maas RL, Gifford DK, Sherwood RI. A multi-parametric flow cytometric assay to analyze DNA-protein interactions. Nucleic Acids Research. 41: e38. PMID 23143268 DOI: 10.1093/nar/gks1034  0.56
2013 Ibebunjo C, Chick JM, Kendall T, Eash JK, Li C, Zhang Y, Vickers C, Wu Z, Clarke BA, Shi J, Cruz J, Fournier B, Brachat S, Gutzwiller S, Ma Q, ... ... Gygi SP, et al. Genomic and proteomic profiling reveals reduced mitochondrial function and disruption of the neuromuscular junction driving rat sarcopenia. Molecular and Cellular Biology. 33: 194-212. PMID 23109432 DOI: 10.1128/MCB.01036-12  0.72
2012 Dominy JE, Lee Y, Jedrychowski MP, Chim H, Jurczak MJ, Camporez JP, Ruan HB, Feldman J, Pierce K, Mostoslavsky R, Denu JM, Clish CB, Yang X, Shulman GI, Gygi SP, et al. The deacetylase Sirt6 activates the acetyltransferase GCN5 and suppresses hepatic gluconeogenesis. Molecular Cell. 48: 900-13. PMID 23142079 DOI: 10.1016/j.molcel.2012.09.030  0.72
2012 Wühr M, Haas W, McAlister GC, Peshkin L, Rad R, Kirschner MW, Gygi SP. Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster. Analytical Chemistry. 84: 9214-21. PMID 23098179 DOI: 10.1021/ac301962s  0.72
2012 Nusinow DP, Kiezun A, O'Connell DJ, Chick JM, Yue Y, Maas RL, Gygi SP, Sunyaev SR. Network-based inference from complex proteomic mixtures using SNIPE. Bioinformatics (Oxford, England). 28: 3115-22. PMID 23060611 DOI: 10.1093/bioinformatics/bts594  0.72
2012 Janas MM, Wang B, Harris AS, Aguiar M, Shaffer JM, Subrahmanyam YV, Behlke MA, Wucherpfennig KW, Gygi SP, Gagnon E, Novina CD. Alternative RISC assembly: binding and repression of microRNA-mRNA duplexes by human Ago proteins. Rna (New York, N.Y.). 18: 2041-55. PMID 23019594 DOI: 10.1261/rna.035675.112  0.72
2012 Thibault G, Shui G, Kim W, McAlister GC, Ismail N, Gygi SP, Wenk MR, Ng DT. The membrane stress response buffers lethal effects of lipid disequilibrium by reprogramming the protein homeostasis network. Molecular Cell. 48: 16-27. PMID 23000174 DOI: 10.1016/j.molcel.2012.08.016  0.48
2012 Cargnello M, Tcherkezian J, Dorn JF, Huttlin EL, Maddox PS, Gygi SP, Roux PP. Phosphorylation of the eukaryotic translation initiation factor 4E-transporter (4E-T) by c-Jun N-terminal kinase promotes stress-dependent P-body assembly. Molecular and Cellular Biology. 32: 4572-84. PMID 22966201 DOI: 10.1128/MCB.00544-12  0.72
2012 Burns KE, McAllister FE, Schwerdtfeger C, Mintseris J, Cerda-Maira F, Noens EE, Wilmanns M, Hubbard SR, Melandri F, Ovaa H, Gygi SP, Darwin KH. Mycobacterium tuberculosis prokaryotic ubiquitin-like protein-deconjugating enzyme is an unusual aspartate amidase. The Journal of Biological Chemistry. 287: 37522-9. PMID 22942282 DOI: 10.1074/jbc.M112.384784  0.72
2012 McAlister GC, Huttlin EL, Haas W, Ting L, Jedrychowski MP, Rogers JC, Kuhn K, Pike I, Grothe RA, Blethrow JD, Gygi SP. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Analytical Chemistry. 84: 7469-78. PMID 22880955 DOI: 10.1021/ac301572t  0.72
2011 Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, ... ... Gygi SP, et al. A protein complex network of Drosophila melanogaster. Cell. 147: 690-703. PMID 22036573 DOI: 10.1016/j.cell.2011.08.047  0.72
2011 Jedrychowski MP, Huttlin EL, Haas W, Sowa ME, Rad R, Gygi SP. Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Molecular & Cellular Proteomics : McP. 10: M111.009910. PMID 21917720 DOI: 10.1074/mcp.M111.009910  0.72
2011 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP. Systematic and quantitative assessment of the ubiquitin-modified proteome. Molecular Cell. 44: 325-40. PMID 21906983 DOI: 10.1016/j.molcel.2011.08.025  0.72
2011 Wu R, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME, Gygi SP. A large-scale method to measure absolute protein phosphorylation stoichiometries. Nature Methods. 8: 677-83. PMID 21725298 DOI: 10.1038/nmeth.1636  0.72
2011 Jirawatnotai S, Hu Y, Michowski W, Elias JE, Becks L, Bienvenu F, Zagozdzon A, Goswami T, Wang YE, Clark AB, Kunkel TA, van Harn T, Xia B, Correll M, Quackenbush J, ... ... Gygi SP, et al. A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Nature. 474: 230-4. PMID 21654808 DOI: 10.1038/nature10155  0.72
2011 Wu R, Dephoure N, Haas W, Huttlin EL, Zhai B, Sowa ME, Gygi SP. Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Molecular & Cellular Proteomics : McP. 10: M111.009654. PMID 21551504 DOI: 10.1074/mcp.M111.009654  0.72
2010 Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell. 143: 1174-89. PMID 21183079 DOI: 10.1016/j.cell.2010.12.001  0.72
2010 Braun CR, Mintseris J, Gavathiotis E, Bird GH, Gygi SP, Walensky LD. Photoreactive stapled BH3 peptides to dissect the BCL-2 family interactome. Chemistry & Biology. 17: 1325-33. PMID 21168768 DOI: 10.1016/j.chembiol.2010.09.015  0.72
2010 Teixeira FR, Yokoo S, Gartner CA, Manfiolli AO, Baqui MM, Assmann EM, Maragno AL, Yu H, de Lanerolle P, Kobarg J, Gygi SP, Gomes MD. Identification of FBXO25-interacting proteins using an integrated proteomics approach. Proteomics. 10: 2746-57. PMID 20473970 DOI: 10.1002/pmic.200900419  0.72
2010 Aguiar M, Haas W, Beausoleil SA, Rush J, Gygi SP. Gas-phase rearrangements do not affect site localization reliability in phosphoproteomics data sets. Journal of Proteome Research. 9: 3103-7. PMID 20377248 DOI: 10.1021/pr1000225  0.72
2010 Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, ... ... Gygi SP, et al. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 463: 374-8. PMID 20090754 DOI: 10.1038/nature08684  0.72
2010 Festa RA, McAllister F, Pearce MJ, Mintseris J, Burns KE, Gygi SP, Darwin KH. Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis [corrected] . Plos One. 5: e8589. PMID 20066036 DOI: 10.1371/journal.pone.0008589  0.72
2010 Elias JE, Gygi SP. Target-decoy search strategy for mass spectrometry-based proteomics. Methods in Molecular Biology (Clifton, N.J.). 604: 55-71. PMID 20013364 DOI: 10.1007/978-1-60761-444-9_5  0.52
2010 Jedrychowski MP, Gartner CA, Gygi SP, Zhou L, Herz J, Kandror KV, Pilch PF. Proteomic analysis of GLUT4 storage vesicles reveals LRP1 to be an important vesicle component and target of insulin signaling. The Journal of Biological Chemistry. 285: 104-14. PMID 19864425 DOI: 10.1074/jbc.M109.040428  0.72
2009 Hemming ML, Elias JE, Gygi SP, Selkoe DJ. Identification of beta-secretase (BACE1) substrates using quantitative proteomics. Plos One. 4: e8477. PMID 20041192 DOI: 10.1371/journal.pone.0008477  0.72
2008 Villén J, Beausoleil SA, Gygi SP. Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics. 8: 4444-52. PMID 18972524 DOI: 10.1002/pmic.200800283  0.6
2008 Hemming ML, Elias JE, Gygi SP, Selkoe DJ. Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements. Plos Biology. 6: e257. PMID 18942891 DOI: 10.1371/journal.pbio.0060257  0.72
2008 Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, Darwin KH. Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Science (New York, N.Y.). 322: 1104-7. PMID 18832610 DOI: 10.1126/science.1163885  0.72
2008 Bakalarski CE, Elias JE, Villén J, Haas W, Gerber SA, Everley PA, Gygi SP. The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses. Journal of Proteome Research. 7: 4756-65. PMID 18798661 DOI: 10.1021/pr800333e  0.72
2008 Dephoure N, Zhou C, Villén J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP. A quantitative atlas of mitotic phosphorylation Proceedings of the National Academy of Sciences of the United States of America. 105: 10762-10767. PMID 18669648 DOI: 10.1073/pnas.0805139105  0.72
2008 Zhai B, Villén J, Beausoleil SA, Mintseris J, Gygi SP. Phosphoproteome analysis of Drosophila melanogaster embryos. Journal of Proteome Research. 7: 1675-82. PMID 18327897 DOI: 10.1021/pr700696a  0.6
2007 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. Profiling of UV-induced ATM/ATR signaling pathways. Proceedings of the National Academy of Sciences of the United States of America. 104: 19855-60. PMID 18077418 DOI: 10.1073/pnas.0707579104  0.72
2007 Everley PA, Gartner CA, Haas W, Saghatelian A, Elias JE, Cravatt BF, Zetter BR, Gygi SP. Assessing enzyme activities using stable isotope labeling and mass spectrometry. Molecular & Cellular Proteomics : McP. 6: 1771-7. PMID 17627935 DOI: 10.1074/mcp.M700057-MCP200  0.72
2007 Gerber SA, Kettenbach AN, Rush J, Gygi SP. The absolute quantification strategy: application to phosphorylation profiling of human separase serine 1126. Methods in Molecular Biology (Clifton, N.J.). 359: 71-86. PMID 17484111 DOI: 10.1007/978-1-59745-255-7_5  0.72
2007 Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature Methods. 4: 207-14. PMID 17327847 DOI: 10.1038/nmeth1019  0.52
2007 Gartner CA, Elias JE, Bakalarski CE, Gygi SP. Catch-and-release reagents for broadscale quantitative proteomics analyses. Journal of Proteome Research. 6: 1482-91. PMID 17311443 DOI: 10.1021/pr060605f  0.72
2007 Villén J, Beausoleil SA, Gerber SA, Gygi SP. Large-scale phosphorylation analysis of mouse liver. Proceedings of the National Academy of Sciences of the United States of America. 104: 1488-93. PMID 17242355 DOI: 10.1073/pnas.0609836104  0.72
2006 Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nature Biotechnology. 24: 1285-92. PMID 16964243 DOI: 10.1038/nbt1240  0.72
2006 Everley PA, Bakalarski CE, Elias JE, Waghorne CG, Beausoleil SA, Gerber SA, Faherty BK, Zetter BR, Gygi SP. Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. Journal of Proteome Research. 5: 1224-31. PMID 16674112 DOI: 10.1021/pr0504891  0.72
2006 Haas W, Faherty BK, Gerber SA, Elias JE, Beausoleil SA, Bakalarski CE, Li X, Villén J, Gygi SP. Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Molecular & Cellular Proteomics : McP. 5: 1326-37. PMID 16635985 DOI: 10.1074/mcp.M500339-MCP200  0.72
2005 Elias JE, Haas W, Faherty BK, Gygi SP. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nature Methods. 2: 667-75. PMID 16118637 DOI: 10.1038/nmeth785  0.52
2005 Dieguez-Acuna FJ, Gerber SA, Kodama S, Elias JE, Beausoleil SA, Faustman D, Gygi SP. Characterization of mouse spleen cells by subtractive proteomics. Molecular & Cellular Proteomics : McP. 4: 1459-70. PMID 16037072 DOI: 10.1074/mcp.M500137-MCP200  0.72
2005 Xu J, Zhong N, Wang H, Elias JE, Kim CY, Woldman I, Pifl C, Gygi SP, Geula C, Yankner BA. The Parkinson's disease-associated DJ-1 protein is a transcriptional co-activator that protects against neuronal apoptosis. Human Molecular Genetics. 14: 1231-41. PMID 15790595 DOI: 10.1093/hmg/ddi134  0.72
2005 Kirkpatrick DS, Gerber SA, Gygi SP. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods (San Diego, Calif.). 35: 265-73. PMID 15722223 DOI: 10.1016/j.ymeth.2004.08.018  0.72
2005 Gartner CA, Wen B, Wan J, Becker RS, Jones G, Gygi SP, Nelson SD. Photochromic agents as tools for protein structure study: lapachenole is a photoaffinity ligand of cytochrome P450 3A4. Biochemistry. 44: 1846-55. PMID 15697210 DOI: 10.1021/bi049231z  0.72
2005 Ballif BA, Roux PP, Gerber SA, MacKeigan JP, Blenis J, Gygi SP. Quantitative phosphorylation profiling of the ERK/p90 ribosomal S6 kinase-signaling cassette and its targets, the tuberous sclerosis tumor suppressors. Proceedings of the National Academy of Sciences of the United States of America. 102: 667-72. PMID 15647351 DOI: 10.1073/pnas.0409143102  0.72
2005 Denison C, Rudner AD, Gerber SA, Bakalarski CE, Moazed D, Gygi SP. A proteomic strategy for gaining insights into protein sumoylation in yeast. Molecular & Cellular Proteomics : McP. 4: 246-54. PMID 15542864 DOI: 10.1074/mcp.M400154-MCP200  0.72
2004 Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell. 119: 789-802. PMID 15607976 DOI: 10.1016/j.cell.2004.11.034  0.72
2004 Starita LM, Machida Y, Sankaran S, Elias JE, Griffin K, Schlegel BP, Gygi SP, Parvin JD. BRCA1-dependent ubiquitination of gamma-tubulin regulates centrosome number. Molecular and Cellular Biology. 24: 8457-66. PMID 15367667 DOI: 10.1128/MCB.24.19.8457-8466.2004  0.52
2004 Ballif BA, Villén J, Beausoleil SA, Schwartz D, Gygi SP. Phosphoproteomic analysis of the developing mouse brain. Molecular & Cellular Proteomics : McP. 3: 1093-101. PMID 15345747 DOI: 10.1074/mcp.M400085-MCP200  0.6
2004 Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, Cohn MA, Cantley LC, Gygi SP. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proceedings of the National Academy of Sciences of the United States of America. 101: 12130-5. PMID 15302935 DOI: 10.1073/pnas.0404720101  0.72
2004 Tanny JC, Kirkpatrick DS, Gerber SA, Gygi SP, Moazed D. Budding yeast silencing complexes and regulation of Sir2 activity by protein-protein interactions. Molecular and Cellular Biology. 24: 6931-46. PMID 15282295 DOI: 10.1128/MCB.24.16.6931-6946.2004  0.72
2004 Gibbons FD, Elias JE, Gygi SP, Roth FP. SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. Journal of the American Society For Mass Spectrometry. 15: 910-2. PMID 15144981 DOI: 10.1016/j.jasms.2004.02.011  0.72
2004 Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nature Biotechnology. 22: 214-9. PMID 14730315 DOI: 10.1038/nbt930  0.72
2004 Vrabioiu AM, Gerber SA, Gygi SP, Field CM, Mitchison TJ. The majority of the Saccharomyces cerevisiae septin complexes do not exchange guanine nucleotides. The Journal of Biological Chemistry. 279: 3111-8. PMID 14597621 DOI: 10.1074/jbc.M310941200  0.72
2003 Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP. A proteomics approach to understanding protein ubiquitination. Nature Biotechnology. 21: 921-6. PMID 12872131 DOI: 10.1038/nbt849  0.72
2003 Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proceedings of the National Academy of Sciences of the United States of America. 100: 6940-5. PMID 12771378 DOI: 10.1073/pnas.0832254100  0.72
2003 Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. Journal of Proteome Research. 2: 43-50. PMID 12643542  0.52
2002 Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. Journal of Proteome Research. 1: 47-54. PMID 12643526 DOI: 10.1021/pr015509n  0.72
2002 Lee H, Griffin TJ, Gygi SP, Rist B, Aebersold R. Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis. Analytical Chemistry. 74: 4353-60. PMID 12236342 DOI: 10.1021/ac025757i  0.72
2002 Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Molecular & Cellular Proteomics : McP. 1: 323-33. PMID 12096114  0.72
2002 Hoppe GJ, Tanny JC, Rudner AD, Gerber SA, Danaie S, Gygi SP, Moazed D. Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Molecular and Cellular Biology. 22: 4167-80. PMID 12024030 DOI: 10.1128/MCB.22.12.4167-4180.2002  0.72
2002 James EA, Gygi SP, Adams ML, Pierce RH, Fausto N, Aebersold RH, Nelson SD, Bruschi SA. Mitochondrial aconitase modification, functional inhibition, and evidence for a supramolecular complex of the TCA cycle by the renal toxicant S-(1,1,2,2-tetrafluoroethyl)-L-cysteine. Biochemistry. 41: 6789-97. PMID 12022883 DOI: 10.1021/bi020038j  0.72
2002 Hamerman JA, Hayashi F, Schroeder LA, Gygi SP, Haas AL, Hampson L, Coughlin P, Aebersold R, Aderem A. Serpin 2a is induced in activated macrophages and conjugates to a ubiquitin homolog. Journal of Immunology (Baltimore, Md. : 1950). 168: 2415-23. PMID 11859133  0.72
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