Steven P. Gygi - Publications

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

443 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
2022 Pfeiffer CT, Paulo JA, Gygi SP, Rockman HA. Proximity labeling for investigating protein-protein interactions. Methods in Cell Biology. 169: 237-266. PMID 35623704 DOI: 10.1016/bs.mcb.2021.12.006  0.322
2021 Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, ... ... Gygi SP, et al. A multi-scale map of cell structure fusing protein images and interactions. Nature. PMID 34819669 DOI: 10.1038/s41586-021-04115-9  0.66
2021 Li J, Cai Z, Vaites LP, Shen N, Mitchell DC, Huttlin EL, Paulo JA, Harry BL, Gygi SP. Proteome-wide mapping of short-lived proteins in human cells. Molecular Cell. PMID 34626566 DOI: 10.1016/j.molcel.2021.09.015  0.7
2021 Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, ... ... Gygi SP, et al. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell. PMID 33961781 DOI: 10.1016/j.cell.2021.04.011  0.81
2021 Hollingsworth LR, Sharif H, Griswold AR, Fontana P, Mintseris J, Dagbay KB, Paulo JA, Gygi SP, Bachovchin DA, Wu H. DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation. Nature. PMID 33731932 DOI: 10.1038/s41586-021-03350-4  0.68
2021 Gassaway BM, Paulo JA, Gygi SP. Categorization of Phosphorylation Site Behavior during the Diauxic Shift in . Journal of Proteome Research. PMID 33630598 DOI: 10.1021/acs.jproteome.0c00943  0.322
2021 Kuljanin M, Mitchell DC, Schweppe DK, Gikandi AS, Nusinow DP, Bulloch NJ, Vinogradova EV, Wilson DL, Kool ET, Mancias JD, Cravatt BF, Gygi SP. Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries. Nature Biotechnology. PMID 33398154 DOI: 10.1038/s41587-020-00778-3  0.818
2020 Rad R, Li J, Mintseris J, O'Connell J, Gygi SP, Schweppe DK. Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage. Journal of Proteome Research. PMID 33190505 DOI: 10.1021/acs.jproteome.0c00563  0.788
2020 Muraoka S, Jedrychowski MP, Yanamandra K, Ikezu S, Gygi SP, Ikezu T. Proteomic Profiling of Extracellular Vesicles Derived from Cerebrospinal Fluid of Alzheimer's Disease Patients: A Pilot Study. Cells. 9. PMID 32854315 DOI: 10.3390/Cells9091959  0.322
2020 Paul AS, Miliu A, Paulo JA, Goldberg JM, Bonilla AM, Berry L, Seveno M, Braun-Breton C, Kosber AL, Elsworth B, Arriola JSN, Lebrun M, Gygi SP, Lamarque MH, Duraisingh MT. Co-option of Plasmodium falciparum PP1 for egress from host erythrocytes. Nature Communications. 11: 3532. PMID 32669539 DOI: 10.1038/S41467-020-17306-1  0.331
2020 Socha A, Yang D, Bulsiewicz A, Yaprianto K, Kupculak M, Liang CC, Hadjicharalambous A, Wu R, Gygi SP, Cohn MA. WRNIP1 Is Recruited to DNA Interstrand Crosslinks and Promotes Repair. Cell Reports. 32: 107850. PMID 32640220 DOI: 10.1016/J.Celrep.2020.107850  0.331
2020 Manohar S, Yu Q, Gygi SP, King RW. The insulin receptor adaptor IRS2 is an APC/C substrate that promotes cell cycle protein expression and a robust spindle assembly checkpoint. Molecular & Cellular Proteomics : McP. PMID 32554797 DOI: 10.1074/Mcp.Ra120.002069  0.358
2020 Hauseman ZJ, Harvey EP, Newman CE, Wales TE, Bucci JC, Mintseris J, Schweppe DK, David L, Fan L, Cohen DT, Herce HD, Mourtada R, Ben-Nun Y, Bloch NB, Hansen SB, ... ... Gygi SP, et al. Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization. Molecular Cell. PMID 32533918 DOI: 10.1016/J.Molcel.2020.05.029  0.772
2020 Jedrychowski MP, Lu GZ, Szpyt J, Mariotti M, Garrity R, Paulo JA, Schweppe DK, Laznik-Bogoslavski D, Kazak L, Murphy MP, Gladyshev VN, Gygi SP, Chouchani ET, Spiegelman BM. Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity. Proceedings of the National Academy of Sciences of the United States of America. PMID 32358195 DOI: 10.1073/Pnas.2001387117  0.808
2020 Sun Y, Ning X, Fan J, Hu J, Jiang Y, Hu Z, Paulo JA, Liu J, Qiu X, Xu H, Fu S, Gygi SP, Zhang J, Zhou C. Loss of tumor suppressor inositol polyphosphate 4-phosphatase type B impairs DNA double-strand break repair by destabilization of DNA tethering protein Rad50. Cell Death & Disease. 11: 292. PMID 32341333 DOI: 10.1038/S41419-020-2491-3  0.31
2020 Yu Q, Xiao H, Jedrychowski MP, Schweppe DK, Navarrete-Perea J, Knott J, Rogers J, Chouchani ET, Gygi SP. Sample multiplexing for targeted pathway proteomics in aging mice. Proceedings of the National Academy of Sciences of the United States of America. PMID 32332170 DOI: 10.1073/Pnas.1919410117  0.814
2020 Yu Q, Paulo JA, Navarrete-Perea J, McAlister GC, Canterbury JD, Bailey DJ, Robitaille AM, Huguet R, Zabrouskov V, Gygi SP, Schweppe DK. Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics. Analytical Chemistry. PMID 32250601 DOI: 10.1021/Acs.Analchem.9B05685  0.791
2020 Li J, Van Vranken JG, Paulo JA, Huttlin EL, Gygi SP. Selection of Heating Temperatures Improves the Sensitivity of Proteome Integral Solubility Alteration (PISA) Assay. Journal of Proteome Research. PMID 32243163 DOI: 10.1021/Acs.Jproteome.0C00063  0.676
2020 Michowski W, Chick JM, Chu C, Kolodziejczyk A, Wang Y, Suski JM, Abraham B, Anders L, Day D, Dunkl LM, Li Cheong Man M, Zhang T, Laphanuwat P, Bacon NA, Liu L, ... ... Gygi SP, et al. Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells. Molecular Cell. PMID 32240602 DOI: 10.1016/J.Molcel.2020.03.010  0.34
2020 Li J, Van Vranken JG, Pontano Vaites L, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, et al. TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nature Methods. PMID 32203386 DOI: 10.1038/S41592-020-0781-4  0.822
2020 Gygi JP, Ramin Rad, Navarrete-Perea J, Younesi S, Gygi SP, Paulo JA. A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search. Journal of the American Society For Mass Spectrometry. PMID 32202424 DOI: 10.1021/Jasms.0C00029  0.375
2020 Sharma S, Zhang T, Michowski W, Rebecca VW, Xiao M, Ferretti R, Suski JM, Bronson RT, Paulo JA, Frederick D, Fassl A, Boland GM, Geng Y, Lees JA, Medema RH, ... ... Gygi SP, et al. Targeting the cyclin-dependent kinase 5 in metastatic melanoma. Proceedings of the National Academy of Sciences of the United States of America. PMID 32193336 DOI: 10.1073/Pnas.1912617117  0.317
2020 Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Wouters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP. Correction to Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry. Analytical Chemistry. PMID 32134636 DOI: 10.1021/acs.analchem.0c00888  0.779
2020 Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP. Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics. Journal of Proteome Research. PMID 32126768 DOI: 10.1021/Acs.Jproteome.9B00860  0.808
2020 Xiao H, Jedrychowski MP, Schweppe DK, Huttlin EL, Yu Q, Heppner DE, Li J, Long J, Mills EL, Szpyt J, He Z, Du G, Garrity R, Reddy A, Vaites LP, ... ... Gygi SP, et al. A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging. Cell. PMID 32109415 DOI: 10.1016/J.Cell.2020.02.012  0.795
2020 Erickson BK, Schweppe DK, Yu Q, Rad R, Haas W, McAlister GC, Gygi SP. Parallel notched gas-phase enrichment for improved proteome identification and quantitation with fast spectral acquisition rates. Journal of Proteome Research. PMID 31990573 DOI: 10.1021/Acs.Jproteome.9B00715  0.785
2020 Nusinow DP, Szpyt J, Ghandi M, Rose CM, McDonald ER, Kalocsay M, Jané-Valbuena J, Gelfand E, Schweppe DK, Jedrychowski M, Golji J, Porter DA, Rejtar T, Wang YK, Kryukov GV, ... ... Gygi SP, et al. Quantitative Proteomics of the Cancer Cell Line Encyclopedia. Cell. 180: 387-402.e16. PMID 31978347 DOI: 10.1016/J.Cell.2019.12.023  0.805
2020 Kennedy JJ, Chowdhury S, Savage SR, Hou X, Huntoon CJ, Ivey RG, Yu Q, Lin C, Huang D, Zhao L, Voytovich UJ, Schoenherr RM, Shire Z, Skates SJ, Whiteaker JR, ... ... Gygi SP, et al. Abstract PR02: Proteogenomic approach to identify mechanisms of platinum refractoriness in high-grade serous ovarian cancers Clinical Cancer Research. 26. DOI: 10.1158/1557-3265.Ovca19-Pr02  0.315
2019 Mintseris J, Gygi SP. High-density chemical cross-linking for modeling protein interactions. Proceedings of the National Academy of Sciences of the United States of America. PMID 31848235 DOI: 10.1073/Pnas.1902931116  0.741
2019 Loo LSW, Vethe H, Soetedjo AAP, Paulo JA, Jasmen J, Jackson N, Bjørlykke Y, Valdez IA, Vaudel M, Barsnes H, Gygi SP, Raeder H, Teo AKK, Kulkarni RN. Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors. Stem Cells (Dayton, Ohio). PMID 31828876 DOI: 10.1002/Stem.3135  0.319
2019 Schweppe DK, Rusin SF, Gygi SP, Paulo JA. An optimized workflow for multiplexed phosphorylation analysis of TMT-labeled peptides using high-Field Asymmetric waveform Ion Mobility Spectrometry (FAIMS). Journal of Proteome Research. PMID 31799850 DOI: 10.1021/Acs.Jproteome.9B00759  0.816
2019 Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D. Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance. Molecular Cell. PMID 31784357 DOI: 10.1016/J.Molcel.2019.10.018  0.408
2019 Guerra-Moreno A, Prado MA, Ang J, Schnell HM, Micoogullari Y, Paulo JA, Finley D, Gygi SP, Hanna J. Thiol-based direct threat sensing by the stress-activated protein kinase Hog1. Science Signaling. 12. PMID 31772124 DOI: 10.1126/Scisignal.Aaw4956  0.346
2019 Li J, Paulo JA, Nusinow DP, Huttlin EL, Gygi SP. Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. Cell Reports. 29: 2092-2104.e4. PMID 31722220 DOI: 10.1016/J.Celrep.2019.10.034  0.812
2019 Gamble J, Chick J, Seltzer K, Graber J, Gygi S, Braun R, Snyder E. An expanded mouse testis transcriptome and mass spectrometry defines novel proteins. Reproduction (Cambridge, England). PMID 31677600 DOI: 10.1530/Rep-19-0092  0.387
2019 Wang Y, Dix MM, Bianco G, Remsberg JR, Lee HY, Kalocsay M, Gygi SP, Forli S, Vite G, Lawrence RM, Parker CG, Cravatt BF. Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs. Nature Chemistry. PMID 31659311 DOI: 10.1038/S41557-019-0351-5  0.396
2019 Muraoka S, Jedrychowski MP, Tatebe H, DeLeo AM, Ikezu S, Tokuda T, Gygi SP, Stern RA, Ikezu T. Proteomic Profiling of Extracellular Vesicles Isolated From Cerebrospinal Fluid of Former National Football League Players at Risk for Chronic Traumatic Encephalopathy. Frontiers in Neuroscience. 13: 1059. PMID 31649498 DOI: 10.3389/Fnins.2019.01059  0.315
2019 Paulo JA, Navarrete-Perea J, Gygi SP. Multiplexed proteome profiling of carbon source perturbations in two yeast species with SL-SP3-TMT. Journal of Proteomics. 103531. PMID 31626996 DOI: 10.1016/J.Jprot.2019.103531  0.402
2019 Lim MY, Paulo JA, Gygi SP. Evaluating False Transfer Rates from the Match-Between-Runs Algorithm with a Two-Proteome Model. Journal of Proteome Research. PMID 31547658 DOI: 10.1021/Acs.Jproteome.9B00492  0.342
2019 Brubaker DK, Paulo JA, Sheth S, Poulin EJ, Popow O, Joughin BA, Strasser SD, Starchenko A, Gygi SP, Lauffenburger DA, Haigis KM. Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation. Cell Systems. PMID 31521603 DOI: 10.1016/J.Cels.2019.07.006  0.319
2019 Paulo JA, Gygi SP. mTMT: An alternative, non-isobaric, tandem mass tag allowing for precursor-based quantification. Analytical Chemistry. PMID 31490667 DOI: 10.1021/Acs.Analchem.9B03162  0.412
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  0.306
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  0.301
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  0.811
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  0.799
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  0.804
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  0.363
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  0.336
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  0.361
2018 Chi B, O'Connell JD, Iocolano AD, Coady JA, Yu Y, Gangopadhyay J, Gygi SP, Reed R. The neurodegenerative diseases ALS and SMA are linked at the molecular level via the ASC-1 complex. Nucleic Acids Research. PMID 30398641 DOI: 10.1093/Nar/Gky1093  0.302
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  0.358
2018 Zukowski A, Phillips J, Park S, Wu R, Gygi SP, Johnson AM. Proteomic profiling of yeast heterochromatin connects direct physical and genetic interactions. Current Genetics. PMID 30310994 DOI: 10.1007/S00294-018-0889-6  0.348
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  0.358
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  0.303
2018 Van Vranken JG, Nowinski SM, Clowers KJ, Jeong MY, Ouyang Y, Berg JA, Gygi JP, Gygi SP, Winge DR, Rutter J. ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly. Molecular Cell. 71: 567-580.e4. PMID 30118679 DOI: 10.1016/J.Molcel.2018.06.039  0.346
2018 Chi B, O'Connell JD, Yamazaki T, Gangopadhyay J, Gygi SP, Reed R. Interactome analyses revealed that the U1 snRNP machinery overlaps extensively with the RNAP II machinery and contains multiple ALS/SMA-causative proteins. Scientific Reports. 8: 8755. PMID 29884807 DOI: 10.1038/S41598-018-27136-3  0.337
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  0.427
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  0.318
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  0.717
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  0.423
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  0.331
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  0.308
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  0.349
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  0.405
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  0.377
2018 Zhao Y, Mudge MC, Soll JM, Rodrigues RB, Byrum AK, Schwarzkopf EA, Bradstreet TR, Gygi SP, Edelson BT, Mosammaparast N. OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates MyD88-Dependent Signaling. Molecular Cell. 69: 505-516.e5. PMID 29395066 DOI: 10.1016/J.Molcel.2018.01.009  0.304
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  0.328
2017 Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, et al. Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling. Cell. PMID 29249356 DOI: 10.1016/J.Cell.2017.11.023  0.319
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  0.729
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  0.779
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  0.776
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  0.339
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  0.815
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  0.342
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  0.619
2017 Boselli M, Lee BH, Robert J, Prado MA, Min SW, Cheng C, Silva MC, Seong C, Elsasser S, Hatle KM, Gahman TC, Gygi SP, Haggarty SJ, Gan L, King RW, et al. An inhibitor of the proteasomal deubiquitinating enzyme USP14 induces tau elimination in cultured neurons. The Journal of Biological Chemistry. PMID 28972160 DOI: 10.1074/Jbc.M117.815126  0.362
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  0.36
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  0.381
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  0.525
2017 Li Y, Sun H, Zhang C, Liu J, Zhang H, Fan F, Everley RA, Ning X, Sun Y, Hu J, Liu J, Zhang J, Ye W, Qiu X, Dai S, ... ... Gygi SP, et al. Identification of translationally controlled tumor protein in promotion of DNA homologous recombination repair in cancer cells by affinity proteomics. Oncogene. PMID 28846114 DOI: 10.1038/Onc.2017.289  0.327
2017 Kamath KS, Krisp C, Chick J, Pascovici D, Gygi SP, Molloy MP. Pseudomonas aeruginosa proteome under hypoxic stress conditions mimicking the cystic fibrosis lung. Journal of Proteome Research. PMID 28832155 DOI: 10.1021/Acs.Jproteome.7B00561  0.353
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  0.399
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  0.305
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  0.508
2017 Yin S, Lopez-Gonzalez R, Kunz RC, Gangopadhyay J, Borufka C, Gygi SP, Gao FB, Reed R. Evidence that C9ORF72 Dipeptide Repeat Proteins Associate with U2 snRNP to Cause Mis-splicing in ALS/FTD Patients. Cell Reports. 19: 2244-2256. PMID 28614712 DOI: 10.1016/J.Celrep.2017.05.056  0.329
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  0.324
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  0.817
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  0.334
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  0.387
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  0.361
2017 Rapali P, Mitteau R, Braun CR, Massoni-Laporte A, Ünlü C, Bataille L, Saint Arramon F, Gygi SP, McCusker D. Scaffold-mediated gating of Cdc42 signaling flux. Elife. 6. PMID 28304276 DOI: 10.7554/Elife.25257  0.341
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  0.736
2017 Thai V, Dephoure N, Weiss A, Ferguson J, Leitao R, Gygi SP, Kellogg DR. Protein kinase C controls binding of Igo/ENSA proteins to protein phosphatase 2A in budding yeast. The Journal of Biological Chemistry. PMID 28100785 DOI: 10.1074/Jbc.M116.753004  0.418
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. Author response: Kinesin superfamily protein Kif26b links Wnt5a-Ror signaling to the control of cell and tissue behaviors in vertebrates Elife. DOI: 10.7554/Elife.26509.034  0.519
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  0.719
2016 Tsanov KM, Pearson DS, Wu Z, Han A, Triboulet R, Seligson MT, Powers JT, Osborne JK, Kane S, Gygi SP, Gregory RI, Daley GQ. LIN28 phosphorylation by MAPK/ERK couples signalling to the post-transcriptional control of pluripotency. Nature Cell Biology. PMID 27992407 DOI: 10.1038/Ncb3453  0.343
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  0.796
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  0.306
2016 White RR, Ponsford AH, Weekes MP, Rodrigues RB, Ascher DB, Mol M, Selkirk ME, Gygi SP, Sanderson CM, Artavanis-Tsakonas K. Ubiquitin-Dependent Modification of Skeletal Muscle by the Parasitic Nematode, Trichinella spiralis. Plos Pathogens. 12: e1005977. PMID 27870901 DOI: 10.1371/Journal.Ppat.1005977  0.309
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  0.393
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  0.75
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  0.731
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  0.399
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  0.404
2016 Yoshida MM, Ting L, Gygi SP, Azuma Y. SUMOylation of DNA topoisomerase IIα regulates histone H3 kinase Haspin and H3 phosphorylation in mitosis. The Journal of Cell Biology. 213: 665-78. PMID 27325792 DOI: 10.1083/Jcb.201511079  0.304
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  0.71
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  0.368
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  0.319
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  0.37
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  0.406
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  0.377
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  0.337
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  0.422
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  0.762
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  0.416
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  0.392
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  0.344
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  0.309
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  0.802
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  0.413
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  0.699
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  0.322
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  0.359
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  0.795
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  0.32
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  0.811
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  0.434
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  0.803
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  0.672
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  0.671
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  0.365
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  0.301
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  0.349
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  0.439
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  0.376
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  0.436
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  0.743
2015 Guarani V, McNeill EM, Paulo JA, Huttlin EL, Fröhlich F, Gygi SP, Vactor DV, Harper JW. Author response: QIL1 is a novel mitochondrial protein required for MICOS complex stability and cristae morphology Elife. DOI: 10.7554/Elife.06265.015  0.672
2015 Westbrook TF, Nair A, Sun T, Karlin KL, Kessler J, Migliaccio I, Nguyen DX, Bernardi RJ, Renwick A, Creighton CJ, Dephoure N, Gygi SP, Shaw CA, Gibbs R, Wheeler D, et al. Abstract P6-11-01: A broad spectrum therapeutic strategy for TNBC revealed by a new pathway that coordinates oncogenic RTKs Cancer Research. 75. DOI: 10.1158/1538-7445.Sabcs14-P6-11-01  0.305
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  0.759
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  0.628
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  0.374
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  0.36
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  0.705
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  0.324
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  0.729
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  0.305
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  0.328
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  0.394
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  0.354
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  0.774
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  0.799
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  0.376
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  0.799
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  0.395
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  0.366
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  0.315
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  0.392
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  0.328
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  0.315
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  0.335
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  0.524
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  0.365
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  0.369
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  0.699
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  0.353
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  0.334
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  0.336
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  0.655
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  0.401
2014 Raju RM, Jedrychowski MP, Wei J, Pinkham JT, Park AS, O'Brien K, Rehren G, Schnappinger D, Gygi SP, Rubin EJ. Validation of proteomic hits reveals that WhiB1 and CarD are likely Clp protease substrates. Plos Pathogens. DOI: 10.1371/Journal.Ppat.1003994.G003  0.314
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  0.333
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  0.389
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  0.358
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  0.313
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  0.339
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  0.707
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  0.331
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  0.366
2013 McAllister FE, Niepel M, Haas W, Huttlin E, Sorger PK, Gygi SP. Mass spectrometry based method to increase throughput for kinome analyses using ATP probes. Analytical Chemistry. 85: 4666-74. PMID 23607489 DOI: 10.1021/Ac303478G  0.693
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  0.328
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  0.605
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  0.399
2013 McAllister FE, Gygi SP. Correlation profiling for determining kinase-substrate relationships. Methods (San Diego, Calif.). 61: 227-35. PMID 23523655 DOI: 10.1016/J.Ymeth.2013.03.012  0.356
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  0.69
2013 Dephoure N, Gould KL, Gygi SP, Kellogg DR. Mapping and analysis of phosphorylation sites: a quick guide for cell biologists. Molecular Biology of the Cell. 24: 535-42. PMID 23447708 DOI: 10.1091/Mbc.E12-09-0677  0.342
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  0.695
2013 Armour SM, Bennett EJ, Braun CR, Zhang XY, McMahon SB, Gygi SP, Harper JW, Sinclair DA. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Molecular and Cellular Biology. 33: 1487-502. PMID 23382074 DOI: 10.1128/Mcb.00971-12  0.353
2013 Nathan JA, Kim HT, Ting L, Gygi SP, Goldberg AL. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? The Embo Journal. 32: 552-65. PMID 23314748 DOI: 10.1038/Emboj.2012.354  0.324
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  0.302
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  0.33
2013 Zhang X, Lavoie G, Fort L, Huttlin EL, Tcherkezian J, Galan JA, Gu H, Gygi SP, Carreno S, Roux PP. Abstract 5191: Gab2 phosphorylation by RSK inhibits Shp2 recruitment and cell motility. Cancer Research. 73: 5191-5191. DOI: 10.1158/1538-7445.Am2013-5191  0.69
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  0.738
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  0.82
2012 Chiang WC, Tishkoff DX, Yang B, Wilson-Grady J, Yu X, Mazer T, Eckersdorff M, Gygi SP, Lombard DB, Hsu AL. C. elegans SIRT6/7 homolog SIR-2.4 promotes DAF-16 relocalization and function during stress. Plos Genetics. 8: e1002948. PMID 23028355 DOI: 10.1371/Journal.Pgen.1002948  0.317
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  0.309
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  0.658
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  0.726
2012 Cohen S, Zhai B, Gygi SP, Goldberg AL. Ubiquitylation by Trim32 causes coupled loss of desmin, Z-bands, and thin filaments in muscle atrophy. The Journal of Cell Biology. 198: 575-89. PMID 22908310 DOI: 10.1083/Jcb.201110067  0.317
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  0.672
2012 Inuzuka H, Gao D, Finley LW, Yang W, Wan L, Fukushima H, Chin YR, Zhai B, Shaik S, Lau AW, Wang Z, Gygi SP, Nakayama K, Teruya-Feldstein J, Toker A, et al. Acetylation-dependent regulation of Skp2 function. Cell. 150: 179-93. PMID 22770219 DOI: 10.1016/J.Cell.2012.05.038  0.312
2012 Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi SP, Forster AC, Jewett MC, Church GM. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. Acs Synthetic Biology. 1: 43-52. PMID 22737598 DOI: 10.1021/Sb3000029  0.395
2012 Kunz RC, McAllister FE, Rush J, Gygi SP. A high-throughput, multiplexed kinase assay using a benchtop orbitrap mass spectrometer to investigate the effect of kinase inhibitors on kinase signaling pathways. Analytical Chemistry. 84: 6233-9. PMID 22724890 DOI: 10.1021/Ac301116Z  0.384
2012 Fukushima H, Matsumoto A, Inuzuka H, Zhai B, Lau AW, Wan L, Gao D, Shaik S, Yuan M, Gygi SP, Jimi E, Asara JM, Nakayama K, Nakayama KI, Wei W. SCF(Fbw7) modulates the NFkB signaling pathway by targeting NFkB2 for ubiquitination and destruction. Cell Reports. 1: 434-43. PMID 22708077 DOI: 10.1016/J.Celrep.2012.04.002  0.346
2012 Christofferson DE, Li Y, Hitomi J, Zhou W, Upperman C, Zhu H, Gerber SA, Gygi S, Yuan J. A novel role for RIP1 kinase in mediating TNFa production Cell Death and Disease. 3. PMID 22695613 DOI: 10.1038/Cddis.2012.64  0.706
2012 Dephoure N, Gygi SP. Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast. Science Signaling. 5: rs2. PMID 22457332 DOI: 10.1126/Scisignal.2002548  0.454
2012 Chen YC, Taylor EB, Dephoure N, Heo JM, Tonhato A, Papandreou I, Nath N, Denko NC, Gygi SP, Rutter J. Identification of a protein mediating respiratory supercomplex stability. Cell Metabolism. 15: 348-60. PMID 22405070 DOI: 10.1016/J.Cmet.2012.02.006  0.319
2012 Dimova NV, Hathaway NA, Lee BH, Kirkpatrick DS, Berkowitz ML, Gygi SP, Finley D, King RW. APC/C-mediated multiple monoubiquitylation provides an alternative degradation signal for cyclin B1. Nature Cell Biology. 14: 168-76. PMID 22286100 DOI: 10.1038/Ncb2425  0.312
2012 Lo HC, Kunz RC, Chen X, Marullo A, Gygi SP, Hollingsworth NM. Cdc7-Dbf4 is a gene-specific regulator of meiotic transcription in yeast. Molecular and Cellular Biology. 32: 541-57. PMID 22106412 DOI: 10.1128/Mcb.06032-11  0.34
2012 Gygi SP, Huttlin EL, Wu R, Haas W, Dephoure N, Sowa M, Zhai B. Reply to Phosphorylation sites of higher stoichiometry are more conserved Nature Methods. 9: 318. DOI: 10.1038/Nmeth.1942  0.653
2012 Morita E, Sandrin V, Chung H, Morham SG, Gygi SP, Rodesch CK, Sundquist WI. Human ESCRT and ALIX proteins interact with proteins of the midbody and function in cytokinesis The Embo Journal. 31: 3228-3228. DOI: 10.1038/Emboj.2012.184  0.384
2011 Banko MR, Allen JJ, Schaffer BE, Wilker EW, Tsou P, White JL, Villén J, Wang B, Kim SR, Sakamoto K, Gygi SP, Cantley LC, Yaffe MB, Shokat KM, Brunet A. Chemical genetic screen for AMPKα2 substrates uncovers a network of proteins involved in mitosis. Molecular Cell. 44: 878-92. PMID 22137581 DOI: 10.1016/J.Molcel.2011.11.005  0.403
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  0.769
2011 Gao D, Inuzuka H, Tan MK, Fukushima H, Locasale JW, Liu P, Wan L, Zhai B, Chin YR, Shaik S, Lyssiotis CA, Gygi SP, Toker A, Cantley LC, Asara JM, et al. mTOR drives its own activation via SCF(βTrCP)-dependent degradation of the mTOR inhibitor DEPTOR. Molecular Cell. 44: 290-303. PMID 22017875 DOI: 10.1016/J.Molcel.2011.08.030  0.32
2011 Shchedrina VA, Everley RA, Zhang Y, Gygi SP, Hatfield DL, Gladyshev VN. Selenoprotein K binds multiprotein complexes and is involved in the regulation of endoplasmic reticulum homeostasis. The Journal of Biological Chemistry. 286: 42937-48. PMID 22016385 DOI: 10.1074/Jbc.M111.310920  0.379
2011 Anderson K, Nordquist KA, Gao X, Hicks KC, Zhai B, Gygi SP, Patel TB. Regulation of cellular levels of Sprouty2 protein by prolyl hydroxylase domain and von Hippel-Lindau proteins. The Journal of Biological Chemistry. 286: 42027-36. PMID 22006925 DOI: 10.1074/Jbc.M111.303222  0.383
2011 Zou W, Greenblatt MB, Shim JH, Kant S, Zhai B, Lotinun S, Brady N, Hu DZ, Gygi SP, Baron R, Davis RJ, Jones D, Glimcher LH. MLK3 regulates bone development downstream of the faciogenital dysplasia protein FGD1 in mice. The Journal of Clinical Investigation. 121: 4383-92. PMID 21965325 DOI: 10.1172/Jci59041  0.317
2011 Ting L, Rad R, Gygi SP, Haas W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nature Methods. 8: 937-40. PMID 21963607 DOI: 10.1038/Nmeth.1714  0.417
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  0.711
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  0.717
2011 Nobles KN, Xiao K, Ahn S, Shukla AK, Lam CM, Rajagopal S, Strachan RT, Huang TY, Bressler EA, Hara MR, Shenoy SK, Gygi SP, Lefkowitz RJ. Distinct phosphorylation sites on the β(2)-adrenergic receptor establish a barcode that encodes differential functions of β-arrestin. Science Signaling. 4: ra51. PMID 21868357 DOI: 10.1126/Scisignal.2001707  0.338
2011 Yi CH, Pan H, Seebacher J, Jang IH, Hyberts SG, Heffron GJ, Vander Heiden MG, Yang R, Li F, Locasale JW, Sharfi H, Zhai B, Rodriguez-Mias R, Luithardt H, Cantley LC, ... ... Gygi SP, et al. Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survival. Cell. 146: 607-20. PMID 21854985 DOI: 10.1016/J.Cell.2011.06.050  0.337
2011 Harvey SL, Enciso G, Dephoure N, Gygi SP, Gunawardena J, Kellogg DR. A phosphatase threshold sets the level of Cdk1 activity in early mitosis in budding yeast. Molecular Biology of the Cell. 22: 3595-608. PMID 21849476 DOI: 10.1091/Mbc.E11-04-0340  0.326
2011 Lee PC, Sowa ME, Gygi SP, Harper JW. Alternative ubiquitin activation/conjugation cascades interact with N-end rule ubiquitin ligases to control degradation of RGS proteins. Molecular Cell. 43: 392-405. PMID 21816346 DOI: 10.1016/J.Molcel.2011.05.034  0.344
2011 Cerda-Maira FA, McAllister F, Bode NJ, Burns KE, Gygi SP, Darwin KH. Reconstitution of the Mycobacterium tuberculosis pupylation pathway in Escherichia coli. Embo Reports. 12: 863-70. PMID 21738222 DOI: 10.1038/Embor.2011.109  0.408
2011 Puram SV, Kim AH, Ikeuchi Y, Wilson-Grady JT, Merdes A, Gygi SP, Bonni A. A CaMKIIβ signaling pathway at the centrosome regulates dendrite patterning in the brain. Nature Neuroscience. 14: 973-83. PMID 21725312 DOI: 10.1038/Nn.2857  0.34
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  0.707
2011 Gopalakrishnan J, Mennella V, Blachon S, Zhai B, Smith AH, Megraw TL, Nicastro D, Gygi SP, Agard DA, Avidor-Reiss T. Sas-4 provides a scaffold for cytoplasmic complexes and tethers them in a centrosome. Nature Communications. 2: 359. PMID 21694707 DOI: 10.1038/Ncomms1367  0.344
2011 Yu Y, Yoon SO, Poulogiannis G, Yang Q, Ma XM, Villén J, Kubica N, Hoffman GR, Cantley LC, Gygi SP, Blenis J. Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science (New York, N.Y.). 332: 1322-6. PMID 21659605 DOI: 10.1126/Science.1199484  0.358
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  0.61
2011 Helmlinger D, Marguerat S, Villén J, Swaney DL, Gygi SP, Bähler J, Winston F. Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex. The Embo Journal. 30: 2843-52. PMID 21642955 DOI: 10.1038/Emboj.2011.181  0.316
2011 Litterman N, Ikeuchi Y, Gallardo G, O'Connell BC, Sowa ME, Gygi SP, Harper JW, Bonni A. An OBSL1-Cul7Fbxw8 ubiquitin ligase signaling mechanism regulates Golgi morphology and dendrite patterning. Plos Biology. 9: e1001060. PMID 21572988 DOI: 10.1371/Journal.Pbio.1001060  0.311
2011 Gu TL, Nardone J, Wang Y, Loriaux M, Villén J, Beausoleil S, Tucker M, Kornhauser J, Ren J, MacNeill J, Gygi SP, Druker BJ, Heinrich MC, Rush J, Polakiewicz RD. Survey of activated FLT3 signaling in leukemia. Plos One. 6: e19169. PMID 21552520 DOI: 10.1371/Journal.Pone.0019169  0.724
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  0.726
2011 Dephoure N, Gygi SP. A solid phase extraction-based platform for rapid phosphoproteomic analysis. Methods (San Diego, Calif.). 54: 379-86. PMID 21440633 DOI: 10.1016/J.Ymeth.2011.03.008  0.427
2011 Ziv I, Matiuhin Y, Kirkpatrick DS, Erpapazoglou Z, Leon S, Pantazopoulou M, Kim W, Gygi SP, Haguenauer-Tsapis R, Reis N, Glickman MH, Kleifeld O. A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis. Molecular & Cellular Proteomics : McP. 10: M111.009753. PMID 21427232 DOI: 10.1074/Mcp.M111.009753  0.345
2011 Inuzuka H, Shaik S, Onoyama I, Gao D, Tseng A, Maser RS, Zhai B, Wan L, Gutierrez A, Lau AW, Xiao Y, Christie AL, Aster J, Settleman J, Gygi SP, et al. SCF(FBW7) regulates cellular apoptosis by targeting MCL1 for ubiquitylation and destruction. Nature. 471: 104-9. PMID 21368833 DOI: 10.1038/Nature09732  0.334
2011 Spirin V, Shpunt A, Seebacher J, Gentzel M, Shevchenko A, Gygi S, Sunyaev S. Assigning spectrum-specific P-values to protein identifications by mass spectrometry. Bioinformatics (Oxford, England). 27: 1128-34. PMID 21349864 DOI: 10.1093/bioinformatics/btr089  0.616
2011 Tolonen AC, Haas W, Chilaka AC, Aach J, Gygi SP, Church GM. Proteome-wide systems analysis of a cellulosic biofuel-producing microbe. Molecular Systems Biology. 7: 461. PMID 21245846 DOI: 10.1038/Msb.2010.116  0.379
2011 Shen H, Ferguson SM, Dephoure N, Park R, Yang Y, Volpicelli-Daley L, Gygi S, Schlessinger J, De Camilli P. Constitutive activated Cdc42-associated kinase (Ack) phosphorylation at arrested endocytic clathrin-coated pits of cells that lack dynamin. Molecular Biology of the Cell. 22: 493-502. PMID 21169560 DOI: 10.1091/Mbc.E10-07-0637  0.31
2011 Braun CR, Mintseris J, Gavathiotis E, Bird GH, Gygi SP, Walensky LD. Abstract LB-241: Photoreactive stapled peptides for target discovery in cancer Cancer Research. 71. DOI: 10.1158/1538-7445.Am2011-Lb-241  0.763
2011 Braun CR, Mintseris J, Gavathiotis E, Bird GH, Gygi SP, Walensky LD. Abstract 4871: Photoreactive stapled peptides to capture cancer proteins and define their sites of interaction Cancer Research. 71: 4871-4871. DOI: 10.1158/1538-7445.Am2011-4871  0.755
2011 Spirin V, Shpunt A, Seebacher J, Gentzel M, Shevchenko A, Gygi S, Sunyaev S. Assigning spectrum-specific P-values to protein identifications by mass spectrometry Bioinformatics. 27: 1128-1134. DOI: 10.1093/Bioinformatics/Btr089  0.635
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  0.812
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  0.735
2010 Bennett EJ, Rush J, Gygi SP, Harper JW. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell. 143: 951-65. PMID 21145461 DOI: 10.1016/J.Cell.2010.11.017  0.318
2010 Xu XM, Turanov AA, Carlson BA, Yoo MH, Everley RA, Nandakumar R, Sorokina I, Gygi SP, Gladyshev VN, Hatfield DL. Targeted insertion of cysteine by decoding UGA codons with mammalian selenocysteine machinery. Proceedings of the National Academy of Sciences of the United States of America. 107: 21430-4. PMID 21115847 DOI: 10.1073/Pnas.1009947107  0.325
2010 Shaw BF, Arthanari H, Narovlyansky M, Durazo A, Frueh DP, Pollastri MP, Lee A, Bilgicer B, Gygi SP, Wagner G, Whitesides GM. Neutralizing positive charges at the surface of a protein lowers its rate of amide hydrogen exchange without altering its structure or increasing its thermostability. Journal of the American Chemical Society. 132: 17411-25. PMID 21090618 DOI: 10.1021/Ja9067035  0.301
2010 Heo JM, Livnat-Levanon N, Taylor EB, Jones KT, Dephoure N, Ring J, Xie J, Brodsky JL, Madeo F, Gygi SP, Ashrafi K, Glickman MH, Rutter J. A stress-responsive system for mitochondrial protein degradation. Molecular Cell. 40: 465-80. PMID 21070972 DOI: 10.1016/J.Molcel.2010.10.021  0.315
2010 O'Connell BC, Adamson B, Lydeard JR, Sowa ME, Ciccia A, Bredemeyer AL, Schlabach M, Gygi SP, Elledge SJ, Harper J. Wade JW. A Genome-wide Camptothecin Sensitivity Screen Identifies a Mammalian MMS22L-NFKBIL2 Complex Required for Genomic Stability Molecular Cell. 40: 645-657. PMID 21055985 DOI: 10.1016/J.Molcel.2010.10.022  0.338
2010 Knowlton ML, Selfors LM, Wrobel CN, Gu TL, Ballif BA, Gygi SP, Polakiewicz R, Brugge JS. Profiling Y561-dependent and -independent substrates of CSF-1R in epithelial cells. Plos One. 5: e13587. PMID 21049007 DOI: 10.1371/Journal.Pone.0013587  0.368
2010 Teixidó-Travesa N, Villén J, Lacasa C, Bertran MT, Archinti M, Gygi SP, Caelles C, Roig J, Lüders J. The gammaTuRC revisited: a comparative analysis of interphase and mitotic human gammaTuRC redefines the set of core components and identifies the novel subunit GCP8. Molecular Biology of the Cell. 21: 3963-72. PMID 20861304 DOI: 10.1091/Mbc.E10-05-0408  0.386
2010 Dufu K, Livingstone MJ, Seebacher J, Gygi SP, Wilson SA, Reed R. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Genes & Development. 24: 2043-53. PMID 20844015 DOI: 10.1101/Gad.1898610  0.368
2010 Gao D, Wan L, Inuzuka H, Berg AH, Tseng A, Zhai B, Shaik S, Bennett E, Tron AE, Gasser JA, Lau A, Gygi SP, Harper JW, DeCaprio JA, Toker A, et al. Rictor forms a complex with Cullin-1 to promote SGK1 ubiquitination and destruction. Molecular Cell. 39: 797-808. PMID 20832730 DOI: 10.1016/J.Molcel.2010.08.016  0.38
2010 Lee BH, Lee MJ, Park S, Oh DC, Elsasser S, Chen PC, Gartner C, Dimova N, Hanna J, Gygi SP, Wilson SM, King RW, Finley D. Enhancement of proteasome activity by a small-molecule inhibitor of USP14. Nature. 467: 179-84. PMID 20829789 DOI: 10.1038/Nature09299  0.778
2010 Moritz A, Li Y, Guo A, Villén J, Wang Y, MacNeill J, Kornhauser J, Sprott K, Zhou J, Possemato A, Ren JM, Hornbeck P, Cantley LC, Gygi SP, Rush J, et al. Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases. Science Signaling. 3: ra64. PMID 20736484 DOI: 10.1126/Scisignal.2000998  0.354
2010 Xiao K, Sun J, Kim J, Rajagopal S, Zhai B, Villén J, Haas W, Kovacs JJ, Shukla AK, Hara MR, Hernandez M, Lachmann A, Zhao S, Lin Y, Cheng Y, ... ... Gygi SP, et al. Global phosphorylation analysis of beta-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR). Proceedings of the National Academy of Sciences of the United States of America. 107: 15299-304. PMID 20686112 DOI: 10.1073/Pnas.1008461107  0.343
2010 Roberts-Galbraith RH, Ohi MD, Ballif BA, Chen JS, McLeod I, McDonald WH, Gygi SP, Yates JR, Gould KL. Dephosphorylation of F-BAR Protein Cdc15 Modulates Its Conformation and Stimulates Its Scaffolding Activity at the Cell Division Site Molecular Cell. 39: 86-99. PMID 20603077 DOI: 10.1016/J.Molcel.2010.06.012  0.363
2010 Jin H, White SR, Shida T, Schulz S, Aguiar M, Gygi SP, Bazan JF, Nachury MV. The conserved Bardet-Biedl syndrome proteins assemble a coat that traffics membrane proteins to cilia. Cell. 141: 1208-19. PMID 20603001 DOI: 10.1016/J.Cell.2010.05.015  0.326
2010 Behrends C, Sowa ME, Gygi SP, Harper JW. Network organization of the human autophagy system. Nature. 466: 68-76. PMID 20562859 DOI: 10.1038/Nature09204  0.426
2010 Greenblatt MB, Shim JH, Zou W, Sitara D, Schweitzer M, Hu D, Lotinun S, Sano Y, Baron R, Park JM, Arthur S, Xie M, Schneider MD, Zhai B, Gygi S, et al. The p38 MAPK pathway is essential for skeletogenesis and bone homeostasis in mice. The Journal of Clinical Investigation. 120: 2457-73. PMID 20551513 DOI: 10.1172/Jci42285  0.314
2010 Isasa M, Katz EJ, Kim W, Yugo V, González S, Kirkpatrick DS, Thomson TM, Finley D, Gygi SP, Crosas B. Monoubiquitination of RPN10 regulates substrate recruitment to the proteasome. Molecular Cell. 38: 733-45. PMID 20542005 DOI: 10.1016/J.Molcel.2010.05.001  0.348
2010 Lee HS, Komarova YA, Nadezhdina ES, Anjum R, Peloquin JG, Schober JM, Danciu O, van Haren J, Galjart N, Gygi SP, Akhmanova A, Borisy GG. Phosphorylation controls autoinhibition of cytoplasmic linker protein-170. Molecular Biology of the Cell. 21: 2661-73. PMID 20519438 DOI: 10.1091/Mbc.E09-12-1036  0.373
2010 Goh LK, Huang F, Kim W, Gygi S, Sorkin A. Multiple mechanisms collectively regulate clathrin-mediated endocytosis of the epidermal growth factor receptor. The Journal of Cell Biology. 189: 871-83. PMID 20513767 DOI: 10.1083/Jcb.201001008  0.319
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  0.799
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  0.71
2010 Ryu H, Al-Ani G, Deckert K, Kirkpatrick D, Gygi SP, Dasso M, Azuma Y. PIASy mediates SUMO-2/3 conjugation of poly(ADP-ribose) polymerase 1 (PARP1) on mitotic chromosomes. The Journal of Biological Chemistry. 285: 14415-23. PMID 20228053 DOI: 10.1074/Jbc.M109.074583  0.319
2010 Kee Y, Yang K, Cohn MA, Haas W, Gygi SP, D'Andrea AD. WDR20 regulates activity of the USP12 x UAF1 deubiquitinating enzyme complex. The Journal of Biological Chemistry. 285: 11252-7. PMID 20147737 DOI: 10.1074/Jbc.M109.095141  0.33
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  0.63
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  0.764
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  0.641
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  0.759
2010 Festa RA, McAllister F, Pearce MJ, Mintseris J, Burns KE, Gygi SP, Darwin KH. Correction: Prokaryotic Ubiquitin-Like Protein (Pup) Proteome of Mycobacterium tuberculosis Plos One. 5. DOI: 10.1371/Annotation/Bf95B2C0-4085-417B-A2B2-7A85Ffe77A9E  0.716
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  0.636
2009 Kaminsky R, Denison C, Bening-Abu-Shach U, Chisholm AD, Gygi SP, Broday L. SUMO regulates the assembly and function of a cytoplasmic intermediate filament protein in C. elegans. Developmental Cell. 17: 724-35. PMID 19922876 DOI: 10.1016/J.Devcel.2009.10.005  0.383
2009 Niu H, Wan L, Busygina V, Kwon Y, Allen JA, Li X, Kunz RC, Kubota K, Wang B, Sung P, Shokat KM, Gygi SP, Hollingsworth NM. Regulation of meiotic recombination via Mek1-mediated Rad54 phosphorylation. Molecular Cell. 36: 393-404. PMID 19917248 DOI: 10.1016/J.Molcel.2009.09.029  0.356
2009 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, et al. Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nature Biotechnology. 27: 933-40. PMID 19801977 DOI: 10.1038/Nbt.1566  0.382
2009 Holt LJ, Tuch BB, Villén J, Johnson AD, Gygi SP, Morgan DO. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science (New York, N.Y.). 325: 1682-6. PMID 19779198 DOI: 10.1126/Science.1172867  0.386
2009 Hao HX, Khalimonchuk O, Schraders M, Dephoure N, Bayley JP, Kunst H, Devilee P, Cremers CW, Schiffman JD, Bentz BG, Gygi SP, Winge DR, Kremer H, Rutter J. SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma. Science (New York, N.Y.). 325: 1139-42. PMID 19628817 DOI: 10.1126/Science.1175689  0.323
2009 Sowa ME, Bennett EJ, Gygi SP, Harper JW. Defining the human deubiquitinating enzyme interaction landscape. Cell. 138: 389-403. PMID 19615732 DOI: 10.1016/J.Cell.2009.04.042  0.419
2009 Svendsen JM, Smogorzewska A, Sowa ME, O'Connell BC, Gygi SP, Elledge SJ, Harper JW. Mammalian BTBD12/SLX4 Assembles A Holliday Junction Resolvase and Is Required for DNA Repair Cell. 138: 63-77. PMID 19596235 DOI: 10.1016/J.Cell.2009.06.030  0.301
2009 Yu Y, Anjum R, Kubota K, Rush J, Villen J, Gygi SP. A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 106: 11606-11. PMID 19564600 DOI: 10.1073/Pnas.0905165106  0.393
2009 Bastiani M, Liu L, Hill MM, Jedrychowski MP, Nixon SJ, Lo HP, Abankwa D, Luetterforst R, Fernandez-Rojo M, Breen MR, Gygi SP, Vinten J, Walser PJ, North KN, Hancock JF, et al. MURC/Cavin-4 and cavin family members form tissue-specific caveolar complexes. The Journal of Cell Biology. 185: 1259-73. PMID 19546242 DOI: 10.1083/Jcb.200903053  0.356
2009 Shim JH, Greenblatt MB, Xie M, Schneider MD, Zou W, Zhai B, Gygi S, Glimcher LH. TAK1 is an essential regulator of BMP signalling in cartilage. The Embo Journal. 28: 2028-41. PMID 19536134 DOI: 10.1038/Emboj.2009.162  0.331
2009 Cohen S, Brault JJ, Gygi SP, Glass DJ, Valenzuela DM, Gartner C, Latres E, Goldberg AL. During muscle atrophy, thick, but not thin, filament components are degraded by MuRF1-dependent ubiquitylation. The Journal of Cell Biology. 185: 1083-95. PMID 19506036 DOI: 10.1083/Jcb.200901052  0.76
2009 Kelly TJ, Lerin C, Haas W, Gygi SP, Puigserver P. GCN5-mediated transcriptional control of the metabolic coactivator PGC-1beta through lysine acetylation. The Journal of Biological Chemistry. 284: 19945-52. PMID 19491097 DOI: 10.1074/Jbc.M109.015164  0.301
2009 Park S, Roelofs J, Kim W, Robert J, Schmidt M, Gygi SP, Finley D. Hexameric assembly of the proteasomal ATPases is templated through their C termini. Nature. 459: 866-70. PMID 19412160 DOI: 10.1038/Nature08065  0.301
2009 Roelofs J, Park S, Haas W, Tian G, McAllister FE, Huo Y, Lee BH, Zhang F, Shi Y, Gygi SP, Finley D. Chaperone-mediated pathway of proteasome regulatory particle assembly. Nature. 459: 861-5. PMID 19412159 DOI: 10.1038/Nature08063  0.354
2009 Kim HT, Kim KP, Uchiki T, Gygi SP, Goldberg AL. S5a promotes protein degradation by blocking synthesis of nondegradable forked ubiquitin chains. The Embo Journal. 28: 1867-77. PMID 19387488 DOI: 10.1038/Emboj.2009.115  0.35
2009 Hurt JA, Obar RA, Zhai B, Farny NG, Gygi SP, Silver PA. A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export. The Journal of Cell Biology. 185: 265-77. PMID 19364924 DOI: 10.1083/Jcb.200811072  0.328
2009 Abe Y, Yoon SO, Kubota K, Mendoza MC, Gygi SP, Blenis J. p90 ribosomal S6 kinase and p70 ribosomal S6 kinase link phosphorylation of the eukaryotic chaperonin containing TCP-1 to growth factor, insulin, and nutrient signaling. The Journal of Biological Chemistry. 284: 14939-48. PMID 19332537 DOI: 10.1074/Jbc.M900097200  0.376
2009 Yuan Z, Lehtinen MK, Merlo P, Villén J, Gygi S, Bonni A. Regulation of neuronal cell death by MST1-FOXO1 signaling. The Journal of Biological Chemistry. 284: 11285-92. PMID 19221179 DOI: 10.1074/Jbc.M900461200  0.302
2009 Besche HC, Haas W, Gygi SP, Goldberg AL. Isolation of mammalian 26S proteasomes and p97/VCP complexes using the ubiquitin-like domain from HHR23B reveals novel proteasome-associated proteins. Biochemistry. 48: 2538-49. PMID 19182904 DOI: 10.1021/Bi802198Q  0.401
2009 Cohn MA, Kee Y, Haas W, Gygi SP, D'Andrea AD. UAF1 is a subunit of multiple deubiquitinating enzyme complexes. The Journal of Biological Chemistry. 284: 5343-51. PMID 19075014 DOI: 10.1074/Jbc.M808430200  0.355
2009 Cohen S, Brault JJ, Gygi SP, Glass DJ, Valenzuela DM, Gartner C, Latres E, Goldberg AL. During muscle atrophy, thick, but not thin, filament components are degraded by MuRF1-dependent ubiquitylation The Journal of Experimental Medicine. 206: i13-i13. DOI: 10.1084/JEM2067OIA13  0.709
2008 Motamedi MR, Hong EJ, Li X, Gerber S, Denison C, Gygi S, Moazed D. HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms. Molecular Cell. 32: 778-90. PMID 19111658 DOI: 10.1016/J.Molcel.2008.10.026  0.717
2008 Mekhail K, Seebacher J, Gygi SP, Moazed D. Role for perinuclear chromosome tethering in maintenance of genome stability. Nature. 456: 667-70. PMID 18997772 DOI: 10.1038/Nature07460  0.369
2008 Matiuhin Y, Kirkpatrick DS, Ziv I, Kim W, Dakshinamurthy A, Kleifeld O, Gygi SP, Reis N, Glickman MH. Extraproteasomal Rpn10 restricts access of the polyubiquitin-binding protein Dsk2 to proteasome. Molecular Cell. 32: 415-25. PMID 18995839 DOI: 10.1016/J.Molcel.2008.10.011  0.39
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  0.721
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  0.649
2008 Villén J, Gygi SP. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nature Protocols. 3: 1630-8. PMID 18833199 DOI: 10.1038/Nprot.2008.150  0.345
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  0.757
2008 Dermody JL, Dreyfuss JM, Villén J, Ogundipe B, Gygi SP, Park PJ, Ponticelli AS, Moore CL, Buratowski S, Bucheli ME. Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation. Plos One. 3: e3273. PMID 18818768 DOI: 10.1371/Journal.Pone.0003273  0.346
2008 Xu L, Sowa ME, Chen J, Li X, Gygi SP, Harper JW. An FTS/Hook/p107(FHIP) complex interacts with and promotes endosomal clustering by the homotypic vacuolar protein sorting complex. Molecular Biology of the Cell. 19: 5059-71. PMID 18799622 DOI: 10.1091/Mbc.E08-05-0473  0.414
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  0.79
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  0.752
2008 Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. The impact of microRNAs on protein output. Nature. 455: 64-71. PMID 18668037 DOI: 10.1038/Nature07242  0.372
2008 Unal E, Heidinger-Pauli JM, Kim W, Guacci V, Onn I, Gygi SP, Koshland DE. A molecular determinant for the establishment of sister chromatid cohesion. Science (New York, N.Y.). 321: 566-9. PMID 18653894 DOI: 10.1126/Science.1157880  0.301
2008 Monahan BJ, Villén J, Marguerat S, Bähler J, Gygi SP, Winston F. Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast. Nature Structural & Molecular Biology. 15: 873-80. PMID 18622392 DOI: 10.1038/Nsmb.1452  0.35
2008 Ménétret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, Akey CW. Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Structure (London, England : 1993). 16: 1126-37. PMID 18611385 DOI: 10.1016/J.Str.2008.05.003  0.306
2008 Egelhofer TA, Villén J, McCusker D, Gygi SP, Kellogg DR. The septins function in G1 pathways that influence the pattern of cell growth in budding yeast. Plos One. 3: e2022. PMID 18431499 DOI: 10.1371/Journal.Pone.0002022  0.323
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  0.821
2008 Wainszelbaum MJ, Charron AJ, Kong C, Kirkpatrick DS, Srikanth P, Barbieri MA, Gygi SP, Stahl PD. The hominoid-specific oncogene TBC1D3 activates Ras and modulates epidermal growth factor receptor signaling and trafficking. The Journal of Biological Chemistry. 283: 13233-42. PMID 18319245 DOI: 10.1074/Jbc.M800234200  0.309
2008 Selenko P, Frueh DP, Elsaesser SJ, Haas W, Gygi SP, Wagner G. In situ observation of protein phosphorylation by high-resolution NMR spectroscopy. Nature Structural & Molecular Biology. 15: 321-9. PMID 18297086 DOI: 10.1038/Nsmb.1395  0.397
2008 Yoon SO, Shin S, Liu Y, Ballif BA, Woo MS, Gygi SP, Blenis J. Ran-binding protein 3 phosphorylation links the Ras and PI3-kinase pathways to nucleocytoplasmic transport. Molecular Cell. 29: 362-75. PMID 18280241 DOI: 10.1016/J.Molcel.2007.12.024  0.321
2008 Wilson-Grady JT, Villén J, Gygi SP. Phosphoproteome analysis of fission yeast. Journal of Proteome Research. 7: 1088-97. PMID 18257517 DOI: 10.1021/Pr7006335  0.434
2008 Ballif BA, Carey GR, Sunyaev SR, Gygi SP. Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. Journal of Proteome Research. 7: 311-8. PMID 18034455 DOI: 10.1021/Pr0701254  0.6
2008 Tan JM, Wong ES, Kirkpatrick DS, Pletnikova O, Ko HS, Tay SP, Ho MW, Troncoso J, Gygi SP, Lee MK, Dawson VL, Dawson TM, Lim KL. Lysine 63-linked ubiquitination promotes the formation and autophagic clearance of protein inclusions associated with neurodegenerative diseases. Human Molecular Genetics. 17: 431-9. PMID 17981811 DOI: 10.1093/Hmg/Ddm320  0.316
2007 Ménétret JF, Schaletzky J, Clemons WM, Osborne AR, Skånland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW. Ribosome binding of a single copy of the SecY complex: implications for protein translocation. Molecular Cell. 28: 1083-92. PMID 18158904 DOI: 10.1016/J.Molcel.2007.10.034  0.335
2007 Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, ... ... Gygi SP, et al. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell. 131: 1190-203. PMID 18083107 DOI: 10.1016/J.Cell.2007.11.025  0.312
2007 Cohn MA, Kowal P, Yang K, Haas W, Huang TT, Gygi SP, D'Andrea AD. A UAF1-containing multisubunit protein complex regulates the Fanconi anemia pathway. Molecular Cell. 28: 786-97. PMID 18082604 DOI: 10.1016/J.Molcel.2007.09.031  0.383
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  0.724
2007 Morita E, Sandrin V, Alam SL, Eckert DM, Gygi SP, Sundquist WI. Identification of human MVB12 proteins as ESCRT-I subunits that function in HIV budding. Cell Host & Microbe. 2: 41-53. PMID 18005716 DOI: 10.1016/J.Chom.2007.06.003  0.345
2007 Greer EL, Dowlatshahi D, Banko MR, Villen J, Hoang K, Blanchard D, Gygi SP, Brunet A. An AMPK-FOXO pathway mediates longevity induced by a novel method of dietary restriction in C. elegans. Current Biology : Cb. 17: 1646-56. PMID 17900900 DOI: 10.1016/J.Cub.2007.08.047  0.33
2007 Bakalarski CE, Haas W, Dephoure NE, Gygi SP. The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics. Analytical and Bioanalytical Chemistry. 389: 1409-19. PMID 17874083 DOI: 10.1007/S00216-007-1563-X  0.393
2007 Morita E, Sandrin V, Chung HY, Morham SG, Gygi SP, Rodesch CK, Sundquist WI. Human ESCRT and ALIX proteins interact with proteins of the midbody and function in cytokinesis. The Embo Journal. 26: 4215-27. PMID 17853893 DOI: 10.1038/Sj.Emboj.7601850  0.383
2007 Greer EL, Oskoui PR, Banko MR, Maniar JM, Gygi MP, Gygi SP, Brunet A. The energy sensor AMP-activated protein kinase directly regulates the mammalian FOXO3 transcription factor. The Journal of Biological Chemistry. 282: 30107-19. PMID 17711846 DOI: 10.1074/Jbc.M705325200  0.336
2007 Zappaterra MD, Lisgo SN, Lindsay S, Gygi SP, Walsh CA, Ballif BA. A comparative proteomic analysis of human and rat embryonic cerebrospinal fluid. Journal of Proteome Research. 6: 3537-48. PMID 17696520 DOI: 10.1021/Pr070247W  0.357
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  0.808
2007 Das R, Yu J, Zhang Z, Gygi MP, Krainer AR, Gygi SP, Reed R. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Molecular Cell. 26: 867-81. PMID 17588520 DOI: 10.1016/J.Molcel.2007.05.036  0.336
2007 Niu H, Li X, Job E, Park C, Moazed D, Gygi SP, Hollingsworth NM. Mek1 kinase is regulated to suppress double-strand break repair between sister chromatids during budding yeast meiosis. Molecular and Cellular Biology. 27: 5456-67. PMID 17526735 DOI: 10.1128/Mcb.00416-07  0.33
2007 Wang B, Matsuoka S, Ballif BA, Zhang D, Smogorzewska A, Gygi SP, Elledge SJ. Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response Science. 316: 1194-1198. PMID 17525340 DOI: 10.1126/Science.1139476  0.347
2007 Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage Science. 316: 1160-1166. PMID 17525332 DOI: 10.1126/Science.1140321  0.39
2007 Bühler M, Haas W, Gygi SP, Moazed D. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell. 129: 707-21. PMID 17512405 DOI: 10.1016/J.Cell.2007.03.038  0.306
2007 Stegmeier F, Sowa ME, Nalepa G, Gygi SP, Harper JW, Elledge SJ. The tumor suppressor CYLD regulates entry into mitosis Proceedings of the National Academy of Sciences of the United States of America. 104: 8869-8874. PMID 17495026 DOI: 10.1073/Pnas.0703268104  0.33
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  0.761
2007 Lan F, Zaratiegui M, Villén J, Vaughn MW, Verdel A, Huarte M, Shi Y, Gygi SP, Moazed D, Martienssen RA, Shi Y. S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription. Molecular Cell. 26: 89-101. PMID 17434129 DOI: 10.1016/J.Molcel.2007.02.023  0.306
2007 McCusker D, Denison C, Anderson S, Egelhofer TA, Yates JR, Gygi SP, Kellogg DR. Cdk1 coordinates cell-surface growth with the cell cycle. Nature Cell Biology. 9: 506-15. PMID 17417630 DOI: 10.1038/Ncb1568  0.326
2007 Smogorzewska A, Matsuoka S, Vinciguerra P, McDonald ER, Hurov KE, Luo J, Ballif BA, Gygi SP, Hofmann K, D'Andrea AD, Elledge SJ. Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair. Cell. 129: 289-301. PMID 17412408 DOI: 10.1016/J.Cell.2007.03.009  0.386
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  0.645
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  0.821
2007 Ma YM, Boucrot E, Villén J, Affar el B, Gygi SP, Göttlinger HG, Kirchhausen T. Targeting of AMSH to endosomes is required for epidermal growth factor receptor degradation. The Journal of Biological Chemistry. 282: 9805-12. PMID 17261583 DOI: 10.1074/Jbc.M611635200  0.306
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  0.813
2007 Johri AK, Margarit I, Broenstrup M, Brettoni C, Hua L, Gygi SP, Telford JL, Grandi G, Paoletti LC. Transcriptional and proteomic profiles of group B Streptococcus type V reveal potential adherence proteins associated with high-level invasion. Infection and Immunity. 75: 1473-83. PMID 17210664 DOI: 10.1128/Iai.00638-06  0.374
2007 Kleijnen MF, Kirkpatrick DS, Gygi SP. The ubiquitin-proteasome system regulates membrane fusion of yeast vacuoles. The Embo Journal. 26: 275-87. PMID 17183369 DOI: 10.1038/Sj.Emboj.7601486  0.302
2006 Moazed D, Bühler M, Buker SM, Colmenares SU, Gerace EL, Gerber SA, Hong EJ, Motamedi MR, Verdel A, Villén J, Gygi SP. Studies on the mechanism of RNAi-dependent heterochromatin assembly. Cold Spring Harbor Symposia On Quantitative Biology. 71: 461-71. PMID 17381328 DOI: 10.1101/Sqb.2006.71.044  0.667
2006 Huang J, Brito IL, Villén J, Gygi SP, Amon A, Moazed D. Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer. Genes & Development. 20: 2887-901. PMID 17043313 DOI: 10.1101/Gad.1472706  0.355
2006 Hanna J, Hathaway NA, Tone Y, Crosas B, Elsasser S, Kirkpatrick DS, Leggett DS, Gygi SP, King RW, Finley D. Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell. 127: 99-111. PMID 17018280 DOI: 10.1016/J.Cell.2006.07.038  0.31
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  0.819
2006 Ballif BA, Cao Z, Schwartz D, Carraway KL, Gygi SP. Identification of 14-3-3epsilon substrates from embryonic murine brain. Journal of Proteome Research. 5: 2372-9. PMID 16944949 DOI: 10.1021/Pr060206K  0.354
2006 Kirkpatrick DS, Hathaway NA, Hanna J, Elsasser S, Rush J, Finley D, King RW, Gygi SP. Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nature Cell Biology. 8: 700-10. PMID 16799550 DOI: 10.1038/Ncb1436  0.363
2006 Lehtinen MK, Yuan Z, Boag PR, Yang Y, Villén J, Becker EB, DiBacco S, de la Iglesia N, Gygi S, Blackwell TK, Bonni A. A conserved MST-FOXO signaling pathway mediates oxidative-stress responses and extends life span. Cell. 125: 987-1001. PMID 16751106 DOI: 10.1016/J.Cell.2006.03.046  0.331
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  0.817
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  0.798
2006 Neher SB, Villén J, Oakes EC, Bakalarski CE, Sauer RT, Gygi SP, Baker TA. Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon. Molecular Cell. 22: 193-204. PMID 16630889 DOI: 10.1016/J.Molcel.2006.03.007  0.368
2006 Huang F, Kirkpatrick D, Jiang X, Gygi S, Sorkin A. Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain. Molecular Cell. 21: 737-48. PMID 16543144 DOI: 10.1016/J.Molcel.2006.02.018  0.301
2006 Huang TT, Nijman SM, Mirchandani KD, Galardy PJ, Cohn MA, Haas W, Gygi SP, Ploegh HL, Bernards R, D'Andrea AD. Regulation of monoubiquitinated PCNA by DUB autocleavage. Nature Cell Biology. 8: 339-47. PMID 16531995 DOI: 10.1038/Ncb1378  0.349
2006 Weiner OD, Rentel MC, Ott A, Brown GE, Jedrychowski M, Yaffe MB, Gygi SP, Cantley LC, Bourne HR, Kirschner MW. Hem-1 complexes are essential for Rac activation, actin polymerization, and myosin regulation during neutrophil chemotaxis. Plos Biology. 4: e38. PMID 16417406 DOI: 10.1371/Journal.Pbio.0040038  0.522
2006 Schwartz D, Gygi SP. An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nature Biotechnology. 23: 1391-8. PMID 16273072 DOI: 10.1038/Nbt1146  0.4
2006 MacLellan DL, Steen H, Adam RM, Garlick M, Zurakowski D, Gygi SP, Freeman MR, Solomon KR. A quantitative proteomic analysis of growth factor-induced compositional changes in lipid rafts of human smooth muscle cells. Proteomics. 5: 4733-42. PMID 16267816 DOI: 10.1002/Pmic.200500044  0.375
2005 Mortensen EM, Haas W, Gygi M, Gygi SP, Kellogg DR. Cdc28-dependent regulation of the Cdc5/Polo kinase. Current Biology : Cb. 15: 2033-7. PMID 16303563 DOI: 10.1016/J.Cub.2005.10.046  0.324
2005 Holz MK, Ballif BA, Gygi SP, Blenis J. mTOR and S6K1 mediate assembly of the translation preinitiation complex through dynamic protein interchange and ordered phosphorylation events. Cell. 123: 569-80. PMID 16286006 DOI: 10.1016/J.Cell.2005.10.024  0.384
2005 Anjum R, Roux PP, Ballif BA, Gygi SP, Blenis J. The tumor suppressor DAP kinase is a target of RSK-mediated survival signaling. Current Biology : Cb. 15: 1762-7. PMID 16213824 DOI: 10.1016/J.Cub.2005.08.050  0.359
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  0.657
2005 Harvey SL, Charlet A, Haas W, Gygi SP, Kellogg DR. Cdk1-dependent regulation of the mitotic inhibitor Wee1. Cell. 122: 407-20. PMID 16096060 DOI: 10.1016/J.Cell.2005.05.029  0.32
2005 Kirkpatrick DS, Denison C, Gygi SP. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nature Cell Biology. 7: 750-7. PMID 16056266 DOI: 10.1038/Ncb0805-750  0.442
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  0.807
2005 Zhao C, Denison C, Huibregtse JM, Gygi S, Krug RM. Human ISG15 conjugation targets both IFN-induced and constitutively expressed proteins functioning in diverse cellular pathways. Proceedings of the National Academy of Sciences of the United States of America. 102: 10200-5. PMID 16009940 DOI: 10.1073/Pnas.0504754102  0.37
2005 Semmes OJ, Cazares LH, Ward MD, Qi L, Moody M, Maloney E, Morris J, Trosset MW, Hisada M, Gygi S, Jacobson S. Discrete serum protein signatures discriminate between human retrovirus-associated hematologic and neurologic disease. Leukemia. 19: 1229-38. PMID 15889159 DOI: 10.1038/Sj.Leu.2403781  0.388
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  0.609
2005 Schmidt M, Haas W, Crosas B, Santamaria PG, Gygi SP, Walz T, Finley D. The HEAT repeat protein Blm10 regulates the yeast proteasome by capping the core particle. Nature Structural & Molecular Biology. 12: 294-303. PMID 15778719 DOI: 10.1038/Nsmb914  0.344
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  0.757
2005 Denison C, Kirkpatrick DS, Gygi SP. Proteomic insights into ubiquitin and ubiquitin-like proteins. Current Opinion in Chemical Biology. 9: 69-75. PMID 15701456 DOI: 10.1016/J.Cbpa.2004.10.010  0.436
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  0.779
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  0.737
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  0.78
2005 Gu T, Nardone J, Lee K, Gygi S, Rush J, Comb M, Polakiewicz R. Tyrosine Phosphoproteomics of FLT3 Signaling. Blood. 106: 1227-1227. DOI: 10.1182/Blood.V106.11.1227.1227  0.396
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  0.676
2004 Takahashi TS, Yiu P, Chou MF, Gygi S, Walter JC. Recruitment of Xenopus Scc2 and cohesin to chromatin requires the pre-replication complex. Nature Cell Biology. 6: 991-6. PMID 15448702 DOI: 10.1038/Ncb1177  0.326
2004 Auty R, Steen H, Myers LC, Persinger J, Bartholomew B, Gygi SP, Buratowski S. Purification of active TFIID from Saccharomyces cerevisiae. Extensive promoter contacts and co-activator function. The Journal of Biological Chemistry. 279: 49973-81. PMID 15448131 DOI: 10.1074/Jbc.M409849200  0.328
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  0.627
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  0.719
2004 Roux PP, Ballif BA, Anjum R, Gygi SP, Blenis J. Tumor-promoting phorbol esters and activated Ras inactivate the tuberous sclerosis tumor suppressor complex via p90 ribosomal S6 kinase. Proceedings of the National Academy of Sciences of the United States of America. 101: 13489-94. PMID 15342917 DOI: 10.1073/Pnas.0405659101  0.323
2004 Richardson CJ, Bröenstrup M, Fingar DC, Jülich K, Ballif BA, Gygi S, Blenis J. SKAR is a specific target of S6 kinase 1 in cell growth control. Current Biology : Cb. 14: 1540-9. PMID 15341740 DOI: 10.1016/J.Cub.2004.08.061  0.329
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  0.805
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  0.726
2004 Ho HY, Rohatgi R, Lebensohn AM, Le Ma, Li J, Gygi SP, Kirschner MW. Toca-1 mediates Cdc42-dependent actin nucleation by activating the N-WASP-WIP complex. Cell. 118: 203-16. PMID 15260990 DOI: 10.1016/J.Cell.2004.06.027  0.495
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  0.635
2004 Everley PA, Krijgsveld J, Zetter BR, Gygi SP. Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Molecular & Cellular Proteomics : McP. 3: 729-35. PMID 15102926 DOI: 10.1074/Mcp.M400021-Mcp200  0.363
2004 Gautreau A, Ho HY, Li J, Steen H, Gygi SP, Kirschner MW. Purification and architecture of the ubiquitous Wave complex. Proceedings of the National Academy of Sciences of the United States of America. 101: 4379-83. PMID 15070726 DOI: 10.1073/Pnas.0400628101  0.49
2004 Peng J, Kim MJ, Cheng D, Duong DM, Gygi SP, Sheng M. Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry. The Journal of Biological Chemistry. 279: 21003-11. PMID 15020595 DOI: 10.1074/Jbc.M400103200  0.41
2004 Brunet A, Sweeney LB, Sturgill JF, Chua KF, Greer PL, Lin Y, Tran H, Ross SE, Mostoslavsky R, Cohen HY, Hu LS, Cheng HL, Jedrychowski MP, Gygi SP, Sinclair DA, et al. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science (New York, N.Y.). 303: 2011-5. PMID 14976264 DOI: 10.1126/Science.1094637  0.304
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  0.643
2004 Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D. RNAi-mediated targeting of heterochromatin by the RITS complex. Science (New York, N.Y.). 303: 672-6. PMID 14704433 DOI: 10.1126/Science.1093686  0.696
2004 Shimura H, Schwartz D, Gygi SP, Kosik KS. CHIP-Hsc70 complex ubiquitinates phosphorylated tau and enhances cell survival. The Journal of Biological Chemistry. 279: 4869-76. PMID 14612456 DOI: 10.1074/Jbc.M305838200  0.324
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  0.749
2003 Hitchcock AL, Auld K, Gygi SP, Silver PA. A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proceedings of the National Academy of Sciences of the United States of America. 100: 12735-40. PMID 14557538 DOI: 10.1073/Pnas.2135500100  0.361
2003 Li J, Steen H, Gygi SP. Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response. Molecular & Cellular Proteomics : McP. 2: 1198-204. PMID 14506205 DOI: 10.1074/Mcp.M300070-Mcp200  0.389
2003 Danial NN, Gramm CF, Scorrano L, Zhang CY, Krauss S, Ranger AM, Datta SR, Greenberg ME, Licklider LJ, Lowell BB, Gygi SP, Korsmeyer SJ. BAD and glucokinase reside in a mitochondrial complex that integrates glycolysis and apoptosis. Nature. 424: 952-6. PMID 12931191 DOI: 10.1038/Nature01825  0.346
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  0.694
2003 Panigrahi AK, Allen TE, Stuart K, Haynes PA, Gygi SP. Mass spectrometric analysis of the editosome and other multiprotein complexes in Trypanosoma brucei. Journal of the American Society For Mass Spectrometry. 14: 728-35. PMID 12837594 DOI: 10.1016/S1044-0305(03)00126-0  0.641
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  0.807
2003 Ayad NG, Rankin S, Murakami M, Jebanathirajah J, Gygi S, Kirschner MW. Tome-1, a trigger of mitotic entry, is degraded during G1 via the APC. Cell. 113: 101-13. PMID 12679038 DOI: 10.1016/S0092-8674(03)00232-0  0.505
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 DOI: 10.1021/Pr025556V  0.662
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  0.698
2002 Li J, Moazed D, Gygi SP. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. The Journal of Biological Chemistry. 277: 49383-8. PMID 12381723 DOI: 10.1074/Jbc.M209294200  0.305
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  0.675
2002 Zhou Z, Licklider LJ, Gygi SP, Reed R. Comprehensive proteomic analysis of the human spliceosome. Nature. 419: 182-5. PMID 12226669 DOI: 10.1038/Nature01031  0.411
2002 Li J, Kinoshita T, Pandey S, Ng CK, Gygi SP, Shimazaki K, Assmann SM. Modulation of an RNA-binding protein by abscisic-acid-activated protein kinase. Nature. 418: 793-7. PMID 12181571 DOI: 10.1038/Nature00936  0.392
2002 Licklider LJ, Thoreen CC, Peng J, Gygi SP. Automation of nanoscale microcapillary liquid chromatography-tandem mass spectrometry with a vented column. Analytical Chemistry. 74: 3076-83. PMID 12141667 DOI: 10.1021/Ac025529O  0.345
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 DOI: 10.1074/Mcp.M200001-Mcp200  0.639
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  0.697
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  0.606
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 DOI: 10.4049/Jimmunol.168.5.2415  0.45
2002 Peng J, Gygi SP. Proteomics: the move to mixtures. Journal of Mass Spectrometry : Jms. 36: 1083-91. PMID 11747101 DOI: 10.1002/Jms.229  0.438
2001 Griffin TJ, Han DK, Gygi SP, Rist B, Lee H, Aebersold R, Parker KC. Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry. Journal of the American Society For Mass Spectrometry. 12: 1238-46. PMID 11766750 DOI: 10.1016/S1044-0305(01)00316-6  0.693
2001 Stemmann O, Zou H, Gerber SA, Gygi SP, Kirschner MW. Dual inhibition of sister chromatid separation at metaphase. Cell. 107: 715-26. PMID 11747808 DOI: 10.1016/S0092-8674(01)00603-1  0.746
2001 Gingras AC, Raught B, Gygi SP, Niedzwiecka A, Miron M, Burley SK, Polakiewicz RD, Wyslouch-Cieszynska A, Aebersold R, Sonenberg N. Hierarchical phosphorylation of the translation inhibitor 4E-BP1. Genes & Development. 15: 2852-64. PMID 11691836 DOI: 10.1101/Gad.912401  0.609
2001 Panigrahi AK, Schnaufer A, Carmean N, Igo RP, Gygi SP, Ernst NL, Palazzo SS, Weston DS, Aebersold R, Salavati R, Stuart KD. Four related proteins of the Trypanosoma brucei RNA editing complex. Molecular and Cellular Biology. 21: 6833-40. PMID 11564867 DOI: 10.1128/Mcb.21.20.6833-6840.2001  0.495
2001 Mayer ML, Gygi SP, Aebersold R, Hieter P. Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. Molecular Cell. 7: 959-70. PMID 11389843 DOI: 10.1016/S1097-2765(01)00254-4  0.465
2001 Griffin TJ, Gygi SP, Rist B, Aebersold R, Loboda A, Jilkine A, Ens W, Standing KG. Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer. Analytical Chemistry. 73: 978-86. PMID 11289445 DOI: 10.1021/Ac001169Y  0.681
2001 Panigrahi AK, Gygi SP, Ernst NL, Igo RP, Palazzo SS, Schnaufer A, Weston DS, Carmean N, Salavati R, Aebersold R, Stuart KD. Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex. Molecular and Cellular Biology. 21: 380-9. PMID 11134327 DOI: 10.1128/Mcb.21.2.380-389.2001  0.483
2000 Nirodi C, NagDas S, Gygi SP, Olson G, Aebersold R, Richmond A. A role for poly(ADP-ribose) polymerase in the transcriptional regulation of the melanoma growth stimulatory activity (CXCL1) gene expression. The Journal of Biological Chemistry. 276: 9366-74. PMID 11112786 DOI: 10.1074/Jbc.M009897200  0.35
2000 Aebersold R, Rist B, Gygi SP. Quantitative proteome analysis: methods and applications. Annals of the New York Academy of Sciences. 919: 33-47. PMID 11083095 DOI: 10.1111/J.1749-6632.2000.Tb06865.X  0.484
2000 Gygi SP, Aebersold R. Mass spectrometry and proteomics. Current Opinion in Chemical Biology. 4: 489-94. PMID 11006534 DOI: 10.1016/S1367-5931(00)00121-6  0.571
2000 Gygi SP, Rist B, Aebersold R. Measuring gene expression by quantitative proteome analysis. Current Opinion in Biotechnology. 11: 396-401. PMID 10975460 DOI: 10.1016/S0958-1669(00)00116-6  0.554
2000 Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proceedings of the National Academy of Sciences of the United States of America. 97: 9390-5. PMID 10920198 DOI: 10.1073/Pnas.160270797  0.72
2000 Raught B, Gingras AC, Gygi SP, Imataka H, Morino S, Gradi A, Aebersold R, Sonenberg N. Serum-stimulated, rapamycin-sensitive phosphorylation sites in the eukaryotic translation initiation factor 4GI. The Embo Journal. 19: 434-44. PMID 10654941 DOI: 10.1093/Emboj/19.3.434  0.637
2000 Liao DF, Jin ZG, Baas AS, Daum G, Gygi SP, Aebersold R, Berk BC. Purification and identification of secreted oxidative stress-induced factors from vascular smooth muscle cells. The Journal of Biological Chemistry. 275: 189-96. PMID 10617604 DOI: 10.1074/Jbc.275.1.189  0.327
2000 Gygi SP, Aebersold R. Using mass spectrometry for quantitative proteomics Trends in Biotechnology. 18: 31-36. DOI: 10.1016/S0167-7799(00)00008-1  0.527
2000 Haynes PA, Goodlett DR, Gygi SP, Watts JD, Figeys D, Aebersold R. Towards an Integrated Analytical Technology for the Generation of Multidimensional Protein Expression Maps Journal of Protein Chemistry. 17: 143-162. DOI: 10.1007/978-1-59259-719-2_9  0.731
1999 Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnology. 17: 994-9. PMID 10504701 DOI: 10.1038/13690  0.803
1999 Gingras AC, Gygi SP, Raught B, Polakiewicz RD, Abraham RT, Hoekstra MF, Aebersold R, Sonenberg N. Regulation of 4E-BP1 phosphorylation: a novel two-step mechanism. Genes & Development. 13: 1422-37. PMID 10364159 DOI: 10.1101/Gad.13.11.1422  0.617
1999 Gygi SP, Han DK, Gingras AC, Sonenberg N, Aebersold R. Protein analysis by mass spectrometry and sequence database searching: tools for cancer research in the post-genomic era. Electrophoresis. 20: 310-9. PMID 10197438 DOI: 10.1002/(Sici)1522-2683(19990201)20:2<310::Aid-Elps310>3.0.Co;2-M  0.658
1999 Gygi SP, Aebersold R. Absolute quantitation of 2-D protein spots. Methods in Molecular Biology (Clifton, N.J.). 112: 417-21. PMID 10027266 DOI: 10.1385/1-59259-584-7:417  0.474
1999 Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Molecular and Cellular Biology. 19: 1720-30. PMID 10022859 DOI: 10.1128/Mcb.19.3.1720  0.513
1998 Figeys D, Gygi SP, McKinnon G, Aebersold R. An Integrated Microfluidics-Tandem Mass Spectrometry System for Automated Protein Analysis Analytical Chemistry. 70: 3728-3734. PMID 9751017 DOI: 10.1021/Ac980320P  0.643
1998 Haynes PA, Gygi SP, Figeys D, Aebersold R. Proteome analysis: biological assay or data archive? Electrophoresis. 19: 1862-71. PMID 9740046 DOI: 10.1002/Elps.1150191104  0.737
1998 Figeys D, Gygi SP, Zhang Y, Watts J, Gu M, Aebersold R. Electrophoresis combined with novel mass spectrometry techniques: Powerful tools for the analysis of proteins and proteomes Electrophoresis. 19: 1811-1818. PMID 9719564 DOI: 10.1002/Elps.1150191045  0.643
1998 Wilkins DG, Valdez AS, Nagasawa PR, Gygi SP, Rollins DE. Incorporation of drugs for the treatment of substance abuse into pigmented and nonpigmented hair. Journal of Pharmaceutical Sciences. 87: 435-40. PMID 9548895 DOI: 10.1021/Js970360T  0.552
1997 Gygi SP, Wilkins DG, Rollins DE. A comparison of phenobarbital and codeine incorporation into pigmented and nonpigmented rat hair. Journal of Pharmaceutical Sciences. 86: 209-14. PMID 9040097 DOI: 10.1021/Js960268H  0.569
1997 Wilkins DG, Nagasawa PR, Gygi SP, Foltz RL, Rollins DE. Quantitative analysis of methadone and two major metabolites in hair by positive chemical ionization ion trap mass spectrometry. Journal of Analytical Toxicology. 20: 355-61. PMID 8889670 DOI: 10.1093/Jat/20.6.355  0.576
1996 Gygi SP, Wilkins DG, Rollins DE. Distribution of codeine and morphine into rat hair after long-term daily dosing with codeine. Journal of Analytical Toxicology. 19: 387-91. PMID 8926732 DOI: 10.1093/Jat/19.6.387  0.564
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