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Papers authored by Gygi SP

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Regulation of meiotic recombination via Mek1-mediated Rad54 phosphorylation.

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Niu H, Wan L, Busygina V, Kwon Y, Allen JA, Li X, Kunz RC, Kubota K, Wang B, Sung P, Shokat KM, Gygi SP, and Hollingsworth NM

Molecular cell 36(3):393-404, 2009 Nov 13 - Who cited this? | PubMed ID: 19917248 | Fulltext

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

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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, and Gygi SP

Nature biotechnology 27(10):933-40, 2009 Oct - Who cited this? | PubMed ID: 19801977 | Fulltext

Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.

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Holt LJ, Tuch BB, Villén J, Johnson AD, Gygi SP, and Morgan DO

Science (New York, N.Y.) 325(5948):1682-6, 2009 Sep 25 - Who cited this? | PubMed ID: 19779198 | Fulltext

SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma.

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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, and Rutter J

Science (New York, N.Y.) 325(5944):1139-42, 2009 Aug 28 - Who cited this? | PubMed ID: 19628817 | Fulltext

Initiation of myoblast to brown fat switch by a PRDM16-C/EBP-beta transcriptional complex.

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Kajimura S, Seale P, Kubota K, Lunsford E, Frangioni JV, Gygi SP, and Spiegelman BM

Nature 460(7259):1154-8, 2009 Aug 27 - Who cited this? | PubMed ID: 19641492 | Fulltext

GCN5-mediated Transcriptional Control of the Metabolic Coactivator PGC-1{beta} through Lysine Acetylation.

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Kelly TJ, Lerin C, Haas W, Gygi SP, and Puigserver P

The Journal of biological chemistry 284(30):19945-52, 2009 Jul 24 - Who cited this? | PubMed ID: 19491097 | Fulltext

Defining the human deubiquitinating enzyme interaction landscape.

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Sowa ME, Bennett EJ, Gygi SP, and Harper JW

Cell 138(2):389-403, 2009 Jul 23 - Who cited this? | PubMed ID: 19615732 | Fulltext

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

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Yu Y, Anjum R, Kubota K, Rush J, Villen J, and Gygi SP

Proceedings of the National Academy of Sciences of the United States of America 106(28):11606-11, 2009 Jul 14 - Who cited this? | PubMed ID: 19564600 | Fulltext

Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair.

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Svendsen JM, Smogorzewska A, Sowa ME, O'Connell BC, Gygi SP, Elledge SJ, and Harper JW

Cell 138(1):63-77, 2009 Jul 10 - Who cited this? | PubMed ID: 19596235 | Fulltext

S5a promotes protein degradation by blocking synthesis of nondegradable forked ubiquitin chains.

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Kim HT, Kim KP, Uchiki T, Gygi SP, and Goldberg AL

The EMBO journal 28(13):1867-77, 2009 Jul 8 - Who cited this? | PubMed ID: 19387488 | Fulltext

MURC/Cavin-4 and cavin family members form tissue-specific caveolar complexes.

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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, Pilch PF,

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The Journal of cell biology 185(7):1259-73, 2009 Jun 29 - Who cited this? | PubMed ID: 19546242 | Fulltext

During muscle atrophy, thick, but not thin, filament components are degraded by MuRF1-dependent ubiquitylation.

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Cohen S, Brault JJ, Gygi SP, Glass DJ, Valenzuela DM, Gartner C, Latres E, and Goldberg AL

The Journal of cell biology 185(6):1083-95, 2009 Jun 15 - Who cited this? | PubMed ID: 19506036 | Fulltext

Chaperone-mediated pathway of proteasome regulatory particle assembly.

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Roelofs J, Park S, Haas W, Tian G, McAllister FE, Huo Y, Lee BH, Zhang F, Shi Y, Gygi SP, and Finley D

Nature 459(7248):861-5, 2009 Jun 11 - Who cited this? | PubMed ID: 19412159 | Fulltext

Hexameric assembly of the proteasomal ATPases is templated through their C termini.

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Park S, Roelofs J, Kim W, Robert J, Schmidt M, Gygi SP, and Finley D

Nature 459(7248):866-70, 2009 Jun 11 - Who cited this? | PubMed ID: 19412160 | Fulltext

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.

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Abe Y, Yoon SO, Kubota K, Mendoza MC, Gygi SP, and Blenis J

The Journal of biological chemistry 284(22):14939-48, 2009 May 29 - Who cited this? | PubMed ID: 19332537 | Fulltext

The Ubiquitin-interacting Motif Protein, S5a, Is Ubiquitinated by All Types of Ubiquitin Ligases by a Mechanism Different from Typical Substrate Recognition.

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Uchiki T, Kim HT, Zhai B, Gygi SP, Johnston JA, O'Bryan JP, and Goldberg AL

The Journal of biological chemistry 284(19):12622-32, 2009 May 8 - Who cited this? | PubMed ID: 19240029 | Fulltext

A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export.

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Hurt JA, Obar RA, Zhai B, Farny NG, Gygi SP, and Silver PA

The Journal of cell biology 185(2):265-77, 2009 Apr 20 - Who cited this? | PubMed ID: 19364924 | Fulltext

UAF1 Is a Subunit of Multiple Deubiquitinating Enzyme Complexes.

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Cohn MA, Kee Y, Haas W, Gygi SP, and D'Andrea AD

The Journal of biological chemistry 284(8):5343-51, 2009 Feb 20 - Who cited this? | PubMed ID: 19075014 | Fulltext

Oxygen-Regulated {beta}2-Adrenergic Receptor Hydroxylation by EGLN3 and Ubiquitylation by pVHL.

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Xie L, Xiao K, Whalen EJ, Forrester MT, Freeman RS, Fong G, Gygi SP, Lefkowitz RJ, and Stamler JS

Science signaling 2(78):ra33, 2009 - Who cited this? | PubMed ID: 19584355 | Fulltext

Mass spectrometric analysis of type 1 inositol 1,4,5-trisphosphate receptor ubiquitination.

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Sliter DA, Kubota K, Kirkpatrick DS, Alzayady KJ, Gygi SP, and Wojcikiewicz RJ

The Journal of biological chemistry 283(51):35319-28, 2008 Dec 19 - Who cited this? | PubMed ID: 18955483 | Fulltext

Role for perinuclear chromosome tethering in maintenance of genome stability.

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Mekhail K, Seebacher J, Gygi SP, and Moazed D

Nature 456(7222):667-70, 2008 Dec 4 - Who cited this? | PubMed ID: 18997772 | Fulltext

The S. pombe SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8.

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Helmlinger D, Marguerat S, Villén J, Gygi SP, Bähler J, and Winston F

Genes & development 22(22):3184-95, 2008 Nov 15 - Who cited this? | PubMed ID: 19056896 | Fulltext

Extraproteasomal Rpn10 restricts access of the polyubiquitin-binding protein Dsk2 to proteasome.

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Matiuhin Y, Kirkpatrick DS, Ziv I, Kim W, Dakshinamurthy A, Kleifeld O, Gygi SP, Reis N, and Glickman MH

Molecular cell 32(3):415-25, 2008 Nov 7 - Who cited this? | PubMed ID: 18995839 | Fulltext

Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis.

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Villén J, Beausoleil SA, and Gygi SP

Proteomics 8(21):4444-52, 2008 Nov - Who cited this? | PubMed ID: 18972524 | Fulltext

Proteomic Profiling of gamma-Secretase Substrates and Mapping of Substrate Requirements.

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Hemming ML, Elias JE, Gygi SP, and Selkoe DJ

PLoS biology 6(10):e257, 2008 Oct 21 - Who cited this? | PubMed ID: 18942891 | Fulltext

Ubiquitin-Like Protein Involved in the Proteasome Pathway of Mycobacterium tuberculosis.

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Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, and Darwin KH

Science (New York, N.Y.), 2008 Oct 2 - Who cited this? | PubMed ID: 18832610 | Fulltext

The Impact of Peptide Abundance and Dynamic Range on Stable-Isotope-Based Quantitative Proteomic Analyses.

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Bakalarski CE, Elias JE, Villén J, Haas W, Gerber SA, Everley PA, and Gygi SP

Journal of proteome research, 2008 Sep 18 - Who cited this? | PubMed ID: 18798661 | Fulltext

An FTS/Hook/p107FHIP Complex Interacts with and Promotes Endosomal Clustering by the Homotypic Vacuolar Protein Sorting (HOPS) Complex.

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Xu L, Sowa ME, Chen J, Li X, Gygi SP, and Wade Harper J

Molecular biology of the cell, 2008 Sep 17 - Who cited this? | PubMed ID: 18799622 | Fulltext

Sir3-Nucleosome Interactions in Spreading of Silent Chromatin in Saccharomyces cerevisiae.

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Buchberger JR, Onishi M, Li G, Seebacher J, Rudner AD, Gygi SP, and Moazed D

Molecular and cellular biology, 2008 Sep 15 - Who cited this? | PubMed ID: 18794362 | Fulltext

A quantitative atlas of mitotic phosphorylation.

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Dephoure N, Zhou C, Villén J, Beausoleil SA, Bakalarski CE, Elledge SJ, and Gygi SP

Proceedings of the National Academy of Sciences of the United States of America 105(31):10762-7, 2008 Aug 5 - Who cited this? | PubMed ID: 18669648 | Fulltext

The impact of microRNAs on protein output.

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Baek D, Villén J, Shin C, Camargo FD, Gygi SP, and Bartel DP

Nature, 2008 Jul 30 - Who cited this? | PubMed ID: 18668037 | Fulltext

A molecular determinant for the establishment of sister chromatid cohesion.

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Unal E, Heidinger-Pauli JM, Kim W, Guacci V, Onn I, Gygi SP, and Koshland DE

Science (New York, N.Y.) 321(5888):566, 2008 Jul 25 - Who cited this? | PubMed ID: 18653894 | Fulltext

Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast.

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Monahan BJ, Villén J, Marguerat S, Bähler J, Gygi SP, and Winston F

Nature structural & molecular biology, 2008 Jul 11 - Who cited this? | PubMed ID: 18622392 | Fulltext

Single Copies of Sec61 and TRAP Associate with a Nontranslating Mammalian Ribosome.

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Ménétret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, and Akey CW

Structure (London, England : 1993) 16(7):1126, 2008 Jul - Who cited this? | PubMed ID: 18611385 | Fulltext

The hominoid-specific oncogene TBC1D3 activates Ras and modulates epidermal growth factor receptor signaling and trafficking.

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Wainszelbaum MJ, Charron AJ, Kong C, Kirkpatrick DS, Srikanth P, Barbieri MA, Gygi SP, and Stahl PD

The Journal of biological chemistry 283(19):13233, 2008 May 9 - Who cited this? | PubMed ID: 18319245 | Fulltext

Phosphoproteome Analysis of Drosophila melanogaster Embryos.

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Zhai B, Villén J, Beausoleil SA, Mintseris J, and Gygi SP

Journal of proteome research 7(4):1675-82, 2008 Apr - Who cited this? | PubMed ID: 18327897 | Fulltext

Phosphoproteome analysis of fission yeast.

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Wilson-Grady JT, Villén J, and Gygi SP

Journal of proteome research 7(3):1088, 2008 Mar - Who cited this? | PubMed ID: 18257517 | Fulltext

In situ observation of protein phosphorylation by high-resolution NMR spectroscopy.

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Selenko P, Frueh DP, Elsaesser SJ, Haas W, Gygi SP, and Wagner G

Nature structural & molecular biology 15(3):321-9, 2008 Mar - Who cited this? | PubMed ID: 18297086 | Fulltext

Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport.

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Yoon SO, Shin S, Liu Y, Ballif BA, Woo MS, Gygi SP, and Blenis J

Molecular cell 29(3):362-75, 2008 Feb 15 - Who cited this? | PubMed ID: 18280241 | Fulltext

Lysine 63-linked ubiquitination promotes the formation and autophagic clearance of protein inclusions associated with neurodegenerative diseases.

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Tan JM, Wong ES, Kirkpatrick DS, Pletnikova O, Ko HS, Tay SP, Ho MW, Troncoso J, Gygi SP, Lee MK, Dawson VL, Dawson TM, and Lim KL

Human molecular genetics 17(3):431-9, 2008 Feb 1 - Who cited this? | PubMed ID: 17981811 | Fulltext

Signaling networks assembled by oncogenic EGFR and c-Met.

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Guo A, Villén J, Kornhauser J, Lee KA, Stokes MP, Rikova K, Possemato A, Nardone J, Innocenti G, Wetzel R, Wang Y, MacNeill J, Mitchell J, Gygi SP, Rush J, Polakiewicz RD,

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Proceedings of the National Academy of Sciences of the United States of America 105(2):692, 2008 Jan 15 - Who cited this? | PubMed ID: 18180459 | Fulltext

The septins function in G1 pathways that influence the pattern of cell growth in budding yeast.

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Egelhofer TA, Villén J, McCusker D, Gygi SP, and Kellogg DR

PLoS ONE 3(4), 2008 - Who cited this? | PubMed ID: 18431499 | Fulltext

Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation.

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Dermody JL, Dreyfuss JM, Villén J, Ogundipe B, Gygi SP, Park PJ, Ponticelli AS, Moore CL, Buratowski S, and Bucheli ME

PLoS ONE 3(9):e3273, 2008 - Who cited this? | PubMed ID: 18818768 | Fulltext

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry.

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Villén J and Gygi SP

Nature protocols 3(10):1630-8, 2008 - Who cited this? | PubMed ID: 18833199 | Fulltext

Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain.

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Ballif BA, Carey GR, Sunyaev SR, and Gygi SP

Journal of proteome research 7(1):311-8, 2008 Jan - Who cited this? | PubMed ID: 18034455 | Fulltext

Ribosome binding of a single copy of the SecY complex: implications for protein translocation.

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Ménétret JF, Schaletzky J, Clemons WM, Osborne AR, Skånland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, and Akey CW

Molecular cell 28(6):1083, 2007 Dec 28 - Who cited this? | PubMed ID: 18158904 | Fulltext

Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.

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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, Wetzel R,

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Cell 131(6):1190, 2007 Dec 14 - Who cited this? | PubMed ID: 18083107 | Fulltext

A UAF1-Containing Multisubunit Protein Complex Regulates the Fanconi Anemia Pathway.

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Cohn MA, Kowal P, Yang K, Haas W, Huang TT, Gygi SP, and D'Andrea AD

Molecular cell 28(5):786-97, 2007 Dec 14 - Who cited this? | PubMed ID: 18082604 | Fulltext

Profiling of UV-induced ATM/ATR signaling pathways.

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Stokes MP, Rush J, MacNeill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, and Comb MJ

Proceedings of the National Academy of Sciences of the United States of America 104(50):19855, 2007 Dec 11 - Who cited this? | PubMed ID: 18077418 | Fulltext

The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics.

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Bakalarski CE, Haas W, Dephoure NE, and Gygi SP

Analytical and bioanalytical chemistry 389(5):1409-19, 2007 Nov - Who cited this? | PubMed ID: 17874083 | Fulltext

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