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Items: 1 to 50 of 474

1.

Interactome analyses revealed that the U1 snRNP machinery overlaps extensively with the RNAP II machinery and contains multiple ALS/SMA-causative proteins.

Chi B, O'Connell JD, Yamazaki T, Gangopadhyay J, Gygi SP, Reed R.

Sci Rep. 2018 Jun 8;8(1):8755. doi: 10.1038/s41598-018-27136-3.

2.

Cardiolipin Synthesis in Brown and Beige Fat Mitochondria Is Essential for Systemic Energy Homeostasis.

Sustarsic EG, Ma T, Lynes MD, Larsen M, Karavaeva I, Havelund JF, Nielsen CH, Jedrychowski MP, Moreno-Torres M, Lundh M, Plucinska K, Jespersen NZ, Grevengoed TJ, Kramar B, Peics J, Hansen JB, Shamsi F, Forss I, Neess D, Keipert S, Wang J, Stohlmann K, Brandslund I, Christensen C, Jørgensen ME, Linneberg A, Pedersen O, Kiebish MA, Qvortrup K, Han X, Pedersen BK, Jastroch M, Mandrup S, Kjær A, Gygi SP, Hansen T, Gillum MP, Grarup N, Emanuelli B, Nielsen S, Scheele C, Tseng YH, Færgeman NJ, Gerhart-Hines Z.

Cell Metab. 2018 Jul 3;28(1):159-174.e11. doi: 10.1016/j.cmet.2018.05.003. Epub 2018 May 31.

3.

Inhibition of the ER stress IRE1α inflammatory pathway protects against cell death in mitochondrial complex I mutant cells.

Soustek MS, Balsa E, Barrow JJ, Jedrychowski M, Vogel R, Jan Smeitink, Gygi SP, Puigserver P.

Cell Death Dis. 2018 May 31;9(6):658. doi: 10.1038/s41419-018-0696-5.

4.

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3.

Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA.

J Proteome Res. 2018 Jun 1;17(6):2226-2236. doi: 10.1021/acs.jproteome.8b00217. Epub 2018 May 16.

5.

Role of Selenof as a Gatekeeper of Secreted Disulfide-Rich Glycoproteins.

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.

Cell Rep. 2018 May 1;23(5):1387-1398. doi: 10.1016/j.celrep.2018.04.009.

6.

Characterization of Plasmodium falciparum Atypical Kinase PfPK7- Dependent Phosphoproteome.

Pease BN, Huttlin EL, Jedrychowski MP, Dorin-Semblat D, Sebastiani D, Segarra DT, Roberts BF, Chakrabarti R, Doerig C, Gygi SP, Chakrabarti D.

J Proteome Res. 2018 Jun 1;17(6):2112-2123. doi: 10.1021/acs.jproteome.8b00062. Epub 2018 Apr 30.

PMID:
29678115
7.

An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies.

Paulo JA, Navarrete-Perea J, Erickson AR, Knott J, Gygi SP.

J Am Soc Mass Spectrom. 2018 Jul;29(7):1505-1511. doi: 10.1007/s13361-018-1946-6. Epub 2018 Apr 18.

PMID:
29671274
8.

Isobaric Tag-Based Protein Profiling of a Nicotine-Treated Alpha7 Nicotinic Receptor-Null Human Haploid Cell Line.

Paulo JA, Gygi SP.

Proteomics. 2018 Jun;18(11):e1700475. doi: 10.1002/pmic.201700475. Epub 2018 May 15.

9.

Phosphorylation of Beta-3 adrenergic receptor at serine 247 by ERK MAP kinase drives lipolysis in obese adipocytes.

Hong S, Song W, Zushin PH, Liu B, Jedrychowski MP, Mina AI, Deng Z, Cabarkapa D, Hall JA, Palmer CJ, Aliakbarian H, Szpyt J, Gygi SP, Tavakkoli A, Lynch L, Perrimon N, Banks AS.

Mol Metab. 2018 Jun;12:25-38. doi: 10.1016/j.molmet.2018.03.012. Epub 2018 Mar 29.

10.

Multiplexed Isobaric Tag-Based Profiling of Seven Murine Tissues Following In Vivo Nicotine Treatment Using a Minimalistic Proteomics Strategy.

Paulo JA, Jedrychowski MP, Chouchani ET, Kazak L, Gygi SP.

Proteomics. 2018 May;18(10):e1700326. doi: 10.1002/pmic.201700326. Epub 2018 May 2.

11.

Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics.

Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, Hou Z, Heo JM, Rubin LL, Sidhu SS, Gygi SP, Harper JW.

Mol Cell. 2018 Apr 19;70(2):211-227.e8. doi: 10.1016/j.molcel.2018.03.012. Epub 2018 Apr 12.

PMID:
29656925
12.

Proteome-Wide Evaluation of Two Common Protein Quantification Methods.

O'Connell JD, Paulo JA, O'Brien JJ, Gygi SP.

J Proteome Res. 2018 May 4;17(5):1934-1942. doi: 10.1021/acs.jproteome.8b00016. Epub 2018 Apr 19.

13.

Filter-Based Protein Digestion (FPD): A Detergent-Free and Scaffold-Based Strategy for TMT Workflows.

Stepanova E, Gygi SP, Paulo JA.

J Proteome Res. 2018 Mar 2;17(3):1227-1234. doi: 10.1021/acs.jproteome.7b00840. Epub 2018 Feb 13.

14.

OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates MyD88-Dependent Signaling.

Zhao Y, Mudge MC, Soll JM, Rodrigues RB, Byrum AK, Schwarzkopf EA, Bradstreet TR, Gygi SP, Edelson BT, Mosammaparast N.

Mol Cell. 2018 Feb 1;69(3):505-516.e5. doi: 10.1016/j.molcel.2018.01.009.

PMID:
29395066
15.

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling.

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, Hochedlinger K.

Cell. 2018 Jan 25;172(3):629-631. doi: 10.1016/j.cell.2017.12.035. No abstract available.

16.

Kinase-independent function of E-type cyclins in liver cancer.

Geng Y, Michowski W, Chick JM, Wang YE, Jecrois ME, Sweeney KE, Liu L, Han RC, Ke N, Zagozdzon A, Sicinska E, Bronson RT, Gygi SP, Sicinski P.

Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):1015-1020. doi: 10.1073/pnas.1711477115. Epub 2018 Jan 16.

PMID:
29339491
17.

Loss of the deubiquitinase USP36 destabilizes the RNA helicase DHX33 and causes preimplantation lethality in mice.

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.

J Biol Chem. 2018 Feb 9;293(6):2183-2194. doi: 10.1074/jbc.M117.788430. Epub 2017 Dec 22.

PMID:
29273634
18.

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling.

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, Hochedlinger K.

Cell. 2018 Jan 11;172(1-2):106-120.e21. doi: 10.1016/j.cell.2017.11.023. Epub 2017 Dec 14. Erratum in: Cell. 2018 Jan 25;172(3):629-631.

PMID:
29249356
19.

Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags.

O'Brien JJ, O'Connell JD, Paulo JA, Thakurta S, Rose CM, Weekes MP, Huttlin EL, Gygi SP.

J Proteome Res. 2018 Jan 5;17(1):590-599. doi: 10.1021/acs.jproteome.7b00699. Epub 2017 Dec 15.

20.

Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg.

Presler M, Van Itallie E, Klein AM, Kunz R, Coughlin ML, Peshkin L, Gygi SP, Wühr M, Kirschner MW.

Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10838-E10847. doi: 10.1073/pnas.1709207114. Epub 2017 Nov 28.

21.

The skeletal phenotype of achondrogenesis type 1A is caused exclusively by cartilage defects.

Bird IM, Kim SH, Schweppe DK, Caetano-Lopes J, Robling AG, Charles JF, Gygi SP, Warman ML, Smits PJ.

Development. 2018 Jan 8;145(1). pii: dev156588. doi: 10.1242/dev.156588.

22.

SAMTOR is an S-adenosylmethionine sensor for the mTORC1 pathway.

Gu X, Orozco JM, Saxton RA, Condon KJ, Liu GY, Krawczyk PA, Scaria SM, Harper JW, Gygi SP, Sabatini DM.

Science. 2017 Nov 10;358(6364):813-818. doi: 10.1126/science.aao3265.

PMID:
29123071
23.

BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data.

Schweppe DK, Huttlin EL, Harper JW, Gygi SP.

J Proteome Res. 2018 Jan 5;17(1):722-726. doi: 10.1021/acs.jproteome.7b00572. Epub 2017 Oct 31.

PMID:
29054129
24.

Cdkal1, a type 2 diabetes susceptibility gene, regulates mitochondrial function in adipose tissue.

Palmer CJ, Bruckner RJ, Paulo JA, Kazak L, Long JZ, Mina AI, Deng Z, LeClair KB, Hall JA, Hong S, Zushin PH, Smith KL, Gygi SP, Hagen S, Cohen DE, Banks AS.

Mol Metab. 2017 Oct;6(10):1212-1225. doi: 10.1016/j.molmet.2017.07.013. Epub 2017 Jul 31.

25.

Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling.

Lim MY, O'Brien J, Paulo JA, Gygi SP.

J Proteome Res. 2017 Nov 3;16(11):4217-4226. doi: 10.1021/acs.jproteome.7b00571.

PMID:
28985074
26.

Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes.

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, Haynes PA, Molloy MP, Martins R, Cristea IM, Gygi SP, Graham SL, Gupta VK.

Sci Rep. 2017 Oct 4;7(1):12685. doi: 10.1038/s41598-017-12858-7.

27.

An inhibitor of the proteasomal deubiquitinating enzyme USP14 induces tau elimination in cultured neurons.

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, Finley D.

J Biol Chem. 2017 Nov 24;292(47):19209-19225. doi: 10.1074/jbc.M117.815126. Epub 2017 Sep 26.

PMID:
28972160
28.

Quantitative multiplexed proteomics of Taenia solium cysts obtained from the skeletal muscle and central nervous system of pigs.

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.

PLoS Negl Trop Dis. 2017 Sep 25;11(9):e0005962. doi: 10.1371/journal.pntd.0005962. eCollection 2017 Sep.

29.

Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins.

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, Finley D, Brown EJ.

Elife. 2017 Sep 21;6. pii: e26435. doi: 10.7554/eLife.26435.

30.

Kinesin superfamily protein Kif26b links Wnt5a-Ror signaling to the control of cell and tissue behaviors in vertebrates.

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, Jao LE, Gygi SP, Greenberg ME, Ho HH.

Elife. 2017 Sep 8;6. pii: e26509. doi: 10.7554/eLife.26509.

31.

Identification of translationally controlled tumor protein in promotion of DNA homologous recombination repair in cancer cells by affinity proteomics.

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, Liu B, Xu H, Fu S, Gygi SP, Zhou C.

Oncogene. 2017 Dec 14;36(50):6839-6849. doi: 10.1038/onc.2017.289. Epub 2017 Aug 28.

32.

Pseudomonas aeruginosa Proteome under Hypoxic Stress Conditions Mimicking the Cystic Fibrosis Lung.

Kamath KS, Krisp C, Chick J, Pascovici D, Gygi SP, Molloy MP.

J Proteome Res. 2017 Oct 6;16(10):3917-3928. doi: 10.1021/acs.jproteome.7b00561. Epub 2017 Aug 31.

PMID:
28832155
33.

UBE2O remodels the proteome during terminal erythroid differentiation.

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, Justice MJ, Gygi SP, Fleming MD, Finley D.

Science. 2017 Aug 4;357(6350). pii: eaan0218. doi: 10.1126/science.aan0218.

34.

Quantitative Temporal in Vivo Proteomics Deciphers the Transition of Virus-Driven Myeloid Cells into M2 Macrophages.

Clements DR, Murphy JP, Sterea A, Kennedy BE, Kim Y, Helson E, Almasi S, Holay N, Konda P, Paulo JA, Sharif T, Lee PW, Weekes MP, Gygi SP, Gujar S.

J Proteome Res. 2017 Sep 1;16(9):3391-3406. doi: 10.1021/acs.jproteome.7b00425. Epub 2017 Aug 23.

35.

Focal Adhesion- and IGF1R-Dependent Survival and Migratory Pathways Mediate Tumor Resistance to mTORC1/2 Inhibition.

Yoon SO, Shin S, Karreth FA, Buel GR, Jedrychowski MP, Plas DR, Dedhar S, Gygi SP, Roux PP, Dephoure N, Blenis J.

Mol Cell. 2017 Aug 3;67(3):512-527.e4. doi: 10.1016/j.molcel.2017.06.033. Epub 2017 Jul 27.

PMID:
28757207
36.

Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation.

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.

Cell Rep. 2017 Jul 18;20(3):721-736. doi: 10.1016/j.celrep.2017.06.074.

37.

Probing the missing mature β-cell proteomic landscape in differentiating patient iPSC-derived cells.

Vethe H, Bjørlykke Y, Ghila LM, Paulo JA, Scholz H, Gygi SP, Chera S, Ræder H.

Sci Rep. 2017 Jul 6;7(1):4780. doi: 10.1038/s41598-017-04979-w.

38.

Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription.

Jih G, Iglesias N, Currie MA, Bhanu NV, Paulo JA, Gygi SP, Garcia BA, Moazed D.

Nature. 2017 Jul 27;547(7664):463-467. doi: 10.1038/nature23267. Epub 2017 Jun 22.

39.

Compensatory metabolic networks in pancreatic cancers upon perturbation of glutamine metabolism.

Biancur DE, Paulo JA, Małachowska B, Quiles Del Rey M, Sousa CM, Wang X, Sohn ASW, Chu GC, Gygi SP, Harper JW, Fendler W, Mancias JD, Kimmelman AC.

Nat Commun. 2017 Jul 3;8:15965. doi: 10.1038/ncomms15965.

40.

Aminoglycoside-driven biosynthesis of selenium-deficient Selenoprotein P.

Renko K, Martitz J, Hybsier S, Heynisch B, Voss L, Everley RA, Gygi SP, Stoedter M, Wisniewska M, Köhrle J, Gladyshev VN, Schomburg L.

Sci Rep. 2017 Jun 29;7(1):4391. doi: 10.1038/s41598-017-04586-9.

41.

UCP1 deficiency causes brown fat respiratory chain depletion and sensitizes mitochondria to calcium overload-induced dysfunction.

Kazak L, Chouchani ET, Stavrovskaya IG, Lu GZ, Jedrychowski MP, Egan DF, Kumari M, Kong X, Erickson BK, Szpyt J, Rosen ED, Murphy MP, Kristal BS, Gygi SP, Spiegelman BM.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):7981-7986. doi: 10.1073/pnas.1705406114. Epub 2017 Jun 19.

42.

Evidence that C9ORF72 Dipeptide Repeat Proteins Associate with U2 snRNP to Cause Mis-splicing in ALS/FTD Patients.

Yin S, Lopez-Gonzalez R, Kunz RC, Gangopadhyay J, Borufka C, Gygi SP, Gao FB, Reed R.

Cell Rep. 2017 Jun 13;19(11):2244-2256. doi: 10.1016/j.celrep.2017.05.056.

43.

The metabolic function of cyclin D3-CDK6 kinase in cancer cell survival.

Wang H, Nicolay BN, Chick JM, Gao X, Geng Y, Ren H, Gao H, Yang G, Williams JA, Suski JM, Keibler MA, Sicinska E, Gerdemann U, Haining WN, Roberts TM, Polyak K, Gygi SP, Dyson NJ, Sicinski P.

Nature. 2017 Jun 15;546(7658):426-430. doi: 10.1038/nature22797. Epub 2017 Jun 7.

44.

ERRα Maintains Mitochondrial Oxidative Metabolism and Constitutes an Actionable Target in PGC1α-Elevated Melanomas.

Luo C, Balsa E, Thomas A, Hatting M, Jedrychowski M, Gygi SP, Widlund HR, Puigserver P.

Mol Cancer Res. 2017 Oct;15(10):1366-1375. doi: 10.1158/1541-7786.MCR-17-0143. Epub 2017 Jun 8.

PMID:
28596418
45.

Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals.

Quirós PM, Prado MA, Zamboni N, D'Amico D, Williams RW, Finley D, Gygi SP, Auwerx J.

J Cell Biol. 2017 Jul 3;216(7):2027-2045. doi: 10.1083/jcb.201702058. Epub 2017 May 31.

46.

Quantitative Phospho-proteomic Analysis of TNFα/NFκB Signaling Reveals a Role for RIPK1 Phosphorylation in Suppressing Necrotic Cell Death.

Mohideen F, Paulo JA, Ordureau A, Gygi SP, Harper JW.

Mol Cell Proteomics. 2017 Jul;16(7):1200-1216. doi: 10.1074/mcp.M117.068189. Epub 2017 May 24.

47.

A Temporal Proteomic Map of Epstein-Barr Virus Lytic Replication in B Cells.

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.

Cell Rep. 2017 May 16;19(7):1479-1493. doi: 10.1016/j.celrep.2017.04.062.

48.

Architecture of the human interactome defines protein communities and disease networks.

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, White AE, Schweppe DK, Rad R, Erickson BK, Obar RA, Guruharsha KG, Li K, Artavanis-Tsakonas S, Gygi SP, Harper JW.

Nature. 2017 May 25;545(7655):505-509. doi: 10.1038/nature22366. Epub 2017 May 17.

49.

Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling.

Paek J, Kalocsay M, Staus DP, Wingler L, Pascolutti R, Paulo JA, Gygi SP, Kruse AC.

Cell. 2017 Apr 6;169(2):338-349.e11. doi: 10.1016/j.cell.2017.03.028.

50.

Proteome-Wide Protein Expression Profiling Across Five Pancreatic Cell Lines.

Paulo JA, Mancias JD, Gygi SP.

Pancreas. 2017 May/Jun;46(5):690-698. doi: 10.1097/MPA.0000000000000800.

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