Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 117

1.

Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation.

Brubaker DK, Paulo JA, Sheth S, Poulin EJ, Popow O, Joughin BA, Strasser SD, Starchenko A, Gygi SP, Lauffenburger DA, Haigis KM.

Cell Syst. 2019 Aug 23. pii: S2405-4712(19)30238-8. doi: 10.1016/j.cels.2019.07.006. [Epub ahead of print]

PMID:
31521603
2.

mTMT: An alternative, non-isobaric, tandem mass tag allowing for precursor-based quantification.

Paulo JA, Gygi SP.

Anal Chem. 2019 Sep 6. doi: 10.1021/acs.analchem.9b03162. [Epub ahead of print]

PMID:
31490667
3.

Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer.

Nissim S, Leshchiner I, Mancias JD, Greenblatt MB, Maertens O, Cassa CA, Rosenfeld JA, Cox AG, Hedgepeth J, Wucherpfennig JI, Kim AJ, Henderson JE, Gonyo P, Brandt A, Lorimer E, Unger B, Prokop JW, Heidel JR, Wang XX, Ukaegbu CI, Jennings BC, Paulo JA, Gableske S, Fierke CA, Getz G, Sunyaev SR, Wade Harper J, Cichowski K, Kimmelman AC, Houvras Y, Syngal S, Williams C, Goessling W.

Nat Genet. 2019 Sep;51(9):1308-1314. doi: 10.1038/s41588-019-0475-y. Epub 2019 Aug 12.

PMID:
31406347
4.

Epstein-Barr-Virus-Induced One-Carbon Metabolism Drives B Cell Transformation.

Wang LW, Shen H, Nobre L, Ersing I, Paulo JA, Trudeau S, Wang Z, Smith NA, Ma Y, Reinstadler B, Nomburg J, Sommermann T, Cahir-McFarland E, Gygi SP, Mootha VK, Weekes MP, Gewurz BE.

Cell Metab. 2019 Sep 3;30(3):539-555.e11. doi: 10.1016/j.cmet.2019.06.003. Epub 2019 Jun 27.

5.

Protein aggregation mediates stoichiometry of protein complexes in aneuploid cells.

Brennan CM, Vaites LP, Wells JN, Santaguida S, Paulo JA, Storchova Z, Harper JW, Marsh JA, Amon A.

Genes Dev. 2019 Aug 1;33(15-16):1031-1047. doi: 10.1101/gad.327494.119. Epub 2019 Jun 13.

PMID:
31196865
6.

Identification of Endogenous Adenomatous Polyposis Coli Interaction Partners and β-Catenin-Independent Targets by Proteomics.

Popow O, Paulo JA, Tatham MH, Volk MS, Rojas-Fernandez A, Loyer N, Newton IP, Januschke J, Haigis KM, Näthke I.

Mol Cancer Res. 2019 Sep;17(9):1828-1841. doi: 10.1158/1541-7786.MCR-18-1154. Epub 2019 Jun 3.

PMID:
31160382
7.

The Effect of Wnt Pathway Modulators on Human iPSC-Derived Pancreatic Beta Cell Maturation.

Vethe H, Ghila L, Berle M, Hoareau L, Haaland ØA, Scholz H, Paulo JA, Chera S, Ræder H.

Front Endocrinol (Lausanne). 2019 May 8;10:293. doi: 10.3389/fendo.2019.00293. eCollection 2019.

8.

Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy.

Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S.

J Proteome Res. 2019 Jun 7;18(6):2666-2675. doi: 10.1021/acs.jproteome.9b00173. Epub 2019 May 29.

PMID:
31095916
9.

TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress.

An H, Ordureau A, Paulo JA, Shoemaker CJ, Denic V, Harper JW.

Mol Cell. 2019 Jun 6;74(5):891-908.e10. doi: 10.1016/j.molcel.2019.03.034. Epub 2019 Apr 18.

PMID:
31006537
10.

Tissue-Specific Oncogenic Activity of KRASA146T.

Poulin EJ, Bera AK, Lu J, Lin YJ, Strasser SD, Paulo JA, Huang TQ, Morales C, Yan W, Cook J, Nowak JA, Brubaker DK, Joughin BA, Johnson CW, DeStefanis RA, Ghazi PC, Gondi S, Wales TE, Iacob RE, Bogdanova L, Gierut JJ, Li Y, Engen JR, Perez-Mancera PA, Braun BS, Gygi SP, Lauffenburger DA, Westover KD, Haigis KM.

Cancer Discov. 2019 Jun;9(6):738-755. doi: 10.1158/2159-8290.CD-18-1220. Epub 2019 Apr 5.

PMID:
30952657
11.
12.

Probing the Global Cellular Responses to Lipotoxicity Caused by Saturated Fatty Acids.

Piccolis M, Bond LM, Kampmann M, Pulimeno P, Chitraju C, Jayson CBK, Vaites LP, Boland S, Lai ZW, Gabriel KR, Elliott SD, Paulo JA, Harper JW, Weissman JS, Walther TC, Farese RV Jr.

Mol Cell. 2019 Apr 4;74(1):32-44.e8. doi: 10.1016/j.molcel.2019.01.036. Epub 2019 Mar 4.

PMID:
30846318
13.

Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin.

Murphy JP, Yu Q, Konda P, Paulo JA, Jedrychowski MP, Kowalewski DJ, Schuster H, Kim Y, Clements D, Jain A, Stevanovic S, Gygi SP, Mancias JD, Gujar S.

Anal Chem. 2019 Apr 16;91(8):5106-5115. doi: 10.1021/acs.analchem.8b05616. Epub 2019 Feb 22.

PMID:
30779550
14.

Diabetes relief in mice by glucose-sensing insulin-secreting human α-cells.

Furuyama K, Chera S, van Gurp L, Oropeza D, Ghila L, Damond N, Vethe H, Paulo JA, Joosten AM, Berney T, Bosco D, Dorrell C, Grompe M, Ræder H, Roep BO, Thorel F, Herrera PL.

Nature. 2019 Mar;567(7746):43-48. doi: 10.1038/s41586-019-0942-8. Epub 2019 Feb 13.

15.

Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence.

Neurohr GE, Terry RL, Lengefeld J, Bonney M, Brittingham GP, Moretto F, Miettinen TP, Vaites LP, Soares LM, Paulo JA, Harper JW, Buratowski S, Manalis S, van Werven FJ, Holt LJ, Amon A.

Cell. 2019 Feb 21;176(5):1083-1097.e18. doi: 10.1016/j.cell.2019.01.018. Epub 2019 Feb 7.

16.

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry.

Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Woulters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP.

Anal Chem. 2019 Mar 19;91(6):4010-4016. doi: 10.1021/acs.analchem.8b05399. Epub 2019 Feb 26.

PMID:
30672687
17.

Active Instrument Engagement Combined with a Real-Time Database Search for Improved Performance of Sample Multiplexing Workflows.

Erickson BK, Mintseris J, Schweppe DK, Navarrete-Perea J, Erickson AR, Nusinow DP, Paulo JA, Gygi SP.

J Proteome Res. 2019 Mar 1;18(3):1299-1306. doi: 10.1021/acs.jproteome.8b00899. Epub 2019 Feb 4.

PMID:
30658528
18.

RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway.

Heo JM, Ordureau A, Swarup S, Paulo JA, Shen K, Sabatini DM, Harper JW.

Sci Adv. 2018 Nov 21;4(11):eaav0443. doi: 10.1126/sciadv.aav0443. eCollection 2018 Nov.

19.

Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice.

Ron-Harel N, Notarangelo G, Ghergurovich JM, Paulo JA, Sage PT, Santos D, Satterstrom FK, Gygi SP, Rabinowitz JD, Sharpe AH, Haigis MC.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):13347-13352. doi: 10.1073/pnas.1804149115. Epub 2018 Dec 10.

20.

TKO6: A Peptide Standard To Assess Interference for Unit-Resolved Isobaric Labeling Platforms.

Paulo JA, Navarrete-Perea J, Guha Thakurta S, Gygi SP.

J Proteome Res. 2019 Jan 4;18(1):565-570. doi: 10.1021/acs.jproteome.8b00902. Epub 2018 Dec 6.

21.

The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments.

O'Brien JJ, Gunawardena HP, Paulo JA, Chen X, Ibrahim JG, Gygi SP, Qaqish BF.

Ann Appl Stat. 2018 Dec;12(4):2075-2095. doi: 10.1214/18-AOAS1144. Epub 2018 Nov 13.

22.

Web-Based Search Tool for Visualizing Instrument Performance Using the Triple Knockout (TKO) Proteome Standard.

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

J Proteome Res. 2019 Feb 1;18(2):687-693. doi: 10.1021/acs.jproteome.8b00737. Epub 2018 Nov 27.

23.

Proteomic Investigation of Murine Neuronal α7-Nicotinic Acetylcholine Receptor Interacting Proteins.

Mulcahy MJ, Paulo JA, Hawrot E.

J Proteome Res. 2018 Nov 2;17(11):3959-3975. doi: 10.1021/acs.jproteome.8b00618. Epub 2018 Oct 4.

24.

Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors.

Martin SES, Tan ZW, Itkonen HM, Duveau DY, Paulo JA, Janetzko J, Boutz PL, Törk L, Moss FA, Thomas CJ, Gygi SP, Lazarus MB, Walker S.

J Am Chem Soc. 2018 Oct 24;140(42):13542-13545. doi: 10.1021/jacs.8b07328. Epub 2018 Oct 4.

PMID:
30285435
25.

Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia.

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, Quesada V, López-Otín C.

Blood. 2018 Nov 29;132(22):2375-2388. doi: 10.1182/blood-2017-09-804401. Epub 2018 Sep 4.

PMID:
30181176
26.

The NAD+ Salvage Pathway Supports PHGDH-Driven Serine Biosynthesis.

Murphy JP, Giacomantonio MA, Paulo JA, Everley RA, Kennedy BE, Pathak GP, Clements DR, Kim Y, Dai C, Sharif T, Gygi SP, Gujar S.

Cell Rep. 2018 Aug 28;24(9):2381-2391.e5. doi: 10.1016/j.celrep.2018.07.086.

27.

Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability.

Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D.

Nature. 2018 Aug;560(7719):504-508. doi: 10.1038/s41586-018-0398-2. Epub 2018 Jul 23.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

MS3-IDQ: Utilizing MS3 Spectra beyond Quantification Yields Increased Coverage of the Phosphoproteome in Isobaric Tag Experiments.

Berberich MJ, Paulo JA, Everley RA.

J Proteome Res. 2018 Apr 6;17(4):1741-1747. doi: 10.1021/acs.jproteome.8b00006. Epub 2018 Feb 26.

35.

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.

36.

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.

37.

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.

38.

Systematic Analysis of Human Cells Lacking ATG8 Proteins Uncovers Roles for GABARAPs and the CCZ1/MON1 Regulator C18orf8/RMC1 in Macroautophagic and Selective Autophagic Flux.

Vaites LP, Paulo JA, Huttlin EL, Harper JW.

Mol Cell Biol. 2017 Dec 13;38(1). pii: e00392-17. doi: 10.1128/MCB.00392-17. Print 2018 Jan 1.

39.

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.

40.

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.

41.

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.

42.

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.

43.

Are forest disturbances amplifying or canceling out climate change-induced productivity changes in European forests?

Reyer CPO, Bathgate S, Blennow K, Borges JG, Bugmann H, Delzon S, Faias SP, Garcia-Gonzalo J, Gardiner B, Gonzalez-Olabarria JR, Gracia C, Hernández JG, Kellomäki S, Kramer K, Lexer MJ, Lindner M, van der Maaten E, Maroschek M, Muys B, Nicoll B, Palahi M, Palma JH, Paulo JA, Peltola H, Pukkala T, Rammer W, Ray D, Sabaté S, Schelhaas MJ, Seidl R, Temperli C, Tomé M, Yousefpour R, Zimmermann NE, Hanewinkel M.

Environ Res Lett. 2017 Mar 16;12(3):034027. doi: 10.1088/1748-9326/aa5ef1.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase.

Scott DC, Hammill JT, Min J, Rhee DY, Connelly M, Sviderskiy VO, Bhasin D, Chen Y, Ong SS, Chai SC, Goktug AN, Huang G, Monda JK, Low J, Kim HS, Paulo JA, Cannon JR, Shelat AA, Chen T, Kelsall IR, Alpi AF, Pagala V, Wang X, Peng J, Singh B, Harper JW, Schulman BA, Guy RK.

Nat Chem Biol. 2017 Aug;13(8):850-857. doi: 10.1038/nchembio.2386. Epub 2017 Jun 5.

50.

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.

Supplemental Content

Loading ...
Support Center