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Items: 1 to 50 of 140

1.

TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples.

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, Paulo JA.

Nat Methods. 2020 Mar 16. doi: 10.1038/s41592-020-0781-4. [Epub ahead of print]

PMID:
32203386
2.

A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search.

Gygi JP, Ramin Rad, Navarrete-Perea J, Younesi S, Gygi SP, Paulo JA.

J Am Soc Mass Spectrom. 2020 Mar 27. doi: 10.1021/jasms.0c00029. [Epub ahead of print]

PMID:
32202424
3.

Targeting the cyclin-dependent kinase 5 in metastatic melanoma.

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, Herlyn M, Gygi SP, Sicinski P.

Proc Natl Acad Sci U S A. 2020 Mar 19. pii: 201912617. doi: 10.1073/pnas.1912617117. [Epub ahead of print]

PMID:
32193336
4.

Chromatin accessibility promotes hematopoietic and leukemia stem cell activity.

Cabal-Hierro L, van Galen P, Prado MA, Higby KJ, Togami K, Mowery CT, Paulo JA, Xie Y, Cejas P, Furusawa T, Bustin M, Long HW, Sykes DB, Gygi SP, Finley D, Bernstein BE, Lane AA.

Nat Commun. 2020 Mar 16;11(1):1406. doi: 10.1038/s41467-020-15221-z.

5.

In vivo Environment Swiftly Restricts Human Pancreatic Progenitors Toward Mono-Hormonal Identity via a HNF1A/HNF4A Mechanism.

Legøy TA, Mathisen AF, Salim Z, Vethe H, Bjørlykke Y, Abadpour S, Paulo JA, Scholz H, Ræder H, Ghila L, Chera S.

Front Cell Dev Biol. 2020 Feb 25;8:109. doi: 10.3389/fcell.2020.00109. eCollection 2020.

6.

Paradoxical mitotic exit induced by a small molecule inhibitor of APC/CCdc20.

Richeson KV, Bodrug T, Sackton KL, Yamaguchi M, Paulo JA, Gygi SP, Schulman BA, Brown NG, King RW.

Nat Chem Biol. 2020 Mar 9. doi: 10.1038/s41589-020-0495-z. [Epub ahead of print]

PMID:
32152539
7.

Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling.

Ordureau A, Paulo JA, Zhang J, An H, Swatek KN, Cannon JR, Wan Q, Komander D, Harper JW.

Mol Cell. 2020 Mar 5;77(5):1124-1142.e10. doi: 10.1016/j.molcel.2019.11.013.

PMID:
32142685
8.

Correction to 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, Wouters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP.

Anal Chem. 2020 Mar 17;92(6):4690. doi: 10.1021/acs.analchem.0c00888. Epub 2020 Mar 5. No abstract available.

PMID:
32134636
9.

Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics.

Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP.

J Proteome Res. 2020 Mar 3. doi: 10.1021/acs.jproteome.9b00860. [Epub ahead of print]

PMID:
32126768
10.

A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging.

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, Paulo JA, Zhang T, Gray NS, Gygi SP, Chouchani ET.

Cell. 2020 Mar 5;180(5):968-983.e24. doi: 10.1016/j.cell.2020.02.012. Epub 2020 Feb 27.

PMID:
32109415
11.

Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling.

Legøy TA, Vethe H, Abadpour S, Strand BL, Scholz H, Paulo JA, Ræder H, Ghila L, Chera S.

Sci Rep. 2020 Jan 15;10(1):414. doi: 10.1038/s41598-019-57305-x.

12.

Pathogenic Pathways in Early-Onset Autosomal Recessive Parkinson's Disease Discovered Using Isogenic Human Dopaminergic Neurons.

Ahfeldt T, Ordureau A, Bell C, Sarrafha L, Sun C, Piccinotti S, Grass T, Parfitt GM, Paulo JA, Yanagawa F, Uozumi T, Kiyota Y, Harper JW, Rubin LL.

Stem Cell Reports. 2020 Jan 14;14(1):75-90. doi: 10.1016/j.stemcr.2019.12.005. Epub 2020 Jan 2.

13.

Quantitative Proteome Responses to Oncolytic Reovirus in GM-CSF- and M-CSF-Differentiated Bone Marrow-Derived Cells.

Giacomantonio MA, Sterea AM, Kim Y, Paulo JA, Clements DR, Kennedy BE, Bydoun MJ, Shi G, Waisman DM, Gygi SP, Giacomantonio CA, Murphy JP, Gujar S.

J Proteome Res. 2020 Feb 7;19(2):708-718. doi: 10.1021/acs.jproteome.9b00583. Epub 2020 Jan 17.

PMID:
31884793
14.

In vivo hyperglycaemia exposure elicits distinct period-dependent effects on human pancreatic progenitor differentiation, conveyed by oxidative stress.

Legøy TA, Ghila L, Vethe H, Abadpour S, Mathisen AF, Paulo JA, Scholz H, Raeder H, Chera S.

Acta Physiol (Oxf). 2020 Apr;228(4):e13433. doi: 10.1111/apha.13433. Epub 2020 Jan 8.

PMID:
31872528
15.

Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors.

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.

Stem Cells. 2019 Dec 11. doi: 10.1002/stem.3135. [Epub ahead of print]

PMID:
31828876
16.

Optimized Workflow for Multiplexed Phosphorylation Analysis of TMT-Labeled Peptides Using High-Field Asymmetric Waveform Ion Mobility Spectrometry.

Schweppe DK, Rusin SF, Gygi SP, Paulo JA.

J Proteome Res. 2020 Jan 3;19(1):554-560. doi: 10.1021/acs.jproteome.9b00759. Epub 2019 Dec 18.

PMID:
31799850
17.

Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance.

Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D.

Mol Cell. 2020 Jan 2;77(1):51-66.e8. doi: 10.1016/j.molcel.2019.10.018. Epub 2019 Nov 26.

PMID:
31784357
18.

Thiol-based direct threat sensing by the stress-activated protein kinase Hog1.

Guerra-Moreno A, Prado MA, Ang J, Schnell HM, Micoogullari Y, Paulo JA, Finley D, Gygi SP, Hanna J.

Sci Signal. 2019 Nov 26;12(609). pii: eaaw4956. doi: 10.1126/scisignal.aaw4956.

PMID:
31772124
19.

Integrated proteogenetic analysis reveals the landscape of a mitochondrial-autophagosome synapse during PARK2-dependent mitophagy.

Heo JM, Harper NJ, Paulo JA, Li M, Xu Q, Coughlin M, Elledge SJ, Harper JW.

Sci Adv. 2019 Nov 6;5(11):eaay4624. doi: 10.1126/sciadv.aay4624. eCollection 2019 Nov.

20.

Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast.

Li J, Paulo JA, Nusinow DP, Huttlin EL, Gygi SP.

Cell Rep. 2019 Nov 12;29(7):2092-2104.e4. doi: 10.1016/j.celrep.2019.10.034.

21.

Brain Region-Specific nAChR and Associated Protein Abundance Alterations Following Chronic Nicotine and/or Menthol Exposure.

Mulcahy MJ, Huard SM, Paulo JA, Wang JH, McKinney S, Henderson BJ, Lester HA.

J Proteome Res. 2020 Jan 3;19(1):36-48. doi: 10.1021/acs.jproteome.9b00286. Epub 2019 Oct 28.

PMID:
31657575
22.

Multiplexed proteome profiling of carbon source perturbations in two yeast species with SL-SP3-TMT.

Paulo JA, Navarrete-Perea J, Gygi SP.

J Proteomics. 2020 Jan 6;210:103531. doi: 10.1016/j.jprot.2019.103531. Epub 2019 Oct 15.

PMID:
31626996
23.

Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model.

Lim MY, Paulo JA, Gygi SP.

J Proteome Res. 2019 Nov 1;18(11):4020-4026. doi: 10.1021/acs.jproteome.9b00492. Epub 2019 Oct 2.

PMID:
31547658
24.

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 Sep 25;9(3):258-270.e6. doi: 10.1016/j.cels.2019.07.006. Epub 2019 Sep 11.

PMID:
31521603
25.

mTMT: An Alternative, Nonisobaric, Tandem Mass Tag Allowing for Precursor-Based Quantification.

Paulo JA, Gygi SP.

Anal Chem. 2019 Oct 1;91(19):12167-12172. doi: 10.1021/acs.analchem.9b03162. Epub 2019 Sep 20.

PMID:
31490667
26.

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
27.

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.

28.

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.

29.

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
30.

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.

31.

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
32.

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
33.

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
34.
35.

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
36.

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
37.

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.

38.

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.

39.

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. Erratum in: Anal Chem. 2020 Mar 17;92(6):4690.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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