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Items: 1 to 50 of 518

1.

An optimized workflow for multiplexed phosphorylation analysis of TMT-labeled peptides using high-Field Asymmetric waveform Ion Mobility Spectrometry (FAIMS).

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

J Proteome Res. 2019 Dec 4. doi: 10.1021/acs.jproteome.9b00759. [Epub ahead of print]

PMID:
31799850
2.

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. 2019 Nov 7. pii: S1097-2765(19)30796-8. doi: 10.1016/j.molcel.2019.10.018. [Epub ahead of print]

PMID:
31784357
3.

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
4.

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.

5.

Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs.

Wang Y, Dix MM, Bianco G, Remsberg JR, Lee HY, Kalocsay M, Gygi SP, Forli S, Vite G, Lawrence RM, Parker CG, Cravatt BF.

Nat Chem. 2019 Dec;11(12):1113-1123. doi: 10.1038/s41557-019-0351-5. Epub 2019 Oct 28.

PMID:
31659311
6.

Proteomic Profiling of Extracellular Vesicles Isolated From Cerebrospinal Fluid of Former National Football League Players at Risk for Chronic Traumatic Encephalopathy.

Muraoka S, Jedrychowski MP, Tatebe H, DeLeo AM, Ikezu S, Tokuda T, Gygi SP, Stern RA, Ikezu T.

Front Neurosci. 2019 Oct 9;13:1059. doi: 10.3389/fnins.2019.01059. eCollection 2019.

7.

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
8.

The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.

Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jiménez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K.

Cell Stem Cell. 2019 Nov 7;25(5):622-638.e13. doi: 10.1016/j.stem.2019.08.018. Epub 2019 Oct 3.

PMID:
31588046
9.

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
10.

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
11.

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
12.

PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression.

Sendinc E, Valle-Garcia D, Dhall A, Chen H, Henriques T, Navarrete-Perea J, Sheng W, Gygi SP, Adelman K, Shi Y.

Mol Cell. 2019 Aug 8;75(3):620-630.e9. doi: 10.1016/j.molcel.2019.05.030. Epub 2019 Jul 3.

PMID:
31279659
13.

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.

14.

Physical and Molecular Landscapes of Mouse Glioma Extracellular Vesicles Define Heterogeneity.

Gyuris A, Navarrete-Perea J, Jo A, Cristea S, Zhou S, Fraser K, Wei Z, Krichevsky AM, Weissleder R, Lee H, Gygi SP, Charest A.

Cell Rep. 2019 Jun 25;27(13):3972-3987.e6. doi: 10.1016/j.celrep.2019.05.089.

15.

Phosphorylation of FANCD2 Inhibits the FANCD2/FANCI Complex and Suppresses the Fanconi Anemia Pathway in the Absence of DNA Damage.

Lopez-Martinez D, Kupculak M, Yang D, Yoshikawa Y, Liang CC, Wu R, Gygi SP, Cohn MA.

Cell Rep. 2019 Jun 4;27(10):2990-3005.e5. doi: 10.1016/j.celrep.2019.05.003.

16.

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
17.

Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program.

Kikani CK, Wu X, Fogarty S, Kang SAW, Dephoure N, Gygi SP, Sabatini DM, Rutter J.

Proc Natl Acad Sci U S A. 2019 May 21;116(21):10382-10391. doi: 10.1073/pnas.1804013116. Epub 2019 May 9.

18.

Dual Sensing of Physiologic pH and Calcium by EFCAB9 Regulates Sperm Motility.

Hwang JY, Mannowetz N, Zhang Y, Everley RA, Gygi SP, Bewersdorf J, Lishko PV, Chung JJ.

Cell. 2019 May 30;177(6):1480-1494.e19. doi: 10.1016/j.cell.2019.03.047. Epub 2019 May 2.

PMID:
31056283
19.

ER and Nutrient Stress Promote Assembly of Respiratory Chain Supercomplexes through the PERK-eIF2α Axis.

Balsa E, Soustek MS, Thomas A, Cogliati S, García-Poyatos C, Martín-García E, Jedrychowski M, Gygi SP, Enriquez JA, Puigserver P.

Mol Cell. 2019 Jun 6;74(5):877-890.e6. doi: 10.1016/j.molcel.2019.03.031. Epub 2019 Apr 22.

PMID:
31023583
20.

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
21.

Targeted Degradation of Glucose Transporters Protects against Arsenic Toxicity.

Jochem M, Ende L, Isasa M, Ang J, Schnell H, Guerra-Moreno A, Micoogullari Y, Bhanu M, Gygi SP, Hanna J.

Mol Cell Biol. 2019 Apr 30;39(10). pii: e00559-18. doi: 10.1128/MCB.00559-18. Print 2019 May 15.

22.

Regulation of MicroRNA Machinery and Development by Interspecies S-Nitrosylation.

Seth P, Hsieh PN, Jamal S, Wang L, Gygi SP, Jain MK, Coller J, Stamler JS.

Cell. 2019 Feb 21;176(5):1014-1025.e12. doi: 10.1016/j.cell.2019.01.037.

PMID:
30794773
23.

Author Correction: Sin1 phosphorylation impairs mTORC2 complex integrity and inhibits downstream Akt signalling to suppress tumorigenesis.

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, Lee TH, Asara JM, Manning BD, Blenis J, Su B, Wei W.

Nat Cell Biol. 2019 May;21(5):662-663. doi: 10.1038/s41556-019-0280-y.

PMID:
30783264
24.

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
25.

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
26.

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
27.

Mitotic regulators TPX2 and Aurora A protect DNA forks during replication stress by counteracting 53BP1 function.

Byrum AK, Carvajal-Maldonado D, Mudge MC, Valle-Garcia D, Majid MC, Patel R, Sowa ME, Gygi SP, Harper JW, Shi Y, Vindigni A, Mosammaparast N.

J Cell Biol. 2019 Feb 4;218(2):422-432. doi: 10.1083/jcb.201803003. Epub 2019 Jan 2.

28.

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.

29.

TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays.

Rose CM, Erickson BK, Schweppe DK, Viner R, Choi J, Rogers J, Bomgarden R, Gygi SP, Kirkpatrick DS.

J Proteome Res. 2019 Feb 1;18(2):594-605. doi: 10.1021/acs.jproteome.8b00767. Epub 2018 Dec 12.

PMID:
30501201
30.

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.

31.

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.

32.

Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma.

Zhou S, Appleman VA, Rose CM, Jun HJ, Yang J, Zhou Y, Bronson RT, Gygi SP, Charest A.

Life Sci Alliance. 2018 Jun 19;1(3):e201800029. doi: 10.26508/lsa.201800029. eCollection 2018 Jun.

33.

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.

34.

The neurodegenerative diseases ALS and SMA are linked at the molecular level via the ASC-1 complex.

Chi B, O'Connell JD, Iocolano AD, Coady JA, Yu Y, Gangopadhyay J, Gygi SP, Reed R.

Nucleic Acids Res. 2018 Dec 14;46(22):11939-11951. doi: 10.1093/nar/gky1093.

35.

Identification of UHRF2 as a novel DNA interstrand crosslink sensor protein.

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.

PLoS Genet. 2018 Oct 18;14(10):e1007643. doi: 10.1371/journal.pgen.1007643. eCollection 2018 Oct.

36.

Proteomic profiling of yeast heterochromatin connects direct physical and genetic interactions.

Zukowski A, Phillips J, Park S, Wu R, Gygi SP, Johnson AM.

Curr Genet. 2019 Apr;65(2):495-505. doi: 10.1007/s00294-018-0889-6. Epub 2018 Oct 12.

PMID:
30310994
37.

Apolipoprotein E is a pancreatic extracellular factor that maintains mature β-cell gene expression.

Mahmoud AI, Galdos FX, Dinan KA, Jedrychowski MP, Davis JC, Vujic A, Rachmin I, Shigley C, Pancoast JR, Lee S, Hollister-Lock J, MacGillivray CM, Gygi SP, Melton DA, Weir GC, Lee RT.

PLoS One. 2018 Oct 10;13(10):e0204595. doi: 10.1371/journal.pone.0204595. eCollection 2018.

38.

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.

39.

Erythrocytes lacking the Langereis blood group protein ABCB6 are resistant to the malaria parasite Plasmodium falciparum.

Egan ES, Weekes MP, Kanjee U, Manzo J, Srinivasan A, Lomas-Francis C, Westhoff C, Takahashi J, Tanaka M, Watanabe S, Brugnara C, Gygi SP, Tani Y, Duraisingh MT.

Commun Biol. 2018 May 3;1:45. doi: 10.1038/s42003-018-0046-2. eCollection 2018.

40.

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.

41.

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.

42.

Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells.

Di Stefano B, Ueda M, Sabri S, Brumbaugh J, Huebner AJ, Sahakyan A, Clement K, Clowers KJ, Erickson AR, Shioda K, Gygi SP, Gu H, Shioda T, Meissner A, Takashima Y, Plath K, Hochedlinger K.

Nat Methods. 2018 Sep;15(9):732-740. doi: 10.1038/s41592-018-0104-1. Epub 2018 Aug 20.

43.

ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly.

Van Vranken JG, Nowinski SM, Clowers KJ, Jeong MY, Ouyang Y, Berg JA, Gygi JP, Gygi SP, Winge DR, Rutter J.

Mol Cell. 2018 Aug 16;71(4):567-580.e4. doi: 10.1016/j.molcel.2018.06.039.

44.

A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine.

Jun HJ, Appleman VA, Wu HJ, Rose CM, Pineda JJ, Yeo AT, Delcuze B, Lee C, Gyuris A, Zhu H, Woolfenden S, Bronisz A, Nakano I, Chiocca EA, Bronson RT, Ligon KL, Sarkaria JN, Gygi SP, Michor F, Mitchison TJ, Charest A.

Nat Commun. 2018 Aug 6;9(1):3116. doi: 10.1038/s41467-018-05036-4.

45.

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.

46.

Accumulation of succinate controls activation of adipose tissue thermogenesis.

Mills EL, Pierce KA, Jedrychowski MP, Garrity R, Winther S, Vidoni S, Yoneshiro T, Spinelli JB, Lu GZ, Kazak L, Banks AS, Haigis MC, Kajimura S, Murphy MP, Gygi SP, Clish CB, Chouchani ET.

Nature. 2018 Aug;560(7716):102-106. doi: 10.1038/s41586-018-0353-2. Epub 2018 Jul 18.

PMID:
30022159
47.

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.

48.

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.

49.

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.

50.

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.

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