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Items: 1 to 50 of 83

1.

The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification.

Abed M, Verschueren E, Budayeva H, Liu P, Kirkpatrick DS, Reja R, Kummerfeld SK, Webster JD, Gierke S, Reichelt M, Anderson KR, Newman RJ, Roose-Girma M, Modrusan Z, Pektas H, Maltepe E, Newton K, Dixit VM.

PLoS One. 2019 Apr 5;14(4):e0214110. doi: 10.1371/journal.pone.0214110. eCollection 2019.

2.

PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease.

Fleck D, Phu L, Verschueren E, Hinkle T, Reichelt M, Bhangale T, Haley B, Wang Y, Graham R, Kirkpatrick DS, Sheng M, Bingol B.

J Neurosci. 2019 Jun 12;39(24):4636-4656. doi: 10.1523/JNEUROSCI.0116-19.2019. Epub 2019 Apr 4.

PMID:
30948477
3.

Muscle specific kinase (MuSK) activation preserves neuromuscular junctions in the diaphragm but is not sufficient to provide a functional benefit in the SOD1G93A mouse model of ALS.

Sengupta-Ghosh A, Dominguez SL, Xie L, Barck KH, Jiang Z, Earr T, Imperio J, Phu L, Budayeva HG, Kirkpatrick DS, Cai H, Eastham-Anderson J, Ngu H, Foreman O, Hedehus M, Reichelt M, Hotzel I, Shang Y, Carano RAD, Ayalon G, Easton A.

Neurobiol Dis. 2019 Apr;124:340-352. doi: 10.1016/j.nbd.2018.12.002. Epub 2018 Dec 4.

PMID:
30528255
4.

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
5.

Interpreting the Language of Polyubiquitin with Linkage-Specific Antibodies and Mass Spectrometry.

Matsumoto ML, Castellanos ER, Zeng YJ, Kirkpatrick DS.

Methods Mol Biol. 2018;1844:385-400. doi: 10.1007/978-1-4939-8706-1_24.

PMID:
30242722
6.

OTULIN limits cell death and inflammation by deubiquitinating LUBAC.

Heger K, Wickliffe KE, Ndoja A, Zhang J, Murthy A, Dugger DL, Maltzman A, de Sousa E Melo F, Hung J, Zeng Y, Verschueren E, Kirkpatrick DS, Vucic D, Lee WP, Roose-Girma M, Newman RJ, Warming S, Hsiao YC, Kőműves LG, Webster JD, Newton K, Dixit VM.

Nature. 2018 Jul;559(7712):120-124. doi: 10.1038/s41586-018-0256-2. Epub 2018 Jun 27.

PMID:
29950720
7.

Disruption of XIAP-RIP2 Association Blocks NOD2-Mediated Inflammatory Signaling.

Goncharov T, Hedayati S, Mulvihill MM, Izrael-Tomasevic A, Zobel K, Jeet S, Fedorova AV, Eidenschenk C, deVoss J, Yu K, Shaw AS, Kirkpatrick DS, Fairbrother WJ, Deshayes K, Vucic D.

Mol Cell. 2018 Feb 15;69(4):551-565.e7. doi: 10.1016/j.molcel.2018.01.016.

8.

Selective autophagy of the adaptor TRIF regulates innate inflammatory signaling.

Samie M, Lim J, Verschueren E, Baughman JM, Peng I, Wong A, Kwon Y, Senbabaoglu Y, Hackney JA, Keir M, Mckenzie B, Kirkpatrick DS, van Lookeren Campagne M, Murthy A.

Nat Immunol. 2018 Mar;19(3):246-254. doi: 10.1038/s41590-017-0042-6. Epub 2018 Jan 22.

PMID:
29358708
9.

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.

10.

Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling pathways to the cell cycle.

Dogan T, Gnad F, Chan J, Phu L, Young A, Chen MJ, Doll S, Stokes MP, Belvin M, Friedman LS, Kirkpatrick DS, Hoeflich KP, Hatzivassiliou G.

J Biol Chem. 2017 Sep 1;292(35):14311-14324. doi: 10.1074/jbc.M117.792754. Epub 2017 Jun 27.

11.

Transcription factor Etv5 is essential for the maintenance of alveolar type II cells.

Zhang Z, Newton K, Kummerfeld SK, Webster J, Kirkpatrick DS, Phu L, Eastham-Anderson J, Liu J, Lee WP, Wu J, Li H, Junttila MR, Dixit VM.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):3903-3908. doi: 10.1073/pnas.1621177114. Epub 2017 Mar 28.

12.

Coordinated ubiquitination and phosphorylation of RIP1 regulates necroptotic cell death.

de Almagro MC, Goncharov T, Izrael-Tomasevic A, Duttler S, Kist M, Varfolomeev E, Wu X, Lee WP, Murray J, Webster JD, Yu K, Kirkpatrick DS, Newton K, Vucic D.

Cell Death Differ. 2017 Jan;24(1):26-37. doi: 10.1038/cdd.2016.78. Epub 2016 Aug 12.

13.

NeuCode Proteomics Reveals Bap1 Regulation of Metabolism.

Baughman JM, Rose CM, Kolumam G, Webster JD, Wilkerson EM, Merrill AE, Rhoads TW, Noubade R, Katavolos P, Lesch J, Stapleton DS, Rabaglia ME, Schueler KL, Asuncion R, Domeyer M, Zavala-Solorio J, Reich M, DeVoss J, Keller MP, Attie AD, Hebert AS, Westphall MS, Coon JJ, Kirkpatrick DS, Dey A.

Cell Rep. 2016 Jul 12;16(2):583-595. doi: 10.1016/j.celrep.2016.05.096. Epub 2016 Jun 30.

14.

Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network.

Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M.

Proteomics. 2016 Jul;16(14):1992-7. doi: 10.1002/pmic.201600118. Epub 2016 Jul 8.

PMID:
27282143
15.

A Biologist's Field Guide to Multiplexed Quantitative Proteomics.

Bakalarski CE, Kirkpatrick DS.

Mol Cell Proteomics. 2016 May;15(5):1489-97. doi: 10.1074/mcp.O115.056986. Epub 2016 Feb 12. Review.

16.

Application of Mass Spectrometry Profiling to Establish Brusatol as an Inhibitor of Global Protein Synthesis.

Vartanian S, Ma TP, Lee J, Haverty PM, Kirkpatrick DS, Yu K, Stokoe D.

Mol Cell Proteomics. 2016 Apr;15(4):1220-31. doi: 10.1074/mcp.M115.055509. Epub 2015 Dec 28.

17.

Discovery of Novel Blood-Brain Barrier Targets to Enhance Brain Uptake of Therapeutic Antibodies.

Zuchero YJ, Chen X, Bien-Ly N, Bumbaca D, Tong RK, Gao X, Zhang S, Hoyte K, Luk W, Huntley MA, Phu L, Tan C, Kallop D, Weimer RM, Lu Y, Kirkpatrick DS, Ernst JA, Chih B, Dennis MS, Watts RJ.

Neuron. 2016 Jan 6;89(1):70-82. doi: 10.1016/j.neuron.2015.11.024. Epub 2015 Dec 10.

18.

Immunoaffinity enrichment coupled to quantitative mass spectrometry reveals ubiquitin-mediated signaling events.

Yu K, Phu L, Varfolomeev E, Bustos D, Vucic D, Kirkpatrick DS.

J Mol Biol. 2015 Jun 5;427(11):2121-34. doi: 10.1016/j.jmb.2015.03.018. Epub 2015 Apr 8.

PMID:
25861760
19.

A novel reaction mediated by human aldehyde oxidase: amide hydrolysis of GDC-0834.

Sodhi JK, Wong S, Kirkpatrick DS, Liu L, Khojasteh SC, Hop CE, Barr JT, Jones JP, Halladay JS.

Drug Metab Dispos. 2015 Jun;43(6):908-15. doi: 10.1124/dmd.114.061804. Epub 2015 Apr 6.

20.

USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria.

Cunningham CN, Baughman JM, Phu L, Tea JS, Yu C, Coons M, Kirkpatrick DS, Bingol B, Corn JE.

Nat Cell Biol. 2015 Feb;17(2):160-9. doi: 10.1038/ncb3097. Epub 2015 Jan 26.

PMID:
25621951
21.

Deubiquitinase DUBA is a post-translational brake on interleukin-17 production in T cells.

Rutz S, Kayagaki N, Phung QT, Eidenschenk C, Noubade R, Wang X, Lesch J, Lu R, Newton K, Huang OW, Cochran AG, Vasser M, Fauber BP, DeVoss J, Webster J, Diehl L, Modrusan Z, Kirkpatrick DS, Lill JR, Ouyang W, Dixit VM.

Nature. 2015 Feb 19;518(7539):417-21. doi: 10.1038/nature13979. Epub 2014 Dec 3.

PMID:
25470037
22.

Ubiquitination profiling identifies sensitivity factors for IAP antagonist treatment.

Varfolomeev E, Izrael-Tomasevic A, Yu K, Bustos D, Goncharov T, Belmont LD, Masselot A, Bakalarski CE, Kirkpatrick DS, Vucic D.

Biochem J. 2015 Feb 15;466(1):45-54. doi: 10.1042/BJ20141195.

PMID:
25423073
23.

Overcoming EMT-associated resistance to anti-cancer drugs via Src/FAK pathway inhibition.

Wilson C, Nicholes K, Bustos D, Lin E, Song Q, Stephan JP, Kirkpatrick DS, Settleman J.

Oncotarget. 2014 Sep 15;5(17):7328-41.

24.

Interrogation of in vivo protein-protein interactions using transgenic mouse models and stable isotope labeling.

Dey A, Wu J, Kirkpatrick DS.

Methods Mol Biol. 2014;1176:179-90. doi: 10.1007/978-1-4939-0992-6_15.

PMID:
25030928
25.

Extended ubiquitin species are protein-based DUB inhibitors.

Krutauz D, Reis N, Nakasone MA, Siman P, Zhang D, Kirkpatrick DS, Gygi SP, Brik A, Fushman D, Glickman MH.

Nat Chem Biol. 2014 Aug;10(8):664-70. doi: 10.1038/nchembio.1574. Epub 2014 Jul 6.

26.

The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy.

Bingol B, Tea JS, Phu L, Reichelt M, Bakalarski CE, Song Q, Foreman O, Kirkpatrick DS, Sheng M.

Nature. 2014 Jun 19;510(7505):370-5. doi: 10.1038/nature13418. Epub 2014 Jun 4.

PMID:
24896179
27.

Phosphoproteomic characterization of DNA damage response in melanoma cells following MEK/PI3K dual inhibition.

Kirkpatrick DS, Bustos DJ, Dogan T, Chan J, Phu L, Young A, Friedman LS, Belvin M, Song Q, Bakalarski CE, Hoeflich KP.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19426-31. doi: 10.1073/pnas.1309473110. Epub 2013 Nov 11. Erratum in: Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):562.

28.

Dual leucine zipper kinase is required for excitotoxicity-induced neuronal degeneration.

Pozniak CD, Sengupta Ghosh A, Gogineni A, Hanson JE, Lee SH, Larson JL, Solanoy H, Bustos D, Li H, Ngu H, Jubb AM, Ayalon G, Wu J, Scearce-Levie K, Zhou Q, Weimer RM, Kirkpatrick DS, Lewcock JW.

J Exp Med. 2013 Nov 18;210(12):2553-67. doi: 10.1084/jem.20122832. Epub 2013 Oct 28.

29.

Peptide level immunoaffinity enrichment enhances ubiquitination site identification on individual proteins.

Anania VG, Pham VC, Huang X, Masselot A, Lill JR, Kirkpatrick DS.

Mol Cell Proteomics. 2014 Jan;13(1):145-56. doi: 10.1074/mcp.M113.031062. Epub 2013 Oct 18.

30.

JNK-mediated phosphorylation of DLK suppresses its ubiquitination to promote neuronal apoptosis.

Huntwork-Rodriguez S, Wang B, Watkins T, Ghosh AS, Pozniak CD, Bustos D, Newton K, Kirkpatrick DS, Lewcock JW.

J Cell Biol. 2013 Sep 2;202(5):747-63. doi: 10.1083/jcb.201303066. Epub 2013 Aug 26.

31.

Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling.

Phillips AH, Zhang Y, Cunningham CN, Zhou L, Forrest WF, Liu PS, Steffek M, Lee J, Tam C, Helgason E, Murray JM, Kirkpatrick DS, Fairbrother WJ, Corn JE.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11379-84. doi: 10.1073/pnas.1302407110. Epub 2013 Jun 25.

32.

OTUB1 modulates c-IAP1 stability to regulate signalling pathways.

Goncharov T, Niessen K, de Almagro MC, Izrael-Tomasevic A, Fedorova AV, Varfolomeev E, Arnott D, Deshayes K, Kirkpatrick DS, Vucic D.

EMBO J. 2013 Apr 17;32(8):1103-14. doi: 10.1038/emboj.2013.62. Epub 2013 Mar 22.

33.

A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway.

Anania VG, Bustos DJ, Lill JR, Kirkpatrick DS, Coscoy L.

Int J Proteomics. 2013;2013:857918. doi: 10.1155/2013/857918. Epub 2013 Feb 3.

34.

HectD1 E3 ligase modifies adenomatous polyposis coli (APC) with polyubiquitin to promote the APC-axin interaction.

Tran H, Bustos D, Yeh R, Rubinfeld B, Lam C, Shriver S, Zilberleyb I, Lee MW, Phu L, Sarkar AA, Zohn IE, Wertz IE, Kirkpatrick DS, Polakis P.

J Biol Chem. 2013 Feb 8;288(6):3753-67. doi: 10.1074/jbc.M112.415240. Epub 2012 Dec 31.

35.

Ser1292 autophosphorylation is an indicator of LRRK2 kinase activity and contributes to the cellular effects of PD mutations.

Sheng Z, Zhang S, Bustos D, Kleinheinz T, Le Pichon CE, Dominguez SL, Solanoy HO, Drummond J, Zhang X, Ding X, Cai F, Song Q, Li X, Yue Z, van der Brug MP, Burdick DJ, Gunzner-Toste J, Chen H, Liu X, Estrada AA, Sweeney ZK, Scearce-Levie K, Moffat JG, Kirkpatrick DS, Zhu H.

Sci Transl Med. 2012 Dec 12;4(164):164ra161. doi: 10.1126/scitranslmed.3004485.

36.

Loss of the tumor suppressor BAP1 causes myeloid transformation.

Dey A, Seshasayee D, Noubade R, French DM, Liu J, Chaurushiya MS, Kirkpatrick DS, Pham VC, Lill JR, Bakalarski CE, Wu J, Phu L, Katavolos P, LaFave LM, Abdel-Wahab O, Modrusan Z, Seshagiri S, Dong K, Lin Z, Balazs M, Suriben R, Newton K, Hymowitz S, Garcia-Manero G, Martin F, Levine RL, Dixit VM.

Science. 2012 Sep 21;337(6101):1541-6. Epub 2012 Aug 9.

37.

Characterizing ubiquitination sites by peptide-based immunoaffinity enrichment.

Bustos D, Bakalarski CE, Yang Y, Peng J, Kirkpatrick DS.

Mol Cell Proteomics. 2012 Dec;11(12):1529-40. doi: 10.1074/mcp.R112.019117. Epub 2012 Jun 23. Review.

38.

Complementary proteomic tools for the dissection of apoptotic proteolysis events.

Pham VC, Pitti R, Anania VG, Bakalarski CE, Bustos D, Jhunjhunwala S, Phung QT, Yu K, Forrest WF, Kirkpatrick DS, Ashkenazi A, Lill JR.

J Proteome Res. 2012 May 4;11(5):2947-54. doi: 10.1021/pr300035k. Epub 2012 Mar 29.

PMID:
22432722
39.

APC/C-mediated multiple monoubiquitylation provides an alternative degradation signal for cyclin B1.

Dimova NV, Hathaway NA, Lee BH, Kirkpatrick DS, Berkowitz ML, Gygi SP, Finley D, King RW.

Nat Cell Biol. 2012 Jan 29;14(2):168-76. doi: 10.1038/ncb2425.

40.

Engineering and structural characterization of a linear polyubiquitin-specific antibody.

Matsumoto ML, Dong KC, Yu C, Phu L, Gao X, Hannoush RN, Hymowitz SG, Kirkpatrick DS, Dixit VM, Kelley RF.

J Mol Biol. 2012 May 4;418(3-4):134-44. doi: 10.1016/j.jmb.2011.12.053. Epub 2011 Dec 29.

41.

Preparation of distinct ubiquitin chain reagents of high purity and yield.

Dong KC, Helgason E, Yu C, Phu L, Arnott DP, Bosanac I, Compaan DM, Huang OW, Fedorova AV, Kirkpatrick DS, Hymowitz SG, Dueber EC.

Structure. 2011 Aug 10;19(8):1053-63. doi: 10.1016/j.str.2011.06.010.

42.

Ubiquitin ligase RNF146 regulates tankyrase and Axin to promote Wnt signaling.

Callow MG, Tran H, Phu L, Lau T, Lee J, Sandoval WN, Liu PS, Bheddah S, Tao J, Lill JR, Hongo JA, Davis D, Kirkpatrick DS, Polakis P, Costa M.

PLoS One. 2011;6(7):e22595. doi: 10.1371/journal.pone.0022595. Epub 2011 Jul 25.

43.

Deubiquitinase USP37 is activated by CDK2 to antagonize APC(CDH1) and promote S phase entry.

Huang X, Summers MK, Pham V, Lill JR, Liu J, Lee G, Kirkpatrick DS, Jackson PK, Fang G, Dixit VM.

Mol Cell. 2011 May 20;42(4):511-23. doi: 10.1016/j.molcel.2011.03.027.

44.

A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis.

Ziv I, Matiuhin Y, Kirkpatrick DS, Erpapazoglou Z, Leon S, Pantazopoulou M, Kim W, Gygi SP, Haguenauer-Tsapis R, Reis N, Glickman MH, Kleifeld O.

Mol Cell Proteomics. 2011 May;10(5):M111.009753. doi: 10.1074/mcp.M111.009753. Epub 2011 Mar 22.

45.

Modulation of K11-linkage formation by variable loop residues within UbcH5A.

Bosanac I, Phu L, Pan B, Zilberleyb I, Maurer B, Dixit VM, Hymowitz SG, Kirkpatrick DS.

J Mol Biol. 2011 May 6;408(3):420-31. doi: 10.1016/j.jmb.2011.03.011. Epub 2011 Mar 10.

PMID:
21396940
46.

Primary cilia membrane assembly is initiated by Rab11 and transport protein particle II (TRAPPII) complex-dependent trafficking of Rabin8 to the centrosome.

Westlake CJ, Baye LM, Nachury MV, Wright KJ, Ervin KE, Phu L, Chalouni C, Beck JS, Kirkpatrick DS, Slusarski DC, Sheffield VC, Scheller RH, Jackson PK.

Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2759-64. doi: 10.1073/pnas.1018823108. Epub 2011 Jan 27.

47.

A novel acetylation of β-tubulin by San modulates microtubule polymerization via down-regulating tubulin incorporation.

Chu CW, Hou F, Zhang J, Phu L, Loktev AV, Kirkpatrick DS, Jackson PK, Zhao Y, Zou H.

Mol Biol Cell. 2011 Feb 15;22(4):448-56. doi: 10.1091/mbc.E10-03-0203. Epub 2010 Dec 22.

48.

c-IAP1 and UbcH5 promote K11-linked polyubiquitination of RIP1 in TNF signalling.

Dynek JN, Goncharov T, Dueber EC, Fedorova AV, Izrael-Tomasevic A, Phu L, Helgason E, Fairbrother WJ, Deshayes K, Kirkpatrick DS, Vucic D.

EMBO J. 2010 Dec 15;29(24):4198-209. doi: 10.1038/emboj.2010.300. Epub 2010 Nov 26.

49.

Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling.

Bosanac I, Wertz IE, Pan B, Yu C, Kusam S, Lam C, Phu L, Phung Q, Maurer B, Arnott D, Kirkpatrick DS, Dixit VM, Hymowitz SG.

Mol Cell. 2010 Nov 24;40(4):548-57. doi: 10.1016/j.molcel.2010.10.009.

50.

Improved quantitative mass spectrometry methods for characterizing complex ubiquitin signals.

Phu L, Izrael-Tomasevic A, Matsumoto ML, Bustos D, Dynek JN, Fedorova AV, Bakalarski CE, Arnott D, Deshayes K, Dixit VM, Kelley RF, Vucic D, Kirkpatrick DS.

Mol Cell Proteomics. 2011 May;10(5):M110.003756. doi: 10.1074/mcp.M110.003756. Epub 2010 Nov 3.

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