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Items: 20

1.

Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers.

Goldstein LD, Lee J, Gnad F, Klijn C, Schaub A, Reeder J, Daemen A, Bakalarski CE, Holcomb T, Shames DS, Hartmaier RJ, Chmielecki J, Seshagiri S, Gentleman R, Stokoe D.

Cell Rep. 2016 Sep 6;16(10):2605-2617. doi: 10.1016/j.celrep.2016.08.010. Epub 2016 Aug 25.

2.

Rapid, semi-automated protein terminal characterization using ISDetect.

Bakalarski CE, Gan Y, Wertz I, Lill JR, Sandoval W.

Nat Biotechnol. 2016 Aug 9;34(8):811-3. doi: 10.1038/nbt.3621. No abstract available.

PMID:
27504771
3.

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.

4.

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
5.

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
6.

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.

7.

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.

8.

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.

9.

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
10.

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.

11.

The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

Bakalarski CE, Elias JE, Villén J, Haas W, Gerber SA, Everley PA, Gygi SP.

J Proteome Res. 2008 Nov;7(11):4756-65. doi: 10.1021/pr800333e. Epub 2008 Sep 18.

12.

A quantitative atlas of mitotic phosphorylation.

Dephoure N, Zhou C, Villén J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP.

Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi: 10.1073/pnas.0805139105. Epub 2008 Jul 31.

13.

Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.

Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ.

Cell. 2007 Dec 14;131(6):1190-203.

14.

The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics.

Bakalarski CE, Haas W, Dephoure NE, Gygi SP.

Anal Bioanal Chem. 2007 Nov;389(5):1409-19. Epub 2007 Sep 14.

PMID:
17874083
15.

ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.

Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ.

Science. 2007 May 25;316(5828):1160-6.

16.

Catch-and-release reagents for broadscale quantitative proteomics analyses.

Gartner CA, Elias JE, Bakalarski CE, Gygi SP.

J Proteome Res. 2007 Apr;6(4):1482-91. Epub 2007 Feb 21.

PMID:
17311443
17.

Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation.

Everley PA, Bakalarski CE, Elias JE, Waghorne CG, Beausoleil SA, Gerber SA, Faherty BK, Zetter BR, Gygi SP.

J Proteome Res. 2006 May;5(5):1224-31.

PMID:
16674112
18.

Optimization and use of peptide mass measurement accuracy in shotgun proteomics.

Haas W, Faherty BK, Gerber SA, Elias JE, Beausoleil SA, Bakalarski CE, Li X, Villén J, Gygi SP.

Mol Cell Proteomics. 2006 Jul;5(7):1326-37. Epub 2006 Apr 23.

19.

Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon.

Neher SB, Villén J, Oakes EC, Bakalarski CE, Sauer RT, Gygi SP, Baker TA.

Mol Cell. 2006 Apr 21;22(2):193-204.

20.

A proteomic strategy for gaining insights into protein sumoylation in yeast.

Denison C, Rudner AD, Gerber SA, Bakalarski CE, Moazed D, Gygi SP.

Mol Cell Proteomics. 2005 Mar;4(3):246-54. Epub 2004 Nov 12.

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