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Items: 37

1.

Residual tissue repositories as a resource for population-based cancer proteomic studies.

Piehowski PD, Petyuk VA, Sontag RL, Gritsenko MA, Weitz KK, Fillmore TL, Moon J, Makhlouf H, Chuaqui RF, Boja ES, Rodriguez H, Lee JSH, Smith RD, Carrick DM, Liu T, Rodland KD.

Clin Proteomics. 2018 Aug 3;15:26. doi: 10.1186/s12014-018-9202-4. eCollection 2018.

2.

Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk.

Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G, Boja ES, Rodriguez H, Kelleher NL.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4140-4145. doi: 10.1073/pnas.1716122115. Epub 2018 Apr 2.

3.

How many human proteoforms are there?

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B.

Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.

4.

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.

Wang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJ, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B.

Mol Cell Proteomics. 2017 Jan;16(1):121-134. doi: 10.1074/mcp.M116.060301. Epub 2016 Nov 11.

5.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators.

Cell. 2016 Jul 28;166(3):755-765. doi: 10.1016/j.cell.2016.05.069. Epub 2016 Jun 29.

6.

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.

Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC.

J Proteome Res. 2016 Mar 4;15(3):691-706. doi: 10.1021/acs.jproteome.5b00859. Epub 2015 Dec 22.

7.

Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts.

Ntai I, LeDuc RD, Fellers RT, Erdmann-Gilmore P, Davies SR, Rumsey J, Early BP, Thomas PM, Li S, Compton PD, Ellis MJ, Ruggles KV, Fenyö D, Boja ES, Rodriguez H, Townsend RR, Kelleher NL.

Mol Cell Proteomics. 2016 Jan;15(1):45-56. doi: 10.1074/mcp.M114.047480. Epub 2015 Oct 26.

8.

Four areas of engagement requiring strengthening in modern proteomics today.

Fehniger TE, Boja ES, Rodriguez H, Baker MS, Marko-Varga G.

J Proteome Res. 2014 Dec 5;13(12):5310-8. doi: 10.1021/pr500472d. Epub 2014 Nov 18.

PMID:
25405748
9.

Biorepository regulatory frameworks: building parallel resources that both promote scientific investigation and protect human subjects.

Marko-Varga G, Baker MS, Boja ES, Rodriguez H, Fehniger TE.

J Proteome Res. 2014 Dec 5;13(12):5319-24. doi: 10.1021/pr500475q. Epub 2014 Nov 18. Review.

PMID:
25277501
10.

Linking cancer genome to proteome: NCI's investment into proteogenomics.

Rivers RC, Kinsinger C, Boja ES, Hiltke T, Mesri M, Rodriguez H.

Proteomics. 2014 Dec;14(23-24):2633-6. doi: 10.1002/pmic.201400193. Epub 2014 Oct 18.

PMID:
25187343
11.

Analytical validation considerations of multiplex mass-spectrometry-based proteomic platforms for measuring protein biomarkers.

Boja ES, Fehniger TE, Baker MS, Marko-Varga G, Rodriguez H.

J Proteome Res. 2014 Dec 5;13(12):5325-32. doi: 10.1021/pr500753r. Epub 2014 Nov 18. Review.

12.

Proteogenomic convergence for understanding cancer pathways and networks.

Boja ES, Rodriguez H.

Clin Proteomics. 2014 Jun 1;11(1):22. doi: 10.1186/1559-0275-11-22. eCollection 2014. Review.

13.

Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies.

Skates SJ, Gillette MA, LaBaer J, Carr SA, Anderson L, Liebler DC, Ransohoff D, Rifai N, Kondratovich M, Težak Ž, Mansfield E, Oberg AL, Wright I, Barnes G, Gail M, Mesri M, Kinsinger CR, Rodriguez H, Boja ES.

J Proteome Res. 2013 Dec 6;12(12):5383-94. doi: 10.1021/pr400132j. Epub 2013 Oct 28.

14.

Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins.

Boja ES, Rodriguez H.

Proteomics. 2012 Apr;12(8):1093-110. doi: 10.1002/pmic.201100387. Review.

PMID:
22577011
15.

Regulatory considerations for clinical mass spectrometry: multiple reaction monitoring.

Boja ES, Rodriguez H.

Clin Lab Med. 2011 Sep;31(3):443-53. doi: 10.1016/j.cll.2011.07.001. No abstract available.

PMID:
21907108
16.

The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science.

Boja ES, Rodriguez H.

Korean J Lab Med. 2011 Apr;31(2):61-71. doi: 10.3343/kjlm.2011.31.2.61. Review.

17.

The journey to regulation of protein-based multiplex quantitative assays.

Boja ES, Jortani SA, Ritchie J, Hoofnagle AN, Težak Ž, Mansfield E, Keller P, Rivers RC, Rahbar A, Anderson NL, Srinivas P, Rodriguez H.

Clin Chem. 2011 Apr;57(4):560-7. doi: 10.1373/clinchem.2010.156034. Epub 2011 Feb 7.

18.

Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells.

Rinschen MM, Yu MJ, Wang G, Boja ES, Hoffert JD, Pisitkun T, Knepper MA.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3882-7. doi: 10.1073/pnas.0910646107. Epub 2010 Feb 5.

19.

Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct.

Bansal AD, Hoffert JD, Pisitkun T, Hwang S, Chou CL, Boja ES, Wang G, Knepper MA.

J Am Soc Nephrol. 2010 Feb;21(2):303-15. doi: 10.1681/ASN.2009070728. Epub 2010 Jan 14.

20.

Quantitative mitochondrial phosphoproteomics using iTRAQ on an LTQ-Orbitrap with high energy collision dissociation.

Boja ES, Phillips D, French SA, Harris RA, Balaban RS.

J Proteome Res. 2009 Oct;8(10):4665-75. doi: 10.1021/pr900387b.

21.

Use of (32)P to study dynamics of the mitochondrial phosphoproteome.

Aponte AM, Phillips D, Hopper RK, Johnson DT, Harris RA, Blinova K, Boja ES, French S, Balaban RS.

J Proteome Res. 2009 Jun;8(6):2679-95. doi: 10.1021/pr800913j.

22.

Mitochondrial NADH fluorescence is enhanced by complex I binding.

Blinova K, Levine RL, Boja ES, Griffiths GL, Shi ZD, Ruddy B, Balaban RS.

Biochemistry. 2008 Sep 9;47(36):9636-45. doi: 10.1021/bi800307y. Epub 2008 Aug 15.

23.
24.

Regulation of ASAP1 by phospholipids is dependent on the interface between the PH and Arf GAP domains.

Che MM, Boja ES, Yoon HY, Gruschus J, Jaffe H, Stauffer S, Schuck P, Fales HM, Randazzo PA.

Cell Signal. 2005 Oct;17(10):1276-88. Epub 2005 Feb 25.

PMID:
16038802
25.

Chronic morphine up-regulates G alpha12 and cytoskeletal proteins in Chinese hamster ovary cells expressing the cloned mu opioid receptor.

Xu H, Wang X, Zimmerman D, Boja ES, Wang J, Bilsky EJ, Rothman RB.

J Pharmacol Exp Ther. 2005 Oct;315(1):248-55. Epub 2005 Jun 29.

PMID:
15987828
26.

Human sperm do not bind to rat zonae pellucidae despite the presence of four homologous glycoproteins.

Hoodbhoy T, Joshi S, Boja ES, Williams SA, Stanley P, Dean J.

J Biol Chem. 2005 Apr 1;280(13):12721-31. Epub 2005 Jan 27.

27.
28.

Mass spectrometry analysis of recombinant human ZP3 expressed in glycosylation-deficient CHO cells.

Zhao M, Boja ES, Hoodbhoy T, Nawrocki J, Kaufman JB, Kresge N, Ghirlando R, Shiloach J, Pannell L, Levine RL, Fales HM, Dean J.

Biochemistry. 2004 Sep 28;43(38):12090-104.

PMID:
15379548
29.
30.

Roles of TRP14, a thioredoxin-related protein in tumor necrosis factor-alpha signaling pathways.

Jeong W, Chang TS, Boja ES, Fales HM, Rhee SG.

J Biol Chem. 2004 Jan 30;279(5):3151-9. Epub 2003 Nov 7.

31.

Specific regulation of the adaptor protein complex AP-3 by the Arf GAP AGAP1.

Nie Z, Boehm M, Boja ES, Vass WC, Bonifacino JS, Fales HM, Randazzo PA.

Dev Cell. 2003 Sep;5(3):513-21.

32.

A homologue of elongation factor 1 gamma regulates methionine sulfoxide reductase A gene expression in Saccharomyces cerevisiae.

Hanbauer I, Boja ES, Moskovitz J.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8199-204. Epub 2003 Jun 24.

33.

Structural characterization of native mouse zona pellucida proteins using mass spectrometry.

Boja ES, Hoodbhoy T, Fales HM, Dean J.

J Biol Chem. 2003 Sep 5;278(36):34189-202. Epub 2003 Jun 10.

34.

Role of proline residues in the folding of serine hydroxymethyltransferase.

Fu TF, Boja ES, Safo MK, Schirch V.

J Biol Chem. 2003 Aug 15;278(33):31088-94. Epub 2003 May 28.

35.

Reversible oxidative modification as a mechanism for regulating retroviral protease dimerization and activation.

Davis DA, Brown CA, Newcomb FM, Boja ES, Fales HM, Kaufman J, Stahl SJ, Wingfield P, Yarchoan R.

J Virol. 2003 Mar;77(5):3319-25.

36.

Reversible glutathionylation regulates actin polymerization in A431 cells.

Wang J, Boja ES, Tan W, Tekle E, Fales HM, English S, Mieyal JJ, Chock PB.

J Biol Chem. 2001 Dec 21;276(51):47763-6. Epub 2001 Oct 29.

37.

Overalkylation of a protein digest with iodoacetamide.

Boja ES, Fales HM.

Anal Chem. 2001 Aug 1;73(15):3576-82.

PMID:
11510821

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