‌Publications

Histone Deacetylase Inhibitors Potentiate Vesicular Stomatitis Virus Oncolysis in Prostate Cancer Cells by Modulating NF-κB-Dependent Autophagy.
Shulak L, Beljanski V, Chiang C, Dutta SM, Van Grevenynghe J, Belgnaoui SM, Nguyên TL, Di Lenardo T, Semmes OJ, Lin R, Hiscott J.
J Virol. 2014 Mar;88(5):2927-40. doi: 10.1128/JVI.03406-13. Epub 2013 Dec 26.
PMID: 24371063
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miR-888 is an expressed prostatic secretions-derived microRNA that promotes prostate cell growth and migration.
Lewis H, Lance R, Troyer D, Beydoun H, Hadley M, Orians J, Benzine T, Madric K, Semmes OJ, Drake R, Esquela-Kerscher A.
Cell Cycle. 2014 Jan 15;13(2):227-39. doi: 10.4161/cc.26984. Epub 2013 Nov 7.
PMID: 24200968
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Histone Deacetylase Inhibitors Potentiate Vesicular Stomatitis Virus Oncolysis in Prostate Cancer Cells by Modulating NF-κB-Dependent Autophagy.
Shulak L, Beljanski V, Chiang C, Dutta SM, Van Grevenynghe J, Belgnaoui SM, Nguyên TL, Di Lenardo T, Semmes OJ, Lin R, Hiscott J.
J Virol. 2014 Mar;88(5):2927-40. doi: 10.1128/JVI.03406-13. Epub 2013 Dec 26.
PMID: 24371063
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Restriction of virus infection but not catalytic dNTPase activity is regulated by phosphorylation of SAMHD1.
Welbourn S, Dutta SM, Semmes OJ, Strebel K.
J Virol. 2013 Nov;87(21):11516-24. doi: 10.1128/JVI.01642-13. Epub 2013 Aug 21.
PMID: 23966382
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Methyltransferase PRMT1 is a binding partner of HBx and a negative regulator of hepatitis B virus transcription.
Benhenda S, Ducroux A, Rivière L, Sobhian B, Ward MD, Dion S, Hantz O, Protzer U, Michel ML, Benkirane M, Semmes OJ, Buendia MA, Neuveut C.
J Virol. 2013 Apr;87(8):4360-71. doi: 10.1128/JVI.02574-12. Epub 2013 Feb 6.
PMID: 23388725
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Focus on cancer proteomics.
Semmes OJ, Conrads T.
Proteomics Clin Appl. 2013 Jun;7(5-6):315. doi: 10.1002/prca.201370034. No abstract available.
PMID: 23780814
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Increased bisecting N-acetylglucosamine and decreased branched chain glycans of N-linked glycoproteins in expressed prostatic secretions associated with prostate cancer progression.
Nyalwidhe JO, Betesh LR, Powers TW, Jones EE, White KY, Burch TC, Brooks J, Watson MT, Lance RS, Troyer DA, Semmes OJ, Mehta A, Drake RR.
Proteomics Clin Appl. 2013 Jun 17. doi: 10.1002/prca.201200134.
PMID: 23775902
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In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.
Principe S, Jones EE, Kim Y, Sinha A, Nyalwidhe JO, Brooks J, Semmes OJ, Troyer DA, Lance RS, Kislinger T, Drake RR.
Proteomics. 2013 May;13(10-11):1667-71. doi: 10.1002/pmic.201200561. Epub 2013 Apr 23.
PMID: 23533145
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The search for biomarkers of human embryo developmental potential in IVF: a comprehensive proteomic approach.
Nyalwidhe J, Burch T, Bocca S, Cazares L, Green-Mitchell S, Cooke M, Birdsall P, Basu G, Semmes OJ, Oehninger S.
Mol Hum Reprod. 2013 Apr;19(4):250-63. doi: 10.1093/molehr/gas063. Epub 2012 Dec 17.
PMID: 23247814
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Restriction of virus infection but not catalytic dNTPase activity is regulated by phosphorylation of SAMHD1.
Welbourn S, Dutta SM, Semmes OJ, Strebel K.
J Virol. 2013 Nov;87(21):11516-24. doi: 10.1128/JVI.01642-13. Epub 2013 Aug 21.
PMID: 23966382
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Increasing the productivity of glycopeptides analysis by using higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation.
Saba J, Dutta S, Hemenway E, Viner R.
Int J Proteomics. 2012;2012:560391. doi: 10.1155/2012/560391. Epub 2012 May 30.
PMID: 22701174
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Evaluation of an accurate mass approach for the simultaneous detection of drug and metabolite distributions via whole-body mass spectrometric imaging.
Shahidi-Latham SK, Dutta SM, Prieto Conaway MC, Rudewicz PJ.
Anal Chem. 2012 Aug 21;84(16):7158-65. doi: 10.1021/ac3015142. Epub 2012 Aug 7.
PMID: 22827834
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BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection.
Lee SH, Kalejta RF, Kerry J, Semmes OJ, O'Connor CM, Khan Z, Garcia BA, Shenk T, Murphy E.
Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9575-80. doi: 10.1073/pnas.1207496109. Epub 2012 May 29.
PMID: 22645331
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NADiA ProsVue prostate-specific antigen slope is an independent prognostic marker for identifying men at reduced risk of clinical recurrence of prostate cancer after radical prostatectomy.
Moul JW, Lilja H, Semmes OJ, Lance RS, Vessella RL, Fleisher M, Mazzola C, Sarno MJ, Stevens B, Klem RE, McDermed JE, Triebell MT, Adams TH.
Urology. 2012 Dec;80(6):1319-25. doi: 10.1016/j.urology.2012.06.080. Epub 2012 Oct 26.
PMID: 23107099
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Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer.
Kim Y, Ignatchenko V, Yao CQ, Kalatskaya I, Nyalwidhe JO, Lance RS, Gramolini AO, Troyer DA, Stein LD, Boutros PC, Medin JA, Semmes OJ, Drake RR, Kislinger T.
Mol Cell Proteomics. 2012 Dec;11(12):1870-84. doi: 10.1074/mcp.M112.017889. Epub 2012 Sep 17.
PMID: 22986220
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Proteomic and pathway analyses reveal a network of inflammatory genes associated with differences in skin tumor promotion susceptibility in DBA/2 and C57BL/6 mice.
Shen J, Abel EL, Riggs PK, Repass J, Hensley SC, Schroeder LJ, Temple A, Chau A, McClellan SA, Rho O, Kiguchi K, Ward MD, Semmes OJ, Person MD, Angel JM, Digiovanni J.
Carcinogenesis. 2012 Nov;33(11):2208-19. doi: 10.1093/carcin/bgs213. Epub 2012 Jul 10.
PMID: 22782996
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Identification of prostate-enriched proteins by in-depth proteomic analyses of expressed prostatic secretions in urine.
Principe S, Kim Y, Fontana S, Ignatchenko V, Nyalwidhe JO, Lance RS, Troyer DA, Alessandro R, Semmes OJ, Kislinger T, Drake RR, Medin JA.
J Proteome Res. 2012 Apr 6;11(4):2386-96. doi: 10.1021/pr2011236. Epub 2012 Feb 29.
PMID: 22339264
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The Sumo-targeted ubiquitin ligase RNF4 regulates the localization and function of the HTLV-1 oncoprotein Tax.
Fryrear KA, Guo X, Kerscher O, Semmes OJ.
Blood. 2012 Feb 2;119(5):1173-81. doi: 10.1182/blood-2011-06-358564. Epub 2011 Nov 21.
PMID: 22106342
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Tissue imaging using nanospray desorption electrospray ionization mass spectrometry.
Laskin J, Heath BS, Roach PJ, Cazares L, Semmes OJ.
Anal Chem. 2012 Jan 3;84(1):141-8. doi: 10.1021/ac2021322. Epub 2011 Dec 1.
PMID: 22098105
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Evaluation of an accurate mass approach for the simultaneous detection of drug and metabolite distributions via whole-body mass spectrometric imaging.
Shahidi-Latham SK, Dutta SM, Prieto Conaway MC, Rudewicz PJ.
Anal Chem. 2012 Aug 21;84(16):7158-65. doi: 10.1021/ac3015142. Epub 2012 Aug 7.
PMID: 22827834
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Increasing the productivity of glycopeptides analysis by using higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation.
Saba J, Dutta S, Hemenway E, Viner R.
Int J Proteomics. 2012;2012:560391. doi: 10.1155/2012/560391. Epub 2012 May 30.
PMID: 22701174
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In vivo solid-phase microextraction: capturing the elusive portion of metabolome.
Vuckovic D, de Lannoy I, Gien B, Shirey RE, Sidisky LM, Dutta S, Pawliszyn J.
Angew Chem Int Ed Engl. 2011 May 27;50(23):5344-8. doi: 10.1002/anie.201006715. Epub 2011 Apr 20. No abstract available.
PMID: 21509917
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Molecular Microscopy of Brain Gangliosides: Illustrating their Distribution in Hippocampal Cell Layers.
Colsch B, Jackson SN, Dutta S, Woods AS.
ACS Chem Neurosci. 2011 Feb 21;2(4):213-222.
PMID: 21961052
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A proteomic study of TAR-RNA binding protein (TRBP)-associated factors.
Chi YH, Semmes OJ, Jeang KT.
Cell Biosci. 2011 Feb 25;1(1):9. doi: 10.1186/2045-3701-1-9.
PMID: 21711701
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Functional and physical interaction between the mismatch repair and FA-BRCA pathways.
Williams SA, Wilson JB, Clark AP, Mitson-Salazar A, Tomashevski A, Ananth S, Glazer PM, Semmes OJ, Bale AE, Jones NJ, Kupfer GM.
Hum Mol Genet. 2011 Nov 15;20(22):4395-410. doi: 10.1093/hmg/ddr366. Epub 2011 Aug 24.
PMID: 21865299
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Using boronolectin in MALDI-MS imaging for the histological analysis of cancer tissue expressing the sialyl Lewis X antigen.
Dai C, Cazares LH, Wang L, Chu Y, Wang SL, Troyer DA, Semmes OJ, Drake RR, Wang B.
Chem Commun (Camb). 2011 Oct 7;47(37):10338-40. doi: 10.1039/c1cc11814e. Epub 2011 Aug 19.
PMID: 21853197
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Improved signal processing and normalization for biomarker protein detection in broad-mass-range TOF mass spectra from clinical samples.
Tracy MB, Cooke WE, Gatlin CL, Cazares LH, Weaver DM, Semmes OJ, Tracy ER, Manos DM, Malyarenko DI.
Proteomics Clin Appl. 2011 Aug;5(7-8):440-7. doi: 10.1002/prca.201000095. Epub 2011 Jul 13.
PMID: 21751409
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Direct and specific binding of the UL16 tegument protein of herpes simplex virus to the cytoplasmic tail of glycoprotein E.
Yeh PC, Han J, Chadha P, Meckes DG Jr, Ward MD, Semmes OJ, Wills JW.
J Virol. 2011 Sep;85(18):9425-36. doi: 10.1128/JVI.05178-11. Epub 2011 Jul 6.
PMID: 21734044
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Human endogenous retrovirus transcription profiles of the kidney and kidney-derived cell lines.
Haupt S, Tisdale M, Vincendeau M, Clements MA, Gauthier DT, Lance R, Semmes OJ, Turqueti-Neves A, Noessner E, Leib-Mösch C, Greenwood AD.
J Gen Virol. 2011 Oct;92(Pt 10):2356-66. doi: 10.1099/vir.0.031518-0. Epub 2011 Jun 22.
PMID: 21697344
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On-tissue identification of insulin: in situ reduction coupled with mass spectrometry imaging.
Green-Mitchell SM, Cazares LH, Semmes OJ, Nadler JL, Nyalwidhe JO.
Proteomics Clin Appl. 2011 Aug;5(7-8):448-53. doi: 10.1002/prca.201000152. Epub 2011 Jun 8.
PMID: 21656913
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MALDI tissue imaging: from biomarker discovery to clinical applications.
Cazares LH, Troyer DA, Wang B, Drake RR, Semmes OJ.
Anal Bioanal Chem. 2011 Jul;401(1):17-27. doi: 10.1007/s00216-011-5003-6. Epub 2011 May 4. Review.
PMID: 21541816
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Targeted identification of metastasis-associated cell-surface sialoglycoproteins in prostate cancer.
Yang L, Nyalwidhe JO, Guo S, Drake RR, Semmes OJ.
Mol Cell Proteomics. 2011 Jun;10(6):M110.007294. doi: 10.1074/mcp.M110.007294. Epub 2011 Mar 29.
PMID: 21447706
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Challenges to developing proteomic-based breast cancer diagnostics.
Drake RR, Cazares LH, Jones EE, Fuller TW, Semmes OJ, Laronga C.
OMICS. 2011 May;15(5):251-9. doi: 10.1089/omi.2010.0120. Epub 2011 Feb 19. Review.
PMID: 21332380
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Enhancement in MALDI-TOF MS analysis of the low molecular weight human serum proteome.
Gatlin CL, White KY, Tracy MB, Wilkins CE, Semmes OJ, Nyalwidhe JO, Drake RR, Malyarenko DI.
J Mass Spectrom. 2011 Jan;46(1):85-9. doi: 10.1002/jms.1864. No abstract available.
PMID: 21190259
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Molecular Microscopy of Brain Gangliosides: Illustrating their Distribution in Hippocampal Cell Layers.
Colsch B, Jackson SN, Dutta S, Woods AS.
ACS Chem Neurosci. 2011 Feb 21;2(4):213-222.
PMID: 21961052
Related citations 
 
In vivo solid-phase microextraction: capturing the elusive portion of metabolome.
Vuckovic D, de Lannoy I, Gien B, Shirey RE, Sidisky LM, Dutta S, Pawliszyn J.
Angew Chem Int Ed Engl. 2011 May 27;50(23):5344-8. doi: 10.1002/anie.201006715. Epub 2011 Apr 20. No abstract available.
PMID: 21509917
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Purification of FANCD2 sub-complexes.
Zhi G, Chen X, Newcomb W, Brown J, Semmes OJ, Kupfer GM.
Br J Haematol. 2010 Jul;150(1):88-92. doi: 10.1111/j.1365-2141.2010.08217.x. Epub 2010 Apr 29.
PMID: 20456353
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Investigation of sialylation aberration in N-linked glycopeptides by lectin and tandem labeling (LTL) quantitative proteomics.
Shetty V, Nickens Z, Shah P, Sinnathamby G, Semmes OJ, Philip R.
Anal Chem. 2010 Nov 15;82(22):9201-10. doi: 10.1021/ac101486d. Epub 2010 Oct 5.
PMID: 20923142
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Recommendations for biomarker identification and qualification in clinical proteomics.
Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, Benigni A, Bennett SE, Bischoff R, Bongcam-Rudloff E, Capasso G, Coon JJ, D'Haese P, Dominiczak AF, Dakna M, Dihazi H, Ehrich JH, Fernandez-Llama P, Fliser D, Frokiaer J, Garin J, Girolami M, Hancock WS, Haubitz M, Hochstrasser D, Holman RR, Ioannidis JP, Jankowski J, Julian BA, Klein JB, Kolch W, Luider T, Massy Z, Mattes WB, Molina F, Monsarrat B, Novak J, Peter K, Rossing P, Sánchez-Carbayo M, Schanstra JP, Semmes OJ, Spasovski G, Theodorescu D, Thongboonkerd V, Vanholder R, Veenstra TD, Weissinger E, Yamamoto T, Vlahou A.
Sci Transl Med. 2010 Aug 25;2(46):46ps42. doi: 10.1126/scitranslmed.3001249.
PMID: 20739680
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The viral oncoprotein tax sequesters DNA damage response factors by tethering MDC1 to chromatin.
Belgnaoui SM, Fryrear KA, Nyalwidhe JO, Guo X, Semmes OJ.
J Biol Chem. 2010 Oct 22;285(43):32897-905. doi: 10.1074/jbc.M110.146373. Epub 2010 Aug 20.
PMID: 20729195
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Interdependent phosphorylation within the kinase domain T-loop Regulates CHK2 activity.
Guo X, Ward MD, Tiedebohl JB, Oden YM, Nyalwidhe JO, Semmes OJ.
J Biol Chem. 2010 Oct 22;285(43):33348-57. doi: 10.1074/jbc.M110.149609. Epub 2010 Aug 16.
PMID: 20713355
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In-depth proteomic analyses of direct expressed prostatic secretions.
Drake RR, Elschenbroich S, Lopez-Perez O, Kim Y, Ignatchenko V, Ignatchenko A, Nyalwidhe JO, Basu G, Wilkins CE, Gjurich B, Lance RS, Semmes OJ, Medin JA, Kislinger T.
J Proteome Res. 2010 May 7;9(5):2109-16. doi: 10.1021/pr1001498.
PMID: 20334419
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Interaction domains of the UL16 and UL21 tegument proteins of herpes simplex virus.
Harper AL, Meckes DG Jr, Marsh JA, Ward MD, Yeh PC, Baird NL, Wilson CB, Semmes OJ, Wills JW.
J Virol. 2010 Mar;84(6):2963-71. doi: 10.1128/JVI.02015-09. Epub 2009 Dec 30.
PMID: 20042500
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The use of ECD/ETD to identify the site of electrostatic interaction in noncovalent complexes.
Jackson SN, Dutta S, Woods AS.
J Am Soc Mass Spectrom. 2009 Feb;20(2):176-9. doi: 10.1016/j.jasms.2008.08.021. Epub 2008 Sep 6.
PMID: 18835725
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Phosphorylation regulates human T-cell leukemia virus type 1 Rex function.
Kesic M, Doueiri R, Ward M, Semmes OJ, Green PL.
Retrovirology. 2009 Nov 17;6:105. doi: 10.1186/1742-4690-6-105.
PMID: 19919707
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Imaging mass spectrometry of a specific fragment of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase kinase 2 discriminates cancer from uninvolved prostate tissue.
Cazares LH, Troyer D, Mendrinos S, Lance RA, Nyalwidhe JO, Beydoun HA, Clements MA, Drake RR, Semmes OJ.
Clin Cancer Res. 2009 Sep 1;15(17):5541-51. doi: 10.1158/1078-0432.CCR-08-2892. Epub 2009 Aug 18.
PMID: 19690195
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Proteomic expression profiling and identification of serum proteins using immobilized trypsin beads with MALDI-TOF/TOF.
Karbassi ID, Nyalwidhe JO, Wilkins CE, Cazares LH, Lance RS, Semmes OJ, Drake RR.
J Proteome Res. 2009 Sep;8(9):4182-92. doi: 10.1021/pr800836c.
PMID: 19603828
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Site-specific phosphorylation regulates human T-cell leukemia virus type 2 Rex function in vivo.
Kesic M, Ward M, Semmes OJ, Green PL.
J Virol. 2009 Sep;83(17):8859-68. doi: 10.1128/JVI.00908-09. Epub 2009 Jun 24.
PMID: 19553333
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Serum proteomic biomarker discovery reflective of stage and obesity in breast cancer patients.
Schaub NP, Jones KJ, Nyalwidhe JO, Cazares LH, Karbassi ID, Semmes OJ, Feliberti EC, Perry RR, Drake RR.
J Am Coll Surg. 2009 May;208(5):970-8; discussion 978-80. doi: 10.1016/j.jamcollsurg.2008.12.024. Epub 2009 Mar 26.
PMID: 19476873
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Clinical collection and protein properties of expressed prostatic secretions as a source for biomarkers of prostatic disease.
Drake RR, White KY, Fuller TW, Igwe E, Clements MA, Nyalwidhe JO, Given RW, Lance RS, Semmes OJ.
J Proteomics. 2009 Aug 20;72(6):907-17. doi: 10.1016/j.jprot.2009.01.007. Epub 2009 Jan 20. Review.
PMID: 19457353
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Dimerization and a novel Tax speckled structure localization signal are required for Tax nuclear localization.
Fryrear KA, Durkin SS, Gupta SK, Tiedebohl JB, Semmes OJ.
J Virol. 2009 Jun;83(11):5339-52. doi: 10.1128/JVI.00232-09. Epub 2009 Mar 25.
PMID: 19321601
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Glycomic characterization of prostate-specific antigen and prostatic acid phosphatase in prostate cancer and benign disease seminal plasma fluids.
White KY, Rodemich L, Nyalwidhe JO, Comunale MA, Clements MA, Lance RS, Schellhammer PF, Mehta AS, Semmes OJ, Drake RR.
J Proteome Res. 2009 Feb;8(2):620-30. doi: 10.1021/pr8007545.
PMID: 19128049
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The use of ECD/ETD to identify the site of electrostatic interaction in noncovalent complexes.
Jackson SN, Dutta S, Woods AS.
J Am Soc Mass Spectrom. 2009 Feb;20(2):176-9. doi: 10.1016/j.jasms.2008.08.021. Epub 2008 Sep 6.
PMID: 18835725
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Physical and in silico approaches identify DNA-PK in a Tax DNA-damage response interactome.
Ramadan E, Ward M, Guo X, Durkin SS, Sawyer A, Vilela M, Osgood C, Pothen A, Semmes OJ.
Retrovirology. 2008 Oct 15;5:92. doi: 10.1186/1742-4690-5-92.
PMID: 18922151
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Human T-cell leukemia virus I tax protein sensitizes p53-mutant cells to DNA damage.
Mihaylova VT, Green AM, Khurgel M, Semmes OJ, Kupfer GM.
Cancer Res. 2008 Jun 15;68(12):4843-52. doi: 10.1158/0008-5472.CAN-07-5070.
PMID: 18559532
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HTLV-1 Tax oncoprotein subverts the cellular DNA damage response via binding to DNA-dependent protein kinase.
Durkin SS, Guo X, Fryrear KA, Mihaylova VT, Gupta SK, Belgnaoui SM, Haoudi A, Kupfer GM, Semmes OJ.
J Biol Chem. 2008 Dec 26;283(52):36311-20. doi: 10.1074/jbc.M804931200. Epub 2008 Oct 27.
PMID: 18957425
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Requirements for protein phosphorylation and the kinase activity of polo-like kinase 1 (Plk1) for the kinetochore function of mitotic arrest deficiency protein 1 (Mad1).
Chi YH, Haller K, Ward MD, Semmes OJ, Li Y, Jeang KT.
J Biol Chem. 2008 Dec 19;283(51):35834-44. doi: 10.1074/jbc.M804967200. Epub 2008 Oct 15.
PMID: 18922800
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National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines for use of tumor markers in clinical practice: quality requirements.
Sturgeon CM, Hoffman BR, Chan DW, Ch'ng SL, Hammond E, Hayes DF, Liotta LA, Petricoin EF, Schmitt M, Semmes OJ, Söletormos G, van der Merwe E, Diamandis EP; National Academy of Clinical Biochemistry.
Clin Chem. 2008 Aug;54(8):e1-e10. doi: 10.1373/clinchem.2007.094144. Epub 2008 Jul 7.
PMID: 18606634
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Staphylococcus aureus clumping factor A binds to complement regulator factor I and increases factor I cleavage of C3b.
Hair PS, Ward MD, Semmes OJ, Foster TJ, Cunnion KM.
J Infect Dis. 2008 Jul 1;198(1):125-33. doi: 10.1086/588825.
PMID: 18544012
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Nuclear trafficking of the human cytomegalovirus pp71 (ppUL82) tegument protein.
Shen W, Westgard E, Huang L, Ward MD, Osborn JL, Chau NH, Collins L, Marcum B, Koach MA, Bibbs J, Semmes OJ, Kerry JA.
Virology. 2008 Jun 20;376(1):42-52. doi: 10.1016/j.virol.2008.03.007. Epub 2008 Apr 18.
PMID: 18423509
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Serum protein expression profiling in pediatric Hodgkin lymphoma: a report from the Children's Oncology Group.
Qi L, Cazares L, Johnson C, de Alarcon P, Kupfer GM, Semmes OJ.
Pediatr Blood Cancer. 2008 Aug;51(2):216-21. doi: 10.1002/pbc.21581.
PMID: 18421715
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Precision enhancement of MALDI-TOF MS using high resolution peak detection and label-free alignment.
Tracy MB, Chen H, Weaver DM, Malyarenko DI, Sasinowski M, Cazares LH, Drake RR, Semmes OJ, Tracy ER, Cooke WE.
Proteomics. 2008 Apr;8(8):1530-8. doi: 10.1002/pmic.200701146.
PMID: 18340636
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MALDI/SELDI protein profiling of serum for the identification of cancer biomarkers.
Cazares LH, Diaz JI, Drake RR, Semmes OJ.
Methods Mol Biol. 2008;428:125-40.
PMID: 18287771
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Tissue sample collection for proteomics analysis.
Diaz JI, Cazares LH, Semmes OJ.
Methods Mol Biol. 2008;428:43-53.
PMID: 18287767
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Signal detection in high-resolution mass spectrometry data.
McLerran DF, Feng Z, Semmes OJ, Cazares L, Randolph TW.
J Proteome Res. 2008 Jan;7(1):276-85. doi: 10.1021/pr700640a.
PMID: 18173224
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Differential capture of serum proteins for expression profiling and biomarker discovery in pre- and posttreatment head and neck cancer samples.
Freed GL, Cazares LH, Fichandler CE, Fuller TW, Sawyer CA, Stack BC Jr, Schraff S, Semmes OJ, Wadsworth JT, Drake RR.
Laryngoscope. 2008 Jan;118(1):61-8.
PMID: 18043497
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SELDI-TOF MS whole serum proteomic profiling with IMAC surface does not reliably detect prostate cancer.
McLerran D, Grizzle WE, Feng Z, Thompson IM, Bigbee WL, Cazares LH, Chan DW, Dahlgren J, Diaz J, Kagan J, Lin DW, Malik G, Oelschlager D, Partin A, Randolph TW, Sokoll L, Srivastava S, Srivastava S, Thornquist M, Troyer D, Wright GL, Zhang Z, Zhu L, Semmes OJ.
Clin Chem. 2008 Jan;54(1):53-60. Epub 2007 Nov 16.
PMID: 18024530
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Analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias.
McLerran D, Grizzle WE, Feng Z, Bigbee WL, Banez LL, Cazares LH, Chan DW, Diaz J, Izbicka E, Kagan J, Malehorn DE, Malik G, Oelschlager D, Partin A, Randolph T, Rosenzweig N, Srivastava S, Srivastava S, Thompson IM, Thornquist M, Troyer D, Yasui Y, Zhang Z, Zhu L, Semmes OJ.
Clin Chem. 2008 Jan;54(1):44-52. Epub 2007 Nov 2.
PMID: 17981926
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Modulation of p53 function by SET8-mediated methylation at lysine 382.
Shi X, Kachirskaia I, Yamaguchi H, West LE, Wen H, Wang EW, Dutta S, Appella E, Gozani O.
Mol Cell. 2007 Aug 17;27(4):636-46.
PMID: 17707234
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Optimization of MALDI-TOF MS detection for enhanced sensitivity of affinity-captured proteins spanning a 100 kDa mass range.
Gatlin-Bunai CL, Cazares LH, Cooke WE, Semmes OJ, Malyarenko DI.
J Proteome Res. 2007 Nov;6(11):4517-24. Epub 2007 Oct 5.
PMID: 17918874
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SELDI protein profiling of dunning R-3327 derived cell lines: identification of molecular markers of prostate cancer progression.
Malik G, Rojahn E, Ward MD, Gretzer MB, Partin AW, Semmes OJ, Veltri RW.
Prostate. 2007 Oct 1;67(14):1565-75.
PMID: 17705230
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Human T-cell leukemia virus type 1 Tax oncoprotein prevents DNA damage-induced chromatin egress of hyperphosphorylated Chk2.
Gupta SK, Guo X, Durkin SS, Fryrear KF, Ward MD, Semmes OJ.
J Biol Chem. 2007 Oct 5;282(40):29431-40. Epub 2007 Aug 13.
PMID: 17698850
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Mining the low molecular weight proteome of blood.
Drake RR, Cazares L, Semmes OJ.
Proteomics Clin Appl. 2007 Aug;1(8):758-68. doi: 10.1002/prca.200700175. Epub 2007 Jul 10.
PMID: 21136732
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Serum biomarkers to differentiate benign and malignant mammographic lesions.
Shin S, Cazares L, Schneider H, Mitchell S, Laronga C, Semmes OJ, Perry RR, Drake RR.
J Am Coll Surg. 2007 May;204(5):1065-71; discussion 1071-3.
PMID: 17481542
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Clinical proteomics: A need to define the field and to begin to set adequate standards.
Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser D, Jankowski J, Julian BA, Kolch W, Massy ZA, Neusuess C, Novak J, Peter K, Rossing K, Schanstra J, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T.
Proteomics Clin Appl. 2007 Feb;1(2):148-56. doi: 10.1002/prca.200600771. Epub 2007 Jan 22.
PMID: 21136664
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Proteomic analysis of reporter genes for molecular imaging of transplanted embryonic stem cells.
Wu JC, Cao F, Dutta S, Xie X, Kim E, Chungfat N, Gambhir S, Mathewson S, Connolly AJ, Brown M, Wang EW.
Proteomics. 2006 Dec;6(23):6234-49.
PMID: 17080479
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Overexpression of alpha-defensin is associated with bladder cancer invasiveness.
Holterman DA, Diaz JI, Blackmore PF, Davis JW, Schellhammer PF, Corica A, Semmes OJ, Vlahou A.
Urol Oncol. 2006 Mar-Apr;24(2):97-108.
PMID: 16520271
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Feature extraction in the analysis of proteomic mass spectra.
Wang X, Zhu W, Pradhan K, Ji C, Ma Y, Semmes OJ, Glimm J, Mitchell J.
Proteomics. 2006 Apr;6(7):2095-100. Erratum in: Proteomics. 2006 Jul;6(14):4203.
PMID: 16502467
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Site-specific phosphorylation differentiates active from inactive forms of the human T-cell leukemia virus type 1 Tax oncoprotein.
Durkin SS, Ward MD, Fryrear KA, Semmes OJ.
J Biol Chem. 2006 Oct 20;281(42):31705-12. Epub 2006 Aug 21.
PMID: 16923801
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Lectin capture strategies combined with mass spectrometry for the discovery of serum glycoprotein biomarkers.
Drake RR, Schwegler EE, Malik G, Diaz J, Block T, Mehta A, Semmes OJ.
Mol Cell Proteomics. 2006 Oct;5(10):1957-67. Epub 2006 Jun 7. Review.
PMID: 16760258
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Human LINE-1 retrotransposon induces DNA damage and apoptosis in cancer cells.
Belgnaoui SM, Gosden RG, Semmes OJ, Haoudi A.
Cancer Cell Int. 2006 May 2;6:13.
PMID: 16670018
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Resampling and deconvolution of linear time-of-flight records for enhanced protein profiling.
Malyarenko DI, Cooke WE, Tracy ER, Drake RR, Shin S, Semmes OJ, Sasinowski M, Manos DM.
Rapid Commun Mass Spectrom. 2006;20(11):1670-8.
PMID: 16637003
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Deconvolution filters to enhance resolution of dense time-of-flight survey spectra in the time-lag optimization range.
Malyarenko DI, Cooke WE, Tracy ER, Trosset MW, Semmes OJ, Sasinowski M, Manos DM.
Rapid Commun Mass Spectrom. 2006;20(11):1661-9.
PMID: 16636999
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Adult T cell leukemia: a tale of two T cells.
Semmes OJ.
J Clin Invest. 2006 Apr;116(4):858-60.
PMID: 16585953
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Application of mass spectrometry to the discovery of biomarkers for detection of prostate cancer.
Semmes OJ, Malik G, Ward M.
J Cell Biochem. 2006 Jun 1;98(3):496-503. Review.
PMID: 16552720
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PDZ binding motif of HTLV-1 Tax promotes virus-mediated T-cell proliferation in vitro and persistence in vivo.
Xie L, Yamamoto B, Haoudi A, Semmes OJ, Green PL.
Blood. 2006 Mar 1;107(5):1980-8. Epub 2005 Nov 1.
PMID: 16263794
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Affinity labeling the dopamine transporter ligand binding site.
Vaughan RA, Parnas ML, Gaffaney JD, Lowe MJ, Wirtz S, Pham A, Reed B, Dutta SM, Murray KK, Justice JB.
J Neurosci Methods. 2005 Apr 15;143(1):33-40. Epub 2004 Dec 2.
PMID: 15763134
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Monomeric IgE enhances human mast cell chemokine production: IL-4 augments and dexamethasone suppresses the response.
Matsuda K, Piliponsky AM, Iikura M, Nakae S, Wang EW, Dutta SM, Kawakami T, Tsai M, Galli SJ.
J Allergy Clin Immunol. 2005 Dec;116(6):1357-63. Epub 2005 Nov 2.
PMID: 16337471
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Impact of HTLV-I Tax on cell cycle progression and the cellular DNA damage repair response.
Marriott SJ, Semmes OJ.
Oncogene. 2005 Sep 5;24(39):5986-95. Review.
PMID: 16155605
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The "omics" haystack: defining sources of sample bias in expression profiling.
Semmes OJ.
Clin Chem. 2005 Sep;51(9):1571-2. No abstract available.
PMID: 16120944
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Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: multi-institution correlation of spectra and identification of biomarkers.
Rai AJ, Stemmer PM, Zhang Z, Adam BL, Morgan WT, Caffrey RE, Podust VN, Patel M, Lim LY, Shipulina NV, Chan DW, Semmes OJ, Leung HC.
Proteomics. 2005 Aug;5(13):3467-74.
PMID: 16052624
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Functional clustering algorithm for high-dimensional proteomics data.
Bensmail H, Aruna B, Semmes OJ, Haoudi A.
J Biomed Biotechnol. 2005 Jun 30;2005(2):80-6.
PMID: 16046812
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The bZIP transcription factor ATFx binds human T-cell leukemia virus type 1 (HTLV-1) Tax and represses HTLV-1 long terminal repeat-mediated transcription.
Forgacs E, Gupta SK, Kerry JA, Semmes OJ.
J Virol. 2005 Jun;79(11):6932-9.
PMID: 15890932
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A novel approach for clustering proteomics data using Bayesian fast Fourier transform.
Bensmail H, Golek J, Moody MM, Semmes JO, Haoudi A.
Bioinformatics. 2005 May 15;21(10):2210-24. Epub 2005 Mar 15.
PMID: 15769836
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SELDI-TOF MS profiling of serum for detection of the progression of chronic hepatitis C to hepatocellular carcinoma.
Schwegler EE, Cazares L, Steel LF, Adam BL, Johnson DA, Semmes OJ, Block TM, Marrero JA, Drake RR.
Hepatology. 2005 Mar;41(3):634-42.
PMID: 15726646
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Serum, salivary and tissue proteomics for discovery of biomarkers for head and neck cancers.
Drake RR, Cazare LH, Semmes OJ, Wadsworth JT.
Expert Rev Mol Diagn. 2005 Jan;5(1):93-100. Review.
PMID: 15723595
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Serum levels of an isoform of apolipoprotein A-II as a potential marker for prostate cancer.
Malik G, Ward MD, Gupta SK, Trosset MW, Grizzle WE, Adam BL, Diaz JI, Semmes OJ.
Clin Cancer Res. 2005 Feb 1;11(3):1073-85.
PMID: 15709174
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the need for review and understanding of SELDI/MALDI mass spectroscopy data prior to analysis.
Grizzle WE, Semmes OJ, Bigbee W, Zhu L, Malik G, Oelschlager DK, Manne B, Manne U.
Cancer Inform. 2005;1:86-97.
PMID: 19305634
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Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility.
Semmes OJ, Feng Z, Adam BL, Banez LL, Bigbee WL, Campos D, Cazares LH, Chan DW, Grizzle WE, Izbicka E, Kagan J, Malik G, McLerran D, Moul JW, Partin A, Prasanna P, Rosenzweig J, Sokoll LJ, Srivastava S, Srivastava S, Thompson I, Welsh MJ, White N, Winget M, Yasui Y, Zhang Z, Zhu L.
Clin Chem. 2005 Jan;51(1):102-12.
PMID: 15613711
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Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques.
Malyarenko DI, Cooke WE, Adam BL, Malik G, Chen H, Tracy ER, Trosset MW, Sasinowski M, Semmes OJ, Manos DM.
Clin Chem. 2005 Jan;51(1):65-74. Epub 2004 Nov 18.
PMID: 15550476
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A nitrocellulose matrix for infrared matrix-assisted laser desorption/ionization of polycyclic aromatic hydrocarbons.
Jackson SN, Dutta SM, Murray KK.
Rapid Commun Mass Spectrom. 2004;18(2):228-30. No abstract available.
PMID: 14745775
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Measurement reproducibility in the early stages of biomarker development.
Liggett WS, Barker PE, Semmes OJ, Cazares LH.
Dis Markers. 2004;20(6):295-307.
PMID: 15665389
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Expression of genes and proteins specific for prostate cancer.
Gelmann EP, Semmes OJ.
J Urol. 2004 Nov;172(5 Pt 2):S23-6; discussion S26-7. Review.
PMID: 15535438
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Retrotransposition-Competent Human LINE-1 Induces Apoptosis in Cancer Cells With Intact p53.
Haoudi A, Semmes OJ, Mason JM, Cannon RE.
J Biomed Biotechnol. 2004;2004(4):185-194.
PMID: 15467158
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Defining the role of mass spectrometry in cancer diagnostics.
Semmes OJ.
Cancer Epidemiol Biomarkers Prev. 2004 Oct;13(10):1555-7. No abstract available.
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Surfaced-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) differentiation of serum protein profiles of BRCA-1 and sporadic breast cancer.
Becker S, Cazares LH, Watson P, Lynch H, Semmes OJ, Drake RR, Laronga C.
Ann Surg Oncol. 2004 Oct;11(10):907-14. Epub 2004 Sep 20.
PMID: 15383419
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The early detection research network surface-enhanced laser desorption and ionization prostate cancer detection study: A study in biomarker validation in genitourinary oncology.
Grizzle WE, Semmes OJ, Basler J, Izbicka E, Feng Z, Kagan J, Adam BL, Troyer D, Srivastava S, Thornquist M, Zhang Z, Thompson IM.
Urol Oncol. 2004 Jul-Aug;22(4):337-43. Review.
PMID: 15283893
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Protein profiling in urine for the diagnosis of bladder cancer.
Vlahou A, Giannopoulos A, Gregory BW, Manousakas T, Kondylis FI, Wilson LL, Schellhammer PF, Wright GL Jr, Semmes OJ.
Clin Chem. 2004 Aug;50(8):1438-41. No abstract available.
PMID: 15277356
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SELDI-TOF serum profiling for prognostic and diagnostic classification of breast cancers.
Laronga C, Becker S, Watson P, Gregory B, Cazares L, Lynch H, Perry RR, Wright GL Jr, Drake RR, Semmes OJ.
Dis Markers. 2003-2004;19(4-5):229-38.
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Serum protein expression profiling for cancer detection: validation of a SELDI-based approach for prostate cancer.
Grizzle WE, Adam BL, Bigbee WL, Conrads TP, Carroll C, Feng Z, Izbicka E, Jendoubi M, Johnsey D, Kagan J, Leach RJ, McCarthy DB, Semmes OJ, Srivastava S, Srivastava S, Thompson IM, Thornquist MD, Verma M, Zhang Z, Zou Z.
Dis Markers. 2003-2004;19(4-5):185-95.
PMID: 15258333
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Computational protein biomarker prediction: a case study for prostate cancer.
Wagner M, Naik DN, Pothen A, Kasukurti S, Devineni RR, Adam BL, Semmes OJ, Wright GL Jr.
BMC Bioinformatics. 2004 Mar 11;5:26.
PMID: 15113409
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Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma.
Pusztai L, Gregory BW, Baggerly KA, Peng B, Koomen J, Kuerer HM, Esteva FJ, Symmans WF, Wagner P, Hortobagyi GN, Laronga C, Semmes OJ, Wright GL Jr, Drake RR, Vlahou A.
Cancer. 2004 May 1;100(9):1814-22.
PMID: 15112261
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Serum protein profiles to identify head and neck cancer.
Wadsworth JT, Somers KD, Cazares LH, Malik G, Adam BL, Stack BC Jr, Wright GL Jr, Semmes OJ.
Clin Cancer Res. 2004 Mar 1;10(5):1625-32.
PMID: 15014013
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Comparative proteomic analysis of de-N-glycosylated serum from hepatitis B carriers reveals polypeptides that correlate with disease status.
Comunale MA, Mattu TS, Lowman MA, Evans AA, London WT, Semmes OJ, Ward M, Drake R, Romano PR, Steel LF, Block TM, Mehta A.
Proteomics. 2004 Mar;4(3):826-38