Publications

  1. Ho TH, Kapur P, Joseph RW, Serie DJ, Eckel-Passow JE, Parasramka M, Cheville JC, Wu KJ, Frenkel E, Rakheja D, Stefanius K, Brugarolas J, Parker AS. Loss of PBRM1 and BAP1 expression is less common in non-clear cell renal cell carcinoma than in clear cell renal cell carcinoma. Urol Oncol. 2014 Nov 24.
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  2. Eckel-Passow JE, Igel DA, Serie DJ, Joseph RW, Ho TH, Cheville JC, Parker AS. Assessing the clinical use of clear cell renal cell carcinoma molecular subtypes identified by RNA expression analysis. Urol Oncol. 2014 Aug 27.
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  3. Walsh KM, Codd V, Smirnov IV, Rice T, Decker PA, Hansen HM, Kollmeyer T, Kosel ML, Molinaro AM, McCoy LS, Bracci PM, Cabriga BS, Pekmezci M, Zheng S, Wiemels JL, Pico AR, Tihan T, Berger MS, Chang SM, Prados MD, Lachance DH, O'Neill BP, Sicotte H, Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. Nat Genet. 2014 Jul; 46(7):731-5. Epub 2014 Jun 08.
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  4. Jenkins RB, Decker P, Kosel M, Eckel-Passow J, Walsh KM, Smirnov IV, Caron A, Kollmeyer T, Rice T, Hansen HM, Molinaro AM, McCoy LS, Bracci PM, Cabriga BS, Marshall R, Pekmezci M, Zheng S, O'Neill B, Buckner J, Giannini C, Perry A, Tihan T, Berger MS, Mutation-based molecular glioma classification: prevalence and association with germline risk snps. Neuro Oncol. 2014 Jul; 16 Suppl 3:iii1.
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  5. Purrington KS, Slager S, Eccles D, Yannoukakos D, Fasching PA, Miron P, Carpenter J, Chang-Claude J, Martin NG, Montgomery GW, Kristensen V, Anton-Culver H, Goodfellow P, Tapper WJ, Rafiq S, Gerty SM, Durcan L, Konstantopoulou I, Fostira F, Vratimos A, Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer. Carcinogenesis. 2014 May; 35(5):1012-9. Epub 2013 Dec 09.
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  6. Joseph RW, Kapur P, Serie DJ, Eckel-Passow JE, Parasramka M, Ho T, Cheville JC, Frenkel E, Rakheja D, Brugarolas J, Parker A. Loss of BAP1 protein expression is an independent marker of poor prognosis in patients with low-risk clear cell renal cell carcinoma. Cancer. 2014 Apr 1; 120(7):1059-67. Epub 2013 Dec 30.
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  7. Eckel-Passow JE, Serie DJ, Bot BM, Joseph RW, Hart SN, Cheville JC, Parker AS. Somatic expression of ENRAGE is associated with obesity status among patients with clear cell renal cell carcinoma. Carcinogenesis. 2014 Apr; 35(4):822-7. Epub 2013 Dec 28.
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  8. Eckel-Passow JE, Serie DJ, Bot BM, Joseph RW, Cheville JC, Parker AS. ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinoma. BMC Urol. 2014; 14:14. Epub 2014 Jan 31.
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  9. Parker AS, Eckel-Passow JE, Serie D, Hilton T, Parasramka M, Joseph RW, Wu KJ, Cheville JC, Leibovich BC. Higher expression of topoisomerase II alpha is an independent marker of increased risk of cancer-specific death in patients with clear cell renal cell carcinoma. Eur Urol. 2014; 66(5):929-35.
  10. Parker AS, Eckel-Passow JE, Serie D, Hilton T, Parasramka M, Joseph RW, Wu KJ, Cheville JC, Leibovich BC. Higher Expression of Topoisomerase II Alpha Is an Independent Marker of Increased Risk of Cancer-specific Death in Patients with Clear Cell Renal Cell Carcinoma. Eur Urol. 2013 Dec 25.
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  11. Joseph RW, Parasramka M, Eckel-Passow JE, Serie D, Wu K, Jiang L, Kalari K, Thompson RH, Huu Ho T, Castle EP, Cheville J, Kwon ED, Thompson EA, Parker A. Inverse Association between Programmed Death Ligand 1 and Genes in the VEGF Pathway in Primary Clear Cell Renal Cell Carcinoma. Cancer Immunol Res. 2013 Dec; 1(6):378-85. Epub 2013 Aug 29.
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  12. Reese SE, Archer KJ, Therneau TM, Atkinson EJ, Vachon CM, de Andrade M, Kocher JP, Eckel-Passow JE. A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. Bioinformatics. 2013 Nov 15; 29(22):2877-83. Epub 2013 Aug 19.
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  13. Al-Hasan MN, Lahr BD, Eckel-Passow JE, Baddour LM. Predictive scoring model of mortality in Gram-negative bloodstream infection. Clin Microbiol Infect. 2013 Oct; 19(10):948-54. Epub 2012 Nov 27.
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  14. Walsh KM, Rice T, Decker PA, Kosel ML, Kollmeyer T, Hansen HM, Zheng S, McCoy LS, Bracci PM, Anderson E, Hsuang G, Wiemels JL, Pico AR, Smirnov I, Molinaro AM, Tihan T, Berger MS, Chang SM, Prados MD, Lachance DH, Sicotte H, Eckel-Passow JE, Wiencke JK, Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis. Neuro Oncol. 2013 Aug; 15(8):1041-7. Epub 2013 Jun 03.
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  15. Waltman LA, Eckel-Passow JE, Sharma RG, Van Dyke DL. Advanced maternal age in polyploidy with concurrent aneuploidy. Am J Med Genet A. 2013 May; 161A(5):1200-2. Epub 2013 Mar 29.
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  16. Rice T, Zheng S, Decker PA, Walsh KM, Bracci P, Xiao Y, McCoy LS, Smirnov I, Patoka JS, Hansen HM, Hsuang G, Wiemels JL, Tihan T, Pico AR, Prados MD, Chang SM, Berger MS, Caron A, Fink S, Kollmeyer T, Rynearson A, Voss J, Kosel ML, Fridley BL, Lachance Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology. Neuro Oncol. 2013 May; 15(5):535-41. Epub 2013 Jan 29.
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  17. Walsh KM, Anderson E, Hansen HM, Decker PA, Kosel ML, Kollmeyer T, Rice T, Zheng S, Xiao Y, Chang JS, McCoy LS, Bracci PM, Wiemels JL, Pico AR, Smirnov I, Lachance DH, Sicotte H, Eckel-Passow JE, Wiencke JK, Jenkins RB, Wrensch MR. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies. Genet Epidemiol. 2013 Feb; 37(2):222-8. Epub 2012 Dec 31.
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  18. Mansfield AS, Sukov WR, Eckel-Passow JE, Sakai Y, Walsh FJ, Lonzo M, Wiktor AE, Dogan A, Jenkins RB. Comparison of fluorescence in situ hybridization (FISH) and dual-ISH (DISH) in the determination of HER2 status in breast cancer. Am J Clin Pathol. 2013 Feb; 139(2):144-50.
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  19. McDonnell SK, Riska SM, Klee EW, Thorland EC, Kay NE, Thibodeau SN, Parker AS, Eckel-Passow JE. Experimental designs for array comparative genomic hybridization technology. Cytogenet Genome Res. 2013; 139(4):250-7. Epub 2013 Mar 27.
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  20. Mahoney DW, Therneau TM, Anderson SK, Jen J, Kocher JP, Reinholz MM, Perez EA, Eckel-Passow JE. Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples. BMC Res Notes. 2013; 6:33. Epub 2013 Jan 30.
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  21. Kalari KR, Necela BM, Tang X, Thompson KJ, Lau M, Eckel-Passow JE, Kachergus JM, Anderson SK, Sun Z, Baheti S, Carr JM, Baker TR, Barman P, Radisky DC, Joseph RW, McLaughlin SA, Chai HS, Camille S, Rossell D, Asmann YW, Thompson EA, Perez EA. An integrated model of the transcriptome of HER2-positive breast cancer. PLoS One. 2013; 8(11):e79298. Epub 2013 Nov 01.
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  22. Joseph RW, Eckel-Passow JE, Sharma R, Liu P, Parker A, Jakob J, Buchbinder E, Bassett RL, Davies MA, Hwu P, Atkins MB, Sullivan RJ. Characterizing the clinical benefit of ipilimumab in patients who progressed on high-dose IL-2. J Immunother. 2012 Nov-Dec; 35(9):711-5.
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  23. Jenkins RB, Xiao Y, Sicotte H, Decker PA, Kollmeyer TM, Hansen HM, Kosel ML, Zheng S, Walsh KM, Rice T, Bracci P, McCoy LS, Smirnov I, Patoka JS, Hsuang G, Wiemels JL, Tihan T, Pico AR, Prados MD, Chang SM, Berger MS, Caron AA, Fink SR, Halder C, A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation. Nat Genet. 2012 Oct; 44(10):1122-5. Epub 2012 Aug 26.
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  24. Berbari EF, Osmon DR, Lahr B, Eckel-Passow JE, Tsaras G, Hanssen AD, Mabry T, Steckelberg J, Thompson R. The Mayo prosthetic joint infection risk score: implication for surgical site infection reporting and risk stratification. Infect Control Hosp Epidemiol. 2012 Aug; 33(8):774-81. Epub 2012 Jun 20.
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  25. Stevens KN, Lindstrom S, Scott CG, Thompson D, Sellers TA, Wang X, Wang A, Atkinson E, Rider DN, Eckel-Passow JE, Varghese JS, Audley T, Brown J, Leyland J, Luben RN, Warren RM, Loos RJ, Wareham NJ, Li J, Hall P, Liu J, Eriksson L, Czene K, Olson JE, Identification of a novel percent mammographic density locus at 12q24. Hum Mol Genet. 2012 Jul 15; 21(14):3299-305. Epub 2012 Apr 24.
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  26. Al-Hasan MN, Eckel-Passow JE, Baddour LM. Impact of healthcare-associated acquisition on community-onset Gram-negative bloodstream infection: a population-based study: healthcare-associated Gram-negative BSI. Eur J Clin Microbiol Infect Dis. 2012 Jun; 31(6):1163-71. Epub 2011 Oct 08.
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  27. Bot BM, Eckel-Passow JE, LeGrand SN, Hilton T, Cheville JC, Igel T, Parker AS. Expression of endothelin 2 and localized clear cell renal cell carcinoma. Hum Pathol. 2012 Jun; 43(6):843-9. Epub 2011 Nov 01.
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  28. Tapia GG, Razonable RR, Eckel-Passow JE, Lahr BD, Afessa B, Keegan MT, Catania J, Baddour LM. A scoring model of factors associated with Candida glabrata candidemia among critically ill patients. Mycoses. 2012 May; 55(3):228-36. Epub 2011 Jul 21.
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  29. Al-Hasan MN, Eckel-Passow JE, Baddour LM. Influence of referral bias on the clinical characteristics of patients with Gram-negative bloodstream infection. Epidemiol Infect. 2011 Nov; 139(11):1750-6. Epub 2011 Feb 01.
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  30. Wiktor AE, Van Dyke DL, Hodnefield JM, Eckel-Passow J, Hanson CA. The significance of isolated Y chromosome loss in bone marrow metaphase cells from males over age 50 years. Leuk Res. 2011 Oct; 35(10):1297-300. Epub 2011 Jun 23.
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  31. Al-Hasan MN, Huskins WC, Lahr BD, Eckel-Passow JE, Baddour LM. Epidemiology and outcome of Gram-negative bloodstream infection in children: a population-based study. Epidemiol Infect. 2011 May; 139(5):791-6. Epub 2010 Jul 02.
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  32. Al-Hasan MN, Eckel-Passow JE, Baddour LM. Cefepime effectiveness in Gram-negative bloodstream infections. J Antimicrob Chemother. 2011 May; 66(5):1156-60. Epub 2011 Mar 08.
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  33. Al-Hasan MN, Lahr BD, Eckel-Passow JE, Baddour LM. Temporal trends in Enterobacter species bloodstream infection: a population-based study from 1998-2007. Clin Microbiol Infect. 2011 Apr; 17(4):539-45.
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  34. Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, Carr JM, Khrebtukova I, Luo S, Zhang L, Schroth GP, Perez EA, Thompson EA. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One. 2011; 6(2):e17490. Epub 2011 Feb 25.
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  35. Eckel-Passow JE, Atkinson EJ, Maharjan S, Kardia SL, de Andrade M. Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform. BMC Bioinformatics. 2011; 12:220. Epub 2011 May 31.
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  36. Smoley SA, Van Dyke DL, Kay NE, Heerema NA, Dell' Aquila ML, Dal Cin P, Koduru P, Aviram A, Rassenti L, Byrd JC, Rai KR, Brown JR, Greaves AW, Eckel-Passow J, Neuberg D, Kipps TJ, Dewald GW. Standardization of fluorescence in situ hybridization studies on chronic lymphocytic leukemia (CLL) blood and marrow cells by the CLL Research Consortium. Cancer Genet Cytogenet. 2010 Dec; 203(2):141-8.
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  37. Kay NE, Eckel-Passow JE, Braggio E, Vanwier S, Shanafelt TD, Van Dyke DL, Jelinek DF, Tschumper RC, Kipps T, Byrd JC, Fonseca R. Progressive but previously untreated CLL patients with greater array CGH complexity exhibit a less durable response to chemoimmunotherapy. Cancer Genet Cytogenet. 2010 Dec; 203(2):161-8.
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  38. Gutierrez A Jr, Tschumper RC, Wu X, Shanafelt TD, Eckel-Passow J, Huddleston PM 3rd, Slager SL, Kay NE, Jelinek DF. LEF-1 is a prosurvival factor in chronic lymphocytic leukemia and is expressed in the preleukemic state of monoclonal B-cell lymphocytosis. Blood. 2010 Oct 21; 116(16):2975-83. Epub 2010 Jul 01.
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  39. El Helou OC, Berbari EF, Lahr BD, Eckel-Passow JE, Razonable RR, Sia IG, Virk A, Walker RC, Steckelberg JM, Wilson WR, Hanssen AD, Osmon DR. Efficacy and safety of rifampin containing regimen for staphylococcal prosthetic joint infections treated with debridement and retention. Eur J Clin Microbiol Infect Dis. 2010 Aug; 29(8):961-7. Epub 2010 May 27.
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  40. Al-Hasan MN, Eckel-Passow JE, Baddour LM. Recurrent gram-negative bloodstream infection: a 10-year population-based cohort study. J Infect. 2010 Jul; 61(1):28-33. Epub 2010 Apr 06.
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  41. Eid AJ, Brown RA, Arthurs SK, Lahr BD, Eckel-Passow JE, Larson TS, Razonable RR. A prospective longitudinal analysis of cytomegalovirus (CMV)-specific CD4+ and CD8+ T cells in kidney allograft recipients at risk of CMV infection. Transpl Int. 2010 May 1; 23(5):506-13. Epub 2009 Nov 27.
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  42. Al-Hasan MN, Eckel-Passow JE, Baddour LM. Bacteremia complicating gram-negative urinary tract infections: a population-based study. J Infect. 2010 Apr; 60(4):278-85. Epub 2010 Jan 28.
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  43. Al-Hasan MN, Lahr BD, Eckel-Passow JE, Baddour LM. Epidemiology and outcome of Klebsiella species bloodstream infection: a population-based study. Mayo Clin Proc. 2010 Feb; 85(2):139-44.
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  44. Eckel-Passow JE, Lohse CM, Sheinin Y, Crispen PL, Krco CJ, Kwon ED. Tissue microarrays: one size does not fit all. Diagn Pathol. 2010; 5:48. Epub 2010 Jul 07.
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  45. Eckel-Passow JE, Mahoney DW, Oberg AL, Zenka RM, Johnson KL, Nair KS, Kudva YC, Bergen HR III, Therneau TM. Bi-linear regression for 18O quantification: Modeling across the elution profile. Journal of Proteomics and Bioinformatics. 2010; 3(12):323-9.
  46. Reinholz MM, Eckel-Passow JE, Anderson SK, Asmann YW, Zschunke MA, Oberg AL, McCullough AE, Dueck AC, Chen B, April CS, Wickham-Garcia E, Jenkins RB, Cunningham JM, Jen J, Perez EA, Fan JB, Lingle WL. Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL(R) platform. BMC Med Genomics. 2010; 3:60. Epub 2010 Dec 20.
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  47. El Atrouni WI, Knoll BM, Lahr BD, Eckel-Passow JE, Sia IG, Baddour LM. Temporal trends in the incidence of Staphylococcus aureus bacteremia in Olmsted County, Minnesota, 1998 to 2005: a population-based study. Clin Infect Dis. 2009 Dec 15; 49(12):e130-8.
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  48. Eid AJ, Brown RA, Hogan WJ, Lahr BD, Eckel-Passow JE, Litzow MR, Razonable RR. Kinetics of interferon-gamma producing cytomegalovirus (CMV)-specific CD4+ and CD8+ T lymphocytes and the risk of subsequent CMV viremia after allogeneic hematopoietic stem cell transplantation. Transpl Infect Dis. 2009 Dec; 11(6):519-28. Epub 2009 Sep 09.
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  49. Al-Hasan MN, Lahr BD, Eckel-Passow JE, Baddour LM. Seasonal variation in Escherichia coli bloodstream infection: a population-based study. Clin Microbiol Infect. 2009 Oct; 15(10):947-50.
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  50. Al-Hasan MN, Lahr BD, Eckel-Passow JE, Baddour LM. Antimicrobial resistance trends of Escherichia coli bloodstream isolates: a population-based study, 1998-2007. J Antimicrob Chemother. 2009 Jul; 64(1):169-74. Epub 2009 May 12.
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  51. Eckel-Passow JE, Oberg AL, Therneau TM, Bergen HR 3rd. An insight into high-resolution mass-spectrometry data. Biostatistics. 2009 Jul; 10(3):481-500. Epub 2009 Mar 26.
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  52. Parker AS, Leibovich BC, Lohse CM, Sheinin Y, Kuntz SM, Eckel-Passow JE, Blute ML, Kwon ED. Development and evaluation of BioScore: a biomarker panel to enhance prognostic algorithms for clear cell renal cell carcinoma. Cancer. 2009 May 15; 115(10):2092-103.
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  53. Al-Hasan MN, Razonable RR, Eckel-Passow JE, Baddour LM. Incidence rate and outcome of Gram-negative bloodstream infection in solid organ transplant recipients. Am J Transplant. 2009 Apr; 9(4):835-43.
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  54. Al-Hasan MN, Wilson JW, Lahr BD, Thomsen KM, Eckel-Passow JE, Vetter EA, Tleyjeh IM, Baddour LM. Beta-lactam and fluoroquinolone combination antibiotic therapy for bacteremia caused by gram-negative bacilli. Antimicrob Agents Chemother. 2009 Apr; 53(4):1386-94. Epub 2009 Jan 21.
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  55. Al-Hasan MN, Wilson JW, Lahr BD, Eckel-Passow JE, Baddour LM. Incidence of Pseudomonas aeruginosa bacteremia: a population-based study. Am J Med. 2008 Aug; 121(8):702-8.
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  56. Hill EG, Schwacke JH, Comte-Walters S, Slate EH, Oberg AL, Eckel-Passow JE, Therneau TM, Schey KL. A statistical model for iTRAQ data analysis. J Proteome Res. 2008 Aug; 7(8):3091-101. Epub 2008 Jun 26.
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  57. Oberg AL, Mahoney DW, Eckel-Passow JE, Malone CJ, Wolfinger RD, Hill EG, Cooper LT, Onuma OK, Spiro C, Therneau TM, Bergen HR 3rd. Statistical analysis of relative labeled mass spectrometry data from complex samples using ANOVA. J Proteome Res. 2008 Jan; 7(1):225-33. Epub 2008 Jan 04.
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  58. Mason CJ, Therneau TM, Eckel-Passow JE, Johnson KL, Oberg AL, Olson JE, Nair KS, Muddiman DC, Bergen HR 3rd. A method for automatically interpreting mass spectra of 18O-labeled isotopic clusters. Mol Cell Proteomics. 2007 Feb; 6(2):305-18. Epub 2006 Oct 26.
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  59. Eckel-Passow JE, Oberg AL, Therneau TM, Mason CJ, Mahoney DW, Johnson KL, Olson JE, Bergen HR 3rd. Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometry. Bioinformatics. 2006 Nov 15; 22(22):2739-45. Epub 2006 Sep 05.
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  60. Eckel-Passow JE, Hoering A, Therneau TM, Ghobrial I. Experimental design and analysis of antibody microarrays: applying methods from cDNA arrays. Cancer Res. 2005 Apr 15; 65(8):2985-9.
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  61. Eckel JE, Gennings C, Therneau TM, Burgoon LD, Boverhof DR, Zacharewski TR. Normalization of two-channel microarray experiments: a semiparametric approach. Bioinformatics. 2005 Apr 1; 21(7):1078-83. Epub 2004 Oct 28.
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  62. Burgoon LD, Eckel-Passow JE, Gennings C, Boverhof DR, Burt JW, Fong CJ, Zacharewski TR. Protocols for the assurance of microarray data quality and process control. Nucleic Acids Res. 2005; 33(19):e172. Epub 2005 Nov 04.
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  63. Johnson KL, Mason CJ, Muddiman DC, Eckel JE. Analysis of the low molecular weight fraction of serum by LC-dual ESI-FT-ICR mass spectrometry: precision of retention time, mass, and ion abundance. Anal Chem. 2004 Sep 1; 76(17):5097-103.
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  64. Eckel JE, Gennings C, Chinchilli VM, Burgoon LD, Zacharewski TR. Empirical bayes gene screening tool for time-course or dose-response microarray data. J Biopharm Stat. 2004 Aug; 14(3):647-70.
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  65. Boverhof DR, Fertuck KC, Burgoon LD, Eckel JE, Gennings C, Zacharewski TR. Temporal- and dose-dependent hepatic gene expression changes in immature ovariectomized mice following exposure to ethynyl estradiol. Carcinogenesis. 2004 Jul; 25(7):1277-91. Epub 2004 Feb 19.
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  66. Fertuck KC, Eckel JE, Gennings C, Zacharewski TR. Identification of temporal patterns of gene expression in the uteri of immature, ovariectomized mice following exposure to ethynylestradiol. Physiol Genomics. 2003 Oct 17; 15(2):127-41. Epub 2003 Oct 17.
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