Publications

  1. Blackburn PR, Hickey RD, Nace RA, Giama NH, Kraft DL, Bordner AJ, Chaiteerakij R, McCormick JB, Radulovic M, Graham RP, Torbenson MS, Tortorelli S, Scott CR, Lindor NM, Milliner DS, Oglesbee D, Al-Qabandi W, Grompe M, Gavrilov DK, El-Youssef M, Clark KJ, Atwal PS, Roberts LR, Klee EW, Ekker SC. Silent Tyrosinemia Type I Without Elevated Tyrosine or Succinylacetone Associated with Liver Cirrhosis and Hepatocellular Carcinoma. Hum Mutat 2016 Oct; 37 (10):1097-105 Epub 2016 Aug 08
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  2. Camilleri M, Carlson P, Valentin N, Acosta A, O'Neill J, Eckert D, Dyer R, Na J, Klee EW, Murray JA. Pilot study of small bowel mucosal gene expression in patients with irritable bowel syndrome with diarrhea. Am J Physiol Gastrointest Liver Physiol 2016 Sep 1; 311 (3):G365-76 Epub 2016 July 21
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  3. Boczek NJ, Sigafoos AN, Zimmermann MT, Maus RL, Cousin MA, Blackburn PR, Urrutia R, Clark KJ, Patterson MC, Wick MJ, Klee EW. Functional characterization of a GFAP variant of uncertain significance in an Alexander disease case within the setting of an individualized medicine clinic. Clin Case Rep 2016 Sep; 4 (9):885-95 Epub 2016 Aug 15
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  4. Ji Y, Skierka JM, Blommel JH, Moore BE, VanCuyk DL, Bruflat JK, Peterson LM, Veldhuizen TL, Fadra N, Peterson SE, Lagerstedt SA, Train LJ, Baudhuin LM, Klee EW, Ferber MJ, Bielinski SJ, Caraballo PJ, Weinshilboum RM, Black JL 3rd. Preemptive Pharmacogenomic Testing for Precision Medicine: A Comprehensive Analysis of Five Actionable Pharmacogenomic Genes Using Next-Generation DNA Sequencing and a Customized CYP2D6 Genotyping Cascade. J Mol Diagn 2016 May; 18 (3):438-45 Epub 2016 Mar 03
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  5. Dimberg EL, Swaika A, Boczek NJ, Sood N, Guthrie K, Klee EW, Agrawal A, Ailawadhi S. Whole Exome Sequencing Leading to the Diagnosis of Dysferlinopathy with a Novel Missense Mutation (c.959G>C) Case Reports in Genetics.;2016().
  6. Individualized Medicine Clinic Members, Lazaridis KN, Schahl KA, Cousin MA, Babovic-Vuksanovic D, Riegert-Johnson DL, Gavrilova RH, McAllister TM, Lindor NM, Abraham RS, Ackerman MJ, Pichurin PN, Deyle DR, Gavrilov DK, Hand JL, Klee EW, Stephens MC, Wick MJ, Atkinson EJ, Linden DR, Ferber MJ, Wieben ED, Farrugia G. Outcome of Whole Exome Sequencing for Diagnostic Odyssey Cases of an Individualized Medicine Clinic: The Mayo Clinic Experience. Mayo Clin Proc 2016 Mar; 91 (3):297-307
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  7. Swaika A, Boczek NJ, Sood N, Guthrie K, Klee EW, Agrawal A, Dimberg EL, Ailawadhi S. Whole Exome Sequencing Leading to the Diagnosis of Dysferlinopathy with a Novel Missense Mutation (c.959G>C). Case Rep Genet 2016; 2016:9280812 Epub 2016 Apr 19
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  8. Oliver GR, Zimmermann MT, Klee EW, Urrutia RA. "The molecule's the thing:" the promise of molecular modeling and dynamic simulations in aiding the prioritization and interpretation of genomic testing results. F1000Res 2016; 5:766 Epub 2016 Apr 27
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  9. Morales-Rosado JA, Cousin MA, Ebbert JO, Klee EW. A Critical Review of Repurposing Apomorphine for Smoking Cessation. Assay Drug Dev Technol 2015 Dec; 13 (10):612-22
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  10. Lindor NM, Schahl KA, Johnson KJ, Hunt KS, Mensink KA, Wieben ED, Klee E, Black JL, Highsmith WE Jr, Thibodeau SN, Ferber MJ, Aypar U, Ji Y, Graham RP, Fiksdal AS, Sarangi V, Ormond KE, Riegert-Johnson DL, McAllister TM, Farrugia G, McCormick JB. Whole-Exome Sequencing of 10 Scientists: Evaluation of the Process and Outcomes. Mayo Clin Proc 2015 Oct; 90 (10):1327-37
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  11. Gleeson FC, Kipp BR, Voss JS, Campion MB, Minot DM, Tu ZJ, Klee EW, Graham RP, Lazaridis KN, Henry MR, Levy MJ. Frequency of mitogen-activated protein kinase and phosphoinositide 3-kinase signaling pathway pathogenic alterations in EUS-FNA sampled malignant lymph nodes in rectal cancer with theranostic potential. Gastrointest Endosc 2015 Sep; 82 (3):550-6.e1 Epub 2015 Apr 14
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  12. Baudhuin LM, Lagerstedt SA, Klee EW, Fadra N, Oglesbee D, Ferber MJ. Confirming Variants in Next-Generation Sequencing Panel Testing by Sanger Sequencing. J Mol Diagn 2015 Jul; 17 (4):456-61 Epub 2015 May 08
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  13. Gleeson FC, Kipp BR, Voss JS, Campion MB, Minot DM, Tu ZJ, Klee EW, Sciallis AP, Graham RP, Lazaridis KN, Henry MR, Levy MJ. Endoscopic ultrasound fine-needle aspiration cytology mutation profiling using targeted next-generation sequencing: personalized care for rectal cancer. Am J Clin Pathol. 2015 Jun; 143(6):879-88.
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  14. Gleeson FC, Kipp BR, Levy MJ, Voss JS, Campion MB, Minot DM, Tu ZJ, Klee EW, Lazaridis KN, Kerr SE. Somatic STK11 and concomitant STK11/KRAS mutational frequency in stage IV lung adenocarcinoma adrenal metastases. J Thorac Oncol 2015 Mar; 10 (3):531-4
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  15. Gleeson FC, Kipp BR, Kerr SE, Voss JS, Graham RP, Campion MB, Minot DM, Tu ZJ, Klee EW, Lazaridis KN, Henry MR, Levy MJ. Kinase genotype analysis of gastric gastrointestinal stromal tumor cytology samples using targeted next-generation sequencing. Clin Gastroenterol Hepatol. 2015 Jan; 13(1):202-6. Epub 2014 Jul 03.
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  16. Oliver GR, Hart SN, Klee EW. Bioinformatics for clinical next generation sequencing. Clin Chem. 2015 Jan; 61(1):124-35. Epub 2014 Dec 01.
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  17. Gleeson FC, Kipp BR, Levy MJ, Voss JS, Campion MB, Minot DM, Tu ZJ, Klee EW, Lazaridis KN, Kerr SE. Lung cancer adrenal gland metastasis: Optimal fine-needle aspirate and touch preparation smear cellularity characteristics for successful theranostic next-generation sequencing. Cancer Cytopathol. 2014 Nov; 122(11):822-32. Epub 2014 Jul 15.
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  18. Shameer K, Klee EW, Dalenberg AK, Kullo IJ. Whole exome sequencing implicates an INO80D mutation in a syndrome of aortic hypoplasia, premature atherosclerosis, and arterial stiffness. Circ Cardiovasc Genet. 2014 Oct; 7(5):607-14. Epub 2014 Aug 13.
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  19. Klee EW, Bondar OP, Goodmanson MK, Trushin SA, Bergstralh EJ, Singh RJ, Anderson NL, Klee GG. Serum concentrations of prostate-specific antigen measured using immune extraction, trypsin digestion, and tandem mass spectrometry quantification of LSEPAELTDAVK peptide. Arch Pathol Lab Med. 2014 Oct; 138(10):1381-6.
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  20. Camilleri M, Carlson P, Acosta A, Busciglio I, Nair AA, Gibbons SJ, Farrugia G, Klee EW. RNA sequencing shows transcriptomic changes in rectosigmoid mucosa in patients with irritable bowel syndrome-diarrhea: a pilot case-control study. Am J Physiol Gastrointest Liver Physiol 2014 Jun 15; 306 (12):G1089-98 Epub 2014 Apr 24
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  21. Klee EW, Bondar OP, Goodmanson MK, Trushin SA, Singh RJ, Anderson NL, Klee GG. Mass spectrometry measurements of prostate-specific antigen (PSA) peptides derived from immune-extracted PSA provide a potential strategy for harmonizing immunoassay differences. Am J Clin Pathol. 2014 Apr; 141(4):527-33.
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  22. Lazaridis KN, McAllister TM, Babovic-Vuksanovic D, Beck SA, Borad MJ, Bryce AH, Chanan-Khan AA, Ferber MJ, Fonseca R, Johnson KJ, Klee EW, Lindor NM, McCormick JB, McWilliams RR, Parker AS, Riegert-Johnson DL, Rohrer Vitek CR, Schahl KA, Schultz C, Stewart K, Then GC, Wieben ED, Farrugia G. Stewart K, Then GC, Wieben ED, Farrugia G. Implementing individualized medicine into the medical practice. Am J Med Genet C Semin Med Genet. 2014 Mar; 166C(1):15-23. Epub 2014 Mar 10.
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  23. Pickart MA, Klee EW. Zebrafish approaches enhance the translational research tackle box. Transl Res. 2014 Feb; 163(2):65-78. Epub 2013 Nov 02.
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  24. Borad MJ, Champion MD, Egan JB, Liang WS, Fonseca R, Bryce AH, McCullough AE, Barrett MT, Hunt K, Patel MD, Young SW, Collins JM, Silva AC, Condjella RM, Block M, McWilliams RR, Lazaridis KN, Klee EW, Bible KC, Harris P, Oliver GR, Bhavsar JD, Nair AA, Middha S, Asmann Y, Kocher JP, Schahl K, Kipp BR, Barr Fritcher EG, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Phillips L, McDonald J, Adkins J, Mastrian SD, Placek P, Watanabe AT, Lobello J, Han H, Von Hoff D, Craig DW, Stewart AK, Carpten JD. Middha S, Asmann Y, Kocher JP, Schahl K, Kipp BR, Barr Fritcher EG, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Phillips L, McDonald J, Adkins J, Mastrian SD, Placek P, Watanabe AT, Lobello J, Han H, et al. Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. PLoS Genet. 2014 Feb; 10(2):e1004135. Epub 2014 Feb 13.
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  25. Camilleri M, Klee EW, Shin A, Carlson P, Li Y, Grover M, Zinsmeister AR. Irritable bowel syndrome-diarrhea: characterization of genotype by exome sequencing, and phenotypes of bile acid synthesis and colonic transit. Am J Physiol Gastrointest Liver Physiol 2014 Jan 1; 306 (1):G13-26 Epub 2013 Nov 07
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  26. Bielinski SJ, Olson JE, Pathak J, Weinshilboum RM, Wang L, Lyke KJ, Ryu E, Targonski PV, Van Norstrand MD, Hathcock MA, Takahashi PY, McCormick JB, Johnson KJ, Maschke KJ, Rohrer Vitek CR, Ellingson MS, Wieben ED, Farrugia G, Morrisette JA, Kruckeberg KJ, Bruflat JK, Peterson LM, Blommel JH, Skierka JM, Ferber MJ, Black JL, Baudhuin LM, Klee EW, Ross JL, Veldhuizen TL, Schultz CG, Caraballo PJ, Freimuth RR, Chute CG, Kullo IJ. KJ, Bruflat JK, Peterson LM, Blommel JH, Skierka JM, Ferber MJ, Black JL, Baudhuin LM, Klee EW, Ross JL, Veldhuizen TL, Schultz CG, Caraballo PJ, Freimuth RR, Chute CG, Kullo IJ. Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol. Mayo Clin Proc. 2014 Jan; 89(1):25-33.
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  27. Veldhuis JD, Bondar OP, Dyer RB, Trushin SA, Klee EW, Singh RJ, Klee GG. Immunological and mass spectrometric assays of SHBG: consistent and inconsistent metabolic associations in healthy men. J Clin Endocrinol Metab. 2014 Jan; 99(1):184-93. Epub 2013 Dec 20.
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  28. Singh M, Bhartiya D, Maini J, Sharma M, Singh AR, Kadarkaraisamy S, Rana R, Sabharwal A, Nanda S, Ramachandran A, Mittal A, Kapoor S, Sehgal P, Asad Z, Kaushik K, Vellarikkal SK, Jagga D, Muthuswami M, Chauhan RK, Leonard E, Priyadarshini R, Halimani M, Malhotra S, Patowary A, Vishwakarma H, Joshi P, Bhardwaj V, Bhaumik A, Bhatt B, Jha A, Kumar A, Budakoti P, Lalwani MK, Meli R, Jalali S, Joshi K, Pal K, Dhiman H, Laddha SV, Jadhav V, Singh N, Pandey V, Sachidanandan C, Ekker SC, Klee EW, Scaria V, Sivasubbu S. Malhotra S, Patowary A, Vishwakarma H, Joshi P, Bhardwaj V, Bhaumik A, Bhatt B, Jha A, Kumar A, Budakoti P, Lalwani MK, Meli R, Jalali S, Joshi K, Pal K, Dhiman H, Laddha SV, Jadhav V, Singh N, Pandey V, Sachidanandan C, Ekker SC, Klee EW, et al. The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. Database (Oxford). 2014; 2014:bau011. Epub 2014 Feb 26.
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  29. Cousin MA, Ebbert JO, Wiinamaki AR, Urban MD, Argue DP, Ekker SC, Klee EW. Larval zebrafish model for FDA-approved drug repositioning for tobacco dependence treatment. PLoS One. 2014; 9(3):e90467. Epub 2014 Mar 21.
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  30. Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher JP, Clark KJ, Stemple DL, Klee EW, Ekker SC, Scaria V, Sivasubbu S. A sequence-based variation map of zebrafish. Zebrafish. 2013 Mar; 10(1):15-20.
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  31. 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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  32. Aggarwal G, Ramachandran V, Javeed N, Arumugam T, Dutta S, Klee GG, Klee EW, Smyrk TC, Bamlet W, Han JJ, Rumie Vittar NB, de Andrade M, Mukhopadhyay D, Petersen GM, Fernandez-Zapico ME, Logsdon CD, Chari ST. Adrenomedullin is up-regulated in patients with pancreatic cancer and causes insulin resistance in beta cells and mice. Gastroenterology. 2012 Dec; 143(6):1510-1517.e1. Epub 2012 Sep 06.
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  33. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics. 2012 Aug 15; 28(16):2180-1. Epub 2012 Jun 10.
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  34. Klee EW, Schneider H, Clark KJ, Cousin MA, Ebbert JO, Hooten WM, Karpyak VM, Warner DO, Ekker SC. Zebrafish: a model for the study of addiction genetics. Hum Genet. 2012 Jun; 131(6):977-1008. Epub 2011 Dec 30.
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  35. Mahapatra S, Klee EW, Young CY, Sun Z, Jimenez RE, Klee GG, Tindall DJ, Donkena KV. Global methylation profiling for risk prediction of prostate cancer. Clin Cancer Res. 2012 May 15; 18(10):2882-95.
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  36. Klee EW, Bondar OP, Goodmanson MK, Dyer RB, Erdogan S, Bergstralh EJ, Bergen HR 3rd, Sebo TJ, Klee GG. Candidate serum biomarkers for prostate adenocarcinoma identified by mRNA differences in prostate tissue and verified with protein measurements in tissue and blood. Clin Chem. 2012 Mar; 58(3):599-609. Epub 2012 Jan 12.
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  37. Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics. 2012 Jan 15; 28(2):277-8. Epub 2011 Nov 15.
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  38. Mahapatra S, Young CY, Kohli M, Karnes RJ, Klee EW, Holmes MW, Tindall DJ, Donkena KV. Antiangiogenic Effects and Therapeutic Targets of Azadirachta indica Leaf Extract in Endothelial Cells. Evid Based Complement Alternat Med. 2012; 2012:303019. Epub 2012 Feb 22.
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  39. Mahapatra S, Karnes RJ, Holmes MW, Young CY, Cheville JC, Kohli M, Klee EW, Tindall DJ, Donkena KV. Novel molecular targets of Azadirachta indica associated with inhibition of tumor growth in prostate cancer. AAPS J. 2011 Sep; 13(3):365-77. Epub 2011 May 11.
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  40. Klee EW, Hoppman-Chaney NL, Ferber MJ. Expanding DNA diagnostic panel testing: is more better? Expert Rev Mol Diagn. 2011 Sep; 11(7):703-9.
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  41. Bielinski SJ, Chai HS, Pathak J, Talwalkar JA, Limburg PJ, Gullerud RE, Sicotte H, Klee EW, Ross JL, Kocher JP, Kullo IJ, Heit JA, Petersen GM, de Andrade M, Chute CG. Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels. Mayo Clin Proc. 2011 Jul; 86(7):606-14. Epub 2011 Jun 06.
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  42. Klee EW, Ebbert JO, Schneider H, Hurt RD, Ekker SC. Zebrafish for the study of the biological effects of nicotine. Nicotine Tob Res. 2011 May; 13(5):301-12. Epub 2011 Mar 08.
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  43. Hoppman-Chaney N, Peterson LM, Klee EW, Middha S, Courteau LK, Ferber MJ. Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics. Clin Chem. 2010 Aug; 56(8):1297-306. Epub 2010 Jun 18.
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  44. Ebbert JO, Wyatt KD, Hays JT, Klee EW, Hurt RD. Varenicline for smoking cessation: efficacy, safety, and treatment recommendations. Patient Prefer Adherence. 2010; 4:355-62. Epub 2010 Oct 05.
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  45. Erdogan E, Klee EW, Thompson EA, Fields AP. Meta-analysis of oncogenic protein kinase Ciota signaling in lung adenocarcinoma. Clin Cancer Res. 2009 Mar 1; 15(5):1527-33. Epub 2009 Feb 17.
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  46. Klee EW, Erdogan S, Tillmans L, Kosari F, Sun Z, Wigle DA, Yang P, Aubry MC, Vasmatzis G. Impact of sample acquisition and linear amplification on gene expression profiling of lung adenocarcinoma: laser capture micro-dissection cell-sampling versus bulk tissue-sampling. BMC Med Genomics. 2009; 2:13. Epub 2009 Mar 09.
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  47. Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, Smith DI, Poland GA, Wieben ED, Kocher JP. 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics. 2009; 10:531. Epub 2009 Nov 16.
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  48. Cheville JC, Karnes RJ, Therneau TM, Kosari F, Munz JM, Tillmans L, Basal E, Rangel LJ, Bergstralh E, Kovtun IV, Savci-Heijink CD, Klee EW, Vasmatzis G. Gene panel model predictive of outcome in men at high-risk of systemic progression and death from prostate cancer after radical retropubic prostatectomy. J Clin Oncol. 2008 Aug 20; 26(24):3930-6.
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  49. Gerszten RE, Accurso F, Bernard GR, Caprioli RM, Klee EW, Klee GG, Kullo I, Laguna TA, Roth FP, Sabatine M, Srinivas P, Wang TJ, Ware LB. Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs. Am J Physiol Lung Cell Mol Physiol. 2008 Jul; 295(1):L16-22. Epub 2008 May 02.
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  50. Klee EW. The zebrafish secretome. Zebrafish. 2008 Summer; 5(2):131-8.
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  51. Kosari F, Munz JM, Savci-Heijink CD, Spiro C, Klee EW, Kube DM, Tillmans L, Slezak J, Karnes RJ, Cheville JC, Vasmatzis G. Identification of prognostic biomarkers for prostate cancer. Clin Cancer Res. 2008 Mar 15; 14(6):1734-43.
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  52. Klee EW. Data mining for biomarker development: a review of tissue specificity analysis. Clin Lab Med. 2008 Mar; 28(1):127-43, viii.
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  53. Vasmatzis G, Klee EW, Kube DM, Therneau TM, Kosari F. Quantitating tissue specificity of human genes to facilitate biomarker discovery. Bioinformatics. 2007 Jun 1; 23(11):1348-55. Epub 2007 Mar 23.
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  54. Bondar OP, Barnidge DR, Klee EW, Davis BJ, Klee GG. LC-MS/MS quantification of Zn-alpha2 glycoprotein: a potential serum biomarker for prostate cancer. Clin Chem. 2007 Apr; 53(4):673-8. Epub 2007 Feb 22.
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  55. Klee EW, Sosa CP. Computational classification of classically secreted proteins. Drug Discov Today. 2007 Mar; 12(5-6):234-40. Epub 2007 Feb 09.
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  56. Klee EW, Finlay JA, McDonald C, Attewell JR, Hebrink D, Dyer R, Love B, Vasmatzis G, Li TM, Beechem JM, Klee GG. Bioinformatics methods for prioritizing serum biomarker candidates. Clin Chem. 2006 Nov; 52(11):2162-4.
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  57. Finlay JA, Klee EW, McDonald C, Attewell JR, Hebrink D, Dyer R, Love B, Vasmatzis G, Li TM, Beechem JM, Klee GG. A systematic method for selection of promising serum protein biomarkers to improve prostate cancer (PCa1) detection. Clin Chem. 2006 Nov; 52(11):2159-62.
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  58. Pickart MA, Klee EW, Nielsen AL, Sivasubbu S, Mendenhall EM, Bill BR, Chen E, Eckfeldt CE, Knowlton M, Robu ME, Larson JD, Deng Y, Schimmenti LA, Ellis LB, Verfaillie CM, Hammerschmidt M, Farber SA, Ekker SC. Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome. PLoS One. 2006; 1:e104. Epub 2006 Dec 20.
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  59. Klee EW, Shim KJ, Pickart MA, Ekker SC, Ellis LB. AMOD: a morpholino oligonucleotide selection tool. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue):W506-11.
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  60. Klee EW, Ellis LB. Evaluating eukaryotic secreted protein prediction. BMC Bioinformatics. 2005; 6:256 Epub 2005 Oct 14.
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  61. Klee EW, Carlson DF, Fahrenkrug SC, Ekker SC, Ellis LB. Identifying secretomes in people, pufferfish and pigs. Nucleic Acids Res. 2004 Feb 27; 32(4):1414-21.
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  62. Klee EW, Ekker SC, Ellis LB. Target selection for Danio rerio functional genomics. Genesis. 2001 Jul; 30(3):123-5.
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