Publications

  1. 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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  2. 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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  3. 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, Implementing individualized medicine into the medical practice. Am J Med Genet C Semin Med Genet. 2014 Mar; 166(1):15-23. Epub 2014 Mar 10.
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  4. 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, 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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  5. 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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  6. 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 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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  7. 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, 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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  8. 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. American Journal of Physiology - Gastrointestinal and Liver Physiology. 2014; 306(1):G13-26.
  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. Klee EW. The zebrafish secretome. Zebrafish. 2008 Summer; 5(2):131-8.
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  31. 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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  32. 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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  33. 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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  34. 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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  35. Klee EW, Sosa CP. Computational classification of classically secreted proteins. Drug Discovery Today Review. 2007 Mar; 12(5-6):234-40.
  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. Klee EW, Ellis LB. Evaluating eukaryotic secreted protein prediction. BMC Bioinformatics. 2005; 6:256 Epub 2005 Oct 14.
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  42. 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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  43. Klee EW, Ekker SC, Ellis LB. Target selection for Danio rerio functional genomics. Genesis. 2001 Jul; 30(3):123-5.
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