Publications

  1. Winham SJ, Cuellar-Barboza AB, Oliveros A, McElroy SL, Crow S, Colby C, Choi DS, Chauhan M, Frye M, Biernacka JM. Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2. Mol Psychiatry. 2014 Sep; 19(9):1010-6. Epub 2013 Dec 10.
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  2. Winham SJ, Cuellar-Barboza AB, McElroy SL, Oliveros A, Crow S, Colby CL, Choi DS, Chauhan M, Frye MA, Biernacka JM. Bipolar disorder with comorbid binge eating history: a genome-wide association study implicates APOB. J Affect Disord. 2014 Aug; 165:151-8. Epub 2014 Apr 19.
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  3. Markopoulou K, Biernacka JM, Armasu SM, Anderson KJ, Ahlskog JE, Chase BA, Chung SJ, Cunningham JM, Farrer M, Frigerio R, Maraganore DM. Does alpha-synuclein have a dual and opposing effect in preclinical vs. clinical Parkinson's disease? Parkinsonism Relat Disord. 2014 Jun; 20(6):584-9; discussion 584. Epub 2014 Mar 05.
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  4. Mrazek DA, Biernacka JM, McAlpine DE, Benitez J, Karpyak VM, Williams MD, Hall-Flavin DK, Netzel PJ, Passov V, Rohland BM, Shinozaki G, Hoberg AA, Snyder KA, Drews MS, Skime MK, Sagen JA, Schaid DJ, Weinshilboum R, Katzelnick DJ. Treatment outcomes of depression: the pharmacogenomic research network antidepressant medication pharmacogenomic study. J Clin Psychopharmacol. 2014 Jun; 34(3):313-7.
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  5. Karpyak VM, Winham SJ, Biernacka JM, Cunningham JM, Lewis KA, Geske JR, Colby CL, Abulseoud OA, Hall-Flavin DK, Loukianova LL, Schneekloth TD, Frye MA, Heit JA, Mrazek DA. Association of GATA4 sequence variation with alcohol dependence. Addict Biol. 2014 Mar; 19(2):312-5. Epub 2012 Aug 02.
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  6. Fridley BL, Abo R, Tan XL, Jenkins GD, Batzler A, Moyer AM, Biernacka JM, Wang L. Integrative gene set analysis: application to platinum pharmacogenomics. OMICS. 2014 Jan; 18(1):34-41. Epub 2013 Nov 07.
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  7. Kolla BP, Schneekloth T, Biernacka J, Mansukhani M, Geske J, Karpyak V, Hall-Flavin D, Louikianova L, Frye MA. The course of sleep disturbances in early alcohol recovery: an observational cohort study. Am J Addict. 2014 Jan-Feb; 23(1):21-6. Epub 2013 Jun 6
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  8. Karpyak VM, Biernacka JM, Geske JR, Jenkins GD, Cunningham JM, Ruegg J, Kononenko O, Leontovich AA, Abulseoud OA, Hall-Flavin DK, Loukianova LL, Schneekloth TD, Skime MK, Frank J, Nothen MM, Rietschel M, Kiefer F, Mann KF, Weinshilboum RM, Frye MA, Choi Genetic markers associated with abstinence length in alcohol-dependent subjects treated with acamprosate. Transl Psychiatry. 2014; 4:e453. Epub 2014 Oct 07.
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  9. Karpyak VM, Winham SJ, Biernacka JM, Cunningham JM, Lewis KA, Geske JR, Colby CL, Abulseoud OA, Hall-Flavin DK, Loukianova LL, Schneekloth TD, Frye MA, Heit JA, Mrazek DA. Association of GATA4 sequence variation with alcohol dependence. Addict Biol. 2014; 19(2):312-5.
  10. Chung SJ, Biernacka JM, Armasu SM, Anderson K, Frigerio R, Aasly JO, Annesi G, Bentivoglio AR, Brighina L, Chartier-Harlin MC, Goldwurm S, Hadjigeorgiou G, Jasinska-Myga B, Jeon BS, Kim YJ, Krüger R, Lesage S, Markopoulou K, Mellick G, Morrison KE, Alpha-synuclein repeat variants and survival in Parkinson's disease. Mov Disord. 2014; 29(8):1053-7.
  11. Winham SJ, Freimuth RR, Biernacka JM. A Weighted Random Forests Approach to Improve Predictive Performance. Stat Anal Data Min. 2013 Dec 1; 6(6):496-505.
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  12. Winham SJ, Biernacka JM. Gene-environment interactions in genome-wide association studies: current approaches and new directions. J Child Psychol Psychiatry. 2013 Oct; 54(10):1120-34. Epub 2013 Jun 28.
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  13. Ji Y, Biernacka JM, Hebbring S, Chai Y, Jenkins GD, Batzler A, Snyder KA, Drews MS, Desta Z, Flockhart D, Mushiroda T, Kubo M, Nakamura Y, Kamatani N, Schaid D, Weinshilboum RM, Mrazek DA. Pharmacogenomics of selective serotonin reuptake inhibitor treatment for major depressive disorder: genome-wide associations and functional genomics. Pharmacogenomics J. 2013 Oct; 13(5):456-63. Epub 2012 Aug 21.
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  14. McElroy SL, Crow S, Biernacka JM, Winham S, Geske J, Cuellar Barboza AB, Prieto ML, Chauhan M, Seymour LR, Mori N, Frye MA. Clinical phenotype of bipolar disorder with comorbid binge eating disorder. J Affect Disord. 2013 Sep 25; 150(3):981-6. Epub 2013 Jun 03.
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  15. Abulseoud OA, Karpyak VM, Schneekloth T, Hall-Flavin DK, Loukianova LL, Geske JR, Biernacka JM, Mrazek DA, Frye MA. A retrospective study of gender differences in depressive symptoms and risk of relapse in patients with alcohol dependence. Am J Addict. 2013 Sep-Oct; 22(5):437-42. Epub 2013 May 30.
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  16. Karpyak VM, Winham SJ, Preuss UW, Zill P, Cunningham JM, Walker DL, Lewis KA, Geske JR, Colby CL, Abulseoud OA, Hall-Flavin DK, Loukianova LL, Schneekloth TD, Frye MA, Bazov I, Heit JA, Bakalkin G, Mrazek DA, Biernacka JM. Association of the PDYN gene with alcohol dependence and the propensity to drink in negative emotional states. Int J Neuropsychopharmacol. 2013 Jun; 16(5):975-85. Epub 2012 Oct 29.
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  17. Chung SJ, Armasu SM, Anderson KJ, Biernacka JM, Lesnick TG, Rider DN, Cunningham JM, Ahlskog JE, Frigerio R, Maraganore DM. Genetic susceptibility loci, environmental exposures, and Parkinson's disease: a case-control study of gene-environment interactions. Parkinsonism Relat Disord. 2013 Jun; 19(6):595-9. Epub 2013 Mar 16.
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  18. Biernacka JM, Geske J, Jenkins GD, Colby C, Rider DN, Karpyak VM, Choi DS, Fridley BL. Genome-wide gene-set analysis for identification of pathways associated with alcohol dependence. Int J Neuropsychopharmacol. 2013 Mar; 16(2):271-8. Epub 2012 May 02.
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  19. Ellsworth KA, Moon I, Eckloff BW, Fridley BL, Jenkins GD, Batzler A, Biernacka JM, Abo R, Brisbin A, Ji Y, Hebbring S, Wieben ED, Mrazek DA, Weinshilboum RM, Wang L. FKBP5 genetic variation: association with selective serotonin reuptake inhibitor treatment outcomes in major depressive disorder. Pharmacogenet Genomics. 2013 Mar; 23(3):156-66.
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  20. Preuss UW, Winham SJ, Biernacka JM, Geske JR, Bakalkin G, Koller G, Zill P, Soyka M, Karpyak VM. PDYN rs2281285 variant association with drinking to avoid emotional or somatic discomfort. PLoS One. 2013; 8(11):e78688. Epub 2013 Nov 06.
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  21. Biernacka JM, Geske JR, Schneekloth TD, Frye MA, Cunningham JM, Choi DS, Tapp CL, Lewis BR, Drews MS, L Pietrzak T, Colby CL, Hall-Flavin DK, Loukianova LL, Heit JA, Mrazek DA, Karpyak VM. Replication of genome wide association studies of alcohol dependence: support for association with variation in ADH1C. PLoS One. 2013; 8(3):e58798. Epub 2013 Mar 13.
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  22. Manchia M, Adli M, Akula N, Ardau R, Aubry JM, Backlund L, Banzato CE, Baune BT, Bellivier F, Bengesser S, Biernacka JM, Brichant-Petitjean C, Bui E, Calkin CV, Cheng AT, Chillotti C, Cichon S, Clark S, Czerski PM, Dantas C, Zompo MD, Depaulo JR, Detera-W Assessment of Response to Lithium Maintenance Treatment in Bipolar Disorder: A Consortium on Lithium Genetics (ConLiGen) Report. PLoS One. 2013; 8(6):e65636. Epub 2013 Jun 19
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  23. Schneekloth TD, Biernacka JM, Hall-Flavin DK, Karpyak VM, Frye MA, Loukianova LL, Stevens SR, Drews MS, Geske JR, Mrazek DA. Alcohol craving as a predictor of relapse. Am J Addict. 2012 Nov; 21 Suppl 1:S20-6.
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  24. Chung SJ, Armasu SM, Biernacka JM, Anderson KJ, Lesnick TG, Rider DN, Cunningham JM, Eric Ahlskog J, Frigerio R, Maraganore DM. Genomic determinants of motor and cognitive outcomes in Parkinson's disease. Parkinsonism Relat Disord. 2012 Aug; 18(7):881-6. Epub 2012 May 30.
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  25. Karpyak VM, Geske JR, Colby CL, Mrazek DA, Biernacka JM. Genetic variability in the NMDA-dependent AMPA trafficking cascade is associated with alcohol dependence. Addict Biol. 2012 Jul; 17(4):798-806. Epub 2011 Jul 18.
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  26. Biernacka JM, Jenkins GD, Wang L, Moyer AM, Fridley BL. Use of the gamma method for self-contained gene-set analysis of SNP data. Eur J Hum Genet. 2012 May; 20(5):565-71. Epub 2011 Dec 14.
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  27. Abo R, Hebbring S, Ji Y, Zhu H, Zeng ZB, Batzler A, Jenkins GD, Biernacka J, Snyder K, Drews M, Fiehn O, Fridley B, Schaid D, Kamatani N, Nakamura Y, Kubo M, Mushiroda T, Kaddurah-Daouk R, Mrazek DA, Weinshilboum RM. Merging pharmacometabolomics with pharmacogenomics using '1000 Genomes' single-nucleotide polymorphism imputation: selective serotonin reuptake inhibitor response pharmacogenomics. Pharmacogenet Genomics. 2012 Apr; 22(4):247-53.
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  28. Schneekloth TD, Jowsey SG, Biernacka JM, Burton MC, Vasquez AR, Bergquist T, Drews MS, Gores GJ. Pretransplant psychiatric and substance use comorbidity in patients with cholangiocarcinoma who received a liver transplant. Psychosomatics. 2012 Mar-Apr; 53(2):116-22.
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  29. Ji Y, Biernacka J, Snyder K, Drews M, Pelleymounter LL, Colby C, Wang L, Mrazek DA, Weinshilboum RM. Catechol O-methyltransferase pharmacogenomics and selective serotonin reuptake inhibitor response. Pharmacogenomics J. 2012 Feb; 12(1):78-85. Epub 2010 Sep 28.
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  30. Biernacka JM, McElroy SL, Crow S, Sharp A, Benitez J, Veldic M, Kung S, Cunningham JM, Post RM, Mrazek D, Frye MA. Pharmacogenomics of antidepressant induced mania: a review and meta-analysis of the serotonin transporter gene (5HTTLPR) association. J Affect Disord. 2012 Jan; 136(1-2):e21-9. Epub 2011 Jun 15.
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  31. Hall-Flavin DK, Winner JG, Allen JD, Jordan JJ, Nesheim RS, Snyder KA, Drews MS, Eisterhold LL, Biernacka JM, Mrazek DA. Using a pharmacogenomic algorithm to guide the treatment of depression. Transl Psychiatry. 2012; 2:e172. Epub 2012 Oct 16.
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  32. Winham SJ, Colby CL, Freimuth RR, Wang X, de Andrade M, Huebner M, Biernacka JM. SNP interaction detection with Random Forests in high-dimensional genetic data. BMC Bioinformatics. 2012; 13:164. Epub 2012 Jul 15
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  33. Lill CM, Roehr JT, McQueen MB, Kavvoura FK, Bagade S, Schjeide BM, Schjeide LM, Meissner E, Zauft U, Allen NC, Liu T, Schilling M, Anderson KJ, Beecham G, Berg D, Biernacka JM, Brice A, DeStefano AL, Do CB, Eriksson N, Factor SA, Farrer MJ, Foroud T, Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database. PLoS Genet. 2012; 8(3):e1002548. Epub 2012 Mar 15.
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  34. Shinozaki G, Jowsey S, Amer H, Biernacka J, Colby C, Walker D, Black J, Rundell J, Stegall M, Mrazek DA. Relationship between FKBP5 polymorphisms and depression symptoms among kidney transplant recipients. Depress Anxiety. 2011 Dec 21; 28(12):1111-8. Epub 2011 Aug 24.
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  35. Biernacka JM, Armasu SM, Cunningham JM, Ahlskog JE, Chung SJ, Maraganore DM. Do interactions between SNCA, MAPT, and LRRK2 genes contribute to Parkinson's disease susceptibility? Parkinsonism Relat Disord. 2011 Dec; 17(10):730-6. Epub 2011 Aug 03.
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  36. Kolla BP, Schneekloth TD, Biernacka JM, Frye MA, Mansukhani MP, Hall-Flavin DK, Karpyak VM, Loukianova LL, Lesnick TG, Mrazek D. Trazodone and alcohol relapse: a retrospective study following residential treatment. Am J Addict. 2011 Nov-Dec; 20(6):525-9. Epub 2011 Sep 29.
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  37. Fridley BL, Biernacka JM. Gene set analysis of SNP data: benefits, challenges, and future directions. Eur J Hum Genet. 2011 Aug; 19(8):837-43. Epub 2011 Apr 13.
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  38. Chung SJ, Armasu SM, Biernacka JM, Lesnick TG, Rider DN, Cunningham JM, Maraganore DM. Variants in estrogen-related genes and risk of Parkinson's disease. Mov Disord. 2011 Jun; 26(7):1234-42. Epub 2011 Apr 05.
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  39. Chung SJ, Armasu SM, Biernacka JM, Lesnick TG, Rider DN, Lincoln SJ, Ortolaza AI, Farrer MJ, Cunningham JM, Rocca WA, Maraganore DM. Common variants in PARK loci and related genes and Parkinson's disease. Mov Disord. 2011 Feb 1; 26(2):280-8. Epub 2010 Dec 13
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  40. McAlpine DE, Biernacka JM, Mrazek DA, O'Kane DJ, Stevens SR, Langman LJ, Courson VL, Bhagia J, Moyer TP. Effect of cytochrome P450 enzyme polymorphisms on pharmacokinetics of venlafaxine. Ther Drug Monit. 2011 Feb; 33(1):14-20.
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  41. Ji Y, Hebbring S, Zhu H, Jenkins GD, Biernacka J, Snyder K, Drews M, Fiehn O, Zeng Z, Schaid D, Mrazek DA, Kaddurah-Daouk R, Weinshilboum RM. Glycine and a glycine dehydrogenase (GLDC) SNP as citalopram/escitalopram response biomarkers in depression: pharmacometabolomics-informed pharmacogenomics. Clin Pharmacol Ther. 2011 Jan; 89(1):97-104. Epub 2010 Nov 24.
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  42. Mrazek DA, Biernacka JM, O'Kane DJ, Black JL, Cunningham JM, Drews MS, Snyder KA, Stevens SR, Rush AJ, Weinshilboum RM. CYP2C19 variation and citalopram response. Pharmacogenet Genomics. 2011 Jan; 21(1):1-9.
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  43. Hall-Flavin DK, Schneekloth TD, Loukianova LL, Karpyak VM, Lesnick TG, Biernacka JM, Mrazek DA, Frye MA. Utilization of residential alcoholism treatment in bipolar disorder. Am J Addict. 2011 Jan-Feb; 20(1):40-4. Epub 2010 Nov 12.
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  44. Schneekloth TD, Biernacka JM, Hall-Flavin DK, Karpyak VM, Frye MA, Loukianova LL, Stevens SR, Drews MS, Geske JR, Mrazek DA. Alcohol Craving as a Predictor of Relapse. Am J Addict. 2011(in Press).
  45. Kim JH, Karpyak VM, Biernacka JM, Nam HW, Lee MR, Preuss UW, Zill P, Yoon G, Colby C, Mrazek DA, Choi DS. Functional role of the polymorphic 647 T/C variant of ENT1 (SLC29A1) and its association with alcohol withdrawal seizures. PLoS One. 2011; 6(1):e16331. Epub 2011 Jan 24.
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  46. Boykoff N, Schneekloth TD, Hall-Flavin D, Loukianova L, Karpyak VM, Stevens SR, Biernacka JM, Mrazek DA, Frye MA. Gender differences in the relationship between depressive symptoms and cravings in alcoholism. Am J Addict. 2010 Jul-Aug; 19(4):352-6.
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  47. Karpyak VM, Biernacka JM, Weg MW, Stevens SR, Cunningham JM, Mrazek DA, Black JL. Interaction of SLC6A4 and DRD2 polymorphisms is associated with a history of delirium tremens. Addict Biol. 2010 Jan; 15(1):23-34.
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  48. Fridley BL, Jenkins GD, Biernacka JM. Self-contained gene-set analysis of expression data: an evaluation of existing and novel methods. PLoS One. 2010; 5(9). Epub 2010 Sep 17.
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  49. Biernacka JM, Cordell HJ. A composite-likelihood approach for identifying polymorphisms that are potentially directly associated with disease. Eur J Hum Genet. 2009 May; 17(5):644-50. Epub 2008 Dec 17.
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  50. Mrazek DA, Rush AJ, Biernacka JM, O'Kane DJ, Cunningham JM, Wieben ED, Schaid DJ, Drews MS, Courson VL, Snyder KA, Black JL 3rd, Weinshilboum RM. SLC6A4 variation and citalopram response. Am J Med Genet B Neuropsychiatr Genet. 2009 Apr 5; 150B(3):341-51.
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  51. Karpyak VM, Kim JH, Biernacka JM, Wieben ED, Mrazek DA, Black JL, Choi DS. Sequence variations of the human MPDZ gene and association with alcoholism in subjects with European ancestry. Alcohol Clin Exp Res. 2009 Apr; 33(4):712-21. Epub 2009 Jan 21.
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  52. Biernacka JM, Tang R, Li J, McDonnell SK, Rabe KG, Sinnwell JP, Rider DN, de Andrade M, Goode EL, Fridley BL. Assessment of genotype imputation methods. BMC Proc. 2009; 3 Suppl 7:S5. Epub 2009 Dec 15.
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  53. Li J, Tang R, Biernacka JM, de Andrade M. Identification of gene-gene interaction using principal components. BMC Proc. 2009; 3 Suppl 7:S78. Epub 2009 Dec 15.
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  54. Fridley BL, McDonnell SK, Rabe KG, Tang R, Biernacka JM, Sinnwell JP, Rider DN, Goode EL. Single versus multiple imputation for genotypic data. BMC Proc. 2009; 3 Suppl 7:S7. Epub 2009 Dec 15.
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  55. Tang R, Sinnwell JP, Li J, Rider DN, de Andrade M, Biernacka JM. Identification of genes and haplotypes that predict rheumatoid arthritis using random forests. BMC Proc. 2009; 3 Suppl 7:S68. Epub 2009 Dec 15.
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  56. Szymczak S, Biernacka JM, Cordell HJ, Gonzalez-Recio O, Konig IR, Zhang H, Sun YV. Machine learning in genome-wide association studies. Genet Epidemiol. 2009; 33 Suppl 1:S51-7.
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  57. Biernacka JM, Cordell HJ. Exploring causality via identification of SNPs or haplotypes responsible for a linkage signal. Genet Epidemiol. 2007 Nov; 31(7):727-40.
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  58. Biernacka JM, Charoen P, Cordell HJ. Joint linkage and association analysis for identification of potentially causal polymorphisms in GAW15 data. BMC Proc. 2007; 1 Suppl 1:S36. Epub 2007 Dec 18.
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  59. Charoen P, Biernacka JM, Cordell HJ. Linkage and association analysis of GAW15 simulated data: fine-mapping of chromosome 6 region. BMC Proc. 2007; 1 Suppl 1:S23. Epub 2007 Dec 18.
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  60. Sherva R, Sun L, Biernacka J, Neuman R. No evidence for multiple loci affecting rheumatoid arthritis risk on chromosome 6p21. BMC Proc. 2007; 1 Suppl 1:S42. Epub 2007 Dec 18.
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  61. Yang Q, Biernacka JM, Chen MH, Houwing-Duistermaat JJ, Bergemann TL, Basu S, Fan R, Liu L, Bourgey M, Clerget-Darpoux F, Lin WY, Elston RC, Cupples LA. Using linkage and association to identify and model genetic ettects: Summary of GAW15 group 4. Genet Epidemiol. 2007; 31(Suppl 1):S34-S42.
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  62. Biernacka JM, Cordell HJ. Perils and pitfalls of permutation tests for distinguishing the effects of neighbouring polymorphisms. Genet Epidemiol. 2006 Nov; 30(7):582-9.
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  63. Farooqi IS, Drop S, Clements A, Keogh JM, Biernacka J, Lowenbein S, Challis BG, O'Rahilly S. Heterozygosity for a POMC-null mutation and increased obesity risk in humans. Diabetes. 2006 Sep; 55(9):2549-53.
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  64. Lewinger JP, Lee SS, Biernacka J, Wu LY, Shi HS, Bull SB. Comparison of family-based association tests in chromosome regions selected by linkage-based confidence intervals. BMC Genet. 2005 Dec 30; 6 Suppl 1:S62. Epub 2005 Dec 30.
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  65. Biernacka JM, Sun L, Bull SB. Tests for the presence of two linked disease susceptibility genes. Genet Epidemiol. 2005 Dec; 29(4):389-401.
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  66. Biernacka JM, Sun L, Bull SB. Simultaneous localization of two linked disease susceptibility genes. Genet Epidemiol. 2005 Jan; 28(1):33-47.
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  67. Biernacka J, Lewinger JP, Chan V, Bull SB. Does simultaneous consideration of multiple regions improve disease gene localization? Genet Epidemiol. 2001; 21 Suppl 1:S504-9.
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