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BCGC Publications

  1. Astermark J, Donfield SM, Gomperts ED, Schwarz J, Menius ED, Pavlova A, Oldenburg J, Kessing B, DiMichele DM, Shapiro AD, Winkler CA, Berntorp E; Hemophilia Inhibitor Genetics Study (HIGS) Combined Cohort. The polygenic nature of inhibitors in hemophilia A: results from the Hemophilia Inhibitor Genetics Study (HIGS) Combined Cohort. Blood. 2013 Feb 21;121(8):1446-54. doi: 10.1182/blood-2012-06-434803. Epub 2012 Dec 6.
  2. Harris M, Burns CM, Becker EA, Braasch AT, Gostick E, Johnson RC, Broman KW, Price DA, Friedrich TC, O'Connor SL. Acute-phase CD8 T cell responses that select for escape variants are needed to control live attenuated simian immunodeficiency virus, Journal of Virology, 2013, 87 (16), 9353–9364
  3. Deep sequencing and Circos analyses of antibody libraries reveal antigen-driven selection of Ig VH genes during HIV-1 infection. Xiao M, Prabakaran P, Chen W, Kessing B, Dimitrov DS. Exp Mol Pathol. 2013 Oct 21. pii: S0014-4800(13)00121-4. doi: 10.1016/j.yexmp.2013.10.004. [Epub ahead of print] PMID: 24158018 [PubMed - as supplied by publisher] Related citations
  4. Tang M, Lautenberger JA, Gao X, Sezgin E, Hendrickson SL, Troyer JL, David VA, Guan L, McIntosh CE, Guo X, Zheng Y, Liao J, Deng H, Malasky M, Kessing B, Winkler CA, Carrington M, Dé The G, Zeng Y, O'Brien SJ. The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove. PLoS Genet. 2012 Nov;8(11):e1003103. doi: 10.1371/journal.pgen.1003103. Epub 2012 Nov 29. PubMed PMID: 23209447.
  5. Alberg AJ, Jorgensen TJ, Ruczinski I, Wheless L, Shugart YY, Berthier-Schaad Y, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Kao WH, Francis L, Alani RM, Smith MW, Strickland PT. DNA repair gene variants in relation to overall cancer risk: a population-based study. Carcinogenesis. 2012 Oct 26. Epub ahead of print PubMed PMID: 23027618.
  6. Jorgensen TJ, Ruczinski I, Yao Shugart Y, Wheless L, Berthier Schaad Y, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Kao WH, Francis L, Alani RM, Strickland PT, Smith MW, Alberg AJ. A population-based study of hedgehog pathway gene variants in relation to the dual risk of basal cell carcinoma plus another cancer. Cancer Epidemiol. 2012 Oct;36(5):e288-93. doi: 10.1016/j.canep.2012.05.001. Epub 2012 Jun 5. PubMed PMID: 22677152; PubMed Central PMCID: PMC3438291.
  7. Ruczinski I, Jorgensen TJ, Shugart YY, Schaad YB, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Kao WH, Wheless L, Francis L, Alani RM, Strickland PT, Smith MW, Alberg AJ. A population-based study of DNA repair gene variants in relation to non-melanoma skin cancer as a marker of a cancer-prone phenotype. Carcinogenesis. 2012 Sep;33(9):1692-8. doi: 10.1093/carcin/bgs170. Epub 2012 May 11. PubMed PMID: 22581838.
  8. Wheless L, Kistner-Griffin E, Jorgensen TJ, Ruczinski I, Berthier-Schaad Y, Kessing B, Hoffman-Bolton J, Francis L, Shugart YY, Strickland PT, Kao WH, Alani RM, Smith MW, Alberg AJ. A community-based study of nucleotide excision repair polymorphisms in relation to the risk of non-melanoma skin cancer. J Invest Dermatol. 2012 May;132(5):1354-62. doi: 10.1038/jid.2012.4. Epub 2012 Feb 16. PubMed PMID: 22336945; PubMed Central PMCID: PMC3326207.
  9. Lessios HA, Lockhart S, Collin R, Sotil G, Sanchez-Jerez P, Zigler KS, Perez AF, Garrido MJ, Geyer LB, Bernardi G, Vacquier VD, Haroun R, Kessing BD. Phylogeography and bindin evolution in Arbacia, a sea urchin genus with an unusual distribution. Mol Ecol. 2012 Jan;21(1):130-44. doi: 10.1111/j.1365-294X.2011.05303.x. Epub 2011 Oct 10. PubMed PMID: 21981354.
  10. Torres AR, Westover JB, Gibbons C, Johnson RC, Ward DC. Activating killer-cell immunoglobulin-like receptors (KIR) and their cognate HLA ligands are significantly increased in autism, Brain, Behavior and Immunity, 2012, 26 (7), 1122-7
  11. Yu, W, Briones, V, Lister, R, McIntosh, CE, Lee, E, Ren, J, Han, Y, Terashima, M, Leighty, R, Ecker, J, Muegge, K. H3K4me1 marks at CG hypomethylated sites in Lsh-/- MEFs preserve an epigenetic memory for gene expression (in Preparation).
  12. Freedman BI, Langefeld CD, Lu L, Divers J, Comeau ME, Kopp JB, Winkler CA, Nelson GW, Johnson RC, Palmer ND, Hicks PJ, Bostrom MA, Cooke JN, McDonough CW, Bowden DW. Differential effects of MYH9 and APOL1 risk variants on FRMD3 association with diabetic ESRD in African Americans, PLoS Genetics, 2011, 7 (6), e1002150
  13. Kopp JB, Nelson GW, Sampath K, Johnson RC, Genovese G, An P, Friedman D, Briggs W, Dart R, Korbet S, Mokrzycki M, Kimmel PL, Limou S, Ahuja TS, Berns JS, Simon E, Smith MC, Trachtman H, Michel DM, Schelling JR, Vlahov D, Pollak M, Winkler CA. APOL1 trypanolytic sequence variants in focal segmental glomerulosclerosis and HIV-associated nephropathy:  genetic risk and clinical phenotype, Journal of the American Society of Nephrology, 2011, 22 (11), 2129-37
  14. Troyer JL, Nelson GW, Lautenberger JA, Chinn L, McIntosh C, Johnson RC, et al. Genome-wide association study implicates PARD3B-based AIDS restriction. J Infect Dis. 2011;203(10):1491-502.# Johnson, R.C., Nelson, G.W., Troyer, J.L., Lautenberger, J.A., Kessing, B.D., Winkler, C.A., O'Brien, S.J. Accounting for multiple comparisons in a genome-wide association study (GWAS) BMC Genomics 11:724 (2010).
  15. Hendrickson, S.L., Lautenberger, J., Chin, L., Malasky, M., Sezgin, E., Kingsley, L.A., Goedert, J.J., Kirk, G.D., Gomperts, E.D., Buchbinder, S.P., Troyer, J., O’Brien, S.J. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. PLoS ONE 5:e12862, 2010.
  16. Herbeck JT, Gottlieb GS, Winkler CA, Nelson GW, An P, Maust BS, et al. Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS. J Infect Dis. 2010;201(4):618-26.
  17. Guo X, Zeng Y, Deng H, Liao J, Zheng Y, Li J, Kessing B, O'Brien SJ. 2010. Genetic Polymorphisms of CYP2E1, GSTP1, NQO1 and MPO and the Risk of Nasopharyngeal Carcinoma in a Han Chinese Population of Southern China. BMC Research Notes 2010, 3:212
  18. Nelson GW, Freedman BI, Bowden DW, Langefeld CD, An P, Hicks PJ, Bostrom MA, Johnson RC, Kopp JB, Winkler CA. Dense mapping of MYH9 localizes the strongest kidney disease associations to the region of introns 13 to 15, Human Molecular Genetics, 2010, 19 (9), 1805-15
  19. O'Connor SL, Lhost JJ, Becker EA, Detmer AM, Johnson RC, Macnair CE, Wiseman RW, Karl JA, Greene JM, Burwitz BJ, Bimber BN, Lank SM, Tuscher JJ, Mee ET, Rose NJ, Desrosiers RC, Hughes AL, Friedrich TC, Carrington M, O'Connor DH. MHC heterozygote advantage in simian immunodeficiency virus-infected Mauritian cynomolgus macaques, Science Transitional Medicine, 2010, 2 (22), 22ra18
  20. Perelman P, Johnson W, Roos C, Seuanez HN, Horvath JE, Moreira MAM, Kessing B, Pontius J, Roelke M, Rumpler Y, Schneider PC, Silva A, O'Brien SJ, Pecon-Slattery J. 2010. A molecular phylogeny of living primates. PLoS Genetics 08/20/10.
  21. Chinn LW, Tang M, Kessing BD, Lautenberger JA, Troyer JL, Malasky MJ, et al. Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection. J Infect Dis. 2010;202(12):1836-45.
  22. Sezgin E, Drosdak A, McIntosh C, Kessing B, Lautenberger JA, Goedert JJ, et al. Examination of disease-based selection, demographic history and population structure in european Y-chromosome haplogroup i. J Hum Genet. 2010;55(9):613-20.
  23. An P, Johnson RC, Phair J, Kirk GD, Yu XF, Donfield S, Buchbinder S, Goedert JJ, Winkler CA. Loss of APOBEC3B Gene Increases Risk of HIV-1 Acquisition, Journal of Infectious Diseases, 2009, 200 (7), 1054-8
  24. Guo X, Johnson RC, Deng H, Liao J, Guan L, Nelson GW, Tang M, Zheng Y, de The G, O’Brien SJ, Winkler CA, Zeng Y. Evaluation of Nonviral Risk Factors for Nasopharyngeal Carcinoma in a High-Risk Population of Southern China, International Journal of Cancer, 2009, 124 (12), 2942-7
  25. GENOME 10K COMMUNITY OF SCIENTISTS. 2009. Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10,000 Vertebrate Species. Journal of Heredity 10:1093
  26. Jorgensen TJ, Ruczinski I, Kessing B, Smith MW, Shugart YY, Alberg AJ. 2009. Hypothesis-Driven Candidate Gene Association Studies: Practical Design and Analytical Considerations. Accepted Am J Epidemiol.
  27. Roelke ME, Brown MA, Troyer JL, Winterbach H, Winterbach C, Hemson G, Smith D, Johnson RC, Pecon-Slattery J, Roca AL, Alexander K, Klein L, Martinelli P, Krishnasamu K, O’Brien SJ. Pathological Manifestations of Feline Immunode?ciency Virus (FIV) Infection in Wild African Lions, Virology, 2009, 390 (1), 1-12
  28. Streeck H, Jolin JS, Qi Y, Yassine-Diab B, Johnson RC, Kwon DS, Addo MM, Brumme C, Routy JP, Little S, Jessen HK, Kelleher AD, Hecht FM, Sekaly RP, Rosenberg ES, Walker BD, Carrington M, Altfeld M. HIV-1-Speci?c CD8+ T Cell Responses During Primary Infection are Major Determinants of the Viral Set Point and Loss of CD4+ T Cells, Journal of Virology, 2009, 83 (15), 7641-8
  29. Winkler CA An P, Johnson RC, Nelson GW, Kirk G. Expression of Duffy Antigen Receptor for Chemokines (DARC) has no Effect on HIV-1 Acquisition or Progression to AIDS in African Americans, Cell Host & Microbe, 2009, 5 (5), 411-13
  30. Troyer JL, Vandewoude S, Pecon-Slattery J, McIntosh C, Franklin S, Antunes A, Johnson W, O'Brien SJ. FIV cross-species transmission: An evolutionary prospective. Vet Immunol Immunopathol 123: 159-166. 2008. PMID: 18299153
  31. Stefanov, S., Lautenberger, J., and Gold, B. An Analysis Pipeline for Genome-wide Association Studies. Cancer Inform 6: 455-461, 2008.
  32. Hendrickson, S.L., Hutcheson, H.B., Ruiz-Pesini, E. Poole, J.C., Lautenberger, J., Sezgin, E., Kingsley, L., Goedert, J.J., Vlahov, D., Donfield, S., Wallace, D.C., and O’Brien, S.J. Mitochondrial DNA Haplogroups influence AIDS Progression. AIDS 22: 2429-2439, 2008.
  33. Hendrickson, S.L., Jacobson, L.P, Nelson, G.W., Phair, J.P., Lautenberger, J., Johnson, R.C., Kingsley, L., Margolick, J.B., Detels, R., Goedert, J.J., and O’Brien, S.J. Host genetic influences on highly active antiretroviral therapy efficacy and AIDS-free survival. J. Acquir. Immune Defic. Syndr 48: 263-271, 2008
  34. Kopp JB, Smith MW, Nelson G, Johnson RC, Freedman BI, Bowden DW, Oleksyk T, McKenzie LM, Kajiyama H, Ahuja TS, Berns JS, Briggs W, Cho ME, Dart RA, Kimmel PL, Korbet SM, Michel DM, Mokrzycki MH, Schelling JR, Simon E, Trachtman H, Vlahov D, Winkler CA. MYH9 is a Major-Effect Risk Gene for Focal Segmental Glomerulosclerosis, Nature Genetics, 2008, 40 (10), 1175-84
  35. Olshen, A.B., Gold, B., Lohmueller, K.E., Struewing, J.P. Satagopan, J., Stefanov, S.A., Eskin, E., Kirchhoff, T., Lautenberger, J.A., Klein, R.J., Friedman, E., Norton, L., Ellis, N.A., Viale, A., Lee, C.S., Borgen, P.I., Clark, A.G., Offit, K., and Boyd, J. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping. BMC Genetics 9: 14, 2008.
  36. Gold, B., Kirchhoff, T., Stefanov, S., Lautenberger, J., Viale, A., Garber, J., Friedman, E., Narod, S., Olshen , A.B., Gregersen , P., Kosarin, K., Olsh, A., Bergeron, J., Ellis, N.A., Klein, R.J., Clark, A.G., Norton, L., Dean, M., Boyd, J., and Offit, K. Genome-wide association study provides evidence for a breast cancer risk locus at 6q 22.33. Proc. Natl. Acad. Sci. U.S.A. 105: 4340-4345, 2008.
  37. Hutcheson, H.B, Lautenberger, J.A., Nelson, G.W., Pontius, J.U., Kessing, B.D., Winkler, C.A., Smith, M.W., Johnson, R., Stephens, R., Phair, J., Goedert, J.J., Donfield, S., and O’Brien, S.J. Detecting AIDS Restriction Genes: From Candidate Genes to Genome-Wide Association Discovery. Vaccine 26: 2951-2965,2008.
  38. Bashirova AA, Bleiber G, Qi Y, Hutcheson H, Yamashita T, Johnson RC, Cheng J, Alter G, Goedert J, Buchbinder S, Hoots K, Vlahov D, May M, Maldarelli F, Jacobson L, O'Brien SJ, Telenti A, Carrington M. Consistent Effects of TSG101 Genetic Variability on Multiple Outcomes of Exposure to Human Immunodeficiency Virus Type 1, Journal of Virology, 2006, 80 (14), 6757-63
  39. Guo, X.C., Scott, K., Liu, Y., Dean, M., David, V., Nelson, G.W., Johnson, R.C., Dilks, H.H., Lautenberger, J., Kessing, B., Martenson, J., Guan, L., Sun, S., Deng, H., Zheng, Y., de The G., Liao, J., Zeng. Y., O’Brien, S.J., and Winkler, C. Genetic factors leading to chronic Epstein-Barr virus infection and nasopharyngeal carcinoma in South East China, study design, methods and feasibility. Hum Genomics 2: 365-375, 2006.Guo XC, Scott K, Liu Y, Dean M, David V, Nelson GW, Johnson RC, Dilks HH, Lautenberger J, Kessing B, Martenson J, Guan L, Sun S, Deng H, Zheng Y, de The G, Liao J, Zeng Y, O'Brien SJ, Winkler CA. Genetic factors leading to chronic Epstein-Barr virus infection and nasopharyngeal carcinoma in South East China: Study design, methods and feasibility, Human Genomics, 2006, 2 (6), 365-75
  40. Modi, W.S., Lautenberger, J., An, P., Scott, K., Goedert, J.J., Kirk, G.D., Buchbinder, S., Phair, J., Donfield, S., O’Brien, S.J., and Winkler, C. Genetic Variation in the CCL18-CCL3-CCL4 Chemokine Gene Cluster Influences HIV Type 1 Transmission and AIDS Disease Progression. Am J Hum Genet 79: 120-128, 2006.
  41. Guo XC, O'Brien SJ, Winkler C., Scott K., Hutcheson H., David V., Kessing B., Zheng Y.M., Liao J., Lui Y., Guy de T. and Y. Zeng. 2006. Association study of chromosome 4 STRs polymorphisms with nasopharyngeal carcinoma. Yi Chuan. 28:783-90
  42. Yant LJ, Friedrich TC, Johnson RC, May G, Maness NJ, Enz AM, Lifson JD, O'Connor DH, Carrington M, Watkins DI. The high frequency MHC Class I allele Mamu-B*17 is associated with control of SIVmac239 Replication, Journal of Virology, 2006, 80 (10), 5074-7
  43. Smith, M.W., Patterson, N., Lautenberger, J.A., Truelove, A.L., McDonald, G.J., Waliszewska, A., Kessing, B.D., Malasky, M.J., Scafe, C., Le, E., De Jager, P.L., Mignault, A.A., Yi, Z., De The, G. Essex, M., Sankale, J.L., Moore, J.H., Poku, K., Phair, J.P., Goedert, J.J., Vlahov, D., Williams, S.M., Tishkoff, S.A., Winkler, C.A., De La Vega, F.M., Woodage, T., Sninsky, J.J., Hafler, D.A., Altshuler, D., Gilbert, D.A., O’Brien, S.J., and Reich, D. A high-density admixture map for disease gene discovery in African Americans. Am J Hum Genet 74: 1001-1013, 2004.
  44. An, P., Vlahov, D., Margolick, J.B., Phair, J., O’Brien, T.R., Lautenberger, J.A., O’Brien, S.J., and Winkler, C.A. A tumor necrosis factor-alpha-inducible promoter variant of interferon-gamma accelerates CD4+ T cell depletion in human immunodeficiency virus-1 infected individuals. J Infect Dis 188: 228-231, 2003.
  45. Smith, M.W., Lautenberger, J.A., Shin, H.D., Chretien, J.P., Shrestha, S., Gilbert, D.A., and O’Brien, S.J. Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet 69: 1080-1094, 2001.
  46. Lautenberger, J.A., Stephens, J.C., O’Brien, S.J., and Smith, M.W. Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am J Hum Genet 66: 969-978, 2000.
  47. Chen, Z.Q., Lautenberger, J.A., Lyons, L.A., McKenzie, L.M., and O’Brien, S.J. A human genome map of comparative anchor tagged sequences. J Heredity 90: 477-484, 1999.