Bibliography:
Linkage Disequilibrium Analysis
(2010)
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+ 2010

  1. A Adeyemo, C Rotimi (2010), "Genetic variants associated with complex human diseases show wide variation across multiple populations", Public Health Genomics, 13(2):72-79.
    [ abstract]

  2. J Asimit, E Zeggini (2010), "Rare variant association analysis methods for complex traits", Annual Review of Genetics, 44:293-308.
    [ abstract]

  3. Kristin L Ayers, Heather J Cordell (2010), "SNP Selection in genome-wide and candidate gene studies via penalized logistic regression", Genetic Epidemiology, 34(8):879-891.
    [ abstract]

  4. International HapMap 3 Consortium, DM Altshuler, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE. (2010), "Integrating common and rare genetic variation in diverse human populations", Nature, 467(7311):52-58

  5. DH Ballard, J Cho, H Zhao (2010), "Comparison of multi-marker association methods to detect association between a candidate region and disease", Genetic Epidemiology, 34:201-212.

  6. V Bansal, O Libiger, A Torkamani, NJ Schork (2010), "Statistical analysis strategies for association studies involving rare variants", Nature Reviews Genetics, 11:773-785.

  7. G Bhatia, V Bansal, O Harismendy, NJ Schork, EJ Topol, K Frazer (2010), "A covering method for detecting genetic associations between rare variants and common phenotypes", PLoS Computational Biology, 6:e1000954.

  8. Seoae Cho, Kyunga Kim, Young Jin Kim, Jong-Keuk Lee, Yoon Shin Cho, Jong-Young Lee, Bok-Ghee Han, Heebal Kim, Jurg Ott, Taesung Park (2010), "Joint identification of multiple genetic variants via elastic-net variable selection in a genome-wide association analysis", Annals of Human Genetics, 74(5):416-428.
    [ abstract]

  9. David Clayton (2010), "On inferring presence of an individual in a mixture: a Bayesian approach", Biostatistics, 11(4):661-673.
    [ abstract]

  10. David N. Cooper (2010), "Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes", Human Genomics, 4(5):284-288.

  11. Ann K Daly (2010), "Genome-wide association studies in pharmacogenomics", Nature Reviews Genetics, 11(4):241-246.
    [ abstract]

  12. T Feng, X Zhu (2010), "Genome-wide searching of rare genetic variants in WTCCC data", Human Genetics, 128:269-280.

  13. J Freudenberg, AT Lee, KA Siminovitch, CI Amos, D Ballard, W Li, PK Gregersen (2010), "Locus category based analysis of a large genome-wide-association study of rheumatoid arthritis", Human Molecular Genetics, 19(19):3863-3872.
    [abstract]

  14. Greg Gibson (2010), "Hints of hidden heritability in GWAS" (news and views), Nature Genetics, 42:558-560.
    [ abstract]

  15. CS Greene, DS Himmelstein, HH Nelson, KT Kelsey, SM Williams, AS Andrew, MR Karagas, JH Moore (2010), "Enabling personal genomics with an explicit test of epistasis", Pacific Symposium on Biocomputing, 15:327-336.

  16. B Han, M Park, X Chen (2010), "A Markov blanket-based method for detecting causal SNPs in GWAS", BMC Bioinformatics, 11(suppl 3):S5,
    [ abstract]

  17. F Han, W Pan (2010), "A data-adaptive sum test for disease association with multiple common or rare variants", Human Heredity, 70:42-54.

  18. F Han, W Pan (2010), "Powerful multi-marker association tests: unifying genomic distance-based regression and logistic regression", Genetic Epidemiology, 34(7):680-688.

  19. H He, WS Oetting, MJ Brott, S Basu (2010), "Pair-wise multifactor dimensionality reduction method to detect gene-gene interactions in a case-control study", Human Heredity, 69:60-70.

  20. TJ Hoffmann, NJ Marini, JS Witte (2010), "Comprehensive approach to analyzing rare genetic variants", PLoS ONE, 5(11):e13584.

  21. YJ Hu, DY Lin, D Zeng (2010), "A general framework for studying genetic effects and gene-environment interactions with missing data", Biostatistics, 11(4):583-598.
    [ abstract]

  22. Mark M. Iles (2010), "The impact of incomplete linkage disequilibrium and genetic model choice on the analysis and interpretation of genome-wide association studies", Annals of Human Genetics, 74(4):375-379.
    [ abstract]

  23. Hyun Min Kang, Noah A. Zaitlen, Eleazar Eskin (2010), "EMINIM: an adaptive and memory-efficient algorithm for genotype imputation", Journal of Computational Biology, 17(3):547-560.
    [ abstract]

  24. Bonnie Kirkpatrick, Eran Halperin, Richard M. Karp (2010), "Haplotype inference in complex pedigrees", Journal of Computational Biology, 17(3):269-280.
    [ abstract]

  25. Julia Kozlitina, Chao Xing, Alexander Pertsemlidis, William R. Schucany "Power of genetic association studies with fixed and random genotype frequencies", Annals of Human Genetics, 74(5):429-438.
    [ abstract]

  26. Claudia Lamina, Helmut Küchenhoff, Jenny Chang-Claude, Bernhard Paulweber, H.-Erich Wichmann, Thomas Illig, Margret R. Hoehe, Florian Kronenberg, Iris M. Heid (2010), "Haplotype misclassification resulting from statistical reconstruction and genotype error, and its impact on association estimates", Annals of Human Genetics, 74(5):452-462.
    [ abstract]

  27. AB Lee, D Luca, L Klei, B Devlin, K Roeder (2010), "Discovering genetic ancestry using spectral graph theory", Genetic Epidemiology, 34:51-59.

  28. Hongzhe Li, Zhi Wei, John Maris (2010), "A hidden Markov random field model for genome-wide association studies", Biostatistics, 11(1):139-150.
    [ abstract]

  29. Tengfei Li, Zhaohai Li, Zhiliang Ying, Hong Zhang (2010), "Influence of population stratification on population-based marker-disease association analysis", Annals of Human Genetics, 74(4):351-360.
    [ abstract]

  30. Y Li, AE Byrnes, M Li (2010), "To identify associations with rare variants, just WHaIT: weighted haplotype and imputation-based tests", American Journal of Human Genetics, 87:728-735.

  31. DJ Liu, SM Leal (2010), "A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions", PLoS Genetics, 6(10):r1001156.

  32. Lan Liu, Yonghui Wu, Stefano Lonardi, Tao Jiang (2010), "Efficient genome-wide TagSNP selection across populations via the linkage disequilibrium criterion", Journal of Computational Biology, 17(1):21-37.
    [ abstract]

  33. JA Longmate, GP Larson, TG Krontiris, SS Sommer (2010), "Three ways of combining genotyping and resequencing in case-control association studies", PLoS ONE , 5(12):e14318.

  34. Jonathan Marchini, Bryan Howie (2010), "Genotype imputation for genome-wide association studies", Nature Reviews Genetics, 11:499-511.
    [ abstract]

  35. Jon McClellan, Mary-Claire King (2010), "Genetic heterogeneity in human disease", Cell, 141(2):210-217.
    [ abstract]

  36. JH Moore, FW Asselbergs, SM Williams (2010), "Bioinformatics challenges for genome-wide association studies", Bioinformatics, 26(4):445-455.

  37. A Morris, E Zeggini (2010), "An evaluation of statistical approaches to rare variant analysis in genetic association studies", Genetic Epidemiology, 34:188-193.

  38. I Mukhopadhyay, E Feingold, D Weeks, A Thalamuthu (2010), "Association tests using kernel-based measures of multi-locus genotype similarity between individuals", Genetic Epidemiology, 34:213-221.

  39. W Pan (2010), "A unified framework for detecting genetic association with multiple SNPs in a candidate gene or region: contrasting genotype scores and LD patterns between cases and controls", Human Heredity, 69:1-13.

  40. W Pan (2010), "Statistical tests of genetic association in the presence of gene-gene and gene-environment interactions", Human Heredity, 69:131-142.

  41. W Pan, F Han, X Shen (2010), "Test selection with application to detecting disease association with multiple SNPs", Human Heredity, 69:120-130.

  42. Ju-Hyun Park, Sholom Wacholder, Mitchell H Gail, Ulrike Peters, Kevin B Jacobs, Stephen J Chanock & Nilanjan Chatterjee (2010), "Estimation of effect size distribution from genome-wide association studies and implications for future discoveries", Nature Genetics, 42:570-575.
    [ abstract]

  43. Bo Peng, Biao Li, Younghun Han, hristopher I Amos (2010), "Power analysis for case-control association studies of samples with known family histories", Human Genetics, 127(6):699-704.

  44. A Price, G Kryukov, P de Bakker, S Purcell, J Staples, L Wei, S Sunyaev (2010), "Pooled association tests for rare vriants in exon-resequencing studies", American Journal of Human Genetics, 86:832-838.

  45. Noah A Rosenberg, Lucy Huang, Ethan M Jewett, Zachary A Szpiech, Ivana Jankovic, Michael Boehnke (2010), "Genome-wide association studies in diverse populations", Nature Reviews Genetics, 11:356-366.
    [ abstract]

  46. DJ Schaid (2010), "Genomic similarity and kernel methods I: advancements by building on mathematical and statistical foundations", Human Heredity, 70:109-131.

  47. DJ Schaid (2010), "Genomic similarity and kernel methods II: methods for genomic information", Human Heredity, 70:132-140.

  48. Dewei She, Yan Li, Hong Zhang, Barry I. Graubard, Zhaohai Li (2010), "Trend tests for genetic association using population-based cross-sectional complex survey data", Biostatistics, 11(1):48-56.
    [ abstract]

  49. Ji-Hyung Shin, Brad McNeney, Jinko Graham (2010), "On the use of allelic transmission rates for assessing gene-by-environment interaction in case-parent trios", Annals of Human Genetics, 74(5):439-451.
    [ abstract]

  50. Daniel Shriner, Adebowale Adeyemo, Guanjie Chen, Charles N. Rotimi (2010), "Practical considerations for imputation of untyped markers in admixed populations", Genetic Epidemiology, 34(3):258-265.
    [ abstract]

  51. Yik Y. Teo (2010), "Exploratory data analysis in large-scale genetic studies", Biostatistics, 11(1):70-81.
    [ abstract]

  52. Yik-Ying Teo, Kerrin S Small, Dominic P Kwiatkowski (2010), "Methodological challenges of genome-wide association analysis in Africa", Nature Reviews Genetics, 11:149-160.
    [ abstract]

  53. Duncan Thomas (2010), "Gene--environment-wide association studies: emerging approaches", Nature Reviews Genetics, 11(4):259-272.
    [ abstract]

  54. Timothy Thornton, Mary Sara McPeek (2010), "ROADTRIPS: case-control association testing with partially or completely unknown population and pedigree structure", American Journal of Human Genetics, 86(2):172-184.
    [ abstract]

  55. Sjozef van Baal, Joël Zlotogora, George Lagoumintzis, Vassiliki Gkantouna, Ioannis Tzimas, Konstantinos Poulas, Athanassios Tsakalidis, Giovanni Romeo, George P. Patrinos (2010), "ETHNOS : A versatile electronic tool for the development and curation of national genetic databases", Human Genomics, 4(5):361-368.

  56. X Wan, C Yang, Q Yang, H Xue, X Fan, N Tang, W Yu (2010), "BOOST: a Boolean representation-based method for Detecting SNP-SNP interactions in genome-wide association studies", American Journal of Human Genetics, 87:325-340.

  57. X Wan, C Yang, Q Yang, H Xue, N Tang, W Yu (2010), "Detecting two-locus associations allowing for interactions in genome-wide association studies", Bioinformatics, 26(20):2517-2525.

  58. Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson LS Tang, Weichuan Yu (2010), "Predictive rule inference for epistatic interaction detection in genome-wide association", Bioinformatics, 26(1):30-37.
    [abstract]

  59. Melanie A Wilson (2010), Bayesian Model Uncertainty and Prior Choice with Applications to Genetic Association Studies. Ph.D Thesis, Department of Statistics, Duke University.
    [PDF]

  60. J Wu, B Devlin, S Ringquist, M Trucco, K Roeder (2010), "Screen and clean: a tool for identifying interactions in genome-wide association studies", Genetic Epidemiology, 34(3):275-285.

  61. MC Wu, P Kraft, MP Epstein, DM Taylor, SJ Chanock, DJ Hunter, X Lin (2010), "Powerful SNP-set analysis for case-control genome-wide association studies", American Journal of Human Genetics, 86:929-942.

  62. C Yang, X Wan, Q Yang, H Xue, N Tang, W Yu (2010), "Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group lasso" BMC Bioinformatics, 11(Suppl 1):S18.

  63. Jian Yang, Beben Benyamin, Brian P McEvoy, Scott Gordon, Anjali K Henders, Dale R Nyholt, Pamela A Madden, Andrew C Heath, Nicholas G Martin, Grant W Montgomery, Michael E Goddard, Peter M Visscher (2010), "Common SNPs explain a large proportion of the heritability for human height", Nature Genetics, 42:565-569.
    [ abstract]

  64. Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel (2010), "Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction", Journal of Computational Biology, 17(3):417-428.
    [ abstract]

  65. Y Zang, WK Fung (2010), "Robust tests for matched case-control genetic association studies", BMC Genetics, 11:91

  66. Yong Zang, Wing Kam Fung, Gang Zheng (2010), "Simple algorithms to calculate asymptotic null distributions of robust tests in case-control genetic association studies in R", Journal of Statistical Software, 33:8.
    [PDF]

  67. M Zawistowski, S Gopalakrishnan, J Ding, Y Li, S Grimm, S Zollner (2010), "Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes", American Journal of Human Genetics, 87:604-617.

  68. L Zhang, YF Pai, J Li, CJ Papasian, HW Deng (2010), "Effecient utilization of rare variants for detection of disease-related genomics regions", PLoS ONE, 5(12):e14288.

  69. Weiping Zhang, Yu Chen (2010), "Double sampling method for genetic association analysis with differential genotyping errors", Biostatistics, Bioinformatics and Biomathematics, 1(1):4.

  70. Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wang (2010), "COE: a general approach for efficient genome-wide two-locus epistasis test in disease association study", Journal of Computational Biology, 17(3): 401-415.
    [ abstract]

  71. Zhaogong Zhang, Adan Niu, Qiuying Sha (2010), "Identification of interacting genes in genome-wide association studies using a model-based two-stage approach", Annals of Human Genetics, 74(5):406-415.
    [ abstract]

  72. Gang Zheng, Zhaohai Li, Mitchell H. Gail, Joseph L. Gastwirth (2010), "Impact of population substructure on trend tests for genetic case-control association studies", Biometrics, 66(1):196-204.
    [ abstract]

  73. H Zhou, ME Sehl, JS Sinsheimer, K Lange (2010), "Association screening of common and rare genetic variants by penalized regression", Bioinformatics, 26:2375-2382.

  74. X Zhu, T Feng, Y Li, Q Lu, RC Elston (2010), "Detecting rare variants for complex traits using family and unrelated data", Genetic Epidemiology, 34:171-187.