Bibliography:
Linkage Disequilibrium Analysis
(2009)
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+ 2009

  1. Attia J, Ioannidis JP, Thakkinstian A, McEvoy M, Scott RJ, Minelli C, Thompson J, Infante-Rivard C, Guyatt G. (2009), "How to use an article about genetic association: A: Background concepts", JAMA, 301(1):74-81.

  2. J Attia, Ioannidis JP, Thakkinstian A, McEvoy M, Scott RJ, Minelli C, Thompson J, Infante-Rivard C, Guyatt G. (2009), "How to use an article about genetic association: B: Are the results of the study valid?", JAMA, 301(2):191-197.

  3. J Attia, Ioannidis JP, Thakkinstian A, McEvoy M, Scott RJ, Minelli C, Thompson J, Infante-Rivard C, Guyatt G. (2009), "How to use an article about genetic association: C: What are the results and will they help me in caring for my patients?", JAMA, 301(3):304-308.

  4. Y Bossé, F Bacot, A Montpetit, J Rung, HQ Qu, JC Engert, C Polychronakos, TJ Hudson, P Froguel, R Sladek, M Desrosiers (2009), "Identification of susceptibility genes for complex diseases using pooling-based genome-wide association scans", Human Genetics, 125(3):305-318.

  5. Richard Bourgon, Eugenio Mancera, Alessandro Brozzi, Lars M. Steinmetz, Wolfgang Huber (2009), "Array-based genotyping in S.cerevisiae using semi-supervised clustering", Bioinformatics, 25(8):1056-1062.
    [abstract]

  6. Brian L Browning, Sharon R Browning (2009), "A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals", American Journal of Human Genetics, 84:210-223.
    [abstract]

  7. Juliet M Chapman, Clive M Onnie, Natalie J Prescott, Sheila A Fisher, John C Mansfield, Christopher G Mathew, Cathryn M Lewis, Claudio J Verzilli, John C Whittaker (2009), "Searching for genotype-ohenotype structure: using hierarchical log-linear models in Crohn disease", American Journal of Human Genetics, 84:178-187.
    [abstract]

  8. Lina Chen , Liangcai Zhang, Yan Zhao, Liangde Xu, Yukui Shang, Qian Wang, Wan Li, Hong Wang and Xia Li (2009), "Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways", Bioinformatics, 25(2):237-242.
    [abstract]

  9. Heather J Cordell (2009), "Detecting gene-gene interactions that underlie human diseases", Nature Reviews Genetics, 10:392-404.
    [ abstract]

  10. R Culverhouse, W Jin, CH Jin, AL Hinrichs, BK Suarez (2009), "Power and false-positive rates for the restricted partition method (RPM) in a large candidate gene data set", BMC Proceedings, 3(suppl 7):S74.

  11. Todd E Druley, Francesco L M Vallania, Daniel J Wegner, Katherine E Varley, Olivia L Knowles, Jacqueline A Bonds, Sarah W Robison, Scott W Doniger, Aaron Hamvas, F Sessions Cole, Justin C Fay, Robi D Mitra (2009), "Quantification of rare allelic variants from pooled genomic DNA", Nature Methods, 6:263-265.
    [ abstract]

  12. M Emily, T Mailund, J Hein, L Schauser, MH Schierup (2009), "Using biological networks to search for interacting loci in genome-wide association studies", European Journal of Human Genetics, 17(10):1231-1240.

  13. Kelly A Frazer, Sarah S Murray, Nicholas J Schork, Eric J Topol (2009), "Human genetic variation and its contribution to complex traits", Nature Reviews Genetics, 10:241-251
    [ abstract]

  14. BL Fridley (2009), "Bayesian variable and model selection methods for genetic association studies", Genetic Epidemiology, 33(1):27-37

  15. Jane Gitschier (2009), "Inferential genotyping of Y chromosomes in Latter-Day Saints founders and comparison to Utah samples in the hapMap project", American Journal of Human Genetics, 84:251-258.
    [abstract]

  16. Derek Gordon, Andrew R Zinn (2009), "Computing power of quantitative trait locus association mapping for haploid loci", BMC Bioinformatics, 10:261.
    [abstract]

  17. CS Greene, NM Penrod, J Kiralis, JH Moore (2009), "Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions", BioData Mining, 2(1):5.

  18. CS Greene, NM Penrod, SM Williams, JH Moore (2009), "Failure to replicate a genetic association may provide important clues about genetic architecture", PLoS ONE, 4(6):e5639.

  19. X Gu, RF Frankowski, GL Rosner, M Relling, B Peng, CI Amos (2009), "A modified forward multiple regression in high-density genome-wide association studies for complex traits", Genetic Epidemiology, to appear.

  20. Shizhong Han, Li Ma, Dawei Li, Bao-Zhu Yang (2009), "Is the tail-strength measure more powerful in tests of genetic association?" (letters to the editor), American Journal of Human Genetics, 84:295-298.

  21. J Hardy, A Singleton (2009), "Genomewide association studies and human disease", New England Journal of Medicine, 360:1759-1768.

  22. AL Hinrichs, R Culverhouse, CH Jin, BK Suarez (2009), "Detecting population stratification using related individuals", BMC Proceedings, 3(suppl 7):S106.

  23. Mun-Gwan Hong, Yudi Pawitan, Patrik K E Magnusson, Jonathan A Prince (2009), "Strategies and issues in the detection of pathway enrichment in genome-wide association studies", Human Genetics, 126(2):289-301.

  24. BN Howie, P Donnelly, J Marchini (2009), "A flexible and accurate genotype imputation method for the next generation of genome-wide association studies", PLoS Genetics, 5:e1000529.

  25. Lucy Huang, Yun Li, Andrew B Singleton, John A Hardy, Gonçalo Abecasis, Noah A Rosenberg, Paul Scheet (2009), "Genotype-imputation accuracy across worldwide human populations", American Journal of Human Genetics, 84:235-250.
    [abstract]

  26. TJ Hudson, DN Cooper (2009), "STREGA: a 'How-To' guide for reporting genetic associations", Human Genetics, 125(2):117-118.

  27. JP Ioannidis (2009), "Personalized genetic prediction: too limited, too expensive, or too soon?", Annals of Internal Medicine, 150(2):139-141.

  28. JP Ioannidis (2009), "Population-wide generalizability of genome-wide discovered associations", Journal of the National Cancer Institute, 101(19):1297-1299.

  29. John PA Ioannidis, Gilles Thomas, Mark J Daly (2009), "Validating, augmenting and refining genome-wide association signals", Nature Reviews Genetics, 10:318-329.
    [ abstract]

  30. AC Janssens, AM González-Zuloeta Ladd, S López-Léon, JP Ioannidis, BA Oostra, MJ Khoury, CM van Duijn (2009), "An empirical comparison of meta-analyses of published gene-disease associations versus consortium analyses", Genetics in Medicine, 11(3):153-162.

  31. J Joo, M Kwak, K Ahn, G Zheng (2009), "A robust genome-wide scan statistic of the Wellcome Trust Case-Control Consortium", Biometrics, to appear.

  32. J Joo, M Kwak, G Zheng (2009), "Improving power for testing genetic association in case-control studies by reducing the alternative space", Biometrics, to appear.

  33. Rachel Karchin (2009), "Next generation tools for the annotation of human SNPs", Briefings in Bioinformatics, 10(1):35-52.
    [abstract]

  34. Ali Katanforoush, Mehdi Sadeghi, Hamid Pezeshk, Elahe Elahi (2009), "Global haplotype partitioning for maximal associated SNP pairs", BMC Bioinformatics, 10:269
    [abstract]

  35. Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka (2009), "Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data", Bioinformatics, 25(21):2735-2743.
    [abstract]

  36. MJ Khoury, Bertram L, Boffetta P, Butterworth AS, Chanock SJ, Dolan SM, Fortier I, Garcia-Closas M, Gwinn M, Higgins JP, Janssens AC, Ostell J, Owen RP, Pagon RA, Rebbeck TR, Rothman N, Bernstein JL, Burton PR, Campbell H, Chockalingam A, Furberg H, Little J, O'Brien TR, Seminara D, Vineis P, Winn DM, Yu W, Ioannidis JP. (2009), "Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation and human diseases", American Journal of Epidemiology, 170(3):269-279.

  37. MJ Khoury, McBride CM, Schully SD, Ioannidis JP, Feero WG, Janssens AC, Gwinn M, Simons-Morton DG, Bernhardt JM, Cargill M, Chanock SJ, Church GM, Coates RJ, Collins FS, Croyle RT, Davis BR, Downing GJ, Duross A, Friedman S, Gail MH, Ginsburg GS, Green RC, Greene MH, Greenland P, Gulcher JR, Hsu A, Hudson KL, Kardia SL, Kimmel PL, Lauer MS, Miller AM, Offit K, Ransohoff DF, Roberts JS, Rasooly RS, Stefansson K, Terry SF, Teutsch SM, Trepanier A, Wanke KL, Witte JS, Xu J. (2009), "The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop", Genetics in Medicine, 11(8):559-567.

  38. MJ Khoury, S Wacholder (2009), "From genome-wide association studies to gene-environment-wide interaction studies -- challenges and opportunities" (invited commentary), American Journal of Epidemiology, 169:227-230.
    [abstract]

  39. Jong Hyun Kim, Woo-Cheol Kim, Michael S. Waterman, Sanghyun Park, and Lei M. Li (2009), "HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome", Bioinformatics, 25(18):2430-2431
    [abstract]

  40. Yoonhee Kim, Robert Wojciechowski, Heejong Sung, Rasika A Mathias, Li Wang, Alison P Klein, Rhoshel K Lenroot, James Malley, Joan E Bailey-Wilson (2009), "Evaluation of random forests performance for genome-wide association studies in the presence of interaction effects", BMC Proceedings, 3(suppl 7):S64.
    [html ]

  41. P Fraft, DJ Hunter (2009), "Genetic risk prediction--are we there yet", New England Journal of Medicine, 360(17):1701-1703.

  42. P Kraft, S Raychaudhuri (2009), "Complex diseases, complex genes: keeping pathways on the right track", Epidemiology, 20(4):508-511.

  43. Peter Kraft, Sholom Wacholder, Marilyn C Cornelis, Frank B Hu, Richard B Hayes, Gilles Thomas, Robert Hoover, David J Hunter, Stephen Chanock (2009), "Beyond odds ratios -- communicating disease risk based on genetic profiles", Nature Reviews Genetics, 10:264-269.
    [ abstract]

  44. M Kwak, J Joo, G Zheng (2009), "A robust test for two-stage design in genome-wide association studies", Biometrics, to appear.

  45. Junghyun Namkung, Kyunga Kim, Sungon Yi, Wonil Chung, Min-Seok Kwon, Taesung Park (2009), "New evaluation measures for multifactor dimensionality reduction classifiers in gene-gene interaction analysis", Bioinformatics, 25(3):338-345.
    [abstract]

  46. Phil Hyoun Lee, Hagit Shatkay (2009), "An integrative scoring system for ranking SNPs by their potential deleterious effects", Bioinformatics, 25(8):1048-1055.
    [abstract]

  47. Q Li, G Zheng, X Liang, K Yu (2009), "Robust tests for single-marker analysis in case-control genetic association studies", Annals of Human Genetics, 73(2):245-252.

  48. Xin Li, Jing Li (2009), "An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions", Journal of Bioinformatics and Computational Biology, 7(4):521-545.
    [ abstract]

  49. J Little, Higgins JP, Ioannidis JP, Moher D, Gagnon F, von Elm E, Khoury MJ, Cohen B, Davey-Smith G, Grimshaw J, Scheet P, Gwinn M, Williamson RE, Zou GY, Hutchings K, Johnson CY, Tait V, Wiens M, Golding J, van Duijn C, McLaughlin J, Paterson A, Wells G, Fortier I, Freedman M, Zecevic M, King R, Infante-Rivard C, Stewart A, Birkett N. (2009), "Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE statement", European Journal of Epidemiology, 24(1):37-55.
    Human Genetics, 125(2):131-151.
    Annals of Internal Medicine, 150(3):206-215.

  50. Quan Long, Daniel MacArthur, Zemin Ning, and Chris Tyler-Smith (2009), "HI: haplotype improver using paired-end short reads", Bioinformatics, 25(18): 2436-2437.
    [abstract]

  51. Bo Eskerod Madsen and Sharon R. Browning (2009), "A groupwise association test for rare mutations using a weighted sum statistic", PLoS Genetics, 5:e1000384.

  52. TA Manolio, FS Collins, NJ Cox, DB Goldstein, LA Hindorff, DJ Hunter, MI McCarthy, EM Ramos, LR Cardon, A Chakravarti, JH Cho, AE Guttmacher, A Kong, L Kruglyak, E Mardis, CN Rotimi, M Slatkin, D Valle, AS Whittemore, M Boehnke, AG Clark, EE Eichler, G Gibson, JL Haines, TF Mackay, SA McCarroll, PM Visscher (2009), "Finding the missing heritability of complex diseases", Nature, 461(7265):747-753.

  53. Heinrich Magnus Manske, Dominic P. Kwiatkowski (2009), "SNP-o-matic", Bioinformatics, 25(18):2434-2435
    [abstract]

  54. Ignacio Medina, David Montaner, Nuria Bonifaci, Miguel Angel Pujana, Jose Carbonell, Joaquin Tarraga, Fatima Al-Shahrour and Joaquin Dopazo, (2009), "Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies", Nucleic Acids Research, 37(suppl 2):W340-W344

  55. David J Miller, Yanxin Zhang, Guoqiang Yu, Yongmei Liu, Li Chen, Carl D Langefeld, David Herrington, and Yue Wang (2009), "An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions", Bioinformatics, 25(19):2478-2485.
    [abstract]

  56. GM Monsees, RM Tamimi, P Fraft (2009), "Genome-wide association scans for secondary traits using case-control samples", Genetic Epidemiology, to appear.

  57. JH Moore (2009), "From genotypes to genometypes: putting the genome back in genome-wide association studies" (comment), European Journal of Human Genetics, 17(10):1205-1206.

  58. JH Moore, SM Williams (2009), "Epistasis and its implications for personal genetics", American Journal of Human Genetics, 85(3):309-320.

  59. SA Mullen, DE Crompton, PW Carney, I Helbig, SF Berkovic (2009), "A neurologist's guide to genome-wide association studies", Neurology, 72(6):558-565

  60. Y Nakamura (2009), "DNA variations in human and medical genetics: 25 years of my experience", Journal of Human Genetics, 54(1):1-8.

  61. PJ Newcombe, C Verzilli, JP Casas, AD Hingorani, L Smeeth, JC Whittaker (2009), "Multilocus Bayesian meta-analysis of gene-disease associations", American Journal of Human Genetics, 84(5):567-580.

  62. C O'Dushlaine, E Kenny, EA Heron, R Segurado, M Gill, DW Morris, A Corvin (2009), "The SNP ratio test: pathway analysis of genome-wide association datasets", Bioinformatics, 25(20):2762-2763.
    [abstract]

  63. KA Pattin, BC White, N Barney, J Gui, HH Nelson, KT Kelsey, AS Andrew, MR Karagas, JH Moore (2009), "A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction", Genetic Epidemiology, 33(1):87-94.

  64. G Peng, L Luo, H Siu, Y Zhu, P Hu, S Hong, J Zhao, X Zhou, JD Reveille, L Jin, CI Amos, M Xiong (2009), "Gene and pathway-based second-wave analysis of genome-wide association studies", European Journal of Human Genetics, to appear.

  65. TV Pereira, NA Patsopoulos, G Salanti, JP Ioannidis (2009), "Discovery properties of genome-wide association signals from cumulatively combined data sets", American Journal of Epidemiology, to appear.

  66. Matthew E. Ritchie, Benilton S. Carvalho, Kurt N. Hetrick, Simon Tavaré, and Rafael A. Irizarry (2009), "R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips", Bioinformatics, 25(19):2621-2623
    [abstract]

  67. M Ryan, M Diekhans, S Lien, Y Liu, R Karchin (2009), "LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures", Bioinformatics, 25(11):1431-1432
    [abstract]

  68. Mina Ryten, Danyah Trabzuni and John Hardy (2009), "Genotypic analysis of gene expression in the dissection of the aetiology of complex neurological and psychiatric diseases", Briefings in Functional Genomics and Proteomics, 8(3):194-198.
    [abstract]

  69. NA Sinnott-Armstrong, CS Greene, F Cancare, JH Moore (2009), "Accelerating epistasis analysis in human genetics with consumer graphics hardware", BMC Research Notes, 2:149.

  70. Christine Sinoquet (2009), "Iterative two-pass algorithm for missing data imputation in SNP arrays", Journal of Bioinformatics and Computational Biology, 7(5):833-852.
    [ abstract]

  71. CC Spencer, Z Su, P Donnelly, J Marchini (2009), "Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip", PLoS Genetics, 5:e1000477

  72. Jingchun Sun, Peilin Jia, Ayman H. Fanous, Bradley T. Webb, Edwin J.C.G. van den Oord, Xiangning Chen, Jozsef Bukszar, Kenneth S. Kendler, and Zhongming Zhao (2009), "A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases?schizophrenia as a case", Bioinformatics, 25(19):2595-6602.
    [abstract]

  73. SA Tishkoff, FA Reed, FR Friedlaender, C Ehret, A Ranciaro, A Froment, JB Hirbo, AA Awomoyi, JM Bodo, O Doumbo, M Ibrahim, AT Juma, MJ Kotze, G Lema, JH Moore, H Mortensen, TB Nyambo, SA Omar, K Powell, GS Pretorius, MW Smith, MA Thera, C Wambebe, JL Weber, SM Williams (2009), "The genetic structure and history of Africans and African Americans", Science, 324(5930):1035-1044.

  74. J Wakefield (2009), "Bayes factors for genome-wide association studies: comparison with P-values", Genetic Epidemiology, 33(1):79-86.
    [ abstract]

  75. J Wakefield, F De Vocht, RJ Hung (2009), "Bayesian mixture modeling of gene-environment and gene-gene interactions", Genetic Epidemiology, to appear.

  76. Jian Wang, Sanjay Shete (2009), "Response to Zang et al. and Han et al." (letters to the editor), American Journal of Human Genetics, 84:298-300.

  77. Lusheng Wang, Zhanyong Wang, Wanling Yang (2009), "Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference", BMC Bioinformatics, 10:216.
    [abstract]

  78. Waranyu Wongseree, Anunchai Assawamakin, Theera Piroonratana, Saravudh Sinsomros, Chanin Limwongse, Nachol Chaiyaratana (2009), "Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses", BMC Bioinformatics, 10:294.
    [abstract]

  79. Tong Tong Wu, Yi Fang Chen, Trevor Hastie, Eric Sobel, and Kenneth Lange (2009), "Genome-wide association analysis by lasso penalized logistic regression", Bioinformatics, 25(6):714-721.
    [abstract]

  80. Can Yang, Zengyou He, Xiang Wan, Qiang Yang, Hong Xue, Weichuan Yu (2009), "SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies", Bioinformatics, 25(4):504-511.
    [abstract]

  81. Y Yang, C He, J Ott (2009), "Testing association with interactions by partitioning chi-squares", Annals of Human Genetics, 73(1):109-117.

  82. Bryndis Yngvadottir, Yali Xue, Steve Searle, Sarah Hunt, Marcos Delgado, Jonathan Morrison, Pamela Whittaker, Panos Deloukas, Chris Tyler-Smith (2009), "A Genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs", American Journal of Human Genetics, 84:224-234.
    [abstract]

  83. K Yu, Q Li, AW Bergen, RM Pfeiffer, PS Rosenberg, N Caporaso, P Kraft, N Chatterjee (2009), "Pathway analysis by adaptive combination of P-values", Genetic Epidemiology, to appear.

  84. David Zamar, Ben Tripp, George Ellis, and Denise Daley (2009), "Path: a tool to facilitate pathway-based genetic association analysis", Bioinformatics, 25(18):2444-2446.
    [abstract]

  85. Yong Zang, Wing K. Fung, Gang Zheng (2009), "Tail strength to combine two p values: their correlation cannot be ignored" (letters to the editor), American Journal of Human Genetics, 84:291-295.

  86. E Zeggini, JP Ioannidis (2009), "Meta-analysis in genome-wide association studies", Pharmacogenomics, 10(2):191-201.

  87. G Zheng, J Joo, Y Yang (2009), "Pearson's test, trend test, and MAX are all trend tests with different types of scores", Annals of Human Genetics, 73(2):133-140.

  88. G Zheng, Z Li, Mh Gail, JL Gastwirth (2009), "Impact of population substructure on trend tests for genetic case-control association studies", Biometrics, to appear.