Bibliography:
Linkage Disequilibrium Analysis
(2005)
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+ 2005

  1. GR Abecasis, D Ghosh, TE Nichols (2005), "Linkage disequilibrium: ancient history drives the new genetics", Human Heredity, 59:118-124.
    [abstract]

  2. GR Abecasis, JE Wigginton (2005), "Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers", American Journal of Human Genetics, 77:754-767.
    [abstract]

  3. TS Anantharaman, V Mysore, B Mishra (2005), "Fast and cheap genome wide haplotype construction via optical mapping", Pacific Symposium on Biocomputing, 10:385-396.

  4. SI Ao, K Yip, M Ng, D Cheung, PY Fong, I Melhado, PC Sham (2005), "CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs", Bioinformatics, 21(8):1735-1736.

  5. YS Aulchenko, AM Bertoli-Avella, CM van Duijn (2005), "A method for pooling alleles from different genotyping experiments", Annals of Human Genetics, 69(2):233-238.
    [abstract]

  6. Vineet Bafna, Vikas Bansal (2005), "Improving recombination lower bounds for haplotype data", Proceedings of the Ninth International Conference on Research in Computational Molecular Biology , pp.?-?

  7. Stuart G Baker (2005), "A simple loglinear model for haplotype effects in a case-control study involving two unphased genotypes", Statistical Applications in Genetics and Molecular Biology, 4(1):14.
    [abstract]

  8. JC Barrett, B Fry, J Maller, MJ Daly (2005), "Haploview: analysis and visualization of LD and haplotype maps", Bioinformatics, 21:263-265.
    [abstract]

  9. T Becker, M Knapp (2005), "Impact of missing genotype data on Monte-Carlo simulation based haplotype analysis", Human Heredity, 59(4):185-189.

  10. T Becker, S Cichon, E Jonson, M Knapp (2005), "Multiple testing in the context of haplotype analysis revisited: application to case-control data", Annals of Human Genetics, 69:747-756.

  11. T Becker, J Schumacher, S Cichon, MP Baur, M Knapp (2005), "Haplotype interaction analysis of unlinked regions", Genetic Epidemiology, 29:313-322.

  12. L Beckmann, DC Thomas, C Fischer, J Chang-Claude (2005), "Haplotype sharing analysis using Mantel statistics", Human Heredity, 59:67-78.
    [abstract]

  13. Tushar R. Bhangale, Mark J. Rieder, Robert J. Livingston and Deborah A. Nickerson (2005), "Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes", Human Molecular Genetics, 14(1):59-69.

  14. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani (2005), "Experimental analysis of a new algorithm for partial haplotype completion", International Journal of Bioinformatics Research and Applications, 1(4):461-473.
    [ abstract]

  15. J Brohede, R Dunne, JD McKay, GN Hannan (2005), "PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays", Nucleic Acids Research, 33(17):e142-e142.
    [abstract]

  16. Alexandre Bureau, Josée Dupuis, Kathleen Falls, Kathryn L Lunetta, Brooke Hayward, Tim P Keith, Paul Van Eerdewegh (2006), "Identifying SNPs predictive of phenotype using random forests", Genetic Epidemiology, 28(2):171-182.
    [ abstract]

  17. PR Burton, MD Tobin, JL Hopper (2005), "Key concepts in genetic epidemiology", Lacent, 366:941-951.

  18. CD Campbell, EL Ogburn, KL Lunetta, HN Lyon, ML Freedman, LC Groop, D Altshuler, KG Ardlie, JN Hirschhorn (2005), "Demonstrating stratification in a European American population", Nature Geneics, 37(8):868-872.

  19. Charles R Cantor (2005), "The use of genetic SNPs as new diagnostic markers in preventive medicine", Annals of New York Academy of Sciences, 1055:48-57.

  20. Rita M Cantor, Gary K Chen, Paivi Pajukanta, Kenneth Lange (2005), "Association testing in a linked region using large pedigrees", American Journal of Human Genetics, 76:538-542.

  21. Christopher S Carlson, Mark J Reider, Deborah A Nickerson (2005), " Comment on 'discrepancies in dbSNP confirmations rates and allele frequency distributions from varying genotyping error rates and patterns" (letter to the editor), Bioinformatics, 21(2):141-143.

  22. Z Chen, G Zheng, K Ghosh, Z Li (2005), "Linkage disequilibrium mapping of quantitative-trait loci by selective genotyping", American Journal of Human Genetics, 77(4):661-669.
    [abstract]

  23. Rong Cheng, Jennie Z. Ma, Robert C. Elston, Ming D. Li (2005), "Fine mapping functional sites or regions from case-Control data using haplotypes of multiple linked SNPs", Annals of Human Genetics, 69(1):102-112.
    [abstract]

  24. Andrew G Clark (2005), "Hot spots unglued" (news and views), Nature Genetics, 37:563-564.

  25. Andrew G Clark, Eric Boerwinkle, James Hixson, Charles F Sing (2005), "Determinants of the success of whole-genome association testing", Genome Research, 15:1463-1467.

  26. Taane G. Clark, Maria De Iorio, Robert C. Griffiths, Martin Farrall (2005), "Finding associations in dense genetic maps: a genetic algorithm approach", Human Heredity, 60:97-108.

  27. GM Clarke, LR Cardon (2005), "Disentangling linkage disequilibrium and linkage from dense SNP Trio data", Genetics, 171(4):2085-2095.
    [html]

  28. TG Clark, M De Iorio, RC Griffiths, M Farrall (2005), "Finding associations in dense genetic maps: a genetic algorithm approach", Human Heredity, 60:97-108.

  29. DG Clayton, NM Walker, DJ Smyth, R Pask, JD Cooper, LM Maier, LJ Smink, AC Lam, NR Ovington, HE Stevens, S Nutland, JM Howson, M Faham, M Moorhead, HB Jones, M Falkowski, P Hardenbol, TD Willis, JA Todd (2005), "Population structure, differential bias and genomic control in a large-scale, case-control association study", Nature Genetics, 37(11):1243-1246.
    [PDF]

  30. HJ Cordell, DG Clayton (2005), "Genetic association studies", Lancet, 366(9491):1121-1131.

  31. Dana C. Crawford, ­Dayna T. Akey, and Deborah A. Nickerson (2005), "The patterns of natural variation in human genes", Annual Review of Genomics and Human Genetics, 6:287-312.
    [abstract]

  32. MJ Daly, D Altshuler (2005), "Partner in crime" (comment), Nature Genetics, 37(4):337-338.

  33. Ariel Darvasi and Sagiv Shifman (2005), "The beauty of admixture" (news and views), Nature Genetics, 37:118-119.
    [abstract] [PDF]

  34. PI de Bakker, R Yelensky, I Pe'er, SB Gabriel, MJ Daly, D Altshuler (2005), "Efficiency and power in genetic association studies", Nature Genetics, 37(11):1217-1223.

  35. Francisco M De la Vega, Hadar Isaac, Andrew Collins, Charles R. Scafe, Bjarni V. Halldórsson, Xiaoping Su, Ross A. Lippert, Yu Wang, Marion Laig-Webster, Ryan T. Koehler, Janet S. Ziegle, Lewis T. Wogan, Junko F. Stevens, Kyle M. Leinen, Sheri J. Olson, Karl J. Guegler, Xiaoqing You, Lily H. Xu, Heinz G. Hemken, Francis Kalush, Mitsuo Itakura, Yi Zheng, Guy de Thé, Stephen J. O'Brien, Andrew G. Clark, Sorin Istrail, Michael W. Hunkapiller, Eugene G. Spier, and Dennis A. Gilbert (2005), "The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern", Genome Research, 15:454-462.

  36. Anna Di Rienzo and Richard R. Hudson (2005), "An evolutionary framework for common diseases: the ancestral-susceptibility model", Trends in Genetics, 21:596-601.

  37. Zhihong Ding, Vladimir Filkov, Dan Gusfield (2005), "A linear-time algorithm for the percect phylogeney haplotyping (PPH) problem", Proceedings of the Ninth International Conference on Research in Computational Molecular Biology , pp.?-?

  38. Michael P Epstein, Colin D Veal, Richard C Trembath, Jonathan NWN Barker, Chun Li, Glen A Satten (2005), "Genetic association analysis using data from triads and unrelated subjects", American Journal of Human Genetics, 76:592-608.

  39. TDT
    WJ Ewens, RS Spielman (2005), "What is the significance of a significant TDT?", Human Heredity, 60(4):206-210.

  40. DM Evans, LR Cardon (2005), "A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations", American Journal of Human Genetics, 76(4):681-687.

  41. Ruzong Fan, Michael Knapp, Matthias Wjst, Caixia Zhao, Momiao Xiong (2005), "High resolution T2 association tests of complex diseases based on family data", Annals of Human Genetics, 69(2):187-208.
    [abstract]

  42. Julian Forton, Dominic Kwiatkowski, Kirk Rockett, Gaia Luoni, Martin Kimber, and Jeremy Hull (2005), "Accuracy of haplotype reconstruction from haplotype-tagging single-nucleotide polymorphisms", American Journal of Human Genetics, 76:438-448.

  43. D Franke, A Philippi, F Tores, J Hager, A Ziegler, IR König (2005), "On confidence intervals for genotype relative risks and attributable risks from case parent trio designs for candidate-gene studies", Human Heredity, 60:81-88.

  44. NB Freimer, C Sabatti (2005), "Guidelines for association studies in Human Molecular Genetics", Human Molecular Genetics, 14(17):2481-2483.

  45. R Fu, DK Dey, KE Holsinger (2005), "Bayesian models for the analysis of genetic structure when populations are correlated", Bioinformatics, 21(8):1516-1529.

  46. Richard Gibbs, et al., (The International HapMap Consortium) (2005), "A haplotype map of the human genome", Nature, 437:1299-1320.
    [PDF]

  47. Jane Gibson, William Tapper, Weihua Zhang, Newton Morton, Andrew Collins (2005), "Cosmopolitan linkage disequilibrium maps", Human Genomics, 2(1):20-27.

  48. Derek Gordon, Stephen J Finch "Factors affecting statistical power in the detection of genetic association", Journal of Clinical Investigation, 115:1408-1418.

  49. Derek Gordon, Chad Haynes, Jon Blumenfeld, Stephen J Finch (2005), "PAWE-3D: visualizing power for association with error in case-control genetic studies of complex traits", Bioinformatics, 21:3935-3937.

  50. Sheng Gu, Andrew J. Pakstis, and Kenneth K. Kidd (2005), "HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations", Bioinformatics, 21:3938-3939.

  51. CY Guo, AL DeStefano, KL Lunetta, J Dupuis, LA Cupples (2005), "Expectation maximization algorithm based haplotype relative risk (EM-HRR): test of linkage disequilibrium using incomplete case-parents trios", Human Heredity, 59:125-135.
    [abstract]

  52. Wei Guo and Wing K Fung (2005), "Combining the case?control methodology with the small size transmission/disequilibrium test for multiallelic markers" European Journal of Human Genetics, 13:1007-1012.

  53. Eran Halperin, Elad Hazan (2005), "HAPLOFREQ -- estimating haplotype frequencies efficiently", Proceedings of the Ninth International Conference on Research in Computational Molecular Biology , pp.?-?

  54. Eran Halperin, Gad Kimmel, Ron Shamir (2005), "Tag SNP selection in genotype data for maximizing SNP prediction accuracy", Bioinformatics, 21(suppl 1):i195-i203.

  55. AT Hattersley, MI McCarthy (2005), "What makes a good genetic association study?", Lancet, 366(9493):1315-1323.

  56. DA Hinds, LL Stuve, GB Nilsen, E Halperin, E Eskin, DG Ballinger, KA Frazer, DR Cox (2005), "Whole-genome patterns of common DNA variation in three human populations", Science, 307:1072-1079.

  57. Jingwu He, Kelly Westbrooks, Alexander Zelikovsky (2005), "Linear reduction method for predictive and informative tag SNP selection", International Journal of Bioinformatics Research and Applications, 1(3):249-260.
    [ abstract]

  58. GA Heiman, P Gorroochurn, SE Hodge, DA Greenberg (2005), "Robustness of case-control studies to population stratification", Cancer Epidemiology Biomarkers & Prevention, 14(6):1579-1580.

  59. Agnar Helgason, Bryndís Yngvadóttir, Birgir Hrafnkelsson, Jeffrey Gulcher, Kári Stefánsson (2005), "An Icelandic example of the impact of population structure on association studies", Nature Genetics, 37:90-95.
    [PDF]

  60. Tero Hiekkalinna, Joseph D Terwilliger, Sampo Sammalisto, Leena Peltonen, Markus Perola (2005), "AUTOGSCAN: powerful tools for automated genome-wide linkage and linkage disequilibrium analysis", Twin Research and Human Genetics, 8(1):16-21.

  61. JN Hirschhorn (2005), "Genetic approaches to studying common diseases and complex traits", Pediatric Research, 57:74R-77R.
    [abstract]

  62. JN Hirschhorn, MJ Daly (2005), "Genome-wide association studies for common diseases and complex traits", Nature Reviews Genetics, 6:95-108.
    [abstract] [PDF]

  63. BD Horne, JL Anderson, JF Carlquist, JB Muhlestein, DG Renlund, TL Bair, RR Pearson, NJ Camp (2005), "Generating genetic risk scores from intermediate phenotypes for use in association studies of clinically significant endpoints", Annals of Human Genetics, 69(2):176-186.
    [abstract]

  64. Ola Hossjer (2005), "Combined association and linkage analysis for general pedigrees and genetic models", Statistical Applications in Genetics and Molecular Biology, 4(1):11.
    [abstract]

  65. Joanna M.M. Howson, Bryan J. Barratt, John A. Todd, Heather J. Cordell (2005), "Comparison of population- and family-based methods for genetic association analysis in the presence of interacting loci", Genetic Epidemiology, 29(1):51-67.
    [abstract]

  66. Xin-Sheng Hu, Fangliang He (2005), "Background selection and population differentiation", Journal of Theoretical Biology, 235:207-219.

  67. Yao-Ting Huang, Kun-Mao Chao, Ting Chen (2005), "An approximation algorithm for haplotype inference by maximum parsimony", Journal of Computational Biology, 12(10):1261-1274.

  68. Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao (2005), "Selecting additional tag SNPs for tolerating missing data in genotyping", BMC Bioinformatics, 6:263.
    [abstract]

  69. David J Hunter (2005), "Gene-environment interactions in human diseases", Nature Reviews Genetics , 6:287-298.
    [abstract]

  70. Mark M Iles (2005), "The effect of SNP marker density on the efficacy of haplotype tagging SNPs - a warning", Annals of Human Genetics, 69(2):209-215.
    [abstract]

  71. Amit R Indap, Gabor T Marth, Craig A Struble, Peter Tonellato, Michael Olivier (2005), "Analysis of concordance of different haplotype block partitioning algorithms", BMC Bioinformatics, 6:303.
    [abstract]

  72. JP Ioannidis (2005), "Why most published research findings are false", PLoS Medicine, 2:e124.

  73. Alec J Jeffreys, Rita Neumann (2005), "Factors influencing recombination frequency and distribution in a human meiotic crossover hotspot", Human Molecular Genetics, 14(15):2277-2287.

  74. J Joo, X Tian, G Zheng, JP Lin, NL Geller (2005), "Selection of single-nucleotide polymorphisms in disease association data", BMC Genetics, 6(Suppl 1):S93.

  75. E Jorgenson, X Liu, JS Witte (2005), "Case-control analyses: Geneopardy!", Genetic Epidemiology, 29(Suppl 1):S86-S90.

  76. R Karchin, LKelly, and A Sali (2005), "Improving functional annotation of non-synonomous SNPs with information theory", Pacific Symposium on Biocomputing, 10:397-408.

  77. GR Kazeem, M Farrall (2005), "Integrating case-control and TDT studies", Annals of Human Genetics, 69(3):329-335.
    [abstract]

  78. X Ke, MM Miretti, J Broxholme, S Hunt, S Beck, DR Bentley, P Deloukas, LR Cardon (2005), "A comparison of tagging methods and their tagging space", Human Molecular Genetics, 14(18):2757-2567.

  79. Gad Kimmel, Ron Shamir (2005), "gerbil: Genotype resolution and block identification using likelihood", Proceedings of National Academy of Sciences, 102(1):158-162.
    [abstract]

  80. Gad Kimmel, Ron Shamir (2005), "The incomplete perfect phylogeny haplotype problem", Journal of Bioinformatics and Computational Biology, 3(2):359-384.

  81. Gad Kimmel, Ron Shamir (2005), "A block-free hidden markov model for genotypes and its application to disease association", Journal of Computational Biology, 12(10):1243-1260.
    [ abstract]

  82. Peter Kraft, David Hunter (2005), "Integrating epidemiology and genetic association: the challenge of gene-environment interaction", Philosophical Transactions of Royal Society of London: B. Biological Sciences, 360(1460):1609-1616.
    [ abstract]

  83. Leonid Kruglyak (2005), "Power tools for human genetics" (news and views), Nature Genetics, 37:1299-1300
    [html]

  84. Kenneth Lange, Janet S. Sinsheimer, Eric Sobel (2005), "Association testing with Mendel", Genetic Epidemiology, 29(1):36-50.
    [abstract]

  85. R Lawrence, DM Evans, LR Cardon (2005), "Prospects and pitfalls in whole genome association studies", Philosophical Transactions of Royal Society of London: B. Biological Sciences, 360(1460):1589-1595.

  86. R Lawrence, DM Evans, AP Morris, X Ke, S Hunt, M Paolucci, J Ragoussis, P Deloukas, D Bentley, LR Cardon (2005), "Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants", Genome Research, 15(11):1503-1510.

  87. Jing Li, Tao Jiang (2005), "Computing the minimum recombinant haplotype configuration from incomplete genotype data on a pedigree by integer linear programming", Journal of Computational Biology, 12(6):719-739.

  88. Jing Li and Tao Jiang (2005), "Haplotype-based linkage disequilibrium mapping via direct data mining", Bioinformatics, 21:4384-4393.
    [abstract]

  89. Mingyao Li, Michael Boehnke, Goncalo R. Abecasis (2005), "Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal", American Journal of Human Genetics, 76:934-949.

  90. Z Li, JL Gastwirth, MH Gail (2005), "Power and related statistical properties of conditional likelihood score tests for association studies in nuclear families with parental genotypes", Annals of Human Genetics, 69(3):296-314.
    [abstract]

  91. Z Li, W Zhou, XS Zhang, L Chen (2005), "A parsimonious tree-grow method for haplotype inference", Bioinformatics, 21(17):3475-3481.

  92. Sooyeol Lim, Joseph Beyene, Celia MT Greenwood (2005), "Continuous covariates in genetic association studies of case-parent triads: gene and gene-environment interaction effects, population stratification, and power analysis", Statistical Applications in Genetics and Molecular Biology, 4(1):20.
    [abstract]

  93. DY Lin (2005), "On rapid simulation of P values in association studies", American Journal of Human Genetics, 77(3):513-514.
    (SR Seaman and B Muller-Myhsok (2005), "Reply to Lin", 77(3):514-515.)

  94. Tie-Fei Liu, Wing-Kin Sung, Yi Li, Jian-Jun Liu, Ankush Mittal, Pei-Lin Mao (2005), "Effective algorithms for tag SNP selection", Journal of Bioinformatics and Computational Biology, 3(5):1089-1106.
    [abstract]

  95. X Liu, E Jorgenson, JS Witte (2005), "Hierarchical modeling in association studies of multiple phenotypes", BMC Genetics, 6(Suppl 1):S104

  96. Zhenqiu Liu, Shili Lin (2005), "Multilocus LD measure and tagging SNP selection with generalized mutual information", Genetic Epidemiology, 29(4):353-364.

  97. Shuangge Ma, Jian Huang (2005), "Regularized ROC method for disease classification and biomarker selection with microarray data", Bioinformatics, 21:4356-4362.
    [abstract]

  98. N Maniatis, NE Morton, J Gibson, CF Xu, LK Hosking, A Collins (2005), "The optimal measure of linkage disequilibrium reduces error in association mapping of affection status", Human Molecular Genetics, 14(1):145-153.

  99. DM Maraganore (2005), "Blood is thicker than water: the strengths of family-based case-control studies", Neurology, 64(3):408-409.

  100. DP Martin, C Williamson, D Posada (2005), "RDP2: recombination detection and analysis from sequence alignments", Bioinformatics, 21:260-262.
    [abstract]

  101. PA McCaskie, KW Carter, SR McCaskie, LJ Palmer (2005), "The effect of missing data on linkage disequilibrium mapping and haplotype association analysis in the GAW14 simulated datasets", BMC Genetics, 6(Suppl 1):S151.

  102. Paul M McKeigue (2005), "Prospects for admixture mapping of complex traits", American Journal of Human Genetics, 76:1-7.

  103. GA McVean, NJ Cardin (2005), "Approximating the coalescent with recombination", Philosophical Transactions of Royal Society of London: B. Biological Sciences, 360(1459):1387-1393.

  104. G McVean, CC Spencer, R Chaix (2005), "Perspectives on human genetic variation from the HapMap Project", PLoS Genetics, 1(4):e54.

  105. Cosetta Minelli, John R Thompson, Keith R Abrams, Ammarin Thakkinstian, John Attia (2005), "The choice of a genetic model in the meta-analysis of molecular association studies", International Journal of Epidemiology, 34(6):1319-1328.

  106. MM Miretti, EC Walsh, X Ke, M Delgado, M Griffiths, S Hunt, J Morrison, P Whittaker, ES Lander, LR Cardon, DR Bentley, JD Rioux, S Beck, P Deloukas (2005), "A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms", American Journal of Human Genetics, 76(4):634-646.

  107. Perseus I Missirlis, Carri-Lyn R Mead, Stefanie L Butland, B.F. Francis Ouellette, Rebecca S Devon, Blair R Leavitt, Robert A Holt (2005), "Satellog: a database for the identification and prioritization of satellite repeats in disease association studies", BMC Bioinformatics, 6:145.
    [abstract]

  108. Giovanni Montana (2005), "HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients", Bioinformatics, 21:4309-4311.
    [abstract]

  109. Sean Mooney (2005), "Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis" Briefings in Bioinformatics, 6(1):44-56.

  110. NE Morton (2005), "Linkage disequilibrium maps and association mapping", Journal of Clinical Investigation, 115:1425-1430.
    [abstract]

  111. Jakob C Mueller, Elin Lõhmussaar, Reedik Mägi, Maido Remm, Thomas Bettecken, Peter Lichtner, Saskia Biskup, Thomas Illig, Arne Pfeufer, Jan Luedemann, Stefan Schreiber, Peter Pramstaller, Irene Pichler, Giovanni Romeo, Anthony Gaddi, Alessandra Testa, Heinz-Erich Wichmann, Andres Metspalu, Thomas Meiting (2005), "Linkage disequilibrium patterns and tagSNP transferability among European populations", American Journal of Human Genetics, 76:387-398.

  112. S Myers, L Bottolo, C Freeman, G McVean, P Donnelly (2005), "A fine-scale map of recombination rates and hotspots across the human genome", Science, 310(5746):321-324.

  113. C Newton-Cheh, JN Hirschhorn (2005), "Genetic association studies of complex traits: design and analysis issues", Mutation Research, 573(1-2):54-69.

  114. Rasmus Nielsen (2005), "Molecular signatures of natural selection" Annual Review of Genetics, 39:197-218.

  115. BV North, D Curtis, PC Sham (2005), "Application of logistic regression to case-control association studies involving two causative loci", Human Heredity, 59:79-87.
    [abstract]

  116. Michael Nothnagel and Klaus Rohde (2005), "The effect of single-nucleotide polymorphism marker selection on patterns of haplotype blocks and haplotype frequency estimates", American Journal of Human Genetics, 77(6):988-998.
    [abstract]

  117. Jun Ohashi, Andrew G Clark (2005), "Application of the stepwise focusing method to optimize the cost-effectiveness of genome-wide association studies with limited research budgets for genotyping and phenotyping", Annals of Human Genetics, 69(3):323-328.
    [abstract]

  118. LJ Palmer, LR Cardon (2005), "Shaking the tree: mapping complex disease genes with linkage disequilibrium", Lancet, 366(9492):1223-1234.
    [PDF]

  119. Z Pan, TA Trikalinos, FK Kavvoura, J Lau, JPA Ioannidis (2005), "Local literature bias in genetic epidemiology: an empirical evaluation of the Chinese literature", PLoS Medicine, 2(12):e419.
    [abstract]

  120. T Pastinen, B Ge, S Gurd, T Gaudin, C Dore, M Lemire, P Lepage, E Harmsen, TJ Hudson (2005), "Mapping common regulatory variants to human haplotypes", Human Molecular Genetics, 14(24):3963-3971.

  121. PD Pharoah, AM Dunning, BA Ponder, DF Easton (2005), "The reliable identification of disease-gene associations" (commentary), Cancer Epidemiology Biomarkers & Prevention, 14:1362.
    [html]

  122. François Pompanon, Aurélie Bonin, Eva Bellemain & Pierre Taberlet (2005), "Genotyping errors: causes, consequences and solutions", Nature Reviews Genetics, 6:847-859.
    [ abstract]

  123. SE Ptak, DA Hinds, K Koehler, B Nickel, N Patil, DG Ballinger, M Przeworski, KA Frazer, S Paabo (2005), "Fine-scale recombination patterns differ between chimpanzees and humans", Nature Genetics, 37(4):429-434.

  124. Eric W Price, Ignazio Carbone (2005), "SNAP: workbench management tool for evolutionary population genetic analysis", Bioinformatics, 21:402-404.

  125. TDT
    S Purcell, PC Sham, MJ Daly (2005), "Parental phenotypes in family-based association analysis", American Journal of Human Genetics, 76(2):249-259.

  126. Hein Putter, Jeanine J Houwing-Duistermaat, Nico JD Nagelkerke (2005), "Combining evidence for association from transmission disequilibrium and case-control studies using single-nucleotide polymorphisms", BMC Genetics, 6(suppl 1):S106.

  127. SR Quade, RC Elston, KA Goddard (2005), "Estimating haplotype frequencies in pooled DNA samples when there is genotyping error", BMC Genetics, 6(1):25.

  128. Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen (2005), "A hidden Markov technique for haplotype reconstruction", Lecture Notes in Computer Science, Vol. 3692, pp.140-151.
    [abstract]

  129. D Reich, N Patterson (2005), "Will admixture mapping work to find disease genes?", Philosophical Transactions of Royal Society of London: B. Biological Sciences, 360(1460):1605-1607.

  130. A Rinaldo, SA Bacanu, B Devlin, V Sonpar, L Wasserman, K Roeder (2005), "Characterization of multilocus linkage disequilibrium", Genetic Epidemiology, 28(3):193-206.

  131. K Roeder, SA Bacanu, V Sonpar, X Zhang, B Devlin (2005), "Analysis of single-locus tests to detect gene/disease associations", Genetic Epidemiology, 28(3):207-219.

  132. Jonathan Rosand (2005), "Epistasis is coming: Are we ready? " (editorial comment), Stroke, 36:1879.
    [abstract]

  133. NA Rosenberg, S Mahajan, S Ramachandran, C Zhao, JK Pritchard, MW Feldman (2005), "Clines, clusters, and the effect of study design on the inference of human population structure", PLoS Genetics, 1:e70.

  134. G Salanti, G Amountza, EE Ntzani, JP Ioannidis (2005), "Hardy-Weinberg equilibrium in genetic association studies: an empirical evaluation of reporting, deviations, and power", European Journal of Human Genetics, 13(7):840-848.

  135. Rany M Salem, Jennifer Wessel, Nicholas J Schork (2005) "A comprehensive literature review of haplotyping software and methods for use with unrelated individuals", Human Genomics, 2(1):39-66.

  136. D Salyakina, SR Seaman, BL Browning, F Dudbridge, B Muller-Myhsok (2005), "Evaluation of Nyholt's procedure for multiple testing correction", Human Heredity, 60(1):19-25.

  137. Sarah L Sawyer, Namita Mukherjee, Andrew J Pakstis, Lars Feuk, Judith R Kidd, Anthony J Brookes, Kenneth K Kidd (2005), "Linkage disequilibrium patterns vary substantially among populations", European Journal of Human Genetics, 13:677-686.

  138. SF Schaffner, C Foo, S Gabriel, D Reich, MJ Daly, D Altshuler (2005), "Calibrating a coalescent simulation of human genome sequence variation", Genome Research, 15(11):1576-1583.

  139. Daniel J Schaid, Shannon K McDonnell, Scott J Hebbring, Julie M Cunningham, Stephen N Thibodeau (2005), "Nonparametric tests of association of multiple genes with human disease", American Journal of Human Genetics, 76:780-793.

  140. Steven J. Schrodi (2005), "A probabilistic approach to large-scale association scans: a semi-Bayesian method to detect disease-predisposing alleles", Statistical Applications in Genetics and Molecular Biology, 4(1):31.
    [abstract]

  141. SR Seaman, B Muller-Myhsok (2005), "Rapid simulation of P values for product methods and multiple-testing adjustment in association studies", American Journal of Human Genetics, 76:399-408.

  142. D Serre, R Nadon, TJ Hudson (2005), "Large-scale recombination rate patterns are conserved among human populations", Genome Research, 15(11):1547-1552.

  143. R Sharan, BV Halldosson, S Istrail (2005), "Islands of tractability for parsimony haplotyping", Proceedings of IEEE Computational Systems Bioinformatics Conference, pp. 65-72.

  144. Mark D Shriver, Rui Mei, Esteban J Parra, Vibhor Sonpar, Indrani Halder, Sarah A Tishkoff, Theodore G Schurr, Sergev I Zhadanov, Ludmila P Osipova, Tom D Brutsaert, Jonathan Friedlaender, Lynn B Jorde, W. Scott Watkins, Michael J Bamshad, Gerardo Gutierrez, Halina Loi, Hajime Matsuzaki, Rick A Kittles, George Argyropoulos, Jose R Fernandez, Joshua M Akey, Keith W Jones (2005), "Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation", Human Genomics, 2(2):81-89.

  145. MJ Sillanpaa, M Bhattacharjee (2005) "Bayesian association-based fine mapping in small chromosomal segments", Genetics, 169:427-439.

  146. CL Simpson, J Knight, LM Butcher, VK Hansen, E Meaburn, LC Schalkwyk, IW Craig, JF Powell, PC Sham, A Al-Chalabi (2005), "A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays", Nucleic Acids Research, 33(3):e25.
    [abstract]

  147. Clara Singer, Iris Grossman, Nili Avidan, Jacques S Beckmann, Itsik Pe'er (2005), "Trick or treat: The effect of placebo on the power of pharmacogenetic association studies", Human Genomics, 2(1):28-38.

  148. AV Smith, DJ Thomas, HM Munro, GR Abecasis (2005), "Sequence features in regions of weak and strong linkage disequilibrium", Genome Research, 15:1519-1534.

  149. Michael W. Smith & Stephen J. O'Brien (2005), "Mapping by admixture linkage disequilibrium: advances, limitations and guidelines" Nature Reviews Genetics, 6:623-632.
    [abstract]

  150. GT Spijker, IM Nolte, RC Jansen, GJ te Meerman (2005), "Genetic association studies in complex disease: disentangling additional predisposing loci from associated neutral loci using a constrained - permutation approach", Annals of Human Genetics, 69(1):90-101.
    [abstract]

  151. C Spinka, RJ Carroll, N Chatterjee (2005), "Analysis of case-control studies of genetic and environmental factors with missing genetic information and haplotype-phase ambiguity", Genetic Epidemiology, 29(2):649-659.

  152. Jason E Stajich, Matthew W Hahn (2006), "Disentangling the effects of demography and selection in human history", Molecular Biology and Evolution, 22(1):63-73.

  153. Hreinn Stefansson, Agnar Helgason, Gudmar Thorleifsson, Valgerdur Steinthorsdottir, Gisli Masson, John Barnard, Adam Baker, Aslaug Jonasdottir, Andres Ingason, Vala G Gudnadottir, Natasa Desnica, Andrew Hicks, Arnaldur Gylfason, Daniel F Gudbjartsson, Gudrun M Jonsdottir, Jesus Sainz, Kari Agnarsson, Birgitta Birgisdottir, Shyamali Ghosh, Adalheidur Olafsdottir, Jean-Baptiste Cazier, Kristleifur Kristjansson, Michael L Frigge, Thorgeir E Thorgeirsson, Jeffrey R Gulcher, Augustine Kong, Kari Stefansson (2005), "A common inversion under selection in Europeans", Nature Genetics, 37:129-137.
    [PDF]

  154. Matthew Stephens and Paul Scheet (2005), "Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation", American Journal of Human Genetics, 76:449-462.

  155. SC Su, CC Kuo, T Chen (2005), "Inference of missing SNPs and information quantity measurements for haplotype blocks", Bioinformatics, 21(9):2001-2007.

  156. Ann-Christine Syvänen (2005), "Toward genome-wide SNP genotyping", Nature Genetics, 37:S5-S10.
    [abstract]

  157. Scott J Tebbutt, Igor V Opushnyev, Ben W Tripp, Ayaz M Kassamali, Wendy L Alexander, Marilyn I Andersen (2005), "SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data", Bioinformatics, 21:124-127.
    [abstract]

  158. H Tang, J Peng, P Wang, NJ Risch (2005), "Estimation of individual admixture: analytical and study design considerations", Genetic Epidemiology, 28(4):289-301.

  159. H Tang, T Quertermous, B Rodriguez, SL Kardia, X Zhu, A Brown, JS Pankow, MA Province, SC Hunt, E Boerwinkle, NJ Schork, NJ Risch (2005), "Genetic structure, self-identified race/ethnicity, and confounding in case-control association studies", American Journal of Human Genetics, 76(2):268-275.

  160. Q Tan, L Christiansen, L Bathum, JH Zhao, AI Yashin, JW Vaupel, K Christensen, TA Kruse (2005), "Estimating haplotype relative risks on human survival in population-based association studies", Human Heredity, 59:88-97.
    [abstract]

  161. W Tapper, A Collins, J Gibson, N Maniatis, S Ennis, NE Morton (2005), "A map of the human genome in linkage disequilibrium units", Proceedings of National Academy of Sciences, 102(33): 11835-11839.
    [PDF]

  162. Ammarin Thakkinstian, Patrick McElduff, Catherine D'Este, David Duffy, John Attia (2005), "A method for meta-analysis of molecular association studies", Statistics in Medicine, 24(9):1291-1306.
    [abstract]

  163. GA Thorisson, AV Smith, L Krishnan, LD Stein (2005), "The International HapMap Project Web site", Genome Research, 15(11):1592-1593.

  164. Alun Thomas (2005), "Characterizing allelic associations from unphased diploid data by graphical modeling", Genetic Epidemiology, 29(1):23-35.
    [abstract]

  165. Duncan C. Thomas, Robert W. Haile, and David Duggan (2005), "Recent developments in genomewide association scans: a workshop summary and review", American Journal of Human Genetics, 77(3):337-345.
    [PDF]

  166. X Tian, J Joo, G Zheng, JP Lin (2005), "Robust trend tests for genetic association in case-control studies using family data", BMC Genetics, 6(Suppl 1):S107.

  167. TDT
    Kristel van Steen, Christoph Lange (2005), "PBAT: A comprehensive software package for genome-wide association analysis of complex family-based studies", Human Genomics, 2(1):67-69.

  168. Veronique Vitart, Andrew D Carothers, Caroline Hayward, Peter Teague, Nicholas D Hastie, Harry Campbell, Alan F Wright (2005), "Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design", American Journal of Human Genetics, 76:763-772.

  169. BF Voight, JF Pritchard (2005), "Confounding from cryptic relatedness in case-control association studies", PLoS Genetics, 1:e32.

  170. CM Wade, MJ Daly (2005), "Genetic variation in laboratory mice", Nature Genetics, 37(11):1175-1180.

  171. Kai Wang, Val C Sheffield (2005), "A constrained-likelihood approach to marker-trait association studies", American Journal of Human Genetics, 77(5):768-780.

  172. Y Wang, R Localio, TR Rebbeck (2005), "Bias correction with a single null marker for population stratification in candidate gene association studies", Human Heredity, 59:165-175.
    [abstract]

  173. Ying Wang and Bruce Rannala (2005), "In Silico analysis of disease-association mapping strategies using the coalescent process and incorporating ascertainment and selection", American Journal of Human Genetics, 76:1066-1073.

  174. RS Wang, LY Wu, ZP Li, XS Zhang (2005), "Haplotype reconstruction from SNP fragments by minimum error correction", Bioinformatics, 21:2456-2462.
    [abstract]

  175. William YS Wang, Bryan J Barratt, David G Clayton, John A Todd (2005), "Genome-wide association studies: theoretical and practical concerns", Nature Reviews Genetics, 6:109-118.
    [abstract] [PDF]

  176. BM Webb-Robertson, SL Havre, and DA Payne (2005), "A Bayesian framework for SNP identification", Pacific Symposium on Biocomputing, 10:421-432.

  177. BS Weir, LR Cardon, AD Anderson, DM Nielsen, WG Hill (2005), "Measures of human population structure show heterogeneity among genomic regions", Genome Research, 15(11):1468-1476.

  178. AS Whittemore (2005), "Genetic association studies: time for a new paradigm?" (commentaries), Cancer Epidemiology, Biomarkers & Prevention, 14:1359.

  179. Scott H Williamson, Ryan Hernandez, Adi Fledel-Alon, Lan Zhu, Rasmus Nielsen, Carlos D Bustamante (2005), "Simultaneous inference of selection and population growth from patterns of variation in the human genome", Proceedings of National Academy of Sciences, 102(22):7882-7887.

  180. Wendy Winckler, Simon R. Myers, Daniel J Richter, Robert C Onofrio, Gavin J McDonald, Ronald E Bontrop, Gilean AT McVean, Stacey B Gabriel, David Reich, Peter Donnelly, David Altshuler (2005), "Comparison of fine-scale recombination rates in humans and chimpanzees", Science, 308:107-111.

  181. Jacqueline K Wittke-Thompson, Anna Pluzhnikov, and Nancy J. Cox (2005), "Rational inferences about departures from Hardy-Weinberg equilibrium", American Journal of Human Genetics, 76:967-986.

  182. NR Wray (2005), "Allele frequencies and the r2 measure of linkage disequilibrium: impact on design and interpretation of association studies" Twin Research and Human Genetics, 8(2):87-94.

  183. Hong Xu, Simon G. Gregory, Elizabeth R. Hauser, Judith E. Stenger, Margaret A. Pericak-Vance, Jeffery M. Vance, Stephan Züchner, and Michael A. Hauser (2005), "SNPselector: a web tool for selecting SNPs for genetic association studies", Bioinformatics, 21:4181-4186.
    [abstract]

  184. HC Yang, CC Pan, RCY Lu, CSJ Fann (2005), "New adjustment factors and sample size calculation in a DNA-pooling experiment with preferential amplification", Genetics, 169:399-410.

  185. Quanhe Yang, Muin J Khoury, JM Friedman, Julian Little, W Dana Flanders (2005), "How many genes underlie the occurrence of common complex diseases in the population?", International Journal of Epidemiology, 34(5):1129-1137.
    [ abstract]

  186. S Yang, J Joo, Z Feng, JP Lin (2005), "A new family-based association test via a least-squares method", BMC Genetics, 6(Suppl 1):S110.

  187. A Yuan, G Chen, C Rotimi, GE Bonney (2005), "A statistical framework for haplotype block inference", Journal of Bioinformatics and Computational Biology, 3(5):1021-1038.
    [abstract]

  188. P Yue, Z Li, J Moult (2005), "Loss of protein structure stability as a major causative factor in monogenic disease", Journal of Molecular Biology, 353(2):459-473.

  189. DV Zaykin, SS Young (2005), "Large recursive partitioning analysis of complex disease pharmacogenetic studies. II. Statistical considerations", Pharmacogenomics, 6(1):77-89.

  190. Dmitri V. Zaykin, Lev A. Zhivotovsky (2005), "Ranks of genuine associations in whole-genome scans", Genetics, 171:813-823.

  191. Eleftheria Zeggini, Anne Barton, Stephen Eyre, Daniel Ward, William Ollier, Jane Worthington, Sally John (2005), "Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition", BMC Genetics, 6:21.

  192. E Zeggini, W Rayner, AP Morris, AT Hattersley, M Walker, GA Hitman, P Deloukas, LR Cardon, MI McCarthy (2005), "An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data sets", Nature Genetics, 37(12):1320-1322.

  193. J Zhang, D Schneider, C Ober, MS McPeek (2005), "Multilocus linkage disequilibrium mapping by the decay of haplotype sharing with samples of related individuals", Genetic Epidemiology, 29(2):128-140.

  194. J Zhang, M Vingron, MR Hoehe (2005), "Haplotype reconstruction for diploid populations", Human Heredity, 59:144-156.
    [abstract]

  195. Kui Zhang, Zhaohui Qin, Ting Chen, Jun S. Liu, Michael S. Waterman, and Fengzhu Sun (2005), "HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms", Bioinformatics, 21:131-134.
    [abstract]

  196. Kui Zhang, Fengzhu Sun, Hongyu Zhao (2005), "HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination", Bioinformatics, 21:90-103.
    [abstract]

  197. Liqing Zhang, Wen-Hsiung Li (2005), "Human SNPs reveal no evidence of frequent positive selection", Molecular Biology and Evolution, 22(12):2504-2507.

  198. Jinying Zhao, Eric Boerwinkle, and Momiao Xiong (2005), "An entropy-based statistic for genomewide association studies", American Journal of Human Genetics, 77:27-40.

  199. Lan-Juan Zhao, Miao-Xin Li, Yan-Fang Guo, Fu-Hua Xu, Jin-Long Li, and Hong-Wen Deng (2005), "SNPP: automating large-scale SNP genotype data management", Bioinformatics, 21:266-268.
    [abstract]

  200. Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang, Xiang-Sun Zhang (2005), "Haplotype assembly from aligned weighted SNP fragments", Computational Biology and Chemistry, 29(4):281-287.
    [abstract]

  201. G Zheng, Z Chen (2005), "Comparison of maximum statistics for hypothesis testing when a nuisance parameter is present only under the alternative", Biometrics, 61(1):254-258.

  202. Gang Zheng, Boris Freidlin, Zhaohai Li, Joseph L. Gastwirth (2005), "Genomic control for association studies under various genetic models", Biometrics, 61(1):186-192.
    [abstract]

  203. G Zheng, J Joo, SK Ganesh, EG Nabel, NL Geller (2005), "On averaging power for genetic association and linkage studies", Human Heredity, 59:14-20.
    [abstract]

  204. Gang Zheng, Xin Tian (2005), "The impact of diagnostic error on testing genetic association in case-control studies", Statistics in Medicine, 24(9):1291-1306.
    [abstract]

  205. Sebastian Zollner, Jonathan K Pritchard (2005), "Coalescent-based association mapping and fine mapping of complex trait loci", Genetics, 169(2):1071-1092.

  206. Sebastian Zollner, Xiaoquan Wen, Jonathan K Pritchard (2005), "Association mapping and fine mapping with TreeLD", Bioinformatics, 21:3168-3170.

  207. TDT
    G Zou, H Zhao (2005), "Family-based association tests for different family structures using pooled DNA", Annals of Human Genetics, 69:429-442.