Bibliography: Linkage Disequilibrium Analysis (2003)

2003

1. Hans Ackerman, Stanley Usen, Richard Mott, Anna Richardson, Fatoumatta Sisay-Joof, Pauline Katundu, Terrie Taylor, Ryk Ward, Malcolm Molyneux, Margaret Pinder, Dominic P Kwiatkowski1 (2003), "Haplotypic analysis of the TNF locus by association efficiency and entropy", Genome Biology, 4(4):R24.

2. T Ahmad, M Neville, SE Marshall, A Armuzzi, K Mulcahy-Hawes, J Crawshaw, H Sato, KL Ling, M Barnardo, S Goldthorpe, R Walton, M Bunce, DP Jewell, KI Welsh (2003), "Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC", Human Molecular Genetics, 12:647-656.
   [abstract]

3. JM Akey, K Zhang, M Xiong, L Jin (2003), "The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium", Molecular Biology and Evolulation, 20(2):232-242.

4. quantitative-trait

   Alexandre Alcais, Laurent Abel (2003), "Removing phenotypic distribution assumptions from tests of linkage disequilibrium for quantitative traits", Genetic Epidemiology, 24(3):191-199.

5. Andrew S Allen, Paul J Rathouz, Glen A Satten (2003), "Informative missingness in genetic association studies: case-parent designs", American Journal of Human Genetics, 72(3):671-680.
   [html]

6. Eric C Anderson, John Novembre (2003), "Fnding haplotype block boundaries by using the minimum-description-length principle", American Journal of Human Genetics, 73:336-354.
   [abstract]

7. Norman Arnheim, Peter Calabrese, Magnus Nordborg (2003), "Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved" (review), American Journal of Human Genetics, 73(1):5-16.
   [PDF]

8. YS Aulchenko, TI Axenovich, I Mackay, CM van Duijn (2003), "miLD and booLD programs for calculation and analysis of corrected linkage disequilibrium", Annals of Human Genetics, 67(4):372-375.

9. V Bafna, D Gusfield, G Lancia, S Yooseph (2003), "Haplotyping as a perfect phylogeny. a direct approach", Journal of Computational Biology, 10(3):323-340.
   [ abstract]

10. V Bafna, BV Halldorsson, R Schwartz, AG Clark, S Istrail (2003), "Haplotypes and informative SNP selection algorithms: don't block out information", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp. 9-18.

11. applications

    I Barroso, J Luan, RPS Middelberg, AH Harding, PW Franks, RW Jakes, D Clayton, AJ Schafer, S O'Rahilly, NJ Wareham (2003), "Candidate gene association study in type 2 diabetes indicates a role for genes involved in beta-cell function as well as insulin action", PLoS Biology, 1(1):41-55.

12. J Bertranpetit, F Calafell, D Comas, A Gonzalez-Neira, A Navarro (2003), "Structure of linkage disequilibrium in humans: genome factors and population stratification", Cold Spring Harbor Symposium on Quantitative Biology, 68:79-88.

13. RG Blazej, BM Paegel, RA Mathies (2003), "Polymorphism ratio sequencing: A new approach for single nucleotide polymorphism discovery and genotyping", Genome Research, 13:287-293.

14. R Bomprezzi, PE Kovanen, R Martin (2003), "New approaches to investigating heterogeneity in complex traits", Journal of Medical Genetics, 40:553-559.
    [PDF]

15. population-structure

    B Borera, R Barrantes, R Marin-Rojas (2003), "Gene admixture in the Costa Rican population", Annals of Human Genetics, 67(1):71-80.
    [ abstract]

16. D Botstein, N Risch (2003), "Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease", Nature Genetics, 33(suppl):228-237.
    [PDF]

17. C Bourgain, S Hoffjan, R Nicolae, D Newman, L Steiner, K Walker, R Reynolds, C Ober, MS McPeek (2003), "Novel case-control test in a founder population identifies P-selectin as an atopy-susceptibility locus", American Journal of Human Genetics, 73(3):612-626.

18. LR Cardon, GR Abecasis (2003), "Using haplotype blocks to map human complex trait loci", Trends in Genetics, 19:135-140.

19. LR Cardon, LJ Palmer (2003), "Population stratification and spurious allelic associations" (review), Lancet, 361:598-604.
    [abstract] [PDF]

20. CS Carlson, MA Eberle, MJ Rieder, JD Smith, L Kruglyak, DA Nickerson (2003), "Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans", Nature Genetics, 33(4):518-521.

21. JM Chapman, JD Cooper, JA Todd, DG Clayton (2003), "Detecting disease associations due to linkage disequilibrium using haplotype tags", Human Heredity, 56:18-31.
    [ abstract]

22. NH Chapman, EA Thompson (2003), "A model for the length of tracts of identity by descent in finite random mating populations", Theoretical Population Biology, 64(2):141-150.

23. HS Chen, X Zhu, H Zhao, S Zhang (2003) "Qualitative semi-parametric test to detect genetic association in case-control design under structured population", Annals of Human Genetics, 67(3):250-264.
    [ abstract]

24. R Cheng, JZ Ma, FA Wright, S Lin, X Gao, D Wang, RC Elston, MD Li (2003), "Nonparametric disequilibrium mapping of functional sites using haplotypes of multiple tightly linked single-nucleotide polymorphism (SNP) markers", Genetics, 164:1175-1187.

25. Ren Hua Chung, Dan Gusfield (2003), "Perfect phylogeny haplotyper: haplotype inferral using a tree model", Bioinformatics, 19:780-781.
    [ abstract]

26. Andrew G Clark (2003), "Finding genes underlying risk of complex disease by linkage disequilibrium mapping", Current Opinion in Genetics & Development, 13(3):296-302.
    [PDF]

27. Andrew G Clark, Rasmus Nielsen, James Signorovitch, Tara C Matise, Stephen Glanowski, Jeremy Heil, Emily S Winn-Deen, Arthur L Holden, Eric Lai (2003), "Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome", American Journal of Human Genetics, 73:285-300.
    [abstract]

28. HM Colhoun, PM McKeigue, G Davey Smith (2003), "Problems of reporting genetic associations with complex outcomes", Lancet, 361(9360):865-872.

29. HE Collins-Schramm, B Chima, DJ Operario, LA Criswell, MF Seldin (2003), "Markers informative for ancestry demonstrate consistent megabase-length linkage disequilibrium in the African American population", Human Genetics, 113(3):211-219.

30. E Cousin, E Genin, S Mace, S Ricard, C Chansac, M de Zompo, JF Deleuze (2003), "Association studies in candidate genes: strategies to select SNPs to be tested" Human Heredity, 56(4):151-159.
    [ abstract]

31. B Devlin, Kathryn Roeder, Larry Wasserman (2003), "Analysis of multilocus models of association", Genetic Epidemiology, 25(1):36-47.
    [abstract]

32. Keyue Ding, Kaixin Zhou, Fuchu He, Yan Shen (2003), "LDA--a java-based linkage disequilibrium analyzer", Bioinformatics, 19:2147-2148.
    [ abstract]

33. F Dudbridge (2003), "Pedigree disequilibrium tests for multilocus haplotypes", Genetic Epidemiology, 25:115-121.
    [abstract]

34. F Dudbridge, BPC Koeleman (2003), "Rank truncated product of P values, with application to genomewide association scans", Genetic Epidemiology, 25(4):360-366.

35. Michael P Epstein, Glen A Satten (2003), "Inference on haplotype effects in case-control studies using unphased genotype data", American Journal of Human Genetics, 73(6):1316-1329.

36. E Eskin, E Halperin, RM Karp (2003), "Effecient reconstruction of haplotype structure via perfect phylogeny", Journal of Bioinformatics and Computational Biology, 1(1):1-20.
    [ abstract]

37. E Eskin, E Halperin, RM Karp (2003), "Large scale reconstruction of haplotypes from genotype data", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.104-113.

38. Laurent Excoffier, Grant Hamilton (2003), "Comment on 'Genetic structure of human populations'", Science, 300:1877.
    [ abstract]

39. L Excoffier, G Laval, DJ Balding (2003), "Gametic phase estimation over large genomic regions using an adaptive window approach", Human Genomics, 1(1):7-19.

40. D Falush, M Stephens, JK Pritchard (2003), "Inference of population structure Using multilocus genotype data: linked loci and correlated allele frequencies", Genetics, 164:1567-1587.
    [abstract]

41. quantitative-trait

    R Fan, M Xiong (2003), "Combined high resolution linkage and association mapping of quantitative trait loci", European Journal of Human Genetics, 11(2):125-137.

42. SA Fisher, A Moody, MM Mirza, AP Cuthbert, J Hampe, A Macpherson, J Sanderson, A Forbes, J Mansfield, S Schreiber, CM Lewis, CG Mathew (2003), "Genetic variation at the chromosome 16 chemokine gene cluster: development of a strategy for association studies in complex disease", Annals of Human Genetics, 67(5):377-390.
    [ abstract]

43. N Freimer, C Sabatti (2003), "The human phenome project", Nature Genetics, 34(1):15-21.

44. J Freudenberg (2003), "Genome-wide prediction of disease-relevant genes and variants", Current Opinion in Drug Discovery & Development, 6:304-309.

45. Chad Garner, Montgomery Slatkin (2003), "On selecting markers for association studies: patterns of linkage disequilibrium between two and three diallelic loci", Genetic Epidemiology, 24(1):57-67.

46. DB Goldstein, GL Cavalleri, KR Ahmadi (2003), "The genetics of common diseases: 10 million times as hard", Cold Spring Harbor Symposium on Quantitative Biology, 68:395-401.

47. G Greenspan, D Geiger (2003), "Model-based inference of haplotype block variation", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.131-137.

48. TDT

    Chi C Gu, DC Rao (2003), "Designing an optimum genetic association study using dense SNP markers and family-based sample", Frontiers in Bioscience, 8:s68-s80.
    [abstract]

49. Indrani Halder, Mark D. Shriver (2003), "Measuring and using admixture to study the genetics of complex diseases", Human Genomics, 1(1):52-62.

50. BV Halldorsson, V Bafna, N Edwards, R Lippert, S Yooseph, S Istrail (2003), "Combinatorial problems arising in SNP and haplotype analysis", Proceedings of the Fourth CDMTCS International Conference on Discrete Mathematics and Theoretical Computer Science (DMTCS 2003), Lecture Notes in Computer Science, volume 2731, eds. CS Calude, MJ Dinneen, V Vajnovszki, pp.26-47 (Springer-Verlag)

51. Mark Harris, Jeremy M. R. Martin, John F. Peden, Christopher J. Rawlings (2003), "SNP cherry picker: maximizing the chance of finding an association with a disease SNP", Bioinformatics, 19:2141-2143.
    [ abstract]

52. population-structure

    Ben J Hayes, Peter M Visscher, Helen C McPartlan, Mike E Goddard (2003), "Novel multilocus measure of linkage disequilibrium to estimate past effective population size", Genome Research, 13(4):635-643.
    [ abstract]

53. A Helgason, G Nicholson, K Stefánsson, P Donnelly (2003), "A Reassessment of genetic diversity in Icelanders: strong evidence from multiple loci for relative homogeneity caused by genetic drift", Annals of Human Genetics, 67(4): 281-297.
    [ abstract]

54. Clive J Hoggart, Esteban J Parra, Mark D Shriver, Carolina Bonilla, Rick A Kittles, David G Clayton, Paul M McKeigue (2003), "Control of confounding of genetic associations in stratified populations", American Journal of Human Genetics, 72(6):1492-1504.
    [abstract] [PDF]

55. Josephine Hoh, Fumihiko Matsuda, Xu Peng, Daniela Markovic, Mark Lathrop, Jurg Ott (2003), "SNP haplotype tagging from DNA pools of two individuals", BMC Bioinformatics, 4:14

56. Josephine Hoh, Jurg Ott (2003), "Mathematical multi-locus approaches to localizing complex human trait genes", Nature Reviews Genetics, 4:701-709.
    [abstract]

57. TJ Hudson (2003), "Wanted: regulatory SNPs" (commentary), Nature Genetics, 33(4):439-440.

58. FC Hsu, KY Liang, TH Beaty, CSGA (2003), "A multipoint linkage disequilibrium mapping approach: incorporating evidence of linkage and linkage disequilibrium from unlinked region", Genetic Epidemiology, 25(1):1-13.
    [ abstract]

59. L Hsu (2003), "Genetic association tests with age at onset", Genetic Epidemiology, 24(2): 118-127.

60. Hideki Innan, Magnus Nordborg (2003), "The extent of linkage disequilibrium and haplotype sharing around a polymorphic site", Genetics, 165(1):437-444. (2003),

61. Hideki Innan, Badri Padhukasahasram, and Magnus Nordborg (2003), "The pattern of polymorphism on human chromosome 21", Genome Research, 13(6a):1158-1168.
    [ abstract]

62. The International HapMap Consortium (2003), "The international HapMap project", Nature, 426:789-796.
    [PDF]

63. John P A Ioannidis, Thomas A Trikalinos, Evangelia E Ntzani, Despina G Contopoulos-Ioannidis (2003), "Genetic associations in large versus small studies: an empirical assessment", Lancet, 361:567-571.
    [PDF]

64. T Ito, S Chiku, E Inoue, M Tomita, T Morisaki, H Morisaki, N Kamatani (2003), "Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data", American Journal of Human Genetics, 72(2):384-398.

65. AS Jannot, L Essioux, MG Reese, F Clerget-Darpoux (2003), "Improved use of SNP information to detect the role of genes", Genetic Epidemiology, 25:158-167.
    [abstract]

66. Manfred Kayser, Silke Brauer, Hiltrud Schädlich, Mechthild Prinz, Mark A. Batzer, Peter A. Zimmerman, BA Boatin, Mark Stoneking (2003), "Y chromosome STR haplotypes and the genetic structure of U.S. populations of african, european, and hispanic ancestry", Genome Research, 13(4):624-634.
    [ abstract]

67. X Ke, LR Cardon (2003), "Efficient selective screening of haplotype tag SNPs", Bioinformatics, 19(2):287-288.
    [ abstract]

68. quantitative-trait

    Riika Kilpikari, Mikko J. Sillanpää (2003), "Bayesian analysis of multilocus association in quantitative and qualitative traits", Genetic Epidemiology, 25:122-125.
    [ abstract]

69. Gad Kimmel, Roded Sharan, Ron Shamir (2003), "Identifying blocks and sub-populations in noisy SNP data", In G Benson, R Page, ed., Algorithms and Bioinformatics: 3rd International Workshop (WABI), Lecture Notes in Bioinformatics, volume 2812. pp. 303-319 (Springer).

70. Rick A. Kittles, Kenneth M. Weiss (2003), "Race, ancestry, and genes: implications for defining disease risk", Annual Review of Genomics and Human Genetics, 4:33-67.
    [ abstract]

71. TDT

    M Knapp, T Becker (2003), "Family-based association analysis with tightly linked markers", Human Heredity, 56(1-3):2-9.
    [ abstract]

72. AS Kondrashov (2003), "Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases", Human Mutation, 21:12-27.

73. SL Lake, H Lyon, K Tantisira, EK Silverman, ST Weiss, NM Laird, DJ Schaid (2003), "Estimation and tests of haplotype-environment interaction when linkage phase is ambiguous", Human Heredity, 55:56-65.

74. TDT

    Christoph Lange, Dawn DeMeo, Edwin K Silverman, Scott T Weiss, Nan M. Laird (2003), "Using the noninformative families in family-based association tests: a powerful new testing strategy", American Journal of Human Genetics, 73(4):801-811.
    [abstract]

75. TDT

    C Lange, H Lyon, D DeMeo, B Raby, EK Silverman, ST West (2003), "A new powerful non-parametric two-stage approach for testing multiple phenotypes in family-based association studies", Human Heredity, 56:10-17.

76. WC Lee (2003), "Testing for Hardy-Weinberg disequilibrium based on cases only: a general approach for sample size calculation", Journal of Genet Mole Biol, 14:159-163.

77. WC Lee (2003), "Searching for disease-susceptibility loci by testing for Hardy-Weinberg disequilibrium in a gene bank of affected individuals", American Journal of Epidemiology, 158:397-400.

78. WC Lee (2003), "Lee Responds to "Testing for Hardy-Weinberg Disequilibrium" American Journal of Epidemiology, 158:404-405.

79. WC Lee (2003), "Using affected sibling pairs to distinguish the direct effect of a susceptibility gene and the indirect effect of linkage disequilibrium", Annals of Human Genetics, 67(2):185-188.
    [ abstract]

80. WC Lee (2003), "Genetic association studies of adult-onset diseases using the case-spouse and case-offspring designs", American Journal of Epidemiology, 158:1023-1032.

81. WC Lee (2003), "Lee responds to 'making the most of genotype asymmetries'" (reply to invited commentary), American Journal of Epidemiology, 158:1036-1038.

82. WC Lee (2003), "Detecting population stratification using a panel of SNPs" (letter), International Journal of Epidemiology, 32:1120.

83. WC Lee, YY Ho (2003), "Potential for gene-gene confounding bias in case-parental control studies", Ann Epidemiology, 13:261-266.

84. TDT

    WC Lee, YC Yen (2003), "Admixture mapping using interval transmission/disequilibrium tests", Annals of Human Genetics, 67:580-588.

85. J Li, T Jiang (2003), "Effecient inference of haplotypes from genotypes on a pedigree", Journal of Bioinformatics and Computational Biology, 1(1):41-69.
    [ abstract]

86. J Li, T Jiang (2003), "Effecient rule-based haplotyping algorithms for pedigree data", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.197-206.

87. L Li, H Kim (2003), "Haplotype reconstruction from SNP alignment", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.207-216.

88. N Li, M Stephens (2003), "Modelling Linkage Disequilibrium, and identifying recombination hotspots using SNP data", Genetics, 165(4):2213-2233.
    [abstract] [PDF]

89. Shuying Sue Li, Najma Khalid, Christopher Carlson, Lue Ping Zhao (2003), "Estimating haplotype frequencies and standard errors for multiple single nucleotide polymorphisms", Biostatistics, 4:513-522.
    [abstract]

90. S Lin, Z Skrivanek, M Irwin (2003), "Haplotying using SIMPLE - caution on ignoring interference", Genetic Epidemiology, 25:384-387.

91. Julian Little, Muin J Khoury (2003), "Mendelian randomisation: a new spin or real progress?", Lancet, 362(9388):930-931.
    [ abstract]

92. Wei-Min Liu, Xiaojun Di, Geoffrey Yang, Hajime Matsuzaki, Jing Huang, Rui Mei, Thomas B Ryder, Teresa A Webster, Shoulian Dong, Guoying Liu, Keith W Jones, Giulia C Kennedy, and David Kulp (2003), "Algorithms for large-scale genotyping microarray", Bioinformatics, 19:2397-2403.
    [ abstract]

93. TDT

    Xin Liu, Derek Gordon (2003), "A general class of association tests for family-based data using weight functions", Genetic Epidemiology, 24(3):208-219.

94. TDT

    Shaw-Hwa Lo, Xin Liu, Yongzhao Shao (2003), "A marginal likelihood model for family-based data", Annals of Human Genetics, 67(4): 357-366.
    [ abstract]

95. KE Lohmueller, CL Pearce, M Pike, ES Lander, JN Hirschhorn (2003), "Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease", Nature Genetics, 33:177-182.

96. population-structure

    C Lonjou, W Zhang, A Collins, WJ Tapper, E Elahi, N Maniatis, NE Morton (2003), "Linkage disequilibrium in human populations", Proceedings of National Academy of Sciences, 100(10):6069-6074.
    [PDF]

97. quantitative-trait

    XY Lou, G Casella, RC Littell, MCK Yang, JA Johnson, R Wu (2003), "A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis", Genetics, 163:1533-1548.

98. Xin Lu, Tianhua Niu, Jun S Liu (2003), "Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms", Genome Research, 13:2112-2117.
    [PDF]

99. H Mannila, M Koivisto, M Perola, T Varilo, W Hennah, J Ekelund, M Lukk, L Peltonen, E Ukkonen (2003), "Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries", American Journal of Human Genetics, 73:86-94.
    [PDF] (retracted because of an identical paper appeared elsewhere)

100. H Mannila, M Koivisto, M Perola, T Varilo, W Hennah, J Ekelund, M Lukk, L Peltonen, E Ukkonen (2003), "Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries," Pacific Symposium on Biocomputing, 73:86-94.

101. G Marnellos (2003), "High-throughput SNP analysis for genetic association studies", Current Opinion in Drug Discovery & Development, 6:317-321.

102. TDT

     ER Martin, MP Bass, JR Gilbert, MA Pericak-Vance, ER Hauser (2003), "Genotype-based association test for general pedigrees: The genotype-PDT", Genetic Epidemiology, 24(4):284-290.
     [abstract]

103. TDT

     Eden R Martin, Meredyth P Bass, Elizabeth R Hauser, Norman L Kaplan (2003), "Accounting for linkage in family-based tests of association with missing parental genotypes", American Journal of Human Genetics, 73(5):1016-1026.
     [abstract]

104. Tara C Matise, Ravi Sachidanandam, Andrew G Clark, Leonid Kruglyak, Ellen Wijsman, Jerzy Kakol, Steven Buyske, Buena Chui, Patrick Cohen, Claudia de Toma, Margaret Ehm, Stephen Glanowski, Chunsheng He, Jeremy Heil, Kyriacos Markianos, Ivy McMullen, Margaret A Pericak-Vance, Arkadiy Silbergleit, Lincoln Stein, Michael Wagner, Alexander F Wilson, Jeffrey D Winick, Emily S Winn-Deen, Carl T Yamashiro, Howard M Cann, Eric Lai, Arthur L. Holden (2003), "A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set", American Journal of Human Genetics, 73:271-284.
     [abstract]

105. Zhaoling Meng, Dmitri V Zaykin, Chun-Fang Xu, Michael Wagner, Margaret G Ehm (2003), "Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes" American Journal of Human Genetics, 73:115-130.
     [abstract]

106. KR Merikangas, N Risch (2003), "Will the genomics revolution revolutionize psychiatry?" American Journal of Psychiatry, 160:625-635.

107. John Molitor, Paul Marjoram, Duncan Thomas (2003), "Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping", Genetic Epidemiology, 25:95-105.
     [abstract]

108. Sean D Mooney, Russ B Altman (2003), "MutDB: annotating human variation with functionally relevant data", Bioinformatics, 19:1858-1860.
     [ abstract]

109. Andrew Morris, Alan Pedder, Karen Ayres (2003), "Linkage disequilibrium assessment via log-linear modeling of SNP haplotype frequencies", Genetic Epidemiology, 25:106-114.
     [abstract]

110. Andrew P Morris, John C Whittaker, Chun-Fang Xu, Louise K Hosking, David J Balding (2003), "Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity", Proceedings of National Academy of Sciences, 100(23):13442-13446.
     [PDF]

111. NE Morton (2003), "Blocks of limited haplotype diversity", in Nature Encyclopedia of the Human Genome, ed. D Cooper (Nature Publishing Group), pp.331-332.

112. DL Newman, S Hoffjan, C Bourgain, M Abney, RI Nicolae, ET Profits, MA Grow, K Walker, L Steiner, R Parry, R Reynolds, MS McPeek, S Cheng, C Ober (2004), "Are common disease susceptibility alleles the same in outbred and founder populations?", European Journal of Human Genetics, 12(7):584-590.

113. Rasmus Nielsen, James Signorovitch (2003), "Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium", Theoretical Population Biology, 63(3):245-255.

114. M Nordborg, H Innan (2003), "The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population", Genetics, 163(3):1201-1213.

115. J Ohashi, K Tokunaga (2003), "The power of genome-wide linkage disequilibrium (LD) testing using microsatellite markers", Journal of Human Genetics, 48:487-491.
     [PDF]

116. Yeong-Gwon Park, Robert Clifford, Kenneth H. Buetow, and Kent W. Hunter (2003), "Multiple cross and inbred strain haplotype mapping of complex-trait candidate genes", Genome Research, 13(1):118-121.
     [ abstract]

117. I Pe'er, JS Backmann (2003), "Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.237-246.

118. TDT

     Ruth M Pfeiffer, Mitchell H Gail (2003), "Sample size calculations for population- and family-based case-control association studies on marker genotypes", Genetic Epidemiology, 25:136-148.
     [abstract] [PDF]

119. haplotype-block

     M S Phillips, R Lawrence, R Sachidanandam, A P Morris, D J Balding, M A Donaldson, J F Studebaker, W M Ankener, S V Alfisi, F -S Kuo, A L Camisa, V Pazorov, K E Scott, B J Carey, J Faith, G Katari, H A Bhatti, J M Cyr, V Derohannessian, C Elosua, A M Forman, N M Grecco, C R Hock, J M Kuebler, J A Lathrop, M A Mockler, E P Nachtman, S L Restine, S A Varde, M J Hozza, C A Gelfand, J Broxholme, G R Abecasis, M T Boyce-Jacino, L R Cardon (2003), "Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots", Nature Genetics, 33:382-387.
     [PDF]

120. Joanna Polanska (2003), "The EM algorithm and its implementation for the estimation of frequencies of SNP-haplotypes", International Journal of Applied Mathematics and Computer Science, 13(3):419-429.
     [PDF]

121. S Purcell, SS Cherny, PC Sham (2003), "Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits", Bioinformatics, 19(1):149-150.

122. Daniel Rabinowitz (2003), "Adjusting for population heterogeneity: a framework for characterizing statistical information and developing efficient test statistics", Genetic Epidemiology, 24(4):284-290.

123. population-structure

     P Rahman, A Jones, J Curtis, S Bartlett, L Peddle, BA Fernandez, NB Freimer (2003), "The Newfoundland population: a unique resource for genetic investigation of complex diseases", Human Molecular Genetics, 12(Suppl 2):R167-R172.
     [abstract]

124. S Ramaswamy, KN Ross, ES Lander, TR Golub (2003), "A molecular signature of metastasis in primary solid tumors", Nature Genetics, 33:49-54.

125. D E Reich, S B Gabriel, D Altshuler (2003), "Quality and completeness of SNP databases", Nature Genetics, 33(4):457-458.

126. KM Rice, P Holmans (2003), "Allowing for genotyping error in analysis of unmatched case-control studies", Annals of Human Genetics, 67(2):165-174.
     [ abstract]

127. K Rohde, R Furst (2003), "Association of genetic traits to estimated haplotypes from SNP genotypes using EM algorithm and Markov chain Monte Carlo techniques", Human Heredity, 56:41-47.
     [ abstract]

128. NA Rosenberg, L Lei, R Ward, JK Pritchard (2003), "Informativeness of genetic markers for inference of ancestry", American Journal of Human Genetics, 73:1402-1422.

129. Noah A. Rosenberg, Jonathan K. Pritchard , James L. Weber, Howard M. Cann, Kenneth K. Kidd, Lev A. Zhivotovsky, Marcus W. Feldman (2003), "Response to 'Comment on Genetic Structure of Human Populations' ", Science, 300:1877.
     [ abstract]

130. Julio Rozas, Juan C. Sanchez-DelBarrio, Xavier Messeguer, and Ricardo Rozas (2003), "DnaSP, DNA polymorphism analyses by the coalescent and other methods", Bioinformatics, 19(18):2496-2497.
     [ abstract]

131. C Sabatti, S Service, N Freimer (2003), "False discovery rates in linkage and association linkage genome screens for complex disorders", Genetics, 164:829-833.

132. Jaya M Satagopan, Robert C Elston (2003), "Optimal two-stage genotyping in population-based association studies", Genetic Epidemiology, 25:149-157.
     [abstract]

133. A Scherag, HH Muller, A Dempfle, J Hebebrand, H Schafer (2003), "Data adaptive interim modification of sample sizes for candidate-gene association studies", Human Heredity, 56:56-62.

134. Russell Schwartz, Bjarni V Halldorsson, Vineet Bafna, Andrew G Clark, Sorin Istrail (2003), "Robustness of inference of haplotype block structure", Journal of Computational Biology, 10(1):13-19.
     [ abstract]

135. Howard Seltman, Kathryn Roeder, B Devlin (2003), "Evolutionary-based association analysis using haplotype data", Genetic Epidemiology, 25(1):48-58.
     [abstract]

136. SK Service, LA Sandkuijl, NB Freimer (2003), "Cost-effective designs for linkage disequilibrium mapping of complex traits", American Journal of Human Genetics, 72(5):1213-1220.

137. S Shete (2003), "A note on the optimal measure of allelic association", Annals of Human Genetics, 67(2):189-191.
     [ abstract]

138. S Shifman, J Kuypers, M Kokoris, B Yakir, A Darvasi (2003), "Linkage disequilibrium patterns of the human genome across populations", Human Molecular Genetics, 12(7):771-776.

139. applications

     MD Shriver, EJ Parra, S Dios, C Bonilla, H Norton, C Jovel, C Pfaff, C Jones, A Massac, N Cameron, A Baron, T Jackson, G Argyropoulos, L Jin, CJ Hoggart, PM McKeigue, RA Kittles (2003), "Skin pigmentation, biogeographical ancestry and admixture mapping", Human Genetics, 112:387-399.

140. TDT

     SL Slager, DJ Schaid, L Wang, SN Thibodeau (2003), "Candidate-gene association studies with pedigree data: controlling for environmental covariates", Genetic Epidemiology, 24(4):273-283

141. George Davey Smith, Shah Ebrahim (2003), "'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease?", International Journal of Epidemiology, 32(1):1-22.

142. MA Spence, DA Greenberg, SE Hodge, VJ Vieland (2003), "The emperor's new methods", American Journal of Human Genetics, 72(5):1084-1087.
     [PDF]

143. John DH Stead, Matthew E Hurles, Alec J Jeffreys (2003), "Global haplotype diversity in the human insulin gene region", Genome Research, 13:2101-2111.
     [abstract]

144. Peter D Stenson, Edward V Ball, Matthew Mort, Andrew D Phillips, Jacqueline A Shiel, Nick ST Thomas, Shaun Abeysinghe, Michael Krawczak, David N Cooper (2003). "Human Gene Mutation Database (HGMD): 2003 update", Human Mutation, 21(6):577-581.

145. M Stephens, P Donnelly (2003), "A comparison of Bayesian methods for haplotype reconstruction from population genotype data", American Journal of Human Genetics, 73(5):1162-1169.
     [abstract]

146. Andrew L Strahs, Mary Sara McPeek (2003), "Multipoint fine-scale linkage disequilibrium mapping: importance of modeling background LD", in Science and Statistics: A Festschrift for Terry Speed (IMS Lecture Notes, Monograph Series Vol 40), ed. D Goldstein, pp.343-366 (IMS).

147. DO Stram, CA Haiman, JN Hirschhorn, D Altshuler, LN Kolonel, BE Henderson, MC Pike (2003), "Choosing haplotype-tagging SNSs based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the multuethnic cohort study", Human Heredity, 55:27-36.

148. DO Stram, C Leigh Pearce, P Bretsky, M Freedman, JN Hirschhorn, D Altshuler, LN Kolonel, BE Henderson, DC Thomas (2003), "Moldelling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals", Human Heredity, 55:179-190.
     [PDF]

149. Michael PH Stumpf, Gilean AT McVean (2003), "Estimating recombination rates from population-genetic data", Nature Reviews Genetics, 4(12):959-968.
     [PDF]

150. Nadia Tahri-Daizadeh, David-Alexandre Tregouet, Viviane Nicaud, Nicolas Manuel, Francois Cambien, Laurence Tiret (2003), "Automated detection of informative combined effects in genetic association studies of complex traits", Genome Research, 13:1952-1960.
     [ abstract]

151. Masazumi Takahashi, Fumihiko Matsuda, Nino Margetic and Mark Lathrop (2003), "Automated identification of single nucleotide polymorphisms from sequencing data", Journal of Bioinformatics and Computational Biology, 1(2):253-265.
     [ abstract]

152. Fuqiang Tang, Elizabeth M Flood, Alexander Pertsemlidis, Harold R Garner (2003), "SNPCEQer II: the integrated detection and analysis of SNPs in DNA sequences", Applied Bioinformatics, 2(3):151-154
     [abstract]

153. WJ Tapper, N Maniatis, NE Morton, A Collins (2003), "A metric linkage disequilibrium map of a human chromosome", Annals of Human Genetics, 67(6):487-494.

154. Alun Thomas (2003), "GCHap: fast MLEs for haplotype frequencies by gene counting", Bioinformatics, 19:2002-2003.
     [ abstract]

155. DC Thomas, DO Stram, D Conti, J Molitor, P Marjoram (2003), "Bayesian spatial modeling of haplotype associations", Human Heredity, 56:32-40.
     [ abstract]

156. G Thomas, H Cann (2003), "Irruption of genomics in the search for disease related genes", Gut, 52:ii1-ii5.
     [abstract]

157. D Thompson, DO Stram, D Goldgar, JS Witte (2004), "Haplotype-tagging single nucleotide polymorphisms and association studies", Human Heredity, 56:48-55.

158. Sarah A Tishkoff, Brian C Verrelli (2003), "Patterns of human genetic diversity: implications for human evolutionary history and disease", Annual Review of Genomics and Human Genetics, 4(1):293-340.
     [ abstract]

159. R Turakulov, S Easteal (2003), "Number of SNPs loci needed to detect population structure", Human Heredity, 55:37-45.

160. haplotype-block

     RC Twells, CA Mein, MS Phillips, JF Hess, R Veijola, M Gilbey, M Bright, M Metzker, BA Lie, A Kingsnorth, E Gregory, Y Nakagawa, H Snook, WY Wang, J Masters, G Johnson, I Eaves, JM Howson, D Clayton, HJ Cordell, S Nutland, H Rance, P Carr, JA Todd (2003), "Haplotype structure, LD blocks, and uneven recombination within the LRP5 gene", Genome Research, 13(5):845-855.
     [ abstract]

161. EJ van den Oord, Y Jiang, BP Riley, KS Kendler, X Chen (2003), "FP-TDI SNP scoring by manual and statistical procedures: a study of error rates and types", Biotechniques, 34(3):610-616, 618-620, 622 passim.

162. population-structure

     T Varilo, T Paunio, A Parker, M Perola, J Meyer, JD Terwilliger, L Peltonen (2003), "The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories", Human Molecular Genetics, 12(1):51-59.
     [abstract] [PDF]

163. Peter M Visscher, Stephanie Le Hellard (2003), "Simple method to analyze SNP-based association studies using DNA pools", Genetic Epidemiology, 24(4):291-296.

164. Jeffrey D Wall, Jonathan K Pritchard (2003), "Assessing the performance of the haplotype block model of linkage disequilibrium", American Journal of Human Genetics, 73(3):502-515.
     [abstract]

165. Jeffrey D Wall, Jonathan K Pritchard (2003), "Haplotype blocks and linkage disequilibrium in the human genome", Nature Reviews Genetics, 4(8):587-597.
     [abstract]

166. Emily C Walsh, Kristie A Mather, Stephen F Schaffner, Lisa Farwell, Mark J Daly, Nick Patterson, Michael Cullen, Mary Carrington, Teodorica L Bugawan, Henry Erlich, Jay Campbell, Jeffrey Barrett, Katie Miller, Glenys Thomson, Eric S Lander, John D. Rioux (2003), "An integrated haplotype map of the human major histocompatibility complex", American Journal of Human Genetics, 73(3):580-590.
     [abstract] [PDF]

167. Lusheng Wang, Ying Xu (2003), "Haplotype inference by maximum parsimony", Bioinformatics, 19:1773-1780.
     [ abstract]

168. Shuang Wang, Kenneth K Kidd, Hongyu Zhao (2003), "On the use of DNA pooling to estimate haplotype frequencies", Genetic Epidemiology, 24(1):74-82.
     [PDF]

169. William YS Wang, Heather J Cordell, John A Todd (2003), "Association mapping of complex diseases in linked regions: estimation of genetic effects and feasibility of testing rare variants", Genetic Epidemiology, 24(1):6-43.

170. Xing Wang (2003), "HIT: a haplotype inference testbed", technical report, Computer Architecture and Parallele Systems Lab, Department of Electrical and Computer Engineering, University of Delaware.
     [PDF]

171. Clarice R Weinberg, Richard W Morris (2003), "Invited commentary: testing for Hardy-Weinberg disequilibrium using a genome single-nucleotide polymorphism scan based on cases only", American Journal of Epidemiology, 158:401-403.

172. Alice S Whittemore, Jerry Halpern (2003), "Genetic association tests for family data with missing parental genotypes: A comparison", Genetic Epidemiology, 25(1):80-91.
     [abstract]

173. C Wiuf, D Posada (2003), "A coalescent model of recombination hotspots", Genetics>, 164(1):407-417.

174. Gane Ka-Shu Wong, Zhiyong Yang, Douglas A. Passey, Miho Kibukawa, Marcia Paddock, Chun-Rong Liu, Lars Bolund, Jun Yu (2003), "A population threshold for functional polymorphisms", Genome Research, 13:1873-1879.

175. haplotype-block

     M Xiong, J Zhao, E Boerwinkle (2003), "Haplotype block linkage disequilibrium mapping", Frontiers in Bioscience, 8:A85-A93.
     [ abstract]

176. Xin Xu, Lu Tian, LJ Wei (2003), "Combining dependent tests for linkage or association across multiple phenotypic traits", Biostatistics, 4:223-229.
     [abstract]

177. Yaning Yang, Jingshan Zhang, Josephine Hoh, Fumihiko Matsuda, Peng Xu, Mark Lathrop, Jurg Ott (2003), "Effeciency of single-nucleotide polymorphism haplotype estimation from pooled DNA", Proceedings of National Academy of Sciences, 100(12):7225-7230.
     [PDF]

178. Jinghui Zhang, William L Rowe, Andrew G Clark, Kenneth H Buetow (2003), "Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations", American Journal of Human Genetics, 73(5):1073-1081.
     [abstract]

179. haplotype-block

     K Zhang, JM Akey, N Wang, M Xiong, R Chakraborty, L Jin (2003), "Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift", Human Genetics, 113(1):51-59.

180. Kun Zhang, Li Jin (2003), "HaploBlockFinder: haplotype block analyses", Bioinformatics, 19:1300-1301.
     [ abstract]

181. K Zhang, F Sun, MS Waterman, T Chen (2003), "Dynamic programming algorithms for haplotype block partitioning: applications to human chromsome 21 haplotype data", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.332-340.

182. K Zhang, F Sun, MS Waterman, T Chen (2003), "Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data", American Journal of Human Genetics, 73:63-73.
     [abstract]

183. Peisen Zhang, Huitao Sheng, Alfredo Morabia, T Conrad Gilliam (2003), "Optimal Step Length EM Algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping", BMC Bioinformatics, 4:3.

184. Shuanglin Zhang, Qiuying Sha, Huann-Sheng Chen, Jianping Dong, Renfang Jiang (2003), "Transmission/disequilibrium test based on haplotype sharing for tightly linked markers", American Journal of Human Genetics, 73(3):566-579.
     [abstract]

185. quantitative-trait

     Shuanglin Zhang, Xiaofeng Zhu, Hongyu Zhao (2003), "On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals", Genetic Epidemiology, 24(1):44-56.

186. Xiaohua Zhang, Kathryn Roeder, Garrick Wallstrom, Bernie Devlin (2003), "Integration of association statistics over genomic regions using Bayesian adaptive regression splines", Human Genomics, 1(1):20-29.

187. H Zhao, R Pfiffer, MH Gail (2003), "Haplotype analysis in population genetics and association studies", Phamacogenomics, 4:171-178.

188. JH Zhao, PC Sham (2003), "Generic number systems and haplotype analysis", Comp. Meth. Prog. Biomed. 70:1-9.

189. LP Zhao, SS Li, N Khalid (2003), "A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies", American Journal of Human Genetics, 72:1231-1250.

190. Zhongming Zhao, Yun-Xin Fu, David Hewett-Emmett, Eric Boerwinkle (2003), "Investigating single nucleotide polymorphism (SNP) density in the genome and its implications for molecular evolution", Gene, 312:207-213.

191. Gang Zheng (2003), "Use of max and min scores for trend tests for association when the genetic model is unknown", Statistics in Medicine, 22(16):2657-2666.
     [ abstract]

192. Xiaofeng Zhu, Denise Yan, Richard S. Cooper, Amy Luke, Morna A. Ikeda, Yen-Pei C. Chang, Alan Weder, Aravinda Chakravarti (2003), "Linkage disequilibrium and haplotype diversity in the genes of the renin-angiotensin system: findings from the family blood pressure program", Genome Research, 13(2):173-181. [ abstract]

193. population-structure

     Ewa Zietkiewicz, Vania Yotova, Dominik Gehl, Tina Wambach, Isabel Arrieta, Mark Batzer, David EC Cole, Peter Hechtman, Feige Kaplan, David Modiano, Jean-Paul Moisan, Roman Michalski, Damian Labuda (2003), "Haplotypes in the Dystrophin DNA segment point to a mosaic origin of modern human diversity", American Journal of Human Genetics, 73(5):994-1015.
     [abstract]

194. E Ziv, EG Burchard (2003), "Human population structure and genetic association studies", Pharmacogenomics, 4(4):431-441.