-
1
-
-
0034892915
-
Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion
-
Ardlie, K., S. Liu-Cordero, M. Eberle, M. Daly, J. Barrett et al., 2001 Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion. Am. J. Hum. Genet. 69: 582-589.
-
(2001)
Am. J. Hum. Genet.
, vol.69
, pp. 582-589
-
-
Ardlie, K.1
Liu-Cordero, S.2
Eberle, M.3
Daly, M.4
Barrett, J.5
-
2
-
-
61449135985
-
Fast and flexible simulation of DNA sequence data
-
Chen, G. K., P. Marjoram, and J. D. Wall, 2009 Fast and flexible simulation of DNA sequence data. Genome Res. 19: 136-142.
-
(2009)
Genome Res.
, vol.19
, pp. 136-142
-
-
Chen, G.K.1
Marjoram, P.2
Wall, J.D.3
-
3
-
-
34548743476
-
Gene conversion: Mechanisms, evolution and human disease
-
Chen, J.-M., D. N. Cooper, N. Chuzhanova, C. Férec, and G. P. Patrinos, 2007 Gene conversion: mechanisms, evolution and human disease. Nat. Rev. Genet. 8: 762-775.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 762-775
-
-
Chen, J.-M.1
Cooper, D.N.2
Chuzhanova, N.3
Férec, C.4
Patrinos, G.P.5
-
4
-
-
27544474337
-
Ascertainment bias in studies of human genomewide polymorphism
-
Clark, A. G., M. J. Hubisz, C. D. Bustamante, S. H. Williamson, and R. Nielsen, 2005 Ascertainment bias in studies of human genomewide polymorphism. Genome Res. 15: 1496-1502.
-
(2005)
Genome Res.
, vol.15
, pp. 1496-1502
-
-
Clark, A.G.1
Hubisz, M.J.2
Bustamante, C.D.3
Williamson, S.H.4
Nielsen, R.5
-
5
-
-
0002629270
-
Maximum likelihood from incomplete data via the EM algorithm
-
Dempster, A. P., N. M. Laird, and D. B. Rubin, 1977 Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. B 39: 1-38.
-
(1977)
J. R. Stat. Soc. B
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
7
-
-
0034835229
-
Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels
-
Frisse, L., R. Hudson, A. Bartoszewicz, J. Wall, J. Donfack et al., 2001 Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69: 831-843.
-
(2001)
Am. J. Hum. Genet.
, vol.69
, pp. 831-843
-
-
Frisse, L.1
Hudson, R.2
Bartoszewicz, A.3
Wall, J.4
Donfack, J.5
-
8
-
-
0029391126
-
Statistical properties of segregating sites
-
Fu, Y., 1995 Statistical properties of segregating sites. Theor. Popul. Biol. 48: 172-197.
-
(1995)
Theor. Popul. Biol.
, vol.48
, pp. 172-197
-
-
Fu, Y.1
-
9
-
-
84857190907
-
Implementing the Nelder-Mead simplex algorithm with adaptive parameters
-
Gao, F., and L. Han, 2012 Implementing the Nelder-Mead simplex algorithm with adaptive parameters. Comput. Optim. Appl. 51: 259-277.
-
(2012)
Comput. Optim. Appl.
, vol.51
, pp. 259-277
-
-
Gao, F.1
Han, L.2
-
10
-
-
0001301442
-
The age of a mutation in a general coalescent tree
-
Griffiths, R., and S. Tavaré, 1998 The age of a mutation in a general coalescent tree. Stoch. Models 14: 273-295.
-
(1998)
Stoch. Models
, vol.14
, pp. 273-295
-
-
Griffiths, R.1
Tavaré, S.2
-
12
-
-
35348983887
-
A second generation human haplotype map of over 3.1 million SNPs
-
HapMap
-
HapMap, 2007 A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-862.
-
(2007)
Nature
, vol.449
, pp. 851-862
-
-
-
13
-
-
0242500969
-
Novel multilocus measure of linkage disequilibrium to estimate past effective population size
-
Hayes, B., P. Visscher, H. McPartlan, and M. Goddard, 2003 Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res. 13: 635-643.
-
(2003)
Genome Res.
, vol.13
, pp. 635-643
-
-
Hayes, B.1
Visscher, P.2
McPartlan, H.3
Goddard, M.4
-
14
-
-
0016565853
-
Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population
-
Hill, W. G., 1975 Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population. Theor. Popul. Biol. 8: 117-126.
-
(1975)
Theor. Popul. Biol.
, vol.8
, pp. 117-126
-
-
Hill, W.G.1
-
15
-
-
0019771734
-
Estimation of effective population size from data on linkage disequilibrium
-
Hill, W. G., 1981 Estimation of effective population size from data on linkage disequilibrium. Genet. Res. 38: 209-216.
-
(1981)
Genet. Res.
, vol.38
, pp. 209-216
-
-
Hill, W.G.1
-
16
-
-
33646226097
-
Linkage disequilibrium in finite populations
-
Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 226-231.
-
(1968)
Theor. Appl. Genet.
, vol.38
, pp. 226-231
-
-
Hill, W.G.1
Robertson, A.2
-
17
-
-
0021909851
-
The sampling distribution of linkage disequilibrium under an infinite allele model without selection
-
Hudson, R. R., 1985 The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109: 611-631.
-
(1985)
Genetics
, vol.109
, pp. 611-631
-
-
Hudson, R.R.1
-
18
-
-
0036180886
-
Extensive linkage disequilibrium in small human populations in Eurasia
-
Kaessmann, H., S. Zöllner, A. C. Gustafsson, V. Wiebe, M. Laan et al., 2002 Extensive linkage disequilibrium in small human populations in Eurasia. Am. J. Hum. Genet. 70: 673-685.
-
(2002)
Am. J. Hum. Genet.
, vol.70
, pp. 673-685
-
-
Kaessmann, H.1
Zöllner, S.2
Gustafsson, A.C.3
Wiebe, V.4
Laan, M.5
-
19
-
-
0026639787
-
Expected behavior of conditional linkage disequilibrium
-
Kaplan, N., and B. Weir, 1992 Expected behavior of conditional linkage disequilibrium. Am. J. Hum. Genet. 51: 333.
-
(1992)
Am. J. Hum. Genet.
, vol.51
, pp. 333
-
-
Kaplan, N.1
Weir, B.2
-
20
-
-
0014494672
-
The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutation
-
Kimura, M., 1969 The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutation. Genetics 61: 893-903.
-
(1969)
Genetics
, vol.61
, pp. 893-903
-
-
Kimura, M.1
-
21
-
-
0033039497
-
Prospects for whole-genome linkage disequilibrium mapping of common disease genes
-
Kruglyak, L., 1999 Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22: 139-144.
-
(1999)
Nat. Genet.
, vol.22
, pp. 139-144
-
-
Kruglyak, L.1
-
22
-
-
0002907949
-
The interaction of selection and linkage. I. General considerations; heterotic models
-
Lewontin, R. C., 1964 The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49: 49-67.
-
(1964)
Genetics
, vol.49
, pp. 49-67
-
-
Lewontin, R.C.1
-
23
-
-
0014127475
-
An estimate of average heterozygosity in man
-
Lewontin, R. C., 1967 An estimate of average heterozygosity in man. Am. J. Hum. Genet. 19: 681-685.
-
(1967)
Am. J. Hum. Genet.
, vol.19
, pp. 681-685
-
-
Lewontin, R.C.1
-
24
-
-
0001180494
-
Moving blocks jacknife and bootstrap capture weak dependence
-
in, edited by R. LePage, and L. Billard. John Wiley & Sons, New York
-
Lieu, R. Y., and K. Singh, 1992 Moving blocks jacknife and bootstrap capture weak dependence, pp. 225-248 in Exploring the "Limits" of the Bootstrap, edited by R. LePage, and L. Billard. John Wiley & Sons, New York.
-
(1992)
Exploring the "Limits" of the Bootstrap
, pp. 225-248
-
-
Lieu, R.Y.1
Singh, K.2
-
25
-
-
0015669794
-
Linkage disequilibrium in two-locus, finite, random mating models without selection or mutation
-
Littler, R., 1973 Linkage disequilibrium in two-locus, finite, random mating models without selection or mutation. Theor. Popul. Biol. 4: 259-275.
-
(1973)
Theor. Popul. Biol.
, vol.4
, pp. 259-275
-
-
Littler, R.1
-
26
-
-
26444452499
-
Stochastic integrals and their application to population genetics
-
in, Protein Polymorphism, and the Neutral Theory, edited by M. Kimura. Springer-Verlag, Berlin
-
Maruyama, T., 1982 Stochastic integrals and their application to population genetics, pp. 151-166 in Molecular Evolution, Protein Polymorphism, and the Neutral Theory, edited by M. Kimura. Springer-Verlag, Berlin.
-
(1982)
Molecular Evolution
, pp. 151-166
-
-
Maruyama, T.1
-
27
-
-
79957956814
-
Human population dispersal "out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs
-
McEvoy, B., J. Powell, M. Goddard, and P. Visscher, 2011 Human population dispersal "out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Res. 21: 821-829.
-
(2011)
Genome Res.
, vol.21
, pp. 821-829
-
-
McEvoy, B.1
Powell, J.2
Goddard, M.3
Visscher, P.4
-
28
-
-
0036811711
-
A genealogical interpretation of linkage disequilibrium
-
McVean, G., 2002 A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991.
-
(2002)
Genetics
, vol.162
, pp. 987-991
-
-
McVean, G.1
-
29
-
-
84889320525
-
Linkage disequilibrium, recombination and selection
-
in, Ed. 3, edited by D. Balding, M. Bishop, and C. Cannings. John Wiley and Sons, Chichester, UK
-
McVean, G., 2007 Linkage disequilibrium, recombination and selection, pp. 909-944 in Handbook of Statistical Genetics, Ed. 3, edited by D. Balding, M. Bishop, and C. Cannings. John Wiley and Sons, Chichester, UK.
-
(2007)
Handbook of Statistical Genetics
, pp. 909-944
-
-
McVean, G.1
-
30
-
-
0014569408
-
Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation
-
Ohta, T., and M. Kimura, 1969 Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics 63: 229.
-
(1969)
Genetics
, vol.63
, pp. 229
-
-
Ohta, T.1
Kimura, M.2
-
31
-
-
0015100342
-
Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population
-
Ohta, T., and M. Kimura, 1971 Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics 68: 571-580.
-
(1971)
Genetics
, vol.68
, pp. 571-580
-
-
Ohta, T.1
Kimura, M.2
-
32
-
-
84975795680
-
Genomes Project Consortium, 2012 An integrated map of genetic variation from 1,092 human genomes
-
1000 Genomes Project Consortium, 2012 An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
-
(1000)
Nature
, vol.491
, pp. 56-65
-
-
-
33
-
-
0003474751
-
-
Ed. 2. Cambridge University Press, New York
-
Press, W. H., S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, 1992 Numerical Recipes in C: The Art of Scientific Computing, Ed. 2. Cambridge University Press, New York.
-
(1992)
Numerical Recipes in C: The Art of Scientific Computing
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
34
-
-
0034977045
-
Linkage disequilibrium in humans: Models and data
-
Pritchard, J., and M. Przeworski, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
-
(2001)
Am. J. Hum. Genet.
, vol.69
, pp. 1-14
-
-
Pritchard, J.1
Przeworski, M.2
-
35
-
-
70349316959
-
Linkage disequilibrium between loci of unknown phase
-
Rogers, A. R., and C. Huff, 2009 Linkage disequilibrium between loci of unknown phase. Genetics 182: 839-844.
-
(2009)
Genetics
, vol.182
, pp. 839-844
-
-
Rogers, A.R.1
Huff, C.2
-
36
-
-
0029983205
-
Ascertainment bias in estimates of average heterozygosity
-
Rogers, A. R., and L. B. Jorde, 1996 Ascertainment bias in estimates of average heterozygosity. Am. J. Hum. Genet. 58: 1033-1041.
-
(1996)
Am. J. Hum. Genet.
, vol.58
, pp. 1033-1041
-
-
Rogers, A.R.1
Jorde, L.B.2
-
37
-
-
84855460566
-
Linkage disequilibrium under recurrent bottlenecks
-
Schaper, E., A. Eriksson, M. Rafajlovic, S. Sagitov, and B. Mehlig, 2012 Linkage disequilibrium under recurrent bottlenecks. Genetics 190: 217-229.
-
(2012)
Genetics
, vol.190
, pp. 217-229
-
-
Schaper, E.1
Eriksson, A.2
Rafajlovic, M.3
Sagitov, S.4
Mehlig, B.5
-
38
-
-
0034940158
-
The value of isolated populations
-
Shifman, S., and A. Darvasi, 2001 The value of isolated populations. Nat. Genet. 28: 309-310.
-
(2001)
Nat. Genet.
, vol.28
, pp. 309-310
-
-
Shifman, S.1
Darvasi, A.2
-
39
-
-
43749105558
-
Linkage disequilibrium-understanding the evolutionary past and mapping the medical future
-
Slatkin, M., 2008 Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nat. Rev. Genet. 9: 477-485.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 477-485
-
-
Slatkin, M.1
-
40
-
-
33750997276
-
Analytic computation of the expectation of the linkage disequilibrium coefficient r2
-
Song, Y., and J. Song, 2007 Analytic computation of the expectation of the linkage disequilibrium coefficient r2. Theor. Popul. Biol. 71: 49-60.
-
(2007)
Theor. Popul. Biol.
, vol.71
, pp. 49-60
-
-
Song, Y.1
Song, J.2
-
41
-
-
0017852492
-
The effect of intragenic recombination on the number of alleles in a finite population
-
Strobeck, C., and K. Morgan, 1978 The effect of intragenic recombination on the number of alleles in a finite population. Genetics 88: 829-844.
-
(1978)
Genetics
, vol.88
, pp. 829-844
-
-
Strobeck, C.1
Morgan, K.2
-
42
-
-
0015070635
-
Linkage disequilibrium and homozygosity of chromosome segments in finite populations
-
Sved, J. A., 1971 Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol. 2: 125-141.
-
(1971)
Theor. Popul. Biol.
, vol.2
, pp. 125-141
-
-
Sved, J.A.1
-
43
-
-
70349263972
-
Correlation measures for linkage disequilibrium within and between populations
-
Sved, J. A., 2009 Correlation measures for linkage disequilibrium within and between populations. Genet. Res. 91: 183-192.
-
(2009)
Genet. Res.
, vol.91
, pp. 183-192
-
-
Sved, J.A.1
-
44
-
-
0015598170
-
Correlation and probability methods for one and two loci
-
Sved, J. A., and M. W. Feldman, 1973 Correlation and probability methods for one and two loci. Theor. Popul. Biol. 4: 129-132.
-
(1973)
Theor. Popul. Biol.
, vol.4
, pp. 129-132
-
-
Sved, J.A.1
Feldman, M.W.2
-
45
-
-
38849164368
-
Apparent mutational hotspots and long distance linkage disequilibrium resulting from a bottleneck
-
Tenaillon, M., F. Austerlitz, and O. Tenaillon, 2008 Apparent mutational hotspots and long distance linkage disequilibrium resulting from a bottleneck. J. Evol. Biol. 21: 541-550.
-
(2008)
J. Evol. Biol.
, vol.21
, pp. 541-550
-
-
Tenaillon, M.1
Austerlitz, F.2
Tenaillon, O.3
-
46
-
-
34147165220
-
Recent human effective population size estimated from linkage disequilibrium
-
Tenesa, A., P. Navarro, B. Hayes, D. Duffy, G. Clarke et al., 2007 Recent human effective population size estimated from linkage disequilibrium. Genome Res. 17: 520-526.
-
(2007)
Genome Res.
, vol.17
, pp. 520-526
-
-
Tenesa, A.1
Navarro, P.2
Hayes, B.3
Duffy, D.4
Clarke, G.5
-
47
-
-
33644763127
-
Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster
-
Thornton, K., and P. Andolfatto, 2006 Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
-
(2006)
Genetics
, vol.172
, pp. 1607-1619
-
-
Thornton, K.1
Andolfatto, P.2
-
48
-
-
0016247512
-
Behavior of pairs of loci in finite monoecious populations
-
Weir, B., and C. Cockerham, 1974 Behavior of pairs of loci in finite monoecious populations. Theor. Popul. Biol. 6: 323-354.
-
(1974)
Theor. Popul. Biol.
, vol.6
, pp. 323-354
-
-
Weir, B.1
Cockerham, C.2
|