-
1
-
-
8844227502
-
Population history and natural selection shape patterns of genetic variation in 132 genes
-
Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L. 2004. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2: e286.
-
(2004)
PLoS Biol.
, vol.2
-
-
Akey, J.M.1
Eberle, M.A.2
Rieder, M.J.3
Carlson, C.S.4
Shriver, M.D.5
Nickerson, D.A.6
Kruglyak, L.7
-
2
-
-
27144491328
-
Adaptive evolution of non-coding DNA in Drosophila
-
DOI 10.1038/nature04107, PII N04107
-
Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437:1149-1152. (Pubitemid 41509351)
-
(2005)
Nature
, vol.437
, Issue.7062
, pp. 1149-1152
-
-
Andolfatto, P.1
-
3
-
-
0242666279
-
Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation
-
DOI 10.1093/molbev/msg204
-
Arndt PF, Petrov DA, Hwa T. 2003. Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation. Mol Biol Evol. 20:1887-1896. (Pubitemid 37420942)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.11
, pp. 1887-1896
-
-
Arndt, P.F.1
Petrov, D.A.2
Hwa, T.3
-
4
-
-
3042544623
-
The genomic rate of adaptive amino acid substitution in Drosophila
-
DOI 10.1093/molbev/msh134
-
Bierne N, Eyre-Walker A. 2004. The genomic rate of adaptive amino acid substitution in Drosophila. Mol Biol Evol. 21:1350-1360. (Pubitemid 38823738)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.7
, pp. 1350-1360
-
-
Bierne, N.1
Eyre-Walker, A.2
-
5
-
-
44949129000
-
Assessing the evolutionary impact of amino acid mutations in the human genome
-
Boyko AR, Williamson SH, Indap AR, et al. 2008. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet. 4: e1000083.
-
(2008)
PLoS Genet.
, vol.4
-
-
Boyko, A.R.1
Williamson, S.H.2
Indap, A.R.3
-
6
-
-
1842667852
-
MAVID: Constrained ancestral alignment of multiple sequences
-
DOI 10.1101/gr.1960404
-
Bray N, Pachter L. 2004. MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14:693-699. (Pubitemid 38500242)
-
(2004)
Genome Research
, vol.14
, Issue.4
, pp. 693-699
-
-
Bray, N.1
Pachter, L.2
-
7
-
-
33745624539
-
The rate of adaptive evolution in enteric bacteria
-
DOI 10.1093/molbev/msk025
-
Charlesworth J, Eyre-Walker A. 2006. The rate of adaptive evolution in enteric bacteria. Mol Biol Evol. 23:1348-1356. (Pubitemid 43992336)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.7
, pp. 1348-1356
-
-
Charlesworth, J.1
Eyre-Walker, A.2
-
8
-
-
33748473348
-
The genomic rate of adaptive evolution
-
DOI 10.1016/j.tree.2006.06.015, PII S0169534706002035
-
Eyre-Walker A. 2006. The genomic rate of adaptive evolution. Trends Ecol. Evol (Amst). 21:569-575. (Pubitemid 44353858)
-
(2006)
Trends in Ecology and Evolution
, vol.21
, Issue.10
, pp. 569-575
-
-
Eyre-Walker, A.1
-
9
-
-
0033611501
-
High genomic deleterious mutation rates in hominids
-
Eyre-Walker A, Keightley PD. 1999. High genomic deleterious mutation rates in hominids. Nature 397:344-347.
-
(1999)
Nature
, vol.397
, pp. 344-347
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
10
-
-
68949202924
-
Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change
-
Eyre-Walker A, Keightley PD. 2009. Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol. 26:2097-2108.
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 2097-2108
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
12
-
-
0034924997
-
Positive and negative selection on the human genome
-
Fay JC, Wyckoff GJ, Wu C. 2001. Positive and negative selection on the human genome. Genetics 158:1227-1234. (Pubitemid 32667107)
-
(2001)
Genetics
, vol.158
, Issue.3
, pp. 1227-1234
-
-
Fay, J.C.1
Wyckoff, G.J.2
Wu, C.-I.3
-
13
-
-
45849116820
-
Selection on amino acid substitutions in Arabidopsis
-
DOI 10.1093/molbev/msn079
-
Foxe JP, Dar V, Zheng H, Nordborg M, Gaut BS, Wright SI. 2008. Selection on amino acid substitutions in Arabidopsis. Mol Biol Evol. 25:1375-1383. (Pubitemid 351882009)
-
(2008)
Molecular Biology and Evolution
, vol.25
, Issue.7
, pp. 1375-1383
-
-
Foxe, J.P.1
Dar, V.-U.-N.2
Zheng, H.3
Nordborg, M.4
Gaut, B.S.5
Wright, S.I.6
-
14
-
-
33751374466
-
Genomic selective constraints in murid noncoding DNA
-
Gaffney DJ, Keightley PD. 2006. Genomic selective constraints in murid noncoding DNA. PLoS Genet. 2: e204.
-
(2006)
PLoS Genet.
, vol.2
-
-
Gaffney, D.J.1
Keightley, P.D.2
-
15
-
-
77954969511
-
Genome wide analyses reveal little evidence for adaptive evolution in many plant species
-
Gossmann TI, Song B, Windsor AJ, Mitchell-Olds T, Dixon CJ, Kapralov MV, Filatov DA, Eyre-Walker A. 2010. Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Mol Biol Evol. 27:1822-1832.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 1822-1832
-
-
Gossmann, T.I.1
Song, B.2
Windsor, A.J.3
Mitchell-Olds, T.4
Dixon, C.J.5
Kapralov, M.V.6
Filatov, D.A.7
Eyre-Walker, A.8
-
17
-
-
49749083390
-
Positive and negative selection on noncoding DNA in Drosophila simulans
-
Haddrill PR, Bachtrog D, Andolfatto P. 2008. Positive and negative selection on noncoding DNA in Drosophila simulans. Mol Biol Evol. 25:1825-1834.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 1825-1834
-
-
Haddrill, P.R.1
Bachtrog, D.2
Andolfatto, P.3
-
18
-
-
76749105263
-
Evidence for pervasive adaptive protein evolution in wild mice
-
Halligan DL, Oliver F, Eyre-Walker A, Harr B, Keightley PD. 2010. Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genet. 6: e1000825.
-
(2010)
PLoS Genet.
, vol.6
-
-
Halligan, D.L.1
Oliver, F.2
Eyre-Walker, A.3
Harr, B.4
Keightley, P.D.5
-
19
-
-
34548346860
-
Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
-
DOI 10.1038/ng2104, PII NG2104
-
Haygood R, Fedrigo O, Hanson B, Yokoyama K, Wray GA. 2007. Promoter regions of many neural-and nutrition-related genes have experienced positive selection during human evolution. Nat Genet. 39:1140-1144. (Pubitemid 47340653)
-
(2007)
Nature Genetics
, vol.39
, Issue.9
, pp. 1140-1144
-
-
Haygood, R.1
Fedrigo, O.2
Hanson, B.3
Yokoyama, K.-D.4
Wray, G.A.5
-
20
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka R, Gentleman R. 1996. R: a language for data analysis and graphics. J Comput Graph Stat. 5:299-314.
-
(1996)
J. Comput. Graph Stat
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
21
-
-
37249042614
-
Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
-
DOI 10.1534/genetics.107.080663
-
Keightley PD, Eyre-Walker A. 2007. Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177:2251-2261. (Pubitemid 350277004)
-
(2007)
Genetics
, vol.177
, Issue.4
, pp. 2251-2261
-
-
Keightley, P.D.1
Eyre-Walker, A.2
-
23
-
-
15744388330
-
Evidence for widespread degradation of gene control regions in hominid genomes
-
Keightley PD, Lercher MJ, Eyre-Walker A. 2005. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 3: e42.
-
(2005)
PLoS Biol.
, vol.3
-
-
Keightley, P.D.1
Lercher, M.J.2
Eyre-Walker, A.3
-
24
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
DOI 10.1007/BF01731581
-
Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111-120. (Pubitemid 11166431)
-
(1980)
Journal of Molecular Evolution
, vol.16
, Issue.2
, pp. 111-120
-
-
Kimura, M.1
-
25
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
26
-
-
1542347028
-
Inference of Positive and Negative Selection on the 5′ Regulatory Regions of Drosophila Genes
-
DOI 10.1093/molbev/msh026
-
Kohn MH, Fang S, Wu C. 2004. Inference of positive and negative selection on the 5′ regulatory regions of Drosophila genes. Mol Biol Evol. 21:374-383. (Pubitemid 38314625)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.2
, pp. 374-383
-
-
Kohn, M.H.1
Fang, S.2
Wu, C.-I.3
-
27
-
-
0027403961
-
Unbiased estimation of the rates of synonymous and nonsynonymous substitution
-
Li WH. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol. 36:96-99.
-
(1993)
J. Mol. Evol.
, vol.36
, pp. 96-99
-
-
Li, W.H.1
-
28
-
-
6344267228
-
Pattern of sequence variation across 213 environmental response genes
-
Livingston RJ, von Niederhausern A, Jegga AG, Crawford DC, Carlson CS, Rieder MJ, Gowrisankar S, Aronow BJ, Weiss RB, Nickerson DA. 2004. Pattern of sequence variation across 213 environmental response genes. Genome Res. 14:1821-1831. (Pubitemid 39386496)
-
(2004)
Genome Research
, vol.14
, Issue.10 A
, pp. 1821-1831
-
-
Livingston, R.J.1
Von Niederhausern, A.2
Jegga, A.G.3
Crawford, D.C.4
Carlson, C.S.5
Rieder, M.J.6
Gowrisankar, S.7
Aronow, B.J.8
Weiss, R.B.9
Nickerson, D.A.10
-
29
-
-
0026428610
-
Adaptive protein evolution at the Adh locus in Drosophila
-
McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654. (Pubitemid 21896661)
-
(1991)
Nature
, vol.351
, Issue.6328
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
30
-
-
0027533924
-
Evolution of the Zfx and Zfy genes: Rates and interdependence between the genes
-
Pamilo P, Bianchi N. 1993. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol. 10:271-281. (Pubitemid 23103001)
-
(1993)
Molecular Biology and Evolution
, vol.10
, Issue.2
, pp. 271-281
-
-
Pamilo, P.1
Bianchi, N.O.2
-
31
-
-
0347380978
-
Bayesian Analysis Suggests that Most Amino Acid Replacements in Drosophila Are Driven by Positive Selection
-
DOI 10.1007/s00239-003-0022-3
-
Sawyer S, Kulathinal R, Bustamante C, Hartl D. 2003. Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. J Mol Evol. 57: S154-S164. (Pubitemid 37544004)
-
(2003)
Journal of Molecular Evolution
, vol.57
, Issue.SUPPL. 1
-
-
Sawyer, S.A.1
Kulathinal, R.J.2
Bustamante, C.D.3
Hartl, D.L.4
-
32
-
-
2442476580
-
The mammalian transcriptome and the function of non-coding DNA sequences
-
Shabalina SA, Spiridonov NA. 2004. The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biol. 5:105.
-
(2004)
Genome Biol.
, vol.5
, pp. 105
-
-
Shabalina, S.A.1
Spiridonov, N.A.2
-
33
-
-
33847781444
-
Adaptive genic evolution in the Drosophila genomes
-
DOI 10.1073/pnas.0610385104
-
Shapiro JA, Huang W, Zhang C, et al. (12 co-authors). 2007. Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci. 104:2271-2276. (Pubitemid 46391387)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.7
, pp. 2271-2276
-
-
Shapiro, J.A.1
Huang, W.2
Zhang, C.3
Hubisz, M.J.4
Lu, J.5
Turissini, D.A.6
Fang, S.7
Wang, H.-Y.8
Hudson, R.R.9
Nielsen, R.10
Chen, Z.11
Wu, C.-I.12
-
34
-
-
77954966377
-
Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size
-
Slotte T, Foxe JP, Hazzouri KM, Wright SI. 2010. Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Mol Biol Evol. 27:1813-1821.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 1813-1821
-
-
Slotte, T.1
Foxe, J.P.2
Hazzouri, K.M.3
Wright, S.I.4
-
35
-
-
0037186564
-
Adaptive protein evolution in Drosophila
-
DOI 10.1038/4151022a
-
Smith NG, Eyre-Walker A. 2002. Adaptive protein evolution in Drosophila. Nature 415:1022-1024. (Pubitemid 34193448)
-
(2002)
Nature
, vol.415
, Issue.6875
, pp. 1022-1024
-
-
Smith, N.G.C.1
Eyre-Walker, A.2
-
36
-
-
0021066244
-
Evolutionary relationship of DNA sequences in finite populations
-
Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460. (Pubitemid 14247444)
-
(1983)
Genetics
, vol.105
, Issue.2
, pp. 437-460
-
-
Tajima, F.1
-
37
-
-
0024313579
-
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
-
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595. (Pubitemid 19274682)
-
(1989)
Genetics
, vol.123
, Issue.3
, pp. 585-595
-
-
Tajima, F.1
-
38
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
Chimpanzee Sequencing and Analysis Consortium
-
The Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87.
-
(2005)
Nature
, vol.437
, pp. 69-87
-
-
-
39
-
-
55449112450
-
High-resolution mapping of expression-QTLs yields insight into human gene regulation
-
Veyrieras J, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK. 2008. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4: e1000214.
-
(2008)
PLoS Genet.
, vol.4
-
-
Veyrieras, J.1
Kudaravalli, S.2
Kim, S.Y.3
Dermitzakis, E.T.4
Gilad, Y.5
Stephens, M.6
Pritchard, J.K.7
-
40
-
-
0016491430
-
On the number of segregating sites in genetical models without recombination
-
Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7:256-276.
-
(1975)
Theor Popul Biol.
, vol.7
, pp. 256-276
-
-
Watterson, G.A.1
-
41
-
-
33745352578
-
Estimating the genomewide rate of adaptive protein evolution in drosophila
-
DOI 10.1534/genetics.106.056911
-
Welch JJ. 2006. Estimating the genomewide rate of adaptive protein evolution in Drosophila. Genetics 173:821-837. (Pubitemid 43945899)
-
(2006)
Genetics
, vol.173
, Issue.2
, pp. 821-837
-
-
Welch, J.J.1
-
42
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
-
DOI 10.1038/nature03441
-
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. 2005. Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals. Nature 434:338-345. (Pubitemid 40469170)
-
(2005)
Nature
, vol.434
, Issue.7031
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
43
-
-
27844543705
-
Human SNPs reveal no evidence of frequent positive selection
-
DOI 10.1093/molbev/msi240
-
Zhang L, Li W. 2005. Human SNPs reveal no evidence of frequent positive selection. Mol Biol Evol. 22:2504-2507. (Pubitemid 41661386)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.12
, pp. 2504-2507
-
-
Zhang, L.1
Li, W.-H.2
|