-
1
-
-
0034681511
-
Evidence for a high frequency of simultaneous double-nucleotide substitutions
-
DOI 10.1126/science.287.5456.1283
-
Averof M, Rokas A, Wolfe KH, Sharp PM. 2000. Evidence for a high-frequency of simultaneous double-nucleotide substitutions. Science 287:1283-1286. (Pubitemid 30112153)
-
(2000)
Science
, vol.287
, Issue.5456
, pp. 1283-1286
-
-
Averof, M.1
Rokas, A.2
Wolfe, K.H.3
Sharp, P.M.4
-
2
-
-
0346991738
-
The Problem of Counting Sites in the Estimation of the Synonymous and Nonsynonymous Substitution Rates: Implications for the Correlation between the Synonymous Substitution Rate and Codon Usage Bias
-
Bierne N, Eyre-Walker A. 2003. The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between synonymous substitution rates and codon usage bias. Genetics 165: 1587-1597. (Pubitemid 38020272)
-
(2003)
Genetics
, vol.165
, Issue.3
, pp. 1587-1597
-
-
Bierne, N.1
Eyre-Walker, A.2
-
3
-
-
0033762460
-
Rates of nucleotide substitution and mammalian nuclear gene evolution: Approximate and maximum-likelihood methods lead to different conclusions
-
Bielawski J, Dunn K, Yang Z. 2000. Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics 156:1299-1308.
-
(2000)
Genetics
, vol.156
, pp. 1299-1308
-
-
Bielawski, J.1
Dunn, K.2
Yang, Z.3
-
4
-
-
31144465926
-
Hearing silence: Non-neutral evolution at synonymous sites in mammals
-
DOI 10.1038/nrg1770, PII NRG1770
-
ChamaryJV, ParmleyJL, Hurst LD. 2006. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet. 7:98-108. (Pubitemid 43128905)
-
(2006)
Nature Reviews Genetics
, vol.7
, Issue.2
, pp. 98-108
-
-
Chamary, J.V.1
Parmley, J.L.2
Hurst, L.D.3
-
5
-
-
47549097539
-
Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
-
DOI 10.1016/j.cell.2008.05.042, PII S0092867408007058
-
Drummond A, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. (Pubitemid 352010328)
-
(2008)
Cell
, vol.134
, Issue.2
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
6
-
-
0028168856
-
A codon-based model of nucleotide substitutions for protein-coding sequences
-
Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitutions for protein-coding sequences. Mol Biol Evol. 11: 725-736.
-
(1994)
Mol Biol Evol
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
7
-
-
84956958332
-
Identification of conflicting selective effects on highly expressed genes
-
Higgs P, Hao W, Golding GB. 2007. Identification of conflicting selective effects on highly expressed genes. Evol Bioinform Online. 3:1-13.
-
(2007)
Evol Bioinform Online
, vol.3
, pp. 1-13
-
-
Higgs, P.1
Hao, W.2
Golding, G.B.3
-
8
-
-
74249110768
-
Human tri-allelic sites: Evidence for a new mutational mechanism
-
Hodgkinson A, Eyre-Walker A. 2010. Human tri-allelic sites: evidence for a new mutational mechanism. Genetics 184:233-243.
-
(2010)
Genetics
, vol.184
, pp. 233-243
-
-
Hodgkinson, A.1
Eyre-Walker, A.2
-
9
-
-
0001521392
-
On the bias of commonly used measures of association for 2 x 2 tables
-
Jewell NP. 1986. On the bias of commonly used measures of association for 2 x 2 tables. Biometrics 42:351-358.
-
(1986)
Biometrics
, vol.42
, pp. 351-358
-
-
Jewell, N.P.1
-
10
-
-
0000732090
-
Evolution of protein molecules
-
Munro HN, editor New York Academic Press
-
Jukes TH, Cantor C 1969. Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York Academic Press. p. 21-132.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.2
-
11
-
-
52449148668
-
The role of compensatory mutation in molecular evolution
-
Kimura M. 1985. The role of compensatory mutation in molecular evolution. J Genet. 64:7-19.
-
(1985)
J Genet
, vol.64
, pp. 7-19
-
-
Kimura, M.1
-
12
-
-
0037224621
-
Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases
-
DOI 10.1002/humu.10147
-
Kondrashov AS. 2002. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Hum Mutat. 21:12-27. (Pubitemid 36070453)
-
(2003)
Human Mutation
, vol.21
, Issue.1
, pp. 12-27
-
-
Kondrashov, A.S.1
-
13
-
-
34547675965
-
An empirical codon model for protein sequence evolution
-
DOI 10.1093/molbev/msm064
-
Kosiol C, Holmes I, Goldman N. 2007. An empirical codon model for protein sequence evolution. Mol Biol Evol. 24:1464-1479. (Pubitemid 47216596)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.7
, pp. 1464-1479
-
-
Kosiol, C.1
Holmes, I.2
Goldman, N.3
-
14
-
-
33845900702
-
Searching for sequence directed mutagenesis in eukaryotes
-
DOI 10.1007/s00239-005-0120-5
-
Ladoukakis ED, Eyre-Walker A. 2007. Searching for sequence directed mutagenesis in eukaryotes. J Mol Evol. 64:1-3. (Pubitemid 46020855)
-
(2007)
Journal of Molecular Evolution
, vol.64
, Issue.1
, pp. 1-3
-
-
Ladoukakis, E.D.1
Eyre-Walker, A.2
-
15
-
-
64949129503
-
Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage
-
Li J, Zhang Z, Vang S, Yu J, Wong GK-S, Wang J. 2009. Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J Mol Evol. 68:414-423.
-
(2009)
J Mol Evol
, vol.68
, pp. 414-423
-
-
Li, J.1
Zhang, Z.2
Vang, S.3
Yu, J.4
Gk-S, W.5
Wang, J.6
-
16
-
-
33244455951
-
Evolutionary conservation of expression profiles between human and mouse orthologous genes
-
DOI 10.1093/molbev/msj054
-
Liao B-Y, Zhang J. 2006. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol. 23:530-540. (Pubitemid 43278264)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.3
, pp. 530-540
-
-
Liao, B.-Y.1
Zhang, J.2
-
17
-
-
0021712452
-
Interaction of silent and replacement changes in eukaryotic coding sequences
-
DOI 10.1007/BF02100090
-
Lipman DJ, Wilbur WJ. 1985. Interaction of silent and replacement changes in eukaryotic coding sequences. J Mol Evol. 21:161-167. (Pubitemid 15106844)
-
(1984)
Journal of Molecular Evolution
, vol.21
, Issue.2
, pp. 161-167
-
-
Lipman, D.J.1
Wilbur, W.J.2
-
18
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
-
Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol. 11:715-724. (Pubitemid 24274880)
-
(1994)
Molecular Biology and Evolution
, vol.11
, Issue.5
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
19
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3:418-426. (Pubitemid 16010523)
-
(1986)
Molecular Biology and Evolution
, vol.3
, Issue.5
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
20
-
-
0029583490
-
Variation in synonymous substitution rates among mammalian genes and the correlation between synonymous and nonsynonymous divergences
-
Ohta T, Ina Y. 1995. Variation in synonymous substitution rates among mammalian genes and the correlation between synonymous and nonsynonymous divergences. J Mol Evol. 41:717-720. (Pubitemid 26020048)
-
(1995)
Journal of Molecular Evolution
, vol.41
, Issue.6
, pp. 717-720
-
-
Ohta, T.1
Ina, Y.2
-
21
-
-
15844406550
-
HyPhy: Hypothesis testing using phylogenies
-
Pond SLK, Frost SDW, Muse SV. 2004. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679.
-
(2004)
Bioinformatics
, vol.21
, pp. 676-679
-
-
Slk, P.1
Sdw, F.2
Muse, S.V.3
-
22
-
-
34547739034
-
Widespread positive selection in synonymous sites of mammalian genes
-
DOI 10.1093/molbev/msm100
-
Resch AM, Carmel L, Marino-Ramirez L, Ogurtsov AY, Shabalina SA, Rogozin IB, Koonin EV. 2007. Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol. 24:1821-1831. (Pubitemid 47236700)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1821-1831
-
-
Resch, A.M.1
Carmel, L.2
Marino-Ramirez, L.3
Ogurtsov, A.Y.4
Shabalina, S.A.5
Rogozin, I.B.6
Koonin, E.V.7
-
23
-
-
72149107901
-
Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment
-
Schneider A, Souvorov A, Sabath N, Landan G, Gonnet GH, Graur D. 2009. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol Evol. 1:114-118.
-
(2009)
Genome Biol Evol
, vol.1
, pp. 114-118
-
-
Schneider, A.1
Souvorov, A.2
Sabath, N.3
Landan, G.4
Gonnet, G.H.5
Graur, D.6
-
24
-
-
0036844415
-
Patterns in spontaneous mutation revealed by human-baboon sequence comparison
-
DOI 10.1016/S0168-9525(02)02757-9, PII S0168952502027579
-
Silva JC, Kondrashov AS. 2002. Patterns in spontaneous mutation revealed by human bamboo sequence comparison. Nat Genet. 18:544-547. (Pubitemid 35284641)
-
(2002)
Trends in Genetics
, vol.18
, Issue.11
, pp. 544-547
-
-
Silva, J.C.1
Kondrashov, A.S.2
-
25
-
-
0037227363
-
Partitioning the variation in mammalian substitution rates
-
Smith NGC, Eyre-Walker A. 2003. Partitioning the variation in mammalian substitution rates. Mol Biol Evol. 20:10-17. (Pubitemid 36077893)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.1
, pp. 10-17
-
-
Smith, N.G.C.1
Eyre-Walker, A.2
-
26
-
-
0032714307
-
The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents
-
Smith NGC, Hurst LD. 1999. The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents. Genetics 153:1395-1402. (Pubitemid 29522150)
-
(1999)
Genetics
, vol.153
, Issue.3
, pp. 1395-1402
-
-
Smith, N.G.C.1
Hurst, L.D.2
-
27
-
-
0037227261
-
A low rate of simultaneous double-nucleotide mutations in primates
-
DOI 10.1093/molbev/msg003
-
Smith NGC, Webster MT, Ellegren H. 2003. A low rate of simultaneous double-nucleotide mutations in primates. Mol Biol Evol. 20:47-53. (Pubitemid 36077898)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.1
, pp. 47-53
-
-
Smith, N.G.C.1
Webster, M.T.2
Ellegren, H.3
-
28
-
-
50649104620
-
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
-
Studer RA, Penel S, Duret L, Robinson-Rechavi M. 2008. Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res. 18:1393-1402.
-
(2008)
Genome Res
, vol.18
, pp. 1393-1402
-
-
Studer, R.A.1
Penel, S.2
Duret, L.3
Robinson-Rechavi, M.4
-
29
-
-
54249105361
-
False-positive reults obtained from the branch-site test of positive selection
-
Suzuki Y. 2008. False-positive reults obtained from the branch-site test of positive selection. Genes Genet Syst. 83:331-338.
-
(2008)
Genes Genet Syst
, vol.83
, pp. 331-338
-
-
Suzuki, Y.1
-
30
-
-
8444247896
-
Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions
-
DOI 10.1093/molbev/msh242
-
Tzeng Y-H, Pan R, Li W-H. 2004. Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 21:2290-2298. (Pubitemid 39488899)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.12
, pp. 2290-2298
-
-
Tzeng, Y.-H.1
Pan, R.2
Li, W.-H.3
-
31
-
-
36048932967
-
Uncovering the mutation-fixation correlation in short lineages
-
Vallender EJ, Lahn BT. 2007. Uncovering the mutation-fixation correlation in short lineages. BMC Evol Biol. 7:168.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 168
-
-
Vallender, E.J.1
Lahn, B.T.2
-
32
-
-
4644373240
-
Estimating the frequency of events that cause multiple-nucleotide changes
-
Whelan S, Goldman N. 2004. Estimating the frequency of events that cause multiple-nucleotide changes. Genetics 167: 2024-2043.
-
(2004)
Genetics
, vol.167
, pp. 2024-2043
-
-
Whelan, S.1
Goldman, N.2
-
33
-
-
0036667703
-
Is the synonymous substitution rate in mammals gene specific?
-
Williams EJB, Hurst LD. 2002. Is the synonymous substitution rate in mammals gene specific? Mol Biol Evol. 198:1395-1398.
-
(2002)
Mol Biol Evol
, vol.198
, pp. 1395-1398
-
-
Ejb, W.1
Hurst, L.D.2
-
34
-
-
0027422858
-
Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat
-
Wolfe KH, Sharp PM. 1993. Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. J Mol Evol. 37:441-456. (Pubitemid 23283730)
-
(1993)
Journal of Molecular Evolution
, vol.37
, Issue.4
, pp. 441-456
-
-
Wolfe, K.H.1
Sharp, P.M.2
-
35
-
-
20644465818
-
A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate
-
DOI 10.1016/j.tig.2005.05.005, PII S0168952505001356
-
Wyckoff GJ, Malcolm CM, Vallender EJ, Lahn BT. 2005. A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate. Trends Genet. 21:381-385. (Pubitemid 40835722)
-
(2005)
Trends in Genetics
, vol.21
, Issue.7
, pp. 381-385
-
-
Wyckoff, G.J.1
Malcom, C.M.2
Vallender, E.J.3
Lahn, B.T.4
-
36
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556. (Pubitemid 27480216)
-
(1997)
Computer Applications in the Biosciences
, vol.13
, Issue.5
, pp. 555-556
-
-
Yang, Z.1
-
38
-
-
0031960185
-
Synonymous and nonsynonymous rate variation in nuclear genes of mammals
-
DOI 10.1007/PL00006320
-
Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 46:409-418. (Pubitemid 28164945)
-
(1998)
Journal of Molecular Evolution
, vol.46
, Issue.4
, pp. 409-418
-
-
Yang, Z.1
Nielsen, R.2
-
39
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang Z, Nielsen R. 2000. Estimating synonymous and nonsynon-ymous substitution rates under realistic evolutionary models. Mol Biol Evol. 17:32-43. (Pubitemid 30056990)
-
(2000)
Molecular Biology and Evolution
, vol.17
, Issue.1
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
|