-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
2
-
-
35748934206
-
Evidence for inefficient selection against deleterious mutations in cytochrome oxidase I of asexual bdelloid rotifers
-
Barraclough T.G., Fontaneto D., Ricci C., and Hernious E.A. Evidence for inefficient selection against deleterious mutations in cytochrome oxidase I of asexual bdelloid rotifers. Mol. Biol. Evol. 24 (2007) 1952-1962
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1952-1962
-
-
Barraclough, T.G.1
Fontaneto, D.2
Ricci, C.3
Hernious, E.A.4
-
3
-
-
35348854895
-
Extensive parallelism in protein evolution
-
Bazykin G.A., Kondrashov F.A., Brudno M., Poliakov A., Dubchak I., and Kondrashov A.S. Extensive parallelism in protein evolution. Biol. Direct 2007 2 (2007) 20
-
(2007)
Biol. Direct
, vol.2007
, Issue.2
, pp. 20
-
-
Bazykin, G.A.1
Kondrashov, F.A.2
Brudno, M.3
Poliakov, A.4
Dubchak, I.5
Kondrashov, A.S.6
-
4
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G., et al. Ultraconserved elements in the human genome. Science 304 (2004) 1321-1325
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
-
5
-
-
31844440056
-
Fast accumulation of nonsynonymous mutations on the female-specific W chromosome in birds
-
Berlin S., and Ellegren H. Fast accumulation of nonsynonymous mutations on the female-specific W chromosome in birds. J. Mol. Evol. 62 (2006) 66-72
-
(2006)
J. Mol. Evol.
, vol.62
, pp. 66-72
-
-
Berlin, S.1
Ellegren, H.2
-
6
-
-
0037041421
-
The cost of inbreeding in Arabidopsis
-
Bustamante C.D., Nielsen R., Sawyer S.A., Olsen K.M., Purugganan M.D., and Hartl D.L. The cost of inbreeding in Arabidopsis. Nature 416 (2002) 531-534
-
(2002)
Nature
, vol.416
, pp. 531-534
-
-
Bustamante, C.D.1
Nielsen, R.2
Sawyer, S.A.3
Olsen, K.M.4
Purugganan, M.D.5
Hartl, D.L.6
-
7
-
-
35348873167
-
Purifying selection maintains highly conserved noncoding sequences in Drosophila
-
Casillas S., Barbadilla A., and Bergman C.M. Purifying selection maintains highly conserved noncoding sequences in Drosophila. Mol. Biol. Evol. 24 (2007) 2222-2234
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 2222-2234
-
-
Casillas, S.1
Barbadilla, A.2
Bergman, C.M.3
-
8
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
Chimpanzee Sequencing and Analysis Consortium
-
Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (2005) 69-87
-
(2005)
Nature
, vol.437
, pp. 69-87
-
-
-
9
-
-
54849419895
-
Comparative genomics and the study of evolution by natural selection
-
Ellegren H. Comparative genomics and the study of evolution by natural selection. Mol. Ecol. 17 (2008) 4586-4596
-
(2008)
Mol. Ecol.
, vol.17
, pp. 4586-4596
-
-
Ellegren, H.1
-
10
-
-
58149328496
-
GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates
-
Galtier N., Duret L., Glémin S., and Ranwez V. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet. 25 (2008) 1-5
-
(2008)
Trends Genet.
, vol.25
, pp. 1-5
-
-
Galtier, N.1
Duret, L.2
Glémin, S.3
Ranwez, V.4
-
11
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
Gene Ontology Consortium
-
Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nat. Genet. 25 (2000) 25-29
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
-
12
-
-
34447522201
-
Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over
-
Haddrill P.R., Halligan D.L., Tomaras D., and Charlesworth B. Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over. Genome Biol. 2007 8 (2007) R18
-
(2007)
Genome Biol.
, vol.2007
, Issue.8
-
-
Haddrill, P.R.1
Halligan, D.L.2
Tomaras, D.3
Charlesworth, B.4
-
14
-
-
0031021191
-
Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells
-
Hughes A.L. Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells. Mol. Biol. Evol. 14 (1997) 1-5
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 1-5
-
-
Hughes, A.L.1
-
15
-
-
0036945805
-
Natural selection and diversification of vertebrate immune effectors
-
Hughes A.L. Natural selection and diversification of vertebrate immune effectors. Immunol. Rev. 190 (2002) 161-168
-
(2002)
Immunol. Rev.
, vol.190
, pp. 161-168
-
-
Hughes, A.L.1
-
16
-
-
15544381275
-
Evidence for abundant slightly deleterious polymorphisms in bacterial populations
-
Hughes A.L. Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics 169 (2005) 533-538
-
(2005)
Genetics
, vol.169
, pp. 533-538
-
-
Hughes, A.L.1
-
17
-
-
33947648538
-
Micro-scale signature of purifying selection in Marburg virus genomes
-
Hughes A.L. Micro-scale signature of purifying selection in Marburg virus genomes. Gene 392 (2007) 266-272
-
(2007)
Gene
, vol.392
, pp. 266-272
-
-
Hughes, A.L.1
-
18
-
-
45249106003
-
Near neutrality: leading edge of the neutral theory of molecular evolution
-
Hughes A.L. Near neutrality: leading edge of the neutral theory of molecular evolution. Ann. N.Y. Acad. Sci. 1133 (2008) 162-179
-
(2008)
Ann. N.Y. Acad. Sci.
, vol.1133
, pp. 162-179
-
-
Hughes, A.L.1
-
19
-
-
0023764283
-
Pattern of nucleotide substitution at MHC class I loci reveals overdominant selection
-
Hughes A.L., and Nei M. Pattern of nucleotide substitution at MHC class I loci reveals overdominant selection. Nature 335 (1988) 167-170
-
(1988)
Nature
, vol.335
, pp. 167-170
-
-
Hughes, A.L.1
Nei, M.2
-
20
-
-
17744385316
-
Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes
-
Hughes A.L., and Friedman R. Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes. Mol. Biol. Evol. 22 (2005) 1320-1324
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1320-1324
-
-
Hughes, A.L.1
Friedman, R.2
-
21
-
-
35248860855
-
More effective purifying selection in RNA viruses than in DNA viruses
-
Hughes A.L., and Hughes M.A. More effective purifying selection in RNA viruses than in DNA viruses. Gene 404 (2007) 117-125
-
(2007)
Gene
, vol.404
, pp. 117-125
-
-
Hughes, A.L.1
Hughes, M.A.2
-
22
-
-
33947507808
-
Coding sequence polymorphism in avian mitochondrial genomes reflects population histories
-
Hughes A.L., and Hughes M.A. Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Mol. Ecol. 16 (2007) 1369-1376
-
(2007)
Mol. Ecol.
, vol.16
, pp. 1369-1376
-
-
Hughes, A.L.1
Hughes, M.A.2
-
23
-
-
48149108739
-
Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes
-
Hughes A.L., and Friedman R. Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics 60 (2008) 495-506
-
(2008)
Immunogenetics
, vol.60
, pp. 495-506
-
-
Hughes, A.L.1
Friedman, R.2
-
24
-
-
0346103664
-
Widespread purifying selection at polymorphic sites in human protein-coding loci
-
Hughes A.L., Packer B., Welch R., Bergen A.W., Chanock S.J., and Yeager M. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 15754-15757
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 15754-15757
-
-
Hughes, A.L.1
Packer, B.2
Welch, R.3
Bergen, A.W.4
Chanock, S.J.5
Yeager, M.6
-
25
-
-
19044362395
-
Gene family content-based phylogeny of prokaryotes: the effect of search criteria
-
Hughes A.L., Ekollu V., Friedman R., and Rose J.R. Gene family content-based phylogeny of prokaryotes: the effect of search criteria. Syst. Biol. 54 (2005) 268-276
-
(2005)
Syst. Biol.
, vol.54
, pp. 268-276
-
-
Hughes, A.L.1
Ekollu, V.2
Friedman, R.3
Rose, J.R.4
-
26
-
-
29144525031
-
High level of functional polymorphism indicates a unique role of natural selection at human immune system loci
-
Hughes A.L., Packer B., Welsch R., Chanock S.J., and Yeager M. High level of functional polymorphism indicates a unique role of natural selection at human immune system loci. Immunogenetics 57 (2005) 821-827
-
(2005)
Immunogenetics
, vol.57
, pp. 821-827
-
-
Hughes, A.L.1
Packer, B.2
Welsch, R.3
Chanock, S.J.4
Yeager, M.5
-
27
-
-
51649122447
-
Synonymous and nonsynonymous polymorphisms and divergences in bacterial genomes
-
Hughes A.L., Friedman R., Rivailler P., and French J.O. Synonymous and nonsynonymous polymorphisms and divergences in bacterial genomes. Mol. Biol. Evol. 25 (2008) 2199-2209
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 2199-2209
-
-
Hughes, A.L.1
Friedman, R.2
Rivailler, P.3
French, J.O.4
-
28
-
-
50549099310
-
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures
-
Irausquin S.J., and Hughes A.L. Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures. J. Gen. Virol. 89 (2008) 1921-1929
-
(2008)
J. Gen. Virol.
, vol.89
, pp. 1921-1929
-
-
Irausquin, S.J.1
Hughes, A.L.2
-
30
-
-
0018415510
-
Two types of amino acid substitutions in protein evolution
-
Miyata T., Miyazawa S., and Yasunaga T. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12 (1979) 219-236
-
(1979)
J. Mol. Evol.
, vol.12
, pp. 219-236
-
-
Miyata, T.1
Miyazawa, S.2
Yasunaga, T.3
-
31
-
-
0027514171
-
Molecular mimicry and the generation of host defense protein diversity
-
Murphy P.M. Molecular mimicry and the generation of host defense protein diversity. Cell 72 (1993) 823-826
-
(1993)
Cell
, vol.72
, pp. 823-826
-
-
Murphy, P.M.1
-
32
-
-
0028279173
-
Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice
-
Nachman M.W., Boyer S.N., and Aquadro C.F. Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 6364-6368
-
(1994)
Proc. Natl. Acad. Sci. U. S. A.
, vol.91
, pp. 6364-6368
-
-
Nachman, M.W.1
Boyer, S.N.2
Aquadro, C.F.3
-
33
-
-
0030011347
-
Nonneutral mitochondrial DNA variation in humans and chimpanzees
-
Nachman M.W., Brown W.M., Stoneking M., and Aquadro C.F. Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics 142 (1996) 953-963
-
(1996)
Genetics
, vol.142
, pp. 953-963
-
-
Nachman, M.W.1
Brown, W.M.2
Stoneking, M.3
Aquadro, C.F.4
-
35
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
-
(1986)
Mol. Biol. Evol.
, vol.3
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
36
-
-
0015722319
-
Slightly deleterious mutant substitutions in evolution
-
Ohta T. Slightly deleterious mutant substitutions in evolution. Nature 246 (1973) 96-98
-
(1973)
Nature
, vol.246
, pp. 96-98
-
-
Ohta, T.1
-
37
-
-
0027318192
-
Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size
-
Ohta T. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc. Natl. Acad. Sci. U. S. A. 90 (1993) 4548-4551
-
(1993)
Proc. Natl. Acad. Sci. U. S. A.
, vol.90
, pp. 4548-4551
-
-
Ohta, T.1
-
38
-
-
0027443866
-
An examination of the generation-time effect on molecular evolution
-
Ohta T. An examination of the generation-time effect on molecular evolution. Proc. Natl. Acad. Sci. U. S. A. 90 (1993) 10676-10680
-
(1993)
Proc. Natl. Acad. Sci. U. S. A.
, vol.90
, pp. 10676-10680
-
-
Ohta, T.1
-
39
-
-
0037058932
-
Near-neutrality in evolution of genes and gene regulation
-
Ohta T. Near-neutrality in evolution of genes and gene regulation. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 16134-16137
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, pp. 16134-16137
-
-
Ohta, T.1
-
40
-
-
0030000951
-
Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans
-
Rand D.M., and Kann L.M. Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol. Biol. Evol. 13 (1996) 735-748
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 735-748
-
-
Rand, D.M.1
Kann, L.M.2
-
41
-
-
34247352040
-
Evolutionary and biomedical insights from the rhesus macaque genome
-
Rhesus Macaque Genome Sequencing and Analysis Consortium
-
Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316 (2007) 222-234
-
(2007)
Science
, vol.316
, pp. 222-234
-
-
-
42
-
-
42249084107
-
Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series
-
Rogozin I.B., Thomson K., Csürös M., Carmel L., and Koonin E.V. Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series. Biol. Direct 2008 3 (2008) 7
-
(2008)
Biol. Direct
, vol.2008
, Issue.3
, pp. 7
-
-
Rogozin, I.B.1
Thomson, K.2
Csürös, M.3
Carmel, L.4
Koonin, E.V.5
-
43
-
-
49749137335
-
Frequent and widespread parallel evolution of protein sequences
-
Rokas A., and Carroll S.B. Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol. 25 (2008) 1943-1953
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 1943-1953
-
-
Rokas, A.1
Carroll, S.B.2
-
44
-
-
58149311049
-
Identification and characterization of new long conserved noncoding sequences in vertebrates
-
Sakuraba Y., et al. Identification and characterization of new long conserved noncoding sequences in vertebrates. Mamm. Genome 19 (2008) 703-712
-
(2008)
Mamm. Genome
, vol.19
, pp. 703-712
-
-
Sakuraba, Y.1
-
45
-
-
1942485886
-
The effect of gene conversion on the divergence between duplicated genes
-
Teshima K.M., and Innan H. The effect of gene conversion on the divergence between duplicated genes. Genetics 166 (2004) 1553-1560
-
(2004)
Genetics
, vol.166
, pp. 1553-1560
-
-
Teshima, K.M.1
Innan, H.2
-
46
-
-
0027968068
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
-
Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
47
-
-
0036729902
-
Molecular evolution of functional genes on the mammalian Y chromosome
-
Wyckoff G.J., Joyce L., and Wu C.-I. Molecular evolution of functional genes on the mammalian Y chromosome. Mol. Biol. Evol. 19 (2002) 1633-1636
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1633-1636
-
-
Wyckoff, G.J.1
Joyce, L.2
Wu, C.-I.3
-
48
-
-
0036135450
-
Protein structures, neighbor effect, and a new index of amino acid similarities
-
Xia X., and Xie Z. Protein structures, neighbor effect, and a new index of amino acid similarities. Mol. Biol. Evol. 19 (2002) 58-67
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 58-67
-
-
Xia, X.1
Xie, Z.2
-
49
-
-
0030683599
-
PAML: a program package for phylogenetic analysis by maximum likelihood
-
Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
50
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang Z., and Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17 (2000) 32-43
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
51
-
-
0030957216
-
Detection of convergent and parallel evolution at the amino acid sequence level
-
Zhang J., and Kumar S. Detection of convergent and parallel evolution at the amino acid sequence level. Mol. Biol. Evol. 14 (1997) 527-536
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 527-536
-
-
Zhang, J.1
Kumar, S.2
|