-
2
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
Wray GA, (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8: 206-216.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
3
-
-
46149104377
-
Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution
-
Carroll SB, (2008) Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134: 25-36.
-
(2008)
Cell
, vol.134
, pp. 25-36
-
-
Carroll, S.B.1
-
4
-
-
51549097146
-
Resurrecting the role of transcription factor change in developmental evolution
-
Lynch VJ, Wagner GP, (2008) Resurrecting the role of transcription factor change in developmental evolution. Evolution 62: 2131-2154.
-
(2008)
Evolution
, vol.62
, pp. 2131-2154
-
-
Lynch, V.J.1
Wagner, G.P.2
-
5
-
-
0037148774
-
Evolution of a transcriptional repression domain in an insect Hox protein
-
Galant R, Carroll SB, (2002) Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415: 910-913.
-
(2002)
Nature
, vol.415
, pp. 910-913
-
-
Galant, R.1
Carroll, S.B.2
-
6
-
-
0037148839
-
Hox protein mutation and macroevolution of the insect body plan
-
Ronshaugen M, McGinnis N, McGinnis W, (2002) Hox protein mutation and macroevolution of the insect body plan. Nature 415: 914-917.
-
(2002)
Nature
, vol.415
, pp. 914-917
-
-
Ronshaugen, M.1
McGinnis, N.2
McGinnis, W.3
-
7
-
-
76749167085
-
Detecting positive selection from genome scans of linkage disequilibrium
-
Huff CD, Harpending HC, Rogers AR, (2010) Detecting positive selection from genome scans of linkage disequilibrium. BMC Genomics 11: 8.
-
(2010)
BMC Genomics
, vol.11
, pp. 8
-
-
Huff, C.D.1
Harpending, H.C.2
Rogers, A.R.3
-
8
-
-
77955759338
-
Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations
-
Pavlidis P, Jensen JD, Stephan W, (2010) Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics 185: 907-922.
-
(2010)
Genetics
, vol.185
, pp. 907-922
-
-
Pavlidis, P.1
Jensen, J.D.2
Stephan, W.3
-
9
-
-
77957108885
-
A powerful score test to detect positive selection in genome-wide scans
-
Zhong M, Lange K, Papp JC, Fan R, (2010) A powerful score test to detect positive selection in genome-wide scans. Europ J Human Genet 18: 1148-1159.
-
(2010)
Europ J Human Genet
, vol.18
, pp. 1148-1159
-
-
Zhong, M.1
Lange, K.2
Papp, J.C.3
Fan, R.4
-
10
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
Clark, A.G.1
Eisen, M.B.2
Smith, D.R.3
Bergman, C.M.4
Oliver, B.5
-
11
-
-
51349094325
-
Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution
-
Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP, (2008) Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution. BMC Genomics 9: 399.
-
(2008)
BMC Genomics
, vol.9
, pp. 399
-
-
Haerty, W.1
Artieri, C.2
Khezri, N.3
Singh, R.S.4
Gupta, B.P.5
-
12
-
-
0030034357
-
Intraspecific nuclear DNA variation in Drosophila
-
Moriyama EN, Powell JR, (1996) Intraspecific nuclear DNA variation in Drosophila. Mol Biol Evol 13: 261-277.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 261-277
-
-
Moriyama, E.N.1
Powell, J.R.2
-
13
-
-
2442500522
-
Nucleotide variation in the tinman and bagpipe homeobox genes of Drosophila melanogaster
-
Balakirev ES, Ayala FJ, (2004a) Nucleotide variation in the tinman and bagpipe homeobox genes of Drosophila melanogaster. Genetics 166: 1845-1856.
-
(2004)
Genetics
, vol.166
, pp. 1845-1856
-
-
Balakirev, E.S.1
Ayala, F.J.2
-
14
-
-
67650337477
-
High nucleotide divergence in developmental regulatory genes contrasts with the structural elements of olfactory pathways in Caenorhabditis
-
Jovelin R, Dunham JP, Sung FS, Phillips PC, (2009) High nucleotide divergence in developmental regulatory genes contrasts with the structural elements of olfactory pathways in Caenorhabditis. Genetics 181: 1387-1397.
-
(2009)
Genetics
, vol.181
, pp. 1387-1397
-
-
Jovelin, R.1
Dunham, J.P.2
Sung, F.S.3
Phillips, P.C.4
-
15
-
-
0033779754
-
The molecular population genetics of regulatory genes
-
Purugganan MD, (2000) The molecular population genetics of regulatory genes. Mol Ecol 9: 1451-1461.
-
(2000)
Mol Ecol
, vol.9
, pp. 1451-1461
-
-
Purugganan, M.D.1
-
17
-
-
0035146393
-
A cluster of Drosophila homeobox genes involved in mesoderm differentiation program
-
Jagla K, Bellard M, Frasch M, (2001) A cluster of Drosophila homeobox genes involved in mesoderm differentiation program. BioEssays 23: 125-133.
-
(2001)
BioEssays
, vol.23
, pp. 125-133
-
-
Jagla, K.1
Bellard, M.2
Frasch, M.3
-
18
-
-
0031020323
-
ladybird, a tandem of homeobox genes that maintain late wingless expression in terminal and dorsal epidermis of the Drosophila embryo
-
Jagla K, Jagla T, Heitzler P, Dretzen G, Bellard F, et al. (1997) ladybird, a tandem of homeobox genes that maintain late wingless expression in terminal and dorsal epidermis of the Drosophila embryo. Development 124: 91-100.
-
(1997)
Development
, vol.124
, pp. 91-100
-
-
Jagla, K.1
Jagla, T.2
Heitzler, P.3
Dretzen, G.4
Bellard, F.5
-
19
-
-
0028337030
-
A distinct class of homeodomain proteins is encoded by two sequentially expressed Drosophila genes from the 93D/E cluster
-
Jagla K, Stanceva I, Dretzen G, Bellard F, Bellard M, (1994) A distinct class of homeodomain proteins is encoded by two sequentially expressed Drosophila genes from the 93D/E cluster. Nucl Acids Res 22: 1202-1207.
-
(1994)
Nucl Acids Res
, vol.22
, pp. 1202-1207
-
-
Jagla, K.1
Stanceva, I.2
Dretzen, G.3
Bellard, F.4
Bellard, M.5
-
20
-
-
2342456392
-
The ladybird homeobox genes are essential for the specification of a subpopulation of neural cells
-
De Graeve F, Jagla T, Daponte J-P, Rickert C, Dastugue B, et al. (2004) The ladybird homeobox genes are essential for the specification of a subpopulation of neural cells. Dev Biol 270: 122-134.
-
(2004)
Dev Biol
, vol.270
, pp. 122-134
-
-
de Graeve, F.1
Jagla, T.2
Daponte, J.-P.3
Rickert, C.4
Dastugue, B.5
-
21
-
-
0033793865
-
Homeobox gene diversification in the calcareous sponge, Sycon raphanus
-
Manuel M, Le Parco Y, (2000) Homeobox gene diversification in the calcareous sponge, Sycon raphanus. Mol Phylogenet Evol 17: 97-107.
-
(2000)
Mol Phylogenet Evol
, vol.17
, pp. 97-107
-
-
Manuel, M.1
Le Parco, Y.2
-
22
-
-
0037381766
-
Gene fishing: the use of a simple protocol to isolate multiple homeodomain classes from diverse invertebrate taxa
-
Lee SE, Gates RD, Jacobs DK, (2003) Gene fishing: the use of a simple protocol to isolate multiple homeodomain classes from diverse invertebrate taxa. J Mol Evol 56: 509-516.
-
(2003)
J Mol Evol
, vol.56
, pp. 509-516
-
-
Lee, S.E.1
Gates, R.D.2
Jacobs, D.K.3
-
23
-
-
0028807783
-
Mouse Lbx1 and human LBX1 define a novel mammalian homeobox gene family related to the Drosophila lady bird genes
-
Jagla K, Dollé P, Mattei M-G, Jagla T, Schuhbaur B, et al. (1995) Mouse Lbx1 and human LBX1 define a novel mammalian homeobox gene family related to the Drosophila lady bird genes. Mech Dev 53: 345-356.
-
(1995)
Mech Dev
, vol.53
, pp. 345-356
-
-
Jagla, K.1
Dollé, P.2
Mattei, M.-G.3
Jagla, T.4
Schuhbaur, B.5
-
24
-
-
0031818514
-
Specification of the hypaxial musculature
-
Dietrich S, Schubert FR, Healy C, Sharpe PT, Lumsden A, (1998) Specification of the hypaxial musculature. Development 125: 2235-2249.
-
(1998)
Development
, vol.125
, pp. 2235-2249
-
-
Dietrich, S.1
Schubert, F.R.2
Healy, C.3
Sharpe, P.T.4
Lumsden, A.5
-
25
-
-
32944458844
-
Cloning and expression pattern of lbx3, a novel chick homeobox gene
-
Kanamoto T, Terada K, Yoshikawa H, Furukawa T, (2006) Cloning and expression pattern of lbx3, a novel chick homeobox gene. Gene Expr Patterns 6: 241-246.
-
(2006)
Gene Expr Patterns
, vol.6
, pp. 241-246
-
-
Kanamoto, T.1
Terada, K.2
Yoshikawa, H.3
Furukawa, T.4
-
26
-
-
0346816492
-
Nucleotide variation of the Est-6 gene region in natural populations of Drosophila melanogaster
-
Balakirev ES, Ayala FJ, (2003) Nucleotide variation of the Est-6 gene region in natural populations of Drosophila melanogaster. Genetics 165: 1901-1914.
-
(2003)
Genetics
, vol.165
, pp. 1901-1914
-
-
Balakirev, E.S.1
Ayala, F.J.2
-
27
-
-
4544293265
-
The β-esterase gene cluster of Drosophila melanogaster: Is ψEst-6 a pseudogene, a functional gene, or both?
-
Balakirev ES, Ayala FJ, (2004b) The β-esterase gene cluster of Drosophila melanogaster: Is ψEst-6 a pseudogene, a functional gene, or both? Genetica 121: 165-179.
-
(2004)
Genetica
, vol.121
, pp. 165-179
-
-
Balakirev, E.S.1
Ayala, F.J.2
-
28
-
-
26444593981
-
Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences
-
Xing Y, Lee C, (2005) Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci U S A 102: 13526-13531.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 13526-13531
-
-
Xing, Y.1
Lee, C.2
-
29
-
-
71749103442
-
Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information
-
Meireles-Filho ACA, Stark A, (2009) Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr Opin Genet Dev 19: 565-570.
-
(2009)
Curr Opin Genet Dev
, vol.19
, pp. 565-570
-
-
Meireles-Filho, A.C.A.1
Stark, A.2
-
30
-
-
0022211482
-
Statistical properties of the number of recombination events in the history of a sample of DNA sequences
-
Hudson RR, Kaplan N, (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
-
(1985)
Genetics
, vol.111
, pp. 147-164
-
-
Hudson, R.R.1
Kaplan, N.2
-
31
-
-
0024356449
-
Statistical tests for detecting gene conversion
-
Sawyer SA, (1989) Statistical tests for detecting gene conversion. Mol Biol Evol 6: 526-538.
-
(1989)
Mol Biol Evol
, vol.6
, pp. 526-538
-
-
Sawyer, S.A.1
-
32
-
-
0028215929
-
Evidence for positive selection in the superoxide dismutase Sod region of Drosophila melanogaster
-
Hudson RR, Bailey K, Skarecky D, Kwiatowski J, Ayala FJ, (1994) Evidence for positive selection in the superoxide dismutase Sod region of Drosophila melanogaster. Genetics 136: 1329-1340.
-
(1994)
Genetics
, vol.136
, pp. 1329-1340
-
-
Hudson, R.R.1
Bailey, K.2
Skarecky, D.3
Kwiatowski, J.4
Ayala, F.J.5
-
33
-
-
0030873114
-
A test of neutrality based on interlocus associations
-
Kelly JK, (1997) A test of neutrality based on interlocus associations. Genetics 146: 1197-1206.
-
(1997)
Genetics
, vol.146
, pp. 1197-1206
-
-
Kelly, J.K.1
-
34
-
-
0032884643
-
Recombination and the power of statistical tests of neutrality
-
Wall JD, (1999) Recombination and the power of statistical tests of neutrality. Genet Res 74: 65-79.
-
(1999)
Genet Res
, vol.74
, pp. 65-79
-
-
Wall, J.D.1
-
35
-
-
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.
-
(1989)
Genetics
, vol.123
, pp. 585-595
-
-
Tajima, F.1
-
36
-
-
0037123374
-
Molecular evolution of the Est-6 gene in Drosophila melanogaster: Contrasting patterns of DNA variability in adjacent functional regions
-
Balakirev ES, Balakirev EI, Ayala FJ, (2002) Molecular evolution of the Est-6 gene in Drosophila melanogaster: Contrasting patterns of DNA variability in adjacent functional regions. Gene 288: 167-177.
-
(2002)
Gene
, vol.288
, pp. 167-177
-
-
Balakirev, E.S.1
Balakirev, E.I.2
Ayala, F.J.3
-
37
-
-
0031805986
-
Statistical tests of neutrality in the age of weak selection
-
Wayne ML, Simonsen K, (1998) Statistical tests of neutrality in the age of weak selection. Trends Ecol Evol 13: 1292-1299.
-
(1998)
Trends Ecol Evol
, vol.13
, pp. 1292-1299
-
-
Wayne, M.L.1
Simonsen, K.2
-
38
-
-
0034809334
-
Statistical tests of selective neutrality in the age of genomics
-
Nielsen R, (2001) Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
-
(2001)
Heredity
, vol.86
, pp. 641-647
-
-
Nielsen, R.1
-
39
-
-
0034897709
-
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
-
Anisimova M, Bielawski JP, Yang Z, (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18: 1585-1592.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1585-1592
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
40
-
-
33645524118
-
Positive and negative selection in the β-esterase gene cluster of the Drosophila melanogaster subgroup
-
Balakirev ES, Anisimova M, Ayala FJ, (2006) Positive and negative selection in the β-esterase gene cluster of the Drosophila melanogaster subgroup. J Mol Evol 62: 496-510.
-
(2006)
J Mol Evol
, vol.62
, pp. 496-510
-
-
Balakirev, E.S.1
Anisimova, M.2
Ayala, F.J.3
-
41
-
-
34547739034
-
Widespread positive selection in synonymous sites of mammalian genes
-
Resch AM, Carmel L, Mariño-Ramírez L, Ogurtsov AY, Shabalina SA, et al. (2007) Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol 24: 1821-1831.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1821-1831
-
-
Resch, A.M.1
Carmel, L.2
Mariño-Ramírez, L.3
Ogurtsov, A.Y.4
Shabalina, S.A.5
-
42
-
-
30744469841
-
Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
-
Parmley JL, Chamary JV, Hurst LD, (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23: 301-309.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 301-309
-
-
Parmley, J.L.1
Chamary, J.V.2
Hurst, L.D.3
-
43
-
-
31144465926
-
Hearing silence: non-neutral evolution at synonymous sites in mammals
-
Chamary JV, Parmley JL, Hurst LD, (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7: 98-108.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 98-108
-
-
Chamary, J.V.1
Parmley, J.L.2
Hurst, L.D.3
-
44
-
-
0034924812
-
Folding of newly translated proteins in vivo: the role of molecular chaperones
-
Frydman J, (2001) Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 70: 603-647.
-
(2001)
Annu Rev Biochem
, vol.70
, pp. 603-647
-
-
Frydman, J.1
-
45
-
-
0028220048
-
Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy
-
Akashi H, (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136: 927-935.
-
(1994)
Genetics
, vol.136
, pp. 927-935
-
-
Akashi, H.1
-
46
-
-
0036889468
-
Evolution of synonymous codon usage in metazoans
-
Duret L, (2002) Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12: 640-649.
-
(2002)
Curr Opin Genet Dev
, vol.12
, pp. 640-649
-
-
Duret, L.1
-
47
-
-
77949447172
-
RNAstructure: software for RNA secondary structure prediction and analysis
-
Reuter JS, Mathews DH, (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11: 129.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 129
-
-
Reuter, J.S.1
Mathews, D.H.2
-
48
-
-
70350002307
-
Structural aspects of RNA helicases in eukaryotic mRNA decay
-
Ling SH, Cheng Z, Song H, (2009) Structural aspects of RNA helicases in eukaryotic mRNA decay. Biosci Rep 29: 339-349.
-
(2009)
Biosci Rep
, vol.29
, pp. 339-349
-
-
Ling, S.H.1
Cheng, Z.2
Song, H.3
-
49
-
-
0030266993
-
RNA structure and the regulation of gene expression
-
Klaff P, Riesner D, Steger G, (1996) RNA structure and the regulation of gene expression. Plant Mol Biol 32: 89-106.
-
(1996)
Plant Mol Biol
, vol.32
, pp. 89-106
-
-
Klaff, P.1
Riesner, D.2
Steger, G.3
-
50
-
-
68949101233
-
Post-transcriptional regulation of gene expression in plants during abiotic stress
-
Floris M, Mahgoub H, Lanet E, Robaglia C, Menand B, (2009) Post-transcriptional regulation of gene expression in plants during abiotic stress. Int J Mol Sci 10: 3168-3185.
-
(2009)
Int J Mol Sci
, vol.10
, pp. 3168-3185
-
-
Floris, M.1
Mahgoub, H.2
Lanet, E.3
Robaglia, C.4
Menand, B.5
-
51
-
-
33845899137
-
Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
-
Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, et al. (2006) Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314: 1930-1933.
-
(2006)
Science
, vol.314
, pp. 1930-1933
-
-
Nackley, A.G.1
Shabalina, S.A.2
Tchivileva, I.E.3
Satterfield, K.4
Korchynskyi, O.5
-
52
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla G, Murray AW, Tollervey D, Plotkin JB, (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science 324: 255-258.
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
53
-
-
79960666882
-
Genomic adaptation of prokaryotic organisms at high temperature
-
Basak S, Mukhopadhyay P, Gupta SK, Ghosh TC, (2010) Genomic adaptation of prokaryotic organisms at high temperature. Bioinformation 4: 352-356.
-
(2010)
Bioinformation
, vol.4
, pp. 352-356
-
-
Basak, S.1
Mukhopadhyay, P.2
Gupta, S.K.3
Ghosh, T.C.4
-
54
-
-
33846510838
-
Large-scale discovery of promoter motifs in Drosophila melanogaster
-
doi:10.1371/journal.pcbi.0030007
-
Down TA, Bergman CM, Hubbard TJP, (2007) Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput Biol 31: e7 doi:10.1371/journal.pcbi.0030007.
-
(2007)
PLoS Comput Biol
, vol.31
-
-
Down, T.A.1
Bergman, C.M.2
Hubbard, T.J.P.3
-
55
-
-
34249676873
-
ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors
-
Papatsenko D, (2007) ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors. Bioinformatics 23: 1032-1034.
-
(2007)
Bioinformatics
, vol.23
, pp. 1032-1034
-
-
Papatsenko, D.1
-
56
-
-
0029026878
-
Maintenance of pre-mRNA secondary structure by epistatic selection
-
Kirby DA, Muse SV, Stephan W, (1995) Maintenance of pre-mRNA secondary structure by epistatic selection. Proc Natl Acad U S A 92: 9047-9051.
-
(1995)
Proc Natl Acad U S A
, vol.92
, pp. 9047-9051
-
-
Kirby, D.A.1
Muse, S.V.2
Stephan, W.3
-
57
-
-
52449148668
-
The role of compensatory neutral mutations in molecular evolution
-
Kimura M, (1985) The role of compensatory neutral mutations in molecular evolution. J Genet 64: 7-19.
-
(1985)
J Genet
, vol.64
, pp. 7-19
-
-
Kimura, M.1
-
58
-
-
34250212837
-
How do synonymous mutations affect fitness?
-
Parmley JL, Hurst LD, (2007) How do synonymous mutations affect fitness? BioEssays 29: 515-519.
-
(2007)
BioEssays
, vol.29
, pp. 515-519
-
-
Parmley, J.L.1
Hurst, L.D.2
-
60
-
-
78650304100
-
Synonymous but not the same: the causes and consequences of codon bias
-
Plotkin JB, Kudla G, (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 12: 32-42.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 32-42
-
-
Plotkin, J.B.1
Kudla, G.2
-
61
-
-
0028797897
-
Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA
-
Akashi H, (1995) Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139: 1067-1076.
-
(1995)
Genetics
, vol.139
, pp. 1067-1076
-
-
Akashi, H.1
-
62
-
-
1842570367
-
DNA variability and divergence at the Notch locus in Drosophila melanogaster and D. simulans: A case of accelerated synonymous site divergence
-
Bauer DuMont VL, Fay JC, Calabrese PP, Aquadro CF, (2004) DNA variability and divergence at the Notch locus in Drosophila melanogaster and D. simulans: A case of accelerated synonymous site divergence. Genetics 167: 171-185.
-
(2004)
Genetics
, vol.167
, pp. 171-185
-
-
Bauer DuMont, V.L.1
Fay, J.C.2
Calabrese, P.P.3
Aquadro, C.F.4
-
63
-
-
77951529989
-
Locus-specific decoupling of base composition evolution at synonymous sites and introns along the Drosophila melanogaster and Drosophila sechellia lineages
-
Bauer DuMont VL, Singh ND, Wright MH, Aquadro CF, (2009) Locus-specific decoupling of base composition evolution at synonymous sites and introns along the Drosophila melanogaster and Drosophila sechellia lineages. Genome Biol Evol 2009: 67-74.
-
(2009)
Genome Biol Evol
, vol.2009
, pp. 67-74
-
-
Bauer DuMont, V.L.1
Singh, N.D.2
Wright, M.H.3
Aquadro, C.F.4
-
64
-
-
33845898825
-
Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila
-
Nielsen R, Bauer DuMont VL, Hubisz MJ, Aquadro CF, (2007) Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila. Mol Biol Evol 24: 228-235.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 228-235
-
-
Nielsen, R.1
Bauer DuMont, V.L.2
Hubisz, M.J.3
Aquadro, C.F.4
-
65
-
-
53549094945
-
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
-
Holloway AK, Begun DJ, Siepel A, Pollard KS, (2008) Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res 18: 1592-1601.
-
(2008)
Genome Res
, vol.18
, pp. 1592-1601
-
-
Holloway, A.K.1
Begun, D.J.2
Siepel, A.3
Pollard, K.S.4
-
66
-
-
34547657193
-
Positive selection for unpreferred codon usage in eukaryotic genomes
-
DOI:10.1186/1471-2148-7-119
-
Neafsey DE, Galagan JE, (2007) Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol 7: 119 DOI:10.1186/1471-2148-7-119.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 119
-
-
Neafsey, D.E.1
Galagan, J.E.2
-
67
-
-
37549022289
-
Patterns of mutation and selection at synonymous sites in Drosophila
-
Singh ND, Bauer DuMont VL, Hubisz MJ, Nielsen R, Aquadro CF, (2007) Patterns of mutation and selection at synonymous sites in Drosophila. Mol Biol Evol 24: 2687-2697.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 2687-2697
-
-
Singh, N.D.1
Bauer DuMont, V.L.2
Hubisz, M.J.3
Nielsen, R.4
Aquadro, C.F.5
-
68
-
-
0021742961
-
Translationally associated helix-destabilizing activity in rabbit reticulocyte lysate
-
Leibhaber SA, Cash FE, Shakin SH, (1984) Translationally associated helix-destabilizing activity in rabbit reticulocyte lysate. J Biol Chem 259: 15597-15602.
-
(1984)
J Biol Chem
, vol.259
, pp. 15597-15602
-
-
Leibhaber, S.A.1
Cash, F.E.2
Shakin, S.H.3
-
70
-
-
27844569825
-
Site-to-site variation of synonymous substitution rates
-
Kosakovsky Pond SL, Muse SV, (2005) Site-to-site variation of synonymous substitution rates. Mol Biol Evol 22: 2375-2385.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2375-2385
-
-
Kosakovsky Pond, S.L.1
Muse, S.V.2
-
71
-
-
0028151259
-
Haplotype divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: roles for both balancing and directional selection?
-
Hanfstingl U, Berry A, Kellogg EA, Costa JT 3rd, Rüdiger W W, et al. (1994) Haplotype divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: roles for both balancing and directional selection? Genetics 138: 811-828.
-
(1994)
Genetics
, vol.138
, pp. 811-828
-
-
Hanfstingl, U.1
Berry, A.2
Kellogg, E.A.3
Costa 3rd, J.T.4
Rüdiger W, W.5
-
72
-
-
0036240921
-
Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway
-
Olsen KM, Womack A, Garrett AR, Suddith JI, Purugganan MD, (2002) Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway. Genetics 160: 1641-1650.
-
(2002)
Genetics
, vol.160
, pp. 1641-1650
-
-
Olsen, K.M.1
Womack, A.2
Garrett, A.R.3
Suddith, J.I.4
Purugganan, M.D.5
-
73
-
-
0032978833
-
Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila
-
Aguadé M, (1999) Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila. Genetics 152: 543-551.
-
(1999)
Genetics
, vol.152
, pp. 543-551
-
-
Aguadé, M.1
-
74
-
-
0035148464
-
Nucleotide polymorphism and natural selection at the Pantophysin Pan I locus in the Atlantic cod, Gadus morhua L
-
Pogson GH, (2001) Nucleotide polymorphism and natural selection at the Pantophysin Pan I locus in the Atlantic cod, Gadus morhua L. Genetics 157: 317-330.
-
(2001)
Genetics
, vol.157
, pp. 317-330
-
-
Pogson, G.H.1
-
75
-
-
60149105525
-
Balancing and directional selection at exon-2 of the MHC DQB1 locus among populations of odontocete cetaceans
-
Vassilakos D, Natoli A, Dahlheim M, Hoelzel R, (2009) Balancing and directional selection at exon-2 of the MHC DQB1 locus among populations of odontocete cetaceans. Mol Biol Evol 26: 681-689.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 681-689
-
-
Vassilakos, D.1
Natoli, A.2
Dahlheim, M.3
Hoelzel, R.4
-
76
-
-
67649560886
-
A complex selection signature at the human AVPRIB gene
-
Cagliani R, Fumagalli M, Pozzoli U, Riva S, Cereda M, et al. (2009) A complex selection signature at the human AVPRIB gene. BMC Evol Biol 9: 123.
-
(2009)
BMC Evol Biol
, vol.9
, pp. 123
-
-
Cagliani, R.1
Fumagalli, M.2
Pozzoli, U.3
Riva, S.4
Cereda, M.5
-
78
-
-
1842575602
-
How two Afrotropical endemics made two cosmopolitan human commensals: the Drosophila melanogaster-D. simulans palaeogeographic riddle
-
Lachaise D, Silvain JF, (2004) How two Afrotropical endemics made two cosmopolitan human commensals: the Drosophila melanogaster-D. simulans palaeogeographic riddle. Genetica 120: 17-39.
-
(2004)
Genetica
, vol.120
, pp. 17-39
-
-
Lachaise, D.1
Silvain, J.F.2
-
79
-
-
22344444998
-
Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations
-
Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P, (2005) Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15: 790-799.
-
(2005)
Genome Res
, vol.15
, pp. 790-799
-
-
Haddrill, P.R.1
Thornton, K.R.2
Charlesworth, B.3
Andolfatto, P.4
-
80
-
-
33846589670
-
The recent demographic and adaptive history of Drosophila melanogaster
-
Stephan W, Li H, (2007) The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98: 65-68.
-
(2007)
Heredity
, vol.98
, pp. 65-68
-
-
Stephan, W.1
Li, H.2
-
81
-
-
0032753344
-
Molecular evolution of two linked genes, Est-6 and Sod, in Drosophila melanogaster
-
Balakirev ES, Balakirev EI, Rodriguez-Trelles F, Ayala FJ, (1999) Molecular evolution of two linked genes, Est-6 and Sod, in Drosophila melanogaster. Genetics 153: 1357-1369.
-
(1999)
Genetics
, vol.153
, pp. 1357-1369
-
-
Balakirev, E.S.1
Balakirev, E.I.2
Rodriguez-Trelles, F.3
Ayala, F.J.4
-
82
-
-
0020641432
-
Expected linkage disequilibrium for a neutral locus linked to a chromosomal arrangement
-
Strobeck C, (1983) Expected linkage disequilibrium for a neutral locus linked to a chromosomal arrangement. Genetics 103: 545-555.
-
(1983)
Genetics
, vol.103
, pp. 545-555
-
-
Strobeck, C.1
-
83
-
-
0023760376
-
The coalescent process in models with selection and recombination
-
Hudson RR, Kaplan N, (1988) The coalescent process in models with selection and recombination. Genetics 120: 831-840.
-
(1988)
Genetics
, vol.120
, pp. 831-840
-
-
Hudson, R.R.1
Kaplan, N.2
-
84
-
-
0023815589
-
The coalescent process in models with selection
-
Kaplan NL, Darden T, Hudson RR, (1988) The coalescent process in models with selection. Genetics 120: 819-29.
-
(1988)
Genetics
, vol.120
, pp. 819-829
-
-
Kaplan, N.L.1
Darden, T.2
Hudson, R.R.3
-
85
-
-
33646484211
-
Balancing selection and its effects on sequences in nearby genome regions
-
DOI:10.1371/journal.pgen.0020064
-
Charlesworth D, (2006) Balancing selection and its effects on sequences in nearby genome regions. PLoS Genet 2 (4): e64 DOI:10.1371/journal.pgen.0020064.
-
(2006)
PLoS Genet
, vol.2
, Issue.4
-
-
Charlesworth, D.1
-
86
-
-
0031450133
-
The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations
-
Charlesworth B, Nordborg M, Charlesworth D, (1997) The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genet Res 70: 155-174.
-
(1997)
Genet Res
, vol.70
, pp. 155-174
-
-
Charlesworth, B.1
Nordborg, M.2
Charlesworth, D.3
-
87
-
-
0020402291
-
Chromosome interactions in Drosophila melanogaster. I. Viability studies
-
Seager RD, Ayala FJ, (1982) Chromosome interactions in Drosophila melanogaster. I. Viability studies. Genetics 102: 467-483.
-
(1982)
Genetics
, vol.102
, pp. 467-483
-
-
Seager, R.D.1
Ayala, F.J.2
-
88
-
-
0027968068
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
89
-
-
0347513220
-
DnaSP, DNA polymorphism analyses by the coalescent and other methods
-
Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R, (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
-
(2003)
Bioinformatics
, vol.19
, pp. 2496-2497
-
-
Rozas, J.1
Sánchez-DelBarrio, J.C.2
Messeguer, X.3
Rozas, R.4
-
90
-
-
0036899966
-
PROSEQ: a software for preparation and evolutionary analysis of DNA sequence data sets
-
Filatov DA, (2002) PROSEQ: a software for preparation and evolutionary analysis of DNA sequence data sets. Mol Ecol Notes 2: 621-624.
-
(2002)
Mol Ecol Notes
, vol.2
, pp. 621-624
-
-
Filatov, D.A.1
-
91
-
-
0023339852
-
A test of neutral molecular evolution based on nucleotide data
-
Hudson RR, Kreitman M, Aguadé M, (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
-
(1987)
Genetics
, vol.116
, pp. 153-159
-
-
Hudson, R.R.1
Kreitman, M.2
Aguadé, M.3
-
92
-
-
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.
-
(1991)
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
93
-
-
0020744702
-
Properties of a neutral allele model with intragenic recombination
-
Hudson RR, (1983) Properties of a neutral allele model with intragenic recombination. Theor Popul Biol 23: 183-201.
-
(1983)
Theor Popul Biol
, vol.23
, pp. 183-201
-
-
Hudson, R.R.1
-
94
-
-
0001935493
-
Gene genealogies and the coalescent process
-
Hudson RR, (1990) Gene genealogies and the coalescent process. Oxf Surv Biol 7: 1-44.
-
(1990)
Oxf Surv Biol
, vol.7
, pp. 1-44
-
-
Hudson, R.R.1
-
95
-
-
0036184745
-
Generating samples under a Wright-Fisher neutral model of genetic variation
-
Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
-
(2002)
Bioinformatics
, vol.18
, pp. 337-338
-
-
Hudson, R.R.1
-
96
-
-
0026512283
-
A statistical test for detecting geographic subdivision
-
Hudson RR, Boos D, Kaplan NL, (1992) A statistical test for detecting geographic subdivision. Mol Biol Evol 9: 138-151.
-
(1992)
Mol Biol Evol
, vol.9
, pp. 138-151
-
-
Hudson, R.R.1
Boos, D.2
Kaplan, N.L.3
-
97
-
-
0036199914
-
A coalescent-based method for detecting and estimating recombination from gene sequences
-
McVean G, Awadalla P, Fearnhead P, (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
-
(2002)
Genetics
, vol.160
, pp. 1231-1241
-
-
McVean, G.1
Awadalla, P.2
Fearnhead, P.3
-
98
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang Z, Nielsen R, Goldman N, Pedersen AM, (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.M.4
-
99
-
-
39749161509
-
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
-
Yang Z, Nielsen R, (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25: 568-579.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 568-579
-
-
Yang, Z.1
Nielsen, R.2
-
100
-
-
34547803197
-
PAML 4: phylogenetic analysis by maximum likelihood
-
Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
101
-
-
58449116673
-
Investigating protein-coding sequence evolution with probabilistic codon substitution models
-
Anisimova M, Kosiol C, (2009) Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol 26: 255-271.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 255-271
-
-
Anisimova, M.1
Kosiol, C.2
-
102
-
-
3142739466
-
Detecting selection in noncoding regions of nucleotide sequences
-
Wong WS, Nielsen R, (2004) Detecting selection in noncoding regions of nucleotide sequences. Genetics 167: 949-958.
-
(2004)
Genetics
, vol.167
, pp. 949-958
-
-
Wong, W.S.1
Nielsen, R.2
-
103
-
-
16344378246
-
Bayes empirical bayes inference of amino acid sites under positive selection
-
Yang Z, Wong WS, Nielsen R, (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22: 1107-1118.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1107-1118
-
-
Yang, Z.1
Wong, W.S.2
Nielsen, R.3
-
104
-
-
0004275709
-
Molecular Evolutionary Genetics
-
New York, Columbia University Press
-
Nei M, (1987) Molecular Evolutionary Genetics. New York Columbia University Press.
-
(1987)
-
-
Nei, M.1
-
105
-
-
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 10: 256-276.
-
(1975)
Theor Popul Biol
, vol.10
, pp. 256-276
-
-
Watterson, G.A.1
|