-
1
-
-
0024389204
-
Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus
-
Crawford DL, Powers DA (1989) Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus. Proc Natl Acad Sci U S A 86: 9365-9369.
-
(1989)
Proc Natl Acad Sci U S A
, vol.86
, pp. 9365-9369
-
-
Crawford, D.L.1
Powers, D.A.2
-
2
-
-
0036812208
-
Nucleotide polymorphism in the Est6 promoter, which is widespread in derived populations of Drosophila melanogaster, changes the level of Esterase 6 expressed in the male ejaculatory duct
-
Odgers WA, Aquadro CF, Coppin CW, Healy MJ, Oakeshott JG (2002) Nucleotide polymorphism in the Est6 promoter, which is widespread in derived populations of Drosophila melanogaster, changes the level of Esterase 6 expressed in the male ejaculatory duct. Genetics 162: 785-797.
-
(2002)
Genetics
, vol.162
, pp. 785-797
-
-
Odgers, W.A.1
Aquadro, C.F.2
Coppin, C.W.3
Healy, M.J.4
Oakeshott, J.G.5
-
3
-
-
19344372220
-
A neutral model of transcriptome evolution
-
doi:10.1371/journal.pbio.0020132
-
Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, et al. (2004) A neutral model of transcriptome evolution. PLoS Biol 2: e132. doi:10.1371/journal.pbio.0020132
-
(2004)
PLoS Biol
, vol.2
-
-
Khaitovich, P.1
Weiss, G.2
Lachmann, M.3
Hellmann, I.4
Enard, W.5
-
4
-
-
33644855479
-
Expression profiling in primates reveals a rapid evolution of human transcription factors
-
Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245.
-
(2006)
Nature
, vol.440
, pp. 242-245
-
-
Gilad, Y.1
Oshlack, A.2
Smyth, G.K.3
Speed, T.P.4
White, K.P.5
-
5
-
-
0037313182
-
Evolution of gene expression in the Drosophila melanogaster subgroup
-
Rifkin SA, Kim J, White KP (2003) Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 33: 138-144.
-
(2003)
Nat Genet
, vol.33
, pp. 138-144
-
-
Rifkin, S.A.1
Kim, J.2
White, K.P.3
-
6
-
-
3042591076
-
Common pattern of evolution of gene expression level and protein sequence in Drosophila
-
Nuzhdin SV, Wayne ML, Harmon KL, McIntyre LM (2004) Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol 21: 1308-1317.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1308-1317
-
-
Nuzhdin, S.V.1
Wayne, M.L.2
Harmon, K.L.3
McIntyre, L.M.4
-
8
-
-
33646882592
-
Adaptive protein evolution and regulatory divergence in Drosophila
-
Good JM, Hayden CA, Wheeler TJ (2006) Adaptive protein evolution and regulatory divergence in Drosophila. Mol Biol Evol 23: 1101-1103.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1101-1103
-
-
Good, J.M.1
Hayden, C.A.2
Wheeler, T.J.3
-
9
-
-
33646568791
-
Positive selection on gene expression in the human brain
-
Khaitovich P, Tang K, Franz H, Kelso J, Hellmann I, et al. (2006) Positive selection on gene expression in the human brain. Curr Biol 16: R356-358.
-
(2006)
Curr Biol
, vol.16
-
-
Khaitovich, P.1
Tang, K.2
Franz, H.3
Kelso, J.4
Hellmann, I.5
-
10
-
-
35948995392
-
Coordinated evolution of coexpression gene clusters in the Drosophila transcriptome
-
In press
-
Mezey JG, Nuzhdin SV, Ye F, Jones CD (2007) Coordinated evolution of coexpression gene clusters in the Drosophila transcriptome. BMC Bioinformatics. In press.
-
(2007)
BMC Bioinformatics
-
-
Mezey, J.G.1
Nuzhdin, S.V.2
Ye, F.3
Jones, C.D.4
-
11
-
-
35948940895
-
Population genomics: Whole-genome analysis of polymorphism and divergence in Drosophila simulans
-
doi:10.1371/journal.pbio. 0050310
-
Begun DJ, Holloway AK, Stevens KS, Hiller LW, Poh Y, Stevens KS, et al. (2007) Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 5: e310. doi:10.1371/journal.pbio. 0050310
-
(2007)
PLoS Biol
, vol.5
-
-
Begun, D.J.1
Holloway, A.K.2
Stevens, K.S.3
Hiller, L.W.4
Poh, Y.5
Stevens, K.S.6
-
12
-
-
0034708480
-
The genome sequence of Drosophila melanogaster
-
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, et al. (2000) The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
-
(2000)
Science
, vol.287
, pp. 2185-2195
-
-
Adams, M.D.1
Celniker, S.E.2
Holt, R.A.3
Evans, C.A.4
Gocayne, J.D.5
-
13
-
-
0016220238
-
The hitch-hiking effect of a favourable gene
-
Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
-
(1974)
Genet Res
, vol.23
, pp. 23-35
-
-
Maynard Smith, J.1
Haigh, J.2
-
14
-
-
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
-
15
-
-
19844365733
-
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
-
Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP (2005) Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res 15: 674-680.
-
(2005)
Genome Res
, vol.15
, pp. 674-680
-
-
Gilad, Y.1
Rifkin, S.A.2
Bertone, P.3
Gerstein, M.4
White, K.P.5
-
16
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, et al. (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20: 1377-1419.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
-
17
-
-
0029988881
-
Control of messenger RNA stability in higher eukaryotes
-
Ross J (1996) Control of messenger RNA stability in higher eukaryotes. Trends Genet 12: 171-175.
-
(1996)
Trends Genet
, vol.12
, pp. 171-175
-
-
Ross, J.1
-
18
-
-
0038343499
-
MicroRNA pathways in flies and worms: Growth, death, fat, stress, and timing
-
Ambros V (2003) MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113: 673-676.
-
(2003)
Cell
, vol.113
, pp. 673-676
-
-
Ambros, V.1
-
20
-
-
33644750115
-
miRBase: MicroRNA sequences, targets and gene nomenclature
-
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140-D144.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Griffiths-Jones, S.1
Grocock, R.J.2
van Dongen, S.3
Bateman, A.4
Enright, A.J.5
-
21
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pal C, Papp B, Hurst LD (2001) Highly expressed genes in yeast evolve slowly. Genetics 158: 927-931.
-
(2001)
Genetics
, vol.158
, pp. 927-931
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
22
-
-
0041817645
-
Translational selection and yeast proteome evolution
-
Akashi H (2003) Translational selection and yeast proteome evolution. Genetics 164: 1291-1303.
-
(2003)
Genetics
, vol.164
, pp. 1291-1303
-
-
Akashi, H.1
-
23
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH (2005) Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A 102: 14338-14343.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
24
-
-
0037472685
-
Serine proteases and their homologs in the Drosophila melanogaster genome: An initial analysis of sequence conservation and phylogenetic relationships
-
Ross J, Jiang H, Kanost MR, Wang Y (2003) Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships. Gene 304: 117-131.
-
(2003)
Gene
, vol.304
, pp. 117-131
-
-
Ross, J.1
Jiang, H.2
Kanost, M.R.3
Wang, Y.4
-
25
-
-
27144491328
-
Adaptive evolution of non-coding DNA in Drosophila
-
Andolfatto P (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
-
(2005)
Nature
, vol.437
, pp. 1149-1152
-
-
Andolfatto, P.1
-
26
-
-
1542347028
-
Inference of positive and negative selection on the 59 regulatory regions of Drosophila genes
-
Kohn MH, Fang S, Wu CI (2004) Inference of positive and negative selection on the 59 regulatory regions of Drosophila genes. Mol Biol Evol 21: 374-383.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 374-383
-
-
Kohn, M.H.1
Fang, S.2
Wu, C.I.3
-
27
-
-
33745583768
-
A genetic signature of interspecies variations in gene expression
-
Tirosh I, Weinberger A, Carmi M, Barkai N (2006) A genetic signature of interspecies variations in gene expression. Nat Genet 38: 830-834.
-
(2006)
Nat Genet
, vol.38
, pp. 830-834
-
-
Tirosh, I.1
Weinberger, A.2
Carmi, M.3
Barkai, N.4
-
28
-
-
0037504137
-
Sex-dependent gene expression and evolution of the Drosophila transcriptome
-
Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL (2003) Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300: 1742-1745.
-
(2003)
Science
, vol.300
, pp. 1742-1745
-
-
Ranz, J.M.1
Castillo-Davis, C.I.2
Meiklejohn, C.D.3
Hartl, D.L.4
-
30
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
-
31
-
-
0031417707
-
Likelihood of ancestor states in adaptive radiation
-
Schluter D, Price T, Mooers AO, Ludwig D (1997) Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711.
-
(1997)
Evolution
, vol.51
, pp. 1699-1711
-
-
Schluter, D.1
Price, T.2
Mooers, A.O.3
Ludwig, D.4
-
32
-
-
35949000143
-
-
Efron B, Tibshirani RJ (1993) An introduction to the bootstrap.Cox DR, Hinkley DV, Reid N, Rubin DB, Silverman BWeditors. Boca Raton (Florida): Chapman & Hall/CRC.
-
Efron B, Tibshirani RJ (1993) An introduction to the bootstrap.Cox DR, Hinkley DV, Reid N, Rubin DB, Silverman BWeditors. Boca Raton (Florida): Chapman & Hall/CRC.
-
-
-
-
33
-
-
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.
-
(1986)
Mol Biol Evol
, vol.3
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
34
-
-
0028267146
-
Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
-
Yang Z, Goldman N, Friday A (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol 11: 316-324.
-
(1994)
Mol Biol Evol
, vol.11
, pp. 316-324
-
-
Yang, Z.1
Goldman, N.2
Friday, A.3
-
35
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611-1618.
-
(2002)
Genome Res
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
-
36
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
-
(1985)
J Mol Evol
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
37
-
-
0030000951
-
Excess amino acid polymorphism in mitochondrial DNA: Contrasts among genes from Drosophila, mice, and humans
-
Rand DM, Kann LM (1996) Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol 13: 735-748.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 735-748
-
-
Rand, D.M.1
Kann, L.M.2
-
38
-
-
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
|