-
1
-
-
0013092230
-
-
(eds Bryson V. & Vogel H.) Academic Press, New York
-
Zuckerkandl, E. & Pauling, L. in Evolving Genes and Proteins (eds Bryson, V. & Vogel, H.) 97-166 (Academic Press, New York, 1965).
-
(1965)
Evolving Genes and Proteins
, pp. 97-166
-
-
Zuckerkandl, E.1
Pauling, L.2
-
2
-
-
0014690698
-
Gene regulation for higher cells: A theory
-
Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349-357 (1969).
-
(1969)
Science
, vol.165
, pp. 349-357
-
-
Britten, R.J.1
Davidson, E.H.2
-
3
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King, M.-C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107-116 (1975).
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.-C.1
Wilson, A.C.2
-
4
-
-
46149104377
-
Evo-devo and an expanding evolutionary syn thesis: A genetic theory of morphological evolution
-
Carroll, S. B. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134, 25-36 (2008).
-
(2008)
Cell
, vol.134
, pp. 25-36
-
-
Carroll, S.B.1
-
5
-
-
51249106485
-
The loci of evolution: How predictable is genetic evolution?
-
Stern, D. L. & Orgogozo, V. The loci of evolution: how predictable is genetic evolution? Evolution 62, 2155-2177 (2008).
-
(2008)
Evolution
, vol.62
, pp. 2155-2177
-
-
Stern, D.L.1
Orgogozo, V.2
-
6
-
-
79952901680
-
Enhancer function: New insights into the regulation of tissue-specific gene expression
-
Ong, C.-T. & Corces, V. G. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nature Rev. Genet. 12, 283-293 (2011).
-
(2011)
Nature Rev. Genet.
, vol.12
, pp. 283-293
-
-
Ong, C.-T.1
Corces, V.G.2
-
7
-
-
77956495708
-
Transcriptional enhancers in animal development and evolution
-
Levine, M. Transcriptional enhancers in animal development and evolution. Curr. Biol. 20, R754-R763 (2010).
-
(2010)
Curr. Biol.
, vol.20
-
-
Levine, M.1
-
8
-
-
79551655285
-
Functional and mechanistic diversity of distal transcription enhancers
-
Bulger, M. & Groudine, M. Functional and mechanistic diversity of distal transcription enhancers. Cell 144, 327-339 (2011).
-
(2011)
Cell
, vol.144
, pp. 327-339
-
-
Bulger, M.1
Groudine, M.2
-
9
-
-
25444493843
-
Reverse transcriptional profiling: Non-correspondence of transcript level variation and proximal promoter polymorphism
-
Brown, R. P. & Feder, M. E. Reverse transcriptional profiling: non-correspondence of transcript level variation and proximal promoter polymorphism. BMC Genomics 6, 110 (2005).
-
(2005)
BMC Genomics
, vol.6
, pp. 110
-
-
Brown, R.P.1
Feder, M.E.2
-
10
-
-
60949088064
-
TATA box polymorphisms in human gene promoters and associated hereditary pathologies
-
Savinkova, L. K. et al. TATA box polymorphisms in human gene promoters and associated hereditary pathologies. Biochemistry 74, 117-129 (2009).
-
(2009)
Biochemistry
, vol.74
, pp. 117-129
-
-
Savinkova, L.K.1
-
11
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
Wray, G. A. The evolutionary significance of cis-regulatory mutations. Nature Rev. Genet. 8, 206-216 (2007).
-
(2007)
Nature Rev. Genet.
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
12
-
-
51149097760
-
Shadow enhancers as a source of evolutionary novelty
-
Hong, J. W., Hendrix, D. A. & Levine, M. S. Shadow enhancers as a source of evolutionary novelty. Science 321, 1314 (2008).
-
(2008)
Science
, vol.321
, pp. 1314
-
-
Hong, J.W.1
Hendrix, D.A.2
Levine, M.S.3
-
13
-
-
77956521381
-
Shadow enhancers foster robustness of Drosophila gastrulation
-
Perry, M. W., Boettiger, A. N., Bothma, J. P. & Levine, M. Shadow enhancers foster robustness of Drosophila gastrulation. Current Biol. 20, 1562-1567 (2010).
-
(2010)
Current Biol
, vol.20
, pp. 1562-1567
-
-
Perry, M.W.1
Boettiger, A.N.2
Bothma, J.P.3
Levine, M.4
-
14
-
-
11144339384
-
Long-range control of gene expression: Emerging mechanisms and disruption in disease
-
Kleinjan, D. A. & van Heyningen, V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8-32 (2005).
-
(2005)
Am. J. Hum. Genet.
, vol.76
, pp. 8-32
-
-
Kleinjan, D.A.1
Van Heyningen, V.2
-
15
-
-
46249134068
-
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
-
Hare, E. E., Peterson, B. K., Iyer, V. N., Meier, R. & Eisen, M. B. Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet. 4, e1000106 (2008).
-
(2008)
PLoS Genet
, vol.4
-
-
Hare, E.E.1
Peterson, B.K.2
Iyer, V.N.3
Meier, R.4
Eisen, M.B.5
-
16
-
-
70149102036
-
Conservation of enhancer location in divergent insects
-
Cande, J., Goltsev, Y. & Levine, M. S. Conservation of enhancer location in divergent insects. Proc. Natl Acad. Sci. USA 106, 14414-14419, (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 14414-14419
-
-
Cande, J.1
Goltsev, Y.2
Levine, M.S.3
-
17
-
-
78649716038
-
Nomadic enhancers: Tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species
-
Kalay, G. & Wittkopp, P. J. Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLoS Genet. 6, e1001222 (2010).
-
(2010)
PLoS Genet
, vol.6
-
-
Kalay, G.1
Wittkopp, P.J.2
-
18
-
-
0036843938
-
Detection of regulatory variation in mouse genes
-
Cowles, C. R., Hirschhorn, J. N., Altshuler, D. & Lander, E. S. Detection of regulatory variation in mouse genes. Nature Genet. 32, 432-437 (2002).
-
(2002)
Nature Genet
, vol.32
, pp. 432-437
-
-
Cowles, C.R.1
Hirschhorn, J.N.2
Altshuler, D.3
Lander, E.S.4
-
19
-
-
3042722019
-
Evolutionary changes in cis and trans gene regulation
-
Wittkopp, P. J., Haerum, B. K. & Clark, A. G. Evolutionary changes in cis and trans gene regulation. Nature 430, 85-88 (2004).
-
(2004)
Nature
, vol.430
, pp. 85-88
-
-
Wittkopp, P.J.1
Haerum, B.K.2
Clark, A.G.3
-
20
-
-
65549086559
-
A yeast hybrid provides insight into the evolution of gene expression regulation
-
Tirosh, I., Reikhav, S., Levy, A. A. & Barkai, N. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324, 659-662 (2009).
-
(2009)
Science
, vol.324
, pp. 659-662
-
-
Tirosh, I.1
Reikhav, S.2
Levy, A.A.3
Barkai, N.4
-
21
-
-
77953010033
-
Regulatory divergence in Drosophila revealed by mRNA-seq
-
McManus, C. J. et al. Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res. 20, 816-825 (2010).
-
(2010)
Genome Res
, vol.20
, pp. 816-825
-
-
McManus, C.J.1
-
22
-
-
63549135783
-
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution
-
He, X., Ling, X. & Sinha, S. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution. PLoS Comput. Biol. 5, e1000299 (2009).
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
He, X.1
Ling, X.2
Sinha, S.3
-
23
-
-
0037208166
-
Transfac: Transcriptional regulation, from patterns to profiles
-
Matys, V. et al. Transfac: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378 (2003).
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 374-378
-
-
Matys, V.1
-
24
-
-
78651272522
-
Yeastract: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface
-
Abdulrehman, D. et al. Yeastract: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res. 39, D136-D140 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Abdulrehman, D.1
-
25
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
Roy, S. et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797 (2010).
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
Roy, S.1
-
26
-
-
78650410139
-
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
-
Gerstein, M. B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775-1787 (2010).
-
(2010)
Science
, vol.330
, pp. 1775-1787
-
-
Gerstein, M.B.1
-
27
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009).
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
-
28
-
-
78651320424
-
The UCSC Genome Browser database: Update 2011
-
Fujita, P. A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876-D882 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Fujita, P.A.1
-
29
-
-
36849073678
-
Sequencing breakthroughs for genomic ecology and evolutionary biology
-
Hudson, M. E. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol. Ecol. Res. 8, 3-17 (2008).
-
(2008)
Mol. Ecol. Res.
, vol.8
, pp. 3-17
-
-
Hudson, M.E.1
-
30
-
-
26644453335
-
Simple and highly efficient BAC recombineering using GalK selection
-
Warming, S., Costantino, N., Court, D. L., Jenkins, N. A. & Copeland, N. G. Simple and highly efficient BAC recombineering using GalK selection. Nucleic Acids Res. 33, e36 (2005).
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Warming, S.1
Costantino, N.2
Court, D.L.3
Jenkins, N.A.4
Copeland, N.G.5
-
31
-
-
77956535595
-
The art of reporter proteins in science: Past, present and future applications
-
Ghim, C. M., Lee, S. K., Takayama, S. & Mitchell, R. J. The art of reporter proteins in science: past, present and future applications. BMB Reports 43, 451-460 (2010).
-
(2010)
BMB Reports
, vol.43
, pp. 451-460
-
-
Ghim, C.M.1
Lee, S.K.2
Takayama, S.3
Mitchell, R.J.4
-
32
-
-
2442458847
-
Construction of transgenic Drosophila by using the site-specific integrase from phage PhiC31
-
Groth, A. C., Fish., M., Nusse, R. & Calos, M. P. Construction of transgenic Drosophila by using the site-specific integrase from phage PhiC31. Genetics 166, 1775-1782 (2004).
-
(2004)
Genetics
, vol.166
, pp. 1775-1782
-
-
Groth, A.C.1
Fish, M.2
Nusse, R.3
Calos, M.P.4
-
33
-
-
85011941304
-
Transgenic tools for members of the genus Drosophila with sequenced genomes
-
Holtzman, S. et al. Transgenic tools for members of the genus Drosophila with sequenced genomes. Fly 4, 349-362 (2010).
-
(2010)
Fly
, vol.4
, pp. 349-362
-
-
Holtzman, S.1
-
34
-
-
13444304173
-
Chance caught on the wing: Cis-regulatory evolution and the origin of pigment patterns in Drosophila
-
Gompel, N., Prud'homme, B., Wittkopp, P. J., Kassner, V. A. & Carroll, S. B. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433, 481-487 (2005).
-
(2005)
Nature
, vol.433
, pp. 481-487
-
-
Gompel, N.1
Prud'Homme, B.2
Wittkopp, P.J.3
Kassner, V.A.4
Carroll, S.B.5
-
35
-
-
49549112519
-
The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila
-
Williams, T. M. et al. The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila. Cell 134, 610-623 (2008).
-
(2008)
Cell
, vol.134
, pp. 610-623
-
-
Williams, T.M.1
-
36
-
-
69349099315
-
Rapid evolution of sex pheromone-producing enzyme expression in Drosophila
-
Shirangi, T. R., Dufour, H. D., Williams, T. M. & Carroll, S. B. Rapid evolution of sex pheromone-producing enzyme expression in Drosophila. PLoS Biol. 7, e1000168 (2009).
-
(2009)
PLoS Biol
, vol.7
-
-
Shirangi, T.R.1
Dufour, H.D.2
Williams, T.M.3
Carroll, S.B.4
-
37
-
-
33744972290
-
A gene-centered C. elegans protein-DNA interaction network
-
Deplancke, B. et al. A gene-centered C. elegans protein-DNA interaction network. Cell 125, 1193-1205 (2006).
-
(2006)
Cell
, vol.125
, pp. 1193-1205
-
-
Deplancke, B.1
-
38
-
-
0035863877
-
DNA-bound transcription factor complexes analysed by mass-spectrometry: Binding of novel proteins to the human c-fos SRE and related sequences
-
Drewett, V. et al. DNA-bound transcription factor complexes analysed by mass-spectrometry: binding of novel proteins to the human c-fos SRE and related sequences. Nucleic Acids Res. 29, 479-487 (2001).
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 479-487
-
-
Drewett, V.1
-
39
-
-
77958096076
-
Determining the specificity of protein-DNA interactions
-
Stormo, G. D. & Zhao, Y. Determining the specificity of protein-DNA interactions. Nature Rev. Genet. 11, 751-760 (2010).
-
(2010)
Nature Rev. Genet.
, vol.11
, pp. 751-760
-
-
Stormo, G.D.1
Zhao, Y.2
-
40
-
-
45449115390
-
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
-
Berger, M. F. et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133, 1266-1276 (2008).
-
(2008)
Cell
, vol.133
, pp. 1266-1276
-
-
Berger, M.F.1
-
41
-
-
33846467150
-
A systems approach to measuring the binding energy landscapes of transcription factors
-
Maerkl, S. J. & Quake, S. R. A systems approach to measuring the binding energy landscapes of transcription factors. Science 315, 233-237 (2007).
-
(2007)
Science
, vol.315
, pp. 233-237
-
-
Maerkl, S.J.1
Quake, S.R.2
-
42
-
-
79959825697
-
Morphological evolution caused by many subtle-effect substitutions in regulatory DNA
-
Frankel, N. et al. Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature 474, 598-603 (2011).
-
(2011)
Nature
, vol.474
, pp. 598-603
-
-
Frankel, N.1
-
43
-
-
39749184167
-
The evolution of gene regulation underlies a morphological difference between two Drosophila sister species
-
Jeong, S. et al. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell 132, 783-793 (2008).
-
(2008)
Cell
, vol.132
, pp. 783-793
-
-
Jeong, S.1
-
44
-
-
51149097366
-
Human-specific gain of function in a developmental enhancer
-
Prabhakar, S. et al. Human-specific gain of function in a developmental enhancer. Science 321, 1346-1350, (2008).
-
(2008)
Science
, vol.321
, pp. 1346-1350
-
-
Prabhakar, S.1
-
45
-
-
79959944339
-
Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences
-
Rebeiz, M., Jikomes, N., Kassner, V. A. & Carroll, S. B. Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences. Proc. Natl Acad. Sci.USA 108, 10036-10043 (2011).
-
(2011)
Proc. Natl Acad. Sci.USA
, vol.108
, pp. 10036-10043
-
-
Rebeiz, M.1
Jikomes, N.2
Kassner, V.A.3
Carroll, S.B.4
-
46
-
-
74549118236
-
Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer
-
Chan, Y. F. et al. Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327, 302-305 (2010).
-
(2010)
Science
, vol.327
, pp. 302-305
-
-
Chan, Y.F.1
-
47
-
-
79952386187
-
Human-specific loss of regulatory DNA and the evolution of human-specific traits
-
McLean, C. Y. et al. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471, 216-219 (2011).
-
(2011)
Nature
, vol.471
, pp. 216-219
-
-
McLean, C.Y.1
-
48
-
-
0030860770
-
Transposable elements as sources of variation in animals and plants
-
Kidwell, M. G. & Lisch, D. Transposable elements as sources of variation in animals and plants. Proc. Natl Acad. Sci. USA 94, 7704-7711 (1997).
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 7704-7711
-
-
Kidwell, M.G.1
Lisch, D.2
-
49
-
-
0037183880
-
A single p450 allele associated with insecticide resistance in Drosophila
-
Daborn, P. J. et al. A single p450 allele associated with insecticide resistance in Drosophila. Science 297, 2253-2256 (2002).
-
(2002)
Science
, vol.297
, pp. 2253-2256
-
-
Daborn, P.J.1
-
50
-
-
34247854158
-
Cis-regulatory elements in the accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1
-
Chung, H. et al. Cis-regulatory elements in the accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics 175, 1071-1077 (2007).
-
(2007)
Genetics
, vol.175
, pp. 1071-1077
-
-
Chung, H.1
-
51
-
-
1242274636
-
Strong selective sweep associated with a transposon insertion in Drosophila simulans
-
Schlenke, T. A. & Begun, D. J. Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc. Natl Acad. USA 101, 1626-1631 (2004).
-
(2004)
Proc. Natl Acad. USA
, vol.101
, pp. 1626-1631
-
-
Schlenke, T.A.1
Begun, D.J.2
-
52
-
-
33646928347
-
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
-
Bejerano, G. et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441, 87-90 (2006).
-
(2006)
Nature
, vol.441
, pp. 87-90
-
-
Bejerano, G.1
-
53
-
-
36749061982
-
Species-specific endogenous retroviruses shape the transcriptional network of the human tumour suppressor protein p53
-
Wang, T. et al. Species-specific endogenous retroviruses shape the transcriptional network of the human tumour suppressor protein p53. Proc. Natl Acad. Sci. USA 104, 18613-18618 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 18613-18618
-
-
Wang, T.1
-
54
-
-
33745227338
-
Regulation of body pigmentation by the abdominal-b hox protein and its gain and loss in Drosophila evolution
-
Jeong, S., Rokas, A. & Carroll, S. B. Regulation of body pigmentation by the abdominal-b hox protein and its gain and loss in Drosophila evolution. Cell 125, 1387-1399 (2006).
-
(2006)
Cell
, vol.125
, pp. 1387-1399
-
-
Jeong, S.1
Rokas, A.2
Carroll, S.B.3
-
55
-
-
79955623470
-
Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules
-
He, B. Z., Holloway, A. K., Maerkl, S. J. & Kreitman, M. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules. PLoS Genet. 7, e1002053 (2011).
-
(2011)
PLoS Genet
, vol.7
-
-
He, B.Z.1
Holloway, A.K.2
Maerkl, S.J.3
Kreitman, M.4
-
56
-
-
77957885770
-
Transcription factor binding variation in the evolution of gene regulation
-
Dowell, R. D. Transcription factor binding variation in the evolution of gene regulation. Trends Genet. 26, 468-475 (2010).
-
(2010)
Trends Genet
, vol.26
, pp. 468-475
-
-
Dowell, R.D.1
-
57
-
-
34249818182
-
Tissue-specific transcriptional regulation has diverged significantly between human and mouse
-
Odom, D. T. et al. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nature Genet. 39, 730-732 (2007).
-
(2007)
Nature Genet
, vol.39
, pp. 730-732
-
-
Odom, D.T.1
-
58
-
-
34547874585
-
Divergence of transcription factor binding sites across related yeast species
-
Borneman, A. R. et al. Divergence of transcription factor binding sites across related yeast species. Science 317, 815-819 (2007).
-
(2007)
Science
, vol.317
, pp. 815-819
-
-
Borneman, A.R.1
-
59
-
-
40149098862
-
The evolution of combinatorial gene regulation in fungi
-
Tuch, B. B., Galgoczy, D. J., Hernday, A. D., Li, H. & Johnson, A. D. The evolution of combinatorial gene regulation in fungi. PLoS Biol. 6, e38 (2008).
-
(2008)
PLoS Biol
, vol.6
-
-
Tuch, B.B.1
Galgoczy, D.J.2
Hernday, A.D.3
Li, H.4
Johnson, A.D.5
-
60
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt, D. et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328, 1036-1040 (2010).
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
-
61
-
-
77950833803
-
Variation in transcription factor binding among humans
-
Kasowski, M. et al. Variation in transcription factor binding among humans. Science 328, 232-235 (2010).
-
(2010)
Science
, vol.328
, pp. 232-235
-
-
Kasowski, M.1
-
62
-
-
54249099196
-
Species-specific transcription in mice carrying human chromosome 21
-
Wilson, M. D. et al. Species-specific transcription in mice carrying human chromosome 21. Science 322, 434-438 (2008).
-
(2008)
Science
, vol.322
, pp. 434-438
-
-
Wilson, M.D.1
-
63
-
-
77951610155
-
Genetic analysis of variation in transcription factor binding in yeast
-
Zheng, W., Zhao, H., Mancera, E., Steinmetz, L. M. & Snyder, M. Genetic analysis of variation in transcription factor binding in yeast. Nature 464, 1187-1191 (2010).
-
(2010)
Nature
, vol.464
, pp. 1187-1191
-
-
Zheng, W.1
Zhao, H.2
Mancera, E.3
Steinmetz, L.M.4
Snyder, M.5
-
64
-
-
77950566643
-
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
-
Bradley, R. K. et al. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 8, e1000343 (2010).
-
(2010)
PLoS Biol
, vol.8
-
-
Bradley, R.K.1
-
65
-
-
0036182414
-
Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes
-
Conte, C., Dastugue, B. & Vaury, C. Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes. Mol. Cell. Biol. 22, 1767-1777 (2002).
-
(2002)
Mol. Cell. Biol.
, vol.22
, pp. 1767-1777
-
-
Conte, C.1
Dastugue, B.2
Vaury, C.3
-
66
-
-
0037226830
-
Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements
-
Lerman, D. N., Michalak, P., Helin, A. B., Bettencourt, B. R. & Feder, M. E. Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements. Mol. Biol. Evol. 20, 135-144 (2003).
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 135-144
-
-
Lerman, D.N.1
Michalak, P.2
Helin, A.B.3
Bettencourt, B.R.4
Feder, M.E.5
-
67
-
-
82455192847
-
De novo genesis of enhancers in vertebrates
-
Eichenlaub, M. P. & Ettwiller, L. De novo genesis of enhancers in vertebrates. PLoS Biol. 9, e1001188 (2011).
-
(2011)
PLoS Biol
, vol.9
-
-
Eichenlaub, M.P.1
Ettwiller, L.2
-
68
-
-
33646191543
-
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene
-
Prud'homme, B. et al. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440, 1050-1053 (2006).
-
(2006)
Nature
, vol.440
, pp. 1050-1053
-
-
Prud'Homme, B.1
-
69
-
-
80155192425
-
Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1
-
Sumiyama, K. & Saitou, N. Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1. Mol. Biol. Evol. 28, 3005-3007 (2011).
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 3005-3007
-
-
Sumiyama, K.1
Saitou, N.2
-
70
-
-
72949110371
-
Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population
-
Rebeiz, M., Pool, J. E., Kassner, V. A., Aquadro, C. F. & Carroll, S. B. Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science 326, 1663-1667 (2009).
-
(2009)
Science
, vol.326
, pp. 1663-1667
-
-
Rebeiz, M.1
Pool, J.E.2
Kassner, V.A.3
Aquadro, C.F.4
Carroll, S.B.5
-
71
-
-
74549195536
-
Multiple functional variants in cis modulate PDYN expression
-
Babbitt, C. C. et al. Multiple functional variants in cis modulate PDYN expression. Mol Biol. Evol. 27, 465-479 (2010).
-
(2010)
Mol Biol. Evol.
, vol.27
, pp. 465-479
-
-
Babbitt, C.C.1
-
72
-
-
0036196885
-
The signature of positive selection at randomly chosen loci
-
Przeworski, M. The signature of positive selection at randomly chosen loci. Genetics 160, 1179-1189 (2002).
-
(2002)
Genetics
, vol.160
, pp. 1179-1189
-
-
Przeworski, M.1
-
73
-
-
34447132938
-
The genetic basis of adaptive pigmentation variation in Drosophila melanogaster
-
Pool, J. E. & Aquadro, C. F. The genetic basis of adaptive pigmentation variation in Drosophila melanogaster. Mol. Ecol. 16, 2844-2851 (2007).
-
(2007)
Mol. Ecol.
, vol.16
, pp. 2844-2851
-
-
Pool, J.E.1
Aquadro, C.F.2
-
74
-
-
70350490025
-
Intraspecific polymorphism to interspecific divergence: Genetics of pigmentation in Drosophila
-
Wittkopp, P. J. et al. Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila. Science 326, 540-544 (2009).
-
(2009)
Science
, vol.326
, pp. 540-544
-
-
Wittkopp, P.J.1
-
75
-
-
20144371089
-
Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles
-
Colosimo, P. F. et al. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307, 1928-1933 (2005).
-
(2005)
Science
, vol.307
, pp. 1928-1933
-
-
Colosimo, P.F.1
-
76
-
-
13144257707
-
The genetic theory of adaptation: A brief history
-
Orr, H. A. The genetic theory of adaptation: a brief history. Nature Rev. Genet. 6, 119-127 (2005).
-
(2005)
Nature Rev. Genet.
, vol.6
, pp. 119-127
-
-
Orr, H.A.1
-
77
-
-
77951544471
-
Mutations and quantitative genetic variation: Lessons from Drosophila
-
Mackay, T. F. Mutations and quantitative genetic variation: lessons from Drosophila. Phil. Trans. R. Soc. B 365, 1229-1239 (2010).
-
(2010)
Phil. Trans. R. Soc. B
, vol.365
, pp. 1229-1239
-
-
-
78
-
-
60349093708
-
Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation
-
Charlesworth, B. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nature Rev. Genet. 10, 195-205 (2009).
-
(2009)
Nature Rev. Genet.
, vol.10
, pp. 195-205
-
-
Charlesworth, B.1
-
79
-
-
37549017103
-
Convergence and parallelism reconsidered: What have we learned about the genetics of adaptation?
-
Arendt, J. & Reznick, D. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends Ecol. Evol. 23, 26-32 (2008).
-
(2008)
Trends Ecol Evol
, vol.23
, pp. 26-32
-
-
Arendt, J.1
Reznick, D.2
-
80
-
-
0038517876
-
Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism
-
Sucena, E., Delon, I., Jones, I., Payre, F. & Stern, D. L. Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism. Nature 424, 935-938 (2003).
-
(2003)
Nature
, vol.424
, pp. 935-938
-
-
Sucena, E.1
Delon, I.2
Jones, I.3
Payre, F.4
Stern, D.L.5
-
81
-
-
59849095985
-
Comment on human-specific gain of function in a developmental enhancer
-
author reply 714
-
Duret, L. & Galtier, N. Comment on "human-specific gain of function in a developmental enhancer". Science 323, 714; author reply 714 (2009).
-
(2009)
Science
, vol.323
, pp. 714
-
-
Duret, L.1
Galtier, N.2
-
82
-
-
78549246207
-
Phenomics: The next challenge
-
Houle, D., Govindaraju, D. R. & Omholt, S. Phenomics: the next challenge. Nature Rev. Genet. 11, 855-866 (2010).
-
(2010)
Nature Rev. Genet.
, vol.11
, pp. 855-866
-
-
Houle, D.1
Govindaraju, D.R.2
Omholt, S.3
-
83
-
-
34247855863
-
The locus of evolution: Evo devo and the genetics of adaptation
-
Hoekstra, H. E. & Coyne, J. A. The locus of evolution: evo devo and the genetics of adaptation. Evolution 61, 995-1016 (2007).
-
(2007)
Evolution
, vol.61
, pp. 995-1016
-
-
Hoekstra, H.E.1
Coyne, J.A.2
-
84
-
-
51549097146
-
Resurrecting the role of transcription factor change in developmental evolution
-
Lynch, V. J. & Wagner, G. P. Resurrecting the role of transcription factor change in developmental evolution. Evolution 62, 2131-2154 (2008).
-
(2008)
Evolution
, vol.62
, pp. 2131-2154
-
-
Lynch, V.J.1
Wagner, G.P.2
-
85
-
-
39749116219
-
Regulatory changes underlying expression differences within and between Drosophila species
-
Wittkopp, P. J., Haerum, B. K. & Clark, A. G. Regulatory changes underlying expression differences within and between Drosophila species. Nature Genet. 40, 346-350 (2008).
-
(2008)
Nature Genet
, vol.40
, pp. 346-350
-
-
Wittkopp, P.J.1
Haerum, B.K.2
Clark, A.G.3
-
86
-
-
77952982347
-
Natural selection on cis and trans regulation in yeasts
-
Emerson, J. J. et al. Natural selection on cis and trans regulation in yeasts. Genome Res. 20, 826-836 (2010).
-
(2010)
Genome Res
, vol.20
, pp. 826-836
-
-
Emerson, J.J.1
-
87
-
-
38349076024
-
Regulatory divergence modifies limb length between mammals
-
Cretekos, C. J. et al. Regulatory divergence modifies limb length between mammals. Genes Dev. 22, 141-151 (2008).
-
(2008)
Genes Dev
, vol.22
, pp. 141-151
-
-
Cretekos, C.J.1
-
88
-
-
80052151984
-
Optix drives the repeated convergent evolution of butterfly wing pattern mimicry
-
Reed, R. D. et al. Optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science 333, 1137-1141 (2011).
-
(2011)
Science
, vol.333
, pp. 1137-1141
-
-
Reed, R.D.1
-
89
-
-
33645472806
-
New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences
-
Gomez-Skarmeta, J. L., Lenhard, B. & Becker, T. S. New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. Dev. Dyn. 235, 870-885 (2006).
-
(2006)
Dev. Dyn.
, vol.235
, pp. 870-885
-
-
Gomez-Skarmeta, J.L.1
Lenhard, B.2
Becker, T.S.3
-
90
-
-
19944434180
-
Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
-
Richards, S. et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 15, 1-18 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 1-18
-
-
Richards, S.1
-
91
-
-
62249204977
-
Big genomes facilitate the comparative identification of regulatory elements
-
Peterson, B. K. et al. Big genomes facilitate the comparative identification of regulatory elements. PLoS ONE 4, e4688 (2009).
-
(2009)
PLoS ONE
, vol.4
-
-
Peterson, B.K.1
-
92
-
-
33747885768
-
Evolution of cis-regulatory sequence and function in Diptera
-
Wittkopp, P. J. Evolution of cis-regulatory sequence and function in Diptera. Heredity 97, 139-147 (2006).
-
(2006)
Heredity
, vol.97
, pp. 139-147
-
-
Wittkopp, P.J.1
-
93
-
-
75149143994
-
Conserved expression without conserved regulatory sequence: The more things change, the more they stay the same
-
Weirauch, M. T. & Hughes, T. R. Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet. 26, 66-74 (2010).
-
(2010)
Trends Genet
, vol.26
, pp. 66-74
-
-
Weirauch, M.T.1
Hughes, T.R.2
-
94
-
-
71749103442
-
Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information
-
Meireles-Filho, A. C. & Stark, A. Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr. Opin. Genet. Dev. 19, 565-570 (2009).
-
(2009)
Curr. Opin. Genet. Dev.
, vol.19
, pp. 565-570
-
-
Meireles-Filho, A.C.1
Stark, A.2
-
95
-
-
0034598832
-
Evidence for stabilizing selection in a eukaryotic enhancer element
-
Ludwig, M. Z., Bergman, C., Patel, N. H. & Kreitman, M. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403, 564-567 (2000).
-
(2000)
Nature
, vol.403
, pp. 564-567
-
-
Ludwig, M.Z.1
Bergman, C.2
Patel, N.H.3
Kreitman, M.4
-
96
-
-
19344368645
-
Functional evolution of a cis-regulatory module
-
Ludwig, M. Z. et al. Functional evolution of a cis-regulatory module. PLoS Biol. 3, e93 (2005).
-
(2005)
PLoS Biol
, vol.3
-
-
Ludwig, M.Z.1
-
97
-
-
0033024612
-
Evidence for redundancy but not trans factor-cis element co-evolution in the regulation of Drosophila Yp genes
-
Piano, F., Parisi, M. J., Karess, R. & Kambysellis, M. P. Evidence for redundancy but not trans factor-cis element co-evolution in the regulation of Drosophila Yp genes. Genetics 152, 605-616, (1999).
-
(1999)
Genetics
, vol.152
, pp. 605-616
-
-
Piano, F.1
Parisi, M.J.2
Karess, R.3
Kambysellis, M.P.4
-
98
-
-
0037125954
-
Evolution of yellow gene regulation and pigmentation in Drosophila
-
Wittkopp, P. J., Vaccaro, K. & Carroll, S. B. Evolution of yellow gene regulation and pigmentation in Drosophila. Curr. Biol. 12, 1547-1556 (2002).
-
(2002)
Curr. Biol.
, vol.12
, pp. 1547-1556
-
-
Wittkopp, P.J.1
Vaccaro, K.2
Carroll, S.B.3
-
99
-
-
79960708456
-
Rapid evolutionary rewiring of a structurally constrained eye enhancer
-
Swanson, C. I., Schwimmer, D. B. & Barolo, S. Rapid evolutionary rewiring of a structurally constrained eye enhancer. Curr. Biol. 21, 1186-1196 (2011).
-
(2011)
Curr. Biol.
, vol.21
, pp. 1186-1196
-
-
Swanson, C.I.1
Schwimmer, D.B.2
Barolo, S.3
-
100
-
-
16644403466
-
Using reporter genes to study cis-regulatory elements
-
Arnone, M. I., Dmochowski, I. J. & Gache, C. Using reporter genes to study cis-regulatory elements. Methods Cell Biol. 74, 621-652 (2004).
-
(2004)
Methods Cell Biol
, vol.74
, pp. 621-652
-
-
Arnone, M.I.1
Dmochowski, I.J.2
Gache, C.3
-
101
-
-
25444442381
-
An aneuploid mouse strain carrying human chromosome 21 with down syndrome phenotypes
-
O'Doherty, A. et al. An aneuploid mouse strain carrying human chromosome 21 with down syndrome phenotypes. Science 309, 2033-2037 (2005).
-
(2005)
Science
, vol.309
, pp. 2033-2037
-
-
O'Doherty, A.1
-
102
-
-
12744263842
-
Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
-
Berman, B. P. et al. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 5, R61 (2004).
-
(2004)
Genome Biol
, vol.5
-
-
Berman, B.P.1
|