-
1
-
-
83555162573
-
Regulatory evolution through divergence of a phosphoswitch in the transcription factor cebpb
-
Lynch, V. J., May, G. & Wagner, G. P. Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB. Nature 480, 383-386 (2011).
-
(2011)
Nature
, vol.480
, pp. 383-386
-
-
Lynch, V.J.1
May, G.2
Wagner, G.P.3
-
2
-
-
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
-
3
-
-
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
-
4
-
-
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
-
5
-
-
46149104377
-
Evo-devo and an expanding evolutionary synthesis 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
-
6
-
-
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
-
7
-
-
49949090861
-
The functional repertoires of metazoan genomes
-
Ponting, C. P. The functional repertoires of metazoan genomes. Nature Rev. Genet. 9, 689-698 (2008).
-
(2008)
Nature Rev. Genet
, vol.9
, pp. 689-698
-
-
Ponting, C.P.1
-
8
-
-
34548346860
-
Promoter regions of many neural-And nutrition-related genes have experienced positive selection during human evolution
-
Haygood, R., Fedrigo, O., Hanson, B., Yokoyama, K. D. & Wray, G. A. Promoter regions of many neural-And nutrition-related genes have experienced positive selection during human evolution. Nature Genet. 39, 1140-1144 (2007).
-
(2007)
Nature Genet
, vol.39
, pp. 1140-1144
-
-
Haygood, R.1
Fedrigo, O.2
Hanson, B.3
Yokoyama, K.D.4
Wray, G.A.5
-
9
-
-
0037066542
-
Intra-And interspecific variation in primate gene expression patterns
-
Enard, W. et al. Intra-And interspecific variation in primate gene expression patterns. Science 296, 340-343 (2002).
-
(2002)
Science
, vol.296
, pp. 340-343
-
-
Enard, W.1
-
10
-
-
22144447840
-
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees
-
Khaitovich, P. et al. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309, 1850-1854 (2005).
-
(2005)
Science
, vol.309
, pp. 1850-1854
-
-
Khaitovich, P.1
-
11
-
-
77953808473
-
Next-generation genomics: An integrative approach
-
Hawkins, R. D., Hon, G. C. & Ren, B. Next-generation genomics: an integrative approach. Nature Rev. Genet. 11, 476-486 (2010).
-
(2010)
Nature Rev. Genet
, vol.11
, pp. 476-486
-
-
Hawkins, R.D.1
Hon, G.C.2
Ren, B.3
-
12
-
-
84863885448
-
Comparative studies of gene expression and the evolution of gene regulation
-
Romero, I. G., Ruvinsky, I. & Gilad, Y. Comparative studies of gene expression and the evolution of gene regulation. Nature Rev. Genet. 13, 505-516 (2012).
-
(2012)
Nature Rev. Genet
, vol.13
, pp. 505-516
-
-
Romero, I.G.1
Ruvinsky, I.2
Gilad, Y.3
-
13
-
-
79952199374
-
Evolutionary history of regulatory variation in human populations
-
Lappalainen, T. & Dermitzakis, E. T. Evolutionary history of regulatory variation in human populations. Hum. Mol. Genet. 19, R197-R203 (2010).
-
(2010)
Hum. Mol. Genet
, vol.19
, pp. R197-R203
-
-
Lappalainen, T.1
Dermitzakis, E.T.2
-
14
-
-
84885639459
-
Expression quantitative trait loci: Present and future
-
Nica, A. & Dermitzakis, E. T. Expression quantitative trait loci: present and future. Phil. Trans. R. Soc. B 368, 20120362 (2013).
-
(2013)
Phil. Trans. R. Soc. B
, vol.368
, pp. 20120362
-
-
Nica, A.1
Dermitzakis, E.T.2
-
15
-
-
56549101959
-
Alternative iso form regulation in human tissue transcriptomes
-
Wang, E. T. et al. Alternative iso form regulation in human tissue transcriptomes. Nature 456, 470-476 (2008).
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
-
16
-
-
84897406127
-
A promoter-level mammalian expression atlas
-
FANTOM Consortium and the RIKEN PMI and CLST (DGT) et al
-
FANTOM Consortium and the RIKEN PMI and CLST (DGT) et al. A promoter-level mammalian expression atlas. Nature 507, 462-470 (2014).
-
(2014)
Nature
, vol.507
, pp. 462-470
-
-
-
17
-
-
78649910014
-
Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation
-
Ozsolak, F. et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143, 1018-1029 (2010).
-
(2010)
Cell
, vol.143
, pp. 1018-1029
-
-
Ozsolak, F.1
-
18
-
-
78751477191
-
Gene silencing by micrornas: Contributions of translational repression and mrna decay
-
Huntzinger, E. & Izaurralde, E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nature Rev. Genet. 12, 99-110 (2011).
-
(2011)
Nature Rev. Genet
, vol.12
, pp. 99-110
-
-
Huntzinger, E.1
Izaurralde, E.2
-
19
-
-
84892599690
-
Piwi proteins and piwi-interacting rnas in the soma
-
Ross, R. J., Weiner, M. M. & Lin, H. PIWI proteins and PIWI-interacting RNAs in the soma. Nature 505, 353-359 (2014).
-
(2014)
Nature
, vol.505
, pp. 353-359
-
-
Ross, R.J.1
Weiner, M.2
Lin, H.3
-
20
-
-
0025012640
-
The product of the h19 gene may function as an rna
-
Brannan, C. I., Dees, E. C., Ingram, R. S. & Tilghman, S. M. The product of the H19 gene may function as an RNA. Mol. Cell. Biol. 10, 28-36 (1990).
-
(1990)
Mol. Cell. Biol
, vol.10
, pp. 28-36
-
-
Brannan, C.I.1
Dees, E.C.2
Ingram, R.S.3
Tilghman, S.M.4
-
21
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding rnas in mammals
-
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
-
22
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding rnas reveals global properties and specific subclasses
-
Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
-
(2011)
Genes Dev
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
-
23
-
-
84865727393
-
The gencode v7 catalog of human long noncoding rnas: Analysis of their gene structure, evolution, and expression
-
Derrien T.,et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression Genome Res. 22, 1775-1789, 2012).
-
(2012)
Genome Res
, vol.22
, pp. 1775-1789
-
-
Derrien, T.1
-
24
-
-
0025961771
-
A gene from the region of the human x inactivation centre is expressed exclusively from the inactive x chromosome
-
Brown, C. J. et al. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349, 38-44 (1991).
-
(1991)
Nature
, vol.349
, pp. 38-44
-
-
Brown, C.J.1
-
25
-
-
84871060911
-
Airn transcriptional overlap, but not its lncrna products, induces imprinted igf2r silencing
-
Latos, P. A.et al. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338, 1469-1472 (2012).
-
(2012)
Science
, vol.338
, pp. 1469-1472
-
-
Latos, P.A.1
-
26
-
-
77957243921
-
Long noncoding rnas with enhancer-like function in human cells
-
Orom, U. A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46-58 (2010).
-
(2010)
Cell
, vol.143
, pp. 46-58
-
-
Orom, U.A.1
-
27
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in human hox loci by noncoding rnas
-
Rinn, J. L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323 (2007).
-
(2007)
Cell
, vol.129
, pp. 1311-1323
-
-
Rinn, J.L.1
-
28
-
-
80054715378
-
A long noncoding rna controls muscle differentiation by functioning as a competing endogenous rna
-
Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358-369 (2011).
-
(2011)
Cell
, vol.147
, pp. 358-369
-
-
Cesana, M.1
-
29
-
-
84863219731
-
The h19 lincrna is a developmental reservoir of mir-675 that suppresses growth and igf1r
-
Keniry, A. et al. The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nature Cell Biol. 14, 659-665 (2012).
-
(2012)
Nature Cell Biol
, vol.14
, pp. 659-665
-
-
Keniry, A.1
-
30
-
-
77952367798
-
Widespre ad transcription at neuronal activity-regulated enhancers
-
Kim, T. K. et al. Widespre ad transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
-
31
-
-
84888232130
-
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding rnas
-
Marques, A. C. et al. Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol. 14, R131 (2013).
-
(2013)
Genome Biol
, vol.14
, pp. R131
-
-
Marques, A.C.1
-
32
-
-
33745125901
-
The xist rna gene evolved in eutheria ns by pseudogenization of a protein-coding gene
-
Duret, L., Chureau, C., Samain, S., Weissenbach, J. & Avner, P. The Xist RNA gene evolved in eutheria ns by pseudogenization of a protein-coding gene. Science 312, 1653-1655 (2006).
-
(2006)
Science
, vol.312
, pp. 1653-1655
-
-
Duret, L.1
Chureau, C.2
Samain, S.3
Weissenbach, J.4
Avner, P.5
-
33
-
-
33644855479
-
Expression profiling in primates reve als a rapid evolution of human transcription factors
-
Gilad, Y., Oshlack, A., Smyth, G. K., Speed, T. P. & White, K. P. Expression profiling in primates reve als a rapid evolution of human transcription factors. Nature 440, 242-245 (2006).
-
(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
-
34
-
-
75649102520
-
Sex-specific and lineage-specific alternative splicing in primates
-
Blekhman, R., Marioni, J. C., Zumbo, P., Stephens, M. & Gilad, Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Res. 20, 180-189 (2010).
-
(2010)
Genome Res
, vol.20
, pp. 180-189
-
-
Blekhman, R.1
Marioni, J.C.2
Zumbo, P.3
Stephens, M.4
Gilad, Y.5
-
35
-
-
1842631448
-
Incongruent expression profiles between human and mouse orthologous genes suggest wide spread neutral evolution of transcription control
-
Yanai, I., Graur, D. & Ophir, R. Incongruent expression profiles between human and mouse orthologous genes suggest wide spread neutral evolution of transcription control. OMICS 8, 15-24 (2004).
-
(2004)
OMICS
, vol.8
, pp. 15-24
-
-
Yanai, I.1
Graur, D.2
Ophir, R.3
-
36
-
-
33244455951
-
Evolutionary conservation of expression profiles between human and mouse orthologous genes
-
Liao, B. Y. & Zhang, J. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol. Biol. Evol. 23, 530-540 (2006).
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 530-540
-
-
Liao, B.Y.1
Zhang, J.2
-
37
-
-
65349162170
-
Conservation of core gene expression in vertebrate tissues
-
Chan, E. T. et al. Conservation of core gene expression in vertebrate tissues. J. Biol. 8, 33 (2009).
-
(2009)
J. Biol
, vol.8
, pp. 33
-
-
Chan, E.T.1
-
38
-
-
13444251367
-
Evolutionary significance of gene expression divergence
-
Jordan, I. K., Marino-Ramirez, L. & Koonin, E. V. Evolutionary significance of gene expression divergence. Gene 345, 119-126 (2005).
-
(2005)
Gene
, vol.345
, pp. 119-126
-
-
Jordan, I.K.1
Marino-Ramirez, L.2
Koonin, E.V.3
-
39
-
-
80054976678
-
The evolution of gene expression levels in mammalian organs
-
Brawand, D. et al. The evolution of gene expression levels in mammalian organs. Nature 478, 343-348 (2011).
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
-
40
-
-
0038617729
-
Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss
-
Modrek, B. & Lee, C. J. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nature Genet. 34, 177-180 (2003).
-
(2003)
Nature Genet
, vol.34
, pp. 177-180
-
-
Modrek, B.1
Lee, C.J.2
-
41
-
-
10944245056
-
Alternative splicing of conserved exons is frequently species-specific in human and mouse
-
Pan, Q. et al. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 21, 73-77 (2005).
-
(2005)
Trends Genet
, vol.21
, pp. 73-77
-
-
Pan, Q.1
-
42
-
-
36248942556
-
Global analysis of alternative splicing differences between humans and chimpanzees
-
Calarco, J. A. et al. Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev. 21, 2963-2975 (2007).
-
(2007)
Genes Dev
, vol.21
, pp. 2963-2975
-
-
Calarco, J.A.1
-
43
-
-
84871436996
-
Evolutionary dynamics of gene and isoform regulation in mammalian tissues
-
Merkin, J., Russell, C., Chen, P. & Burge, C. B. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338, 1593-1599 (2012).
-
(2012)
Science
, vol.338
, pp. 1593-1599
-
-
Merkin, J.1
Russell, C.2
Chen, P.3
Burge, C.B.4
-
44
-
-
84871410405
-
The evolutionary landscape of alternative splicing in vertebrate species
-
References 43 and 44 present the first large-scale evolutionary comparison of alternative splicing patterns, which reveals rapid evolution of exon skipping frequencies
-
Barbosa-Morais, N. L. et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 338, 1587-1593 ( 2012). References 43 and 44 present the first large-scale evolutionary comparison of alternative splicing patterns, which reveals rapid evolution of exon skipping frequencies.
-
(2012)
Science
, vol.338
, pp. 1587-1593
-
-
Barbosa-Morais, N.L.1
-
45
-
-
84861903786
-
A quantitative atlas of polyadenylation in five mammals
-
Derti A.,et al. A quantitative atlas of polyadenylation in five mammals Genome Res., 22, 1173-1183, 2012)
-
(2012)
Genome Res
, vol.22
, pp. 1173-1183
-
-
Derti, A.1
-
46
-
-
84871974893
-
Birth and expression evolution of mammalian microrna genes
-
Meunier, J. et al. Birth and expression evolution of mammalian microRNA genes. Genome Res. 23, 34-45 (2013).
-
(2013)
Genome Res
, vol.23
, pp. 34-45
-
-
Meunier, J.1
-
47
-
-
84866979410
-
Reducing ligation bias of small rnas in libraries for next generation sequencing
-
Sorefan, K. et al. Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence 3, 4 (2012).
-
(2012)
Silence
, vol.3
, pp. 4
-
-
Sorefan, K.1
-
48
-
-
84896706999
-
Biases in small rna deep sequencing data
-
Raabe, C. A., Tang, T. H., Brosi us, J. & Rozhdestvensky, T. S. Biases in small RNA deep sequencing data. Nucleic Acids Res. 42, 1414-1426 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 1414-1426
-
-
Raabe, C.A.1
Tang, T.H.2
Brosi Us, J.3
Rozhdestvensky, T.S.4
-
49
-
-
84864449330
-
Compa rative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of mirnas
-
Roux, J., Gonzalez-Porta, M. & Robinson-Rechavi, M. Compa rative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Res. 40, 5890-5900 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5890-5900
-
-
Roux, J.1
Gonzalez-Porta, M.2
Robinson-Rechavi, M.3
-
50
-
-
84864629645
-
Ra pid turnover of long noncoding rnas and the evolution of gene expression
-
Kutter, C. et al. Ra pid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet. 8, e1002841 (2012).
-
(2012)
PLoS Genet
, vol.8
, pp. e1002841
-
-
Kutter, C.1
-
51
-
-
84895908120
-
The evolution of lncrna repertoires and expression patterns in tetrapods
-
Necsulea, A. et al. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505, 635-640 (2014).
-
(2014)
Nature
, vol.505
, pp. 635-640
-
-
Necsulea, A.1
-
52
-
-
84898747543
-
Evolutionary dynamics and tissue specificity of human long noncoding rnas in six mammals
-
Washietl, S., Kellis, M. & Garber, M. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res. 24, 616-628 (2014).
-
(2014)
Genome Res
, vol.24
, pp. 616-628
-
-
Washietl, S.1
Kellis, M.2
Garber, M.3
-
53
-
-
77954399763
-
Long noncoding rna genes: Conservation of sequence and brain expression among diverse amniotes
-
Chodroff, R. A. et al. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol. 11, R72 (2010).
-
(2010)
Genome Biol
, vol.11
, pp. R72
-
-
Chodroff, R.A.1
-
54
-
-
80053383499
-
Pol iii binding in six mammals shows conservation among amino acid isotypes despite divergence among trna genes
-
Kutter, C. et al. Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nature Genet. 43, 948-955 (2011).
-
(2011)
Nature Genet
, vol.43
, pp. 948-955
-
-
Kutter, C.1
-
55
-
-
0030076124
-
Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis
-
Li, W. H., Ellsworth, D. L., Krushkal, J., Chang, B. H. & Hewett-Emmett, D. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet Evol. 5, 182-187 (1996).
-
(1996)
Mol. Phylogenet Evol
, vol.5
, pp. 182-187
-
-
Li, W.H.1
Ellsworth, D.L.2
Krushkal, J.3
Chang, B.4
Hewett-Emmett, D.5
-
56
-
-
15744388330
-
Evidence for widespread degradation of gene control regions in hominid genomes
-
Keightley, P. D., Lercher, M. J. & Eyre-Walker, A. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 3, e42 (2005).
-
(2005)
PLoS Biol
, vol.3
, pp. e42
-
-
Keightley, P.1
Lercher, M.J.2
Eyre-Walker, A.3
-
57
-
-
0344436038
-
Dna sequence variation in a non-coding region of low recombination on the human x chromosome
-
Kaessmann, H., Heissig, F., von Haeseler, A. & Paabo, S. DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nature Genet. 22, 78-81 (1999).
-
(1999)
Nature Genet
, vol.22
, pp. 78-81
-
-
Kaessmann, H.1
Heissig, F.2
Von Haeseler, A.3
Paabo, S.4
-
58
-
-
1842837782
-
Dna polymorphism in a worldwide sample of human x chromosomes
-
Yu, N., Fu, Y. X. & Li, W. H. DNA polymorphism in a worldwide sample of human X chromosomes. Mol. Biol. Evol. 19, 2131-2141 (2002).
-
(2002)
Mol. Biol. Evol
, vol.19
, pp. 2131-2141
-
-
Yu, N.1
Fu, Y.X.2
Li, W.H.3
-
59
-
-
0033527718
-
Extensive nuclear dna sequence diversity among chimpanzees
-
Kaessmann, H., Wiebe, V. & Paabo, S. Extensive nuclear DNA sequence diversity among chimpanzees. Science 286, 1159-1162 (1999).
-
(1999)
Science
, vol.286
, pp. 1159-1162
-
-
Kaessmann, H.1
Wiebe, V.2
Paabo, S.3
-
60
-
-
43449123631
-
Genome analysis of the platypus reveals unique signatures of evolution
-
Warren, W. C. et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453, 175-183 (2008).
-
(2008)
Nature
, vol.453
, pp. 175-183
-
-
Warren, W.C.1
-
61
-
-
19344372220
-
A neutral model of transcriptome evolution
-
Khaitovich, P. et al. A neutral model of transcriptome evolution. PLoS Biol. 2, E132 (2004).
-
(2004)
PLoS Biol
, vol.2
, pp. E132
-
-
Khaitovich, P.1
-
62
-
-
33747519617
-
Evolution of primate gene expression
-
Khaitovich, P., Enard, W., Lachmann, M. & Paabo, S. Evolution of primate gene expression. Nature Rev. Genet. 7, 693-702 (2006).
-
(2006)
Nature Rev. Genet
, vol.7
, pp. 693-702
-
-
Khaitovich, P.1
Enard, W.2
Lachmann, M.3
Paabo, S.4
-
63
-
-
84891724119
-
Evolution of the correlation between expression divergence and protein divergence in mammals
-
Warnefors, M. & Kaessmann, H. Evolution of the correlation between expression divergence and protein divergence in mammals. Genome Biol. Evol. 5, 1324-1335 (2013).
-
(2013)
Genome Biol. Evol
, vol.5
, pp. 1324-1335
-
-
Warnefors, M.1
Kaessmann, H.2
-
64
-
-
84855175650
-
Microrna-driven developmental remodeling in the brain distinguishes humans from other primates
-
Somel, M. et al. MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates. PLoS Biol. 9, e1001214 (2011).
-
(2011)
PLoS Biol
, vol.9
, pp. e1001214
-
-
Somel, M.1
-
65
-
-
20444430245
-
A scan for positively selected genes in the genomes of humans and chimpanzees
-
Nielsen, R. et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3, e170 (2005).
-
(2005)
PLoS Biol
, vol.3
, pp. e170
-
-
Nielsen, R.1
-
66
-
-
84879795456
-
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis
-
Soumillon M.,et al. Cellular source and mechanisms of high transcriptome complexity in the mammalian testis Cell Rep. 3, 2179-2190, 2013).
-
(2013)
Cell Rep
, vol.3
, pp. 2179-2190
-
-
Soumillon, M.1
-
67
-
-
78649231644
-
Origins evolution, and phenotypic impact of new genes
-
Kaessmann, H. Origins, evolution, and phenotypic impact of new genes. Genome Res. 20, 1313-1326 (2010).
-
(2010)
Genome Res
, vol.20
, pp. 1313-1326
-
-
Kaessmann, H.1
-
68
-
-
57749177443
-
Rna-based gene duplication: Mechanistic and evolutionary insights
-
Kaessmann, H., Vinckenbosch, N. & Long, M. RNA-based gene duplication: mechanistic and evolutionary insights. Nature Rev. Genet. 10, 19-31 (2009).
-
(2009)
Nature Rev. Genet
, vol.10
, pp. 19-31
-
-
Kaessmann, H.1
Vinckenbosch, N.2
Long, M.3
-
69
-
-
77958508497
-
Evolution of neuronal and endothelial transcriptomes in primates
-
Giger, T. et al. Evolution of neuronal and endothelial transcriptomes in primates. Genome Biol. Evol. 2, 284-292 (2010).
-
(2010)
Genome Biol. Evol
, vol.2
, pp. 284-292
-
-
Giger, T.1
-
70
-
-
33746681910
-
Tissue-specific expression and regulation of sexually dimorphic genes in mice
-
Yang, X. et al. Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res. 16, 995-1004 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 995-1004
-
-
Yang, X.1
-
71
-
-
46249118379
-
An evolutionarily conserved sexual signature in the primate brain
-
Reinius, B. et al. An evolutionarily conserved sexual signature in the primate brain. PLoS Genet. 4, e1000100 (2008).
-
(2008)
PLoS Genet
, vol.4
, pp. e1000100
-
-
Reinius, B.1
-
72
-
-
43749100749
-
Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes
-
Veyrunes, F. et al. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res. 18, 965-973 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 965-973
-
-
Veyrunes, F.1
-
73
-
-
84899484057
-
Origins and functional evolution of y chromosomes across mammals
-
Cortez, D. et al. Origins and functional evolution of Y chromosomes across mammals. Nature 508, 488-493 (2014).
-
(2014)
Nature
, vol.508
, pp. 488-493
-
-
Cortez, D.1
-
74
-
-
84899473294
-
Mammalian y chromosomes retain widely expressed dosage-sensitive regulators
-
Bellott, D. W. et al. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508, 494-499 (2014).
-
(2014)
Nature
, vol.508
, pp. 494-499
-
-
Bellott, D.W.1
-
75
-
-
0012486875
-
Model for evolution of y chromosomes and dosage compensation
-
Charlesworth, B. Model for evolution of Y chromosomes and dosage compensation. Proc. Natl Acad. Sci. USA 75, 5618-5622 (1978).
-
(1978)
Proc. Natl Acad. Sci. USA
, vol.75
, pp. 5618-5622
-
-
Charlesworth, B.1
-
77
-
-
84861541065
-
Mechanisms and evolutionary patterns of mammalian and avian dosage compensation
-
Julien, P. et al. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 10, e1001328 (2012).
-
(2012)
PLoS Biol
, vol.10
, pp. e1001328
-
-
Julien, P.1
-
78
-
-
84863955476
-
Expression reduction in mammalian x chromosome evolution refutes ohno's hypothesis of dosage compensation
-
Lin, F., Xing, K., Zhang, J. & He, X. Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation. Proc. Natl Acad. Sci. USA 109, 11752-11757 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 11752-11757
-
-
Lin, F.1
Xing, K.2
Zhang, J.3
He, X.4
-
79
-
-
84901029300
-
X chromosome regulation: Diverse patterns in development, tissues and disease
-
Deng, X., Berletch, J. B., Nguyen, D. K. & Disteche, C. M. X chromosome regulation: diverse patterns in development, tissues and disease. Nature Rev. Genet. 15, 367-378 (2014).
-
(2014)
Nature Rev. Genet
, vol.15
, pp. 367-378
-
-
Deng, X.1
Berletch, J.B.2
Nguyen, D.K.3
Disteche, C.M.4
-
80
-
-
78149404797
-
Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the x chromosome
-
Zhang, Y. E., Vibranovski, M. D., Landback, P., Marais, G. A. & Long, M. Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. PLoS Biol. 8, e1000494 (2010).
-
(2010)
PLoS Biol
, vol.8
, pp. e1000494
-
-
Zhang, Y.1
Vibranovski, M.2
Landback, P.3
Marais, G.4
Long, M.5
-
81
-
-
0021554565
-
Sex chromosomes and the evolution of sexual dimorphism
-
Rice, W. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38, 735-742 (1984).
-
(1984)
Evolution
, vol.38
, pp. 735-742
-
-
Rice, W.1
-
82
-
-
34250626425
-
Meiotic sex chromosome inactivation
-
Turner, J. M. Meiotic sex chromosome inactivation. Development 134, 1823-1831 (2007).
-
(2007)
Development
, vol.134
, pp. 1823-1831
-
-
Turner, J.M.1
-
83
-
-
44349137392
-
The mouse x chromosome is enriched for multicopy testis genes showing postmeiotic expression
-
Mueller, J. L. et al. The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nature Genet. 40, 794-799 (2008).
-
(2008)
Nature Genet
, vol.40
, pp. 794-799
-
-
Mueller, J.L.1
-
84
-
-
4444358439
-
Bmp4 and morphological variation of beaks in darwin's finches
-
Abzhanov, A., Protas, M., Grant, B. R., Grant, P. R. & Tabin, C. J. Bmp4 and morphological variation of beaks in Darwin's finches. Science 305, 1462-1465 (2004).
-
(2004)
Science
, vol.305
, pp. 1462-1465
-
-
Abzhanov, A.1
Protas, M.2
Grant, B.R.3
Grant, P.R.4
Tabin, C.J.5
-
85
-
-
84879311724
-
Developmental basis of phallus reduction during bird evolution
-
Herrera, A. M., Shuster, S. G., Perriton, C. L. & Cohn, M. J. Developmental basis of phallus reduction during bird evolution. Curr. Biol. 23, 1065-1074 (2013).
-
(2013)
Curr. Biol
, vol.23
, pp. 1065-1074
-
-
Herrera, A.M.1
Shuster, S.G.2
Perriton, C.L.3
Cohn, M.J.4
-
86
-
-
79952063440
-
The developmental role of agouti in color pattern evolution
-
Mancea u, M., Domingues, V.S., Mallarino, R. & Hoekstra, H.E. The developmental role of Agouti in color pattern evolution. Science 331, 1062-1065 (2011).
-
(2011)
Science
, vol.331
, pp. 1062-1065
-
-
Mancea, U.M.1
Domingues, V.S.2
Mallarino, R.3
Hoekstra, H.E.4
-
87
-
-
84903516869
-
A molecular basis for classic blond hair color in europeans
-
Guenther C. A.,Tasic B.,Luo L.,Bedell M. A.,Kingsley D. M. A molecular basis for classic blond hair color in Europeans Nature Genet. 46, 748-752, 2014).
-
(2014)
Nature Genet
, vol.46
, pp. 748-752
-
-
Guenther, C.A.1
Tasic, B.2
Luo, L.3
Bedell, M.A.4
Kingsley, D.M.5
-
88
-
-
59049088893
-
Optimization of gene expression by natural selection
-
Bedford, T. & Hartl, D. L. Optimization of gene expression by natural selection. Proc. Natl Acad. Sci. USA 106, 1133-1138 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 1133-1138
-
-
Bedford, T.1
Hartl, D.L.2
-
89
-
-
84859984293
-
A selection index for gene expression evolution and its application to the divergence between humans and chimpanzees
-
Warnefors, M. & Eyre-Walker, A. A selection index for gene expression evolution and its application to the divergence between humans and chimpanzees. PLoS ONE 7, e34935 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e34935
-
-
Warnefors, M.1
Eyre-Walker, A.2
-
90
-
-
84891786317
-
Modeling gene expression evolution with an extended ornstein-uhlenbeck process accounting for within-species variation
-
Rohlfs, R. V., Harrigan, P. & Nielsen, R. Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within-species variation. Mol. Biol. Evol. 31, 201-211 (2014).
-
(2014)
Mol. Biol. Evol
, vol.31
, pp. 201-211
-
-
Rohlfs, R.V.1
Harrigan, P.2
Nielsen, R.3
-
91
-
-
57149084867
-
Gene regulation in primates evolves under tissue-specific selection pressures
-
Blekhman, R., Oshlack, A., Chabot, A. E., Smyth, G. K. & Gilad, Y. Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet. 4, e1000271 (2008).
-
(2008)
PLoS Genet
, vol.4
, pp. e1000271
-
-
Blekhman, R.1
Oshlack, A.2
Chabot, A.E.3
Smyth, G.K.4
Gilad, Y.5
-
92
-
-
0030772835
-
Stabilizing selection and the comparative analysis of adaptation
-
Hansen, T. F. Stabilizing selection and the comparative analysis of adaptation. Evolution 51, 1341-1351 (1997).
-
(1997)
Evolution
, vol.51
, pp. 1341-1351
-
-
Hansen, T.F.1
-
93
-
-
11944264347
-
Phylogenetic comparative analysis: A modelling approach for adaptive evolution
-
Butler, M. A. & King, A. A. Phylogenetic comparative analysis: a modelling approach for adaptive evolution. Am. Nat. 164, 683-695 (2004).
-
(2004)
Am. Nat
, vol.164
, pp. 683-695
-
-
Butler, M.A.1
King, A.A.2
-
94
-
-
79958259071
-
Genomic signatures of diet-related shifts during human origins
-
Babbitt, C. C., Warner, L. R., Fedrigo, O., Wall, C. E. & Wray, G. A. Genomic signatures of diet-related shifts during human origins. Proc. Biol. Sci. 278, 961-969 (2011).
-
(2011)
Proc. Biol. Sci
, vol.278
, pp. 961-969
-
-
Babbitt, C.C.1
Warner, L.R.2
Fedrigo, O.3
Wall, C.E.4
Wray, G.A.5
-
95
-
-
13244281707
-
Prefrontal white matter volume is disproportionately larger in humans tha n in other primates
-
Schoenemann, P. T., Sheehan, M. J. & Glotzer, L. D. Prefrontal white matter volume is disproportionately larger in humans tha n in other primates. Nature Neurosci. 8, 242-252 (2005).
-
(2005)
Nature Neurosci
, vol.8
, pp. 242-252
-
-
Schoenemann, P.T.1
Sheehan, M.J.2
Glotzer, L.D.3
-
96
-
-
34248641119
-
Adaptation or biased gene conversion Extending the null hypothesis of molecular evolution
-
Galtier, N. & Duret, L. Adaptation or biased gene conversion Extending the null hypothesis of molecular evolution. Trends Genet. 23, 273-277 (2007).
-
(2007)
Trends Genet
, vol.23
, pp. 273-277
-
-
Galtier, N.1
Duret, L.2
-
97
-
-
58149328496
-
Gc-biased gene conversion promotes the fixation of deleterious amino acid changes in primates
-
Galtier, N., Duret, L., Glemin, S. & Ranwez, V. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet. 25, 1-5 (2009).
-
(2009)
Trends Genet
, vol.25
, pp. 1-5
-
-
Galtier, N.1
Duret, L.2
Glemin, S.3
Ranwez, V.4
-
98
-
-
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
-
99
-
-
59849095985
-
Comment on " human-specific gain of function in a developmental enhancer"
-
Duret, L. & Galtier, N. Comment on " Human-specific gain of function in a developmental enhancer".Science 323, 714 (2009).
-
(2009)
Science
, vol.323
, pp. 714
-
-
Duret, L.1
Galtier, N.2
-
100
-
-
84888838351
-
Primate transcript and protein expression levels evolve under compensatory selection pressures
-
Khan, Z. et al. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science 342, 1100-1104 (2013).
-
(2013)
Science
, vol.342
, pp. 1100-1104
-
-
Khan, Z.1
-
101
-
-
57749195712
-
Rna-seq a revolutionary tool for transcriptomics
-
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev. Genet. 10, 57-63 (2009).
-
(2009)
Nature Rev. Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
102
-
-
84864994884
-
Iterative signature algorithm for the analysis of large-scale gene expression data
-
Bergmann, S., Ihmels, J. & Barkai, N. Iterative signature algorithm for the analysis of large-scale gene expression data. Phys. Rev. E Stat. Nonlin Soft Matter Phys. 67, 031902 (2003).
-
(2003)
Phys. Rev. e Stat. Nonlin Soft Matter Phys
, vol.67
, pp. 031902
-
-
Bergmann, S.1
Ihmels, J.2
Barkai, N.3
-
103
-
-
84858967131
-
Comparative modular analysis of gene expression in vertebrate organs
-
Piasecka, B., Kutalik, Z., Roux, J., Bergmann, S. & Robinson-Rechavi, M. Comparative modular analysis of gene expression in vertebrate organs. BMC Genomics 13, 124 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 124
-
-
Piasecka, B.1
Kutalik, Z.2
Roux, J.3
Bergmann, S.4
Robinson-Rechavi, M.5
-
104
-
-
33845231723
-
Conservation and evolution of gene coexpression networks in human and chimpanzee brains
-
Oldham, M.C., Horvath, S. & Geschwind, D.H. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc. Natl Acad. Sci. USA 103, 17973-17978 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 17973-17978
-
-
Oldham, M.C.1
Horvath, S.2
Geschwind, D.H.3
-
105
-
-
84865374280
-
Human-specific transcriptional networks in the brain
-
Kono pka, G. et al. Human-specific transcriptional networks in the brain. Neuron 75, 601-617 (2012).
-
(2012)
Neuron
, vol.75
, pp. 601-617
-
-
Konopka, G.1
-
106
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stu art, J. M., Segal, E., Koller, D. & Kim, S. K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-255 (2003).
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
107
-
-
0033977618
-
Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
-
Duret, L. & Mouchiroud, D. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17, 68-74 (2000).
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 68-74
-
-
Duret, L.1
Mouchiroud, D.2
-
108
-
-
77952359315
-
Contrasts between adaptive coding and noncoding changes during human evolution
-
Haygood, R., Babbitt, C. C., Fedrigo, O. & Wray, G. A. Contrasts between adaptive coding and noncoding changes during human evolution. Proc. Natl Acad. Sci. USA 107, 7853-7857 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 7853-7857
-
-
Haygood, R.1
Babbitt, C.C.2
Fedrigo, O.3
Wray, G.A.4
-
109
-
-
84905484562
-
Cis and trans effects of human genomic variants on gene expression
-
Bryois J.,et al. Cis and trans effects of human genomic variants on gene expression PLoS Genet. 10, e1004461, 2014).
-
(2014)
PLoS Genet
, vol.10
, pp. e1004461
-
-
Bryois, J.1
-
110
-
-
29144492108
-
Ancient and recent positive selection transformed opioid cis-regulation in humans
-
Rockman, M. V. et al. Ancient and recent positive selection transformed opioid cis-regulation in humans. PLoS Biol. 3, e387 (2005).
-
(2005)
PLoS Biol
, vol.3
, pp. e387
-
-
Rockman, M.V.1
-
111
-
-
55049123524
-
Rapidly evolving human promoter regions
-
Taylor, M. S. et al. Rapidly evolving human promoter regions. Nature Genet. 40, 1262-1263 (2008).
-
(2008)
Nature Genet
, vol.40
, pp. 1262-1263
-
-
Taylor, M.S.1
-
112
-
-
70149100044
-
Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence
-
Torgerson, D. G. et al. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet. 5, e1000592 (2009).
-
(2009)
PLoS Genet
, vol.5
, pp. e1000592
-
-
Torgerson, D.G.1
-
113
-
-
84892714881
-
Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents
-
Halligan, D. L. et al. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genet. 9, e1003995 (2013).
-
(2013)
PLoS Genet
, vol.9
, pp. e1003995
-
-
Halligan, D.L.1
-
114
-
-
50849144848
-
Selective constraints in experimentally defined primate regulatory regions
-
Gaffney, D. J., Blekhman, R. & Majewski, J. Selective constraints in experimentally defined primate regulatory regions. PLoS Genet. 4, e1000157 (2008).
-
(2008)
PLoS Genet
, vol.4
, pp. e1000157
-
-
Gaffney, D.J.1
Blekhman, R.2
Majewski, J.3
-
115
-
-
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
-
116
-
-
84863393570
-
Waves of retrotransposon expansion remodel genome organization and ctcf binding in multiple mammalian lineages
-
Schmidt, D. et al. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148, 335-348 (2012).
-
(2012)
Cell
, vol.148
, pp. 335-348
-
-
Schmidt, D.1
-
117
-
-
84884678913
-
Dynamics of dna methylation in recent human and great ape evolution
-
Hernando-Herraez, I. et al. Dynamics of DNA methylation in recent human and great ape evolution. PLoS Genet. 9, e1003763 (2013).
-
(2013)
PLoS Genet
, vol.9
, pp. e1003763
-
-
Hernando-Herraez, I.1
-
118
-
-
79952265169
-
Genome-wide study of dna methylation patterns and gene expression levels in multiple human and chimpanzee tissues
-
Pai, A. A., Bell, J. T., Marioni, J. C., Pritchard, J. K. & Gilad, Y. A. Genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Gene t. 7, e1001316 (2011).
-
(2011)
PLoS Gene T
, vol.7
, pp. e1001316
-
-
Pai, A.A.1
Bell, J.T.2
Marioni, J.C.3
Pritchard, J.K.4
Gilad, Y.A.5
-
119
-
-
84870260582
-
Human-specific histone methylation signatures at transcription start sites in prefrontal neurons
-
Shulha, H. P. et al. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol. 10, e1001427 (2012).
-
(2012)
PLoS Biol
, vol.10
, pp. e1001427
-
-
Shulha, H.P.1
-
120
-
-
79955403252
-
Gene expression differences among primates are associated with changes in a histone epigenetic modification
-
Cain, C. E., Blekhman, R., Marioni, J. C. & Gilad, Y. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics 187, 1225-1234 (2011).
-
(2011)
Genetics
, vol.187
, pp. 1225-1234
-
-
Cain, C.E.1
Blekhman, R.2
Marioni, J.C.3
Gilad, Y.4
-
121
-
-
80055092199
-
Microrna expression and regulation in human, chimpanzee, and macaque brains
-
Hu, H. Y. et al. MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genet. 7, e1002327 (2011).
-
(2011)
PLoS Genet
, vol.7
, pp. e1002327
-
-
Hu, H.Y.1
-
122
-
-
77956275374
-
Microrna, mrn a, and protein expression link development and aging in human and macaque brain
-
Somel, M. et al. MicroRNA, mRN A, and protein expression link development and aging in human and macaque brain. Genome Res. 20, 1207-1218 (2010).
-
(2010)
Genome Res
, vol.20
, pp. 1207-1218
-
-
Somel, M.1
-
123
-
-
84869485949
-
Evolution of the human-specific microrna mir-941
-
Hu, H. Y. et al. Evolution of the human-specific microRNA miR-941. Nature Commun. 3, 1145 (2012).
-
(2012)
Nature Commun
, vol.3
, pp. 1145
-
-
Hu, H.Y.1
-
124
-
-
84875369248
-
Circular rnas are a large class of animal rnas with regulatory potency
-
Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333-338 (2013).
-
(2013)
Nature
, vol.495
, pp. 333-338
-
-
Memczak, S.1
-
125
-
-
84875372911
-
Natural rna circles function as efficient microrna sponges
-
Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384-388 (2013).
-
(2013)
Nature
, vol.495
, pp. 384-388
-
-
Hansen, T.1
-
126
-
-
65249099621
-
Transcriptional neoteny in the human brain
-
Somel, M. et al. Transcriptional neoteny in the human brain. Proc. Natl Acad. Sci. USA 106, 5743-5748 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 5743-5748
-
-
Somel, M.1
-
127
-
-
79953113902
-
Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis
-
Irie, N. & Kuratani, S. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nature Commun. 2, 248 (2011).
-
(2011)
Nature Commun
, vol.2
, pp. 248
-
-
Irie, N.1
Kuratani, S.2
-
128
-
-
84894630323
-
Entering the era of single-cell transcriptomics in biology and medicine
-
Sandberg, R. Entering the era of single-cell transcriptomics in biology and medicine. Nature Methods 11, 22-24 (2013).
-
(2013)
Nature Methods
, vol.11
, pp. 22-24
-
-
Sandberg, R.1
-
129
-
-
84897394513
-
The functional consequences of variation in transcription factor binding
-
Cusanovich, D. A., Pavlovic, B., Pritchard, J. K. & Gilad, Y. The functional consequences of variation in transcription factor binding. PLoS Genet. 10, e1004226 (2014).
-
(2014)
PLoS Genet
, vol.10
, pp. e1004226
-
-
Cusanovich, D.A.1
Pavlovic, B.2
Pritchard, J.3
Gilad, Y.4
-
130
-
-
84865739425
-
Architecture of the human regulatory network derived from encode data
-
Gerstein M. B.,et al. Architecture of the human regulatory network derived from ENCODE data Nature 489, 91-100, 2012).
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
-
131
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380 (2012).
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
-
132
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary dna microarray
-
Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 , 467-470 (1995).
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
133
-
-
79957665988
-
Microarrays deep sequencing and the true measure of the transcriptome
-
Malone, J. H. & Oliver, B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol. 9, 34 (2011).
-
(2011)
BMC Biol
, vol.9
, pp. 34
-
-
Malone, J.H.1
Oliver, B.2
-
134
-
-
33750482555
-
Functionality of intergenic transcription: An evolutionary comparison
-
Khaitovich, P. et al. Functionality of intergenic transcription: an evolutionary comparison. PLoS Genet. 2, e171 (2006).
-
(2006)
PLoS Genet
, vol.2
, pp. e171
-
-
Khaitovich, P.1
-
135
-
-
34447336411
-
Using dna microarrays to study gene expression in closely related species
-
Oshlack, A., Chabot, A. E., Smyth, G. K. & Gilad, Y. Using DNA microarrays to study gene expression in closely related species. Bioinformatics 23, 1235-1242 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 1235-1242
-
-
Oshlack, A.1
Chabot, A.E.2
Smyth, G.K.3
Gilad, Y.4
-
136
-
-
0242268390
-
Elevated gene expression levels distinguish human from non-human primate brains
-
Caceres, M. et al. Elevated gene expression levels distinguish human from non-human primate brains. Proc. Natl Acad. Sci. USA 100, 13030-13035 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 13030-13035
-
-
Caceres, M.1
-
137
-
-
65649083411
-
Estimating accuracy of rna-seq and microarrays with proteomics
-
Fu, X. et al. Estimating accuracy of RNA-seq and microarrays with proteomics. BMC Genomics 10, 161 (2009).
-
(2009)
BMC Genomics
, vol.10
, pp. 161
-
-
Fu, X.1
-
138
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using rna-seq
-
Garber, M., Grabherr, M. G., Guttman, M. & Trapnell, C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods 8, 469-477 (2011).
-
(2011)
Nature Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
139
-
-
84859552481
-
Comparative rna sequencing reveals substantial genetic variation in endangered primates
-
Perry, G. H. et al. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 22, 602-610 (2011).
-
(2011)
Genome Res
, vol.22
, pp. 602-610
-
-
Perry, G.H.1
-
140
-
-
84864101947
-
Transcription factors are targeted by differentially expressed mirnas in primates
-
Dannemann, M. et al. Transcription factors are targeted by differentially expressed miRNAs in primates. Genome Biol. Evol. 4, 552-564 (2012).
-
(2012)
Genome Biol. Evol
, vol.4
, pp. 552-564
-
-
Dannemann, M.1
-
141
-
-
84888419634
-
Evolutionary and ontogenetic changes in rna editing in human, chimpanzee, and macaque brains
-
Li, Z. et al. Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains. RNA 19, 1693-1702 (2013).
-
(2013)
RNA
, vol.19
, pp. 1693-1702
-
-
Li, Z.1
-
142
-
-
84908156465
-
Conserved microrna e diting in mammalian evolution, development and disease
-
Warnefors, M., Liechti, A., Halbert, J., Valloton, D. & Kaessmann, H. Conserved microRNA e diting in mammalian evolution, development and disease. Genome Biol. 15, R83 (2014).
-
(2014)
Genome Biol
, vol.15
, pp. R83
-
-
Warnefors, M.1
Liechti, A.2
Halbert, J.3
Valloton, D.4
Kaessmann, H.5
-
143
-
-
77957914800
-
Evolution of alternative splicing in primate brain transcriptomes
-
Lin, L. et al. Evolution of alternative splicing in primate brain transcriptomes. Hum. Mol. Genet. 19, 2958-2973 (2010).
-
(2010)
Hum. Mol. Genet
, vol.19
, pp. 2958-2973
-
-
Lin, L.1
-
144
-
-
77955090515
-
Both noncoding and protein-coding rnas contribute to gene expression evolution in the primate brain
-
Babbitt, C. C. et al. Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain. Genome Biol. Evol. 2, 67-79 (2010).
-
(2010)
Genome Biol. Evol
, vol.2
, pp. 67-79
-
-
Babbitt, C.C.1
-
145
-
-
34547803197
-
Paml 4: Phylogenetic analysis by maximum likelihood
-
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
146
-
-
59949096873
-
Ensemblcompara genetrees: Complete, duplication-Aware phylogenetic trees in vertebrates
-
Vilella, A. J. et al. EnsemblCompara GeneTrees: complete, duplication-Aware phylogenetic trees in vertebrates. Genome Res. 19, 327-335 (2009).
-
(2009)
Genome Res
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
-
147
-
-
84891768365
-
Ensembl 2014
-
Flicek, P. et al. Ensembl 2014. Nucleic Acids Res. 42, D749-D755 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D749-D755
-
-
Flicek, P.1
|