-
2
-
-
80053555789
-
More than just a focus: the chromatin response to DNA damage and its role in genome integrity maintenance
-
Lukas J., et al. More than just a focus: the chromatin response to DNA damage and its role in genome integrity maintenance. Nat. Cell Biol. 2011, 13:1161-1169.
-
(2011)
Nat. Cell Biol.
, vol.13
, pp. 1161-1169
-
-
Lukas, J.1
-
3
-
-
79955482843
-
Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development
-
Okamoto I., et al. Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development. Nature 2011, 472:370-374.
-
(2011)
Nature
, vol.472
, pp. 370-374
-
-
Okamoto, I.1
-
4
-
-
66049083160
-
X inactivation and the complexities of silencing a sex chromosome
-
Chow J., Heard E. X inactivation and the complexities of silencing a sex chromosome. Curr. Opin. Cell Biol. 2009, 21:359-366.
-
(2009)
Curr. Opin. Cell Biol.
, vol.21
, pp. 359-366
-
-
Chow, J.1
Heard, E.2
-
5
-
-
84864867828
-
Establishment of epigenetic patterns in development
-
Leeb M., Wutz A. Establishment of epigenetic patterns in development. Chromosoma 2012, 121:251-262.
-
(2012)
Chromosoma
, vol.121
, pp. 251-262
-
-
Leeb, M.1
Wutz, A.2
-
6
-
-
0024870633
-
The biological homology concept
-
Wagner G.P. The biological homology concept. Annu. Rev. Ecol. Syst. 1989, 20:51-69.
-
(1989)
Annu. Rev. Ecol. Syst.
, vol.20
, pp. 51-69
-
-
Wagner, G.P.1
-
7
-
-
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 2010, 330:1775-1787.
-
(2010)
Science
, vol.330
, pp. 1775-1787
-
-
Gerstein, M.B.1
-
8
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
Consortium modENCODE., et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010, 330:1787-1797.
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
Consortium, M.1
-
9
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Consortium R.E., et al. Integrative analysis of 111 reference human epigenomes. Nature 2015, 518:317-330.
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
Consortium, R.E.1
-
10
-
-
84865121188
-
An encyclopedia of mouse DNA elements (Mouse ENCODE)
-
Mouse ENCODE Consortium, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012, 13:418.
-
(2012)
Genome Biol.
, vol.13
, pp. 418
-
-
-
11
-
-
0014421064
-
Evolutionary rate at the molecular level
-
Kimura M. Evolutionary rate at the molecular level. Nature 1968, 217:624-626.
-
(1968)
Nature
, vol.217
, pp. 624-626
-
-
Kimura, M.1
-
12
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio L.A., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006, 444:499-502.
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
-
13
-
-
84866150923
-
Human developmental enhancers conserved between deuterostomes and protostomes
-
Clarke S.L., et al. Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 2012, 8:e1002852.
-
(2012)
PLoS Genet.
, vol.8
-
-
Clarke, S.L.1
-
14
-
-
34250365369
-
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
-
Margulies E.H., et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007, 17:760-774.
-
(2007)
Genome Res.
, vol.17
, pp. 760-774
-
-
Margulies, E.H.1
-
15
-
-
39049086371
-
Qualifying the relationship between sequence conservation and molecular function
-
Cooper G.M., Brown C.D. Qualifying the relationship between sequence conservation and molecular function. Genome Res. 2008, 18:201-205.
-
(2008)
Genome Res.
, vol.18
, pp. 201-205
-
-
Cooper, G.M.1
Brown, C.D.2
-
16
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King M.C., Wilson A.C. Evolution at two levels in humans and chimpanzees. Science 1975, 188:107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
17
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
Wray G.A. The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 2007, 8:206-216.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
18
-
-
77953271655
-
Comparative assessment of methods for aligning multiple genome sequences
-
Chen X., Tompa M. Comparative assessment of methods for aligning multiple genome sequences. Nat. Biotechnol. 2010, 28:567-572.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 567-572
-
-
Chen, X.1
Tompa, M.2
-
19
-
-
0014690698
-
Gene regulation for higher cells: a theory
-
Britten R.J., Davidson E.H. Gene regulation for higher cells: a theory. Science 1969, 165:349-357.
-
(1969)
Science
, vol.165
, pp. 349-357
-
-
Britten, R.J.1
Davidson, E.H.2
-
21
-
-
77954100084
-
Transposable elements have rewired the core regulatory network of human embryonic stem cells
-
Kunarso G., et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet. 2010, 42:631-634.
-
(2010)
Nat. Genet.
, vol.42
, pp. 631-634
-
-
Kunarso, G.1
-
22
-
-
77956641239
-
ChIP-Seq identification of weakly conserved heart enhancers
-
Blow M.J., et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 2010, 42:806-810.
-
(2010)
Nat. Genet.
, vol.42
, pp. 806-810
-
-
Blow, M.J.1
-
23
-
-
84929320904
-
Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility
-
Dogan N., et al. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin 2015, 8:16.
-
(2015)
Epigenetics Chromatin
, vol.8
, pp. 16
-
-
Dogan, N.1
-
24
-
-
0028143457
-
Comparative analysis of Igf-2/H19 imprinted domain: identification of a highly conserved intergenic DNase I hypersensitive region
-
Koide T., et al. Comparative analysis of Igf-2/H19 imprinted domain: identification of a highly conserved intergenic DNase I hypersensitive region. Genomics 1994, 24:1-8.
-
(1994)
Genomics
, vol.24
, pp. 1-8
-
-
Koide, T.1
-
25
-
-
0031593199
-
Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights
-
Hardison R., et al. Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene 1997, 205:73-94.
-
(1997)
Gene
, vol.205
, pp. 73-94
-
-
Hardison, R.1
-
26
-
-
0344011426
-
Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci
-
Follows G.A., et al. Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci. Nucleic Acids Res. 2003, 31:5805-5816.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5805-5816
-
-
Follows, G.A.1
-
27
-
-
33751234242
-
The human and mouse H19 imprinting control regions harbor an evolutionarily conserved silencer element that functions on transgenes in Drosophila
-
Arney K.L., et al. The human and mouse H19 imprinting control regions harbor an evolutionarily conserved silencer element that functions on transgenes in Drosophila. Dev. Genes Evol. 2006, 216:811-819.
-
(2006)
Dev. Genes Evol.
, vol.216
, pp. 811-819
-
-
Arney, K.L.1
-
28
-
-
48249141249
-
Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians
-
Smits G., et al. Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians. Nat. Genet. 2008, 40:971-976.
-
(2008)
Nat. Genet.
, vol.40
, pp. 971-976
-
-
Smits, G.1
-
29
-
-
0033634728
-
M6P/IGF2R imprinting evolution in mammals
-
Killian J.K., et al. M6P/IGF2R imprinting evolution in mammals. Mol. Cell 2000, 5:707-716.
-
(2000)
Mol. Cell
, vol.5
, pp. 707-716
-
-
Killian, J.K.1
-
30
-
-
84926098534
-
Sequence-level mechanisms of human epigenome evolution
-
Prendergast J.G.D., et al. Sequence-level mechanisms of human epigenome evolution. Genome Biol. Evol. 2014, 6:1758-1771.
-
(2014)
Genome Biol. Evol.
, vol.6
, pp. 1758-1771
-
-
Prendergast, J.G.D.1
-
31
-
-
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. 2013, 9:e1003763-e1003812.
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003763-e1003812
-
-
Hernando-Herraez, I.1
-
32
-
-
84949024094
-
The interplay between DNA methylation and sequence divergence in recent human evolution
-
Hernando-Herraez I., et al. The interplay between DNA methylation and sequence divergence in recent human evolution. Nucleic Acids Res. 2015, 43:8204-8214.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 8204-8214
-
-
Hernando-Herraez, I.1
-
33
-
-
84924561748
-
Evolutionary changes in promoter and enhancer activity during human corticogenesis
-
Reilly S.K., et al. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 2015, 347:1155-1159.
-
(2015)
Science
, vol.347
, pp. 1155-1159
-
-
Reilly, S.K.1
-
34
-
-
84861977900
-
Comparative epigenomic annotation of regulatory DNA
-
Xiao S., et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012, 149:1381-1392.
-
(2012)
Cell
, vol.149
, pp. 1381-1392
-
-
Xiao, S.1
-
35
-
-
33745772571
-
New methods for detecting lineage-specific selection
-
Springer Berlin Heidelberg
-
Siepel A., et al. New methods for detecting lineage-specific selection. Research in Computational Molecular Biology 2006, Vol. 3909:190-205. Springer Berlin Heidelberg.
-
(2006)
Research in Computational Molecular Biology
, vol.3909
, pp. 190-205
-
-
Siepel, A.1
-
36
-
-
84879911829
-
The evolution of lineage-specific regulatory activities in the human embryonic limb
-
Cotney J., et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 2013, 154:185-196.
-
(2013)
Cell
, vol.154
, pp. 185-196
-
-
Cotney, J.1
-
37
-
-
0026001046
-
CpG islands: features and distribution in the genomes of vertebrates
-
Aïssani B., Bernardi G. CpG islands: features and distribution in the genomes of vertebrates. Gene 1991, 106:173-183.
-
(1991)
Gene
, vol.106
, pp. 173-183
-
-
Aïssani, B.1
Bernardi, G.2
-
38
-
-
84879049092
-
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
-
Long H.K., et al. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife 2013, 2:e00348.
-
(2013)
Elife
, vol.2
-
-
Long, H.K.1
-
39
-
-
0021924990
-
Effect of regional DNA methylation on gene expression
-
Keshet I., et al. Effect of regional DNA methylation on gene expression. Proc. Natl. Acad. Sci. U.S.A. 1985, 82:2560-2564.
-
(1985)
Proc. Natl. Acad. Sci. U.S.A.
, vol.82
, pp. 2560-2564
-
-
Keshet, I.1
-
40
-
-
0023057868
-
In vitro methylation inhibits the promotor activity of a cloned intracisternal A-particle LTR
-
Feenastr A., et al. In vitro methylation inhibits the promotor activity of a cloned intracisternal A-particle LTR. Nucleic Acids Res. 1986, 14:4343-4352.
-
(1986)
Nucleic Acids Res.
, vol.14
, pp. 4343-4352
-
-
Feenastr, A.1
-
41
-
-
38949212693
-
A novel CpG island set identifies tissue-specific methylation at developmental gene loci
-
Illingworth R., et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 2008, 6:e22.
-
(2008)
PLoS Biol.
, vol.6
, pp. e22
-
-
Illingworth, R.1
-
42
-
-
79952265169
-
A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues
-
Pai A.A., et al. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet. 2011, 7:e1001316.
-
(2011)
PLoS Genet.
, vol.7
-
-
Pai, A.A.1
-
43
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002, 16:6-21.
-
(2002)
Genes Dev.
, vol.16
, pp. 6-21
-
-
Bird, A.1
-
44
-
-
84923345958
-
Intermediate DNA methylation is a conserved signature of genome regulation
-
Elliott G., et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nat. Commun. 2015, 6:6363.
-
(2015)
Nat. Commun.
, vol.6
, pp. 6363
-
-
Elliott, G.1
-
45
-
-
43749098985
-
DNA methylation landscapes: provocative insights from epigenomics
-
Suzuki M.M., Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 2008, 9:465-476.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 465-476
-
-
Suzuki, M.M.1
Bird, A.2
-
46
-
-
80054994283
-
Identification of genetic elements that autonomously determine DNA methylation states
-
Lienert F., et al. Identification of genetic elements that autonomously determine DNA methylation states. Nat. Genet. 2011, 43:1091-1097.
-
(2011)
Nat. Genet.
, vol.43
, pp. 1091-1097
-
-
Lienert, F.1
-
47
-
-
84899093961
-
DNA methylation and evolution of duplicate genes
-
Keller T.E., Yi S.V. DNA methylation and evolution of duplicate genes. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:5932-5937.
-
(2014)
Proc. Natl. Acad. Sci. U.S.A.
, vol.111
, pp. 5932-5937
-
-
Keller, T.E.1
Yi, S.V.2
-
48
-
-
0027960055
-
Sp1 sites in the mouse Aprt gene promoter are required to prevent methylation of the CpG island
-
Macleod D., et al. Sp1 sites in the mouse Aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 1994, 8:2282-2292.
-
(1994)
Genes Dev.
, vol.8
, pp. 2282-2292
-
-
Macleod, D.1
-
49
-
-
84892690160
-
Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions
-
Feldmann A., et al. Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet. 2013, 9:e1003994.
-
(2013)
PLoS Genet.
, vol.9
-
-
Feldmann, A.1
-
50
-
-
84922621952
-
Function and information content of DNA methylation
-
Schübeler D. Function and information content of DNA methylation. Nature 2015, 517:321-326.
-
(2015)
Nature
, vol.517
, pp. 321-326
-
-
Schübeler, D.1
-
51
-
-
84922295278
-
Enhancer evolution across 20 mammalian species
-
Villar D., et al. Enhancer evolution across 20 mammalian species. Cell 2015, 160:554-566.
-
(2015)
Cell
, vol.160
, pp. 554-566
-
-
Villar, D.1
-
52
-
-
77952734605
-
Conservation and divergence of methylation patterning in plants and animals
-
Feng S., et al. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:8689-8694.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 8689-8694
-
-
Feng, S.1
-
53
-
-
77952355762
-
Genome-wide evolutionary analysis of eukaryotic DNA methylation
-
Zemach A., et al. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010, 328:916-919.
-
(2010)
Science
, vol.328
, pp. 916-919
-
-
Zemach, A.1
-
54
-
-
69949132191
-
Chromatin organization marks exon-intron structure
-
Schwartz S., et al. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 2009, 16:990-995.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 990-995
-
-
Schwartz, S.1
-
55
-
-
84859033105
-
DNA methylation rebalances gene dosage after mammalian gene duplications
-
Chang A.Y-F., Liao B-Y. DNA methylation rebalances gene dosage after mammalian gene duplications. Mol. Biol. Evol. 2012, 29:133-144.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 133-144
-
-
Chang, A.Y.-F.1
Liao, B.-Y.2
-
56
-
-
84866081028
-
Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution
-
Zeng J., et al. Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. Am. J. Hum. Genet. 2012, 91:455-465.
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 455-465
-
-
Zeng, J.1
-
57
-
-
84940752163
-
Early developmental and evolutionary origins of gene body DNA methylation patterns in mammalian placentas
-
Schroeder D.I., et al. Early developmental and evolutionary origins of gene body DNA methylation patterns in mammalian placentas. PLoS Genet. 2015, 11:e1005442.
-
(2015)
PLoS Genet.
, vol.11
-
-
Schroeder, D.I.1
-
58
-
-
61349098460
-
Differential chromatin marking of introns and expressed exons by H3K36me3
-
Kolasinska-Zwierz P., et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 2009, 41:376-381.
-
(2009)
Nat. Genet.
, vol.41
, pp. 376-381
-
-
Kolasinska-Zwierz, P.1
-
59
-
-
77149175671
-
Regulation of alternative splicing by histone modifications
-
Luco R.F., et al. Regulation of alternative splicing by histone modifications. Science 2010, 327:996-1000.
-
(2010)
Science
, vol.327
, pp. 996-1000
-
-
Luco, R.F.1
-
60
-
-
84956647649
-
Regulation of mismatch repair by histone code and posttranslational modifications in eukaryotic cells
-
Li F., et al. Regulation of mismatch repair by histone code and posttranslational modifications in eukaryotic cells. DNA Repair 2016, 38:68-74.
-
(2016)
DNA Repair
, vol.38
, pp. 68-74
-
-
Li, F.1
-
61
-
-
84938830634
-
Chromatin signature identifies monoallelic gene expression across mammalian cell types
-
Nag A., et al. Chromatin signature identifies monoallelic gene expression across mammalian cell types. G3 2015, 5:1713-1720.
-
(2015)
G3
, vol.5
, pp. 1713-1720
-
-
Nag, A.1
-
62
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman N.D., et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009, 459:108-112.
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
-
63
-
-
84890397089
-
Predicting enhancer transcription and activity from chromatin modifications
-
Zhu Y., et al. Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Res. 2013, 41:10032-10043.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 10032-10043
-
-
Zhu, Y.1
-
64
-
-
84355163093
-
DNA-binding factors shape the mouse methylome at distal regulatory regions
-
Stadler M.B., et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011, 480:490-495.
-
(2011)
Nature
, vol.480
, pp. 490-495
-
-
Stadler, M.B.1
-
66
-
-
84872020892
-
Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state
-
Wilczynski B., et al. Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. PLoS Comput. Biol. 2012, 8:e1002798.
-
(2012)
PLoS Comput. Biol.
, vol.8
-
-
Wilczynski, B.1
-
67
-
-
84891390867
-
Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts
-
Hsu C-H., Ovcharenko I. Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2013, 368:20120366.
-
(2013)
Philos. Trans. R. Soc. Lond. B: Biol. Sci.
, vol.368
, pp. 20120366
-
-
Hsu, C.-H.1
Ovcharenko, I.2
-
68
-
-
77957220857
-
Comparative epigenomic analysis of murine and human adipogenesis
-
Mikkelsen T.S., et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 2010, 143:156-169.
-
(2010)
Cell
, vol.143
, pp. 156-169
-
-
Mikkelsen, T.S.1
-
69
-
-
84948457844
-
Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest
-
Prescott S.L., et al. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell 2015, 163:68-83.
-
(2015)
Cell
, vol.163
, pp. 68-83
-
-
Prescott, S.L.1
-
70
-
-
84904250693
-
Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
-
Tena J.J., et al. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period. Genome Res. 2014, 24:1075-1085.
-
(2014)
Genome Res.
, vol.24
, pp. 1075-1085
-
-
Tena, J.J.1
-
71
-
-
84868484735
-
Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
-
Rada-Iglesias A., et al. Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell 2012, 11:633-648.
-
(2012)
Cell Stem Cell
, vol.11
, pp. 633-648
-
-
Rada-Iglesias, A.1
-
72
-
-
84925680345
-
Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework
-
Yokoyama K.D., et al. Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework. PLoS Comput. Biol. 2014, 10:e1003771.
-
(2014)
PLoS Comput. Biol.
, vol.10
-
-
Yokoyama, K.D.1
-
73
-
-
84881141882
-
Cooperativity and rapid evolution of cobound transcription factors in closely related mammals
-
Stefflova K., et al. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell 2013, 154:530-540.
-
(2013)
Cell
, vol.154
, pp. 530-540
-
-
Stefflova, K.1
-
74
-
-
0028853170
-
NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region
-
Stamatoyannopoulos J.A., et al. NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region. EMBO J. 1995, 14:106-116.
-
(1995)
EMBO J.
, vol.14
, pp. 106-116
-
-
Stamatoyannopoulos, J.A.1
-
75
-
-
84911494217
-
Principles of regulatory information conservation between mouse and human
-
Cheng Y., et al. Principles of regulatory information conservation between mouse and human. Nature 2014, 515:371-375.
-
(2014)
Nature
, vol.515
, pp. 371-375
-
-
Cheng, Y.1
-
76
-
-
84911936991
-
Widespread contribution of transposable elements to the innovation of gene regulatory networks
-
Sundaram V., et al. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 2014, 24:1963-1976.
-
(2014)
Genome Res.
, vol.24
, pp. 1963-1976
-
-
Sundaram, V.1
-
77
-
-
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. Nat. Genet. 2007, 39:730-732.
-
(2007)
Nat. Genet.
, vol.39
, pp. 730-732
-
-
Odom, D.T.1
-
78
-
-
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 2010, 328:1036-1040.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
-
79
-
-
84864073098
-
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection
-
Shibata Y., et al. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet. 2012, 8:e1002789.
-
(2012)
PLoS Genet.
, vol.8
-
-
Shibata, Y.1
-
80
-
-
84911462077
-
A comparative encyclopedia of DNA elements in the mouse genome
-
Yue F., et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature 2014, 515:355-364.
-
(2014)
Nature
, vol.515
, pp. 355-364
-
-
Yue, F.1
-
81
-
-
19944430797
-
Genomic maps and comparative analysis of histone modifications in human and mouse
-
Bernstein B.E., et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 2005, 120:169-181.
-
(2005)
Cell
, vol.120
, pp. 169-181
-
-
Bernstein, B.E.1
-
82
-
-
84928236059
-
Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates
-
Chalopin D., et al. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol. Evol. 2015, 7:567-580.
-
(2015)
Genome Biol. Evol.
, vol.7
, pp. 567-580
-
-
Chalopin, D.1
-
83
-
-
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 2006, 441:87-90.
-
(2006)
Nature
, vol.441
, pp. 87-90
-
-
Bejerano, G.1
-
84
-
-
84877749322
-
Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?
-
de Souza F.S.J., et al. Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?. Mol. Biol. Evol. 2013, 30:1239-1251.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 1239-1251
-
-
de Souza, F.S.J.1
-
85
-
-
42349096534
-
Transposable elements and the evolution of regulatory networks
-
Feschotte C. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 2008, 9:397-405.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 397-405
-
-
Feschotte, C.1
-
86
-
-
0035986888
-
Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover
-
Dermitzakis E.T., Clark A.G. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 2002, 19:1114-1121.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1114-1121
-
-
Dermitzakis, E.T.1
Clark, A.G.2
-
87
-
-
33744824906
-
Evolutionary turnover of mammalian transcription start sites
-
Frith M.C. Evolutionary turnover of mammalian transcription start sites. Genome Res. 2006, 16:713-722.
-
(2006)
Genome Res.
, vol.16
, pp. 713-722
-
-
Frith, M.C.1
-
88
-
-
84911470871
-
Conservation of trans-acting circuitry during mammalian regulatory evolution
-
Stergachis A.B., et al. Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature 2014, 515:365-370.
-
(2014)
Nature
, vol.515
, pp. 365-370
-
-
Stergachis, A.B.1
-
89
-
-
0028104109
-
Spl elements protect a CpG island from de novo methylation
-
Brandeis M., et al. Spl elements protect a CpG island from de novo methylation. Nature 1994, 371:435-438.
-
(1994)
Nature
, vol.371
, pp. 435-438
-
-
Brandeis, M.1
-
90
-
-
59149084538
-
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
-
Irizarry R.A., et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 2009, 41:178-186.
-
(2009)
Nat. Genet.
, vol.41
, pp. 178-186
-
-
Irizarry, R.A.1
-
91
-
-
76549135113
-
Colloquium paper: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease
-
Feinberg A.P., Irizarry R.A. Colloquium paper: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:1757-1764.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 1757-1764
-
-
Feinberg, A.P.1
Irizarry, R.A.2
-
92
-
-
84855278198
-
Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development
-
Göke J., et al. Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development. PLoS Comput. Biol. 2011, 7:e1002304.
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Göke, J.1
-
93
-
-
51149203927
-
Canalization of development and the inheritance of acquired characters
-
Waddington C.H. Canalization of development and the inheritance of acquired characters. Nature 1942, 150:563-565.
-
(1942)
Nature
, vol.150
, pp. 563-565
-
-
Waddington, C.H.1
-
94
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
-
95
-
-
84882766972
-
Developmental fate and cellular maturity encoded in human regulatory DNA landscapes
-
Stergachis A.B., et al. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 2013, 154:888-903.
-
(2013)
Cell
, vol.154
, pp. 888-903
-
-
Stergachis, A.B.1
-
96
-
-
0026546877
-
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
-
Frommer M., et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:1827-1831.
-
(1992)
Proc. Natl. Acad. Sci. U.S.A.
, vol.89
, pp. 1827-1831
-
-
Frommer, M.1
-
97
-
-
27144500218
-
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
-
Meissner A., et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005, 33:5868-5877.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5868-5877
-
-
Meissner, A.1
-
98
-
-
77954504873
-
Conserved role of intragenic DNA methylation in regulating alternative promoters
-
Maunakea A.K., et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010, 466:253-257.
-
(2010)
Nature
, vol.466
, pp. 253-257
-
-
Maunakea, A.K.1
-
99
-
-
84863256915
-
Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA
-
Blackledge N.P., et al. Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. Nucleic Acids Res. 2012, 40:e32.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e32
-
-
Blackledge, N.P.1
-
100
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski A., et al. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
-
101
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman R.E., et al. The accessible chromatin landscape of the human genome. Nature 2012, 489:75-82.
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
-
102
-
-
0036645169
-
Transcription factor complex formation and chromatin fine structure alterations at the murine c-Fms (CSF-1 receptor) locus during maturation of myeloid precursor cells
-
Tagoh H., et al. Transcription factor complex formation and chromatin fine structure alterations at the murine c-Fms (CSF-1 receptor) locus during maturation of myeloid precursor cells. Genes Dev. 2002, 16:1721-1737.
-
(2002)
Genes Dev.
, vol.16
, pp. 1721-1737
-
-
Tagoh, H.1
-
103
-
-
1642512344
-
Evolution of eyes and photoreceptor cell types
-
Arendt D. Evolution of eyes and photoreceptor cell types. Int. J. Dev. Biol. 2003, 47:563-571.
-
(2003)
Int. J. Dev. Biol.
, vol.47
, pp. 563-571
-
-
Arendt, D.1
-
104
-
-
34249034031
-
The developmental genetics of homology
-
Wagner G.P. The developmental genetics of homology. Nat. Rev. Genet. 2007, 8:473-479.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 473-479
-
-
Wagner, G.P.1
-
105
-
-
84876940752
-
Divergence of mammalian higher order chromatin structure is associated with developmental loci
-
Chambers E.V., et al. Divergence of mammalian higher order chromatin structure is associated with developmental loci. PLoS Comput. Biol. 2013, 9:e1003017.
-
(2013)
PLoS Comput. Biol.
, vol.9
-
-
Chambers, E.V.1
|