-
1
-
-
0022540321
-
CpG-rich islands and the function of DNA methylation
-
Bird, A.P. (1986) CpG-rich islands and the function of DNA methylation. Nature, 321, 209-213
-
(1986)
Nature
, vol.321
, pp. 209-213
-
-
Bird, A.P.1
-
2
-
-
67349255210
-
CpG islands-'a rough guide'
-
Illingworth, R.S. and Bird, A.P. (2009) CpG islands-'a rough guide'. FEBS Lett., 583, 1713-1720
-
(2009)
FEBS Lett
, vol.583
, pp. 1713-1720
-
-
Illingworth, R.S.1
Bird, A.P.2
-
3
-
-
43749098985
-
DNAmethylation landscapes: provocative insights from epigenomics
-
Suzuki, M.M. and Bird, A. (2008)DNAmethylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet., 9, 465-476
-
(2008)
Nat. Rev. Genet
, vol.9
, pp. 465-476
-
-
Suzuki, M.M.1
Bird, A.2
-
4
-
-
79956330964
-
CpG islands and the regulation of transcription
-
Deaton, A.M. and Bird, A. (2011) CpG islands and the regulation of transcription. Genes Dev., 25, 1010-1022
-
(2011)
Genes Dev
, vol.25
, pp. 1010-1022
-
-
Deaton, A.M.1
Bird, A.2
-
5
-
-
38949212693
-
A novel CpG island set identifies tissue-specific methylation at developmental gene loci
-
Illingworth, R., Kerr, A., Desousa, D., Jorgensen, H., Ellis, P., Stalker, J., Jackson, D., Clee, C., Plumb, R., Rogers, J. et al. (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol., 6, e22
-
(2008)
PLoS Biol
, vol.6
-
-
Illingworth, R.1
Kerr, A.2
Desousa, D.3
Jorgensen, H.4
Ellis, P.5
Stalker, J.6
Jackson, D.7
Clee, C.8
Plumb, R.9
Rogers, J.10
-
6
-
-
0035839057
-
The role of DNAmethylation in mammalian epigenetics
-
Jones, P.A. and Takai, D. (2001) The role of DNAmethylation in mammalian epigenetics. Science, 293, 1068-1070
-
(2001)
Science
, vol.293
, pp. 1068-1070
-
-
Jones, P.A.1
Takai, D.2
-
7
-
-
34249279527
-
Stability and flexibility of epigenetic gene regulation in mammalian development
-
Reik, W. (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature, 447, 425-432
-
(2007)
Nature
, vol.447
, pp. 425-432
-
-
Reik, W.1
-
8
-
-
34047116826
-
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
-
Weber, M., Hellmann, I., Stadler, M.B., Ramos, L., Paabo, S., Rebhan, M. and Schubeler, D. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet., 39, 457-466
-
(2007)
Nat. Genet
, vol.39
, pp. 457-466
-
-
Weber, M.1
Hellmann, I.2
Stadler, M.B.3
Ramos, L.4
Paabo, S.5
Rebhan, M.6
Schubeler, D.7
-
9
-
-
0020489781
-
Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells
-
Ehrlich, M., Gama-Sosa, M.A., Huang, L.H., Midgett, R.M., Kuo, K.C., McCune, R.A. and Gehrke, C. (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res., 10, 2709-2721
-
(1982)
Nucleic Acids Res
, vol.10
, pp. 2709-2721
-
-
Ehrlich, M.1
Gama-Sosa, M.A.2
Huang, L.H.3
Midgett, R.M.4
Kuo, K.C.5
McCune, R.A.6
Gehrke, C.7
-
10
-
-
0020522019
-
Tissue-specific differences in DNA methylation in various mammals
-
Gama-Sosa, M.A., Midgett, R.M., Slagel, V.A., Githens, S., Kuo, K.C., Gehrke, C.W. and Ehrlich, M. (1983) Tissue-specific differences in DNA methylation in various mammals. Biochim. Biophys. Acta, 740, 212-219
-
(1983)
Biochim. Biophys. Acta
, vol.740
, pp. 212-219
-
-
Gama-Sosa, M.A.1
Midgett, R.M.2
Slagel, V.A.3
Githens, S.4
Kuo, K.C.5
Gehrke, C.W.6
Ehrlich, M.7
-
11
-
-
77649267695
-
Dynamic changes in the human methylome during differentiation
-
Laurent, L., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C.T., Low, H.M., Kin Sung, K.W., Rigoutsos, I., Loring, J. et al. (2010) Dynamic changes in the human methylome during differentiation. Genome Res., 20, 320-331
-
(2010)
Genome Res
, vol.20
, pp. 320-331
-
-
Laurent, L.1
Wong, E.2
Li, G.3
Huynh, T.4
Tsirigos, A.5
Ong, C.T.6
Low, H.M.7
Kin Sung, K.W.8
Rigoutsos, I.9
Loring, J.10
-
12
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister, R., Pelizzola, M., Dowen, R.H., Hawkins, R.D., Hon, G., Tonti-Filippini, J., Nery, J.R., Lee, L., Ye, Z., Ngo, Q.M. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
Tonti-Filippini, J.6
Nery, J.R.7
Lee, L.8
Ye, Z.9
Ngo, Q.M.10
-
13
-
-
84866081028
-
Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution
-
Zeng, J., Konopka, G., Hunt, B.G., Preuss, T.M., Geschwind, D. and Yi, S.V. (2012) Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. Am. J. Hum. Genet., 91, 455-465
-
(2012)
Am. J. Hum. Genet
, vol.91
, pp. 455-465
-
-
Zeng, J.1
Konopka, G.2
Hunt, B.G.3
Preuss, T.M.4
Geschwind, D.5
Yi, S.V.6
-
14
-
-
34250160167
-
Mechanisms regulating imprinted genes in clusters
-
Edwards, C.A. and Ferguson-Smith, A.C. (2007) Mechanisms regulating imprinted genes in clusters. Curr. Opin. Cell Biol., 19, 281-289
-
(2007)
Curr. Opin. Cell Biol
, vol.19
, pp. 281-289
-
-
Edwards, C.A.1
Ferguson-Smith, A.C.2
-
15
-
-
84879663784
-
Global epigenomic reconfiguration during mammalian brain development
-
Lister, R., Mukamel, E.A., Nery, J.R., Urich, M., Puddifoot, C.A., Johnson, N.D., Lucero, J., Huang, Y., Dwork, A.J., Schultz, M.D. et al. (2013) Global epigenomic reconfiguration during mammalian brain development. Science, 341, 1237905
-
(2013)
Science
, vol.341
-
-
Lister, R.1
Mukamel, E.A.2
Nery, J.R.3
Urich, M.4
Puddifoot, C.A.5
Johnson, N.D.6
Lucero, J.7
Huang, Y.8
Dwork, A.J.9
Schultz, M.D.10
-
16
-
-
0037068312
-
CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future
-
Esteller, M. (2002) CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future. Oncogene, 21, 5427-5440
-
(2002)
Oncogene
, vol.21
, pp. 5427-5440
-
-
Esteller, M.1
-
17
-
-
80053144962
-
A decade of exploring the cancer epigenome-biological and translational implications
-
Baylin, S.B. and Jones, P.A. (2011) A decade of exploring the cancer epigenome-biological and translational implications. Nat. Rev. Cancer, 11, 726-734
-
(2011)
Nat. Rev. Cancer
, vol.11
, pp. 726-734
-
-
Baylin, S.B.1
Jones, P.A.2
-
18
-
-
0034305821
-
DNA methylation in health and disease
-
Robertson, K.D. and Wolffe, A.P. (2000) DNA methylation in health and disease. Nat. Rev. Genet., 1, 11-19
-
(2000)
Nat. Rev. Genet
, vol.1
, pp. 11-19
-
-
Robertson, K.D.1
Wolffe, A.P.2
-
19
-
-
0023216891
-
CpG islands in vertebrate genomes
-
Gardiner-Garden, M. and Frommer, M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282
-
(1987)
J. Mol. Biol
, vol.196
, pp. 261-282
-
-
Gardiner-Garden, M.1
Frommer, M.2
-
20
-
-
0035999991
-
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences
-
Ponger, L. and Mouchiroud, D. (2002) CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics, 18, 631-633
-
(2002)
Bioinformatics
, vol.18
, pp. 631-633
-
-
Ponger, L.1
Mouchiroud, D.2
-
21
-
-
0037133565
-
Comprehensive analysis of CpG islands in human chromosomes 21 and 22
-
Takai, D. and Jones, P.A. (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl Acad. Sci. USA, 99, 3740-3745
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 3740-3745
-
-
Takai, D.1
Jones, P.A.2
-
22
-
-
84879049092
-
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
-
Long, H.K., Sims, D., Heger, A., Blackledge, N.P., Kutter, C., Wright, M.L., Grutzner, F., Odom, D.T., Patient, R., Ponting, C.P. et al. (2013) Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife, 2, e00348
-
(2013)
Elife
, vol.2
-
-
Long, H.K.1
Sims, D.2
Heger, A.3
Blackledge, N.P.4
Kutter, C.5
Wright, M.L.6
Grutzner, F.7
Odom, D.T.8
Patient, R.9
Ponting, C.P.10
-
23
-
-
84899143629
-
Fundamental diversity of human CpG islands at multiple biological levels
-
Zeng, J., Nagrajan, H.K. and Yi, S.V. (2014) Fundamental diversity of human CpG islands at multiple biological levels. Epigenetics, 9, 483-491
-
(2014)
Epigenetics
, vol.9
, pp. 483-491
-
-
Zeng, J.1
Nagrajan, H.K.2
Yi, S.V.3
-
24
-
-
78049419464
-
Orphan CpG islands identify numerous conserved promoters in themammalian genome
-
Illingworth, R.S., Gruenewald-Schneider, U., Webb, S., Kerr, A. R., James, K.D., Turner, D.J., Smith, C., Harrison, D.J., Andrews, R. and Bird, A.P. (2010) Orphan CpG islands identify numerous conserved promoters in themammalian genome. PLoS Genet., 6, e1001134
-
(2010)
PLoS Genet
, vol.6
-
-
Illingworth, R.S.1
Gruenewald-Schneider, U.2
Webb, S.3
Kerr, A.R.4
James, K.D.5
Turner, D.J.6
Smith, C.7
Harrison, D.J.8
Andrews, R.9
Bird, A.P.10
-
25
-
-
79957577720
-
Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection
-
Cohen, N.M., Kenigsberg, E. and Tanay, A. (2011) Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell, 145, 773-786
-
(2011)
Cell
, vol.145
, pp. 773-786
-
-
Cohen, N.M.1
Kenigsberg, E.2
Tanay, A.3
-
26
-
-
84886834154
-
Identification of active regulatory regions fromDNA methylation data
-
Burger, L., Gaidatzis, D., Schubeler, D. and Stadler, M.B. (2013) Identification of active regulatory regions fromDNA methylation data. Nucleic Acids Res., 41, e155
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Burger, L.1
Gaidatzis, D.2
Schubeler, D.3
Stadler, M.B.4
-
27
-
-
84355163093
-
DNA-binding factors shape the mouse methylome at distal regulatory regions
-
Stadler, M.B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Scholer, A., Wirbelauer, C., Oakeley, E.J., Gaidatzis, D., Tiwari, V.K. et al. (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, 480, 490-495
-
(2011)
Nature
, vol.480
, pp. 490-495
-
-
Stadler, M.B.1
Murr, R.2
Burger, L.3
Ivanek, R.4
Lienert, F.5
Scholer, A.6
Wirbelauer, C.7
Oakeley, E.J.8
Gaidatzis, D.9
Tiwari, V.K.10
-
28
-
-
84878282421
-
Epigenomic analysis of multilineage differentiation of human embryonic stem cells
-
Xie, W., Schultz, M.D., Lister, R., Hou, Z., Rajagopal, N., Ray, P., Whitaker, J.W., Tian, S., Hawkins, R.D., Leung, D. et al. (2013) Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell, 153, 1134-1148
-
(2013)
Cell
, vol.153
, pp. 1134-1148
-
-
Xie, W.1
Schultz, M.D.2
Lister, R.3
Hou, Z.4
Rajagopal, N.5
Ray, P.6
Whitaker, J.W.7
Tian, S.8
Hawkins, R.D.9
Leung, D.10
-
29
-
-
77957940722
-
The NIH Roadmap Epigenomics Mapping Consortium
-
Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M.A., Beaudet, A.L., Ecker, J.R. et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol., 28, 1045-1048
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 1045-1048
-
-
Bernstein, B.E.1
Stamatoyannopoulos, J.A.2
Costello, J.F.3
Ren, B.4
Milosavljevic, A.5
Meissner, A.6
Kellis, M.7
Marra, M.A.8
Beaudet, A.L.9
Ecker, J.R.10
-
30
-
-
84898758414
-
Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
-
Court, F., Tayama, C., Romanelli, V., Martin-Trujillo, A., Iglesias-Platas, I., Okamura, K., Sugahara, N., Simon, C., Moore, H., Harness, J.V. et al. (2014) Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res., 24, 554-569
-
(2014)
Genome Res
, vol.24
, pp. 554-569
-
-
Court, F.1
Tayama, C.2
Romanelli, V.3
Martin-Trujillo, A.4
Iglesias-Platas, I.5
Okamura, K.6
Sugahara, N.7
Simon, C.8
Moore, H.9
Harness, J.V.10
-
31
-
-
80052918929
-
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment
-
Hodges, E., Molaro, A., Dos Santos, C.O., Thekkat, P., Song, Q., Uren, P.J., Park, J., Butler, J., Rafii, S., McCombie, W.R. et al. (2011) Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell, 44, 17-28
-
(2011)
Mol. Cell
, vol.44
, pp. 17-28
-
-
Hodges, E.1
Molaro, A.2
Dos Santos, C.O.3
Thekkat, P.4
Song, Q.5
Uren, P.J.6
Park, J.7
Butler, J.8
Rafii, S.9
McCombie, W.R.10
-
32
-
-
84898950243
-
Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
-
Kunde-Ramamoorthy, G., Coarfa, C., Laritsky, E., Kessler, N.J., Harris, R.A., Xu, M., Chen, R., Shen, L., Milosavljevic, A. and Waterland, R.A. (2014) Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Res., 42, e43
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Kunde-Ramamoorthy, G.1
Coarfa, C.2
Laritsky, E.3
Kessler, N.J.4
Harris, R.A.5
Xu, M.6
Chen, R.7
Shen, L.8
Milosavljevic, A.9
Waterland, R.A.10
-
33
-
-
80052937538
-
Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
-
Molaro, A., Hodges, E., Fang, F., Song, Q., McCombie, W.R., Hannon, G.J. and Smith, A.D. (2011) Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell, 146, 1029-1041
-
(2011)
Cell
, vol.146
, pp. 1029-1041
-
-
Molaro, A.1
Hodges, E.2
Fang, F.3
Song, Q.4
McCombie, W.R.5
Hannon, G.J.6
Smith, A.D.7
-
34
-
-
84882884517
-
Charting a dynamic DNA methylation landscape of the human genome
-
Ziller, M.J., Gu, H., Muller, F., Donaghey, J., Tsai, L.T., Kohlbacher, O., De Jager, P.L., Rosen, E.D., Bennett, D.A., Bernstein, B.E. et al. (2013) Charting a dynamic DNA methylation landscape of the human genome. Nature, 500, 477-481
-
(2013)
Nature
, vol.500
, pp. 477-481
-
-
Ziller, M.J.1
Gu, H.2
Muller, F.3
Donaghey, J.4
Tsai, L.T.5
Kohlbacher, O.6
De Jager, P.L.7
Rosen, E.D.8
Bennett, D.A.9
Bernstein, B.E.10
-
35
-
-
15244353967
-
X-inactivation profile reveals extensive variability in X-linked gene expression in females
-
Carrel, L. and Willard, H.F. (2005) X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature, 434, 400-404
-
(2005)
Nature
, vol.434
, pp. 400-404
-
-
Carrel, L.1
Willard, H.F.2
-
36
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner, A., Mikkelsen, T.S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B.E., Nusbaum, C., Jaffe, D.B. et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature, 454, 766-770
-
(2008)
Nature
, vol.454
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
Wernig, M.4
Hanna, J.5
Sivachenko, A.6
Zhang, X.7
Bernstein, B.E.8
Nusbaum, C.9
Jaffe, D.B.10
-
37
-
-
0029150196
-
Specific Alu binding protein from human sperm chromatin prevents DNA methylation
-
Chesnokov, I.N. and Schmid, C.W. (1995) Specific Alu binding protein from human sperm chromatin prevents DNA methylation. J. Biol. Chem., 270, 18539-18542
-
(1995)
J. Biol. Chem
, vol.270
, pp. 18539-18542
-
-
Chesnokov, I.N.1
Schmid, C.W.2
-
38
-
-
0028575909
-
Alu repeated DNAs are differentially methylated in primate germ cells
-
Rubin, C.M., VandeVoort, C.A., Teplitz, R.L. and Schmid, C.W. (1994) Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res., 22, 5121-5127
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 5121-5127
-
-
Rubin, C.M.1
VandeVoort, C.A.2
Teplitz, R.L.3
Schmid, C.W.4
-
39
-
-
59149084538
-
The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores
-
Irizarry, R.A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M. et al. (2009) The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186
-
(2009)
Nat. Genet
, vol.41
, pp. 178-186
-
-
Irizarry, R.A.1
Ladd-Acosta, C.2
Wen, B.3
Wu, Z.4
Montano, C.5
Onyango, P.6
Cui, H.7
Gabo, K.8
Rongione, M.9
Webster, M.10
-
40
-
-
70649095120
-
Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
-
Doi, A., Park, I.H., Wen, B., Murakami, P., Aryee, M.J., Irizarry, R., Herb, B., Ladd-Acosta, C., Rho, J., Loewer, S. et al. (2009) Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet., 41, 1350-1353
-
(2009)
Nat. Genet
, vol.41
, pp. 1350-1353
-
-
Doi, A.1
Park, I.H.2
Wen, B.3
Murakami, P.4
Aryee, M.J.5
Irizarry, R.6
Herb, B.7
Ladd-Acosta, C.8
Rho, J.9
Loewer, S.10
-
41
-
-
84897406127
-
A promoter-level mammalian expression atlas
-
FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest, A.R., Kawaji, H., Rehli, M., Baillie, J.K., de Hoon, M.J., Haberle, V., Lassman, T., Kulakovskiy, I.V., Lizio, M. et al. (2014) A promoter-level mammalian expression atlas. Nature, 507, 462-470
-
(2014)
Nature
, vol.507
, pp. 462-470
-
-
Forrest, A.R.1
Kawaji, H.2
Rehli, M.3
Baillie, J.K.4
de Hoon, M.J.5
Haberle, V.6
Lassman, T.7
Kulakovskiy, I.V.8
Lizio, M.9
-
42
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
43
-
-
0037806031
-
The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells
-
Mitsui, K., Tokuzawa, Y., Itoh, H., Segawa, K., Murakami, M., Takahashi, K., Maruyama, M., Maeda, M. and Yamanaka, S. (2003) The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell, 113, 631-642
-
(2003)
Cell
, vol.113
, pp. 631-642
-
-
Mitsui, K.1
Tokuzawa, Y.2
Itoh, H.3
Segawa, K.4
Murakami, M.5
Takahashi, K.6
Maruyama, M.7
Maeda, M.8
Yamanaka, S.9
-
44
-
-
0038143611
-
Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells
-
Chambers, I., Colby, D., Robertson, M., Nichols, J., Lee, S., Tweedie, S. and Smith, A. (2003) Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell, 113, 643-655
-
(2003)
Cell
, vol.113
, pp. 643-655
-
-
Chambers, I.1
Colby, D.2
Robertson, M.3
Nichols, J.4
Lee, S.5
Tweedie, S.6
Smith, A.7
-
45
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst, J., Kheradpour, P., Mikkelsen, T.S., Shoresh, N., Ward, L. D., Epstein, C.B., Zhang, X., Wang, L., Issner, R., Coyne, M. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
Epstein, C.B.6
Zhang, X.7
Wang, L.8
Issner, R.9
Coyne, M.10
-
46
-
-
84929628130
-
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation
-
Lou, S., Lee, H.M., Qin, H., Li, J.W., Gao, Z., Liu, X., Chan, L.L., Kl Lam, V., So, W.Y., Wang, Y. et al. (2014) Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biol., 15, 408
-
(2014)
Genome Biol
, vol.15
, pp. 408
-
-
Lou, S.1
Lee, H.M.2
Qin, H.3
Li, J.W.4
Gao, Z.5
Liu, X.6
Chan, L.L.7
Kl Lam, V.8
So, W.Y.9
Wang, Y.10
-
47
-
-
47649091157
-
DNA methylation and structural and functional bimodality of vertebrate promoters
-
Elango, N. and Yi, S.V. (2008) DNA methylation and structural and functional bimodality of vertebrate promoters. Mol. Biol. Evol., 25, 1602-1608
-
(2008)
Mol. Biol. Evol
, vol.25
, pp. 1602-1608
-
-
Elango, N.1
Yi, S.V.2
-
48
-
-
31944432339
-
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
-
Saxonov, S., Berg, P. and Brutlag, D.L. (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl Acad. Sci. USA, 103, 1412-1417
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 1412-1417
-
-
Saxonov, S.1
Berg, P.2
Brutlag, D.L.3
-
49
-
-
83455162761
-
What are the determinants of gene expression levels and breadths in the human genome?
-
Park, J., Xu, K., Park, T. and Yi, S.V. (2012) What are the determinants of gene expression levels and breadths in the human genome? Hum. Mol. Genet., 21, 46-56
-
(2012)
Hum. Mol. Genet
, vol.21
, pp. 46-56
-
-
Park, J.1
Xu, K.2
Park, T.3
Yi, S.V.4
-
50
-
-
77954504873
-
Conserved role of intragenic DNAmethylation in regulating alternative promoters
-
Maunakea, A.K., Nagarajan, R.P., Bilenky, M., Ballinger, T.J., D'Souza, C., Fouse, S.D., Johnson, B.E., Hong, C., Nielsen, C., Zhao, Y. et al. (2010) Conserved role of intragenic DNAmethylation in regulating alternative promoters. Nature, 466, 253-257
-
(2010)
Nature
, vol.466
, pp. 253-257
-
-
Maunakea, A.K.1
Nagarajan, R.P.2
Bilenky, M.3
Ballinger, T.J.4
D'Souza, C.5
Fouse, S.D.6
Johnson, B.E.7
Hong, C.8
Nielsen, C.9
Zhao, Y.10
-
51
-
-
80455176999
-
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
-
Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Sandberg, R. and Oberdoerffer, S. (2011) CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature, 479, 74-79
-
(2011)
Nature
, vol.479
, pp. 74-79
-
-
Shukla, S.1
Kavak, E.2
Gregory, M.3
Imashimizu, M.4
Shutinoski, B.5
Kashlev, M.6
Oberdoerffer, P.7
Sandberg, R.8
Oberdoerffer, S.9
-
52
-
-
84891798006
-
NONCODEv4: exploring the world of long non-coding RNA genes
-
Xie, C., Yuan, J., Li, H., Li, M., Zhao, G., Bu, D., Zhu, W., Wu, W., Chen, R. and Zhao, Y. (2014) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res., 42, D98-D103
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D98-D103
-
-
Xie, C.1
Yuan, J.2
Li, H.3
Li, M.4
Zhao, G.5
Bu, D.6
Zhu, W.7
Wu, W.8
Chen, R.9
Zhao, Y.10
-
53
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927
-
(2011)
Genes Dev
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
Trapnell, C.2
Goff, L.3
Koziol, M.4
Tazon-Vega, B.5
Regev, A.6
Rinn, J.L.7
-
54
-
-
77952908743
-
A large fraction of extragenic RNA pol II transcription sites overlap enhancers
-
De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B.K., Muller, H., Ragoussis, J., Wei, C.L. and Natoli, G. (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol., 8, e1000384
-
(2010)
PLoS Biol
, vol.8
-
-
De Santa, F.1
Barozzi, I.2
Mietton, F.3
Ghisletti, S.4
Polletti, S.5
Tusi, B.K.6
Muller, H.7
Ragoussis, J.8
Wei, C.L.9
Natoli, G.10
-
55
-
-
77957243921
-
Long noncoding RNAs with enhancer-like function in human cells
-
Orom, U.A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q. et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell, 143, 46-58
-
(2010)
Cell
, vol.143
, pp. 46-58
-
-
Orom, U.A.1
Derrien, T.2
Beringer, M.3
Gumireddy, K.4
Gardini, A.5
Bussotti, G.6
Lai, F.7
Zytnicki, M.8
Notredame, C.9
Huang, Q.10
-
56
-
-
74549161822
-
Epigenetic control of the expression of a primate-specific microRNA cluster in human cancer cells
-
Tsai, K.W., Kao, H.W., Chen, H.C., Chen, S.J. and Lin, W.C. (2009) Epigenetic control of the expression of a primate-specific microRNA cluster in human cancer cells. Epigenetics, 4, 587-592
-
(2009)
Epigenetics
, vol.4
, pp. 587-592
-
-
Tsai, K.W.1
Kao, H.W.2
Chen, H.C.3
Chen, S.J.4
Lin, W.C.5
-
57
-
-
77956164185
-
The primate-specific microRNA gene cluster (C19MC) is imprinted in the placenta
-
Noguer-Dance, M., Abu-Amero, S., Al-Khtib, M., Lefevre, A., Coullin, P., Moore, G.E. and Cavaille, J. (2010) The primate-specific microRNA gene cluster (C19MC) is imprinted in the placenta. Hum. Mol. Genet., 19, 3566-3582
-
(2010)
Hum. Mol. Genet
, vol.19
, pp. 3566-3582
-
-
Noguer-Dance, M.1
Abu-Amero, S.2
Al-Khtib, M.3
Lefevre, A.4
Coullin, P.5
Moore, G.E.6
Cavaille, J.7
-
58
-
-
0032714383
-
The human MAGEL2 gene and its mouse homologue are paternally expressed and mapped to the Prader-Willi region
-
Boccaccio, I., Glatt-Deeley, H., Watrin, F., Roeckel, N., Lalande, M. and Muscatelli, F. (1999) The human MAGEL2 gene and its mouse homologue are paternally expressed and mapped to the Prader-Willi region. Hum. Mol. Genet., 8, 2497-2505
-
(1999)
Hum. Mol. Genet
, vol.8
, pp. 2497-2505
-
-
Boccaccio, I.1
Glatt-Deeley, H.2
Watrin, F.3
Roeckel, N.4
Lalande, M.5
Muscatelli, F.6
-
59
-
-
35948981875
-
Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters
-
Shen, L., Kondo, Y., Guo, Y., Zhang, J., Zhang, L., Ahmed, S., Shu, J., Chen, X., Waterland, R.A. and Issa, J.P. (2007) Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet., 3, 2023-2036
-
(2007)
PLoS Genet
, vol.3
, pp. 2023-2036
-
-
Shen, L.1
Kondo, Y.2
Guo, Y.3
Zhang, J.4
Zhang, L.5
Ahmed, S.6
Shu, J.7
Chen, X.8
Waterland, R.A.9
Issa, J.P.10
-
60
-
-
84879611157
-
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
-
Xie, M., Hong, C., Zhang, B., Lowdon, R.F., Xing, X., Li, D., Zhou, X., Lee, H.J., Maire, C.L., Ligon, K.L. et al. (2013) DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat. Genet., 45, 836-841
-
(2013)
Nat. Genet
, vol.45
, pp. 836-841
-
-
Xie, M.1
Hong, C.2
Zhang, B.3
Lowdon, R.F.4
Xing, X.5
Li, D.6
Zhou, X.7
Lee, H.J.8
Maire, C.L.9
Ligon, K.L.10
-
61
-
-
42349096534
-
Transposable elements and the evolution of regulatory networks
-
Feschotte, C. (2008) Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet., 9, 397-405
-
(2008)
Nat. Rev. Genet
, vol.9
, pp. 397-405
-
-
Feschotte, C.1
-
62
-
-
33947303168
-
Transposable elements and the epigenetic regulation of the genome
-
Slotkin, R.K. and Martienssen, R. (2007) Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet., 8, 272-285
-
(2007)
Nat. Rev. Genet
, vol.8
, pp. 272-285
-
-
Slotkin, R.K.1
Martienssen, R.2
-
63
-
-
84863256915
-
Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of nonmethylated DNA
-
Blackledge, N.P., Long, H.K., Zhou, J.C., Kriaucionis, S., Patient, R. and Klose, R.J. (2012) Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of nonmethylated DNA. Nucleic Acids Res., 40, e32
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Blackledge, N.P.1
Long, H.K.2
Zhou, J.C.3
Kriaucionis, S.4
Patient, R.5
Klose, R.J.6
-
64
-
-
0024342297
-
Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes
-
Cooper, D.N. and Krawczak, M. (1989) Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum. Genet., 83, 181-188
-
(1989)
Hum. Genet
, vol.83
, pp. 181-188
-
-
Cooper, D.N.1
Krawczak, M.2
-
65
-
-
40149097494
-
Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation
-
Elango, N., Kim, S.H., Vigoda, E. and Yi, S.V. (2008) Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Comput. Biol., 4, e1000015
-
(2008)
PLoS Comput. Biol
, vol.4
-
-
Elango, N.1
Kim, S.H.2
Vigoda, E.3
Yi, S.V.4
-
66
-
-
84863565553
-
Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data
-
Liu, Y., Siegmund, K.D., Laird, P.W. and Berman, B.P. (2012) Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol., 13, R61
-
(2012)
Genome Biol
, vol.13
, pp. R61
-
-
Liu, Y.1
Siegmund, K.D.2
Laird, P.W.3
Berman, B.P.4
-
67
-
-
84943543379
-
Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin
-
Yang, X., Shao, X., Gao, L. and Zhang, S. (2015) Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin. Hum. Mol. Genet., 24, 4374-4384
-
(2015)
Hum. Mol. Genet
, vol.24
, pp. 4374-4384
-
-
Yang, X.1
Shao, X.2
Gao, L.3
Zhang, S.4
-
68
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreiman, G.10
-
69
-
-
84856498057
-
DNA methylome analysis using short bisulfite sequencing data
-
Krueger, F., Kreck, B., Franke, A. and Andrews, S.R. (2012) DNA methylome analysis using short bisulfite sequencing data. Nat. Methods, 9, 145-151
-
(2012)
Nat. Methods
, vol.9
, pp. 145-151
-
-
Krueger, F.1
Kreck, B.2
Franke, A.3
Andrews, S.R.4
-
70
-
-
79957868920
-
Bismark: aflexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger, F. and Andrews, S.R. (2011) Bismark: aflexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
71
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
Genomes Project, Consortium, Abecasis, G.R., Auton, A., Brooks, L.D., DePristo, M.A., Durbin, R.M., Handsaker, R.E., Kang, H.M., Marth, G.T. and McVean, G.A. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature, 491, 56-65
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
Genomes Project Consortium Abecasis, G.R.1
Auton, A.2
Brooks, L.D.3
DePristo, M.A.4
Durbin, R.M.5
Handsaker, R.E.6
Kang, H.M.7
Marth, G.T.8
McVean, G.A.9
-
72
-
-
84864326252
-
Genomic dark matter: the reliability of short read mapping illustrated by the Genome Mappability Score
-
Lee, H. and Schatz, M.C. (2012) Genomic dark matter: the reliability of short read mapping illustrated by the Genome Mappability Score. Bioinformatics, 28, 2097-2105
-
(2012)
Bioinformatics
, vol.28
, pp. 2097-2105
-
-
Lee, H.1
Schatz, M.C.2
-
74
-
-
84883368195
-
Software for computing and annotating genomic ranges
-
Lawrence, M., Huber, W., Pages, H., Aboyoun, P., Carlson, M., Gentleman, R., Morgan, M.T. and Carey, V.J. (2013) Software for computing and annotating genomic ranges. PLoS Comput. Biol., 9, e1003118
-
(2013)
PLoS Comput. Biol
, vol.9
-
-
Lawrence, M.1
Huber, W.2
Pages, H.3
Aboyoun, P.4
Carlson, M.5
Gentleman, R.6
Morgan, M.T.7
Carey, V.J.8
-
75
-
-
33846689706
-
Using GOstats to test gene lists for GO term association
-
Falcon, S. and Gentleman, R. (2007) Using GOstats to test gene lists for GO term association. Bioinformatics, 23, 257-258
-
(2007)
Bioinformatics
, vol.23
, pp. 257-258
-
-
Falcon, S.1
Gentleman, R.2
|