-
1
-
-
0002947085
-
The epigenotype
-
Waddington, C. H. 1942. The epigenotype. Endeavour 1:18-20.
-
(1942)
Endeavour
, vol.1
, pp. 18-20
-
-
Waddington, C.H.1
-
2
-
-
0036960243
-
The changing concept of epigenetics
-
Jablonka, E., and M. J. Lamb. 2002. The changing concept of epigenetics. Ann. N. Y. Acad. Sci. 981:82-96.
-
(2002)
Ann. N. Y. Acad. Sci.
, vol.981
, pp. 82-96
-
-
Jablonka, E.1
Lamb, M.J.2
-
3
-
-
0022000776
-
A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA
-
Bird, A., M. Taggart, M. Frommer, O. J. Miller, and D. Macleod. 1985. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40:91-99.
-
(1985)
Cell
, vol.40
, pp. 91-99
-
-
Bird, A.1
Taggart, M.2
Frommer, M.3
Miller, O.J.4
Macleod, D.5
-
4
-
-
0023216891
-
CpG islands in vertebrate genomes
-
Gardiner-Garden, M., and M. Frommer. 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
-
5
-
-
59149084538
-
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
-
Irizarry, R. A., C. Ladd-Acosta, B. Wen, 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
-
6
-
-
70649095120
-
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
-
Doi, A., I. H. Park, B. Wen, 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
-
7
-
-
0016439429
-
DNA modification mechanisms and gene activity during development
-
Holliday, R., and J. E. Pugh. 1975. DNA modification mechanisms and gene activity during development. Science 187:226-232.
-
(1975)
Science
, vol.187
, pp. 226-232
-
-
Holliday, R.1
Pugh, J.E.2
-
8
-
-
0016692220
-
X inactivation, differentiation, and DNA methylation
-
Riggs, A. D. 1975. X inactivation, differentiation, and DNA methylation. Cytogenet. Cell Genet. 14:9-25.
-
(1975)
Cytogenet. Cell Genet.
, vol.14
, pp. 9-25
-
-
Riggs, A.D.1
-
9
-
-
34848923648
-
DNA methylation: potential for diagnosis, prognosis and therapy - prediction in oncology
-
Haedicke, W., and R. Lesche. 2006. DNA methylation: potential for diagnosis, prognosis and therapy - prediction in oncology. Verh. Dtsch. Ges. Pathol. 90:39-45.
-
(2006)
Verh. Dtsch. Ges. Pathol.
, vol.90
, pp. 39-45
-
-
Haedicke, W.1
Lesche, R.2
-
10
-
-
0029843950
-
Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands
-
Herman, J. G., J. R. Graff, S. Myohanen, B. D. Nelkin, and S. B. Baylin. 1996. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93:9821-9826.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 9821-9826
-
-
Herman, J.G.1
Graff, J.R.2
Myohanen, S.3
Nelkin, B.D.4
Baylin, S.B.5
-
11
-
-
33845443302
-
Epigenetic diagnostics of cancer - the application of DNA methylation markers
-
Paluszczak, J., and W. Baer-Dubowska. 2006. Epigenetic diagnostics of cancer - the application of DNA methylation markers. J. Appl. Genet. 47:365-375.
-
(2006)
J. Appl. Genet.
, vol.47
, pp. 365-375
-
-
Paluszczak, J.1
Baer-Dubowska, W.2
-
12
-
-
77955450160
-
CILDA. The implications of heterogeneous DNA methylation for the accurate quantification of methylation
-
Mikeska, T. 2010. CILDA. The implications of heterogeneous DNA methylation for the accurate quantification of methylation. Epigenomics 2:561-573.
-
(2010)
Epigenomics
, vol.2
, pp. 561-573
-
-
Mikeska, T.1
-
13
-
-
80052461558
-
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
-
Ito, S., L. Shen, Q. Dai, et al. 2011. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333:1300-1303.
-
(2011)
Science
, vol.333
, pp. 1300-1303
-
-
Ito, S.1
Shen, L.2
Dai, Q.3
-
14
-
-
66149123748
-
The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain
-
Kriaucionis, S., and N. Heintz. 2009. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324:929-930.
-
(2009)
Science
, vol.324
, pp. 929-930
-
-
Kriaucionis, S.1
Heintz, N.2
-
15
-
-
0015298215
-
The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid
-
Penn, N. W., R. Suwalski, C. O'Riley, K. Bojanowski, and R. Yura. 1972. The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem. J. 126:781-790.
-
(1972)
Biochem. J.
, vol.126
, pp. 781-790
-
-
Penn, N.W.1
Suwalski, R.2
O'Riley, C.3
Bojanowski, K.4
Yura, R.5
-
16
-
-
66149146320
-
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
-
Tahiliani, M., K. P. Koh, Y. Shen, et al. 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930-935.
-
(2009)
Science
, vol.324
, pp. 930-935
-
-
Tahiliani, M.1
Koh, K.P.2
Shen, Y.3
-
17
-
-
84856058152
-
Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers
-
Haffner, M. C., A. Chaux, A. K. Meeker, et al. 2011. Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers. Oncotarget 2:627-637.
-
(2011)
Oncotarget
, vol.2
, pp. 627-637
-
-
Haffner, M.C.1
Chaux, A.2
Meeker, A.K.3
-
18
-
-
79960560477
-
The presence of 5-hydroxymethylcytosine at the gene promoter and not in the gene body negatively regulates gene expression
-
Robertson, J., A. B. Robertson, and A. Klungland. 2011. The presence of 5-hydroxymethylcytosine at the gene promoter and not in the gene body negatively regulates gene expression. Biochem. Biophys. Res. Commun. 411:40-43.
-
(2011)
Biochem. Biophys. Res. Commun.
, vol.411
, pp. 40-43
-
-
Robertson, J.1
Robertson, A.B.2
Klungland, A.3
-
19
-
-
79956323623
-
Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation
-
Ficz, G., M. R. Branco, S. Seisenberger, et al. 2011. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473:398-402.
-
(2011)
Nature
, vol.473
, pp. 398-402
-
-
Ficz, G.1
Branco, M.R.2
Seisenberger, S.3
-
20
-
-
79955948324
-
Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells
-
Xu, Y., F. Wu, L. Tan, et al. 2011. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol. Cell 42:451-464.
-
(2011)
Mol. Cell
, vol.42
, pp. 451-464
-
-
Xu, Y.1
Wu, F.2
Tan, L.3
-
21
-
-
84873411803
-
Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation
-
doi: 10.1038/onc.2012.67.
-
Yang, H., Y. Liu, F. Bai, et al. 2012. Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene. doi: 10.1038/onc.2012.67.
-
(2012)
Oncogene
-
-
Yang, H.1
Liu, Y.2
Bai, F.3
-
22
-
-
0027316298
-
Restriction landmark genomic scanning method and its various applications
-
Hayashizaki, Y., S. Hirotsune, Y. Okazaki, et al. 1993. Restriction landmark genomic scanning method and its various applications. Electrophoresis 14:251-258.
-
(1993)
Electrophoresis
, vol.14
, pp. 251-258
-
-
Hayashizaki, Y.1
Hirotsune, S.2
Okazaki, Y.3
-
23
-
-
0026052179
-
A genomic scanning method for higher organisms using restriction sites as landmarks
-
Hatada, I., Y. Hayashizaki, S. Hirotsune, H. Komatsubara, and T. Mukai. 1991. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc. Natl. Acad. Sci. USA 88:9523-9527.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 9523-9527
-
-
Hatada, I.1
Hayashizaki, Y.2
Hirotsune, S.3
Komatsubara, H.4
Mukai, T.5
-
24
-
-
0037068375
-
The study of aberrant methylation in cancer via restriction landmark genomic scanning
-
Smiraglia, D. J., and C. Plass. 2002. The study of aberrant methylation in cancer via restriction landmark genomic scanning. Oncogene 21:5414-5426.
-
(2002)
Oncogene
, vol.21
, pp. 5414-5426
-
-
Smiraglia, D.J.1
Plass, C.2
-
25
-
-
33746756014
-
Comparative isoschizomer profiling of cytosine methylation: the HELP assay
-
Khulan, B., R. F. Thompson, K. Ye, et al. 2006. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 16:1046-1055.
-
(2006)
Genome Res.
, vol.16
, pp. 1046-1055
-
-
Khulan, B.1
Thompson, R.F.2
Ye, K.3
-
26
-
-
67651149735
-
High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
-
Oda, M., J. L. Glass, R. F. Thompson, et al. 2009. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 37:3829-3839.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 3829-3839
-
-
Oda, M.1
Glass, J.L.2
Thompson, R.F.3
-
27
-
-
65549107163
-
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
-
Brunner, A. L., D. S. Johnson, S. W. Kim, et al. 2009. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19:1044-1056.
-
(2009)
Genome Res.
, vol.19
, pp. 1044-1056
-
-
Brunner, A.L.1
Johnson, D.S.2
Kim, S.W.3
-
28
-
-
34247156577
-
Using LUMA: a luminometric-based assay for global DNA-methylation
-
Karimi, M., S. Johansson, and T. J. Ekstrom. 2006. Using LUMA: a luminometric-based assay for global DNA-methylation. Epigenetics 1:45-48.
-
(2006)
Epigenetics
, vol.1
, pp. 45-48
-
-
Karimi, M.1
Johansson, S.2
Ekstrom, T.J.3
-
29
-
-
33744938449
-
LUMA (LUminometric Methylation Assay) - a high throughput method to the analysis of genomic DNA methylation
-
Karimi, M., S. Johansson, D. Stach, et al. 2006. LUMA (LUminometric Methylation Assay) - a high throughput method to the analysis of genomic DNA methylation. Exp. Cell Res. 312:1989-1995.
-
(2006)
Exp. Cell Res.
, vol.312
, pp. 1989-1995
-
-
Karimi, M.1
Johansson, S.2
Stach, D.3
-
30
-
-
64349091471
-
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
-
Ball, M. P., J. B. Li, Y. Gao, et al. 2009. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27:361-368.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 361-368
-
-
Ball, M.P.1
Li, J.B.2
Gao, Y.3
-
31
-
-
0033563165
-
Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification
-
Toyota, M., C. Ho, N. Ahuja, et al. 1999. Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res. 59:2307-2312.
-
(1999)
Cancer Res.
, vol.59
, pp. 2307-2312
-
-
Toyota, M.1
Ho, C.2
Ahuja, N.3
-
32
-
-
34948830291
-
High-throughput methylation profiling by MCA coupled to CpG island microarray
-
Estecio, M. R., P. S. Yan, A. E. Ibrahim, et al. 2007. High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res. 17:1529-1536.
-
(2007)
Genome Res.
, vol.17
, pp. 1529-1536
-
-
Estecio, M.R.1
Yan, P.S.2
Ibrahim, A.E.3
-
33
-
-
18444364803
-
A microarray-based method for detecting methylated loci
-
Hatada, I., A. Kato, S. Morita, et al. 2002. A microarray-based method for detecting methylated loci. J. Hum. Genet. 47:448-451.
-
(2002)
J. Hum. Genet.
, vol.47
, pp. 448-451
-
-
Hatada, I.1
Kato, A.2
Morita, S.3
-
34
-
-
33646456046
-
Microarray analysis of promoter methylation in lung cancers
-
Fukasawa, M., M. Kimura, S. Morita, et al. 2006. Microarray analysis of promoter methylation in lung cancers. J. Hum. Genet. 51:368-374.
-
(2006)
J. Hum. Genet.
, vol.51
, pp. 368-374
-
-
Fukasawa, M.1
Kimura, M.2
Morita, S.3
-
35
-
-
77952085655
-
Profiling DNA methylomes from microarray to genome-scale sequencing
-
Huang, Y. W., T. H. Huang, and L. S. Wang. 2010. Profiling DNA methylomes from microarray to genome-scale sequencing. Technol. Cancer Res. Treat. 9:139-147.
-
(2010)
Technol. Cancer Res. Treat.
, vol.9
, pp. 139-147
-
-
Huang, Y.W.1
Huang, T.H.2
Wang, L.S.3
-
36
-
-
0026634757
-
McrBC: a multisubunit GTP-dependent restriction endonuclease
-
Sutherland, E., L. Coe, and E. A. Raleigh. 1992. McrBC: a multisubunit GTP-dependent restriction endonuclease. J. Mol. Biol. 225:327-348.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 327-348
-
-
Sutherland, E.1
Coe, L.2
Raleigh, E.A.3
-
37
-
-
43149098062
-
Comprehensive high-throughput arrays for relative methylation (CHARM)
-
Irizarry, R. A., C. Ladd-Acosta, B. Carvalho, et al. 2008. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18:780-790.
-
(2008)
Genome Res.
, vol.18
, pp. 780-790
-
-
Irizarry, R.A.1
Ladd-Acosta, C.2
Carvalho, B.3
-
38
-
-
33845643047
-
MMASS: an optimized array-based method for assessing CpG island methylation
-
Ibrahim, A. E., N. P. Thorne, K. Baird, et al. 2006. MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res. 34:e136.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Ibrahim, A.E.1
Thorne, N.P.2
Baird, K.3
-
39
-
-
33845356420
-
Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets
-
Ordway, J. M., J. A. Bedell, R. W. Citek, et al. 2006. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis 27:2409-2423.
-
(2006)
Carcinogenesis
, vol.27
, pp. 2409-2423
-
-
Ordway, J.M.1
Bedell, J.A.2
Citek, R.W.3
-
40
-
-
44449175595
-
Identification of novel high-frequency DNA methylation changes in breast cancer
-
Ordway, J. M., M. A. Budiman, Y. Korshunova, et al. 2007. Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS One 2:e1314.
-
(2007)
PLoS One
, vol.2
-
-
Ordway, J.M.1
Budiman, M.A.2
Korshunova, Y.3
-
41
-
-
0033047813
-
Methylation profiling of CpG islands in human breast cancer cells
-
Huang, T. H., M. R. Perry, and D. E. Laux. 1999. Methylation profiling of CpG islands in human breast cancer cells. Hum. Mol. Genet. 8:459-470.
-
(1999)
Hum. Mol. Genet.
, vol.8
, pp. 459-470
-
-
Huang, T.H.1
Perry, M.R.2
Laux, D.E.3
-
42
-
-
63049098369
-
Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays
-
Kron, K., V. Pethe, L. Briollais, et al. 2009. Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays. PLoS One 4:e4830.
-
(2009)
PLoS One
, vol.4
-
-
Kron, K.1
Pethe, V.2
Briollais, L.3
-
43
-
-
79959885041
-
Association of tissue promoter methylation levels of APC, TGFbeta2, HOXD3, and RASSF1A with prostate cancer progression
-
Liu, L., K. J. Kron, V. V. Pethe, et al. 2011. Association of tissue promoter methylation levels of APC, TGFbeta2, HOXD3, and RASSF1A with prostate cancer progression. Int. J. Cancer 129:2454-2462.
-
(2011)
Int. J. Cancer
, vol.129
, pp. 2454-2462
-
-
Liu, L.1
Kron, K.J.2
Pethe, V.V.3
-
44
-
-
46249117780
-
Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation
-
Kerkel, K., A. Spadola, E. Yuan, et al. 2008. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat. Genet. 40:904-908.
-
(2008)
Nat. Genet.
, vol.40
, pp. 904-908
-
-
Kerkel, K.1
Spadola, A.2
Yuan, E.3
-
45
-
-
33645737308
-
A single nucleotide polymorphism chip-based method for combined genetic and epigenetic profiling: validation in decitabine therapy and tumor/normal comparisons
-
Yuan, E., F. Haghighi, S. White, et al. 2006. A single nucleotide polymorphism chip-based method for combined genetic and epigenetic profiling: validation in decitabine therapy and tumor/normal comparisons. Cancer Res. 66:3443-3451.
-
(2006)
Cancer Res.
, vol.66
, pp. 3443-3451
-
-
Yuan, E.1
Haghighi, F.2
White, S.3
-
46
-
-
0031017268
-
Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines
-
Kane, M. F., M. Loda, G. M. Gaida, et al. 1997. Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res. 57:808-811.
-
(1997)
Cancer Res.
, vol.57
, pp. 808-811
-
-
Kane, M.F.1
Loda, M.2
Gaida, G.M.3
-
47
-
-
0028152397
-
Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis
-
Lee, W. H., R. A. Morton, J. I. Epstein, et al. 1994. Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis. Proc. Natl. Acad. Sci. USA 91:11733-11737.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 11733-11737
-
-
Lee, W.H.1
Morton, R.A.2
Epstein, J.I.3
-
48
-
-
0026041906
-
Direct correlation between methylation status and expression of the human O-6-methylguanine DNA methyltransferase gene
-
Pieper, R. O., J. F. Costello, R. A. Kroes, B. W. Futscher, U. Marathi, and L. C. Erickson. 1991. Direct correlation between methylation status and expression of the human O-6-methylguanine DNA methyltransferase gene. Cancer Commun. 3:241-253.
-
(1991)
Cancer Commun.
, vol.3
, pp. 241-253
-
-
Pieper, R.O.1
Costello, J.F.2
Kroes, R.A.3
Futscher, B.W.4
Marathi, U.5
Erickson, L.C.6
-
49
-
-
77954061853
-
Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA
-
Nestor, C., A. Ruzov, R. Meehan, and D. Dunican. 2010. Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Biotechniques 48:317-319.
-
(2010)
Biotechniques
, vol.48
, pp. 317-319
-
-
Nestor, C.1
Ruzov, A.2
Meehan, R.3
Dunican, D.4
-
50
-
-
79960127277
-
Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes
-
Kinney, S. M., H. G. Chin, R. Vaisvila, et al. 2011. Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes. J. Biol. Chem. 286:24685-24693.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 24685-24693
-
-
Kinney, S.M.1
Chin, H.G.2
Vaisvila, R.3
-
51
-
-
0028040618
-
Molecular cloning and expression of a novel hydroxymethylcytosine-specific restriction enzyme (PvuRts1I) modulated by glucosylation of DNA
-
Janosi, L., H. Yonemitsu, H. Hong, and A. Kaji. 1994. Molecular cloning and expression of a novel hydroxymethylcytosine-specific restriction enzyme (PvuRts1I) modulated by glucosylation of DNA. J. Mol. Biol. 242:45-61.
-
(1994)
J. Mol. Biol.
, vol.242
, pp. 45-61
-
-
Janosi, L.1
Yonemitsu, H.2
Hong, H.3
Kaji, A.4
-
52
-
-
23044514626
-
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
-
Weber, M., J. J. Davies, D. Wittig, et al. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37:853-862.
-
(2005)
Nat. Genet.
, vol.37
, pp. 853-862
-
-
Weber, M.1
Davies, J.J.2
Wittig, D.3
-
53
-
-
46949098742
-
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
-
Down, T. A., V. K. Rakyan, D. J. Turner, et al. 2008. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26:779-785.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 779-785
-
-
Down, T.A.1
Rakyan, V.K.2
Turner, D.J.3
-
54
-
-
33845880624
-
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
-
Zilberman, D., M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff. 2007. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39:61-69.
-
(2007)
Nat. Genet.
, vol.39
, pp. 61-69
-
-
Zilberman, D.1
Gehring, M.2
Tran, R.K.3
Ballinger, T.4
Henikoff, S.5
-
55
-
-
33748629119
-
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
-
Zhang, X., J. Yazaki, A. Sundaresan, et al. 2006. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126:1189-1201.
-
(2006)
Cell
, vol.126
, pp. 1189-1201
-
-
Zhang, X.1
Yazaki, J.2
Sundaresan, A.3
-
56
-
-
0028340280
-
Purification of CpG islands using a methylated DNA binding column
-
Cross, S. H., J. A. Charlton, X. Nan, and A. P. Bird. 1994. Purification of CpG islands using a methylated DNA binding column. Nat. Genet. 6:236-244.
-
(1994)
Nat. Genet.
, vol.6
, pp. 236-244
-
-
Cross, S.H.1
Charlton, J.A.2
Nan, X.3
Bird, A.P.4
-
57
-
-
27744443057
-
Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer
-
Rauch, T., and G. P. Pfeifer. 2005. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab. Invest. 85:1172-1180.
-
(2005)
Lab. Invest.
, vol.85
, pp. 1172-1180
-
-
Rauch, T.1
Pfeifer, G.P.2
-
58
-
-
33745700202
-
Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia
-
Gebhard, C., L. Schwarzfischer, T. H. Pham, et al. 2006. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res. 66:6118-6128.
-
(2006)
Cancer Res.
, vol.66
, pp. 6118-6128
-
-
Gebhard, C.1
Schwarzfischer, L.2
Pham, T.H.3
-
59
-
-
4043112183
-
Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2)
-
Valinluck, V., H. H. Tsai, D. K. Rogstad, A. Burdzy, A. Bird, and L. C. Sowers. 2004. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 32:4100-4108.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 4100-4108
-
-
Valinluck, V.1
Tsai, H.H.2
Rogstad, D.K.3
Burdzy, A.4
Bird, A.5
Sowers, L.C.6
-
60
-
-
77954362183
-
Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine
-
Jin, S. G., S. Kadam, and G. P. Pfeifer. 2010. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 38:e125.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Jin, S.G.1
Kadam, S.2
Pfeifer, G.P.3
-
61
-
-
78650826181
-
Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates
-
Globisch, D., M. Munzel, M. Muller, et al. 2010. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 5:e15367.
-
(2010)
PLoS One
, vol.5
-
-
Globisch, D.1
Munzel, M.2
Muller, M.3
-
62
-
-
79952763586
-
Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine
-
Iqbal, K., S. G. Jin, G. P. Pfeifer, and P. E. Szabo. 2011. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc. Natl. Acad. Sci. USA 108:3642-3647.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 3642-3647
-
-
Iqbal, K.1
Jin, S.G.2
Pfeifer, G.P.3
Szabo, P.E.4
-
63
-
-
78651280460
-
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
-
Song, C. X., K. E. Szulwach, Y. Fu, et al. 2010. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 29:68-72.
-
(2010)
Nat. Biotechnol.
, vol.29
, pp. 68-72
-
-
Song, C.X.1
Szulwach, K.E.2
Fu, Y.3
-
64
-
-
78650175023
-
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2
-
Ko, M., Y. Huang, A. M. Jankowska, et al. 2010. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468:839-843.
-
(2010)
Nature
, vol.468
, pp. 839-843
-
-
Ko, M.1
Huang, Y.2
Jankowska, A.M.3
-
65
-
-
79955571248
-
A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA
-
Robertson, A. B., J. A. Dahl, C. B. Vagbo, P. Tripathi, H. E. Krokan, and A. Klungland. 2011. A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res. 39:e55.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Robertson, A.B.1
Dahl, J.A.2
Vagbo, C.B.3
Tripathi, P.4
Krokan, H.E.5
Klungland, A.6
-
66
-
-
0014936031
-
Reaction of sodium bisulfite with uracil, cytosine, and their derivatives
-
Hayatsu, H., Y. Wataya, K. Kai, and S. Iida. 1970. Reaction of sodium bisulfite with uracil, cytosine, and their derivatives. Biochemistry 9:2858-2865.
-
(1970)
Biochemistry
, vol.9
, pp. 2858-2865
-
-
Hayatsu, H.1
Wataya, Y.2
Kai, K.3
Iida, S.4
-
67
-
-
77749277177
-
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing
-
Huang, Y., W. A. Pastor, Y. Shen, M. Tahiliani, D. R. Liu, and A. Rao. 2010. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 5:e8888.
-
(2010)
PLoS One
, vol.5
-
-
Huang, Y.1
Pastor, W.A.2
Shen, Y.3
Tahiliani, M.4
Liu, D.R.5
Rao, A.6
-
68
-
-
84861221693
-
Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
-
Booth, M. J., M. R. Branco, G. Ficz, et al. 2012. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336:934-937.
-
(2012)
Science
, vol.336
, pp. 934-937
-
-
Booth, M.J.1
Branco, M.R.2
Ficz, G.3
-
69
-
-
79956308473
-
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
-
Pastor, W. A., U. J. Pape, Y. Huang, et al. 2011. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473:394-397.
-
(2011)
Nature
, vol.473
, pp. 394-397
-
-
Pastor, W.A.1
Pape, U.J.2
Huang, Y.3
-
70
-
-
78049401678
-
Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA
-
Szwagierczak, A., S. Bultmann, C. S. Schmidt, F. Spada, and H. Leonhardt. 2010. Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res. 38:e181.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Szwagierczak, A.1
Bultmann, S.2
Schmidt, C.S.3
Spada, F.4
Leonhardt, H.5
-
71
-
-
79951906658
-
Methyltransferase-directed derivatization of 5-hydroxymethylcytosine in DNA
-
Liutkeviciute, Z., E. Kriukiene, I. Grigaityte, V. Masevicius, and S. Klimasauskas. 2011. Methyltransferase-directed derivatization of 5-hydroxymethylcytosine in DNA. Angew. Chem. Int. Ed. Engl. 50:2090-2093.
-
(2011)
Angew. Chem. Int. Ed. Engl.
, vol.50
, pp. 2090-2093
-
-
Liutkeviciute, Z.1
Kriukiene, E.2
Grigaityte, I.3
Masevicius, V.4
Klimasauskas, S.5
-
72
-
-
77957322330
-
Whole methylome analysis by ultra-deep sequencing using two-base encoding
-
Bormann Chung, C. A., V. L. Boyd, K. J. McKernan, et al. 2012. Whole methylome analysis by ultra-deep sequencing using two-base encoding. PLoS One 5:e9320.
-
(2012)
PLoS One
, vol.5
-
-
Bormann Chung, C.A.1
Boyd, V.L.2
McKernan, K.J.3
-
73
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister, R., M. Pelizzola, R. H. Dowen, 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
-
74
-
-
40749109894
-
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
-
Cokus, S. J., S. Feng, X. Zhang, et al. 2008. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215-219.
-
(2008)
Nature
, vol.452
, pp. 215-219
-
-
Cokus, S.J.1
Feng, S.2
Zhang, X.3
-
75
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister, R., R. C. O'Malley, J. Tonti-Filippini, et al. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
-
76
-
-
27144500218
-
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
-
Meissner, A., A. Gnirke, G. W. Bell, B. Ramsahoye, E. S. Lander, and R. Jaenisch. 2005. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33:5868-5877.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5868-5877
-
-
Meissner, A.1
Gnirke, A.2
Bell, G.W.3
Ramsahoye, B.4
Lander, E.S.5
Jaenisch, R.6
-
77
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner, A., T. S. Mikkelsen, H. Gu, 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
-
78
-
-
0035041886
-
A novel MSP/DHPLC method for the investigation of the methylation status of imprinted genes enables the molecular detection of low cell mosaicisms
-
Baumer, A., U. Wiedemann, M. Hergersberg, and A. Schinzel. 2001. A novel MSP/DHPLC method for the investigation of the methylation status of imprinted genes enables the molecular detection of low cell mosaicisms. Hum. Mutat. 17:423-430.
-
(2001)
Hum. Mutat.
, vol.17
, pp. 423-430
-
-
Baumer, A.1
Wiedemann, U.2
Hergersberg, M.3
Schinzel, A.4
-
79
-
-
0026546877
-
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
-
Frommer, M., L. E. McDonald, D. S. Millar, et al. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 89:1827-1831.
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 1827-1831
-
-
Frommer, M.1
McDonald, L.E.2
Millar, D.S.3
-
80
-
-
34548734299
-
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing
-
Taylor, K. H., R. S. Kramer, J. W. Davis, et al. 2007. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res. 67:8511-8518.
-
(2007)
Cancer Res.
, vol.67
, pp. 8511-8518
-
-
Taylor, K.H.1
Kramer, R.S.2
Davis, J.W.3
-
81
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies, M., M. Egholm, W. E. Altman, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
-
82
-
-
46449103738
-
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
-
Valouev, A., J. Ichikawa, T. Tonthat, et al. 2008. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 18:1051-1063.
-
(2008)
Genome Res.
, vol.18
, pp. 1051-1063
-
-
Valouev, A.1
Ichikawa, J.2
Tonthat, T.3
-
83
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
Bentley, D. R., S. Balasubramanian, H. P. Swerdlow, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
-
(2008)
Nature
, vol.456
, pp. 53-59
-
-
Bentley, D.R.1
Balasubramanian, S.2
Swerdlow, H.P.3
-
84
-
-
24644462173
-
Accurate multiplex polony sequencing of an evolved bacterial genome
-
Shendure, J., G. J. Porreca, N. B. Reppas, et al. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728-1732.
-
(2005)
Science
, vol.309
, pp. 1728-1732
-
-
Shendure, J.1
Porreca, G.J.2
Reppas, N.B.3
-
85
-
-
44949127038
-
Helicos BioSciences
-
Milos, P. 2008. Helicos BioSciences. Pharmacogenomics 9:477-480.
-
(2008)
Pharmacogenomics
, vol.9
, pp. 477-480
-
-
Milos, P.1
-
86
-
-
79959923864
-
Pipeline for large-scale microdroplet bisulfite pcr-based sequencing allows the tracking of hepitype evolution in tumors
-
Herrmann, A., A. Haake, O. Ammerpohl, et al. 2011. Pipeline for large-scale microdroplet bisulfite pcr-based sequencing allows the tracking of hepitype evolution in tumors. PLoS One 6:e21332.
-
(2011)
PLoS One
, vol.6
-
-
Herrmann, A.1
Haake, A.2
Ammerpohl, O.3
-
87
-
-
80053520872
-
Application of microdroplet PCR for large-scale targeted bisulfite sequencing
-
Komori, H. K., S. A. Lamere, A. Torkamani, et al. 2011. Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res. 21:1738-1745.
-
(2011)
Genome Res.
, vol.21
, pp. 1738-1745
-
-
Komori, H.K.1
Lamere, S.A.2
Torkamani, A.3
-
88
-
-
64449088698
-
Continuous base identification for single-molecule nanopore DNA sequencing
-
Clarke, J., H. C. Wu, L. Jayasinghe, A. Patel, S. Reid, and H. Bayley. 2009. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 4:265-270.
-
(2009)
Nat. Nanotechnol.
, vol.4
, pp. 265-270
-
-
Clarke, J.1
Wu, H.C.2
Jayasinghe, L.3
Patel, A.4
Reid, S.5
Bayley, H.6
-
89
-
-
77952967431
-
Direct detection of DNA methylation during single-molecule, real-time sequencing
-
Flusberg, B. A., D. R. Webster, J. H. Lee, et al. 2000. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7:461-465.
-
(2000)
Nat. Methods
, vol.7
, pp. 461-465
-
-
Flusberg, B.A.1
Webster, D.R.2
Lee, J.H.3
-
90
-
-
77958487369
-
Identification of epigenetic DNA modifications with a protein nanopore
-
Wallace, E. V., D. Stoddart, A. J. Heron, et al. 2010. Identification of epigenetic DNA modifications with a protein nanopore. Chem. Commun. (Camb.) 46:8195-8197.
-
(2010)
Chem. Commun. (Camb.)
, vol.46
, pp. 8195-8197
-
-
Wallace, E.V.1
Stoddart, D.2
Heron, A.J.3
-
91
-
-
77952967431
-
Direct detection of DNA methylation during single-molecule, real-time sequencing
-
Flusberg, B. A., D. R. Webster, J. H. Lee, et al. 2010. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7:461-465.
-
(2010)
Nat. Methods
, vol.7
, pp. 461-465
-
-
Flusberg, B.A.1
Webster, D.R.2
Lee, J.H.3
-
92
-
-
40449137021
-
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion
-
Reinders, J., C. Delucinge Vivier, G. Theiler, D. Chollet, P. Descombes, and J. Paszkowski. 2008. Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Genome Res. 18:469-476.
-
(2008)
Genome Res.
, vol.18
, pp. 469-476
-
-
Reinders, J.1
Delucinge Vivier, C.2
Theiler, G.3
Chollet, D.4
Descombes, P.5
Paszkowski, J.6
-
93
-
-
33644649616
-
High-throughput DNA methylation profiling using universal bead arrays
-
Bibikova, M., Z. Lin, L. Zhou, et al. 2006. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16:383-393.
-
(2006)
Genome Res.
, vol.16
, pp. 383-393
-
-
Bibikova, M.1
Lin, Z.2
Zhou, L.3
-
94
-
-
85077242196
-
-
® assay platform. [Technical report], Illumina, Inc., San Diego, CA.
-
® assay platform. [Technical report], Illumina, Inc., San Diego, CA.
-
(2008)
-
-
Weisenberger, D.J.1
Van Den Berg, D.2
Pan, F.3
Berman, B.P.4
Laird, P.W.5
-
95
-
-
0036613250
-
A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer
-
Suzuki, H., E. Gabrielson, W. Chen, et al. 2002. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat. Genet. 31:141-149.
-
(2002)
Nat. Genet.
, vol.31
, pp. 141-149
-
-
Suzuki, H.1
Gabrielson, E.2
Chen, W.3
-
96
-
-
0018860957
-
Cellular differentiation, cytidine analogs and DNA methylation
-
Jones, P. A., and S. M. Taylor. 1980. Cellular differentiation, cytidine analogs and DNA methylation. Cell 20:85-93.
-
(1980)
Cell
, vol.20
, pp. 85-93
-
-
Jones, P.A.1
Taylor, S.M.2
-
97
-
-
29144506935
-
Real-time PCR: overview and applications
-
Houghton, S. G., and F. R. Cockerill III. 2006. Real-time PCR: overview and applications. Surgery 139:1-5.
-
(2006)
Surgery
, vol.139
, pp. 1-5
-
-
Houghton, S.G.1
Cockerill III, F.R.2
-
98
-
-
49249091385
-
DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight
-
Weisenberger, D. J., B. N. Trinh, M. Campan, et al. 2008. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 36:4689-4698.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 4689-4698
-
-
Weisenberger, D.J.1
Trinh, B.N.2
Campan, M.3
-
99
-
-
0030874380
-
Methylation of discrete regions of the O6-methylguanine DNA methyltransferase (MGMT) CpG island is associated with heterochromatinization of the MGMT transcription start site and silencing of the gene
-
Watts, G. S., R. O. Pieper, J. F. Costello, Y. M. Peng, W. S. Dalton, and B. W. Futscher. 1997. Methylation of discrete regions of the O6-methylguanine DNA methyltransferase (MGMT) CpG island is associated with heterochromatinization of the MGMT transcription start site and silencing of the gene. Mol. Cell. Biol. 17:5612-5619.
-
(1997)
Mol. Cell. Biol.
, vol.17
, pp. 5612-5619
-
-
Watts, G.S.1
Pieper, R.O.2
Costello, J.F.3
Peng, Y.M.4
Dalton, W.S.5
Futscher, B.W.6
-
100
-
-
0032521402
-
The role of DNA methylation in expression of the p19/p16 locus in human bladder cancer cell lines
-
Gonzalgo, M. L., T. Hayashida, C. M. Bender, et al. 1998. The role of DNA methylation in expression of the p19/p16 locus in human bladder cancer cell lines. Cancer Res. 58:1245-1252.
-
(1998)
Cancer Res.
, vol.58
, pp. 1245-1252
-
-
Gonzalgo, M.L.1
Hayashida, T.2
Bender, C.M.3
-
101
-
-
0033135049
-
Methylation of CpG in a small region of the hMLH1 promoter invariably correlates with the absence of gene expression
-
Deng, G., A. Chen, J. Hong, H. S. Chae, and Y. S. Kim. 1999. Methylation of CpG in a small region of the hMLH1 promoter invariably correlates with the absence of gene expression. Cancer Res. 59:2029-2033.
-
(1999)
Cancer Res.
, vol.59
, pp. 2029-2033
-
-
Deng, G.1
Chen, A.2
Hong, J.3
Chae, H.S.4
Kim, Y.S.5
-
102
-
-
64349106730
-
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming
-
Deng, J., R. Shoemaker, B. Xie, et al. 2009. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat. Biotechnol. 27:353-360.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 353-360
-
-
Deng, J.1
Shoemaker, R.2
Xie, B.3
-
103
-
-
35748953750
-
Multiplex amplification of large sets of human exons
-
Porreca, G. J., K. Zhang, J. B. Li, et al. 2007. Multiplex amplification of large sets of human exons. Nat. Methods 4:931-936.
-
(2007)
Nat. Methods
, vol.4
, pp. 931-936
-
-
Porreca, G.J.1
Zhang, K.2
Li, J.B.3
-
104
-
-
0038678777
-
Sensitive and quantitative universal pyrosequencing methylation analysis of CpG sites
-
Colella, S., L. Shen, K. A. Baggerly, J. P. Issa, and R. Krahe. 2003. Sensitive and quantitative universal pyrosequencing methylation analysis of CpG sites. Biotechniques 35:146-150.
-
(2003)
Biotechniques
, vol.35
, pp. 146-150
-
-
Colella, S.1
Shen, L.2
Baggerly, K.A.3
Issa, J.P.4
Krahe, R.5
-
105
-
-
0038002236
-
Analysis and quantification of multiple methylation variable positions in cpg islands by pyrosequencing
-
Tost, J., J. Dunker, and I. G. Gut. 2003. Analysis and quantification of multiple methylation variable positions in cpg islands by pyrosequencing. Biotechniques 35:152-156.
-
(2003)
Biotechniques
, vol.35
, pp. 152-156
-
-
Tost, J.1
Dunker, J.2
Gut, I.G.3
-
106
-
-
61549137178
-
Emerging methods for analysis of the cancer methylome
-
Chang, J. W., T. H. Huang, and Y. C. Wang. 2008. Emerging methods for analysis of the cancer methylome. Pharmacogenomics 9:1869-1878.
-
(2008)
Pharmacogenomics
, vol.9
, pp. 1869-1878
-
-
Chang, J.W.1
Huang, T.H.2
Wang, Y.C.3
-
107
-
-
27644548948
-
Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry
-
Ehrich, M., M. R. Nelson, P. Stanssens, et al. 2005. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102:15785-15790.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15785-15790
-
-
Ehrich, M.1
Nelson, M.R.2
Stanssens, P.3
-
108
-
-
0037106658
-
Synthesis of stable-isotope enriched 5-methylpyrimidines and their use as probes of base reactivity in DNA
-
Burdzy, A., K. T. Noyes, V. Valinluck, and L. C. Sowers. 2002. Synthesis of stable-isotope enriched 5-methylpyrimidines and their use as probes of base reactivity in DNA. Nucleic Acids Res. 30:4068-4074.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4068-4074
-
-
Burdzy, A.1
Noyes, K.T.2
Valinluck, V.3
Sowers, L.C.4
-
109
-
-
77950187447
-
Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons
-
Feng, J., Y. Zhou, S. L. Campbell, et al. 2010. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat. Neurosci. 13:423-430.
-
(2010)
Nat. Neurosci.
, vol.13
, pp. 423-430
-
-
Feng, J.1
Zhou, Y.2
Campbell, S.L.3
-
110
-
-
79953217366
-
A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples
-
Le, T., K. P. Kim, G. Fan, and K. F. Faull. 2011. A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal. Biochem. 412:203-209.
-
(2011)
Anal. Biochem.
, vol.412
, pp. 203-209
-
-
Le, T.1
Kim, K.P.2
Fan, G.3
Faull, K.F.4
-
111
-
-
68149163117
-
PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment
-
Kristensen, L. S., and L. L. Hansen. 2009. PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment. Clin. Chem. 55:1471-1483.
-
(2009)
Clin. Chem.
, vol.55
, pp. 1471-1483
-
-
Kristensen, L.S.1
Hansen, L.L.2
-
112
-
-
0033607147
-
In situ detection of the hypermethylation-induced inactivation of the p16 gene as an early event in oncogenesis
-
Nuovo, G. J., T. W. Plaia, S. A. Belinsky, S. B. Baylin, and J. G. Herman. 1999. In situ detection of the hypermethylation-induced inactivation of the p16 gene as an early event in oncogenesis. Proc. Natl. Acad. Sci. USA 96:12754-12759.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 12754-12759
-
-
Nuovo, G.J.1
Plaia, T.W.2
Belinsky, S.A.3
Baylin, S.B.4
Herman, J.G.5
-
113
-
-
0034654669
-
MethyLight: a high-throughput assay to measure DNA methylation
-
Eads, C. A., K. D. Danenberg, K. Kawakami, et al. 2000. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 28:E32.
-
(2000)
Nucleic Acids Res.
, vol.28
-
-
Eads, C.A.1
Danenberg, K.D.2
Kawakami, K.3
-
114
-
-
0034949862
-
In-tube DNA methylation profiling by fluorescence melting curve analysis
-
Worm, J., A. Aggerholm, and P. Guldberg. 2001. In-tube DNA methylation profiling by fluorescence melting curve analysis. Clin. Chem. 47:1183-1189.
-
(2001)
Clin. Chem.
, vol.47
, pp. 1183-1189
-
-
Worm, J.1
Aggerholm, A.2
Guldberg, P.3
-
115
-
-
34247849498
-
Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation
-
Wojdacz, T. K., and A. Dobrovic. 2007. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res. 35:e41.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Wojdacz, T.K.1
Dobrovic, A.2
-
116
-
-
42449142344
-
Sensitive melting analysis after real time- methylation specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection
-
Kristensen, L. S., T. Mikeska, M. Krypuy, and A. Dobrovic. 2008. Sensitive melting analysis after real time- methylation specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection. Nucleic Acids Res. 36:e42.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Kristensen, L.S.1
Mikeska, T.2
Krypuy, M.3
Dobrovic, A.4
-
117
-
-
17444437545
-
A real-time PCR assay for DNA-methylation using methylation-specific blockers
-
Cottrell, S. E., J. Distler, N. S. Goodman, et al. 2004. A real-time PCR assay for DNA-methylation using methylation-specific blockers. Nucleic Acids Res. 32:e10.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Cottrell, S.E.1
Distler, J.2
Goodman, N.S.3
-
118
-
-
36649005341
-
MS-FLAG, a novel real-time signal generation method for methylation-specific PCR
-
Bonanno, C., E. Shehi, D. Adlerstein, and G. M. Makrigiorgos. 2007. MS-FLAG, a novel real-time signal generation method for methylation-specific PCR. Clin. Chem. 53:2119-2127.
-
(2007)
Clin. Chem.
, vol.53
, pp. 2119-2127
-
-
Bonanno, C.1
Shehi, E.2
Adlerstein, D.3
Makrigiorgos, G.M.4
-
119
-
-
77954159684
-
DNA methylation of HOXD3 as a marker of prostate cancer progression
-
Kron, K. J., L. Liu, V. V. Pethe, et al. 2010. DNA methylation of HOXD3 as a marker of prostate cancer progression. Lab. Invest. 90:1060-1067.
-
(2010)
Lab. Invest.
, vol.90
, pp. 1060-1067
-
-
Kron, K.J.1
Liu, L.2
Pethe, V.V.3
-
120
-
-
77955448176
-
Methylated APC and GSTP1 genes in serum DNA correlate with the presence of circulating blood tumor cells and are associated with a more aggressive and advanced breast cancer disease
-
Matuschek, C., E. Bolke, G. Lammering, et al. 2010. Methylated APC and GSTP1 genes in serum DNA correlate with the presence of circulating blood tumor cells and are associated with a more aggressive and advanced breast cancer disease. Eur. J. Med. Res. 15:277-286.
-
(2010)
Eur. J. Med. Res.
, vol.15
, pp. 277-286
-
-
Matuschek, C.1
Bolke, E.2
Lammering, G.3
-
121
-
-
78149463044
-
Specific variants in the MLH1 gene region may drive DNA methylation, loss of protein expression, and MSI-H colorectal cancer
-
Mrkonjic, M., N. M. Roslin, C. M. Greenwood, et al. 2010. Specific variants in the MLH1 gene region may drive DNA methylation, loss of protein expression, and MSI-H colorectal cancer. PLoS One 5:e13314.
-
(2010)
PLoS One
, vol.5
-
-
Mrkonjic, M.1
Roslin, N.M.2
Greenwood, C.M.3
-
122
-
-
79955773267
-
Promoter methylation of Wnt antagonists DKK1 and SFRP1 are associated with opposing tumor subtypes in a large cohort of colorectal cancers
-
Rawson, J. B., M. Manno, M. Mrkonjic, et al. 2011. Promoter methylation of Wnt antagonists DKK1 and SFRP1 are associated with opposing tumor subtypes in a large cohort of colorectal cancers. Carcinogenesis 32:741-747.
-
(2011)
Carcinogenesis
, vol.32
, pp. 741-747
-
-
Rawson, J.B.1
Manno, M.2
Mrkonjic, M.3
-
123
-
-
70249147655
-
Sensitive digital quantification of DNA methylation in clinical samples
-
Li, M., W. D. Chen, N. Papadopoulos, et al. 2009. Sensitive digital quantification of DNA methylation in clinical samples. Nat. Biotechnol. 27:858-863.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 858-863
-
-
Li, M.1
Chen, W.D.2
Papadopoulos, N.3
-
124
-
-
0030738231
-
Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE)
-
Gonzalgo, M. L., and P. A. Jones. 1997. Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE). Nucleic Acids Res. 25:2529-2531.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 2529-2531
-
-
Gonzalgo, M.L.1
Jones, P.A.2
-
125
-
-
0036753290
-
DNA methylation: a profile of methods and applications
-
4, 6-49.
-
Fraga, M. F., and M. Esteller. 2002. DNA methylation: a profile of methods and applications. Biotechniques 33:632, 4, 6-49.
-
(2002)
Biotechniques
, vol.33
, pp. 632
-
-
Fraga, M.F.1
Esteller, M.2
-
126
-
-
0041719983
-
A rapid, quantitative, non-radioactive bisulfite-SNuPE- IP RP HPLC assay for methylation analysis at specific CpG sites
-
El-Maarri, O., U. Herbiniaux, J. Walter, and J. Oldenburg. 2002. A rapid, quantitative, non-radioactive bisulfite-SNuPE- IP RP HPLC assay for methylation analysis at specific CpG sites. Nucleic Acids Res. 30:e25.
-
(2002)
Nucleic Acids Res.
, vol.30
-
-
El-Maarri, O.1
Herbiniaux, U.2
Walter, J.3
Oldenburg, J.4
-
127
-
-
23944445098
-
Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions
-
Kaminsky, Z. A., A. Assadzadeh, J. Flanagan, and A. Petronis. 2005. Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions. Nucleic Acids Res. 33:e95.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Kaminsky, Z.A.1
Assadzadeh, A.2
Flanagan, J.3
Petronis, A.4
-
128
-
-
79951495448
-
MIRA-SNuPE, a quantitative, multiplex method for measuring allele-specific DNA methylation
-
Lee, D. H., D. A. Tran, P. Singh, et al. 2011. MIRA-SNuPE, a quantitative, multiplex method for measuring allele-specific DNA methylation. Epigenetics 6:212-223.
-
(2011)
Epigenetics
, vol.6
, pp. 212-223
-
-
Lee, D.H.1
Tran, D.A.2
Singh, P.3
-
129
-
-
0030825309
-
COBRA: a sensitive and quantitative DNA methylation assay
-
Xiong, Z., and P. W. Laird. 1997. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 25:2532-2534.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 2532-2534
-
-
Xiong, Z.1
Laird, P.W.2
-
130
-
-
33947671871
-
Quantification of DNA methylation in electrofluidics chips (Bio-COBRA)
-
Brena, R. M., H. Auer, K. Kornacker, and C. Plass. 2006. Quantification of DNA methylation in electrofluidics chips (Bio-COBRA). Nat. Protoc. 1:52-58.
-
(2006)
Nat. Protoc.
, vol.1
, pp. 52-58
-
-
Brena, R.M.1
Auer, H.2
Kornacker, K.3
Plass, C.4
-
131
-
-
18844465619
-
Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS)
-
Frigola, J., M. Ribas, R. A. Risques, and M. A. Peinado. 2002. Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS). Nucleic Acids Res. 30:e28.
-
(2002)
Nucleic Acids Res.
, vol.30
-
-
Frigola, J.1
Ribas, M.2
Risques, R.A.3
Peinado, M.A.4
-
132
-
-
0031050736
-
Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR
-
Gonzalgo, M. L., G. Liang, C. H. Spruck III, J. M. Zingg, W. M. Rideout III, and P. A. Jones. 1997. Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR. Cancer Res. 57:594-599.
-
(1997)
Cancer Res.
, vol.57
, pp. 594-599
-
-
Gonzalgo, M.L.1
Liang, G.2
Spruck III, C.H.3
Zingg, J.M.4
Rideout III, W.M.5
Jones, P.A.6
-
133
-
-
0030888263
-
Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique
-
Huang, T. H., D. E. Laux, B. C. Hamlin, P. Tran, H. Tran, and D. B. Lubahn. 1997. Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique. Cancer Res. 57:1030-1034.
-
(1997)
Cancer Res.
, vol.57
, pp. 1030-1034
-
-
Huang, T.H.1
Laux, D.E.2
Hamlin, B.C.3
Tran, P.4
Tran, H.5
Lubahn, D.B.6
-
134
-
-
34047116826
-
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
-
Weber, M., I. Hellmann, M. B. Stadler, et al. 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
-
135
-
-
33644853936
-
Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation
-
Yegnasubramanian, S., X. Lin, M. C. Haffner, A. M. DeMarzo, and W. G. Nelson. 2006. Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation. Nucleic Acids Res. 34:e19.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Yegnasubramanian, S.1
Lin, X.2
Haffner, M.C.3
DeMarzo, A.M.4
Nelson, W.G.5
-
136
-
-
79955538247
-
Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain
-
Guo, J. U., Y. Su, C. Zhong, G. L. Ming, and H. Song. 2011. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145:423-434.
-
(2011)
Cell
, vol.145
, pp. 423-434
-
-
Guo, J.U.1
Su, Y.2
Zhong, C.3
Ming, G.L.4
Song, H.5
-
137
-
-
79956302047
-
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
-
Williams, K., J. Christensen, M. T. Pedersen, et al. 2011. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473:343-348.
-
(2011)
Nature
, vol.473
, pp. 343-348
-
-
Williams, K.1
Christensen, J.2
Pedersen, M.T.3
-
138
-
-
84856058152
-
Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers
-
Haffner, M. C., A. Chaux, A. K. Meeker, et al. 2011. Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers. Oncotarget 2:627-637.
-
(2011)
Oncotarget
, vol.2
, pp. 627-637
-
-
Haffner, M.C.1
Chaux, A.2
Meeker, A.K.3
|