-
1
-
-
22844457491
-
DNA methylation and human disease
-
Robertson, K.D. (2005) DNA methylation and human disease. Nat. Rev. Genet., 6, 597-610.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 597-610
-
-
Robertson, K.D.1
-
2
-
-
79952111066
-
Chromatin remodeling in mammary gland differentiation and breast tumorigenesis
-
Huang, T.H. and Esteller, M. (2010) Chromatin remodeling in mammary gland differentiation and breast tumorigenesis. Cold Spring Harb. Perspect. Biol., 2, a004515.
-
(2010)
Cold Spring Harb. Perspect. Biol.
, vol.2
-
-
Huang, T.H.1
Esteller, M.2
-
3
-
-
0036274359
-
The fundamental role of epigenetic events in cancer
-
Jones, P.A. and Baylin, S.B. (2002) The fundamental role of epigenetic events in cancer. Nat. Rev. Genet., 3, 415-428.
-
(2002)
Nat. Rev. Genet.
, vol.3
, pp. 415-428
-
-
Jones, P.A.1
Baylin, S.B.2
-
4
-
-
17444417521
-
Cancer epigenetics
-
Laird, P.W. (2005) Cancer epigenetics. Hum. Mol. Genet, 14(Spec No. 1), R65-R76.
-
(2005)
Hum. Mol. Genet
, vol.14
, Issue.1 SPEC.
-
-
Laird, P.W.1
-
5
-
-
0038576158
-
The power and the promise of DNA methylation markers
-
Laird, P.W. (2003) The power and the promise of DNA methylation markers. Nat. Rev. Cancer, 3, 253-266.
-
(2003)
Nat. Rev. Cancer
, vol.3
, pp. 253-266
-
-
Laird, P.W.1
-
6
-
-
33746407333
-
The emerging science of epigenomics
-
Callinan, P.A. and Feinberg, A.P. (2006) The emerging science of epigenomics. Hum. Mol. Genet., 15(Spec No. 1), R95-R101.
-
(2006)
Hum. Mol. Genet.
, vol.15
, Issue.1 SPEC.
-
-
Callinan, P.A.1
Feinberg, A.P.2
-
7
-
-
79952088316
-
Next generation sequencing: Advances in characterizing the methylome
-
Taylor, K.H., Shi, H. and Caldwell, C.W. (2010) Next generation sequencing: advances in characterizing the methylome. Genes, 1, 143-165.
-
(2010)
Genes
, vol.1
, pp. 143-165
-
-
Taylor, K.H.1
Shi, H.2
Caldwell, C.W.3
-
8
-
-
79952118443
-
Genome-wide DNA methylation profiling. Wiley Interdisciplin
-
Bibikova, M. and Fan, J.-B. Genome-wide DNA methylation profiling. Wiley Interdisciplin. Rev. Syst. Biol. Med., 2, 210-223.
-
Rev. Syst. Biol. Med.
, vol.2
, pp. 210-223
-
-
Bibikova, M.1
Fan, J.-B.2
-
9
-
-
77249137168
-
Principles and challenges of genome-wide DNA methylation analysis
-
Laird, P.W. (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 191-203
-
-
Laird, P.W.1
-
10
-
-
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
-
11
-
-
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
-
12
-
-
77955458087
-
High-throughput method for analyzing methylation of CpGs in targeted genomic regions
-
Nautiyal, S., Carlton, V.E., Lu, Y., Ireland, J.S., Flaucher, D., Moorhead, M., Gray, J.W., Spellman, P., Mindrinos, M., Berg, P. et al. (2010) High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc. Natl Acad. Sci. USA, 107, 12587-12592.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 12587-12592
-
-
Nautiyal, S.1
Carlton, V.E.2
Lu, Y.3
Ireland, J.S.4
Flaucher, D.5
Moorhead, M.6
Gray, J.W.7
Spellman, P.8
Mindrinos, M.9
Berg, P.10
-
13
-
-
78649297854
-
Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
-
Teer, J.K., Bonnycastle, L.L., Chines, P.S., Hansen, N.F., Aoyama, N., Swift, A.J., Abaan, H.O., Albert, T.J., Margulies, E.H., Green, E.D. et al. (2010) Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res., 20, 1420-1431.
-
(2010)
Genome Res.
, vol.20
, pp. 1420-1431
-
-
Teer, J.K.1
Bonnycastle, L.L.2
Chines, P.S.3
Hansen, N.F.4
Aoyama, N.5
Swift, A.J.6
Abaan, H.O.7
Albert, T.J.8
Margulies, E.H.9
Green, E.D.10
-
14
-
-
64349091471
-
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
-
Ball, M.P., Li, J.B., Gao, Y., Lee, J.H., LeProust, E.M., Park, I.H., Xie, B., Daley, G.Q. and Church, G.M. (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
Lee, J.H.4
Leproust, E.M.5
Park, I.H.6
Xie, B.7
Daley, G.Q.8
Church, G.M.9
-
15
-
-
64349106730
-
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming
-
Deng, J., Shoemaker, R., Xie, B., Gore, A., LeProust, E.M., Antosiewicz-Bourget, J., Egli, D., Maherali, N., Park, I.H., Yu, J. 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
Gore, A.4
Leproust, E.M.5
Antosiewicz-Bourget, J.6
Egli, D.7
Maherali, N.8
Park, I.H.9
Yu, J.10
-
16
-
-
69749092741
-
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
-
Hodges, E., Smith, A.D., Kendall, J., Xuan, Z., Ravi, K., Rooks, M., Zhang, M.Q., Ye, K., Bhattacharjee, A., Brizuela, L. et al. (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res., 19, 1593-1605.
-
(2009)
Genome Res.
, vol.19
, pp. 1593-1605
-
-
Hodges, E.1
Smith, A.D.2
Kendall, J.3
Xuan, Z.4
Ravi, K.5
Rooks, M.6
Zhang, M.Q.7
Ye, K.8
Bhattacharjee, A.9
Brizuela, L.10
-
17
-
-
59849113821
-
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
-
Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C. et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol., 27, 182-189.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 182-189
-
-
Gnirke, A.1
Melnikov, A.2
Maguire, J.3
Rogov, P.4
Leproust, E.M.5
Brockman, W.6
Fennell, T.7
Giannoukos, G.8
Fisher, S.9
Russ, C.10
-
18
-
-
35748953750
-
Multiplex amplification of large sets of human exons
-
Porreca, G.J., Zhang, K., Li, J.B., Xie, B., Austin, D., Vassallo, S.L., LeProust, E.M., Peck, B.J., Emig, C.J., Dahl, F. 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
Xie, B.4
Austin, D.5
Vassallo, S.L.6
Leproust, E.M.7
Peck, B.J.8
Emig, C.J.9
Dahl, F.10
-
19
-
-
50549102884
-
PRIMEGENS-v2: Genome-wide primer design for analyzing DNA methylation patterns of CpG islands
-
Srivastava, G.P., Guo, J., Shi, H. and Xu, D. (2008) PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics, 24, 1837-1842.
-
(2008)
Bioinformatics
, vol.24
, pp. 1837-1842
-
-
Srivastava, G.P.1
Guo, J.2
Shi, H.3
Xu, D.4
-
20
-
-
53849146020
-
Model-based Analysis of ChIP-Seq (MACS)
-
Zhang, Y., Liu, T., Meyer, C., Eeckhoute, J., Johnson, D., Bernstein, B., Nusbaum, C., Myers, R., Brown, M., Li, W. et al. (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
-
(2008)
Genome Biol.
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.3
Eeckhoute, J.4
Johnson, D.5
Bernstein, B.6
Nusbaum, C.7
Myers, R.8
Brown, M.9
Li, W.10
-
21
-
-
80455159046
-
-
Fung, G. (ed.) iConcept Press Ltd, Annerley, Australia
-
Srivastava, G.P., Kushwaha, G., Shi, H. and Xu, D. (2010) In Fung, G. (ed.), A Practical Guide to Bioinformatics Analysis. iConcept Press Ltd, Annerley, Australia.
-
(2010)
A Practical Guide to Bioinformatics Analysis
-
-
Srivastava, G.P.1
Kushwaha, G.2
Shi, H.3
Xu, D.4
-
22
-
-
0141954011
-
Differential distribution of DNA methylation within the RASSF1A CpG island in breast cancer
-
Yan, P.S., Shi, H., Rahmatpanah, F., Hsiau, T.H., Hsiau, A.H., Leu, Y.W., Liu, J.C. and Huang, T.H. (2003) Differential distribution of DNA methylation within the RASSF1A CpG island in breast cancer. Cancer Res., 63, 6178-6186.
-
(2003)
Cancer Res.
, vol.63
, pp. 6178-6186
-
-
Yan, P.S.1
Shi, H.2
Rahmatpanah, F.3
Hsiau, T.H.4
Hsiau, A.H.5
Leu, Y.W.6
Liu, J.C.7
Huang, T.H.8
-
23
-
-
18344390653
-
DNMT1 and DNMT3b cooperate to silence genes in human cancer cells
-
Rhee, I., Bachman, K.E., Park, B.H., Jair, K.W., Yen, R.W., Schuebel, K.E., Cui, H., Feinberg, A.P., Lengauer, C., Kinzler, K.W. et al. (2002) DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature, 416, 552-556.
-
(2002)
Nature
, vol.416
, pp. 552-556
-
-
Rhee, I.1
Bachman, K.E.2
Park, B.H.3
Jair, K.W.4
Yen, R.W.5
Schuebel, K.E.6
Cui, H.7
Feinberg, A.P.8
Lengauer, C.9
Kinzler, K.W.10
-
24
-
-
0034720284
-
CpG methylation is maintained in human cancer cells lacking DNMT1
-
Rhee, I., Jair, K.W., Yen, R.W., Lengauer, C., Herman, J.G., Kinzler, K.W., Vogelstein, B., Baylin, S.B. and Schuebel, K.E. (2000) CpG methylation is maintained in human cancer cells lacking DNMT1. Nature, 404, 1003-1007.
-
(2000)
Nature
, vol.404
, pp. 1003-1007
-
-
Rhee, I.1
Jair, K.W.2
Yen, R.W.3
Lengauer, C.4
Herman, J.G.5
Kinzler, K.W.6
Vogelstein, B.7
Baylin, S.B.8
Schuebel, K.E.9
-
25
-
-
33748998743
-
Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts sugges|s an essential role for DNMT1 in cell survival
-
Egger, G., Jeong, S., Escobar, S.G., Cortez, C.C., Li, T.W., Saito, Y., Yoo, C.B., Jones, P.A. and Liang, G. (2006) Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts sugges|s an essential role for DNMT1 in cell survival. Proc. Natl Acad. Sci. USA, 103, 14080-14085.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 14080-14085
-
-
Egger, G.1
Jeong, S.2
Escobar, S.G.3
Cortez, C.C.4
Li, T.W.5
Saito, Y.6
Yoo, C.B.7
Jones, P.A.8
Liang, G.9
-
26
-
-
0041779528
-
Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases
-
Paz, M.F., Wei, S., Cigudosa, J.C., Rodriguez-Perales, S., Peinado, M.A., Huang, T.H. and Esteller, M. (2003) Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases. Hum. Mol. Genet., 12, 2209-2219.
-
(2003)
Hum. Mol. Genet.
, vol.12
, pp. 2209-2219
-
-
Paz, M.F.1
Wei, S.2
Cigudosa, J.C.3
Rodriguez-Perales, S.4
Peinado, M.A.5
Huang, T.H.6
Esteller, M.7
-
27
-
-
79958754527
-
Validation of a DNA methylation microarray for 450, 000 CpG sites in the human genome
-
Sandoval, J., Heyn, H.A., Moran, S., Serra-Musach, J., Pujana, M.A., Bibikova, M. and Esteller, M. (2011) Validation of a DNA methylation microarray for 450, 000 CpG sites in the human genome. Epigenetics, 6, 692-702.
-
(2011)
Epigenetics
, vol.6
, pp. 692-702
-
-
Sandoval, J.1
Heyn, H.A.2
Moran, S.3
Serra-Musach, J.4
Pujana, M.A.5
Bibikova, M.6
Esteller, M.7
-
28
-
-
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
-
29
-
-
78649773164
-
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
-
Adey, A., Morrison, H., Asan., Xun, X., Kitzman, J., Turner, E., Stackhouse, B., MacKenzie, A., Caruccio, N., Zhang, X. et al. (2011) Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol., 11, R119.
-
(2011)
Genome Biol.
, vol.11
-
-
Adey, A.1
Asan, M.H.2
Xun, X.3
Kitzman, J.4
Turner, E.5
Stackhouse, B.6
MacKenzie, A.7
Caruccio, N.8
Zhang, X.9
-
30
-
-
78650762588
-
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
-
Fisher, S., Barry, A., Abreu, J., Minie, B., Delorey, T., Fennell, T., Allen, A., Ambrogio, L., Berlin, A., Blumenstiel, B. et al. (2011) A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol., 12, R1.
-
(2011)
Genome Biol.
, vol.12
-
-
Fisher, S.1
Barry, A.2
Abreu, J.3
Minie, B.4
Delorey, T.5
Fennell, T.6
Allen, A.7
Ambrogio, L.8
Berlin, A.9
Blumenstiel, B.10
-
31
-
-
77449153454
-
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
-
Gu, H. Bock, C., Mikkelsen, T.S., Jager, N., Smith, Z.D., Tomazou, E., Gnirke, A., Lander, E.S. and Meissner, A. (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods, 7, 133-136.
-
(2010)
Nat. Methods
, vol.7
, pp. 133-136
-
-
Gu, H.1
Bock, C.2
Mikkelsen, T.S.3
Jager, N.4
Smith, Z.D.5
Tomazou, E.6
Gnirke, A.7
Lander, E.S.8
Meissner, A.9
-
32
-
-
33845209913
-
A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes
-
Neve, R.M., Chin, K., Fridlyand, J., Yeh, J., Baehner, F.L., Fevr, T., Clark, L., Bayani, N., Coppe, J.P., Tong, F. et al. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell, 10, 515-527.
-
(2006)
Cancer Cell
, vol.10
, pp. 515-527
-
-
Neve, R.M.1
Chin, K.2
Fridlyand, J.3
Yeh, J.4
Baehner, F.L.5
Fevr, T.6
Clark, L.7
Bayani, N.8
Coppe, J.P.9
Tong, F.10
-
33
-
-
5444227862
-
Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach
-
Gius, D., Cui, H., Bradbury, C.M., Cook, J., Smart, D.K., Zhao, S., Young, L., Brandenburg, S.A., Hu, Y., Bisht, K.S. et al. (2004) Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach. Cancer Cell, 6, 361-371.
-
(2004)
Cancer Cell
, vol.6
, pp. 361-371
-
-
Gius, D.1
Cui, H.2
Bradbury, C.M.3
Cook, J.4
Smart, D.K.5
Zhao, S.6
Young, L.7
Brandenburg, S.A.8
Hu, Y.9
Bisht, K.S.10
-
34
-
-
33847763576
-
Genetic unmasking of an epigenetically silenced microRNA in human cancer cells
-
Lujambio, A., Ropero, S., Ballestar, E., Fraga, M.F., Cerrato, C., Setien, F., Casado, S., Suarez-Gauthier, A., Sanchez-Cespedes, M., Git, A. et al. (2007) Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res., 67, 1424-1429.
-
(2007)
Cancer Res.
, vol.67
, pp. 1424-1429
-
-
Lujambio, A.1
Ropero, S.2
Ballestar, E.3
Fraga, M.F.4
Cerrato, C.5
Setien, F.6
Casado, S.7
Suarez-Gauthier, A.8
Sanchez-Cespedes, M.9
Git, A.10
|