-
1
-
-
33947315736
-
Cancer epigenomics: DNA methylomes and histonemodification maps
-
Esteller M (2007) Cancer epigenomics: DNA methylomes and histonemodification maps. Nat Rev Genet 8: 286-298.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 286-298
-
-
Esteller, M.1
-
2
-
-
33847065486
-
The Epigenomics of Cancer
-
DOI 10.1016/j.cell.2007.01.029, PII S0092867407001274
-
Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128: 683-692. (Pubitemid 46273572)
-
(2007)
Cell
, vol.128
, Issue.4
, pp. 683-692
-
-
Jones, P.A.1
Baylin, S.B.2
-
3
-
-
77649157895
-
Genomic imprinting: The influence of differential methylation in the two sexes
-
Biliya S, Bulla LA (2010) Genomic imprinting: the influence of differential methylation in the two sexes. Experimental Biology and Medicine 235: 139-147.
-
(2010)
Experimental Biology and Medicine
, vol.235
, pp. 139-147
-
-
Biliya, S.1
Bulla, L.A.2
-
4
-
-
79961022818
-
Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation
-
Cotton AM, Lam L, Affleck JG, Wilson IM, Penaherrera MS, et al. (2011) Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation. Human Genetics 130: 187-201.
-
(2011)
Human Genetics
, vol.130
, pp. 187-201
-
-
Cotton, A.M.1
Lam, L.2
Affleck, J.G.3
Wilson, I.M.4
Penaherrera, M.S.5
-
5
-
-
77957932941
-
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
-
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28: 1097-1105.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1097-1105
-
-
Harris, R.A.1
Wang, T.2
Coarfa, C.3
Nagarajan, R.P.4
Hong, C.5
-
6
-
-
22844457491
-
DNA methylation and human disease
-
Robertson KD (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
-
7
-
-
77449127799
-
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
-
Serre D, Lee BH, Ting AH (2010) MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 38: 391-399.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 391-399
-
-
Serre, D.1
Lee, B.H.2
Ting, A.H.3
-
8
-
-
39149133183
-
Methyl-DNA immunoprecipitation (MeDIP): Hunting down the DNA methylome
-
39 passim
-
Jacinto FV, Ballestar E, Esteller M (2008) Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44: 35, 37, 39 passim.
-
(2008)
Biotechniques
, vol.44
-
-
Jacinto, F.V.1
Ballestar, E.2
Esteller, M.3
-
9
-
-
46949098742
-
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
-
DOI 10.1038/nbt1414, PII NBT1414
-
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, et al. (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26: 779-785. (Pubitemid 351961453)
-
(2008)
Nature Biotechnology
, vol.26
, Issue.7
, pp. 779-785
-
-
Down, T.A.1
Rakyan, V.K.2
Turner, D.J.3
Flicek, P.4
Li, H.5
Kulesha, E.6
Graf, S.7
Johnson, N.8
Herrero, J.9
Tomazou, E.M.10
Thorne, N.P.11
Backdahl, L.12
Herberth, M.13
Howe, K.L.14
Jackson, D.K.15
Miretti, M.M.16
Marioni, J.C.17
Birney, E.18
Hubbard, T.J.P.19
Durbin, R.20
Tavare, S.21
Beck, S.22
more..
-
10
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, 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
-
11
-
-
49649125042
-
Genomescale DNA methylation maps of pluripotent and differentiated cells
-
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, et al. (2008) Genomescale 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
-
12
-
-
77957937011
-
Genome-wide mapping of DNA methylation: A quantitative technology comparison
-
Bock C, Tomazou EM, Brinkman A, Müller F, Simmer F, et al. (2010) Genome-wide mapping of DNA methylation: a quantitative technology comparison. Nature biotechnology 28: 1106.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 1106
-
-
Bock, C.1
Tomazou, E.M.2
Brinkman, A.3
Müller, F.4
Simmer, F.5
-
13
-
-
68949141599
-
BSMAP: Whole genome bisulfite sequence MAPping program
-
Li YX, Li W (2009) BSMAP: whole genome bisulfite sequence MAPping program. Bmc Bioinformatics 10.
-
(2009)
Bmc Bioinformatics
, vol.10
-
-
Li, Y.X.1
Li, W.2
-
15
-
-
70350697851
-
Updates to the RMAP short-read mapping software
-
Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, et al. (2009) Updates to the RMAP short-read mapping software. Bioinformatics 25: 2841-2842.
-
(2009)
Bioinformatics
, vol.25
, pp. 2841-2842
-
-
Smith, A.D.1
Chung, W.Y.2
Hodges, E.3
Kendall, J.4
Hannon, G.5
-
16
-
-
79957868920
-
Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger F, Andrews SR (2011) Bismark: a flexible 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
-
17
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
18
-
-
79953177468
-
Aligning short sequencing reads with Bowtie
-
Chapter 11: Unit 11 17
-
Langmead B (2010) Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics Chapter 11: Unit 11 17.
-
(2010)
Curr Protoc Bioinformatics
-
-
Langmead, B.1
-
19
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
20
-
-
34547093155
-
CyMATE: A new tool for methylation analysis of plant genomic DNA after bisulphite sequencing
-
DOI 10.1111/j.1365-313X.2007.03152.x
-
Hetzl J, Foerster AM, Raidl G, Mittelsten Scheid O (2007) CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing. Plant J 51: 526-536. (Pubitemid 47106545)
-
(2007)
Plant Journal
, vol.51
, Issue.3
, pp. 526-536
-
-
Hetzl, J.1
Foerster, A.M.2
Raidl, G.3
Scheid, O.M.4
-
21
-
-
34548684770
-
CpG PatternFinder: A Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA
-
Xu YH, Manoharan HT, Pitot HC (2007) CpG PatternFinder: a Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA. Biotechniques 43: 334, 336-340, 342.
-
(2007)
Biotechniques
, vol.43
-
-
Xu, Y.H.1
Manoharan, H.T.2
Pitot, H.C.3
-
22
-
-
84876387793
-
GBSA: A comprehensive software for analysing whole genome bisulfite sequencing data
-
Benoukraf T, Wongphayak S, Hadi LH, Wu M, Soong R (2012) GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data. Nucleic Acids Res 41: e55.
-
(2012)
Nucleic Acids Res
, vol.41
-
-
Benoukraf, T.1
Wongphayak, S.2
Hadi, L.H.3
Wu, M.4
Soong, R.5
-
23
-
-
84878866495
-
COHCAP: An integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis
-
Warden CD, Lee H, Tompkins JD, Li X, Wang C, et al. (2013) COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res.
-
(2013)
Nucleic Acids Res
-
-
Warden, C.D.1
Lee, H.2
Tompkins, J.D.3
Li, X.4
Wang, C.5
-
24
-
-
84866860221
-
methylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles
-
Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, et al. (2012) methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 13: R87.
-
(2012)
Genome Biol
, vol.13
-
-
Akalin, A.1
Kormaksson, M.2
Li, S.3
Garrett-Bakelman, F.E.4
Figueroa, M.E.5
-
25
-
-
84866853818
-
BSmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
-
Hansen KD, Langmead B, Irizarry RA (2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol 13: R83.
-
(2012)
Genome Biol
, vol.13
-
-
Hansen, K.D.1
Langmead, B.2
Irizarry, R.A.3
-
26
-
-
84865091830
-
SAAP-RRBS: Streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing
-
Sun ZF, Baheti S, Middha S, Kanwar R, Zhang YJ, et al. (2012) SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics 28: 2180-2181.
-
(2012)
Bioinformatics
, vol.28
, pp. 2180-2181
-
-
Sun, Z.F.1
Baheti, S.2
Middha, S.3
Kanwar, R.4
Zhang, Y.J.5
-
27
-
-
84887606048
-
RRBS-Analyser: A Comprehensive Web Server for Reduced Representation Bisulfite Sequencing Data Analysis
-
Wang T, Liu Q, Li X, Wang X, Li J, et al. (2013) RRBS-Analyser: A Comprehensive Web Server for Reduced Representation Bisulfite Sequencing Data Analysis. Hum Mutat.
-
(2013)
Hum Mutat
-
-
Wang, T.1
Liu, Q.2
Li, X.3
Wang, X.4
Li, J.5
-
28
-
-
79956006215
-
QDMR: A quantitative method for identification of differentially methylated regions by entropy
-
Zhang Y, Liu H, Lv J, Xiao X, Zhu J, et al. (2011) QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res 39: e58.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Zhang, Y.1
Liu, H.2
Lv, J.3
Xiao, X.4
Zhu, J.5
-
29
-
-
2142738304
-
WebLogo: A sequence logo generator
-
DOI 10.1101/gr.849004
-
Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190. (Pubitemid 38811555)
-
(2004)
Genome Research
, vol.14
, Issue.6
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.-M.3
Brenner, S.E.4
-
30
-
-
80054902457
-
wapRNA: A web-based application for the processing of RNA sequences
-
Zhao W, Liu W, Tian D, Tang B, Wang Y, et al. (2011) wapRNA: a web-based application for the processing of RNA sequences. Bioinformatics 27: 3076-3077.
-
(2011)
Bioinformatics
, vol.27
, pp. 3076-3077
-
-
Zhao, W.1
Liu, W.2
Tian, D.3
Tang, B.4
Wang, Y.5
|