-
1
-
-
84866860221
-
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
-
Akalin, A., Kormaksson, M., Li, S., Garrett-Bakelman, F. E., Figueroa, M. E., Melnick, A., et al. (2012). methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 13, R87. doi: 10.1186/gb-2012-13-10-r87
-
(2012)
Genome Biol
, vol.13
, pp. R87
-
-
Akalin, A.1
Kormaksson, M.2
Li, S.3
Garrett-Bakelman, F.E.4
Figueroa, M.E.5
Melnick, A.6
-
2
-
-
84897548625
-
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays
-
Aryee, M. J., Jaffe, A. E., Corrada-Bravo, H., Ladd-Acosta, C., Feinberg, A. P., Hansen, K. D., et al. (2014). Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays. Bioinformatics 30, 1363-1369. doi: 10.1093/bioinformatics/btu049
-
(2014)
Bioinformatics
, vol.30
, pp. 1363-1369
-
-
Aryee, M.J.1
Jaffe, A.E.2
Corrada-Bravo, H.3
Ladd-Acosta, C.4
Feinberg, A.P.5
Hansen, K.D.6
-
3
-
-
84889649328
-
Perspectives of international human epigenome consortium
-
Bae, J. B. (2013). Perspectives of international human epigenome consortium. Genom. Inform. 11, 7-14. doi: 10.5808/GI.2013.11.1.7
-
(2013)
Genom. Inform.
, vol.11
, pp. 7-14
-
-
Bae, J.B.1
-
4
-
-
38349022394
-
False discovery rates for spatial signals
-
Benjamini, Y., and Heller, R. (2007). False discovery rates for spatial signals. J. Am. Stat. Assoc. 102, 1272-1281. doi: 10.1198/016214507000000941
-
(2007)
J. Am. Stat. Assoc.
, vol.102
, pp. 1272-1281
-
-
Benjamini, Y.1
Heller, R.2
-
5
-
-
64349095390
-
An operational definition of epigenetics
-
Berger, S. L., Kouzarides, T., Shiekhattar, R., and Shilatifard, A. (2009). An operational definition of epigenetics. Genes Dev. 23, 781-783. doi: 10.1101/gad.1787609
-
(2009)
Genes Dev
, vol.23
, pp. 781-783
-
-
Berger, S.L.1
Kouzarides, T.2
Shiekhattar, R.3
Shilatifard, A.4
-
6
-
-
77957940722
-
The NIH roadmap epigenomics mapping consortium
-
Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., et al. (2010). The NIH roadmap epigenomics mapping consortium. Nat. Biotechnol. 28, 1045-1048. doi: 10.1038/nbt1010-1045
-
(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
-
7
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
Bird, A. (2002). DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6-21. doi: 10.1101/gad.947102
-
(2002)
Genes Dev
, vol.16
, pp. 6-21
-
-
Bird, A.1
-
8
-
-
84871688621
-
Analysing and interpreting DNA methylation data
-
Bock, C. (2012). Analysing and interpreting DNA methylation data. Nat. Rev. Genet. 13, 705-719. doi: 10.1038/nrg3273
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 705-719
-
-
Bock, C.1
-
9
-
-
84861221693
-
Quantitative sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at single-base resolution
-
Booth, M. J., Branco, M. R., Ficz, G., Oxley, D., Krueger, F., Reik, W., et al. (2012). Quantitative sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at single-base resolution. Science 336, 934-937. doi: 10.1126/science.1220671
-
(2012)
Science
, vol.336
, pp. 934-937
-
-
Booth, M.J.1
Branco, M.R.2
Ficz, G.3
Oxley, D.4
Krueger, F.5
Reik, W.6
-
10
-
-
84869992095
-
Genome-wide DNA Methylation Events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-Dependent mechanism with miR-26a Hypermethylation
-
Borno, S. T., Fischer, A., Kerick, M., Falth, M., Laible, M., Brase, J. C., et al. (2012). Genome-wide DNA Methylation Events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-Dependent mechanism with miR-26a Hypermethylation. Cancer Discov. 2, 1024-1035. doi: 10.1158/2159-8290.CD-12-0041
-
(2012)
Cancer Discov
, vol.2
, pp. 1024-1035
-
-
Borno, S.T.1
Fischer, A.2
Kerick, M.3
Falth, M.4
Laible, M.5
Brase, J.C.6
-
12
-
-
78649291183
-
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
-
Chavez, L., Jozefczuk, J., Grimm, C., Dietrich, J., Timmermann, B., Lehrach, H., et al. (2010). Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res. 20, 1441-1450. doi: 10.1101/gr.110114.110
-
(2010)
Genome Res
, vol.20
, pp. 1441-1450
-
-
Chavez, L.1
Jozefczuk, J.2
Grimm, C.3
Dietrich, J.4
Timmermann, B.5
Lehrach, H.6
-
13
-
-
79952395270
-
Cancer genomics: from discovery science to personalized medicine
-
Chin, L., Andersen, J. N., and Futreal, P. A. (2011). Cancer genomics: from discovery science to personalized medicine. Nat. Med. 17, 297-303. doi: 10.1038/nm.2323
-
(2011)
Nat. Med.
, vol.17
, pp. 297-303
-
-
Chin, L.1
Andersen, J.N.2
Futreal, P.A.3
-
14
-
-
34547528183
-
DNA methylation: bisulphite modification and analysis
-
Clark, S. J., Statham, A., Stirzaker, C., Molloy, P. L., and Frommer, M. (2006). DNA methylation: bisulphite modification and analysis. Nat. Protoc. 1, 2353-2364. doi: 10.1038/nprot.2006.324
-
(2006)
Nat. Protoc.
, vol.1
, pp. 2353-2364
-
-
Clark, S.J.1
Statham, A.2
Stirzaker, C.3
Molloy, P.L.4
Frommer, M.5
-
15
-
-
84904751825
-
Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments
-
Dolzhenko, E., and Smith, A. D. (2014). Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments. BMC Bioinformatics 15:215. doi: 10.1186/1471-2105-15-215
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 215
-
-
Dolzhenko, E.1
Smith, A.D.2
-
16
-
-
46949098742
-
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
-
Down, T. A., Rakyan, V. K., Turner, D. J., Flicek, P., Li, H., Kulesha, E., et al. (2008). A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26, 779-785. doi: 10.1038/nbt1414
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 779-785
-
-
Down, T.A.1
Rakyan, V.K.2
Turner, D.J.3
Flicek, P.4
Li, H.5
Kulesha, E.6
-
17
-
-
78649475003
-
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
-
Du, P., Zhang, X., Huang, C.-C., Jafari, N., Kibbe, W. A., Hou, L., et al. (2010). Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 11:587. doi: 10.1186/1471-2105-11-587
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 587
-
-
Du, P.1
Zhang, X.2
Huang, C.-C.3
Jafari, N.4
Kibbe, W.A.5
Hou, L.6
-
18
-
-
84860808258
-
Genomic landscape of human allele-specific DNA methylation
-
Fang, F., Hodges, E., Molaro, A., Dean, M., Hannon, G. J., and Smith, A. D. (2012). Genomic landscape of human allele-specific DNA methylation. Proc. Natl. Acad. Sci. U.S.A. 109, 7332-7337. doi: 10.1073/pnas.1201310109
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 7332-7337
-
-
Fang, F.1
Hodges, E.2
Molaro, A.3
Dean, M.4
Hannon, G.J.5
Smith, A.D.6
-
19
-
-
84899843749
-
A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data
-
Feng, H., Conneely, K. N., and Wu, H. (2014). A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res. 42, e69. doi: 10.1093/nar/gku154
-
(2014)
Nucleic Acids Res
, vol.42
, pp. e69
-
-
Feng, H.1
Conneely, K.N.2
Wu, H.3
-
20
-
-
77952967431
-
Direct detection of DNA methylation during single-molecule, real-time sequencing
-
Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., et al. (2010). Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7, 461-465. doi: 10.1038/nmeth.1459
-
(2010)
Nat. Methods
, vol.7
, pp. 461-465
-
-
Flusberg, B.A.1
Webster, D.R.2
Lee, J.H.3
Travers, K.J.4
Olivares, E.C.5
Clark, T.A.6
-
21
-
-
84890526238
-
Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing
-
Guo, H., Zhu, P., Wu, X., Li, X., Wen, L., and Tang, F. (2013). Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res. 23, 2126-2135. doi: 10.1101/gr.161679.113
-
(2013)
Genome Res
, vol.23
, pp. 2126-2135
-
-
Guo, H.1
Zhu, P.2
Wu, X.3
Li, X.4
Wen, L.5
Tang, F.6
-
22
-
-
84858068675
-
Removing technical variability in RNA-seq data using conditional quantile normalization
-
Hansen, K. D., Irizarry, R. A., and Wu, Z. (2012a). Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics 13, 204-216. doi: 10.1093/biostatistics/kxr054
-
(2012)
Biostatistics
, vol.13
, pp. 204-216
-
-
Hansen, K.D.1
Irizarry, R.A.2
Wu, Z.3
-
23
-
-
84866853818
-
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
-
Hansen, K. D., Langmead, B., and Irizarry, R. A. (2012b). BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 13:R83. doi: 10.1186/gb-2012-13-10-r83
-
(2012)
Genome Biol
, vol.13
, pp. R83
-
-
Hansen, K.D.1
Langmead, B.2
Irizarry, R.A.3
-
24
-
-
84879895082
-
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data
-
Hebestreit, K., Dugas, M., and Klein, H. U. (2013). Detection of significantly differentially methylated regions in targeted bisulfite sequencing data. Bioinformatics 29, 1647-1653. doi: 10.1093/bioinformatics/btt263
-
(2013)
Bioinformatics
, vol.29
, pp. 1647-1653
-
-
Hebestreit, K.1
Dugas, M.2
Klein, H.U.3
-
25
-
-
84860637797
-
DNA methylation arrays as surrogate measures of cell mixture distribution
-
Houseman, E., Accomando, W., Koestler, D., Christensen, B., Marsit, C., Nelson, H., et al. (2012). DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13:86. doi: 10.1186/1471-2105-13-86
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 86
-
-
Houseman, E.1
Accomando, W.2
Koestler, D.3
Christensen, B.4
Marsit, C.5
Nelson, H.6
-
26
-
-
77749277177
-
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing
-
Huang, Y., Pastor, W. A., Shen, Y., Tahiliani, M., Liu, D. R., and Rao, A. (2010). The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS ONE 5:e8888. doi: 10.1371/journal.pone.0008888
-
(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
-
27
-
-
77951115122
-
International network of cancer genome projects
-
Hudson, T. J., Anderson, W., Artez, A., Barker, A. D., Bell, C., Bernabé, R. R., et al. (2010). International network of cancer genome projects. Nature 464, 993-998. doi: 10.1038/nature08987
-
(2010)
Nature
, vol.464
, pp. 993-998
-
-
Hudson, T.J.1
Anderson, W.2
Artez, A.3
Barker, A.D.4
Bell, C.5
Bernabé, R.R.6
-
28
-
-
84893192328
-
Accounting for cellular heterogeneity is critical in epigenome-wide association studies
-
Jaffe, A. E., and Irizarry, R. A. (2014). Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 15, R31. doi: 10.1186/gb-2014-15-2-r31
-
(2014)
Genome Biol
, vol.15
, pp. R31
-
-
Jaffe, A.E.1
Irizarry, R.A.2
-
29
-
-
84863386102
-
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
-
Jaffe, A. E., Murakami, P., Lee, H., Leek, J. T., Fallin, M. D., Feinberg, A. P., et al. (2012). Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int. J. Epidemiol. 41, 200-209. doi: 10.1093/ije/dyr238
-
(2012)
Int. J. Epidemiol.
, vol.41
, pp. 200-209
-
-
Jaffe, A.E.1
Murakami, P.2
Lee, H.3
Leek, J.T.4
Fallin, M.D.5
Feinberg, A.P.6
-
30
-
-
77956398037
-
Generalizing moving averages for tiling arrays using combined p-value statistics
-
Kechris, K. J., Biehs, B., and Kornberg, T. B. (2010). Generalizing moving averages for tiling arrays using combined p-value statistics. Stat. Appl. Genet. Mol. Biol. 9:29. doi: 10.2202/1544-6115.1434
-
(2010)
Stat. Appl. Genet. Mol. Biol.
, vol.9
, pp. 29
-
-
Kechris, K.J.1
Biehs, B.2
Kornberg, T.B.3
-
31
-
-
84898654757
-
Whole-genome haplotyping using long reads and statistical methods
-
Kuleshov, V., Xie, D., Chen, R., Pushkarev, D., Ma, Z., Blauwkamp, T., et al. (2014). Whole-genome haplotyping using long reads and statistical methods. Nat. Biotechnol. 32, 261-266. doi: 10.1038/nbt.2833
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 261-266
-
-
Kuleshov, V.1
Xie, D.2
Chen, R.3
Pushkarev, D.4
Ma, Z.5
Blauwkamp, T.6
-
32
-
-
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. doi: 10.1038/nrg2732
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 191-203
-
-
Laird, P.W.1
-
34
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
Leek, J. T., and Storey, J. D. (2007). Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3:e161. doi: 10.1371/journal.pgen.0030161
-
(2007)
PLoS Genet
, vol.3
-
-
Leek, J.T.1
Storey, J.D.2
-
35
-
-
84876130617
-
An optimized algorithm for detecting and annotating regional differential methylation
-
Li, S., Garrett-Bakelman, F. E., Akalin, A., Zumbo, P., Levine, R., To, B. L., et al. (2013). An optimized algorithm for detecting and annotating regional differential methylation. BMC Bioinformatics 14(Suppl. 5):S10. doi: 10.1186/1471-2105-14-S5-S10
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S10
-
-
Li, S.1
Garrett-Bakelman, F.E.2
Akalin, A.3
Zumbo, P.4
Levine, R.5
To, B.L.6
-
36
-
-
84892740765
-
MEDIPS: Genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
-
Lienhard, M., Grimm, C., Morkel, M., Herwig, R., and Chavez, L. (2014). MEDIPS: Genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics 30, 284-286. doi: 10.1093/bioinformatics/btt650
-
(2014)
Bioinformatics
, vol.30
, pp. 284-286
-
-
Lienhard, M.1
Grimm, C.2
Morkel, M.3
Herwig, R.4
Chavez, L.5
-
37
-
-
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., et al. (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322. doi: 10.1038/nature08514
-
(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
-
38
-
-
84903210850
-
De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly
-
Lun, A. T., and Smyth, G. K. (2014). De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly. Nucleic Acids Res. 42, e95. doi: 10.1093/nar/gku351
-
(2014)
Nucleic Acids Res
, vol.42
, pp. e95
-
-
Lun, A.T.1
Smyth, G.K.2
-
39
-
-
84862173149
-
SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips
-
Maksimovic, J., Gordon, L., Oshlack, A., and Makismovic, J. (2012). SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol. 13, R44. doi: 10.1186/gb-2012-13-6-r44
-
(2012)
Genome Biol
, vol.13
, pp. R44
-
-
Maksimovic, J.1
Gordon, L.2
Oshlack, A.3
Makismovic, J.4
-
40
-
-
84884950833
-
BLUEPRINT: mapping human blood cell epigenomes
-
Martens, J. H. H., and Stunnenberg, H. G. (2013). BLUEPRINT: mapping human blood cell epigenomes. Haematologica 98, 1487-1489. doi: 10.3324/haematol.2013.094243
-
(2013)
Haematologica
, vol.98
, pp. 1487-1489
-
-
Martens, J.H.H.1
Stunnenberg, H.G.2
-
41
-
-
80052009948
-
Mechanisms for the inheritance of chromatin states
-
Moazed, D. (2011). Mechanisms for the inheritance of chromatin states. Cell 146, 510-518. doi: 10.1016/j.cell.2011.07.013
-
(2011)
Cell
, vol.146
, pp. 510-518
-
-
Moazed, D.1
-
42
-
-
84907033475
-
MethylSig: a whole genome DNA methylation analysis pipeline
-
Park, Y., Figueroa, M. E., Rozek, L. S., and Sartor, M. A. (2014). MethylSig: a whole genome DNA methylation analysis pipeline. Bioinformatics 30, 2414-2422. doi: 10.1093/bioinformatics/btu339
-
(2014)
Bioinformatics
, vol.30
, pp. 2414-2422
-
-
Park, Y.1
Figueroa, M.E.2
Rozek, L.S.3
Sartor, M.A.4
-
43
-
-
84869421697
-
Comb-p: Software for combining, analyzing, grouping and correcting spatially correlated P-values
-
Pedersen, B. S., Schwartz, D. A., Yang, I. V., and Kechris, K. J. (2012). Comb-p: Software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinformatics 28, 2986-2988. doi: 10.1093/bioinformatics/bts545
-
(2012)
Bioinformatics
, vol.28
, pp. 2986-2988
-
-
Pedersen, B.S.1
Schwartz, D.A.2
Yang, I.V.3
Kechris, K.J.4
-
44
-
-
53549104134
-
MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
-
Pelizzola, M., Koga, Y., Urban, A. E., Krauthammer, M., Weissman, S., Halaban, R., et al. (2008). MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res. 18, 1652-1659. doi: 10.1101/gr.080721.108
-
(2008)
Genome Res
, vol.18
, pp. 1652-1659
-
-
Pelizzola, M.1
Koga, Y.2
Urban, A.E.3
Krauthammer, M.4
Weissman, S.5
Halaban, R.6
-
45
-
-
84876806540
-
A data-driven approach to preprocessing Illumina 450K methylation array data
-
Pidsley, R., Y Wong, C. C., Volta, M., Lunnon, K., Mill, J., Schalkwyk, L. C., et al. (2013). A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics 14:293. doi: 10.1186/1471-2164-14-293
-
(2013)
BMC Genomics
, vol.14
, pp. 293
-
-
Pidsley, R.Y.1
Wong, C.C.2
Volta, M.3
Lunnon, K.4
Mill, J.5
Schalkwyk, L.C.6
-
46
-
-
84874396923
-
Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array
-
Price, M. E., Cotton, A. M., Lam, L. L., Farré, P., Emberly, E., Brown, C. J., et al. (2013). Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin 6, 4. doi: 10.1186/1756-8935-6-4
-
(2013)
Epigenetics Chromatin
, vol.6
, pp. 4
-
-
Price, M.E.1
Cotton, A.M.2
Lam, L.L.3
Farré, P.4
Emberly, E.5
Brown, C.J.6
-
47
-
-
84897558199
-
BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach
-
Riebler, A., Menigatti, M., Song, J. Z., Statham, A. L., Stirzaker, C., Mahmud, N., et al. (2014). BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach. Genome Biol. 15, R35. doi: 10.1186/gb-2014-15-2-r35
-
(2014)
Genome Biol
, vol.15
, pp. R35
-
-
Riebler, A.1
Menigatti, M.2
Song, J.Z.3
Statham, A.L.4
Stirzaker, C.5
Mahmud, N.6
-
48
-
-
84909644283
-
Normalization of RNA-seq data using factor analysis of control genes or samples
-
Risso, D., Ngai, J., Speed, T. P., and Sandrine, D. (2014). Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32, 896-902. doi: 10.1038/nbt.2931.
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 896-902
-
-
Risso, D.1
Ngai, J.2
Speed, T.P.3
Sandrine, D.4
-
49
-
-
77955446294
-
Protocol matters: which methylome are you actually studying?
-
Robinson, M. D., Statham, A. L., Speed, T. P., and Clark, S. J. (2010). Protocol matters: which methylome are you actually studying? Epigenomics 2, 587-598. doi: 10.2217/epi.10.36
-
(2010)
Epigenomics
, vol.2
, pp. 587-598
-
-
Robinson, M.D.1
Statham, A.L.2
Speed, T.P.3
Clark, S.J.4
-
50
-
-
84870495795
-
Copy-number-aware differential analysis of quantitative DNA sequencing data
-
Robinson, M. D., Strbenac, D., Stirzaker, C., Statham, A. L., Song, J., Speed, T. P., et al. (2012). Copy-number-aware differential analysis of quantitative DNA sequencing data. Genome Res. 22, 2489-2496. doi: 10.1101/gr.139055.112
-
(2012)
Genome Res
, vol.22
, pp. 2489-2496
-
-
Robinson, M.D.1
Strbenac, D.2
Stirzaker, C.3
Statham, A.L.4
Song, J.5
Speed, T.P.6
-
51
-
-
84856008906
-
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
-
Ross-Innes, C. S., Stark, R., Teschendorff, A. E., Holmes, K. A., Ali, H. R., Dunning, M. J., et al. (2012). Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389-393. doi: 10.1038/nature10730
-
(2012)
Nature
, vol.481
, pp. 389-393
-
-
Ross-Innes, C.S.1
Stark, R.2
Teschendorff, A.E.3
Holmes, K.A.4
Ali, H.R.5
Dunning, M.J.6
-
52
-
-
77957943791
-
Tackling the epigenome: challenges and opportunities for collaboration
-
Satterlee, J. S., Schübeler, D., and Ng, H.-H. (2010). Tackling the epigenome: challenges and opportunities for collaboration. Nat. Biotechnol. 28, 1039-1044. doi: 10.1038/nbt1010-1039
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1039-1044
-
-
Satterlee, J.S.1
Schübeler, D.2
Ng, H.-H.3
-
53
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3:3. doi: 10.2202/1544-6115.1027
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
, pp. 3
-
-
Smyth, G.K.1
-
54
-
-
84890026239
-
A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure
-
Sofer, T., Schifano, E. D., Hoppin, J. A., Hou, L., and Baccarelli, A. A. (2013). A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure. Bioinformatics 29, 2884-2891. doi: 10.1093/bioinformatics/btt498
-
(2013)
Bioinformatics
, vol.29
, pp. 2884-2891
-
-
Sofer, T.1
Schifano, E.D.2
Hoppin, J.A.3
Hou, L.4
Baccarelli, A.A.5
-
55
-
-
84891904054
-
A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics
-
Song, Q., Decato, B., Hong, E. E., Zhou, M., Fang, F., Qu, J., et al. (2013). A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLoS ONE 8:e81148. doi: 10.1371/journal.pone.0081148
-
(2013)
PLoS ONE
, vol.8
-
-
Song, Q.1
Decato, B.2
Hong, E.E.3
Zhou, M.4
Fang, F.5
Qu, J.6
-
56
-
-
84861916932
-
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
-
Statham, A. L., Robinson, M. D., Song, J. Z., Coolen, M. W., Stirzaker, C., and Clark, S. J. (2012). Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res. 22, 1120-1127. doi: 10.1101/gr.132076.111
-
(2012)
Genome Res
, vol.22
, pp. 1120-1127
-
-
Statham, A.L.1
Robinson, M.D.2
Song, J.Z.3
Coolen, M.W.4
Stirzaker, C.5
Clark, S.J.6
-
57
-
-
84903709420
-
DMAP: differential methylation analysis package for RRBS and WGBS data
-
Stockwell, P. A., Chatterjee, A., Rodger, E. J., and Morison, I. M. (2014). DMAP: differential methylation analysis package for RRBS and WGBS data. Bioinformatics 30, 1814-1822. doi: 10.1093/bioinformatics/btu126
-
(2014)
Bioinformatics
, vol.30
, pp. 1814-1822
-
-
Stockwell, P.A.1
Chatterjee, A.2
Rodger, E.J.3
Morison, I.M.4
-
58
-
-
84899049695
-
MOABS: model based analysis of bisulfite sequencing data
-
Sun, D., Xi, Y., Rodriguez, B., Park, H. J., Tong, P., Meong, M., et al. (2014). MOABS: model based analysis of bisulfite sequencing data. Genome Biol. 15, R38. doi: 10.1186/gb-2014-15-2-r38
-
(2014)
Genome Biol
, vol.15
, pp. R38
-
-
Sun, D.1
Xi, Y.2
Rodriguez, B.3
Park, H.J.4
Tong, P.5
Meong, M.6
-
59
-
-
84858983373
-
DNA methylation signatures for breast cancer classification and prognosis
-
Szyf, M. (2012). DNA methylation signatures for breast cancer classification and prognosis. Genome Med. 4:26. doi: 10.1186/gm325
-
(2012)
Genome Med
, vol.4
, pp. 26
-
-
Szyf, M.1
-
60
-
-
84874624739
-
Dynamic DNA methylation across diverse human cell lines and tissues
-
Varley, K. E., Gertz, J., Bowling, K. M., Parker, S. L., Reddy, T. E., Pauli-Behn, F., et al. (2013). Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 23, 555-567. doi: 10.1101/gr.147942.112
-
(2013)
Genome Res
, vol.23
, pp. 555-567
-
-
Varley, K.E.1
Gertz, J.2
Bowling, K.M.3
Parker, S.L.4
Reddy, T.E.5
Pauli-Behn, F.6
-
61
-
-
84863230488
-
IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data
-
Wang, D., Yan, L., Hu, Q., Sucheston, L. E., Higgins, M. J., Ambrosone, C. B., et al. (2012). IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data. Bioinformatics 28, 729-730. doi: 10.1093/bioinformatics/bts013
-
(2012)
Bioinformatics
, vol.28
, pp. 729-730
-
-
Wang, D.1
Yan, L.2
Hu, Q.3
Sucheston, L.E.4
Higgins, M.J.5
Ambrosone, C.B.6
-
62
-
-
84878866495
-
COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis
-
Warden, C. D., Lee, H., Tompkins, J. D., Li, X., Wang, C., Riggs, A. D., et al. (2013). COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res. 41:e117. doi: 10.1093/nar/gkt242
-
(2013)
Nucleic Acids Res
, vol.41
, pp. e117
-
-
Warden, C.D.1
Lee, H.2
Tompkins, J.D.3
Li, X.4
Wang, C.5
Riggs, A.D.6
-
63
-
-
3342989681
-
Epigenetic programming by maternal behavior
-
Weaver, I. C. G., Cervoni, N., Champagne, F. A., D'Alessio, A. C., Sharma, S., Seckl, J. R., et al. (2004). Epigenetic programming by maternal behavior. Nat. Neurosci. 7, 847-854. doi: 10.1038/nn1276
-
(2004)
Nat. Neurosci.
, vol.7
, pp. 847-854
-
-
Weaver, I.C.G.1
Cervoni, N.2
Champagne, F.A.3
D'Alessio, A.C.4
Sharma, S.5
Seckl, J.R.6
-
64
-
-
84883668746
-
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
-
Zhang, B., Zhou, Y., Lin, N., Lowdon, R. F., Hong, C., Nagarajan, R. P., et al. (2013). Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 23, 1522-1540. doi: 10.1101/gr.156539.113
-
(2013)
Genome Res
, vol.23
, pp. 1522-1540
-
-
Zhang, B.1
Zhou, Y.2
Lin, N.3
Lowdon, R.F.4
Hong, C.5
Nagarajan, R.P.6
-
65
-
-
84882884517
-
Charting a dynamic DNA methylation landscape of the human genome
-
Ziller, M. J., Gu, H., Müller, F., Donaghey, J., Tsai, L. T.-Y., Kohlbacher, O., et al. (2013). Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477-481. doi: 10.1038/nature12433
-
(2013)
Nature
, vol.500
, pp. 477-481
-
-
Ziller, M.J.1
Gu, H.2
Müller, F.3
Donaghey, J.4
Tsai, L.-Y.5
Kohlbacher, O.6
-
66
-
-
84895540377
-
Epigenome-wide association studies without the need for cell-type composition
-
Zou, J., Lippert, C., Heckerman, D., Heckerman, M., and Listgarten, J. (2014). Epigenome-wide association studies without the need for cell-type composition. Nat. Methods 11, 309-311. doi: 10.1038/nmeth.2815
-
(2014)
Nat. Methods
, vol.11
, pp. 309-311
-
-
Zou, J.1
Lippert, C.2
Heckerman, D.3
Heckerman, M.4
Listgarten, J.5
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