-
1
-
-
79956330964
-
CpG islands and the regulation of transcription
-
Deaton, A. M. & Bird, A. CpG islands and the regulation of transcription. Genes Dev. 25, 1010-1022 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 1010-1022
-
-
Deaton, A.M.1
Bird, A.2
-
2
-
-
0032401808
-
Aging and DNA methylation in colorectal mucosa and cancer
-
Ahuja, N., Li, Q., Mohan, A. L., Baylin, S. B. & Issa, J. P. Aging and DNA methylation in colorectal mucosa and cancer. Cancer Res. 58, 5489-5494 (1998).
-
(1998)
Cancer Res.
, vol.58
, pp. 5489-5494
-
-
Ahuja, N.1
Li, Q.2
Mohan, A.L.3
Baylin, S.B.4
Issa, J.P.5
-
3
-
-
23044514669
-
Epigenetic differences arise during the lifetime of monozygotic twins
-
Fraga, M. F. et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl Acad. Sci. USA 102, 10604-10609 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 10604-10609
-
-
Fraga, M.F.1
-
4
-
-
77950650405
-
Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer
-
Teschendorff, A. E. et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res. 20, 440-446 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 440-446
-
-
Teschendorff, A.E.1
-
5
-
-
77950657253
-
Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains
-
Rakyan, V. K. et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 20, 434-439 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 434-439
-
-
Rakyan, V.K.1
-
6
-
-
77649240380
-
Widespread and tissue specific age-related DNA methylation changes in mice
-
Maegawa, S. et al. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 20, 332-340 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 332-340
-
-
Maegawa, S.1
-
7
-
-
0033913645
-
Aging, methylation and cancer
-
Ahuja, N. & Issa, J. P. Aging, methylation and cancer. Histol. Histopathol. 15, 835-842 (2000).
-
(2000)
Histol. Histopathol.
, vol.15
, pp. 835-842
-
-
Ahuja, N.1
Issa, J.P.2
-
8
-
-
84886111619
-
DNA methylation age of human tissues and cell types
-
Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, R115 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R115
-
-
Horvath, S.1
-
9
-
-
77953469917
-
Epigenetics as a unifying principle in the aetiology of complex traits and diseases
-
Petronis, A. Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 465, 721-727 (2010).
-
(2010)
Nature
, vol.465
, pp. 721-727
-
-
Petronis, A.1
-
10
-
-
29244469466
-
The epigenetic progenitor origin of human cancer
-
Feinberg, A. P., Ohlsson, R. & Henikoff, S. The epigenetic progenitor origin of human cancer. Nat. Rev. Genet. 7, 21-33 (2006).
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 21-33
-
-
Feinberg, A.P.1
Ohlsson, R.2
Henikoff, S.3
-
11
-
-
77957948773
-
Taking the measure of the methylome
-
Beck, S. Taking the measure of the methylome. Nat. Biotechnol. 28, 1026-1028 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1026-1028
-
-
Beck, S.1
-
12
-
-
79958754527
-
Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome
-
Sandoval, J. et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6, 692-702 (2011).
-
(2011)
Epigenetics
, vol.6
, pp. 692-702
-
-
Sandoval, J.1
-
13
-
-
84962545867
-
Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences
-
Moran, S., Arribas, C. & Esteller, M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics 8, 389-399 (2016).
-
(2016)
Epigenomics
, vol.8
, pp. 389-399
-
-
Moran, S.1
Arribas, C.2
Esteller, M.3
-
14
-
-
84995912090
-
The International Human Epigenome Consortium: A blueprint for scientific collaboration and discovery
-
The International Human Epigenome Consortium & Hirst, M
-
Stunnenberg, H. G., The International Human Epigenome Consortium & Hirst, M. The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery. Cell 167, 1145-1149 (2016).
-
(2016)
Cell
, vol.167
, pp. 1145-1149
-
-
Stunnenberg, H.G.1
-
15
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics Consortium et al
-
Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015).
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
-
16
-
-
85014528183
-
Identification of methylation haplotype blocks AIDS in deconvolution of heterogeneous tissue samples and tumor tissue-of?Origin mapping from plasma DNA
-
Guo, S. et al. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of?origin mapping from plasma DNA. Nat. Genet. 49, 635-642 (2017).
-
(2017)
Nat. Genet.
, vol.49
, pp. 635-642
-
-
Guo, S.1
-
17
-
-
84944259040
-
DNA methylation changes of whole blood cells in response to active smoking exposure in adults: A systematic review of DNA methylation studies
-
Gao, X., Jia, M., Zhang, Y., Breitling, L. P. & Brenner, H. DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies. Clin. Epigenet. 7, 113 (2015).
-
(2015)
Clin. Epigenet.
, vol.7
, pp. 113
-
-
Gao, X.1
Jia, M.2
Zhang, Y.3
Breitling, L.P.4
Brenner, H.5
-
18
-
-
85010888461
-
Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity
-
Wahl, S. et al. Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity. Nature 541, 81-86 (2017).
-
(2017)
Nature
, vol.541
, pp. 81-86
-
-
Wahl, S.1
-
19
-
-
84992392020
-
Epigenetic signatures of cigarette smoking
-
Joehanes, R. et al. Epigenetic signatures of cigarette smoking. Circ. Cardiovasc. Genet. 9, 436-447 (2016).
-
(2016)
Circ. Cardiovasc. Genet.
, vol.9
, pp. 436-447
-
-
Joehanes, R.1
-
20
-
-
85014611626
-
Prolonged high-fat diet induces gradual and fat depot-specific DNA methylation changes in adult mice
-
Zwamborn, R. A. et al. Prolonged high-fat diet induces gradual and fat depot-specific DNA methylation changes in adult mice. Sci. Rep. 7, 43261 (2017).
-
(2017)
Sci. Rep.
, vol.7
, pp. 43261
-
-
Zwamborn, R.A.1
-
21
-
-
84871688621
-
Analysing and interpreting DNA methylation data
-
Bock, C. Analysing and interpreting DNA methylation data. Nat. Genet. 13, 705-719 (2012).
-
(2012)
Nat. Genet.
, vol.13
, pp. 705-719
-
-
Bock, C.1
-
22
-
-
84927752388
-
Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data
-
Morris, T. J. & Beck, S. Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data. Methods 72, 3-8 (2015).
-
(2015)
Methods
, vol.72
, pp. 3-8
-
-
Morris, T.J.1
Beck, S.2
-
23
-
-
84908566266
-
Comprehensive analysis of DNA methylation data with RnBeads
-
Assenov, Y. et al. Comprehensive analysis of DNA methylation data with RnBeads. Nat. Methods 11, 1138-1140 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 1138-1140
-
-
Assenov, Y.1
-
24
-
-
85021798825
-
DeepBlueR: Large-scale epigenomic analysis in R
-
Albrecht, F., List, M., Bock, C. & Lengauer, T. DeepBlueR: large-scale epigenomic analysis in R. Bioinformatics 33, 2063-2064 (2017).
-
(2017)
Bioinformatics
, vol.33
, pp. 2063-2064
-
-
Albrecht, F.1
List, M.2
Bock, C.3
Lengauer, T.4
-
25
-
-
84928819497
-
An epigenome-wide association study of total serum immunoglobulin e concentration
-
Liang, L. et al. An epigenome-wide association study of total serum immunoglobulin E concentration. Nature 520, 670-674 (2015).
-
(2015)
Nature
, vol.520
, pp. 670-674
-
-
Liang, L.1
-
26
-
-
84938984463
-
The prognostic landscape of genes and infiltrating immune cells across human cancers
-
Gentles, A. J. et al. The prognostic landscape of genes and infiltrating immune cells across human cancers. Nat. Med. 21, 938-945 (2015).
-
(2015)
Nat. Med.
, vol.21
, pp. 938-945
-
-
Gentles, A.J.1
-
27
-
-
77949533111
-
An epigenetic signature in peripheral blood predicts active ovarian cancer
-
Teschendorff, A. E. et al. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS ONE 4, e8274 (2009).
-
(2009)
PLoS ONE
, vol.4
, pp. e8274
-
-
Teschendorff, A.E.1
-
28
-
-
84901760091
-
Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients
-
Langevin, S. M. et al. Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients. Epigenetics 9, 884-895 (2014).
-
(2014)
Epigenetics
, vol.9
, pp. 884-895
-
-
Langevin, S.M.1
-
29
-
-
84864822325
-
Peripheral blood immune cell methylation profiles are associated with nonhematopoietic cancers
-
Koestler, D. C. et al. Peripheral blood immune cell methylation profiles are associated with nonhematopoietic cancers. Cancer Epidemiol. Biomarkers Prev. 21, 1293-1302 (2012).
-
(2012)
Cancer Epidemiol. Biomarkers Prev.
, vol.21
, pp. 1293-1302
-
-
Koestler, D.C.1
-
30
-
-
84873576566
-
Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis
-
Liu, Y. et al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat. Biotechnol. 31, 142-147 (2013).
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 142-147
-
-
Liu, Y.1
-
31
-
-
84860637797
-
DNA methylation arrays as surrogate measures of cell mixture distribution
-
Houseman, E. A. et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformat. 13, 86 (2012).
-
(2012)
BMC Bioinformat.
, vol.13
, pp. 86
-
-
Houseman, E.A.1
-
32
-
-
84900824657
-
Reference-free cell mixture adjustments in analysis of DNA methylation data
-
Houseman, E. A., Molitor, J. & Marsit, C. J. Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics 30, 1431-1439 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1431-1439
-
-
Houseman, E.A.1
Molitor, J.2
Marsit, C.J.3
-
33
-
-
84976503563
-
Reference-free deconvolution of DNA methylation data and mediation by cell composition effects
-
Houseman, E. A. et al. Reference-free deconvolution of DNA methylation data and mediation by cell composition effects. BMC Bioinformat. 17, 259 (2016).
-
(2016)
BMC Bioinformat.
, vol.17
, pp. 259
-
-
Houseman, E.A.1
-
34
-
-
85003794522
-
Epigenomic deconvolution of breast tumors reveals metabolic coupling between constituent cell types
-
Onuchic, V. et al. Epigenomic deconvolution of breast tumors reveals metabolic coupling between constituent cell types. Cell Rep. 17, 2075-2086 (2016).
-
(2016)
Cell Rep.
, vol.17
, pp. 2075-2086
-
-
Onuchic, V.1
-
35
-
-
84960082583
-
Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL)
-
Koestler, D. C. et al. Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). BMC Bioinformat. 17, 120 (2016).
-
(2016)
BMC Bioinformat.
, vol.17
, pp. 120
-
-
Koestler, D.C.1
-
36
-
-
1942422934
-
Model uncertainty, data mining and statistical inference
-
Chatfield, C. Model uncertainty, data mining and statistical inference. J. R. Statist. Soc. A 158, 419-466 (1995).
-
(1995)
J. R. Statist. Soc. A
, vol.158
, pp. 419-466
-
-
Chatfield, C.1
-
37
-
-
84928927858
-
Robust enumeration of cell subsets from tissue expression profiles
-
Newman, A. M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12, 453-457 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 453-457
-
-
Newman, A.M.1
-
38
-
-
84899115256
-
Quantitative reconstruction of leukocyte subsets using DNA methylation
-
Accomando, W. P., Wiencke, J. K., Houseman, E. A., Nelson, H. H. & Kelsey, K. T. Quantitative reconstruction of leukocyte subsets using DNA methylation. Genome Biol. 15, R50 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. R50
-
-
Accomando, W.P.1
Wiencke, J.K.2
Houseman, E.A.3
Nelson, H.H.4
Kelsey, K.T.5
-
39
-
-
85012965214
-
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies
-
Teschendorff, A. E., Breeze, C. E., Zheng, S. C. & Beck, S. A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. BMC Bioinformat. 18, 105 (2017).
-
(2017)
BMC Bioinformat.
, vol.18
, pp. 105
-
-
Teschendorff, A.E.1
Breeze, C.E.2
Zheng, S.C.3
Beck, S.4
-
40
-
-
85016166382
-
CancerLocator: Non-invasive cancer diagnosis and tissue-of?Origin prediction using methylation profiles of cell-free DNA
-
Kang, S. et al. CancerLocator: non-invasive cancer diagnosis and tissue-of?origin prediction using methylation profiles of cell-free DNA. Genome Biol. 18, 53 (2017).
-
(2017)
Genome Biol.
, vol.18
, pp. 53
-
-
Kang, S.1
-
41
-
-
84924551236
-
MethylPurify: Tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes
-
Zheng, X. et al. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol. 15, 419 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 419
-
-
Zheng, X.1
-
42
-
-
84947546879
-
Predicting tumor purity from methylation microarray data
-
Zhang, N. et al. Predicting tumor purity from methylation microarray data. Bioinformatics 31, 3401-3405 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 3401-3405
-
-
Zhang, N.1
-
43
-
-
85010962092
-
Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies
-
Zheng, X., Zhang, N., Wu, H. J. & Wu, H. Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. Genome Biol. 18, 17 (2017).
-
(2017)
Genome Biol.
, vol.18
, pp. 17
-
-
Zheng, X.1
Zhang, N.2
Wu, H.J.3
Wu, H.4
-
44
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
Leek, J. T. & Storey, J. D. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3, 1724-1735 (2007).
-
(2007)
PLoS Genet.
, vol.3
, pp. 1724-1735
-
-
Leek, J.T.1
Storey, J.D.2
-
45
-
-
57749084635
-
A general framework for multiple testing dependence
-
Leek, J. T. & Storey, J. D. A general framework for multiple testing dependence. Proc. Natl Acad. Sci. USA 105, 18718-18723 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 18718-18723
-
-
Leek, J.T.1
Storey, J.D.2
-
46
-
-
84859098571
-
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
-
Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E. & Storey, J. D. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28, 882-883 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 882-883
-
-
Leek, J.T.1
Johnson, W.E.2
Parker, H.S.3
Jaffe, A.E.4
Storey, J.D.5
-
47
-
-
84964747508
-
An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies
-
McGregor, K. et al. An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies. Genome Biol. 17, 84 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 84
-
-
McGregor, K.1
-
48
-
-
85014341578
-
Correcting for cell-type heterogeneity in epigenome-wide association studies: Revisiting previous analyses
-
Zheng, S. C. et al. Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses. Nat. Methods 14, 216-217 (2017).
-
(2017)
Nat. Methods
, vol.14
, pp. 216-217
-
-
Zheng, S.C.1
-
49
-
-
85018522240
-
Comparison of different cell type correction methods for genome-scale epigenetics studies
-
Kaushal, A. et al. Comparison of different cell type correction methods for genome-scale epigenetics studies. BMC Bioinformat. 18, 216 (2017).
-
(2017)
BMC Bioinformat.
, vol.18
, pp. 216
-
-
Kaushal, A.1
-
50
-
-
79957851822
-
Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies
-
Teschendorff, A. E., Zhuang, J. & Widschwendter, M. Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. Bioinformatics 27, 1496-1505 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 1496-1505
-
-
Teschendorff, A.E.1
Zhuang, J.2
Widschwendter, M.3
-
51
-
-
84994715829
-
Correlation of smoking-associated DNA methylation changes in buccal cells with DNA methylation changes in epithelial cancer
-
Teschendorff, A. E. et al. Correlation of smoking-associated DNA methylation changes in buccal cells with DNA methylation changes in epithelial cancer. JAMA Oncol. 1, 476-485 (2015).
-
(2015)
JAMA Oncol.
, vol.1
, pp. 476-485
-
-
Teschendorff, A.E.1
-
52
-
-
0042826822
-
Independent component analysis: Algorithms and applications
-
Hyvärinen, A. & Oja, E. Independent component analysis: algorithms and applications. Neural Netw. 13, 411-430 (2000).
-
(2000)
Neural Netw.
, vol.13
, pp. 411-430
-
-
Hyvärinen, A.1
Oja, E.2
-
53
-
-
84895540377
-
Epigenome-wide association studies without the need for cell-type composition
-
Zou, J., Lippert, C., Heckerman, D., Aryee, M. & Listgarten, J. Epigenome-wide association studies without the need for cell-type composition. Nat. Methods 11, 309-311 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 309-311
-
-
Zou, J.1
Lippert, C.2
Heckerman, D.3
Aryee, M.4
Listgarten, J.5
-
54
-
-
84961720054
-
Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies
-
Rahmani, E. et al. Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies. Nat. Methods 13, 443-445 (2016).
-
(2016)
Nat. Methods
, vol.13
, pp. 443-445
-
-
Rahmani, E.1
-
55
-
-
84961357451
-
DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer
-
Teschendorff, A. E. et al. DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer. Nat. Commun. 7, 10478 (2016).
-
(2016)
Nat. Commun.
, vol.7
, pp. 10478
-
-
Teschendorff, A.E.1
-
56
-
-
84862250978
-
Using control genes to correct for unwanted variation in microarray data
-
Gagnon-Bartsch, J. A. & Speed, T. P. Using control genes to correct for unwanted variation in microarray data. Biostatistics 13, 539-552 (2012).
-
(2012)
Biostatistics
, vol.13
, pp. 539-552
-
-
Gagnon-Bartsch, J.A.1
Speed, T.P.2
-
57
-
-
84893192328
-
Accounting for cellular heterogeneity is critical in epigenome-wide association studies
-
Jaffe, A. E. & Irizarry, R. A. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 15, R31 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. R31
-
-
Jaffe, A.E.1
Irizarry, R.A.2
-
58
-
-
85016146302
-
MeDeCom: Discovery and quantification of latent components of heterogeneous methylomes
-
Lutsik, P. et al. MeDeCom: discovery and quantification of latent components of heterogeneous methylomes. Genome Biol. 18, 55 (2017).
-
(2017)
Genome Biol.
, vol.18
, pp. 55
-
-
Lutsik, P.1
-
59
-
-
84965014445
-
DNA methylation of cord blood cell types: Applications for mixed cell birth studies
-
Bakulski, K. M. et al. DNA methylation of cord blood cell types: Applications for mixed cell birth studies. Epigenetics 11, 354-362 (2016).
-
(2016)
Epigenetics
, vol.11
, pp. 354-362
-
-
Bakulski, K.M.1
-
60
-
-
84963614956
-
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
-
Tirosh, I. et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352, 189-196 (2016).
-
(2016)
Science
, vol.352
, pp. 189-196
-
-
Tirosh, I.1
-
61
-
-
85011097316
-
Correcting for cell-type effects in DNA methylation studies: Reference-based method outperforms latent variable approaches in empirical studies
-
Hattab, M. W. et al. Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies. Genome Biol. 18, 24 (2017).
-
(2017)
Genome Biol.
, vol.18
, pp. 24
-
-
Hattab, M.W.1
-
62
-
-
33845432928
-
Adjusting batch effects in microarray expression data using empirical Bayes methods
-
Johnson, W. E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118-127 (2007).
-
(2007)
Biostatistics
, vol.8
, pp. 118-127
-
-
Johnson, W.E.1
Li, C.2
Rabinovic, A.3
-
63
-
-
84868206265
-
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues
-
Landan, G. et al. Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat. Genet. 44, 1207-1214 (2012).
-
(2012)
Nat. Genet.
, vol.44
, pp. 1207-1214
-
-
Landan, G.1
-
64
-
-
84904460344
-
Dynamic heterogeneity and DNA methylation in embryonic stem cells
-
Singer, Z. S. et al. Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol. Cell 55, 319-331 (2014).
-
(2014)
Mol. Cell
, vol.55
, pp. 319-331
-
-
Singer, Z.S.1
-
66
-
-
84919469035
-
Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia
-
Landau, D. A. et al. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell 26, 813-825 (2014).
-
(2014)
Cancer Cell
, vol.26
, pp. 813-825
-
-
Landau, D.A.1
-
67
-
-
84975321367
-
Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia
-
Li, S. et al. Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. Nat. Med. 22, 792-799 (2016).
-
(2016)
Nat. Med.
, vol.22
, pp. 792-799
-
-
Li, S.1
-
68
-
-
84858828509
-
Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation
-
Teschendorff, A. E. et al. Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation. Genome Med. 4, 24 (2012).
-
(2012)
Genome Med.
, vol.4
, pp. 24
-
-
Teschendorff, A.E.1
-
69
-
-
84929173375
-
Dynamic evolution of clonal epialleles revealed by methclone
-
Li, S. et al. Dynamic evolution of clonal epialleles revealed by methclone. Genome Biol. 15, 472 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 472
-
-
Li, S.1
-
70
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
van 't Veer, L. J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002).
-
(2002)
Nature
, vol.415
, pp. 530-536
-
-
Van't Veer, L.J.1
-
71
-
-
78649475003
-
Comparison of Beta-value and M?Value methods for quantifying methylation levels by microarray analysis
-
Du, P. et al. Comparison of Beta-value and M?value methods for quantifying methylation levels by microarray analysis. BMC Bioinformat. 11, 587 (2010).
-
(2010)
BMC Bioinformat.
, vol.11
, pp. 587
-
-
Du, P.1
-
72
-
-
84928376648
-
Non-specific filtering of beta-distributed data
-
Wang, X., Laird, P. W., Hinoue, T., Groshen, S. & Siegmund, K. D. Non-specific filtering of beta-distributed data. BMC Bioinformat. 15, 199 (2014).
-
(2014)
BMC Bioinformat.
, vol.15
, pp. 199
-
-
Wang, X.1
Laird, P.W.2
Hinoue, T.3
Groshen, S.4
Siegmund, K.D.5
-
73
-
-
84859931424
-
A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform
-
Zhuang, J., Widschwendter, M. & Teschendorff, A. E. A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform. BMC Bioinformat. 13, 59 (2012).
-
(2012)
BMC Bioinformat.
, vol.13
, pp. 59
-
-
Zhuang, J.1
Widschwendter, M.2
Teschendorff, A.E.3
-
74
-
-
84893852621
-
A comprehensive overview of Infinium HumanMethylation450 data processing
-
Dedeurwaerder, S. et al. A comprehensive overview of Infinium HumanMethylation450 data processing. Briefings Bioinformat. 15, 929-941 (2014).
-
(2014)
Briefings Bioinformat.
, vol.15
, pp. 929-941
-
-
Dedeurwaerder, S.1
-
75
-
-
85020640961
-
Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes
-
Zhou, W., Laird, P. W. & Shen, H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res. 45, e22 (2017).
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. e22
-
-
Zhou, W.1
Laird, P.W.2
Shen, H.3
-
76
-
-
84963641653
-
Genetic and environmental influences interact with age and sex in shaping the human methylome
-
van Dongen, J. et al. Genetic and environmental influences interact with age and sex in shaping the human methylome. Nat. Commun. 7, 11115 (2016).
-
(2016)
Nat. Commun.
, vol.7
, pp. 11115
-
-
Van Dongen, J.1
-
77
-
-
84988511927
-
Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms
-
Slieker, R. C. et al. Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms. Genome Biol. 17, 191 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 191
-
-
Slieker, R.C.1
-
78
-
-
12344330424
-
LimmaGUI: A graphical user interface for linear modeling of microarray data
-
Wettenhall, J. M. & Smyth, G. K. limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20, 3705-3706 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 3705-3706
-
-
Wettenhall, J.M.1
Smyth, G.K.2
-
79
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth, G. K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article3 (2004).
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
, pp. Article3
-
-
Smyth, G.K.1
-
80
-
-
84926507971
-
Limma powers differential expression analyses for RNA-sequencing and microarray studies
-
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e47
-
-
Ritchie, M.E.1
-
81
-
-
33751505540
-
DNA methylation profiling of human chromosomes 6, 20 and 22
-
Eckhardt, F. et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378-1385 (2006).
-
(2006)
Nat. Genet.
, vol.38
, pp. 1378-1385
-
-
Eckhardt, F.1
-
82
-
-
84978285850
-
Saturation analysis for whole-genome bisulfite sequencing data
-
Libertini, E. et al. Saturation analysis for whole-genome bisulfite sequencing data. Nat. Biotechnol. 34, 691-693 (2016).
-
(2016)
Nat. Biotechnol.
, vol.34
, pp. 691-693
-
-
Libertini, E.1
-
83
-
-
84976571454
-
Information recovery from low coverage whole-genome bisulfite sequencing
-
Libertini, E. et al. Information recovery from low coverage whole-genome bisulfite sequencing. Nat. Commun. 7, 11306 (2016).
-
(2016)
Nat. Commun.
, vol.7
, pp. 11306
-
-
Libertini, E.1
-
84
-
-
84881499370
-
Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes
-
VanderKraats, N. D., Hiken, J. F., Decker, K. F. & Edwards, J. R. Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes. Nucleic Acids Res. 41, 6816-6827 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 6816-6827
-
-
VanderKraats, N.D.1
Hiken, J.F.2
Decker, K.F.3
Edwards, J.R.4
-
85
-
-
85027177188
-
Modeling complex patterns of differential DNA methylation that associate with gene expression changes
-
Schlosberg, C. E., VanderKraats, N. D. & Edwards, J. R. Modeling complex patterns of differential DNA methylation that associate with gene expression changes. Nucleic Acids Res. 45, 5100-5111 (2017).
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. 5100-5111
-
-
Schlosberg, C.E.1
VanderKraats, N.D.2
Edwards, J.R.3
-
86
-
-
84863386102
-
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
-
Jaffe, A. E. et al. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int. J. Epidemiol. 41, 200-209 (2012).
-
(2012)
Int. J. Epidemiol.
, vol.41
, pp. 200-209
-
-
Jaffe, A.E.1
-
87
-
-
84897548625
-
Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
-
Aryee, M. J. et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 30, 1363-1369 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1363-1369
-
-
Aryee, M.J.1
-
88
-
-
43149098062
-
Comprehensive high-throughput arrays for relative methylation (CHARM)
-
Irizarry, R. A. et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18, 780-790 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 780-790
-
-
Irizarry, R.A.1
-
89
-
-
84655162785
-
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains
-
Berman, B. P. et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat. Genet. 44, 40-46 (2012).
-
(2012)
Nat. Genet.
, vol.44
, pp. 40-46
-
-
Berman, B.P.1
-
90
-
-
84906837231
-
Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors
-
Timp, W. et al. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Med. 6, 61 (2014).
-
(2014)
Genome Med.
, vol.6
, pp. 61
-
-
Timp, W.1
-
91
-
-
84924407381
-
An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging
-
Yuan, T. et al. An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet. 11, e1004996 (2015).
-
(2015)
PLoS Genet.
, vol.11
, pp. e1004996
-
-
Yuan, T.1
-
92
-
-
84939211019
-
Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin
-
Vandiver, A. R. et al. Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol. 16, 80 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 80
-
-
Vandiver, A.R.1
-
93
-
-
79960927422
-
Increased methylation variation in epigenetic domains across cancer types
-
Hansen, K. D. et al. Increased methylation variation in epigenetic domains across cancer types. Nature Genet. 43, 768-777 (2011).
-
(2011)
Nature Genet.
, vol.43
, pp. 768-777
-
-
Hansen, K.D.1
-
94
-
-
84893711405
-
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B?Cell immortalization
-
Hansen, K. D. et al. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B?cell immortalization. Genome Res. 24, 177-184 (2014).
-
(2014)
Genome Res.
, vol.24
, pp. 177-184
-
-
Hansen, K.D.1
-
95
-
-
84929147900
-
De novo identification of differentially methylated regions in the human genome
-
Peters, T. J. et al. De novo identification of differentially methylated regions in the human genome. Epigenetics Chromatin 8, 6 (2015).
-
(2015)
Epigenetics Chromatin
, vol.8
, pp. 6
-
-
Peters, T.J.1
-
96
-
-
84869421697
-
Comb?P: Software for combining, analyzing, grouping and correcting spatially correlated P?Values
-
Pedersen, B. S., Schwartz, D. A., Yang, I. V. & Kechris, K. J. Comb?p: software for combining, analyzing, grouping and correcting spatially correlated P?values. Bioinformatics 28, 2986-2988 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 2986-2988
-
-
Pedersen, B.S.1
Schwartz, D.A.2
Yang, I.V.3
Kechris, K.J.4
-
98
-
-
84861752999
-
Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions
-
Teschendorff, A. E. & Widschwendter, M. Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions. Bioinformatics 28, 1487-1494 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1487-1494
-
-
Teschendorff, A.E.1
Widschwendter, M.2
-
99
-
-
78650650451
-
Adaptive index models for marker-based risk stratification
-
Tian, L. & Tibshirani, R. Adaptive index models for marker-based risk stratification. Biostatistics 12, 68-86 (2011).
-
(2011)
Biostatistics
, vol.12
, pp. 68-86
-
-
Tian, L.1
Tibshirani, R.2
-
100
-
-
84964316090
-
DiffVar: A new method for detecting differential variability with application to methylation in cancer and aging
-
Phipson, B. & Oshlack, A. DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging. Genome Biol. 15, 465 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 465
-
-
Phipson, B.1
Oshlack, A.2
-
101
-
-
84907714293
-
On the potential of models for location and scale for genome-wide DNA methylation data
-
Wahl, S. et al. On the potential of models for location and scale for genome-wide DNA methylation data. BMC Bioinformat. 15, 232 (2014).
-
(2014)
BMC Bioinformat.
, vol.15
, pp. 232
-
-
Wahl, S.1
-
102
-
-
84891422343
-
A powerful statistical method for identifying differentially methylated markers in complex diseases
-
Ahn, S. & Wang, T. A powerful statistical method for identifying differentially methylated markers in complex diseases. Pac. Symp. Biocomput. 2013, 69-79 (2012).
-
(2012)
Pac. Symp. Biocomput.
, vol.2013
, pp. 69-79
-
-
Ahn, S.1
Wang, T.2
-
103
-
-
84963946861
-
Stochastic epigenetic outliers can define field defects in cancer
-
Teschendorff, A. E., Jones, A. & Widschwendter, M. Stochastic epigenetic outliers can define field defects in cancer. BMC Bioinformat. 17, 178 (2016).
-
(2016)
BMC Bioinformat.
, vol.17
, pp. 178
-
-
Teschendorff, A.E.1
Jones, A.2
Widschwendter, M.3
-
104
-
-
84872806231
-
Genome-wide methylation profiles reveal quantitative views of human aging rates
-
Hannum, G. et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol. Cell 49, 359-367 (2013).
-
(2013)
Mol. Cell
, vol.49
, pp. 359-367
-
-
Hannum, G.1
-
105
-
-
83755224300
-
Significance analysis and statistical dissection of variably methylated regions
-
Jaffe, A. E., Feinberg, A. P., Irizarry, R. A. & Leek, J. T. Significance analysis and statistical dissection of variably methylated regions. Biostatistics 13, 166-178 (2012).
-
(2012)
Biostatistics
, vol.13
, pp. 166-178
-
-
Jaffe, A.E.1
Feinberg, A.P.2
Irizarry, R.A.3
Leek, J.T.4
-
106
-
-
85016117149
-
Potential energy landscapes identify the information-theoretic nature of the epigenome
-
Jenkinson, G., Pujadas, E., Goutsias, J. & Feinberg, A. P. Potential energy landscapes identify the information-theoretic nature of the epigenome. Nat. Genet. 49, 719-729 (2017).
-
(2017)
Nat. Genet.
, vol.49
, pp. 719-729
-
-
Jenkinson, G.1
Pujadas, E.2
Goutsias, J.3
Feinberg, A.P.4
-
107
-
-
85003856277
-
EFORGE: A tool for identifying cell type-specific signal in epigenomic data
-
Breeze, C. E. et al. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Rep. 17, 2137-2150 (2016).
-
(2016)
Cell Rep.
, vol.17
, pp. 2137-2150
-
-
Breeze, C.E.1
-
108
-
-
84882884517
-
Charting a dynamic DNA methylation landscape of the human genome
-
Ziller, M. J. et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477-481 (2013).
-
(2013)
Nature
, vol.500
, pp. 477-481
-
-
Ziller, M.J.1
-
109
-
-
84880544162
-
Gene-set analysis is severely biased when applied to genome-wide methylation data
-
Geeleher, P. et al. Gene-set analysis is severely biased when applied to genome-wide methylation data. Bioinformatics 29, 1851-1857 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 1851-1857
-
-
Geeleher, P.1
-
110
-
-
84959862869
-
MissMethyl: An R package for analyzing data from Illumina's HumanMethylation450 platform
-
Phipson, B., Maksimovic, J. & Oshlack, A. missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform. Bioinformatics 32, 286-288 (2016).
-
(2016)
Bioinformatics
, vol.32
, pp. 286-288
-
-
Phipson, B.1
Maksimovic, J.2
Oshlack, A.3
-
111
-
-
84882454737
-
An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways
-
West, J., Beck, S., Wang, X. & Teschendorff, A. E. An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways. Sci. Rep. 3, 1630 (2013).
-
(2013)
Sci. Rep.
, vol.3
, pp. 1630
-
-
West, J.1
Beck, S.2
Wang, X.3
Teschendorff, A.E.4
-
112
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
113
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
114
-
-
84977481546
-
Epigenome-wide association studies and the interpretation of disease-omics
-
Birney, E., Smith, G. D. & Greally, J. M. Epigenome-wide association studies and the interpretation of disease-omics. PLoS Genet. 12, e1006105 (2016).
-
(2016)
PLoS Genet.
, vol.12
, pp. e1006105
-
-
Birney, E.1
Smith, G.D.2
Greally, J.M.3
-
115
-
-
85020763883
-
Associating cellular epigenetic models with human phenotypes
-
Lappalainen, T. & Greally, J. M. Associating cellular epigenetic models with human phenotypes. Nat. Rev. Genet. 18, 441-451 (2017).
-
(2017)
Nat. Rev. Genet.
, vol.18
, pp. 441-451
-
-
Lappalainen, T.1
Greally, J.M.2
-
116
-
-
84976327016
-
Blood lipids influence DNA methylation in circulating cells
-
Dekkers, K. F. et al. Blood lipids influence DNA methylation in circulating cells. Genome Biol. 17, 138 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 138
-
-
Dekkers, K.F.1
-
117
-
-
77649246145
-
Histone modification levels are predictive for gene expression
-
Karlic, R., Chung, H. R., Lasserre, J., Vlahovicek, K. & Vingron, M. Histone modification levels are predictive for gene expression. Proc. Natl Acad. Sci. USA 107, 2926-2931 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 2926-2931
-
-
Karlic, R.1
Chung, H.R.2
Lasserre, J.3
Vlahovicek, K.4
Vingron, M.5
-
118
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
-
119
-
-
85015350236
-
Systematic identification of genetic influences on methylation across the human life course
-
Gaunt, T. R. et al. Systematic identification of genetic influences on methylation across the human life course. Genome Biol. 17, 61 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 61
-
-
Gaunt, T.R.1
-
120
-
-
84907584646
-
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels
-
Banovich, N. E. et al. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet. 10, e1004663 (2014).
-
(2014)
PLoS Genet.
, vol.10
, pp. e1004663
-
-
Banovich, N.E.1
-
121
-
-
78651552406
-
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
-
Bell, J. T. et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 12, R10 (2011).
-
(2011)
Genome Biol.
, vol.12
, pp. R10
-
-
Bell, J.T.1
-
122
-
-
85002263457
-
Disease variants alter transcription factor levels and methylation of their binding sites
-
Bonder, M. J. et al. Disease variants alter transcription factor levels and methylation of their binding sites. Nat. Genet. 49, 131-138 (2017).
-
(2017)
Nat. Genet.
, vol.49
, pp. 131-138
-
-
Bonder, M.J.1
-
123
-
-
85010825671
-
Genome-wide methylation data mirror ancestry information
-
Rahmani, E. et al. Genome-wide methylation data mirror ancestry information. Epigenetics Chromatin 10, 1 (2017).
-
(2017)
Epigenetics Chromatin
, vol.10
, pp. 1
-
-
Rahmani, E.1
-
124
-
-
84858648623
-
Two-step epigenetic Mendelian randomization: A strategy for establishing the causal role of epigenetic processes in pathways to disease
-
Relton, C. L. & Davey Smith, G. Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease. Int. J. Epidemiol. 41, 161-176 (2012).
-
(2012)
Int. J. Epidemiol.
, vol.41
, pp. 161-176
-
-
Relton, C.L.1
Davey Smith, G.2
-
125
-
-
85031708100
-
Mendelian randomization analysis identifies CpG sites as putative mediators for genetic influences on cardiovascular disease risk
-
Richardson, T. G. et al. Mendelian randomization analysis identifies CpG sites as putative mediators for genetic influences on cardiovascular disease risk. Am. J. Hum. Genet. 101, 590-602 (2017).
-
(2017)
Am. J. Hum. Genet.
, vol.101
, pp. 590-602
-
-
Richardson, T.G.1
-
126
-
-
85032335608
-
Exploring a causal role of DNA methylation in the relationship between maternal vitamin B12 during pregnancy and child's IQ at age 8, cognitive performance and educational attainment: A two-step Mendelian randomization study
-
Caramaschi, D. et al. Exploring a causal role of DNA methylation in the relationship between maternal vitamin B12 during pregnancy and child's IQ at age 8, cognitive performance and educational attainment: a two-step Mendelian randomization study. Hum. Mol. Genet. 26, 3001-3013 (2017).
-
(2017)
Hum. Mol. Genet.
, vol.26
, pp. 3001-3013
-
-
Caramaschi, D.1
-
127
-
-
84874816208
-
DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes
-
Aran, D., Sabato, S. & Hellman, A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol. 14, R21 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R21
-
-
Aran, D.1
Sabato, S.2
Hellman, A.3
-
128
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
-
129
-
-
84963601453
-
Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
-
Whalen, S., Truty, R. M. & Pollard, K. S. Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nat. Genet. 48, 488-496 (2016).
-
(2016)
Nat. Genet.
, vol.48
, pp. 488-496
-
-
Whalen, S.1
Truty, R.M.2
Pollard, K.S.3
-
130
-
-
84907997839
-
Gene body methylation can alter gene expression and is a therapeutic target in cancer
-
Yang, X. et al. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell 26, 577-590 (2014).
-
(2014)
Cancer Cell
, vol.26
, pp. 577-590
-
-
Yang, X.1
-
131
-
-
31344466008
-
DNA methylation and gene silencing in cancer
-
Baylin, S. B. DNA methylation and gene silencing in cancer. Nat. Clin. Pract. Oncol. 2 (Suppl. 1), S4-S11 (2005).
-
(2005)
Nat. Clin. Pract. Oncol.
, vol.2
, pp. S4-S11
-
-
Baylin, S.B.1
-
132
-
-
84863986133
-
Functions of DNA methylation: Islands, start sites, gene bodies and beyond
-
Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484-492 (2012).
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 484-492
-
-
Jones, P.A.1
-
133
-
-
84867145980
-
On the presence and role of human gene-body DNA methylation
-
Jjingo, D., Conley, A. B., Yi, S. V., Lunyak, V. V. & Jordan, I. K. On the presence and role of human gene-body DNA methylation. Oncotarget 3, 462-474 (2012).
-
(2012)
Oncotarget
, vol.3
, pp. 462-474
-
-
Jjingo, D.1
Conley, A.B.2
Yi, S.V.3
Lunyak, V.V.4
Jordan, I.K.5
-
134
-
-
84906251108
-
A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control
-
Jiao, Y., Widschwendter, M. & Teschendorff, A. E. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Bioinformatics 30, 2360-2366 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2360-2366
-
-
Jiao, Y.1
Widschwendter, M.2
Teschendorff, A.E.3
-
135
-
-
79251567720
-
DNA methylation of the first exon is tightly linked to transcriptional silencing
-
Brenet, F. et al. DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS ONE 6, e14524 (2011).
-
(2011)
PLoS ONE
, vol.6
, pp. e14524
-
-
Brenet, F.1
-
136
-
-
0032901199
-
Cytosine methylation and mammalian development
-
Walsh, C. P. & Bestor, T. H. Cytosine methylation and mammalian development. Genes Dev. 13, 26-34 (1999).
-
(1999)
Genes Dev.
, vol.13
, pp. 26-34
-
-
Walsh, C.P.1
Bestor, T.H.2
-
137
-
-
70449331456
-
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
-
Shen, R., Olshen, A. B. & Ladanyi, M. Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 25, 2906-2912 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2906-2912
-
-
Shen, R.1
Olshen, A.B.2
Ladanyi, M.3
-
138
-
-
84949257291
-
The integrative epigenomic-transcriptomic landscape of ER positive breast cancer
-
Gao, Y. et al. The integrative epigenomic-transcriptomic landscape of ER positive breast cancer. Clin. Epigenet. 7, 126 (2015).
-
(2015)
Clin. Epigenet.
, vol.7
, pp. 126
-
-
Gao, Y.1
-
139
-
-
84875016233
-
Pattern discovery and cancer gene identification in integrated cancer genomic data
-
Mo, Q. et al. Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc. Natl Acad. Sci. USA 110, 4245-4250 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 4245-4250
-
-
Mo, Q.1
-
140
-
-
84941021874
-
Role of DNA methylation in modulating transcription factor occupancy
-
Maurano, M. T. et al. Role of DNA methylation in modulating transcription factor occupancy. Cell Rep. 12, 1184-1195 (2015).
-
(2015)
Cell Rep.
, vol.12
, pp. 1184-1195
-
-
Maurano, M.T.1
-
141
-
-
84951325892
-
Competition between DNA methylation and transcription factors determines binding of NRF1
-
Domcke, S. et al. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528, 575-579 (2015).
-
(2015)
Nature
, vol.528
, pp. 575-579
-
-
Domcke, S.1
-
142
-
-
84980361817
-
Transcription factors as readers and effectors of DNA methylation
-
Zhu, H., Wang, G. & Qian, J. Transcription factors as readers and effectors of DNA methylation. Nat. Rev. Genet. 17, 551-565 (2016).
-
(2016)
Nat. Rev. Genet.
, vol.17
, pp. 551-565
-
-
Zhu, H.1
Wang, G.2
Qian, J.3
-
143
-
-
85018754019
-
Impact of cytosine methylation on DNA binding specificities of human transcription factors
-
Yin, Y. et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 356, eaaj2239 (2017).
-
(2017)
Science
, vol.356
, pp. eaaj2239
-
-
Yin, Y.1
-
144
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322 (2009).
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
-
145
-
-
84355163093
-
DNA-binding factors shape the mouse methylome at distal regulatory regions
-
Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490-495 (2011).
-
(2011)
Nature
, vol.480
, pp. 490-495
-
-
Stadler, M.B.1
-
146
-
-
84885848576
-
Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2
-
Guilhamon, P. et al. Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2. Nat. Commun. 4, 2166 (2013).
-
(2013)
Nat. Commun.
, vol.4
, pp. 2166
-
-
Guilhamon, P.1
-
147
-
-
84938923353
-
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes
-
Yao, L., Shen, H., Laird, P. W., Farnham, P. J. & Berman, B. P. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 16, 105 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 105
-
-
Yao, L.1
Shen, H.2
Laird, P.W.3
Farnham, P.J.4
Berman, B.P.5
-
148
-
-
84903516439
-
Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing
-
Hovestadt, V. et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature 510, 537-541 (2014).
-
(2014)
Nature
, vol.510
, pp. 537-541
-
-
Hovestadt, V.1
-
149
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Dunham, I.1
-
150
-
-
85040645383
-
Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits
-
Rhie, S. K. et al. Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin 9, 50 (2016).
-
(2016)
Epigenetics Chromatin
, vol.9
, pp. 50
-
-
Rhie, S.K.1
-
151
-
-
85026383892
-
Identification of novel prostate cancer drivers using RegNetDriver: A framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network
-
Dhingra, P. et al. Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome Biol. 18, 141 (2017).
-
(2017)
Genome Biol.
, vol.18
, pp. 141
-
-
Dhingra, P.1
-
152
-
-
84887620842
-
A high-resolution map of the three-dimensional chromatin interactome in human cells
-
Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290-294 (2013).
-
(2013)
Nature
, vol.503
, pp. 290-294
-
-
Jin, F.1
-
153
-
-
84919949716
-
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
-
Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014).
-
(2014)
Cell
, vol.159
, pp. 1665-1680
-
-
Rao, S.S.1
-
154
-
-
84889021277
-
Role of DNA methylation and epigenetic silencing of HAND2 in endometrial cancer development
-
Jones, A. et al. Role of DNA methylation and epigenetic silencing of HAND2 in endometrial cancer development. PLoS Med. 10, e1001551 (2013).
-
(2013)
PLoS Med.
, vol.10
, pp. e1001551
-
-
Jones, A.1
-
155
-
-
80053446196
-
Protein networks as logic functions in development and cancer
-
Dutkowski, J. & Ideker, T. Protein networks as logic functions in development and cancer. PLoS Computat. Biol. 7, e1002180 (2011).
-
(2011)
PLoS Computat. Biol.
, vol.7
, pp. e1002180
-
-
Dutkowski, J.1
Ideker, T.2
-
156
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang, H. Y., Lee, E., Liu, Y. T., Lee, D. & Ideker, T. Network-based classification of breast cancer metastasis. Mol. Systems Biol. 3, 140 (2007).
-
(2007)
Mol. Systems Biol.
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
Lee, D.4
Ideker, T.5
-
157
-
-
78649703966
-
Rewiring of genetic networks in response to DNA damage
-
Bandyopadhyay, S. et al. Rewiring of genetic networks in response to DNA damage. Science 330, 1385-1389 (2010).
-
(2010)
Science
, vol.330
, pp. 1385-1389
-
-
Bandyopadhyay, S.1
-
158
-
-
84988968777
-
NEpiC: A network-assisted algorithm for epigenetic studies using mean and variance combined signals
-
Ruan, P., Shen, J., Santella, R. M., Zhou, S. & Wang, S. NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals. Nucleic Acids Res. 44, e134 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. e134
-
-
Ruan, P.1
Shen, J.2
Santella, R.M.3
Zhou, S.4
Wang, S.5
-
159
-
-
85011067014
-
Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data
-
Ma, X., Liu, Z., Zhang, Z., Huang, X. & Tang, W. Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. BMC Bioinformat. 18, 72 (2017).
-
(2017)
BMC Bioinformat.
, vol.18
, pp. 72
-
-
Ma, X.1
Liu, Z.2
Zhang, Z.3
Huang, X.4
Tang, W.5
-
160
-
-
85009809651
-
SMITE: An R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information
-
Wijetunga, N. A. et al. SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. BMC Bioinformat. 18, 41 (2017).
-
(2017)
BMC Bioinformat.
, vol.18
, pp. 41
-
-
Wijetunga, N.A.1
-
161
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
The Cancer Genome Atlas Research Network et al
-
The Cancer Genome Atlas Research Network et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113-1120 (2013).
-
(2013)
Nat. Genet.
, vol.45
, pp. 1113-1120
-
-
-
162
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Koboldt, D. C. et al. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
Koboldt, D.C.1
-
163
-
-
84983605252
-
The multi-omic landscape of transcription factor inactivation in cancer
-
Teschendorff, A. E. et al. The multi-omic landscape of transcription factor inactivation in cancer. Genome Med. 8, 89 (2016).
-
(2016)
Genome Med.
, vol.8
, pp. 89
-
-
Teschendorff, A.E.1
-
164
-
-
84868152524
-
Discovery of multi-dimensional modules by integrative analysis of cancer genomic data
-
Zhang, S. et al. Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Res. 40, 9379-9391 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 9379-9391
-
-
Zhang, S.1
-
165
-
-
84859992638
-
Integrative subtype discovery in glioblastoma using iCluster
-
Shen, R. et al. Integrative subtype discovery in glioblastoma using iCluster. PLoS ONE 7, e35236 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e35236
-
-
Shen, R.1
-
166
-
-
84992189556
-
R.JIVE for exploration of multi-source molecular data
-
O'Connell, M. J. & Lock, E. F. R.JIVE for exploration of multi-source molecular data. Bioinformatics 32, 2877-2879 (2016).
-
(2016)
Bioinformatics
, vol.32
, pp. 2877-2879
-
-
O'Connell, M.J.1
Lock, E.F.2
-
167
-
-
84876058478
-
Joint and Individual Variation Explained (JIVE) for integrated analysis of multiple data types
-
Lock, E. F., Hoadley, K. A., Marron, J. S. & Nobel, A. B. Joint and Individual Variation Explained (JIVE) for integrated analysis of multiple data types. Ann. Appl. Statist. 7, 523-542 (2013).
-
(2013)
Ann. Appl. Statist.
, vol.7
, pp. 523-542
-
-
Lock, E.F.1
Hoadley, K.A.2
Marron, J.S.3
Nobel, A.B.4
-
169
-
-
84980335767
-
Tensor decomposition for multiple-tissue gene expression experiments
-
Hore, V. et al. Tensor decomposition for multiple-tissue gene expression experiments. Nat. Genet. 48, 1094-1100 (2016).
-
(2016)
Nat. Genet.
, vol.48
, pp. 1094-1100
-
-
Hore, V.1
-
170
-
-
85016465042
-
Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment
-
Wang, T. et al. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol. 18, 57 (2017).
-
(2017)
Genome Biol.
, vol.18
, pp. 57
-
-
Wang, T.1
-
171
-
-
85016516711
-
Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions
-
Cole, J. J. et al. Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biol. 18, 58 (2017).
-
(2017)
Genome Biol.
, vol.18
, pp. 58
-
-
Cole, J.J.1
-
172
-
-
85016505395
-
Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism
-
Hahn, O. et al. Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. Genome Biol. 18, 56 (2017).
-
(2017)
Genome Biol.
, vol.18
, pp. 56
-
-
Hahn, O.1
-
173
-
-
84950107042
-
Hypomethylation of smoking-related genes is associated with future lung cancer in four prospective cohorts
-
Fasanelli, F. et al. Hypomethylation of smoking-related genes is associated with future lung cancer in four prospective cohorts. Nat. Commun. 6, 10192 (2015).
-
(2015)
Nat. Commun.
, vol.6
, pp. 10192
-
-
Fasanelli, F.1
-
174
-
-
76549135113
-
Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease
-
Feinberg, A. P. & Irizarry, R. A. Evolution in health and medicine Sackler colloquium: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc. Natl Acad. Sci. USA 107 (Suppl. 1), 1757-1764 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 1757-1764
-
-
Feinberg, A.P.1
Irizarry, R.A.2
-
175
-
-
79960912486
-
Epigenetic variation and cellular Darwinism
-
Issa, J. P. Epigenetic variation and cellular Darwinism. Nat. Genet. 43, 724-726 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 724-726
-
-
Issa, J.P.1
-
176
-
-
85009792040
-
Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis
-
McDonald, O. G. et al. Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis. Nat. Genet. 49, 367-376 (2017).
-
(2017)
Nat. Genet.
, vol.49
, pp. 367-376
-
-
McDonald, O.G.1
-
177
-
-
84859166725
-
The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer
-
Zhuang, J. et al. The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer. PLoS Genet. 8, e1002517 (2012).
-
(2012)
PLoS Genet.
, vol.8
, pp. e1002517
-
-
Zhuang, J.1
-
178
-
-
84940090291
-
Reconstructing A/B compartments as revealed by Hi?C using long-range correlations in epigenetic data
-
Fortin, J. P. & Hansen, K. D. Reconstructing A/B compartments as revealed by Hi?C using long-range correlations in epigenetic data. Genome Biol. 16, 180 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 180
-
-
Fortin, J.P.1
Hansen, K.D.2
-
179
-
-
84943372238
-
DNA methylation age of blood predicts future onset of lung cancer in the women's health initiative
-
Levine, M. E. et al. DNA methylation age of blood predicts future onset of lung cancer in the women's health initiative. Aging 7, 690-700 (2015).
-
(2015)
Aging
, vol.7
, pp. 690-700
-
-
Levine, M.E.1
-
180
-
-
84989345511
-
Correlation of an epigenetic mitotic clock with cancer risk
-
Yang, Z. et al. Correlation of an epigenetic mitotic clock with cancer risk. Genome Biol. 17, 205 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 205
-
-
Yang, Z.1
-
181
-
-
84926674860
-
DNA methylation age of blood predicts all-cause mortality in later life
-
Marioni, R. E. et al. DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol. 16, 25 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 25
-
-
Marioni, R.E.1
-
182
-
-
85015616657
-
DNA methylation signatures in peripheral blood strongly predict all-cause mortality
-
Zhang, Y. et al. DNA methylation signatures in peripheral blood strongly predict all-cause mortality. Nat. Commun. 8, 14617 (2017).
-
(2017)
Nat. Commun.
, vol.8
, pp. 14617
-
-
Zhang, Y.1
-
183
-
-
85001610245
-
Frailty is associated with the epigenetic clock but not with telomere length in a German cohort
-
Breitling, L. P. et al. Frailty is associated with the epigenetic clock but not with telomere length in a German cohort. Clin. Epigenet. 8, 21 (2016).
-
(2016)
Clin. Epigenet.
, vol.8
, pp. 21
-
-
Breitling, L.P.1
-
184
-
-
84962407100
-
Identification of tissue-specific cell death using methylation patterns of circulating DNA
-
Lehmann-Werman, R. et al. Identification of tissue-specific cell death using methylation patterns of circulating DNA. Proc. Natl Acad. Sci. USA 113, E1826-E1834 (2016).
-
(2016)
Proc. Natl Acad. Sci. USA
, vol.113
, pp. E1826-E1834
-
-
Lehmann-Werman, R.1
-
185
-
-
85016574289
-
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq
-
Venteicher, A. S. et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science 355, eaai8478 (2017).
-
(2017)
Science
, vol.355
, pp. eaai8478
-
-
Venteicher, A.S.1
-
186
-
-
84982161976
-
Single-cell multimodal profiling reveals cellular epigenetic heterogeneity
-
Cheow, L. F. et al. Single-cell multimodal profiling reveals cellular epigenetic heterogeneity. Nat. Methods 13, 833-836 (2016).
-
(2016)
Nat. Methods
, vol.13
, pp. 833-836
-
-
Cheow, L.F.1
-
187
-
-
84995804537
-
From profiles to function in epigenomics
-
Stricker, S. H., Koferle, A. & Beck, S. From profiles to function in epigenomics. Nat. Rev. Genet. 18, 51-66 (2017).
-
(2017)
Nat. Rev. Genet.
, vol.18
, pp. 51-66
-
-
Stricker, S.H.1
Koferle, A.2
Beck, S.3
-
188
-
-
84980022857
-
Deep learning for computational biology
-
Angermueller, C., Parnamaa, T., Parts, L. & Stegle, O. Deep learning for computational biology. Mol. Syst. Biol. 12, 878 (2016).
-
(2016)
Mol. Syst. Biol.
, vol.12
, pp. 878
-
-
Angermueller, C.1
Parnamaa, T.2
Parts, L.3
Stegle, O.4
-
189
-
-
84926632357
-
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
-
Ernst, J. & Kellis, M. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nat. Biotechnol. 33, 364-376 (2015).
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 364-376
-
-
Ernst, J.1
Kellis, M.2
-
190
-
-
84881171093
-
Statistical mechanics of pluripotency
-
MacArthur, B. D. & Lemischka, I. R. Statistical mechanics of pluripotency. Cell 154, 484-489 (2013).
-
(2013)
Cell
, vol.154
, pp. 484-489
-
-
MacArthur, B.D.1
Lemischka, I.R.2
-
191
-
-
85020213929
-
Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome
-
Teschendorff, A. & Enver, T. Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome. Nat. Commun. 8, 15599 (2017).
-
(2017)
Nat. Commun.
, vol.8
, pp. 15599
-
-
Teschendorff, A.1
Enver, T.2
-
192
-
-
84905460448
-
The dynamics of DNA methylation covariation patterns in carcinogenesis
-
Teschendorff, A. E. et al. The dynamics of DNA methylation covariation patterns in carcinogenesis. PLoS Computat. Biol. 10, e1003709 (2014).
-
(2014)
PLoS Computat. Biol.
, vol.10
, pp. e1003709
-
-
Teschendorff, A.E.1
-
193
-
-
84927955044
-
Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes
-
Lang, A. H., Li, H., Collins, J. J. & Mehta, P. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes. PLoS Computat. Biol. 10, e1003734 (2014).
-
(2014)
PLoS Computat. Biol.
, vol.10
, pp. e1003734
-
-
Lang, A.H.1
Li, H.2
Collins, J.J.3
Mehta, P.4
-
194
-
-
85009096649
-
Cell fate decision as high-dimensional critical state transition
-
Mojtahedi, M. et al. Cell fate decision as high-dimensional critical state transition. PLoS Biol. 14, e2000640 (2016).
-
(2016)
PLoS Biol.
, vol.14
, pp. e2000640
-
-
Mojtahedi, M.1
-
195
-
-
74549148040
-
Decomposition of gene expression state space trajectories
-
Mar, J. C. & Quackenbush, J. Decomposition of gene expression state space trajectories. PLoS Computat. Biol. 5, e1000626 (2009).
-
(2009)
PLoS Computat. Biol.
, vol.5
, pp. e1000626
-
-
Mar, J.C.1
Quackenbush, J.2
-
196
-
-
84901439430
-
Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data
-
Teschendorff, A. E., Sollich, P. & Kuehn, R. Signalling entropy: a novel network-theoretical framework for systems analysis and interpretation of functional omic data. Methods 67, 282-293 (2014).
-
(2014)
Methods
, vol.67
, pp. 282-293
-
-
Teschendorff, A.E.1
Sollich, P.2
Kuehn, R.3
-
198
-
-
84985904907
-
Single cell pluripotency regulatory networks
-
Stumpf, P. S., Ewing, R. & MacArthur, B. D. Single cell pluripotency regulatory networks. Proteomics 16, 2303-2312 (2016).
-
(2016)
Proteomics
, vol.16
, pp. 2303-2312
-
-
Stumpf, P.S.1
Ewing, R.2
MacArthur, B.D.3
-
199
-
-
0023020183
-
The moderator-mediator variable distinction in social psychological research: Conceptual, strategic, and statistical considerations
-
Baron, R. M. & Kenny, D. A. The moderator-mediator variable distinction in social psychological research: conceptual, strategic, and statistical considerations. J. Pers. Soc. Psychol. 51, 1173-1182 (1986).
-
(1986)
J. Pers. Soc. Psychol.
, vol.51
, pp. 1173-1182
-
-
Baron, R.M.1
Kenny, D.A.2
-
200
-
-
84906838227
-
Mendelian randomization: Genetic anchors for causal inference in epidemiological studies
-
Davey Smith, G. & Hemani, G. Mendelian randomization: genetic anchors for causal inference in epidemiological studies. Hum. Mol. Genet. 23, R89-R98 (2014).
-
(2014)
Hum. Mol. Genet.
, vol.23
, pp. R89-R98
-
-
Davey Smith, G.1
Hemani, G.2
-
201
-
-
85010976480
-
Association of body mass index with DNA methylation and gene expression in blood cells and relations to cardiometabolic disease: A Mendelian randomization approach
-
Mendelson, M. M. et al. Association of body mass index with DNA methylation and gene expression in blood cells and relations to cardiometabolic disease: a Mendelian randomization approach. PLoS Med. 14, e1002215 (2017).
-
(2017)
PLoS Med.
, vol.14
, pp. e1002215
-
-
Mendelson, M.M.1
-
202
-
-
85014046988
-
Genome-wide DNA methylation study in human placenta identifies novel loci associated with maternal smoking during pregnancy
-
Morales, E. et al. Genome-wide DNA methylation study in human placenta identifies novel loci associated with maternal smoking during pregnancy. Int. J. Epidemiol. 45, 1644-1655 (2016).
-
(2016)
Int. J. Epidemiol.
, vol.45
, pp. 1644-1655
-
-
Morales, E.1
-
203
-
-
84927740135
-
Mendelian randomization supports causality between maternal hyperglycemia and epigenetic regulation of leptin gene in newborns
-
Allard, C. et al. Mendelian randomization supports causality between maternal hyperglycemia and epigenetic regulation of leptin gene in newborns. Epigenetics 10, 342-351 (2015).
-
(2015)
Epigenetics
, vol.10
, pp. 342-351
-
-
Allard, C.1
-
204
-
-
84936755918
-
Mendelian randomization with invalid instruments: Effect estimation and bias detection through Egger regression
-
Bowden, J., Davey Smith, G. & Burgess, S. Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression. Int. J. Epidemiol. 44, 512-525 (2015).
-
(2015)
Int. J. Epidemiol.
, vol.44
, pp. 512-525
-
-
Bowden, J.1
Davey Smith, G.2
Burgess, S.3
-
205
-
-
84963670568
-
Consistent estimation in Mendelian randomization with some invalid instruments using a weighted median estimator
-
Bowden, J., Davey Smith, G., Haycock, P. C. & Burgess, S. Consistent estimation in Mendelian randomization with some invalid instruments using a weighted median estimator. Genet. Epidemiol. 40, 304-314 (2016).
-
(2016)
Genet. Epidemiol.
, vol.40
, pp. 304-314
-
-
Bowden, J.1
Davey Smith, G.2
Haycock, P.C.3
Burgess, S.4
-
206
-
-
84908120809
-
Investigating the possible causal association of smoking with depression and anxiety using Mendelian randomisation meta-analysis: The CARTA consortium
-
Taylor, A. E. et al. Investigating the possible causal association of smoking with depression and anxiety using Mendelian randomisation meta-analysis: the CARTA consortium. BMJ Open 4, e006141 (2014).
-
(2014)
BMJ Open
, vol.4
, pp. e006141
-
-
Taylor, A.E.1
-
208
-
-
84942243321
-
Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data
-
Maksimovic, J., Gagnon-Bartsch, J. A., Speed, T. P. & Oshlack, A. Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data. Nucleic Acids Res. 43, e106 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e106
-
-
Maksimovic, J.1
Gagnon-Bartsch, J.A.2
Speed, T.P.3
Oshlack, A.4
-
209
-
-
84866853818
-
BSmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
-
Hansen, K. D., Langmead, B. & Irizarry, R. A. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 13, R83 (2012).
-
(2012)
Genome Biol.
, vol.13
, pp. R83
-
-
Hansen, K.D.1
Langmead, B.2
Irizarry, R.A.3
-
210
-
-
85015991570
-
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
-
Schmidt, F. et al. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. Nucleic Acids Res. 45, 54-66 (2017).
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. 54-66
-
-
Schmidt, F.1
-
212
-
-
85013155806
-
Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types
-
Chun, S. et al. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Nat. Genet. 49, 600-605 (2017).
-
(2017)
Nat. Genet.
, vol.49
, pp. 600-605
-
-
Chun, S.1
-
213
-
-
84901631426
-
Bayesian test for colocalisation between pairs of genetic association studies using summary statistics
-
Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014).
-
(2014)
PLoS Genet.
, vol.10
, pp. e1004383
-
-
Giambartolomei, C.1
-
214
-
-
84968649781
-
Detection and interpretation of shared genetic influences on 42 human traits
-
Pickrell, J. K. et al. Detection and interpretation of shared genetic influences on 42 human traits. Nat. Genet. 48, 709-717 (2016).
-
(2016)
Nat. Genet.
, vol.48
, pp. 709-717
-
-
Pickrell, J.K.1
-
215
-
-
84961927084
-
Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets
-
Zhu, Z. et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nat. Genet. 48, 481-487 (2016).
-
(2016)
Nat. Genet.
, vol.48
, pp. 481-487
-
-
Zhu, Z.1
|