-
1
-
-
0022000776
-
A fraction of the mouse genome that is derived from islands of nonmethylated
-
Bird, A., Taggart, M., Frommer, M., Miller, O.J. & Macleod, D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40, 91-99 (1985).
-
(1985)
CpG-rich DNA. Cell
, vol.40
, pp. 91-99
-
-
Bird, A.1
Taggart, M.2
Frommer, M.3
Miller, O.J.4
MacLeod, D.5
-
2
-
-
59149084538
-
The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores
-
Irizarry, R.A. et al. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 41, 178-186 (2009).
-
(2009)
Nat. Genet
, vol.41
, pp. 178-186
-
-
Irizarry, R.A.1
-
3
-
-
78649906060
-
DNMT3A mutations in acute myeloid leukemia
-
Ley, T.J. et al. DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med. 363, 2424-2433 (2010).
-
(2010)
N. Engl. J. Med
, vol.363
, pp. 2424-2433
-
-
Ley, T.J.1
-
4
-
-
79953176952
-
Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia
-
Yan, X.J. et al. Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat. Genet. 43, 309-315 (2011).
-
(2011)
Nat. Genet
, vol.43
, pp. 309-315
-
-
Yan, X.J.1
-
5
-
-
66249137734
-
Mutation in TET2 in myeloid cancers
-
Delhommeau, F. et al. Mutation in TET2 in myeloid cancers. N. Engl. J. Med. 360, 2289-2301 (2009).
-
(2009)
N. Engl. J. Med
, vol.360
, pp. 2289-2301
-
-
Delhommeau, F.1
-
6
-
-
67651065502
-
Genetic characterization of TET1TET2, and TET3 alterations in myeloid malignancies
-
Abdel-Wahab, O. et al. Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies. Blood 114, 144-147 (2009).
-
(2009)
Blood
, vol.114
, pp. 144-147
-
-
Abdel-Wahab, O.1
-
7
-
-
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
-
8
-
-
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
-
9
-
-
84855281409
-
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
-
Ziller, M.J. et al. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 7, e1002389 (2011).
-
(2011)
PLoS Genet
, vol.7
-
-
Ziller, M.J.1
-
10
-
-
80052918929
-
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment
-
Hodges, E. et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell 44, 17-28 (2011).
-
(2011)
Mol. Cell
, vol.44
, pp. 17-28
-
-
Hodges, E.1
-
11
-
-
0023216891
-
CpG islands in vertebrate genomes
-
Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261-282 (1987).
-
(1987)
J. Mol. Biol
, vol.196
, pp. 261-282
-
-
Gardiner-Garden, M.1
Frommer, M.2
-
12
-
-
34249937354
-
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
-
Lowe, C.B., Bejerano, G. & Haussler, D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Natl. Acad. Sci. USA 104, 8005-8010 (2007).
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 8005-8010
-
-
Lowe, C.B.1
Bejerano, G.2
Haussler, D.3
-
13
-
-
45549093494
-
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
-
Hendrix, D.A., Hong, J.W., Zeitlinger, J., Rokhsar, D.S. & Levine, M.S. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 105, 7762-7767 (2008).
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 7762-7767
-
-
Hendrix, D.A.1
Hong, J.W.2
Zeitlinger, J.3
Rokhsar, D.S.4
Levine, M.S.5
-
14
-
-
79960114353
-
The Drosophila gene disruption project: Progress using transposons with distinctive site specificities
-
Bellen, H.J. et al. The Drosophila gene disruption project: progress using transposons with distinctive site specificities. Genetics 188, 731-743 (2011).
-
(2011)
Genetics
, vol.188
, pp. 731-743
-
-
Bellen, H.J.1
-
15
-
-
65149092197
-
Transcriptional features of genomic regulatory blocks
-
Akalin, A. et al. Transcriptional features of genomic regulatory blocks. Genome Biol. 10, R38 (2009).
-
(2009)
Genome Biol
, vol.10
-
-
Akalin, A.1
-
16
-
-
34248153777
-
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
-
Kikuta, H. et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17, 545-555 (2007).
-
(2007)
Genome Res
, vol.17
, pp. 545-555
-
-
Kikuta, H.1
-
17
-
-
84876216563
-
Master transcription factors and mediator establish super-enhancers at key cell identity genes
-
Whyte, W.A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319 (2013).
-
(2013)
Cell
, vol.153
, pp. 307-319
-
-
Whyte, W.A.1
-
18
-
-
77957348625
-
Combinatorial transcriptional control in blood stem/progenitor cells: Genome-wide analysis of ten major transcriptional regulators
-
Wilson, N.K. et al. Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 7, 532-544 (2010).
-
(2010)
Cell Stem Cell
, vol.7
, pp. 532-544
-
-
Wilson, N.K.1
-
19
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006).
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
-
20
-
-
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
-
21
-
-
77649271805
-
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
-
Coolen, M.W. et al. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat. Cell Biol. 12, 235-246 (2010).
-
(2010)
Nat. Cell Biol
, vol.12
, pp. 235-246
-
-
Coolen, M.W.1
-
22
-
-
84872395684
-
Regional activation of the cancer genome by long-range epigenetic remodeling
-
Bert, S.A. et al. Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell 23, 9-22 (2013).
-
(2013)
Cancer Cell
, vol.23
, pp. 9-22
-
-
Bert, S.A.1
-
23
-
-
84863393263
-
Prognostic relevance of integrated genetic profiling in acute myeloid leukemia
-
Patel, J.P. et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N. Engl. J. Med. 366, 1079-1089 (2012).
-
(2012)
N. Engl. J. Med
, vol.366
, pp. 1079-1089
-
-
Patel, J.P.1
-
24
-
-
84555207349
-
Dnmt3a is essential for hematopoietic stem cell differentiation
-
Challen, G.A. et al. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat. Genet. 44, 23-31 (2012).
-
(2012)
Nat. Genet
, vol.44
, pp. 23-31
-
-
Challen, G.A.1
-
25
-
-
84878260646
-
TETonic shift: Biological roles of TET proteins in DNA demethylation and transcription
-
Pastor, W.A., Aravind, L. & Rao, A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol. 14, 341-356 (2013).
-
(2013)
Nat. Rev. Mol. Cell Biol
, vol.14
, pp. 341-356
-
-
Pastor, W.A.1
Aravind, L.2
Rao, A.3
-
26
-
-
80054097425
-
Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos
-
Inoue, A. & Zhang, Y. Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 334, 194 (2011).
-
Science
, vol.334
, Issue.194
, pp. 2011
-
-
Inoue, A.1
Zhang, Y.2
-
27
-
-
79956308473
-
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
-
Pastor, W.A. et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473, 394-397 (2011).
-
(2011)
Nature
, vol.473
, pp. 394-397
-
-
Pastor, W.A.1
-
28
-
-
84861221693
-
Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
-
Booth, M.J. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336, 934-937 (2012).
-
(2012)
Science
, vol.336
, pp. 934-937
-
-
Booth, M.J.1
-
29
-
-
84880318248
-
Landmark analysis of DNMT3A mutations in hematological malignancies
-
Roller, A. et al. Landmark analysis of DNMT3A mutations in hematological malignancies. Leukemia 27, 1573-1578 (2013).
-
(2013)
Leukemia
, vol.27
, pp. 1573-1578
-
-
Roller, A.1
-
30
-
-
33847065486
-
The epigenomics of cancer
-
Jones, P.A. & Baylin, S.B. The epigenomics of cancer. Cell 128, 683-692 (2007).
-
(2007)
Cell
, vol.128
, pp. 683-692
-
-
Jones, P.A.1
Baylin, S.B.2
-
31
-
-
84879049092
-
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
-
Long, H.K. et al. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. eLife 2, e00348 (2013).
-
(2013)
ELife
, vol.2
-
-
Long, H.K.1
-
32
-
-
84878282421
-
Epigenomic analysis of multilineage differentiation of human embryonic stem cells
-
Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134-1148 (2013).
-
(2013)
Cell
, vol.153
, pp. 1134-1148
-
-
Xie, W.1
-
33
-
-
78650175023
-
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2
-
Ko, M. et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468, 839-843 (2010).
-
(2010)
Nature
, vol.468
, pp. 839-843
-
-
Ko, M.1
-
34
-
-
0029958876
-
Isolation and functional properties of murine hematopoietic stem cells that are replicating in vivo
-
Goodell, M.A., Brose, K., Paradis, G., Conner, A.S. & Mulligan, R.C. Isolation and functional properties of murine hematopoietic stem cells that are replicating in vivo. J. Exp. Med. 183, 1797-1806 (1996).
-
(1996)
J. Exp. Med
, vol.183
, pp. 1797-1806
-
-
Goodell, M.A.1
Brose, K.2
Paradis, G.3
Conner, A.S.4
Mulligan, R.C.5
-
35
-
-
84871647883
-
Flow cytometry analysis of murine hematopoietic stem cells
-
Mayle, A., Luo, M., Jeong, M. & Goodell, M.A. Flow cytometry analysis of murine hematopoietic stem cells. Cytometry A 83, 27-37 (2013).
-
(2013)
Cytometry A
, vol.83
, pp. 27-37
-
-
Mayle, A.1
Luo, M.2
Jeong, M.3
Goodell, M.A.4
-
36
-
-
79952788617
-
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
-
Gu, H. et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat. Protoc. 6, 468-481 (2011).
-
(2011)
Nat. Protoc
, vol.6
, pp. 468-481
-
-
Gu, H.1
-
37
-
-
84869075314
-
The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine
-
Huang, Y., Pastor, W.A., Zepeda-Martinez, J.A. & Rao, A. The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine. Nat. Protoc. 7, 1897-1908 (2012).
-
(2012)
Nat. Protoc
, vol.7
, pp. 1897-1908
-
-
Huang, Y.1
Pastor, W.A.2
Zepeda-Martinez, J.A.3
Rao, A.4
-
38
-
-
79957868920
-
Bismark a flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger, F. & Andrews, S.R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
39
-
-
44949138461
-
A rapid micro chromatin immunoprecipitation assay (microChIP)
-
Dahl, J.A. & Collas, P. A rapid micro chromatin immunoprecipitation assay (microChIP). Nat. Protoc. 3, 1032-1045 (2008).
-
(2008)
Nat. Protoc
, vol.3
, pp. 1032-1045
-
-
Dahl, J.A.1
Collas, P.2
-
40
-
-
68949141599
-
BSMAP whole genome bisulfite sequence mapping program
-
Xi, Y. & Li, W. BSMAP: whole genome Bisulfite Sequence MAPping program. BMC Bioinformatics 10, 232 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 232
-
-
Xi, Y.1
Li, W.2
-
41
-
-
84899050224
-
BSeQC: Quality control of bisulfite sequencing experiments
-
doi:10.1093/bioinformatics/btt548 11 October 2013
-
Lin, X. et al. BSeQC: quality control of bisulfite sequencing experiments. Bioinformatics doi:10.1093/bioinformatics/btt548 (11 October 2013).
-
Bioinformatics
-
-
Lin, X.1
-
42
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
-
43
-
-
67650711615
-
SOAP2: An improved ultrafast tool for short read alignment
-
Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
-
44
-
-
80052495940
-
Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA
-
He, Y.-F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303-1307 (2011).
-
(2011)
Science
, vol.333
, pp. 1303-1307
-
-
He, Y.-F.1
-
45
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
46
-
-
41149167129
-
Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'
-
Kuhn, A., Luthi-Carter, R. & Delorenzi, M. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics 9, 26 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 26
-
-
Kuhn, A.1
Luthi-Carter, R.2
Delorenzi, M.3
-
47
-
-
34447560961
-
Analysis of gene expression data using BRB-ArrayTools
-
Simon, R. et al. Analysis of gene expression data using BRB-ArrayTools. Cancer Inform. 3, 11-17 (2007).
-
(2007)
Cancer Inform
, vol.3
, pp. 11-17
-
-
Simon, R.1
-
48
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863-14868 (1998).
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
|