-
1
-
-
84875745673
-
Interplay between the cancer genome and epigenome
-
Shen, H. & Laird, P. W. Interplay between the cancer genome and epigenome. Cell 153, 38-55 (2013).
-
(2013)
Cell
, vol.153
, pp. 38-55
-
-
Shen, H.1
Laird, P.W.2
-
2
-
-
84860821444
-
Molecular subgroups of medulloblastoma: The current consensus
-
Taylor, M. D. et al. Molecular subgroups of medulloblastoma: the current consensus. Acta Neuropathol. 123, 465-472 (2012).
-
(2012)
Acta Neuropathol
, vol.123
, pp. 465-472
-
-
Taylor, M.D.1
-
3
-
-
84864419974
-
Dissecting the genomic complexity underlying medulloblastoma
-
Jones, D. T. W. et al. Dissecting the genomic complexity underlying medulloblastoma. Nature 488, 100-105 (2012).
-
(2012)
Nature
, vol.488
, pp. 100-105
-
-
Jones, D.T.W.1
-
4
-
-
84870215426
-
Medulloblastomics: The end of the beginning
-
Northcott, P. A. et al. Medulloblastomics: the end of the beginning. Nature Rev. Cancer 12, 818-834 (2012).
-
(2012)
Nature Rev. Cancer
, vol.12
, pp. 818-834
-
-
Northcott, P.A.1
-
5
-
-
84878588603
-
Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays
-
Hovestadt, V. et al. Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays. Acta Neuropathol. 125, 913-916 (2013).
-
(2013)
Acta Neuropathol
, vol.125
, pp. 913-916
-
-
Hovestadt, V.1
-
6
-
-
84879663784
-
Global epigenomic reconfiguration during mammalian brain development
-
Lister, R. et al. Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905 (2013).
-
(2013)
Science
, vol.341
, pp. 1237905
-
-
Lister, R.1
-
7
-
-
34547411860
-
Epigenome scans and cancer genome sequencing converge on WNK2, a kinase-independent suppressor of cell growth
-
Hong, C. et al. Epigenome scans and cancer genome sequencing converge on WNK2, a kinase-independent suppressor of cell growth. Proc. Natl Acad. Sci. USA 104, 10974-10979 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 10974-10979
-
-
Hong, C.1
-
8
-
-
25844509347
-
Canonical WNT signaling promotes osteogenesis by directly stimulating Runx2 gene expression
-
Gaur, T. et al. Canonical WNT signaling promotes osteogenesis by directly stimulating Runx2 gene expression. J. Biol. Chem. 280, 33132-33140 (2005).
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 33132-33140
-
-
Gaur, T.1
-
9
-
-
70649095120
-
Differential methylation of tissue-And cancer-specific CpG island shores distinguishes humaninduced pluripotent stemcells, embryonic stemcells and fibroblasts
-
Doi, A. et al. Differential methylation of tissue-And cancer-specific CpG island shores distinguishes humaninduced pluripotent stemcells, embryonic stemcells and fibroblasts. Nature Genet. 41, 1350-1353 (2009).
-
(2009)
Nature Genet
, vol.41
, pp. 1350-1353
-
-
Doi, A.1
-
10
-
-
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, 768-775 (2011).
-
(2011)
Nature Genet
, vol.43
, pp. 768-775
-
-
Hansen, K.D.1
-
11
-
-
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. Nature Genet. 41, 178-186 (2009).
-
(2009)
Nature Genet
, vol.41
, pp. 178-186
-
-
Irizarry, R.A.1
-
12
-
-
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
-
13
-
-
48449101742
-
Medulloblastoma can be initiated by deletion of Patched in lineage-restricted progenitors or stem cells
-
Yang, Z. J. et al. Medulloblastoma can be initiated by deletion of Patched in lineage-restricted progenitors or stem cells. Cancer Cell 14, 135-145 (2008).
-
(2008)
Cancer Cell
, vol.14
, pp. 135-145
-
-
Yang, Z.J.1
-
14
-
-
79954991010
-
Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome
-
Cho, Y. J. et al. Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome. J. Clin. Oncol. 29, 1424-1430 (2011).
-
(2011)
J. Clin. Oncol.
, vol.29
, pp. 1424-1430
-
-
Cho, Y.J.1
-
15
-
-
84875933577
-
Lin28: Primal regulator of growth andmetabolismin stem cells
-
Shyh-Chang, N.&Daley, G. Q. Lin28: primal regulator of growth andmetabolismin stem cells. Cell Stem Cell 12, 395-406 (2013).
-
(2013)
Cell Stem Cell
, vol.12
, pp. 395-406
-
-
Shyh-Chang, N.1
Daley, G.Q.2
-
16
-
-
84868210731
-
LIN28 Binduces neuroblastomaandenhances MYC Nlevels via let-7 suppression
-
Molenaar, J. J. et al. LIN28Binduces neuroblastomaandenhancesMYCNlevels via let-7 suppression. Nature Genet. 44, 1199-1206 (2012).
-
(2012)
Nature Genet
, vol.44
, pp. 1199-1206
-
-
Molenaar, J.J.1
-
17
-
-
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. Nature Genet. 44, 40-46 (2012).
-
(2012)
Nature Genet
, vol.44
, pp. 40-46
-
-
Berman, B.P.1
-
18
-
-
84856528270
-
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
-
Hon, G. C. et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 22, 246-258 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 246-258
-
-
Hon, G.C.1
-
19
-
-
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
-
20
-
-
59149083658
-
Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells
-
Wen, B.,Wu, H., Shinkai, Y., Irizarry, R. A. & Feinberg, A. P. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nature Genet. 41, 246-250 (2009).
-
(2009)
Nature Genet
, vol.41
, pp. 246-250
-
-
Wen, B.1
Wu, H.2
Shinkai, Y.3
Irizarry, R.A.4
Feinberg, A.P.5
-
21
-
-
84865248380
-
Chromatin organization is a major influence on regional mutation rates in human cancer cells
-
Schuster-Böckler, B. & Lehner, B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488, 504-507 (2012).
-
(2012)
Nature
, vol.488
, pp. 504-507
-
-
Schuster-Böckler, B.1
Lehner, B.2
-
22
-
-
78751693154
-
Replication timing-related and gene body-specific methylation of active human genes
-
Aran, D., Toperoff, G., Rosenberg, M. & Hellman, A. Replication timing-related and gene body-specific methylation of active human genes. Hum. Mol. Genet. 20, 670-680 (2011).
-
(2011)
Hum. Mol. Genet.
, vol.20
, pp. 670-680
-
-
Aran, D.1
Toperoff, G.2
Rosenberg, M.3
Hellman, A.4
-
23
-
-
84891372425
-
Large conserved domains of low DNA methylation maintained by Dnmt3a
-
Jeong, M. et al. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nature Genet. 46, 17-23 (2014).
-
(2014)
Nature Genet
, vol.46
, pp. 17-23
-
-
Jeong, M.1
-
24
-
-
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
-
25
-
-
34248358308
-
Hyperconserved CpG domains underlie Polycomb-binding sites
-
Tanay, A., O'Donnell, A. H., Damelin, M. & Bestor, T. H. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc. Natl Acad. Sci. USA 104, 5521-5526 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 5521-5526
-
-
Tanay, A.1
O'Donnell, A.H.2
Damelin, M.3
Bestor, T.H.4
-
26
-
-
84879917277
-
FoxG1 interacts with Bmi1 to regulate self-renewal and tumorigenicity ofmedulloblastomastemcells
-
Manoranjan, B. et al. FoxG1 interacts with Bmi1 to regulate self-renewal and tumorigenicity ofmedulloblastomastemcells. Stem Cells 31, 1266-1277 (2013).
-
(2013)
Stem Cells
, vol.31
, pp. 1266-1277
-
-
Manoranjan, B.1
-
27
-
-
33846569960
-
A stem cell-like chromatin pattern may predispose tumor suppressor genes toDNA hypermethylation and heritable silencing
-
Ohm, J. E. et al. A stem cell-like chromatin pattern may predispose tumor suppressor genes toDNA hypermethylation and heritable silencing. Nature Genet. 39, 237-242 (2007).
-
(2007)
Nature Genet
, vol.39
, pp. 237-242
-
-
Ohm, J.E.1
-
28
-
-
33846649587
-
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer
-
Schlesinger, Y. et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nature Genet. 39, 232-236 (2007).
-
(2007)
Nature Genet
, vol.39
, pp. 232-236
-
-
Schlesinger, Y.1
-
29
-
-
84861640022
-
OTX2 directly activates cell cycle genes and inhibits differentiation in medulloblastoma cells
-
Bunt, J. et al. OTX2 directly activates cell cycle genes and inhibits differentiation in medulloblastoma cells. Int. J. Cancer 131, E21-E32 (2012).
-
(2012)
Int. J. Cancer
, vol.131
-
-
Bunt, J.1
-
30
-
-
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
-
31
-
-
84871275799
-
HD-MB03 is a novel Group 3 medulloblastoma model demonstrating sensitivity to histone deacetylase inhibitor treatment
-
Milde, T. et al. HD-MB03 is a novel Group 3 medulloblastoma model demonstrating sensitivity to histone deacetylase inhibitor treatment. J. Neurooncol. 110, 335-348 (2012).
-
(2012)
J. Neurooncol.
, vol.110
, pp. 335-348
-
-
Milde, T.1
-
32
-
-
84870544677
-
Recurrentmutation of the ID3 gene in Burkitt lymphomaidentified by integrated genome, exome and transcriptome sequencing
-
Richter, J. et al. Recurrentmutation of the ID3 gene in Burkitt lymphomaidentified by integrated genome, exome and transcriptome sequencing. Nature Genet. 44, 1316-1320 (2012).
-
(2012)
Nature Genet
, vol.44
, pp. 1316-1320
-
-
Richter, J.1
-
33
-
-
79952264847
-
Hotspots ofaberrantepigenomic reprogramming inhumaninduced pluripotent stem cells
-
Lister, R. et al.Hotspots ofaberrantepigenomic reprogramming inhumaninduced pluripotent stem cells. Nature 471, 68-73 (2011).
-
(2011)
Nature
, vol.471
, pp. 68-73
-
-
Lister, R.1
-
34
-
-
84880983541
-
Recurrent somatic alterations ofFGFR1 andNTRK2 in pilocytic astrocytoma
-
Jones, D. T. W. et al. Recurrent somatic alterations ofFGFR1 andNTRK2 in pilocytic astrocytoma. Nature Genet. 45, 927-932 (2013).
-
(2013)
Nature Genet
, vol.45
, pp. 927-932
-
-
Jones, D.T.W.1
-
35
-
-
37349130959
-
Identification of micro RNA sandothersmall regulatory RNA susing cDNA library sequencing
-
Hafner, M. et al. Identification of micro RNA sandothersmall regulatory RNAs using cDNA library sequencing. Methods 44, 3-12 (2008).
-
(2008)
Methods
, vol.44
, pp. 3-12
-
-
Hafner, M.1
-
36
-
-
80053901555
-
Joint binding of OTX 2 and MY Cin promotor regions is associated with high gene expression in medulloblastoma
-
Bunt, J. et al. Joint binding of OTX 2 and MY Cin promotor regions is associated with high gene expression in medulloblastoma. PLoS ONE 6, e26058 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Bunt, J.1
-
37
-
-
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
-
38
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
39
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
-
40
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 28, 511-515 (2010).
-
(2010)
Nature Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
-
41
-
-
78651293534
-
MiRBase: Integrating microRNAannotation and deep-sequencing data
-
Kozomara, A.& Griffiths-Jones, S. miRBase: integrating microRNAannotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
42
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.4
-
43
-
-
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
-
45
-
-
84886834154
-
Identification of active regulatory regions from DNA methylation data
-
Burger, L., Gaidatzis, D., Schubeler, D. & Stadler, M. B. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Burger, L.1
Gaidatzis, D.2
Schubeler, D.3
Stadler, M.B.4
-
46
-
-
84872540994
-
DNA-binding specificities of human transcription factors
-
Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327-339 (2013).
-
(2013)
Cell
, vol.152
, pp. 327-339
-
-
Jolma, A.1
-
47
-
-
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
-
48
-
-
48249090873
-
Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivo
-
Li, H. et al. Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivo. Proc. Natl Acad. Sci. USA 105, 9397-9402 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 9397-9402
-
-
Li, H.1
|