-
1
-
-
84881166117
-
Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes
-
Narlikar, G. J., Sundaramoorthy, R. & Owen-Hughes, T. Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes. Cell 154, 490-503 (2013).
-
(2013)
Cell
, vol.154
, pp. 490-503
-
-
Narlikar, G.J.1
Sundaramoorthy, R.2
Owen-Hughes, T.3
-
3
-
-
70249121045
-
The logic of chromatin architecture and remodelling at promoters
-
Cairns, B. R. The logic of chromatin architecture and remodelling at promoters. Nature 461, 193-198 (2009).
-
(2009)
Nature
, vol.461
, pp. 193-198
-
-
Cairns, B.R.1
-
4
-
-
84862643713
-
Genome-wide nucleosome specificity and directionality of chromatin remodelers
-
Yen, K., Vinayachandran, V., Batta, K., Koerber, R. T. & Pugh, B. F. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell 149, 1461-1473 (2012).
-
(2012)
Cell
, vol.149
, pp. 1461-1473
-
-
Yen, K.1
Vinayachandran, V.2
Batta, K.3
Koerber, R.T.4
Pugh, B.F.5
-
5
-
-
0345698603
-
Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes
-
Simic, R. et al. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 22, 1846-1856 (2003).
-
(2003)
EMBO J
, vol.22
, pp. 1846-1856
-
-
Simic, R.1
-
6
-
-
84866114872
-
Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange
-
Smolle, M. et al. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nature Struct. Mol. Biol. 19, 884-892 (2012).
-
(2012)
Nature Struct. Mol. Biol.
, vol.19
, pp. 884-892
-
-
Smolle, M.1
-
7
-
-
84869089058
-
Genome-wide nucleosome positioning during embryonic stem cell development. Nature Struct
-
Teif, V. B. et al. Genome-wide nucleosome positioning during embryonic stem cell development. Nature Struct. Mol. Biol. 19, 1185-1192 (2012).
-
(2012)
Mol. Biol.
, vol.19
, pp. 1185-1192
-
-
Teif, V.B.1
-
8
-
-
84856962477
-
Enhancer decommissioning by LSD1 during embryonic stem cell differentiation
-
Whyte, W. A. et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482, 221-225 (2012).
-
(2012)
Nature
, vol.482
, pp. 221-225
-
-
Whyte, W.A.1
-
9
-
-
84870485829
-
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
-
Fenouil, R. et al. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res. 22, 2399-2408 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 2399-2408
-
-
Fenouil, R.1
-
10
-
-
79954562232
-
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
-
Min, I. M. et al. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev. 25, 742-754 (2011).
-
(2011)
Genes Dev
, vol.25
, pp. 742-754
-
-
Min, I.M.1
-
11
-
-
34250369627
-
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
-
Giresi, P. G., Kim, J., McDaniell, R. M., Iyer, V. R. & Lieb, J. D. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 17, 877-885 (2007).
-
(2007)
Genome Res
, vol.17
, pp. 877-885
-
-
Giresi, P.G.1
Kim, J.2
McDaniell, R.M.3
Iyer, V.R.4
Lieb, J.D.5
-
12
-
-
84930962818
-
A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters
-
Yildirim, O. et al. A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters. PLoS Genet. 10, e1004515 (2014).
-
(2014)
PLoS Genet
, vol.10
-
-
Yildirim, O.1
-
13
-
-
84899117608
-
Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells
-
Yukawa, M. et al. Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. PLoS ONE 9, e92689 (2014).
-
(2014)
PLoS ONE
, vol.9
-
-
Yukawa, M.1
-
14
-
-
84873581550
-
H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
-
Hu, G. et al. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell 12, 180-192 (2013).
-
(2013)
Cell Stem Cell
, vol.12
, pp. 180-192
-
-
Hu, G.1
-
15
-
-
84860351082
-
The transcriptional and epigenomic foundations of ground state pluripotency
-
Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590-604 (2012).
-
(2012)
Cell
, vol.149
, pp. 590-604
-
-
Marks, H.1
-
16
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931-21936 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 21931-21936
-
-
Creyghton, M.P.1
-
17
-
-
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
-
18
-
-
79961002967
-
EsBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function
-
Ho, L. et al. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nature Cell Biol. 13, 903-913 (2011).
-
(2011)
Nature Cell Biol.
, vol.13
, pp. 903-913
-
-
Ho, L.1
-
19
-
-
67649669255
-
A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
-
Ramirez-Carrozzi, V. R. et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138, 114-128 (2009).
-
(2009)
Cell
, vol.138
, pp. 114-128
-
-
Ramirez-Carrozzi, V.R.1
-
20
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods 10, 1213-1218 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
21
-
-
0037352031
-
A highly efficient recombineering-based method for generating conditional knockout mutations
-
Liu, P., Jenkins, N. A. & Copeland, N. G. A highly efficient recombineering-based method for generating conditional knockout mutations. Genome Res. 13, 476-484 (2003).
-
(2003)
Genome Res
, vol.13
, pp. 476-484
-
-
Liu, P.1
Jenkins, N.A.2
Copeland, N.G.3
-
22
-
-
0037313844
-
Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture
-
Ying, Q. L., Stavridis, M., Griffiths, D., Li, M. & Smith, A. Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nature Biotechnol. 21, 183-186 (2003).
-
(2003)
Nature Biotechnol
, vol.21
, pp. 183-186
-
-
Ying, Q.L.1
Stavridis, M.2
Griffiths, D.3
Li, M.4
Smith, A.5
-
23
-
-
0035227286
-
Manipulating mouse embryonic stem cells
-
Tessarollo, L. Manipulating mouse embryonic stem cells. Methods Mol. Biol. 158, 47-63 (2001).
-
(2001)
Methods Mol. Biol.
, vol.158
, pp. 47-63
-
-
Tessarollo, L.1
-
24
-
-
84891767394
-
RefSeq: An update on mammalian reference sequences
-
Pruitt, K. D. et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 42, D756-D763 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D756-D763
-
-
Pruitt, K.D.1
-
25
-
-
79953699973
-
SeqMINER: An integrated ChIP-seq data interpretation platform
-
Ye, T. et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 39, e35 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
, pp. e35
-
-
Ye, T.1
-
26
-
-
43349089437
-
GeneTrack-a genomic data processing and visualization framework
-
Albert, I., Wachi, S., Jiang, C. & Pugh, B. F. GeneTrack-a genomic data processing and visualization framework. Bioinformatics 24, 1305-1306 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 1305-1306
-
-
Albert, I.1
Wachi, S.2
Jiang, C.3
Pugh, B.F.4
-
27
-
-
84866127830
-
Identifying ChIP-seq enrichment using MACS
-
Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nature Protocols 7, 1728-1740 (2012).
-
(2012)
Nature Protocols
, vol.7
, pp. 1728-1740
-
-
Feng, J.1
Liu, T.2
Qin, B.3
Zhang, Y.4
Liu, X.S.5
-
28
-
-
79952012015
-
Loss-of-function studies in mouse embryonic stem cells using the pHYPER shRNA plasmid vector
-
Berlivet, S., Houlard, M. & Gérard, M. Loss-of-function studies in mouse embryonic stem cells using the pHYPER shRNA plasmid vector. Methods Mol. Biol. 650, 85-100 (2010).
-
(2010)
Methods Mol. Biol.
, vol.650
, pp. 85-100
-
-
Berlivet, S.1
Houlard, M.2
Gérard, M.3
-
29
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-628 (2008).
-
(2008)
Nature Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
30
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
31
-
-
67649524640
-
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
-
Giresi, P. G. & Lieb, J. D. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48, 233-239 (2009).
-
(2009)
Methods
, vol.48
, pp. 233-239
-
-
Giresi, P.G.1
Lieb, J.D.2
-
32
-
-
84855288772
-
Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells
-
Carrière, L. et al. Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. Nucleic Acids Res. 40, 270-283 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 270-283
-
-
Carrière, L.1
-
33
-
-
83255164884
-
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
-
Rhee, H. S. & Pugh, B. F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419 (2011).
-
(2011)
Cell
, vol.147
, pp. 1408-1419
-
-
Rhee, H.S.1
Pugh, B.F.2
-
34
-
-
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
-
35
-
-
65249173999
-
An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network
-
Ho, L. et al. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc. Natl Acad. Sci. USA 106, 5187-5191 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 5187-5191
-
-
Ho, L.1
-
36
-
-
77957139539
-
Mediator and cohesin connect gene expression and chromatin architecture
-
Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430-435 (2010).
-
(2010)
Nature
, vol.467
, pp. 430-435
-
-
Kagey, M.H.1
-
37
-
-
77951920690
-
C-Myc regulates transcriptional pause release
-
Rahl, P. B. et al. c-Myc regulates transcriptional pause release. Cell 141, 432-445 (2010).
-
(2010)
Cell
, vol.141
, pp. 432-445
-
-
Rahl, P.B.1
|