-
1
-
-
84875196326
-
Determinants of nucleosome positioning
-
Struhl K, Segal E. Determinants of nucleosome positioning. Nat StructMol Biol 2013;20:267-73.
-
(2013)
Nat StructMol Biol
, vol.20
, pp. 267-273
-
-
Struhl, K.1
Segal, E.2
-
2
-
-
0021099544
-
Modulation of chromatin structure associated with derepression of the acid phosphatase gene of Saccharomyces cerevisiae
-
Bergman LW, Kramer RA. Modulation of chromatin structure associated with derepression of the acid phosphatase gene of Saccharomyces cerevisiae. J Biol Chem 1983;258: 7223-7.
-
(1983)
J Biol Chem
, vol.258
, pp. 7223-7227
-
-
Bergman, L.W.1
Kramer, R.A.2
-
3
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones DE, Cui K, Cuddapah S, et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008;132:887-98.
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
-
4
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
Valouev A, Johnson SM, Boyd SD, et al. Determinants of nucleosome organization in primary human cells. Nature 2011;474:516-20.
-
(2011)
Nature
, vol.474
, pp. 516-520
-
-
Valouev, A.1
Johnson, S.M.2
Boyd, S.D.3
-
5
-
-
43749099875
-
Nucleosome organization in the Drosophila genome
-
Mavrich TN, Jiang C, Ioshikhes IP, et al. Nucleosome organization in the Drosophila genome. Nature 2008;453: 358-62.
-
(2008)
Nature
, vol.453
, pp. 358-362
-
-
Mavrich, T.N.1
Jiang, C.2
Ioshikhes, I.P.3
-
6
-
-
46449103738
-
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
-
Valouev A, Ichikawa J, Tonthat T, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008;18: 1051-63.
-
(2008)
Genome Res
, vol.18
, pp. 1051-1063
-
-
Valouev, A.1
Ichikawa, J.2
Tonthat, T.3
-
7
-
-
80555156654
-
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
-
Tsankov A, Yanagisawa Y, Rhind N, et al. Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res 2011;21:1851-62.
-
(2011)
Genome Res
, vol.21
, pp. 1851-1862
-
-
Tsankov, A.1
Yanagisawa, Y.2
Rhind, N.3
-
8
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
Lee W, Tillo D, Bray N, et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 2007;39: 1235-44.
-
(2007)
Nat Genet
, vol.39
, pp. 1235-1244
-
-
Lee, W.1
Tillo, D.2
Bray, N.3
-
9
-
-
37249077649
-
Chromatin remodelling at promoters suppresses antisense transcription
-
Whitehouse I, Rando OJ, Delrow J, et al. Chromatin remodelling at promoters suppresses antisense transcription. Nature 2007;450:1031-5.
-
(2007)
Nature
, vol.450
, pp. 1031-1035
-
-
Whitehouse, I.1
Rando, O.J.2
Delrow, J.3
-
10
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
-
Mavrich TN, Ioshikhes IP, Venters BJ, et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 2008;18: 1073-83.
-
(2008)
Genome Res
, vol.18
, pp. 1073-1083
-
-
Mavrich, T.N.1
Ioshikhes, I.P.2
Venters, B.J.3
-
11
-
-
57149119464
-
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
-
Field Y, Kaplan N, Fondufe-Mittendorf Y, et al. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 2008;4: e1000216.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Field, Y.1
Kaplan, N.2
Fondufe-Mittendorf, Y.3
-
12
-
-
41749091787
-
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
-
Shivaswamy S, Bhinge A, Zhao Y, et al. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol 2008; 6:e65.
-
(2008)
PLoS Biol
, vol.6
-
-
Shivaswamy, S.1
Bhinge, A.2
Zhao, Y.3
-
13
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 2009;458:362-6.
-
(2009)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
-
14
-
-
75349098018
-
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
-
Jiang C, Pugh BF. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol 2009;10:R109.
-
(2009)
Genome Biol
, vol.10
, pp. R109
-
-
Jiang, C.1
Pugh, B.F.2
-
15
-
-
0029928550
-
Mapping nucleosome position at single base-pair resolution by using sitedirected hydroxyl radicals
-
Flaus A, Luger K, Tan S, et al. Mapping nucleosome position at single base-pair resolution by using sitedirected hydroxyl radicals. Proc Natl Acad Sci USA 1996;93: 1370-5.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 1370-1375
-
-
Flaus, A.1
Luger, K.2
Tan, S.3
-
16
-
-
0033031977
-
Base-pair resolution mapping of nucleosome positions using site-directed hydroxyl radicals
-
Flaus A, Richmond TJ. Base-pair resolution mapping of nucleosome positions using site-directed hydroxyl radicals. Methods Enzymol 1999;304:251-63.
-
(1999)
Methods Enzymol
, vol.304
, pp. 251-263
-
-
Flaus, A.1
Richmond, T.J.2
-
17
-
-
84862979650
-
A map of nucleosome positions in yeast at base-pair resolution
-
Brogaard K, Xi L, Wang JP, et al. A map of nucleosome positions in yeast at base-pair resolution. Nature 2012;486: 496-501.
-
(2012)
Nature
, vol.486
, pp. 496-501
-
-
Brogaard, K.1
Xi, L.2
Wang, J.P.3
-
18
-
-
84865500837
-
A chemical approach to mapping nucleosomes at base pair resolution in yeast
-
Brogaard KR, Xi L, Wang JP, et al. A chemical approach to mapping nucleosomes at base pair resolution in yeast. Methods Enzymol 2012;513:315-34.
-
(2012)
Methods Enzymol
, vol.513
, pp. 315-334
-
-
Brogaard, K.R.1
Xi, L.2
Wang, J.P.3
-
19
-
-
84890280929
-
Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning
-
Moyle-Heyrman G, Zaichuk T, Xi L, et al. Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. ProcNatlAcad SciUSA 2013;110: 20158-63.
-
(2013)
ProcNatlAcad SciUSA
, vol.110
, pp. 20158-20163
-
-
Moyle-Heyrman, G.1
Zaichuk, T.2
Xi, L.3
-
20
-
-
0023948705
-
Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene
-
Solomon MJ, Larsen PL, Varshavsky A. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 1988;53:937-47.
-
(1988)
Cell
, vol.53
, pp. 937-947
-
-
Solomon, M.J.1
Larsen, P.L.2
Varshavsky, A.3
-
21
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson DS, Mortazavi A, Myers RM, et al. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007; 316:1497-502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
-
22
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007;129:823-37.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
-
23
-
-
84869502241
-
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions
-
Furey TS. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 2012;13:840-52.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 840-852
-
-
Furey, T.S.1
-
24
-
-
84865511446
-
Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-seq
-
Wal M, Pugh BF. Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-seq. Methods Enzymol 2012;513:233-50.
-
(2012)
Methods Enzymol
, vol.513
, pp. 233-250
-
-
Wal, M.1
Pugh, B.F.2
-
25
-
-
84865777819
-
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
-
Landt SG, Marinov GK, Kundaje A, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. GenomeRes 2012;22:1813-31.
-
(2012)
GenomeRes
, vol.22
, pp. 1813-1831
-
-
Landt, S.G.1
Marinov, G.K.2
Kundaje, A.3
-
26
-
-
84897676120
-
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
-
Zhang J, Kobert K, Flouri T, et al. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 2014;30: 614-20.
-
(2014)
Bioinformatics
, vol.30
, pp. 614-620
-
-
Zhang, J.1
Kobert, K.2
Flouri, T.3
-
27
-
-
57449095143
-
Identifying positioned nucleosomes with epigenetic marks in human from ChIPseq
-
Zhang Y, Shin H, Song JS, et al. Identifying positioned nucleosomes with epigenetic marks in human from ChIPseq. BMCGenomics 2008;9:537.
-
(2008)
BMCGenomics
, vol.9
, pp. 537
-
-
Zhang, Y.1
Shin, H.2
Song, J.S.3
-
28
-
-
79960434317
-
nucleR: a package for nonparametric nucleosome positioning
-
Flores O, Orozco M. nucleR: a package for nonparametric nucleosome positioning. Bioinformatics 2011;27: 2149-50.
-
(2011)
Bioinformatics
, vol.27
, pp. 2149-2150
-
-
Flores, O.1
Orozco, M.2
-
29
-
-
74949110964
-
High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
-
Weiner A, Hughes A, Yassour M, et al. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res 2010;20:90-100.
-
(2010)
Genome Res
, vol.20
, pp. 90-100
-
-
Weiner, A.1
Hughes, A.2
Yassour, M.3
-
30
-
-
34047111213
-
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
-
Albert I, Mavrich TN, Tomsho LP, et al. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 2007;446:572-6.
-
(2007)
Nature
, vol.446
, pp. 572-576
-
-
Albert, I.1
Mavrich, T.N.2
Tomsho, L.P.3
-
31
-
-
77955410104
-
Nucleosome sequence preferences influence in vivo nucleosome organization
-
author reply 920-2
-
Kaplan N, Moore I, Fondufe-Mittendorf Y, et al. Nucleosome sequence preferences influence in vivo nucleosome organization. Nat Struct Mol Biol 2010;17:918-20; author reply 920-2.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 918-920
-
-
Kaplan, N.1
Moore, I.2
Fondufe-Mittendorf, Y.3
-
32
-
-
84863290812
-
Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data
-
Zhang X, Robertson G, Woo S, et al. Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data. PLoS One 2012;7:e32095.
-
(2012)
PLoS One
, vol.7
-
-
Zhang, X.1
Robertson, G.2
Woo, S.3
-
33
-
-
77349100416
-
New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome
-
Feng J, Dai X, Xiang Q, et al. New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome. BMC Genomics 2010;11:33.
-
(2010)
BMC Genomics
, vol.11
, pp. 33
-
-
Feng, J.1
Dai, X.2
Xiang, Q.3
-
34
-
-
83255187902
-
Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns
-
Tsui K, Dubuis S, Gebbia M, et al. Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns. Mol Cell Biol 2011;31: 4348-4355.
-
(2011)
Mol Cell Biol
, vol.31
, pp. 4348-4355
-
-
Tsui, K.1
Dubuis, S.2
Gebbia, M.3
-
35
-
-
83755224395
-
Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes
-
Cole HA, Howard BH, Clark DJ. Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes. Nucleic Acids Res 2011;39:9521-35.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 9521-9535
-
-
Cole, H.A.1
Howard, B.H.2
Clark, D.J.3
-
36
-
-
84874271270
-
NCBI GEO: archive for functional genomics data sets-update
-
Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res 2013;41:D991-5.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D991-D995
-
-
Barrett, T.1
Wilhite, S.E.2
Ledoux, P.3
-
37
-
-
77950962157
-
Conserved nucleosome positioning defines replication origins
-
Eaton ML, Galani K, Kang S, et al. Conserved nucleosome positioning defines replication origins. Genes Dev 2010;24: 748-53.
-
(2010)
Genes Dev
, vol.24
, pp. 748-753
-
-
Eaton, M.L.1
Galani, K.2
Kang, S.3
-
38
-
-
80053140931
-
A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization
-
Gkikopoulos T, Schofi P, Singh V, et al. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 2011;333:1758-60.
-
(2011)
Science
, vol.333
, pp. 1758-1760
-
-
Gkikopoulos, T.1
Schofi, P.2
Singh, V.3
-
39
-
-
84864059329
-
In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae
-
Gossett AJ, Lieb JD. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 2012;8:e1002771.
-
(2012)
PLoS Genet
, vol.8
-
-
Gossett, A.J.1
Lieb, J.D.2
-
40
-
-
77952245290
-
Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences
-
Tirosh I, Sigal N, Barkai N. Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol Syst Biol 2010;6:365.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 365
-
-
Tirosh, I.1
Sigal, N.2
Barkai, N.3
-
41
-
-
77955045449
-
The role of nucleosome positioning in the evolution of gene regulation
-
Tsankov AM, Thompson DA, Socha A, et al. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 2010;8:e1000414.
-
(2010)
PLoS Biol
, vol.8
-
-
Tsankov, A.M.1
Thompson, D.A.2
Socha, A.3
-
42
-
-
84874773048
-
A role for the nucleoporin Nup170p in chromatin structure and gene silencing
-
Van de Vosse DW, Wan Y, Lapetina DL, et al. A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell 2013;152:969-83.
-
(2013)
Cell
, vol.152
, pp. 969-983
-
-
Van de Vosse, D.W.1
Wan, Y.2
Lapetina, D.L.3
-
43
-
-
79955559703
-
Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation
-
Xi Y, Yao J, Chen R, et al. Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation. GenomeRes 2011;21:718-24.
-
(2011)
GenomeRes
, vol.21
, pp. 718-724
-
-
Xi, Y.1
Yao, J.2
Chen, R.3
-
44
-
-
84873395730
-
Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor
-
Chen K, Wilson MA, Hirsch C, et al. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. GenomeRes 2013;23:312-22.
-
(2013)
GenomeRes
, vol.23
, pp. 312-322
-
-
Chen, K.1
Wilson, M.A.2
Hirsch, C.3
-
45
-
-
84885187482
-
Gene promoters dictate histone occupancy within genes
-
Perales R, Erickson B, Zhang L, et al. Gene promoters dictate histone occupancy within genes. EMBOJ 2013;32:2645-56.
-
(2013)
EMBOJ
, vol.32
, pp. 2645-2656
-
-
Perales, R.1
Erickson, B.2
Zhang, L.3
-
46
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
-
47
-
-
0003833285
-
-
Philadelphia: Society for Industrial and Applied Mathematics
-
Daubechies I. Ten Lectures on Wavelets. Philadelphia: Society for Industrial and Applied Mathematics, 1992.
-
(1992)
Ten Lectures on Wavelets
-
-
Daubechies, I.1
|