-
2
-
-
33847065486
-
The epigenomics of cancer
-
Jones PA,Baylin SB: The epigenomics of cancer. Cell 128(4), 683-692 (2007).
-
(2007)
Cell
, vol.128
, Issue.4
, pp. 683-692
-
-
Jones Pabaylin, S.B.1
-
3
-
-
33947315736
-
Cancer epigenomics: DNA methylomes and histone-modification maps
-
DOI 10.1038/nrg2005, PII NRG2005
-
Esteller M: Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet. 8(4), 286-298 (2007). (Pubitemid 46439286)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.4
, pp. 286-298
-
-
Esteller, M.1
-
4
-
-
39149130361
-
Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming
-
DOI 10.1016/j.cell.2008.01.015, PII S0092867408001153
-
Jaenisch R,Young R: Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132(4), 567-582 (2008). (Pubitemid 351253686)
-
(2008)
Cell
, vol.132
, Issue.4
, pp. 567-582
-
-
Jaenisch, R.1
Young, R.2
-
6
-
-
33847047461
-
Epigenetics: A Landscape Takes Shape
-
DOI 10.1016/j.cell.2007.02.006, PII S0092867407001869
-
Goldberg AD, Allis CD, Bernstein E: Epigenetics: a landscape takes shape. Cell 128(4), 635-638 (2007). (Pubitemid 46273578)
-
(2007)
Cell
, vol.128
, Issue.4
, pp. 635-638
-
-
Goldberg, A.D.1
Allis, C.D.2
Bernstein, E.3
-
7
-
-
33847032960
-
The Mammalian Epigenome
-
DOI 10.1016/j.cell.2007.01.033, PII S0092867407001286
-
Bernstein BE, Meissner A, Lander ES: The mammalian epigenome. Cell 128(4), 669-681 (2007). (Pubitemid 46273573)
-
(2007)
Cell
, vol.128
, Issue.4
, pp. 669-681
-
-
Bernstein, B.E.1
Meissner, A.2
Lander, E.S.3
-
8
-
-
34249337761
-
Perceptions of epigenetics
-
DOI 10.1038/nature05913, PII NATURE05913
-
Bird A: Perceptions of epigenetics. Nature 447(7143), 396-398 (2007). (Pubitemid 46816744)
-
(2007)
Nature
, vol.447
, Issue.7143
, pp. 396-398
-
-
Bird, A.1
-
9
-
-
34249026300
-
High-Resolution Profiling of Histone Methylations in the Human Genome
-
DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
-
Barski A, Cuddapah S, Cui K et al.: High-resolution profiling of histone methylations in the human genome. Cell 129(4), 823-837 (2007). (Pubitemid 46802390)
-
(2007)
Cell
, vol.129
, Issue.4
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.-Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
10
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
DOI 10.1038/ng.154, PII NG154
-
Wang Z, Zang C, Rosenfeld JA et al.: Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40(7), 897-903 (2008). (Pubitemid 351913645)
-
(2008)
Nature Genetics
, vol.40
, Issue.7
, pp. 897-903
-
-
Wang, Z.1
Zang, C.2
Rosenfeld, J.A.3
Schones, D.E.4
Barski, A.5
Cuddapah, S.6
Cui, K.7
Roh, T.-Y.8
Peng, W.9
Zhang, M.Q.10
Zhao, K.11
-
11
-
-
35848961668
-
How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers
-
DOI 10.1038/nsmb1338, PII NSMB1338
-
Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ: How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14(11), 1025-1040 (2007). (Pubitemid 350060344)
-
(2007)
Nature Structural and Molecular Biology
, vol.14
, Issue.11
, pp. 1025-1040
-
-
Taverna, S.D.1
Li, H.2
Ruthenburg, A.J.3
Allis, C.D.4
Patel, D.J.5
-
12
-
-
0035169663
-
Methyl-CpG-binding proteins: Targeting specific gene repression
-
DOI 10.1046/j.1432-1327.2001.01869.x
-
Ballestar E,Wolffe AP: Methyl-CpG-binding proteins. Targeting specific gene repression. Eur. J. Biochem. 268(1), 1-6 (2001). (Pubitemid 32052241)
-
(2001)
European Journal of Biochemistry
, vol.268
, Issue.1
, pp. 1-6
-
-
Ballestar, E.1
Wolffe, A.P.2
-
13
-
-
41349089522
-
Gene regulation in the third dimension
-
DOI 10.1126/science.1152850
-
Dekker J: Gene regulation in the third dimension. Science 319(5871), 1793-1794 (2008). (Pubitemid 351451557)
-
(2008)
Science
, vol.319
, Issue.5871
, pp. 1793-1794
-
-
Dekker, J.1
-
14
-
-
77952242784
-
The transcriptional interactome: Gene expression in 3.D
-
Schoenfelder S, Clay I,Fraser P: The transcriptional interactome: gene expression in 3D. Curr. Opin. Genet. Dev. 20(2), 127-133 (2010).
-
(2010)
Curr. Opin. Genet. Dev.
, vol.20
, Issue.2
, pp. 127-133
-
-
Schoenfelder, S.1
Clay I.Fraser, P.2
-
15
-
-
41749091787
-
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
-
Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR: Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 6(3), e65 (2008).
-
(2008)
PloS. Biol.
, vol.6
, Issue.3
-
-
Shivaswamy, S.1
Bhinge, A.2
Zhao, Y.3
Jones, S.4
Hirst, M.5
Iyer, V.R.6
-
16
-
-
39749145198
-
Dynamic Regulation of Nucleosome Positioning in the Human Genome
-
DOI 10.1016/j.cell.2008.02.022, PII S0092867408002705
-
Schones DE, Cui K, Cuddapah S et al.: Dynamic regulation of nucleosome positioning in the human genome. Cell 132(5), 887-898 (2008). (Pubitemid 351312809)
-
(2008)
Cell
, vol.132
, Issue.5
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.-Y.4
Barski, A.5
Wang, Z.6
Wei, G.7
Zhao, K.8
-
17
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
-
DOI 10.1101/gr.078261.108
-
Mavrich TN, Ioshikhes IP, Venters BJ et al.: A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 18(7), 1073-1083 (2008). (Pubitemid 351931158)
-
(2008)
Genome Research
, vol.18
, Issue.7
, pp. 1073-1083
-
-
Mavrich, T.N.1
Ioshikhes, I.P.2
Venters, B.J.3
Jiang, C.4
Tomsho, L.P.5
Qi, J.6
Schuster, S.C.7
Albert, I.8
Pugh, B.F.9
-
18
-
-
22744432660
-
Molecular biology: Genome-scale identification of nucleosome positions in S. cerevisiae
-
DOI 10.1126/science.1112178
-
Yuan GC, Liu YJ, Dion MF et al.: Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309(5734), 626-630 (2005). (Pubitemid 41033649)
-
(2005)
Science
, vol.309
, Issue.5734
, pp. 626-630
-
-
Yuan, G.-C.1
Liu, Y.-J.2
Dion, M.F.3
Slack, M.D.4
Wu, L.F.5
Altschuler, S.J.6
Rando, O.J.7
-
19
-
-
33846862405
-
High-throughput mapping of the chromatin structure of human promoters
-
DOI 10.1038/nbt1279, PII NBT1279
-
Ozsolak F, Song JS, Liu XS, Fisher DE: High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol. 25(2), 244-248 (2007). (Pubitemid 46227125)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.2
, pp. 244-248
-
-
Ozsolak, F.1
Song, J.S.2
Liu, X.S.3
Fisher, D.E.4
-
20
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
DOI 10.1038/ng2117, PII NG2117
-
Lee W, Tillo D, Bray N et al.: A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet. 39(10), 1235-1244 (2007). (Pubitemid 47482684)
-
(2007)
Nature Genetics
, vol.39
, Issue.10
, pp. 1235-1244
-
-
Lee, W.1
Tillo, D.2
Bray, N.3
Morse, R.H.4
Davis, R.W.5
Hughes, T.R.6
Nislow, C.7
-
21
-
-
58449116917
-
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
-
Sasaki S, Mello CC, Shimada A et al.: Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323(5912), 401-404 (2009).
-
(2009)
Science
, vol.323
, Issue.5912
, pp. 401-404
-
-
Sasaki, S.1
Mello, C.C.2
Shimada, A.3
-
22
-
-
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 458(7236), 362-366 (2009).
-
(2009)
Nature
, vol.458
, Issue.7236
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
-
23
-
-
46449103738
-
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
-
DOI 10.1101/gr.076463.108
-
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. 18(7), 1051-1063 (2008). (Pubitemid 351931156)
-
(2008)
Genome Research
, vol.18
, Issue.7
, pp. 1051-1063
-
-
Valouev, A.1
Ichikawa, J.2
Tonthat, T.3
Stuart, J.4
Ranade, S.5
Peckham, H.6
Zeng, K.7
Malek, J.A.8
Costa, G.9
McKernan, K.10
Sidow, A.11
Fire, A.12
Johnson, S.M.13
-
24
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
DOI 10.1038/nature06008, PII NATURE06008
-
Mikkelsen TS, Ku M, Jaffe DB et al.: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153), 553-560 (2007). (Pubitemid 47206934)
-
(2007)
Nature
, vol.448
, Issue.7153
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.-K.9
Koche, R.P.10
Lee, W.11
Mendenhall, E.12
O'Donovan, A.13
Presser, A.14
Russ, C.15
Xie, X.16
Meissner, A.17
Wernig, M.18
Jaenisch, R.19
Nusbaum, C.20
Lander, E.S.21
Bernstein, B.E.22
more..
-
25
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein BE, Mikkelsen TS, Xie X et al.: A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125(2), 315-326 (2006).
-
(2006)
Cell
, vol.125
, Issue.2
, pp. 315-326
-
-
Bernstein, B.E.1
Mikkelsen, T.S.2
Xie, X.3
-
26
-
-
34250307630
-
The landscape of histone modifications across 1% of the human genome in five human cell lines
-
DOI 10.1101/gr.5704207
-
Koch CM, Andrews RM, Flicek P et al.: The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res. 17(6), 691-707 (2007). (Pubitemid 46919707)
-
(2007)
Genome Research
, vol.17
, Issue.6
, pp. 691-707
-
-
Koch, C.M.1
Andrews, R.M.2
Flicek, P.3
Dillon, S.C.4
Karaoz, U.5
Clelland, G.K.6
Wilcox, S.7
Beare, D.M.8
Fowler, J.C.9
Couttet, P.10
James, K.D.11
Lefebvre, G.C.12
Bruce, A.W.13
Dovey, O.M.14
Ellis, P.D.15
Dhami, P.16
Langford, C.F.17
Weng, Z.18
Birney, E.19
Carter, N.P.20
Vetrie, D.21
Dunham, I.22
more..
-
27
-
-
0037172993
-
Methylation of histone H3 Lys 4 in coding regions of active genes
-
DOI 10.1073/pnas.082249499
-
Bernstein BE, Humphrey EL, Erlich RL et al.: Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl Acad. Sci. USA 99(13), 8695-8700 (2002). (Pubitemid 34693622)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.13
, pp. 8695-8700
-
-
Bernstein, B.E.1
Humphrey, E.L.2
Erlich, R.L.3
Schneider, R.4
Bouman, P.5
Liu, J.S.6
Kouzarides, T.7
Schreiber, S.L.8
-
28
-
-
0037123767
-
Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases
-
DOI 10.1016/S0092-8674(02)00746-8
-
Robyr D, Suka Y, Xenarios I et al.: Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109(4), 437-446 (2002). (Pubitemid 34564471)
-
(2002)
Cell
, vol.109
, Issue.4
, pp. 437-446
-
-
Robyr, D.1
Suka, Y.2
Xenarios, I.3
Kurdistani, S.K.4
Wang, A.5
Suka, N.6
Grunstein, M.7
-
29
-
-
2642570305
-
The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
-
DOI 10.1101/gad.1198204
-
Schubeler D, Macalpine DM, Scalzo D et al.: The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18(11), 1263-1271 (2004). (Pubitemid 38720594)
-
(2004)
Genes and Development
, vol.18
, Issue.11
, pp. 1263-1271
-
-
Schubeler, D.1
MacAlpine, D.M.2
Scalzo, D.3
Wirbelauer, C.4
Kooperberg, C.5
Van Leeuwen, F.6
Gottschling, D.E.7
O'Neill, L.P.8
Turner, B.M.9
Delrow, J.10
Bell, S.P.11
Groudine, M.12
-
30
-
-
26444508841
-
Single-nucleosome mapping of histone modifications in S cerevisiae
-
Liu CL, Kaplan T, Kim M et al.: Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 3(10), e328 (2005).
-
(2005)
Plos. Biol.
, vol.3
, Issue.10
-
-
Liu, C.L.1
Kaplan, T.2
Kim, M.3
-
31
-
-
23944462969
-
Genome-wide map of nucleosome acetylation and methylation in yeast
-
DOI 10.1016/j.cell.2005.06.026, PII S0092867405006458
-
Pokholok DK, Harbison CT, Levine S et al.: Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122(4), 517-527 (2005). (Pubitemid 41191151)
-
(2005)
Cell
, vol.122
, Issue.4
, pp. 517-527
-
-
Pokholok, D.K.1
Harbison, C.T.2
Levine, S.3
Cole, M.4
Hannett, N.M.5
Tong, I.L.6
Bell, G.W.7
Walker, K.8
Rolfe, P.A.9
Herbolsheimer, E.10
Zeitlinger, J.11
Lewitter, F.12
Gifford, D.K.13
Young, R.A.14
-
32
-
-
19944430797
-
Genomic maps and comparative analysis of histone modifications in human and mouse
-
DOI 10.1016/j.cell.2005.01.001, PII S0092867405000395
-
Bernstein BE, Kamal M, Lindblad-Toh K et al.: Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120(2), 169-181 (2005). (Pubitemid 40174761)
-
(2005)
Cell
, vol.120
, Issue.2
, pp. 169-181
-
-
Bernstein, B.E.1
Kamal, M.2
Lindblad-Toh, K.3
Bekiranov, S.4
Bailey, D.K.5
Huebert, D.J.6
McMahon, S.7
Karlsson, E.K.8
Kulbokas III, E.J.9
Gingeras, T.R.10
Schreiber, S.L.11
Lander, E.S.12
-
33
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
DOI 10.1038/ng1966, PII NG1966
-
Heintzman ND, Stuart RK, Hon G et al.: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39(3), 311-318 (2007). (Pubitemid 46328487)
-
(2007)
Nature Genetics
, vol.39
, Issue.3
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
Hawkins, R.D.6
Barrera, L.O.7
Van Calcar, S.8
Qu, C.9
Ching, K.A.10
Wang, W.11
Weng, Z.12
Green, R.D.13
Crawford, G.E.14
Ren, B.15
-
34
-
-
3543008920
-
High-resolution genome-wide mapping of histone modifications
-
DOI 10.1038/nbt990
-
Roh TY, Ngau WC, Cui K, Landsman D, Zhao K: High-resolution genome-wide mapping of histone modifications. Nat. Biotechnol. 22(8), 1013-1016 (2004). (Pubitemid 39014479)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.8
, pp. 1013-1016
-
-
Roh, T.-Y.1
Ngau, W.C.2
Cui, K.3
Landsman, D.4
Zhao, K.5
-
35
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman M, Amit I, Garber M et al.: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235), 223-227 (2009).
-
(2009)
Nature
, vol.458
, Issue.7235
, pp. 223-227
-
-
Guttman, M.1
Amit, I.2
Garber, M.3
-
36
-
-
48949099045
-
Inferring causal relationships among different histone modifications and gene expression
-
Yu H, Zhu S, Zhou B, Xue H,Han JD: Inferring causal relationships among different histone modifications and gene expression. Genome Res. 18(8), 1314-1324 (2008).
-
(2008)
Genome. Res.
, vol.18
, Issue.8
, pp. 1314-1324
-
-
Yu, H.1
Zhu, S.2
Zhou, B.3
Xue, H.4
Han, J.D.5
-
37
-
-
77649246145
-
Histone modification levels are predictive for gene expression
-
USA
-
Karlic R, Chung HR, Lasserre J, Vlahovicek K, Vingron M: Histone modification levels are predictive for gene expression. Proc. Natl Acad. Sci. USA 107(7), 2926-2931 (2010).
-
(2010)
Proc. Natl. Acad. Sci.
, vol.107
, Issue.7
, pp. 2926-2931
-
-
Karlic, R.1
Chung, H.R.2
Lasserre, J.3
Vlahovicek, K.4
Vingron, M.5
-
39
-
-
77950262538
-
Nucleosome dynamics define transcriptional enhancers
-
He HH, Meyer CA, Shin H et al.: Nucleosome dynamics define transcriptional enhancers. Nat. Genet. 42(4), 343-347 (2010).
-
(2010)
Nat. Genet.
, vol.42
, Issue.4
, pp. 343-347
-
-
He, H.H.1
Meyer, C.A.2
Shin, H.3
-
40
-
-
58049191558
-
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation
-
Cui K, Zang C, Roh TY et al.: Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4(1), 80-93 (2009).
-
(2009)
Cell Stem. Cell.
, vol.4
, Issue.1
, pp. 80-93
-
-
Cui, K.1
Zang, C.2
Roh, T.Y.3
-
41
-
-
34047111213
-
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
-
DOI 10.1038/nature05632, PII NATURE05632
-
Albert I, Mavrich TN, Tomsho LP et al.: Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446(7135), 572-576 (2007). (Pubitemid 46514724)
-
(2007)
Nature
, vol.446
, Issue.7135
, pp. 572-576
-
-
Albert, I.1
Mavrich, T.N.2
Tomsho, L.P.3
Qi, J.4
Zanton, S.J.5
Schuster, S.C.6
Pugh, B.F.7
-
42
-
-
43749099875
-
Nucleosome organization in the Drosophila genome
-
DOI 10.1038/nature06929, PII NATURE06929
-
Mavrich TN, Jiang C, Ioshikhes IP et al.: Nucleosome organization in the Drosophila genome. Nature 453(7193), 358-362 (2008). (Pubitemid 351693129)
-
(2008)
Nature
, vol.453
, Issue.7193
, pp. 358-362
-
-
Mavrich, T.N.1
Jiang, C.2
Ioshikhes, I.P.3
Li, X.4
Venters, B.J.5
Zanton, S.J.6
Tomsho, L.P.7
Qi, J.8
Glaser, R.L.9
Schuster, S.C.10
Gilmour, D.S.11
Albert, I.12
Pugh, B.F.13
-
43
-
-
57449095143
-
Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq
-
Zhang Y, Shin H, Song JS, Lei Y,Liu XS: Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 9, 537 (2008).
-
(2008)
BMC Genomics
, vol.9
, pp. 537
-
-
Zhang, Y.1
Shin, H.2
Song, J.S.3
Lei, Y.4
Liu, X.S.5
-
44
-
-
36248989105
-
ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters
-
DOI 10.1016/j.cell.2007.11.017, PII S0092867407014699
-
Schmid CD, Bucher P: ChIP-Seq data reveal nucleosome architecture of human promoters. Cell 131(5), 831-832; author reply 832-833 (2007). (Pubitemid 350138097)
-
(2007)
Cell
, vol.131
, Issue.5
, pp. 831-832
-
-
Schmid, C.D.1
Bucher, P.2
-
45
-
-
77249137168
-
Principles and challenges of genome-wide DNA methylation analysis
-
Laird PW: Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet. 11(3), 191-203 (2010).
-
(2010)
Nat. Rev. Genet.
, vol.11
, Issue.3
, pp. 191-203
-
-
Laird, P.W.1
-
46
-
-
65549107163
-
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
-
Brunner AL, Johnson DS, Kim SW et al.: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19(6), 1044-1056 (2009).
-
(2009)
Genome. Res.
, vol.19
, Issue.6
, pp. 1044-1056
-
-
Brunner, A.L.1
Johnson, D.S.2
Kim, S.W.3
-
47
-
-
64349091471
-
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
-
Ball MP, Li JB, Gao Y et al.: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27(4), 361-368 (2009).
-
(2009)
Nat. Biotechnol.
, vol.27
, Issue.4
, pp. 361-368
-
-
Ball, M.P.1
Li, J.B.2
Gao, Y.3
-
48
-
-
67649132826
-
An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines
-
Li J, Gao F, Li N et al.: An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics 10, 223 (2009).
-
(2009)
BMC Genomics
, vol.10
, pp. 223
-
-
Li, J.1
Gao, F.2
Li, N.3
-
49
-
-
39149133183
-
Methyl-DNA immunoprecipitation MeDIP: Hunting down the DNA methylome
-
39 passim
-
Jacinto FV, Ballestar E, Esteller M: Methyl- DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44(1), 35, 37, 39 passim (2008).
-
(2008)
Biotechniques
, vol.44
, Issue.1
, pp. 35-37
-
-
Jacinto, F.V.1
Ballestar, E.2
Esteller, M.3
-
50
-
-
38649126918
-
Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation
-
DOI 10.1016/j.stem.2007.12.011, PII S193459090700327X
-
Fouse SD, Shen Y, Pellegrini M et al.: Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/ Nanog, PcG complex, and histone H3 K4/ K27 trimethylation. Cell Stem Cell 2(2), 160-169 (2008). (Pubitemid 351168712)
-
(2008)
Cell Stem Cell
, vol.2
, Issue.2
, pp. 160-169
-
-
Fouse, S.D.1
Shen, Y.2
Pellegrini, M.3
Cole, S.4
Meissner, A.5
Van Neste, L.6
Jaenisch, R.7
Fan, G.8
-
51
-
-
46949098742
-
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
-
DOI 10.1038/nbt1414, PII NBT1414
-
Down TA, Rakyan VK, Turner DJ et al.: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26(7), 779-785 (2008). (Pubitemid 351961453)
-
(2008)
Nature Biotechnology
, vol.26
, Issue.7
, pp. 779-785
-
-
Down, T.A.1
Rakyan, V.K.2
Turner, D.J.3
Flicek, P.4
Li, H.5
Kulesha, E.6
Graf, S.7
Johnson, N.8
Herrero, J.9
Tomazou, E.M.10
Thorne, N.P.11
Backdahl, L.12
Herberth, M.13
Howe, K.L.14
Jackson, D.K.15
Miretti, M.M.16
Marioni, J.C.17
Birney, E.18
Hubbard, T.J.P.19
Durbin, R.20
Tavare, S.21
Beck, S.22
more..
-
52
-
-
78649291183
-
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
-
Chavez L, Jozefczuk J, Grimm C et al.: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res. 20(10), 1441-1450 (2010).
-
(2010)
Genome Res.
, vol.20
, Issue.10
, pp. 1441-1450
-
-
Chavez, L.1
Jozefczuk, J.2
Grimm, C.3
-
53
-
-
77957174102
-
Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated
-
Choy MK, Movassagh M, Goh HG, Bennett MR, Down TA, Foo RS: Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated. BMC Genomics 11, 519 (2010).
-
(2010)
BMC Genomics.
, vol.11
, pp. 519
-
-
Choy, M.K.1
Movassagh, M.2
Goh, H.G.3
Bennett, M.R.4
Down, T.A.5
Foo, R.S.6
-
54
-
-
77950409567
-
Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing
-
Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G: Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics 11, 137 (2010).
-
(2010)
BMC Genomics.
, vol.11
, pp. 137
-
-
Ruike, Y.1
Imanaka, Y.2
Sato, F.3
Shimizu, K.4
Tsujimoto, G.5
-
55
-
-
78049419464
-
Orphan cpg islands identify numerous conserved promoters in the mammalian genome
-
Illingworth RS, Gruenewald-Schneider U, Webb S et al.: Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 6(9), e1001134 (2010).
-
(2010)
Plos. Genet.
, vol.6
, Issue.9
-
-
Illingworth, R.S.1
Gruenewald-Schneider, U.2
Webb, S.3
-
56
-
-
40749109894
-
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
-
DOI 10.1038/nature06745, PII NATURE06745
-
Cokus SJ, Feng S, Zhang X et al.: Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452(7184), 215-219 (2008). (Pubitemid 351380251)
-
(2008)
Nature
, vol.452
, Issue.7184
, pp. 215-219
-
-
Cokus, S.J.1
Feng, S.2
Zhang, X.3
Chen, Z.4
Merriman, B.5
Haudenschild, C.D.6
Pradhan, S.7
Nelson, S.F.8
Pellegrini, M.9
Jacobsen, S.E.10
-
57
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in arabidopsis
-
Lister R, O'Malley RC, Tonti-Filippini J et al.: Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3), 523-536 (2008).
-
(2008)
Cell
, vol.133
, Issue.3
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
-
58
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister R, Pelizzola M, Dowen RH et al.: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271), 315-322 (2009).
-
(2009)
Nature
, vol.462
, Issue.7271
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
-
59
-
-
77952123054
-
Single base-resolution methylome of the silkworm reveals a sparse epigenomic map
-
Xiang H, Zhu J, Chen Q et al.: Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat. Biotechnol. 28(5), 516-520 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, Issue.5
, pp. 516-520
-
-
Xiang, H.1
Zhu, J.2
Chen, Q.3
-
60
-
-
77249148019
-
Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency
-
Popp C, Dean W, Feng S et al.: Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463(7284), 1101-1105 (2010).
-
(2010)
Nature
, vol.463
, Issue.7284
, pp. 1101-1105
-
-
Popp, C.1
Dean, W.2
Feng, S.3
-
61
-
-
27144500218
-
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
-
DOI 10.1093/nar/gki901
-
Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R: Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33(18), 5868-5877 (2005). (Pubitemid 41742606)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.18
, pp. 5868-5877
-
-
Meissner, A.1
Gnirke, A.2
Bell, G.W.3
Ramsahoye, B.4
Lander, E.S.5
Jaenisch, R.6
-
62
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner A, Mikkelsen TS, Gu H et al.: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454(7205), 766-770 (2008).
-
(2008)
Nature
, vol.454
, Issue.7205
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
-
63
-
-
77952967431
-
Direct detection of DNA methylation during single-molecule real-time sequencing
-
Flusberg BA, Webster DR, Lee JH et al.: Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7(6), 461-465 (2010).
-
(2010)
Nat. Methods
, vol.7
, Issue.6
, pp. 461-465
-
-
Flusberg, B.A.1
Webster, D.R.2
Lee, J.H.3
-
64
-
-
64449088698
-
Continuous base identification for single-molecule nanopore DNA sequencing
-
Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H: Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 4(4), 265-270 (2009).
-
(2009)
Nat. Nanotechnol.
, vol.4
, Issue.4
, pp. 265-270
-
-
Clarke, J.1
Wu, H.C.2
Jayasinghe, L.3
Patel, A.4
Reid, S.5
Bayley, H.6
-
65
-
-
77955433253
-
Whole genome DNA methylation analysis based on high throughput sequencing technology
-
Epub ahead of print
-
Li N, Ye M, Li Y et al.: Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods (2010) (Epub ahead of print).
-
(2010)
Methods
-
-
Li, N.1
Ye, M.2
Li, Y.3
-
66
-
-
77955446294
-
Protocol matters: Which methylome are you actually studying
-
Robinson MD, Statham AL, Speed TP, Clark SJ: Protocol matters: which methylome are you actually studying? Epigenomics 2(4), 587-598 (2010).
-
(2010)
Epigenomics
, vol.2
, Issue.4
, pp. 587-598
-
-
Robinson, M.D.1
Statham, A.L.2
Speed, T.P.3
Clark, S.J.4
-
67
-
-
77957932941
-
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
-
Harris RA, Wang T, Coarfa C et al.: Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol. 28(10), 1097-1105 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, Issue.10
, pp. 1097-1105
-
-
Harris, R.A.1
Wang, T.2
Coarfa, C.3
-
68
-
-
77957937011
-
Quantitative comparison of genome-wide DNA methylation mapping technologies
-
Bock C, Tomazou EM, Brinkman AB et al.: Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol. 28(10), 1106-1114 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, Issue.10
, pp. 1106-1114
-
-
Bock, C.1
Tomazou, E.M.2
Brinkman, A.B.3
-
69
-
-
77449127799
-
MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
-
Serre D, Lee BH, Ting AH: MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 38(2), 391-399 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, Issue.2
, pp. 391-399
-
-
Serre, D.1
Lee, B.H.2
Ting, A.H.3
-
70
-
-
77957951913
-
Whole-genome DNA methylation profiling using MethylCap-seq
-
Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG: Whole-genome DNA methylation profiling using MethylCap-seq. Methods 52(3), 232-236 (2010).
-
(2010)
Methods
, vol.52
, Issue.3
, pp. 232-236
-
-
Brinkman, A.B.1
Simmer, F.2
Ma, K.3
Kaan, A.4
Zhu, J.5
Stunnenberg, H.G.6
-
71
-
-
77954504873
-
Conserved role of intragenic DNA methylation in regulating alternative promoters
-
Maunakea AK, Nagarajan RP, Bilenky M et al.: Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466(7303), 253-257 (2010).
-
(2010)
Nature
, vol.466
, Issue.7303
, pp. 253-257
-
-
Maunakea, A.K.1
Nagarajan, R.P.2
Bilenky, M.3
-
72
-
-
84856306090
-
Genome-wide DNA methylation profiling using Infinium assay
-
Bibikova M, Le J, Barnes B et al.: Genome-wide DNA methylation profiling using Infinium assay. Epigenomics 1(1), 177-200 (2009).
-
(2009)
Epigenomics
, vol.1
, Issue.1
, pp. 177-200
-
-
Bibikova, M.1
Le, J.2
Barnes, B.3
-
73
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E, Van Berkum NL, Williams L et al.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289-293 (2009).
-
(2009)
Science
, vol.326
, Issue.5950
, pp. 289-293
-
-
Lieberman-Aiden, E.1
Van Berkum, N.L.2
Williams, L.3
-
74
-
-
70449103609
-
An oestrogen-receptor-alpha-bound human chromatin interactome
-
Fullwood MJ, Liu MH, Pan YF et al.: An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462(7269), 58-64 (2009).
-
(2009)
Nature
, vol.462
, Issue.7269
, pp. 58-64
-
-
Fullwood, M.J.1
Liu, M.H.2
Pan, Y.F.3
-
75
-
-
0037083376
-
Capturing chromosome conformation
-
DOI 10.1126/science.1067799
-
Dekker J, Rippe K, Dekker M,Kleckner N: Capturing chromosome conformation. Science 295(5558), 1306-1311 (2002). (Pubitemid 34157624)
-
(2002)
Science
, vol.295
, Issue.5558
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
76
-
-
78650458168
-
Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulatio
-
Tanizawa H, Iwasaki O, Tanaka A et al.: Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res. 38(22), 8164-8177 (2010).
-
(2010)
Nucleic Acids. Res.
, vol.38
, Issue.22
, pp. 8164-8177
-
-
Tanizawa, H.1
Iwasaki, O.2
Tanaka, A.3
-
77
-
-
77952744854
-
A three-dimensional model of the yeast genome
-
Duan Z, Andronescu M, Schutz K et al.: A three-dimensional model of the yeast genome. Nature 465(7296), 363-367 (2010).
-
(2010)
Nature
, vol.465
, Issue.7296
, pp. 363-367
-
-
Duan, Z.1
Andronescu, M.2
Schutz, K.3
-
78
-
-
77949497797
-
BRAT: Bisulfite-treated reads analysis tool
-
Harris EY, Ponts N, Levchuk A, Roch KL, Lonardi S: BRAT: bisulfite-treated reads analysis tool. Bioinformatics 26(4), 572-573 (2010).
-
(2010)
Bioinformatics
, vol.26
, Issue.4
, pp. 572-573
-
-
Harris, E.Y.1
Ponts, N.2
Levchuk, A.3
Roch, K.L.4
Lonardi, S.5
-
79
-
-
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
-
81
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
-
Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25(15), 1952-1958 (2009).
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1952-1958
-
-
Zang, C.1
Schones, D.E.2
Zeng, C.3
Cui, K.4
Zhao, K.5
Peng, W.6
-
82
-
-
53749092745
-
An HMM approach to genome-wide identification of differential histone modification sites from chip-seq data
-
Xu H, Wei CL, Lin F, Sung WK: An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 24(20), 2344-2349 (2008).
-
(2008)
Bioinformatics
, vol.24
, Issue.20
, pp. 2344-2349
-
-
Xu, H.1
Wei, C.L.2
Lin, F.3
Sung, W.K.4
-
83
-
-
55549118625
-
ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome
-
Hon G, Ren B, Wang W: ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput. Biol. 4(10), e1000201 (2008).
-
(2008)
Plos Comput. Biol.
, vol.4
, Issue.10
-
-
Hon, G.1
Ren, B.2
Wang, W.3
-
84
-
-
77449153454
-
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
-
Gu H, Bock C, Mikkelsen TS et al.: Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods 7(2), 133-136 (2010).
-
(2010)
Nat. Methods.
, vol.7
, Issue.2
, pp. 133-136
-
-
Gu, H.1
Bock, C.2
Mikkelsen, T.S.3
-
85
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10(3), R25 (2009).
-
(2009)
Genome Biol.
, vol.10
, Issue.3
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
86
-
-
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(14), 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
87
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5), 589-595 (2010).
-
(2010)
Bioinformatics
, vol.26
, Issue.5
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
88
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18(11), 1851-1858 (2008).
-
(2008)
Genome. Res.
, vol.18
, Issue.11
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
89
-
-
67650711615
-
SOAP2: An improved ultrafast tool for short read alignment
-
Li R, Yu C, Li Y et al.: SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15), 1966-1967 (2009).
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
-
90
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
Suppl
-
Pepke S, Wold B, Mortazavi A: Computation for ChIP-seq and RNA-seq studies. Nat. Methods 6(11 Suppl), S22-32 (2009).
-
(2009)
Nat. Methods.
, vol.6
, Issue.11
-
-
Pepke, S.1
Wold, B.2
Mortazavi, A.3
-
91
-
-
55749094855
-
An integrated software system for analyzing chip-chip and chip-seq data
-
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 26(11), 1293-1300 (2008).
-
(2008)
Nat. Biotechnol.
, vol.26
, Issue.11
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
Wong, W.H.6
-
92
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
DOI 10.1126/science.1141319
-
Johnson DS, Mortazavi A, Myers RM, Wold B: Genome-wide mapping of in vivo protein-DNA interactions. Science 316(5830), 1497-1502 (2007). (Pubitemid 46906620)
-
(2007)
Science
, vol.316
, Issue.5830
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
93
-
-
73049112582
-
Extracting transcription factor targets from chip-seq data
-
Tuteja G, White P, Schug J, Kaestner KH: Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res. 37(17), e113 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, Issue.17
-
-
Tuteja, G.1
White, P.2
Schug, J.3
Kaestner, K.H.4
-
94
-
-
53849146020
-
Model-based analysis of chip-seq MACS
-
Zhang Y, Liu T, Meyer Ca et al.: Model-based analysis of ChIP-Seq (MACS).Genome Biol. 9(9), R137 (2008).
-
(2008)
Genome. Biol.
, vol.9
, Issue.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
-
95
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky J, Euskirchen G, Auerbach RK et al.: PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 27(1), 66-75 (2009).
-
(2009)
Nat. Biotechnol.
, vol.27
, Issue.1
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
-
96
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
-
Valouev A, Johnson DS, Sundquist A et al.: Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5(9), 829-834 (2008).
-
(2008)
Nat. Methods
, vol.5
, Issue.9
, pp. 829-834
-
-
Valouev, A.1
Johnson, D.S.2
Sundquist, A.3
-
97
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from chip-seq data
-
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K: Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 36(16), 5221-5231 (2008).
-
(2008)
Nucleic Acids. Res.
, vol.36
, Issue.16
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
98
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko PV, Tolstorukov MY, Park PJ: Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 26(12), 1351-1359 (2008).
-
(2008)
Nat. Biotechnol.
, vol.26
, Issue.12
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
99
-
-
60849117520
-
Empirical methods for controlling false positives and estimating confidence in chip-seq peaks
-
Nix DA, Courdy SJ, Boucher KM: Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9, 523 (2008).
-
(2008)
BMC Bioinformatics.
, vol.9
, pp. 523
-
-
Nix, D.A.1
Courdy, S.J.2
Boucher, K.M.3
-
100
-
-
48249140621
-
FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
-
Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ: FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24(15), 1729-1730 (2008).
-
(2008)
Bioinformatics.
, vol.24
, Issue.15
, pp. 1729-1730
-
-
Fejes, A.P.1
Robertson, G.2
Bilenky, M.3
Varhol, R.4
Bainbridge, M.5
Jones, S.J.6
-
101
-
-
54949147307
-
F-Seq: A feature density estimator for high-throughput sequence tags
-
Boyle AP, Guinney J, Crawford GE, Furey TS: F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24(21), 2537-2538 (2008).
-
(2008)
Bioinformatics
, vol.24
, Issue.21
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
102
-
-
77955368935
-
Evaluation of algorithm performance in chip-seq peak detection
-
Wilbanks EG, Facciotti MT: Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One 5(7), e11471 (2010).
-
(2010)
Plos One
, vol.5
, Issue.7
-
-
Wilbanks, E.G.1
Facciotti, M.T.2
-
103
-
-
77952157350
-
Third-generation sequencing fireworks at marco Island
-
Munroe DJ, Harris Tjr: Third-generation sequencing fireworks at Marco Island. Nat. Biotech. 28(5), 426-428 (2010).
-
(2010)
Nat. Biotech.
, vol.28
, Issue.5
, pp. 426-428
-
-
Munroe, D.J.1
Harris Jr., T.2
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