-
1
-
-
0037451302
-
Transcription factor YY1 functions as a PcG protein in vivo
-
Atchison L, Ghias A, Wilkinson F, Bonini N, Atchison ML. 2003. Transcription factor YY1 functions as a PcG protein in vivo. EMBO J 22:1347-1358.
-
(2003)
EMBO J
, vol.22
, pp. 1347-1358
-
-
Atchison, L.1
Ghias, A.2
Wilkinson, F.3
Bonini, N.4
Atchison, M.L.5
-
2
-
-
33646872978
-
Chromatin signatures of pluripotent cell lines
-
Azuara V, Perry P, Sauer S, Spivakov M, Jørgensen HF, John RM, Gouti M, Casanova M, Warnes G, Merkenschlager M, et al. 2006. Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8:532-538.
-
(2006)
Nat Cell Biol
, vol.8
, pp. 532-538
-
-
Azuara, V.1
Perry, P.2
Sauer, S.3
Spivakov, M.4
Jørgensen, H.F.5
John, R.M.6
Gouti, M.7
Casanova, M.8
Warnes, G.9
Merkenschlager, M.10
-
3
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, et al. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315-326.
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
Mikkelsen, T.S.2
Xie, X.3
Kamal, M.4
Huebert, D.J.5
Cuff, J.6
Fry, B.7
Meissner, A.8
Wernig, M.9
Plath, K.10
-
4
-
-
77957940722
-
The NIH roadmap epigenomics mapping consortium
-
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, et al. 2010. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 28:1045-1048.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1045-1048
-
-
Bernstein, B.E.1
Stamatoyannopoulos, J.A.2
Costello, J.F.3
Ren, B.4
Milosavljevic, A.5
Meissner, A.6
Kellis, M.7
Marra, M.A.8
Beaudet, A.L.9
Ecker, J.R.10
-
5
-
-
0032087892
-
The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1
-
Brown JL, Mucci D, Whiteley M, Dirksen ML, Kassis JA. 1998. The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol Cell 1:1057-1064.
-
(1998)
Mol Cell
, vol.1
, pp. 1057-1064
-
-
Brown, J.L.1
Mucci, D.2
Whiteley, M.3
Dirksen, M.L.4
Kassis, J.A.5
-
6
-
-
65549107163
-
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
-
Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, et al. 2009. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res 19:1044-1056.
-
(2009)
Genome Res
, vol.19
, pp. 1044-1056
-
-
Brunner, A.L.1
Johnson, D.S.2
Kim, S.W.3
Valouev, A.4
Reddy, T.E.5
Neff, N.F.6
Anton, E.7
Medina, C.8
Nguyen, L.9
Chiao, E.10
-
7
-
-
84855593661
-
An integrative variant analysis suite for whole exome next-generation sequencing data
-
doi:10.1186/1471-2105-13-8
-
Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F. 2012. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 13:8. doi:10.1186/1471-2105-13-8.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 8
-
-
Challis, D.1
Yu, J.2
Evani, U.S.3
Jackson, A.R.4
Paithankar, S.5
Coarfa, C.6
Milosavljevic, A.7
Gibbs, R.A.8
Yu, F.9
-
8
-
-
0037232925
-
CtBP family proteins: More than transcriptional corepressors
-
Chinnadurai G. 2003. CtBP family proteins: More than transcriptional corepressors. Bioessays 25:9-12.
-
(2003)
Bioessays
, vol.25
, pp. 9-12
-
-
Chinnadurai, G.1
-
9
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
10
-
-
78650747491
-
Discovery and characterization of chromatin states for systematic annotation of the human genome
-
Ernst J, Kellis M. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28:817-825.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 817-825
-
-
Ernst, J.1
Kellis, M.2
-
11
-
-
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. 2008. FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24:1729-1730.
-
(2008)
Bioinformatics
, vol.24
, pp. 1729-1730
-
-
Fejes, A.P.1
Robertson, G.2
Bilenky, M.3
Varhol, R.4
Bainbridge, M.5
Jones, S.J.6
-
12
-
-
77957932941
-
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
-
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, et al. 2010. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28:1097-1105
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1097-1105
-
-
Harris, R.A.1
Wang, T.2
Coarfa, C.3
Nagarajan, R.P.4
Hong, C.5
Downey, S.L.6
Johnson, B.E.7
Fouse, S.D.8
Delaney, A.9
Zhao, Y.10
-
13
-
-
77953809032
-
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
-
Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, et al. 2010. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6:479-491.
-
(2010)
Cell Stem Cell
, vol.6
, pp. 479-491
-
-
Hawkins, R.D.1
Hon, G.C.2
Lee, L.K.3
Ngo, Q.4
Lister, R.5
Pelizzola, M.6
Edsall, L.E.7
Kuan, S.8
Luu, Y.9
Klugman, S.10
-
14
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, et al. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39:311-318.
-
(2007)
Nat Genet
, vol.39
, 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
-
15
-
-
0036314926
-
Overlapping and unique roles for C-terminal binding protein 1 (CtBP1) and CtBP2 during mouse development
-
Hildebrand JD, Soriano P. 2002. Overlapping and unique roles for C-terminal binding protein 1 (CtBP1) and CtBP2 during mouse development. Mol Cell Biol 22:5296-5307.
-
(2002)
Mol Cell Biol
, vol.22
, pp. 5296-5307
-
-
Hildebrand, J.D.1
Soriano, P.2
-
16
-
-
84862785201
-
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
-
Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. 2012. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods 9:473-476.
-
(2012)
Nat Methods
, vol.9
, pp. 473-476
-
-
Hoffman, M.M.1
Buske, O.J.2
Wang, J.3
Weng, Z.4
Bilmes, J.A.5
Noble, W.S.6
-
17
-
-
55549118625
-
ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome
-
doi:10.1371/journal.pcbi.1000201
-
Hon G, Ren B, Wang W. 2008. ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol 4: e1000201. doi:10.1371/journal.pcbi.1000201.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Hon, G.1
Ren, B.2
Wang, W.3
-
18
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang DA, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57.
-
(2009)
Nat Protoc
, vol.4
, pp. 44-57
-
-
Huang, D.A.1
Sherman, B.T.2
Lempicki, R.A.3
-
19
-
-
75949114262
-
W-ChIPMotifs: A web application tool for de novo motif discovery from ChIP-based high-throughput data
-
Jin VX, Apostolos J, Nagisetty NS, Farnham PJ. 2009. W-ChIPMotifs: A web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics 25:3191-3193.
-
(2009)
Bioinformatics
, vol.25
, pp. 3191-3193
-
-
Jin, V.X.1
Apostolos, J.2
Nagisetty, N.S.3
Farnham, P.J.4
-
20
-
-
0036079158
-
The human genome browser at UCSC
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12:996-1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
21
-
-
3042781030
-
Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27
-
Kirmizis A, Bartley SM, Kuzmichev A, Margueron R, Reinberg D, Green R, Farnham PJ. 2004. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev 18:1592-1605.
-
(2004)
Genes Dev
, vol.18
, pp. 1592-1605
-
-
Kirmizis, A.1
Bartley, S.M.2
Kuzmichev, A.3
Margueron, R.4
Reinberg, D.5
Green, R.6
Farnham, P.J.7
-
22
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
23
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315-322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
Tonti-Filippini, J.6
Nery, J.R.7
Lee, L.8
Ye, Z.9
Ngo, Q.M.10
-
24
-
-
80052022462
-
Cistrome: An integrative platform for transcriptional regulation studies
-
doi:10.1186/gb-2011-12-8-r83
-
Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, et al. 2011. Cistrome: An integrative platform for transcriptional regulation studies. Genome Biol 12: R83. doi:10.1186/gb-2011-12-8-r83.
-
(2011)
Genome Biol
, vol.12
-
-
Liu, T.1
Ortiz, J.A.2
Taing, L.3
Meyer, C.A.4
Lee, B.5
Zhang, Y.6
Shin, H.7
Wong, S.S.8
Ma, J.9
Lei, Y.10
-
25
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-770.
-
(2008)
Nature
, vol.454
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
Wernig, M.4
Hanna, J.5
Sivachenko, A.6
Zhang, X.7
Bernstein, B.E.8
Nusbaum, C.9
Jaffe, D.B.10
-
26
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committedcells
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committedcells. Nature 448:553-560.
-
(2007)
Nature
, vol.448
, 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
-
27
-
-
77954758157
-
Polycomb group protein-mediated repression of transcription
-
Morey L, Helin K. 2010. Polycomb group protein-mediated repression of transcription. Trends Biochem Sci 35:323-332.
-
(2010)
Trends Biochem Sci
, vol.35
, pp. 323-332
-
-
Morey, L.1
Helin, K.2
-
28
-
-
33847084602
-
Genome regulation by polycomb and trithorax proteins
-
Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G. 2007. Genome regulation by polycomb and trithorax proteins. Cell 128:735-745.
-
(2007)
Cell
, vol.128
, pp. 735-745
-
-
Schuettengruber, B.1
Chourrout, D.2
Vervoort, M.3
Leblanc, B.4
Cavalli, G.5
-
29
-
-
7544224445
-
YY1 DNA binding and PcG recruitment requires CtBP
-
Srinivasan L, Atchison ML. 2004. YY1 DNA binding and PcG recruitment requires CtBP. Genes Dev 18:2596-2601.
-
(2004)
Genes Dev
, vol.18
, pp. 2596-2601
-
-
Srinivasan, L.1
Atchison, M.L.2
-
30
-
-
2942574510
-
Hierarchical recruitment of polycomb group silencing complexes
-
Wang L, Brown JL, Cao R, Zhang Y, Kassis JA, Jones RS. 2004. Hierarchical recruitment of polycomb group silencing complexes. Mol Cell 14:637-646.
-
(2004)
Mol Cell
, vol.14
, pp. 637-646
-
-
Wang, L.1
Brown, J.L.2
Cao, R.3
Zhang, Y.4
Kassis, J.A.5
Jones, R.S.6
-
31
-
-
78650613168
-
Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2)
-
Xu C, Bian C, Yang W, Galka M, Ouyang H, Chen C, Qiu W, Liu H, Jones AE, MacKenzie F, et al. 2010. Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc Natl Acad Sci 107:19266-19271.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 19266-19271
-
-
Xu, C.1
Bian, C.2
Yang, W.3
Galka, M.4
Ouyang, H.5
Chen, C.6
Qiu, W.7
Liu, H.8
Jones, A.E.9
MacKenzie, F.10
-
32
-
-
79953699973
-
SeqMINER: An integrated ChIP-seq data interpretation platform
-
doi:10.1093/nar/gkq1287
-
Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L. 2011. seqMINER: An integrated ChIP-seq data interpretation platform. Nucleic Acids Res 39: e35. doi:10.1093/nar/gkq1287.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Ye, T.1
Krebs, A.R.2
Choukrallah, M.A.3
Keime, C.4
Plewniak, F.5
Davidson, I.6
Tora, L.7
-
33
-
-
82355171753
-
The human epigenome browser at Washington University
-
Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, et al. 2011. The Human Epigenome Browser at Washington University. Nat Methods 8:989-990.
-
(2011)
Nat Methods
, vol.8
, pp. 989-990
-
-
Zhou, X.1
Maricque, B.2
Xie, M.3
Li, D.4
Sundaram, V.5
Martin, E.A.6
Koebbe, B.C.7
Nielsen, C.8
Hirst, M.9
Farnham, P.10
|