-
1
-
-
38349169664
-
Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight?
-
Filipowicz, W., Bhattacharyya, S.N. and Sonenberg, N. (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet., 9, 102-114.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 102-114
-
-
Filipowicz, W.1
Bhattacharyya, S.N.2
Sonenberg, N.3
-
2
-
-
77949875682
-
MicroRNA control of signal transduction
-
Inui, M., Martello, G. and Piccolo, S. (2010) MicroRNA control of signal transduction. Nat. Rev. Mol. Cell Biol., 11, 252-263.
-
(2010)
Nat. Rev. Mol. Cell Biol.
, vol.11
, pp. 252-263
-
-
Inui, M.1
Martello, G.2
Piccolo, S.3
-
3
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
Maeda, N.6
Oyama, R.7
Ravasi, T.8
Lenhard, B.9
Wells, C.10
-
4
-
-
38649114329
-
Specific expression of long noncoding RNAs in the mouse brain
-
Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F. and Mattick, J.S. (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl Acad. Sci. USA, 105, 716-721.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 716-721
-
-
Mercer, T.R.1
Dinger, M.E.2
Sunkin, S.M.3
Mehler, M.F.4
Mattick, J.S.5
-
5
-
-
84857066786
-
Modular regulatory principles of large non-coding RNAs
-
Guttman, M. and Rinn, J.L. (2012) Modular regulatory principles of large non-coding RNAs. Nature, 482, 339-346.
-
(2012)
Nature
, vol.482
, pp. 339-346
-
-
Guttman, M.1
Rinn, J.L.2
-
6
-
-
78651397147
-
Large non-coding RNAs: Missing links in cancer?
-
Huarte, M. and Rinn, J.L. (2010) Large non-coding RNAs: missing links in cancer? Hum. Mol. Genet., 19, R152-R161.
-
(2010)
Hum. Mol. Genet.
, vol.19
-
-
Huarte, M.1
Rinn, J.L.2
-
7
-
-
84867900638
-
Long non-coding RNAs and cancer: A new frontier of translational research?
-
Spizzo, R., Almeida, M.I., Colombatti, A. and Calin, G.A. (2012) Long non-coding RNAs and cancer: a new frontier of translational research? Oncogene, 31, 4577-4587.
-
(2012)
Oncogene
, vol.31
, pp. 4577-4587
-
-
Spizzo, R.1
Almeida, M.I.2
Colombatti, A.3
Calin, G.A.4
-
8
-
-
82155186923
-
The emergence of IncRNAs in cancer biology
-
Prensner, J.R. and Chinnaiyan, A.M. (2011) The emergence of IncRNAs in cancer biology. Cancer Discov., 1, 391-407.
-
(2011)
Cancer Discov.
, vol.1
, pp. 391-407
-
-
Prensner, J.R.1
Chinnaiyan, A.M.2
-
9
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa, M., Li, N., Bailey, T.L., Church, G.M., De Moor, B., Eskin, E., Favorov, A.V., Frith, M.C., Fu, Y., Kent, W.J. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
-
10
-
-
70349312354
-
ChIP-seq: Advantages and challenges of a maturing technology
-
Park, P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 669-680
-
-
Park, P.J.1
-
11
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
Pepke, S., Wold, B. and Mortazavi, A. (2009) Computation for ChIP-seq and RNA-seq studies. Nat. Methods, 6, S22-S32.
-
(2009)
Nat. Methods
, vol.6
-
-
Pepke, S.1
Wold, B.2
Mortazavi, A.3
-
12
-
-
68949213578
-
Insights from genomic profiling of transcription factors
-
Farnham, P.J. (2009) Insights from genomic profiling of transcription factors. Nat. Rev. Genet., 10, 605-616.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 605-616
-
-
Farnham, P.J.1
-
13
-
-
78651339534
-
NCBI GEO: Archive for functional genomics data sets-10 years on
-
Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M. et al. (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res., 39, D1005-D1010.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Evangelista, C.5
Kim, I.F.6
Tomashevsky, M.7
Marshall, K.A.8
Phillippy, K.H.9
Sherman, P.M.10
-
14
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
-
(2011)
PLoS Biol.
, vol.9
-
-
-
15
-
-
79953046943
-
A cis-regulatory map of the Drosophila genome
-
Negre, N., Brown, C.D., Ma, L., Bristow, C.A., Miller, S.W., Wagner, U., Kheradpour, P., Eaton, M.L., Loriaux, P., Sealfon, R. et al. (2011) A cis-regulatory map of the Drosophila genome. Nature, 471, 527-531.
-
(2011)
Nature
, vol.471
, pp. 527-531
-
-
Negre, N.1
Brown, C.D.2
Ma, L.3
Bristow, C.A.4
Miller, S.W.5
Wagner, U.6
Kheradpour, P.7
Eaton, M.L.8
Loriaux, P.9
Sealfon, R.10
-
16
-
-
78650410139
-
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
-
Gerstein, M.B., Lu, Z.J., Van Nostrand, E.L., Cheng, C., Arshinoff, B.I., Liu, T., Yip, K.Y., Robilotto, R., Rechtsteiner, A., Ikegami, K. et al. (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science, 330, 1775-1787.
-
(2010)
Science
, vol.330
, pp. 1775-1787
-
-
Gerstein, M.B.1
Lu, Z.J.2
Van Nostrand, E.L.3
Cheng, C.4
Arshinoff, B.I.5
Liu, T.6
Yip, K.Y.7
Robilotto, R.8
Rechtsteiner, A.9
Ikegami, K.10
-
17
-
-
84859865967
-
The UCSC Genome Browser database: Extensions and updates 2011
-
Dreszer, T.R., Karolchik, D., Zweig, A.S., Hinrichs, A.S., Raney, B.J., Kuhn, R.M., Meyer, L.R., Wong, M., Sloan, C.A., Rosenbloom, K.R. et al. (2012) The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res., 40, D918-D923.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Dreszer, T.R.1
Karolchik, D.2
Zweig, A.S.3
Hinrichs, A.S.4
Raney, B.J.5
Kuhn, R.M.6
Meyer, L.R.7
Wong, M.8
Sloan, C.A.9
Rosenbloom, K.R.10
-
18
-
-
75549083247
-
JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles
-
Portales-Casamar, E., Thongjuea, S., Kwon, A.T., Arenillas, D., Zhao, X., Valen, E., Yusuf, D., Lenhard, B., Wasserman, W.W. and Sandelin, A. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
Valen, E.6
Yusuf, D.7
Lenhard, B.8
Wasserman, W.W.9
Sandelin, A.10
-
19
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
Reuter, I.7
Chekmenev, D.8
Krull, M.9
Hornischer, K.10
-
20
-
-
80052022462
-
Cistrome: An integrative platform for transcriptional regulation studies
-
Liu, T., Ortiz, J.A., Taing, L., Meyer, C.A., Lee, B., Zhang, Y., Shin, H., Wong, S.S., Ma, J., Lei, Y. et al. (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol., 12, 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
-
21
-
-
78651303899
-
UniPROBE, update 2011: Expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
-
Robasky, K. and Bulyk, M.L. (2011) UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res., 39, D124-D128.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Robasky, K.1
Bulyk, M.L.2
-
22
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
-
(2011)
Genes Dev.
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
Trapnell, C.2
Goff, L.3
Koziol, M.4
Tazon-Vega, B.5
Regev, A.6
Rinn, J.L.7
-
23
-
-
84864098110
-
Identification and properties of 1119 candidate lincRNA loci in the Drosophila melanogaster genome
-
Young, R.S., Marques, A.C., Tibbit, C., Haerty, W., Bassett, A.R., Liu, J.L. and Ponting, C.P. (2012) Identification and properties of 1119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol. Evol., 4, 427-442.
-
(2012)
Genome Biol. Evol.
, vol.4
, pp. 427-442
-
-
Young, R.S.1
Marques, A.C.2
Tibbit, C.3
Haerty, W.4
Bassett, A.R.5
Liu, J.L.6
Ponting, C.P.7
-
24
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol., 28, 503-510.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
Donaghey, J.4
Robinson, J.5
Adiconis, X.6
Fan, L.7
Koziol, M.J.8
Gnirke, A.9
Nusbaum, C.10
-
25
-
-
80052869283
-
LincRNAs act in the circuitry controlling pluripotency and differentiation
-
Guttman, M., Donaghey, J., Carey, B.W., Garber, M., Grenier, J.K., Munson, G., Young, G., Lucas, A.B., Ach, R., Bruhn, L. et al. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 477, 295-300.
-
(2011)
Nature
, vol.477
, pp. 295-300
-
-
Guttman, M.1
Donaghey, J.2
Carey, B.W.3
Garber, M.4
Grenier, J.K.5
Munson, G.6
Young, G.7
Lucas, A.B.8
Ach, R.9
Bruhn, L.10
-
26
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
Amit, I.2
Garber, M.3
French, C.4
Lin, M.F.5
Feldser, D.6
Huarte, M.7
Zuk, O.8
Carey, B.W.9
Cassady, J.P.10
-
27
-
-
80051898233
-
A transcriptomic atlas of mouse neocortical layers
-
Belgard, T.G., Marques, A.C., Oliver, P.L., Abaan, H.O., Sirey, T.M., Hoerder-Suabedissen, A., Garcia-Moreno, F., Molnar, Z., Margulies, E.H. and Ponting, C.P. (2011) A transcriptomic atlas of mouse neocortical layers. Neuron, 71, 605-616.
-
(2011)
Neuron
, vol.71
, pp. 605-616
-
-
Belgard, T.G.1
Marques, A.C.2
Oliver, P.L.3
Abaan, H.O.4
Sirey, T.M.5
Hoerder-Suabedissen, A.6
Garcia-Moreno, F.7
Molnar, Z.8
Margulies, E.H.9
Ponting, C.P.10
-
28
-
-
84858221706
-
Ensembl 2012
-
Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Carvalho-Silva, D.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
-
29
-
-
78651325932
-
IncRNAdb: A reference database for long noncoding RNAs
-
Amaral, P.P., Clark, M.B., Gascoigne, D.K., Dinger, M.E. and Mattick, J.S. (2011) IncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res., 39, D146-D151.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Amaral, P.P.1
Clark, M.B.2
Gascoigne, D.K.3
Dinger, M.E.4
Mattick, J.S.5
-
30
-
-
78651293534
-
MiRBase: Integrating microRNA annotation and deep-sequencing data
-
Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
31
-
-
78651307694
-
StarBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
-
Yang, J.H., Li, J.H., Shao, P., Zhou, H., Chen, Y.Q. and Qu, L.H. (2011) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res, 39, D202-D209.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Yang, J.H.1
Li, J.H.2
Shao, P.3
Zhou, H.4
Chen, Y.Q.5
Qu, L.H.6
-
32
-
-
77952214662
-
GREAT improves functional interpretation of cis-regulatory regions
-
McLean, C.Y., Bristor, D., Hiller, M., Clarke, S.L., Schaar, B.T., Lowe, C.B., Wenger, A.M. and Bejerano, G. (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol., 28, 495-501.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 495-501
-
-
McLean, C.Y.1
Bristor, D.2
Hiller, M.3
Clarke, S.L.4
Schaar, B.T.5
Lowe, C.B.6
Wenger, A.M.7
Bejerano, G.8
-
33
-
-
8144225486
-
MicroRNA genes are transcribed by RNA polymerase II
-
Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S., Baek, S.H. and Kim, V.N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23, 4051-4060.
-
(2004)
EMBO J.
, vol.23
, pp. 4051-4060
-
-
Lee, Y.1
Kim, M.2
Han, J.3
Yeom, K.H.4
Lee, S.5
Baek, S.H.6
Kim, V.N.7
-
34
-
-
34249817549
-
Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis
-
Chang, T.C., Wentzel, E.A., Kent, O.A., Ramachandran, K., Mullendore, M., Lee, K.H., Feldmann, G., Yamakuchi, M., Ferlito, M., Lowenstein, C.J. et al. (2007) Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol. Cell., 26, 745-752.
-
(2007)
Mol. Cell.
, vol.26
, pp. 745-752
-
-
Chang, T.C.1
Wentzel, E.A.2
Kent, O.A.3
Ramachandran, K.4
Mullendore, M.5
Lee, K.H.6
Feldmann, G.7
Yamakuchi, M.8
Ferlito, M.9
Lowenstein, C.J.10
-
35
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
36
-
-
75549084786
-
DeepBase: A database for deeply annotating and mining deep sequencing data
-
Yang, J.H., Shao, P., Zhou, H., Chen, Y.Q. and Qu, L.H. (2010) deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 38, D123-D130.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Yang, J.H.1
Shao, P.2
Zhou, H.3
Chen, Y.Q.4
Qu, L.H.5
-
37
-
-
84867499417
-
Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs
-
Lai, X., Schmitz, U., Gupta, S.K., Bhattacharya, A., Kunz, M., Wolkenhauer, O. and Vera, J. (2012) Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs. Nucleic Acids Res., 40, 8818-8834.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 8818-8834
-
-
Lai, X.1
Schmitz, U.2
Gupta, S.K.3
Bhattacharya, A.4
Kunz, M.5
Wolkenhauer, O.6
Vera, J.7
-
38
-
-
20444479428
-
C-Myc-regulated microRNAs modulate E2F1 expression
-
O'Donnell, K.A., Wentzel, E.A., Zeller, K.I., Dang, C.V. and Mendell, J.T. (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature, 435, 839-843.
-
(2005)
Nature
, vol.435
, pp. 839-843
-
-
O'Donnell, K.A.1
Wentzel, E.A.2
Zeller, K.I.3
Dang, C.V.4
Mendell, J.T.5
-
39
-
-
77957954445
-
Liver-enriched transcription factors regulate microRNA-122 that targets CUTL1 during liver development
-
Xu, H., He, J.H., Xiao, Z.D., Zhang, Q.Q., Chen, Y.Q., Zhou, H. and Qu, L.H. (2010) Liver-enriched transcription factors regulate microRNA-122 that targets CUTL1 during liver development. Hepatology, 52, 1431-1442.
-
(2010)
Hepatology
, vol.52
, pp. 1431-1442
-
-
Xu, H.1
He, J.H.2
Xiao, Z.D.3
Zhang, Q.Q.4
Chen, Y.Q.5
Zhou, H.6
Qu, L.H.7
-
40
-
-
75549092303
-
TransmiR: A transcription factor-microRNA regulation database
-
Wang, J., Lu, M., Qiu, C. and Cui, Q. (2010) TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res., 38, D119-D122.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Wang, J.1
Lu, M.2
Qiu, C.3
Cui, Q.4
-
41
-
-
77956520986
-
CircuitsDB: A database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse
-
Friard, O., Re, A., Taverna, D., De Bortoli, M. and Cora, D. (2010) CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC Bioinformatics, 11, 435.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 435
-
-
Friard, O.1
Re, A.2
Taverna, D.3
De Bortoli, M.4
Cora, D.5
-
42
-
-
79955778027
-
HmChIP: A database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data
-
Chen, L., Wu, G. and Ji, H. (2011) hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. Bioinformatics, 27, 1447-1448.
-
(2011)
Bioinformatics
, vol.27
, pp. 1447-1448
-
-
Chen, L.1
Wu, G.2
Ji, H.3
-
43
-
-
79954414897
-
Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network
-
Ang, Y.S., Tsai, S.Y., Lee, D.F., Monk, J., Su, J., Ratnakumar, K., Ding, J., Ge, Y., Darr, H., Chang, B. et al. (2011) Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell, 145, 183-197.
-
(2011)
Cell
, vol.145
, pp. 183-197
-
-
Ang, Y.S.1
Tsai, S.Y.2
Lee, D.F.3
Monk, J.4
Su, J.5
Ratnakumar, K.6
Ding, J.7
Ge, Y.8
Darr, H.9
Chang, B.10
-
44
-
-
77956641239
-
ChIP-Seq identification of weakly conserved heart enhancers
-
Blow, M.J., McCulley, D.J., Li, Z., Zhang, T., Akiyama, J.A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F. et al. (2010) ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet., 42, 806-810.
-
(2010)
Nat. Genet.
, vol.42
, pp. 806-810
-
-
Blow, M.J.1
McCulley, D.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
Holt, A.6
Plajzer-Frick, I.7
Shoukry, M.8
Wright, C.9
Chen, F.10
-
45
-
-
77957234538
-
Identification of beta-catenin binding regions in colon cancer cells using ChIP-Seq
-
Bottomly, D., Kyler, S.L., McWeeney, S.K. and Yochum, G.S. (2010) Identification of beta-catenin binding regions in colon cancer cells using ChIP-Seq. Nucleic Acids Res., 38, 5735-5745.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 5735-5745
-
-
Bottomly, D.1
Kyler, S.L.2
McWeeney, S.K.3
Yochum, G.S.4
-
46
-
-
77950566643
-
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
-
Bradley, R.K., Li, X.Y., Trapnell, C., Davidson, S., Pachter, L., Chu, H.C., Tonkin, L.A., Biggin, M.D. and Eisen, M.B. (2010) Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. Plos Biol, 8, e1000343.
-
(2010)
Plos Biol
, vol.8
-
-
Bradley, R.K.1
Li, X.Y.2
Trapnell, C.3
Davidson, S.4
Pachter, L.5
Chu, H.C.6
Tonkin, L.A.7
Biggin, M.D.8
Eisen, M.B.9
-
47
-
-
55949112523
-
A human snoRNA with microRNA-like functions
-
Ender, C., Krek, A., Friedlander, M.R., Beitzinger, M., Weinmann, L., Chen, W., Pfeffer, S., Rajewsky, N. and Meister, G. (2008) A human snoRNA with microRNA-like functions. Mol. Cell, 32, 519-528.
-
(2008)
Mol. Cell
, vol.32
, pp. 519-528
-
-
Ender, C.1
Krek, A.2
Friedlander, M.R.3
Beitzinger, M.4
Weinmann, L.5
Chen, W.6
Pfeffer, S.7
Rajewsky, N.8
Meister, G.9
-
48
-
-
70449696134
-
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
-
Cheng, Y., Wu, W., Kumar, S.A., Yu, D., Deng, W., Tripic, T., King, D.C., Chen, K.B., Zhang, Y., Drautz, D. et al. (2009) Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res., 19, 2172-2184.
-
(2009)
Genome Res.
, vol.19
, pp. 2172-2184
-
-
Cheng, Y.1
Wu, W.2
Kumar, S.A.3
Yu, D.4
Deng, W.5
Tripic, T.6
King, D.C.7
Chen, K.B.8
Zhang, Y.9
Drautz, D.10
-
49
-
-
77952062004
-
Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs
-
Cicatiello, L., Mutarelli, M., Grober, O.M.V., Paris, O., Ferraro, L., Ravo, M., Tarallo, R., Luo, S.J., Schroth, G.P., Seifert, M. et al. (2010) Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. Am. J. Pathol., 176, 2113-2130.
-
(2010)
Am. J. Pathol.
, vol.176
, pp. 2113-2130
-
-
Cicatiello, L.1
Mutarelli, M.2
Grober, O.M.V.3
Paris, O.4
Ferraro, L.5
Ravo, M.6
Tarallo, R.7
Luo, S.J.8
Schroth, G.P.9
Seifert, M.10
-
50
-
-
74049139555
-
Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263
-
Frietze, S., Lan, X., Jin, V.X. and Farnham, P.J. (2010) Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J. Biol. Chem., 285, 1393-1403.
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 1393-1403
-
-
Frietze, S.1
Lan, X.2
Jin, V.X.3
Farnham, P.J.4
-
51
-
-
70449675049
-
Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy
-
Fujiwara, T., O'Geen, H., Keles, S., Blahnik, K., Linnemann, A.K., Kang, Y.A., Choi, K., Farnham, P.J. and Bresnick, E.H. (2009) Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol. Cell, 36, 667-681.
-
(2009)
Mol. Cell
, vol.36
, pp. 667-681
-
-
Fujiwara, T.1
O'Geen, H.2
Keles, S.3
Blahnik, K.4
Linnemann, A.K.5
Kang, Y.A.6
Choi, K.7
Farnham, P.J.8
Bresnick, E.H.9
-
52
-
-
78651370470
-
Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation
-
Grober, O.M., Mutarelli, M., Giurato, G., Ravo, M., Cicatiello, L., De Filippo, M.R., Ferraro, L., Nassa, G., Papa, M.F., Paris, O. et al. (2011) Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation. BMC Genomics, 12, 36.
-
(2011)
BMC Genomics
, vol.12
, pp. 36
-
-
Grober, O.M.1
Mutarelli, M.2
Giurato, G.3
Ravo, M.4
Cicatiello, L.5
De Filippo, M.R.6
Ferraro, L.7
Nassa, G.8
Papa, M.F.9
Paris, O.10
-
53
-
-
79955027617
-
Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart
-
He, A., Kong, S.W., Ma, Q. and Pu, W.T. (2011) Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc. Natl Acad. Sci. USA, 108, 5632-5637.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 5632-5637
-
-
He, A.1
Kong, S.W.2
Ma, Q.3
Pu, W.T.4
-
54
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H. and Glass, C.K. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576-589.
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
Benner, C.2
Spann, N.3
Bertolino, E.4
Lin, Y.C.5
Laslo, P.6
Cheng, J.X.7
Murre, C.8
Singh, H.9
Glass, C.K.10
-
55
-
-
75349088911
-
The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells
-
Heng, J.C.D., Feng, B., Han, J.Y., Jiang, J.M., Kraus, P., Ng, J.H., Orlov, Y.L., Huss, M., Yang, L., Lufkin, T. et al. (2010) The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell, 6, 167-174.
-
(2010)
Cell Stem Cell
, vol.6
, pp. 167-174
-
-
Heng, J.C.D.1
Feng, B.2
Han, J.Y.3
Jiang, J.M.4
Kraus, P.5
Ng, J.H.6
Orlov, Y.L.7
Huss, M.8
Yang, L.9
Lufkin, T.10
-
56
-
-
74249118523
-
DNA specificity determinants associate with distinct transcription factor functions
-
Hollenhorst, P.C., Chandler, K.J., Poulsen, R.L., Johnson, W.E., Speck, N.A. and Graves, B.J. (2009) DNA specificity determinants associate with distinct transcription factor functions. Plos Genet., 5, e1000778.
-
(2009)
Plos Genet.
, vol.5
-
-
Hollenhorst, P.C.1
Chandler, K.J.2
Poulsen, R.L.3
Johnson, W.E.4
Speck, N.A.5
Graves, B.J.6
-
57
-
-
77949916244
-
On the detection and refinement of transcription factor binding sites using ChIP-Seq data
-
Hu, M., Yu, J.D., Taylor, J.M.G., Chinnaiyan, A.M. and Qin, Z.H.S. (2010) On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Res., 38, 2154-2167.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 2154-2167
-
-
Hu, M.1
Yu, J.D.2
Taylor, J.M.G.3
Chinnaiyan, A.M.4
Qin, Z.H.S.5
-
58
-
-
58849156573
-
A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress
-
Kang, J.S., Gemberling, M., Nakamura, M., Whitby, F.G., Handa, H., Fairbrother, W.G. and Tantin, D. (2009) A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress. Genes Dev., 23, 208-222.
-
(2009)
Genes Dev.
, vol.23
, pp. 208-222
-
-
Kang, J.S.1
Gemberling, M.2
Nakamura, M.3
Whitby, F.G.4
Handa, H.5
Fairbrother, W.G.6
Tantin, D.7
-
59
-
-
80051537445
-
Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs
-
Kim, S.W., Yoon, S.J., Chuong, E., Oyolu, C., Wills, A.E., Gupta, R. and Baker, J. (2011) Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs. Dev. Biol., 357, 492-504.
-
(2011)
Dev. Biol.
, vol.357
, pp. 492-504
-
-
Kim, S.W.1
Yoon, S.J.2
Chuong, E.3
Oyolu, C.4
Wills, A.E.5
Gupta, R.6
Baker, J.7
-
60
-
-
77950893589
-
A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation
-
Kleine-Kohlbrecher, D., Christensen, J., Vandamme, J., Abarrategui, I., Bak, M., Tommerup, N., Shi, X., Gozani, O., Rappsilber, J., Salcini, A.E. et al. (2010) A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Mol. Cell, 38, 165-178.
-
(2010)
Mol. Cell
, vol.38
, pp. 165-178
-
-
Kleine-Kohlbrecher, D.1
Christensen, J.2
Vandamme, J.3
Abarrategui, I.4
Bak, M.5
Tommerup, N.6
Shi, X.7
Gozani, O.8
Rappsilber, J.9
Salcini, A.E.10
-
61
-
-
77957371805
-
Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus
-
Kouwenhoven, E.N., van Heeringen, S.J., Tena, J.J., Oti, M., Dutilh, B.E., Alonso, M.E., de la Calle-Mustienes, E., Smeenk, L., Rinne, T., Parsaulian, L. et al. (2010) Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. Plos Genet., 6, e1001065.
-
(2010)
Plos Genet.
, vol.6
-
-
Kouwenhoven, E.N.1
Van Heeringen, S.J.2
Tena, J.J.3
Oti, M.4
Dutilh, B.E.5
Alonso, M.E.6
De La Calle-Mustienes, E.7
Smeenk, L.8
Rinne, T.9
Parsaulian, L.10
-
62
-
-
77954100084
-
Transposable elements have rewired the core regulatory network of human embryonic stem cells
-
Kunarso, G., Chia, N.Y., Jeyakani, J., Hwang, C., Lu, X.Y., Chan, Y.S., Ng, H.H. and Bourque, G. (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet., 42, 631-634.
-
(2010)
Nat. Genet.
, vol.42
, pp. 631-634
-
-
Kunarso, G.1
Chia, N.Y.2
Jeyakani, J.3
Hwang, C.4
Lu, X.Y.5
Chan, Y.S.6
Ng, H.H.7
Bourque, G.8
-
63
-
-
79956053726
-
Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis
-
Lee, B.K., Bhinge, A.A. and Iyer, V.R. (2011) Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis. Nucleic Acids Res., 39, 3558-3573.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 3558-3573
-
-
Lee, B.K.1
Bhinge, A.A.2
Iyer, V.R.3
-
64
-
-
77950634721
-
Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages
-
Lefterova, M.I., Steger, D.J., Zhuo, D., Qatanani, M., Mullican, S.E., Tuteja, G., Manduchi, E., Grant, G.R. and Lazar, M.A. (2010) Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol. Cell. Biol., 30, 2078-2089.
-
(2010)
Mol. Cell. Biol.
, vol.30
, pp. 2078-2089
-
-
Lefterova, M.I.1
Steger, D.J.2
Zhuo, D.3
Qatanani, M.4
Mullican, S.E.5
Tuteja, G.6
Manduchi, E.7
Grant, G.R.8
Lazar, M.A.9
-
65
-
-
77953763449
-
A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate
-
Lin, Y.C., Jhunjhunwala, S., Benner, C., Heinz, S., Welinder, E., Mansson, R., Sigvardsson, M., Hagman, J., Espinoza, C.A., Dutkowski, J. et al. (2010) A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat. Immunol., 11, 635-643.
-
(2010)
Nat. Immunol.
, vol.11
, pp. 635-643
-
-
Lin, Y.C.1
Jhunjhunwala, S.2
Benner, C.3
Heinz, S.4
Welinder, E.5
Mansson, R.6
Sigvardsson, M.7
Hagman, J.8
Espinoza, C.A.9
Dutkowski, J.10
-
66
-
-
79957950591
-
Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes
-
Lo, K.A., Bauchmann, M.K., Baumann, A.P., Donahue, C.J., Thiede, M.A., Hayes, L.S., des Etages, S.A. and Fraenkel, E. (2011) Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes. PLoS One, 6, e19778.
-
(2011)
PLoS One
, vol.6
-
-
Lo, K.A.1
Bauchmann, M.K.2
Baumann, A.P.3
Donahue, C.J.4
Thiede, M.A.5
Hayes, L.S.6
Des Etages, S.A.7
Fraenkel, E.8
-
67
-
-
77954586080
-
A quantitative model of transcriptional regulation reveals the influence of binding location on expression
-
MacIsaac, K.D., Lo, K.A., Gordon, W., Motola, S., Mazor, T. and Fraenkel, E. (2010) A quantitative model of transcriptional regulation reveals the influence of binding location on expression. PLoS Comput. Biol., 6, e1000773.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
MacIsaac, K.D.1
Lo, K.A.2
Gordon, W.3
Motola, S.4
Mazor, T.5
Fraenkel, E.6
-
68
-
-
80052454883
-
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes (vol 18, pg 708, 2011)
-
Martin, D., Pantoja, C., Minan, A.F., Valdes-Quezada, C., Molto, E., Matesanz, F., Bogdanovic, O., de la Calle-Mustienes, E., Dominguez, O., Taher, L. et al. (2011) Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes (vol 18, pg 708, 2011). Nat. Struct. Mol. Biol., 18, 1084-1084.
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 1084-1084
-
-
Martin, D.1
Pantoja, C.2
Minan, A.F.3
Valdes-Quezada, C.4
Molto, E.5
Matesanz, F.6
Bogdanovic, O.7
De La Calle-Mustienes, E.8
Dominguez, O.9
Taher, L.10
-
69
-
-
79959813762
-
GATA4 regulates estrogen receptor-alpha-mediated osteoblast transcription
-
Miranda-Carboni, G.A., Guemes, M., Bailey, S., Anaya, E., Corselli, M., Peault, B. and Krum, S.A. (2011) GATA4 regulates estrogen receptor-alpha- mediated osteoblast transcription. Mol. Endocrinol., 25, 1126-1136.
-
(2011)
Mol. Endocrinol.
, vol.25
, pp. 1126-1136
-
-
Miranda-Carboni, G.A.1
Guemes, M.2
Bailey, S.3
Anaya, E.4
Corselli, M.5
Peault, B.6
Krum, S.A.7
-
70
-
-
79955929062
-
RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity
-
Nitzsche, A., Paszkowski-Rogacz, M., Matarese, F., Janssen-Megens, E.M., Hubner, N.C., Schulz, H., de Vries, I., Ding, L., Huebner, N., Mann, M. et al. (2011) RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PLoS One, 6, e19470.
-
(2011)
PLoS One
, vol.6
-
-
Nitzsche, A.1
Paszkowski-Rogacz, M.2
Matarese, F.3
Janssen-Megens, E.M.4
Hubner, N.C.5
Schulz, H.6
De Vries, I.7
Ding, L.8
Huebner, N.9
Mann, M.10
-
71
-
-
77949414371
-
JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells
-
Pasini, D., Cloos, P.A., Walfridsson, J., Olsson, L., Bukowski, J.P., Johansen, J.V., Bak, M., Tommerup, N., Rappsilber, J. and Helin, K. (2010) JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature, 464, 306-310.
-
(2010)
Nature
, vol.464
, pp. 306-310
-
-
Pasini, D.1
Cloos, P.A.2
Walfridsson, J.3
Olsson, L.4
Bukowski, J.P.5
Johansen, J.V.6
Bak, M.7
Tommerup, N.8
Rappsilber, J.9
Helin, K.10
-
72
-
-
72249119297
-
Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells
-
Peng, J.C., Valouev, A., Swigut, T., Zhang, J., Zhao, Y., Sidow, A. and Wysocka, J. (2009) Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell, 139, 1290-1302.
-
(2009)
Cell
, vol.139
, pp. 1290-1302
-
-
Peng, J.C.1
Valouev, A.2
Swigut, T.3
Zhang, J.4
Zhao, Y.5
Sidow, A.6
Wysocka, J.7
-
73
-
-
77649268269
-
Close association of RNA polymerase II and many transcription factors with Pol III genes
-
Raha, D., Wang, Z., Moqtaderi, Z., Wu, L., Zhong, G., Gerstein, M., Struhl, K. and Snyder, M. (2010) Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc. Natl Acad. Sci. USA, 107, 3639-3644.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 3639-3644
-
-
Raha, D.1
Wang, Z.2
Moqtaderi, Z.3
Wu, L.4
Zhong, G.5
Gerstein, M.6
Struhl, K.7
Snyder, M.8
-
74
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y.J., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657.
-
(2007)
Nat. Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.J.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
-
75
-
-
75149194937
-
Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer
-
Ross-Innes, C.S., Stark, R., Holmes, K.A., Schmidt, D., Spyrou, C., Russell, R., Massie, C.E., Vowler, S.L., Eldridge, M. and Carroll, J.S. (2010) Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer. Genes Dev., 24, 171-182.
-
(2010)
Genes Dev.
, vol.24
, pp. 171-182
-
-
Ross-Innes, C.S.1
Stark, R.2
Holmes, K.A.3
Schmidt, D.4
Spyrou, C.5
Russell, R.6
Massie, C.E.7
Vowler, S.L.8
Eldridge, M.9
Carroll, J.S.10
-
76
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky, J., Euskirchen, G., Auerbach, R.K., Zhang, Z.D.D., Gibson, T., Bjornson, R., Carriero, N., Snyder, M. and Gerstein, M.B. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol., 27, 66-75.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.D.4
Gibson, T.5
Bjornson, R.6
Carriero, N.7
Snyder, M.8
Gerstein, M.B.9
-
77
-
-
79952275149
-
The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs
-
Schlesinger, J., Schueler, M., Grunert, M., Fischer, J.J., Zhang, Q., Krueger, T., Lange, M., Tonjes, M., Dunkel, I. and Sperling, S.R. (2011) The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs. Plos Genet., 7, e1001313.
-
(2011)
Plos Genet.
, vol.7
-
-
Schlesinger, J.1
Schueler, M.2
Grunert, M.3
Fischer, J.J.4
Zhang, Q.5
Krueger, T.6
Lange, M.7
Tonjes, M.8
Dunkel, I.9
Sperling, S.R.10
-
78
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt, D., Wilson, M.D., Ballester, B., Schwalie, P.C., Brown, G.D., Marshall, A., Kutter, C., Watt, S., Martinez-Jimenez, C.P., Mackay, S. et al. (2010) Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science, 328, 1036-1040.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
Wilson, M.D.2
Ballester, B.3
Schwalie, P.C.4
Brown, G.D.5
Marshall, A.6
Kutter, C.7
Watt, S.8
Martinez-Jimenez, C.P.9
Mackay, S.10
-
79
-
-
79953756730
-
Species-specific strategies underlying conserved functions of metabolic transcription factors
-
Soccio, R.E., Tuteja, G., Everett, L.J., Li, Z., Lazar, M.A. and Kaestner, K.H. (2011) Species-specific strategies underlying conserved functions of metabolic transcription factors. Mol. Endocrinol., 25, 694-706.
-
(2011)
Mol. Endocrinol.
, vol.25
, pp. 694-706
-
-
Soccio, R.E.1
Tuteja, G.2
Everett, L.J.3
Li, Z.4
Lazar, M.A.5
Kaestner, K.H.6
-
80
-
-
77952331646
-
Propagation of adipogenic signals through an epigenomic transition state
-
Steger, D.J., Grant, G.R., Schupp, M., Tomaru, T., Lefterova, M.I., Schug, J., Manduchi, E., Stoeckert, C.J. and Lazar, M.A. (2010) Propagation of adipogenic signals through an epigenomic transition state. Genes Dev., 24, 1035-1044.
-
(2010)
Genes Dev.
, vol.24
, pp. 1035-1044
-
-
Steger, D.J.1
Grant, G.R.2
Schupp, M.3
Tomaru, T.4
Lefterova, M.I.5
Schug, J.6
Manduchi, E.7
Stoeckert, C.J.8
Lazar, M.A.9
-
81
-
-
77955629953
-
Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation
-
Stender, J.D., Kim, K., Charn, T.H., Komm, B., Chang, K.C., Kraus, W.L., Benner, C., Glass, C.K. and Katzenellenbogen, B.S. (2010) Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol. Cell. Biol., 30, 3943-3955.
-
(2010)
Mol. Cell. Biol.
, vol.30
, pp. 3943-3955
-
-
Stender, J.D.1
Kim, K.2
Charn, T.H.3
Komm, B.4
Chang, K.C.5
Kraus, W.L.6
Benner, C.7
Glass, C.K.8
Katzenellenbogen, B.S.9
-
82
-
-
77953289247
-
Early B cell factor 1 regulates B cell gene networks by activation, repression, and transcription-independent poising of chromatin
-
Treiber, T., Mandel, E.M., Pott, S., Gyory, I., Firner, S., Liu, E.T. and Grosschedl, R. (2010) Early B cell factor 1 regulates B cell gene networks by activation, repression, and transcription-independent poising of chromatin. Immunity, 32, 714-725.
-
(2010)
Immunity
, vol.32
, pp. 714-725
-
-
Treiber, T.1
Mandel, E.M.2
Pott, S.3
Gyory, I.4
Firner, S.5
Liu, E.T.6
Grosschedl, R.7
-
83
-
-
78149485097
-
Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2
-
Verzi, M.P., Shin, H., He, H.H., Sulahian, R., Meyer, C.A., Montgomery, R.K., Fleet, J.C., Brown, M., Liu, X.S. and Shivdasani, R.A. (2010) Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev. Cell, 19, 713-726.
-
(2010)
Dev. Cell
, vol.19
, pp. 713-726
-
-
Verzi, M.P.1
Shin, H.2
He, H.H.3
Sulahian, R.4
Meyer, C.A.5
Montgomery, R.K.6
Fleet, J.C.7
Brown, M.8
Liu, X.S.9
Shivdasani, R.A.10
-
84
-
-
79956111870
-
Essential and redundant functions of caudal family proteins in activating adult intestinal genes
-
Verzi, M.P., Shin, H., Ho, L.L., Liu, X.S. and Shivdasani, R.A. (2011) Essential and redundant functions of caudal family proteins in activating adult intestinal genes. Mol. Cell. Biol., 31, 2026-2039.
-
(2011)
Mol. Cell. Biol.
, vol.31
, pp. 2026-2039
-
-
Verzi, M.P.1
Shin, H.2
Ho, L.L.3
Liu, X.S.4
Shivdasani, R.A.5
-
85
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel, A., Blow, M.J., Li, Z., Zhang, T., Akiyama, J.A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F. et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature, 457, 854-858.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
Holt, A.6
Plajzer-Frick, I.7
Shoukry, M.8
Wright, C.9
Chen, F.10
-
86
-
-
77954584837
-
Estrogen receptor beta binds to and regulates three distinct classes of target genes
-
Vivar, O.I., Zhao, X.Y., Saunier, E.F., Griffin, C., Mayba, O.S., Tagliaferri, M., Cohen, I., Speed, T.P. and Leitman, D.C. (2010) Estrogen receptor beta binds to and regulates three distinct classes of target genes. J. Biol. Chem., 285, 22059-22066.
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 22059-22066
-
-
Vivar, O.I.1
Zhao, X.Y.2
Saunier, E.F.3
Griffin, C.4
Mayba, O.S.5
Tagliaferri, M.6
Cohen, I.7
Speed, T.P.8
Leitman, D.C.9
-
87
-
-
75349104610
-
Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation
-
Walker, E., Chang, W.Y., Hunkapiller, J., Cagney, G., Garcha, K., Torchia, J., Krogan, N.J., Reiter, J.F. and Stanford, W.L. (2010) Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation. Cell Stem Cell, 6, 153-166.
-
(2010)
Cell Stem Cell
, vol.6
, pp. 153-166
-
-
Walker, E.1
Chang, W.Y.2
Hunkapiller, J.3
Cagney, G.4
Garcha, K.5
Torchia, J.6
Krogan, N.J.7
Reiter, J.F.8
Stanford, W.L.9
-
88
-
-
79959198166
-
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA
-
Wang, D., Garcia-Bassets, I., Benner, C., Li, W., Su, X., Zhou, Y., Qiu, J., Liu, W., Kaikkonen, M.U., Ohgi, K.A. et al. (2011) Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature, 474, 390-394.
-
(2011)
Nature
, vol.474
, pp. 390-394
-
-
Wang, D.1
Garcia-Bassets, I.2
Benner, C.3
Li, W.4
Su, X.5
Zhou, Y.6
Qiu, J.7
Liu, W.8
Kaikkonen, M.U.9
Ohgi, K.A.10
-
89
-
-
79959559692
-
The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle
-
Warnatz, H.J., Schmidt, D., Manke, T., Piccini, I., Sultan, M., Borodina, T., Balzereit, D., Wruck, W., Soldatov, A., Vingron, M. et al. (2011) The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. J. Biol. Chem., 286, 23521-23532.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 23521-23532
-
-
Warnatz, H.J.1
Schmidt, D.2
Manke, T.3
Piccini, I.4
Sultan, M.5
Borodina, T.6
Balzereit, D.7
Wruck, W.8
Soldatov, A.9
Vingron, M.10
-
90
-
-
77954954652
-
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
-
Wei, G.H., Badis, G., Berger, M.F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A.R. et al. (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J., 29, 2147-2160.
-
(2010)
EMBO J.
, vol.29
, pp. 2147-2160
-
-
Wei, G.H.1
Badis, G.2
Berger, M.F.3
Kivioja, T.4
Palin, K.5
Enge, M.6
Bonke, M.7
Jolma, A.8
Varjosalo, M.9
Gehrke, A.R.10
-
91
-
-
66549085342
-
ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
-
Welboren, W.J., van Driel, M.A., Janssen-Megens, E.M., van Heeringen, S.J., Sweep, F.C., Span, P.N. and Stunnenberg, H.G. (2009) ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. EMBO J., 28, 1418-1428.
-
(2009)
EMBO J.
, vol.28
, pp. 1418-1428
-
-
Welboren, W.J.1
Van Driel, M.A.2
Janssen-Megens, E.M.3
Van Heeringen, S.J.4
Sweep, F.C.5
Span, P.N.6
Stunnenberg, H.G.7
-
92
-
-
77957348625
-
Combinatorial transcriptional control in blood stem/progenitor cells: Genome-wide analysis of ten major transcriptional regulators
-
Wilson, N.K., Foster, S.D., Wang, X., Knezevic, K., Schutte, J., Kaimakis, P., Chilarska, P.M., Kinston, S., Ouwehand, W.H., Dzierzak, E. et al. (2010) Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell, 7, 532-544.
-
(2010)
Cell Stem Cell
, vol.7
, pp. 532-544
-
-
Wilson, N.K.1
Foster, S.D.2
Wang, X.3
Knezevic, K.4
Schutte, J.5
Kaimakis, P.6
Chilarska, P.M.7
Kinston, S.8
Ouwehand, W.H.9
Dzierzak, E.10
-
93
-
-
78349252731
-
Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA
-
Yao, H., Brick, K., Evrard, Y., Xiao, T., Camerini-Otero, R.D. and Felsenfeld, G. (2010) Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev., 24, 2543-2555.
-
(2010)
Genes Dev.
, vol.24
, pp. 2543-2555
-
-
Yao, H.1
Brick, K.2
Evrard, Y.3
Xiao, T.4
Camerini-Otero, R.D.5
Felsenfeld, G.6
-
94
-
-
80051571400
-
Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
-
Yu, H.B., Johnson, R., Kunarso, G. and Stanton, L.W. (2011) Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells. Genome Res., 21, 1284-1293.
-
(2011)
Genome Res.
, vol.21
, pp. 1284-1293
-
-
Yu, H.B.1
Johnson, R.2
Kunarso, G.3
Stanton, L.W.4
-
95
-
-
77952103123
-
An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression
-
Yu, J.D., Yu, J.J., Mani, R.S., Cao, Q., Brenner, C.J., Cao, X.H., Wang, X.J., Wu, L.T., Li, J., Hu, M. et al. (2010) An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell, 17, 443-454.
-
(2010)
Cancer Cell
, vol.17
, pp. 443-454
-
-
Yu, J.D.1
Yu, J.J.2
Mani, R.S.3
Cao, Q.4
Brenner, C.J.5
Cao, X.H.6
Wang, X.J.7
Wu, L.T.8
Li, J.9
Hu, M.10
-
96
-
-
70449638281
-
Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis
-
Yu, M., Riva, L., Xie, H.F., Schindler, Y., Moran, T.B., Cheng, Y., Yu, D.N., Hardison, R., Weiss, M.J., Orkin, S.H. et al. (2009) Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol. Cell, 36, 682-695.
-
(2009)
Mol. Cell
, vol.36
, pp. 682-695
-
-
Yu, M.1
Riva, L.2
Xie, H.F.3
Schindler, Y.4
Moran, T.B.5
Cheng, Y.6
Yu, D.N.7
Hardison, R.8
Weiss, M.J.9
Orkin, S.H.10
-
97
-
-
79959473094
-
Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb
-
Zhao, L., Glazov, E.A., Pattabiraman, D.R., Al-Owaidi, F., Zhang, P., Brown, M.A., Leo, P.J. and Gonda, T.J. (2011) Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb. Nucleic Acids Res., 39, 4664-4679.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 4664-4679
-
-
Zhao, L.1
Glazov, E.A.2
Pattabiraman, D.R.3
Al-Owaidi, F.4
Zhang, P.5
Brown, M.A.6
Leo, P.J.7
Gonda, T.J.8
-
98
-
-
77649225979
-
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response
-
Zhong, M., Niu, W., Lu, Z.J., Sarov, M., Murray, J.I., Janette, J., Raha, D., Sheaffer, K.L., Lam, H.Y., Preston, E. et al. (2010) Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. Plos Genet., 6, e1000848.
-
(2010)
Plos Genet.
, vol.6
-
-
Zhong, M.1
Niu, W.2
Lu, Z.J.3
Sarov, M.4
Murray, J.I.5
Janette, J.6
Raha, D.7
Sheaffer, K.L.8
Lam, H.Y.9
Preston, E.10
|