-
1
-
-
80052014052
-
Inflammation meets cancer, with NF-kappaB as the matchmaker
-
Ben-Neriah, Y. & Karin, M. Inflammation meets cancer, with NF-kappaB as the matchmaker. Nat. Immunol. 12, 715-723 (2011).
-
(2011)
Nat. Immunol.
, vol.12
, pp. 715-723
-
-
Ben-Neriah, Y.1
Karin, M.2
-
2
-
-
84858734708
-
NF-kappaB and chromatin: Ten years on the path from basic mechanisms to candidate drugs
-
Natoli, G. NF-kappaB and chromatin: ten years on the path from basic mechanisms to candidate drugs. Immunol. Rev. 246, 183-192 (2012).
-
(2012)
Immunol. Rev.
, vol.246
, pp. 183-192
-
-
Natoli, G.1
-
3
-
-
77950346282
-
Immunity inflammation, and cancer
-
Grivennikov, S. I., Greten, F. R. & Karin, M. Immunity, inflammation, and cancer. Cell 140, 883-899 (2010).
-
(2010)
Cell
, vol.140
, pp. 883-899
-
-
Grivennikov, S.I.1
Greten, F.R.2
Karin, M.3
-
5
-
-
84877823153
-
Mutant p53 prolongs NF-kappaB activation and promotes chronic inflammation and inflammation-associated colorectal cancer
-
Cooks, T. et al. Mutant p53 prolongs NF-kappaB activation and promotes chronic inflammation and inflammation-associated colorectal cancer. Cancer Cell 23, 634-646 (2013).
-
(2013)
Cancer Cell
, vol.23
, pp. 634-646
-
-
Cooks, T.1
-
6
-
-
84919480782
-
Mutant p53 reprograms TNF signaling in cancer cells through interaction with the tumor suppressor DAB2IP
-
Di Minin, G. et al. Mutant p53 reprograms TNF signaling in cancer cells through interaction with the tumor suppressor DAB2IP. Mol. Cell 56, 617-629 (2014).
-
(2014)
Mol. Cell
, vol.56
, pp. 617-629
-
-
Di Minin, G.1
-
7
-
-
84896098750
-
Mutant p53 in cancer: New functions and therapeutic opportunities
-
Muller, P. A. & Vousden, K. H. Mutant p53 in cancer: new functions and therapeutic opportunities. Cancer Cell 25, 304-317 (2014).
-
(2014)
Cancer Cell
, vol.25
, pp. 304-317
-
-
Muller, P.A.1
Vousden, K.H.2
-
8
-
-
33748211158
-
Gain of function of mutant p53: The mutant p53/NF-Y protein complex reveals an aberrant transcriptional mechanism of cell cycle regulation
-
Di Agostino, S. et al. Gain of function of mutant p53: the mutant p53/NF-Y protein complex reveals an aberrant transcriptional mechanism of cell cycle regulation. Cancer Cell 10, 191-202 (2006).
-
(2006)
Cancer Cell
, vol.10
, pp. 191-202
-
-
Di Agostino, S.1
-
9
-
-
78650210727
-
Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response
-
Barish, G. D. et al. Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes Dev. 24, 2760-2765 (2010).
-
(2010)
Genes Dev.
, vol.24
, pp. 2760-2765
-
-
Barish, G.D.1
-
10
-
-
79959911826
-
Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding
-
Biddie, S. C. et al. Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. Mol. Cell 43, 145-155 (2011).
-
(2011)
Mol. Cell
, vol.43
, pp. 145-155
-
-
Biddie, S.C.1
-
11
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
12
-
-
77950634721
-
Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages
-
Lefterova, M. I. et al. Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol. Cell Biol. 30, 2078-2089 (2010).
-
(2010)
Mol. Cell Biol.
, vol.30
, pp. 2078-2089
-
-
Lefterova, M.I.1
-
13
-
-
80155137594
-
Master transcription factors determine cell-type-specific responses to TGF-beta signaling
-
Mullen, A. C. et al. Master transcription factors determine cell-type-specific responses to TGF-beta signaling. Cell 147, 565-576 (2011).
-
(2011)
Cell
, vol.147
, pp. 565-576
-
-
Mullen, A.C.1
-
14
-
-
55749101777
-
Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis
-
Nielsen, R. et al. Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev. 22, 2953-2967 (2008).
-
(2008)
Genes Dev.
, vol.22
, pp. 2953-2967
-
-
Nielsen, R.1
-
15
-
-
80155123782
-
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration
-
Trompouki, E. et al. Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell 147,577-589 (2011).
-
(2011)
Cell
, vol.147
, pp. 577-589
-
-
Trompouki, E.1
-
16
-
-
84857781464
-
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
-
Chepelev, I., Wei, G., Wangsa, D., Tang, Q. & Zhao, K. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res. 22, 490-503 (2012).
-
(2012)
Cell Res.
, vol.22
, pp. 490-503
-
-
Chepelev, I.1
Wei, G.2
Wangsa, D.3
Tang, Q.4
Zhao, K.5
-
17
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108-112 (2009).
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
-
18
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311-318 (2007).
-
(2007)
Nat. Genet.
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
-
19
-
-
77952908743
-
A large fraction of extragenic RNA pol II transcription sites overlap enhancers
-
De Santa, F. et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010).
-
(2010)
PLoS Biol.
, vol.8
, pp. e1000384
-
-
De Santa, F.1
-
20
-
-
79955836460
-
A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells
-
Hah, N. et al. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145, 622-634 (2011).
-
(2011)
Cell
, vol.145
, pp. 622-634
-
-
Hah, N.1
-
21
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
-
22
-
-
79953748673
-
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
-
Wang, K. C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120-124 (2011).
-
(2011)
Nature
, vol.472
, pp. 120-124
-
-
Wang, K.C.1
-
23
-
-
84862636275
-
Mutant p53: One name, many proteins
-
Freed-Pastor, W. A. & Prives, C. Mutant p53: one name, many proteins. Genes Dev. 26, 1268-1286 (2012).
-
(2012)
Genes Dev.
, vol.26
, pp. 1268-1286
-
-
Freed-Pastor, W.A.1
Prives, C.2
-
24
-
-
79952184341
-
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
-
John, S. et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43, 264-268 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 264-268
-
-
John, S.1
-
25
-
-
84859869155
-
Mutant p53 cooperates with ETS2 to promote etoposide resistance
-
Do, P. M. et al. Mutant p53 cooperates with ETS2 to promote etoposide resistance. Genes Dev. 26, 830-845 (2012).
-
(2012)
Genes Dev.
, vol.26
, pp. 830-845
-
-
Do, P.M.1
-
26
-
-
84941220446
-
Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth
-
Zhu, J. et al. Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth. Nature 525, 206-211 (2015).
-
(2015)
Nature
, vol.525
, pp. 206-211
-
-
Zhu, J.1
-
27
-
-
0032189348
-
Proteasome inhibitors: Valuable new tools for cell biologists
-
Lee, D. H. & Goldberg, A. L. Proteasome inhibitors: valuable new tools for cell biologists. Trends Cell Biol. 8, 397-403 (1998).
-
(1998)
Trends Cell Biol.
, vol.8
, pp. 397-403
-
-
Lee, D.H.1
Goldberg, A.L.2
-
28
-
-
0027983669
-
Crystal structure of a p53 tumor suppressor-DNA complex: Understanding tumorigenic mutations
-
Cho, Y., Gorina, S., Jeffrey, P. D. & Pavletich, N. P. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 265, 346-355 (1994).
-
(1994)
Science
, vol.265
, pp. 346-355
-
-
Cho, Y.1
Gorina, S.2
Jeffrey, P.D.3
Pavletich, N.P.4
-
29
-
-
84923786414
-
The selection and function of cell type-specific enhancers
-
Heinz, S., Romanoski, C. E., Benner, C. & Glass, C. K. The selection and function of cell type-specific enhancers. Nat. Rev. Mol Cell Biol. 16,144-154 (2015).
-
(2015)
Nat. Rev. Mol Cell Biol.
, vol.16
, pp. 144-154
-
-
Heinz, S.1
Romanoski, C.E.2
Benner, C.3
Glass, C.K.4
-
30
-
-
34047198167
-
Transcription regulation by mutant p53
-
Weisz, L., Oren, M. & Rotter, V. Transcription regulation by mutant p53. Oncogene 26, 2202-2211 (2007).
-
(2007)
Oncogene
, vol.26
, pp. 2202-2211
-
-
Weisz, L.1
Oren, M.2
Rotter, V.3
-
31
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008).
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
32
-
-
0035710746
-
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method
-
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods 25, 402-408 (2001).
-
(2001)
Methods
, vol.25
, pp. 402-408
-
-
Livak, K.J.1
Schmittgen, T.D.2
-
33
-
-
80053064498
-
A strand-specific library preparation protocol for RNA sequencing
-
Borodina, T., Adjaye, J. & Sultan, M. A strand-specific library preparation protocol for RNA sequencing. Methods Enzymol. 500,79-98 (2011).
-
(2011)
Methods Enzymol.
, vol.500
, pp. 79-98
-
-
Borodina, T.1
Adjaye, J.2
Sultan, M.3
-
34
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
-
35
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
36
-
-
84951019738
-
Meta- and orthogonal integration of influenza "oMICs" data defines a role for UBR4 in virus budding
-
Tripathi, S. et al. Meta- and orthogonal integration of influenza "OMICs" data defines a role for UBR4 in virus budding. Cell Host Microbe 18, 723-735 (2015).
-
(2015)
Cell Host Microbe
, vol.18
, pp. 723-735
-
-
Tripathi, S.1
-
37
-
-
36849083946
-
A phosphomimetic mutation in the Sall1 repression motif disrupts recruitment of the nucleosome remodeling and deacetylase complex and repression of Gbx2
-
Lauberth, S. M., Bilyeu, A. C., Firulli, B. A., Kroll, K. L. & Rauchman, M. A phosphomimetic mutation in the Sall1 repression motif disrupts recruitment of the nucleosome remodeling and deacetylase complex and repression of Gbx2. J. Bio. Chem. 282, 34858-34868 (2007).
-
(2007)
J. Bio. Chem.
, vol.282
, pp. 34858-34868
-
-
Lauberth, S.M.1
Bilyeu, A.C.2
Firulli, B.A.3
Kroll, K.L.4
Rauchman, M.5
-
38
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
39
-
-
85017133693
-
DeepTools2: A next generation web server for deep-sequencing data analysis
-
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nuc eic Acids Res. 44, W160-W165 (2016).
-
(2016)
Nuc Eic Acids Res.
, vol.44
, pp. W160-W165
-
-
Ramirez, F.1
|