-
1
-
-
0027278557
-
Instability and decay of the primary structure of DNA
-
T. Lindahl, Instability and decay of the primary structure of DNA. Nature 362, 709-715 (1993).
-
(1993)
Nature
, vol.362
, pp. 709-715
-
-
Lindahl, T.1
-
2
-
-
78649336706
-
The DNA damage response: Making it safe to play with knives
-
A. Ciccia, S. J. Elledge, The DNA damage response: Making it safe to play with knives. Mol. Cell 40, 179-204 (2010).
-
(2010)
Mol. Cell
, vol.40
, pp. 179-204
-
-
Ciccia, A.1
Elledge, S.J.2
-
3
-
-
84865620494
-
Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: The molecular choreography
-
L. H. Thompson, Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: The molecular choreography. Mutat. Res. 751, 158-246 (2012).
-
(2012)
Mutat. Res.
, vol.751
, pp. 158-246
-
-
Thompson, L.H.1
-
5
-
-
84870738828
-
Diseases associated with defective responses to DNA damage
-
M. O'Driscoll, Diseases associated with defective responses to DNA damage. Cold Spring Harb. Perspect. Biol. 4, a012773 (2012).
-
(2012)
Cold Spring Harb. Perspect. Biol.
, vol.4
-
-
O'Driscoll, M.1
-
7
-
-
84873635293
-
Genome instability and aging
-
J. Vijg, Y. Suh, Genome instability and aging. Annu. Rev. Physiol. 75, 645-668 (2013).
-
(2013)
Annu. Rev. Physiol.
, vol.75
, pp. 645-668
-
-
Vijg, J.1
Suh, Y.2
-
8
-
-
84856436035
-
Targeting DNA damage and repair: Embracing the pharmacological era for successful cancer therapy
-
K. Aziz, S. Nowsheen, G. Pantelias, G. Iliakis, V. G. Gorgoulis, A. G. Georgakilas, Targeting DNA damage and repair: Embracing the pharmacological era for successful cancer therapy. Pharmacol. Ther. 133, 334-350 (2012).
-
(2012)
Pharmacol. Ther.
, vol.133
, pp. 334-350
-
-
Aziz, K.1
Nowsheen, S.2
Pantelias, G.3
Iliakis, G.4
Gorgoulis, V.G.5
Georgakilas, A.G.6
-
9
-
-
84859864552
-
Targeting the DNA damage response in oncology: Past, present and future perspectives
-
B. Basu, T. A. Yap, L. R. Molife, J. S. de Bono, Targeting the DNA damage response in oncology: Past, present and future perspectives. Curr. Opin. Oncol. 24, 316-324 (2012).
-
(2012)
Curr. Opin. Oncol.
, vol.24
, pp. 316-324
-
-
Basu, B.1
Yap, T.A.2
Molife, L.R.3
De Bono, J.S.4
-
10
-
-
84894353718
-
DNA damage response: Three levels of DNA repair regulation
-
B. M. Sirbu, D. Cortez, DNA damage response: Three levels of DNA repair regulation. Cold Spring Harb. Perspect. Biol. 5, a012724 (2013).
-
(2013)
Cold Spring Harb. Perspect. Biol.
, vol.5
-
-
Sirbu, B.M.1
Cortez, D.2
-
11
-
-
84877824046
-
Programmed induction of DNA double strand breaks during meiosis: Setting up communication between DNA and the chromosome structure
-
V. Borde, B. de Massy, Programmed induction of DNA double strand breaks during meiosis: Setting up communication between DNA and the chromosome structure. Curr. Opin. Genet. Dev. 23, 147-155 (2013).
-
(2013)
Curr. Opin. Genet. Dev.
, vol.23
, pp. 147-155
-
-
Borde, V.1
De Massy, B.2
-
12
-
-
84873320525
-
Mechanisms of programmed DNA lesions and genomic instability in the immune system
-
F. W. Alt, Y. Zhang, F. L. Meng, C. Guo, B. Schwer, Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell 152, 417-429 (2013).
-
(2013)
Cell
, vol.152
, pp. 417-429
-
-
Alt, F.W.1
Zhang, Y.2
Meng, F.L.3
Guo, C.4
Schwer, B.5
-
13
-
-
84875423827
-
The ATM protein kinase: Regulating the cellular response to genotoxic stress, and more
-
Y. Shiloh, Y. Ziv, The ATM protein kinase: Regulating the cellular response to genotoxic stress, and more. Nat. Rev. Mol. Cell Biol. 14, 197-210 (2013).
-
(2013)
Nat. Rev. Mol. Cell Biol.
, vol.14
, pp. 197-210
-
-
Shiloh, Y.1
Ziv, Y.2
-
14
-
-
79952235291
-
Dynamics of DNA damage response proteins at DNA breaks: A focus on protein modifications
-
S. E. Polo, S. P. Jackson, Dynamics of DNA damage response proteins at DNA breaks: A focus on protein modifications. Genes Dev. 25, 409-433 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 409-433
-
-
Polo, S.E.1
Jackson, S.P.2
-
15
-
-
78649703966
-
Rewiring of genetic networks in response to DNA damage
-
S. Bandyopadhyay, M. Mehta, D. Kuo, M. K. Sung, R. Chuang, E. J. Jaehnig, B. Bodenmiller, K. Licon, W. Copeland, M. Shales, D. Fiedler, J. Dutkowski, A. Guénolé, H. van Attikum, K. M. Shokat, R. D. Kolodner, W. K. Huh, R. Aebersold, M. C. Keogh, N. J. Krogan, T. Ideker, Rewiring of genetic networks in response to DNA damage. Science 330, 1385-1389 (2010).
-
(2010)
Science
, vol.330
, pp. 1385-1389
-
-
Bandyopadhyay, S.1
Mehta, M.2
Kuo, D.3
Sung, M.K.4
Chuang, R.5
Jaehnig, E.J.6
Bodenmiller, B.7
Licon, K.8
Copeland, W.9
Shales, M.10
Fiedler, D.11
Dutkowski, J.12
Guénolé, A.13
Van Attikum, H.14
Shokat, K.M.15
Kolodner, R.D.16
Huh, W.K.17
Aebersold, R.18
Keogh, M.C.19
Krogan, N.J.20
Ideker, T.21
more..
-
16
-
-
84892431829
-
Checkpoint kinases regulate a global network of transcription factors in response to DNA damage
-
E. J. Jaehnig, D. Kuo, H. Hombauer, T. G. Ideker, R. D. Kolodner, Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. Cell Rep. 4, 174-188 (2013).
-
(2013)
Cell Rep.
, vol.4
, pp. 174-188
-
-
Jaehnig, E.J.1
Kuo, D.2
Hombauer, H.3
Ideker, T.G.4
Kolodner, R.D.5
-
17
-
-
84872821321
-
Dissection of DNA damage responses using multiconditional genetic interaction maps
-
A. Guénolé, R. Srivas, K. Vreeken, Z. Z.Wang, S.Wang, N. J. Krogan, T. Ideker, H. van Attikum, Dissection of DNA damage responses using multiconditional genetic interaction maps. Mol. Cell 49, 346-358 (2013).
-
(2013)
Mol. Cell
, vol.49
, pp. 346-358
-
-
Guénolé, A.1
Srivas, R.2
Vreeken, K.3
Wang, Z.Z.4
Wang, S.5
Krogan, N.J.6
Ideker, T.7
Van Attikum, H.8
-
18
-
-
84883559012
-
Unraveling DNA damage response-signaling networks through systems approaches
-
L. von Stechow, B. van de Water, E. H. Danen, Unraveling DNA damage response-signaling networks through systems approaches. Arch. Toxicol. 87, 1635-1648 (2013).
-
(2013)
Arch. Toxicol.
, vol.87
, pp. 1635-1648
-
-
Von Stechow, L.1
Van De Water, B.2
Danen, E.H.3
-
19
-
-
84876093576
-
DNA damage-induced cell death: From specific DNA lesions to the DNA damage response and apoptosis
-
W. P. Roos, B. Kaina, DNA damage-induced cell death: From specific DNA lesions to the DNA damage response and apoptosis. Cancer Lett. 332, 237-248 (2013).
-
(2013)
Cancer Lett.
, vol.332
, pp. 237-248
-
-
Roos, W.P.1
Kaina, B.2
-
20
-
-
78751570979
-
RNA sequencing: Advances, challenges and opportunities
-
F. Ozsolak, P. M. Milos, RNA sequencing: Advances, challenges and opportunities. Nat. Rev. Genet. 12, 87-98 (2011).
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 87-98
-
-
Ozsolak, F.1
Milos, P.M.2
-
21
-
-
84869502241
-
ChIP-seq and beyond: New and improved methodologies to detect and characterize protein-DNA interactions
-
T. S. Furey, ChIP-seq and beyond: New and improved methodologies to detect and characterize protein-DNA interactions. Nat. Rev. Genet. 13, 840-852 (2012).
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 840-852
-
-
Furey, T.S.1
-
22
-
-
70349312354
-
ChIP-seq: Advantages and challenges of a maturing technology
-
P. J. Park, ChIP-seq: Advantages and challenges of a maturing technology. Nat. Rev. Genet. 10, 669-680 (2009).
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 669-680
-
-
Park, P.J.1
-
23
-
-
0025193312
-
Establishment and characterisation of a new tumorigenic cell line with a normal karyotype derived from a human breast adenocarcinoma
-
J. Gioanni, D. Le François, E. Zanghellini, C. Mazeau, F. Ettore, J. C. Lambert, M. Schneider, B. Dutrillaux, Establishment and characterisation of a new tumorigenic cell line with a normal karyotype derived from a human breast adenocarcinoma. Br. J. Cancer 62, 8-13 (1990).
-
(1990)
Br. J. Cancer
, vol.62
, pp. 8-13
-
-
Gioanni, J.1
Le François, D.2
Zanghellini, E.3
Mazeau, C.4
Ettore, F.5
Lambert, J.C.6
Schneider, M.7
Dutrillaux, B.8
-
24
-
-
45549084168
-
p53 target gene AEN is a nuclear exonuclease required for p53-dependent apoptosis
-
T. Kawase, H. Ichikawa, T. Ohta, N. Nozaki, F. Tashiro, R. Ohki, Y. Taya, p53 target gene AEN is a nuclear exonuclease required for p53-dependent apoptosis. Oncogene 27, 3797-3810 (2008).
-
(2008)
Oncogene
, vol.27
, pp. 3797-3810
-
-
Kawase, T.1
Ichikawa, H.2
Ohta, T.3
Nozaki, N.4
Tashiro, F.5
Ohki, R.6
Taya, Y.7
-
25
-
-
77951536199
-
ISG20L1 is a p53 family target gene that modulates genotoxic stress-induced autophagy
-
K. G. Eby, J. M. Rosenbluth, D. J. Mays, C. B. Marshall, C. E. Barton, S. Sinha, K. N. Johnson, L. Tang, J. A. Pietenpol, ISG20L1 is a p53 family target gene that modulates genotoxic stress-induced autophagy. Mol. Cancer 9, 95 (2010).
-
(2010)
Mol. Cancer
, vol.9
, pp. 95
-
-
Eby, K.G.1
Rosenbluth, J.M.2
Mays, D.J.3
Marshall, C.B.4
Barton, C.E.5
Sinha, S.6
Johnson, K.N.7
Tang, L.8
Pietenpol, J.A.9
-
26
-
-
33748774114
-
Upon intracellular processing, the C-terminal death domain-containing fragment of the p53-inducible PIDD/LRDD protein translocates to the nucleoli and interacts with nucleolin
-
R. Pick, S. Badura, S. Bösser, M. Zörnig, Upon intracellular processing, the C-terminal death domain-containing fragment of the p53-inducible PIDD/LRDD protein translocates to the nucleoli and interacts with nucleolin. Biochem. Biophys. Res. Commun. 349, 1329-1338 (2006).
-
(2006)
Biochem. Biophys. Res. Commun.
, vol.349
, pp. 1329-1338
-
-
Pick, R.1
Badura, S.2
Bösser, S.3
Zörnig, M.4
-
27
-
-
59049083119
-
PH domain-only protein PHLDA3 is a p53-regulated repressor of Akt
-
T. Kawase, R. Ohki, T. Shibata, S. Tsutsumi, N. Kamimura, J. Inazawa, T. Ohta, H. Ichikawa, H. Aburatani, F. Tashiro, Y. Taya, PH domain-only protein PHLDA3 is a p53-regulated repressor of Akt. Cell 136, 535-550 (2009).
-
(2009)
Cell
, vol.136
, pp. 535-550
-
-
Kawase, T.1
Ohki, R.2
Shibata, T.3
Tsutsumi, S.4
Kamimura, N.5
Inazawa, J.6
Ohta, T.7
Ichikawa, H.8
Aburatani, H.9
Tashiro, F.10
Taya, Y.11
-
28
-
-
84879987789
-
lincRNAs: Genomics, evolution, and mechanisms
-
I. Ulitsky, D. P. Bartel, lincRNAs: Genomics, evolution, and mechanisms. Cell 154, 26-46 (2013).
-
(2013)
Cell
, vol.154
, pp. 26-46
-
-
Ulitsky, I.1
Bartel, D.P.2
-
29
-
-
84875200257
-
Long noncoding RNAs: Cellular address codes in development and disease
-
P. J. Batista, H. Y. Chang, Long noncoding RNAs: Cellular address codes in development and disease. Cell 152, 1298-1307 (2013).
-
(2013)
Cell
, vol.152
, pp. 1298-1307
-
-
Batista, P.J.1
Chang, H.Y.2
-
30
-
-
84861904178
-
Genome regulation by long noncoding RNAs
-
J. L. Rinn, H. Y. Chang, Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145-166 (2012).
-
(2012)
Annu. Rev. Biochem.
, vol.81
, pp. 145-166
-
-
Rinn, J.L.1
Chang, H.Y.2
-
31
-
-
84876093209
-
p53 induces transcriptional and translational programs to suppress cell proliferation and growth
-
F. Loayza-Puch, J. Drost, K. Rooijers, R. Lopes, R. Elkon, R. Agami, p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol. 14, R32 (2013).
-
(2013)
Genome Biol.
, vol.14
-
-
Loayza-Puch, F.1
Drost, J.2
Rooijers, K.3
Lopes, R.4
Elkon, R.5
Agami, R.6
-
32
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
T. K. Kim, M. Hemberg, J. M. Gray, A. M. Costa, D. M. Bear, J. Wu, D. A. Harmin, M. Laptewicz, K. Barbara-Haley, S. Kuersten, E. Markenscoff- Papadimitriou, D. Kuhl, H. Bito, P. F. Worley, G. Kreiman, M. E. Greenberg, Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
Hemberg, M.2
Gray, J.M.3
Costa, A.M.4
Bear, D.M.5
Wu, J.6
Harmin, D.A.7
Laptewicz, M.8
Barbara-Haley, K.9
Kuersten, S.10
Markenscoff-Papadimitriou, E.11
Kuhl, D.12
Bito, H.13
Worley, P.F.14
Kreiman, G.15
Greenberg, M.E.16
-
33
-
-
84873456575
-
eRNAs are required for p53-dependent enhancer activity and gene transcription
-
C. A. Melo, J. Drost, P. J. Wijchers, H. van de Werken, E. de Wit, J. A. Oude Vrielink, R. Elkon, S. A. Melo, N. Léveillé, R. Kalluri, W. de Laat, R. Agami, eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol. Cell 49, 524-535 (2013).
-
(2013)
Mol. Cell
, vol.49
, pp. 524-535
-
-
Melo, C.A.1
Drost, J.2
Wijchers, P.J.3
Van De Werken, H.4
De Wit, E.5
Oude Vrielink, J.A.6
Elkon, R.7
Melo, S.A.8
Léveillé, N.9
Kalluri, R.10
De Laat, W.11
Agami, R.12
-
34
-
-
34250851115
-
A microRNA component of the p53 tumour suppressor network
-
L. He, X. He, L. P. Lim, E. de Stanchina, Z. Xuan, Y. Liang, W. Xue, L. Zender, J. Magnus, D. Ridzon, A. L. Jackson, P. S. Linsley, C. Chen, S. W. Lowe, M. A. Cleary, G. J. Hannon, A microRNA component of the p53 tumour suppressor network. Nature 447, 1130-1134 (2007).
-
(2007)
Nature
, vol.447
, pp. 1130-1134
-
-
He, L.1
He, X.2
Lim, L.P.3
De Stanchina, E.4
Xuan, Z.5
Liang, Y.6
Xue, W.7
Zender, L.8
Magnus, J.9
Ridzon, D.10
Jackson, A.L.11
Linsley, P.S.12
Chen, C.13
Lowe, S.W.14
Cleary, M.A.15
Hannon, G.J.16
-
35
-
-
34249822779
-
Transcriptional activation of miR-34a contributes to p53-mediated apoptosis
-
N. Raver-Shapira, E. Marciano, E. Meiri, Y. Spector, N. Rosenfeld, N. Moskovits, Z. Bentwich, M. Oren, Transcriptional activation of miR-34a contributes to p53-mediated apoptosis. Mol. Cell 26, 731-743 (2007).
-
(2007)
Mol. Cell
, vol.26
, pp. 731-743
-
-
Raver-Shapira, N.1
Marciano, E.2
Meiri, E.3
Spector, Y.4
Rosenfeld, N.5
Moskovits, N.6
Bentwich, Z.7
Oren, M.8
-
36
-
-
84864022892
-
E2F7, a novel target, is upregulated by p53 and mediates DNA damage-dependent transcriptional repression
-
L. A. Carvajal, P. J. Hamard, C. Tonnessen, J. J. Manfredi, E2F7, a novel target, is upregulated by p53 and mediates DNA damage-dependent transcriptional repression. Genes Dev. 26, 1533-1545 (2012).
-
(2012)
Genes Dev.
, vol.26
, pp. 1533-1545
-
-
Carvajal, L.A.1
Hamard, P.J.2
Tonnessen, C.3
Manfredi, J.J.4
-
37
-
-
84864011866
-
The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence
-
O. Aksoy, A. Chicas, T. Zeng, Z. Zhao, M. McCurrach, X. Wang, S. W. Lowe, The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence. Genes Dev. 26, 1546-1557 (2012).
-
(2012)
Genes Dev.
, vol.26
, pp. 1546-1557
-
-
Aksoy, O.1
Chicas, A.2
Zeng, T.3
Zhao, Z.4
McCurrach, M.5
Wang, X.6
Lowe, S.W.7
-
38
-
-
84860369516
-
Critical role for antiapoptotic Bcl-xL and Mcl-1 in human macrophage survival and cellular IAP1/2 (cIAP1/2) in resistance to HIV-Vpr-induced apoptosis
-
A. Busca, M. Saxena, A. Kumar, Critical role for antiapoptotic Bcl-xL and Mcl-1 in human macrophage survival and cellular IAP1/2 (cIAP1/2) in resistance to HIV-Vpr-induced apoptosis. J. Biol. Chem. 287, 15118-15133 (2012).
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 15118-15133
-
-
Busca, A.1
Saxena, M.2
Kumar, A.3
-
39
-
-
84887911347
-
Platinum-resistance in ovarian cancer cells is mediated by IL-6 secretion via the increased expression of its target cIAP-2
-
S. Cohen, I. Bruchim, D. Graiver, Z. Evron, V. Oron-Karni, M. Pasmanik-Chor, R. Eitan, J. Bernheim, H. Levavi, A. Fishman, E. Flescher, Platinum-resistance in ovarian cancer cells is mediated by IL-6 secretion via the increased expression of its target cIAP-2. J. Mol. Med. 91, 357-368 (2013).
-
(2013)
J. Mol. Med.
, vol.91
, pp. 357-368
-
-
Cohen, S.1
Bruchim, I.2
Graiver, D.3
Evron, Z.4
Oron-Karni, V.5
Pasmanik-Chor, M.6
Eitan, R.7
Bernheim, J.8
Levavi, H.9
Fishman, A.10
Flescher, E.11
-
40
-
-
0036337748
-
A20 inhibits tumor necrosis factor (TNF) alpha-induced apoptosis by disrupting recruitment of TRADD and RIP to the TNF receptor 1 complex in Jurkat T cells
-
K. L. He, A. T. Ting, A20 inhibits tumor necrosis factor (TNF) alpha-induced apoptosis by disrupting recruitment of TRADD and RIP to the TNF receptor 1 complex in Jurkat T cells. Mol. Cell. Biol. 22, 6034-6045 (2002).
-
(2002)
Mol. Cell. Biol.
, vol.22
, pp. 6034-6045
-
-
He, K.L.1
Ting, A.T.2
-
41
-
-
34447507710
-
A20/TNFAIP3, a new estrogen-regulated gene that confers tamoxifen resistance in breast cancer cells
-
J. A. Vendrell, S. Ghayad, S. Ben-Larbi, C. Dumontet, N. Mechti, P. A. Cohen, A20/TNFAIP3, a new estrogen-regulated gene that confers tamoxifen resistance in breast cancer cells. Oncogene 26, 4656-4667 (2007).
-
(2007)
Oncogene
, vol.26
, pp. 4656-4667
-
-
Vendrell, J.A.1
Ghayad, S.2
Ben-Larbi, S.3
Dumontet, C.4
Mechti, N.5
Cohen, P.A.6
-
42
-
-
33646547951
-
Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4
-
M. Gilchrist, V. Thorsson, B. Li, A. G. Rust, M. Korb, J. C. Roach, K. Kennedy, T. Hai, H. Bolouri, A. Aderem, Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441, 173-178 (2006).
-
(2006)
Nature
, vol.441
, pp. 173-178
-
-
Gilchrist, M.1
Thorsson, V.2
Li, B.3
Rust, A.G.4
Korb, M.5
Roach, J.C.6
Kennedy, K.7
Hai, T.8
Bolouri, H.9
Aderem, A.10
-
43
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
N. D. Heintzman, G. C. Hon, R. D. Hawkins, P. Kheradpour, A. Stark, L. F. Harp, Z. Ye, L. K. Lee, R. K. Stuart, C. W. Ching, K. A. Ching, J. E. Antosiewicz-Bourget, H. Liu, X. Zhang, R. D. Green, V. V. Lobanenkov, R. Stewart, J. A. Thomson, G. E. Crawford, M. Kellis, B. Ren, 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
Hon, G.C.2
Hawkins, R.D.3
Kheradpour, P.4
Stark, A.5
Harp, L.F.6
Ye, Z.7
Lee, L.K.8
Stuart, R.K.9
Ching, C.W.10
Ching, K.A.11
Antosiewicz-Bourget, J.E.12
Liu, H.13
Zhang, X.14
Green, R.D.15
Lobanenkov, V.V.16
Stewart, R.17
Thomson, J.A.18
Crawford, G.E.19
Kellis, M.20
Ren, B.21
more..
-
44
-
-
34249299791
-
The complex language of chromatin regulation during transcription
-
S. L. Berger, The complex language of chromatin regulation during transcription. Nature 447, 407-412 (2007).
-
(2007)
Nature
, vol.447
, pp. 407-412
-
-
Berger, S.L.1
-
45
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Z. Wang, M. Gerstein, M. Snyder, RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63 (2009).
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
46
-
-
33644843626
-
Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue
-
S. Rashi-Elkeles, R. Elkon, N. Weizman, C. Linhart, N. Amariglio, G. Sternberg, G. Rechavi, A. Barzilai, R. Shamir, Y. Shiloh, Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue. Oncogene 25, 1584-1592 (2006).
-
(2006)
Oncogene
, vol.25
, pp. 1584-1592
-
-
Rashi-Elkeles, S.1
Elkon, R.2
Weizman, N.3
Linhart, C.4
Amariglio, N.5
Sternberg, G.6
Rechavi, G.7
Barzilai, A.8
Shamir, R.9
Shiloh, Y.10
-
47
-
-
0141785046
-
Functional genomics as a window on radiation stress signaling
-
S. A. Amundson, M. Bittner, A. J. Fornace Jr., Functional genomics as a window on radiation stress signaling. Oncogene 22, 5828-5833 (2003).
-
(2003)
Oncogene
, vol.22
, pp. 5828-5833
-
-
Amundson, S.A.1
Bittner, M.2
Fornace Jr., A.J.3
-
48
-
-
70350343183
-
Cell response to ionising radiation analysed by gene expression patterns
-
L. Roy, G. Gruel, A. Vaurijoux, Cell response to ionising radiation analysed by gene expression patterns. Ann. Ist. Super. Sanita 45, 272-277 (2009).
-
(2009)
Ann. Ist. Super. Sanita
, vol.45
, pp. 272-277
-
-
Roy, L.1
Gruel, G.2
Vaurijoux, A.3
-
49
-
-
0026318356
-
Participation of p53 protein in the cellular response to DNA damage
-
M. B. Kastan, O. Onyekwere, D. Sidransky, B. Vogelstein, R. W. Craig, Participation of p53 protein in the cellular response to DNA damage. Cancer Res. 51, 6304-6311 (1991).
-
(1991)
Cancer Res.
, vol.51
, pp. 6304-6311
-
-
Kastan, M.B.1
Onyekwere, O.2
Sidransky, D.3
Vogelstein, B.4
Craig, R.W.5
-
50
-
-
0026496885
-
A mammalian cell cycle checkpoint pathway utilizing p53 and GADD45 is defective in ataxia-telangiectasia
-
M. B. Kastan, Q. Zhan, W. S. el-Deiry, F. Carrier, T. Jacks, W. V. Walsh, B. S. Plunkett, B. Vogelstein, A. J. Fornace Jr., A mammalian cell cycle checkpoint pathway utilizing p53 and GADD45 is defective in ataxia- telangiectasia. Cell 71, 587-597 (1992).
-
(1992)
Cell
, vol.71
, pp. 587-597
-
-
Kastan, M.B.1
Zhan, Q.2
El-Deiry, W.S.3
Carrier, F.4
Jacks, T.5
Walsh, W.V.6
Plunkett, B.S.7
Vogelstein, B.8
Fornace Jr., A.J.9
-
51
-
-
0032508608
-
Activation of the ATM kinase by ionizing radiation and phosphorylation of p53
-
C. E. Canman, D. S. Lim, K. A. Cimprich, Y. Taya, K. Tamai, K. Sakaguchi, E. Appella, M. B. Kastan, J. D. Siliciano, Activation of the ATM kinase by ionizing radiation and phosphorylation of p53. Science 281, 1677-1679 (1998).
-
(1998)
Science
, vol.281
, pp. 1677-1679
-
-
Canman, C.E.1
Lim, D.S.2
Cimprich, K.A.3
Taya, Y.4
Tamai, K.5
Sakaguchi, K.6
Appella, E.7
Kastan, M.B.8
Siliciano, J.D.9
-
52
-
-
0032508504
-
Enhanced phosphorylation of p53 by ATM in response to DNA damage
-
S. Banin, L. Moyal, S. Shieh, Y. Taya, C. W. Anderson, L. Chessa, N. I. Smorodinsky, C. Prives, Y. Reiss, Y. Shiloh, Y. Ziv, Enhanced phosphorylation of p53 by ATM in response to DNA damage. Science 281, 1674-1677 (1998).
-
(1998)
Science
, vol.281
, pp. 1674-1677
-
-
Banin, S.1
Moyal, L.2
Shieh, S.3
Taya, Y.4
Anderson, C.W.5
Chessa, L.6
Smorodinsky, N.I.7
Prives, C.8
Reiss, Y.9
Shiloh, Y.10
Ziv, Y.11
-
53
-
-
84862307800
-
Eukaryotic DNA damage checkpoint activation in response to double-strand breaks
-
K. Finn, N. F. Lowndes, M. Grenon, Eukaryotic DNA damage checkpoint activation in response to double-strand breaks. Cell. Mol. Life Sci. 69, 1447-1473 (2012).
-
(2012)
Cell. Mol. Life Sci.
, vol.69
, pp. 1447-1473
-
-
Finn, K.1
Lowndes, N.F.2
Grenon, M.3
-
54
-
-
84055190692
-
Distinct p53 genomic binding patterns in normal and cancer-derived human cells
-
K. Botcheva, S. R. McCorkle, W. R. McCombie, J. J. Dunn, C. W. Anderson, Distinct p53 genomic binding patterns in normal and cancer-derived human cells. Cell Cycle 10, 4237-4249 (2011).
-
(2011)
Cell Cycle
, vol.10
, pp. 4237-4249
-
-
Botcheva, K.1
McCorkle, S.R.2
McCombie, W.R.3
Dunn, J.J.4
Anderson, C.W.5
-
55
-
-
84869090231
-
Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis
-
F. Nikulenkov, C. Spinnler, H. Li, C. Tonelli, Y. Shi, M. Turunen, T. Kivioja, I. Ignatiev, A. Kel, J. Taipale, G. Selivanova, Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis. Cell Death Differ. 19, 1992-2002 (2012).
-
(2012)
Cell Death Differ.
, vol.19
, pp. 1992-2002
-
-
Nikulenkov, F.1
Spinnler, C.2
Li, H.3
Tonelli, C.4
Shi, Y.5
Turunen, M.6
Kivioja, T.7
Ignatiev, I.8
Kel, A.9
Taipale, J.10
Selivanova, G.11
-
56
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
G. Robertson, M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao, T. Zeng, G. Euskirchen, B. Bernier, R. Varhol, A. Delaney, N. Thiessen, O. L. Griffith, A. He, M. Marra, M. Snyder, S. Jones, Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651-657 (2007).
-
(2007)
Nat. Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
Thiessen, N.11
Griffith, O.L.12
He, A.13
Marra, M.14
Snyder, M.15
Jones, S.16
-
57
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium, B. E. Bernstein, E. Birney, I. Dunham, E. D. Green, C. Gunter, M. Snyder, An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Bernstein, B.E.1
Birney, E.2
Dunham, I.3
Green, E.D.4
Gunter, C.5
Snyder, M.6
-
58
-
-
84856525447
-
Deconstructing p53 transcriptional networks in tumor suppression
-
K. T. Bieging, L. D. Attardi, Deconstructing p53 transcriptional networks in tumor suppression. Trends Cell Biol. 22, 97-106 (2012).
-
(2012)
Trends Cell Biol.
, vol.22
, pp. 97-106
-
-
Bieging, K.T.1
Attardi, L.D.2
-
59
-
-
84857443702
-
The p53 network: Cellular and systemic DNA damage responses in aging and cancer
-
H. C. Reinhardt, B. Schumacher, The p53 network: Cellular and systemic DNA damage responses in aging and cancer. Trends Genet. 28, 128-136 (2012).
-
(2012)
Trends Genet.
, vol.28
, pp. 128-136
-
-
Reinhardt, H.C.1
Schumacher, B.2
-
60
-
-
84857342600
-
The p53 circuit board
-
K. D. Sullivan, C. L. Gallant-Behm, R. E. Henry, J. L. Fraikin, J. M. Espinosa, The p53 circuit board. Biochim. Biophys. Acta 1825, 229-244 (2012).
-
(2012)
Biochim. Biophys. Acta
, vol.1825
, pp. 229-244
-
-
Sullivan, K.D.1
Gallant-Behm, C.L.2
Henry, R.E.3
Fraikin, J.L.4
Espinosa, J.M.5
-
61
-
-
77954641944
-
Radiation-induced cell death mechanisms
-
D. Eriksson, T. Stigbrand, Radiation-induced cell death mechanisms. Tumour Biol. 31, 363-372 (2010).
-
(2010)
Tumour Biol.
, vol.31
, pp. 363-372
-
-
Eriksson, D.1
Stigbrand, T.2
-
63
-
-
84882450932
-
Various modes of cell death induced by DNA damage
-
O. Surova, B. Zhivotovsky, Various modes of cell death induced by DNA damage. Oncogene 32, 3789-3797 (2013).
-
(2013)
Oncogene
, vol.32
, pp. 3789-3797
-
-
Surova, O.1
Zhivotovsky, B.2
-
64
-
-
0035736138
-
If not apoptosis, then what? Treatment-induced senescence and mitotic catastrophe in tumor cells
-
I. B. Roninson, E. V. Broude, B. D. Chang, If not apoptosis, then what? Treatment-induced senescence and mitotic catastrophe in tumor cells. Drug Resist. Updat. 4, 303-313 (2001).
-
(2001)
Drug Resist. Updat.
, vol.4
, pp. 303-313
-
-
Roninson, I.B.1
Broude, E.V.2
Chang, B.D.3
-
66
-
-
84877826693
-
Restoring p53 function in human melanoma cells by inhibiting MDM2 and cyclin B1/CDK1-phosphorylated nuclear iASPP
-
M. Lu, H. Breyssens, V. Salter, S. Zhong, Y. Hu, C. Baer, I. Ratnayaka, A. Sullivan, N. R. Brown, J. Endicott, S. Knapp, B. M. Kessler, M. R. Middleton, C. Siebold, E. Y. Jones, E. V. Sviderskaya, J. Cebon, T. John, O. L. Caballero, C. R. Goding, X. Lu, Restoring p53 function in human melanoma cells by inhibiting MDM2 and cyclin B1/CDK1-phosphorylated nuclear iASPP. Cancer Cell 23, 618-633 (2013).
-
(2013)
Cancer Cell
, vol.23
, pp. 618-633
-
-
Lu, M.1
Breyssens, H.2
Salter, V.3
Zhong, S.4
Hu, Y.5
Baer, C.6
Ratnayaka, I.7
Sullivan, A.8
Brown, N.R.9
Endicott, J.10
Knapp, S.11
Kessler, B.M.12
Middleton, M.R.13
Siebold, C.14
Jones, E.Y.15
Sviderskaya, E.V.16
Cebon, J.17
John, T.18
Caballero, O.L.19
Goding, C.R.20
Lu, X.21
more..
-
67
-
-
84858722471
-
DNA damage-dependent NF-κB activation: NEMO turns nuclear signaling inside out
-
K. W. McCool, S. Miyamoto, DNA damage-dependent NF-κB activation: NEMO turns nuclear signaling inside out. Immunol. Rev. 246, 311-326 (2012).
-
(2012)
Immunol. Rev.
, vol.246
, pp. 311-326
-
-
McCool, K.W.1
Miyamoto, S.2
-
68
-
-
79952534189
-
Regulation of chromatin by histone modifications
-
A. J. Bannister, T. Kouzarides, Regulation of chromatin by histone modifications. Cell Res. 21, 381-395 (2011).
-
(2011)
Cell Res.
, vol.21
, pp. 381-395
-
-
Bannister, A.J.1
Kouzarides, T.2
-
69
-
-
79960600521
-
p53 binding to nucleosomes within the p21 promoter in vivo leads to nucleosome loss and transcriptional activation
-
O. Laptenko, R. Beckerman, E. Freulich, C. Prives, p53 binding to nucleosomes within the p21 promoter in vivo leads to nucleosome loss and transcriptional activation. Proc. Natl. Acad. Sci. U.S.A. 108, 10385-10390 (2011).
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 10385-10390
-
-
Laptenko, O.1
Beckerman, R.2
Freulich, E.3
Prives, C.4
-
70
-
-
78649264722
-
p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy
-
E. Lidor Nili, Y. Field, Y. Lubling, J. Widom, M. Oren, E. Segal, p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res. 20, 1361-1368 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1361-1368
-
-
Lidor Nili, E.1
Field, Y.2
Lubling, Y.3
Widom, J.4
Oren, M.5
Segal, E.6
-
71
-
-
79957547966
-
The protein kinase landscape of the DNA damage response
-
A. Bensimon, R. Aebersold, Y. Shiloh, Beyond ATM: The protein kinase landscape of the DNA damage response. FEBS Lett. 585, 1625-1639 (2011).
-
(2011)
FEBS Lett.
, vol.585
, pp. 1625-1639
-
-
Bensimon, A.1
Aebersold, R.2
Shiloh, Y.3
Beyond, A.T.M.4
-
72
-
-
84883474258
-
Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells
-
D. Menendez, T. A. Nguyen, J. M. Freudenberg, V. J. Mathew, C. W. Anderson, R. Jothi, M. A. Resnick, Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells. Nucleic Acids Res. 41, 7286-7301 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 7286-7301
-
-
Menendez, D.1
Nguyen, T.A.2
Freudenberg, J.M.3
Mathew, V.J.4
Anderson, C.W.5
Jothi, R.6
Resnick, M.A.7
-
73
-
-
9744271049
-
Identification and characterization of a novel and specific inhibitor of the ataxia-telangiectasia mutated kinase ATM
-
I. Hickson, Y. Zhao, C. J. Richardson, S. J. Green, N. M. Martin, A. I. Orr, P. M. Reaper, S. P. Jackson, N. J. Curtin, G. C. Smith, Identification and characterization of a novel and specific inhibitor of the ataxia-telangiectasia mutated kinase ATM. Cancer Res. 64, 9152-9159 (2004).
-
(2004)
Cancer Res.
, vol.64
, pp. 9152-9159
-
-
Hickson, I.1
Zhao, Y.2
Richardson, C.J.3
Green, S.J.4
Martin, N.M.5
Orr, A.I.6
Reaper, P.M.7
Jackson, S.P.8
Curtin, N.J.9
Smith, G.C.10
-
74
-
-
84862293682
-
A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods
-
M. Sultan, S. Dökel, V. Amstislavskiy, D. Wuttig, H. Sültmann, H. Lehrach, M. L. Yaspo, A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods. Biochem. Biophys. Res. Commun. 422, 643-646 (2012).
-
(2012)
Biochem. Biophys. Res. Commun.
, vol.422
, pp. 643-646
-
-
Sultan, M.1
Dökel, S.2
Amstislavskiy, V.3
Wuttig, D.4
Sültmann, H.5
Lehrach, H.6
Yaspo, M.L.7
-
75
-
-
79959559692
-
The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle
-
H. J. Warnatz, D. Schmidt, T. Manke, I. Piccini, M. Sultan, T. Borodina, D. Balzereit, W. Wruck, A. Soldatov, M. Vingron, H. Lehrach, M. L. Yaspo, 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).
-
(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
Lehrach, H.11
Yaspo, M.L.12
-
77
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
C. Trapnell, L. Pachter, S. L. Salzberg, TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
78
-
-
84883364264
-
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
-
S. Anders, D. J. McCarthy, Y. Chen, M. Okoniewski, G. K. Smyth, W. Huber, M. D. Robinson, Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc. 8, 1765-1786 (2013).
-
(2013)
Nat. Protoc.
, vol.8
, pp. 1765-1786
-
-
Anders, S.1
McCarthy, D.J.2
Chen, Y.3
Okoniewski, M.4
Smyth, G.K.5
Huber, W.6
Robinson, M.D.7
-
79
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
B. Langmead, C. Trapnell, M. Pop, S. L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
80
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
H. Ji, H. Jiang, W. Ma, D. S. Johnson, R. M. Myers, W. H. Wong, An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 26, 1293-1300 (2008).
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
Wong, W.H.6
-
81
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
T. L. Bailey, C. Elkan, Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
82
-
-
46449123335
-
Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
-
C. Linhart, Y. Halperin, R. Shamir, Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. Genome Res. 18, 1180-1189 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 1180-1189
-
-
Linhart, C.1
Halperin, Y.2
Shamir, R.3
-
83
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
R. A. Irizarry, B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis, U. Scherf, T. P. Speed, Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264 (2003).
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
Speed, T.P.7
-
84
-
-
34548561818
-
beadarray: R classes and methods for Illumina bead-based data
-
M. J. Dunning, M. L. Smith, M. E. Ritchie, S. Tavaré, beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 23, 2183-2184 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 2183-2184
-
-
Dunning, M.J.1
Smith, M.L.2
Ritchie, M.E.3
Tavaré, S.4
-
85
-
-
0141506116
-
CLICK and EXPANDER: A system for clustering and visualizing gene expression data
-
R. Sharan, A. Maron-Katz, R. Shamir, CLICK and EXPANDER: A system for clustering and visualizing gene expression data. Bioinformatics 19, 1787-1799 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 1787-1799
-
-
Sharan, R.1
Maron-Katz, A.2
Shamir, R.3
-
86
-
-
76649122816
-
Expander: From expression microarrays to networks and functions
-
I. Ulitsky, A. Maron-Katz, S. Shavit, D. Sagir, C. Linhart, R. Elkon, A. Tanay, R. Sharan, Y. Shiloh, R. Shamir, Expander: From expression microarrays to networks and functions. Nat. Protocols 5, 303-322 (2010).
-
(2010)
Nat. Protocols
, vol.5
, pp. 303-322
-
-
Ulitsky, I.1
Maron-Katz, A.2
Shavit, S.3
Sagir, D.4
Linhart, C.5
Elkon, R.6
Tanay, A.7
Sharan, R.8
Shiloh, Y.9
Shamir, R.10
-
87
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
W. Huang da, B. T. Sherman, R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols 4, 44-57 (2009).
-
(2009)
Nat. Protocols
, vol.4
, pp. 44-57
-
-
Da Huang, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
88
-
-
78651290281
-
SPIKE: A database of highly curated human signaling pathways
-
A. Paz, Z. Brownstein, Y. Ber, S. Bialik, E. David, D. Sagir, I. Ulitsky, R. Elkon, A. Kimchi, K. B. Avraham, Y. Shiloh, R. Shamir, SPIKE: A database of highly curated human signaling pathways. Nucleic Acids Res. 39, D793-D799 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Paz, A.1
Brownstein, Z.2
Ber, Y.3
Bialik, S.4
David, E.5
Sagir, D.6
Ulitsky, I.7
Elkon, R.8
Kimchi, A.9
Avraham, K.B.10
Shiloh, Y.11
Shamir, R.12
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