-
1
-
-
84940502214
-
Predicting effective microRNA target sites in mammalian mRNAs
-
Agarwal, V., Bell, G.W., Nam, J.-W., Bartel, D.P., Predicting effective microRNA target sites in mammalian mRNAs. eLife, 4, 2015, e05005.
-
(2015)
eLife
, vol.4
, pp. e05005
-
-
Agarwal, V.1
Bell, G.W.2
Nam, J.-W.3
Bartel, D.P.4
-
2
-
-
84902324667
-
Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms
-
Allen, M.A., Andrysik, Z., Dengler, V.L., Mellert, H.S., Guarnieri, A., Freeman, J.A., Sullivan, K.D., Galbraith, M.D., Luo, X., Kraus, W.L., et al. Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. eLife, 3, 2014, e02200.
-
(2014)
eLife
, vol.3
, pp. e02200
-
-
Allen, M.A.1
Andrysik, Z.2
Dengler, V.L.3
Mellert, H.S.4
Guarnieri, A.5
Freeman, J.A.6
Sullivan, K.D.7
Galbraith, M.D.8
Luo, X.9
Kraus, W.L.10
-
3
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., Zhao, K., High-resolution profiling of histone methylations in the human genome. Cell 129 (2007), 823–837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.-Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
4
-
-
42949171936
-
Recurrent initiation: a mechanism for triggering p53 pulses in response to DNA damage
-
Batchelor, E., Mock, C.S., Bhan, I., Loewer, A., Lahav, G., Recurrent initiation: a mechanism for triggering p53 pulses in response to DNA damage. Mol. Cell 30 (2008), 277–289.
-
(2008)
Mol. Cell
, vol.30
, pp. 277-289
-
-
Batchelor, E.1
Mock, C.S.2
Bhan, I.3
Loewer, A.4
Lahav, G.5
-
5
-
-
79955809529
-
Stimulus-dependent dynamics of p53 in single cells
-
Batchelor, E., Loewer, A., Mock, C., Lahav, G., Stimulus-dependent dynamics of p53 in single cells. Mol. Syst. Biol., 7, 2011, 488.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 488
-
-
Batchelor, E.1
Loewer, A.2
Mock, C.3
Lahav, G.4
-
6
-
-
84905049901
-
Trimmomatic: a flexible trimmer for Illumina sequence data
-
Bolger, A.M., Lohse, M., Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 (2014), 2114–2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
7
-
-
84982950001
-
Local and global regulation of transcription initiation in bacteria
-
Browning, D.F., Busby, S.J.W., Local and global regulation of transcription initiation in bacteria. Nat. Rev. Microbiol. 14 (2016), 638–650.
-
(2016)
Nat. Rev. Microbiol.
, vol.14
, pp. 638-650
-
-
Browning, D.F.1
Busby, S.J.W.2
-
8
-
-
0037134020
-
A system for stable expression of short interfering RNAs in mammalian cells
-
Brummelkamp, T.R., Bernards, R., Agami, R., A system for stable expression of short interfering RNAs in mammalian cells. Science 296 (2002), 550–553.
-
(2002)
Science
, vol.296
, pp. 550-553
-
-
Brummelkamp, T.R.1
Bernards, R.2
Agami, R.3
-
9
-
-
0033611568
-
p53 represses ribosomal gene transcription
-
Budde, A., Grummt, I., p53 represses ribosomal gene transcription. Oncogene 18 (1999), 1119–1124.
-
(1999)
Oncogene
, vol.18
, pp. 1119-1124
-
-
Budde, A.1
Grummt, I.2
-
10
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J., Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10 (2013), 1213–1218.
-
(2013)
Nat. Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
11
-
-
84949212255
-
ATAC-seq: a method for assaying chromatin accessibility genome-wide
-
Buenrostro, J.D., Wu, B., Chang, H.Y., Greenleaf, W.J., ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 109 (2015), 21.29.1–21.29.9.
-
(2015)
Curr. Protoc. Mol. Biol.
, vol.109
, pp. 21.29.1-21.29.9
-
-
Buenrostro, J.D.1
Wu, B.2
Chang, H.Y.3
Greenleaf, W.J.4
-
12
-
-
84904800365
-
A comprehensive and high-resolution genome-wide response of p53 to stress
-
Chang, G.S., Chen, X.A., Park, B., Rhee, H.S., Li, P., Han, K.H., Mishra, T., Chan-Salis, K.Y., Li, Y., Hardison, R.C., et al. A comprehensive and high-resolution genome-wide response of p53 to stress. Cell Rep. 8 (2014), 514–527.
-
(2014)
Cell Rep.
, vol.8
, pp. 514-527
-
-
Chang, G.S.1
Chen, X.A.2
Park, B.3
Rhee, H.S.4
Li, P.5
Han, K.H.6
Mishra, T.7
Chan-Salis, K.Y.8
Li, Y.9
Hardison, R.C.10
-
13
-
-
84873351389
-
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing
-
Chen, K., Xi, Y., Pan, X., Li, Z., Kaestner, K., Tyler, J., Dent, S., He, X., Li, W., DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 23 (2013), 341–351.
-
(2013)
Genome Res.
, vol.23
, pp. 341-351
-
-
Chen, K.1
Xi, Y.2
Pan, X.3
Li, Z.4
Kaestner, K.5
Tyler, J.6
Dent, S.7
He, X.8
Li, W.9
-
14
-
-
74249124132
-
p53-independent upregulation of miR-34a during oncogene-induced senescence represses MYC
-
Christoffersen, N.R., Shalgi, R., Frankel, L.B., Leucci, E., Lees, M., Klausen, M., Pilpel, Y., Nielsen, F.C., Oren, M., Lund, A.H., p53-independent upregulation of miR-34a during oncogene-induced senescence represses MYC. Cell Death Differ. 17 (2010), 236–245.
-
(2010)
Cell Death Differ.
, vol.17
, pp. 236-245
-
-
Christoffersen, N.R.1
Shalgi, R.2
Frankel, L.B.3
Leucci, E.4
Lees, M.5
Klausen, M.6
Pilpel, Y.7
Nielsen, F.C.8
Oren, M.9
Lund, A.H.10
-
15
-
-
84958927854
-
Long non-coding RNA PVT1 and cancer
-
Cui, M., You, L., Ren, X., Zhao, W., Liao, Q., Zhao, Y., Long non-coding RNA PVT1 and cancer. Biochem. Biophys. Res. Commun. 471 (2016), 10–14.
-
(2016)
Biochem. Biophys. Res. Commun.
, vol.471
, pp. 10-14
-
-
Cui, M.1
You, L.2
Ren, X.3
Zhao, W.4
Liao, Q.5
Zhao, Y.6
-
16
-
-
0001087931
-
Extreme instability of myc mRNA in normal and transformed human cells
-
Dani, C., Blanchard, J.M., Piechaczyk, M., El Sabouty, S., Marty, L., Jeanteur, P., Extreme instability of myc mRNA in normal and transformed human cells. Proc. Natl. Acad. Sci. USA 81 (1984), 7046–7050.
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 7046-7050
-
-
Dani, C.1
Blanchard, J.M.2
Piechaczyk, M.3
El Sabouty, S.4
Marty, L.5
Jeanteur, P.6
-
17
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Dunham, I., Kundaje, A., Aldred, S.F., Collins, P.J., Davis, C.A., Doyle, F., Epstein, C.B., Frietze, S., Harrow, J., Kaul, R., et al., ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489 (2012), 57–74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Dunham, I.1
Kundaje, A.2
Aldred, S.F.3
Collins, P.J.4
Davis, C.A.5
Doyle, F.6
Epstein, C.B.7
Frietze, S.8
Harrow, J.9
Kaul, R.10
-
18
-
-
0026849821
-
Definition of a consensus binding site for p53
-
el-Deiry, W.S., Kern, S.E., Pietenpol, J.A., Kinzler, K.W., Vogelstein, B., Definition of a consensus binding site for p53. Nat. Genet. 1 (1992), 45–49.
-
(1992)
Nat. Genet.
, vol.1
, pp. 45-49
-
-
el-Deiry, W.S.1
Kern, S.E.2
Pietenpol, J.A.3
Kinzler, K.W.4
Vogelstein, B.5
-
19
-
-
84897584387
-
MYC Degradation
-
Farrell, A.S., Sears, R.C., MYC Degradation. Cold Spring Harb. Perspect. Med., 4, 2014, a014365.
-
(2014)
Cold Spring Harb. Perspect. Med.
, vol.4
, pp. a014365
-
-
Farrell, A.S.1
Sears, R.C.2
-
20
-
-
84990852918
-
Systematic mapping of functional enhancer-promoter connections with CRISPR interference
-
Fulco, C.P., Munschauer, M., Anyoha, R., Munson, G., Grossman, S.R., Perez, E.M., Kane, M., Cleary, B., Lander, E.S., Engreitz, J.M., Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science 354 (2016), 769–773.
-
(2016)
Science
, vol.354
, pp. 769-773
-
-
Fulco, C.P.1
Munschauer, M.2
Anyoha, R.3
Munson, G.4
Grossman, S.R.5
Perez, E.M.6
Kane, M.7
Cleary, B.8
Lander, E.S.9
Engreitz, J.M.10
-
21
-
-
33745451921
-
Oscillations and variability in the p53 system
-
Geva-Zatorsky, N., Rosenfeld, N., Itzkovitz, S., Milo, R., Sigal, A., Dekel, E., Yarnitzky, T., Liron, Y., Polak, P., Lahav, G., Alon, U., Oscillations and variability in the p53 system. Mol. Syst. Biol., 2, 2006, 0033.
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 0033
-
-
Geva-Zatorsky, N.1
Rosenfeld, N.2
Itzkovitz, S.3
Milo, R.4
Sigal, A.5
Dekel, E.6
Yarnitzky, T.7
Liron, Y.8
Polak, P.9
Lahav, G.10
Alon, U.11
-
22
-
-
33749249590
-
NF-kappaB activation by double-strand breaks
-
Habraken, Y., Piette, J., NF-kappaB activation by double-strand breaks. Biochem. Pharmacol. 72 (2006), 1132–1141.
-
(2006)
Biochem. Pharmacol.
, vol.72
, pp. 1132-1141
-
-
Habraken, Y.1
Piette, J.2
-
23
-
-
44349089776
-
Multiple mechanisms contribute to inhibit transcription in response to DNA damage
-
Heine, G.F., Horwitz, A.A., Parvin, J.D., Multiple mechanisms contribute to inhibit transcription in response to DNA damage. J. Biol. Chem. 283 (2008), 9555–9561.
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 9555-9561
-
-
Heine, G.F.1
Horwitz, A.A.2
Parvin, J.D.3
-
24
-
-
84934275896
-
Proteostasis control by the unfolded protein response
-
Hetz, C., Chevet, E., Oakes, S.A., Proteostasis control by the unfolded protein response. Nat. Cell Biol. 17 (2015), 829–838.
-
(2015)
Nat. Cell Biol.
, vol.17
, pp. 829-838
-
-
Hetz, C.1
Chevet, E.2
Oakes, S.A.3
-
25
-
-
23844476499
-
p53-Dependent transcriptional repression of c-myc is required for G1 cell cycle arrest
-
Ho, J.S.L., Ma, W., Mao, D.Y.L., Benchimol, S., p53-Dependent transcriptional repression of c-myc is required for G1 cell cycle arrest. Mol. Cell. Biol. 25 (2005), 7423–7431.
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 7423-7431
-
-
Ho, J.S.L.1
Ma, W.2
Mao, D.Y.L.3
Benchimol, S.4
-
26
-
-
0642365202
-
Efficient labeling of fission yeast Schizosaccharomyces pombe with thymidine and BUdR
-
Hodson, J.A., Bailis, J.M., Forsburg, S.L., Efficient labeling of fission yeast Schizosaccharomyces pombe with thymidine and BUdR. Nucleic Acids Res., 31, 2003, e134.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. e134
-
-
Hodson, J.A.1
Bailis, J.M.2
Forsburg, S.L.3
-
27
-
-
54949149565
-
Apoptotic signaling by c-MYC
-
Hoffman, B., Liebermann, D.A., Apoptotic signaling by c-MYC. Oncogene 27 (2008), 6462–6472.
-
(2008)
Oncogene
, vol.27
, pp. 6462-6472
-
-
Hoffman, B.1
Liebermann, D.A.2
-
28
-
-
84880513002
-
Genome-wide identification of genes with amplification and/or fusion in small cell lung cancer
-
Iwakawa, R., Takenaka, M., Kohno, T., Shimada, Y., Totoki, Y., Shibata, T., Tsuta, K., Nishikawa, R., Noguchi, M., Sato-Otsubo, A., et al. Genome-wide identification of genes with amplification and/or fusion in small cell lung cancer. Genes Chromosomes Cancer 52 (2013), 802–816.
-
(2013)
Genes Chromosomes Cancer
, vol.52
, pp. 802-816
-
-
Iwakawa, R.1
Takenaka, M.2
Kohno, T.3
Shimada, Y.4
Totoki, Y.5
Shibata, T.6
Tsuta, K.7
Nishikawa, R.8
Noguchi, M.9
Sato-Otsubo, A.10
-
29
-
-
0040298568
-
Caspase-3 is required for DNA fragmentation and morphological changes associated with apoptosis
-
Jänicke, R.U., Sprengart, M.L., Wati, M.R., Porter, A.G., Caspase-3 is required for DNA fragmentation and morphological changes associated with apoptosis. J. Biol. Chem. 273 (1998), 9357–9360.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 9357-9360
-
-
Jänicke, R.U.1
Sprengart, M.L.2
Wati, M.R.3
Porter, A.G.4
-
30
-
-
80054789799
-
Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation
-
Ji, H., Wu, G., Zhan, X., Nolan, A., Koh, C., De Marzo, A., Doan, H.M., Fan, J., Cheadle, C., Fallahi, M., et al. Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation. PLoS ONE, 6, 2011, e26057.
-
(2011)
PLoS ONE
, vol.6
, pp. e26057
-
-
Ji, H.1
Wu, G.2
Zhan, X.3
Nolan, A.4
Koh, C.5
De Marzo, A.6
Doan, H.M.7
Fan, J.8
Cheadle, C.9
Fallahi, M.10
-
31
-
-
84876996918
-
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L., TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, 2013, R36.
-
(2013)
Genome Biol.
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
32
-
-
84887506884
-
Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis
-
Kim, H.P., Cho, G.A., Han, S.W., Shin, J.Y., Jeong, E.G., Song, S.H., Lee, W.C., Lee, K.H., Bang, D., Seo, J.S., et al. Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis. Oncogene 33 (2014), 5434–5441.
-
(2014)
Oncogene
, vol.33
, pp. 5434-5441
-
-
Kim, H.P.1
Cho, G.A.2
Han, S.W.3
Shin, J.Y.4
Jeong, E.G.5
Song, S.H.6
Lee, W.C.7
Lee, K.H.8
Bang, D.9
Seo, J.S.10
-
33
-
-
0842332406
-
Dynamics of the p53-Mdm2 feedback loop in individual cells
-
Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A.J., Elowitz, M.B., Alon, U., Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat. Genet. 36 (2004), 147–150.
-
(2004)
Nat. Genet.
, vol.36
, pp. 147-150
-
-
Lahav, G.1
Rosenfeld, N.2
Sigal, A.3
Geva-Zatorsky, N.4
Levine, A.J.5
Elowitz, M.B.6
Alon, U.7
-
34
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 (2012), 357–359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
35
-
-
52149094807
-
How the c-myc promoter works and why it sometimes does not
-
Levens, D., How the c-myc promoter works and why it sometimes does not. J. Natl. Cancer Inst. Monogr. 2008 (2008), 41–43.
-
(2008)
J. Natl. Cancer Inst. Monogr.
, vol.2008
, pp. 41-43
-
-
Levens, D.1
-
36
-
-
84887191036
-
Cellular MYCro economics: balancing MYC function with MYC expression
-
Levens, D., Cellular MYCro economics: balancing MYC function with MYC expression. Cold Spring Harb. Perspect. Med., 3, 2013, a014233.
-
(2013)
Cold Spring Harb. Perspect. Med.
, vol.3
, pp. a014233
-
-
Levens, D.1
-
37
-
-
70349442548
-
The first 30 years of p53: growing ever more complex
-
Levine, A.J., Oren, M., The first 30 years of p53: growing ever more complex. Nat. Rev. Cancer 9 (2009), 749–758.
-
(2009)
Nat. Rev. Cancer
, vol.9
, pp. 749-758
-
-
Levine, A.J.1
Oren, M.2
-
38
-
-
0027420554
-
Complementation by wild-type p53 of interleukin-6 effects on M1 cells: induction of cell cycle exit and cooperativity with c-myc suppression
-
Levy, N., Yonish-Rouach, E., Oren, M., Kimchi, A., Complementation by wild-type p53 of interleukin-6 effects on M1 cells: induction of cell cycle exit and cooperativity with c-myc suppression. Mol. Cell. Biol. 13 (1993), 7942–7952.
-
(1993)
Mol. Cell. Biol.
, vol.13
, pp. 7942-7952
-
-
Levy, N.1
Yonish-Rouach, E.2
Oren, M.3
Kimchi, A.4
-
39
-
-
84862777719
-
Distinct regulatory mechanisms and functions for p53-activated and p53-repressed DNA damage response genes in embryonic stem cells
-
Li, M., He, Y., Dubois, W., Wu, X., Shi, J., Huang, J., Distinct regulatory mechanisms and functions for p53-activated and p53-repressed DNA damage response genes in embryonic stem cells. Mol. Cell 46 (2012), 30–42.
-
(2012)
Mol. Cell
, vol.46
, pp. 30-42
-
-
Li, M.1
He, Y.2
Dubois, W.3
Wu, X.4
Shi, J.5
Huang, J.6
-
40
-
-
84867021989
-
Transcriptional amplification in tumor cells with elevated c-Myc
-
Lin, C.Y., Lovén, J., Rahl, P.B., Paranal, R.M., Burge, C.B., Bradner, J.E., Lee, T.I., Young, R.A., Transcriptional amplification in tumor cells with elevated c-Myc. Cell 151 (2012), 56–67.
-
(2012)
Cell
, vol.151
, pp. 56-67
-
-
Lin, C.Y.1
Lovén, J.2
Rahl, P.B.3
Paranal, R.M.4
Burge, C.B.5
Bradner, J.E.6
Lee, T.I.7
Young, R.A.8
-
41
-
-
84868010349
-
Revisiting global gene expression analysis
-
Lovén, J., Orlando, D.A., Sigova, A.A., Lin, C.Y., Rahl, P.B., Burge, C.B., Levens, D.L., Lee, T.I., Young, R.A., Revisiting global gene expression analysis. Cell 151 (2012), 476–482.
-
(2012)
Cell
, vol.151
, pp. 476-482
-
-
Lovén, J.1
Orlando, D.A.2
Sigova, A.A.3
Lin, C.Y.4
Rahl, P.B.5
Burge, C.B.6
Levens, D.L.7
Lee, T.I.8
Young, R.A.9
-
42
-
-
0141864362
-
c-Myc augments gamma irradiation-induced apoptosis by suppressing Bcl-XL
-
Maclean, K.H., Keller, U.B., Rodriguez-Galindo, C., Nilsson, J.A., Cleveland, J.L., c-Myc augments gamma irradiation-induced apoptosis by suppressing Bcl-XL. Mol. Cell. Biol. 23 (2003), 7256–7270.
-
(2003)
Mol. Cell. Biol.
, vol.23
, pp. 7256-7270
-
-
Maclean, K.H.1
Keller, U.B.2
Rodriguez-Galindo, C.3
Nilsson, J.A.4
Cleveland, J.L.5
-
43
-
-
84891352625
-
Promoter activity dynamics in the lag phase of Escherichia coli
-
Madar, D., Dekel, E., Bren, A., Zimmer, A., Porat, Z., Alon, U., Promoter activity dynamics in the lag phase of Escherichia coli. BMC Syst. Biol., 7, 2013, 136.
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. 136
-
-
Madar, D.1
Dekel, E.2
Bren, A.3
Zimmer, A.4
Porat, Z.5
Alon, U.6
-
44
-
-
79952303452
-
The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo
-
Meerbrey, K.L., Hu, G., Kessler, J.D., Roarty, K., Li, M.Z., Fang, J.E., Herschkowitz, J.I., Burrows, A.E., Ciccia, A., Sun, T., et al. The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo. Proc. Natl. Acad. Sci. USA 108 (2011), 3665–3670.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 3665-3670
-
-
Meerbrey, K.L.1
Hu, G.2
Kessler, J.D.3
Roarty, K.4
Li, M.Z.5
Fang, J.E.6
Herschkowitz, J.I.7
Burrows, A.E.8
Ciccia, A.9
Sun, T.10
-
45
-
-
0038054341
-
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
-
Mootha, V.K., Lindgren, C.M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34 (2003), 267–273.
-
(2003)
Nat. Genet.
, vol.34
, pp. 267-273
-
-
Mootha, V.K.1
Lindgren, C.M.2
Eriksson, K.-F.3
Subramanian, A.4
Sihag, S.5
Lehar, J.6
Puigserver, P.7
Carlsson, E.8
Ridderstråle, M.9
Laurila, E.10
-
46
-
-
84867134177
-
Frequent PVT1 rearrangement and novel chimeric genes PVT1-NBEA and PVT1-WWOX occur in multiple myeloma with 8q24 abnormality
-
Nagoshi, H., Taki, T., Hanamura, I., Nitta, M., Otsuki, T., Nishida, K., Okuda, K., Sakamoto, N., Kobayashi, S., Yamamoto-Sugitani, M., et al. Frequent PVT1 rearrangement and novel chimeric genes PVT1-NBEA and PVT1-WWOX occur in multiple myeloma with 8q24 abnormality. Cancer Res. 72 (2012), 4954–4962.
-
(2012)
Cancer Res.
, vol.72
, pp. 4954-4962
-
-
Nagoshi, H.1
Taki, T.2
Hanamura, I.3
Nitta, M.4
Otsuki, T.5
Nishida, K.6
Okuda, K.7
Sakamoto, N.8
Kobayashi, S.9
Yamamoto-Sugitani, M.10
-
47
-
-
84867010006
-
c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells
-
Nie, Z., Hu, G., Wei, G., Cui, K., Yamane, A., Resch, W., Wang, R., Green, D.R., Tessarollo, L., Casellas, R., et al. c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell 151 (2012), 68–79.
-
(2012)
Cell
, vol.151
, pp. 68-79
-
-
Nie, Z.1
Hu, G.2
Wei, G.3
Cui, K.4
Yamane, A.5
Resch, W.6
Wang, R.7
Green, D.R.8
Tessarollo, L.9
Casellas, R.10
-
48
-
-
84864425646
-
Subgroup-specific structural variation across 1,000 medulloblastoma genomes
-
Northcott, P.A., Shih, D.J.H., Peacock, J., Garzia, L., Morrissy, A.S., Zichner, T., Stütz, A.M., Korshunov, A., Reimand, J., Schumacher, S.E., et al. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature 488 (2012), 49–56.
-
(2012)
Nature
, vol.488
, pp. 49-56
-
-
Northcott, P.A.1
Shih, D.J.H.2
Peacock, J.3
Garzia, L.4
Morrissy, A.S.5
Zichner, T.6
Stütz, A.M.7
Korshunov, A.8
Reimand, J.9
Schumacher, S.E.10
-
49
-
-
84899926214
-
Endogenous c-Myc is essential for p53-induced apoptosis in response to DNA damage in vivo
-
Phesse, T.J., Myant, K.B., Cole, A.M., Ridgway, R.A., Pearson, H., Muncan, V., van den Brink, G.R., Vousden, K.H., Sears, R., Vassilev, L.T., et al. Endogenous c-Myc is essential for p53-induced apoptosis in response to DNA damage in vivo. Cell Death Differ. 21 (2014), 956–966.
-
(2014)
Cell Death Differ.
, vol.21
, pp. 956-966
-
-
Phesse, T.J.1
Myant, K.B.2
Cole, A.M.3
Ridgway, R.A.4
Pearson, H.5
Muncan, V.6
van den Brink, G.R.7
Vousden, K.H.8
Sears, R.9
Vassilev, L.T.10
-
50
-
-
84962676782
-
p53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks
-
Porter, J.R., Fisher, B.E., Batchelor, E., p53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks. Cell Syst. 2 (2016), 272–282.
-
(2016)
Cell Syst.
, vol.2
, pp. 272-282
-
-
Porter, J.R.1
Fisher, B.E.2
Batchelor, E.3
-
51
-
-
33646589650
-
Cockayne syndrome B protein regulates the transcriptional program after UV irradiation
-
Proietti-De-Santis, L., Drané, P., Egly, J.-M., Cockayne syndrome B protein regulates the transcriptional program after UV irradiation. EMBO J. 25 (2006), 1915–1923.
-
(2006)
EMBO J.
, vol.25
, pp. 1915-1923
-
-
Proietti-De-Santis, L.1
Drané, P.2
Egly, J.-M.3
-
52
-
-
84862270480
-
p53 dynamics control cell fate
-
Purvis, J.E., Karhohs, K.W., Mock, C., Batchelor, E., Loewer, A., Lahav, G., p53 dynamics control cell fate. Science 336 (2012), 1440–1444.
-
(2012)
Science
, vol.336
, pp. 1440-1444
-
-
Purvis, J.E.1
Karhohs, K.W.2
Mock, C.3
Batchelor, E.4
Loewer, A.5
Lahav, G.6
-
53
-
-
42449114966
-
Transcriptional control of human p53-regulated genes
-
Riley, T., Sontag, E., Chen, P., Levine, A., Transcriptional control of human p53-regulated genes. Nat. Rev. Mol. Cell Biol. 9 (2008), 402–412.
-
(2008)
Nat. Rev. Mol. Cell Biol.
, vol.9
, pp. 402-412
-
-
Riley, T.1
Sontag, E.2
Chen, P.3
Levine, A.4
-
54
-
-
0034641753
-
UV-induced inhibition of transcription involves repression of transcription initiation and phosphorylation of RNA polymerase II
-
Rockx, D.A.P., Mason, R., van Hoffen, A., Barton, M.C., Citterio, E., Bregman, D.B., van Zeeland, A.A., Vrieling, H., Mullenders, L.H.F., UV-induced inhibition of transcription involves repression of transcription initiation and phosphorylation of RNA polymerase II. Proc. Natl. Acad. Sci. USA 97 (2000), 10503–10508.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10503-10508
-
-
Rockx, D.A.P.1
Mason, R.2
van Hoffen, A.3
Barton, M.C.4
Citterio, E.5
Bregman, D.B.6
van Zeeland, A.A.7
Vrieling, H.8
Mullenders, L.H.F.9
-
55
-
-
62549148270
-
p53 represses c-Myc through induction of the tumor suppressor miR-145
-
Sachdeva, M., Zhu, S., Wu, F., Wu, H., Walia, V., Kumar, S., Elble, R., Watabe, K., Mo, Y.-Y., p53 represses c-Myc through induction of the tumor suppressor miR-145. Proc. Natl. Acad. Sci. USA 106 (2009), 3207–3212.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 3207-3212
-
-
Sachdeva, M.1
Zhu, S.2
Wu, F.3
Wu, H.4
Walia, V.5
Kumar, S.6
Elble, R.7
Watabe, K.8
Mo, Y.-Y.9
-
56
-
-
0037126303
-
Myc suppression of the p21(Cip1) Cdk inhibitor influences the outcome of the p53 response to DNA damage
-
Seoane, J., Le, H.-V., Massagué, J., Myc suppression of the p21(Cip1) Cdk inhibitor influences the outcome of the p53 response to DNA damage. Nature 419 (2002), 729–734.
-
(2002)
Nature
, vol.419
, pp. 729-734
-
-
Seoane, J.1
Le, H.-V.2
Massagué, J.3
-
57
-
-
0036176452
-
Overexpression of c-Myc alters G(1)/S arrest following ionizing radiation
-
Sheen, J.-H., Dickson, R.B., Overexpression of c-Myc alters G(1)/S arrest following ionizing radiation. Mol. Cell. Biol. 22 (2002), 1819–1833.
-
(2002)
Mol. Cell. Biol.
, vol.22
, pp. 1819-1833
-
-
Sheen, J.-H.1
Dickson, R.B.2
-
58
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., Mesirov, J.P., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102 (2005), 15545–15550.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
59
-
-
84959209018
-
GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler
-
Takaku, M., Grimm, S.A., Shimbo, T., Perera, L., Menafra, R., Stunnenberg, H.G., Archer, T.K., Machida, S., Kurumizaka, H., Wade, P.A., GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biol., 17, 2016, 36.
-
(2016)
Genome Biol.
, vol.17
, pp. 36
-
-
Takaku, M.1
Grimm, S.A.2
Shimbo, T.3
Perera, L.4
Menafra, R.5
Stunnenberg, H.G.6
Archer, T.K.7
Machida, S.8
Kurumizaka, H.9
Wade, P.A.10
-
60
-
-
84931049513
-
Sambamba: fast processing of NGS alignment formats
-
Tarasov, A., Vilella, A.J., Cuppen, E., Nijman, I.J., Prins, P., Sambamba: fast processing of NGS alignment formats. Bioinformatics 31 (2015), 2032–2034.
-
(2015)
Bioinformatics
, vol.31
, pp. 2032-2034
-
-
Tarasov, A.1
Vilella, A.J.2
Cuppen, E.3
Nijman, I.J.4
Prins, P.5
-
61
-
-
85009754856
-
Genome-wide analysis of p53-regulated transcription in Myc-driven lymphomas
-
Tonelli, C., Morelli, M.J., Sabò, A., Verrecchia, A., Rotta, L., Capra, T., Bianchi, S., Campaner, S., Amati, B., Genome-wide analysis of p53-regulated transcription in Myc-driven lymphomas. Oncogene 36 (2017), 2921–2929.
-
(2017)
Oncogene
, vol.36
, pp. 2921-2929
-
-
Tonelli, C.1
Morelli, M.J.2
Sabò, A.3
Verrecchia, A.4
Rotta, L.5
Capra, T.6
Bianchi, S.7
Campaner, S.8
Amati, B.9
-
62
-
-
55249084500
-
Translational control of c-MYC by rapamycin promotes terminal myeloid differentiation
-
Wall, M., Poortinga, G., Hannan, K.M., Pearson, R.B., Hannan, R.D., McArthur, G.A., Translational control of c-MYC by rapamycin promotes terminal myeloid differentiation. Blood 112 (2008), 2305–2317.
-
(2008)
Blood
, vol.112
, pp. 2305-2317
-
-
Wall, M.1
Poortinga, G.2
Hannan, K.M.3
Pearson, R.B.4
Hannan, R.D.5
McArthur, G.A.6
-
63
-
-
82255173966
-
The unfolded protein response: from stress pathway to homeostatic regulation
-
Walter, P., Ron, D., The unfolded protein response: from stress pathway to homeostatic regulation. Science 334 (2011), 1081–1086.
-
(2011)
Science
, vol.334
, pp. 1081-1086
-
-
Walter, P.1
Ron, D.2
-
64
-
-
0033867975
-
Repression of RNA polymerase I transcription by the tumor suppressor p53
-
Zhai, W., Comai, L., Repression of RNA polymerase I transcription by the tumor suppressor p53. Mol. Cell. Biol. 20 (2000), 5930–5938.
-
(2000)
Mol. Cell. Biol.
, vol.20
, pp. 5930-5938
-
-
Zhai, W.1
Comai, L.2
-
65
-
-
53849146020
-
Model-based analysis of ChIP-seq (MACS)
-
Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., Liu, X.S., Model-based analysis of ChIP-seq (MACS). Genome Biol., 9, 2008, R137.
-
(2008)
Genome Biol.
, vol.9
, pp. R137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
66
-
-
84956634373
-
Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
-
Zhang, X., Choi, P.S., Francis, J.M., Imielinski, M., Watanabe, H., Cherniack, A.D., Meyerson, M., Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers. Nat. Genet. 48 (2016), 176–182.
-
(2016)
Nat. Genet.
, vol.48
, pp. 176-182
-
-
Zhang, X.1
Choi, P.S.2
Francis, J.M.3
Imielinski, M.4
Watanabe, H.5
Cherniack, A.D.6
Meyerson, M.7
|