-
2
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz, J., Siggia, E. D. & Cohen, B. A. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457, 215-218 (2009).
-
(2009)
Nature
, vol.457
, pp. 215-218
-
-
Gertz, J.1
Siggia, E.D.2
Cohen, B.A.3
-
3
-
-
79952672993
-
Impulse control: Temporal dynamics in gene transcription
-
Yosef, N. & Regev, A. Impulse control: Temporal dynamics in gene transcription. Cell 144, 886-896 (2011).
-
(2011)
Cell
, vol.144
, pp. 886-896
-
-
Yosef, N.1
Regev, A.2
-
4
-
-
84874765320
-
Encoding and decoding cellular information through signaling dynamics
-
Purvis, J. E. & Lahav, G. Encoding and decoding cellular information through signaling dynamics. Cell 152, 945-956 (2013).
-
(2013)
Cell
, vol.152
, pp. 945-956
-
-
Purvis, J.E.1
Lahav, G.2
-
5
-
-
84889256682
-
Functional roles of pulsing in genetic circuits
-
Levine, J. H., Lin, Y. & Elowitz, M. B. Functional roles of pulsing in genetic circuits. Science 342, 1193-1200 (2013).
-
(2013)
Science
, vol.342
, pp. 1193-1200
-
-
Levine, J.H.1
Lin, Y.2
Elowitz, M.B.3
-
6
-
-
0842332406
-
Dynamics of the p53-Mdm2 feedback loop in individual cells
-
Lahav, G. et al. Dynamics of the p53-Mdm2 feedback loop in individual cells. Nature Genet. 36, 147-150 (2004).
-
(2004)
Nature Genet.
, vol.36
, pp. 147-150
-
-
Lahav, G.1
-
7
-
-
7444254365
-
Oscillations in NF-kB signaling control the dynamics of gene expression
-
Nelson, D. E. et al. Oscillations in NF-kB signaling control the dynamics of gene expression. Science 306, 704-708 (2004).
-
(2004)
Science
, vol.306
, pp. 704-708
-
-
Nelson, D.E.1
-
8
-
-
52949098296
-
Frequency-modulatednuclear localizationbursts coordinate gene regulation
-
Cai, L., Dalal, C. K. &Elowitz, M. B. Frequency-modulatednuclear localizationbursts coordinate gene regulation. Nature 455, 485-490 (2008).
-
(2008)
Nature
, vol.455
, pp. 485-490
-
-
Cai, L.1
Dalal, C.K.2
Elowitz, M.B.3
-
9
-
-
80054837496
-
Stochastic pulse regulation in bacterial stress response
-
Locke, J. C., Young, J. W., Fontes, M., Hernández Jiménez, M. J. & Elowitz, M. B. Stochastic pulse regulation in bacterial stress response. Science 334, 366-369 (2011).
-
(2011)
Science
, vol.334
, pp. 366-369
-
-
Locke, J.C.1
Young, J.W.2
Fontes, M.3
Hernández Jiménez, M.J.4
Elowitz, M.B.5
-
10
-
-
84855424553
-
Signal-dependent dynamics of transcription factor translocation controls gene expression
-
Hao, N. & O'Shea, E. K. Signal-dependent dynamics of transcription factor translocation controls gene expression. Nature Struct. Mol. Biol. 19, 31-39 (2012).
-
(2012)
Nature Struct. Mol. Biol.
, vol.19
, pp. 31-39
-
-
Hao, N.1
O'Shea, E.K.2
-
11
-
-
71149092283
-
Dynamicsandvariability of ERK2 response to EGF in individual living cells
-
Cohen-Saidon, C., Cohen, A. A., Sigal, A., Liron, Y. &Alon, U. Dynamicsandvariability of ERK2 response to EGF in individual living cells. Mol. Cell 36, 885-893 (2009).
-
(2009)
Mol. Cell
, vol.36
, pp. 885-893
-
-
Cohen-Saidon, C.1
Cohen, A.A.2
Sigal, A.3
Liron, Y.4
Alon, U.5
-
12
-
-
84874629638
-
Rate of environmental change determines stress response specificity
-
Young, J. W., Locke, J. C. & Elowitz, M. B. Rate of environmental change determines stress response specificity. Proc. Natl Acad. Sci. USA 110, 4140-4145 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 4140-4145
-
-
Young, J.W.1
Locke, J.C.2
Elowitz, M.B.3
-
13
-
-
84856463001
-
Pulsed feedback defers cellular differentiation
-
Levine, J. H., Fontes, M. E., Dworkin, J. & Elowitz, M. B. Pulsed feedback defers cellular differentiation. PLoS Biol. 10, e1001252 (2012).
-
(2012)
PLoS Biol.
, vol.10
, pp. e1001252
-
-
Levine, J.H.1
Fontes, M.E.2
Dworkin, J.3
Elowitz, M.B.4
-
14
-
-
34250155259
-
Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: Evidence for periodic PKA activation
-
Garmendia-Torres, C., Goldbeter, A. & Jacquet, M. Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation. Curr. Biol. 17, 1044-1049 (2007).
-
(2007)
Curr. Biol.
, vol.17
, pp. 1044-1049
-
-
Garmendia-Torres, C.1
Goldbeter, A.2
Jacquet, M.3
-
15
-
-
84872813837
-
Tunable signal processing through modular control of transcription factor translocation
-
Hao, N., Budnik, B. A., Gunawardena, J. & O'Shea, E. K. Tunable signal processing through modular control of transcription factor translocation. Science 339, 460-464 (2013).
-
(2013)
Science
, vol.339
, pp. 460-464
-
-
Hao, N.1
Budnik, B.A.2
Gunawardena, J.3
O'Shea, E.K.4
-
16
-
-
84889261450
-
Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression
-
Hansen, A. S. & O'Shea, E. K. Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Mol. Syst. Biol. 9, 704 (2013).
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 704
-
-
Hansen, A.S.1
O'Shea, E.K.2
-
17
-
-
84879583718
-
Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses
-
Petrenko, N., Chereji, R. V., McClean, M. N., Morozov, A. V. & Broach, J. R. Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses. Mol. Biol. Cell 24, 2045-2057 (2013).
-
(2013)
Mol. Biol. Cell
, vol.24
, pp. 2045-2057
-
-
Petrenko, N.1
Chereji, R.V.2
McClean, M.N.3
Morozov, A.V.4
Broach, J.R.5
-
18
-
-
77952903562
-
Signalling ballet in space and time
-
Kholodenko, B. N., Hancock, J. F. & Kolch, W. Signalling ballet in space and time. Nature Rev. Mol. Cell Biol. 11, 414-426 (2010).
-
(2010)
Nature Rev. Mol. Cell Biol.
, vol.11
, pp. 414-426
-
-
Kholodenko, B.N.1
Hancock, J.F.2
Kolch, W.3
-
19
-
-
77954541844
-
Single-cell NF-kB dynamics reveal digital activation and analogue information processing
-
Tay, S. et al. Single-cell NF-kB dynamics reveal digital activation and analogue information processing. Nature 466, 267-271 (2010).
-
(2010)
Nature
, vol.466
, pp. 267-271
-
-
Tay, S.1
-
20
-
-
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, 488 (2011).
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 488
-
-
Batchelor, E.1
Loewer, A.2
Mock, C.3
Lahav, G.4
-
21
-
-
84872796463
-
Frequency-modulated pulses of ERK activity transmit quantitative proliferation signals
-
Albeck, J. G., Mills, G. B. &Brugge, J. S. Frequency-modulated pulses of ERK activity transmit quantitative proliferation signals. Mol. Cell 49, 249-261 (2013).
-
(2013)
Mol. Cell
, vol.49
, pp. 249-261
-
-
Albeck, J.G.1
Mills, G.B.2
Brugge, J.S.3
-
22
-
-
84872768987
-
Dynamic response diversity ofNFATisoforms inindividual living cells
-
Yissachar, N. et al. Dynamic response diversity ofNFATisoforms inindividual living cells. Mol. Cell 49, 322-330 (2013).
-
(2013)
Mol. Cell
, vol.49
, pp. 322-330
-
-
Yissachar, N.1
-
23
-
-
54949151933
-
Dynamic Notch signaling in neural progenitor cells and a revised view of lateral inhibition
-
Kageyama, R., Ohtsuka, T., Shimojo, H. & Imayoshi, I. Dynamic Notch signaling in neural progenitor cells and a revised view of lateral inhibition. Nature Neurosci. 11, 1247-1251 (2008).
-
(2008)
Nature Neurosci.
, vol.11
, pp. 1247-1251
-
-
Kageyama, R.1
Ohtsuka, T.2
Shimojo, H.3
Imayoshi, I.4
-
24
-
-
0029879360
-
The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE)
-
Mart?ńez-Pastor, M. T. et al. The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J. 15, 2227-2235 (1996).
-
(1996)
EMBO J.
, vol.15
, pp. 2227-2235
-
-
Martńez-Pastor, M.T.1
-
25
-
-
0030003064
-
Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae
-
Schmitt, A. P. & McEntee, K. Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 93, 5777-5782 (1996).
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 5777-5782
-
-
Schmitt, A.P.1
McEntee, K.2
-
26
-
-
0031910875
-
Msn2p and Msn4p control a large number of genes induced at the diauxic transition which are repressed by cyclicAMPin Saccharomyces cerevisiae
-
Boy-Marcotte, E., Perrot, M., Bussereau, F., Boucherie, H. & Jacquet, M. Msn2p and Msn4p control a large number of genes induced at the diauxic transition which are repressed by cyclicAMPin Saccharomyces cerevisiae. J. Bacteriol. 180, 1044-1052 (1998).
-
(1998)
J. Bacteriol.
, vol.180
, pp. 1044-1052
-
-
Boy-Marcotte, E.1
Perrot, M.2
Bussereau, F.3
Boucherie, H.4
Jacquet, M.5
-
27
-
-
0033813390
-
Stress-controlled transcriptionfactors, stress-induced genesandstress tolerance in budding yeast
-
Estruch, F. Stress-controlled transcriptionfactors, stress-induced genesandstress tolerance in budding yeast. FEMS Microbiol. Rev. 24, 469-486 (2000).
-
(2000)
FEMS Microbiol. Rev.
, vol.24
, pp. 469-486
-
-
Estruch, F.1
-
28
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A. P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
-
29
-
-
0035982899
-
The control of the yeastH2O2 response by theMsn2/4 transcription factors
-
Hasan, R. et al. The control of the yeastH2O2 response by theMsn2/4 transcription factors. Mol. Microbiol. 45, 233-241 (2002).
-
(2002)
Mol. Microbiol.
, vol.45
, pp. 233-241
-
-
Hasan, R.1
-
30
-
-
84859586432
-
The response to heat shock and oxidative stress in Saccharomyces cerevisiae
-
Morano, K. A., Grant, C. M. & Moye-Rowley, W. S. The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics 190, 1157-1195 (2012).
-
(2012)
Genetics
, vol.190
, pp. 1157-1195
-
-
Morano, K.A.1
Grant, C.M.2
Moye-Rowley, W.S.3
-
31
-
-
0025944734
-
Control of yeast GAL genes by MIG1 repressor: A transcriptional cascade in the glucose response
-
Nehlin, J. O., Carlberg, M. & Ronne, H. Control of yeast GAL genes by MIG1 repressor: A transcriptional cascade in the glucose response. EMBO J. 10, 3373-3377 (1991).
-
(1991)
EMBO J.
, vol.10
, pp. 3373-3377
-
-
Nehlin, J.O.1
Carlberg, M.2
Ronne, H.3
-
32
-
-
0029783926
-
Two zinc-finger-containing repressors are responsible for glucose repression of SUC2 expression
-
Lutfiyya, L. L. &Johnston, M. Two zinc-finger-containing repressors are responsible for glucose repression of SUC2 expression. Mol. Cell. Biol. 16, 4790-4797 (1996).
-
(1996)
Mol. Cell. Biol.
, vol.16
, pp. 4790-4797
-
-
Lutfiyya, L.L.1
Johnston, M.2
-
33
-
-
0033118209
-
Glucose repression in yeast
-
Carlson, M. Glucose repression in yeast. Curr. Opin. Microbiol. 2, 202-207 (1999).
-
(1999)
Curr. Opin. Microbiol.
, vol.2
, pp. 202-207
-
-
Carlson, M.1
-
34
-
-
84891806965
-
The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
-
Teixeira, M. C. et al. The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic Acids Res. 42, D161-D166 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D161-D166
-
-
Teixeira, M.C.1
-
35
-
-
0032518996
-
Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity
-
Görner, W. et al. Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev. 12, 586-597 (1998).
-
(1998)
Genes Dev.
, vol.12
, pp. 586-597
-
-
Görner, W.1
-
36
-
-
0030883032
-
Regulated nuclear translocation of the Mig1 glucose repressor
-
De Vit, M. J., Waddle, J. A. & Johnston, M. Regulated nuclear translocation of the Mig1 glucose repressor. Mol. Biol. Cell 8, 1603-1618 (1997).
-
(1997)
Mol. Biol. Cell
, vol.8
, pp. 1603-1618
-
-
De Vit, M.J.1
Waddle, J.A.2
Johnston, M.3
-
37
-
-
0031740335
-
Snf1 protein kinase regulates phosphorylation of the Mig1 repressor in Saccharomyces cerevisiae
-
Treitel, M. A., Kuchin, S. & Carlson, M. Snf1 protein kinase regulates phosphorylation of the Mig1 repressor in Saccharomyces cerevisiae. Mol. Cell. Biol. 18, 6273-6280 (1998).
-
(1998)
Mol. Cell. Biol.
, vol.18
, pp. 6273-6280
-
-
Treitel, M.A.1
Kuchin, S.2
Carlson, M.3
-
38
-
-
84908150919
-
Pulsatile dynamics in the yeast proteome
-
Dalal, C. K., Cai, L., Lin, Y., Rahbar, K. & Elowitz, M. B. Pulsatile dynamics in the yeast proteome. Curr. Biol. 24, 2189-2194 (2014).
-
(2014)
Curr. Biol.
, vol.24
, pp. 2189-2194
-
-
Dalal, C.K.1
Cai, L.2
Lin, Y.3
Rahbar, K.4
Elowitz, M.B.5
-
39
-
-
30944467113
-
A guide to choosing fluorescent proteins
-
Shaner, N. C., Steinbach, P. A. & Tsien, R. Y. A guide to choosing fluorescent proteins. Nature Methods 2, 905-909 (2005).
-
(2005)
Nature Methods
, vol.2
, pp. 905-909
-
-
Shaner, N.C.1
Steinbach, P.A.2
Tsien, R.Y.3
-
40
-
-
79955407832
-
Real-timeobservation of transcription initiation and elongation on an endogenous yeast gene
-
Larson, D. R., Zenklusen, D., Wu, B., Chao, J. A. & Singer, R. H. Real-timeobservation of transcription initiation and elongation on an endogenous yeast gene. Science 332, 475-478 (2011).
-
(2011)
Science
, vol.332
, pp. 475-478
-
-
Larson, D.R.1
Zenklusen, D.2
Wu, B.3
Chao, J.A.4
Singer, R.H.5
-
41
-
-
0038712724
-
Multiple positive and negative elements involved in the regulation of expression of GSY1 in Saccharomyces cerevisiae
-
Unnikrishnan, I., Miller, S., Meinke, M. & LaPorte, D. C. Multiple positive and negative elements involved in the regulation of expression of GSY1 in Saccharomyces cerevisiae. J. Biol. Chem. 278, 26450-26457 (2003).
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 26450-26457
-
-
Unnikrishnan, I.1
Miller, S.2
Meinke, M.3
LaPorte, D.C.4
-
42
-
-
0028302901
-
Multi-neuronal signals from the retina: Acquisition and analysis
-
Meister, M., Pine, J. & Baylor, D. A. Multi-neuronal signals from the retina: Acquisition and analysis. J. Neurosci. Methods 51, 95-106 (1994).
-
(1994)
J. Neurosci. Methods
, vol.51
, pp. 95-106
-
-
Meister, M.1
Pine, J.2
Baylor, D.A.3
-
43
-
-
28644434811
-
A dual role for PP1 in shaping the Msn2-dependent transcriptional response to glucose starvation
-
DeWever, V., Reiter, W., Ballarini, A., Ammerer, G. & Brocard, C. A dual role for PP1 in shaping the Msn2-dependent transcriptional response to glucose starvation. EMBO J. 24, 4115-4123 (2005).
-
(2005)
EMBO J.
, vol.24
, pp. 4115-4123
-
-
DeWever, V.1
Reiter, W.2
Ballarini, A.3
Ammerer, G.4
Brocard, C.5
-
45
-
-
0032535029
-
Synaptic modifications in cultured hippocampal neurons: Dependence on spike timing, synaptic strength, and postsynaptic cell type
-
Bi, G. Q. & Poo, M. M. Synaptic modifications in cultured hippocampal neurons: dependence on spike timing, synaptic strength, and postsynaptic cell type. J. Neurosci. 18, 10464-10472 (1998).
-
(1998)
J. Neurosci.
, vol.18
, pp. 10464-10472
-
-
Bi, G.Q.1
Poo, M.M.2
-
47
-
-
34347206860
-
High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method
-
Gietz, R. D. & Schiestl, R. H. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nature Protocols 2, 31-34 (2007).
-
(2007)
Nature Protocols
, vol.2
, pp. 31-34
-
-
Gietz, R.D.1
Schiestl, R.H.2
-
48
-
-
3042722112
-
Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae
-
Sheff, M. A. & Thorn, K. S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21, 661-670 (2004).
-
(2004)
Yeast
, vol.21
, pp. 661-670
-
-
Sheff, M.A.1
Thorn, K.S.2
-
49
-
-
0032873415
-
Threenewdominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae
-
Goldstein, A. L. &McCusker, J. H. Threenewdominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15, 1541-1553 (1999).
-
(1999)
Yeast
, vol.15
, pp. 1541-1553
-
-
Goldstein, A.L.1
McCusker, J.H.2
-
50
-
-
0031761689
-
Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae
-
Lutfiyya, L. L. et al. Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. Genetics 150, 1377-1391 (1998).
-
(1998)
Genetics
, vol.150
, pp. 1377-1391
-
-
Lutfiyya, L.L.1
-
51
-
-
77957714521
-
Computer control of microscopes using mManager
-
Edelstein, A., Amodaj, N., Hoover, K., Vale, R. & Stuurman, N. Computer control of microscopes using mManager. Curr. Protoc. Mol. Biol. Unit 14. 20 (2010).
-
(2010)
Curr. Protoc. Mol. Biol. Unit
, pp. 1420
-
-
Edelstein, A.1
Amodaj, N.2
Hoover, K.3
Vale, R.4
Stuurman, N.5
-
52
-
-
48449087576
-
Robust single-particle tracking in live-cell time-lapse sequences
-
Jaqaman, K. et al. Robust single-particle tracking in live-cell time-lapse sequences. Nature Methods 5, 695-702 (2008).
-
(2008)
Nature Methods
, vol.5
, pp. 695-702
-
-
Jaqaman, K.1
-
53
-
-
70549086797
-
Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae
-
Teste, M. A., Duquenne, M., Fraņois, J. M. & Parrou, J. L. Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol. Biol. 10, 99 (2009).
-
(2009)
BMC Mol. Biol.
, vol.10
, pp. 99
-
-
Teste, M.A.1
Duquenne, M.2
Fraņois, J.M.3
Parrou, J.L.4
-
54
-
-
84862245279
-
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
-
Ye, J. et al. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134 (2012).
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 134
-
-
Ye, J.1
-
55
-
-
77955801615
-
The Galaxy Team. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks, J., Nekrutenko, A., Taylor, J., The Galaxy Team. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R86
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
56
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 7, 562-578 (2012).
-
(2012)
Nature Protocols
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
-
57
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
|