-
1
-
-
77955102352
-
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
-
Taniguchi Y, et al. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329:533-538.
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
-
2
-
-
77955174763
-
Single-allele analysis of transcription kinetics in living mammalian cells
-
Yunger S, Rosenfeld L, Garini Y, Shav-Tal Y (2010) Single-allele analysis of transcription kinetics in living mammalian cells. Nat Methods 7:631-633.
-
(2010)
Nat Methods
, vol.7
, pp. 631-633
-
-
Yunger, S.1
Rosenfeld, L.2
Garini, Y.3
Shav-Tal, Y.4
-
3
-
-
28944434119
-
Real-time kinetics of gene activity in individual bacteria
-
DOI 10.1016/j.cell.2005.09.031, PII S0092867405010378
-
Golding I, Paulsson J, Zawilski SM, Cox EC (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123:1025-1036. (Pubitemid 41785418)
-
(2005)
Cell
, vol.123
, Issue.6
, pp. 1025-1036
-
-
Golding, I.1
Paulsson, J.2
Zawilski, S.M.3
Cox, E.C.4
-
4
-
-
38349185928
-
Effects of molecular memory and bursting on fluctuations in gene expression
-
Pedraza JM, Paulsson J (2008) Effects of molecular memory and bursting on fluctuations in gene expression. Science 319:339-343.
-
(2008)
Science
, vol.319
, pp. 339-343
-
-
Pedraza, J.M.1
Paulsson, J.2
-
5
-
-
33645027986
-
Stochastic protein expression in individual cells at the single molecule level
-
Cai L, Friedman N, Xie XS (2006) Stochastic protein expression in individual cells at the single molecule level. Nature 440:358-362.
-
(2006)
Nature
, vol.440
, pp. 358-362
-
-
Cai, L.1
Friedman, N.2
Xie, X.S.3
-
6
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman JR, et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441:840-846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.1
-
7
-
-
33745287724
-
Noise in protein expression scales with natural protein abundance
-
DOI 10.1038/ng1807, PII N1807
-
Bar-Even A, et al. (2006) Noise in protein expression scales with natural protein abundance. Nat Genet 38:636-643. (Pubitemid 43927304)
-
(2006)
Nature Genetics
, vol.38
, Issue.6
, pp. 636-643
-
-
Bar-Even, A.1
Paulsson, J.2
Maheshri, N.3
Carmi, M.4
O'Shea, E.5
Pilpel, Y.6
Barkai, N.7
-
8
-
-
79957608918
-
General properties of transcriptional time series in Escherichia coli
-
So LH, et al. (2011) General properties of transcriptional time series in Escherichia coli. Nat Genet 43:554-560.
-
(2011)
Nat Genet
, vol.43
, pp. 554-560
-
-
So, L.H.1
-
9
-
-
0242416539
-
Noise in eukaryotic gene expression
-
DOI 10.1038/nature01546
-
Blake WJ, M KÆrn, Cantor CR, Collins JJ (2003) Noise in eukaryotic gene expression. Nature 422:633-637. (Pubitemid 36460419)
-
(2003)
Nature
, vol.422
, Issue.6932
, pp. 633-637
-
-
Blake, W.J.1
Kaern, M.2
Cantor, C.R.3
Collins, J.J.4
-
10
-
-
49449090300
-
Using noise to probe and characterize gene circuits
-
Cox CD, McCollum JM, Allen MS, Dar RD, Simpson ML (2008) Using noise to probe and characterize gene circuits. Proc Natl Acad Sci USA 105:10809-10814.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 10809-10814
-
-
Cox, C.D.1
McCollum, J.M.2
Allen, M.S.3
Dar, R.D.4
Simpson, M.L.5
-
11
-
-
31844449923
-
Gene network shaping of inherent noise spectra
-
DOI 10.1038/nature04194, PII NATURE04194
-
Austin DW, et al. (2006) Gene network shaping of inherent noise spectra. Nature 439:608-611. (Pubitemid 43185386)
-
(2006)
Nature
, vol.439
, Issue.7076
, pp. 608-611
-
-
Austin, D.W.1
Allen, M.S.2
McCollum, J.M.3
Dar, R.D.4
Wilgus, J.R.5
Sayler, G.S.6
Samatova, N.F.7
Cox, C.D.8
Simpson, M.L.9
-
12
-
-
41349095731
-
Transient-mediated fate determination in a transcriptional circuit of HIV
-
DOI 10.1038/ng.116, PII NG116
-
Weinberger LS, Dar RD, Simpson ML (2008) Transient-mediated fate determination in a transcriptional circuit of HIV. Nat Genet 40:466-470. (Pubitemid 351450884)
-
(2008)
Nature Genetics
, vol.40
, Issue.4
, pp. 466-470
-
-
Weinberger, L.S.1
Dar, R.D.2
Simpson, M.L.3
-
13
-
-
3042601065
-
Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation
-
DOI 10.1016/j.jtbi.2004.04.017, PII S0022519304001481
-
Simpson ML, Cox CD, Sayler GS (2004) Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation. J Theor Biol 229:383-394. (Pubitemid 38844942)
-
(2004)
Journal of Theoretical Biology
, vol.229
, Issue.3
, pp. 383-394
-
-
Simpson, M.L.1
Cox, C.D.2
Sayler, G.S.3
-
14
-
-
0035193294
-
Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations
-
Kepler TB, Elston TC (2001) Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations. Biophys J 81:3116-3136. (Pubitemid 33111463)
-
(2001)
Biophysical Journal
, vol.81
, Issue.6
, pp. 3116-3136
-
-
Kepler, T.B.1
Elston, T.C.2
-
15
-
-
33845257870
-
Variability and memory of protein levels in human cells
-
DOI 10.1038/nature05316, PII NATURE05316
-
Sigal A, et al. (2006) Variability and memory of protein levels in human cells. Nature 444:643-646. (Pubitemid 44864444)
-
(2006)
Nature
, vol.444
, Issue.7119
, pp. 643-646
-
-
Sigal, A.1
Milo, R.2
Cohen, A.3
Geva-Zatorsky, N.4
Klein, Y.5
Liron, Y.6
Rosenfeld, N.7
Danon, T.8
Perzov, N.9
Alon, U.10
-
16
-
-
57349097152
-
Dynamic proteomics of individual cancer cells in response to a drug
-
Cohen AA, et al. (2008) Dynamic proteomics of individual cancer cells in response to a drug. Science 322:1511-1516.
-
(2008)
Science
, vol.322
, pp. 1511-1516
-
-
Cohen, A.A.1
-
17
-
-
77951604611
-
Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression
-
Singh A, Razooky B, Cox CD, Simpson ML, Weinberger LS (2010) Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression. Biophys J 98:L32-L34.
-
(2010)
Biophys J
, vol.98
-
-
Singh, A.1
Razooky, B.2
Cox, C.D.3
Simpson, M.L.4
Weinberger, L.S.5
-
18
-
-
79955381895
-
Mammalian genes are transcribed with widely different bursting kinetics
-
Suter DM, et al. (2011) Mammalian genes are transcribed with widely different bursting kinetics. Science 332:472-474.
-
(2011)
Science
, vol.332
, pp. 472-474
-
-
Suter, D.M.1
-
19
-
-
78049436913
-
HIV promoter integration site primarily modulates transcriptional burst size rather than frequency
-
Skupsky R, Burnett JC, Foley JE, Schaffer DV, Arkin AP (2010) HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. PLoS Comput Biol 6:e1000952.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Skupsky, R.1
Burnett, J.C.2
Foley, J.E.3
Schaffer, D.V.4
Arkin, A.P.5
-
20
-
-
26444524237
-
Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences
-
Mitchell RS, et al. (2004) Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol 2:1127-1137.
-
(2004)
PLoS Biol
, vol.2
, pp. 1127-1137
-
-
Mitchell, R.S.1
-
21
-
-
0037162715
-
HIV-1 integration in the human genome favors active genes and local hotspots
-
DOI 10.1016/S0092-8674(02)00864-4
-
Schroder AR, et al. (2002) HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110:521-529. (Pubitemid 35232295)
-
(2002)
Cell
, vol.110
, Issue.4
, pp. 521-529
-
-
Schroder, A.R.W.1
Shinn, P.2
Chen, H.3
Berry, C.4
Ecker, J.R.5
Bushman, F.6
-
22
-
-
0035794637
-
The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation
-
DOI 10.1093/emboj/20.7.1726
-
Jordan A, Defechereux P, Verdin E (2001) The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation. EMBO J 20:1726-1738. (Pubitemid 32299409)
-
(2001)
EMBO Journal
, vol.20
, Issue.7
, pp. 1726-1738
-
-
Jordan, A.1
Defechereux, P.2
Verdin, E.3
-
23
-
-
0025170955
-
Use of the human elongation factor 1alpha promoter as a versatile and efficient expression system
-
DOI 10.1016/0378-1119(90)90091-5
-
Kim DW, Uetsuki T, Kaziro Y, Yamaguchi N, Sugano S (1990) Use of the human elongation factor 1 alpha promoter as a versatile and efficient expression system. Gene 91:217-223. (Pubitemid 20269505)
-
(1990)
Gene
, vol.91
, Issue.2
, pp. 217-223
-
-
Kim, D.W.1
Uetsuki, T.2
Kaziro, Y.3
Yamaguchi, N.4
Sugano, S.5
-
24
-
-
0034322159
-
Lentiviral vectors for enhanced gene expression in human hematopoietic cells
-
Ramezani A, Hawley TS, Hawley RG (2000) Lentiviral vectors for enhanced gene expression in human hematopoietic cells. Mol Ther 2:458-469.
-
(2000)
Mol Ther
, vol.2
, pp. 458-469
-
-
Ramezani, A.1
Hawley, T.S.2
Hawley, R.G.3
-
25
-
-
79955488304
-
Dynamic analysis of stochastic transcription cycles
-
Harper CV, et al. (2011) Dynamic analysis of stochastic transcription cycles. PLoS Biol 9:e1000607.
-
(2011)
PLoS Biol
, vol.9
-
-
Harper, C.V.1
-
26
-
-
0023513563
-
Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product
-
DOI 10.1038/330489a0
-
Kao SY, Calman AF, Luciw PA, Peterlin BM (1987) Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product. Nature 330:489-493. (Pubitemid 18006431)
-
(1987)
Nature
, vol.330
, Issue.6147
, pp. 489-493
-
-
Kao, S.-Y.1
Calman, A.F.2
Luciw, P.A.3
Peterlin, B.M.4
-
27
-
-
80052305523
-
Activation of HIV transcription by the viral Tat protein requires a demethylation step mediated by lysine-specific demethylase 1 (LSD1/KDM1)
-
Sakane N, et al. (2011) Activation of HIV transcription by the viral Tat protein requires a demethylation step mediated by lysine-specific demethylase 1 (LSD1/KDM1). PLoS Pathog 7:e1002184.
-
(2011)
PLoS Pathog
, vol.7
-
-
Sakane, N.1
-
28
-
-
84860990368
-
Rapid transcriptional pulsing dynamics of high expressing retroviral transgenes in embryonic stem cells
-
Lo MY, Rival-Gervier S, Pasceri P, Ellis J (2012) Rapid transcriptional pulsing dynamics of high expressing retroviral transgenes in embryonic stem cells. PLoS One 7:e37130.
-
(2012)
PLoS One
, vol.7
-
-
Lo, M.Y.1
Rival-Gervier, S.2
Pasceri, P.3
Ellis, J.4
-
29
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
DOI 10.1371/journal.pbio.0040309
-
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S (2006) Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4:1707-1719. (Pubitemid 44610091)
-
(2006)
PLoS Biology
, vol.4
, Issue.10
, pp. 1707-1719
-
-
Raj, A.1
Peskin, C.S.2
Tranchina, D.3
Vargas, D.Y.4
Tyagi, S.5
-
30
-
-
84866083176
-
Dynamics of protein noise can distinguish between alternative sources of gene-expression variability
-
Singh A, Razooky B, Dar RD, Weinberger LS (2012) Dynamics of protein noise can distinguish between alternative sources of gene-expression variability. Mol Syst Biol 8:1-9.
-
(2012)
Mol Syst Biol
, vol.8
, pp. 1-9
-
-
Singh, A.1
Razooky, B.2
Dar, R.D.3
Weinberger, L.S.4
-
31
-
-
67650724069
-
Regulation and function of NF-kappaB transcription factors in the immune system
-
Vallabhapurapu S, KarinM(2009) Regulation and function of NF-kappaB transcription factors in the immune system. Annu Rev Immunol 27:693-733.
-
(2009)
Annu Rev Immunol
, vol.27
, pp. 693-733
-
-
Vallabhapurapu, S.1
Karin, M.2
-
32
-
-
0029919356
-
Transcriptional activation and chromatin remodeling of the HIV-1 promoter in response to histone acetylation
-
VanLint C, Emiliani S, Ott M, Verdin E (1996) Transcriptional activation and chromatin remodeling of the HIV-1 promoter in response to histone acetylation. EMBO J 15:1112-1120. (Pubitemid 26077840)
-
(1996)
EMBO Journal
, vol.15
, Issue.5
, pp. 1112-1120
-
-
Van Lint, C.1
Emiliani, S.2
Ott, M.3
Verdin, E.4
-
33
-
-
4444376712
-
Signaling to NF-kappaB
-
Hayden MS, Ghosh S (2004) Signaling to NF-kappaB. Genes Dev 18:2195-2224.
-
(2004)
Genes Dev
, vol.18
, pp. 2195-2224
-
-
Hayden, M.S.1
Ghosh, S.2
-
34
-
-
30444431914
-
NF-kappaB p50 promotes HIV latency through HDAC recruitment and repression of transcriptional initiation
-
DOI 10.1038/sj.emboj.7600900, PII 7600900
-
Williams SA, et al. (2006) NF-kappaB p50 promotes HIV latency through HDAC recruitment and repression of transcriptional initiation. EMBO J 25:139-149. (Pubitemid 43077303)
-
(2006)
EMBO Journal
, vol.25
, Issue.1
, pp. 139-149
-
-
Williams, S.A.1
Chen, L.-F.2
Kwon, H.3
Ruiz-Jarabo, C.M.4
Verdin, E.5
Greene, W.C.6
-
35
-
-
0034892960
-
Activation of human immunodeficiency virus transcription in T cells revisited: NF-kappaB p65 stimulates transcriptional elongation
-
DOI 10.1128/JVI.75.18.8524-8537.2001
-
West MJ, Lowe AD, Karn J (2001) Activation of human immunodeficiency virus transcription in T cells revisited: NF-kappaB p65 stimulates transcriptional elongation. J Virol 75:8524-8537. (Pubitemid 32768957)
-
(2001)
Journal of Virology
, vol.75
, Issue.18
, pp. 8524-8537
-
-
West, M.J.1
Lowe, A.D.2
Karn, J.3
-
36
-
-
0034741714
-
NF-kappaB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II
-
DOI 10.1016/S1097-2765(01)00314-8
-
Barboric M, Nissen RM, Kanazawa S, Jabrane-Ferrat N, Peterlin BM (2001) NF-kappaB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II. Mol Cell 8:327-337. (Pubitemid 32831550)
-
(2001)
Molecular Cell
, vol.8
, Issue.2
, pp. 327-337
-
-
Barboric, M.1
Nissen, R.M.2
Kanazawa, S.3
Jabrane-Ferrat, N.4
Peterlin, B.M.5
-
37
-
-
34249810678
-
Sustained induction of NF-kappaB is required for efficient expression of latent human immunodeficiency virus type l
-
DOI 10.1128/JVI.02074-06
-
Williams SA, Kwon H, Chen LF, Greene WC (2007) Sustained induction of NF-kappa B is required for efficient expression of latent human immunodeficiency virus type 1. J Virol 81:6043-6056. (Pubitemid 46847040)
-
(2007)
Journal of Virology
, vol.81
, Issue.11
, pp. 6043-6056
-
-
Williams, S.A.1
Kwon, H.2
Chen, L.-F.3
Greene, W.C.4
-
38
-
-
0037044575
-
The IkappaB-NF-kappaB signaling module: Temporal control and selective gene activation
-
DOI 10.1126/science.1071914
-
Hoffmann A, Levchenko A, Scott ML, Baltimore D (2002) The IkappaB-NF-kappaB signaling module: Temporal control and selective gene activation. Science 298:1241-1245. (Pubitemid 35285493)
-
(2002)
Science
, vol.298
, Issue.5596
, pp. 1241-1245
-
-
Hoffmann, A.1
Levchenko, A.2
Scott, M.L.3
Baltimore, D.4
-
40
-
-
52949098296
-
Frequency-modulated nuclear localization bursts coordinate gene regulation
-
Cai L, Dalal CK, Elowitz MB (2008) Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455:485-490.
-
(2008)
Nature
, vol.455
, pp. 485-490
-
-
Cai, L.1
Dalal, C.K.2
Elowitz, M.B.3
-
41
-
-
22744441386
-
Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity
-
DOI 10.1016/j.cell.2005.06.006, PII S0092867405005490
-
Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV (2005) Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122:169-182. (Pubitemid 41032982)
-
(2005)
Cell
, vol.122
, Issue.2
, pp. 169-182
-
-
Weinberger, L.S.1
Burnett, J.C.2
Toettcher, J.E.3
Arkin, A.P.4
Schaffer, D.V.5
-
42
-
-
33846360341
-
An HIV feedback resistor: Auto-regulatory circuit deactivator and noise buffer
-
Weinberger LS, Shenk T (2007) An HIV feedback resistor: Auto-regulatory circuit deactivator and noise buffer. PLoS Biol 5:67-81.
-
(2007)
PLoS Biol
, vol.5
, pp. 67-81
-
-
Weinberger, L.S.1
Shenk, T.2
-
43
-
-
0017030517
-
General method for numerically simulating stochastic time evolution of coupled chemical-reactions
-
Gillespie DT (1976) General method for numerically simulating stochastic time evolution of coupled chemical-reactions. J Comput Phys 22:403-434.
-
(1976)
J Comput Phys
, vol.22
, pp. 403-434
-
-
Gillespie, D.T.1
-
44
-
-
31344458755
-
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
-
DOI 10.1016/j.compbiolchem.2005.10.007, PII S1476927105001088
-
McCollum JM, Peterson GD, Cox CD, Simpson ML, Samatova NF (2006) The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Comput Biol Chem 30:39-49. (Pubitemid 43144430)
-
(2006)
Computational Biology and Chemistry
, vol.30
, Issue.1
, pp. 39-49
-
-
McCollum, J.M.1
Peterson, G.D.2
Cox, C.D.3
Simpson, M.L.4
Samatova, N.F.5
|