-
1
-
-
33745287724
-
Noise in protein expression scales with natural protein abundance
-
doi:10.1038/ng1807
-
Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M., O'Shea, E., Pilpel, Y., et al. (2006). Noise in protein expression scales with natural protein abundance. Nat. Genet. 38, 636-643. doi:10.1038/ng1807.
-
(2006)
Nat. Genet.
, vol.38
, pp. 636-643
-
-
Bar-Even, A.1
Paulsson, J.2
Maheshri, N.3
Carmi, M.4
O'Shea, E.5
Pilpel, Y.6
-
2
-
-
84872513867
-
In vivo facilitated diffusion model
-
doi:10.1371/journal.pone.0053956
-
Bauer, M., and Metzler, R. (2013). In vivo facilitated diffusion model. PLoS ONE 8:e53956. doi:10.1371/journal.pone.0053956.
-
(2013)
PLoS ONE
, vol.8
-
-
Bauer, M.1
Metzler, R.2
-
3
-
-
25144450143
-
Contributions of low molecule number and chromosomal positioning to stochastic gene expression
-
doi:10.1038/ng1616
-
Becskei, A., Kaufmann, B. B., and van Oudenaarden, A. (2005). Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat. Genet. 37, 937-944. doi:10.1038/ng1616.
-
(2005)
Nat. Genet.
, vol.37
, pp. 937-944
-
-
Becskei, A.1
Kaufmann, B.B.2
van Oudenaarden, A.3
-
4
-
-
0019887628
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
-
doi:10.1021/bi00527a028
-
Berg, O. G., Winter, R. B., and von Hippel, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20, 6929-6948. doi:10.1021/bi00527a028.
-
(1981)
Biochemistry
, vol.20
, pp. 6929-6948
-
-
Berg, O.G.1
Winter, R.B.2
von Hippel, P.H.3
-
5
-
-
47249153641
-
Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA
-
doi:10.1093/nar/gkn376
-
Bonnet, I., Biebricher, A., Porte, P.-L., Loverdo, C., Benichou, O., Voituriez, R., et al. (2008). Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res. 36, 4118-4127. doi:10.1093/nar/gkn376.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 4118-4127
-
-
Bonnet, I.1
Biebricher, A.2
Porte, P.-L.3
Loverdo, C.4
Benichou, O.5
Voituriez, R.6
-
6
-
-
84867517832
-
Facilitated diffusion on mobile DNA:configurational traps and sequence heterogeneity
-
doi:10.1103/PhysRevLett.109.168103
-
Brackley, C. A., Cates, M. E., and Marenduzzo, D. (2012). Facilitated diffusion on mobile DNA:configurational traps and sequence heterogeneity. Phys. Rev. Lett. 109:168103. doi:10.1103/PhysRevLett.109.168103.
-
(2012)
Phys. Rev. Lett.
, vol.109
, pp. 168103
-
-
Brackley, C.A.1
Cates, M.E.2
Marenduzzo, D.3
-
7
-
-
84884268708
-
Intracellular facilitated diffusion:searchers, crowders, and blockers
-
doi:10.1103/PhysRevLett.111.108101
-
Brackley, C. A., Cates, M. E., and Marenduzzo, D. (2013). Intracellular facilitated diffusion:searchers, crowders, and blockers. Phys. Rev. Lett. 111:108101. doi:10.1103/PhysRevLett.111.108101.
-
(2013)
Phys. Rev. Lett.
, vol.111
, pp. 108101
-
-
Brackley, C.A.1
Cates, M.E.2
Marenduzzo, D.3
-
8
-
-
61449155349
-
Models of transcription factor binding:sensitivity of activation functions to model assumptions
-
doi:10.1016/j.jtbi.2008.11.026
-
Chu, D., Zabet, N. R., and Mitavskiy, B. (2009). Models of transcription factor binding:sensitivity of activation functions to model assumptions. J. Theor. Biol. 257, 419-429. doi:10.1016/j.jtbi.2008.11.026.
-
(2009)
J. Theor. Biol.
, vol.257
, pp. 419-429
-
-
Chu, D.1
Zabet, N.R.2
Mitavskiy, B.3
-
9
-
-
34249932435
-
Probing transcription factor dynamics at the single-molecule level in a living cell
-
doi:10.1126/science.1141967
-
Elf, J., Li, G.-W., and Xie, X. S. (2007). Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191-1194. doi:10.1126/science.1141967.
-
(2007)
Science
, vol.316
, pp. 1191-1194
-
-
Elf, J.1
Li, G.-W.2
Xie, X.S.3
-
10
-
-
33646945653
-
Strong physical constraints on sequence-specific target location by proteins on DNA molecules
-
doi:10.1093/nar/gkl271
-
Flyvbjerg, H., Keatch, S. A., and Dryden, D. T. (2006). Strong physical constraints on sequence-specific target location by proteins on DNA molecules. Nucleic Acids Res. 34, 2550-2557. doi:10.1093/nar/gkl271.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 2550-2557
-
-
Flyvbjerg, H.1
Keatch, S.A.2
Dryden, D.T.3
-
11
-
-
84857712855
-
Facilitated diffusion on confined DNA
-
doi:10.1103/PhysRevE.85.021919
-
Foffano, G., Marenduzzo, D., and Orlandini, E. (2012). Facilitated diffusion on confined DNA. Phys. Rev. E 85:021919. doi:10.1103/PhysRevE.85.021919.
-
(2012)
Phys. Rev. E
, vol.85
, pp. 021919
-
-
Foffano, G.1
Marenduzzo, D.2
Orlandini, E.3
-
12
-
-
80051728360
-
How do hox transcription factors find their target genes in the nucleus of living cells?
-
doi:10.1051/jbio/2011012
-
Gehring, W. J. (2011). How do hox transcription factors find their target genes in the nucleus of living cells? Biol. Aujourdhui 205, 75-85. doi:10.1051/jbio/2011012.
-
(2011)
Biol. Aujourdhui
, vol.205
, pp. 75-85
-
-
Gehring, W.J.1
-
13
-
-
0037126028
-
Physical constraints and functional characteristics of transcription factor-DNA interactions
-
doi:10.1073/pnas.192693599
-
Gerland, U., Moroz, J. D., and Hwa, T. (2002). Physical constraints and functional characteristics of transcription factor-DNA interactions. PNAS 99, 12015-12020. doi:10.1073/pnas.192693599.
-
(2002)
PNAS
, vol.99
, pp. 12015-12020
-
-
Gerland, U.1
Moroz, J.D.2
Hwa, T.3
-
14
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
doi:10.1016/0021-9991(76)90041-3
-
Gillespie, D. T. (1976). A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22, 403-434. doi:10.1016/0021-9991(76)90041-3.
-
(1976)
J. Comput. Phys.
, vol.22
, pp. 403-434
-
-
Gillespie, D.T.1
-
15
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
doi:10.1021/j100540a008
-
Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361. doi:10.1021/j100540a008.
-
(1977)
J. Phys. Chem.
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
16
-
-
3042579602
-
How do site-specific DNA-binding proteins find their targets?
-
doi:10.1093/nar/gkh624
-
Halford, S. E., and Marko, J. F. (2004). How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32, 3040-3052. doi:10.1093/nar/gkh624.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3040-3052
-
-
Halford, S.E.1
Marko, J.F.2
-
17
-
-
84862624197
-
The lac repressor displays facilitated diffusion in living cells
-
doi:10.1126/science.1221648
-
Hammar, P., Leroy, P., Mahmutovic, A., Marklund, E. G., Berg, O. G., and Elf, J. (2012). The lac repressor displays facilitated diffusion in living cells. Science 336, 1595-1598. doi:10.1126/science.1221648.
-
(2012)
Science
, vol.336
, pp. 1595-1598
-
-
Hammar, P.1
Leroy, P.2
Mahmutovic, A.3
Marklund, E.G.4
Berg, O.G.5
Elf, J.6
-
18
-
-
33846002036
-
Transcriptional regulation by competing transcription factor modules
-
doi:10.1371/journal.pcbi.0020164
-
Hermsen, R., Tans, S., and ten Wolde, P. R. (2006). Transcriptional regulation by competing transcription factor modules. PLoS Comput. Biol. 2, 1552-1560. doi:10.1371/journal.pcbi.0020164.
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. 1552-1560
-
-
Hermsen, R.1
Tans, S.2
ten Wolde, P.R.3
-
19
-
-
0027749617
-
Visualization of single molecules of rna polymerase sliding along dna
-
doi:10.1126/science.8248804
-
Kabata, H., Kurosawa, O., I, Arai, M. W., Margarson, S., Glass, R., and Shimamoto, N. (1993). Visualization of single molecules of rna polymerase sliding along dna. Science 262, 1561-1563. doi:10.1126/science.8248804.
-
(1993)
Science
, vol.262
, pp. 1561-1563
-
-
Kabata, H.1
Kurosawa, O.I.2
Arai, M.W.3
Margarson, S.4
Glass, R.5
Shimamoto, N.6
-
20
-
-
63849284078
-
Effects of macromolecular crowding and dna looping on gene regulation kinetics
-
doi:10.1038/nphys1222
-
Li, G.-W., Berg, O. G., and Elf, J. (2009). Effects of macromolecular crowding and dna looping on gene regulation kinetics. Nat. Phys. 5, 294-297. doi:10.1038/nphys1222.
-
(2009)
Nat. Phys.
, vol.5
, pp. 294-297
-
-
Li, G.-W.1
Berg, O.G.2
Elf, J.3
-
21
-
-
84877274846
-
Obstacles may facilitate and direct dna search by proteins
-
doi:10.1016/j.bpj.2013.03.030
-
Marcovitz, A., and Levy, Y. (2013). Obstacles may facilitate and direct dna search by proteins. Biophys. J. 104, 2042-2050. doi:10.1016/j.bpj.2013.03.030.
-
(2013)
Biophys. J.
, vol.104
, pp. 2042-2050
-
-
Marcovitz, A.1
Levy, Y.2
-
22
-
-
72149127671
-
How a protein searches for its site on DNA:the mechanism of facilitated diffusion
-
doi:10.1088/1751-8113/42/43/434013
-
Mirny, L., Slutsky, M., Wunderlich, Z., Tafvizi, A., Leith, J., and Kosmrlj, A. (2009). How a protein searches for its site on DNA:the mechanism of facilitated diffusion. J. Phys. A Math. Theor. 42:434013. doi:10.1088/1751-8113/42/43/434013.
-
(2009)
J. Phys. A Math. Theor.
, vol.42
, pp. 434013
-
-
Mirny, L.1
Slutsky, M.2
Wunderlich, Z.3
Tafvizi, A.4
Leith, J.5
Kosmrlj, A.6
-
23
-
-
84055217487
-
Effects of macromolecular crowding on genetic networks
-
doi:10.1016/j.bpj.2011.10.053
-
Morelli, M. J., Allen, R. J., and ten Wolde, P. R. (2011). Effects of macromolecular crowding on genetic networks. Biophys. J. 101, 2882-2891. doi:10.1016/j.bpj.2011.10.053.
-
(2011)
Biophys. J.
, vol.101
, pp. 2882-2891
-
-
Morelli, M.J.1
Allen, R.J.2
ten Wolde, P.R.3
-
24
-
-
77952002322
-
Theory of site-specific interactions of the combinatorial transcription factors with DNA
-
doi:10.1088/1751-8113/43/19/195003
-
Murugan, R. (2010). Theory of site-specific interactions of the combinatorial transcription factors with DNA. J. Phys. A Math. Theor. 43:195003. doi:10.1088/1751-8113/43/19/195003.
-
(2010)
J. Phys. A Math. Theor.
, vol.43
, pp. 195003
-
-
Murugan, R.1
-
25
-
-
20344389483
-
Models of stochastic gene expression
-
doi:10.1016/j.plrev.2005.03.003
-
Paulsson, J. (2005). Models of stochastic gene expression. Phys. Life Rev. 2, 157-175. doi:10.1016/j.plrev.2005.03.003.
-
(2005)
Phys. Life Rev.
, vol.2
, pp. 157-175
-
-
Paulsson, J.1
-
26
-
-
0014945567
-
The lac represser-operator interaction:III
-
doi:10.1016/0022-2836(70)90074-4
-
Riggs, A. D., Bourgeois, S., and Cohn, M. (1970). The lac represser-operator interaction:III. kinetic studies. J. Mol. Biol. 53, 401-417. doi:10.1016/0022-2836(70)90074-4.
-
(1970)
kinetic studies. J. Mol. Biol.
, vol.53
, pp. 401-417
-
-
Riggs, A.D.1
Bourgeois, S.2
Cohn, M.3
-
27
-
-
31544443526
-
Escherichia coli k-12:a cooperatively developed annotation snapshot-2005
-
doi:10.1093/nar/gkj405
-
Riley, M., Abe, T., Arnaud, M. B., Berlyn, M. K., Blattner, F. R., Chaudhuri, R. R., et al. (2006). Escherichia coli k-12:a cooperatively developed annotation snapshot-2005. Nucleic Acids Res. 34, 1-9. doi:10.1093/nar/gkj405.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1-9
-
-
Riley, M.1
Abe, T.2
Arnaud, M.B.3
Berlyn, M.K.4
Blattner, F.R.5
Chaudhuri, R.R.6
-
28
-
-
15544371346
-
Gene regulation at the single-cell level
-
doi:10.1126/science.1106914
-
Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S., and Elowitz, M. B. (2005). Gene regulation at the single-cell level. Science 307, 1962-1965. doi:10.1126/science.1106914.
-
(2005)
Science
, vol.307
, pp. 1962-1965
-
-
Rosenfeld, N.1
Young, J.W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
29
-
-
0026771275
-
Sliding and intermolecular transfer of the lac repressor:kinetic perturbation of a reaction intermediate by a distant dna sequence
-
doi:10.1073/pnas.89.11.4903
-
Ruusala, T., and Crothers, D. M. (1992). Sliding and intermolecular transfer of the lac repressor:kinetic perturbation of a reaction intermediate by a distant dna sequence. PNAS 89, 4903-4907. doi:10.1073/pnas.89.11.4903.
-
(1992)
PNAS
, vol.89
, pp. 4903-4907
-
-
Ruusala, T.1
Crothers, D.M.2
-
30
-
-
84861426505
-
Mode of regulation and the insulation of bacterial gene expression
-
doi:10.1016/j.molcel.2012.04.032
-
Sasson, V., Shachrai, I., Bren, A., Dekel, E., and Alon, U. (2012). Mode of regulation and the insulation of bacterial gene expression. Mol. Cell 46, 399-407. doi:10.1016/j.molcel.2012.04.032.
-
(2012)
Mol. Cell
, vol.46
, pp. 399-407
-
-
Sasson, V.1
Shachrai, I.2
Bren, A.3
Dekel, E.4
Alon, U.5
-
31
-
-
10044223573
-
Kinetics of protein-DNA interaction:facilitated target location in sequence-dependent potential
-
doi:10.1529/biophysj.104.050765
-
Slutsky, M., and Mirny, L. A. (2004). Kinetics of protein-DNA interaction:facilitated target location in sequence-dependent potential. Biophys. J. 87, 4021-4035. doi:10.1529/biophysj.104.050765.
-
(2004)
Biophys. J.
, vol.87
, pp. 4021-4035
-
-
Slutsky, M.1
Mirny, L.A.2
-
32
-
-
0034072450
-
DNA binding sites:representation and discovery
-
doi:10.1093/bioinformatics/16.1.16
-
Stormo, G. D. (2000). DNA binding sites:representation and discovery. Bioinformatics 16, 16-23. doi:10.1093/bioinformatics/16.1.16.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
33
-
-
0032032780
-
Specificity, free energy and information content in protein-DNA interactions
-
doi:10.1016/S0968-0004(98)01187-6
-
Stormo, G. D., and Fields, D. S. (1998). Specificity, free energy and information content in protein-DNA interactions. Trends Biochem. Sci. 23, 109-113. doi:10.1016/S0968-0004(98)01187-6.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 109-113
-
-
Stormo, G.D.1
Fields, D.S.2
-
34
-
-
33845442827
-
Diffusion of transcription factors can drastically enhance the noise in gene expression
-
doi:10.1529/biophysj.106.086157
-
van Zon, J. S., Morelli, M. J., Tanase-Nicola, S., and ten Wolde, P. R. (2006). Diffusion of transcription factors can drastically enhance the noise in gene expression. Biophys. J. 91, 4350-4367. doi:10.1529/biophysj.106.086157.
-
(2006)
Biophys. J.
, vol.91
, pp. 4350-4367
-
-
van Zon, J.S.1
Morelli, M.J.2
Tanase-Nicola, S.3
ten Wolde, P.R.4
-
35
-
-
77749239764
-
Quantitative study of synthetic hox transcription factor-dna interactions in live cells
-
doi:10.1073/pnas.0914612107
-
Vukojevic, V., Papadopoulos, D. K., Terenius, L., Gehring, W. J., and Rigler, R. (2010). Quantitative study of synthetic hox transcription factor-dna interactions in live cells. PNAS 107, 4093-4098. doi:10.1073/pnas.0914612107.
-
(2010)
PNAS
, vol.107
, pp. 4093-4098
-
-
Vukojevic, V.1
Papadopoulos, D.K.2
Terenius, L.3
Gehring, W.J.4
Rigler, R.5
-
36
-
-
84885391743
-
Stochastic Reaction-Diffusion Processes with Embedded Lower Dimensional Structures
-
Technical report, Department of Information Technology, Uppsala University.
-
Wang, S., Elf, J., Hellander, S., and Lotstedt, P. (2012). Stochastic Reaction-Diffusion Processes with Embedded Lower Dimensional Structures. Technical report, Department of Information Technology, Uppsala University.
-
(2012)
-
-
Wang, S.1
Elf, J.2
Hellander, S.3
Lotstedt, P.4
-
37
-
-
70350741354
-
An ensemble model of competitive multi-factor binding of the genome
-
doi:10.1101/gr.093450.109
-
Wasson, T., and Hartemink, A. J. (2009). An ensemble model of competitive multi-factor binding of the genome. Genome Res. 19, 2101-2112. doi:10.1101/gr.093450.109.
-
(2009)
Genome Res.
, vol.19
, pp. 2101-2112
-
-
Wasson, T.1
Hartemink, A.J.2
-
38
-
-
46349108554
-
Spatial effects on the speed and reliability of protein-DNA search
-
doi:10.1093/nar/gkn173
-
Wunderlich, Z., and Mirny, L. A. (2008). Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Res. 36, 3570-3578. doi:10.1093/nar/gkn173.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 3570-3578
-
-
Wunderlich, Z.1
Mirny, L.A.2
-
39
-
-
70349961774
-
Different gene regulation strategies revealed by analysis of binding motifs
-
doi:10.1016/j.tig.2009.08.003
-
Wunderlich, Z., and Mirny, L. A. (2009). Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 25, 434-440. doi:10.1016/j.tig.2009.08.003.
-
(2009)
Trends Genet.
, vol.25
, pp. 434-440
-
-
Wunderlich, Z.1
Mirny, L.A.2
-
40
-
-
84865819662
-
System size reduction in stochastic simulations of the facilitated diffusion mechanism
-
doi:10.1186/1752-0509-6-121
-
Zabet, N. R. (2012). System size reduction in stochastic simulations of the facilitated diffusion mechanism. BMC Syst. Biol. 6:121. doi:10.1186/1752-0509-6-121.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 121
-
-
Zabet, N.R.1
-
41
-
-
84861756737
-
A comprehensive computational model of facilitated diffusion in prokaryotes
-
doi:10.1093/bioinformatics/bts178
-
Zabet, N. R., and Adryan, B. (2012a). A comprehensive computational model of facilitated diffusion in prokaryotes. Bioinformatics 28, 1517-1524. doi:10.1093/bioinformatics/bts178.
-
(2012)
Bioinformatics
, vol.28
, pp. 1517-1524
-
-
Zabet, N.R.1
Adryan, B.2
-
42
-
-
84867364776
-
Computational models for large-scale simulations of facilitated diffusion
-
doi:10.1039/c2mb25201e
-
Zabet, N. R., and Adryan, B. (2012b). Computational models for large-scale simulations of facilitated diffusion. Mol. Biosyst. 8, 2815-2827. doi:10.1039/c2mb25201e.
-
(2012)
Mol. Biosyst.
, vol.8
, pp. 2815-2827
-
-
Zabet, N.R.1
Adryan, B.2
-
43
-
-
84860495813
-
GRiP:a computational tool to simulate transcription factor binding in prokaryotes
-
doi:10.1093/bioinformatics/bts132
-
Zabet, N. R., and Adryan, B. (2012c). GRiP:a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics 28, 1287-1289. doi:10.1093/bioinformatics/bts132.
-
(2012)
Bioinformatics
, vol.28
, pp. 1287-1289
-
-
Zabet, N.R.1
Adryan, B.2
-
44
-
-
77953170555
-
Computational limits to binary genes
-
doi:10.1098/rsif.2009.0474
-
Zabet, N. R., and Chu, D. F. (2010). Computational limits to binary genes. J. R. Soc. Interface 7, 945-954. doi:10.1098/rsif.2009.0474.
-
(2010)
J. R. Soc. Interface
, vol.7
, pp. 945-954
-
-
Zabet, N.R.1
Chu, D.F.2
|