-
1
-
-
4444293086
-
-
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
-
Ptashne, M. 2004. A Genetic Switch. 3rd. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
-
(2004)
A Genetic Switch. 3rd
-
-
Ptashne, M.1
-
2
-
-
4444256116
-
Regulatory circuit design and evolution using phage lambda
-
Atsumi, S., and J. W. Little. 2004. Regulatory circuit design and evolution using phage lambda. Genes Dev. 18:2086-2094.
-
(2004)
Genes Dev
, vol.18
, pp. 2086-2094
-
-
Atsumi, S.1
Little, J.W.2
-
3
-
-
0035890132
-
Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny
-
Dodd, I. B., A. J. Perkins, D. Tsemitsidis, and J. B. Egan. 2001. Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes Dev. 15:3013-3022.
-
(2001)
Genes Dev
, vol.15
, pp. 3013-3022
-
-
Dodd, I.B.1
Perkins, A.J.2
Tsemitsidis, D.3
Egan, J.B.4
-
4
-
-
1042278041
-
Cooperativity in long-range gene regulation by the lambda CI repressor
-
Dodd, I. B., K. E. Shearwin, A. J. Perkins, T. Burr, A. Hochschild, and J. B. Egan. 2004. Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev. 18:344-354.
-
(2004)
Genes Dev
, vol.18
, pp. 344-354
-
-
Dodd, I.B.1
Shearwin, K.E.2
Perkins, A.J.3
Burr, T.4
Hochschild, A.5
Egan, J.B.6
-
5
-
-
0033517148
-
Robustness of a gene regulatory circuit
-
Little, J. W., D. P. Shepley, and D. W. Wert. 1999. Robustness of a gene regulatory circuit. EMBO J. 18:4299-4307.
-
(1999)
EMBO J
, vol.18
, pp. 4299-4307
-
-
Little, J.W.1
Shepley, D.P.2
Wert, D.W.3
-
6
-
-
0242663281
-
Single-cell analysis of lambda immunity regulation
-
Baek, K., S. Svenningsen, H. Eisen, K. Sneppen, and S. Brown. 2003. Single-cell analysis of lambda immunity regulation. J. Mol. Biol. 334:363-372.
-
(2003)
J. Mol. Biol
, vol.334
, pp. 363-372
-
-
Baek, K.1
Svenningsen, S.2
Eisen, H.3
Sneppen, K.4
Brown, S.5
-
7
-
-
0034703473
-
Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding II: Cooperative interactions of cro dimers
-
Darling, P. J., J. M. Holt, and G. K. Ackers. 2000. Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding II: cooperative interactions of cro dimers. J. Mol. Biol. 302:625-638.
-
(2000)
J. Mol. Biol
, vol.302
, pp. 625-638
-
-
Darling, P.J.1
Holt, J.M.2
Ackers, G.K.3
-
8
-
-
0001422329
-
Quantitative model for gene regulation by lambda phage repressor
-
Ackers, G. K., A. D. Johnson, and M. A. Shea. 1982. Quantitative model for gene regulation by lambda phage repressor. Proc. Natl. Acad. Sci. USA. 79:1129-1133.
-
(1982)
Proc. Natl. Acad. Sci. USA
, vol.79
, pp. 1129-1133
-
-
Ackers, G.K.1
Johnson, A.D.2
Shea, M.A.3
-
9
-
-
0025122786
-
Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity
-
Reinitz, J., and J. R. Vaisnys. 1990. Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity. J. Theor. Biol. 145:295-318.
-
(1990)
J. Theor. Biol
, vol.145
, pp. 295-318
-
-
Reinitz, J.1
Vaisnys, J.R.2
-
10
-
-
4243911221
-
Epigenetics as a first exit problem
-
Aurell, E., and K. Sneppen. 2002. Epigenetics as a first exit problem. Phys. Rev. Lett. 88:048101.
-
(2002)
Phys. Rev. Lett
, vol.88
, pp. 048101
-
-
Aurell, E.1
Sneppen, K.2
-
11
-
-
7644234438
-
Calculating biological behaviors of epigenetic states in the phage lambda life cycle
-
Zhu, X. M., L. Yin, L. Hood, and P. Ao. 2004. Calculating biological behaviors of epigenetic states in the phage lambda life cycle. Funct. Integr. Genomics. 4:188-195.
-
(2004)
Funct. Integr. Genomics
, vol.4
, pp. 188-195
-
-
Zhu, X.M.1
Yin, L.2
Hood, L.3
Ao, P.4
-
12
-
-
5644304343
-
Nonspecific binding of the OR repressors CI and Cro of bacteriophage lambda
-
Bakk, A., and R. Metzler. 2004. Nonspecific binding of the OR repressors CI and Cro of bacteriophage lambda. J. Theor. Biol. 231:525-533.
-
(2004)
J. Theor. Biol
, vol.231
, pp. 525-533
-
-
Bakk, A.1
Metzler, R.2
-
13
-
-
1842788224
-
In vivo non-specific binding of lambda CI and Cro repressors is significant
-
Bakk, A., and R. Metzler. 2004. In vivo non-specific binding of lambda CI and Cro repressors is significant. FEBS Lett. 563:66-68.
-
(2004)
FEBS Lett
, vol.563
, pp. 66-68
-
-
Bakk, A.1
Metzler, R.2
-
14
-
-
0346057952
-
Sensitivity of OR in phage lambda
-
Bakk, A., R. Metzler, and K. Sneppen. 2004. Sensitivity of OR in phage lambda. Biophys. J. 86:58-66.
-
(2004)
Biophys. J
, vol.86
, pp. 58-66
-
-
Bakk, A.1
Metzler, R.2
Sneppen, K.3
-
15
-
-
0346688719
-
Why the lysogenic state of phage lambda is so stable: A mathematical modeling approach
-
Santillan, M., and M. C. Mackey. 2004. Why the lysogenic state of phage lambda is so stable: a mathematical modeling approach. Biophys. J. 86:75-84.
-
(2004)
Biophys. J
, vol.86
, pp. 75-84
-
-
Santillan, M.1
Mackey, M.C.2
-
16
-
-
0344630293
-
On the relation between fluctuation and response in biological systems
-
Sato, K., Y. Ito, T. Yomo, and K. Kaneko. 2003. On the relation between fluctuation and response in biological systems. Proc. Natl. Acad. Sci. USA. 100:14086-14090.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 14086-14090
-
-
Sato, K.1
Ito, Y.2
Yomo, T.3
Kaneko, K.4
-
18
-
-
15744393452
-
DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise
-
Vilar, J. M., and L. Saiz. 2005. DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise. Curr. Opin. Genet. Dev. 15:136-144.
-
(2005)
Curr. Opin. Genet. Dev
, vol.15
, pp. 136-144
-
-
Vilar, J.M.1
Saiz, L.2
-
19
-
-
0019887628
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
-
Berg, O. G., R. B. Winter, and P. H. von Hippel. 1981. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry. 20:6929-6948.
-
(1981)
Biochemistry
, vol.20
, pp. 6929-6948
-
-
Berg, O.G.1
Winter, R.B.2
von Hippel, P.H.3
-
20
-
-
0019867850
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli Lac repressor-operator interaction: Kinetic measurements and conclusions
-
Winter, R. B., O. G. Berg, and P. H. von Hippel. 1981. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli Lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry. 20:6961-6977.
-
(1981)
Biochemistry
, vol.20
, pp. 6961-6977
-
-
Winter, R.B.1
Berg, O.G.2
von Hippel, P.H.3
-
21
-
-
0032986554
-
One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements
-
Shimamoto, N. 1999. One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements. J. Biol. Chem. 274:15293-15296.
-
(1999)
J. Biol. Chem
, vol.274
, pp. 15293-15296
-
-
Shimamoto, N.1
-
22
-
-
18044403216
-
Dynamics of DNA-protein interaction deduced from in vitro DNA evolution
-
Dubertret, B., S. Liu, Q. Ouyang, and A. Libchaber. 2001. Dynamics of DNA-protein interaction deduced from in vitro DNA evolution. Phys. Rev. Lett. 86:6022-6025.
-
(2001)
Phys. Rev. Lett
, vol.86
, pp. 6022-6025
-
-
Dubertret, B.1
Liu, S.2
Ouyang, Q.3
Libchaber, A.4
-
23
-
-
0037451299
-
Protein motion from non-specific to specific DNA by three-dimensional routes aided by super-coiling
-
Gowers, D. M., and S. E. Halford. 2003. Protein motion from non-specific to specific DNA by three-dimensional routes aided by super-coiling. EMBO J. 22:1410-1418.
-
(2003)
EMBO J
, vol.22
, pp. 1410-1418
-
-
Gowers, D.M.1
Halford, S.E.2
-
24
-
-
27644460480
-
Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA
-
Gowers, D. M., G. G. Wilson, and S. E. Halford. 2005. Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc. Natl. Acad. Sci. USA. 102:15883-15888.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15883-15888
-
-
Gowers, D.M.1
Wilson, G.G.2
Halford, S.E.3
-
25
-
-
3142657230
-
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
-
Kalodimos, C. G., N. Biris, A. M. Bonvin, M. M. Levandoski, M. Guennuegues, R. Boelens, and R. Kaptein. 2004. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science. 305:386-389.
-
(2004)
Science
, vol.305
, pp. 386-389
-
-
Kalodimos, C.G.1
Biris, N.2
Bonvin, A.M.3
Levandoski, M.M.4
Guennuegues, M.5
Boelens, R.6
Kaptein, R.7
-
26
-
-
23244432464
-
Target search of N sliding proteins on a DNA
-
Sokolov, I. M., R. Metzler, K. Pant, and M. C. Williams. 2005. Target search of N sliding proteins on a DNA. Biophys. J. 89:895-902.
-
(2005)
Biophys. J
, vol.89
, pp. 895-902
-
-
Sokolov, I.M.1
Metzler, R.2
Pant, K.3
Williams, M.C.4
-
27
-
-
30344463841
-
Optimal target search on a fast-folding polymer chain with volume exchange
-
Lomholt, M. A., T. Ambjornsson, and R. Metzler. 2005. Optimal target search on a fast-folding polymer chain with volume exchange. Phys. Rev. Lett. 95:260603.
-
(2005)
Phys. Rev. Lett
, vol.95
, pp. 260603
-
-
Lomholt, M.A.1
Ambjornsson, T.2
Metzler, R.3
-
28
-
-
21244475671
-
A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: Dependence on DNA length and presence of obstacles
-
Zhou, H. X. 2005. A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles. Biophys. J. 88:1608-1615.
-
(2005)
Biophys. J
, vol.88
, pp. 1608-1615
-
-
Zhou, H.X.1
-
29
-
-
4444236055
-
Kinetics of target site localization of a protein on DNA: A stochastic approach
-
Coppey, M., O. Benichou, R. Voituriez, and M. Moreau. 2004. Kinetics of target site localization of a protein on DNA: a stochastic approach. Biophys. J. 87:1640-1649.
-
(2004)
Biophys. J
, vol.87
, pp. 1640-1649
-
-
Coppey, M.1
Benichou, O.2
Voituriez, R.3
Moreau, M.4
-
30
-
-
10044223573
-
Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential
-
Slutsky, M., and L. A. Mirny. 2004. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys. J. 87:4021-4035.
-
(2004)
Biophys. J
, vol.87
, pp. 4021-4035
-
-
Slutsky, M.1
Mirny, L.A.2
-
31
-
-
33645816459
-
How proteins search for their specific sites on DNA: The role of DNA conformation
-
Hu, T., A. Y. Grosberg, and B. I. Shklovskii. 2006. How proteins search for their specific sites on DNA: the role of DNA conformation. Biophys. J. 90:2731-2744.
-
(2006)
Biophys. J
, vol.90
, pp. 2731-2744
-
-
Hu, T.1
Grosberg, A.Y.2
Shklovskii, B.I.3
-
32
-
-
0024531901
-
Facilitated target location in biological systems
-
von Hippel, P. H., and O. G. Berg. 1989. Facilitated target location in biological systems. J. Biol. Chem. 264:675-678.
-
(1989)
J. Biol. Chem
, vol.264
, pp. 675-678
-
-
von Hippel, P.H.1
Berg, O.G.2
-
33
-
-
2042475515
-
Nonspecific DNA binding of genome regulating proteins as a biological control mechanism: Measurement of DNA-bound Escherichia coli Lac repressor in vivo
-
Huang, Y. K., A. Revzin, A. P. Butler, P. O'Conner, D. W. Noble, and P. H. Von Hippel. 1977. Nonspecific DNA binding of genome regulating proteins as a biological control mechanism: Measurement of DNA-bound Escherichia coli Lac repressor in vivo. Proc. Natl. Acad. Sci. USA. 74:4228-4232.
-
(1977)
Proc. Natl. Acad. Sci. USA
, vol.74
, pp. 4228-4232
-
-
Huang, Y.K.1
Revzin, A.2
Butler, A.P.3
O'Conner, P.4
Noble, D.W.5
Von Hippel, P.H.6
-
34
-
-
0031453895
-
The role of DNA bending in Cro protein-DNA interactions
-
Gromiha, M. M., M. G. Munteanu, I. Simon, and S. Pongor. 1997. The role of DNA bending in Cro protein-DNA interactions. Biophys. Chem. 69:153-160.
-
(1997)
Biophys. Chem
, vol.69
, pp. 153-160
-
-
Gromiha, M.M.1
Munteanu, M.G.2
Simon, I.3
Pongor, S.4
-
35
-
-
0036013781
-
Is there a code for protein-DNA recognition? Probab(ilistical)ly
-
Benos, P. V., A. S. Lapedes, and G. D. Stormo. 2002. Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays. 24:466-475.
-
(2002)
Bioessays
, vol.24
, pp. 466-475
-
-
Benos, P.V.1
Lapedes, A.S.2
Stormo, G.D.3
-
36
-
-
33744821974
-
-
Saiz, L., and J. M. Vilar. 2006. Stochastic dynamics of macromolecular-assembly networks. Mol. Syst. Biol. 2:2006.0024 (Epub ahead of print).
-
Saiz, L., and J. M. Vilar. 2006. Stochastic dynamics of macromolecular-assembly networks. Mol. Syst. Biol. 2:2006.0024 (Epub ahead of print).
-
-
-
-
37
-
-
1842607238
-
Secondary structure switching in Cro protein evolution
-
Newlove, T., J. H. Konieczka, and M. H. Cordes. 2004. Secondary structure switching in Cro protein evolution. Structure. 12:569-581.
-
(2004)
Structure
, vol.12
, pp. 569-581
-
-
Newlove, T.1
Konieczka, J.H.2
Cordes, M.H.3
-
38
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361.
-
(1977)
J. Phys. Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
39
-
-
22144443131
-
Nonlinear protein degradation and the function of genetic circuits
-
Buchler, N. E., U. Gerland, and T. Hwa. 2005. Nonlinear protein degradation and the function of genetic circuits. Proc. Natl. Acad. Sci. USA. 102:9559-9564.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 9559-9564
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
40
-
-
0014945080
-
Immunity phase-shift in defective lysogens: Non-mutational hereditary change of early regulation of lambda prophage
-
Neubauer, Z., and E. Calef. 1970. Immunity phase-shift in defective lysogens: non-mutational hereditary change of early regulation of lambda prophage. J. Mol. Biol. 51:1-13.
-
(1970)
J. Mol. Biol
, vol.51
, pp. 1-13
-
-
Neubauer, Z.1
Calef, E.2
-
41
-
-
0017649239
-
The essential role of the cro gene in lytic development by bacteriophage lambda
-
Folkmanis, A., W. Maltzman, P. Mellon, A. Skalka, and H. Echols. 1977. The essential role of the cro gene in lytic development by bacteriophage lambda. Virology. 81:352-362.
-
(1977)
Virology
, vol.81
, pp. 352-362
-
-
Folkmanis, A.1
Maltzman, W.2
Mellon, P.3
Skalka, A.4
Echols, H.5
-
42
-
-
15444379609
-
On the role of Cro in lambda prophage induction
-
Svenningsen, S. L., N. Costantino, D. L. Court, and S. Adhya. 2005. On the role of Cro in lambda prophage induction. Proc. Natl. Acad. Sci. USA. 102:4465-4469.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 4465-4469
-
-
Svenningsen, S.L.1
Costantino, N.2
Court, D.L.3
Adhya, S.4
-
43
-
-
37649030145
-
Stability puzzles in phage lambda
-
Aurell, E., S. Brown, J. Johanson, and K. Sneppen. 2002. Stability puzzles in phage lambda. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65:051914.
-
(2002)
Phys. Rev. E Stat. Nonlin. Soft Matter Phys
, vol.65
, pp. 051914
-
-
Aurell, E.1
Brown, S.2
Johanson, J.3
Sneppen, K.4
-
44
-
-
0037418253
-
Retroevolution of lambda Cro toward a stable monomer
-
LeFevre, K. R., and M. H. Cordes. 2003. Retroevolution of lambda Cro toward a stable monomer. Proc. Natl. Acad. Sci. USA. 100:2345-2350.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 2345-2350
-
-
LeFevre, K.R.1
Cordes, M.H.2
-
45
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
-
Arkin, A., J. Ross, and H. H. McAdams. 1998. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 149:1633-1648.
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
|