-
1
-
-
0032479079
-
Going the distance: A current view of enhancer action
-
E.M. Blackwood, and J.T. Kadonaga Going the distance: a current view of enhancer action Science 281 1998 60 63
-
(1998)
Science
, vol.281
, pp. 60-63
-
-
Blackwood, E.M.1
Kadonaga, J.T.2
-
2
-
-
76749118994
-
A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes
-
Y. Liu, and H. Chen J. Yan A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes Genes Dev. 24 2010 339 344
-
(2010)
Genes Dev.
, vol.24
, pp. 339-344
-
-
Liu, Y.1
Chen, H.2
Yan, J.3
-
3
-
-
0025216961
-
DNA looping in cellular repression of transcription of the galactose operon
-
N. Mandal, and W. Su H. Echols DNA looping in cellular repression of transcription of the galactose operon Genes Dev. 4 1990 410 418
-
(1990)
Genes Dev.
, vol.4
, pp. 410-418
-
-
Mandal, N.1
Su, W.2
Echols, H.3
-
4
-
-
78751479182
-
Salmonella enterica response regulator SsrB relieves H-NS silencing by displacing H-NS bound in polymerization mode and directly activates transcription
-
D. Walthers, and Y. Li L.J. Kenney Salmonella enterica response regulator SsrB relieves H-NS silencing by displacing H-NS bound in polymerization mode and directly activates transcription J. Biol. Chem. 286 2011 1895 1902
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 1895-1902
-
-
Walthers, D.1
Li, Y.2
Kenney, L.J.3
-
5
-
-
50649121477
-
Advances in single-molecule fluorescence methods for molecular biology
-
C. Joo, and H. Balci T. Ha Advances in single-molecule fluorescence methods for molecular biology Annu. Rev. Biochem. 77 2008 51 76
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 51-76
-
-
Joo, C.1
Balci, H.2
Ha, T.3
-
6
-
-
44449087047
-
Single-molecule force spectroscopy: Optical tweezers, magnetic tweezers and atomic force microscopy
-
K.C. Neuman, and A. Nagy Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy Nat. Methods 5 2008 491 505
-
(2008)
Nat. Methods
, vol.5
, pp. 491-505
-
-
Neuman, K.C.1
Nagy, A.2
-
7
-
-
44449097780
-
Do-it-yourself guide: How to use the modern single-molecule toolkit
-
N.G. Walter, and C.Y. Huang M.A. Sobhy Do-it-yourself guide: how to use the modern single-molecule toolkit Nat. Methods 5 2008 475 489
-
(2008)
Nat. Methods
, vol.5
, pp. 475-489
-
-
Walter, N.G.1
Huang, C.Y.2
Sobhy, M.A.3
-
8
-
-
77953512028
-
Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription
-
L. Finzi, and D.D. Dunlap Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription J. Biol. Chem. 285 2010 18973 18978
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 18973-18978
-
-
Finzi, L.1
Dunlap, D.D.2
-
10
-
-
0028956979
-
Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules
-
L. Finzi, and J. Gelles Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules Science 267 1995 378 380
-
(1995)
Science
, vol.267
, pp. 378-380
-
-
Finzi, L.1
Gelles, J.2
-
11
-
-
31544452261
-
Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
-
B. van den Broek, and F. Vanzi G.J. Wuite Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI Nucleic Acids Res. 34 2006 167 174
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 167-174
-
-
Van Den Broek, B.1
Vanzi, F.2
Wuite, G.J.3
-
12
-
-
33746207766
-
Lac repressor hinge flexibility and DNA looping: Single molecule kinetics by tethered particle motion
-
F. Vanzi, and C. Broggio F.S. Pavone Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion Nucleic Acids Res. 34 2006 3409 3420
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3409-3420
-
-
Vanzi, F.1
Broggio, C.2
Pavone, F.S.3
-
13
-
-
0141482089
-
Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping
-
G. Lia, and D. Bensimon L. Finzi Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping Proc. Natl. Acad. Sci. USA 100 2003 11373 11377
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 11373-11377
-
-
Lia, G.1
Bensimon, D.2
Finzi, L.3
-
14
-
-
0035890132
-
Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny
-
I.B. Dodd, and A.J. Perkins J.B. Egan Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny Genes Dev. 15 2001 3013 3022
-
(2001)
Genes Dev.
, vol.15
, pp. 3013-3022
-
-
Dodd, I.B.1
Perkins, A.J.2
Egan, J.B.3
-
15
-
-
44449154784
-
DNA looping can enhance lysogenic CI transcription in phage lambda
-
L.M. Anderson, and H. Yang DNA looping can enhance lysogenic CI transcription in phage lambda Proc. Natl. Acad. Sci. USA 105 2008 5827 5832
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 5827-5832
-
-
Anderson, L.M.1
Yang, H.2
-
16
-
-
33645236709
-
Role of the lytic repressor in prophage induction of phage lambda as analyzed by a module-replacement approach
-
S. Atsumi, and J.W. Little Role of the lytic repressor in prophage induction of phage lambda as analyzed by a module-replacement approach Proc. Natl. Acad. Sci. USA 103 2006 4558 4563
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 4558-4563
-
-
Atsumi, S.1
Little, J.W.2
-
17
-
-
80052563421
-
Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro
-
D. Lewis, and P. Le S. Adhya Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro Proc. Natl. Acad. Sci. USA 108 2011 14807 14812
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 14807-14812
-
-
Lewis, D.1
Le, P.2
Adhya, S.3
-
18
-
-
33748780364
-
Tethered particle motion as a diagnostic of DNA tether length
-
P.C. Nelson, and C. Zurla D. Dunlap Tethered particle motion as a diagnostic of DNA tether length J. Phys. Chem. B 110 2006 17260 17267
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 17260-17267
-
-
Nelson, P.C.1
Zurla, C.2
Dunlap, D.3
-
19
-
-
66249111861
-
Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor
-
C. Zurla, and C. Manzo L. Finzi Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor Nucleic Acids Res. 37 2009 2789 2795
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2789-2795
-
-
Zurla, C.1
Manzo, C.2
Finzi, L.3
-
20
-
-
77954571156
-
Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments
-
C. Manzo, and L. Finzi Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments Methods Enzymol. 475 2010 199 220
-
(2010)
Methods Enzymol.
, vol.475
, pp. 199-220
-
-
Manzo, C.1
Finzi, L.2
-
21
-
-
12344282980
-
Detection of intensity change points in time-resolved single-molecule measurements
-
L.P. Watkins, and H. Yang Detection of intensity change points in time-resolved single-molecule measurements J. Phys. Chem. B 109 2005 617 628
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 617-628
-
-
Watkins, L.P.1
Yang, H.2
-
22
-
-
70350455297
-
AFM studies of λ repressor oligomers securing DNA loops
-
H. Wang, and L. Finzi D. Dunlap AFM studies of λ repressor oligomers securing DNA loops Curr. Pharm. Biotechnol. 10 2009 494 501
-
(2009)
Curr. Pharm. Biotechnol.
, vol.10
, pp. 494-501
-
-
Wang, H.1
Finzi, L.2
Dunlap, D.3
-
23
-
-
0035668536
-
Making contacts on a nucleic acid polymer
-
K. Rippe Making contacts on a nucleic acid polymer Trends Biochem. Sci. 26 2001 733 740
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 733-740
-
-
Rippe, K.1
-
24
-
-
0034852959
-
Fractal methods to analyze ion channel kinetics
-
L.S. Liebovitch, and D. Scheurle M. Zochowski Fractal methods to analyze ion channel kinetics Methods 24 2001 359 375
-
(2001)
Methods
, vol.24
, pp. 359-375
-
-
Liebovitch, L.S.1
Scheurle, D.2
Zochowski, M.3
-
25
-
-
0008101112
-
Distributions of activation energy barriers that produce stretched exponential probability distributions for the time spent in each state of the two state reaction AB
-
L.S. Liebovitch, and T.I. Tóth Distributions of activation energy barriers that produce stretched exponential probability distributions for the time spent in each state of the two state reaction AB Bull. Math. Biol. 53 1991 443 455
-
(1991)
Bull. Math. Biol.
, vol.53
, pp. 443-455
-
-
Liebovitch, L.S.1
Tóth, T.I.2
-
26
-
-
36749116443
-
First passage time approach to diffusion controlled reactions
-
A. Szabo, K. Schulten, and Z. Schulten First passage time approach to diffusion controlled reactions J. Chem. Phys. 72 1980 4350 4357
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 4350-4357
-
-
Szabo, A.1
Schulten, K.2
Schulten, Z.3
-
27
-
-
38549136462
-
Long-time stretched exponential kinetics in single DNA duplex dissociation
-
P.L. Biancaniello, A.J. Kim, and J.C. Crocker Long-time stretched exponential kinetics in single DNA duplex dissociation Biophys. J. 94 2008 891 896
-
(2008)
Biophys. J.
, vol.94
, pp. 891-896
-
-
Biancaniello, P.L.1
Kim, A.J.2
Crocker, J.C.3
-
28
-
-
0035826712
-
Non-Arrhenius kinetics for the loop closure of a DNA hairpin
-
M.I. Wallace, and L. Ying D. Klenerman Non-Arrhenius kinetics for the loop closure of a DNA hairpin Proc. Natl. Acad. Sci. USA 98 2001 5584 5589
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 5584-5589
-
-
Wallace, M.I.1
Ying, L.2
Klenerman, D.3
-
29
-
-
20044379583
-
Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules
-
O. Flomenbom, and K. Velonia J. Klafter Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules Proc. Natl. Acad. Sci. USA 102 2005 2368 2372
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 2368-2372
-
-
Flomenbom, O.1
Velonia, K.2
Klafter, J.3
-
30
-
-
61349151084
-
Unified explanation of the fluorescence decay and blinking characteristics of semiconductor nanocrystals
-
M. Tachiya, and K. Seki Unified explanation of the fluorescence decay and blinking characteristics of semiconductor nanocrystals Appl. Phys. Lett. 94 2009 081104
-
(2009)
Appl. Phys. Lett.
, vol.94
, pp. 081104
-
-
Tachiya, M.1
Seki, K.2
-
31
-
-
33645693765
-
Transition in the temperature-dependence of GFP fluorescence: From proton wires to proton exit
-
P. Leiderman, D. Huppert, and N. Agmon Transition in the temperature-dependence of GFP fluorescence: from proton wires to proton exit Biophys. J. 90 2006 1009 1018
-
(2006)
Biophys. J.
, vol.90
, pp. 1009-1018
-
-
Leiderman, P.1
Huppert, D.2
Agmon, N.3
-
32
-
-
0027173716
-
Highly cooperative DNA binding by the coliphage HK022 repressor
-
N.G. Carlson, and J.W. Little Highly cooperative DNA binding by the coliphage HK022 repressor J. Mol. Biol. 230 1993 1108 1130
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 1108-1130
-
-
Carlson, N.G.1
Little, J.W.2
-
33
-
-
0042622638
-
DNA looping and physical constraints on transcription regulation
-
J.M.G. Vilar, and S. Leibler DNA looping and physical constraints on transcription regulation J. Mol. Biol. 331 2003 981 989
-
(2003)
J. Mol. Biol.
, vol.331
, pp. 981-989
-
-
Vilar, J.M.G.1
Leibler, S.2
-
34
-
-
33645322437
-
Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda
-
C. Zurla, and A. Franzini L. Finzi Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda J. Phys. Condens. Matter 18 2006 S225 S234
-
(2006)
J. Phys. Condens. Matter
, vol.18
-
-
Zurla, C.1
Franzini, A.2
Finzi, L.3
-
35
-
-
0007208716
-
Interactions between DNA-bound repressors govern regulation by the lambda phage repressor
-
A.D. Johnson, B.J. Meyer, and M. Ptashne Interactions between DNA-bound repressors govern regulation by the lambda phage repressor Proc. Natl. Acad. Sci. USA 76 1979 5061 5065
-
(1979)
Proc. Natl. Acad. Sci. USA
, vol.76
, pp. 5061-5065
-
-
Johnson, A.D.1
Meyer, B.J.2
Ptashne, M.3
-
36
-
-
0018850588
-
Gene regulation at the right operator (OR) bacteriophage lambda. I. OR3 and autogenous negative control by repressor
-
R. Maurer, B.J. Meyer, and M. Ptashne Gene regulation at the right operator (OR) bacteriophage lambda. I. OR3 and autogenous negative control by repressor J. Mol. Biol. 139 1980 147 161
-
(1980)
J. Mol. Biol.
, vol.139
, pp. 147-161
-
-
Maurer, R.1
Meyer, B.J.2
Ptashne, M.3
-
37
-
-
0018817388
-
Gene regulation at the right operator (OR) of bacteriophage lambda. II. OR1, OR2, and OR3: Their roles in mediating the effects of repressor and cro
-
B.J. Meyer, R. Maurer, and M. Ptashne Gene regulation at the right operator (OR) of bacteriophage lambda. II. OR1, OR2, and OR3: their roles in mediating the effects of repressor and cro J. Mol. Biol. 139 1980 163 194
-
(1980)
J. Mol. Biol.
, vol.139
, pp. 163-194
-
-
Meyer, B.J.1
Maurer, R.2
Ptashne, M.3
-
38
-
-
0029691136
-
On the rate of approximations for maximum likelihood tests in change-point models
-
E. Gombay, and L. Horvath On the rate of approximations for maximum likelihood tests in change-point models J. Multivar. Anal. 56 1996 120 152
-
(1996)
J. Multivar. Anal.
, vol.56
, pp. 120-152
-
-
Gombay, E.1
Horvath, L.2
-
40
-
-
0032269108
-
How many clusters? Which clustering method? Answers via model-based cluster analysis
-
C. Fraley, and A.E. Raftery How many clusters? Which clustering method? Answers via model-based cluster analysis Comput. J. 41 1998 578 588
-
(1998)
Comput. J.
, vol.41
, pp. 578-588
-
-
Fraley, C.1
Raftery, A.E.2
-
41
-
-
0035998835
-
Model-based clustering, discriminant analysis, and density estimation
-
C. Fraley, and A.E. Raftery Model-based clustering, discriminant analysis, and density estimation J. Am. Stat. Assoc. 97 2002 611 631
-
(2002)
J. Am. Stat. Assoc.
, vol.97
, pp. 611-631
-
-
Fraley, C.1
Raftery, A.E.2
-
42
-
-
0001340183
-
Clustering methods based on likelihood ratio criteria
-
A.J. Scott, and M.J. Symons Clustering methods based on likelihood ratio criteria Biometrics 27 1971 387 397
-
(1971)
Biometrics
, vol.27
, pp. 387-397
-
-
Scott, A.J.1
Symons, M.J.2
|