-
1
-
-
84899024465
-
Physical constraints determine the logic of bacterial promoter architectures
-
Ezer D, Zabet NR, Adryan B. Physical constraints determine the logic of bacterial promoter architectures. Nucleic Acids Res 2014; 42 (7):4196-207. http://dx.doi.org/10.1093/nar/gku078.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.7
, pp. 4196-4207
-
-
Ezer, D.1
Zabet, N.R.2
Adryan, B.3
-
2
-
-
33846002036
-
Transcriptional regulation by competing transcription factor modules
-
Hermsen R, Tans S, ten Wolde PR. Transcriptional regulation by competing transcription factor modules. PLoS Comput Biol 2006; 2 (12):e164. http://dx.doi.org/10.1371/journal.pcbi.0020164.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.12
, pp. e164
-
-
Hermsen, R.1
Tans, S.2
Ten Wolde, P.R.3
-
3
-
-
84876216563
-
Master transcription factors and mediator establish super-enhancers at key cell identity genes
-
Whyte WA, Orlando DA, Hnisz D, Abraham B.J., Lin CY, Kagey MH, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 2013; 153 (2):307-19. http://dx.doi.org/10.1016/j.cell.2013.03.035.
-
(2013)
Cell
, vol.153
, Issue.2
, pp. 307-319
-
-
Whyte, W.A.1
Orlando, D.A.2
Hnisz, D.3
Abraham, B.J.4
Lin, C.Y.5
Kagey, M.H.6
-
4
-
-
84855895602
-
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells
-
Cheng C, Gerstein M. Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res 2012; 40 (2):553-68. http://dx.doi.org/10.1093/nar/gkr752.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.2
, pp. 553-568
-
-
Cheng, C.1
Gerstein, M.2
-
5
-
-
84865249952
-
Transcription factors: From enhancer binding to developmental control
-
Spitz F, Furlong EEM. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 2012; 13 (9):613-26. http://dx.doi.org/10.1038/nrg3207.
-
(2012)
Nat Rev Genet
, vol.13
, Issue.9
, pp. 613-626
-
-
Spitz, F.1
Furlong, E.E.M.2
-
6
-
-
84881520887
-
Cellular resolution models for even skipped regulation in the entire drosophila embryo
-
[n/a]
-
Ilsley GR, Fisher J, Apweiler R., DePace AH, Luscombe NM. Cellular resolution models for even skipped regulation in the entire Drosophila embryo. eLife 2013; 2. http://dx.doi.org/10.7554/eLife.00522 [n/a].
-
(2013)
ELife
, vol.2
-
-
Ilsley, G.R.1
Fisher, J.2
Apweiler, R.3
Depace, A.H.4
Luscombe, N.M.5
-
7
-
-
36249017917
-
Programming gene expression with combinatorial promoters
-
[n/a]
-
Cox III RS, Surette MG, Elowitz MB. Programming gene expression with combinatorial promoters. Mol Syst Biol 2007; 3 (1). http://dx.doi.org/10.1038/msb4100187 [n/a].
-
(2007)
Mol Syst Biol
, vol.3
, Issue.1
-
-
Cox, R.S.1
Surette, M.G.2
Elowitz, M.B.3
-
8
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz J, Siggia ED, Cohen BA. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 2009; 457:215-8. http://dx.doi.org/10.1038/nature07521.
-
(2009)
Nature
, vol.457
, pp. 215-218
-
-
Gertz, J.1
Siggia, E.D.2
Cohen, B.A.3
-
9
-
-
84862002321
-
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
-
Sharon E, Kalma Y, Sharp A., Raveh-Sadka T, Levo M, Zeevi D., et al. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol 2012; 30 (6):521-30. http://dx.doi.org/10.1038/nbt.2205.
-
(2012)
Nat Biotechnol
, vol.30
, Issue.6
, pp. 521-530
-
-
Sharon, E.1
Kalma, Y.2
Sharp, A.3
Raveh-Sadka, T.4
Levo, M.5
Zeevi, D.6
-
10
-
-
84883457107
-
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model
-
Smith RP, Taher L, Patwardhan R.P., Kim MJ, Inoue F, Shendure J, et al. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet 2013:1021-8. http://dx.doi.org/10.1038/ng.2713.
-
(2013)
Nat Genet
, pp. 1021-1028
-
-
Smith, R.P.1
Taher, L.2
Patwardhan, R.P.3
Kim, M.J.4
Inoue, F.5
Shendure, J.6
-
11
-
-
84872651936
-
Drosophila blastoderm patterning
-
Jaeger J, Manu J Reinitz. Drosophila blastoderm patterning. Curr Opin Genet Dev 2012; 22 (6):533-41. http://dx.doi.org/10.1016/j.gde.2012.10.005.
-
(2012)
Curr Opin Genet Dev
, vol.22
, Issue.6
, pp. 533-541
-
-
Jaeger, J.1
Reinitz, M.J.2
-
12
-
-
84862624197
-
The lac repressor displays facilitated diffusion in living cells
-
Hammar P, Leroy P, Mahmutovic A., Marklund EG, Berg OG, Elf J. The lac repressor displays facilitated diffusion in living cells. Science 2012; 336 (6088):1595-8. http://dx.doi.org/10.1126/science.1221648.
-
(2012)
Science
, vol.336
, Issue.6088
, pp. 1595-1598
-
-
Hammar, P.1
Leroy, P.2
Mahmutovic, A.3
Marklund, E.G.4
Berg, O.G.5
Elf, J.6
-
13
-
-
78651107675
-
Nucleosome-mediated cooperativity between transcription factors
-
Mirny LA. Nucleosome-mediated cooperativity between transcription factors. PNAS 2010; 107 (52):22534-9. http://dx.doi.org/10.1073/pnas.0913805107.
-
(2010)
PNAS
, vol.107
, Issue.52
, pp. 22534-22539
-
-
Mirny, L.A.1
-
14
-
-
70350741354
-
An ensemble model of competitive multi-factor binding of the genome
-
Wasson T, Hartemink AJ. An ensemble model of competitive multi-factor binding of the genome. Genome Res 2009; 19:2101-12. http://dx.doi.org/10.1101/gr.093450.109.
-
(2009)
Genome Res
, vol.19
, pp. 2101-2112
-
-
Wasson, T.1
Hartemink, A.J.2
-
15
-
-
84884659690
-
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy
-
Cheng Q, Kazemian M, Pham H., Blatti C, Celniker SE, Wolfe S.A., et al. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genet 2013; 9 (8):e1003571. http://dx.doi.org/10.1371/journal.pgen.1003571.
-
(2013)
PLoS Genet
, vol.9
, Issue.8
-
-
Cheng, Q.1
Kazemian, M.2
Pham, H.3
Blatti, C.4
Celniker, S.E.5
Wolfe, S.A.6
-
16
-
-
0030912313
-
Common themes in the function of transcription and splicing enhancers
-
Hertel KJ, Lynch KW, Maniatis T. Common themes in the function of transcription and splicing enhancers. Curr Opin Cell Biol 1997; 9 (3):350-7. http://dx.doi.org/10.1016/S0955-0674(97)80007-5.
-
(1997)
Curr Opin Cell Biol
, vol.9
, Issue.3
, pp. 350-357
-
-
Hertel, K.J.1
Lynch, K.W.2
Maniatis, T.3
-
17
-
-
0026011628
-
Synergistic activation of a human promoter in vivo by transcription factor sp1
-
Anderson GM, Freytag SO. Synergistic activation of a human promoter in vivo by transcription factor Sp1. Mol Cell Biol 1991; 11 (4):1935-43. http://dx.doi.org/10.1128/MCB.11.4.1935.
-
(1991)
Mol Cell Biol
, vol.11
, Issue.4
, pp. 1935-1943
-
-
Anderson, G.M.1
Freytag, S.O.2
-
18
-
-
78049450019
-
Thermodynamics-based models of transcription-al regulation by enhancers: The roles of synergistic activation, cooperative binding and short-range repression
-
He X, Samee MAH, Blatti C, Sinha S. Thermodynamics-based models of transcription-al regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Comput Biol 2010; 6 (9):e1000935. http://dx.doi.org/10.1371/journal.pcbi.1000935.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.9
-
-
He, X.1
Samee, M.A.H.2
Blatti, C.3
Sinha, S.4
-
19
-
-
0025318699
-
How different Eukaryotic transcriptional activators can cooperate promiscuously
-
Lin YS, Carey M, Ptashne M., Green MR. How different eukaryotic transcriptional activators can cooperate promiscuously. Nature 1990; 345 (6273):359-61. http:// dx.doi.org/10.1038/345359a0.
-
(1990)
Nature
, vol.345
, Issue.6273
, pp. 359-361
-
-
Lin, Y.S.1
Carey, M.2
Ptashne, M.3
Green, M.R.4
-
21
-
-
77951874066
-
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
-
Gotea V, Visel A, Westlund J.M., Nobrega MA, Pennacchio LA, Ovcharenko I. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 2010; 20 (5):565-77. http://dx.doi.org/10.1101/gr.104471.109.
-
(2010)
Genome Res
, vol.20
, Issue.5
, pp. 565-577
-
-
Gotea, V.1
Visel, A.2
Westlund, J.M.3
Nobrega, M.A.4
Pennacchio, L.A.5
Ovcharenko, I.6
-
22
-
-
40449124692
-
Systematic functional characterization of cis-regulatory motifs in human core promoters
-
Sinha S, Adler AS, Field Y, Chang H.Y., Segal E. Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res 2008; 18 (3):477-88. http://dx.doi.org/10.1101/gr.6828808.
-
(2008)
Genome Res
, vol.18
, Issue.3
, pp. 477-488
-
-
Sinha, S.1
Adler, A.S.2
Field, Y.3
Chang, H.Y.4
Segal, E.5
-
23
-
-
33646844116
-
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome
-
Zhang C, Xuan Z, Otto S., Hover JR, McCorkle SR, Mandel G, et al. A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res 2006; 34 (8):2238-46. http://dx.doi.org/10.1093/nar/gkl248.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.8
, pp. 2238-2246
-
-
Zhang, C.1
Xuan, Z.2
Otto, S.3
Hover, J.R.4
McCorkle, S.R.5
Mandel, G.6
-
24
-
-
84863230316
-
Massively parallel functional dissection of mammalian enhancers in vivo
-
Patwardhan RP, Hiatt JB, Witten D.M., Kim MJ, Smith RP, May D, et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol 2012; 30 (3):265-70. http://dx.doi.org/10.1038/nbt.2136.
-
(2012)
Nat Biotechnol
, vol.30
, Issue.3
, pp. 265-270
-
-
Patwardhan, R.P.1
Hiatt, J.B.2
Witten, D.M.3
Kim, M.J.4
Smith, R.P.5
May, D.6
-
25
-
-
84863229330
-
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
-
Melnikov A, Murugan A, Zhang X., Tesileanu T, Wang L, Rogov P., et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol 2012; 30 (3):271-7. http://dx.doi.org/10.1038/nbt.2137.
-
(2012)
Nat Biotechnol
, vol.30
, Issue.3
, pp. 271-277
-
-
Melnikov, A.1
Murugan, A.2
Zhang, X.3
Tesileanu, T.4
Wang, L.5
Rogov, P.6
-
26
-
-
84880362638
-
Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
-
White MA, Myers CA, Corbo J.C., Cohen BA. Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. PNAS 2013; 110 (29):11952-7. http://dx.doi.org/10.1073/pnas.1307449110.
-
(2013)
PNAS
, vol.110
, Issue.29
, pp. 11952-11957
-
-
White, M.A.1
Myers, C.A.2
Corbo, J.C.3
Cohen, B.A.4
-
27
-
-
78651299341
-
RegulonDB version 7.0: Transcriptional regulation of escherichia coli K-12 integrated within genetic sensory response units (Gensor units)
-
Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz Rascado L, Solano-Lira H, et al. RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor units). Nucleic Acids Res 2011; 39 (Suppl. 1):D98-D105.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D98-D105
-
-
Gama-Castro, S.1
Salgado, H.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Muñiz Rascado, L.5
Solano-Lira, H.6
-
28
-
-
78651335916
-
REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in drosophila
-
Gallo SM, Gerrard DT, Miner D, Simich M., Des Soye B, Bergman CM, et al. REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res 2011; 39 (Suppl. 1):D118-23.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D118-23
-
-
Gallo, S.M.1
Gerrard, D.T.2
Miner, D.3
Simich, M.4
Des Soye, B.5
Bergman, C.M.6
-
29
-
-
61449155349
-
Models of transcription factor binding: Sensitivity of activation functions to model assumptions
-
Chu D, Zabet NR, Mitavskiy B. Models of transcription factor binding: sensitivity of activation functions to model assumptions. J Theor Biol 2009; 257 (3):419-29. http://dx.doi.org/10.1016/j.jtbi.2008.11.026.
-
(2009)
J Theor Biol
, vol.257
, Issue.3
, pp. 419-429
-
-
Chu, D.1
Zabet, N.R.2
Mitavskiy, B.3
-
30
-
-
15744387380
-
Transcriptional regulation by the numbers: Models
-
Bintu L, Buchler NE, Garcia H.G., Gerland U., Hwa T, Kondev J, et al. Transcriptional regulation by the numbers: models. Curr Opin Genet Dev 2005; 15:116-24. http:// dx.doi.org/10.1016/j.gde.2005.02.007.
-
(2005)
Curr Opin Genet Dev
, vol.15
, pp. 116-124
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
-
31
-
-
77953170555
-
Computational limits to binary genes
-
Zabet NR, Chu DF. Computational limits to binary genes. J R Soc Interface 2010; 7: 945-54. http://dx.doi.org/10.1098/rsif.2009.0474.
-
(2010)
J R Soc Interface
, vol.7
, pp. 945-954
-
-
Zabet, N.R.1
Chu, D.F.2
-
32
-
-
0037965981
-
On schemes of combinatorial transcription logic
-
Buchler NE, Gerland U, Hwa T. On schemes of combinatorial transcription logic. PNAS 2003; 100 (9):5136-41. http://dx.doi.org/10.1073/pnas.0930314100.
-
(2003)
PNAS
, vol.100
, Issue.9
, pp. 5136-5141
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
33
-
-
33646167129
-
Plasticity of the cis-regulatory input function of a gene
-
Mayo AE, Setty Y, Shavit S., Zaslaver A, Alon U. Plasticity of the cis-regulatory input function of a gene. PLoS Biol 2006; 4 (4):e45. http://dx.doi.org/10.1371/journal.pbio.0040045.
-
(2006)
PLoS Biol
, vol.4
, Issue.4
, pp. e45
-
-
Mayo, A.E.1
Setty, Y.2
Shavit, S.3
Zaslaver, A.4
Alon, U.5
-
34
-
-
75949115944
-
Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs
-
Giorgetti L, Siggers T, Tiana G., Caprara G, Notarbartolo S, Corona T., et al. Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol Cell 2010; 37 (3): 418-28. http://dx.doi.org/10.1016/j.molcel.2010.01.016.
-
(2010)
Mol Cell
, vol.37
, Issue.3
, pp. 418-428
-
-
Giorgetti, L.1
Siggers, T.2
Tiana, G.3
Caprara, G.4
Notarbartolo, S.5
Corona, T.6
-
35
-
-
84902212429
-
Regulation of gene expression in the genomic context
-
Atkinson TJ, Halfon MS. Regulation of gene expression in the genomic context. Comput Struct Biotechnol J 2014; 9 (13):1-21. http://dx.doi.org/10.5936/csbj.201401001.
-
(2014)
Comput Struct Biotechnol J
, vol.9
, Issue.13
, pp. 1-21
-
-
Atkinson, T.J.1
Halfon, M.S.2
-
36
-
-
84870901239
-
Cellular crowding imposes global constraints on the chemistry and evolution of proteomes
-
Levy ED, De S, Teichmann SA. Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. PNAS 2012; 109 (50):20461-6. http://dx.doi.org/10.1073/pnas.1209312109.
-
(2012)
PNAS
, vol.109
, Issue.50
, pp. 20461-20466
-
-
Levy, E.D.1
De, S.2
Teichmann, S.A.3
-
37
-
-
80055092183
-
Inferring transcription factor complexes from ChIP-seq data
-
Whitington T, Frith MC, Johnson J, Bailey TL. Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Res 2011; 39 (15):e98. http://dx.doi.org/10.1093/nar/gkr341.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.15
, pp. e98
-
-
Whitington, T.1
Frith, M.C.2
Johnson, J.3
Bailey, T.L.4
-
38
-
-
17044431033
-
The role of binding site cluster strength in bicoid-dependent patterning in drosophila
-
Ochoa-Espinosa A, Yucel G, Kaplan L., Pare A, Pura N, Oberstein A., et al. The role of binding site cluster strength in bicoid-dependent patterning in Drosophila. PNAS 2005; 102 (14):4960-5. http://dx.doi.org/10.1073/pnas.0500373102.
-
(2005)
PNAS
, vol.102
, Issue.14
, pp. 4960-4965
-
-
Ochoa-Espinosa, A.1
Yucel, G.2
Kaplan, L.3
Pare, A.4
Pura, N.5
Oberstein, A.6
-
39
-
-
0032499071
-
Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions
-
Vashee S, Melcher K, Ding W., Johnston SA, Kodadek T. Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions. Curr Biol 1998; 8 (8):452-8. http://dx.doi.org/10.1016/S0960-9822(98)70179-4.
-
(1998)
Curr Biol
, vol.8
, Issue.8
, pp. 452-458
-
-
Vashee, S.1
Melcher, K.2
Ding, W.3
Johnston, S.A.4
Kodadek, T.5
-
40
-
-
67649826220
-
From DNA sequence to transcriptional behaviour: A quantitative approach
-
Segal E, Widom J. From DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet 2009; 10:443-56. http://dx.doi.org/10.1038/nrg2591.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 443-456
-
-
Segal, E.1
Widom, J.2
-
41
-
-
0014945567
-
The lac represser-operator interaction: III. Kinetic studies
-
Riggs AD, Bourgeois S, Cohn M. The lac represser-operator interaction: III. Kinetic studies. J Mol Biol 1970; 53 (3):401-17. http://dx.doi.org/10.1016/0022-2836(70)90074-4.
-
(1970)
J Mol Biol
, vol.53
, Issue.3
, pp. 401-417
-
-
Riggs, A.D.1
Bourgeois, S.2
Cohn, M.3
-
42
-
-
84867364776
-
Computational models for large-scale simulations of facilitated diffusion
-
Zabet NR, Adryan B. Computational models for large-scale simulations of facilitated diffusion. Mol BioSyst 2012; 8 (11):2815-27. http://dx.doi.org/10.1039/C2MB25201E.
-
(2012)
Mol BioSyst
, vol.8
, Issue.11
, pp. 2815-2827
-
-
Zabet, N.R.1
Adryan, B.2
-
43
-
-
0019887628
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
-
Berg OG, Winter RB, von Hippel PH. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 1981; 20 (24):6929-48.
-
(1981)
Biochemistry
, vol.20
, Issue.24
, pp. 6929-6948
-
-
Berg, O.G.1
Winter, R.B.2
Von Hippel, P.H.3
-
44
-
-
65549171477
-
An end to 40 years of mistakes in DNA-protein association kinetics?
-
Halford SE. An end to 40 years of mistakes in DNA-protein association kinetics? Biochem Soc Trans 2009; 37:343-8. http://dx.doi.org/10.1042/BST0370343.
-
(2009)
Biochem Soc Trans
, vol.37
, pp. 343-348
-
-
Halford, S.E.1
-
45
-
-
0023645192
-
Kinetic studies on cro repressor-operator DNA interaction
-
Kim JG, Takeda Y, Matthews B.W., Anderson WF. Kinetic studies on Cro repressor-operator DNA interaction. J Mol Biol 1987; 196 (1):149-58. http://dx.doi.org/10.1016/0022-2836(87)90517-1.
-
(1987)
J Mol Biol
, vol.196
, Issue.1
, pp. 149-158
-
-
Kim, J.G.1
Takeda, Y.2
Matthews, B.W.3
Anderson, W.F.4
-
46
-
-
0032986554
-
One-dimensional diffusion of proteins along DNA
-
Shimamoto N. One-dimensional diffusion of proteins along DNA. J Biol Chem 1999; 274 (22):15293-6. http://dx.doi.org/10.1074/jbc.274.22.15293.
-
(1999)
J Biol Chem
, vol.274
, Issue.22
, pp. 15293-15296
-
-
Shimamoto, N.1
-
47
-
-
0027749617
-
Visualization of single molecules of RNA polymerase sliding along DNA
-
Kabata OKH, Arai MWI, Margarson SA, Glass R.E., Shimamoto N. Visualization of single molecules of RNA polymerase sliding along DNA. Science 1993; 262 (5139): 1561-3. http://dx.doi.org/10.1126/science.8248804.
-
(1993)
Science
, vol.262
, Issue.5139
, pp. 1561-1563
-
-
Kabata, O.K.H.1
Arai, M.W.I.2
Margarson, S.A.3
Glass, R.E.4
Shimamoto, N.5
-
48
-
-
33645807371
-
A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
-
Blainey PC, van Oijen AM, Banerjee A, Verdine GL, Xie XS. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. PNAS 2006; 103 (15):5752-7. http://dx.doi.org/10.1073/pnas.0509723103.
-
(2006)
PNAS
, vol.103
, Issue.15
, pp. 5752-5757
-
-
Blainey, P.C.1
Van Oijen, A.M.2
Banerjee, A.3
Verdine, G.L.4
Xie, X.S.5
-
49
-
-
84867351024
-
Sequence-dependent sliding kinetics of p53
-
Leith JS, Tafvizi A, Huang F., Uspal WE, Doyle PS, Fersht AR, et al. Sequence-dependent sliding kinetics of p53. PNAS 2012; 109 (41):16552-7. http://dx.doi.org/10.1073/pnas.1120452109.
-
(2012)
PNAS
, vol.109
, Issue.41
, pp. 16552-16557
-
-
Leith, J.S.1
Tafvizi, A.2
Huang, F.3
Uspal, W.E.4
Doyle, P.S.5
Fersht, A.R.6
-
50
-
-
34249932435
-
Probing transcription factor dynamics at the single-molecule level in a living cell
-
Elf J, Li G-W, Xie XS. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 2007; 316:1191-4. http://dx.doi.org/10.1126/science.114196.
-
(2007)
Science
, vol.316
, pp. 1191-1194
-
-
Elf, J.1
Li, G.-W.2
Xie, X.S.3
-
51
-
-
77749239764
-
Quantitative study of synthetic hox transcription factor-DNA interactions in live cells
-
Vukojevic V, Papadopoulos DK, Terenius L, Gehring W.J., Rigler R. Quantitative study of synthetic Hox transcription factor-DNA interactions in live cells. PNAS 2010; 107 (9):4093-8. http://dx.doi.org/10.1073/pnas.0914612107.
-
(2010)
PNAS
, vol.107
, Issue.9
, pp. 4093-4098
-
-
Vukojevic, V.1
Papadopoulos, D.K.2
Terenius, L.3
Gehring, W.J.4
Rigler, R.5
-
52
-
-
84896338378
-
Single-molecule dynamics of enhanceosome assembly in embryonic stem cells
-
Chen J, Zhang Z, Li L., Chen B-C, Revyakin A, Hajj B., et al. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell 2014; 156 (6):1274-85. http://dx.doi.org/10.1016/j.cell.2014.01.062.
-
(2014)
Cell
, vol.156
, Issue.6
, pp. 1274-1285
-
-
Chen, J.1
Zhang, Z.2
Li, L.3
Chen, B.-C.4
Revyakin, A.5
Hajj, B.6
-
53
-
-
79955407832
-
Real-time observation of transcription initiation and elongation on an endogenous yeast gene
-
Larson DR, Zenklusen D, Wu B., Chao JA, Singer RH. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 2011; 332 (6028):475-8. http://dx.doi.org/10.1126/science.1202142.
-
(2011)
Science
, vol.332
, Issue.6028
, pp. 475-478
-
-
Larson, D.R.1
Zenklusen, D.2
Wu, B.3
Chao, J.A.4
Singer, R.H.5
-
54
-
-
84873558007
-
The promoter-search mechanism of escherichia coli RNA polymerase is dominated by three-dimensional diffusion
-
Wang F, Redding S, Finkelstein I.J., Gorman J., Reichman DR, Greene EC. The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion. Nat Struct Mol Biol 2013; 20 (2):174-81. http://dx.doi.org/10.1038/nsmb.2472.
-
(2013)
Nat Struct Mol Biol
, vol.20
, Issue.2
, pp. 174-181
-
-
Wang, F.1
Redding, S.2
Finkelstein, I.J.3
Gorman, J.4
Reichman, D.R.5
Greene, E.C.6
-
55
-
-
77951800353
-
An effective model for natural selection in promoters
-
Hoffman MM, Birney E. An effective model for natural selection in promoters. Genome Res 2010; 20 (5):685-92. http://dx.doi.org/10.1101/gr.096719.109.
-
(2010)
Genome Res
, vol.20
, Issue.5
, pp. 685-692
-
-
Hoffman, M.M.1
Birney, E.2
-
56
-
-
0026771275
-
Sliding and intermolecular transfer of the lac repressor: Kinetic perturbation of a reaction intermediate by a distant DNA sequence
-
Ruusala T, Crothers DM. Sliding and intermolecular transfer of the lac repressor: kinetic perturbation of a reaction intermediate by a distant DNA sequence. PNAS 1992; 89 (11):4903-7 [URL http://www.pnas.org/content/89/11/4903.Abstract].
-
(1992)
PNAS
, vol.89
, Issue.11
, pp. 4903-4907
-
-
Ruusala, T.1
Crothers, D.M.2
-
57
-
-
84907527856
-
Probing the effect of promoters on noise in gene expression using thousands of designed sequences
-
[n/a]
-
Sharon E, van Dijk D, Kalma Y, Keren L., Yakhini OMZ, Segal E. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Res 2014. http://dx.doi.org/10.1101/gr.168773.113 [n/a].
-
(2014)
Genome Res
-
-
Sharon, E.1
Van Dijk, D.2
Kalma, Y.3
Keren, L.4
Yakhini, O.M.Z.5
Segal, E.6
-
58
-
-
84867517832
-
Facilitated diffusion on mobile DNA: Config-urational traps and sequence heterogeneity
-
Brackley CA, Cates ME, Marenduzzo D. Facilitated diffusion on mobile DNA: config-urational traps and sequence heterogeneity. Phys Rev Lett 2012; 109 (16):168103. http://dx.doi.org/10.1103/PhysRevLett.109.168103.
-
(2012)
Phys Rev Lett
, vol.109
, Issue.16
-
-
Brackley, C.A.1
Cates, M.E.2
Marenduzzo, D.3
-
59
-
-
67649982898
-
Modeling promoter search by E. Coli RNA polymerase: One-dimensional diffusion in a sequence-dependent energy landscape
-
Weindl J, Dawy Z, Hanus P., Zech J, Mueller JC. Modeling promoter search by E. coli RNA polymerase: one-dimensional diffusion in a sequence-dependent energy landscape. J Theor Biol 2009; 259 (3):628-34.
-
(2009)
J Theor Biol
, vol.259
, Issue.3
, pp. 628-634
-
-
Weindl, J.1
Dawy, Z.2
Hanus, P.3
Zech, J.4
Mueller, J.C.5
-
60
-
-
72149127671
-
How a protein searches for its site on DNA: The mechanism of facilitated diffusion
-
Mirny L, Slutsky M, Wunderlich Z., Tafvizi A, Leith J, Kosmrlj A. How a protein searches for its site on DNA: the mechanism of facilitated diffusion. J Phys A Math Theor 2009; 42:434013. http://dx.doi.org/10.1088/1751-8113/42/43/434013.
-
(2009)
J Phys a Math Theor
, vol.42
-
-
Mirny, L.1
Slutsky, M.2
Wunderlich, Z.3
Tafvizi, A.4
Leith, J.5
Kosmrlj, A.6
-
61
-
-
33846467150
-
A systems approach to measuring the binding energy landscapes of transcription factors
-
Maerkl SJ, Quake SR. A systems approach to measuring the binding energy landscapes of transcription factors. Science (New York, NY) 2007; 315 (5809):233-7. http://dx.doi.org/10.1126/science.1131007.
-
(2007)
Science (New York, NY)
, vol.315
, Issue.5809
, pp. 233-237
-
-
Maerkl, S.J.1
Quake, S.R.2
-
62
-
-
84871844925
-
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in drosophila
-
Fisher WW, Li JJ, Hammonds A.S., Brown JB, Pfeiffer BD, Weiszmann R, et al. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. PNAS 2012; 109 (52):21330-5. http://dx.doi.org/10.1073/pnas.1209589110.
-
(2012)
PNAS
, vol.109
, Issue.52
, pp. 21330-21335
-
-
Fisher, W.W.1
Li, J.J.2
Hammonds, A.S.3
Brown, J.B.4
Pfeiffer, B.D.5
Weiszmann, R.6
-
63
-
-
33846002036
-
Transcriptional regulation by competing transcription factor modules
-
Hermsen R, Tans S, ten Wolde PR. Transcriptional regulation by competing transcription factor modules. PLoS Comput Biol 2006; 2:1552-60. http://dx.doi.org/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
-
64
-
-
76749088015
-
Evolutionary mirages: Selection on binding site composition creates the illusion of conserved grammars in drosophila enhancers
-
Lusk RW, Eisen MB. Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet 2010; 6 (1):e1000829. http://dx.doi.org/10.1371/journal.pgen.1000829.
-
(2010)
PLoS Genet
, vol.6
, Issue.1
-
-
Lusk, R.W.1
Eisen, M.B.2
-
65
-
-
84863404645
-
Evolutionary origins of transcription factor binding site clusters
-
He X, Duque TSPC, Sinha S. Evolutionary origins of transcription factor binding site clusters. Mol Biol Evol 2012; 29 (3):1059-70. http://dx.doi.org/10.1093/molbev/msr277.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.3
, pp. 1059-1070
-
-
He, X.1
Duque, T.S.P.C.2
Sinha, S.3
-
66
-
-
0036515546
-
Fitness landscapes and evolvability
-
Smith T, Husbands P, Layzell P., O'Shea M. Fitness landscapes and evolvability. Evol Comput 2002; 10 (1):1-34. http://dx.doi.org/10.1162/106365602317301754.
-
(2002)
Evol Comput
, vol.10
, Issue.1
, pp. 1-34
-
-
Smith, T.1
Husbands, P.2
Layzell, P.3
O'Shea, M.4
-
67
-
-
70349961774
-
Different gene regulation strategies revealed by analysis of binding motifs
-
Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet 2009; 25 (10):434-40. http://dx.doi.org/10.1016/j.tig.2009.08.003.
-
(2009)
Trends Genet
, vol.25
, Issue.10
, pp. 434-440
-
-
Wunderlich, Z.1
Mirny, L.A.2
-
68
-
-
44449084835
-
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
-
Polavarapu N, Mariño Ramirez L, Landsman D, McDonald JF, Jordan IK. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics 2008; 9:226.
-
(2008)
BMC Genomics
, vol.9
, pp. 226
-
-
Polavarapu, N.1
Mariño Ramirez, L.2
Landsman, D.3
McDonald, J.F.4
Jordan, I.K.5
-
69
-
-
80055083209
-
Formation of regulatory modules by local sequence duplication
-
Nourmohammad A, Lässig M. Formation of regulatory modules by local sequence duplication. PLoS Comput Biol 2011; 7 (10):e1002167.
-
(2011)
PLoS Comput Biol
, vol.7
, Issue.10
-
-
Nourmohammad, A.1
Lässig, M.2
-
70
-
-
84898058764
-
Direct measurement of transcription factor issociation excludes a simple operator occupancy model for gene regulation
-
Hammar P, Walldén M, Fange D., Persson F, Baltekin O, Ullman G., et al. Direct measurement of transcription factor issociation excludes a simple operator occupancy model for gene regulation. Nat Genet 2014; 46:405-8. http://dx.doi.org/10.1038/ng.2905.
-
(2014)
Nat Genet
, vol.46
, pp. 405-408
-
-
Hammar, P.1
Walldén, M.2
Fange, D.3
Persson, F.4
Baltekin, O.5
Ullman, G.6
-
71
-
-
43149119497
-
Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching
-
Mueller F, Wach P, McNally JG. Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching. Biophys J 2008; 94 (8):3323-39. http://dx.doi.org/10.1529/biophysj.107.123182.
-
(2008)
Biophys J
, vol.94
, Issue.8
, pp. 3323-3339
-
-
Mueller, F.1
Wach, P.2
McNally, J.G.3
-
72
-
-
84857097177
-
RNA-guided genetic silencing systems in bacteria and archaea
-
Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012; 482 (7385):331-8. http://dx.doi.org/10.1038/nature10886.
-
(2012)
Nature
, vol.482
, Issue.7385
, pp. 331-338
-
-
Wiedenheft, B.1
Sternberg, S.H.2
Doudna, J.A.3
|