-
2
-
-
18944401160
-
Eukaryotic transcription activation: right on target
-
Green MR. Eukaryotic transcription activation: right on target. Mol Cell 2005;18: 399-402.
-
(2005)
Mol Cell
, vol.18
, pp. 399-402
-
-
Green, M.R.1
-
3
-
-
18844394569
-
Dynamic regulation of pol II transcription by the mammalian Mediator complex
-
Malik S, Roeder RG. Dynamic regulation of pol II transcription by the mammalian Mediator complex. Trends Biochem Sci 2005;30: 256-63.
-
(2005)
Trends Biochem Sci
, vol.30
, pp. 256-263
-
-
Malik, S.1
Roeder, R.G.2
-
6
-
-
0032409038
-
Recruitment of the RNA polymerase II holoenzyme and its implications in gene regulation
-
Barberis A, Gaudreau L. Recruitment of the RNA polymerase II holoenzyme and its implications in gene regulation. Biol Chem 1998;379: 1397-405.
-
(1998)
Biol Chem
, vol.379
, pp. 1397-1405
-
-
Barberis, A.1
Gaudreau, L.2
-
7
-
-
18844378166
-
The mammalian Mediator complex and its role in transcriptional regulation
-
Conaway RC, Sato S, Tomomori-Sato C, et al. The mammalian Mediator complex and its role in transcriptional regulation. Trends Biochem Sci 2005;30: 250-5.
-
(2005)
Trends Biochem Sci
, vol.30
, pp. 250-255
-
-
Conaway, R.C.1
Sato, S.2
Tomomori-sato, C.3
-
9
-
-
84876529769
-
TFClass: an expandable hierarchical classification of human transcription factors
-
Wingender E, Schoeps T, Donitz J. TFClass: an expandable hierarchical classification of human transcription factors. Nucleic Acids Res 2013;41: D165-70.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D165-D170
-
-
Wingender, E.1
Schoeps, T.2
Donitz, J.3
-
10
-
-
77950519937
-
Origins of specificity in protein-DNA recognition
-
Rohs R, Jin X, West SM, et al. Origins of specificity in protein-DNA recognition. Annu Rev Biochem 2010;79: 233-69.
-
(2010)
Annu Rev Biochem
, vol.79
, pp. 233-269
-
-
Rohs, R.1
Jin, X.2
West, S.M.3
-
11
-
-
0025995844
-
A structural taxonomy of DNA-binding domains
-
Harrison SC. A structural taxonomy of DNA-binding domains. Nature 1991;353: 715-9.
-
(1991)
Nature
, vol.353
, pp. 715-719
-
-
Harrison, S.C.1
-
12
-
-
0028328872
-
Zinc finger phage: affinity selection of fingers with new DNA-binding specificities
-
Rebar EJ, Pabo CO. Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science 1994;263: 671-3.
-
(1994)
Science
, vol.263
, pp. 671-673
-
-
Rebar, E.J.1
Pabo, C.O.2
-
14
-
-
45449111373
-
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
-
Noyes MB, Christensen RG, Wakabayashi A, et al. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 2008;133: 1277-89.
-
(2008)
Cell
, vol.133
, pp. 1277-1289
-
-
Noyes, M.B.1
Christensen, R.G.2
Wakabayashi, A.3
-
15
-
-
45449115390
-
Variation in home-odomain DNA binding revealed by high-resolution analysis of sequence preferences
-
Berger MF, Badis G, Gehrke AR, et al. Variation in home-odomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 2008;133: 1266-76.
-
(2008)
Cell
, vol.133
, pp. 1266-1276
-
-
Berger, M.F.1
Badis, G.2
Gehrke, A.R.3
-
16
-
-
67650594823
-
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors
-
Grove CA, De Masi F, Barrasa MI, et al. A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell 2009;138: 314-27.
-
(2009)
Cell
, vol.138
, pp. 314-327
-
-
Grove, C.A.1
De Masi, F.2
Barrasa, M.I.3
-
17
-
-
84880681583
-
DNA-binding specificity changes in the evolution of forkhead transcription factors
-
Nakagawa S, Gisselbrecht SS, Rogers JM, et al. DNA-binding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci USA 2013;110: 12349-54.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 12349-12354
-
-
Nakagawa, S.1
Gisselbrecht, S.S.2
Rogers, J.M.3
-
18
-
-
0025773296
-
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A
-
Pavletich NP, Pabo CO. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 1991;252: 809-17.
-
(1991)
Science
, vol.252
, pp. 809-817
-
-
Pavletich, N.P.1
Pabo, C.O.2
-
19
-
-
83255188878
-
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
-
Slattery M, Riley T, Liu P, et al. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 2011;147: 1270-82.
-
(2011)
Cell
, vol.147
, pp. 1270-1282
-
-
Slattery, M.1
Riley, T.2
Liu, P.3
-
20
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990;249: 505-10.
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
21
-
-
0025572707
-
Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection
-
Blackwell TK, Weintraub H. Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science 1990;250: 1104-10.
-
(1990)
Science
, vol.250
, pp. 1104-1110
-
-
Blackwell, T.K.1
Weintraub, H.2
-
22
-
-
0029862991
-
In vitro evolution of the DNA binding sites of Escherichia coli methionine repressor, MetJ
-
He YY, Stockley PG, Gold L. In vitro evolution of the DNA binding sites of Escherichia coli methionine repressor, MetJ. J Mol Biol 1996;255: 55-66.
-
(1996)
J Mol Biol
, vol.255
, pp. 55-66
-
-
He, Y.Y.1
Stockley, P.G.2
Gold, L.3
-
23
-
-
0031571660
-
Quantitative specificity of the Mnt repressor
-
Fields DS, He Y, Al-Uzri AY, et al. Quantitative specificity of the Mnt repressor. J Mol Biol 1997;271: 178-94.
-
(1997)
J Mol Biol
, vol.271
, pp. 178-194
-
-
Fields, D.S.1
He, Y.2
Al-uzri, A.Y.3
-
24
-
-
84872540994
-
DNA-binding specificities of human transcription factors
-
Jolma A, Yan J, Whitington T, et al. DNA-binding specificities of human transcription factors. Cell 2013;152: 327-39.
-
(2013)
Cell
, vol.152
, pp. 327-339
-
-
Jolma, A.1
Yan, J.2
Whitington, T.3
-
25
-
-
74549209548
-
Inferring binding energies from selected binding sites
-
Zhao Y, Granas D, Stormo GD. Inferring binding energies from selected binding sites. PLoS Comput Biol 2009;5: e1000590.
-
(2009)
PLoS Comput Biol
, vol.5
, pp. e1000590
-
-
Zhao, Y.1
Granas, D.2
Stormo, G.D.3
-
26
-
-
0035912721
-
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
-
Bulyk ML, Huang X, Choo Y, et al. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci USA 2001;98: 7158-63.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 7158-7163
-
-
Bulyk, M.L.1
Huang, X.2
Choo, Y.3
-
27
-
-
46149107652
-
Specific DNA-binding by apicomplexan AP2 transcription factorsional
-
De Silva EK, Gehrke AR, Olszewski K, et al. Specific DNA-binding by apicomplexan AP2 transcription factorsional. Proc Natl Acad Sci USA 2008;105: 8393-8.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 8393-8398
-
-
De Silva, E.K.1
Gehrke, A.R.2
Olszewski, K.3
-
28
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis G, Berger MF, Philippakis AA, et al. Diversity and complexity in DNA recognition by transcription factors. Science 2009;324: 1720-3.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
-
29
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
-
Valouev A, Johnson DS, Sundquist A, et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 2008;5: 829-34.
-
(2008)
Nat Methods
, vol.5
, pp. 829-834
-
-
Valouev, A.1
Johnson, D.S.2
Sundquist, A.3
-
30
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison CT, Gordon DB, Lee TI, et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004;431: 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
-
31
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson DS, Mortazavi A, Myers RM, et al. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007;316: 1497-502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
-
32
-
-
15544375816
-
DIP-chip: rapid and accurate determination of DNA-binding specificity
-
Liu X, Noll DM, Lieb JD, et al. DIP-chip: rapid and accurate determination of DNA-binding specificity. Genome Res 2005;15: 421-7.
-
(2005)
Genome Res
, vol.15
, pp. 421-427
-
-
Liu, X.1
Noll, D.M.2
Lieb, J.D.3
-
33
-
-
84859582058
-
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
-
Lickwar CR, Mueller F, Hanlon SE, et al. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 2012;484: 251-5.
-
(2012)
Nature
, vol.484
, pp. 251-255
-
-
Lickwar, C.R.1
Mueller, F.2
Hanlon, S.E.3
-
34
-
-
0024406857
-
A novel genetic system to detect protein-protein interactions
-
Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 1989;340: 245-6.
-
(1989)
Nature
, vol.340
, pp. 245-246
-
-
Fields, S.1
Song, O.2
-
35
-
-
7444267933
-
A gateway-compatible yeast one-hybrid system
-
Deplancke B, Dupuy D, Vidal M, et al. A gateway-compatible yeast one-hybrid system. Genome Res 2004;14: 2093-101.
-
(2004)
Genome Res
, vol.14
, pp. 2093-2101
-
-
Deplancke, B.1
Dupuy, D.2
Vidal, M.3
-
36
-
-
33744972290
-
A gene-centered C. elegans protein-DNA interaction network
-
Deplancke B, Mukhopadhyay A, Ao W, et al. A gene-centered C. elegans protein-DNA interaction network. Cell 2006;125: 1193-205.
-
(2006)
Cell
, vol.125
, pp. 1193-1205
-
-
Deplancke, B.1
Mukhopadhyay, A.2
Ao, W.3
-
37
-
-
0030907304
-
Activation of prokaryotic transcription through arbitrary protein-protein contacts
-
Dove SL, Joung JK, Hochschild A. Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 1997;386: 627-30.
-
(1997)
Nature
, vol.386
, pp. 627-630
-
-
Dove, S.L.1
Joung, J.K.2
Hochschild, A.3
-
38
-
-
0028051844
-
Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein
-
Joung JK, Koepp DM, Hochschild A. Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein. Science 1994;265: 1863-6.
-
(1994)
Science
, vol.265
, pp. 1863-1866
-
-
Joung, J.K.1
Koepp, D.M.2
Hochschild, A.3
-
39
-
-
0034691202
-
A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions
-
Joung JK, Ramm EI, Pabo CO. A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci USA 2000;97: 7382-7.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 7382-7387
-
-
Joung, J.K.1
Ramm, E.I.2
Pabo, C.O.3
-
40
-
-
23444446753
-
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
-
Meng X, Brodsky MH, Wolfe SA. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol 2005;23: 988-94.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 988-994
-
-
Meng, X.1
Brodsky, M.H.2
Wolfe, S.A.3
-
41
-
-
0023643078
-
The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80
-
Ma J, Ptashne M. The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80. Cell 1987;50: 137-42.
-
(1987)
Cell
, vol.50
, pp. 137-142
-
-
Ma, J.1
Ptashne, M.2
-
42
-
-
0023652389
-
Deletion analysis of GAL4 defines two transcriptional activating segments
-
Ma J, Ptashne M. Deletion analysis of GAL4 defines two transcriptional activating segments. Cell 1987;48: 847-53.
-
(1987)
Cell
, vol.48
, pp. 847-853
-
-
Ma, J.1
Ptashne, M.2
-
43
-
-
0022622235
-
Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein
-
Keegan L, Gill G, Ptashne M. Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science 1986;231: 699-704.
-
(1986)
Science
, vol.231
, pp. 699-704
-
-
Keegan, L.1
Gill, G.2
Ptashne, M.3
-
44
-
-
0000976047
-
Amino terminus of the yeast GAL4 gene product is sufficient for nuclear localization
-
Silver PA, Keegan LP, Ptashne M. Amino terminus of the yeast GAL4 gene product is sufficient for nuclear localization. Proc Natl Acad Sci USA 1984;81: 5951-5.
-
(1984)
Proc Natl Acad Sci USA
, vol.81
, pp. 5951-5955
-
-
Silver, P.A.1
Keegan, L.P.2
Ptashne, M.3
-
45
-
-
0023649257
-
Mutants of GAL4 protein altered in an activation function
-
Gill G, Ptashne M. Mutants of GAL4 protein altered in an activation function. Cell 1987;51: 121-6.
-
(1987)
Cell
, vol.51
, pp. 121-126
-
-
Gill, G.1
Ptashne, M.2
-
46
-
-
0023649184
-
A new class of yeast transcriptional activators
-
Ma J, Ptashne M. A new class of yeast transcriptional activators. Cell 1987;51: 113-19.
-
(1987)
Cell
, vol.51
, pp. 113-119
-
-
Ma, J.1
Ptashne, M.2
-
47
-
-
0025940629
-
The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest
-
Chien CT, Bartel PL, Sternglanz R, et al. The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc Natl Acad Sci USA 1991;88: 9578-82.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 9578-9582
-
-
Chien, C.T.1
Bartel, P.L.2
Sternglanz, R.3
-
48
-
-
0026639625
-
Protein interaction cloning in yeast: identification of mammalian proteins that react with the leucine zipper of Jun
-
Chevray PM, Nathans D. Protein interaction cloning in yeast: identification of mammalian proteins that react with the leucine zipper of Jun. Proc Natl Acad Sci USA 1992;89: 5789-93.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 5789-5793
-
-
Chevray, P.M.1
Nathans, D.2
-
50
-
-
0030832043
-
Transcriptional activation upon pheromone stimulation mediated by a small domain of Saccharomycescerevisiae Ste12p
-
Pi H, Chien CT, Fields S. Transcriptional activation upon pheromone stimulation mediated by a small domain of Saccharomycescerevisiae Ste12p. MolCellBiol 1997;17: 6410-18.
-
(1997)
MolCellBiol
, vol.17
, pp. 6410-6418
-
-
Pi, H.1
Chien, C.T.2
Fields, S.3
-
51
-
-
0027476456
-
Synergistic activation of transcription by Escherichia coli cAMP receptor protein
-
Joung JK, Le LU, Hochschild A. Synergistic activation of transcription by Escherichia coli cAMP receptor protein. Proc Natl Acad Sci USA 1993;90: 3083-7.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 3083-3087
-
-
Joung, J.K.1
Le, L.U.2
Hochschild, A.3
-
52
-
-
0032489504
-
Protein-protein contacts that activate and repress prokaryotic transcription
-
Hochschild A, Dove SL. Protein-protein contacts that activate and repress prokaryotic transcription. Cell 1998;92: 597-600.
-
(1998)
Cell
, vol.92
, pp. 597-600
-
-
Hochschild, A.1
Dove, S.L.2
-
53
-
-
0032032533
-
Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target
-
Dove SL, Hochschild A. Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target. Genes Dev 1998;12: 745-54.
-
(1998)
Genes Dev
, vol.12
, pp. 745-754
-
-
Dove, S.L.1
Hochschild, A.2
-
54
-
-
34250661506
-
Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system
-
Meng X, Wolfe SA. Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat Protoc 2006;1: 30-45.
-
(2006)
Nat Protoc
, vol.1
, pp. 30-45
-
-
Meng, X.1
Wolfe, S.A.2
-
55
-
-
43349107222
-
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
-
Noyes MB, Meng X, Wakabayashi A, et al. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res 2008;36: 2547-60.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 2547-2560
-
-
Noyes, M.B.1
Meng, X.2
Wakabayashi, A.3
-
56
-
-
80555139629
-
Analysis of specific protein-DNA interactions by bacterial one-hybrid assay
-
Noyes MB. Analysis of specific protein-DNA interactions by bacterial one-hybrid assay. Methods Mol Biol 2012;786: 79-95.
-
(2012)
Methods Mol Biol
, vol.786
, pp. 79-95
-
-
Noyes, M.B.1
-
57
-
-
79960225382
-
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
-
e83
-
Christensen RG, Gupta A, Zuo Z, et al. A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity. Nucleic Acids Res 2011;39:e83, 1-15.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 1-15
-
-
Christensen, R.G.1
Gupta, A.2
Zuo, Z.3
-
58
-
-
84899846624
-
An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins
-
Gupta A, Christensen RG, Bell HA, et al. An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res 2014;42: 4800-12.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 4800-4812
-
-
Gupta, A.1
Christensen, R.G.2
Bell, H.A.3
-
59
-
-
84878683632
-
Global analysis of Drosophila Cys(2)-His(2) zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
-
Enuameh MS, Asriyan Y, Richards A, et al. Global analysis of Drosophila Cys(2)-His(2) zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res 2013;23: 928-40.
-
(2013)
Genome Res
, vol.23
, pp. 928-940
-
-
Enuameh, M.S.1
Asriyan, Y.2
Richards, A.3
-
60
-
-
84863514508
-
Recognition models to predict DNA-binding specificities of homeodomain proteins
-
Christensen RG, Enuameh MS, Noyes MB, et al. Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics 2012;28: 184-9.
-
(2012)
Bioinformatics
, vol.28
, pp. 184-189
-
-
Christensen, R.G.1
Enuameh, M.S.2
Noyes, M.B.3
-
61
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994;2: 28-36.
-
(1994)
Proc Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
62
-
-
84861982214
-
An optimized two-finger archive for ZFN-mediated gene targeting
-
Gupta A, Christensen RG, Rayla AL, et al. An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods 2012;9: 588-90.
-
(2012)
Nat Methods
, vol.9
, pp. 588-590
-
-
Gupta, A.1
Christensen, R.G.2
Rayla, A.L.3
-
63
-
-
84876352590
-
Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases
-
Zhu C, Gupta A, Hall VL, et al. Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases. Nucleic Acids Res 2013;41: 2455-65.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 2455-2465
-
-
Zhu, C.1
Gupta, A.2
Hall, V.L.3
-
64
-
-
84867157760
-
Exploring the DNA-recognition potential of homeodomains
-
Chu SW, Noyes MB, Christensen RG, et al. Exploring the DNA-recognition potential of homeodomains. Genome Res 2012;22: 1889-98.
-
(2012)
Genome Res
, vol.22
, pp. 1889-1898
-
-
Chu, S.W.1
Noyes, M.B.2
Christensen, R.G.3
-
65
-
-
44949162060
-
Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases
-
Meng X, Noyes MB, Zhu LJ, et al. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol 2008;26: 695-701.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 695-701
-
-
Meng, X.1
Noyes, M.B.2
Zhu, L.J.3
-
66
-
-
84896731976
-
Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets
-
Persikov AV, Rowland EF, Oakes BL, et al. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res 2014;42: 1497-508.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 1497-1508
-
-
Persikov, A.V.1
Rowland, E.F.2
Oakes, B.L.3
-
67
-
-
0142091373
-
Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection
-
Hurt JA, Thibodeau SA, Hirsh AS, et al. Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci USA 2003;100: 12271-6.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12271-12276
-
-
Hurt, J.A.1
Thibodeau, S.A.2
Hirsh, A.S.3
-
68
-
-
47349097567
-
Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification
-
Maeder ML, Thibodeau-Beganny S, Osiak A, et al. Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 2008;31: 294-301.
-
(2008)
Mol Cell
, vol.31
, pp. 294-301
-
-
Maeder, M.L.1
Thibodeau-beganny, S.2
Osiak, A.3
-
69
-
-
78650863981
-
Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA)
-
Sander JD, Dahlborg EJ, Goodwin MJ, et al. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 2011;8: 67-9.
-
(2011)
Nat Methods
, vol.8
, pp. 67-69
-
-
Sander, J.D.1
Dahlborg, E.J.2
Goodwin, M.J.3
-
70
-
-
0037123602
-
Structural basis of transcription initiation: an RNA polymerase holo-enzyme-DNA complex
-
Murakami KS, Masuda S, Campbell EA, et al. Structural basis of transcription initiation: an RNA polymerase holo-enzyme-DNA complex. Science 2002;296: 1285-90.
-
(2002)
Science
, vol.296
, pp. 1285-1290
-
-
Murakami, K.S.1
Masuda, S.2
Campbell, E.A.3
-
71
-
-
0022913522
-
The cloning and sequence of the gene encoding the omega subunit of Escherichia coli RNA polymerase
-
Gentry DR, Burgess RR. The cloning and sequence of the gene encoding the omega subunit of Escherichia coli RNA polymerase. Gene 1986;48: 33-40.
-
(1986)
Gene
, vol.48
, pp. 33-40
-
-
Gentry, D.R.1
Burgess, R.R.2
-
72
-
-
0024593347
-
rpoZ, encoding the omega subunit of Escherichia coli RNA polymerase, is in the same operon as spoT
-
Gentry DR, Burgess RR. rpoZ, encoding the omega subunit of Escherichia coli RNA polymerase, is in the same operon as spoT. J Bacteriol 1989;171: 1271-7.
-
(1989)
J Bacteriol
, vol.171
, pp. 1271-1277
-
-
Gentry, D.R.1
Burgess, R.R.2
-
73
-
-
0025886298
-
The omega subunit of Escherichia coli K-12 RNA polymerase is not required for stringent RNA control in vivo
-
Gentry D, Xiao H, Burgess R, et al. The omega subunit of Escherichia coli K-12 RNA polymerase is not required for stringent RNA control in vivo. J Bacteriol 1991;173: 3901-3.
-
(1991)
J Bacteriol
, vol.173
, pp. 3901-3903
-
-
Gentry, D.1
Xiao, H.2
Burgess, R.3
-
74
-
-
78651321628
-
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
-
Zhu LJ, Christensen RG, Kazemian M, et al. FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res 2011;39: D111-17.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D111-D117
-
-
Zhu, L.J.1
Christensen, R.G.2
Kazemian, M.3
-
75
-
-
84891752831
-
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites
-
Shazman S, Lee H, Socol Y, et al. OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Res 2014;42: D167-71.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D167-D171
-
-
Shazman, S.1
Lee, H.2
Socol, Y.3
-
76
-
-
84867414332
-
Characterization of the DNA-binding properties of the Mohawk homeobox transcription factor
-
Anderson DM, George R, Noyes MB, et al. Characterization of the DNA-binding properties of the Mohawk homeobox transcription factor. J Biol Chem 2012;287: 35351-9.
-
(2012)
J Biol Chem
, vol.287
, pp. 35351-35359
-
-
Anderson, D.M.1
George, R.2
Noyes, M.B.3
-
77
-
-
84860350869
-
A system of repressor gradients spatially organizes the boundaries of Bicoid-dependent target genes
-
Chen H, Xu Z, Mei C, et al. A system of repressor gradients spatially organizes the boundaries of Bicoid-dependent target genes. Cell 2012;149: 618-29.
-
(2012)
Cell
, vol.149
, pp. 618-629
-
-
Chen, H.1
Xu, Z.2
Mei, C.3
-
78
-
-
80052477170
-
Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer
-
Struffi P, Corado M, Kaplan L, et al. Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer. Development 2011;138: 4291-9.
-
(2011)
Development
, vol.138
, pp. 4291-4299
-
-
Struffi, P.1
Corado, M.2
Kaplan, L.3
-
79
-
-
77958545415
-
Investigating giant (Gt) repression in the formation of partially overlapping pair-rule stripes
-
Ribeiro TC, Ventrice G, Machado-Lima A, et al. Investigating giant (Gt) repression in the formation of partially overlapping pair-rule stripes. Dev Dyn 2010;239: 2989-99.
-
(2010)
Dev Dyn
, vol.239
, pp. 2989-2999
-
-
Ribeiro, T.C.1
Ventrice, G.2
Machado-lima, A.3
-
80
-
-
79952273012
-
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
-
Kaplan T, Li XY, Sabo PJ, et al. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet 2011;7: e1001290.
-
(2011)
PLoS Genet
, vol.7
, pp. e1001290
-
-
Kaplan, T.1
Li, X.Y.2
Sabo, P.J.3
-
81
-
-
79953700593
-
Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila
-
Slattery M, Ma L, Negre N, et al. Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila. PloS One 2011;6: e14686.
-
(2011)
PloS One
, vol.6
, pp. e14686
-
-
Slattery, M.1
Ma, L.2
Negre, N.3
-
82
-
-
83155181419
-
Huckebein is part of a combinatorial repression code in the anterior blastoderm
-
Andrioli LP, Digiampietri LA, de Barros LP, et al. Huckebein is part of a combinatorial repression code in the anterior blastoderm. Dev Biol 2012;361: 177-85.
-
(2012)
Dev Biol
, vol.361
, pp. 177-185
-
-
Andrioli, L.P.1
Digiampietri, L.A.2
de Barros, L.P.3
-
83
-
-
77956830473
-
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials
-
Kazemian M, Blatti C, Richards A, et al. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol 2010;8: e1000456.
-
(2010)
PLoS Biol
, vol.8
, pp. e1000456
-
-
Kazemian, M.1
Blatti, C.2
Richards, A.3
-
84
-
-
84884659690
-
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy
-
Cheng Q, Kazemian M, Pham H, et al. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genet 2013;9: e1003571.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003571
-
-
Cheng, Q.1
Kazemian, M.2
Pham, H.3
-
85
-
-
84884959191
-
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development
-
Kazemian M, Pham H, Wolfe SA, et al. Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. Nucleic Acids Res 2013;41: 8237-52.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 8237-8252
-
-
Kazemian, M.1
Pham, H.2
Wolfe, S.A.3
-
86
-
-
84906790368
-
Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding
-
Siggers T, Reddy J, Barron B, et al. Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Mol Cell 2014;55: 640-8.
-
(2014)
Mol Cell
, vol.55
, pp. 640-648
-
-
Siggers, T.1
Reddy, J.2
Barron, B.3
-
87
-
-
77954954652
-
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
-
Wei GH, Badis G, Berger MF, et al. Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J 2010;29: 2147-60.
-
(2010)
EMBO J
, vol.29
, pp. 2147-2160
-
-
Wei, G.H.1
Badis, G.2
Berger, M.F.3
-
89
-
-
77953633943
-
The discovery of zinc fingers and their applications in gene regulation and genome manipulation
-
Klug A. The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem 2010;79: 213-31.
-
(2010)
Annu Rev Biochem
, vol.79
, pp. 213-231
-
-
Klug, A.1
-
90
-
-
70349617470
-
Chemokine signaling guides regional patterning of the first embryonic artery
-
Siekmann AF, Standley C, Fogarty KE, et al. Chemokine signaling guides regional patterning of the first embryonic artery. Genes Dev 2009;23: 2272-7.
-
(2009)
Genes Dev
, vol.23
, pp. 2272-2277
-
-
Siekmann, A.F.1
Standley, C.2
Fogarty, K.E.3
-
91
-
-
78651341148
-
Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases
-
Gupta A, Meng X, Zhu LJ, et al. Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res 2011;39: 381-92.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 381-392
-
-
Gupta, A.1
Meng, X.2
Zhu, L.J.3
-
92
-
-
80053069040
-
Evaluation and application of modularly assembled zinc-finger nucleases in zebra-fish
-
Zhu C, Smith T, McNulty J, et al. Evaluation and application of modularly assembled zinc-finger nucleases in zebra-fish. Development 2011;138: 4555-64.
-
(2011)
Development
, vol.138
, pp. 4555-4564
-
-
Zhu, C.1
Smith, T.2
McNulty, J.3
-
93
-
-
0010182724
-
A specific transcription factor that can bind either the 5S RNA gene or 5S RNA
-
Pelham HR, Brown DD. A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. Proc Natl Acad Sci USA 1980;77: 4170-4.
-
(1980)
Proc Natl Acad Sci USA
, vol.77
, pp. 4170-4174
-
-
Pelham, H.R.1
Brown, D.D.2
-
94
-
-
44849089416
-
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains
-
Brayer KJ, Segal DJ. Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem Biophys 2008;50: 111-31.
-
(2008)
Cell Biochem Biophys
, vol.50
, pp. 111-131
-
-
Brayer, K.J.1
Segal, D.J.2
-
95
-
-
84891757744
-
De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins
-
Persikov AV, Singh M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res 2014;42: 97-108.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 97-108
-
-
Persikov, A.V.1
Singh, M.2
-
96
-
-
84867372779
-
Massively parallel measurements of molecular interaction kinetics on a microfluidic platform
-
Geertz M, Shore D, Maerkl SJ. Massively parallel measurements of molecular interaction kinetics on a microfluidic platform. Proc Natl Acad Sci USA 2012;109: 16540-5.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 16540-16545
-
-
Geertz, M.1
Shore, D.2
Maerkl, S.J.3
-
97
-
-
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 2007;315: 233-7.
-
(2007)
Science
, vol.315
, pp. 233-237
-
-
Maerkl, S.J.1
Quake, S.R.2
-
98
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson G, Hirst M, Bainbridge M, et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007;4: 651-7.
-
(2007)
Nat Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
-
99
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
-
Jothi R, Cuddapah S, Barski A, et al. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 2008;36: 5221-31.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
-
100
-
-
36248989105
-
ChIP-Seq data reveal nucleosome architecture of human promoters
-
author reply 832-3
-
Schmid CD, Bucher P. ChIP-Seq data reveal nucleosome architecture of human promoters. Cell 2007;131:831-2; author reply 832-3.
-
(2007)
Cell
, vol.131
, pp. 831-832
-
-
Schmid, C.D.1
Bucher, P.2
-
101
-
-
79551685675
-
A TALE nuclease architecture for efficient genome editing
-
Miller JC, Tan S, Qiao G, et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 2011;29: 143-8.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 143-148
-
-
Miller, J.C.1
Tan, S.2
Qiao, G.3
-
102
-
-
79960836456
-
Genetic engineering of human pluripotent cells using TALE nucleases
-
Hockemeyer D, Wang H, Kiani S, et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol 2011;29: 731-4.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 731-734
-
-
Hockemeyer, D.1
Wang, H.2
Kiani, S.3
-
103
-
-
84865070369
-
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
-
Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012;337: 816-21.
-
(2012)
Science
, vol.337
, pp. 816-821
-
-
Jinek, M.1
Chylinski, K.2
Fonfara, I.3
-
104
-
-
84874617789
-
Efficient genome editing in zebrafish using a CRISPR-Cas system
-
Hwang WY, Fu Y, Reyon D, et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 2013;31: 227-9.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 227-229
-
-
Hwang, W.Y.1
Fu, Y.2
Reyon, D.3
-
105
-
-
84881475586
-
Heritable genome editing in C. elegans via a CRISPR-Cas9 system
-
Friedland AE, Tzur YB, Esvelt KM, et al. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 2013;10: 741-3.
-
(2013)
Nat Methods
, vol.10
, pp. 741-743
-
-
Friedland, A.E.1
Tzur, Y.B.2
Esvelt, K.M.3
-
106
-
-
33745436961
-
Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers
-
2006.2011
-
Giesecke AV, Fang R, Joung JK. Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers. Mol Syst Biol 2006;2: 2006.2011.
-
(2006)
Mol Syst Biol
, vol.2
-
-
Giesecke, A.V.1
Fang, R.2
Joung, J.K.3
|