-
1
-
-
0000127073
-
Sequence-specific recognition of double helical nucleic acids by proteins
-
Seeman, N.C., Rosenberg, J.M. and Rich, A. (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA, 73, 804-808.
-
(1976)
Proc. Natl Acad. Sci. USA
, vol.73
, pp. 804-808
-
-
Seeman, N.C.1
Rosenberg, J.M.2
Rich, A.3
-
2
-
-
77950519937
-
Origins of specificity in protein-DNA recognition
-
Rohs, R., Jin, X., West, S.M., Joshi, R., Honig, B. and Mann, R.S. (2010) Origins of specificity in protein-DNA recognition. Annu. Rev. Biochem., 79, 233-269.
-
(2010)
Annu. Rev. Biochem.
, vol.79
, pp. 233-269
-
-
Rohs, R.1
Jin, X.2
West, S.M.3
Joshi, R.4
Honig, B.5
Mann, R.S.6
-
3
-
-
0035930331
-
Recognition of specific DNA sequences
-
Garvie, C.W. and Wolberger, C. (2001) Recognition of specific DNA sequences. Mol. Cell, 8, 937-946.
-
(2001)
Mol. Cell
, vol.8
, pp. 937-946
-
-
Garvie, C.W.1
Wolberger, C.2
-
5
-
-
0035976713
-
Do water molecules mediate protein-DNA recognition?
-
Reddy, C.K., Das, A. and Jayaram, B. (2001) Do water molecules mediate protein-DNA recognition? J. Mol. Biol., 314, 619-632.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 619-632
-
-
Reddy, C.K.1
Das, A.2
Jayaram, B.3
-
6
-
-
0035914475
-
Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition
-
Miller, J.C. and Pabo, C.O. (2001) Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition. J. Mol. Biol., 313, 309-315.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 309-315
-
-
Miller, J.C.1
Pabo, C.O.2
-
7
-
-
0345531145
-
A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water
-
Baldwin, E.P., Martin, S.S., Abel, J., Gelato, K.A., Kim, H., Schultz, P.G. and Santoro, S.W. (2003) A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water. Chem. Biol., 10, 1085-1094.
-
(2003)
Chem. Biol.
, vol.10
, pp. 1085-1094
-
-
Baldwin, E.P.1
Martin, S.S.2
Abel, J.3
Gelato, K.A.4
Kim, H.5
Schultz, P.G.6
Santoro, S.W.7
-
8
-
-
0024294634
-
Crystal structure of trp repressor/operator complex at atomic resolution
-
Otwinowski, Z., Schevitz, R.W., Zhang, R.G., Lawson, C.L., Joachimiak, A., Marmorstein, R.Q., Luisi, B.F. and Sigler, P.B. (1988) Crystal structure of trp repressor/operator complex at atomic resolution. Nature, 335, 321-329.
-
(1988)
Nature
, vol.335
, pp. 321-329
-
-
Otwinowski, Z.1
Schevitz, R.W.2
Zhang, R.G.3
Lawson, C.L.4
Joachimiak, A.5
Marmorstein, R.Q.6
Luisi, B.F.7
Sigler, P.B.8
-
9
-
-
70350686719
-
The role of DNA shape in protein-DNA recognition
-
Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature, 461, 1248-1253.
-
(2009)
Nature
, vol.461
, pp. 1248-1253
-
-
Rohs, R.1
West, S.M.2
Sosinsky, A.3
Liu, P.4
Mann, R.S.5
Honig, B.6
-
10
-
-
84876982103
-
Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen
-
Chang, Y.P., Xu, M., Machado, A.C., Yu, X.J., Rohs, R. and Chen, X.S. (2013) Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen. Cell Reports, 3, 1117-1127.
-
(2013)
Cell Reports
, vol.3
, pp. 1117-1127
-
-
Chang, Y.P.1
Xu, M.2
Machado, A.C.3
Yu, X.J.4
Rohs, R.5
Chen, X.S.6
-
11
-
-
0030046809
-
Intercalation, DNA kinking, and the control of transcription
-
Werner, M.H., Gronenborn, A.M. and Clore, G.M. (1996) Intercalation, DNA kinking, and the control of transcription. Science, 271, 778-784.
-
(1996)
Science
, vol.271
, pp. 778-784
-
-
Werner, M.H.1
Gronenborn, A.M.2
Clore, G.M.3
-
12
-
-
0027483012
-
Co-crystal structure of TBP recognizing the minor groove of a TATA element
-
Kim, J.L., Nikolov, D.B. and Burley, S.K. (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520-527.
-
(1993)
Nature
, vol.365
, pp. 520-527
-
-
Kim, J.L.1
Nikolov, D.B.2
Burley, S.K.3
-
13
-
-
26444478194
-
Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites
-
Rohs, R., Sklenar, H. and Shakked, Z. (2005) Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites. Structure, 13, 1499-1509.
-
(2005)
Structure
, vol.13
, pp. 1499-1509
-
-
Rohs, R.1
Sklenar, H.2
Shakked, Z.3
-
14
-
-
0034682882
-
Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
-
Pabo, C.O. and Nekludova, L. (2000) Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J. Mol. Biol., 301, 597-624.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 597-624
-
-
Pabo, C.O.1
Nekludova, L.2
-
15
-
-
0027937601
-
Stereochemical basis of DNA recognition by Zn fingers
-
Suzuki, M., Gerstein, M. and Yagi, N. (1994) Stereochemical basis of DNA recognition by Zn fingers. Nucleic Acids Res., 22, 3397-3405.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 3397-3405
-
-
Suzuki, M.1
Gerstein, M.2
Yagi, N.3
-
16
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Baker
-
Kortemme, T., Morozov, A.V. and Baker, D. (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol., 326, 1239-1259.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
-
17
-
-
34047153962
-
Structure-based prediction of C2H2 zinc-finger binding specificity: Sensitivity to docking geometry
-
Siggers, T.W. and Honig, B. (2007) Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res., 35, 1085-1097.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 1085-1097
-
-
Siggers, T.W.1
Honig, B.2
-
18
-
-
11844279783
-
Structural alignment of protein-DNA interfaces: Insights into the determinants of binding specificity
-
Siggers, T.W., Silkov, A. and Honig, B. (2005) Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity. J. Mol. Biol., 345, 1027-1045.
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 1027-1045
-
-
Siggers, T.W.1
Silkov, A.2
Honig, B.3
-
19
-
-
0033596120
-
Regulation of DNA binding by Rel/NF-kappaB transcription factors: Structural views
-
Chen, F.E. and Ghosh, G. (1999) Regulation of DNA binding by Rel/NF-kappaB transcription factors: structural views. Oncogene, 18, 6845-6852.
-
(1999)
Oncogene
, vol.18
, pp. 6845-6852
-
-
Chen, F.E.1
Ghosh, G.2
-
20
-
-
0031964687
-
A novel DNA recognition mode by the NF-kappa B p65 homodimer
-
Chen, Y.Q., Ghosh, S. and Ghosh, G. (1998) A novel DNA recognition mode by the NF-kappa B p65 homodimer. Nat. Struct. Biol., 5, 67-73.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 67-73
-
-
Chen, Y.Q.1
Ghosh, S.2
Ghosh, G.3
-
21
-
-
0034654832
-
NF-kappaB p65 (RelA) homodimer uses distinct mechanisms to recognize DNA targets
-
Chen, Y.Q., Sengchanthalangsy, L.L., Hackett, A. and Ghosh, G. (2000) NF-kappaB p65 (RelA) homodimer uses distinct mechanisms to recognize DNA targets. Structure, 8, 419-428.
-
(2000)
Structure
, vol.8
, pp. 419-428
-
-
Chen, Y.Q.1
Sengchanthalangsy, L.L.2
Hackett, A.3
Ghosh, G.4
-
22
-
-
79959389606
-
Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers
-
Yanover, C. and Bradley, P. (2011) Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers. Nucleic Acids Res., 39, 4564-4576.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 4564-4576
-
-
Yanover, C.1
Bradley, P.2
-
23
-
-
45449115390
-
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
-
Berger, M.F., Badis, G., Gehrke, A.R., Talukder, S., Philippakis, A.A., Pena-Castillo, L., Alleyne, T.M., Mnaimneh, S., Botvinnik, O.B., Chan, E.T. et al. (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell, 133, 1266-1276.
-
(2008)
Cell
, vol.133
, pp. 1266-1276
-
-
Berger, M.F.1
Badis, G.2
Gehrke, A.R.3
Talukder, S.4
Philippakis, A.A.5
Pena-Castillo, L.6
Alleyne, T.M.7
Mnaimneh, S.8
Botvinnik, O.B.9
Chan, E.T.10
-
24
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis, G., Berger, M.F., Philippakis, A.A., Talukder, S., Gehrke, A.R., Jaeger, S.A., Chan, E.T., Metzler, G., Vedenko, A., Chen, X. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
25
-
-
42949083192
-
Unexpected failure rates for modular assembly of engineered zinc fingers
-
Ramirez, C.L., Foley, J.E., Wright, D.A., Muller-Lerch, F., Rahman, S.H., Cornu, T.I., Winfrey, R.J., Sander, J.D., Fu, F., Townsend, J.A. et al. (2008) Unexpected failure rates for modular assembly of engineered zinc fingers. Nat. Methods, 5, 374-375.
-
(2008)
Nat. Methods
, vol.5
, pp. 374-375
-
-
Ramirez, C.L.1
Foley, J.E.2
Wright, D.A.3
Muller-Lerch, F.4
Rahman, S.H.5
Cornu, T.I.6
Winfrey, R.J.7
Sander, J.D.8
Fu, F.9
Townsend, J.A.10
-
26
-
-
77954954652
-
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
-
Wei, G.H., Badis, G., Berger, M.F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A.R. et al. (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J., 29, 2147-2160.
-
(2010)
EMBO J.
, vol.29
, pp. 2147-2160
-
-
Wei, G.H.1
Badis, G.2
Berger, M.F.3
Kivioja, T.4
Palin, K.5
Enge, M.6
Bonke, M.7
Jolma, A.8
Varjosalo, M.9
Gehrke, A.R.10
-
27
-
-
33645508729
-
Counter-selectable marker for bacterial-based interaction trap systems
-
Meng, X., Smith, R.M., Giesecke, A.V., Joung, J.K. and Wolfe, S.A. (2006) Counter-selectable marker for bacterial-based interaction trap systems. Biotechniques, 40, 179-184.
-
(2006)
Biotechniques
, vol.40
, pp. 179-184
-
-
Meng, X.1
Smith, R.M.2
Giesecke, A.V.3
Joung, J.K.4
Wolfe, S.A.5
-
28
-
-
43349107222
-
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
-
Noyes, M.B., Meng, X., Wakabayashi, A., Sinha, S., Brodsky, M.H. and Wolfe, S.A. (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res., 36, 2547-2560.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 2547-2560
-
-
Noyes, M.B.1
Meng, X.2
Wakabayashi, A.3
Sinha, S.4
Brodsky, M.H.5
Wolfe, S.A.6
-
29
-
-
33750882505
-
Compact universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
Berger, M.F., Philippakis, A.A., Qureshi, A.M., He, F.S., Estep, P.W. 3rd and Bulyk, M.L. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429-1435.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1429-1435
-
-
Berger, M.F.1
Philippakis, A.A.2
Qureshi, A.M.3
He, F.S.4
Estep Iii., P.W.5
Bulyk, M.L.6
-
30
-
-
0033028741
-
Quantifying DNA-protein interactions by double-stranded DNA arrays
-
Bulyk, M.L., Gentalen, E., Lockhart, D.J. and Church, G.M. (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat. Biotechnol., 17, 573-577.
-
(1999)
Nat. Biotechnol.
, vol.17
, pp. 573-577
-
-
Bulyk, M.L.1
Gentalen, E.2
Lockhart, D.J.3
Church, G.M.4
-
31
-
-
9644268153
-
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
-
Mukherjee, S., Berger, M.F., Jona, G., Wang, X.S., Muzzey, D., Snyder, M., Young, R.A. and Bulyk, M.L. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet., 36, 1331-1339.
-
(2004)
Nat. Genet.
, vol.36
, pp. 1331-1339
-
-
Mukherjee, S.1
Berger, M.F.2
Jona, G.3
Wang, X.S.4
Muzzey, D.5
Snyder, M.6
Young, R.A.7
Bulyk, M.L.8
-
32
-
-
2342507824
-
Quantitative high-throughput analysis of transcription factor binding specificities
-
Linnell, J., Mott, R., Field, S., Kwiatkowski, D.P., Ragoussis, J. and Udalova, I.A. (2004) Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res., 32, e44.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Linnell, J.1
Mott, R.2
Field, S.3
Kwiatkowski, D.P.4
Ragoussis, J.5
Udalova, I.A.6
-
33
-
-
34047123640
-
Accuracy and reproducibility of protein-DNA microarray technology
-
Field, S., Udalova, I. and Ragoussis, J. (2007) Accuracy and reproducibility of protein-DNA microarray technology. Adv Biochem. Eng. Biotechnol., 104, 87-110.
-
(2007)
Adv Biochem. Eng. Biotechnol.
, vol.104
, pp. 87-110
-
-
Field, S.1
Udalova, I.2
Ragoussis, J.3
-
34
-
-
67949120337
-
Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays
-
Bonham, A.J., Neumann, T., Tirrell, M. and Reich, N.O. (2009) Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays. Nucleic Acids Res., 37, e94.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Bonham, A.J.1
Neumann, T.2
Tirrell, M.3
Reich, N.O.4
-
35
-
-
33846467150
-
A systems approach to measuring the binding energy landscapes of transcription factors
-
Maerkl, S.J. and Quake, S.R. (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science, 315, 233-237.
-
(2007)
Science
, vol.315
, pp. 233-237
-
-
Maerkl, S.J.1
Quake, S.R.2
-
36
-
-
75649122221
-
Bind-n-Seq: High-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing
-
Zykovich, A., Korf, I. and Segal, D.J. (2009) Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res., 37, e151.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Zykovich, A.1
Korf, I.2
Segal, D.J.3
-
37
-
-
79960860669
-
Extensive characterization of NF-kappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits
-
Wong, D., Teixeira, A., Oikonomopoulos, S., Humburg, P., Lone, I.N., Saliba, D., Siggers, T., Bulyk, M., Angelov, D., Dimitrov, S. et al. (2011) Extensive characterization of NF-kappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol., 12, R70.
-
(2011)
Genome Biol.
, vol.12
-
-
Wong, D.1
Teixeira, A.2
Oikonomopoulos, S.3
Humburg, P.4
Lone, I.N.5
Saliba, D.6
Siggers, T.7
Bulyk, M.8
Angelov, D.9
Dimitrov, S.10
-
38
-
-
74549209548
-
Inferring binding energies from selected binding sites
-
Zhao, Y., Granas, D. and Stormo, G.D. (2009) Inferring binding energies from selected binding sites. PLoS Comput. Biol., 5, e1000590.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Zhao, Y.1
Granas, D.2
Stormo, G.D.3
-
39
-
-
77953006022
-
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
-
Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J.M., Yan, J., Sillanpaa, M.J. et al. (2010) Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res., 20, 861-873.
-
(2010)
Genome Res.
, vol.20
, pp. 861-873
-
-
Jolma, A.1
Kivioja, T.2
Toivonen, J.3
Cheng, L.4
Wei, G.5
Enge, M.6
Taipale, M.7
Vaquerizas, J.M.8
Yan, J.9
Sillanpaa, M.J.10
-
40
-
-
83255188878
-
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
-
Slattery, M., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H.J. et al. (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell, 147, 1270-1282.
-
(2011)
Cell
, vol.147
, pp. 1270-1282
-
-
Slattery, M.1
Riley, T.2
Liu, P.3
Abe, N.4
Gomez-Alcala, P.5
Dror, I.6
Zhou, T.7
Rohs, R.8
Honig, B.9
Bussemaker, H.J.10
-
41
-
-
41649086194
-
High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
-
Tantin, D., Gemberling, M., Callister, C. and Fairbrother, W.G. (2008) High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes. Genome Res., 18, 631-639.
-
(2008)
Genome Res.
, vol.18
, pp. 631-639
-
-
Tantin, D.1
Gemberling, M.2
Callister, C.3
Fairbrother, W.G.4
-
42
-
-
32244448130
-
Defining the sequence-recognition profile of DNA-binding molecules
-
Warren, C.L., Kratochvil, N.C., Hauschild, K.E., Foister, S., Brezinski, M.L., Dervan, P.B., Phillips, G.N. Jr and Ansari, A.Z. (2006) Defining the sequence-recognition profile of DNA-binding molecules. Proc. Natl Acad. Sci. USA, 103, 867-872.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 867-872
-
-
Warren, C.L.1
Kratochvil, N.C.2
Hauschild, K.E.3
Foister, S.4
Brezinski, M.L.5
Dervan, P.B.6
Phillips Jr., G.N.7
Ansari, A.Z.8
-
43
-
-
79960277492
-
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument
-
Nutiu, R., Friedman, R.C., Luo, S., Khrebtukova, I., Silva, D., Li, R., Zhang, L., Schroth, G.P. and Burge, C.B. (2011) Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat. Biotechnol., 29, 659-664.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 659-664
-
-
Nutiu, R.1
Friedman, R.C.2
Luo, S.3
Khrebtukova, I.4
Silva, D.5
Li, R.6
Zhang, L.7
Schroth, G.P.8
Burge, C.B.9
-
44
-
-
77958190479
-
Dramatic changes in transcription factor binding over evolutionary time
-
Weirauch, M.T. and Hughes, T.R. Dramatic changes in transcription factor binding over evolutionary time. Genome Biol., 11, 122.
-
Genome Biol.
, vol.11
, pp. 122
-
-
Weirauch, M.T.1
Hughes, T.R.2
-
45
-
-
84876955991
-
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape
-
Gordan, R., Shen, N., Dror, I., Zhou, T., Horton, J., Rohs, R. and Bulyk, M.L. (2013) Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Reports, 3, 1093-1104.
-
(2013)
Cell Reports
, vol.3
, pp. 1093-1104
-
-
Gordan, R.1
Shen, N.2
Dror, I.3
Zhou, T.4
Horton, J.5
Rohs, R.6
Bulyk, M.L.7
-
46
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo, G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
47
-
-
0016821121
-
Recognition sequences of repressor and polymerase in the operators of bacteriophage lambda
-
Maniatis, T., Ptashne, M., Backman, K., Kield, D., Flashman, S., Jeffrey, A. and Maurer, R. (1975) Recognition sequences of repressor and polymerase in the operators of bacteriophage lambda. Cell, 5, 109-113.
-
(1975)
Cell
, vol.5
, pp. 109-113
-
-
Maniatis, T.1
Ptashne, M.2
Backman, K.3
Kield, D.4
Flashman, S.5
Jeffrey, A.6
Maurer, R.7
-
48
-
-
83455164709
-
Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex
-
Siggers, T., Duyzend, M.H., Reddy, J., Khan, S. and Bulyk, M.L. (2011) Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol. Syst. Biol., 7, 555.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 555
-
-
Siggers, T.1
Duyzend, M.H.2
Reddy, J.3
Khan, S.4
Bulyk, M.L.5
-
49
-
-
0021760026
-
Computer methods to locate signals in nucleic acid sequences
-
Staden, R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res., 12, 505-519.
-
(1984)
Nucleic Acids Res.
, vol.12
, pp. 505-519
-
-
Staden, R.1
-
50
-
-
22344457014
-
EnoLOGOS: A versatile web tool for energy normalized sequence logos
-
Workman, C.T., Yin, Y., Corcoran, D.L., Ideker, T., Stormo, G.D. and Benos, P.V. (2005) enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res., 33, W389-W392.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Workman, C.T.1
Yin, Y.2
Corcoran, D.L.3
Ideker, T.4
Stormo, G.D.5
Benos, P.V.6
-
51
-
-
0035875327
-
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay
-
Man, T.K. and Stormo, G.D. (2001) Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res., 29, 2471-2478.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2471-2478
-
-
Man, T.K.1
Stormo, G.D.2
-
52
-
-
0036493201
-
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
-
Bulyk, M.L., Johnson, P.L. and Church, G.M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res., 30, 1255-1261.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1255-1261
-
-
Bulyk, M.L.1
Johnson, P.L.2
Church, G.M.3
-
53
-
-
34249654609
-
Position dependencies in transcription factor binding sites
-
Tomovic, A. and Oakeley, E.J. (2007) Position dependencies in transcription factor binding sites. Bioinformatics, 23, 933-941.
-
(2007)
Bioinformatics
, vol.23
, pp. 933-941
-
-
Tomovic, A.1
Oakeley, E.J.2
-
54
-
-
2342445980
-
Modeling within-motif dependence for transcription factor binding site predictions
-
Zhou, Q. and Liu, J.S. (2004) Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics, 20, 909-916.
-
(2004)
Bioinformatics
, vol.20
, pp. 909-916
-
-
Zhou, Q.1
Liu, J.S.2
-
55
-
-
78049440479
-
High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions
-
Agius, P., Arvey, A., Chang, W., Noble, W.S. and Leslie, C. (2010) High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. PLoS Comput. Biol., 6, pii: e1000916.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Agius, P.1
Arvey, A.2
Chang, W.3
Noble, W.S.4
Leslie, C.5
-
56
-
-
20744440509
-
Identification of transcription factor binding sites with variable-order Bayesian networks
-
Ben-Gal, I., Shani, A., Gohr, A., Grau, J., Arviv, S., Shmilovici, A., Posch, S. and Grosse, I. (2005) Identification of transcription factor binding sites with variable-order Bayesian networks. Bioinformatics, 21, 2657-2666.
-
(2005)
Bioinformatics
, vol.21
, pp. 2657-2666
-
-
Ben-Gal, I.1
Shani, A.2
Gohr, A.3
Grau, J.4
Arviv, S.5
Shmilovici, A.6
Posch, S.7
Grosse, I.8
-
57
-
-
17644369311
-
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites
-
Gershenzon, N.I., Stormo, G.D. and Ioshikhes, I.P. (2005) Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res., 33, 2290-2301.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2290-2301
-
-
Gershenzon, N.I.1
Stormo, G.D.2
Ioshikhes, I.P.3
-
58
-
-
84863866025
-
Improved models for transcription factor binding site identification using nonindependent interactions
-
Zhao, Y., Ruan, S., Pandey, M. and Stormo, G.D. (2012) Improved models for transcription factor binding site identification using nonindependent interactions. Genetics, 191, 781-790.
-
(2012)
Genetics
, vol.191
, pp. 781-790
-
-
Zhao, Y.1
Ruan, S.2
Pandey, M.3
Stormo, G.D.4
-
59
-
-
84873594686
-
Evaluation of methods for modeling transcription factor sequence specificity
-
Weirauch, M.T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T.R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S. et al. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol., 31, 126-134.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 126-134
-
-
Weirauch, M.T.1
Cote, A.2
Norel, R.3
Annala, M.4
Zhao, Y.5
Riley, T.R.6
Saez-Rodriguez, J.7
Cokelaer, T.8
Vedenko, A.9
Talukder, S.10
-
60
-
-
84879970323
-
Stability selection for regression-based models of transcription factor-DNA binding specificity
-
Mordelet, F., Horton, J., Hartemink, A.J., Engelhardt, B.E. and Gordan, R. (2013) Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinformatics, 29, i117-i125.
-
(2013)
Bioinformatics
, vol.29
-
-
Mordelet, F.1
Horton, J.2
Hartemink, A.J.3
Engelhardt, B.E.4
Gordan, R.5
-
61
-
-
79952116707
-
Dinucleotide weight matrices for predicting transcription factor binding sites: Generalizing the position weight matrix
-
Siddharthan, R. (2010) Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix. PLoS One, 5, e9722.
-
(2010)
PLoS One
, vol.5
-
-
Siddharthan, R.1
-
62
-
-
84884695174
-
The next generation of transcription factor binding site prediction
-
Mathelier, A. and Wasserman, W.W. (2013) The next generation of transcription factor binding site prediction. PLoS Comput. Biol., 9, e1003214.
-
(2013)
PLoS Comput. Biol.
, vol.9
-
-
Mathelier, A.1
Wasserman, W.W.2
-
63
-
-
0027511507
-
Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen
-
Jiang, J. and Levine, M. (1993) Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen. Cell, 72, 741-752.
-
(1993)
Cell
, vol.72
, pp. 741-752
-
-
Jiang, J.1
Levine, M.2
-
64
-
-
84866983699
-
A model of spatially restricted transcription in opposing gradients of activators and repressors
-
White, M.A., Parker, D.S., Barolo, S. and Cohen, B.A. (2012) A model of spatially restricted transcription in opposing gradients of activators and repressors. Mol. Syst Biol., 8, 614.
-
(2012)
Mol. Syst Biol.
, vol.8
, pp. 614
-
-
White, M.A.1
Parker, D.S.2
Barolo, S.3
Cohen, B.A.4
-
65
-
-
0038765091
-
Direct and concentration-dependent regulation of the proneural gene Neurogenin2 by Pax6
-
Scardigli, R., Baumer, N., Gruss, P., Guillemot, F. and Le Roux, I. (2003) Direct and concentration-dependent regulation of the proneural gene Neurogenin2 by Pax6. Development, 130, 3269-3281.
-
(2003)
Development
, vol.130
, pp. 3269-3281
-
-
Scardigli, R.1
Baumer, N.2
Gruss, P.3
Guillemot, F.4
Le Roux, I.5
-
66
-
-
0024380401
-
The gradient morphogen bicoid is a concentration-dependent transcriptional activator
-
Struhl, G., Struhl, K. and Macdonald, P.M. (1989) The gradient morphogen bicoid is a concentration-dependent transcriptional activator. Cell, 57, 1259-1273.
-
(1989)
Cell
, vol.57
, pp. 1259-1273
-
-
Struhl, G.1
Struhl, K.2
Macdonald, P.M.3
-
67
-
-
77952352833
-
Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity
-
Rowan, S., Siggers, T., Lachke, S.A., Yue, Y., Bulyk, M.L. and Maas, R.L. (2010) Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity. Genes Dev., 24, 980-985.
-
(2010)
Genes Dev.
, vol.24
, pp. 980-985
-
-
Rowan, S.1
Siggers, T.2
Lachke, S.A.3
Yue, Y.4
Bulyk, M.L.5
Maas, R.L.6
-
68
-
-
0036468361
-
Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4
-
Gaudet, J. and Mango, S.E. (2002) Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science, 295, 821-825.
-
(2002)
Science
, vol.295
, pp. 821-825
-
-
Gaudet, J.1
Mango, S.E.2
-
69
-
-
77950339177
-
Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites
-
Jaeger, S.A., Chan, E.T., Berger, M.F., Stottmann, R., Hughes, T.R. and Bulyk, M.L. (2010) Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. Genomics, 95, 185-195.
-
(2010)
Genomics
, vol.95
, pp. 185-195
-
-
Jaeger, S.A.1
Chan, E.T.2
Berger, M.F.3
Stottmann, R.4
Hughes, T.R.5
Bulyk, M.L.6
-
70
-
-
33746691336
-
Extensive low-affinity transcriptional interactions in the yeast genome
-
Tanay, A. (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res., 16, 962-972.
-
(2006)
Genome Res.
, vol.16
, pp. 962-972
-
-
Tanay, A.1
-
71
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U. and Gaul, U. (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature, 451, 535-540.
-
(2008)
Nature
, vol.451
, pp. 535-540
-
-
Segal, E.1
Raveh-Sadka, T.2
Schroeder, M.3
Unnerstall, U.4
Gaul, U.5
-
72
-
-
83855162723
-
Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-kappaB family DNA binding
-
Siggers, T., Chang, A.B., Teixeira, A., Wong, D., Williams, K.J., Ahmed, B., Ragoussis, J., Udalova, I.A., Smale, S.T. and Bulyk, M.L. (2012) Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-kappaB family DNA binding. Nat. Immunol., 13, 95-102.
-
(2012)
Nat. Immunol.
, vol.13
, pp. 95-102
-
-
Siggers, T.1
Chang, A.B.2
Teixeira, A.3
Wong, D.4
Williams, K.J.5
Ahmed, B.6
Ragoussis, J.7
Udalova, I.A.8
Smale, S.T.9
Bulyk, M.L.10
-
73
-
-
63849315606
-
High-resolution DNA-binding specificity analysis of yeast transcription factors
-
Zhu, C., Byers, K.J., McCord, R.P., Shi, Z., Berger, M.F., Newburger, D.E., Saulrieta, K., Smith, Z., Shah, M.V., Radhakrishnan, M. et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res., 19, 556-566.
-
(2009)
Genome Res.
, vol.19
, pp. 556-566
-
-
Zhu, C.1
Byers, K.J.2
McCord, R.P.3
Shi, Z.4
Berger, M.F.5
Newburger, D.E.6
Saulrieta, K.7
Smith, Z.8
Shah, M.V.9
Radhakrishnan, M.10
-
74
-
-
83755196322
-
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
-
Gordan, R., Murphy, K.F., McCord, R.P., Zhu, C., Vedenko, A. and Bulyk, M.L. (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol., 12, R125.
-
(2011)
Genome Biol.
, vol.12
-
-
Gordan, R.1
Murphy, K.F.2
McCord, R.P.3
Zhu, C.4
Vedenko, A.5
Bulyk, M.L.6
-
75
-
-
84880681583
-
DNA-binding specificity changes in the evolution of forkhead transcription factors
-
Nakagawa, S., Gisselbrecht, S.S., Rogers, J.M., Hartl, D.L. and Bulyk, M.L. (2013) DNA-binding specificity changes in the evolution of forkhead transcription factors. Proc. Natl Acad. Sci. USA, 110, 12349-12354.
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 12349-12354
-
-
Nakagawa, S.1
Gisselbrecht, S.S.2
Rogers, J.M.3
Hartl, D.L.4
Bulyk, M.L.5
-
76
-
-
81055149802
-
Nuclear receptor HNF4alpha binding sequences are widespread in Alu repeats
-
Bolotin, E., Chellappa, K., Hwang-Verslues, W., Schnabl, J.M., Yang, C. and Sladek, F.M. (2011) Nuclear receptor HNF4alpha binding sequences are widespread in Alu repeats. BMC Genomics, 12, 560.
-
(2011)
BMC Genomics
, vol.12
, pp. 560
-
-
Bolotin, E.1
Chellappa, K.2
Hwang-Verslues, W.3
Schnabl, J.M.4
Yang, C.5
Sladek, F.M.6
-
77
-
-
84867157760
-
-
Chu, S.W., Noyes, M.B., Christensen, R.G., Pierce, B.G., Zhu, L.J., Weng, Z., Stormo, G.D. and Wolfe, S.A. (2012) Exploring the DNA-recognition potential of homeodomains. Genome Res., 22, 1889-1898.
-
(2012)
Exploring the DNA-recognition Potential of Homeodomains. Genome Res.
, vol.22
, pp. 1889-1898
-
-
Chu, S.W.1
Noyes, M.B.2
Christensen, R.G.3
Pierce, B.G.4
Zhu, L.J.5
Weng, Z.6
Stormo, G.D.7
Wolfe, S.A.8
-
78
-
-
45449111373
-
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
-
Noyes, M.B., Christensen, R.G., Wakabayashi, A., Stormo, G.D., Brodsky, M.H. and Wolfe, S.A. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell, 133, 1277-1289.
-
(2008)
Cell
, vol.133
, pp. 1277-1289
-
-
Noyes, M.B.1
Christensen, R.G.2
Wakabayashi, A.3
Stormo, G.D.4
Brodsky, M.H.5
Wolfe, S.A.6
-
79
-
-
84863228237
-
Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors
-
Fang, B., Mane-Padros, D., Bolotin, E., Jiang, T. and Sladek, F.M. (2012) Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors. Nucleic Acids Res., 40, 5343-5356.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 5343-5356
-
-
Fang, B.1
Mane-Padros, D.2
Bolotin, E.3
Jiang, T.4
Sladek, F.M.5
-
80
-
-
84883590358
-
DNAshape: A method for the high-throughput prediction of DNA structural features on a genomic scale
-
Zhou, T., Yang, L., Lu, Y., Dror, I., Dantas Machado, A.C., Ghane, T., Di Felice, R. and Rohs, R. (2013) DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res., 41, W56-W62.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Zhou, T.1
Yang, L.2
Lu, Y.3
Dror, I.4
Dantas Machado, A.C.5
Ghane, T.6
Di Felice, R.7
Rohs, R.8
-
81
-
-
57749121616
-
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
-
Badis, G., Chan, E.T., van Bakel, H., Pena-Castillo, L., Tillo, D., Tsui, K., Carlson, C.D., Gossett, A.J., Hasinoff, M.J., Warren, C.L. et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol. Cell, 32, 878-887.
-
(2008)
Mol. Cell
, vol.32
, pp. 878-887
-
-
Badis, G.1
Chan, E.T.2
Van Bakel, H.3
Pena-Castillo, L.4
Tillo, D.5
Tsui, K.6
Carlson, C.D.7
Gossett, A.J.8
Hasinoff, M.J.9
Warren, C.L.10
-
82
-
-
0029036735
-
Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains
-
Kim, J. and Struhl, K. (1995) Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains. Nucleic Acids Res., 23, 2531-2537.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 2531-2537
-
-
Kim, J.1
Struhl, K.2
-
83
-
-
0036724089
-
Classification of human B-ZIP proteins based on dimerization properties
-
Vinson, C., Myakishev, M., Acharya, A., Mir, A.A., Moll, J.R. and Bonovich, M. (2002) Classification of human B-ZIP proteins based on dimerization properties. Mol. Cell. Biol., 22, 6321-6335.
-
(2002)
Mol. Cell. Biol.
, vol.22
, pp. 6321-6335
-
-
Vinson, C.1
Myakishev, M.2
Acharya, A.3
Mir, A.A.4
Moll, J.R.5
Bonovich, M.6
-
84
-
-
78650039587
-
Coevolution within a transcriptional network by compensatory trans and cis mutations
-
Kuo, D., Licon, K., Bandyopadhyay, S., Chuang, R., Luo, C., Catalana, J., Ravasi, T., Tan, K. and Ideker, T. (2010) Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res., 20, 1672-1678.
-
(2010)
Genome Res.
, vol.20
, pp. 1672-1678
-
-
Kuo, D.1
Licon, K.2
Bandyopadhyay, S.3
Chuang, R.4
Luo, C.5
Catalana, J.6
Ravasi, T.7
Tan, K.8
Ideker, T.9
-
85
-
-
0035369335
-
Nuclear-receptor interactions on DNA-response elements
-
Khorasanizadeh, S. and Rastinejad, F. (2001) Nuclear-receptor interactions on DNA-response elements. Trends Biochem. Sci., 26, 384-390.
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 384-390
-
-
Khorasanizadeh, S.1
Rastinejad, F.2
-
86
-
-
0028122988
-
Regulation of retinoid signalling by receptor polarity and allosteric control of ligand binding
-
Kurokawa, R., DiRenzo, J., Boehm, M., Sugarman, J., Gloss, B., Rosenfeld, M.G., Heyman, R.A. and Glass, C.K. (1994) Regulation of retinoid signalling by receptor polarity and allosteric control of ligand binding. Nature, 371, 528-531.
-
(1994)
Nature
, vol.371
, pp. 528-531
-
-
Kurokawa, R.1
Direnzo, J.2
Boehm, M.3
Sugarman, J.4
Gloss, B.5
Rosenfeld, M.G.6
Heyman, R.A.7
Glass, C.K.8
-
87
-
-
0033647653
-
An overview of the structures of protein-DNA complexes
-
Luscombe, N.M., Austin, S.E., Berman, H.M. and Thornton, J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, REVIEWS001.
-
(2000)
Genome Biol.
, vol.1
-
-
Luscombe, N.M.1
Austin, S.E.2
Berman, H.M.3
Thornton, J.M.4
-
88
-
-
0026342692
-
Evi-1, a murine zinc finger proto-oncogene, encodes a sequence-specific DNA-binding protein
-
Perkins, A.S., Fishel, R., Jenkins, N.A. and Copeland, N.G. (1991) Evi-1, a murine zinc finger proto-oncogene, encodes a sequence-specific DNA-binding protein. Mol. Cell. Biol., 11, 2665-2674.
-
(1991)
Mol. Cell. Biol.
, vol.11
, pp. 2665-2674
-
-
Perkins, A.S.1
Fishel, R.2
Jenkins, N.A.3
Copeland, N.G.4
-
89
-
-
0027232223
-
Four of the seven zinc fingers of the Evi-1 myeloid-transforming gene are required for sequence-specific binding to GA(C/T)AAGA(T/C)AAGATAA
-
Delwel, R., Funabiki, T., Kreider, B.L., Morishita, K. and Ihle, J.N. (1993) Four of the seven zinc fingers of the Evi-1 myeloid-transforming gene are required for sequence-specific binding to GA(C/T)AAGA(T/C)AAGATAA. Mol. Cell. Biol., 13, 4291-4300.
-
(1993)
Mol. Cell. Biol.
, vol.13
, pp. 4291-4300
-
-
Delwel, R.1
Funabiki, T.2
Kreider, B.L.3
Morishita, K.4
Ihle, J.N.5
-
90
-
-
0028241701
-
The carboxyl domain of zinc fingers of the Evi-1 myeloid transforming gene binds a consensus sequence of GAAGATGAG
-
Funabiki, T., Kreider, B.L. and Ihle, J.N. (1994) The carboxyl domain of zinc fingers of the Evi-1 myeloid transforming gene binds a consensus sequence of GAAGATGAG. Oncogene, 9, 1575-1581.
-
(1994)
Oncogene
, vol.9
, pp. 1575-1581
-
-
Funabiki, T.1
Kreider, B.L.2
Ihle, J.N.3
-
91
-
-
0028200262
-
Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules
-
Klemm, J.D., Rould, M.A., Aurora, R., Herr, W. and Pabo, C.O. (1994) Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell, 77, 21-32.
-
(1994)
Cell
, vol.77
, pp. 21-32
-
-
Klemm, J.D.1
Rould, M.A.2
Aurora, R.3
Herr, W.4
Pabo, C.O.5
-
92
-
-
0027092288
-
The DNA binding specificity of the bipartite POU domain and its subdomains
-
Verrijzer, C.P., Alkema, M.J., van Weperen, W.W., Van Leeuwen, H.C., Strating, M.J. and van der Vliet, P.C. (1992) The DNA binding specificity of the bipartite POU domain and its subdomains. EMBO J., 11, 4993-5003.
-
(1992)
EMBO J.
, vol.11
, pp. 4993-5003
-
-
Verrijzer, C.P.1
Alkema, M.J.2
Van Weperen, W.W.3
Van Leeuwen, H.C.4
Strating, M.J.5
Van Der Vliet, P.C.6
-
93
-
-
0024425433
-
Octamer transcription factors bind to two different sequence motifs of the immunoglobulin heavy chain promoter
-
Kemler, I., Schreiber, E., Muller, M.M., Matthias, P. and Schaffner, W. (1989) Octamer transcription factors bind to two different sequence motifs of the immunoglobulin heavy chain promoter. EMBO J., 8, 2001-2008.
-
(1989)
EMBO J.
, vol.8
, pp. 2001-2008
-
-
Kemler, I.1
Schreiber, E.2
Muller, M.M.3
Matthias, P.4
Schaffner, W.5
-
94
-
-
0030953793
-
The DNA binding pattern of the retinoid X receptor is regulated by ligand-dependent modulation of its oligomeric state
-
Kersten, S., Gronemeyer, H. and Noy, N. (1997) The DNA binding pattern of the retinoid X receptor is regulated by ligand-dependent modulation of its oligomeric state. J. Biol. Chem., 272, 12771-12777.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 12771-12777
-
-
Kersten, S.1
Gronemeyer, H.2
Noy, N.3
-
95
-
-
84872540994
-
DNA-binding specificities of human transcription factors
-
Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K.R., Rastas, P., Morgunova, E., Enge, M., Taipale, M., Wei, G. et al. (2013) DNA-binding specificities of human transcription factors. Cell, 152, 327-339.
-
(2013)
Cell
, vol.152
, pp. 327-339
-
-
Jolma, A.1
Yan, J.2
Whitington, T.3
Toivonen, J.4
Nitta, K.R.5
Rastas, P.6
Morgunova, E.7
Enge, M.8
Taipale, M.9
Wei, G.10
-
96
-
-
0028963743
-
Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain
-
Kim, J.B., Spotts, G.D., Halvorsen, Y.D., Shih, H.M., Ellenberger, T., Towle, H.C. and Spiegelman, B.M. (1995) Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain. Mol. Cell. Biol., 15, 2582-2588.
-
(1995)
Mol. Cell. Biol.
, vol.15
, pp. 2582-2588
-
-
Kim, J.B.1
Spotts, G.D.2
Halvorsen, Y.D.3
Shih, H.M.4
Ellenberger, T.5
Towle, H.C.6
Spiegelman, B.M.7
-
97
-
-
0032524465
-
Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution
-
Parraga, A., Bellsolell, L., Ferre-D'Amare, A.R. and Burley, S.K. (1998) Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution. Structure, 6, 661-672.
-
(1998)
Structure
, vol.6
, pp. 661-672
-
-
Parraga, A.1
Bellsolell, L.2
Ferre-D'Amare, A.R.3
Burley, S.K.4
-
98
-
-
84868588824
-
Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses
-
Fordyce, P.M., Pincus, D., Kimmig, P., Nelson, C.S., El-Samad, H., Walter, P. and DeRisi, J.L. (2012) Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses. Proc. Natl Acad. Sci. USA, 109, E3084-E3093.
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
-
-
Fordyce, P.M.1
Pincus, D.2
Kimmig, P.3
Nelson, C.S.4
El-Samad, H.5
Walter, P.6
Derisi, J.L.7
-
99
-
-
79952266465
-
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
-
Pique-Regi, R., Degner, J.F., Pai, A.A., Gaffney, D.J., Gilad, Y. and Pritchard, J.K. (2011) Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res., 21, 447-455.
-
(2011)
Genome Res.
, vol.21
, pp. 447-455
-
-
Pique-Regi, R.1
Degner, J.F.2
Pai, A.A.3
Gaffney, D.J.4
Gilad, Y.5
Pritchard, J.K.6
-
100
-
-
0742306815
-
Computational prediction of transcription-factor binding site locations
-
Bulyk, M.L. (2003) Computational prediction of transcription-factor binding site locations. Genome Biol., 5, 201.
-
(2003)
Genome Biol.
, vol.5
, pp. 201
-
-
Bulyk, M.L.1
-
101
-
-
0037819447
-
Transcription regulation and animal diversity
-
Levine, M. and Tjian, R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
-
(2003)
Nature
, vol.424
, pp. 147-151
-
-
Levine, M.1
Tjian, R.2
-
102
-
-
0029154633
-
Molecular mechanisms of cell-type determination in budding yeast
-
Johnson, A.D. (1995) Molecular mechanisms of cell-type determination in budding yeast. Curr. Opin Genet. Dev., 5, 552-558.
-
(1995)
Curr. Opin Genet. Dev.
, vol.5
, pp. 552-558
-
-
Johnson, A.D.1
-
103
-
-
0033056554
-
Multiprotein-DNA complexes in transcriptional regulation
-
Wolberger, C. (1999) Multiprotein-DNA complexes in transcriptional regulation. Annu. Rev. Biophys. Biomol. Struct., 28, 29-56.
-
(1999)
Annu. Rev. Biophys. Biomol. Struct.
, vol.28
, pp. 29-56
-
-
Wolberger, C.1
-
104
-
-
0001294043
-
-
McKnight, S.L. and Yamamoto, K.R. (eds), Cold Spring Harbor Lab. Press, Cold Spring Harbor, NY
-
Johnson, A.D. (1992) In: McKnight, S.L. and Yamamoto, K.R. (eds), Transcriptional Regulation. Cold Spring Harbor Lab. Press, Cold Spring Harbor, NY, pp. 975-1006.
-
(1992)
Transcriptional Regulation
, pp. 975-1006
-
-
Johnson, A.D.1
-
105
-
-
84873647198
-
Probing allostery through DNA
-
Kim, S., Brostromer, E., Xing, D., Jin, J., Chong, S., Ge, H., Wang, S., Gu, C., Yang, L., Gao, Y.Q. et al. (2013) Probing allostery through DNA. Science, 339, 816-819.
-
(2013)
Science
, vol.339
, pp. 816-819
-
-
Kim, S.1
Brostromer, E.2
Xing, D.3
Jin, J.4
Chong, S.5
Ge, H.6
Wang, S.7
Gu, C.8
Yang, L.9
Gao, Y.Q.10
-
106
-
-
0035697276
-
Structural studies of Ets-1/Pax5 complex formation on DNA
-
Garvie, C.W., Hagman, J. and Wolberger, C. (2001) Structural studies of Ets-1/Pax5 complex formation on DNA. Mol. Cell, 8, 1267-1276.
-
(2001)
Mol. Cell
, vol.8
, pp. 1267-1276
-
-
Garvie, C.W.1
Hagman, J.2
Wolberger, C.3
-
107
-
-
35548931586
-
Functional specificity of a Hox protein mediated by the recognition of minor groove structure
-
Joshi, R., Passner, J.M., Rohs, R., Jain, R., Sosinsky, A., Crickmore, M.A., Jacob, V., Aggarwal, A.K., Honig, B. and Mann, R.S. (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell, 131, 530-543.
-
(2007)
Cell
, vol.131
, pp. 530-543
-
-
Joshi, R.1
Passner, J.M.2
Rohs, R.3
Jain, R.4
Sosinsky, A.5
Crickmore, M.A.6
Jacob, V.7
Aggarwal, A.K.8
Honig, B.9
Mann, R.S.10
-
108
-
-
0008231153
-
The control of trunk Hox specificity and activity by Extradenticle
-
Ryoo, H.D. and Mann, R.S. (1999) The control of trunk Hox specificity and activity by Extradenticle. Genes Dev., 13, 1704-1716.
-
(1999)
Genes Dev.
, vol.13
, pp. 1704-1716
-
-
Ryoo, H.D.1
Mann, R.S.2
-
109
-
-
0032498230
-
The enhanceosome and transcriptional synergy
-
Carey, M. (1998) The enhanceosome and transcriptional synergy. Cell, 92, 5-8.
-
(1998)
Cell
, vol.92
, pp. 5-8
-
-
Carey, M.1
-
110
-
-
0030960672
-
Transcriptional activation by recruitment
-
Ptashne, M. and Gann, A. (1997) Transcriptional activation by recruitment. Nature, 386, 569-577.
-
(1997)
Nature
, vol.386
, pp. 569-577
-
-
Ptashne, M.1
Gann, A.2
-
111
-
-
0031604766
-
Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription
-
Merika, M., Williams, A.J., Chen, G., Collins, T. and Thanos, D. (1998) Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription. Mol. Cell, 1, 277-287.
-
(1998)
Mol. Cell
, vol.1
, pp. 277-287
-
-
Merika, M.1
Williams, A.J.2
Chen, G.3
Collins, T.4
Thanos, D.5
-
112
-
-
0031310825
-
The mechanism of transcriptional synergy of an in vitro assembled interferon-beta enhanceosome
-
Kim, T.K. and Maniatis, T. (1997) The mechanism of transcriptional synergy of an in vitro assembled interferon-beta enhanceosome. Mol. Cell, 1, 119-129.
-
(1997)
Mol. Cell
, vol.1
, pp. 119-129
-
-
Kim, T.K.1
Maniatis, T.2
-
113
-
-
0034194473
-
CIITA is a transcriptional coactivator that is recruited to MHC class II promoters by multiple synergistic interactions with an enhanceosome complex
-
Masternak, K., Muhlethaler-Mottet, A., Villard, J., Zufferey, M., Steimle, V. and Reith, W. (2000) CIITA is a transcriptional coactivator that is recruited to MHC class II promoters by multiple synergistic interactions with an enhanceosome complex. Genes Dev., 14, 1156-1166.
-
(2000)
Genes Dev.
, vol.14
, pp. 1156-1166
-
-
Masternak, K.1
Muhlethaler-Mottet, A.2
Villard, J.3
Zufferey, M.4
Steimle, V.5
Reith, W.6
-
114
-
-
84859409089
-
Tcra enhancer activation by inducible transcription factors downstream of pre-TCR signaling
-
del Blanco, B., Garcia-Mariscal, A., Wiest, D.L. and Hernandez-Munain, C. (2012) Tcra enhancer activation by inducible transcription factors downstream of pre-TCR signaling. J. Immunol., 188, 3278-3293.
-
(2012)
J. Immunol.
, vol.188
, pp. 3278-3293
-
-
Del Blanco, B.1
Garcia-Mariscal, A.2
Wiest, D.L.3
Hernandez-Munain, C.4
-
115
-
-
0025257112
-
Regulation of major histocompatibility complex class-II genes: X, y and other letters of the alphabet
-
Benoist, C. and Mathis, D. (1990) Regulation of major histocompatibility complex class-II genes: X, Y and other letters of the alphabet. Annu. Rev. Immunol., 8, 681-715.
-
(1990)
Annu. Rev. Immunol.
, vol.8
, pp. 681-715
-
-
Benoist, C.1
Mathis, D.2
-
116
-
-
0036185782
-
Allosteric regulation of estrogen receptor structure
-
Hall, J.M., McDonnell, D.P. and Korach, K.S. (2002) Allosteric regulation of estrogen receptor structure, function, and coactivator recruitment by different estrogen response elements. Mol. Endocrinol., 16, 469-486.
-
(2002)
Function, and Coactivator Recruitment by Different Estrogen Response Elements. Mol. Endocrinol.
, vol.16
, pp. 469-486
-
-
Hall, J.M.1
McDonnell, D.P.2
Korach, K.S.3
-
117
-
-
4644252538
-
One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers
-
Leung, T.H., Hoffmann, A. and Baltimore, D. (2004) One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell, 118, 453-464.
-
(2004)
Cell
, vol.118
, pp. 453-464
-
-
Leung, T.H.1
Hoffmann, A.2
Baltimore, D.3
-
118
-
-
65249167505
-
DNA binding site sequence directs glucocorticoid receptor structure and activity
-
Meijsing, S.H., Pufall, M.A., So, A.Y., Bates, D.L., Chen, L. and Yamamoto, K.R. (2009) DNA binding site sequence directs glucocorticoid receptor structure and activity. Science, 324, 407-410.
-
(2009)
Science
, vol.324
, pp. 407-410
-
-
Meijsing, S.H.1
Pufall, M.A.2
So, A.Y.3
Bates, D.L.4
Chen, L.5
Yamamoto, K.R.6
-
119
-
-
83755172769
-
Role of sequence encoded kappaB DNA geometry in gene regulation by Dorsal
-
Mrinal, N., Tomar, A. and Nagaraju, J. (2011) Role of sequence encoded kappaB DNA geometry in gene regulation by Dorsal. Nucleic Acids Res., 39, 9574-9591.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 9574-9591
-
-
Mrinal, N.1
Tomar, A.2
Nagaraju, J.3
-
120
-
-
84868093966
-
The transcriptional specificity of NF-kappaB dimers is coded within the kappaB DNA response elements
-
Wang, V.Y., Huang, W., Asagiri, M., Spann, N., Hoffmann, A., Glass, C. and Ghosh, G. (2012) The transcriptional specificity of NF-kappaB dimers is coded within the kappaB DNA response elements. Cell Reports, 2, 824-839.
-
(2012)
Cell Reports
, vol.2
, pp. 824-839
-
-
Wang, V.Y.1
Huang, W.2
Asagiri, M.3
Spann, N.4
Hoffmann, A.5
Glass, C.6
Ghosh, G.7
-
121
-
-
4344595718
-
Combinatorial control of gene expression
-
Remenyi, A., Scholer, H.R. and Wilmanns, M. (2004) Combinatorial control of gene expression. Nat. Struct. Mol. Biol., 11, 812-815.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 812-815
-
-
Remenyi, A.1
Scholer, H.R.2
Wilmanns, M.3
-
122
-
-
0031964687
-
A novel DNA recognition mode by the NF-kappa B p65 homodimer
-
Chen, Y.Q., Ghosh, S. and Ghosh, G. (1998) A novel DNA recognition mode by the NF-kappa B p65 homodimer. Nat. Struct. Biol., 5, 67-73.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 67-73
-
-
Chen, Y.Q.1
Ghosh, S.2
Ghosh, G.3
-
123
-
-
0026708394
-
Independent modes of transcriptional activation by the p50 and p65 subunits of NF-kappa B
-
Fujita, T., Nolan, G.P., Ghosh, S. and Baltimore, D. (1992) Independent modes of transcriptional activation by the p50 and p65 subunits of NF-kappa B. Genes Dev., 6, 775-787.
-
(1992)
Genes Dev.
, vol.6
, pp. 775-787
-
-
Fujita, T.1
Nolan, G.P.2
Ghosh, S.3
Baltimore, D.4
-
124
-
-
0034634340
-
Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification
-
Scully, K.M., Jacobson, E.M., Jepsen, K., Lunyak, V., Viadiu, H., Carriere, C., Rose, D.W., Hooshmand, F., Aggarwal, A.K. and Rosenfeld, M.G. (2000) Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification. Science, 290, 1127-1131.
-
(2000)
Science
, vol.290
, pp. 1127-1131
-
-
Scully, K.M.1
Jacobson, E.M.2
Jepsen, K.3
Lunyak, V.4
Viadiu, H.5
Carriere, C.6
Rose, D.W.7
Hooshmand, F.8
Aggarwal, A.K.9
Rosenfeld, M.G.10
-
125
-
-
0034791092
-
Differential dimer activities of the transcription factor Oct-1 by DNA-induced interface swapping
-
Remenyi, A., Tomilin, A., Pohl, E., Lins, K., Philippsen, A., Reinbold, R., Scholer, H.R. and Wilmanns, M. (2001) Differential dimer activities of the transcription factor Oct-1 by DNA-induced interface swapping. Mol. Cell, 8, 569-580.
-
(2001)
Mol. Cell
, vol.8
, pp. 569-580
-
-
Remenyi, A.1
Tomilin, A.2
Pohl, E.3
Lins, K.4
Philippsen, A.5
Reinbold, R.6
Scholer, H.R.7
Wilmanns, M.8
-
126
-
-
0033569643
-
Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: Specific recognition of a protein-DNA interface
-
Chasman, D., Cepek, K., Sharp, P.A. and Pabo, C.O. (1999) Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface. Genes Dev., 13, 2650-2657.
-
(1999)
Genes Dev.
, vol.13
, pp. 2650-2657
-
-
Chasman, D.1
Cepek, K.2
Sharp, P.A.3
Pabo, C.O.4
-
127
-
-
0024277940
-
A tissue-specific transcription factor containing a homeodomain specifies a pituitary phenotype
-
Ingraham, H.A., Chen, R.P., Mangalam, H.J., Elsholtz, H.P., Flynn, S.E., Lin, C.R., Simmons, D.M., Swanson, L. and Rosenfeld, M.G. (1988) A tissue-specific transcription factor containing a homeodomain specifies a pituitary phenotype. Cell, 55, 519-529.
-
(1988)
Cell
, vol.55
, pp. 519-529
-
-
Ingraham, H.A.1
Chen, R.P.2
Mangalam, H.J.3
Elsholtz, H.P.4
Flynn, S.E.5
Lin, C.R.6
Simmons, D.M.7
Swanson, L.8
Rosenfeld, M.G.9
-
128
-
-
0025339078
-
The POU-specific domain of Pit-1 is essential for sequence-specific, high affinity DNA binding and DNA-dependent Pit-1-Pit-1 interactions
-
Ingraham, H.A., Flynn, S.E., Voss, J.W., Albert, V.R., Kapiloff, M.S., Wilson, L. and Rosenfeld, M.G. (1990) The POU-specific domain of Pit-1 is essential for sequence-specific, high affinity DNA binding and DNA-dependent Pit-1-Pit-1 interactions. Cell, 61, 1021-1033.
-
(1990)
Cell
, vol.61
, pp. 1021-1033
-
-
Ingraham, H.A.1
Flynn, S.E.2
Voss, J.W.3
Albert, V.R.4
Kapiloff, M.S.5
Wilson, L.6
Rosenfeld, M.G.7
-
129
-
-
0034949170
-
DNA recognition by the herpes simplex virus transactivator VP16: A novel DNA-binding structure
-
Babb, R., Huang, C.C., Aufiero, D.J. and Herr, W. (2001) DNA recognition by the herpes simplex virus transactivator VP16: a novel DNA-binding structure. Mol. Cell Biol., 21, 4700-4712.
-
(2001)
Mol. Cell Biol.
, vol.21
, pp. 4700-4712
-
-
Babb, R.1
Huang, C.C.2
Aufiero, D.J.3
Herr, W.4
-
130
-
-
0029944825
-
A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediates the transcription activation of yeast sulfur metabolism
-
Kuras, L., Cherest, H., Surdin-Kerjan, Y. and Thomas, D. (1996) A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediates the transcription activation of yeast sulfur metabolism. EMBO J., 15, 2519-2529.
-
(1996)
EMBO J.
, vol.15
, pp. 2519-2529
-
-
Kuras, L.1
Cherest, H.2
Surdin-Kerjan, Y.3
Thomas, D.4
-
131
-
-
0032476584
-
Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA
-
Blaiseau, P.L. and Thomas, D. (1998) Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J., 17, 6327-6336.
-
(1998)
EMBO J.
, vol.17
, pp. 6327-6336
-
-
Blaiseau, P.L.1
Thomas, D.2
-
132
-
-
79960860669
-
Extensive characterization of NF-KappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits
-
Wong, D., Teixeira, A., Oikonomopoulos, S., Humburg, P., Lone, I.N., Saliba, D., Siggers, T., Bulyk, M., Angelov, D., Dimitrov, S. et al. (2011) Extensive characterization of NF-KappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol., 12, R70.
-
(2011)
Genome Biol.
, vol.12
-
-
Wong, D.1
Teixeira, A.2
Oikonomopoulos, S.3
Humburg, P.4
Lone, I.N.5
Saliba, D.6
Siggers, T.7
Bulyk, M.8
Angelov, D.9
Dimitrov, S.10
-
133
-
-
79959892923
-
Combinatorial binding of transcription factors in the pluripotency control regions of the genome
-
Ferraris, L., Stewart, A.P., Kang, J., DeSimone, A.M., Gemberling, M., Tantin, D. and Fairbrother, W.G. (2011) Combinatorial binding of transcription factors in the pluripotency control regions of the genome. Genome Res., 21, 1055-1064.
-
(2011)
Genome Res.
, vol.21
, pp. 1055-1064
-
-
Ferraris, L.1
Stewart, A.P.2
Kang, J.3
Desimone, A.M.4
Gemberling, M.5
Tantin, D.6
Fairbrother, W.G.7
-
134
-
-
75449100306
-
Integrated approach for the identification of human hepatocyte nuclear factor 4alpha target genes using protein binding microarrays
-
Bolotin, E., Liao, H., Ta, T.C., Yang, C., Hwang-Verslues, W., Evans, J.R., Jiang, T. and Sladek, F.M. (2010) Integrated approach for the identification of human hepatocyte nuclear factor 4alpha target genes using protein binding microarrays. Hepatology, 51, 642-653.
-
(2010)
Hepatology
, vol.51
, pp. 642-653
-
-
Bolotin, E.1
Liao, H.2
Ta, T.C.3
Yang, C.4
Hwang-Verslues, W.5
Evans, J.R.6
Jiang, T.7
Sladek, F.M.8
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