-
1
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
Babu, M. M., Luscombe, N. M., Aravind, L., et al. 2004. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14, 283-291
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 283-291
-
-
Babu, M.M.1
Luscombe, N.M.2
Aravind, L.3
-
2
-
-
33745620176
-
Integrated assessment and prediction of transcription factor binding
-
Beyer, A., Workman, C., Hollunder, J., et al. 2006. Integrated assessment and prediction of transcription factor binding. PLoS Comput. Biol. 2, e70
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. e70
-
-
Beyer, A.1
Workman, C.2
Hollunder, J.3
-
3
-
-
0032831938
-
Association of the cell cycle transcription factor mbp1 with the skn7 response regulator in budding yeast
-
Bouquin, N., Johnson, A. L., Morgan, B. A., and Johnston, L. H. 1999. Association of the cell cycle transcription factor mbp1 with the skn7 response regulator in budding yeast. Mol. Biol. Cell 10, 3389-3400
-
(1999)
Mol. Biol. Cell
, vol.10
, pp. 3389-3400
-
-
Bouquin, N.1
Johnson, A.L.2
Morgan, B.A.3
Johnston, L.H.4
-
4
-
-
0022328481
-
A eukaryotic transcriptional activator bearing the dna specificity of a prokaryotic repressor
-
Brent, R., and Ptashne, M. 1985. A eukaryotic transcriptional activator bearing the dna specificity of a prokaryotic repressor. Cell 43, 729-736
-
(1985)
Cell
, vol.43
, pp. 729-736
-
-
Brent, R.1
Ptashne, M.2
-
5
-
-
0034617294
-
Adenovirus e1a down-regulates lmp2 transcription by interfering with the binding of stat1 to irf1
-
Chatterjee-Kishore, M., van den Akker, F., and Stark, G. R. 2000. Adenovirus e1a down-regulates lmp2 transcription by interfering with the binding of stat1 to irf1. J. Biol. Chem. 275, 20406-20411
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 20406-20411
-
-
Chatterjee-Kishore, M.1
Van Den Akker, F.2
Stark, G.R.3
-
6
-
-
33745432883
-
Regulation of mating and filamentation genes by two distinct ste12 complexes in saccharomyces cerevisiae
-
Chou, S., Lane, S., and Liu, H. 2006. Regulation of mating and filamentation genes by two distinct ste12 complexes in saccharomyces cerevisiae. Mol. Cell. Biol. 26, 4794-4805
-
(2006)
Mol. Cell. Biol.
, vol.26
, pp. 4794-4805
-
-
Chou, S.1
Lane, S.2
Liu, H.3
-
7
-
-
84865790047
-
An integrated encyclopedia of dna elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium. 2012. An integrated encyclopedia of dna elements in the human genome. Nature 489, 57-74
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
8
-
-
41849115550
-
A semi-supervised method for predicting transcription factor-gene interactions in escherichia coli
-
Ernst, J., Beg, Q. K., Kay, K. A., et al. 2008. A semi-supervised method for predicting transcription factor-gene interactions in escherichia coli. PLoS Comput. Biol. 4, e1000044
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. e1000044
-
-
Ernst, J.1
Beg, Q.K.2
Kay, K.A.3
-
9
-
-
33846521053
-
Reconstructing dynamic regulatory maps
-
Ernst, J., Vainas, O., Harbison, C., et al. 2007. Reconstructing dynamic regulatory maps. Mol. Syst. Biol., 3, 74
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 74
-
-
Ernst, J.1
Vainas, O.2
Harbison, C.3
-
10
-
-
84857862981
-
Contribution of a tank-binding kinase 1-interferon (ifn) regulatory factor 7 pathway to ifn-c-induced gene expression
-
Farlik, M., Rapp, B., Marie, I., et al. 2012. Contribution of a tank-binding kinase 1-interferon (ifn) regulatory factor 7 pathway to ifn-c-induced gene expression. Mol. Cell. Biol. 32, 1032-1043
-
(2012)
Mol. Cell. Biol.
, vol.32
, pp. 1032-1043
-
-
Farlik, M.1
Rapp, B.2
Marie, I.3
-
12
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A., Spellman, P., Kao, C., et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Sci. Signal. 11, 4241
-
(2000)
Sci. Signal.
, vol.11
, pp. 4241
-
-
Gasch, A.1
Spellman, P.2
Kao, C.3
-
13
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz, J., Siggia, E. D., and Cohen, B. A. 2008. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457, 215-218
-
(2008)
Nature
, vol.457
, pp. 215-218
-
-
Gertz, J.1
Siggia, E.D.2
Cohen, B.A.3
-
14
-
-
84879979131
-
Identifying proteins controlling key disease signaling pathways
-
Gitter, A., and Bar-Joseph, Z. 2013. Identifying proteins controlling key disease signaling pathways. Bioinformatics 29, i227-i236
-
(2013)
Bioinformatics
, vol.29
, pp. i227-i236
-
-
Gitter, A.1
Bar-Joseph, Z.2
-
15
-
-
84873392956
-
Linking the signaling cascades and dynamic regulatory networks controlling stress responses
-
Gitter, A., Carmi, M., Barkai, N., and Bar-Joseph, Z. 2013. Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res., 23, 365-376
-
(2013)
Genome Res.
, vol.23
, pp. 365-376
-
-
Gitter, A.1
Carmi, M.2
Barkai, N.3
Bar-Joseph, Z.4
-
16
-
-
0024380583
-
Structurally similar but functionally distinct factors, irf-1 and irf-2, bind to the same regulatory elements of ifn and ifn-inducible genes
-
Harada, H., Fujita, T., Miyamoto, M., et al. 1989. Structurally similar but functionally distinct factors, irf-1 and irf-2, bind to the same regulatory elements of ifn and ifn-inducible genes. Cell 58, 729-739
-
(1989)
Cell
, vol.58
, pp. 729-739
-
-
Harada, H.1
Fujita, T.2
Miyamoto, M.3
-
17
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C. T., Gordon, D. B., Lee, T. I., et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
-
18
-
-
80052320333
-
Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection
-
Huang, Y., Zaas, A. K., Rao, A., et al. 2011. Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection. PLoS Genet. 7, e1002234
-
(2011)
PLoS Genet.
, vol.7
, pp. e1002234
-
-
Huang, Y.1
Zaas, A.K.2
Rao, A.3
-
19
-
-
84879421185
-
The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment
-
Laurenti, E., Doulatov, S., Zandi, S., et al. 2013. The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment. Nat. Immunol. 14, 756-763
-
(2013)
Nat. Immunol.
, vol.14
, pp. 756-763
-
-
Laurenti, E.1
Doulatov, S.2
Zandi, S.3
-
20
-
-
0141792394
-
Correlating protein-dna and protein-protein interaction networks
-
Manke, T., Bringas, R., and Vingron, M. 2003. Correlating protein-dna and protein-protein interaction networks. J. Mol. Biol., 333, 75-85
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 75-85
-
-
Manke, T.1
Bringas, R.2
Vingron, M.3
-
21
-
-
80054088836
-
Dissecting the retinoid-induced differentiation of f9 embryonal stem cells by integrative genomics
-
Mendoza-Parra, M. A., Walia, M., Sankar, M., and Gronemeyer, H. 2011. Dissecting the retinoid-induced differentiation of f9 embryonal stem cells by integrative genomics. Mol. Syst. Biol. 7, 538
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 538
-
-
Mendoza-Parra, M.A.1
Walia, M.2
Sankar, M.3
Gronemeyer, H.4
-
22
-
-
24144495286
-
Identifying cooperative transcriptional regulations using protein-protein interactions
-
Nagamine, N., Kawada, Y., and Sakakibara, Y. 2005. Identifying cooperative transcriptional regulations using protein-protein interactions. Nucleic Acids Res. 33, 4828-4837
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 4828-4837
-
-
Nagamine, N.1
Kawada, Y.2
Sakakibara, Y.3
-
23
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
Pilpel, Y., Sudarsanam, P., and Church, G. M. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29, 153-159
-
(2001)
Nat. Genet.
, vol.29
, pp. 153-159
-
-
Pilpel, Y.1
Sudarsanam, P.2
Church, G.M.3
-
24
-
-
0033916138
-
The skn7 response regulator of saccharomyces cerevisiae interacts with hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress
-
Raitt, D. C., Johnson, A. L., Erkine, A. M., et al. 2000. The skn7 response regulator of saccharomyces cerevisiae interacts with hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress. Mol. Biol. Cell 11, 2335-2347
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 2335-2347
-
-
Raitt, D.C.1
Johnson, A.L.2
Erkine, A.M.3
-
25
-
-
77955817629
-
Comprehensive reanalysis of transcription factor knockout expression data in saccharomyces cerevisiae reveals many new targets
-
Reimand, J., Vaquerizas, J. M., Todd, A. E., et al. 2010. Comprehensive reanalysis of transcription factor knockout expression data in saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res. 38, 4768-4777
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 4768-4777
-
-
Reimand, J.1
Vaquerizas, J.M.2
Todd, A.E.3
-
26
-
-
0034704248
-
Genome-wide location and function of dna binding proteins
-
Ren, B., Robert, F., Wyrick, J. J., et al. 2000. Genome-wide location and function of dna binding proteins. Science 290, 2306-2309
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
-
27
-
-
66449128185
-
Specific and global regulation of mrna stability during osmotic stress in saccharomyces cerevisiae
-
Romero-Santacreu, L., Moreno, J., Pérez-Ortín, J., and Alepuz, P. 2009. Specific and global regulation of mrna stability during osmotic stress in saccharomyces cerevisiae. RNA 15, 1110-1120
-
(2009)
RNA
, vol.15
, pp. 1110-1120
-
-
Romero-Santacreu, L.1
Moreno, J.2
Pérez-Ortn, J.3
Alepuz, P.4
-
28
-
-
78650331647
-
Identification of functional elements and regulatory circuits by drosophila modencode
-
Roy, S., Ernst, J., Kharchenko, P. V., et al. 2010. Identification of functional elements and regulatory circuits by drosophila modencode. Science 330, 1787-1797
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
Roy, S.1
Ernst, J.2
Kharchenko, P.V.3
-
29
-
-
34347336512
-
Potential interface between ribosomal protein production and pre-rrna processing
-
Rudra, D., Mallick, J., Zhao, Y., and Warner, J. R. 2007. Potential interface between ribosomal protein production and pre-rrna processing. Mol. Cell. Biol. 27, 4815-4824
-
(2007)
Mol. Cell. Biol.
, vol.27
, pp. 4815-4824
-
-
Rudra, D.1
Mallick, J.2
Zhao, Y.3
Warner, J.R.4
-
30
-
-
84864921682
-
Drem 2. 0: Improved reconstruction of dynamic regulatory networks from time-series expression data
-
Schulz, M., Devanny, W., Gitter, A., et al. 2012. Drem 2. 0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst. Biol. 6, 104
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 104
-
-
Schulz, M.1
Devanny, W.2
Gitter, A.3
-
31
-
-
84884599189
-
Reconstructing dynamic microrna-regulated interaction networks
-
Schulz, M. H., Pandit, K. V., Cardenas, C. L. L., et al. 2013. Reconstructing dynamic microrna-regulated interaction networks. Proc. Natl. Acad. Sci. USA 110, 15686-15691
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 15686-15691
-
-
Schulz, M.H.1
Pandit, K.V.2
Cardenas, C.L.L.3
-
32
-
-
40449124692
-
Systematic functional characterization of cis-regulatory motifs in human core promoters
-
Sinha, S., Adler, A. S., Field, Y., et al. 2008. Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res. 18, 477-488
-
(2008)
Genome Res.
, vol.18
, pp. 477-488
-
-
Sinha, S.1
Adler, A.S.2
Field, Y.3
-
33
-
-
33644873184
-
Biogrid: A general repository for interaction datasets
-
Stark, C., Breitkreutz, B.-J., Reguly, T., et al. 2006. Biogrid: a general repository for interaction datasets. Nucleic Acids Res. 34, D535-D539
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D535-D539
-
-
Stark, C.1
Breitkreutz, B.-J.2
Reguly, T.3
-
34
-
-
33644855121
-
Genome-wide prediction and characterization of interactions between transcription factors in saccharomyces cerevisiae
-
Yu, X., Lin, J., Masuda, T., et al. (2006b). Genome-wide prediction and characterization of interactions between transcription factors in saccharomyces cerevisiae. Nucleic Acids Res. 34, 917-927
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 917-927
-
-
Yu, X.1
Lin, J.2
Masuda, T.3
-
35
-
-
33750217984
-
Computational analysis of tissue-specific combinatorial gene regulation: Predicting interaction between transcription factors in human tissues
-
Yu, X., Lin, J., Zack, D. J., and Qian, J. (2006a). Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res. 34, 4925-4936
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 4925-4936
-
-
Yu, X.1
Lin, J.2
Zack, D.J.3
Qian, J.4
-
36
-
-
0032549745
-
Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
-
Yuh, C.-H., Bolouri, H., and Davidson, E. H. 1998. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279, 1896-1902
-
(1998)
Science
, vol.279
, pp. 1896-1902
-
-
Yuh, C.-H.1
Bolouri, H.2
Davidson, E.H.3
-
37
-
-
79960567195
-
Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque
-
Zinman, G., Brower-Sinning, R., Emeche, C. H., et al. 2011. Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PloS One 6, e22401
-
(2011)
PloS One
, vol.6
, pp. e22401
-
-
Zinman, G.1
Brower-Sinning, R.2
Emeche, C.H.3
-
38
-
-
70449132583
-
Combinatorial binding predicts spatio-temporal cis-regulatory activity
-
Zinzen, R. P., Girardot, C., Gagneur, J., et al. 2009. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nat
-
(2009)
Nat
-
-
Zinzen, R.P.1
Girardot, C.2
Gagneur, J.3
|