-
1
-
-
0030986188
-
The hardwiring of development: Organization and function of genomic regulatory systems
-
Arnone, M. I. and Davidson, E. H. The hardwiring of development: organization and function of genomic regulatory systems. Development 124, 1851-1864 (1997).
-
(1997)
Development
, vol.124
, pp. 1851-1864
-
-
Arnone, M.I.1
Davidson, E.H.2
-
2
-
-
0024508141
-
Synergistic activation and repression of transcription by Drosophila homeobox proteins
-
Han, K., Levine, M. S. and Manley, J. L. Synergistic activation and repression of transcription by Drosophila homeobox proteins. Cell 56, 573-583 (1989).
-
(1989)
Cell
, vol.56
, pp. 573-583
-
-
Han, K.1
Levine, M.S.2
Manley, J.L.3
-
3
-
-
84901804887
-
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
-
Yáñez-Cuna, J. O. et al. Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Res. 24, 1147-1156 (2014).
-
(2014)
Genome Res.
, vol.24
, pp. 1147-1156
-
-
Yáñez-Cuna, J.O.1
-
4
-
-
0030960672
-
Transcriptional activation by recruitment
-
Ptashne, M. and Gann, A. Transcriptional activation by recruitment. Nature 386, 569-577 (1997).
-
(1997)
Nature
, vol.386
, pp. 569-577
-
-
Ptashne, M.1
Gann, A.2
-
5
-
-
4544352146
-
Activation of the Gal1 gene of yeast by pairs of non-classical activators
-
Cheng, J. X., Gandolfi, M. and Ptashne, M. Activation of the Gal1 gene of yeast by pairs of non-classical activators. Curr. Biol. 14, 1675-1679 (2004).
-
(2004)
Curr. Biol.
, vol.14
, pp. 1675-1679
-
-
Cheng, J.X.1
Gandolfi, M.2
Ptashne, M.3
-
6
-
-
84903942172
-
Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation
-
Keung, A. J., Bashor, C. J., Kiriakov, S., Collins, J. J. and Khalil, A. S. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158, 110-120 (2014).
-
(2014)
Cell
, vol.158
, pp. 110-120
-
-
Keung, A.J.1
Bashor, C.J.2
Kiriakov, S.3
Collins, J.J.4
Khalil, A.S.5
-
7
-
-
0038010275
-
Drosophila homeodomain protein REPO controls glial differentiation by cooperating with ETS and BTB transcription factors
-
Yuasa, Y. et al. Drosophila homeodomain protein REPO controls glial differentiation by cooperating with ETS and BTB transcription factors. Development 130, 2419-2428 (2003).
-
(2003)
Development
, vol.130
, pp. 2419-2428
-
-
Yuasa, Y.1
-
8
-
-
79961072841
-
Functional synthetic Antennapedia genes and the dual roles of YPWM motif and linker size in transcriptional activation and repression
-
Papadopoulos, D. K. et al. Functional synthetic Antennapedia genes and the dual roles of YPWM motif and linker size in transcriptional activation and repression. Proc. Natl Acad. Sci. USA 108, 11959-11964 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 11959-11964
-
-
Papadopoulos, D.K.1
-
9
-
-
0030030902
-
The Eve stripe 2 enhancer employs multiple modes of transcriptional synergy
-
Arnosti, D. N., Barolo, S., Levine, M. and Small, S. The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development 122, 205-214 (1996).
-
(1996)
Development
, vol.122
, pp. 205-214
-
-
Arnosti, D.N.1
Barolo, S.2
Levine, M.3
Small, S.4
-
10
-
-
0034923280
-
A UAS site substitution approach to the in vivo dissection of promoters: Interplay between the GATAb activator and the AEF-1 repressor at a Drosophila ecdysone response unit
-
Brodu, V., Mugat, B., Fichelson, P., Lepesant, J. A. and Antoniewski, C. A UAS site substitution approach to the in vivo dissection of promoters: interplay between the GATAb activator and the AEF-1 repressor at a Drosophila ecdysone response unit. Development 128, 2593-2602 (2001).
-
(2001)
Development
, vol.128
, pp. 2593-2602
-
-
Brodu, V.1
Mugat, B.2
Fichelson, P.3
Lepesant, J.A.4
Antoniewski, C.5
-
11
-
-
82355191645
-
Automated protein-DNA interaction screening of Drosophila regulatory elements
-
Hens, K. et al. Automated protein-DNA interaction screening of Drosophila regulatory elements. Nature Methods 8, 1065-1070 (2011).
-
(2011)
Nature Methods
, vol.8
, pp. 1065-1070
-
-
Hens, K.1
-
12
-
-
84898025687
-
Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin
-
Shlyueva, D. et al. Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin. Mol. Cell 54, 180-192 (2014).
-
(2014)
Mol. Cell
, vol.54
, pp. 180-192
-
-
Shlyueva, D.1
-
13
-
-
84925543087
-
Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation
-
Zabidi, M. A. et al. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature 518, 556-559 (2015).
-
(2015)
Nature
, vol.518
, pp. 556-559
-
-
Zabidi, M.A.1
-
14
-
-
23444458415
-
Transcriptional activation modulated by homopolymeric glutamine and proline stretches
-
Gerber, H. P. et al. Transcriptional activation modulated by homopolymeric glutamine and proline stretches. Science 263, 808-811 (1994).
-
(1994)
Science
, vol.263
, pp. 808-811
-
-
Gerber, H.P.1
-
15
-
-
0037148774
-
Evolution of a transcriptional repression domain in an insect Hox protein
-
Galant, R. and Carroll, S. B. Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415, 910-913 (2002).
-
(2002)
Nature
, vol.415
, pp. 910-913
-
-
Galant, R.1
Carroll, S.B.2
-
16
-
-
84864050448
-
The NSL complex regulates housekeeping genes in Drosophila
-
Lam, K. C. et al. The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet. 8, e1002736 (2012).
-
(2012)
PLoS Genet.
, vol.8
, pp. e1002736
-
-
Lam, K.C.1
-
17
-
-
33747603251
-
TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter
-
Wright, K. J., Marr, M. T. and Tjian, R. TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter. Proc. Natl Acad. Sci. USA 103, 12347-12352 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 12347-12352
-
-
Wright, K.J.1
Marr, M.T.2
Tjian, R.3
-
18
-
-
0037380161
-
Recent advances in understanding chromatin remodeling by Swi/Snf complexes
-
Martens, J. A. and Winston, F. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13, 136-142 (2003).
-
(2003)
Curr. Opin. Genet. Dev.
, vol.13
, pp. 136-142
-
-
Martens, J.A.1
Winston, F.2
-
19
-
-
8844250940
-
IXL, a new subunit of the mammalian Mediator complex, functions as a transcriptional suppressor
-
Wang, Y. et al. IXL, a new subunit of the mammalian Mediator complex, functions as a transcriptional suppressor. Biochem. Biophys. Res. Commun. 325, 1330-1338 (2004).
-
(2004)
Biochem. Biophys. Res. Commun.
, vol.325
, pp. 1330-1338
-
-
Wang, Y.1
-
20
-
-
0346993714
-
A novel docking site on Mediator is critical for activation by VP16 in mammalian cells
-
Mittler, G. et al. A novel docking site on Mediator is critical for activation by VP16 in mammalian cells. EMBO J. 22, 6494-6504 (2003).
-
(2003)
EMBO J.
, vol.22
, pp. 6494-6504
-
-
Mittler, G.1
-
21
-
-
0037716755
-
Independent recruitment in vivo by Gal4 of two complexes required for transcription
-
Bryant, G. O. and Ptashne, M. Independent recruitment in vivo by Gal4 of two complexes required for transcription. Mol. Cell 11, 1301-1309 (2003).
-
(2003)
Mol. Cell
, vol.11
, pp. 1301-1309
-
-
Bryant, G.O.1
Ptashne, M.2
-
22
-
-
84901315026
-
Genetic control of specificity to steroid-triggered responses in Drosophila
-
Ihry, R. J. and Bashirullah, A. Genetic control of specificity to steroid-triggered responses in Drosophila. Genetics 196, 767-780 (2014).
-
(2014)
Genetics
, vol.196
, pp. 767-780
-
-
Ihry, R.J.1
Bashirullah, A.2
-
23
-
-
4344601432
-
MED16 and MED23 of Mediator are coactivators of lipopolysaccharide-and heat-shock-induced transcriptional activators
-
Kim, T. W. et al. MED16 and MED23 of Mediator are coactivators of lipopolysaccharide-and heat-shock-induced transcriptional activators. Proc. Natl Acad. Sci. USA 101, 12153-12158 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 12153-12158
-
-
Kim, T.W.1
-
24
-
-
80054812877
-
The Chriz-Z4 complex recruits JIL-1 to polytene chromosomes, a requirement for interband-specific phosphorylation of H3S10
-
Gan, M., Moebus, S., Eggert, H. and Saumweber, H. The Chriz-Z4 complex recruits JIL-1 to polytene chromosomes, a requirement for interband-specific phosphorylation of H3S10. J. Biosci. 36, 425-438 (2011).
-
(2011)
J. Biosci.
, vol.36
, pp. 425-438
-
-
Gan, M.1
Moebus, S.2
Eggert, H.3
Saumweber, H.4
-
25
-
-
80155171417
-
A protein complex network of Drosophila melanogaster
-
Guruharsha, K. G. et al. A protein complex network of Drosophila melanogaster. Cell 147, 690-703 (2011).
-
(2011)
Cell
, vol.147
, pp. 690-703
-
-
Guruharsha, K.G.1
-
26
-
-
0032478737
-
Interaction of short-range repressors with Drosophila CtBP in the embryo
-
Nibu, Y., Zhang, H. and Levine, M. Interaction of short-range repressors with Drosophila CtBP in the embryo. Science 280, 101-104 (1998).
-
(1998)
Science
, vol.280
, pp. 101-104
-
-
Nibu, Y.1
Zhang, H.2
Levine, M.3
-
27
-
-
0345600247
-
A protein interaction map of Drosophila melanogaster
-
Giot, L. et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736 (2003).
-
(2003)
Science
, vol.302
, pp. 1727-1736
-
-
Giot, L.1
-
28
-
-
84907386652
-
Transcription factor networks in Drosophila melanogaster
-
Rhee, D. Y. et al. Transcription factor networks in Drosophila melanogaster. Cell Rep. 8, 2031-2043 (2014).
-
(2014)
Cell Rep.
, vol.8
, pp. 2031-2043
-
-
Rhee, D.Y.1
-
29
-
-
78651343711
-
DroID 2011: A comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
-
Murali, T. et al. DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res. 39, D736-D743 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D736-D743
-
-
Murali, T.1
-
30
-
-
38049181018
-
A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway
-
Amelio, A. L. et al. A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway. Proc. Natl Acad. Sci. USA 104, 20314-20319 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 20314-20319
-
-
Amelio, A.L.1
-
31
-
-
84891808813
-
FlyBase Consortium. FlyBase 102-advanced approaches to interrogating FlyBase
-
St Pierre, S. E., Ponting, L., Stefancsik, R. and McQuilton, P. FlyBase Consortium. FlyBase 102-advanced approaches to interrogating FlyBase. Nucleic Acids Res. 42, D780-D788 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D780-D788
-
-
St Pierre, S.E.1
Ponting, L.2
Stefancsik, R.3
McQuilton, P.4
-
32
-
-
84891782659
-
Pfam: The protein families database
-
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222-D230 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
-
33
-
-
84874381107
-
Genome-wide quantitative enhancer activity maps identified by STARR-seq
-
Arnold, C. D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074-1077 (2013).
-
(2013)
Science
, vol.339
, pp. 1074-1077
-
-
Arnold, C.D.1
-
34
-
-
77954260412
-
WebPrInSeS: Automated full-length clone sequence identification and verification using highthroughput sequencing data
-
Massouras, A., Decouttere, F., Hens, K. and Deplancke, B. WebPrInSeS: automated full-length clone sequence identification and verification using highthroughput sequencing data. Nucleic Acids Res. 38, W378-W384 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W378-W384
-
-
Massouras, A.1
Decouttere, F.2
Hens, K.3
Deplancke, B.4
-
35
-
-
47749087494
-
Tools for neuroanatomy and neurogenetics in Drosophila
-
Pfeiffer, B. D. et al. Tools for neuroanatomy and neurogenetics in Drosophila. Proc. Natl Acad. Sci. USA 105, 9715-9720 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 9715-9720
-
-
Pfeiffer, B.D.1
-
36
-
-
0015189068
-
The culture of cells from insects and ticks. I. Cultivation of dipteran cells in vitro
-
Schneider, I. The culture of cells from insects and ticks. I. Cultivation of dipteran cells in vitro. Curr. Top. Microbiol. Immunol. 55, 1-12 (1971).
-
(1971)
Curr. Top. Microbiol. Immunol.
, vol.55
, pp. 1-12
-
-
Schneider, I.1
-
37
-
-
0028234384
-
Newly established cell lines from Drosophila larval CNS express neural specific characteristics
-
Ui, K. et al. Newly established cell lines from Drosophila larval CNS express neural specific characteristics. In Vitro Cell. Dev. Biol. Anim. 30, 209-216 (1994).
-
(1994)
Vitro Cell. Dev. Biol. Anim.
, vol.30
, pp. 209-216
-
-
Ui, K.1
-
38
-
-
0014696872
-
Isolation, in tissue culture, of Drosophila melangaster cell lines
-
[transl.]
-
Echalier, G. and Ohanessian, A. Isolation, in tissue culture, of Drosophila melangaster cell lines. C. R. Acad. Sci. Hebd. Seances Acad. Sci. D 268, 1771-1773 (1969) [transl.].
-
(1969)
C. R. Acad. Sci. Hebd. Seances Acad. Sci. D
, vol.268
, pp. 1771-1773
-
-
Echalier, G.1
Ohanessian, A.2
-
39
-
-
70449519397
-
A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila
-
Saito, K. et al. A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila. Nature 461, 1296-1299 (2009).
-
(2009)
Nature
, vol.461
, pp. 1296-1299
-
-
Saito, K.1
-
40
-
-
33747156647
-
A protocol for combined Photinus and Renilla luciferase quantification compatible with protein assays
-
Hampf, M. and Gossen, M. A protocol for combined Photinus and Renilla luciferase quantification compatible with protein assays. Anal. Biochem. 356, 94-99 (2006).
-
(2006)
Anal. Biochem.
, vol.356
, pp. 94-99
-
-
Hampf, M.1
Gossen, M.2
-
42
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-W208 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W202-W208
-
-
Bailey, T.L.1
-
43
-
-
0031743421
-
Profile hidden Markov models
-
Eddy, S. R. Profile hidden Markov models. Bioinformatics 14, 755-763 (1998).
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
44
-
-
84859051901
-
ELM-the database of eukaryotic linear motifs
-
Dinkel, H. et al. ELM-the database of eukaryotic linear motifs. Nucleic Acids Res. 40, D242-D251 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D242-D251
-
-
Dinkel, H.1
-
45
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25-29 (2000).
-
(2000)
Nature Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
46
-
-
0012252471
-
Systematic determination of patterns of gene expression during Drosophila embryogenesis
-
Tomancak, P. et al. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 3, (2002).
-
(2002)
Genome Biol.
, vol.3
-
-
Tomancak, P.1
-
47
-
-
78651321628
-
FlyFactorSurvey: A database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
-
Zhu, L. J. et al. FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res. 39, D111-D117 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D111-D117
-
-
Zhu, L.J.1
-
48
-
-
36049018312
-
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
-
Stark, A. et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219-232 (2007).
-
(2007)
Nature
, vol.450
, pp. 219-232
-
-
Stark, A.1
-
49
-
-
0344551898
-
Multiclass spectral clustering
-
IEEE
-
Yu, S. X. and Shi, J. Multiclass spectral clustering. In ICCV, 313-319 (IEEE, 2003).
-
(2003)
ICCV
, pp. 313-319
-
-
Yu, S.X.1
Shi, J.2
-
50
-
-
80555140075
-
Scikit-learn: Machine learning in Python
-
Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Machine Learn. Res. 12 2825-2830 (2011).
-
(2011)
J. Machine Learn. Res.
, vol.12
, pp. 2825-2830
-
-
Pedregosa, F.1
-
53
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
The modENCODE Consortium et al.
-
The modENCODE Consortium et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797 (2010).
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
-
54
-
-
78951477322
-
Refinement of tools for targeted gene expression in Drosophila
-
Pfeiffer, B. D. et al. Refinement of tools for targeted gene expression in Drosophila. Genetics 186, 735-755 (2010).
-
(2010)
Genetics
, vol.186
, pp. 735-755
-
-
Pfeiffer, B.D.1
|