-
1
-
-
77956495708
-
Transcriptional enhancers in animal development and evolution
-
Levine, M. Transcriptional enhancers in animal development and evolution. Curr. Biol. 20, R754-R763 (2010).
-
(2010)
Curr. Biol.
, vol.20
-
-
Levine, M.1
-
2
-
-
84905657230
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
The modENCODE Consortium
-
The modENCODE Consortium. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 489, 57-74 (2010).
-
(2010)
Science
, vol.489
, pp. 57-74
-
-
-
3
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
4
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502 (2006).
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
-
5
-
-
84868114222
-
A GAL4-driver line resource for Drosophila neurobiology
-
Jenett, A. et al. A GAL4-driver line resource for Drosophila neurobiology. Cell Rep. 2, 991-1001 (2012).
-
(2012)
Cell Rep.
, vol.2
, pp. 991-1001
-
-
Jenett, A.1
-
6
-
-
84868097251
-
A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS
-
Manning, L. et al. A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS. Cell Rep. 2, 1002-1013 (2012).
-
(2012)
Cell Rep.
, vol.2
, pp. 1002-1013
-
-
Manning, L.1
-
7
-
-
84868088171
-
A survey of 6, 300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster
-
Jory, A. et al. A survey of 6, 300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Rep. 2, 1014-1024 (2012).
-
(2012)
Cell Rep.
, vol.2
, pp. 1014-1024
-
-
Jory, A.1
-
8
-
-
70449132583
-
Combinatorial binding predicts spatio-temporal cis-regulatory activity
-
Zinzen, R. P., Girardot, C., Gagneur, J., Braun, M. & Furlong, E. E. M. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462, 65-70 (2009).
-
(2009)
Nature
, vol.462
, pp. 65-70
-
-
Zinzen, R.P.1
Girardot, C.2
Gagneur, J.3
Braun, M.4
Furlong, E.E.M.5
-
9
-
-
84871693720
-
Deciphering the transcriptional cis-regulatory code
-
Yánez-Cuna, J. O., Kvon, E. Z. & Stark, A. Deciphering the transcriptional cis-regulatory code. Trends Genet. 29, 11-22 (2013).
-
(2013)
Trends Genet.
, vol.29
, pp. 11-22
-
-
Yánez-Cuna, J.O.1
Kvon, E.Z.2
Stark, A.3
-
10
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009).
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
-
11
-
-
84864462544
-
Amap ofthe cis-regulatory sequencesin the mouse genome
-
Shen, Y. et al. Amap ofthe cis-regulatory sequencesin the mouse genome. Nature 448, 116-120 (2012).
-
(2012)
Nature
, vol.448
, pp. 116-120
-
-
Shen, Y.1
-
12
-
-
76949094155
-
Developmental gene regulationin the era ofgenomics
-
Zeitlinger, J. & Stark, A. Developmental gene regulationin the era ofgenomics. Dev. Biol. 339, 230-239 (2010).
-
(2010)
Dev. Biol.
, vol.339
, pp. 230-239
-
-
Zeitlinger, J.1
Stark, A.2
-
13
-
-
0034708613
-
A brief history of Drosophila's contributions to genome research
-
Rubin, G. M. & Lewis, E. B. A brief history of Drosophila's contributions to genome research. Science 287, 2216-2218 (2000).
-
(2000)
Science
, vol.287
, pp. 2216-2218
-
-
Rubin, G.M.1
Lewis, E.B.2
-
14
-
-
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, RESEARCH0088 (2002).
-
(2002)
Genome Biol.
, vol.3
-
-
Tomancak, P.1
-
15
-
-
78651335916
-
REDfly v3. 0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila
-
Gallo, S. M. et al. REDfly v3. 0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res. 39, D118-D123 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Gallo, S.M.1
-
16
-
-
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
-
18
-
-
79953043801
-
The developmental transcriptome of Drosophila melanogaster
-
Graveley, B. R. et al. The developmental transcriptome of Drosophila melanogaster. Nature 471, 473-479 (2011).
-
(2011)
Nature
, vol.471
, pp. 473-479
-
-
Graveley, B.R.1
-
19
-
-
84856239091
-
Tissue-specific analysis of chromatin state identifies temporal signaturesofenhancer activity during embryonic development
-
Bonn, S. et al. Tissue-specific analysis of chromatin state identifies temporal signaturesofenhancer activity during embryonic development. Nature Genet. 44, 148-156 (2012).
-
(2012)
Nature Genet.
, vol.44
, pp. 148-156
-
-
Bonn, S.1
-
20
-
-
79955760882
-
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
-
Thomas, S. et al. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 12, R43 (2011).
-
(2011)
Genome Biol.
, vol.12
-
-
Thomas, S.1
-
21
-
-
84856747483
-
Three-dimensional folding and functional organization principles of the Drosophila genome
-
Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458-472 (2012).
-
(2012)
Cell
, vol.148
, pp. 458-472
-
-
Sexton, T.1
-
22
-
-
76749089660
-
A comprehensive map of insulator elements for the Drosophila genome
-
Nègre, N. et al. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 6, e1000814 (2010).
-
(2010)
PLoS Genet.
, vol.6
-
-
Nègre, N.1
-
23
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Drosophila 12 Genomes Consortium
-
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (2007).
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
-
24
-
-
51149097760
-
Shadow enhancers as a source of evolutionary novelty
-
Hong, J.-W., Hendrix, D. A. & Levine, M. S. Shadow enhancers as a source of evolutionary novelty. Science 321, 1314 (2008)
-
(2008)
Science
, vol.321
, pp. 1314
-
-
Hong, J.-W.1
Hendrix, D.A.2
Levine, M.S.3
-
25
-
-
0037047146
-
Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex
-
Calhoun, V. C., Stathopoulos, A. & Levine, M. Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex. Proc. Natl Acad. Sci. USA 99, 9243-9247 (2002).
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 9243-9247
-
-
Calhoun, V.C.1
Stathopoulos, A.2
Levine, M.3
-
26
-
-
0025943096
-
Expression of the cut locus in the Drosophila wing margin is required for cell type specification and is regulated by a distant enhancer
-
Jack, J., Dorsett, D., Delotto, Y. & Liu, S. Expression of the cut locus in the Drosophila wing margin is required for cell type specification and is regulated by a distant enhancer. Development 113, 735-747 (1991).
-
(1991)
Development
, vol.113
, pp. 735-747
-
-
Jack, J.1
Dorsett, D.2
Delotto, Y.3
Liu, S.4
-
27
-
-
79953162491
-
Geneexpressionintimeandspace: Additivevshierarchical organization of cis-regulatory regions
-
Maeda, R. K. & Karch, F. Geneexpressionintimeandspace: additivevshierarchical organization of cis-regulatory regions. Curr. Opin. Genet. Dev. 21, 187-193 (2011).
-
(2011)
Curr. Opin. Genet. Dev.
, vol.21
, pp. 187-193
-
-
Maeda, R.K.1
Karch, F.2
-
28
-
-
84875249885
-
An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape
-
Marinić, M., Aktas, T., Ruf, S. & Spitz, F. An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Dev. Cell 24, 530-542 (2013).
-
(2013)
Dev. Cell
, vol.24
, pp. 530-542
-
-
Marinić, M.1
Aktas, T.2
Ruf, S.3
Spitz, F.4
-
29
-
-
84865257761
-
Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
-
Yánez-Cuna, J. O., Dinh, H. Q., Kvon, E. Z., Shlyueva, D. & Stark, A. Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding. Genome Res. 22, 2018-2030 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 2018-2030
-
-
Yánez-Cuna, J.O.1
Dinh, H.Q.2
Kvon, E.Z.3
Shlyueva, D.4
Stark, A.5
-
30
-
-
56749183626
-
The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila
-
Liang, H.-L. et al. The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila. Nature 456, 400-403 (2008).
-
(2008)
Nature
, vol.456
, pp. 400-403
-
-
Liang, H.-L.1
-
31
-
-
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
-
32
-
-
64849106452
-
Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos
-
Weiszmann, R., Hammonds, A. S. & Celniker, S. E. Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos. Nature Protocols 4, 605-618 (2009).
-
(2009)
Nature Protocols
, vol.4
, pp. 605-618
-
-
Weiszmann, R.1
Hammonds, A.S.2
Celniker, S.E.3
-
33
-
-
49649125105
-
Fluorescent in situ hybridization protocols in Drosophila embryos and tissues
-
Lécuyer, E., Parthasarathy, N. & Krause, H. M. Fluorescent in situ hybridization protocols in Drosophila embryos and tissues. Methods Mol. Biol. 420, 289-302 (2008).
-
(2008)
Methods Mol. Biol.
, vol.420
, pp. 289-302
-
-
Lécuyer, E.1
Parthasarathy, N.2
Krause, H.M.3
-
34
-
-
84860503075
-
HOT regions functionaspatterned developmental enhancers and haveadistinct cis-regulatory signature
-
Kvon, E. Z., Stampfel, G., Yánez-Cuna, J. O., Dickson, B. J. & Stark, A. HOT regions functionaspatterned developmental enhancers and haveadistinct cis-regulatory signature. Genes Dev. 26, 908-913 (2012).
-
(2012)
Genes Dev.
, vol.26
, pp. 908-913
-
-
Kvon, E.Z.1
Stampfel, G.2
Yánez-Cuna, J.O.3
Dickson, B.J.4
Stark, A.5
-
35
-
-
84871844925
-
DNAregionsboundatlow occupancybytranscription factors do not drive patterned reporter gene expression in Drosophila
-
Fisher, W. W. et al. DNAregionsboundatlow occupancybytranscription factors do not drive patterned reporter gene expression in Drosophila. Proc. Natl Acad. Sci. USA 109, 21330-21335 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 21330-21335
-
-
Fisher, W.W.1
-
36
-
-
76149094177
-
Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape
-
Frise, E., Hammonds, A. S. & Celniker, S. E. Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Mol. Syst. Biol. 6, 345 (2010).
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 345
-
-
Frise, E.1
Hammonds, A.S.2
Celniker, S.E.3
-
37
-
-
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
-
38
-
-
84891808813
-
The FlyBase Consortium. FlyBase 102-advanced approaches to interrogating FlyBase
-
St Pierre, S. E., Ponting, L., Stefancsik, R. & McQuilton, P. The FlyBase Consortium. FlyBase 102-advanced approaches to interrogating FlyBase. Nucleic Acids Res. 42, D780-D788 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
St Pierre, S.E.1
Ponting, L.2
Stefancsik, R.3
McQuilton, P.4
-
39
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
40
-
-
0026744792
-
Regulation of even-skipped stripe2 inthe Drosophila embryo
-
Small, S., Blair, A. & Levine, M. Regulation of even-skipped stripe2 inthe Drosophila embryo. EMBO J. 11, 4047-4057 (1992).
-
(1992)
EMBO J.
, vol.11
, pp. 4047-4057
-
-
Small, S.1
Blair, A.2
Levine, M.3
-
41
-
-
33846112470
-
VISTA Enhancer Browser-a database of tissue-specific human enhancers
-
Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88-D92 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Visel, A.1
Minovitsky, S.2
Dubchak, I.3
Pennacchio, L.A.4
-
43
-
-
1642289044
-
Coordinate enhancers share common organizational features in the Drosophila genome
-
Erives, A. & Levine, M. Coordinate enhancers share common organizational features in the Drosophila genome. Proc. Natl Acad. Sci. USA 101, 3851-3856 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 3851-3856
-
-
Erives, A.1
Levine, M.2
-
44
-
-
80052007879
-
Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo
-
Perry, M. W., Boettiger, A. N. & Levine, M. Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc. Natl Acad. Sci. USA 108, 13570-13575 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 13570-13575
-
-
Perry, M.W.1
Boettiger, A.N.2
Levine, M.3
-
45
-
-
0035872950
-
Pannier is a transcriptional target and partner of Tinman during Drosophila cardiogenesis
-
Gajewski, K. et al. Pannier is a transcriptional target and partner of Tinman during Drosophila cardiogenesis. Dev. Biol. 233, 425-436 (2001).
-
(2001)
Dev. Biol.
, vol.233
, pp. 425-436
-
-
Gajewski, K.1
-
46
-
-
80055073174
-
Zelda bindinginthe early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition
-
Harrison, M. M., Li, X.-Y., Kaplan, T., Botchan, M. R. & Eisen, M. B. Zelda bindinginthe early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLoS Genet. 7, e1002266 (2011).
-
(2011)
PLoS Genet.
, vol.7
-
-
Harrison, M.M.1
Li, X.-Y.2
Kaplan, T.3
Botchan, M.R.4
Eisen, M.B.5
-
47
-
-
80055074510
-
Temporal coordination of gene networks by Zelda in the early Drosophila embryo
-
Nien, C.-Y. et al. Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLoS Genet. 7, e1002339 (2011).
-
(2011)
PLoS Genet.
, vol.7
-
-
Nien, C.-Y.1
-
48
-
-
0026314893
-
The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development
-
Nambu, J. R., Lewis, J. O., Wharton, K. A. & Crews, S. T. The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development. Cell 67, 1157-1167 (1991).
-
(1991)
Cell
, vol.67
, pp. 1157-1167
-
-
Nambu, J.R.1
Lewis, J.O.2
Wharton, K.A.3
Crews, S.T.4
-
49
-
-
17044431033
-
The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila
-
Ochoa-Espinosa, A. et al. The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. Proc. Natl Acad. Sci. USA 102, 4960-4965 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4960-4965
-
-
Ochoa-Espinosa, A.1
-
50
-
-
0029890668
-
Twist: A myogenic switch in Drosophila
-
Baylies, M. K. & Bate, M. twist: a myogenic switch in Drosophila. Science 272, 1481-1484 (1996).
-
(1996)
Science
, vol.272
, pp. 1481-1484
-
-
Baylies, M.K.1
Bate, M.2
-
51
-
-
0028087974
-
D-mef2: A Drosophila mesoderm-specific MADS box-containing gene with a biphasic expressionprofile duringembryogenesis
-
Nguyen, H. T., Bodmer, R., Abmayr, S. M., McDermott, J. C. & Spoerel, N. A. D-mef2: a Drosophila mesoderm-specific MADS box-containing gene with a biphasic expressionprofile duringembryogenesis. Proc. NatlAcad. Sci. USA 91, 7520-7524 (1994).
-
(1994)
Proc. NatlAcad. Sci. USA
, vol.91
, pp. 7520-7524
-
-
Nguyen, H.T.1
Bodmer, R.2
Abmayr, S.M.3
McDermott, J.C.4
Spoerel, N.A.5
|