-
1
-
-
84865249952
-
Transcription factors: from enhancer binding to developmental control
-
Spitz F, Furlong EE, (2012) Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 13: 613-626.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 613-626
-
-
Spitz, F.1
Furlong, E.E.2
-
2
-
-
84856704764
-
A transcription factor collective defines cardiac cell fate and reflects lineage history
-
Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, et al. (2012) A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell 148: 473-486.
-
(2012)
Cell
, vol.148
, pp. 473-486
-
-
Junion, G.1
Spivakov, M.2
Girardot, C.3
Braun, M.4
Gustafson, E.H.5
-
3
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, et al. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27.
-
(2008)
PLoS Biol
, vol.6
-
-
Li, X.Y.1
MacArthur, S.2
Bourgon, R.3
Nix, D.4
Pollard, D.A.5
-
4
-
-
68849103482
-
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
-
MacArthur S, Li XY, Li J, Brown JB, Chu HC, et al. (2009) Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 10: R80.
-
(2009)
Genome Biol
, vol.10
-
-
MacArthur, S.1
Li, X.Y.2
Li, J.3
Brown, J.B.4
Chu, H.C.5
-
5
-
-
33847271755
-
A core transcriptional network for early mesoderm development in Drosophila melanogaster
-
Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, et al. (2007) A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev 21: 436-449.
-
(2007)
Genes Dev
, vol.21
, pp. 436-449
-
-
Sandmann, T.1
Girardot, C.2
Brehme, M.3
Tongprasit, W.4
Stolc, V.5
-
6
-
-
33847189172
-
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
-
Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, et al. (2007) Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev 21: 385-390.
-
(2007)
Genes Dev
, vol.21
, pp. 385-390
-
-
Zeitlinger, J.1
Zinzen, R.P.2
Stark, A.3
Kellis, M.4
Zhang, H.5
-
7
-
-
70449132583
-
Combinatorial binding predicts spatio-temporal cis-regulatory activity
-
Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE, (2009) Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462: 65-70.
-
(2009)
Nature
, vol.462
, pp. 65-70
-
-
Zinzen, R.P.1
Girardot, C.2
Gagneur, J.3
Braun, M.4
Furlong, E.E.5
-
8
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
-
9
-
-
77956641239
-
ChIP-Seq identification of weakly conserved heart enhancers
-
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, et al. (2010) ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42: 806-810.
-
(2010)
Nat Genet
, vol.42
, pp. 806-810
-
-
Blow, M.J.1
McCulley, D.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
-
10
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Bernstein, B.E.1
Birney, E.2
Dunham, I.3
Green, E.D.4
Gunter, C.5
-
11
-
-
84856239091
-
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
-
Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, et al. (2012) Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44: 148-156.
-
(2012)
Nat Genet
, vol.44
, pp. 148-156
-
-
Bonn, S.1
Zinzen, R.P.2
Girardot, C.3
Gustafson, E.H.4
Perez-Gonzalez, A.5
-
12
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
-
13
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
Hon, G.C.2
Hawkins, R.D.3
Kheradpour, P.4
Stark, A.5
-
14
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311-318.
-
(2007)
Nat Genet
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
-
15
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, 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
Kheradpour, P.4
Negre, N.5
-
16
-
-
84874416769
-
Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network
-
Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, et al. (2012) Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network. Proc Natl Acad Sci U S A 109: 20768-20773.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 20768-20773
-
-
Busser, B.W.1
Huang, D.2
Rogacki, K.R.3
Lane, E.A.4
Shokri, L.5
-
17
-
-
0034730326
-
Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors
-
Halfon MS, Carmena A, Gisselbrecht S, Sackerson CM, Jimenez F, et al. (2000) Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors. Cell 103: 63-74.
-
(2000)
Cell
, vol.103
, pp. 63-74
-
-
Halfon, M.S.1
Carmena, A.2
Gisselbrecht, S.3
Sackerson, C.M.4
Jimenez, F.5
-
18
-
-
0026722283
-
dorsal-twist interactions establish snail expression in the presumptive mesoderm of the Drosophila embryo
-
Ip YT, Park RE, Kosman D, Yazdanbakhsh K, Levine M, (1992) dorsal-twist interactions establish snail expression in the presumptive mesoderm of the Drosophila embryo. Genes Dev 6: 1518-1530.
-
(1992)
Genes Dev
, vol.6
, pp. 1518-1530
-
-
Ip, Y.T.1
Park, R.E.2
Kosman, D.3
Yazdanbakhsh, K.4
Levine, M.5
-
19
-
-
80052477170
-
Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer
-
Struffi P, Corado M, Kaplan L, Yu D, Rushlow C, et al. (2011) Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer. Development 138: 4291-4299.
-
(2011)
Development
, vol.138
, pp. 4291-4299
-
-
Struffi, P.1
Corado, M.2
Kaplan, L.3
Yu, D.4
Rushlow, C.5
-
20
-
-
77950580571
-
Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer
-
Swanson CI, Evans NC, Barolo S, (2010) Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer. Dev Cell 18: 359-370.
-
(2010)
Dev Cell
, vol.18
, pp. 359-370
-
-
Swanson, C.I.1
Evans, N.C.2
Barolo, S.3
-
21
-
-
0037016730
-
Physical interaction of the activator protein-1 factors c-Fos and c-Jun with Cbfa1 for collagenase-3 promoter activation
-
D'Alonzo RC, Selvamurugan N, Karsenty G, Partridge NC, (2002) Physical interaction of the activator protein-1 factors c-Fos and c-Jun with Cbfa1 for collagenase-3 promoter activation. J Biol Chem 277: 816-822.
-
(2002)
J Biol Chem
, vol.277
, pp. 816-822
-
-
D'Alonzo, R.C.1
Selvamurugan, N.2
Karsenty, G.3
Partridge, N.C.4
-
22
-
-
1642289044
-
Coordinate enhancers share common organizational features in the Drosophila genome
-
Erives A, Levine M, (2004) Coordinate enhancers share common organizational features in the Drosophila genome. Proc Natl Acad Sci U S A 101: 3851-3856.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 3851-3856
-
-
Erives, A.1
Levine, M.2
-
23
-
-
0031801013
-
Multiple DNA elements for sterol regulatory element-binding protein and NF-Y are responsible for sterol-regulated transcription of the genes for human 3-hydroxy-3-methylglutaryl coenzyme A synthase and squalene synthase
-
Inoue J, Sato R, Maeda M, (1998) Multiple DNA elements for sterol regulatory element-binding protein and NF-Y are responsible for sterol-regulated transcription of the genes for human 3-hydroxy-3-methylglutaryl coenzyme A synthase and squalene synthase. J Biochem 123: 1191-1198.
-
(1998)
J Biochem
, vol.123
, pp. 1191-1198
-
-
Inoue, J.1
Sato, R.2
Maeda, M.3
-
24
-
-
34250017968
-
An atomic model of the interferon-beta enhanceosome
-
Panne D, Maniatis T, Harrison SC, (2007) An atomic model of the interferon-beta enhanceosome. Cell 129: 1111-1123.
-
(2007)
Cell
, vol.129
, pp. 1111-1123
-
-
Panne, D.1
Maniatis, T.2
Harrison, S.C.3
-
25
-
-
0029617947
-
Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome
-
Thanos D, Maniatis T, (1995) Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83: 1091-1100.
-
(1995)
Cell
, vol.83
, pp. 1091-1100
-
-
Thanos, D.1
Maniatis, T.2
-
26
-
-
33745658106
-
Computational models for neurogenic gene expression in the Drosophila embryo
-
Zinzen RP, Senger K, Levine M, Papatsenko D, (2006) Computational models for neurogenic gene expression in the Drosophila embryo. Curr Biol 16: 1358-1365.
-
(2006)
Curr Biol
, vol.16
, pp. 1358-1365
-
-
Zinzen, R.P.1
Senger, K.2
Levine, M.3
Papatsenko, D.4
-
27
-
-
84873486967
-
Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures
-
Jin H, Stojnic R, Adryan B, Ozdemir A, Stathopoulos A, et al. (2013) Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures. PLoS Genet 9: e1003195.
-
(2013)
PLoS Genet
, vol.9
-
-
Jin, H.1
Stojnic, R.2
Adryan, B.3
Ozdemir, A.4
Stathopoulos, A.5
-
28
-
-
34548690542
-
Functional architecture and evolution of transcriptional elements that drive gene coexpression
-
Brown CD, Johnson DS, Sidow A, (2007) Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 317: 1557-1560.
-
(2007)
Science
, vol.317
, pp. 1557-1560
-
-
Brown, C.D.1
Johnson, D.S.2
Sidow, A.3
-
29
-
-
60549089720
-
Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence
-
Liberman LM, Stathopoulos A, (2009) Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence. Dev Biol 327: 578-589.
-
(2009)
Dev Biol
, vol.327
, pp. 578-589
-
-
Liberman, L.M.1
Stathopoulos, A.2
-
30
-
-
44349089659
-
The words of the regulatory code are arranged in a variable manner in highly conserved enhancers
-
Rastegar S, Hess I, Dickmeis T, Nicod JC, Ertzer R, et al. (2008) The words of the regulatory code are arranged in a variable manner in highly conserved enhancers. Dev Biol 318: 366-377.
-
(2008)
Dev Biol
, vol.318
, pp. 366-377
-
-
Rastegar, S.1
Hess, I.2
Dickmeis, T.3
Nicod, J.C.4
Ertzer, R.5
-
31
-
-
79960708456
-
Rapid evolutionary rewiring of a structurally constrained eye enhancer
-
Swanson CI, Schwimmer DB, Barolo S, (2011) Rapid evolutionary rewiring of a structurally constrained eye enhancer. Curr Biol 21: 1186-1196.
-
(2011)
Curr Biol
, vol.21
, pp. 1186-1196
-
-
Swanson, C.I.1
Schwimmer, D.B.2
Barolo, S.3
-
32
-
-
79958204355
-
The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity
-
Parker DS, White MA, Ramos AI, Cohen BA, Barolo S, (2011) The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity. Sci Signal 4: ra38.
-
(2011)
Sci Signal
, vol.4
-
-
Parker, D.S.1
White, M.A.2
Ramos, A.I.3
Cohen, B.A.4
Barolo, S.5
-
33
-
-
79951548111
-
Changes in selective effects over time facilitate turnover of enhancer sequences
-
Bullaughey K, (2011) Changes in selective effects over time facilitate turnover of enhancer sequences. Genetics 187: 567-582.
-
(2011)
Genetics
, vol.187
, pp. 567-582
-
-
Bullaughey, K.1
-
34
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz J, Siggia ED, Cohen BA, (2009) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457: 215-218.
-
(2009)
Nature
, vol.457
, pp. 215-218
-
-
Gertz, J.1
Siggia, E.D.2
Cohen, B.A.3
-
35
-
-
84862002321
-
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
-
Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, et al. (2012) Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol 30: 521-530.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 521-530
-
-
Sharon, E.1
Kalma, Y.2
Sharp, A.3
Raveh-Sadka, T.4
Levo, M.5
-
36
-
-
84863229330
-
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
-
Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, et al. (2012) Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol 30: 271-277.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 271-277
-
-
Melnikov, A.1
Murugan, A.2
Zhang, X.3
Tesileanu, T.4
Wang, L.5
-
37
-
-
84863230316
-
Massively parallel functional dissection of mammalian enhancers in vivo
-
Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, et al. (2012) Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol 30: 265-270.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 265-270
-
-
Patwardhan, R.P.1
Hiatt, J.B.2
Witten, D.M.3
Kim, M.J.4
Smith, R.P.5
-
38
-
-
84874640391
-
Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
-
Zichner T, Garfield DA, Rausch T, Stutz AM, Cannavo E, et al. (2013) Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Genome research 23: 568-579.
-
(2013)
Genome Research
, vol.23
, pp. 568-579
-
-
Zichner, T.1
Garfield, D.A.2
Rausch, T.3
Stutz, A.M.4
Cannavo, E.5
-
39
-
-
84870693546
-
Genomic variation and its impact on gene expression in Drosophila melanogaster
-
Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, et al. (2012) Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS genetics 8: e1003055.
-
(2012)
PLoS Genetics
, vol.8
-
-
Massouras, A.1
Waszak, S.M.2
Albarca-Aguilera, M.3
Hens, K.4
Holcombe, W.5
-
40
-
-
84872506987
-
Phenotypic impact of genomic structural variation: insights from and for human disease
-
Weischenfeldt J, Symmons O, Spitz F, Korbel JO, (2013) Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet 14: 125-138.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 125-138
-
-
Weischenfeldt, J.1
Symmons, O.2
Spitz, F.3
Korbel, J.O.4
-
41
-
-
58549102472
-
cis-Regulatory networks during development: a view of Drosophila
-
Bonn S, Furlong EE, (2008) cis-Regulatory networks during development: a view of Drosophila. Curr Opin Genet Dev 18: 513-520.
-
(2008)
Curr Opin Genet Dev
, vol.18
, pp. 513-520
-
-
Bonn, S.1
Furlong, E.E.2
-
42
-
-
70549096299
-
Conservation and divergence in developmental networks: a view from Drosophila myogenesis
-
Ciglar L, Furlong EE, (2009) Conservation and divergence in developmental networks: a view from Drosophila myogenesis. Curr Opin Cell Biol 21: 754-760.
-
(2009)
Curr Opin Cell Biol
, vol.21
, pp. 754-760
-
-
Ciglar, L.1
Furlong, E.E.2
-
43
-
-
33847660443
-
An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases
-
Bischof J, Maeda RK, Hediger M, Karch F, Basler K, (2007) An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc Natl Acad Sci U S A 104: 3312-3317.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 3312-3317
-
-
Bischof, J.1
Maeda, R.K.2
Hediger, M.3
Karch, F.4
Basler, K.5
-
44
-
-
78650362376
-
Emerging properties of animal gene regulatory networks
-
Davidson EH, (2010) Emerging properties of animal gene regulatory networks. Nature 468: 911-920.
-
(2010)
Nature
, vol.468
, pp. 911-920
-
-
Davidson, E.H.1
-
45
-
-
0037398319
-
Homotypic regulatory clusters in Drosophila
-
Lifanov AP, Makeev VJ, Nazina AG, Papatsenko DA, (2003) Homotypic regulatory clusters in Drosophila. Genome Res 13: 579-588.
-
(2003)
Genome Res
, vol.13
, pp. 579-588
-
-
Lifanov, A.P.1
Makeev, V.J.2
Nazina, A.G.3
Papatsenko, D.A.4
-
46
-
-
77951874066
-
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
-
Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, et al. (2010) Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 20: 565-577.
-
(2010)
Genome Res
, vol.20
, pp. 565-577
-
-
Gotea, V.1
Visel, A.2
Westlund, J.M.3
Nobrega, M.A.4
Pennacchio, L.A.5
-
47
-
-
0028206856
-
Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen
-
Hanes SD, Riddihough G, Ish-Horowicz D, Brent R, (1994) Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen. Mol Cell Biol 14: 3364-3375.
-
(1994)
Mol Cell Biol
, vol.14
, pp. 3364-3375
-
-
Hanes, S.D.1
Riddihough, G.2
Ish-Horowicz, D.3
Brent, R.4
-
48
-
-
0028021851
-
Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila
-
Simpson-Brose M, Treisman J, Desplan C, (1994) Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila. Cell 78: 855-865.
-
(1994)
Cell
, vol.78
, pp. 855-865
-
-
Simpson-Brose, M.1
Treisman, J.2
Desplan, C.3
-
49
-
-
0029028177
-
Multiple modes of dorsal-bHLH transcriptional synergy in the Drosophila embryo
-
Szymanski P, Levine M, (1995) Multiple modes of dorsal-bHLH transcriptional synergy in the Drosophila embryo. EMBO J 14: 2229-2238.
-
(1995)
EMBO J
, vol.14
, pp. 2229-2238
-
-
Szymanski, P.1
Levine, M.2
-
50
-
-
78650136358
-
Common motifs shared by conserved enhancers of Drosophila midline glial genes
-
Fulkerson E, Estes PA, (2010) Common motifs shared by conserved enhancers of Drosophila midline glial genes. J Exp Zool B Mol Dev Evol 316: 61-75.
-
(2010)
J Exp Zool B Mol Dev Evol
, vol.316
, pp. 61-75
-
-
Fulkerson, E.1
Estes, P.A.2
-
51
-
-
37249037083
-
A combinatorial code of maternal GATA, Ets and beta-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm
-
Rothbacher U, Bertrand V, Lamy C, Lemaire P, (2007) A combinatorial code of maternal GATA, Ets and beta-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm. Development 134: 4023-4032.
-
(2007)
Development
, vol.134
, pp. 4023-4032
-
-
Rothbacher, U.1
Bertrand, V.2
Lamy, C.3
Lemaire, P.4
-
52
-
-
0025325446
-
A synthetic homeodomain binding site acts as a cell type specific, promoter specific enhancer in Drosophila embryos
-
Vincent JP, Kassis JA, O'Farrell PH, (1990) A synthetic homeodomain binding site acts as a cell type specific, promoter specific enhancer in Drosophila embryos. EMBO J 9: 2573-2578.
-
(1990)
EMBO J
, vol.9
, pp. 2573-2578
-
-
Vincent, J.P.1
Kassis, J.A.2
O'Farrell, P.H.3
-
53
-
-
33845351102
-
Transgenic Wnt/TCF pathway reporters: all you need is Lef?
-
Barolo S, (2006) Transgenic Wnt/TCF pathway reporters: all you need is Lef? Oncogene 25: 7505-7511.
-
(2006)
Oncogene
, vol.25
, pp. 7505-7511
-
-
Barolo, S.1
-
54
-
-
0030979996
-
LEF-1, a nuclear factor coordinating signaling inputs from wingless and decapentaplegic
-
Riese J, Yu X, Munnerlyn A, Eresh S, Hsu SC, et al. (1997) LEF-1, a nuclear factor coordinating signaling inputs from wingless and decapentaplegic. Cell 88: 777-787.
-
(1997)
Cell
, vol.88
, pp. 777-787
-
-
Riese, J.1
Yu, X.2
Munnerlyn, A.3
Eresh, S.4
Hsu, S.C.5
-
55
-
-
0033637705
-
A notch-independent activity of suppressor of hairless is required for normal mechanoreceptor physiology
-
Barolo S, Walker RG, Polyanovsky AD, Freschi G, Keil T, et al. (2000) A notch-independent activity of suppressor of hairless is required for normal mechanoreceptor physiology. Cell 103: 957-969.
-
(2000)
Cell
, vol.103
, pp. 957-969
-
-
Barolo, S.1
Walker, R.G.2
Polyanovsky, A.D.3
Freschi, G.4
Keil, T.5
-
56
-
-
0035844087
-
Control of a genetic regulatory network by a selector gene
-
Guss KA, Nelson CE, Hudson A, Kraus ME, Carroll SB, (2001) Control of a genetic regulatory network by a selector gene. Science 292: 1164-1167.
-
(2001)
Science
, vol.292
, pp. 1164-1167
-
-
Guss, K.A.1
Nelson, C.E.2
Hudson, A.3
Kraus, M.E.4
Carroll, S.B.5
-
57
-
-
0035498955
-
biniou (FoxF), a central component in a regulatory network controlling visceral mesoderm development and midgut morphogenesis in Drosophila
-
Zaffran S, Kuchler A, Lee HH, Frasch M, (2001) biniou (FoxF), a central component in a regulatory network controlling visceral mesoderm development and midgut morphogenesis in Drosophila. Genes Dev 15: 2900-2915.
-
(2001)
Genes Dev
, vol.15
, pp. 2900-2915
-
-
Zaffran, S.1
Kuchler, A.2
Lee, H.H.3
Frasch, M.4
-
58
-
-
34948861002
-
Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network
-
Jakobsen JS, Braun M, Astorga J, Gustafson EH, Sandmann T, et al. (2007) Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network. Genes Dev 21: 2448-2460.
-
(2007)
Genes Dev
, vol.21
, pp. 2448-2460
-
-
Jakobsen, J.S.1
Braun, M.2
Astorga, J.3
Gustafson, E.H.4
Sandmann, T.5
-
59
-
-
0028821180
-
Ultrabithorax protein is necessary but not sufficient for full activation of decapentaplegic expression in the visceral mesoderm
-
Sun B, Hursh DA, Jackson D, Beachy PA, (1995) Ultrabithorax protein is necessary but not sufficient for full activation of decapentaplegic expression in the visceral mesoderm. EMBO J 14: 520-535.
-
(1995)
EMBO J
, vol.14
, pp. 520-535
-
-
Sun, B.1
Hursh, D.A.2
Jackson, D.3
Beachy, P.A.4
-
60
-
-
0033828572
-
decapentaplegic is a direct target of dTcf repression in the Drosophila visceral mesoderm
-
Yang X, van Beest M, Clevers H, Jones T, Hursh DA, et al. (2000) decapentaplegic is a direct target of dTcf repression in the Drosophila visceral mesoderm. Development 127: 3695-3702.
-
(2000)
Development
, vol.127
, pp. 3695-3702
-
-
Yang, X.1
van Beest, M.2
Clevers, H.3
Jones, T.4
Hursh, D.A.5
-
61
-
-
0242620396
-
Schnurri mediates Dpp-dependent repression of brinker transcription
-
Marty T, Muller B, Basler K, Affolter M, (2000) Schnurri mediates Dpp-dependent repression of brinker transcription. Nat Cell Biol 2: 745-749.
-
(2000)
Nat Cell Biol
, vol.2
, pp. 745-749
-
-
Marty, T.1
Muller, B.2
Basler, K.3
Affolter, M.4
-
62
-
-
0035029174
-
Direct competition between Brinker and Drosophila Mad in Dpp target gene transcription
-
Saller E, Bienz M, (2001) Direct competition between Brinker and Drosophila Mad in Dpp target gene transcription. EMBO Rep 2: 298-305.
-
(2001)
EMBO Rep
, vol.2
, pp. 298-305
-
-
Saller, E.1
Bienz, M.2
-
63
-
-
80155137594
-
Master transcription factors determine cell-type-specific responses to TGF-beta signaling
-
Mullen AC, Orlando DA, Newman JJ, Loven J, Kumar RM, et al. (2011) Master transcription factors determine cell-type-specific responses to TGF-beta signaling. Cell 147: 565-576.
-
(2011)
Cell
, vol.147
, pp. 565-576
-
-
Mullen, A.C.1
Orlando, D.A.2
Newman, J.J.3
Loven, J.4
Kumar, R.M.5
-
64
-
-
80155123782
-
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration
-
Trompouki E, Bowman TV, Lawton LN, Fan ZP, Wu DC, et al. (2011) Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell 147: 577-589.
-
(2011)
Cell
, vol.147
, pp. 577-589
-
-
Trompouki, E.1
Bowman, T.V.2
Lawton, L.N.3
Fan, Z.P.4
Wu, D.C.5
-
65
-
-
0030018425
-
Mothers against dpp encodes a conserved cytoplasmic protein required in DPP/TGF-beta responsive cells
-
Newfeld SJ, Chartoff EH, Graff JM, Melton DA, Gelbart WM, (1996) Mothers against dpp encodes a conserved cytoplasmic protein required in DPP/TGF-beta responsive cells. Development 122: 2099-2108.
-
(1996)
Development
, vol.122
, pp. 2099-2108
-
-
Newfeld, S.J.1
Chartoff, E.H.2
Graff, J.M.3
Melton, D.A.4
Gelbart, W.M.5
-
66
-
-
0025295925
-
Induction across germ layers in Drosophila mediated by a genetic cascade
-
Immergluck K, Lawrence PA, Bienz M, (1990) Induction across germ layers in Drosophila mediated by a genetic cascade. Cell 62: 261-268.
-
(1990)
Cell
, vol.62
, pp. 261-268
-
-
Immergluck, K.1
Lawrence, P.A.2
Bienz, M.3
-
67
-
-
35748960549
-
Dpp signalling orchestrates dorsal closure by regulating cell shape changes both in the amnioserosa and in the epidermis
-
Fernandez BG, Arias AM, Jacinto A, (2007) Dpp signalling orchestrates dorsal closure by regulating cell shape changes both in the amnioserosa and in the epidermis. Mech Dev 124: 884-897.
-
(2007)
Mech Dev
, vol.124
, pp. 884-897
-
-
Fernandez, B.G.1
Arias, A.M.2
Jacinto, A.3
-
68
-
-
17944378083
-
A murine model of Holt-Oram syndrome defines roles of the T-box transcription factor Tbx5 in cardiogenesis and disease
-
Bruneau BG, Nemer G, Schmitt JP, Charron F, Robitaille L, et al. (2001) A murine model of Holt-Oram syndrome defines roles of the T-box transcription factor Tbx5 in cardiogenesis and disease. Cell 106: 709-721.
-
(2001)
Cell
, vol.106
, pp. 709-721
-
-
Bruneau, B.G.1
Nemer, G.2
Schmitt, J.P.3
Charron, F.4
Robitaille, L.5
-
69
-
-
0030799792
-
The cardiac transcription factors Nkx2-5 and GATA-4 are mutual cofactors
-
Durocher D, Charron F, Warren R, Schwartz RJ, Nemer M, (1997) The cardiac transcription factors Nkx2-5 and GATA-4 are mutual cofactors. EMBO J 16: 5687-5696.
-
(1997)
EMBO J
, vol.16
, pp. 5687-5696
-
-
Durocher, D.1
Charron, F.2
Warren, R.3
Schwartz, R.J.4
Nemer, M.5
-
70
-
-
0035872950
-
Pannier is a transcriptional target and partner of Tinman during Drosophila cardiogenesis
-
Gajewski K, Zhang Q, Choi CY, Fossett N, Dang A, et al. (2001) Pannier is a transcriptional target and partner of Tinman during Drosophila cardiogenesis. Dev Biol 233: 425-436.
-
(2001)
Dev Biol
, vol.233
, pp. 425-436
-
-
Gajewski, K.1
Zhang, Q.2
Choi, C.Y.3
Fossett, N.4
Dang, A.5
-
71
-
-
0038801547
-
Cardiogenesis in the Drosophila model: control mechanisms during early induction and diversification of cardiac progenitors
-
Zaffran S, Xu X, Lo PC, Lee HH, Frasch M, (2002) Cardiogenesis in the Drosophila model: control mechanisms during early induction and diversification of cardiac progenitors. Cold Spring Harb Symp Quant Biol 67: 1-12.
-
(2002)
Cold Spring Harb Symp Quant Biol
, vol.67
, pp. 1-12
-
-
Zaffran, S.1
Xu, X.2
Lo, P.C.3
Lee, H.H.4
Frasch, M.5
-
72
-
-
0036608009
-
Control of cardiac development by an evolutionarily conserved transcriptional network
-
Cripps RM, Olson EN, (2002) Control of cardiac development by an evolutionarily conserved transcriptional network. Dev Biol 246: 14-28.
-
(2002)
Dev Biol
, vol.246
, pp. 14-28
-
-
Cripps, R.M.1
Olson, E.N.2
-
73
-
-
0027282774
-
The gene tinman is required for specification of the heart and visceral muscles in Drosophila
-
Bodmer R, (1993) The gene tinman is required for specification of the heart and visceral muscles in Drosophila. Development 118: 719-729.
-
(1993)
Development
, vol.118
, pp. 719-729
-
-
Bodmer, R.1
-
74
-
-
0027237596
-
tinman and bagpipe: two homeo box genes that determine cell fates in the dorsal mesoderm of Drosophila
-
Azpiazu N, Frasch M, (1993) tinman and bagpipe: two homeo box genes that determine cell fates in the dorsal mesoderm of Drosophila. Genes Dev 7: 1325-1340.
-
(1993)
Genes Dev
, vol.7
, pp. 1325-1340
-
-
Azpiazu, N.1
Frasch, M.2
-
75
-
-
28844432418
-
The Dorsocross T-box genes are key components of the regulatory network controlling early cardiogenesis in Drosophila
-
Reim I, Frasch M, (2005) The Dorsocross T-box genes are key components of the regulatory network controlling early cardiogenesis in Drosophila. Development 132: 4911-4925.
-
(2005)
Development
, vol.132
, pp. 4911-4925
-
-
Reim, I.1
Frasch, M.2
-
76
-
-
0033398273
-
The zinc finger proteins Pannier and GATA4 function as cardiogenic factors in Drosophila
-
Gajewski K, Fossett N, Molkentin JD, Schulz RA, (1999) The zinc finger proteins Pannier and GATA4 function as cardiogenic factors in Drosophila. Development 126: 5679-5688.
-
(1999)
Development
, vol.126
, pp. 5679-5688
-
-
Gajewski, K.1
Fossett, N.2
Molkentin, J.D.3
Schulz, R.A.4
-
77
-
-
0028903248
-
Induction of visceral and cardiac mesoderm by ectodermal Dpp in the early Drosophila embryo
-
Frasch M, (1995) Induction of visceral and cardiac mesoderm by ectodermal Dpp in the early Drosophila embryo. Nature 374: 464-467.
-
(1995)
Nature
, vol.374
, pp. 464-467
-
-
Frasch, M.1
-
78
-
-
0036011238
-
The patterns of wingless, decapentaplegic, and tinman position the Drosophila heart
-
Lockwood WK, Bodmer R, (2002) The patterns of wingless, decapentaplegic, and tinman position the Drosophila heart. Mech Dev 114: 13-26.
-
(2002)
Mech Dev
, vol.114
, pp. 13-26
-
-
Lockwood, W.K.1
Bodmer, R.2
-
79
-
-
0035215246
-
The functions of pannier during Drosophila embryogenesis
-
Herranz H, Morata G, (2001) The functions of pannier during Drosophila embryogenesis. Development 128: 4837-4846.
-
(2001)
Development
, vol.128
, pp. 4837-4846
-
-
Herranz, H.1
Morata, G.2
-
80
-
-
0038444550
-
Gata factor Pannier is required to establish competence for heart progenitor formation
-
Klinedinst SL, Bodmer R, (2003) Gata factor Pannier is required to establish competence for heart progenitor formation. Development 130: 3027-3038.
-
(2003)
Development
, vol.130
, pp. 3027-3038
-
-
Klinedinst, S.L.1
Bodmer, R.2
-
81
-
-
0030087518
-
Epistasis and pleiotropy as natural properties of transcriptional regulation
-
Gibson G, (1996) Epistasis and pleiotropy as natural properties of transcriptional regulation. Theor Popul Biol 49: 58-89.
-
(1996)
Theor Popul Biol
, vol.49
, pp. 58-89
-
-
Gibson, G.1
-
82
-
-
0001422329
-
Quantitative model for gene regulation by lambda phage repressor
-
Ackers GK, Johnson AD, Shea MA, (1982) Quantitative model for gene regulation by lambda phage repressor. Proc Natl Acad Sci U S A 79: 1129-1133.
-
(1982)
Proc Natl Acad Sci U S A
, vol.79
, pp. 1129-1133
-
-
Ackers, G.K.1
Johnson, A.D.2
Shea, M.A.3
-
83
-
-
79959991126
-
Building enhancers from the ground up: a synthetic biology approach
-
Amit R, Garcia HG, Phillips R, Fraser SE, (2011) Building enhancers from the ground up: a synthetic biology approach. Cell 146: 105-118.
-
(2011)
Cell
, vol.146
, pp. 105-118
-
-
Amit, R.1
Garcia, H.G.2
Phillips, R.3
Fraser, S.E.4
-
84
-
-
0015526977
-
Equilibrium and kinetic studies of Escherichia coli lac repressor-inducer interactions
-
Laiken SL, Gross CA, Von Hippel PH, (1972) Equilibrium and kinetic studies of Escherichia coli lac repressor-inducer interactions. J Mol Biol 66: 143-155.
-
(1972)
J Mol Biol
, vol.66
, pp. 143-155
-
-
Laiken, S.L.1
Gross, C.A.2
Von Hippel, P.H.3
-
85
-
-
29444442484
-
Switches in bacteriophage lambda development
-
Oppenheim AB, Kobiler O, Stavans J, Court DL, Adhya S, (2005) Switches in bacteriophage lambda development. Annu Rev Genet 39: 409-429.
-
(2005)
Annu Rev Genet
, vol.39
, pp. 409-429
-
-
Oppenheim, A.B.1
Kobiler, O.2
Stavans, J.3
Court, D.L.4
Adhya, S.5
-
86
-
-
20444382737
-
Regulation of transcription: from lambda to eukaryotes
-
Ptashne M, (2005) Regulation of transcription: from lambda to eukaryotes. Trends Biochem Sci 30: 275-279.
-
(2005)
Trends Biochem Sci
, vol.30
, pp. 275-279
-
-
Ptashne, M.1
-
87
-
-
76149087772
-
Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo
-
Fakhouri WD, Ay A, Sayal R, Dresch J, Dayringer E, et al. (2010) Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo. Mol Syst Biol 6: 341.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 341
-
-
Fakhouri, W.D.1
Ay, A.2
Sayal, R.3
Dresch, J.4
Dayringer, E.5
-
88
-
-
56849103052
-
Evolution acts on enhancer organization to fine-tune gradient threshold readouts
-
Crocker J, Tamori Y, Erives A, (2008) Evolution acts on enhancer organization to fine-tune gradient threshold readouts. PLoS Biol 6: e263.
-
(2008)
PLoS Biol
, vol.6
-
-
Crocker, J.1
Tamori, Y.2
Erives, A.3
-
89
-
-
0035477640
-
Molecular integration of inductive and mesoderm-intrinsic inputs governs even-skipped enhancer activity in a subset of pericardial and dorsal muscle progenitors
-
Knirr S, Frasch M, (2001) Molecular integration of inductive and mesoderm-intrinsic inputs governs even-skipped enhancer activity in a subset of pericardial and dorsal muscle progenitors. Dev Biol 238: 13-26.
-
(2001)
Dev Biol
, vol.238
, pp. 13-26
-
-
Knirr, S.1
Frasch, M.2
-
90
-
-
77953728005
-
Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors
-
BabuRajendran N, Palasingam P, Narasimhan K, Sun W, Prabhakar S, et al. (2010) Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors. Nucleic Acids Res 38: 3477-3488.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 3477-3488
-
-
BabuRajendran, N.1
Palasingam, P.2
Narasimhan, K.3
Sun, W.4
Prabhakar, S.5
-
91
-
-
0042161874
-
Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior
-
LaRonde-LeBlanc NA, Wolberger C, (2003) Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior. Genes Dev 17: 2060-2072.
-
(2003)
Genes Dev
, vol.17
, pp. 2060-2072
-
-
LaRonde-LeBlanc, N.A.1
Wolberger, C.2
-
92
-
-
0032145411
-
Smad proteins act in combination with synergistic and antagonistic regulators to target Dpp responses to the Drosophila mesoderm
-
Xu X, Yin Z, Hudson JB, Ferguson EL, Frasch M, (1998) Smad proteins act in combination with synergistic and antagonistic regulators to target Dpp responses to the Drosophila mesoderm. Genes Dev 12: 2354-2370.
-
(1998)
Genes Dev
, vol.12
, pp. 2354-2370
-
-
Xu, X.1
Yin, Z.2
Hudson, J.B.3
Ferguson, E.L.4
Frasch, M.5
-
93
-
-
67749106610
-
Synchronous and stochastic patterns of gene activation in the Drosophila embryo
-
Boettiger AN, Levine M, (2009) Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science 325: 471-473.
-
(2009)
Science
, vol.325
, pp. 471-473
-
-
Boettiger, A.N.1
Levine, M.2
-
94
-
-
79955795581
-
Paused RNA polymerase II as a developmental checkpoint
-
Levine M, (2011) Paused RNA polymerase II as a developmental checkpoint. Cell 145: 502-511.
-
(2011)
Cell
, vol.145
, pp. 502-511
-
-
Levine, M.1
-
95
-
-
77956521381
-
Shadow enhancers foster robustness of Drosophila gastrulation
-
Perry MW, Boettiger AN, Bothma JP, Levine M, (2010) Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol 20: 1562-1567.
-
(2010)
Curr Biol
, vol.20
, pp. 1562-1567
-
-
Perry, M.W.1
Boettiger, A.N.2
Bothma, J.P.3
Levine, M.4
-
96
-
-
51149097760
-
Shadow enhancers as a source of evolutionary novelty
-
Hong JW, Hendrix DA, Levine MS, (2008) Shadow enhancers as a source of evolutionary novelty. Science 321: 1314.
-
(2008)
Science
, vol.321
, pp. 1314
-
-
Hong, J.W.1
Hendrix, D.A.2
Levine, M.S.3
-
97
-
-
77957742483
-
Evolution of insect dorsoventral patterning mechanisms
-
Perry MW, Cande JD, Boettiger AN, Levine M, (2009) Evolution of insect dorsoventral patterning mechanisms. Cold Spring Harb Symp Quant Biol 74: 275-279.
-
(2009)
Cold Spring Harb Symp Quant Biol
, vol.74
, pp. 275-279
-
-
Perry, M.W.1
Cande, J.D.2
Boettiger, A.N.3
Levine, M.4
-
98
-
-
77954960062
-
Phenotypic robustness conferred by apparently redundant transcriptional enhancers
-
Frankel N, Davis GK, Vargas D, Wang S, Payre F, et al. (2010) Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature 466: 490-493.
-
(2010)
Nature
, vol.466
, pp. 490-493
-
-
Frankel, N.1
Davis, G.K.2
Vargas, D.3
Wang, S.4
Payre, F.5
-
99
-
-
81755177824
-
Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness
-
Ludwig MZ, Manu, Kittler R, White KP, Kreitman M, (2011) Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness. PLoS Genet 7: e1002364.
-
(2011)
PLoS Genet
, vol.7
-
-
Ludwig, M.Z.1
Manu2
Kittler, R.3
White, K.P.4
Kreitman, M.5
-
100
-
-
0033782266
-
GFP and beta-galactosidase transformation vectors for promoter/enhancer analysis in Drosophila
-
728, 730, 732
-
Barolo S, Carver LA, Posakony JW, (2000) GFP and beta-galactosidase transformation vectors for promoter/enhancer analysis in Drosophila. Biotechniques 29: 726, 728, 730, 732.
-
(2000)
Biotechniques
, vol.29
, pp. 726
-
-
Barolo, S.1
Carver, L.A.2
Posakony, J.W.3
-
101
-
-
0035979735
-
Patterns of gene expression during Drosophila mesoderm development
-
Furlong EE, Andersen EC, Null B, White KP, Scott MP, (2001) Patterns of gene expression during Drosophila mesoderm development. Science 293: 1629-1633.
-
(2001)
Science
, vol.293
, pp. 1629-1633
-
-
Furlong, E.E.1
Andersen, E.C.2
Null, B.3
White, K.P.4
Scott, M.P.5
-
102
-
-
79952983516
-
Mathematical modeling of gene expression: a guide for the perplexed biologist
-
Ay A, Arnosti DN, (2011) Mathematical modeling of gene expression: a guide for the perplexed biologist. Crit Rev Biochem Mol Biol 46: 137-151.
-
(2011)
Crit Rev Biochem Mol Biol
, vol.46
, pp. 137-151
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Ay, A.1
Arnosti, D.N.2
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