-
1
-
-
0030030902
-
The eve stripe 2 enhancer employs multiple modes of transcriptional synergy
-
Arnosti DN, Barolo S, Levine M, Small S. 1996. The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development 122: 205-214.
-
(1996)
Development
, vol.122
, pp. 205-214
-
-
Arnosti, D.N.1
Barolo, S.2
Levine, M.3
Small, S.4
-
2
-
-
79958090979
-
DREME: Motif discovery in transcription factor ChIP-seq data
-
Bailey TL. 2011. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27: 1653-1659.
-
(2011)
Bioinformatics
, vol.27
, pp. 1653-1659
-
-
Bailey, T.L.1
-
3
-
-
33745410216
-
Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange
-
Bateman JR, Lee AM, Wu CT. 2006. Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange. Genetics 173: 769-777.
-
(2006)
Genetics
, vol.173
, pp. 769-777
-
-
Bateman, J.R.1
Lee, A.M.2
Wu, C.T.3
-
4
-
-
0024022215
-
The role of localization of bicoid RNA in organizing the anterior pattern of the Drosophila embryo
-
Berleth T, Burri M, Thoma G, Bopp D, Richstein S, Frigerio G, Noll M, Nusslein-Volhard C. 1988. The role of localization of bicoid RNA in organizing the anterior pattern of the Drosophila embryo. EMBO J 7: 1749-1756.
-
(1988)
EMBO J
, vol.7
, pp. 1749-1756
-
-
Berleth, T.1
Burri, M.2
Thoma, G.3
Bopp, D.4
Richstein, S.5
Frigerio, G.6
Noll, M.7
Nusslein-Volhard, C.8
-
5
-
-
27644469434
-
Spatial regulation of microRNA gene expression in the Drosophila embryo
-
Biemar F, Zinzen R, Ronshaugen M, Sementchenko V, Manak JR, Levine MS. 2005. Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc Natl Acad Sci 102: 15907-15911.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 15907-15911
-
-
Biemar, F.1
Zinzen, R.2
Ronshaugen, M.3
Sementchenko, V.4
Manak, J.R.5
Levine, M.S.6
-
6
-
-
80054728495
-
Animal transcription networks as highly connected, quantitative continua
-
Biggin MD. 2011. Animal transcription networks as highly connected, quantitative continua. Dev Cell 21: 611-626.
-
(2011)
Dev Cell
, vol.21
, pp. 611-626
-
-
Biggin, M.D.1
-
7
-
-
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, Delhomme N, Ghavi-Helm Y, Wilczynski B, Riddell A, Furlong EE. 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
Delhomme, N.6
Ghavi-Helm, Y.7
Wilczynski, B.8
Riddell, A.9
Furlong, E.E.10
-
8
-
-
84860350869
-
A system of repressor gradients spatially organizes the boundaries of Bicoid-dependent target genes
-
Chen H, Xu Z, Mei C, Yu D, Small S. 2012. A system of repressor gradients spatially organizes the boundaries of Bicoid-dependent target genes. Cell 149: 618-629.
-
(2012)
Cell
, vol.149
, pp. 618-629
-
-
Chen, H.1
Xu, Z.2
Mei, C.3
Yu, D.4
Small, S.5
-
9
-
-
30044449116
-
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
-
Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, et al. 2006. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res 16: 123-131.
-
(2006)
Genome Res
, vol.16
, pp. 123-131
-
-
Crawford, G.E.1
Holt, I.E.2
Whittle, J.3
Webb, B.D.4
Tai, D.5
Davis, S.6
Margulies, E.H.7
Chen, Y.8
Bernat, J.A.9
Ginsburg, D.10
-
10
-
-
34249092299
-
Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo
-
De Renzis S, Elemento O, Tavazoie S, Wieschaus EF. 2007. Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol 5: e117.
-
(2007)
PLoS Biol
, vol.5
-
-
De Renzis, S.1
Elemento, O.2
Tavazoie, S.3
Wieschaus, E.F.4
-
11
-
-
0023679744
-
The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner
-
Driever W, Nusslein-Volhard C. 1988a. The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner. Cell 54: 95-104.
-
(1988)
Cell
, vol.54
, pp. 95-104
-
-
Driever, W.1
Nusslein-Volhard, C.2
-
12
-
-
0023677769
-
A gradient of bicoid protein in Drosophila embryos
-
Driever W, Nusslein-Volhard C. 1988b. A gradient of bicoid protein in Drosophila embryos. Cell 54: 83-93.
-
(1988)
Cell
, vol.54
, pp. 83-93
-
-
Driever, W.1
Nusslein-Volhard, C.2
-
13
-
-
0024569785
-
The bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo
-
Driever W, Nusslein-Volhard C. 1989. The bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo. Nature 337: 138-143.
-
(1989)
Nature
, vol.337
, pp. 138-143
-
-
Driever, W.1
Nusslein-Volhard, C.2
-
14
-
-
0024457385
-
Rescue of bicoid mutant Drosophila embryos by bicoid fusion proteins containing heterologous activating sequences
-
Driever W, Ma J, Nusslein-Volhard C, Ptashne M. 1989. Rescue of bicoid mutant Drosophila embryos by bicoid fusion proteins containing heterologous activating sequences. Nature 342: 149-154.
-
(1989)
Nature
, vol.342
, pp. 149-154
-
-
Driever, W.1
Ma, J.2
Nusslein-Volhard, C.3
Ptashne, M.4
-
15
-
-
80054687054
-
Measurement and perturbation of morphogen lifetime: Effects on gradient shape
-
Drocco JA, Grimm O, Tank DW, Wieschaus E. 2011. Measurement and perturbation of morphogen lifetime: effects on gradient shape. Biophys J 101: 1807-1815.
-
(2011)
Biophys J
, vol.101
, pp. 1807-1815
-
-
Drocco, J.A.1
Grimm, O.2
Tank, D.W.3
Wieschaus, E.4
-
16
-
-
34249932435
-
Probing transcription factor dynamics at the single-molecule level in a living cell
-
Elf J, Li GW, Xie XS. 2007. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316: 1191-1194.
-
(2007)
Science
, vol.316
, pp. 1191-1194
-
-
Elf, J.1
Li, G.W.2
Xie, X.S.3
-
17
-
-
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 101: 3851-3856.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 3851-3856
-
-
Erives, A.1
Levine, M.2
-
18
-
-
77957333745
-
Dynamic chromatin organization during foregut development mediated by the organ selector gene PHA-4/FoxA
-
Fakhouri TH, Stevenson J, Chisholm AD, Mango SE. 2010. Dynamic chromatin organization during foregut development mediated by the organ selector gene PHA-4/FoxA. PLoS Genet 6: e1001060.
-
(2010)
PLoS Genet
, vol.6
-
-
Fakhouri, T.H.1
Stevenson, J.2
Chisholm, A.D.3
Mango, S.E.4
-
19
-
-
84871844925
-
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila
-
Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, et al. 2012. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci 109: 21330-21335.
-
(2012)
Proc Natl Acad Sci
, vol.109
, pp. 21330-21335
-
-
Fisher, W.W.1
Li, J.J.2
Hammonds, A.S.3
Brown, J.B.4
Pfeiffer, B.D.5
Weiszmann, R.6
McArthur, S.7
Thomas, S.8
Stamatoyannopoulos, J.A.9
Eisen, M.B.10
-
20
-
-
0033037862
-
Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients
-
Fujioka M, Emi-Sarker Y, Yusibova GL, Goto T, Jaynes JB. 1999. Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients. Development 126: 2527-2538.
-
(1999)
Development
, vol.126
, pp. 2527-2538
-
-
Fujioka, M.1
Emi-Sarker, Y.2
Yusibova, G.L.3
Goto, T.4
Jaynes, J.B.5
-
21
-
-
0031793177
-
Targeting gene expression to the head: The Drosophila orthodenticle gene is a direct target of the Bicoid morphogen
-
Gao Q, Finkelstein R. 1998. Targeting gene expression to the head: the Drosophila orthodenticle gene is a direct target of the Bicoid morphogen. Development 125: 4185-4193.
-
(1998)
Development
, vol.125
, pp. 4185-4193
-
-
Gao, Q.1
Finkelstein, R.2
-
22
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, et al. 2005. Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15: 1451-1455.
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
-
23
-
-
34250369627
-
FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin
-
Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. 2007. FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin. Genome Res 17: 877-885.
-
(2007)
Genome Res
, vol.17
, pp. 877-885
-
-
Giresi, P.G.1
Kim, J.2
McDaniell, R.M.3
Iyer, V.R.4
Lieb, J.D.5
-
24
-
-
34447104600
-
Stability and nuclear dynamics of the bicoid morphogen gradient
-
Gregor T, Wieschaus EF, McGregor AP, Bialek W, Tank DW. 2007. Stability and nuclear dynamics of the bicoid morphogen gradient. Cell 130: 141-152.
-
(2007)
Cell
, vol.130
, pp. 141-152
-
-
Gregor, T.1
Wieschaus, E.F.2
McGregor, A.P.3
Bialek, W.4
Tank, D.W.5
-
26
-
-
0029950139
-
Drosophila goosecoid participates in neural development but not in body axis formation
-
Hahn M, Jackle H. 1996. Drosophila goosecoid participates in neural development but not in body axis formation. EMBO J 15: 3077-3084.
-
(1996)
EMBO J
, vol.15
, pp. 3077-3084
-
-
Hahn, M.1
Jackle, H.2
-
27
-
-
80055073174
-
Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-tozygotic transition
-
Harrison MM, Li XY, Kaplan T, Botchan MR, Eisen MB. 2011. Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-tozygotic transition. PLoS Genet 7: e1002266.
-
(2011)
PLoS Genet
, vol.7
-
-
Harrison, M.M.1
Li, X.Y.2
Kaplan, T.3
Botchan, M.R.4
Eisen, M.B.5
-
28
-
-
0035198222
-
Interaction of gap genes in the Drosophila head: Tailless regulates expression of empty spiracles in early embryonic patterning and brain development
-
Hartmann B, Reichert H, Walldorf U. 2001. Interaction of gap genes in the Drosophila head: tailless regulates expression of empty spiracles in early embryonic patterning and brain development. Mech Dev 109: 161-172.
-
(2001)
Mech Dev
, vol.109
, pp. 161-172
-
-
Hartmann, B.1
Reichert, H.2
Walldorf, U.3
-
29
-
-
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, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, 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
Hawkins, R.D.6
Barrera, L.O.7
Van Calcar, S.8
Qu, C.9
Ching, K.A.10
-
30
-
-
0025353654
-
Cis-acting control elements for Kruppel expression in the Drosophila embryo
-
Hoch M, Schroder C, Seifert E, Jackle H. 1990. Cis-acting control elements for Kruppel expression in the Drosophila embryo. EMBO J 9: 2587-2595.
-
(1990)
EMBO J
, vol.9
, pp. 2587-2595
-
-
Hoch, M.1
Schroder, C.2
Seifert, E.3
Jackle, H.4
-
31
-
-
0025688974
-
Decoding positional information: Regulation of the pair-rule gene hairy
-
Howard KR, Struhl G. 1990. Decoding positional information: regulation of the pair-rule gene hairy. Development 110: 1223-1231.
-
(1990)
Development
, vol.110
, pp. 1223-1231
-
-
Howard, K.R.1
Struhl, G.2
-
32
-
-
84863054702
-
Pattern formation by graded and uniform signals in the early Drosophila embryo
-
Kanodia JS, Liang HL, Kim Y, Lim B, Zhan M, Lu H, Rushlow CA, Shvartsman SY. 2012. Pattern formation by graded and uniform signals in the early Drosophila embryo. Biophys J 102: 427-433.
-
(2012)
Biophys J
, vol.102
, pp. 427-433
-
-
Kanodia, J.S.1
Liang, H.L.2
Kim, Y.3
Lim, B.4
Zhan, M.5
Lu, H.6
Rushlow, C.A.7
Shvartsman, S.Y.8
-
33
-
-
70349996336
-
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse
-
Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Gottgens B, Halfon MS, Sinha S. 2009. Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Dev Cell 17: 568-579.
-
(2009)
Dev Cell
, vol.17
, pp. 568-579
-
-
Kantorovitz, M.R.1
Kazemian, M.2
Kinston, S.3
Miranda-Saavedra, D.4
Zhu, Q.5
Robinson, G.E.6
Gottgens, B.7
Halfon, M.S.8
Sinha, S.9
-
34
-
-
79952273012
-
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
-
Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. 2011. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet 7: e1001290.
-
(2011)
PLoS Genet
, vol.7
-
-
Kaplan, T.1
Li, X.Y.2
Sabo, P.J.3
Thomas, S.4
Stamatoyannopoulos, J.A.5
Biggin, M.D.6
Eisen, M.B.7
-
36
-
-
84860503075
-
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature
-
Kvon EZ, Stampfel G, Yanez-Cuna JO, Dickson BJ, Stark A. 2012. HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev 26: 908-913.
-
(2012)
Genes Dev
, vol.26
, pp. 908-913
-
-
Kvon, E.Z.1
Stampfel, G.2
Yanez-Cuna, J.O.3
Dickson, B.J.4
Stark, A.5
-
37
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
38
-
-
0343247787
-
Mechanism and Bicoid-dependent control of hairy stripe 7 expression in the posterior region of the Drosophila embryo
-
La Rosee A, Hader T, Taubert H, Rivera-Pomar R, Jackle H. 1997. Mechanism and Bicoid-dependent control of hairy stripe 7 expression in the posterior region of the Drosophila embryo. EMBO J 16: 4403-4411.
-
(1997)
EMBO J
, vol.16
, pp. 4403-4411
-
-
La Rosee, A.1
Hader, T.2
Taubert, H.3
Rivera-Pomar, R.4
Jackle, H.5
-
39
-
-
84888038427
-
Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-tozygotic transition
-
Lee MT, Bonneau AR, Takacs CM, Bazzini AA, Divito KR, Fleming ES, Giraldez AJ. 2013. Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-tozygotic transition. Nature 503: 360-364.
-
(2013)
Nature
, vol.503
, pp. 360-364
-
-
Lee, M.T.1
Bonneau, A.R.2
Takacs, C.M.3
Bazzini, A.A.4
Divito, K.R.5
Fleming, E.S.6
Giraldez, A.J.7
-
40
-
-
84883134422
-
Pou5f1 transcription factor controls zygotic gene activation in vertebrates
-
Leichsenring M, Maes J, Mossner R, Driever W, Onichtchouk D. 2013. Pou5f1 transcription factor controls zygotic gene activation in vertebrates. Science 341: 1005-1009.
-
(2013)
Science
, vol.341
, pp. 1005-1009
-
-
Leichsenring, M.1
Maes, J.2
Mossner, R.3
Driever, W.4
Onichtchouk, D.5
-
41
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, 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
McArthur, S.2
Bourgon, R.3
Nix, D.4
Pollard, D.A.5
Iyer, V.N.6
Hechmer, A.7
Simirenko, L.8
Stapleton, M.9
Luengo Hendriks, C.L.10
-
42
-
-
79953709415
-
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
-
Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. 2011. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol 12: R34.
-
(2011)
Genome Biol
, vol.12
-
-
Li, X.Y.1
Thomas, S.2
Sabo, P.J.3
Eisen, M.B.4
Stamatoyannopoulos, J.A.5
Biggin, M.D.6
-
43
-
-
56749183626
-
The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila
-
Liang HL, Nien CY, Liu HY, Metzstein MM, Kirov N, Rushlow C. 2008. The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila. Nature 456: 400-403.
-
(2008)
Nature
, vol.456
, pp. 400-403
-
-
Liang, H.L.1
Nien, C.Y.2
Liu, H.Y.3
Metzstein, M.M.4
Kirov, N.5
Rushlow, C.6
-
44
-
-
60549089720
-
Design flexibility in cisregulatory control of gene expression: Synthetic and comparative evidence
-
Liberman LM, Stathopoulos A. 2009. Design flexibility in cisregulatory 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
-
46
-
-
0016437021
-
A comparison of lac repressor binding to operator and to nonoperator DNA
-
Lin S, Riggs AD. 1975. A comparison of lac repressor binding to operator and to nonoperator DNA. Biochem Biophys Res Commun 62: 704-710.
-
(1975)
Biochem Biophys Res Commun
, vol.62
, pp. 704-710
-
-
Lin, S.1
Riggs, A.D.2
-
47
-
-
79953674509
-
The Formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA
-
Little S, Tkacik G, Kneeland T, Wieschaus E, Gregor T. 2011. The Formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA. PLoS Biol 9: e1000596.
-
(2011)
PLoS Biol
, vol.9
-
-
Little, S.1
Tkacik, G.2
Kneeland, T.3
Wieschaus, E.4
Gregor, T.5
-
48
-
-
80052022462
-
Cistrome: An integrative platform for transcriptional regulation studies
-
Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, et al. 2011. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 12: R83.
-
(2011)
Genome Biol
, vol.12
-
-
Liu, T.1
Ortiz, J.A.2
Taing, L.3
Meyer, C.A.4
Lee, B.5
Zhang, Y.6
Shin, H.7
Wong, S.S.8
Ma, J.9
Lei, Y.10
-
49
-
-
84876840287
-
Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network
-
Liu F, Morrison AH, Gregor T. 2013. Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network. Proc Natl Acad Sci 110: 6724-6729.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 6724-6729
-
-
Liu, F.1
Morrison, A.H.2
Gregor, T.3
-
50
-
-
76049091247
-
Antagonistic action of Bicoid and the repressor Capicua determines the spatial limits of Drosophila head gene expression domains
-
Lohr U, Chung HR, Beller M, Jackle H. 2009. Antagonistic action of Bicoid and the repressor Capicua determines the spatial limits of Drosophila head gene expression domains. Proc Natl Acad Sci 106: 21695-21700.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 21695-21700
-
-
Lohr, U.1
Chung, H.R.2
Beller, M.3
Jackle, H.4
-
51
-
-
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, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keranen SV, 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
-
-
McArthur, S.1
Li, X.Y.2
Li, J.3
Brown, J.B.4
Chu, H.C.5
Zeng, L.6
Grondona, B.P.7
Hechmer, A.8
Simirenko, L.9
Keranen, S.V.10
-
52
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
modEncode Consortium
-
modEncode Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L 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
Eaton, M.L.6
Landolin, J.M.7
Bristow, C.A.8
Ma, L.9
-
53
-
-
80055074510
-
Temporal coordination of gene networks by Zelda in the early Drosophila embryo
-
Nien CY, Liang HL, Butcher S, Sun Y, Fu S, Gocha T, Kirov N, Manak JR, Rushlow C. 2011. Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLoS Genet 7: e1002339.
-
(2011)
PLoS Genet
, vol.7
-
-
Nien, C.Y.1
Liang, H.L.2
Butcher, S.3
Sun, Y.4
Fu, S.5
Gocha, T.6
Kirov, N.7
Manak, J.R.8
Rushlow, C.9
-
54
-
-
45449111373
-
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
-
Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. 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
-
55
-
-
17044431033
-
The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila
-
Ochoa-Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, Oberstein A, Papatsenko D, Small S. 2005. The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. Proc Natl Acad Sci 102: 4960-4965.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 4960-4965
-
-
Ochoa-Espinosa, A.1
Yucel, G.2
Kaplan, L.3
Pare, A.4
Pura, N.5
Oberstein, A.6
Papatsenko, D.7
Small, S.8
-
56
-
-
62649174030
-
Anterior-posterior positional information in the absence of a strong Bicoid gradient
-
Ochoa-Espinosa A, Yu D, Tsirigos A, Struffi P, Small S. 2009. Anterior-posterior positional information in the absence of a strong Bicoid gradient. Proc Natl Acad Sci 106: 3823-3828.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 3823-3828
-
-
Ochoa-Espinosa, A.1
Yu, D.2
Tsirigos, A.3
Struffi, P.4
Small, S.5
-
57
-
-
3042760021
-
Global nature of dynamic protein-chromatin interactions in vivo: Three-dimensional genome scanning and dynamic interaction networks of chromatin proteins
-
Phair RD, Scaffidi P, Elbi C, Vecerova J, Dey A, Ozato K, Brown DT, Hager G, Bustin M, Misteli T. 2004. Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol 24: 6393-6402.
-
(2004)
Mol Cell Biol
, vol.24
, pp. 6393-6402
-
-
Phair, R.D.1
Scaffidi, P.2
Elbi, C.3
Vecerova, J.4
Dey, A.5
Ozato, K.6
Brown, D.T.7
Hager, G.8
Bustin, M.9
Misteli, T.10
-
58
-
-
77955764031
-
The time to measure positional information: Maternal hunchback is required for the synchrony of the Bicoid transcriptional response at the onset of zygotic transcription
-
Porcher A, Abu-Arish A, Huart S, Roelens B, Fradin C, Dostatni N. 2010. The time to measure positional information: maternal hunchback is required for the synchrony of the Bicoid transcriptional response at the onset of zygotic transcription. Development 137: 2795-2804.
-
(2010)
Development
, vol.137
, pp. 2795-2804
-
-
Porcher, A.1
Abu-Arish, A.2
Huart, S.3
Roelens, B.4
Fradin, C.5
Dostatni, N.6
-
59
-
-
0025853591
-
Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes
-
Riddihough G, Ish-Horowicz D. 1991. Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes. Genes Dev 5: 840-854.
-
(1991)
Genes Dev
, vol.5
, pp. 840-854
-
-
Riddihough, G.1
Ish-Horowicz, D.2
-
60
-
-
34848816094
-
Statistical tests to compare motif count exceptionalities
-
Robin S, Schbath S, Vandewalle V. 2007. Statistical tests to compare motif count exceptionalities. BMC Bioinformatics 8: 84.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 84
-
-
Robin, S.1
Schbath, S.2
Vandewalle, V.3
-
61
-
-
84856008906
-
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
-
Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, et al. 2012. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481: 389-393.
-
(2012)
Nature
, vol.481
, pp. 389-393
-
-
Ross-Innes, C.S.1
Stark, R.2
Teschendorff, A.E.3
Holmes, K.A.4
Ali, H.R.5
Dunning, M.J.6
Brown, G.D.7
Gojis, O.8
Ellis, I.O.9
Green, A.R.10
-
62
-
-
84872669981
-
Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient
-
Rushlow CA, Shvartsman SY. 2012. Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient. Curr Opin Genet Dev 22: 542-546.
-
(2012)
Curr Opin Genet Dev
, vol.22
, pp. 542-546
-
-
Rushlow, C.A.1
Shvartsman, S.Y.2
-
63
-
-
84859528845
-
The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
-
Satija R, Bradley RK. 2012. The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo. Genome Res 22: 656-665.
-
(2012)
Genome Res
, vol.22
, pp. 656-665
-
-
Satija, R.1
Bradley, R.K.2
-
64
-
-
19344375742
-
Transcriptional control in the segmentation gene network of Drosophila
-
Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U. 2004. Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol 2: E271.
-
(2004)
PLoS Biol
, vol.2
-
-
Schroeder, M.D.1
Pearce, M.2
Fak, J.3
Fan, H.4
Unnerstall, U.5
Emberly, E.6
Rajewsky, N.7
Siggia, E.D.8
Gaul, U.9
-
65
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, 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
-
66
-
-
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
-
67
-
-
0033818568
-
In vivo analysis of lacZ fusion genes in transgenic Drosophila melanogaster
-
Small S. 2000. In vivo analysis of lacZ fusion genes in transgenic Drosophila melanogaster. Methods Enzymol 326: 146-159.
-
(2000)
Methods Enzymol
, vol.326
, pp. 146-159
-
-
Small, S.1
-
68
-
-
0026744792
-
Regulation of even-skipped stripe 2 in the Drosophila embryo
-
Small S, Blair A, Levine M. 1992. Regulation of even-skipped stripe 2 in the Drosophila embryo. EMBO J 11: 4047-4057.
-
(1992)
EMBO J
, vol.11
, pp. 4047-4057
-
-
Small, S.1
Blair, A.2
Levine, M.3
-
69
-
-
84870058502
-
Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome
-
Soufi A, Donahue G, Zaret KS. 2012. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151: 994-1004.
-
(2012)
Cell
, vol.151
, pp. 994-1004
-
-
Soufi, A.1
Donahue, G.2
Zaret, K.S.3
-
70
-
-
33745744347
-
Mutations of the Drosophila zinc finger-encoding gene vielfaltig impair mitotic cell divisions and cause improper chromosome segregation
-
Staudt N, Fellert S, Chung HR, Jackle H, Vorbruggen G. 2006. Mutations of the Drosophila zinc finger-encoding gene vielfaltig impair mitotic cell divisions and cause improper chromosome segregation. Mol Biol Cell 17: 2356-2365.
-
(2006)
Mol Biol Cell
, vol.17
, pp. 2356-2365
-
-
Staudt, N.1
Fellert, S.2
Chung, H.R.3
Jackle, H.4
Vorbruggen, G.5
-
71
-
-
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, Small S. 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
Small, S.6
-
72
-
-
0024380401
-
The gradient morphogen bicoid is a concentration-dependent transcriptional activator
-
Struhl G, Struhl K, Macdonald PM. 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
-
73
-
-
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
-
74
-
-
33745106890
-
The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription
-
ten Bosch JR, Benavides JA, Cline TW. 2006. The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription. Development 133: 1967-1977.
-
(2006)
Development
, vol.133
, pp. 1967-1977
-
-
ten Bosch, J.R.1
Benavides, J.A.2
Cline, T.W.3
-
75
-
-
84871995408
-
GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility
-
Theodorou V, Stark R, Menon S, Carroll JS. 2013. GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility. Genome Res 23: 12-22.
-
(2013)
Genome Res
, vol.23
, pp. 12-22
-
-
Theodorou, V.1
Stark, R.2
Menon, S.3
Carroll, J.S.4
-
76
-
-
79955760882
-
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
-
Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, et al. 2011. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol 12: R43.
-
(2011)
Genome Biol
, vol.12
-
-
Thomas, S.1
Li, X.Y.2
Sabo, P.J.3
Sandstrom, R.4
Thurman, R.E.5
Canfield, T.K.6
Giste, E.7
Fisher, W.8
Hammonds, A.9
Celniker, S.E.10
-
77
-
-
0024397687
-
A single amino acid can determine the DNA binding specificity of homeodomain proteins
-
Treisman J, Gonczy P, Vashishtha M, Harris E, Desplan C. 1989. A single amino acid can determine the DNA binding specificity of homeodomain proteins. Cell 59: 553-562.
-
(1989)
Cell
, vol.59
, pp. 553-562
-
-
Treisman, J.1
Gonczy, P.2
Vashishtha, M.3
Harris, E.4
Desplan, C.5
-
78
-
-
33749400902
-
Temporal regulation of foregut development by HTZ-1/H2A. Z and PHA-4/FoxA
-
Updike DL, Mango SE. 2006. Temporal regulation of foregut development by HTZ-1/H2A. Z and PHA-4/FoxA. PLoS Genet 2: e161.
-
(2006)
PLoS Genet
, vol.2
-
-
Updike, D.L.1
Mango, S.E.2
-
79
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, 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
Holt, A.6
Plajzer-Frick, I.7
Shoukry, M.8
Wright, C.9
Chen, F.10
-
80
-
-
0027982060
-
Two homeo domain proteins bind with similar specificity to a wide range of DNA sites in Drosophila embryos
-
Walter J, Dever CA, Biggin MD. 1994. Two homeo domain proteins bind with similar specificity to a wide range of DNA sites in Drosophila embryos. Genes Dev 8: 1678-1692.
-
(1994)
Genes Dev
, vol.8
, pp. 1678-1692
-
-
Walter, J.1
Dever, C.A.2
Biggin, M.D.3
-
81
-
-
0028817034
-
Trans-and cis-acting requirements for blastodermal expression of the head gap gene buttonhead
-
Wimmer EA, Simpson-Brose M, Cohen SM, Desplan C, Jackle H. 1995. Trans-and cis-acting requirements for blastodermal expression of the head gap gene buttonhead. Mech Dev 53: 235-245.
-
(1995)
Mech Dev
, vol.53
, pp. 235-245
-
-
Wimmer, E.A.1
Simpson-Brose, M.2
Cohen, S.M.3
Desplan, C.4
Jackle, H.5
-
82
-
-
84865257761
-
Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
-
Yanez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A. 2012. Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding. Genome Res 22: 2018-2030.
-
(2012)
Genome Res
, vol.22
, pp. 2018-2030
-
-
Yanez-Cuna, J.O.1
Dinh, H.Q.2
Kvon, E.Z.3
Shlyueva, D.4
Stark, A.5
-
83
-
-
80455144479
-
Pioneer transcription factors: Establishing competence for gene expression
-
Zaret KS, Carroll JS. 2011. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 25: 2227-2241.
-
(2011)
Genes Dev
, vol.25
, pp. 2227-2241
-
-
Zaret, K.S.1
Carroll, J.S.2
-
84
-
-
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, Young RA, Levine M. 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
Young, R.A.6
Levine, M.7
-
85
-
-
53849146020
-
Model-based analysis of ChIP-seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based analysis of ChIP-seq (MACS). Genome Biol 9: R137.
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
-
86
-
-
84890397089
-
Predicting enhancer transcription and activity from chromatin modifications
-
Zhu Y, Sun L, Chen Z, Whitaker JW, Wang T, Wang W. 2013. Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Res 41: 10032-10043.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 10032-10043
-
-
Zhu, Y.1
Sun, L.2
Chen, Z.3
Whitaker, J.W.4
Wang, T.5
Wang, W.6
-
87
-
-
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
|