-
1
-
-
84861167698
-
Developmental regulation of chromatin conformation by Hox proteins in Drosophila
-
Agelopoulos, M., D. J. McKay, and R. S. Mann, 2012 Developmental regulation of chromatin conformation by Hox proteins in Drosophila. Cell Rep. 1: 350-359.
-
(2012)
Cell Rep
, vol.1
, pp. 350-359
-
-
Agelopoulos, M.1
McKay, D.J.2
Mann, R.S.3
-
2
-
-
79958090979
-
DREME: Motif discovery in transcription factor ChIP-seq data
-
Bailey, T. L., 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
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey, T. L., and C. Elkan, 1994 Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2: 28-36.
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
4
-
-
0031901903
-
Methods and statistics for combining motif match scores
-
Bailey, T. L., and M. Gribskov, 1998 Methods and statistics for combining motif match scores. J. Comput. Biol. 5: 211-221.
-
(1998)
J. Comput. Biol
, vol.5
, pp. 211-221
-
-
Bailey, T.L.1
Gribskov, M.2
-
5
-
-
84866937220
-
Inferring direct DNA binding from ChIP-seq
-
Bailey, T. L., and P. Machanick, 2012 Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res. 40: e128.
-
(2012)
Nucleic Acids Res
, vol.e128
, pp. 40
-
-
Bailey, T.L.1
Machanick, P.2
-
6
-
-
0036943581
-
Yan regulates Lozenge during Drosophila eye development
-
Behan, K. J., C. D. Nichols, T. L. Cheung, A. Farlow, B. M. Hogan et al., 2002 Yan regulates Lozenge during Drosophila eye development. Dev. Genes Evol. 212: 267-276.
-
(2002)
Dev. Genes Evol
, vol.212
, pp. 267-276
-
-
Behan, K.J.1
Nichols, C.D.2
Cheung, T.L.3
Farlow, A.4
Hogan, B.M.5
-
7
-
-
84856239091
-
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
-
Bonn, S., R. P. Zinzen, C. Girardot, E. H. Gustafson, A. Perez-Gonzalez 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
-
8
-
-
73649114935
-
Dissecting the regulatory switches of development: Lessons from enhancer evolution in Drosophila
-
Borok, M. J., D. A. Tran, M. C. Ho, and R. A. Drewell, 2010 Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila. Development 137: 5-13.
-
(2010)
Development
, vol.137
, pp. 5-13
-
-
Borok, M.J.1
Tran, D.A.2
Ho, M.C.3
Drewell, R.A.4
-
9
-
-
79551655285
-
Functional and mechanistic diversity of distal transcription enhancers
-
Bulger, M., and M. Groudine, 2011 Functional and mechanistic diversity of distal transcription enhancers. Cell 144: 327-339.
-
(2011)
Cell
, vol.144
, pp. 327-339
-
-
Bulger, M.1
Groudine, M.2
-
10
-
-
84865067902
-
New negative feedback regulators of EGFR signaling in Drosophila
-
Butchar, J. P., D. Cain, S. N. Manivannan, A. D. McCue, L. Bonanno et al., 2012 New negative feedback regulators of EGFR signaling in Drosophila. Genetics 191: 1213-1226.
-
(2012)
Genetics
, vol.191
, pp. 1213-1226
-
-
Butchar, J.P.1
Cain, D.2
Manivannan, S.N.3
McCue, A.D.4
Bonanno, L.5
-
11
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline, M. S., M. Smoot, E. Cerami, A. Kuchinsky, N. Landys et al., 2007 Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2: 2366-2382.
-
(2007)
Nat. Protoc
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
-
12
-
-
0035499392
-
Transcriptional repression: The long and the short of it
-
Courey, A. J., and S. Jia, 2001 Transcriptional repression: the long and the short of it. Genes Dev. 15: 2786-2796.
-
(2001)
Genes Dev
, vol.15
, pp. 2786-2796
-
-
Courey, A.J.1
Jia, S.2
-
13
-
-
80051928360
-
Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression
-
Dunipace, L., A. Ozdemir, and A. Stathopoulos, 2011 Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression. Development 138: 4075-4084.
-
(2011)
Development
, vol.138
, pp. 4075-4084
-
-
Dunipace, L.1
Ozdemir, A.2
Stathopoulos, A.3
-
14
-
-
0034730331
-
Combinatorial signaling in the specification of unique cell fates
-
Flores, G. V., H. Duan, H. Yan, R. Nagaraj, W. Fu et al., 2000 Combinatorial signaling in the specification of unique cell fates. Cell 103: 75-85.
-
(2000)
Cell
, vol.103
, pp. 75-85
-
-
Flores, G.V.1
Duan, H.2
Yan, H.3
Nagaraj, R.4
Fu, W.5
-
15
-
-
77954960062
-
Phenotypic robustness conferred by apparently redundant transcriptional enhancers
-
Frankel, N., G. K. Davis, D. Vargas, S. Wang, F. Payre 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
-
16
-
-
0034777594
-
Detection of cis-element clusters in higher eukaryotic DNA
-
Frith, M. C., U. Hansen, and Z. Weng, 2001 Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 17: 878-889.
-
(2001)
Bioinformatics
, vol.17
, pp. 878-889
-
-
Frith, M.C.1
Hansen, U.2
Weng, Z.3
-
17
-
-
0029904093
-
EGF receptor signaling induces pointed P1 transcription and inactivates Yan protein in the Drosophila embryonic ventral ectoderm
-
Gabay, L., H. Scholz, M. Golembo, A. Klaes, B. Z. Shilo et al., 1996 EGF receptor signaling induces pointed P1 transcription and inactivates Yan protein in the Drosophila embryonic ventral ectoderm. Development 122: 3355-3362.
-
(1996)
Development
, vol.122
, pp. 3355-3362
-
-
Gabay, L.1
Scholz, H.2
Golembo, M.3
Klaes, A.4
Shilo, B.Z.5
-
18
-
-
0029671192
-
Argos transcription is induced by the Drosophila EGF receptor pathway to form an inhibitory feedback loop
-
Golembo, M., R. Schweitzer, M. Freeman, and B. Z. Shilo, 1996 Argos transcription is induced by the Drosophila EGF receptor pathway to form an inhibitory feedback loop. Development 122: 223-230.
-
(1996)
Development
, vol.122
, pp. 223-230
-
-
Golembo, M.1
Schweitzer, R.2
Freeman, M.3
Shilo, B.Z.4
-
19
-
-
77954641668
-
Modeling bistable cell-fate choices in the Drosophila eye: Qualitative and quantitative perspectives
-
Graham, T. G., S. M. Tabei, A. R. Dinner, and I. Rebay, 2010 Modeling bistable cell-fate choices in the Drosophila eye: qualitative and quantitative perspectives. Development 137: 2265-2278.
-
(2010)
Development
, vol.137
, pp. 2265-2278
-
-
Graham, T.G.1
Tabei, S.M.2
Dinner, A.R.3
Rebay, I.4
-
20
-
-
77953315305
-
DNA binding by the ETS protein TEL (ETV6) is regulated by autoinhibition and self-association
-
Green, S. M., H. J. Coyne 3rd. L. P. McIntosh, and B. J. Graves, 2010 DNA binding by the ETS protein TEL (ETV6) is regulated by autoinhibition and self-association. J. Biol. Chem. 285: 18496-18504.
-
(2010)
J. Biol. Chem
, vol.285
, pp. 18496-18504
-
-
Green, S.M.1
Coyne, H.J.2
McIntosh, L.P.3
Graves, B.J.4
-
21
-
-
2442458847
-
Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31
-
Groth, A. C., M. Fish, R. Nusse, and M. P. Calos, 2004 Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. Genetics 166: 1775-1782.
-
(2004)
Genetics
, vol.166
, pp. 1775-1782
-
-
Groth, A.C.1
Fish, M.2
Nusse, R.3
Calos, M.P.4
-
22
-
-
0034730326
-
Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors
-
Halfon, M. S., A. Carmena, S. Gisselbrecht, C. M. Sackerson, F. Jimenez 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
-
23
-
-
79955471381
-
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
-
He, Q., A. F. Bardet, B. Patton, J. Purvis, J. Johnston et al., 2011 High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat. Genet. 43: 414-420.
-
(2011)
Nat. Genet
, vol.43
, pp. 414-420
-
-
He, Q.1
Bardet, A.F.2
Patton, B.3
Purvis, J.4
Johnston, J.5
-
24
-
-
51149097760
-
Shadow enhancers as a source of evolutionary novelty
-
Hong, J. W., D. A. Hendrix, and M. S. Levine, 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
-
25
-
-
0034684621
-
Sequence and functional properties of Ets genes in the model organism Drosophila
-
Hsu, T., and R. A. Schulz, 2000 Sequence and functional properties of Ets genes in the model organism Drosophila. Oncogene 19: 6409-6416.
-
(2000)
Oncogene
, vol.19
, pp. 6409-6416
-
-
Hsu, T.1
Schulz, R.A.2
-
26
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang, D. W., B. T. Sherman, and R. A. Lempicki, 2009a Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37: 1-13.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1-13
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
27
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources
-
Huang, D. W., B. T. Sherman, and R. A. Lempicki, 2009b Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc. 4: 44-57.
-
(2009)
Nat. Protoc
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
28
-
-
0031839403
-
The Drosophila Medea gene is required downstream of dpp and encodes a functional homolog of human Smad4
-
Hudson, J. B., S. D. Podos, K. Keith, S. L. Simpson, and E. L. Ferguson, 1998 The Drosophila Medea gene is required downstream of dpp and encodes a functional homolog of human Smad4. Development 125: 1407-1420.
-
(1998)
Development
, vol.125
, pp. 1407-1420
-
-
Hudson, J.B.1
Podos, S.D.2
Keith, K.3
Simpson, S.L.4
Ferguson, E.L.5
-
29
-
-
77954056894
-
On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence
-
Huen, D. S., and S. Russell, 2010 On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence. BMC Bioinformatics 11: 359.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 359
-
-
Huen, D.S.1
Russell, S.2
-
30
-
-
33747587864
-
Model-based analysis of tiling-arrays for ChIP-chip
-
Johnson, W. E., W. Li, C. A. Meyer, R. Gottardo, J. S. Carroll et al., 2006 Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA 103: 12457-12462.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 12457-12462
-
-
Johnson, W.E.1
Li, W.2
Meyer, C.A.3
Gottardo, R.4
Carroll, J.S.5
-
31
-
-
14644432436
-
Genome wide analysis of transcript levels after perturbation of the EGFR pathway in the Drosophila ovary
-
Jordan, K. C., S. D. Hatfield, M. Tworoger, E. J. Ward, K. A. Fischer et al., 2005 Genome wide analysis of transcript levels after perturbation of the EGFR pathway in the Drosophila ovary. Dev. Dyn. 232: 709-724.
-
(2005)
Dev. Dyn
, vol.232
, pp. 709-724
-
-
Jordan, K.C.1
Hatfield, S.D.2
Tworoger, M.3
Ward, E.J.4
Fischer, K.A.5
-
32
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko, P. V., M. Y. Tolstorukov, and P. J. Park, 2008 Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 26: 1351-1359.
-
(2008)
Nat. Biotechnol
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
33
-
-
0035421962
-
Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression
-
Kim, C. A., M. L. Phillips, W. Kim, M. Gingery, H. H. Tran et al., 2001 Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression. EMBO J. 20: 4173-4182.
-
(2001)
EMBO J
, vol.20
, pp. 4173-4182
-
-
Kim, C.A.1
Phillips, M.L.2
Kim, W.3
Gingery, M.4
Tran, H.H.5
-
34
-
-
0036260660
-
The SAM domain of polyhomeotic forms a helical polymer
-
Kim, C. A., M. Gingery, R. M. Pilpa, and J. U. Bowie, 2002 The SAM domain of polyhomeotic forms a helical polymer. Nat. Struct. Biol. 9: 453-457.
-
(2002)
Nat. Struct. Biol
, vol.9
, pp. 453-457
-
-
Kim, C.A.1
Gingery, M.2
Pilpa, R.M.3
Bowie, J.U.4
-
35
-
-
23044476138
-
Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer
-
Kim, C. A., M. R. Sawaya, D. Cascio, W. Kim, and J. U. Bowie, 2005 Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer. J. Biol. Chem. 280: 27769-27775.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 27769-27775
-
-
Kim, C.A.1
Sawaya, M.R.2
Cascio, D.3
Kim, W.4
Bowie, J.U.5
-
36
-
-
0027518831
-
The Drosophila gene pointed encodes two ETSlike proteins which are involved in the development of the midline glial cells
-
Klambt, C., 1993 The Drosophila gene pointed encodes two ETSlike proteins which are involved in the development of the midline glial cells. Development 117: 163-176.
-
(1993)
Development
, vol.117
, pp. 163-176
-
-
Klambt, C.1
-
37
-
-
58149178565
-
The UCSC Genome Browser Database: Update 2009
-
Kuhn, R. M., D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith et al., 2009 The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37: D755-D761.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Kuhn, R.M.1
Karolchik, D.2
Zweig, A.S.3
Wang, T.4
Smith, K.E.5
-
38
-
-
74949088391
-
Integration of data obtained by different experimental methods to determine the motifs in DNA sequences recognized by transcription-regulating factors
-
Kulakovskii, I. V., and V. Makeev, 2009 Integration of data obtained by different experimental methods to determine the motifs in DNA sequences recognized by transcription-regulating factors. Biofizika 54: 965-974.
-
(2009)
Biofizika
, vol.54
, pp. 965-974
-
-
Kulakovskii, I.V.1
Makeev, V.2
-
39
-
-
69849099700
-
Motif discovery and motif finding from genome-mapped DNase footprint data
-
Kulakovskiy, I. V., A. V. Favorov, and V. J. Makeev, 2009 Motif discovery and motif finding from genome-mapped DNase footprint data. Bioinformatics 25: 2318-2325.
-
(2009)
Bioinformatics
, vol.25
, pp. 2318-2325
-
-
Kulakovskiy, I.V.1
Favorov, A.V.2
Makeev, V.J.3
-
40
-
-
84865777819
-
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
-
Landt, S. G., G. K. Marinov, A. Kundaje, P. Kheradpour, F. Pauli et al., 2012 ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22: 1813-1831.
-
(2012)
Genome Res
, vol.22
, pp. 1813-1831
-
-
Landt, S.G.1
Marinov, G.K.2
Kundaje, A.3
Kheradpour, P.4
Pauli, F.5
-
41
-
-
24944522339
-
Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila
-
Lebrecht, D., M. Foehr, E. Smith, F. J. Lopes, C. E. Vanario-Alonso et al., 2005 Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. Proc. Natl. Acad. Sci. USA 102: 13176-13181.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 13176-13181
-
-
Lebrecht, D.1
Foehr, M.2
Smith, E.3
Lopes, F.J.4
Vanario-Alonso, C.E.5
-
42
-
-
33845925394
-
Chromatin immunoprecipitation and microarray-based analysis of protein location
-
Lee, T. I., S. E. Johnstone, and R. A. Young, 2006 Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 1: 729-748.
-
(2006)
Nat. Protoc
, vol.1
, pp. 729-748
-
-
Lee, T.I.1
Johnstone, S.E.2
Young, R.A.3
-
43
-
-
29244437868
-
A microRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye
-
Li, X., and R. W. Carthew, 2005 A microRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye. Cell 123: 1267-1277.
-
(2005)
Cell
, vol.123
, pp. 1267-1277
-
-
Li, X.1
Carthew, R.W.2
-
44
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li, X. Y., S. MacArthur, R. Bourgon, D. Nix, D. A. Pollard et al., 2008 Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 6: e27.
-
(2008)
PLoS Biol
, vol.e27
, pp. 6
-
-
Li, X.Y.1
Macarthur, S.2
Bourgon, R.3
Nix, D.4
Pollard, D.A.5
-
45
-
-
79953709415
-
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
-
Li, X. Y., S. Thomas, P. J. Sabo, M. B. Eisen, J. A. Stamatoyannopoulos et al., 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
-
46
-
-
81755177824
-
Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness
-
Ludwig, M. Z., and R. Manu Kittler, K. P. White, and M. Kreitman, 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
Manu, K.R.2
White, K.P.3
Kreitman, M.4
-
47
-
-
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., X. Y. Li, J. Li, J. B. Brown, H. C. Chu 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
-
48
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
modENCODE Consortium
-
modENCODE Consortium, S. Roy, J. Ernst, P. V. Kharchenko, P. Kheradpour 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
-
49
-
-
33646856965
-
Chromosomal distribution of PcG proteins during Drosophila development
-
Negre, N., J. Hennetin, L. V. Sun, S. Lavrov, M. Bellis et al., 2006 Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol. 4: e170.
-
(2006)
PLoS Biol
, vol.4
-
-
Negre, N.1
Hennetin, J.2
Sun, L.V.3
Lavrov, S.4
Bellis, M.5
-
50
-
-
79953046943
-
A cis-regulatory map of the Drosophila genome
-
Negre, N., C. D. Brown, L. Ma, C. A. Bristow, S. W. Miller et al., 2011 A cis-regulatory map of the Drosophila genome. Nature 471: 527-531.
-
(2011)
Nature
, vol.471
, pp. 527-531
-
-
Negre, N.1
Brown, C.D.2
Ma, L.3
Bristow, C.A.4
Miller, S.W.5
-
51
-
-
0019133661
-
Mutations affecting segment number and polarity in Drosophila
-
Nusslein-Volhard, C., and E. Wieschaus, 1980 Mutations affecting segment number and polarity in Drosophila. Nature 287: 795-801.
-
(1980)
Nature
, vol.287
, pp. 795-801
-
-
Nusslein-Volhard, C.1
Wieschaus, E.2
-
52
-
-
0031444518
-
Spitz and Wingless, emanating from distinct borders, cooperate to establish cell fate across the Engrailed domain in the Drosophila epidermis
-
O'Keefe, L., S. T. Dougan, L. Gabay, E. Raz, B. Z. Shilo et al., 1997 Spitz and Wingless, emanating from distinct borders, cooperate to establish cell fate across the Engrailed domain in the Drosophila epidermis. Development 124: 4837-4845.
-
(1997)
Development
, vol.124
, pp. 4837-4845
-
-
O'Keefe, L.1
Dougan, S.T.2
Gabay, L.3
Raz, E.4
Shilo, B.Z.5
-
53
-
-
80053563150
-
Yan, an ETS-domain transcription factor, negatively modulates the Wingless pathway in the Drosophila eye
-
Olson, E. R., R. Pancratov, S. S. Chatterjee, B. Changkakoty, Z. Pervaiz et al., 2011 Yan, an ETS-domain transcription factor, negatively modulates the Wingless pathway in the Drosophila eye. EMBO Rep. 12: 1047-1054.
-
(2011)
EMBO Rep
, vol.12
, pp. 1047-1054
-
-
Olson, E.R.1
Pancratov, R.2
Chatterjee, S.S.3
Changkakoty, B.4
Pervaiz, Z.5
-
54
-
-
0028239896
-
The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway
-
O'Neill, E. M., I. Rebay, R. Tjian, and G. M. Rubin, 1994 The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway. Cell 78: 137-147.
-
(1994)
Cell
, vol.78
, pp. 137-147
-
-
O'Neill, E.M.1
Rebay, I.2
Tjian, R.3
Rubin, G.M.4
-
55
-
-
77956521381
-
Shadow enhancers foster robustness of Drosophila gastrulation
-
Perry, M. W., A. N. Boettiger, J. P. Bothma, and M. Levine, 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
-
56
-
-
80052007879
-
Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo
-
Perry, M. W., A. N. Boettiger, and M. Levine, 2011 Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 108: 13570-13575.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 13570-13575
-
-
Perry, M.W.1
Boettiger, A.N.2
Levine, M.3
-
57
-
-
0033067603
-
The yan gene is highly conserved in Drosophila and its expression suggests a complex role throughout development
-
Price, M. D., and Z. Lai, 1999 The yan gene is highly conserved in Drosophila and its expression suggests a complex role throughout development. Dev. Genes Evol. 209: 207-217.
-
(1999)
Dev. Genes Evol
, vol.209
, pp. 207-217
-
-
Price, M.D.1
Lai, Z.2
-
59
-
-
3242688256
-
Derepression by depolymerization; structural insights into the regulation of Yan by Mae
-
Qiao, F., H. Song, C. A. Kim, M. R. Sawaya, J. B. Hunter et al., 2004 Derepression by depolymerization; structural insights into the regulation of Yan by Mae. Cell 118: 163-173.
-
(2004)
Cell
, vol.118
, pp. 163-173
-
-
Qiao, F.1
Song, H.2
Kim, C.A.3
Sawaya, M.R.4
Hunter, J.B.5
-
60
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A. R., and I. M. Hall, 2010 BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
61
-
-
0029019928
-
Yan functions as a general inhibitor of differentiation and is negatively regulated by activation of the Ras1/MAPK pathway
-
Rebay, I., and G. M. Rubin, 1995 Yan functions as a general inhibitor of differentiation and is negatively regulated by activation of the Ras1/MAPK pathway. Cell 81: 857-866.
-
(1995)
Cell
, vol.81
, pp. 857-866
-
-
Rebay, I.1
Rubin, G.M.2
-
62
-
-
0030797351
-
Drosophila Jun kinase regulates expression of decapentaplegic via the ETS-domain protein Aop and the AP-1 transcription factor DJun during dorsal closure
-
Riesgo-Escovar, J. R., and E. Hafen, 1997 Drosophila Jun kinase regulates expression of decapentaplegic via the ETS-domain protein Aop and the AP-1 transcription factor DJun during dorsal closure. Genes Dev. 11: 1717-1727.
-
(1997)
Genes Dev
, vol.11
, pp. 1717-1727
-
-
Riesgo-Escovar, J.R.1
Hafen, E.2
-
63
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson, G., M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao et al., 2007 Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4: 651-657.
-
(2007)
Nat. Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
-
64
-
-
84863337963
-
The growth-suppressive function of the polycomb group protein polyhomeotic is mediated by polymerization of its sterile alpha motif (SAM) domain
-
Robinson, A. K., B. Z. Leal, L. V. Chadwell, R. Wang, U. Ilangovan et al., 2012 The growth-suppressive function of the polycomb group protein polyhomeotic is mediated by polymerization of its sterile alpha motif (SAM) domain. J. Biol. Chem. 287: 8702-8713.
-
(2012)
J. Biol. Chem
, vol.287
, pp. 8702-8713
-
-
Robinson, A.K.1
Leal, B.Z.2
Chadwell, L.V.3
Wang, R.4
Ilangovan, U.5
-
65
-
-
0029562617
-
The role of yan in mediating the choice between cell division and differentiation
-
Rogge, R., P. J. Green, J. Urano, S. Horn-Saban, M. Mlodzik et al., 1995 The role of yan in mediating the choice between cell division and differentiation. Development 121: 3947-3958.
-
(1995)
Development
, vol.121
, pp. 3947-3958
-
-
Rogge, R.1
Green, P.J.2
Urano, J.3
Horn-Saban, S.4
Mlodzik, M.5
-
66
-
-
0037006801
-
Notch activation of yan expression is antagonized by RTK/pointed signaling in the Drosophila eye
-
Rohrbaugh, M., E. Ramos, D. Nguyen, M. Price, Y. Wen et al., 2002 Notch activation of yan expression is antagonized by RTK/pointed signaling in the Drosophila eye. Curr. Biol. 12: 576-581.
-
(2002)
Curr. Biol
, vol.12
, pp. 576-581
-
-
Rohrbaugh, M.1
Ramos, E.2
Nguyen, D.3
Price, M.4
Wen, Y.5
-
67
-
-
0035022705
-
Long-range repression by multiple polycomb group (PcG) proteins targeted by fusion to a defined DNA-binding domain in Drosophila
-
Roseman, R. R., K. Morgan, D. R. Mallin, R. Roberson, T. J. Parnell et al., 2001 Long-range repression by multiple polycomb group (PcG) proteins targeted by fusion to a defined DNA-binding domain in Drosophila. Genetics 158: 291-307.
-
(2001)
Genetics
, vol.158
, pp. 291-307
-
-
Roseman, R.R.1
Morgan, K.2
Mallin, D.R.3
Roberson, R.4
Parnell, T.J.5
-
68
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
Roy, S., J. Ernst, P. V. Kharchenko, P. Kheradpour, N. Negre 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
-
69
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky, J., G. Euskirchen, R. K. Auerbach, Z. D. Zhang, T. Gibson et al., 2009 PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 27: 66-75.
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
-
70
-
-
0027438201
-
Genetic dissection of pointed, a Drosophila gene encoding two ETS-related proteins
-
Scholz, H., J. Deatrick, A. Klaes, and C. Klambt, 1993 Genetic dissection of pointed, a Drosophila gene encoding two ETS-related proteins. Genetics 135: 455-468.
-
(1993)
Genetics
, vol.135
, pp. 455-468
-
-
Scholz, H.1
Deatrick, J.2
Klaes, A.3
Klambt, C.4
-
71
-
-
0031159623
-
Control of midline glia development in the embryonic Drosophila CNS
-
Scholz, H., E. Sadlowski, A. Klaes, and C. Klambt, 1997 Control of midline glia development in the embryonic Drosophila CNS. Mech. Dev. 64: 137-151.
-
(1997)
Mech. Dev
, vol.64
, pp. 137-151
-
-
Scholz, H.1
Sadlowski, E.2
Klaes, A.3
Klambt, C.4
-
72
-
-
33745225872
-
Genome-wide analysis of Polycomb targets in Drosophila melanogaster
-
Schwartz, Y. B., T. G. Kahn, D. A. Nix, X. Y. Li, R. Bourgon et al., 2006 Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat. Genet. 38: 700-705.
-
(2006)
Nat. Genet
, vol.38
, pp. 700-705
-
-
Schwartz, Y.B.1
Kahn, T.G.2
Nix, D.A.3
Li, X.Y.4
Bourgon, R.5
-
73
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
Segal, E., T. Raveh-Sadka, M. Schroeder, U. Unnerstall, and U. Gaul, 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
-
74
-
-
0028940853
-
Genetic characterization and cloning of mothers against dpp, a gene required for decapentaplegic function in Drosophila melanogaster
-
Sekelsky, J. J., S. J. Newfeld, L. A. Raftery, E. H. Chartoff, and W. M. Gelbart, 1995 Genetic characterization and cloning of mothers against dpp, a gene required for decapentaplegic function in Drosophila melanogaster. Genetics 139: 1347-1358.
-
(1995)
Genetics
, vol.139
, pp. 1347-1358
-
-
Sekelsky, J.J.1
Newfeld, S.J.2
Raftery, L.A.3
Chartoff, E.H.4
Gelbart, W.M.5
-
75
-
-
23744450036
-
Antagonistic regulation of Yan nuclear export by Mae and Crm1 may increase the stringency of the Ras response
-
Song, H., M. Nie, F. Qiao, J. U. Bowie, and A. J. Courey, 2005 Antagonistic regulation of Yan nuclear export by Mae and Crm1 may increase the stringency of the Ras response. Genes Dev. 19: 1767-1772.
-
(2005)
Genes Dev
, vol.19
, pp. 1767-1772
-
-
Song, H.1
Nie, M.2
Qiao, F.3
Bowie, J.U.4
Courey, A.J.5
-
76
-
-
78651324347
-
The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored
-
Szklarczyk, D., A. Franceschini, M. Kuhn, M. Simonovic, A. Roth et al., 2011 The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39: D561-D568.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
-
77
-
-
0037249501
-
PANTHER: A browsable database of gene products organized by biological function, using curated protein family and subfamily classification
-
Thomas, P. D., A. Kejariwal, M. J. Campbell, H. Mi, K. Diemer et al., 2003 PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 31: 334-341.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 334-341
-
-
Thomas, P.D.1
Kejariwal, A.2
Campbell, M.J.3
Mi, H.4
Diemer, K.5
-
78
-
-
33745258986
-
Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster
-
Tolhuis, B., E. de Wit, I. Muijrers, H. Teunissen, W. Talhout et al., 2006 Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat. Genet. 38: 694-699.
-
(2006)
Nat. Genet
, vol.38
, pp. 694-699
-
-
Tolhuis, B.1
de Wit, E.2
Muijrers, I.3
Teunissen, H.4
Talhout, W.5
-
79
-
-
0012252471
-
Systematic determination of patterns of gene expression during Drosophila embryogenesis
-
RESEARCH0088
-
Tomancak, P., A. Beaton, R. Weiszmann, E. Kwan, S. Shu et al., 2002 Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 3: RESEARCH0088.
-
(2002)
Genome Biol
, vol.3
-
-
Tomancak, P.1
Beaton, A.2
Weiszmann, R.3
Kwan, E.4
Shu, S.5
-
80
-
-
38349127974
-
Global analysis of patterns of gene expression during Drosophila embryogenesis
-
Tomancak, P., B. P. Berman, A. Beaton, R. Weiszmann, E. Kwan et al., 2007 Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 8: R145.
-
(2007)
Genome Biol
, vol.8
-
-
Tomancak, P.1
Berman, B.P.2
Beaton, A.3
Weiszmann, R.4
Kwan, E.5
-
81
-
-
0037348614
-
CRM1-mediated nuclear export and regulated activity of the Receptor Tyrosine Kinase antagonist YAN require specific interactions with MAE
-
Tootle, T. L., P. S. Lee, and I. Rebay, 2003 CRM1-mediated nuclear export and regulated activity of the Receptor Tyrosine Kinase antagonist YAN require specific interactions with MAE. Development 130: 845-857.
-
(2003)
Development
, vol.130
, pp. 845-857
-
-
Tootle, T.L.1
Lee, P.S.2
Rebay, I.3
-
82
-
-
3342971065
-
Native interface of the SAM domain polymer of TEL
-
Tran, H. H., C. A. Kim, S. Faham, M. C. Siddall, and J. U. Bowie, 2002 Native interface of the SAM domain polymer of TEL. BMC Struct. Biol. 2: 5.
-
(2002)
BMC Struct. Biol
, vol.2
, pp. 5
-
-
Tran, H.H.1
Kim, C.A.2
Faham, S.3
Siddall, M.C.4
Bowie, J.U.5
-
83
-
-
7044232153
-
MAE, a dual regulator of the EGFR signaling pathway, is a target of the Ets transcription factors PNT and YAN
-
Vivekanand, P., T. L. Tootle, and I. Rebay, 2004 MAE, a dual regulator of the EGFR signaling pathway, is a target of the Ets transcription factors PNT and YAN. Mech. Dev. 121: 1469-1479.
-
(2004)
Mech. Dev
, vol.121
, pp. 1469-1479
-
-
Vivekanand, P.1
Tootle, T.L.2
Rebay, I.3
-
84
-
-
77954954652
-
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
-
Wei, G. H., G. Badis, M. F. Berger, T. Kivioja, K. Palin et al., 2010 Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J. 29: 2147-2160.
-
(2010)
EMBO J
, vol.29
, pp. 2147-2160
-
-
Wei, G.H.1
Badis, G.2
Berger, M.F.3
Kivioja, T.4
Palin, K.5
-
85
-
-
0034730329
-
Overlapping activators and repressors delimit transcriptional response to receptor tyrosine kinase signals in the Drosophila eye
-
Xu, C., R. C. Kauffmann, J. Zhang, S. Kladny, and R. W. Carthew, 2000 Overlapping activators and repressors delimit transcriptional response to receptor tyrosine kinase signals in the Drosophila eye. Cell 103: 87-97.
-
(2000)
Cell
, vol.103
, pp. 87-97
-
-
Xu, C.1
Kauffmann, R.C.2
Zhang, J.3
Kladny, S.4
Carthew, R.W.5
-
86
-
-
76749109939
-
Sterile alpha motif domain-mediated self-association plays an essential role in modulating the activity of the Drosophila ETS family transcriptional repressor Yan
-
Zhang, J., T. G. Graham, P. Vivekanand, L. Cote, M. Cetera et al., 2010 Sterile alpha motif domain-mediated self-association plays an essential role in modulating the activity of the Drosophila ETS family transcriptional repressor Yan. Mol. Cell. Biol. 30: 1158-1170.
-
(2010)
Mol. Cell. Biol
, vol.30
, pp. 1158-1170
-
-
Zhang, J.1
Graham, T.G.2
Vivekanand, P.3
Cote, L.4
Cetera, M.5
-
87
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y., T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson 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
-
88
-
-
77649225979
-
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response
-
Zhong, M., W. Niu, Z. J. Lu, M. Sarov, J. I. Murray et al., 2010 Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 6: e1000848.
-
(2010)
PLoS Genet
, vol.6
-
-
Zhong, M.1
Niu, W.2
Lu, Z.J.3
Sarov, M.4
Murray, J.I.5
-
89
-
-
70449132583
-
Combinatorial binding predicts spatio-temporal cis-regulatory activity
-
Zinzen, R. P., C. Girardot, J. Gagneur, M. Braun, and E. E. Furlong, 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
|