-
1
-
-
76949094155
-
Developmental gene regulation in the era of genomics
-
Zeitlinger J., Stark A. Developmental gene regulation in the era of genomics. Dev. Biol. 2010, 339:230-239.
-
(2010)
Dev. Biol.
, vol.339
, pp. 230-239
-
-
Zeitlinger, J.1
Stark, A.2
-
2
-
-
84860503075
-
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature
-
Kvon E.Z., et al. HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev. 2012, 26:908-913.
-
(2012)
Genes Dev.
, vol.26
, pp. 908-913
-
-
Kvon, E.Z.1
-
3
-
-
84863882671
-
Mechanisms of transcriptional precision in animal development
-
Lagha M., et al. Mechanisms of transcriptional precision in animal development. Trends Genet. 2012, 10.1016/j.tig.2012.03.006.
-
(2012)
Trends Genet.
-
-
Lagha, M.1
-
4
-
-
54249099196
-
Species-specific transcription in mice carrying human chromosome 21
-
Wilson M.D., et al. Species-specific transcription in mice carrying human chromosome 21. Science 2008, 322:434-438.
-
(2008)
Science
, vol.322
, pp. 434-438
-
-
Wilson, M.D.1
-
5
-
-
84865257761
-
Uncovering cis-regulatory sequence requirements for context specific transcription factor binding
-
Yanez-Cuna J.O., et al. Uncovering cis-regulatory sequence requirements for context specific transcription factor binding. Genome Res. 2012, 10.1101/gr.132811.111.
-
(2012)
Genome Res.
-
-
Yanez-Cuna, J.O.1
-
6
-
-
80054994283
-
Identification of genetic elements that autonomously determine DNA methylation states
-
Lienert F., et al. Identification of genetic elements that autonomously determine DNA methylation states. Nat. Genet. 2011, 43:1091-1097.
-
(2011)
Nat. Genet.
, vol.43
, pp. 1091-1097
-
-
Lienert, F.1
-
7
-
-
71749103442
-
Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information
-
Meireles-Filho A.C.A., Stark A. Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr. Opin. Genet. Dev. 2009, 19:565-570.
-
(2009)
Curr. Opin. Genet. Dev.
, vol.19
, pp. 565-570
-
-
Meireles-Filho, A.C.A.1
Stark, A.2
-
8
-
-
17044396348
-
Logic functions of the genomic cis-regulatory code
-
Istrail S., Davidson E.H. Logic functions of the genomic cis-regulatory code. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:4954-4959.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 4954-4959
-
-
Istrail, S.1
Davidson, E.H.2
-
9
-
-
77950833803
-
Variation in transcription factor binding among humans
-
Kasowski M., et al. Variation in transcription factor binding among humans. Science 2010, 328:232-235.
-
(2010)
Science
, vol.328
, pp. 232-235
-
-
Kasowski, M.1
-
10
-
-
84859916280
-
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
-
Reddy T.E., et al. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res. 2012, 22:860-869.
-
(2012)
Genome Res.
, vol.22
, pp. 860-869
-
-
Reddy, T.E.1
-
11
-
-
77950566643
-
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
-
Bradley R.K., et al. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 2010, 8:e1000343.
-
(2010)
PLoS Biol.
, vol.8
-
-
Bradley, R.K.1
-
12
-
-
79955471381
-
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
-
He Q., et al. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat. Genet. 2011, 43:414-420.
-
(2011)
Nat. Genet.
, vol.43
, pp. 414-420
-
-
He, Q.1
-
13
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt D., et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 2010, 328:1036-1040.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
-
14
-
-
46149104377
-
Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution
-
Carroll S.B. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 2008, 134:25-36.
-
(2008)
Cell
, vol.134
, pp. 25-36
-
-
Carroll, S.B.1
-
15
-
-
34548690542
-
Functional architecture and evolution of transcriptional elements that drive gene coexpression
-
Brown C.D., et al. Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 2007, 317:1557-1560.
-
(2007)
Science
, vol.317
, pp. 1557-1560
-
-
Brown, C.D.1
-
16
-
-
70449132583
-
Combinatorial binding predicts spatio-temporal cis-regulatory activity
-
Zinzen R.P., et al. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 2009, 462:65-70.
-
(2009)
Nature
, vol.462
, pp. 65-70
-
-
Zinzen, R.P.1
-
17
-
-
19344368645
-
Functional evolution of a cis-regulatory module
-
Ludwig M.Z., et al. Functional evolution of a cis-regulatory module. PLoS Biol. 2005, 3:e93.
-
(2005)
PLoS Biol.
, vol.3
-
-
Ludwig, M.Z.1
-
18
-
-
77950580571
-
Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer
-
Swanson C.I., et al. Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer. Dev. Cell 2010, 18:359-370.
-
(2010)
Dev. Cell
, vol.18
, pp. 359-370
-
-
Swanson, C.I.1
-
19
-
-
81755177824
-
Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness
-
Ludwig M.Z., et al. Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness. PLoS Genet. 2011, 7:e1002364.
-
(2011)
PLoS Genet.
, vol.7
-
-
Ludwig, M.Z.1
-
20
-
-
34347406754
-
The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron
-
Etchberger J.F., et al. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron. Genes Dev. 2007, 21:1653-1674.
-
(2007)
Genes Dev.
, vol.21
, pp. 1653-1674
-
-
Etchberger, J.F.1
-
21
-
-
1642289044
-
Coordinate enhancers share common organizational features in the Drosophila genome
-
Erives A., Levine M. Coordinate enhancers share common organizational features in the Drosophila genome. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:3851-3856.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 3851-3856
-
-
Erives, A.1
Levine, M.2
-
22
-
-
3042710549
-
A regulatory code for neurogenic gene expression in the Drosophila embryo
-
Markstein M., et al. A regulatory code for neurogenic gene expression in the Drosophila embryo. Development 2004, 131:2387-2394.
-
(2004)
Development
, vol.131
, pp. 2387-2394
-
-
Markstein, M.1
-
23
-
-
0036848430
-
Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms
-
Andrioli L.P.M., et al. Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms. Development 2002, 129:4931-4940.
-
(2002)
Development
, vol.129
, pp. 4931-4940
-
-
Andrioli, L.P.M.1
-
24
-
-
79960708456
-
Rapid evolutionary rewiring of a structurally constrained eye enhancer
-
Swanson C.I., et al. Rapid evolutionary rewiring of a structurally constrained eye enhancer. Curr. Biol. 2011, 21:1186-1196.
-
(2011)
Curr. Biol.
, vol.21
, pp. 1186-1196
-
-
Swanson, C.I.1
-
25
-
-
0029617947
-
Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome
-
Thanos D., Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 1995, 83:1091-1100.
-
(1995)
Cell
, vol.83
, pp. 1091-1100
-
-
Thanos, D.1
Maniatis, T.2
-
26
-
-
43749099875
-
Nucleosome organization in the Drosophila genome
-
Mavrich T.N., et al. Nucleosome organization in the Drosophila genome. Nature 2008, 453:358-362.
-
(2008)
Nature
, vol.453
, pp. 358-362
-
-
Mavrich, T.N.1
-
27
-
-
65249089637
-
Local DNA topography correlates with functional noncoding regions of the human genome
-
Parker S.C.J., et al. Local DNA topography correlates with functional noncoding regions of the human genome. Science 2009, 324:389-392.
-
(2009)
Science
, vol.324
, pp. 389-392
-
-
Parker, S.C.J.1
-
28
-
-
84863229330
-
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
-
Melnikov A., et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat. Biotechnol. 2012, 30:271-277.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 271-277
-
-
Melnikov, A.1
-
29
-
-
84863230316
-
Massively parallel functional dissection of mammalian enhancers in vivo
-
Patwardhan R.P., et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nat. Biotechnol. 2012, 30:265-270.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 265-270
-
-
Patwardhan, R.P.1
-
30
-
-
84862002321
-
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
-
Sharon E., et al. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat. Biotechnol. 2012, 10.1038/nbt.2205.
-
(2012)
Nat. Biotechnol.
-
-
Sharon, E.1
-
31
-
-
33745658106
-
Computational models for neurogenic gene expression in the Drosophila embryo
-
Zinzen R.P., et al. Computational models for neurogenic gene expression in the Drosophila embryo. Curr. Biol. 2006, 16:1358-1365.
-
(2006)
Curr. Biol.
, vol.16
, pp. 1358-1365
-
-
Zinzen, R.P.1
-
32
-
-
79958204355
-
The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity
-
Parker D.S., et al. The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity. Sci. Signal. 2011, 4:ra38.
-
(2011)
Sci. Signal.
, vol.4
-
-
Parker, D.S.1
-
33
-
-
77958096076
-
Determining the specificity of protein-DNA interactions
-
Stormo G.D., Zhao Y. Determining the specificity of protein-DNA interactions. Nat. Rev. Genet. 2010, 11:751-760.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 751-760
-
-
Stormo, G.D.1
Zhao, Y.2
-
34
-
-
79952113732
-
Motif discovery using expectation maximization and Gibbs' sampling
-
Stormo G.D. Motif discovery using expectation maximization and Gibbs' sampling. Methods Mol. Biol. 2010, 674:85-95.
-
(2010)
Methods Mol. Biol.
, vol.674
, pp. 85-95
-
-
Stormo, G.D.1
-
35
-
-
33646229522
-
Practical strategies for discovering regulatory DNA sequence motifs
-
MacIsaac K.D., Fraenkel E. Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput. Biol. 2006, 2:e36.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
MacIsaac, K.D.1
Fraenkel, E.2
-
36
-
-
77955015475
-
Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification
-
Aerts S., et al. Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. PLoS Biol. 2010, 8:e1000435.
-
(2010)
PLoS Biol.
, vol.8
-
-
Aerts, S.1
-
37
-
-
41449086977
-
Systematic identification of mammalian regulatory motifs' target genes and functions
-
Warner J.B., et al. Systematic identification of mammalian regulatory motifs' target genes and functions. Nat. Methods 2008, 5:347-353.
-
(2008)
Nat. Methods
, vol.5
, pp. 347-353
-
-
Warner, J.B.1
-
38
-
-
33745106890
-
The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription
-
ten Bosch J.R., et al. The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription. Development 2006, 133:1967-1977.
-
(2006)
Development
, vol.133
, pp. 1967-1977
-
-
ten Bosch, J.R.1
-
39
-
-
56749183626
-
The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila
-
Liang H-L., et al. The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila. Nature 2008, 456:400-403.
-
(2008)
Nature
, vol.456
, pp. 400-403
-
-
Liang, H.-L.1
-
40
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li X-Y., et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008, 6:e27.
-
(2008)
PLoS Biol.
, vol.6
-
-
Li, X.-Y.1
-
41
-
-
80055074510
-
Temporal coordination of gene networks by Zelda in the early Drosophila embryo
-
Nien C-Y., et al. Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLoS Genet. 2011, 7:e1002339.
-
(2011)
PLoS Genet.
, vol.7
-
-
Nien, C.-Y.1
-
42
-
-
80055073174
-
Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition
-
Harrison M.M., et al. Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLoS Genet. 2011, 7:e1002266.
-
(2011)
PLoS Genet.
, vol.7
-
-
Harrison, M.M.1
-
43
-
-
80052477170
-
Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer
-
Struffi P., et al. Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer. Development 2011, 10.1242/dev.065987.
-
(2011)
Development
-
-
Struffi, P.1
-
44
-
-
84871688165
-
Characterization of enhancer function from genome-wide analyses
-
Maston G.A., et al. Characterization of enhancer function from genome-wide analyses. Annu. Rev. Genomics Hum. Genet. 2012, 10.1146/annurev-genom-090711-163723.
-
(2012)
Annu. Rev. Genomics Hum. Genet.
-
-
Maston, G.A.1
-
45
-
-
84865708757
-
An expansive human regulatory lexicon encoded in transcription factor footprints
-
Neph S., et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012, 489:83-90.
-
(2012)
Nature
, vol.489
, pp. 83-90
-
-
Neph, S.1
-
46
-
-
83255164884
-
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
-
Rhee H.S., Pugh B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 2011, 147:1408-1419.
-
(2011)
Cell
, vol.147
, pp. 1408-1419
-
-
Rhee, H.S.1
Pugh, B.F.2
-
47
-
-
57749121616
-
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
-
Badis G., et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol. Cell 2008, 32:878-887.
-
(2008)
Mol. Cell
, vol.32
, pp. 878-887
-
-
Badis, G.1
-
48
-
-
43349107222
-
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
-
Noyes M.B., et al. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res. 2008, 36:2547-2560.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 2547-2560
-
-
Noyes, M.B.1
-
49
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis G., et al. Diversity and complexity in DNA recognition by transcription factors. Science 2009, 324:1720-1723.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
-
50
-
-
77953006022
-
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
-
Jolma A., et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 2010, 20:861-873.
-
(2010)
Genome Res.
, vol.20
, pp. 861-873
-
-
Jolma, A.1
-
51
-
-
45449115390
-
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
-
Berger M.F., et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 2008, 133:1266-1276.
-
(2008)
Cell
, vol.133
, pp. 1266-1276
-
-
Berger, M.F.1
-
52
-
-
82355191640
-
Enhanced Y1H assays for Arabidopsis
-
Gaudinier A., et al. Enhanced Y1H assays for Arabidopsis. Nat. Methods 2011, 8:1053-1055.
-
(2011)
Nat. Methods
, vol.8
, pp. 1053-1055
-
-
Gaudinier, A.1
-
53
-
-
33744972290
-
A gene-centered C. elegans protein-DNA interaction network
-
Deplancke B., et al. A gene-centered C. elegans protein-DNA interaction network. Cell 2006, 125:1193-1205.
-
(2006)
Cell
, vol.125
, pp. 1193-1205
-
-
Deplancke, B.1
-
54
-
-
82355191645
-
Automated protein-DNA interaction screening of Drosophila regulatory elements
-
Hens K., et al. Automated protein-DNA interaction screening of Drosophila regulatory elements. Nat. Methods 2011, 8:1065-1070.
-
(2011)
Nat. Methods
, vol.8
, pp. 1065-1070
-
-
Hens, K.1
-
55
-
-
84863890567
-
Genomic approaches towards finding cis-regulatory modules in animals
-
Hardison R.C., Taylor J. Genomic approaches towards finding cis-regulatory modules in animals. Nat. Rev. Genet. 2012, 13:469-483.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 469-483
-
-
Hardison, R.C.1
Taylor, J.2
-
56
-
-
80155137594
-
Master transcription factors determine cell-type-specific responses to TGF-β signaling
-
Mullen A.C., et al. Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell 2011, 147:565-576.
-
(2011)
Cell
, vol.147
, pp. 565-576
-
-
Mullen, A.C.1
-
57
-
-
80155123782
-
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration
-
Trompouki E., et al. Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell 2011, 147:577-589.
-
(2011)
Cell
, vol.147
, pp. 577-589
-
-
Trompouki, E.1
-
58
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz S., et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 2010, 38:576-589.
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
59
-
-
77951610155
-
Genetic analysis of variation in transcription factor binding in yeast
-
Zheng W., et al. Genetic analysis of variation in transcription factor binding in yeast. Nature 2010, 464:1187-1191.
-
(2010)
Nature
, vol.464
, pp. 1187-1191
-
-
Zheng, W.1
-
60
-
-
77953132064
-
A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites
-
Khoueiry P., et al. A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Curr. Biol. 2010, 20:792-802.
-
(2010)
Curr. Biol.
, vol.20
, pp. 792-802
-
-
Khoueiry, P.1
-
61
-
-
73649107243
-
Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila
-
Ho M.C.W., et al. Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. PLoS Genet. 2009, 5:e1000709.
-
(2009)
PLoS Genet.
, vol.5
-
-
Ho, M.C.W.1
-
62
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G., et al. Ultraconserved elements in the human genome. Science 2004, 304:1321-1325.
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
-
63
-
-
38649123306
-
Ultraconservation identifies a small subset of extremely constrained developmental enhancers
-
Visel A., et al. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat. Genet. 2008, 40:158-160.
-
(2008)
Nat. Genet.
, vol.40
, pp. 158-160
-
-
Visel, A.1
-
64
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
Bussemaker H.J., et al. Regulatory element detection using correlation with expression. Nat. Genet. 2001, 27:167-171.
-
(2001)
Nat. Genet.
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
-
65
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
Pilpel Y., et al. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 2001, 29:153-159.
-
(2001)
Nat. Genet.
, vol.29
, pp. 153-159
-
-
Pilpel, Y.1
-
66
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer M.A., Tavazoie S. Predicting gene expression from sequence. Cell 2004, 117:185-198.
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
67
-
-
36949030484
-
Predicting gene expression from sequence: a reexamination
-
Yuan Y., et al. Predicting gene expression from sequence: a reexamination. PLoS Comput. Biol. 2007, 3:e243.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Yuan, Y.1
-
68
-
-
0037154273
-
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
-
Berman B.P., et al. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:757-762.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 757-762
-
-
Berman, B.P.1
-
69
-
-
19344375742
-
Transcriptional control in the segmentation gene network of Drosophila
-
Schroeder M.D., et al. Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol. 2004, 2:E271.
-
(2004)
PLoS Biol.
, vol.2
-
-
Schroeder, M.D.1
-
70
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel A., et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009, 457:854-858.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
-
71
-
-
83055181959
-
Discriminative prediction of mammalian enhancers from DNA sequence
-
Lee D., et al. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011, 21:2167-2180.
-
(2011)
Genome Res.
, vol.21
, pp. 2167-2180
-
-
Lee, D.1
-
72
-
-
77649259719
-
Genome-wide discovery of human heart enhancers
-
Narlikar L., et al. Genome-wide discovery of human heart enhancers. Genome Res. 2010, 20:381-392.
-
(2010)
Genome Res.
, vol.20
, pp. 381-392
-
-
Narlikar, L.1
-
73
-
-
84859235405
-
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis
-
Busser B.W., et al. A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PLoS Genet. 2012, 8:e1002531.
-
(2012)
PLoS Genet.
, vol.8
-
-
Busser, B.W.1
-
74
-
-
77957034280
-
Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny
-
Rouault H., et al. Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny. Proc. Natl. Acad. Sci. U.S.A. 2010, 10.1073/pnas.1002876107.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
-
-
Rouault, H.1
-
75
-
-
47149110727
-
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
-
Van Loo P., et al. ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?. Genome Biol. 2008, 9:R66.
-
(2008)
Genome Biol.
, vol.9
-
-
Van Loo, P.1
-
76
-
-
67649826220
-
From DNA sequence to transcriptional behaviour: a quantitative approach
-
Segal E., Widom J. From DNA sequence to transcriptional behaviour: a quantitative approach. Nat. Rev. Genet. 2009, 10:443-456.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 443-456
-
-
Segal, E.1
Widom, J.2
-
77
-
-
33044497095
-
Transcriptional control in Drosophila
-
Reinitz J., et al. Transcriptional control in Drosophila. Complexus 2003, 1:54-64.
-
(2003)
Complexus
, vol.1
, pp. 54-64
-
-
Reinitz, J.1
-
78
-
-
33749137281
-
Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene
-
Janssens H., et al. Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat. Genet. 2006, 38:1159-1165.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1159-1165
-
-
Janssens, H.1
-
79
-
-
77956830473
-
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials
-
Kazemian M., et al. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol. 2010, 8:e1000456.
-
(2010)
PLoS Biol.
, vol.8
-
-
Kazemian, M.1
-
80
-
-
77958053631
-
Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects
-
Dresch J.M., et al. Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. BMC Syst. Biol. 2010, 4:142.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 142
-
-
Dresch, J.M.1
-
81
-
-
76149087772
-
Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo
-
Fakhouri W.D., et al. Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo. Mol. Syst. Biol. 2010, 6:341.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 341
-
-
Fakhouri, W.D.1
-
82
-
-
78049450019
-
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
-
He X., et al. Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Comput. Biol. 2010, 6:e1000935.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
He, X.1
-
83
-
-
54149090863
-
The evolution of cell types in animals: emerging principles from molecular studies
-
Arendt D. The evolution of cell types in animals: emerging principles from molecular studies. Nat. Rev. Genet. 2008, 9:868-882.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 868-882
-
-
Arendt, D.1
-
84
-
-
0034598832
-
Evidence for stabilizing selection in a eukaryotic enhancer element
-
Ludwig M.Z., et al. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 2000, 403:564-567.
-
(2000)
Nature
, vol.403
, pp. 564-567
-
-
Ludwig, M.Z.1
-
85
-
-
80052152362
-
Transphyletic conservation of developmental regulatory state in animal evolution
-
Royo J.L., et al. Transphyletic conservation of developmental regulatory state in animal evolution. Proc. Natl. Acad. Sci. U.S.A. 2011, 10.1073/pnas.1109037108.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
-
-
Royo, J.L.1
-
86
-
-
0028944665
-
Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila
-
Halder G., et al. Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. Science 1995, 267:1788-1792.
-
(1995)
Science
, vol.267
, pp. 1788-1792
-
-
Halder, G.1
-
87
-
-
32444446240
-
Gene regulatory networks and the evolution of animal body plans
-
Davidson E.H., Erwin D.H. Gene regulatory networks and the evolution of animal body plans. Science 2006, 311:796-800.
-
(2006)
Science
, vol.311
, pp. 796-800
-
-
Davidson, E.H.1
Erwin, D.H.2
-
88
-
-
54349112123
-
Evolution of the holozoan ribosome biogenesis regulon
-
Brown S.J., et al. Evolution of the holozoan ribosome biogenesis regulon. BMC Genomics 2008, 9:442.
-
(2008)
BMC Genomics
, vol.9
, pp. 442
-
-
Brown, S.J.1
-
89
-
-
74549118236
-
Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer
-
Chan Y.F., et al. Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 2010, 327:302-305.
-
(2010)
Science
, vol.327
, pp. 302-305
-
-
Chan, Y.F.1
-
90
-
-
79952386187
-
Human-specific loss of regulatory DNA and the evolution of human-specific traits
-
McLean C.Y., et al. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 2011, 471:216-219.
-
(2011)
Nature
, vol.471
, pp. 216-219
-
-
McLean, C.Y.1
-
91
-
-
13444304173
-
Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila
-
Gompel N., et al. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 2005, 433:481-487.
-
(2005)
Nature
, vol.433
, pp. 481-487
-
-
Gompel, N.1
-
92
-
-
79959825697
-
Morphological evolution caused by many subtle-effect substitutions in regulatory DNA
-
Frankel N., et al. Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature 2011, 474:598-603.
-
(2011)
Nature
, vol.474
, pp. 598-603
-
-
Frankel, N.1
-
93
-
-
70249088327
-
Genomic views of distant-acting enhancers
-
Visel A., et al. Genomic views of distant-acting enhancers. Nature 2009, 461:199-205.
-
(2009)
Nature
, vol.461
, pp. 199-205
-
-
Visel, A.1
-
94
-
-
0019811465
-
Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences
-
Banerji J., et al. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell 1981, 27:299-308.
-
(1981)
Cell
, vol.27
, pp. 299-308
-
-
Banerji, J.1
-
95
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
The modENCODE Consortium, et al.
-
The modENCODE Consortium, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010, 10.1126/science.1198374.
-
(2010)
Science
-
-
-
96
-
-
78650410139
-
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project
-
Gerstein M.B., et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project. Science 2010, 10.1126/science.1196914.
-
(2010)
Science
-
-
Gerstein, M.B.1
-
97
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium, et al.
-
ENCODE Project Consortium, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
98
-
-
0012252471
-
Systematic determination of patterns of gene expression during Drosophila embryogenesis
-
research0088.1-0088.14
-
Tomancak P., et al. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002, 3. research0088.1-0088.14.
-
(2002)
Genome Biol.
, vol.3
-
-
Tomancak, P.1
-
99
-
-
0342817350
-
Types of visible variations induced by X-rays in Drosophila
-
Muller H. Types of visible variations induced by X-rays in Drosophila. J. Genet. 1930, 22:299-334.
-
(1930)
J. Genet.
, vol.22
, pp. 299-334
-
-
Muller, H.1
-
100
-
-
84865249952
-
Transcription factors: from enhancer binding to developmental control
-
Spitz F., Furlong E.E.M. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 2012, 13:613-626.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 613-626
-
-
Spitz, F.1
Furlong, E.E.M.2
-
101
-
-
84870222914
-
Disentangling the many layers of eukaryotic transcriptional regulation
-
Lelli K.M., et al. Disentangling the many layers of eukaryotic transcriptional regulation. Annu. Rev. Genet. 2012, 10.1146/annurev-genet-110711-155437.
-
(2012)
Annu. Rev. Genet.
-
-
Lelli, K.M.1
-
102
-
-
79953176250
-
Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor
-
Ruf S., et al. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat. Genet. 2011, 43:379-386.
-
(2011)
Nat. Genet.
, vol.43
, pp. 379-386
-
-
Ruf, S.1
-
103
-
-
77957776228
-
Systematic protein location mapping reveals five principal chromatin types in Drosophila cells
-
Filion G.J., et al. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 2010, 10.1016/j.cell.2010.09.009.
-
(2010)
Cell
-
-
Filion, G.J.1
-
104
-
-
79957864084
-
Chromatin globules: a common motif of higher order chromosome structure?
-
Sanyal A., et al. Chromatin globules: a common motif of higher order chromosome structure?. Curr. Opin. Cell Biol. 2011, 23:325-331.
-
(2011)
Curr. Opin. Cell Biol.
, vol.23
, pp. 325-331
-
-
Sanyal, A.1
-
105
-
-
84855297335
-
A decade of 3C technologies: insights into nuclear organization
-
de Wit E., de Laat W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 2012, 26:11-24.
-
(2012)
Genes Dev.
, vol.26
, pp. 11-24
-
-
de Wit, E.1
de Laat, W.2
-
106
-
-
33745586053
-
FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
-
Adryan B., Teichmann S.A. FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics 2006, 22:1532-1533.
-
(2006)
Bioinformatics
, vol.22
, pp. 1532-1533
-
-
Adryan, B.1
Teichmann, S.A.2
-
107
-
-
44649193565
-
The RNA polymerase II core promoter - the gateway to transcription
-
Juven-Gershon T., et al. The RNA polymerase II core promoter - the gateway to transcription. Curr. Opin. Cell Biol. 2008, 20:253-259.
-
(2008)
Curr. Opin. Cell Biol.
, vol.20
, pp. 253-259
-
-
Juven-Gershon, T.1
-
108
-
-
84872256757
-
Machine learning and its applications to biology
-
Tarca A.L., et al. Machine learning and its applications to biology. PLoS Comput. Biol. 2007, 3:e116.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Tarca, A.L.1
-
109
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio L.A., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006, 444:499-502.
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
-
110
-
-
78651335916
-
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
-
Gallo S.M., et al. REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res. 2010, 10.1093/nar/gkq999.
-
(2010)
Nucleic Acids Res.
-
-
Gallo, S.M.1
-
111
-
-
84861529303
-
Enhancers as information integration hubs in development: lessons from genomics
-
Buecker C., Wysocka J. Enhancers as information integration hubs in development: lessons from genomics. Trends Genet. 2012, 28:276-284.
-
(2012)
Trends Genet.
, vol.28
, pp. 276-284
-
-
Buecker, C.1
Wysocka, J.2
-
112
-
-
12744263842
-
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
-
Berman B.P., et al. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 2004, 5:R61.
-
(2004)
Genome Biol.
, vol.5
-
-
Berman, B.P.1
-
113
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Drosophila 12 Genomes Consortium, et al.
-
Drosophila 12 Genomes Consortium, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007, 450:203-218.
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
-
114
-
-
84856998493
-
959 Nematode Genomes: a semantic wiki for coordinating sequencing projects
-
Kumar S., et al. 959 Nematode Genomes: a semantic wiki for coordinating sequencing projects. Nucleic Acids Res. 2012, 40:D1295-D1300.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Kumar, S.1
-
115
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
Lindblad-Toh K., et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 2011, 478:476-482.
-
(2011)
Nature
, vol.478
, pp. 476-482
-
-
Lindblad-Toh, K.1
-
116
-
-
14644390333
-
A model of the statistical power of comparative genome sequence analysis
-
Eddy S.R. A model of the statistical power of comparative genome sequence analysis. PLoS Biol. 2005, 3:e10.
-
(2005)
PLoS Biol.
, vol.3
-
-
Eddy, S.R.1
-
117
-
-
36049018312
-
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
-
Stark A., et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007, 450:219-232.
-
(2007)
Nature
, vol.450
, pp. 219-232
-
-
Stark, A.1
-
118
-
-
77956641239
-
ChIP-Seq identification of weakly conserved heart enhancers
-
Blow M.J., et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 2010, 42:806-810.
-
(2010)
Nat. Genet.
, vol.42
, pp. 806-810
-
-
Blow, M.J.1
-
120
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
Segal E., et al. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 2008, 451:535-540.
-
(2008)
Nature
, vol.451
, pp. 535-540
-
-
Segal, E.1
|