-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
-
2
-
-
0028292659
-
Fly Base - the Drosophila genetic database
-
Ashburner, M. and Drysdale, R. (1994) Fly Base - the Drosophila genetic database. Development, 120, 2077-2079.
-
(1994)
Development
, vol.120
, pp. 2077-2079
-
-
Ashburner, M.1
Drysdale, R.2
-
3
-
-
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. (2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA, 99, 757-762.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 757-762
-
-
Berman, B.P.1
-
4
-
-
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. (2004) Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol., 5, R61.
-
(2004)
Genome Biol.
, vol.5
-
-
Berman, B.P.1
-
5
-
-
0036107903
-
Discovery of regulatory elements by a computational method for phylogenetic footprinting
-
Blanchette, M. and Tompa, M. (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res., 12, 739-749.
-
(2002)
Genome Res.
, vol.12
, pp. 739-749
-
-
Blanchette, M.1
Tompa, M.2
-
6
-
-
27744473016
-
Using hexamers to predict cis-regulatory motifs in Drosophila
-
Chan, B.Y. and Kibler, D. (2005) Using hexamers to predict cis-regulatory motifs in Drosophila. BMC Bioinformatics, 6, 262.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 262
-
-
Chan, B.Y.1
Kibler, D.2
-
7
-
-
0034919548
-
Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis
-
Cliften, P.F. et al. (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res., 11, 1175-1186.
-
(2001)
Genome Res.
, vol.11
, pp. 1175-1186
-
-
Cliften, P.F.1
-
8
-
-
22344442009
-
Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements
-
Corcoran, D.L. et al. (2005) Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements. Genome Res., 15, 840-847.
-
(2005)
Genome Res.
, vol.15
, pp. 840-847
-
-
Corcoran, D.L.1
-
9
-
-
1642289044
-
Coordinate enhancers share common organizational features in the Drosophila genome
-
Erives, A. and Levine, M. (2004) Coordinate enhancers share common organizational features in the Drosophila genome. Proc. Natl Acad. Sci. USA, 101, 3851-3856.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 3851-3856
-
-
Erives, A.1
Levine, M.2
-
10
-
-
32144456548
-
REDfly: a Regulatory Element Database for Drosophila
-
Gallo, S.M. et al. (2006) REDfly: a Regulatory Element Database for Drosophila. Bioinformatics, 22, 381-383.
-
(2006)
Bioinformatics
, vol.22
, pp. 381-383
-
-
Gallo, S.M.1
-
11
-
-
0034284481
-
Conserved noncoding sequences are reliable guides to regulatory elements
-
Hardison, R.C. (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet., 16, 369-372.
-
(2000)
Trends Genet.
, vol.16
, pp. 369-372
-
-
Hardison, R.C.1
-
12
-
-
46249134068
-
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
-
Hare, E.E. et al. (2008) Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet., 4, e1000106.
-
(2008)
PLoS Genet.
, vol.4
-
-
Hare, E.E.1
-
13
-
-
51149097760
-
Shadow enhancers as a source of evolutionary novelty
-
Hong, J.W. et al. (2008) Shadow enhancers as a source of evolutionary novelty. Science, 321, 1314.
-
(2008)
Science
, vol.321
, pp. 1314
-
-
Hong, J.W.1
-
14
-
-
46249100442
-
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
-
Ivan, A. et al. (2008) Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol., 9, R22.
-
(2008)
Genome Biol.
, vol.9
-
-
Ivan, A.1
-
15
-
-
34547844142
-
A statistical method for alignment-free comparison of regulatory sequences
-
Kantorovitz, M.R. et al. (2007) A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics, 23, i249-i255.
-
(2007)
Bioinformatics
, vol.23
-
-
Kantorovitz, M.R.1
-
16
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis, M. et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
-
17
-
-
70249151095
-
Identifying cis-regulatory sequences by word profile similarity
-
Leung, G. and Eisen, M.B. (2009) Identifying cis-regulatory sequences by word profile similarity. PLoS ONE, 4, e6901.
-
(2009)
PLoS ONE
, vol.4
-
-
Leung, G.1
Eisen, M.B.2
-
18
-
-
0036105591
-
rVista for comparative sequence-based discovery of functional transcription factor binding sites
-
Loots, G.G. et al. (2002) rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res., 12, 832-839.
-
(2002)
Genome Res.
, vol.12
, pp. 832-839
-
-
Loots, G.G.1
-
19
-
-
0031889035
-
Functional analysis of eve strip 2 enhancer evolution in Drosophila: rules governing conservation and change
-
Ludwig, M.Z. et al. (1998) Functional analysis of eve strip 2 enhancer evolution in Drosophila: rules governing conservation and change. Development, 125, 949-958.
-
(1998)
Development
, vol.125
, pp. 949-958
-
-
Ludwig, M.Z.1
-
20
-
-
0034598832
-
Evidence for stabilizing selection in a eukaryotic enhancer element
-
Ludwig, M.Z. et al. (2002) Evidence for stabilizing selection in a eukaryotic enhancer element. Nature, 403, 564-567.
-
(2002)
Nature
, vol.403
, pp. 564-567
-
-
Ludwig, M.Z.1
-
21
-
-
0036889175
-
Functional evolution of noncoding DNA
-
Ludwig, M.Z. (2002) Functional evolution of noncoding DNA. Curr. Opin. Genet. Dev., 12, 634-639.
-
(2002)
Curr. Opin. Genet. Dev.
, vol.12
, pp. 634-639
-
-
Ludwig, M.Z.1
-
22
-
-
0036777340
-
Decoding cis-regulatory DNAs in the Drosophila genome
-
Markstein, M. and Levine, M. (2002) Decoding cis-regulatory DNAs in the Drosophila genome. Curr. Opin. Genet. Dev., 12, 601-606.
-
(2002)
Curr. Opin. Genet. Dev.
, vol.12
, pp. 601-606
-
-
Markstein, M.1
Levine, M.2
-
23
-
-
2942517992
-
Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency
-
Nazina, A.G. and Papatsenko, D.A. (2003) Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency. BMC Bioinformatics, 4, 65.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 65
-
-
Nazina, A.G.1
Papatsenko, D.A.2
-
24
-
-
17044380888
-
Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo
-
Papatsenko, D. and Levine, M. (2005) Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. Proc. Natl Acad. Sci. USA, 102, 4966-5971.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4966-5971
-
-
Papatsenko, D.1
Levine, M.2
-
25
-
-
0036956224
-
Comparing gene expression profiles in genes with similar promoter regions
-
Park, P.J. et al. (2002) Comparing gene expression profiles in genes with similar promoter regions. Bioinformatics, 18, 1576-1584.
-
(2002)
Bioinformatics
, vol.18
, pp. 1576-1584
-
-
Park, P.J.1
-
26
-
-
1542537849
-
Combining phylogenetic and hidden markov models in biosequence analysis
-
Siepel, A. and Haussler, D. (2004) Combining phylogenetic and hidden markov models in biosequence analysis. J. Comput. Biol., 11, 413-428.
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 413-428
-
-
Siepel, A.1
Haussler, D.2
-
27
-
-
34547540506
-
Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting
-
Sosinsky, A. et al. (2007) Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc. Natl Acad. Sci. USA, 104, 6305-6310.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 6305-6310
-
-
Sosinsky, A.1
-
28
-
-
38349127974
-
Global analysis of patterns of gene expression during Drosophila embryogenesis
-
Tomancak, P. 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
-
29
-
-
1342309208
-
Metrics for comparing regulatory sequences on the basis of pattern counts
-
van Helden, J. (2004) Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics, 20, 399-406.
-
(2004)
Bioinformatics
, vol.20
, pp. 399-406
-
-
van Helden, J.1
-
30
-
-
0037342499
-
Alignment-free sequence comparison-a review
-
Vinga, S. and Almeida, J. (2003) Alignment-free sequence comparison-a review. Bioinformatics, 19, 513-523.
-
(2003)
Bioinformatics
, vol.19
, pp. 513-523
-
-
Vinga, S.1
Almeida, J.2
-
31
-
-
0344906814
-
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
-
Wang, T. and Stormo, G.D. (2003) Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics, 19, 2369-2380
-
(2003)
Bioinformatics
, vol.19
, pp. 2369-2380
-
-
Wang, T.1
Stormo, G.D.2
-
32
-
-
0032903438
-
Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis
-
Wolff, C. et al. (1999) Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis. Mech. Dev., 80, 87-99.
-
(1999)
Mech. Dev.
, vol.80
, pp. 87-99
-
-
Wolff, C.1
|