-
1
-
-
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
-
2
-
-
1542748076
-
-
Aligning multiple genomic sequences with the threaded blockset aligner
-
Blanchette,M. et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14, 708-715.
-
(2004)
Genome Res
, vol.14
, pp. 708-715
-
-
Blanchette, M.1
-
3
-
-
0242418246
-
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
-
Boffelli,D. et al. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science, 299, 1391-1394.
-
(2003)
Science
, vol.299
, pp. 1391-1394
-
-
Boffelli, D.1
-
4
-
-
34547874585
-
Divergence of transcription factor binding sites across related yeast species
-
Borneman,A.R. et al. (2007) Divergence of transcription factor binding sites across related yeast species. Science, 317, 815-819.
-
(2007)
Science
, vol.317
, pp. 815-819
-
-
Borneman, A.R.1
-
5
-
-
0037398368
-
Lagan and multi-lagan: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno,M. et al. (2003) Lagan and multi-lagan: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13 721-731.
-
(2003)
Genome Res
, vol.13
, pp. 721-731
-
-
Brudno, M.1
-
6
-
-
0042121237
-
Multiple sequence alignment with the clustal series of programs
-
Chenna,R. et al. (2003) Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res., 31, 3497-3500.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
-
7
-
-
34249723155
-
Frequent gain and loss of functional transcription factor binding sites
-
Doniger,S.W. and Fay,J.C. (2007) Frequent gain and loss of functional transcription factor binding sites. PLoS Comput. Biol., 3, e99.
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Doniger, S.W.1
Fay, J.C.2
-
8
-
-
14644390333
-
A model of the statistical power of comparative genome sequence analysis
-
Eddy,S.R. (2005) A model of the statistical power of comparative genome sequence analysis. PLoS Biol., 3, e10.
-
(2005)
PLoS Biol
, vol.3
-
-
Eddy, S.R.1
-
9
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein,J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol., 17, 368-376.
-
(1981)
J. Mol. Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
10
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz,J. (2008) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature, 457, 215-218.
-
(2008)
Nature
, vol.457
, pp. 215-218
-
-
Gertz, J.1
-
11
-
-
33745737494
-
Myc-binding-site recognition in the human genome is determined by chromatin context
-
764-U225
-
Guccione,E. (2006) Myc-binding-site recognition in the human genome is determined by chromatin context. Nat. Cell Biol., 8, 764-U225.
-
(2006)
Nat. Cell Biol
, vol.8
-
-
Guccione, E.1
-
12
-
-
33746835021
-
Computational identification of transcriptional regulatory elements in DNA sequence
-
GuhaThakurta,D. (2006) Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res., 34, 3585-3598.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3585-3598
-
-
GuhaThakurta, D.1
-
13
-
-
0026738749
-
Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes
-
Gumucio,D.L. et al. (1992) Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes. Mol. Cell Biol., 12, 4919-4929.
-
(1992)
Mol. Cell Biol
, vol.12
, pp. 4919-4929
-
-
Gumucio, D.L.1
-
14
-
-
0031875569
-
Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
-
Halpern,A.L. and Bruno,W.J. (1998) Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies. Mol. Biol. Evol., 15, 910-917.
-
(1998)
Mol. Biol. Evol
, vol.15
, pp. 910-917
-
-
Halpern, A.L.1
Bruno, W.J.2
-
15
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa,M. et al. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160-174.
-
(1985)
J. Mol. Evol
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
-
16
-
-
47249087256
-
The statistical power of phylogenetic motif models
-
Vingron,M. and Wong,L, eds, Springer, pp
-
Hawkins,J.C. and Bailey,T.L. (2008) The statistical power of phylogenetic motif models. In Vingron,M. and Wong,L. (eds), 12th Annual International Conference on Computational Biology, RECOMB 2008 Springer, pp. 112-126.
-
(2008)
12th Annual International Conference on Computational Biology, RECOMB 2008
, pp. 112-126
-
-
Hawkins, J.C.1
Bailey, T.L.2
-
17
-
-
0037100671
-
Mafft: A novel method for rapid multiple sequence alignment based on fast fourier transform
-
Katoh,K. et al. (2002) Mafft: A novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res., 30, 3059-3066.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
-
18
-
-
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
-
19
-
-
38849171836
-
Reliable prediction of regulator targets using 12 Drosophila genomes
-
Kheradpour,P. et al. (2007) Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res., 17, 1919-1931.
-
(2007)
Genome Res
, vol.17
, pp. 1919-1931
-
-
Kheradpour, P.1
-
20
-
-
33847076849
-
Chromatin modifications and their function
-
Kouzarides,T. (2007) Chromatin modifications and their function. Cell 128, 693-705.
-
(2007)
Cell
, vol.128
, pp. 693-705
-
-
Kouzarides, T.1
-
21
-
-
0037819447
-
Transcription regulation and animal diversity
-
Levine,M. and Tjian,R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
-
(2003)
Nature
, vol.424
, pp. 147-151
-
-
Levine, M.1
Tjian, R.2
-
22
-
-
33749381311
-
Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
-
Liu,X. (2006) Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res., 16, 1517-1528.
-
(2006)
Genome Res
, vol.16
, pp. 1517-1528
-
-
Liu, X.1
-
23
-
-
22144491990
-
MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
-
Moses,A.M. et al. (2004) MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol., 5, R98.
-
(2004)
Genome Biol
, vol.5
-
-
Moses, A.M.1
-
24
-
-
33750442876
-
Large-scale turnover of functional transcription factor binding sites in drosophila
-
Moses,A.M. et al. (2006) Large-scale turnover of functional transcription factor binding sites in drosophila. PLoS Comput. Biol. 2, e130.
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Moses, A.M.1
-
25
-
-
36949023082
-
A nucleosome-guided map of transcription factor binding sites in yeast
-
Narlikar,L. et al. (2007) A nucleosome-guided map of transcription factor binding sites in yeast. PLos Comput. Biol., 3, e215.
-
(2007)
PLos Comput. Biol
, vol.3
-
-
Narlikar, L.1
-
26
-
-
0025265665
-
Searching for patterns in protein and nucleic acid sequences
-
Staden,R. (1990) Searching for patterns in protein and nucleic acid sequences. Methods Enzymol., 183, 193-211.
-
(1990)
Methods Enzymol
, vol.183
, pp. 193-211
-
-
Staden, R.1
-
28
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
29
-
-
0023890867
-
Measuring the accuracy of diagnostic systems
-
Swets,J.A. (1988) Measuring the accuracy of diagnostic systems. Science, 240, 1285-1293.
-
(1988)
Science
, vol.240
, pp. 1285-1293
-
-
Swets, J.A.1
-
30
-
-
40149098862
-
The evolution of combinatorial gene regulation in fungi
-
Tuch,B.B. et al. (2008) The evolution of combinatorial gene regulation in fungi. PLoS Biol., 6, e38.
-
(2008)
PLoS Biol
, vol.6
-
-
Tuch, B.B.1
-
31
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
Wasserman,W.W. and Sandelin,A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet., 5, 276-287.
-
(2004)
Nat. Rev. Genet
, vol.5
, pp. 276-287
-
-
Wasserman, W.W.1
Sandelin, A.2
-
32
-
-
58549106607
-
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites
-
Whitington,T. et al. (2008) High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Res., 37, 14-25.
-
(2008)
Nucleic Acids Res
, vol.37
, pp. 14-25
-
-
Whitington, T.1
-
33
-
-
0032861774
-
SCPD: A promoter database of the yeast Saccharomyces cerevisiae
-
Zhu,J. and Zhang,M.Q. (1999) SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.
-
(1999)
Bioinformatics
, vol.15
, pp. 607-611
-
-
Zhu, J.1
Zhang, M.Q.2
|