-
1
-
-
0343114274
-
Short palindromic repetitive DNA elements in enterobacteria: A survey
-
Bachellier,S. et al. (1999) Short palindromic repetitive DNA elements in enterobacteria: A survey. Res. Microbiol., 150, 627-639.
-
(1999)
Res. Microbiol.
, vol.150
, pp. 627-639
-
-
Bachellier, S.1
-
2
-
-
0031786214
-
Integration host factor and cyclic AMP receptor protein are required for TyrR-mediated activation of tpl in Citrobacter freundii
-
Bai,Q. and Somerville,R.L. (1998) Integration host factor and cyclic AMP receptor protein are required for TyrR-mediated activation of tpl in Citrobacter freundii. J. Bacteriol., 180, 6173-6186.
-
(1998)
J. Bacteriol.
, vol.180
, pp. 6173-6186
-
-
Bai, Q.1
Somerville, R.L.2
-
3
-
-
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
-
4
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey,T.L. et al. (2009) MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res., 37, W202-W208.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Bailey, T.L.1
-
5
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey,T.L. and Elkan,C. (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
-
6
-
-
0031877016
-
Combining evidence using p-values: Application to sequence homology searches
-
Bailey,T.L. and Gribskov,M. (1998) Combining evidence using p-values: Application to sequence homology searches. Bioinformatics, 14, 48-54.
-
(1998)
Bioinformatics
, vol.14
, pp. 48-54
-
-
Bailey, T.L.1
Gribskov, M.2
-
7
-
-
0000353178
-
A maximization technique occurring in the statistical analysis of probabilistic functions ofMarkov chains
-
Baum,L.E. et al. (1970) A maximization technique occurring in the statistical analysis of probabilistic functions ofMarkov chains. Ann. Math. Stat., 41, 164-171.
-
(1970)
Ann. Math. Stat.
, vol.41
, pp. 164-171
-
-
Baum, L.E.1
-
8
-
-
78650497790
-
On the power and limits of evolutionary conservation- unraveling bacterial gene regulatory networks
-
Baumbach,J. (2010) On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks. Nucleic Acids Res., 38, 7877-7884.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 7877-7884
-
-
Baumbach, J.1
-
9
-
-
20744440509
-
Identification of transcription factor binding sites with variable- order Bayesian networks
-
Ben-Gal,I. et al. (2005) Identification of transcription factor binding sites with variable- order Bayesian networks. Bioinformatics, 21, 2657-2666.
-
(2005)
Bioinformatics
, vol.21
, pp. 2657-2666
-
-
Ben-Gal, I.1
-
10
-
-
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, 739-748.
-
(2002)
Genome Res.
, vol.12
, pp. 739-748
-
-
Blanchette, M.1
Tompa, M.2
-
11
-
-
80055069400
-
Unraveling networks of co-regulated genes on the sole basis of genome sequences
-
Brohee,S. et al. (2011) Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res., 39, 6340-6358.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 6340-6358
-
-
Brohee, S.1
-
12
-
-
33646832750
-
Detecting uber-operons in prokaryotic genomes
-
Che,D. et al. (2006) Detecting uber-operons in prokaryotic genomes. Nucleic Acids Res., 34, 2418-2427.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 2418-2427
-
-
Che, D.1
-
13
-
-
42649103655
-
W-alignace: An improved gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/chip-chip data
-
Chen,X. et al. (2008) W-AlignACE: An improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data. Bioinformatics, 24, 1121-1128.
-
(2008)
Bioinformatics
, vol.24
, pp. 1121-1128
-
-
Chen, X.1
-
14
-
-
33747148392
-
Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA
-
Cho,B.K. et al. (2006) Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology, 152, 2207-2219.
-
(2006)
Microbiology
, vol.152
, pp. 2207-2219
-
-
Cho, B.K.1
-
15
-
-
0026813814
-
Contribution of the fnr and arca gene products in coordinate regulation of cytochrome o and d oxidase (cyoabcde and cydab) genes in escherichia coli
-
Cotter,P.A. and Gunsalus,R.P. (1992) Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxidase (cyoABCDE and cydAB) genes in Escherichia coli. FEMS Microbiol. Lett., 70, 31-36.
-
(1992)
FEMS Microbiol. Lett.
, vol.70
, pp. 31-36
-
-
Cotter, P.A.1
Gunsalus, R.P.2
-
16
-
-
49549088391
-
Efficient representation and P-value computation for high-order Markov motifs
-
da Fonseca,P.G. et al. (2008) Efficient representation and P-value computation for high-order Markov motifs. Bioinformatics, 24, i160-i166.
-
(2008)
Bioinformatics
, vol.24
-
-
Da Fonseca, P.G.1
-
17
-
-
33846668510
-
Operon prediction using both genome-specific and general genomic information
-
Dam,P. et al. (2007) Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res., 35, 288-298.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 288-298
-
-
Dam, P.1
-
18
-
-
38549144819
-
A survey of DNA motif finding algorithms
-
Das,M.K. and Dai,H.K. (2007) A survey of DNA motif finding algorithms. BMC Bioinformatics, 8 (Suppl. 7), S21.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 7
-
-
Das, M.K.1
Dai, H.K.2
-
20
-
-
76949089832
-
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
-
Dillon,S.C. and Dorman,C.J. (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat. Rev. Microbiol., 8, 185-195.
-
(2010)
Nat. Rev. Microbiol.
, vol.8
, pp. 185-195
-
-
Dillon, S.C.1
Dorman, C.J.2
-
21
-
-
33645232936
-
Characterization of CprK1, a CRP/FNR-type transcriptional regulator of halorespiration from Desulfitobacterium hafniense
-
Gabor,K. et al. (2006) Characterization of CprK1, a CRP/FNR-type transcriptional regulator of halorespiration from Desulfitobacterium hafniense. J. Bacteriol., 188, 2604-2613.
-
(2006)
J. Bacteriol.
, vol.188
, pp. 2604-2613
-
-
Gabor, K.1
-
22
-
-
0031452318
-
Arac/XylS family of transcriptional regulators
-
Gallegos,M.T. et al. (1997) Arac/XylS family of transcriptional regulators. Microbiol. Mol. Biol. Rev., 61, 393-410.
-
(1997)
Microbiol. Mol. Biol. Rev.
, vol.61
, pp. 393-410
-
-
Gallegos, M.T.1
-
23
-
-
0031026282
-
Functional characterization of roles of GalR and GalS as regulators of the gal regulon
-
Geanacopoulos,M. and Adhya,S. (1997) Functional characterization of roles of GalR and GalS as regulators of the gal regulon. J. Bacteriol., 179, 228-234.
-
(1997)
J. Bacteriol.
, vol.179
, pp. 228-234
-
-
Geanacopoulos, M.1
Adhya, S.2
-
24
-
-
4444325079
-
CisML: An XML-based format for sequence motif detection software
-
Haverty,P.M. and Weng,Z. (2004) CisML: An XML-based format for sequence motif detection software. Bioinformatics, 20, 1815-1817.
-
(2004)
Bioinformatics
, vol.20
, pp. 1815-1817
-
-
Haverty, P.M.1
Weng, Z.2
-
25
-
-
78651281217
-
EcoCyc: A comprehensive database of Escherichia coli biology
-
Keseler,I.M. et al. (2011) EcoCyc: A comprehensive database of Escherichia coli biology. Nucleic Acids Res., 39, D583-D590.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Keseler, I.M.1
-
26
-
-
0344153756
-
Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: Exploiting the metabolic spectrum by controlling alternative gene programs
-
Korner,H. et al. (2003) Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: Exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol. Rev., 27, 559-592.
-
(2003)
FEMS Microbiol. Rev.
, vol.27
, pp. 559-592
-
-
Korner, H.1
-
27
-
-
33745198703
-
High guanine and cytosine content increases mRNA levels in mammalian cells
-
Kudla,G. et al. (2006) High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol., 4, e180.
-
(2006)
PLoS Biol.
, vol.4
-
-
Kudla, G.1
-
28
-
-
79954591091
-
A new framework for identifying cis-regulatory motifs in prokaryotes
-
Li,G. et al. (2011) A new framework for identifying cis-regulatory motifs in prokaryotes. Nucleic Acids Res., 39, e42.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Li, G.1
-
29
-
-
0036956513
-
Collaborative regulation of escherichia coli glutamate-dependent acid resistance by two arac-like regulators gadx and gadw (yhiw)
-
Ma,Z. et al. (2002) Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW). J. Bacteriol., 184, 7001-7012.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 7001-7012
-
-
Ma, Z.1
-
30
-
-
0037440734
-
Evolution of transcription factors and the gene regulatory network in Escherichia coli
-
Madan Babu,M. and Teichmann,S.A. (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. NucleicAcids Res., 31, 1234-1244.
-
(2003)
NucleicAcids Res.
, vol.31
, pp. 1234-1244
-
-
Madan Babu, M.1
Teichmann, S.A.2
-
31
-
-
58149200939
-
DOOR: A database for prokaryotic operons
-
Mao,F. et al. (2009) DOOR: A database for prokaryotic operons. Nucleic Acids Res., 37, D459-D463.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Mao, F.1
-
33
-
-
79951570672
-
Theoretical and empirical quality assessment of transcription factor-binding motifs
-
Medina-Rivera,A. et al. (2011) Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res., 39, 808-824.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 808-824
-
-
Medina-Rivera, A.1
-
34
-
-
33846928720
-
Integration of regulatory signals through involvement of multiple global regulators: Control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR
-
Paul,L. et al. (2007) Integration of regulatory signals through involvement of multiple global regulators: Control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR. BMC Microbiol., 7, 2.
-
(2007)
BMC Microbiol.
, vol.7
, pp. 2
-
-
Paul, L.1
-
35
-
-
1542407109
-
Escherichia coli prereplication complex assembly is regulated by dynamic interplay among Fis IHF and DnaA
-
Ryan,V.T. et al. (2004) Escherichia coli prereplication complex assembly is regulated by dynamic interplay among Fis, IHF and DnaA. Mol. Microbiol., 51, 1347-1359.
-
(2004)
Mol. Microbiol.
, vol.51
, pp. 1347-1359
-
-
Ryan, V.T.1
-
36
-
-
84876543942
-
RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
-
Salgado,H. et al. (2013) RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res., 41, D203-D213.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Salgado, H.1
-
37
-
-
0344906914
-
Consensus sequence Zen
-
Schneider,T.D. (2002) Consensus sequence Zen. Appl. Bioinformatics, 1, 111-119.
-
(2002)
Appl. Bioinformatics
, vol.1
, pp. 111-119
-
-
Schneider, T.D.1
-
38
-
-
0023042012
-
Information content of binding sites on nucleotide sequences
-
Schneider,T.D. et al. (1986) Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415-431.
-
(1986)
J. Mol. Biol.
, vol.188
, pp. 415-431
-
-
Schneider, T.D.1
-
39
-
-
36549078564
-
PhyME: A software tool for finding motifs in sets of orthologous sequences
-
Sinha,S. (2007) PhyME: A software tool for finding motifs in sets of orthologous sequences. Methods Mol. Biol., 395, 309-318.
-
(2007)
Methods Mol. Biol.
, vol.395
, pp. 309-318
-
-
Sinha, S.1
-
40
-
-
0025195709
-
The CytR repressor antagonizes cyclic AMPcyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12
-
Sogaard-Andersen,L. et al. (1990) The CytR repressor antagonizes cyclic AMPcyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12. J. Bacteriol., 172, 5706-5713.
-
(1990)
J. Bacteriol.
, vol.172
, pp. 5706-5713
-
-
Sogaard-Andersen, L.1
-
41
-
-
0025008358
-
Tandem DNA-bound cAMP-CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli
-
Sogaard-Andersen,L. et al. (1990) Tandem DNA-bound cAMP-CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli. Mol. Microbiol., 4, 1595-1601.
-
(1990)
Mol. Microbiol.
, vol.4
, pp. 1595-1601
-
-
Sogaard-Andersen, L.1
-
42
-
-
0025729663
-
A novel function of the camp-crp complex in escherichia coli: Camp-crp functions as an adaptor for the cytr repressor in the deo operon
-
Sogaard-Andersen,L. et al. (1991) A novel function of the cAMP-CRP complex in Escherichia coli: CAMP-CRP functions as an adaptor for the CytR repressor in the deo operon. Mol. Microbiol., 5, 969-975.
-
(1991)
Mol. Microbiol.
, vol.5
, pp. 969-975
-
-
Sogaard-Andersen, L.1
-
43
-
-
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
-
44
-
-
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
-
45
-
-
79958105825
-
Improved similarity scores for comparing motifs
-
Tanaka,E. et al. (2011) Improved similarity scores for comparing motifs. Bioinformatics, 27, 1603-1609.
-
(2011)
Bioinformatics
, vol.27
, pp. 1603-1609
-
-
Tanaka, E.1
-
46
-
-
48449090922
-
RSAT: Regulatory sequence analysis tools
-
Thomas-Chollier,M. et al. (2008) RSAT: Regulatory sequence analysis tools. Nucleic Acids Res., 36, W119-W127.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Thomas-Chollier, M.1
-
47
-
-
62749095223
-
-
MIT Press and McGraw-Hill, Cambridge, MA, USA
-
Thomas,H. et al. (2001) Introduction to Algorithms. MIT Press and McGraw-Hill, Cambridge, MA, USA
-
(2001)
Introduction to Algorithms.
-
-
Thomas, H.1
-
48
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa,M. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 137-144
-
-
Tompa, M.1
-
49
-
-
54249135920
-
GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: Transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites
-
Tramonti,A. et al. (2008) GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: Transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites. Mol. Microbiol., 70, 965-982.
-
(2008)
Mol. Microbiol.
, vol.70
, pp. 965-982
-
-
Tramonti, A.1
-
51
-
-
0026682712
-
Isorepressor of the gal regulon in Escherichia coli
-
Weickert,M.J. and Adhya,S. (1992) Isorepressor of the gal regulon in Escherichia coli. J. Mol. Biol., 226, 69-83.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 69-83
-
-
Weickert, M.J.1
Adhya, S.2
-
52
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals
-
Xie,X. et al. (2005) Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals. Nature, 434, 338-345.
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
|