-
1
-
-
38049007503
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Multidimensional annotation of the Escherichia coli K-12 genome
-
Karp P.D., Keseler I.M., Shearer A., Latendresse M., Krummenacker M., Paley S.M., Paulsen I., Collado-Vides J., Gama-Castro S., Peralta-Gil M., et al. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 35 (2007) 7577-7590
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 7577-7590
-
-
Karp, P.D.1
Keseler, I.M.2
Shearer, A.3
Latendresse, M.4
Krummenacker, M.5
Paley, S.M.6
Paulsen, I.7
Collado-Vides, J.8
Gama-Castro, S.9
Peralta-Gil, M.10
-
3
-
-
57549107143
-
Regulation by transcription factors in bacteria: beyond description
-
Balleza E., Lopez-Bojorquez L.N., Martinez-Antonio A., Resendis-Antonio O., Lazada-Chavez I., Balderas-Marinez Y.I., Encarnacion S., and Collado-Vides J. Regulation by transcription factors in bacteria: beyond description. FEMS Microbiol Rev 33 (2009) 133-151
-
(2009)
FEMS Microbiol Rev
, vol.33
, pp. 133-151
-
-
Balleza, E.1
Lopez-Bojorquez, L.N.2
Martinez-Antonio, A.3
Resendis-Antonio, O.4
Lazada-Chavez, I.5
Balderas-Marinez, Y.I.6
Encarnacion, S.7
Collado-Vides, J.8
-
4
-
-
46849106965
-
Functional organisation of Escherichia coli transcriptional regulatory network
-
Martinez-Antonio A., Janga S.C., and Thieffry D. Functional organisation of Escherichia coli transcriptional regulatory network. J Mol Biol 381 (2008) 238-247
-
(2008)
J Mol Biol
, vol.381
, pp. 238-247
-
-
Martinez-Antonio, A.1
Janga, S.C.2
Thieffry, D.3
-
5
-
-
49349103536
-
Methods for studying global patterns of DNA binding by transcription factors and RNA polymerase
-
Grainger D.C., and Busby S.J. Methods for studying global patterns of DNA binding by transcription factors and RNA polymerase. Biochem Soc Trans 36 (2008) 754-757
-
(2008)
Biochem Soc Trans
, vol.36
, pp. 754-757
-
-
Grainger, D.C.1
Busby, S.J.2
-
6
-
-
56149116568
-
Global regulators of transcription in Escherichia coli: mechanisms of action and methods for study
-
Grainger D.C., and Busby S.J. Global regulators of transcription in Escherichia coli: mechanisms of action and methods for study. Adv Appl Microbiol 65 (2008) 93-113
-
(2008)
Adv Appl Microbiol
, vol.65
, pp. 93-113
-
-
Grainger, D.C.1
Busby, S.J.2
-
7
-
-
65549122479
-
Dissecting regulatory networks in host-pathogen interaction using ChIP-on-chip technology
-
Sala C., Grainger D.C., and Cole S.T. Dissecting regulatory networks in host-pathogen interaction using ChIP-on-chip technology. Cell Host Microbe 5 (2009) 430-437
-
(2009)
Cell Host Microbe
, vol.5
, pp. 430-437
-
-
Sala, C.1
Grainger, D.C.2
Cole, S.T.3
-
8
-
-
0037007079
-
Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle
-
Laub M.T., Chen S.L., Shapiro L., and McAdams H.H. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci U S A 99 (2002) 4632-4637
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 4632-4637
-
-
Laub, M.T.1
Chen, S.L.2
Shapiro, L.3
McAdams, H.H.4
-
9
-
-
34250619055
-
Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization
-
This minireview presents a succinct overview of current ChIP technology and highlights some of its more surprising applications. See also citation [7].
-
Wade J.T., Struhl K., Busby S.J., and Grainger D.C. Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization. Mol Microbiol 65 (2007) 21-26. This minireview presents a succinct overview of current ChIP technology and highlights some of its more surprising applications. See also citation [7].
-
(2007)
Mol Microbiol
, vol.65
, pp. 21-26
-
-
Wade, J.T.1
Struhl, K.2
Busby, S.J.3
Grainger, D.C.4
-
10
-
-
0346256789
-
The Spo0A regulon of Bacillus subtilis
-
Molle V., Fujita M., Jensen S.T., Eichenberger P., Gonzalez-Pastor J.E., Liu J.S., and Losick R. The Spo0A regulon of Bacillus subtilis. Mol Microbiol 50 (2003) 1683-1701
-
(2003)
Mol Microbiol
, vol.50
, pp. 1683-1701
-
-
Molle, V.1
Fujita, M.2
Jensen, S.T.3
Eichenberger, P.4
Gonzalez-Pastor, J.E.5
Liu, J.S.6
Losick, R.7
-
11
-
-
0037336206
-
Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis
-
Molle V., Nakaura Y., Shivers R.P., Yamaguchi H., Losick R., Fujita Y., and Sonenshein A.L. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol 185 (2003) 1911-1922
-
(2003)
J Bacteriol
, vol.185
, pp. 1911-1922
-
-
Molle, V.1
Nakaura, Y.2
Shivers, R.P.3
Yamaguchi, H.4
Losick, R.5
Fujita, Y.6
Sonenshein, A.L.7
-
13
-
-
33745460953
-
In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis
-
Danielli A., Roncarati D., Delany I., Chiarini V., Rappuoli R., and Scarlato V. In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis. J Bacteriol 188 (2006) 4654-4662
-
(2006)
J Bacteriol
, vol.188
, pp. 4654-4662
-
-
Danielli, A.1
Roncarati, D.2
Delany, I.3
Chiarini, V.4
Rappuoli, R.5
Scarlato, V.6
-
14
-
-
33947415761
-
Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays
-
Rodrigue S., Brodeur J., Jacques P.E., Gervais A.L., Brzezinski R., and Gaudreau L. Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays. J Bacteriol 189 (2007) 1505-1513
-
(2007)
J Bacteriol
, vol.189
, pp. 1505-1513
-
-
Rodrigue, S.1
Brodeur, J.2
Jacques, P.E.3
Gervais, A.L.4
Brzezinski, R.5
Gaudreau, L.6
-
15
-
-
60649096132
-
Genome-wide regulon and crystal structure of BlaI (Rv1846c) from Mycobacterium tuberculosis
-
This paper reports the unusual combination of a high resolution structure and a genomic analysis for a previously uncharacterised Mycobacterium tuberculosis transcription factor and illustrates the power of applying ChIP-on-chip in a 'difficult' organism.
-
Sala C., Haouz A., Saul F.A., Miras I., Rosenkrands I., Alzari P.M., and Cole S.T. Genome-wide regulon and crystal structure of BlaI (Rv1846c) from Mycobacterium tuberculosis. Mol Microbiol 71 (2009) 1102-1116. This paper reports the unusual combination of a high resolution structure and a genomic analysis for a previously uncharacterised Mycobacterium tuberculosis transcription factor and illustrates the power of applying ChIP-on-chip in a 'difficult' organism.
-
(2009)
Mol Microbiol
, vol.71
, pp. 1102-1116
-
-
Sala, C.1
Haouz, A.2
Saul, F.A.3
Miras, I.4
Rosenkrands, I.5
Alzari, P.M.6
Cole, S.T.7
-
16
-
-
33747148392
-
Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA
-
Cho B.K., Knight E.M., and Palsson B.Ø. Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology 152 (2006) 2207-2219
-
(2006)
Microbiology
, vol.152
, pp. 2207-2219
-
-
Cho, B.K.1
Knight, E.M.2
Palsson, B.O.3
-
17
-
-
29144431508
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Studies of the distribution of E. coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome
-
Grainger D.C., Hurd D., Harrison M., Holdstock J., and Busby S.J. Studies of the distribution of E. coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc Natl Acad Sci U S A 102 (2005) 17693-17698
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 17693-17698
-
-
Grainger, D.C.1
Hurd, D.2
Harrison, M.3
Holdstock, J.4
Busby, S.J.5
-
18
-
-
33846659467
-
Transcription factor distribution in Escherichia coli: studies with FNR protein
-
Grainger D.C., Aiba H., Hurd D., Browning D.F., and Busby S.J. Transcription factor distribution in Escherichia coli: studies with FNR protein. Nucleic Acids Res 35 (2007) 269-278
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 269-278
-
-
Grainger, D.C.1
Aiba, H.2
Hurd, D.3
Browning, D.F.4
Busby, S.J.5
-
19
-
-
27644580858
-
Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites
-
Wade J.T., Reppas N.B., Church G.M., and Struhl K. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev 19 (2005) 2619-2630
-
(2005)
Genes Dev
, vol.19
, pp. 2619-2630
-
-
Wade, J.T.1
Reppas, N.B.2
Church, G.M.3
Struhl, K.4
-
20
-
-
58049200606
-
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli
-
Cho B.K., Barrett C.L., Knight E.M., Park Y.S., and Palsson B.Ø. Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc Natl Acad Sci U S A 105 (2008) 19462-19467
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 19462-19467
-
-
Cho, B.K.1
Barrett, C.L.2
Knight, E.M.3
Park, Y.S.4
Palsson, B.O.5
-
21
-
-
4944225301
-
Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays
-
Grainger D.C., Overton T.W., Reppas N., Wade J.T., Tamai E., Hobman J.L., Constantinidou C., Struhl K., Church G., and Busby S.J. Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol 186 (2004) 6938-6943
-
(2004)
J Bacteriol
, vol.186
, pp. 6938-6943
-
-
Grainger, D.C.1
Overton, T.W.2
Reppas, N.3
Wade, J.T.4
Tamai, E.5
Hobman, J.L.6
Constantinidou, C.7
Struhl, K.8
Church, G.9
Busby, S.J.10
-
22
-
-
47049086640
-
Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR
-
An excellent source of in-depth protocols for ChIP-on-chip analysis and the mathematical treatment of ChIP-on-chip data.
-
Efromovich S., Grainger D., Bodenmiller D., and Spiro S. Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR. Methods Enzymol 437 (2008) 211-233. An excellent source of in-depth protocols for ChIP-on-chip analysis and the mathematical treatment of ChIP-on-chip data.
-
(2008)
Methods Enzymol
, vol.437
, pp. 211-233
-
-
Efromovich, S.1
Grainger, D.2
Bodenmiller, D.3
Spiro, S.4
-
23
-
-
51549086290
-
Escherichia coli NsrR regulates a pathway for the oxidation of 3-nitrotyramine to 4-hydroxy-3-nitrophenylacetate
-
Rankin L.D., Bodenmiller D.M., Partridge J.D., Nishino S.F., Spain J.C., and Spiro S. Escherichia coli NsrR regulates a pathway for the oxidation of 3-nitrotyramine to 4-hydroxy-3-nitrophenylacetate. J Bacteriol 190 (2008) 6170-6177
-
(2008)
J Bacteriol
, vol.190
, pp. 6170-6177
-
-
Rankin, L.D.1
Bodenmiller, D.M.2
Partridge, J.D.3
Nishino, S.F.4
Spain, J.C.5
Spiro, S.6
-
24
-
-
47249152834
-
The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
-
Shimada T., Ishihama A., Busby S.J., and Grainger D.C. The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res 36 (2008) 3950-3955
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 3950-3955
-
-
Shimada, T.1
Ishihama, A.2
Busby, S.J.3
Grainger, D.C.4
-
25
-
-
66149148317
-
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content
-
Lewis N.E., Cho B.K., Knight E.M., and Palsson B.Ø. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol 191 (2009) 3437-3444
-
(2009)
J Bacteriol
, vol.191
, pp. 3437-3444
-
-
Lewis, N.E.1
Cho, B.K.2
Knight, E.M.3
Palsson, B.O.4
-
26
-
-
33750898424
-
Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase
-
Oshima T., Ishikawa S., Kurokawa K., Aiba H., and Ogasawara N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res 13 (2006) 141-153
-
(2006)
DNA Res
, vol.13
, pp. 141-153
-
-
Oshima, T.1
Ishikawa, S.2
Kurokawa, K.3
Aiba, H.4
Ogasawara, N.5
-
27
-
-
64049096202
-
Differential binding profiles of StpA in wild-type and H-NS mutant cells: a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis
-
Uyar E., Kurokawa K., Yoshimura M., Ishikawa S., Ogasawara N., and Oshima T. Differential binding profiles of StpA in wild-type and H-NS mutant cells: a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis. J Bacteriol 191 (2009) 2388-2391
-
(2009)
J Bacteriol
, vol.191
, pp. 2388-2391
-
-
Uyar, E.1
Kurokawa, K.2
Yoshimura, M.3
Ishikawa, S.4
Ogasawara, N.5
Oshima, T.6
-
28
-
-
44849093465
-
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
-
Fis is one of the most abundant nucleoid-associated proteins in rapidly growing E. coli. This study shows that Fis binds at hundreds of target sites, the majority of which are in gene regulatory regions. This has important consequences for the organisation of the folded chromosome and shows that the influence of Fis is more pervasive than previously thought. See also citation [29].
-
Cho B.K., Knight E.M., Barrett C.L., and Palsson B.Ø. Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res 18 (2008) 900-910. Fis is one of the most abundant nucleoid-associated proteins in rapidly growing E. coli. This study shows that Fis binds at hundreds of target sites, the majority of which are in gene regulatory regions. This has important consequences for the organisation of the folded chromosome and shows that the influence of Fis is more pervasive than previously thought. See also citation [29].
-
(2008)
Genome Res
, vol.18
, pp. 900-910
-
-
Cho, B.K.1
Knight, E.M.2
Barrett, C.L.3
Palsson, B.O.4
-
29
-
-
33750000118
-
Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
-
Grainger D.C., Hurd D., Goldberg M.D., and Busby S.J. Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res 34 (2006) 4642-4652
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4642-4652
-
-
Grainger, D.C.1
Hurd, D.2
Goldberg, M.D.3
Busby, S.J.4
-
30
-
-
33748055114
-
H-NS mediates the silencing of laterally acquired genes in bacteria
-
Lucchini S., Rowley G., Goldberg M.D., Hurd D., Harrison M., and Hinton J.C. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog 2 (2006) e81
-
(2006)
PLoS Pathog
, vol.2
-
-
Lucchini, S.1
Rowley, G.2
Goldberg, M.D.3
Hurd, D.4
Harrison, M.5
Hinton, J.C.6
-
31
-
-
33746008173
-
Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella
-
Navarre W.W., Porwollik S., Wang Y., McClelland M., Rosen H., Libby S.J., and Fang F.C. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313 (2006) 236-238
-
(2006)
Science
, vol.313
, pp. 236-238
-
-
Navarre, W.W.1
Porwollik, S.2
Wang, Y.3
McClelland, M.4
Rosen, H.5
Libby, S.J.6
Fang, F.C.7
-
32
-
-
33751534830
-
The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting
-
Reppas N.B., Wade J.T., Church G.M., and Struhl K. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell 24 (2006) 747-757
-
(2006)
Mol Cell
, vol.24
, pp. 747-757
-
-
Reppas, N.B.1
Wade, J.T.2
Church, G.M.3
Struhl, K.4
-
33
-
-
33748350078
-
Extensive functional overlap between sigma factors in Escherichia coli
-
Wade J.T., Roa D.C., Grainger D.C., Hurd D., Busby S.J., Struhl K., and Nudler E. Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol 13 (2006) 806-814
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 806-814
-
-
Wade, J.T.1
Roa, D.C.2
Grainger, D.C.3
Hurd, D.4
Busby, S.J.5
Struhl, K.6
Nudler, E.7
-
34
-
-
27644473223
-
Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo
-
Raffaelle M., Kanin E.T., Vogt J., Burgess R.R., and Ansari A.Z. Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo. Mol Cell 20 (2005) 357-366
-
(2005)
Mol Cell
, vol.20
, pp. 357-366
-
-
Raffaelle, M.1
Kanin, E.T.2
Vogt, J.3
Burgess, R.R.4
Ansari, A.Z.5
-
35
-
-
58149312711
-
Regulator trafficking on bacterial transcription units in vivo
-
This remarkable paper presents a picture of the comings and goings of different factors throughout the bacterial transcription cycle. The work is a stunning technical feat illustrating the power of high-density arrays and rigorous data analysis. See also citation [32].
-
Mooney R.A., Davis S.E., Peters J.M., Rowland J.L., Ansari A.Z., and Landick R. Regulator trafficking on bacterial transcription units in vivo. Mol Cell 33 (2009) 97-108. This remarkable paper presents a picture of the comings and goings of different factors throughout the bacterial transcription cycle. The work is a stunning technical feat illustrating the power of high-density arrays and rigorous data analysis. See also citation [32].
-
(2009)
Mol Cell
, vol.33
, pp. 97-108
-
-
Mooney, R.A.1
Davis, S.E.2
Peters, J.M.3
Rowland, J.L.4
Ansari, A.Z.5
Landick, R.6
-
36
-
-
33846260077
-
The bacteriophage λQ anti-terminator protein regulates late gene expression as a stable component of the transcription elongation complex
-
Deighan P., and Hochschild A. The bacteriophage λQ anti-terminator protein regulates late gene expression as a stable component of the transcription elongation complex. Mol Microbiol 63 (2007) 911-920
-
(2007)
Mol Microbiol
, vol.63
, pp. 911-920
-
-
Deighan, P.1
Hochschild, A.2
-
37
-
-
24344447800
-
Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays
-
Herring C.D., Raffaelle M., Allen T.E., Kanin E.I., Landick R., Ansari A.Z., and Palsson B.Ø. Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J Bacteriol 187 (2005) 6166-6174
-
(2005)
J Bacteriol
, vol.187
, pp. 6166-6174
-
-
Herring, C.D.1
Raffaelle, M.2
Allen, T.E.3
Kanin, E.I.4
Landick, R.5
Ansari, A.Z.6
Palsson, B.O.7
-
38
-
-
63249132195
-
DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes
-
Butala M., Busby S.J., and Lee D.J. DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes. Nucleic Acids Res 37 (2009) e37
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Butala, M.1
Busby, S.J.2
Lee, D.J.3
-
39
-
-
64149123778
-
Next-generation sequencing: from basic research to diagnostics
-
Voelkerding K.V., Darnes S.A., and Durtschi J.D. Next-generation sequencing: from basic research to diagnostics. Clin Chem 55 (2009) 641-658
-
(2009)
Clin Chem
, vol.55
, pp. 641-658
-
-
Voelkerding, K.V.1
Darnes, S.A.2
Durtschi, J.D.3
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