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Items: 1 to 20 of 103

1.

The transcription unit architecture of the Escherichia coli genome.

Cho BK, Zengler K, Qiu Y, Park YS, Knight EM, Barrett CL, Gao Y, Palsson BØ.

Nat Biotechnol. 2009 Nov;27(11):1043-9. doi: 10.1038/nbt.1582. Epub 2009 Nov 1.

2.

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.

Cho BK, Kim D, Knight EM, Zengler K, Palsson BO.

BMC Biol. 2014 Jan 24;12:4. doi: 10.1186/1741-7007-12-4.

3.

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.

Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E.

PLoS One. 2009 Oct 19;4(10):e7526. doi: 10.1371/journal.pone.0007526.

4.

Genome-wide detection of novel regulatory RNAs in E. coli.

Raghavan R, Groisman EA, Ochman H.

Genome Res. 2011 Sep;21(9):1487-97. doi: 10.1101/gr.119370.110. Epub 2011 Jun 10.

5.

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling.

Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ.

PLoS Genet. 2012;8(8):e1002867. doi: 10.1371/journal.pgen.1002867. Epub 2012 Aug 9.

6.

Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.

Seo JH, Hong JS, Kim D, Cho BK, Huang TW, Tsai SF, Palsson BO, Charusanti P.

BMC Genomics. 2012 Nov 29;13:679. doi: 10.1186/1471-2164-13-679.

7.

Extensive functional overlap between sigma factors in Escherichia coli.

Wade JT, Castro Roa D, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E.

Nat Struct Mol Biol. 2006 Sep;13(9):806-14. Epub 2006 Aug 6.

PMID:
16892065
8.

Identification of regulatory RNA in bacterial genomes by genome-scale mapping of transcription start sites.

Singh N, Wade JT.

Methods Mol Biol. 2014;1103:1-10. doi: 10.1007/978-1-62703-730-3_1.

PMID:
24318882
9.

Complex regulation of the global regulatory gene csrA: CsrA-mediated translational repression, transcription from five promoters by Eσ⁷⁰ and Eσ(S), and indirect transcriptional activation by CsrA.

Yakhnin H, Yakhnin AV, Baker CS, Sineva E, Berezin I, Romeo T, Babitzke P.

Mol Microbiol. 2011 Aug;81(3):689-704. doi: 10.1111/j.1365-2958.2011.07723.x. Epub 2011 Jun 23.

10.

Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes.

Sinoquet C, Demey S, Braun F.

Nucleic Acids Res. 2008 Jun;36(10):3332-40. doi: 10.1093/nar/gkn135. Epub 2008 Apr 25.

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13.

sigma factor selectivity of Escherichia coli RNA polymerase: role for CRP, IHF and lrp transcription factors.

Colland F, Barth M, Hengge-Aronis R, Kolb A.

EMBO J. 2000 Jun 15;19(12):3028-37.

14.

Integration host factor-mediated expression of the ilvGMEDA operon of Escherichia coli.

Pagel JM, Hatfield GW.

J Biol Chem. 1991 Jan 25;266(3):1985-96.

15.

Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays.

Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BØ.

J Bacteriol. 2005 Sep;187(17):6166-74.

16.

Functional studies of potential intrastrand triplex elements in the Escherichia coli genome.

Hoyne PR, Maher LJ 3rd.

J Mol Biol. 2002 Apr 26;318(2):373-86.

PMID:
12051844
18.
20.

Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes.

Huerta AM, Francino MP, Morett E, Collado-Vides J.

PLoS Genet. 2006 Nov 10;2(11):e185. Epub 2006 Sep 12.

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