PubMed

Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome.

Sivaraman K, Seshasayee AS, Swaminathan K, Muthukumaran G, Pennathur G.

Theor Biol Med Model. 2005 May 31;2:20.PMID: 15927055 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Apr 25.PMID: 18440978 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.

Kim SY, Kim Y.

BMC Bioinformatics. 2006 Jul 4;7:330.PMID: 16817975 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide localization of mobile elements: experimental, statistical and biological considerations.

Martinez-Vaz BM, Xie Y, Pan W, Khodursky AB.

BMC Genomics. 2005 Jun 1;6(1):81.PMID: 15929794 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1.PMID: 19426448 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 19838305 [PubMed - indexed for MEDLINE]Related articlesFree article

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455.PMID: 18950538 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting bacterial transcription units using sequence and expression data.

Bockhorst J, Qiu Y, Glasner J, Liu M, Blattner F, Craven M.

Bioinformatics. 2003;19 Suppl 1:i34-43.PMID: 12855435 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals.

Vanet A, Marsan L, Labigne A, Sagot MF.

J Mol Biol. 2000 Mar 24;297(2):335-53.PMID: 10715205 [PubMed - indexed for MEDLINE]Related articles

A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli.

Bulyk ML, McGuire AM, Masuda N, Church GM.

Genome Res. 2004 Feb;14(2):201-8.PMID: 14762058 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.

Yan B, Núñez C, Ueki T, Esteve-Núñez A, Puljic M, Adkins RM, Methé BA, Lovley DR, Krushkal J.

Gene. 2006 Dec 15;384:73-95. Epub 2006 Jul 20.PMID: 17014972 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 17096598 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene promoter scan methodology for identifying and classifying coregulated promoters.

Zwir I, Harari O, Groisman EA.

Methods Enzymol. 2007;422:361-85.PMID: 17628149 [PubMed - indexed for MEDLINE]Related articles

Combining microarray and genomic data to predict DNA binding motifs.

Mao L, Mackenzie C, Roh JH, Eraso JM, Kaplan S, Resat H.

Microbiology. 2005 Oct;151(Pt 10):3197-213.PMID: 16207904 [PubMed - indexed for MEDLINE]Related articlesFree article

Consequences of reductive evolution for gene expression in an obligate endosymbiont.

Wilcox JL, Dunbar HE, Wolfinger RD, Moran NA.

Mol Microbiol. 2003 Jun;48(6):1491-500.PMID: 12791133 [PubMed - indexed for MEDLINE]Related articles

Cis-acting sites contributing to expression of divergently transcribed DAL1 and DAL4 genes in S. cerevisiae: a word of caution when correlating cis-acting sequences with genome-wide expression analyses.

van der Merwe GK, van Vuuren HJ, Cooper TG.

Curr Genet. 2001 May;39(3):156-65.PMID: 11409177 [PubMed - indexed for MEDLINE]Related articles

Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens.

Yan B, Lovley DR, Krushkal J.

Biosystems. 2007 Sep-Oct;90(2):421-41. Epub 2006 Oct 26.PMID: 17184904 [PubMed - indexed for MEDLINE]Related articles

Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation.

Rawal P, Kummarasetti VB, Ravindran J, Kumar N, Halder K, Sharma R, Mukerji M, Das SK, Chowdhury S.

Genome Res. 2006 May;16(5):644-55.PMID: 16651665 [PubMed - indexed for MEDLINE]Related articlesFree article

Selective promoter recognition by chlamydial sigma28 holoenzyme.

Shen L, Feng X, Yuan Y, Luo X, Hatch TP, Hughes KT, Liu JS, Zhang YX.

J Bacteriol. 2006 Nov;188(21):7364-77. Epub 2006 Aug 25.PMID: 16936033 [PubMed - indexed for MEDLINE]Related articlesFree article

Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70.

Cavanagh AT, Klocko AD, Liu X, Wassarman KM.

Mol Microbiol. 2008 Mar;67(6):1242-56. Epub 2008 Jan 15.PMID: 18208528 [PubMed - indexed for MEDLINE]Related articles