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Prediction of highly expressed genes in microbes based on chromatin accessibility.

Willenbrock H, Ussery DW.

BMC Mol Biol. 2007 Feb 13;8:11.PMID: 17295928 [PubMed - indexed for MEDLINE]Related articlesFree article

Codon usages in different gene classes of the Escherichia coli genome.

Karlin S, Mrázek J, Campbell AM.

Mol Microbiol. 1998 Sep;29(6):1341-55.PMID: 9781873 [PubMed - indexed for MEDLINE]Related articles

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome.

dos Reis M, Wernisch L, Savva R.

Nucleic Acids Res. 2003 Dec 1;31(23):6976-85.PMID: 14627830 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome.

Roymondal U, Das S, Sahoo S.

DNA Res. 2009 Feb;16(1):13-30. Epub 2009 Jan 8.PMID: 19131380 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicted highly expressed genes of diverse prokaryotic genomes.

Karlin S, Mrázek J.

J Bacteriol. 2000 Sep;182(18):5238-50.PMID: 10960111 [PubMed - indexed for MEDLINE]Related articlesFree article

An environmental signature for 323 microbial genomes based on codon adaptation indices.

Willenbrock H, Friis C, Juncker AS, Ussery DW.

Genome Biol. 2006;7(12):R114.PMID: 17156429 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes.

Mondal UK, Sur S, Bothra AK, Sen A.

Indian J Med Microbiol. 2008 Oct-Dec;26(4):313-21.PMID: 18974482 [PubMed - indexed for MEDLINE]Related articlesFree article

Codon-anticodon assignment and detection of codon usage trends in seven microbial genomes.

Nakamura Y, Tabata S.

Microb Comp Genomics. 1997;2(4):299-312.PMID: 9689228 [PubMed - indexed for MEDLINE]Related articles

A DNA structural atlas for Escherichia coli.

Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW.

J Mol Biol. 2000 Jun 16;299(4):907-30.PMID: 10843847 [PubMed - indexed for MEDLINE]Related articles

Analysis of codon usage patterns of bacterial genomes using the self-organizing map.

Wang HC, Badger J, Kearney P, Li M.

Mol Biol Evol. 2001 May;18(5):792-800.PMID: 11319263 [PubMed - indexed for MEDLINE]Related articlesFree article

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.

Jansen R, Bussemaker HJ, Gerstein M.

Nucleic Acids Res. 2003 Apr 15;31(8):2242-51.PMID: 12682375 [PubMed - indexed for MEDLINE]Related articlesFree article

Characterizations of highly expressed genes of four fast-growing bacteria.

Karlin S, Mrázek J, Campbell A, Kaiser D.

J Bacteriol. 2001 Sep;183(17):5025-40.PMID: 11489855 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism.

Wu G, Culley DE, Zhang W.

Microbiology. 2005 Jul;151(Pt 7):2175-87.PMID: 16000708 [PubMed - indexed for MEDLINE]Related articlesFree article

Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae.

Martín-Galiano AJ, Wells JM, de la Campa AG.

Microbiology. 2004 Jul;150(Pt 7):2313-25.PMID: 15256573 [PubMed - indexed for MEDLINE]Related articlesFree article

The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes.

Sen A, Sur S, Bothra AK, Benson DR, Normand P, Tisa LS.

Antonie Van Leeuwenhoek. 2008 May;93(4):335-46. Epub 2008 Feb 22.PMID: 18293096 [PubMed - indexed for MEDLINE]Related articles

Differences in codon bias cannot explain differences in translational power among microbes.

Dethlefsen L, Schmidt TM.

BMC Bioinformatics. 2005 Jan 6;6:3.PMID: 15636642 [PubMed - indexed for MEDLINE]Related articlesFree article

[RNA responsible for conferring a DNase I sensitive structure on albumin gene in assembled chromatin]

Lv ZJ, Wang XF, Zhai Y, Song SX.

Yi Chuan. 2003 Jan;25(1):30-6. Chinese. PMID: 15639815 [PubMed]Related articles

Predicting gene expression level from codon usage bias.

Henry I, Sharp PM.

Mol Biol Evol. 2007 Jan;24(1):10-2. Epub 2006 Oct 12.PMID: 17038449 [PubMed - indexed for MEDLINE]Related articlesFree article

Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes.

Couturier E, Rocha EP.

Mol Microbiol. 2006 Mar;59(5):1506-18.PMID: 16468991 [PubMed - indexed for MEDLINE]Related articles

Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of Escherichia coli genome.

Kahali B, Basak S, Ghosh TC.

J Biomol Struct Dyn. 2008 Jun;25(6):655-61.PMID: 18399699 [PubMed - indexed for MEDLINE]Related articles