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Results: 1 to 20 of 100

1.

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]
Free PMC Article
2.

Contributions of speed and accuracy to translational selection in bacteria.

Ran W, Higgs PG.

PLoS One. 2012;7(12):e51652. doi: 10.1371/journal.pone.0051652. Epub 2012 Dec 14.

PMID:
23272132
[PubMed - indexed for MEDLINE]
Free PMC Article
3.
4.

A genetic optimization approach for isolating translational efficiency bias.

Raiford DW, Krane DE, Doom TE, Raymer ML.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):342-52. doi: 10.1109/TCBB.2009.24.

PMID:
21233519
[PubMed - indexed for MEDLINE]
5.
6.

CBDB: the codon bias database.

Hilterbrand A, Saelens J, Putonti C.

BMC Bioinformatics. 2012 Apr 26;13:62. doi: 10.1186/1471-2105-13-62.

PMID:
22536831
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization.

Rocha EP.

Genome Res. 2004 Nov;14(11):2279-86. Epub 2004 Oct 12. Erratum in: Genome Res. 2004 Dec;14(12):2510.

PMID:
15479947
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles.

Botzman M, Margalit H.

Genome Biol. 2011 Oct 27;12(10):R109. doi: 10.1186/gb-2011-12-10-r109.

PMID:
22032172
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Codon adaptation index as a measure of dominating codon bias.

Carbone A, Zinovyev A, Képès F.

Bioinformatics. 2003 Nov 1;19(16):2005-15.

PMID:
14594704
[PubMed - indexed for MEDLINE]
Free Article
10.

Transfer RNA gene numbers may not be completely responsible for the codon usage bias in asparagine, isoleucine, phenylalanine, and tyrosine in the high expression genes in bacteria.

Satapathy SS, Dutta M, Buragohain AK, Ray SK.

J Mol Evol. 2012 Aug;75(1-2):34-42. doi: 10.1007/s00239-012-9524-1. Epub 2012 Oct 2. Erratum in: J Mol Evol. 2012 Oct;75(3-4):151-3.

PMID:
23053196
[PubMed - indexed for MEDLINE]
11.

Preferential usage of some minor codons in bacteria.

Ohno H, Sakai H, Washio T, Tomita M.

Gene. 2001 Oct 3;276(1-2):107-15.

PMID:
11591477
[PubMed - indexed for MEDLINE]
12.

Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias.

Rashmi M, Swati D.

Bioinformation. 2013 Nov 11;9(18):912-8. doi: 10.6026/97320630009912. eCollection 2013.

PMID:
24307769
[PubMed]
Free PMC Article
13.

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]
Free Article
14.

Relative codon adaptation: a generic codon bias index for prediction of gene expression.

Fox JM, Erill I.

DNA Res. 2010 Jun;17(3):185-96. doi: 10.1093/dnares/dsq012. Epub 2010 May 7.

PMID:
20453079
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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]
Free PMC Article
16.

Translational selection is ubiquitous in prokaryotes.

Supek F, Skunca N, Repar J, Vlahovicek K, Smuc T.

PLoS Genet. 2010 Jun 24;6(6):e1001004. doi: 10.1371/journal.pgen.1001004.

PMID:
20585573
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Codon bias signatures, organization of microorganisms in codon space, and lifestyle.

Carbone A, Képès F, Zinovyev A.

Mol Biol Evol. 2005 Mar;22(3):547-61. Epub 2004 Nov 10. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1158.

PMID:
15537809
[PubMed - indexed for MEDLINE]
Free Article
18.

SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation.

Kloster M, Tang C.

Nucleic Acids Res. 2008 Jun;36(11):3819-27. doi: 10.1093/nar/gkn288. Epub 2008 May 21.

PMID:
18495752
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency.

Merkl R.

J Mol Evol. 2003 Oct;57(4):453-66.

PMID:
14708578
[PubMed - indexed for MEDLINE]
20.

Relative codon adaptation index, a sensitive measure of codon usage bias.

Lee S, Weon S, Lee S, Kang C.

Evol Bioinform Online. 2010 May 5;6:47-55.

PMID:
20535230
[PubMed]
Free PMC Article

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