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Items: 1 to 20 of 194

1.

Universal pattern and diverse strengths of successive synonymous codon bias in three domains of life, particularly among prokaryotic genomes.

Guo FB, Ye YN, Zhao HL, Lin D, Wei W.

DNA Res. 2012 Dec;19(6):477-85. doi: 10.1093/dnares/dss027. Epub 2012 Nov 6.

2.

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.

3.

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids.

Wald N, Alroy M, Botzman M, Margalit H.

Nucleic Acids Res. 2012 Aug;40(15):7074-83. doi: 10.1093/nar/gks348. Epub 2012 May 11.

4.

Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.

Shao ZQ, Zhang YM, Feng XY, Wang B, Chen JQ.

PLoS One. 2012;7(3):e33547. doi: 10.1371/journal.pone.0033547. Epub 2012 Mar 14.

5.

Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content.

Sandberg R, Bränden CI, Ernberg I, Cöster J.

Gene. 2003 Jun 5;311:35-42.

PMID:
12853136
6.

Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes.

Grosjean H, de Crécy-Lagard V, Marck C.

FEBS Lett. 2010 Jan 21;584(2):252-64. doi: 10.1016/j.febslet.2009.11.052. Review.

7.

Mutation bias is the driving force of codon usage in the Gallus gallus genome.

Rao Y, Wu G, Wang Z, Chai X, Nie Q, Zhang X.

DNA Res. 2011 Dec;18(6):499-512. doi: 10.1093/dnares/dsr035. Epub 2011 Oct 27.

8.
9.

Non-random arrangement of synonymous codons in archaea coding sequences.

Zhang YM, Shao ZQ, Yang LT, Sun XQ, Mao YF, Chen JQ, Wang B.

Genomics. 2013 Jun;101(6):362-7. doi: 10.1016/j.ygeno.2013.04.008. Epub 2013 Apr 17.

10.
11.

The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria.

Ran W, Higgs PG.

Mol Biol Evol. 2010 Sep;27(9):2129-40. doi: 10.1093/molbev/msq102. Epub 2010 Apr 19.

PMID:
20403966
12.

Gene functionality's influence on the second codon: A large-scale survey of second codon composition in three domains.

Tang SL, Chang BC, Halgamuge SK.

Genomics. 2010 Aug;96(2):92-101. doi: 10.1016/j.ygeno.2010.04.001. Epub 2010 Apr 21.

13.

Variation in the strength of selected codon usage bias among bacteria.

Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE.

Nucleic Acids Res. 2005 Feb 23;33(4):1141-53. Print 2005.

14.

Codon-pair usage and genome evolution.

Wang FP, Li H.

Gene. 2009 Mar 15;433(1-2):8-15. doi: 10.1016/j.gene.2008.12.016. Epub 2008 Dec 29.

PMID:
19159666
15.

Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage.

Higgs PG, Ran W.

Mol Biol Evol. 2008 Nov;25(11):2279-91. doi: 10.1093/molbev/msn173. Epub 2008 Aug 6.

PMID:
18687657
16.

Solving the riddle of codon usage preferences: a test for translational selection.

dos Reis M, Savva R, Wernisch L.

Nucleic Acids Res. 2004 Sep 24;32(17):5036-44. Print 2004.

17.

A role for tRNA modifications in genome structure and codon usage.

Novoa EM, Pavon-Eternod M, Pan T, Ribas de Pouplana L.

Cell. 2012 Mar 30;149(1):202-13. doi: 10.1016/j.cell.2012.01.050.

18.

Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea.

Ran W, Kristensen DM, Koonin EV.

MBio. 2014 Mar 25;5(2):e00956-14. doi: 10.1128/mBio.00956-14.

19.

Codon bias as a factor in regulating expression via translation rate in the human genome.

Lavner Y, Kotlar D.

Gene. 2005 Jan 17;345(1):127-38. Epub 2004 Dec 24.

PMID:
15716084
20.

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

Behura SK, Severson DW.

Biol Rev Camb Philos Soc. 2013 Feb;88(1):49-61. doi: 10.1111/j.1469-185X.2012.00242.x. Epub 2012 Aug 14. Review.

PMID:
22889422

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