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Items: 1 to 20 of 137

1.

Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes.

Bohlin J, Brynildsrud O, Vesth T, Skjerve E, Ussery DW.

PLoS One. 2013 Jul 26;8(7):e69878. doi: 10.1371/journal.pone.0069878. Print 2013.

3.
4.

Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage.

Lightfield J, Fram NR, Ely B.

PLoS One. 2011 Mar 10;6(3):e17677. doi: 10.1371/journal.pone.0017677.

5.

Investigations of oligonucleotide usage variance within and between prokaryotes.

Bohlin J, Skjerve E, Ussery DW.

PLoS Comput Biol. 2008 Apr 18;4(4):e1000057. doi: 10.1371/journal.pcbi.1000057. Erratum in: PLoS Comput Biol. 2009 Jul;5(7). doi: 10.1371/annotation/91dc9016-fc1e-495e-8828-22608c3efe44. PLoS Comput Biol. 2009 Jul;5(7). doi: 10.1371/annotation/45b4b21a-d0d1-40d2-8efd-c30b28baf1eb. PLoS Comput Biol. 2009 Jul;5(7). doi: 10.1371/annotation/4eb76620-9599-40f5-bb05-54f252e48f3b. PLoS Comput Biol. 2009 Jul;5(7). doi: 10.1371/annotation/27a4f12b-e6e6-4d19-bf53-09ce05dfe1b9. PLoS Comput Biol. 2009 Jul;5(7). doi: 10.1371/annotation/3785bc7c-4548-4554-8331-74cc68b8f356.

6.

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
7.

The genome of Campylobacter jejuni: codon and amino acid usage.

Fuglsang A.

APMIS. 2003 Jun;111(6):605-18.

PMID:
12969016
8.
9.

Study of completed archaeal genomes and proteomes: hypothesis of strong mutational AT pressure existed in their common predecessor.

Khrustalev VV, Barkovsky EV.

Genomics Proteomics Bioinformatics. 2010 Mar;8(1):22-32. doi: 10.1016/S1672-0229(10)60003-4.

10.

Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages.

Chen LL, Zhang CT.

Biochem Biophys Res Commun. 2003 Jun 20;306(1):310-7.

PMID:
12788106
11.

Inferring parameters shaping amino acid usage in prokaryotic genomes via Bayesian MCMC methods.

Naya H, Gianola D, Romero H, Urioste JI, Musto H.

Mol Biol Evol. 2006 Jan;23(1):203-11. Epub 2005 Sep 14.

PMID:
16162860
12.

Hydrophobicity and aromaticity are primary factors shaping variation in amino acid usage of chicken proteome.

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

PLoS One. 2014 Oct 16;9(10):e110381. doi: 10.1371/journal.pone.0110381. eCollection 2014.

13.
14.

Causes and implications of codon usage bias in RNA viruses.

Belalov IS, Lukashev AN.

PLoS One. 2013;8(2):e56642. doi: 10.1371/journal.pone.0056642. Epub 2013 Feb 25.

15.

CodonO: codon usage bias analysis within and across genomes.

Angellotti MC, Bhuiyan SB, Chen G, Wan XF.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W132-6. Epub 2007 May 30.

16.

Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes.

Tse H, Cai JJ, Tsoi HW, Lam EP, Yuen KY.

BMC Genomics. 2010 Sep 9;11:491. doi: 10.1186/1471-2164-11-491.

17.

Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes.

Wang B, Liu J, Jin L, Feng XY, Chen JQ.

J Integr Plant Biol. 2010 Dec;52(12):1100-8. doi: 10.1111/j.1744-7909.2010.00998.x. Epub 2010 Oct 22.

PMID:
21106008
18.

Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations.

Schmid P, Flegel WA.

J Transl Med. 2011 Jun 8;9:87. doi: 10.1186/1479-5876-9-87.

19.

A general model of codon bias due to GC mutational bias.

Palidwor GA, Perkins TJ, Xia X.

PLoS One. 2010 Oct 27;5(10):e13431. doi: 10.1371/journal.pone.0013431.

20.

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.

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