References
- Gustafsson C, Govindarajan S, Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol 2004;22:346-353. https://doi.org/10.1016/j.tibtech.2004.04.006
- Kurland CG. Major codon preference: theme and variations. Biochem Soc Trans 1993;21:841-846. https://doi.org/10.1042/bst0210841
- Sharp PM, Lloyd AT. Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure. Nucleic Acids Res 1993;21:179-183. https://doi.org/10.1093/nar/21.2.179
- Akashi H. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 1994;136:927-935.
- Baker SF, Nogales A, Martinez-Sobrido L. Downregulating viral gene expression: codon usage bias manipulation for the generation of novel influenza A virus vaccines. Future Virol 2015;10:715-730. https://doi.org/10.2217/fvl.15.31
- Akashi H. Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 1995;139:1067-1076.
- Hartl DL, Moriyama EN, Sawyer SA. Selection intensity for codon bias. Genetics 1994;138:227-234.
- Wu G, Culley DE, Zhang W. Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism. Microbiology 2005;151(Pt 7):2175-2187. https://doi.org/10.1099/mic.0.27833-0
- Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 1981;151:389-409. https://doi.org/10.1016/0022-2836(81)90003-6
- Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 1985;2:13-34.
- Karlin S, Mrazek J. Predicted highly expressed genes of diverse prokaryotic genomes. J Bacteriol 2000;182:5238-5250. https://doi.org/10.1128/JB.182.18.5238-5250.2000
- Karlin S, Mrazek J, Ma J, Brocchieri L. Predicted highly expressed genes in archaeal genomes. Proc Natl Acad Sci U S A 2005;102:7303-7308. https://doi.org/10.1073/pnas.0502313102
- Carbone A, Kepes F, Zinovyev A. Codon bias signatures, organization of microorganisms in codon space, and lifestyle. Mol Biol Evol 2005;22:547-561. https://doi.org/10.1093/molbev/msi040
- Kurland CG. Codon bias and gene expression. FEBS Lett 1991;285:165-169. https://doi.org/10.1016/0014-5793(91)80797-7
- Supek F, Vlahovicek K. Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. BMC Bioinformatics 2005;6:182. https://doi.org/10.1186/1471-2105-6-182
- Supek F, Vlahovicek K. Correction: comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. BMC Bioinformatics 2010;11:463. https://doi.org/10.1186/1471-2105-11-463
- Sharp PM, Li WH. The Codon Adaptation Index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987;15:1281-1295. https://doi.org/10.1093/nar/15.3.1281
- Fox JM, Erill I. Relative codon adaptation: a generic codon bias index for prediction of gene expression. DNA Res 2010;17:185-196. https://doi.org/10.1093/dnares/dsq012
- Roymondal U, Das S, Sahoo S. Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome. DNA Res 2009;16:13-30. https://doi.org/10.1093/dnares/dsn029
- Das S, Roymondal U, Sahoo S. Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance. Gene 2009;443:121-131. https://doi.org/10.1016/j.gene.2009.04.022
- Das S, Roymondal U, Chottopadhyay B, Sahoo S. Gene expression profile of the cynobacterium synechocystis genome. Gene 2012;497:344-352. https://doi.org/10.1016/j.gene.2012.01.023
- Lee S, Weon S, Lee S, Kang C. Relative codon adaptation index, a sensitive measure of codon usage bias. Evol Bioinform Online 2010;6:47-55.
- Hockenberry AJ, Sirer MI, Amaral LA, Jewett MC. Quantifying position-dependent codon usage bias. Mol Biol Evol 2014;31:1880-1893. https://doi.org/10.1093/molbev/msu126
- Sahoo S, Das S. Analyzing gene expression and codon usage bias in diverse genomes using a variety of models. Curr Bioinform 2014;9:102-112. https://doi.org/10.2174/1574893608999140109114247
- Sahoo S, Das S. Analyzing gene expression and codon usage bias in Metallosphaera sedula. J Bioinform Intell Control 2014;3:72-80. https://doi.org/10.1166/jbic.2014.1069
- Amils R. Crenarchaeota. In: Encyclopedia of Astrobiology (Amils R, Gargaud M, Cernicharo Quintanilla J, Cleaves HJ, Irvine WM, Pinti D, et al., eds.). Berlin: Springer-Verlag, 2011. p. 390.
- Donati ER, Castro C, Urbieta MS. Thermophilic microorganisms in biomining. World J Microbiol Biotechnol 2016;32:179. https://doi.org/10.1007/s11274-016-2140-2
- Lillford PJ, Holt CB. In vitro uses of biological cryoprotectants. Philos Trans R Soc Lond B Biol Sci 2002;357:945-951. https://doi.org/10.1098/rstb.2002.1083
- Rubinsky B, Arav A, Fletcher GL. Hypothermic protection: a fundamental property of "antifreeze" proteins. Biochem Biophys Res Commun 1991;180:566-571. https://doi.org/10.1016/S0006-291X(05)81102-7
- Barns SM, Delwiche CF, Palmer JD, Pace NR. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci U S A 1996;93:9188-9193. https://doi.org/10.1073/pnas.93.17.9188
- Shields DC. Switches in species-specific codon preferences: the influence of mutation biases. J Mol Evol 1990;31:71-80. https://doi.org/10.1007/BF02109476
- Das S, Chakrabarti J, Ghosh Z, Sahoo S, Mallick B. A new measure to study phylogenetic relations in the brown algal order Ectocarpales: the "codon impact parameter". J Biosci 2005;30:699-709. https://doi.org/10.1007/BF02703570
- Galtier N, Lobry JR. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 1997;44:632-636. https://doi.org/10.1007/PL00006186
- Lynn DJ, Singer GA, Hickey DA. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 2002;30:4272-4277. https://doi.org/10.1093/nar/gkf546
- Sueoka N. On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci U S A 1962;48:582-592. https://doi.org/10.1073/pnas.48.4.582
- Graham DE, Overbeek R, Olsen GJ, Woese CR. An archaeal genomic signature. Proc Natl Acad Sci U S A 2000;97:3304-3308. https://doi.org/10.1073/pnas.97.7.3304
- Goodacre NF, Gerloff DL, Uetz P. Protein domains of unknown function are essential in bacteria. MBio 2013;5:e00744-e00713.
- Snijders AP, Walther J, Peter S, Kinnman I, de Vos MG, van de Werken HJ, et al. Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis. Proteomics 2006;6:1518-1529. https://doi.org/10.1002/pmic.200402070
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