Relative synonymous codon usage and codon pair analysis of depression associated genes by Rekha Khandia, Pankaj Gurjar, Mohammad Amjad Kamal, Nigel H. Greig

“…Information based on codon usage, preferred codons, rare, and codon context might be used in constructing a deliverable synthetic construct to correct the gene expression level of the human body, which is altered in the depressive state. …”
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Extended stop codon context predicts nonsense codon readthrough efficiency in human cells by Kotchaphorn Mangkalaphiban, Lianwu Fu, Ming Du, Kari Thrasher, Kim M. Keeling, David M. Bedwell, Allan Jacobson

“…Abstract Protein synthesis terminates when a stop codon enters the ribosome’s A-site. Although termination is efficient, stop codon readthrough can occur when a near-cognate tRNA outcompetes release factors during decoding. …”
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Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides by Jamie R Wangen, Rachel Green

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Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli by Napolitano, Michael G., Landon, Matthieu, Gregg, Christopher J., Lajoie, Marc J., Govindarajan, Lakshmi, Mosberg, Joshua A., Kuznetsov, Gleb, Vargas-Rodriguez, Oscar, Isaacs, Farren J., Söll, Dieter, Goodman, Daniel Bryan, Church, George M

“…The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). …”
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Codon Usage Bias in Phytoplankton by Marc Krasovec, Dmitry A. Filatov

Subjects: “…codon usage bias…”
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The imprint of codons on protein structure. by Deane, C, Saunders, R

“…Here, past and present research regarding synonymous codons and codon translation speed are reviewed within the context of protein structure attainment.…”

Codon usage bias in phytoplankton by Krasovec, M, Filatov, DA

“…Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is known about it in phytoplankton. …”

Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon by Aviv A. Rosenberg, Ailie Marx, Alex M. Bronstein

“…This study uncovers a dependence between local amino acid conformation in folded proteins and the identity of the codon from which that amino acid was translated.…”
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Stop codons in bacteria are not selectively equivalent by Povolotskaya Inna S, Kondrashov Fyodor A, Ledda Alice, Vlasov Peter K

“…<p>Abstract</p> <p>Background</p> <p>The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. …”
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Genome landscapes and bacteriophage codon usage. by Julius B Lucks, David R Nelson, Grzegorz R Kudla, Joshua B Plotkin

“…Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonymous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. …”
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Chaperonin activity modulates codon adaptation by Sangjo Han, Philip M Kim

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Tendencies in Echinococcus sp. codon usage by Fernando Alvarez, Beatriz Garat, Hector Musto, Marina Picon, Ricardo Ehrlich

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Trypanosomatidae codon usage and GC distribution by Guilhermina Alonso, Palmira Guevara, Jose L. Ramirez

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Evolution of codon usage bias in diatoms by Krasovec, M, Filatov, D

“…Codon usage bias (CUB)—preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. …”

Heterogeneity in codon usages of sobemovirus genes. by Zhou, H, Wang, H, Huang, L, Naylor, M, Clifford, P

“…Most interestingly, the codon usages of the viral ORF-2 that encodes the replicase showed affinity to that of the plants whereas codon usages of the other viral ORFs were not relevant to the host species. …”

An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus by Lingqi Wang, Haiting Zhao, Zhilei Wang, Shiwen Ding, Lang Qin, Runzhou Jiang, Xiaolong Deng, Zhen He, Liangjun Li

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Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchy. by Rachele Rossi, Mingyan Fang, Lin Zhu, Chongyi Jiang, Cong Yu, Cristina Flesia, Chao Nie, Wenyan Li, Alessandra Ferlini

“…We designed a novel strategy to define codon usage bias (CUB) in 6 specific small cohorts of human genes. …”
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Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias by Sailen Barik

“…A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. …”
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On the origin of the genetic code: a 27-codon hypothetical precursor of an intricate 64-codon intermediate shaped the modern code by Dujon, Bernard

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Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool by Doyle, Francis, Leonardi, Andrea, Endres, Lauren, Tenenbaum, Scott A., Begley, Thomas J., Dedon, Peter C

“…There are 64 possible codons in the genetic code, with codons for the ∼20 amino acids and 3 stop codons having 1- to 6-fold degeneracy. …”
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