Distinct responses to rare codons in select Drosophila tissues by Scott R Allen, Rebeccah K Stewart, Michael Rogers, Ivan Jimenez Ruiz, Erez Cohen, Alain Laederach, Christopher M Counter, Jessica K Sawyer, Donald T Fox

Subjects: “…codon bias…”
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Synonymous Codon Usage Analysis of Three Narcissus Potyviruses by Zhen He, Shiwen Ding, Jiyuan Guo, Lang Qin, Xiaowei Xu

Subjects: “…codon usage bias…”
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Codon usage patterns across seven Rosales species by Yao Zhang, Zenan Shen, Xiangrui Meng, Liman Zhang, Zhiguo Liu, Mengjun Liu, Fa Zhang, Jin Zhao

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Analysis of codon usage and nucleotide composition bias in polioviruses by Gu Yuan-xing, Ding Yao-zhong, Ma Li-na, Chen Hao-tai, Zhou Jian-hua, Liu Wen-qian, Wang Meng, Zhang Jie, Liu Yong-sheng

“…</p> <p>Methods</p> <p>The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents and dinucleotides were investigated and a comparative analysis of codon usage pattern for open reading frames (ORFs) among 48 polioviruses isolates including 31 of genotype 1, 13 of genotype 2 and 4 of genotype 3.…”
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Stop Codon Context-Specific Induction of Translational Readthrough by Mirco Schilff, Yelena Sargsyan, Julia Hofhuis, Sven Thoms

“…Premature termination codon (PTC) mutations account for approximately 10% of pathogenic variants in monogenic diseases. …”
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Codon-optimization in gene therapy: promises, prospects and challenges by Anastasiia Iu Paremskaia, Anna A. Kogan, Anastasiia Murashkina, Daria A. Naumova, Anakha Satish, Ivan S. Abramov, Ivan S. Abramov, Sofya G. Feoktistova, Olga N. Mityaeva, Andrei A. Deviatkin, Pavel Yu Volchkov, Pavel Yu Volchkov

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Analysis of codon usage bias of thioredoxin in apicomplexan protozoa by Dawei Wang, Baoling Yang

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Next-generation development and application of codon model in evolution by Manoj Kumar Gupta, Ramakrishna Vadde

Subjects: “…codon substitution models…”
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Analysis of codon usage patterns in 48 Aconitum species by Meihua Yang, Jiahao Liu, Wanqing Yang, Zhen Li, Yonglin Hai, Baozhong Duan, Haizhu Zhang, Xiaoli Yang, Conglong Xia

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ICOR: improving codon optimization with recurrent neural networks by Rishab Jain, Aditya Jain, Elizabeth Mauro, Kevin LeShane, Douglas Densmore

Subjects: “…Codon optimization…”
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Measuring the tolerance of the genetic code to altered codon size by Erika Alden DeBenedictis, Dieter Söll, Kevin M Esvelt

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Evolution of termination codons of proteins and the TAG-TGA paradox by Mária Trexler, László Bányai, Krisztina Kerekes, László Patthy

“…Our analyses of human mutation data revealed that out of the eighteen sense codons that can give rise to a nonsense codon by single base substitution, the CGA codon is exceptional: it gives rise to the TGA stop codon at an order of magnitude higher rate than the other codons. …”
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Ribosome Fate during Decoding of UGA-Sec Codons by Paul R. Copeland, Michael T. Howard

“…Decoding of genetic information into polypeptides occurs during translation, generally following the codon assignment rules of the organism’s genetic code. …”
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Readthrough events in plants reveal plasticity of stop codons by Yuqian Zhang, Hehuan Li, Yanting Shen, Shunxi Wang, Lei Tian, Haoqiang Yin, Jiawei Shi, Anqi Xing, Jinghua Zhang, Usman Ali, Abdul Sami, Xueyan Chen, Chenxuan Gao, Yangtao Zhao, Yajing Lyu, Xiaoxu Wang, Yanhui Chen, Zhixi Tian, Shu-Biao Wu, Liuji Wu

“…Summary: Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. …”
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Elucidation of Codon Usage Signatures across the Domains of Life by Novoa Pardo, Eva Maria, Jungreis, Irwin, Jaillon, Olivier, Kellis, Manolis

“…Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being "synonymous," these codons are not equally used. …”
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Codon: A Framework for Pythonic Domain-Specific Languages by Ramirez, Gabriel L.

“…In this thesis, we propose Codon, a framework for implementing high-performance DSLs based on Python. …”
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Measuring the tolerance of the genetic code to altered codon size by DeBenedictis, Erika Alden, Söll, Dieter, Esvelt, Kevin M

“…<jats:p>Translation using four-base codons occurs in both natural and synthetic systems. …”
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Positive selection for unpreferred codon usage in eukaryotic genomes by Neafsey, Daniel E., Galagan, James E.

“…We looked for evidence of directional selection resulting in increased unpreferred codon usage (and presumably reduced translational efficiency) in three divergent clusters of eukaryotic genomes using a simple optimal-codon-based metric (Kp/Ku). …”
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Evolutionary lability of context-dependent codon bias in bacteria. by Mcvean, G, Hurst, G

“…In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. …”

A phylogenetic codon substitution model for antibody lineages by Pybus, O, Hoehn, K, Lunter, G