Evolutionary Regression and Species-Specific Codon Usage of TLR15 by Carlos G. P. Voogdt, Mark E. Merchant, Jaap A. Wagenaar, Jaap A. Wagenaar, Jos P. M. van Putten

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Supplementary material for "Evolutionary dynamics of abundant stop codon readthrough" by Jungreis, Irwin, Fields, Gabriel, Lin, Michael F., Chan, Clara S., Waterhouse, Robert, Kellis, Manolis

“…Evolutionary dynamics of abundant stop codon readthrough. Molecular Biology and Evolution. doi:10.1093/molbev/msw189…”
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tRNA epitranscriptomics and biased codon are linked to proteome expression in by Ng, Chee Sheng, Sinha, Ameya, Aniweh, Yaw, Nah, Qianhui, Babu, Indrakanti Ramesh, Gu, Chen, Chionh, Yok Hian, Dedon, Peter C, Preiser, Peter R

“…Quantitative analysis of ~2,100 proteins across the IDC revealed that up- and down-regulated proteins in late but not early stages have a marked codon bias that directly correlates with parallel changes in tRNA modifications and enhanced translational efficiency. …”
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Codon: A Compiler for High-Performance Pythonic Applications and DSLs by Shajii, Ariya, Ramirez, Gabriel, Smajlovi?, Haris, Ray, Jessica, Berger, Bonnie, Amarasinghe, Saman, Numanagi?, Ibrahim

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Dysfunctional tRNA reprogramming and codon-biased translation in cancer by Dedon, Peter C, Begley, Thomas J

“…Many cancers hijack translation to increase the synthesis of tumor-driving proteins, the messenger mRNAs of which have specific codon usage patterns. Termed 'codon-biased translation' and originally identified in stress response regulation, this mechanism is supported by diverse studies demonstrating how the 50 RNA modifications of the epitranscriptome, specific tRNAs, and codon-biased mRNAs are used by oncogenic programs to promote proliferation and chemoresistance. …”
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Inferring 3D Shapes from 2D Codons by Richards, Whitman, Koenderink, Jan J., Hoffman, D.D.

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Oligonucleotide design and codon optimization for PCR-based gene synthesis by Steiner, Paul Jamesen

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Evidence of abundant stop codon readthrough in Drosophila and other Metazoa by Jungreis, Irwin, Lin, Michael F., Spokony, Rebecca, Chan, Clara Sophia, Negre, Nicolas, Victorsen, Alec, White, Kevin P., Kellis, Manolis

“…While translational stop codon readthrough is often used by viral genomes, it has been observed for only a handful of eukaryotic genes. …”
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Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast by Jungreis, Irwin, Kellis, Manolis, Chan, Clara Sophia

“…Recent analysis of genomic signatures in mammals, flies, and worms indicates that functional translational stop codon readthrough is considerably more abundant in metazoa than previously recognized, but this analysis provides only limited clues about the function or mechanism of readthrough. …”
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Evidence of efficient stop codon readthrough in four mammalian genes by Loughran, Gary, Chou, Ming-Yuan, Ivanov, Ivaylo P., Jungreis, Irwin, Kellis, Manolis, Kiran, Anmol M., Baranov, Pavel V., Atkins, John F.

“…Stop codon readthrough is used extensively by viruses to expand their gene expression. …”
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Codon choice directs constitutive mRNA levels in trypanosomes by Nascimento, J, Kelly, S, Sunter, J, Carrington, M

“…First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. …”

Synonymous codon usage influences the local protein structure observed by Saunders, R, Deane, C

“…CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. …”

Synonymous codon usage influences the local protein structure observed. by Saunders, R, Deane, C

“…CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. …”

Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance. by Wu, X, Jörnvall, H, Berndt, K, Oppermann, U

“…Expression patterns in Escherichia coli of two small archaeal proteins with a natural content of about 30% rare codons were analyzed. The proteins, a histone-like protein from Sulfolobus shibatae (Ssh10), and a glutaredoxin-like protein from Methanobacterium thermoautotrophicum (mtGrx), were produced with expression plasmids encoding wild-type genes, codon-optimized synthetic, and GST-fusion genes. …”

Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina by Kun Zhang, Yiheng Wang, Yue Zhang, Xiaofei Shan

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MICROPROPAGATION AND START CODON TARGETED CHARACTERIZATION OF FOUR STEVIA CULTIVARS IN EGYPT by Reham Abd ElHamid, F. Abd ElTawab, A. Abdel Razik, A. Allam, A. ELDoliefy

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Codon Bias Can Determine Sorting of a Potassium Channel Protein by Anja J. Engel, Marina Kithil, Markus Langhans, Oliver Rauh, Matea Cartolano, James L. Van Etten, Anna Moroni, Gerhard Thiel

Subjects: “…codon usage…”
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Novel start codons introduce novel coding sequences in the human genomes by He Zhang, Yang Xie

“…Abstract Start-gain mutations can introduce novel start codons and generate novel coding sequences that may affect the function of genes. …”
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Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus by Yue Gao, Yan Lu, Yang Song, Lan Jing

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Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code by Alexander Nesterov-Mueller, Roman Popov, Hervé Seligmann

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