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   Articles with "synonymous codon" as a keyword



The nucleotide usages significantly impact synonymous codon usage in Mycoplasma hyorhinis

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recommendations! Published in 2021 at "Journal of Basic Microbiology"

DOI: 10.1002/jobm.202000592

Abstract: Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics… read more here.

Keywords: synonymous codon; hyorhinis; codon usage; mycoplasma hyorhinis ... See more keywords

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

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recommendations! Published in 2022 at "Virology"

DOI: 10.1016/j.virol.2022.01.011

Abstract: SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we… read more here.

Keywords: analysis; sars cov; codon usage; synonymous codon ... See more keywords

Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli

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recommendations! Published in 2024 at "Genome Biology and Evolution"

DOI: 10.1093/gbe/evae080

Abstract: Abstract Rosenberg AA, Marx A, Bronstein AM (Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nat Commun. 2022:13:2815) recently found a surprising correlation between synonymous codon usage and… read more here.

Keywords: synonymous codon; bond angles; codon usage; codon ... See more keywords

A synonymous codon variant altering splicing of RBCK1 expands the phenotype and genotype spectra of polyglucosan body myopathy 1.

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recommendations! Published in 2023 at "Clinical genetics"

DOI: 10.1111/cge.14350

Abstract: Polyglucosan body myopathy type 1 (PGBM1, OMIM #615895.) is a rare autosomal recessive disorder caused by RBCK1 mutations. The patients displayed polyglucosan accumulation in skeletal and cardiac muscles, giving rise to loss of ambulation and… read more here.

Keywords: codon variant; synonymous codon; polyglucosan body; body myopathy ... See more keywords

Synonymous codon changes at the 5′-end of the gene strongly impact the heterologous protein expression in Escherichia coli

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recommendations! Published in 2017 at "Applied Biochemistry and Microbiology"

DOI: 10.1134/s0003683817030024

Abstract: This study describes the impact of 5′-end codon modulation on the expression of a heterologous gene, human granulocyte colony stimulating factor (GCSF), in Escherichia coli. Fourteen different constructs (pGCSF-01 to pGCSF-14) carrying single or multiple… read more here.

Keywords: synonymous codon; gcsf; escherichia coli; expression ... See more keywords

RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU)

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recommendations! Published in 2025 at "BMC Bioinformatics"

DOI: 10.1186/s12859-025-06166-5

Abstract: Synonymous codon usage bias, a significant factor in gene expression and genome evolution, was extensively studied in genomics and molecular biology. Although the genetic code is universal, significant variations in synonymous codon usage have been… read more here.

Keywords: codon usage; package; synonymous codon; rscu ... See more keywords

Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat

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recommendations! Published in 2020 at "PLoS ONE"

DOI: 10.1371/journal.pone.0242624

Abstract: Synonymous codon usage bias (SCUB) of both nuclear and organellar genes can mirror the evolutionary specialization of plants. The polyploidization process exposes the nucleus to genomic shock, a syndrome which promotes, among other genetic variants,… read more here.

Keywords: synonymous codon; chloroplast genomes; wheat; codon usage ... See more keywords

Alteration of synonymous codon usage bias accompanies polyploidization in wheat

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recommendations! Published in 2022 at "Frontiers in Genetics"

DOI: 10.3389/fgene.2022.979902

Abstract: The diploidization of polyploid genomes is accompanied by genomic variation, including synonymous nucleotide substitutions that may lead to synonymous codon usage bias (SCUB). SCUB can mirror the evolutionary specialization of plants, but its effect on… read more here.

Keywords: codon usage; hexaploid wheat; wheat; synonymous codon ... See more keywords

Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

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recommendations! Published in 2023 at "Frontiers in Microbiology"

DOI: 10.3389/fmicb.2023.1134228

Abstract: Introduction Codon basis is a common and complex natural phenomenon observed in many kinds of organisms. Methods In the present study, we analyzed the base bias of 12 mitochondrial core protein-coding genes (PCGs) shared by… read more here.

Keywords: codon usage; codon; amanita species; synonymous codon ... See more keywords

Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae

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recommendations! Published in 2018 at "International Journal of Molecular Sciences"

DOI: 10.3390/ijms19124010

Abstract: The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding… read more here.

Keywords: synonymous codon; codon usages; codon usage; family ... See more keywords

The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes

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recommendations! Published in 2023 at "International Journal of Molecular Sciences"

DOI: 10.3390/ijms24021185

Abstract: Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid… read more here.

Keywords: codon usage; codon; synonymous codon; amino acid ... See more keywords