ArticleGenome biology2005
Comparative context analysis of codon pairs on an ORFeome scale.
Article in Genome biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
49 citing papers in PubMed.
- Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization.Annals of medicine and surgery (2012) · 2024Article
- Article
- Article
- Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts.Pathogens (Basel, Switzerland) · 2023Article
- Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation.Vaccines · 2022Article
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- Codon usage bias.Molecular biology reports · 2022Review
- tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast.RNA biology · 2021Article
- The Use of the Rare TTA Codon inIndian journal of microbiology · 2021Article
- Codon usage bias analysis of genes linked with esophagus cancer.Bioinformation · 2021Article
- Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines.Frontiers in microbiology · 2021Review
- NipahVR: a resource of multi-targeted putative therapeutics and epitopes for the Nipah virus.Database : the journal of biological databases and curation · 2020Article
- Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding.Frontiers in microbiology · 2020Review
- CoronaVR: A Computational Resource and Analysis of Epitopes and Therapeutics for Severe Acute Respiratory Syndrome Coronavirus-2.Frontiers in microbiology · 2020Article
- Attenuation of Viruses by Large-Scale Recoding of their Genomes: the Selection Is Always Biased.Current clinical microbiology reports · 2018Review
- Attenuation and protective efficacy of Rift Valley fever phlebovirus rMP12-GM50 strain.Vaccine · 2017Article
- Codon usage and codon pair patterns in non-grass monocot genomes.Annals of botany · 2017Review
- Review
- The Yin and Yang of codon usage.Human molecular genetics · 2016Review
- ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis.Scientific reports · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.