ArticleProceedings of the National Academy of Sciences of the United States of America2009
Genome rhetoric and the emergence of compositional bias.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Article
- Decoding Codon Usage Patterns in High-Risk Human Papillomavirus Genomes: A Comprehensive Analysis.Current microbiology · 2025Article
- Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.Polish journal of microbiology · 2024Article
- Strand asymmetries across genomic processes.Computational and structural biotechnology journal · 2023Review
- Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis.Frontiers in microbiology · 2022Article
- Article
- Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus.Pathogens (Basel, Switzerland) · 2021Article
- Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism.The Plant cell · 2021Article
- Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype.Frontiers in microbiology · 2021Article
- Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers candidate therapeutics for COVID-19.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Article
- ExonSkipDB: functional annotation of exon skipping event in human.Nucleic acids research · 2020Article
- Analysis of Nipah Virus Codon Usage and Adaptation to Hosts.Frontiers in microbiology · 2019Article
- Novel metrics for quantifying bacterial genome composition skews.BMC genomics · 2018Article
- Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus.Evolutionary bioinformatics online · 2018Article
- Energy efficiency trade-offs drive nucleotide usage in transcribed regions.Nature communications · 2016Article
- Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses.PloS one · 2016Article
- The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli.BMC evolutionary biology · 2015Article
- Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development.Virology journal · 2012Article
- A detailed comparative analysis on the overall codon usage patterns in hepatitis A virus.Virus research · 2011Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Genomes exhibit diverse patterns of species-specific GC content, GC and AT skews, codon bias, and mutation bias. Despite intensive investigations and the rapid accumulation of sequence data, the causes of these a priori different genome biases have not been agreed on and seem multifactorial and idiosyncratic. We show that these biases can arise generically from an instability of the coevolutionary dynamics between genome composition and resource allocation for translation, transcription, and replication. Thus, we offer a unifying framework for understanding and analyzing different genome biases. We develop a test of multistability of nucleotide composition of completely sequenced genomes and reveal a bistability for Borrelia burgdorferi, a genome with pronounced replication-related biases. These results indicate that evolution generates rhetoric, it improves the efficiency of the genome's communication with the cell without modifying the message, and this leads to bias.
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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.