ArticleProceedings of the National Academy of Sciences of the United States of America2014
Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. 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, 42 citations in OpenAlex.
- Repeats mimic pathogen-associated patterns across a vast evolutionary landscape.Cell genomics · 2025Article
- Deciphering the Code of Viral-Host Adaptation Through Maximum-Entropy Nucleotide Bias Models.Molecular biology and evolution · 2025Article
- Concepts and Methods for Predicting Viral Evolution.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Machine learning methods for predicting human-adaptive influenza A virus reassortment based on intersegment constraint.Frontiers in microbiology · 2025Article
- Concepts and methods for predicting viral evolution.bioRxiv : the preprint server for biology · 2024Article
- Article
- Reduced B cell antigenicity of Omicron lowers host serologic response.Cell reports · 2022Article
- The low abundance of CpG in the SARS-CoV-2 genome is not an evolutionarily signature of ZAP.Scientific reports · 2022Article
- The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2.Molecular biology and evolution · 2021Article
- Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses.Viruses · 2020Article
- Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus.International journal of molecular sciences · 2019Article
- A tumor-specific endogenous repetitive element is induced by herpesviruses.Nature communications · 2019Article
- Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV.PLoS genetics · 2018Article
- Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes.Cell reports · 2018Article
- Influenza Virus-Host Co-evolution. A Predator-Prey Relationship?Frontiers in immunology · 2018Review
- Minority report: targeting emerging viruses before their emergence.Gene therapy · 2017Article
- Time-series oligonucleotide count to assign antiviral siRNAs with long utility fit in the big data era.Gene therapy · 2017Article
- Getting the flu: 5 key facts about influenza virus evolution.PLoS pathogens · 2017Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
We outline a theory to quantify the interplay of entropic and selective forces on nucleotide organization and apply it to the genomes of single-stranded RNA viruses. We quantify these forces as intensive variables that can easily be compared between sequences, outline a computationally efficient transfer-matrix method for their calculation, and apply this method to influenza and HIV viruses. We find viruses altering their dinucleotide motif use under selective forces, with these forces on CpG dinucleotides growing stronger in influenza the longer it replicates in humans. For a subset of genes in the human genome, many involved in antiviral innate immunity, the forces acting on CpG dinucleotides are even greater than the forces observed in viruses, suggesting that both effects are in response to similar selective forces involving the innate immune system. We further find that the dynamics of entropic forces balancing selective forces can be used to predict how long it will take a virus to adapt to a new host, and that it would take H1N1 several centuries to adapt to humans from birds, typically contributing many of its synonymous substitutions to the forcible removal of CpG dinucleotides. By examining the probability landscape of dinucleotide motifs, we predict where motifs are likely to appear using only a single-force parameter and uncover the localization of UpU motifs in HIV. Essentially, we extend the natural language and concepts of statistical physics, such as entropy and conjugated forces, to understanding viral sequences and, more generally, constrained genome evolution.
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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.