ArticleBioMed research international2014
Large-scale genomic analysis of codon usage in dengue virus and evaluation of its phylogenetic dependence.
Article in BioMed research international, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 29 citations in OpenAlex.
- Article
- Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity.Microorganisms · 2024Article
- Genetic background of adaptation of Crimean-Congo haemorrhagic fever virus to the different tick hosts.PloS one · 2024Article
- Recent advances in the biological activities of microbial exopolysaccharides.World journal of microbiology & biotechnology · 2023Review
- Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype.Frontiers in microbiology · 2021Article
- Origin and evolution of emerging Liao ning Virus (genus Seadornavirus, family Reoviridae).Virology journal · 2020Article
- Analysis of codon usage patterns and influencing factors in Nipah virus.Virus research · 2019Article
- Computational screening of medicinal plant phytochemicals to discover potent pan-serotype inhibitors against dengue virus.Scientific reports · 2019Article
- Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus.BioMed research international · 2019Article
- Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Article
- Article
- Genome Investigations of Vector Competence in Aedes aegypti to Inform Novel Arbovirus Disease Control Approaches.Insects · 2016Review
- Nucleotide composition of the Zika virus RNA genome and its codon usage.Virology journal · 2016Article
- Article
- Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes.PeerJ · 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
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1-4 (DENV1-4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1-4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution.
Indexed as
Identifiers
What OpenQuestion holds
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.