ArticlePLoS computational biology2006
Codon usage domains over bacterial chromosomes.
Article in PLoS computational biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 48 citations in OpenAlex.
- GIPSy2: high-performance and scalable genomic island prediction software.Scientific reports · 2026Article
- Current Status of Endolysin-Based Treatments against Gram-Negative Bacteria.Antibiotics (Basel, Switzerland) · 2021Review
- Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers.Scientific reports · 2017Article
- Coevolution of the Organization and Structure of Prokaryotic Genomes.Cold Spring Harbor perspectives in biology · 2016Review
- From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.Cellular and molecular life sciences : CMLS · 2015Review
- GC3-biased gene domains in mammalian genomes.Bioinformatics (Oxford, England) · 2015Article
- Genome-wide patterns of codon bias are shaped by natural selection in the purple sea urchin, Strongylocentrotus purpuratus.G3 (Bethesda, Md.) · 2013Article
- Base composition and translational selection are insufficient to explain codon usage bias in plant viruses.Viruses · 2013Article
- A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation.Nucleic acids research · 2012Article
- Unsupervised two-way clustering of metagenomic sequences.Journal of biomedicine & biotechnology · 2012Article
- Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3).BMC microbiology · 2011Article
- Metagenomic analyses: past and future trends.Applied and environmental microbiology · 2011Review
- Hidden chromosome symmetry: in silico transformation reveals symmetry in 2D DNA walk trajectories of 671 chromosomes.PloS one · 2009Article
- From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later.Microbiology (Reading, England) · 2009Article
- Bacteria as computers making computers.FEMS microbiology reviews · 2009Review
- SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation.Nucleic acids research · 2008Article
- Genomics of an extreme psychrophile, Psychromonas ingrahamii.BMC genomics · 2008Article
- Binning sequences using very sparse labels within a metagenome.BMC bioinformatics · 2008Article
- Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants.Genome biology · 2008Article
- Causes for the intriguing presence of tRNAs in phages.Genome research · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information theory, specifically designed to cluster genes according to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One of the clusters identified in each of the organisms is found to be related to expression levels, as expected, but other groups feature an over-representation of genes belonging to different functional groups, namely horizontally transferred genes, motility, and intermediary metabolism. Furthermore, we show that genes with a similar bias tend to be close to each other on the chromosome and organized in coherent domains, more extended than operons, demonstrating a role of translation in structuring bacterial chromosomes. It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context.
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.