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Elucidation of Codon Usage Signatures across the Domains of Life

https://doi.org/10.1101/421487
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/jmbi.1996.0428openalex-snapshot
Co-variation of tRNA Abundance and Codon Usage inEscherichia coliat Different Growth Rates
inferredcites →https://doi.org/10.1016/0022-2836(89)90260-xopenalex-snapshot
Codon usage determines translation rate in Escherichia coli
inferredcites →https://doi.org/10.1016/j.cell.2010.02.036openalex-snapshot
A Role for Codon Order in Translation Dynamics
inferredcites →https://doi.org/10.1016/j.cell.2010.03.031openalex-snapshot
An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation
inferredcites →https://doi.org/10.1016/j.cell.2012.01.050openalex-snapshot
A Role for tRNA Modifications in Genome Structure and Codon Usage
inferredcites →https://doi.org/10.1016/j.cell.2015.02.029openalex-snapshot
Codon Optimality Is a Major Determinant of mRNA Stability
inferredcites →https://doi.org/10.1016/j.celrep.2014.08.012openalex-snapshot
Local Correlations in Codon Preferences Do Not Support a Model of tRNA Recycling
inferredcites →https://doi.org/10.1016/j.molcel.2015.07.018openalex-snapshot
Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding
inferredcites →https://doi.org/10.1016/j.tibs.2008.10.002openalex-snapshot
A pause for thought along the co-translational folding pathway
inferredcites →https://doi.org/10.1016/j.tig.2012.07.006openalex-snapshot
Speeding with control: codon usage, tRNAs, and ribosomes
inferredcites →https://doi.org/10.1016/s0168-9525(00)02041-2openalex-snapshot
tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
inferredcites →https://doi.org/10.1038/325728a0openalex-snapshot
Coevolution of codon usage and transfer RNA abundance
inferredcites →https://doi.org/10.1038/msb.2011.14openalex-snapshot
Determinants of translation efficiency and accuracy
inferredcites →https://doi.org/10.1038/nature04785openalex-snapshot
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
inferredcites →https://doi.org/10.1038/nature10965openalex-snapshot
The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria
inferredcites →https://doi.org/10.1038/nbt1270openalex-snapshot
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
inferredcites →https://doi.org/10.1038/nmeth.1358openalex-snapshot
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
inferredcites →https://doi.org/10.1038/nmeth.3103openalex-snapshot
Binning metagenomic contigs by coverage and composition
inferredcites →https://doi.org/10.1038/nmeth976openalex-snapshot
Accurate phylogenetic classification of variable-length DNA fragments
inferredcites →https://doi.org/10.1038/nrg2899openalex-snapshot
Synonymous but not the same: the causes and consequences of codon bias
inferredcites →https://doi.org/10.1038/s41559-017-0425-yopenalex-snapshot
Evolutionary determinants of genome-wide nucleotide composition
inferredcites →https://doi.org/10.1038/srep24175openalex-snapshot
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
inferredcites →https://doi.org/10.1073/pnas.0307827100openalex-snapshot
Codon usage between genomes is constrained by genome-wide mutational processes
inferredcites →https://doi.org/10.1073/pnas.0909910107openalex-snapshot
Translation efficiency is determined by both codon bias and folding energy
inferredcites →https://doi.org/10.1073/pnas.091427698openalex-snapshot
Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes
inferredcites →https://doi.org/10.1073/pnas.96.8.4482openalex-snapshot
Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis , Drosophila , and Arabidopsis
inferredcites →https://doi.org/10.1080/15476286.2016.1172755openalex-snapshot
Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors
inferredcites →https://doi.org/10.1093/bib/bbs033openalex-snapshot
Functional assignment of metagenomic data: challenges and applications
inferredcites →https://doi.org/10.1093/bioinformatics/btq619openalex-snapshot
NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
inferredcites →https://doi.org/10.1093/bioinformatics/btw290openalex-snapshot
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
inferredcites →https://doi.org/10.1093/genetics/129.3.897openalex-snapshot
The selection-mutation-drift theory of synonymous codon usage.
inferredcites →https://doi.org/10.1093/genetics/136.3.927openalex-snapshot
Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.
inferredcites →https://doi.org/10.1093/molbev/msn173openalex-snapshot
Coevolution of Codon Usage and tRNA Genes Leads to Alternative Stable States of Biased Codon Usage
inferredcites →https://doi.org/10.1093/nar/10.22.7055openalex-snapshot
Codon usage in bacteria: correlation with gene expressivity
inferredcites →https://doi.org/10.1093/nar/14.13.5125openalex-snapshot
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
inferredcites →https://doi.org/10.1093/nar/16.7.3013openalex-snapshot
The AGG codon is translated slowly inE. colieven at very low expression levels
inferredcites →https://doi.org/10.1093/nar/gkr225openalex-snapshot
Taxonomic classification of metagenomic shotgun sequences with CARMA3
inferredcites →https://doi.org/10.1093/nar/gks1205openalex-snapshot
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
inferredcites →https://doi.org/10.1093/nar/gkv1309openalex-snapshot
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025646openalex-snapshot
Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040335openalex-snapshot
Codon usage and tRNA content in unicellular and multicellular organisms.
inferredcites →https://doi.org/10.1098/rstb.2009.0305openalex-snapshot
Forces that influence the evolution of codon bias
inferredcites →https://doi.org/10.1126/science.1170160openalex-snapshot
Coding-Sequence Determinants of Gene Expression in Escherichia coli
inferredcites →https://doi.org/10.1146/annurev.genet.42.110807.091442openalex-snapshot
Selection on Codon Bias
inferredcites →https://doi.org/10.1186/1471-2105-10-56openalex-snapshot
TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
inferredcites →https://doi.org/10.1186/1471-2105-5-163openalex-snapshot
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
inferredcites →https://doi.org/10.1186/gb-2001-2-4-research0010openalex-snapshot
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
inferredcites →https://doi.org/10.1186/s12862-015-0441-yopenalex-snapshot
The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli.
inferredcites →https://doi.org/10.1207/s15327906mbr0102_10openalex-snapshot
The Scree Test For The Number Of Factors
inferredcites →https://doi.org/10.1371/journal.pbio.1001508openalex-snapshot
Positively Charged Residues Are the Major Determinants of Ribosomal Velocity
inferredcites →https://doi.org/10.1371/journal.pcbi.1004957openalex-snapshot
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pgen.1000556openalex-snapshot
General Rules for Optimal Codon Choice
inferredcites →https://doi.org/10.1371/journal.pgen.1002603openalex-snapshot
Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency
inferredcites →https://doi.org/10.1371/journal.pgen.1004392openalex-snapshot
The Effects of Codon Context on In Vivo Translation Speed
inferredcites →https://doi.org/10.1371/journal.pgen.1004941openalex-snapshot
GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands
inferredcites →https://doi.org/10.1371/journal.pone.0013431openalex-snapshot
A General Model of Codon Bias Due to GC Mutational Bias
inferredcites →https://doi.org/10.15252/embj.201694699openalex-snapshot
Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition
inferredcites →https://doi.org/10.7554/elife.01257openalex-snapshot
Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments
inferredcites →https://doi.org/10.7554/elife.01339openalex-snapshot
tRNA genes rapidly change in evolution to meet novel translational demands
inferredcites →https://doi.org/10.7554/elife.03735openalex-snapshot
Measurement of average decoding rates of the 61 sense codons in vivo

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1111/jeb.14212openalex-snapshot
Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: The showcase of polypyrimidine tract binding proteins
inferred← citeshttps://doi.org/10.64898/2025.12.07.692868openalex-snapshot
Conservation of non-consensus nucleotides in transcription factor binding sites
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