(Q38625586)

4 September 2017

title

The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function (English)

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4 September 2017

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Fran Supek

1

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publication date

4 November 2015

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Journal of Molecular Evolution

4 September 2017

published in

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4 September 2017

volume

82

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4 September 2017

issue

1

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4 September 2017

page(s)

65-73

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tRNA's wobble decoding of the genome: 40 years of modification

4 September 2017

cites work

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon usage: nature's roadmap to expression and folding of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Efficient translation initiation dictates codon usage at gene start

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The evolution, impact and properties of exonic splice enhancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The relation of codon bias to tissue-specific gene expression in Arabidopsis thaliana.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

A role for codon order in translation dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Computational prediction of genomic functional cores specific to different microbes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon usage between genomes is constrained by genome-wide mutational processes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The effects of codon context on in vivo translation speed

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

BacMap: an up-to-date electronic atlas of annotated bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Cotranslational protein folding--fact or fiction?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

A system of RNA modifications and biased codon use controls cellular stress response at the level of translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Selective charging of tRNA isoacceptors induced by amino-acid starvation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Tissue-specific differences in human transfer RNA expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Selective charging of tRNA isoacceptors explains patterns of codon usage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

mRNA-programmed translation pauses in the targeting of E. coli membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Coevolution of gene expression among interacting proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Determinants of translation efficiency and accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

A dual program for translation regulation in cellular proliferation and differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Causes and effects of N-terminal codon bias in bacterial genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon usage in bacteria: correlation with gene expressivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

21 January 2018

Selection on Codon Bias

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

General rules for optimal codon choice

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Exposing synonymous mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Predicted highly expressed genes of diverse prokaryotic genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Predicted highly expressed genes in archaeal genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Spatial and temporal regulation of protein expression by bldA within a Streptomyces lividans colony

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Inferring gene function from evolutionary change in signatures of translation efficiency

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Coding-sequence determinants of gene expression in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Rare codons regulate KRas oncogenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Accumulation of bldA-specified tRNA is temporally regulated in Streptomyces coelicolor A3(2).

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Speed controls in translating secretory proteins in eukaryotes--an evolutionary perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Environment specific substitution tables for thermophilic proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon usage bias and tRNA abundance in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Sequence-based prediction of protein-protein interactions by means of codon usage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Universal function-specificity of codon usage

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Testing the ortholog conjecture with comparative functional genomic data from mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Assessment of compositional heterogeneity within and between eukaryotic genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Speeding with control: codon usage, tRNAs, and ribosomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

A role for tRNA modifications in genome structure and codon usage

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Tracing specific synonymous codon-secondary structure correlations through evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Rare codons capacitate Kras-driven de novo tumorigenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Synonymous but not the same: the causes and consequences of codon bias

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Effects of codon usage on gene expression: empirical studies on Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon optimality is a major determinant of mRNA stability

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon Bias as a Means to Fine-Tune Gene Expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Quantification of codon selection for comparative bacterial genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The replication-related organization of bacterial genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Understanding the contribution of synonymous mutations to human disease

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Synonymous codon usage influences the local protein structure observed

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

DNA sequence evolution: the sounds of silence

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Variation in the strength of selected codon usage bias among bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Synonymous codon usage in Escherichia coli: selection for translational accuracy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

On relevance of codon usage to expression of synthetic and natural genes in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Translational selection is ubiquitous in prokaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Multiple roles of the coding sequence 5' end in gene expression regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Translation efficiency is determined by both codon bias and folding energy

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The signature of selection mediated by expression on human genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Selection for translation efficiency on synonymous polymorphisms in recent human evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Codon-by-codon modulation of translational speed and accuracy via mRNA folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Translationally optimal codons associate with structurally sensitive sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00239-015-9714-8

The UK10K project identifies rare variants in health and disease

21 January 2018

1 reference

12 December 2020

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

1 reference

12 December 2020

How optimized is the translational machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae?

1 reference

12 December 2020

The selection-mutation-drift theory of synonymous codon usage

1 reference

12 December 2020

Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species

1 reference

12 December 2020

Inferring lifestyle from gene expression patterns

1 reference

12 December 2020

A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes

1 reference

12 December 2020

Codon usage and tRNA content in unicellular and multicellular organisms

1 reference

12 December 2020

10.1007/S00239-015-9714-8

Identifiers

DOI

1 reference

Dimensions Publication ID

4 September 2017

1030716275

0 references

1 reference