(Q33619109)

28 July 2017

Translational selection is ubiquitous in prokaryotes (English)

1 reference

28 July 2017

0 references

Fran Supek

1

0 references

Kristian Vlahoviček

object named as

Kristian Vlahovicek

4

0 references

author name string

Nives Skunca

2

1 reference

PubMed ID

20585573

28 July 2017

Jelena Repar

3

1 reference

PubMed ID

20585573

28 July 2017

Tomislav Smuc

5

1 reference

28 July 2017

24 June 2010

1 reference

28 July 2017

1 reference

28 July 2017

6

1 reference

28 July 2017

6

1 reference

28 July 2017

e1001004

1 reference

Creative Commons Attribution 4.0 International

28 July 2017

start time

24 June 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

General rules for optimal codon choice

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

IslandViewer: an integrated interface for computational identification and visualization of genomic islands

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Protein abundance profiling of the Escherichia coli cytosol

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Universal patterns of purifying selection at noncoding positions in bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Widespread positive selection in synonymous sites of mammalian genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Environment specific substitution tables for thermophilic proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Protein and DNA sequence determinants of thermophilic adaptation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

A "silent" polymorphism in the MDR1 gene changes substrate specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Ammonium toxicity and potassium limitation in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Psychrophilic microorganisms: challenges for life

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

A problem in multivariate analysis of codon usage data and a possible solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Predicted highly expressed genes in archaeal genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Variation in the strength of selected codon usage bias among bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Selective charging of tRNA isoacceptors induced by amino-acid starvation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Differences in codon bias cannot explain differences in translational power among microbes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Solving the riddle of codon usage preferences: a test for translational selection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

The replication-related organization of bacterial genomes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Decoding the genome: a modified view

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

The COG database: an updated version includes eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Use and misuse of correspondence analysis in codon usage studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Asymmetric directional mutation pressures in bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Alkyl hydroperoxide reductase is the primary scavenger of endogenous hydrogen peroxide in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Predicted highly expressed genes of diverse prokaryotic genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Gene ontology: tool for the unification of biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Global dinucleotide signatures and analysis of genomic heterogeneity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

The RNA Modification Database: 1999 update

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Replicational and transcriptional selection on codon usage in Borrelia burgdorferi

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Amelioration of bacterial genomes: rates of change and exchange

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

21 June 2018

Codon selection in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Queuosine modification of the wobble base in tRNAHis influences 'in vivo' decoding properties

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2891978

Base composition bias might result from competition for metabolic resources.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Error minimization explains the codon usage of highly expressed genes in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Specific correlations between relative synonymous codon usage and protein secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Computational prediction of genomic functional cores specific to different microbes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Absence of translationally selected synonymous codon usage bias in Helicobacter pylori.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Codon bias signatures, organization of microorganisms in codon space, and lifestyle

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

INCA: synonymous codon usage analysis and clustering by means of self-organizing map.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Genomic comparisons among gamma-proteobacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival Forests

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Synonymous codon usage in Pseudomonas aeruginosa PA01.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

The Baumgartner-Weiss-Schindler test for the detection of differentially expressed genes in replicated microarray experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Microeconomic principles explain an optimal genome size in bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

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/10.1371%2FJOURNAL.PGEN.1001004

An introduction to ROC analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1001004

Inferring lifestyle from gene expression patterns

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20585573

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20585573

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.1001004

1 reference

28 July 2017

1 reference

28 July 2017

1 reference

PubMed ID

20585573