Environmental shaping of codon usage and functional adaptation across microbial communities (Q37236759)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

title

Environmental shaping of codon usage and functional adaptation across microbial communities (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Tina Perica

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Kristian Vlahoviček

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

author name string

Vedran Lucić

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

István Nagy

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

language of work or name

English

0 references

publication date

5 August 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

volume

41

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

issue

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

page(s)

8842-8852

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 3.0 Unported

6 March 2020

copyright license

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The shared antibiotic resistome of soil bacteria and human pathogens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Ecological adaptation in bacteria: speciation driven by codon selection

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Draft genome sequence of an antibiotic-resistant Propionibacterium acnes strain, PRP-38, from the novel type IC cluster

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Genome sequence of Propionibacterium acnes type II strain ATCC 11828.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Codon bias, tRNA pools and horizontal gene transfer

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Bacterial community assembly based on functional genes rather than species

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Complete genome sequence of Propionibacterium acnes type IB strain 6609.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Enterotypes of the human gut microbiome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Association between translation efficiency and horizontal gene transfer within microbial communities

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

High Frequency of Horizontal Gene Transfer in the Oceans

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

The bacterial pan-genome:a new paradigm in microbiology.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Translational selection is ubiquitous in prokaryotes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

The systemic imprint of growth and its uses in ecological (meta)genomics

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

General rules for optimal codon choice

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

The fate of new bacterial genes.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

STRING 8--a global view on proteins and their functional interactions in 630 organisms

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Horizontal gene transfer in eukaryotic evolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Microbial diversity and the genetic nature of microbial species

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Metaproteomics provides functional insight into activated sludge wastewater treatment

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

MEGAN analysis of metagenomic data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

An obesity-associated gut microbiome with increased capacity for energy harvest

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Metagenomic analysis of the human distal gut microbiome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

From genomics to chemical genomics: new developments in KEGG

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Environments shape the nucleotide composition of genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Comparative metagenomics of microbial communities

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Variation in the strength of selected codon usage bias among bacteria

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

The complete genome sequence of Propionibacterium acnes, a commensal of human skin

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Environmental genome shotgun sequencing of the Sargasso Sea

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Community structure and metabolism through reconstruction of microbial genomes from the environment

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

The COG database: an updated version includes eukaryotes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

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.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Predicted highly expressed genes of diverse prokaryotic genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

A whole-genome assembly of Drosophila

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Prokaryotes: the unseen majority

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

The estimation of intraclass correlation in the analysis of family data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Codon usage and tRNA content in unicellular and multicellular organisms

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new "killer bugs" are created because of a sympatric lifestyle

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Horizontal gene transfer in evolution: facts and challenges.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799439

Shotgun metaproteomics of the human distal gut microbiota

3 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT673

21 January 2018

Identifiers

DOI

10.1093/NAR/GKT673

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

PubMed publication ID

23921637

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23921637%20AND%20SRC:MED&resulttype=core&format=json