Ribosomal proteins: toward a next generation standard for prokaryotic systematics? (Q48608592)

13 February 2018

title

Ribosomal proteins: toward a next generation standard for prokaryotic systematics? (English)

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13 February 2018

author

Vincent Daubin

5

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13 February 2018

Mathieu Groussin

object named as

Mathieu Groussin

2

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Emmanuel Talla

3

object named as

Emmanuel Talla

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13 February 2018

author name string

Hemalatha Golaconda Ramulu

1

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13 February 2018

Remi Planel

4

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13 February 2018

Céline Brochier-Armanet

6

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13 February 2018

publication date

28 February 2014

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13 February 2018

Molecular Phylogenetics and Evolution

published in

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13 February 2018

volume

75

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13 February 2018

page(s)

103-117

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13 February 2018

ProtTest: selection of best-fit models of protein evolution

cites work

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Lateral gene transfer as a support for the tree of life

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov., Magnetococcales ord. nov.) at the base of the Alphaproteobacteria

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

A review of long-branch attraction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Efficient likelihood computations with nonreversible models of evolution.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Eubacterial phylogeny based on translational apparatus proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Universal trees based on large combined protein sequence data sets.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Saturation and base composition bias explain phylogenomic conflict in Plasmodium.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogenomics and the reconstruction of the tree of life

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Roundup 2.0: enabling comparative genomics for over 1800 genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

MUSCLE: multiple sequence alignment with high accuracy and high throughput

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Hydrogenosomes, mitochondria and early eukaryotic evolution.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Genome Streamlining in a Cosmopolitan Oceanic Bacterium

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogeny of prokaryotes: does it exist and why should we care?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Ancient phylogenetic relationships

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Horizontal gene transfer among genomes: the complexity hypothesis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

RETRACTED: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Recent developments in the MAFFT multiple sequence alignment program

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The quest for orthologs: finding the corresponding gene across genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Mitochondrial Genome Evolution and the Origin of Eukaryotes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Clustal W and Clustal X version 2.0

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

An improved general amino acid replacement matrix

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The hierarchical system of the 'Alphaproteobacteria': description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Isolation and characterization of a magnetotactic bacterial culture from the Mediterranean Sea.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Let them fall where they may: congruence analysis in massive phylogenetically messy data sets

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Tracking microbial biodiversity through molecular and genomic ecology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

FUNYBASE: a FUNgal phYlogenomic dataBASE

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Archaeal phylogeny based on ribosomal proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Genomics and evolution of heritable bacterial symbionts

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

SAR11 clade dominates ocean surface bacterioplankton communities.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

MUST, a computer package of Management Utilities for Sequences and Trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Horizontal gene transfer and phylogenetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The rooting of the universal tree of life is not reliable

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

How good are deep phylogenetic trees?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The tree and net components of prokaryote evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Cultivation of the ubiquitous SAR11 marine bacterioplankton clade.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

An approximately unbiased test of phylogenetic tree selection

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

CONSEL: for assessing the confidence of phylogenetic tree selection

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogenetic affiliation and ultrastructure of uncultured magnetic bacteria with unusually large magnetosomes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Proteobacteria classis nov., a Name for the Phylogenetic Taxon That Includes the "Purple Bacteria and Their Relatives"

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

7 January 2021

Trees in the web of life

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Novel accurate bacterial discrimination by MALDI-time-of-flight MS based on ribosomal proteins coding in S10-spc-alpha operon at strain level S10-GERMS.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

A phylum-level bacterial phylogenetic marker database

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogeny of gammaproteobacteria

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

A robust species tree for the alphaproteobacteria

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogenetic structure of the prokaryotic domain: The primary kingdoms

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

Phylogenomics of prokaryotic ribosomal proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.02.013

10.1016/J.YMPEV.2014.02.013

7 January 2021

Identifiers

DOI

1 reference

13 February 2018

1 reference

13 February 2018