(Q30489524)

14 October 2017

Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model (English)

1 reference

14 October 2017

1 reference

0 references

Miklós Csurös

1

1 reference

PMC publication ID

2726834

14 October 2017

István Miklós

series ordinal

2

1 reference

14 October 2017

30 June 2009

1 reference

Molecular Biology and Evolution

14 October 2017

1 reference

14 October 2017

26

1 reference

14 October 2017

9

1 reference

14 October 2017

2087-2095

1 reference

Modelling prokaryote gene content

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Reduced selection leads to accelerated gene loss in Shigella

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Adaptations to energy stress dictate the ecology and evolution of the Archaea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Streamlining and simplification of microbial genome architecture

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

The origin and evolution of Archaea: a state of the art

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Orthologs, paralogs, and evolutionary genomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Concerted and birth-and-death evolution of multigene families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Horizontal gene transfer, genome innovation and evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Evolutionary and functional genomics of the Archaea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Estimating the tempo and mode of gene family evolution from comparative genomic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

The net of life: reconstructing the microbial phylogenetic network

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Higher-level classification of the Archaea: evolution of methanogenesis and methanogens

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

MUSCLE: multiple sequence alignment with high accuracy and high throughput

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Lateral Gene Transfer and the Origins of Prokaryotic Groups

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Geographic barriers isolate endemic populations of hyperthermophilic archaea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Genome trees and the tree of life

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

The genome of M. acetivorans reveals extensive metabolic and physiological diversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Deletional bias and the evolution of bacterial genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Whole genome-based phylogenetic analysis of free-living microorganisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

The genomic tree as revealed from whole proteome comparisons

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Genome phylogeny based on gene content

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

A genomic perspective on protein families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Gene families: the taxonomy of protein paralogs and chimeras

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Evolutionary trees from DNA sequences: A maximum likelihood approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2726834

Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP123

Evidence for genetic drift in the diversification of a geographically isolated population of the hyperthermophilic archaeon Pyrococcus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP123

Reconstruction of highly heterogeneous gene-content evolution across the three domains of life.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP123

Population size and rate of evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP123

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP123

Orthology, paralogy and proposed classification for paralog subtypes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP123

Archaeal phylogeny based on ribosomal proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP123

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP123

PHYLOGENIES FROM RESTRICTION SITES: A MAXIMUM-LIKELIHOOD APPROACH.

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19570746

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSP123

1 reference

14 October 2017

1 reference

PMC publication ID

2726834

14 October 2017

PubMed publication ID

19570746

1 reference

PMC publication ID

2726834