Decoding the genomic tree of life (Q24527375)

2

Jacqueline A

Servin

1 reference

19 October 2023

Ryan G Skophammer

3

Ryan G

Skophammer

1 reference

19 October 2023

Craig W Herbold

4

Craig W

Herbold

1 reference

19 October 2023

Maria C Rivera

5

Maria C

Rivera

1 reference

19 October 2023

James A Lake

6

James A

Proceedings of the National Academy of Sciences of the United States of America

Lake

1 reference

19 October 2023

language of work or name

English

0 references

publication date

3 May 2005

0 references

published in

0 references

volume

102 Suppl 1

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page(s)

6608-13

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issue

Supplement 1

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cites work

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24 March 2017

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Horizontal gene transfer among genomes: the complexity hypothesis

24 March 2017

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Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes

24 March 2017

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Molecular archaeology of the Escherichia coli genome

24 March 2017

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Prokaryotes: the unseen majority

24 March 2017

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Archaea and the prokaryote-to-eukaryote transition

24 March 2017

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The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

24 March 2017

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Determining divergence times with a protein clock: update and reevaluation

24 March 2017

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Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics

24 March 2017

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Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum

24 March 2017

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Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya

24 March 2017

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The ring of life provides evidence for a genome fusion origin of eukaryotes

24 March 2017

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The complete genome of the hyperthermophilic bacterium Aquifex aeolicus

24 March 2017

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The complete genome sequence of the gram-positive bacterium Bacillus subtilis

24 March 2017

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The complete genome sequence of Escherichia coli K-12

24 March 2017

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24 March 2017

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Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii

24 March 2017

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Higher-plant chloroplast and cytosolic fructose-1,6-bisphosphatase isoenzymes: origins via duplication rather than prokaryote-eukaryote divergence

24 March 2017

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Phylogenetic classification and the universal tree

24 March 2017

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Evidence for a clade of nematodes, arthropods and other moulting animals

7 April 2017

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Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC6803. II. Sequence Determination of the Entire Genome and Assignment of Potential Protein-coding Regions

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Prokaryotic evolution in light of gene transfer

7 April 2017

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The closest living relatives of land plants

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Horizontal gene transfer in prokaryotes: quantification and classification

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

A kingdom-level phylogeny of eukaryotes based on combined protein data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Genome phylogeny based on gene content

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

The hydrogen hypothesis for the first eukaryote

7 April 2017

1 reference

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The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code

7 April 2017

1 reference

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Examining bacterial species under the specter of gene transfer and exchange

10 May 2017

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Phylogeny determined by protein domain content

27 September 2017

1 reference

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A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Rooting the eukaryote tree by using a derived gene fusion

27 September 2017

1 reference

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Lateral and oblique gene transfer

27 September 2017

1 reference

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Universal trees based on large combined protein sequence data sets.

27 September 2017

1 reference

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Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Assessing evolutionary relationships among microbes from whole-genome analysis

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Gene content phylogeny of herpesviruses

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Lateral gene transfer in prokaryotes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Evolution of organellar genomes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

The nature of the last universal common ancestor

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Whole genome-based phylogenetic analysis of free-living microorganisms

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Early evolution: prokaryotes, the new kids on the block

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

The genomic tree as revealed from whole proteome comparisons

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Horizontal gene transfer: pitfalls and promises

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Animal evolution. The end of the intermediate taxa?

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Genomic evidence for two functionally distinct gene classes.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Three insertion sequences from the cyanobacterium Synechocystis PCC6803 support the occurrence of horizontal DNA transfer among bacteria

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Compositional biases of bacterial genomes and evolutionary implications

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Was the nucleus the first endosymbiont?

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Evidence from 18S ribosomal DNA that the lophophorates are protostome animals

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Mapping evolution with ribosome structure: intralineage constancy and interlineage variation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Evidence that eukaryotes and eocyte prokaryotes are immediate relatives

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Evidence of recent lateral gene transfer among hyperthermophilic archaea

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

The mosaic nature of the eukaryotic nucleus.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Horizontal gene transfer accelerates genome innovation and evolution.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Whole-Genome Analysis of Photosynthetic Prokaryotes

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Using homolog groups to create a whole-genomic tree of free-living organisms: an update.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Protein synthesis. Believe it or not-translation in the nucleus

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

The rooting of the universal tree of life is not reliable.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

Evolutionary anomalies among the aminoacyl-tRNA synthetases

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1131872

The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?

29 November 2018

1 reference

12 December 2020

Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis

1 reference

12 December 2020

Deciding among green plants for whole genome studies

1 reference

12 December 2020

1 reference

12 December 2020

Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases

1 reference

12 December 2020

Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0501996102

1 reference

release_7efjumg6kfhgjbrzwxzrlysg4u

0 references

0 references

1171238

1 reference

1 reference

1 reference