Discovering novel biology by in silico archaeology (Q36262997)

13 August 2017

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title

Discovering novel biology by in silico archaeology (English)

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13 August 2017

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3

John van der Oost

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Willem de Vos

series ordinal

2

object named as

Willem M de Vos

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13 August 2017

Thijs J G Ettema

1

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PubMed ID

16175172

13 August 2017

language of work or name

English

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publication date

1 November 2005

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Nature Reviews Microbiology

13 August 2017

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13 August 2017

3

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13 August 2017

11

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13 August 2017

859-869

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https://scigraph.springernature.com/pub.10.1038/nrmicro1268

13 August 2017

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EVOLUTIONARY BIOLOGY: The Birth of the Nucleus

21 January 2018

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Are archaebacteria merely derived ‘prokaryotes’?

21 January 2018

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

21 January 2018

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Default taxonomy: Ernst Mayr's view of the microbial world.

21 January 2018

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21 January 2018

Two empires or three?

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Evidence that eukaryotes and eocyte prokaryotes are immediate relatives

21 January 2018

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21 January 2018

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The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont

21 January 2018

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Life in hot springs and hydrothermal vents

21 January 2018

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Extremophiles and their adaptation to hot environments

21 January 2018

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Methanogenic Archaea and human periodontal disease

21 January 2018

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Diverse microbial communities inhabit Antarctic sponges.

21 January 2018

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Environmental genome shotgun sequencing of the Sargasso Sea

21 January 2018

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

21 January 2018

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Archaeal tetraether lipids: unique structures and applications

21 January 2018

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Widespread occurrence of structurally diverse tetraether membrane lipids: evidence for the ubiquitous presence of low-temperature relatives of hyperthermophiles

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Archaeal genomics: do archaea have a mixed heritage?

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

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Central Dogma of Molecular Biology

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

DNA replication in the hyperthermophilic archaeon Sulfolobus solfataricus

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

21 January 2018

Transcription in Archaea

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Functional organization of the yeast proteome by systematic analysis of protein complexes

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

An exosome-like complex in Sulfolobus solfataricus

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Comparative genomics of Archaea: how much have we learned in six years, and what's next?

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Lineage-specific loss and divergence of functionally linked genes in eukaryotes

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Evidence of recent lateral gene transfer among hyperthermophilic archaea

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Gene and context: integrative approaches to genome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Aminoacyl-tRNAs: setting the limits of the genetic code

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Archaeal shikimate kinase, a new member of the GHMP-kinase family

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Systematic discovery of analogous enzymes in thiamin biosynthesis

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Prediction of protein function and pathways in the genome era.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Cloning and characterization of a RNAse L inhibitor. A new component of the interferon-regulated 2-5A pathway

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRMICRO1268

Identification of a host protein essential for assembly of immature HIV-1 capsids

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Effects of depletion and overexpression of the Trypanosoma brucei ribonuclease L inhibitor homologue.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Biogenesis of cytosolic ribosomes requires the essential iron-sulphur protein Rli1p and mitochondria

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Functional link between ribosome formation and biogenesis of iron-sulfur proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Serial analysis of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Integrating high-throughput and computational data elucidates bacterial networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Genomic analysis of regulatory network dynamics reveals large topological changes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

21 January 2018

The digital code of DNA.

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Basic local alignment search tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Rapid and sensitive sequence comparison with FASTP and FASTA

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Evolution of domain families

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

21 January 2018

Evolution and tinkering

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

SMART 4.0: towards genomic data integration

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

The Pfam protein families database

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

CDD: a curated Entrez database of conserved domain alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Recent improvements to the PROSITE database

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Distinguishing Homologous from Analogous Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Orthology, paralogy and proposed classification for paralog subtypes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

A genomic perspective on protein families

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Genetic regulatory mechanisms in the synthesis of proteins

21 January 2018

2 references

https://api.crossref.org/works/10.1038%2FNRMICRO1268

21 January 2018

https://api.crossref.org/works/10.1038%2FNRMICRO1268

inferred from DOI database lookup

7 January 2021

based on heuristic

Measuring genome evolution

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Conservation of gene order: a fingerprint of proteins that physically interact

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Exploitation of gene context

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Who's your neighbor? New computational approaches for functional genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Non-orthologous gene displacement

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Detecting protein function and protein-protein interactions from genome sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Protein interaction maps for complete genomes based on gene fusion events

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Distribution of membrane lipids of planktonic Crenarchaeota in the Arabian Sea

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

The phylum Nanoarchaeota: Present knowledge and future perspectives of a unique form of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Complete Genome Sequence of an Aerobic Hyper-thermophilic Crenarchaeon, Aeropyrum pernix K1

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

The complete genome of the crenarchaeon Sulfolobus solfataricus P2

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Complete Genome Sequence of an Aerobic Thermoacidophilic Crenarchaeon, Sulfolobus tokodaii strain7

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Genome sequence of Halobacterium species NRC-1

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology

21 January 2018

2 references

https://api.crossref.org/works/10.1038%2FNRMICRO1268

21 January 2018

https://api.crossref.org/works/10.1038%2FNRMICRO1268

inferred from DOI database lookup

7 January 2021

based on heuristic

Complete Sequence and Gene Organization of the Genome of a Hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Genome sequence of Picrophilus torridus and its implications for life around pH 0

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

PGTdb: a database providing growth temperatures of prokaryotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

The phylogeny of prokaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Interactions between methanogenic bacteria and hydrogenic ciliates in the rumen

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Bacterial Mode of Replication with Eukaryotic-Like Machinery in a Hyperthermophilic Archaeon

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

Modularity in the gain and loss of genes: applications for function prediction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

The complete set of tRNA species in Nanoarchaeum equitans

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

31 March 2020

Complexity and tinkering

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO1268

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NRMICRO1268

1 reference

PubMed ID

16175172

Dimensions Publication ID

13 August 2017

0 references

1 reference

PubMed ID

16175172