Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Current Biology

• Publication date

  2015-03-16

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1016/j.cub.2015.01.014PMID 25702576
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2013influential reference
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  2013cited by this paper
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  2013influential reference
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  2011influential reference
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  2011cited by this paper
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• Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

  2010cited by this paper
• Enigmatic, ultrasmall, uncultivated Archaea

  2010influential reference
• Autotrophic carbon fixation in archaea

  2010cited by this paper
• Community-wide analysis of microbial genome sequence signatures

  2009cited by this paper
• Search for a 'Tree of Life' in the thicket of the phylogenetic forest

  2009cited by this paper
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  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
• Hydrogenases and H(+)-reduction in primary energy conservation.

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• Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

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  2007cited by this paper
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  2007cited by this paper
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  2007cited by this paper
• Peptide and Protein Antibiotics from the Domain Archaea: Halocins and Sulfolobicins

  2007cited by this paper
• SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

  2007cited by this paper
• RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

  2006cited by this paper
• Structures and mechanisms of glycosyltransferases.

  2006cited by this paper
• Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis

  2006cited by this paper
• AMP-forming acetyl-CoA synthetases in Archaea show unexpected diversity in substrate utilization.

  2006cited by this paper
• Isolation of an autotrophic ammonia-oxidizing marine archaeon

  2005cited by this paper
• MUSCLE: a multiple sequence alignment method with reduced time and space complexity

  2004cited by this paper
• Stringent control in the archaeal genus Sulfolobus.

  2004cited by this paper
• Community structure and metabolism through reconstruction of microbial genomes from the environment

  2004cited by this paper
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.

  2004cited by this paper
• The unique features of glycolytic pathways in Archaea.

  2003cited by this paper
• A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

  2003cited by this paper
• The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism

  2003cited by this paper
• A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont

  2002influential reference
• Enzymes of hydrogen metabolism in Pyrococcus furiosus.

  2000cited by this paper
• The rhamnose pathway.

  2000cited by this paper
• Genetic diversity of archaea in deep-sea hydrothermal vent environments.

  1999cited by this paper
• Population Structure and Phylogenetic Characterization of Marine Benthic Archaea in Deep-Sea Sediments

  1999cited by this paper
• Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring

  1998cited by this paper
• Membrane-bound proton-translocating pyrophosphatase of Syntrophus gentianae, a syntrophically benzoate-degrading fermenting bacterium.

  1998cited by this paper
• tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

  1997cited by this paper
• Purification and properties of acetyl-CoA synthetase (ADP-forming), an archaeal enzyme of acetate formation and ATP synthesis, from the hyperthermophile Pyrococcus furiosus.

  1997cited by this paper
• Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences.

  1996cited by this paper
• Archaea in coastal marine environments.

  1992cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

  1990cited by this paper
• Isolation and chemical composition of the cytoplasmic membrane of the archaebacterium Methanospirillum hungatei.

  1983cited by this paper

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  2025cites this paper
• DPANN Archaea and CPR Bacteria: insights into early cellular evolution?

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• Circular 23S rRNA within archaeal ribosomes

  2025cites this paper
• DPANN archaea.

  2025cites this paper
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  2025cites this paper
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  2023cites this paper
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  2023cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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  2022cites this paper
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