ReviewBiochemical Society transactions2019
Towards functional characterization of archaeal genomic dark matter.
Review in Biochemical Society transactions, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 59 citations in OpenAlex.
- Characterization of aliA and aliB deletion mutants reveals a dominant role of AliA in Haloferax volcanii lipoprotein lipidation.The Journal of biological chemistry · 2026Article
- Comparative pangenome analysis of methanogenic archaea from diverse ecosystems reveals potential targets for methane mitigation in rumen microbiome.Journal of animal science and technology · 2026Article
- Potential metabolic viability on asteroid chemistry.Communications chemistry · 2026Article
- Article
- Biotechnological Applications of Archaea.Progress in molecular and subcellular biology · 2026Review
- Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.Environmental microbiology reports · 2025Article
- Uncovering the prevalence, key biogenesis enzymes, and biological significance of archaeal lipoproteins.Nature communications · 2025Article
- Review
- Article
- Advancing archaeal research through FAIR resource and data sharing, and inclusive community building.Communications biology · 2025Review
- Article
- A metric and its derived protein network for evaluation of ortholog database inconsistency.BMC bioinformatics · 2025Article
- Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods.Journal of microbiology and biotechnology · 2024Review
- Regulatory sequence-based discovery of anti-defense genes in archaeal viruses.Nature communications · 2024Article
- Article
- Widespread photosynthesis reaction centre barrel proteins are necessary for haloarchaeal cell division.Nature microbiology · 2024Article
- Article
- Diversity, Origin and Evolution of the ESCRT Systems.bioRxiv : the preprint server for biology · 2024Article
- Article
- A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes.Environmental microbiome · 2024Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A substantial fraction of archaeal genes, from ∼30% to as much as 80%, encode 'hypothetical' proteins or genomic 'dark matter'. Archaeal genomes typically contain a higher fraction of dark matter compared with bacterial genomes, primarily, because isolation and cultivation of most archaea in the laboratory, and accordingly, experimental characterization of archaeal genes, are difficult. In the present study, we present quantitative characteristics of the archaeal genomic dark matter and discuss comparative genomic approaches for functional prediction for 'hypothetical' proteins. We propose a list of top priority candidates for experimental characterization with a broad distribution among archaea and those that are characteristic of poorly studied major archaeal groups such as Thaumarchaea, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) and Asgard.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.