ArticleeLife2022
Unifying the known and unknown microbial coding sequence space.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
71 citing papers in PubMed, 124 citations in OpenAlex.
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- Differential proteomics of bacteria grownmSystems · 2026Article
- "Quadrupling" the protein family space with global metagenomics.Nucleic acids research · 2026Article
- From functional annotation to functional meaning in microbiome research.Environmental microbiome · 2026Review
- ESM2-Guided Context-Aware Annotation Completion Supplements Carbohydrate Metabolism Coverage in Silage Microbial Metagenomes.Microorganisms · 2026Article
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- Genome shuffling enables quantitative trait locus mapping in Bacillus subtilis.Nature communications · 2026Article
- Strain-Specific Loci in Bacterial Genomes: Whole-Genome Discovery, Genomic Context, and Application for Multi-Strain qPCR Monitoring.Microorganisms · 2026Article
- The microbial unknome, a repertoire for microbial chatting?Heredity · 2026Review
- Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.bioRxiv : the preprint server for biology · 2026Article
- A robust, sensitive phylogenetic method enables gene-level metagenomic analyses.bioRxiv : the preprint server for biology · 2026Article
- Predicting functions of uncharacterized gene products from microbial communities.Nature biotechnology · 2026Article
- Linear-time prediction of proteome-scale microbial protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- Urban greenspaces harbour distinct plasmid communities enriched in heavy metal resistance and competitive traits in arid soils.Microbiology (Reading, England) · 2026Article
- Clustering the protein universe of life using DIAMOND DeepClust.Nature methods · 2026Article
- Cosmopolitan Gene Families With Known Functions Are Hotspots for the Evolution of Novel Genes in Stony Corals.Genome biology and evolution · 2026Article
- Water mass specific genes dominate the Southern Ocean microbiome.Nature communications · 2026Article
- Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling.Nature microbiology · 2026Article
- Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 14 institutions in 10 countries.
Funding
Abstract
Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40-60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for
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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.