ArticleCommunications biology2025
FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life.
Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Protein Language Model Embeddings Recover Evolutionary and Functional Organization Across the Ras Superfamily.Journal of molecular evolution · 2026Article
- FANTASIA suite: a reproducible and configurable framework for embedding-based functional annotation of proteins.NAR genomics and bioinformatics · 2026Article
- Genomic Exaptation and Regulatory Landscape Shifts as Key Mechanisms Enabling Flatworm Terrestrialization.Genome biology and evolution · 2026Article
- Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species.Scientific data · 2026Article
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Article
- Artificial intelligence to shed light on the algal dark proteomes.Patterns (New York, N.Y.) · 2025Article
- Ballistic Microscopy (BaM).bioRxiv : the preprint server for biology · 2025Article
- Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course "Evolutionary and Comparative Genomics".Bioinformatics advances · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Protein functional annotation is crucial in biology, but many protein-coding genes remain uncharacterized, especially in non-model organisms. FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) integrates protein language models for large-scale functional annotation. Applied to ~1000 animal proteomes, FANTASIA predicts functions to virtually all proteins, including up to 50% that remained unannotated by traditional homology-based methods. This enables the discovery of novel gene functions, enhancing our understanding of molecular evolution and organismal biology. FANTASIA holds particular promise for functional discovery in non-model taxa, offering advantages over homology-based tools in sensitivity and generalizability. FANTASIA is available on GitHub at https://github.com/CBBIO/FANTASIA .
Indexed as
Identifiers
What OpenQuestion holds
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.