ArticleScience advances2025
Gaia: An AI-enabled genomic context-aware platform for protein sequence annotation.
Article in Science advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Widespread genomic islands are hotspots of genome variations and mosaicism in giant viruses.Nature communications · 2026Article
- The microbial unknome, a repertoire for microbial chatting?Heredity · 2026Review
- Adaptation ofbioRxiv : the preprint server for biology · 2026Article
- Linear-time prediction of proteome-scale microbial protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Balancing of immune activation and suppression during phage infection.bioRxiv : the preprint server for biology · 2026Article
- ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Hunting for new lineages and mechanisms of life.Nature microbiology · 2026Article
- Gap Analysis of Metabolic Conversions of Off-Flavors and Antinutrients in Plant-Based Substrates.Comprehensive reviews in food science and food safety · 2026Review
- Genome-Informed Identification of Species-Specific Diagnostic Markers for Listeria Using Pangenome Analysis.Pathogens (Basel, Switzerland) · 2026Article
- Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.The ISME journal · 2026Article
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Article
- Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.The ISME journal · 2025Article
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Authors and funding
8 authors.
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Abstract
Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets. Gaia leverages gLM2, a mixed-modality genomic language model trained on both amino acid sequences and their genomic neighborhoods to generate embeddings that integrate sequence-structure-context information. This approach allows for the identification of functionally and/or evolutionarily related genes that are found in conserved genomic contexts, which may be missed by traditional sequence- or structure-based search alone. Gaia enables real-time search of a curated database comprising more than 85 million protein clusters from 131,744 microbial genomes. We compare the homolog retrieval performance of Gaia search against other embedding and alignment-based approaches. We provide Gaia as a web-based, freely available tool.
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