ArticleNature methods2026
Highly accurate ab initio gene annotation with ANNEVO.
Article in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Opinion and perspectives on artificial intelligence biology.Quantitative biology (Beijing, China) · 2026Article
- PlantGFM: A Genomic Foundation Model for Discovery and Creation of Plant Genes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Transposable elements in the era of data science EMBO course: a call for open, accessible, and collaborative TE resources.Mobile DNA · 2026Article
- Biological Characterization, Domestication, and the Molecular Basis of Iron Enrichment in a WildJournal of fungi (Basel, Switzerland) · 2026Article
- Draft hybrid genome assembly of the photosynthetic sacoglossan Elysia crispata provides insights into sacoglossan biology.BMC genomics · 2026Article
- Article
- Biological foundation models illuminate annotation blind spots in evolutionarily divergent genomes.bioRxiv : the preprint server for biology · 2026Article
- A chromosome-level genome assembly of Vanilla planifolia uncovers the genomic architecture underlying partial endoreplication.BMC genomics · 2026Article
- AccuratebioRxiv : the preprint server for biology · 2026Article
- Genomic Analysis and Population Divergence Driven by Geographic Isolation inEcology and evolution · 2026Article
- Comparative genomics acrossFrontiers in genetics · 2026Article
- GeneCAD: Plant Genome Annotation with a DNA Foundation Model.bioRxiv : the preprint server for biology · 2025Article
- Linking phenotype to genotype using comprehensive genomic comparisons.Current opinion in genetics & development · 2025Review
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Authors and funding
13 authors.
Funding
Abstract
Accurate gene annotation is essential for deciphering the mapping from genomic sequences to their functional roles. However, current methods struggle to model complex gene transmission patterns, such as vertical inheritance and horizontal gene transfer. Here we introduce ANNEVO, a mixture of experts-based genomic language model that directly models distal sequence dependencies and joint evolutionary relationships from diverse genomes, enabling precise ab initio gene annotation. Through extensive benchmarking on 566 phylogenetically diverse species, we demonstrate that ANNEVO substantially outperforms existing ab initio methods and achieves performance comparable to state-of-the-art annotation pipelines. Furthermore, ANNEVO's independence from external evidence allows it to deliver more complete annotations than reference annotations for a broad range of species while correcting errors within them. These advancements will improve genome sequence interpretation and provide a framework capable of integrating evolutionary insights.
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