ArticleNature methods2026
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model.
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 90 papers.
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Who cites it
90 citing papers in PubMed.
- Chromosome-Level Genome of Simulium vittatum Links Black Fly Cytogenetics to Genome Organization and Evolution.bioRxiv : the preprint server for biology · 2026Article
- Chromosome-scale genome assembly and genomic prediction of essential oil compounds in Atractylodes lancea for genomics-assisted breeding.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Validation of the International Weed Genomics Consortium genome annotation pipeline through reannotation of the model species Arabidopsis thaliana.The plant genome · 2026Article
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- Expanding the triangle of U: comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits.Annals of botany · 2026Article
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- Chromosome-scale genome assembly and annotation of the white star apple (Gambeya albida).Scientific data · 2026Article
- Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.Genome research · 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
- A dual genome-methylome map of clonal evolution in grapevine.Genome biology · 2026Article
- Chromosome-Scale Genome Assemblies of Duckweeds Provide Insights Into Genomic Plasticity, Aquatic Adaptation, and Morphological Reduction.Genome biology and evolution · 2026Article
- Contrasting evolutionary patterns of helper and sensor NRC NLRs in lettuce reflect functional divergence following subfunctionalization.PLoS genetics · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity.Nature communications · 2026Article
- Long-Read Sequencing and Comparative Genome Analyses of Seven Emergomyces Type-Strains.Mycopathologia · 2026Article
- An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation.G3 (Bethesda, Md.) · 2026Article
30 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
Abstract
The accurate identification of genes is vital for understanding biological function, yet this remains challenging across many newly sequenced or less-studied species. Here we present Helixer, an artificial intelligence-based tool for ab initio gene prediction that delivers highly accurate gene models across fungal, plant, vertebrate and invertebrate genomes. Unlike traditional methods, Helixer operates without requiring additional experimental data such as RNA sequencing, making it broadly applicable to diverse species. We show that Helixer's pretrained models achieve accuracy on par with or exceeding current tools, producing gene annotations that closely match expert-curated references across multiple evaluation metrics. Its design enables immediate use on genomes without retraining, providing an efficient, accessible solution for genome annotation in both research and applied settings. The tool is available as an open-source software for local installation via GitHub. An online web interface is also available as well as through the Galaxy ToolShed.
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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.