ArticleProceedings of the National Academy of Sciences of the United States of America2025
Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Translating functional molecular knowledge into crop-breeding success.Nature reviews. Genetics · 2026Review
- Predicting transcriptional regulators in plants in the era of artificial intelligence.Current opinion in plant biology · 2026Review
- AI-driven technological breakthroughs and practical pathways for biodiversity conservation and ecological management.iScience · 2026Review
- Genolator enables protein function interpretation using a multimodal large language model fusing genomic and structural interpretation with natural language interaction.Genome biology · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- A sequence-based classifier distinguishes phenotype-associated genes from other gene models in plants.Genome research · 2026Article
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Integrating deep learning and pangenomics to recover missing heritability from wild structural variations.BMC genomics · 2026Review
- Single-Cell and Spatial Omics Technologies in Rice Abiotic Stress Biology: A Methodological Review.International journal of molecular sciences · 2026Review
- Prioritization of deleterious mutations informs genomic prediction and increases the rate of gain in common bean (Phaseolus vulgaris L.), a simulation study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- PlantGFM: A Genomic Foundation Model for Discovery and Creation of Plant Genes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomic constraint and hypervariability correlate with fitness effects in elite tetraploid potato breeding material.PLoS genetics · 2026Article
- Artificial intelligence in plant salt stress research: from predictive models to multi-omics integration.Journal of experimental botany · 2026Review
- Identification of race-specific QTL and candidate genes for Aphanomyces root rot resistance in alfalfa (Medicago sativa L.).G3 (Bethesda, Md.) · 2026Article
- Application of deep learning in crop research: From genomics to phenomics.The plant genome · 2026Review
- CodonMoE: DNA language models for codon-dependent mRNA prediction.Bioinformatics (Oxford, England) · 2026Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- Identification of Genetic Variation Associated With Heat Tolerance in Cowpea (Vigna unguiculata L. Walp.).Molecular ecology · 2026Article
- The DNA dialect: a comprehensive guide to pretrained genomic language models.Molecular systems biology · 2026Review
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Authors and funding
12 authors.
Funding
Abstract
Interpreting function and fitness effects in diverse plant genomes requires transferable models. Language models (LMs) pretrained on large-scale biological sequences can capture evolutionary conservation and offer cross-species prediction better than supervised models through fine-tuning limited labeled data. We introduce PlantCaduceus, a plant DNA LM that learns evolutionary conservation patterns in 16 angiosperm genomes by modeling both DNA strands simultaneously. When fine-tuned on a small set of labeled
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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.