ArticleNature communications2024
A long-context language model for deciphering and generating bacteriophage genomes.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- DESIGN: a framework for generative AI-enabled crop molecular design-driven breeding.Science China. Life sciences · 2026Review
- Review
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- AI-assisted phage formulation delivered via injectable hydrogels for localized control of implant-associated infections.Bioactive materials · 2026Article
- PlantGFM: A Genomic Foundation Model for Discovery and Creation of Plant Genes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- ATACompass enables cross-species cell identity mapping for scATAC-seq without gene annotations.Cell reports methods · 2026Article
- Decoding viral protein sequences by large language models.Briefings in bioinformatics · 2026Review
- Foundation models in omics research: a comprehensive survey.Briefings in bioinformatics · 2026Review
- Artificial Intelligence in Bacteriophage Science: A Comprehensive Narrative Review of Applications, Challenges, and Translational Opportunities.Antibiotics (Basel, Switzerland) · 2026Review
- Probing the limits of genetic recoding using multi-omics-guided evolution.Nature communications · 2026Article
- AI-empowered human microbiome research.Gut · 2026Review
- CodonMoE: DNA language models for codon-dependent mRNA prediction.Bioinformatics (Oxford, England) · 2026Article
- DNAwhisper: An Integrated Deep Learning Pyramidal Framework for Multi-Trait Genomic Prediction and Adaptive Marker Prioritisation.Plant biotechnology journal · 2026Article
- PlasmidGPT: A generative framework for plasmid analysis and generation.Science advances · 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
- The human skin virome: Ecological dynamics, aberrant profiles, and therapeutic opportunities.Cell host & microbe · 2026Review
- A survey on large language models in biology and chemistry.Experimental & molecular medicine · 2026Review
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.bioRxiv : the preprint server for biology · 2026Article
- The DNA dialect: a comprehensive guide to pretrained genomic language models.Molecular systems biology · 2026Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Inspired by the success of large language models (LLMs), we develop a long-context generative model for genomes. Our multiscale transformer model, megaDNA, is pre-trained on unannotated bacteriophage genomes with nucleotide-level tokenization. We demonstrate the foundational capabilities of our model including the prediction of essential genes, genetic variant effects, regulatory element activity and taxonomy of unannotated sequences. Furthermore, it generates de novo sequences up to 96 K base pairs, which contain potential regulatory elements and annotated proteins with phage-related functions.
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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.