<scp>AI</scp> foundation models in plant biology

Rapid technological progress has enabled plant biologists to accumulate unprecedented volumes of multi-scale, multi-modal data, yet this abundance of data has intensified the challenge of translating complexity into biological understanding. Foundation models (FMs), large-scale artificial intelligence (AI) systems pretrained on millions of sequences, structures, or images and adaptable to diverse tasks are breaking through this barrier. Across plant science, these FMs are already making an impact: genomic FMs decode regulatory grammar, protein FMs enable rational protein engineering, vision FMs score phenotypes at breeding-population scale, single-cell FMs annotate cell types across species, and FM-powered AI agents accelerate knowledge retrieval and automate research workflows. While experimental validation remains indispensable, foundation models empower plant scientists to accelerate scientific discovery.

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Publication Details

Journal
New Phytologist
Published
2026-06-30
DOI
https://doi.org/10.1111/nph.71395
Primary Topic
Plant Molecular Biology Research
Type
article
Field-Weighted Citation Impact
0.00

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article

AI foundation models in plant biology

Haopeng Yu
New Phytologist
Plant Molecular Biology Research
article

AI foundation models in plant biology

Haopeng Yu
article en

Abstract

Rapid technological progress has enabled plant biologists to accumulate unprecedented volumes of multi-scale, multi-modal data, yet this abundance of data has intensified the challenge of translating complexity into biological understanding. Foundation models (FMs), large-scale artificial intelligence (AI) systems pretrained on millions of sequences, structures, or images and adaptable to diverse tasks are breaking through this barrier. Across plant science, these FMs are already making an impact: genomic FMs decode regulatory grammar, protein FMs enable rational protein engineering, vision FMs score phenotypes at breeding-population scale, single-cell FMs annotate cell types across species, and FM-powered AI agents accelerate knowledge retrieval and automate research workflows. While experimental validation remains indispensable, foundation models empower plant scientists to accelerate scientific discovery.

New Phytologist
John Innes Centre (GB), Norwich Research Park (GB)
Human Frontier Science Program, Biotechnology and Biological Sciences Research Council
Openalex Percentile: Top 10%
Plant Molecular Biology Research
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