Clemson University researchers are launching a three-year, $830,055 NSF project to use artificial intelligence to study gene regulation at the single-cell level in plants, aiming to understand how individual cells respond to drought, heat, and disease.

Initial work will focus on Arabidopsis as a model plant due to its rapid life cycle and ease of study, with later phases involving computer-based simulations and laboratory validation of predictions in genetically modified plants under stress conditions.

Researchers will employ interpretable AI methods and develop new mathematical models to capture dynamic gene regulatory networks over time, using flow matching to model continuous gene expression changes and generative flow networks to rank multiple regulatory networks with confidence scores.

A key goal is targeted crop improvement by identifying cell-type–specific genetic switches, and the project includes an Artificial Intelligence and Genomics Teaching Camp (AGTC) to expose high school students to AI and genomics concepts, fostering early interest in these fields.

The project seeks to move beyond bulk RNA analysis by examining cell-type–specific gene activity, revealing how different cells contribute to stress responses and how precision genetic editing might target the most important cells for drought tolerance, heat resilience, or disease defense.