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Life at Earlham Institute
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Plants survive drought, heat and disease by rapidly changing which genes are switched on, where, and when. But we still cannot reliably design the regulatory DNA that controls these expression patterns. This PhD asks an ambitious question: can explainable AI discover plant DNA “design rules” that are strong enough to survive experimental testing?
You will join Earlham Institute’s AI for Biology group and work at the interface of frontier AI, plant genomics and engineering biology. The project will apply plant nucleotide foundation models, and develop explainable AI and active learning methods to identify sequence features that control gene expression.
Rather than training large-scale foundation models from scratch, you will build on the group’s existing platforms and focus on the central scientific challenge: turning AI explanations into testable biological hypotheses.
The project will move from prediction to experiment. Supported by Prof. Anthony Hall’s plant genomics expertise and Dr Carolina Grandellis’s Earlham Biofoundry team, you will design compact libraries of cis-regulatory modules, assemble them into a standard reporter system and test them in potato protoplast assays. Successful and failed designs will both be valuable: they will reveal which AI-derived rules are biologically meaningful, where models fail, and how future design cycles should be improved.
You will receive training in explainable AI, active learning and plant regulatory genomics, alongside hands-on Biofoundry training in DNA assembly and reporter assays. You will also develop skills in experimental design, reproducible software and FAIR data management.
The project will be conducted at the Earlham Institute, a world-class BBSRC research centre of excellence in genomics, engineering and computational biology, and AI.
You will join a highly collaborative and supportive research community, interact with AI researchers, plant scientists, bioinformaticians, automation specialists, and have access to training and career development opportunities across the Norwich Research Park through the Norwich Research Park Biosciences Doctoral Training Partnership.
