Decoding and Designing DNA Replication Origins Using Genome Language Models (NIEDUSZYNSKI_E27DTP)
How does a cell know where and when to copy its DNA? And can we use artificial intelligence to design entirely new genetic elements that control this process? This exciting interdisciplinary PhD project will tackle a fundamental question in biology: how DNA replication origins are encoded and regulated within genomes.
Working at the interface of computational biology, synthetic biology, and genomics, you will combine cutting-edge genome language models (AI systems trained on whole genomes) with high-throughput experimental approaches to uncover the rules that govern DNA replication. You will develop predictive models of replication origin function, design hundreds of synthetic DNA sequences, and test their performance in yeast using advanced molecular biology and nanopore sequencing technologies.
The project brings together complementary expertise from the Li, Hall, Grandellis and Nieduszynski groups, providing training in machine learning, genome engineering, automation, CRISPR-based genome editing, next-generation sequencing, and data analysis. You will also have access to world-class facilities, including the Earlham Biofoundry and advanced genomics platforms.
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 and have access to training and career development opportunities across the Norwich Research Park through the Norwich Research Park Biosciences Doctoral Training Partnership
Beyond answering fundamental questions about chromosome biology, this research aims to enable the rational design of stable synthetic chromosomes, a key challenge in the future of engineering biology. The project offers outstanding opportunities for collaboration, international conference presentations, and publication, while developing highly sought-after computational and experimental skills relevant to both academia and biotechnology industries.
Join us to help decode the language of genomes and design the chromosomes of the future.