PhD Studentship: Learning the kinetic rules of DNA amplification through high-throughput EXPAR and machine learning

EXPAR is an extremely rapid isothermal DNA amplification reaction, but its behaviour changes substantially with DNA sequence and reaction conditions. An assay that works well for one sequence can become slow, unreliable or dominated by spontaneous amplification when only a few bases are changed. This makes new EXPAR assays difficult to design and still requires substantial empirical optimisation.

This PhD will develop a high-throughput experimental approach to determine the rules that govern EXPAR. The student will measure complete amplification curves across many DNA sequences while systematically varying polymerase and nicking enzyme concentration, buffer, temperature, template design and starting target concentration. Statistical design of experiments, Bayesian optimisation and machine learning will then be used to identify the important factors and efficiently explore this large parameter space.

Our central hypothesis is that these data contain transferable sequence-kinetic relationships that can be used to predict how previously unseen DNA targets will amplify. This will be tested prospectively using new sequences. Single-nucleotide variants (SNVs) will provide a particularly demanding test because the assay must discriminate DNA sequences that differ by only one base. This provides a stringent way to determine whether the models capture sequence-dependent EXPAR behaviour rather than simply fitting individual targets.

The outcome will be quantitative design rules for EXPAR rather than an optimised recipe for one target. This will make rapid nucleic-acid amplification more predictable, reproducible and transferable between biological sequences.

The project will be supervised by Dr Robert E Simpson. For more information, see: https://warwick.ac.uk/fac/cross_fac/mibtp/phd/supervisors/RSimpson/

Funding notes:

The MIBTP provides fully funded four-year PhD studentships, covering tuition fees, a tax-free annual stipend of £21,805 (2026/27 rate), approximately £4,500 per year for research consumables, and additional funding for travel and conferences.

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