Dr Robert Simpson

Supervisor Details

Contact Details

Department of Electronic, Electrical and Systems Engineering, University of Birmingham

Scientific Background

Research Interests

I am an Associate Professor in Electronic, Electrical and Systems Engineering at the University of Birmingham, with a research background spanning functional materials, photonics, sensing and computational modelling. My current bioscience research combines sensitive photonic measurements with DNA recognition and amplification to investigate molecular detection and single-nucleotide discrimination. I bring expertise in sensor design, experimental characterisation, statistical design of experiments, and Bayesian optimisation. This enables me to advise students on connecting biological questions with quantitative experiments, understanding sources of variability and developing reliable measurement methods.

I have experience supervising doctoral researchers through to completion and supporting researchers who have progressed into academic careers. My approach encourages independence, critical thinking and open discussion, alongside practical guidance on experimental planning, analysis and scientific communication. Having taught statistical design methods and innovation by design, I also use structured design techniques to support interdisciplinary discussion and ensure different perspectives are considered. Working with colleagues in chemistry and bioscience, I can help MIBTP students develop the engineering and analytical skills needed to investigate biological systems, while supporting collaboration across disciplinary boundaries.

Scientific Inspiration

My scientific inspiration is Thomas Young because his “Renaissance” approach to science crossed disciplinary boundaries. He made important contribution to optics (interference of light with the double-slit experiment), human vision (proposing that colour depends on three types of receptor), mechanics (Young’s modulus) and ancient languages (deciphering Egyptian hieroglyphs using the Rosetta Stone). The contributions show how much one person can achieve by interdisciplinary thinking. Personally, I enjoy bringing ideas from materials science, photonics and engineering into bioscience, and working with people whose expertise extends my knowledge. Young legacy shows that following an interesting question across boundaries can lead to discoveries with lasting impact.

Supervision Style

In three words or phrases: Adaptive, Fun, Interactive.

Provision of Training

Here is the deal: Year 1-- I teach you; Year 2- we teach one another; Year 3- you teach me. My expectation is that you will become the world's expert in your PhD thesis. Therefore, by the end of the PhD, I hope that I will be learning from you.

Progression Monitoring and Management

We will have weekly progress meetings + adhoc meetings as and when require. I also try to adap to different student styles. Indeed, one of my current students prefer to have walking meetings, where we stroll around campus and make voice notes as we go.

Communication

I prefer to meet in person. We predominatly use Teams, Whatsapp, and Email to communicate.

Meetings

PhD Students can expect scheduled meetings with me at least once per week. These meetings will be a mixture of face-to-face and via video chat or telephone. I am usually contactable for an instant response on every working day.

Work Patterns

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings) I expect students to manage their own time.

Notice Period for Feedback

I need at least 2 weeks' notice to provide feedback on written work of up to 5,000 words.

MIBTP Project Details

Primary supervisor for:

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

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

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

Secondary Supervisor(s): Professor James Tucker

University of Registration: University of Birmingham

BBSRC Research Themes:

Understanding the Rules of Life (Systems Biology)

Project Outline

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.

Kinetic co-design of DNA amplification and ultrasensitive photonic sensing

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Kinetic co-design of DNA amplification and ultrasensitive photonic sensing

Secondary Supervisor(s): Professor James Tucker

University of Registration: University of Birmingham

BBSRC Research Themes:

Understanding the Rules of Life (Systems Biology)

Project Outline

Rapid DNA assays normally treat amplification and detection as separate problems. The amplification reaction is made as fast as possible and the resulting DNA is then measured. For the beyond-PCR exponential amplication reactions (EXPARs), however, this can create a design contradiction: aggressive reaction conditions can accelerate both target-triggered amplification and spontaneous background amplification. This reduces the time available to distinguish a true target reaction from background.

Here, we propose a different approach. Our central hypothesis is that more reliable and earlier sequence discrimination can be achieved by deliberately slowing EXPAR to suppress spontaneous amplification, then using an ultrasensitive photonic detector to measure the first products generated by the target-triggered reaction.

The student will control EXPAR kinetics by varying the precursor concentrations, reaction temperature, and target DNA abundance. They will measure target-triggered initiation, amplification rate and spontaneous background onset. These reactions will then be coupled to our novel optical sensor, which is designed to detect very small changes in DNA concentration. The key parameter will, therefore, be the time window in which target-triggered amplification is detectable while background remains below the detection threshold.

Statistical, kinetic and Bayesian models will be used to optimise this coupled biochemical-photonic system. Single-nucleotide variants (SNVs) will provide a demanding test because the system must distinguish DNA sequences that differ by only one base. This will test whether kinetic co-design can improve sequence discrimination when target and reference strands are otherwise almost identical.

Co-supervisor on a project with Professor James Tucker.