Personal Statement
I work in metatranscriptomics, microbiome research, and clinical diagnostics. I focus on improving how we detect infections and track pathogens.

In the INTEGRATE study, I analysed over 1,000 stool samples from patients with diarrhoea. This is the UK’s largest study comparing traditional lab tests to next-generation sequencing (Cunningham-Oakes et al., 2025). We used DNA (metagenomics) and RNA (metatranscriptomics) to detect pathogens directly from a patient sample (no culturing needed). This approach found infections that standard tests missed and revealed which genes were active during infection. RNA stayed stable in older, unpreserved samples and improved detection of pathogens like Cryptosporidium, Salmonella, and Adenovirus compared to clinical tests. This makes it a powerful tool for tracking outbreaks. By combining RNA and DNA, we got the clearest view yet of what causes gut infections and how microbes behave inside the gut.

Research Overview
Using RNA for diagnostics: I showed that RNA from older clinical samples can still detect key public health pathogens like Adenovirus, Cryptosporidium, and Salmonella (Cunningham-Oakes et al., 2025. Genome Medicine). This opens the door to better tracking of infections.

Faster, better testing in hospitals: Working with The Centre for Genomic Research and Liverpool Clinical Laboratories, we got NHS approval for bacterial tests that return results in under 24 hours. This helped support better use of antibiotics and won a Royal College of Pathologists Achievement Award.

Rapid response to outbreaks: I used RNA sequencing to track a new variant of Canine Enteric Coronavirus during a 2022 outbreak. We found changes in the spike gene that may affect how it spreads and escapes immunity

Industrial bioinformatics: During my PhD, I sequenced over 1,000 bacteria from industrial settings. This work contributed to Unilever’s Genomic Preservation Science Strategy.