Postdoctoral bioinformatician, gamer, powerlifter and father of one, based in Liverpool.

During my PhD at Cardiff University, I researched the genomics of bacteria with tolerance and resistance to industrial preservatives (see my most recent review on this topic). Recently, my focus has been on metagenomics and novel pathogen identification in unexplained diarrhoeal disease.

I’m always open to meet and/or collaborate, so if there is anything you would like to discuss, get in touch.

Interests
  • Genomic epidemiology
  • Computational biology
  • Microbial pathogenesis
  • Bioinformatics
Education

  • PhD in Microbiology and Bioinformatics, 2016 - 2020

    Cardiff University

  • BSc in Pharmacology with Extra Mural Year, 2012 - 2016

    King's College London

Skills and expertise

Bioinformatics
Microbiology
Pathogens
Linux
R
Statistics

Experience

 
 
 
 
 
University of Liverpool, Darby Lab
Postdoctoral Research Associate
University of Liverpool, Darby Lab
Apr 2021 – Present Liverpool
I currently work in the HPRU-GI, and lab of Prof. Alistair Darby, performing bioinformatic research, primarily on the genomics of gastrointestinal infections. All current work is described in more detail under “Projects”.
 
 
 
 
 
Unilever R&D, Port Sunlight, Home Care division
Bioinformatician
Unilever R&D, Port Sunlight, Home Care division
May 2020 – Apr 2021 Liverpool
Resident Bioinformatician for the Unilever Home Care division, responsible for evaluating and establishing new techniques and bioinformatics pipelines for multi-omic data. Oversaw the administration, validation and application of novel computational and statistical methods for business needs.
 
 
 
 
 
Cardiff University, MMI group
BBSRC-CASE PhD Student (Unilever partnership)
Cardiff University, MMI group
Oct 2016 – Mar 2020
Worked as a Microbiologist and Bioinformatician, utilising whole genome sequencing, bioinformatics and big-data analysis to systematically map antimicrobial resistance genes, metabolic pathways and mutations that underpin bacterial resistance to cosmetic preservatives.

Projects

(Relevant primary research linked)

*
All Diarrhoeal pathogens Rotavirus vaccines Clinical genomics
Last updated on Jan 11, 2022
INTEGRATE
INTEGRATE

Using ~2000 metagenomic samples collected from cases of diarrhoea, we aim to to investigate the overlap of diagnostics achieved by metagenomic sequencing, culturing and molecular (PCR) methodologies, for known pathogens. We also aim to identify novel pathogens where conventional gastrointestinal species of interest are not detected.
Last updated on Jan 10, 2022
RoVI
RoVI

Follow-up to the primary publication. We aim to use shotgun metagenomics to identify risk factors for impaired oral rotavirus vaccine efficacy in low-income countries, via microbiome and pathway analysis.
Last updated on Jan 10, 2022
Viral surveillance
Viral surveillance

We aim to take novel sequencing and informatic approaches and develop them for application to respiratory and enteric pathogens. The end goal is an assay that can be used for routine sequencing in a clinical setting. This would minimise detection time and provide information regarding the transmission of strains within hours.

All Publications

Edward Cunningham-Oakes, Tom Pointon, Barry Murphy, Thomas R. Connor, Eshwar Mahenthiralingam (2020). Genome Sequence of Pluralibacter gergoviae ECO77, a Multireplicon Isolate of Industrial Origin. Microbial Resource Announcments.

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Gordon Webster, Alex J. Mullins, Edward Cunningham-Oakes, Arun Renganathan, Jamuna Bai Aswathanarayan, Eshwar Mahenthiralingam, Ravishankar Rai Vittal (2020). Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India. FEMS Microbiology Ecology.

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Edward Cunningham-Oakes, Rebecca Weiser, Tom Pointon, Eshwar Mahenthiralingam (2019). Understanding the challenges of non-food industrial product contamination. FEMS Microbiology Letters.

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Gordon Webster, Alex J Mullins, Aimee S Bettridge, Cerith Jones, Edward Cunningham-Oakes, Thomas R. Connor, Julian Parkhill, Eshwar Mahenthiralingam (2019). The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential. Microbial Resource Announcements.

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Gordon Webster, Alex J Mullins, Andrew J Watkins, Edward Cunningham-Oakes, Andrew J Weightman, Eshwar Mahenthiralingam, Henrik Sass (2019). Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments. Microbial Resource Announcements.

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Rebecca Weiser, Angharad E. Green, Matthew J. Bull, Edward Cunningham-Oakes, Keith A. Jolley, Martin C. J. Maiden, Amanda J. Hall, Craig Winstanley, Andrew J. Weightman, Denise Donoghue, Alejandro Amezquita, Thomas R. Connor, Eshwar Mahenthiralingam (2019). Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes. Microbial Genomics.

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Ainsley Beaton, Cédric Lood, Edward Cunningham-Oakes, Alison MacFadyen, Alex J Mullins, Walid El Bestawy, João Botelho, Sylvie Chevalier, Shannon Coleman, Chloe Dalzell, Stephen K Dolan, Alberto Faccenda, Maarten G K Ghequire, Steven Higgins, Alexander Kutschera, Jordan Murray, Martha Redway, Talal Salih, Ana C da Silva, Brian A Smith, Nathan Smits, Ryan Thomson, Stuart Woodcock, Martin Welch, Pierre Cornelis, Rob Lavigne, Vera van Noort, Nicholas P Tucker (2018). Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies. FEMS Microbiology Letters.

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Edward Cunningham-Oakes, Odel Soren, Caroline Moussa, Getika Rathor, Yingjun Liu, Anthony Coates, Yanmin Hu (2015). Nordihydroguaiaretic acid enhances the activities of aminoglycosides against methicillin- sensitive and resistant Staphylococcus aureus in vitro and in vivo. Frontiers in Microbiology.

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