Summary

I am a Principal Research Fellow in Genomics and Bioinformatics, and the Bioinformatics Lead at the Centre for Enzyme Innovation (CEI) at the University of Portsmouth. Our focus is to develop enzymatic solutions to solve global environmental problems, such as management of the prevalance of waste plastic in the environment. I also collaborate with researchers across the faculty on a number of different projects, in particular those utilising high-throughput next generation sequencing methods.

Biography

I am a Principal Research Fellow in Genomics and Bioinformatics at the University of Portsmouth, where I am the Bioinformatics Lead at the Centre for Enzyme Innovation (CEI). Our goal is to identify and develop enzymatic solutions to help solve global environmental issues such as the current plastics crisis.

The CEI have previously characterised and engineered an enzyme able to efficiently catalyse the breakdown of Polyethylene terephthalate (PET) plastics. We aim to explore the natural world to find further exciting candidate enzymes with unique properties, to use bioengineering to further improve these properties, and to develop these enzymes for deployment at an industrial scale.

Since 2020, I have led the south coast sequencing hub for the COVID-19 Genomics UK (COG-UK) Consortium. This is a network of research institutes, public health agencies and NHS Trusts, working together to understand the spread of the virus across the UK. Through the use of whole genome sequencing of virus samples, we are able to further understand how the virus spreads, identify direct transmission chains in hospitals and other settings, and identify potential variants of concern.

In addition, I collaborate across the faculty on research projects utilising powerful techniques such as high-throughput sequencing (both Illumina and Nanopore-based technologies), which require extensive processing and rigorous statistical analyses. I also work to build bioinformatics tools for the use of the wider research community.

I have developed a Bioinformatics-specific compute cluster here at the University where I have developed analysis pipelines for whole genome sequencing, genome/transcriptome assembly, RNA-seq, ChIP-seq, CLIP-seq, BS-seq, amplicon sequencing, and other typical sequencing data types used by researchers throughout the University.

Previous to my appointment, I worked in the group of Prof. Tony Kouzarides at the Wellcome Trust/CRUK Gurdon Institute where I worked as the bioinformatics lead. My main research focus was to analyse the role of histone and RNA modifications, and in particular their role in diseases such as cancer. Much of my work involved the analysis of high-throughput sequencing data, in particular ChIP-seq and RNA-seq. 

Prior to this, I held a Post-Doctoral Fellowship at the Wellcome Trust Sanger Institute where I worked under Dr. Matt Hurles as a Mathematical and Statistical Biologist. My work focused on the analysis of large scale copy-number variations in the human genome and their role in common diseases such as breast cancer and Crohn's Disease.

My initial training was in Mathematics, having achieved a Bachelor's degree at the University of Warwick in 2003. I joined the MOAC Doctoral Training Centre in its first year, where students were taken from a number of different backgrounds and trained with a focus on inter-disciplinary science to communicate at the interface between the Life Sciences. I completed my MSc in 2004, and was awarded a PhD in Mathematical Biology and Biophysical Chemistry in January 2009.

Outside of work, I am a keen runner and regularly take part in ultra-marathons, often running over 100 miles at a time. I am also an avid martial artist and hold a black belt (1st Degree) in the Korean art of Tae Kwon Do.

Research interests

My primary research interests lie in the analysis of high-throughput sequencing data and the development of tools and pipelines for the processing and analysis of these data sets. I have expertise in the analysis and interpretation of many different data types, including 16s rDNA amplicon sequencing for metagenomics diversity analysis, de novo assembly of novel genomes/transcriptomes, RNA seq for differential expression analysis, whole genome/exome sequencing for genotyping analyses, ChIP seq for epigenetics analyses, and CLIP seq for ncRNA regulation analyses. I work with both Illumina and Nanopore sequencing technologies. 

I currently collaborate on numerous projects throughout the University in a number of diverse research areas:

• Analysis of microbial biofilm diversity and the effects of antifouling technologies
• Understanding the enzymatic activity of wood-eating gribbles for biofuel development
• Analysis of diverse gene expression pathways in bacterial communities
• Identification of novel biomarkers for prosthetic joint infection
• Understanding the pathogenesis and treatment of Duchenne muscular dystrophy
• Paleogenetics (e.g. genotyping of crew members from the Mary Rose)
• Transcriptional profiling of novel marine organisms
• Identification of therapeutic targets and biosensors for the SARS-CoV-2 virus

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