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PhD

Northumbria University, Newcastle, UK

Bioinformatics

• Thesis title: Global, viral and protein scale functional annotation tools for -omics and structural bioinformatics.

BSc (Hons)

Newcastle University, Newcastle, UK

Biochemistry

• Dissertation title: Proteomic analysis of the E3-ubiquitin ligase DTX3L interactome

Senior Research Assistant

COVID19 Sequencing Group, Northumbria University

Part of the COVID19 Genomics Consortium (COG-UK) Sequencing efforts at Northumbria University and developed a novel structural and functional annotation tool for SARS-CoV-2 proteins (see Projects). Undertook routine analysis of SARS-CoV-2 sequencing data as part of the sequencing efforts, including running and troubleshooting Nextflow pipelines, handling sensitive metadata linkage, and developing SOPs.

• Sequence Informatics
• Pipelines
• SARS-CoV-2

Industrial Placement Student

Exploratory Biomarkers Group, GlaxoSmithKline

1-year industrial placement. The focus of work was development and optimisation of assays to support preclinical/clinical safety and efficacy studies of large and small molecule drugs. Utilised commercial immunoassay and flow cytometry platforms and performed downstream data analysis.

• Flow Cytometry
• Immunoassay

ProCogGraph: A graph-based mapping of cognate ligand domain interactions

Bioinformatics Advances

(first author) Developed a graph database of protein domain:ligand interactions, and used this to explore the types of interactions proteins have with their cognate (i.e. in vivo) ligands.

OMEinfo: global geographic metadata for -omics experiments

Bioinformatics Advances

(first author) Developed a tool for geospatial metadata annotation to provide globally consistent metadata, which I found to be inconsistent in some built-environment microbiome studies. OMEinfo has wide applicability to any studies which utilise location as a feature of interest.

Environmental microbiome in the home and daycare settings during the {COVID}-19 pandemic, and potential risk of non-communicable disease in children

Environ. Microbiol. Rep.

(co-author) I performed data analysis of 16S built-environment microbiome samples, using Kraken2 for taxonomic annotation and various R packages for statistical analysis of results.

SPEAR: Systematic ProtEin AnnotatoR

Bioinformatics

(first author) Developed a tool for structural and functional annotation of all proteins in the SARS-CoV-2 genome, to assist in identification of potentially important variants at point of sequencing.

Bacterial Diversity in House Dust: Characterization of a Core Indoor Microbiome

Front. Environ. Sci

(co-author) I performed data analysis of 16S built-environment microbiome samples, using Kraken2 for taxonomic annotation and various R packages for statistical analysis of results.