Shannon Massey

• Bioinformatics Analyst for several regulated end-to-end workflows, including AmPORE-TB and BioPharma quality control workflows: mRNA Quality Control and Plasmid Quality Control.
• Adherence to strict guidelines for medical device software, including GAMP5 and IEC-62304 to ensure workflows meet industry standards.
• Working with External Consultants to ensure documentation is completed to a thorough standard to pass potential audits.
• Adept at using JAMA, Jira, Master Control, GitLab and Linux-based command-line.
• Quality Control of workflow software, including writing documentation for Software Lifecycle Management, Risk Management, Software Component Items and ensuring traceability matrices are available to track customer requirements and the implementation of those requirements.
• Presented at the Bioinformatics Offsite Conference (October 2024) and generated scientific posters for London Calling (May 2025).

PhD Project: Analysing the Impact of Sexual Recombination on the Segregation of Virulence Genes in African trypanosomes

Lab techniques:

• Established parasite cell cultures (Trypanosoma brucei brucei )
• Established ultra-high molecular weight DNA extraction pipeline for long-read sequencing, to generate DNA libraries for PacBio HiFi sequencing and ONT Nanopore sequencing
• Library preparation and DNA sequencing

Bioinformatics techniques:

• Whole genome assembly combining both long and short read data (Nanopore, PacBio HiFi, Illumina WGS & Hi-C scaffolding) (HiFiASM, Flye)
• Variant calling pipelines including SNP, indels, heterozygosity, and identifying genomic distributions for both whole genome assemblies, and pangenome assemblies (minimap2, bcftools/ vcftools, samtools, vg-giraffe, vg-tools)
• Pangenomics approaches (Minigraph-Cactus)
• Base-level resolution of meiotic recombination events (script customisation)
• Linux (Bash), R

Other Relevant Skills:

• Technical knowledge of long-read sequencing technologies, including PacBio SMRT sequencing (SMRTbell library generation, SMRT cells, Sequel II and IIe instruments, and optimisation modes (CCS and CLR)), and Oxford Nanopore Technologies nanopore sequencing (MinION Mk1B, GridION X5, R9.4.1 flow cells). Experience with ultra-long read DNA extractions and DNA library preparations.
• Technical knowledge of short-read sequencing technologies, including Illumina NGS and Hi-C, NovaSeq 6000 and NextSeq 2000, and short read DNA extractions and DNA library preparations.
• Completed multiple DNA sequencing runs on both MinION Mk1B and GridION X5, including library generation.
• Extensive knowledge of genome sequencing and associated tools for both long and short read sequencing, from laboratory techniques to downstream data analysis pipelines.

Drug Metabolism

• Performed routine LC-MS data analysis
• Quality control
• Utilised automated liquid handling systems for routine in vitro compound clearance and inhibition assays

Professor Charles Lacey

• Optimisation of PBMC isolation methods as part of a pre-study for a clinical trial

Professor Sally Roberts

• Characterisation and co-culture of mesenchymal stem cells (MSCs) and chondrocytes in different serum types as part of the ASCOT clinical trial (Phase I and II)