The Mason Lab started in November 2019 when Andrew started a 3-year Independent Research Fellowship in Cancer Informatics funded by York Against Cancer to commemorate the charity’s 30^th anniversary. This position will mature into a Lectureship in Cancer Informatics in 2022 as part of The University of York’s Department of Biology and York Biomedical Research Institute.

Lab members over time

Linux onboarding information for group members

Current lab members

Vlad Ungureanu PhD Student (Co-supervisee)

Vlad completed an MEng in Electronic and Computer Engineering at the University of York before working as a graduate software developer.
In February 2020 he returned to York on a GCRF-funded RA position (predominantly within the Mason lab) which included transcriptomic clustering from low n, high feature datasets and development of an RNAseq visualisation tool. He began a 3-year inter-disciplinary PhD at York in October 2020, and is working on methods to incorporate multiple sequencing data types to improve clinical utility of sequencing-derived bladder cancer subtypes.

Saleh Alsuhyami PhD Student

Saleh achieved his bachelor from the University of Taif (Saudi Arabia) with second honors in Lab Sciences and Clinical Biotechnology in 2014. He then worked in Namerah General Hospital for 18 months before moving into academia supported by The University of Bisha (Saudi Arabia). This started with an MSc in Medical and Molecular Virology from The University of Manchester completed in 2020, and now with a PhD at York. Saleh started his PhD on Human Endogenous Retroviruses (HERVs) and their dysregulation in urothelial carcinoma in April 2024.

Marcello Beltrami Bioinformatician

Marcello graduated with a first class Microbiology BSc from the University of Reading. During his second year he realized that there was a possibility of merging two of his biggest passions: computer science and biology. As a result, he pursued a Masters in Bioinformatics at the University of Birmingham, where his research project involved analysing RNA-seq data of glioblastoma multiforme cell lines to determine the effect of drug resistance mutations on pathway regulation. Marcello joined the Mason lab as a Bioinformatics Technician in September 2024.

Charlotte Garton MSc by Research student

Charlotte completed her BSc in Biology at the University of York, where she developed a keen interest in cancer biology, epigenetics, and bioinformatics. Her undergraduate studies included a year in industry, during which she focused on whole genome sequencing of Salmonella enterica for serotype prediction and single nucleotide variant (SNV) analysis. For her final year project, she studied transcription factor binding and epigenetic modifications in prostate cancer. In September 2024, Charlotte began her MSc project, utilising a multi-modal bioinformatics approach to investigate sex-specific dysregulation of the COMPASS complex in bladder cancer.

Hugo Aguado MSc by Research student

Hugo joined the Mason Lab in June 2024 for a summer studentship after finishing his BSc Genetics degree from the University of York. His summer project investigated the impact of changing genome annotations on TPM stability from TCGA's BLCA cohort. Building on this interest in improving annotation specificity, Hugo began an MSc by Research in September 2024, co-supervised by Dr Katherine Bridge (CBR), using long and short read polyA sequencing to identify tissue- and cancer-specific splicing changes and the impact on expression quantification.

Joy Njeru MBiomedSci project student

Joy joined the lab in September 2024 for her MBiomedSci, project. With a background in Accounting and Finance, Joy brings an interdisciplinary perspective to healthcare and research. Her passion for understanding biological systems has led her to explore bioinformatics, where data-driven insights can revolutionise medical science. She aims to develop her expertise in data analysis and contribute to cutting-edge research in genomics, disease mapping, and personalised medicine. With a strong interest in cancer biology and bioinformatics, she is excited to develop new skills that will enhance her understanding of bladder cancer and other diseases.

George Hatton PhD Student (Co-supervisee)

George gained a 1st class MBiol in Biology from the University of York in 2023, completing his final year project in the Jack Birch Unit on the induction and localisation of anti-viral APOBEC3 proteins during BK Polyomavirus infection. George then successfully applied for a 3-year York Against Cancer-sponsored PhD studentship in Biomedical Science continuing the work of his Master’s. The PhD will expand on our knowledge of the role BK plays in bladder cancer oncogenesis, with George developing wet lab and bioinformatic skills supervised by Dr Simon Baker, Dr Andrew Mason and Prof Jenny Southgate.

Anastasia Kaltsa MSc by Research Student (Co-supervisee)

Anastasia obtained her medical degree from Aristotle University in Greece and moved to the UK for her specialty training in Obstetrics and Gynaecology. She is currently a year 4 trainee in the Yorkshire and the Humber Deanery. She developed a special interest in Urogynaecology and successfully applied for a part-time MSc by research project in the Jack Birch Unit, supervised by Prof Jenny Southgate and Dr Andrew Mason. The project focuses on benign urogynaecological conditions, providing knowledge and research experience to pursue her subspecialty training.

Past lab members

Katie Skinner Bioinformatician

Katie joined the lab in October 2020 after gaining a distinction in the Bioinformatics MSc programme at Queen Mary University in London. Katie led our first work with single-cell transcriptomics, in addition to bulk RNAseq and mutational signature projects.
Katie emigrated to the United States in August 2021 to commence her PhD programme in Cancer Informatics at Emory University in Atlanta, GA.

Sarah Becker Undergraduate project student

Sarah joined the Mason Lab in August 2021 for a 7-week internship between the first and second years of her BSc Biology degree at the University of York. Sarah's project used RNAseq data generated from human urothelium cultured in hypoxic conditions, and will form part of an upcoming publication. In September 2023 Sarah will begin a PhD on stress and endometrial cancer at The University of Brighton.

Charlotte Tunnicliffe MBiol project student

Charlotte completed her University of York final year integrated masters project in 2021/22, gaining a 1st. Charlotte characterised the mutational signatures of the 100kGP bladder cancer cohort. She then explored the dominance of APOBEC mutagenesis and its extended mutational footprint.

Eleanor Woodward MBiol project student

Eleanor completed her University of York final year integrated masters project in 2021/22, gaining a 1st, and went on to pursue a PhD in cancer informatics at The University of Newcastle. Eleanor characterised non-coding mutation hotspots in the 100kGP bladder cancer cohort, their relation to coding hotspots, and the likelihood of APOBEC mutagenesis.

Emilia Cross FRAME undergraduate project student

Emilia successfully applied for a FRAME summer studentship to work in the lab in Summer 2022 on a project to study APOBEC tissue specificity in bladder cancer, using the 100kGP cohort. Following her project, Emilia has now entered her final year as a University of York integrated masters student. Emilia has developed a keen interest in cancer bioinformatics and hopes to pursue a research career in this area. Emilia commenced a cancer omics PhD at Imperial College London in Summer 2024.

Fernando Vazquez Lopez Undergraduate project student

Fernando joined the lab for summer 2022 to study avian oncogenic endogenous retroviruses using whole genome sequencing data; hoping to gain direct research experience to help him pursue a career in applied bioinformatics. He has since commenced a PhD (2023 start) at The University of Southampton, applying AI to improve diagnosis of IBD with Dr James Ashton.

Grace Dobbs Postdoctoral research associate

Grace gained a 1st class honours degree in Biomedical Sciences at Newcastle University, and then moved to The University of York to complete her PhD with Professor Dawn Coverley. Grace’s PhD focused on the role of the Cip1-interacting zinc finger protein 1 (CIZ1) during the transition to quiescence.
Grace joined the Mason lab as a postdoctoral researcher in July 2022 after successfully applying for a 8-month BBSRC White Rose DCDF fellowship to develop her skills in bioinformatics. Grace will build on her PhD research by analysing mutational signatures induced in CIZ1-null colony cultures which emerged due to unstable quiescence, further applying this work to explore CIZ1 biology in a pan-cancer analysis. Grace's fellowship concluded in February 2023 before she headed off on a 3-month trip round Latin America!

Ben Musgrove MBiol project student

Ben completed his integrated masters final year project in the lab using the 100kGP bladder cancer cohort to understand copy number alterations, gaining a 1st. After graduating Ben will use his analytical and data science skills in the energy sector.

Sarah Forrester Postdoctoral research associate

Sarah gained her PhD at the University of Liverpool using multi ‘omic approaches to analyse parasite genomic data in 2016 and has worked since then on a range of microbial systems and used a variety of bioinformatic methods. She performs HPC-driven microbial genomics research and delivers bioinformatics training, including as a Software Sustainability Institute Fellow.
Since 2020 she has been working in the Chong lab using long read metagenomics and metabolomics to look at methanogenic archaea which are involved in the decomposition of organic matter during anaerobic digestion. Sarah joined the Mason Lab part-time in June 2023 to apply her data analysis skills to support data analysis in both avian and urothelial cancer projects.

Mae Wells Research Assistant

Mae completed her University of York final year integrated masters project in the lab, working on clonal evolution in the 100kGP bladder cancer cohort, earning a first class degree overall. After graduating Mae returned to the group to continue her work on the 100kGP bladder cancer cohort, developing her skills in bioinformatics and presenting her work to academic and clinical audiences. Mae really enjoyed the different pace of research as a career rather than as a student!

Mwenda Rintari MBiol project student

Mwenda joined the lab in September 2023 to undertake his final year MBiol project. With a passion for data science and omics, Mwenda's project offers him a great opportunity to enhance his bioinformatics skills. The project will generate WGS and RNAseq data from patients with metachronous upper tract and bladder urothelial carcinoma to evaluate the role of clonal seeding in UC recurrence. This project is supported by York Against Cancer and Action Bladder Cancer UK. Mwenda is now pursuing a PhD in cancer omics.

Richard Gawne Bioinformatician

Richard gained a 1st class BSc Molecular Cell Biology degree at the University of York, followed by a distinction in the Bioinformatics MSc at the University of Birmingham. His MSc research project involved analysing RNA-seq data to investigate the genetic basis of a corneal disorder known as keratoconus. Richard returned to York to join the Mason Lab in October 2021 and provided broad bioinformatic support and expertise on multiple projects. Richard left the group in September 2024 to begin a prestigious NHS STP position on the Genomics and Bioinformatics track.

Ellie Robinson Bioinformatics MSc project student

Ellie graduated in 2023 with a 1st class BSc in Biomedical Science from Liverpool John Moores University. Ellie joined the Mason lab in June 2024 to undertake the final project of her MSc in Bioinformatics at the University of York. Ellie’s project involves exploring the relevance of an *in vitro* urothelial hypoxia signature in benign and malignant bladder disease.

Charlie Barker Undergraduate project student

Charlie joined the Mason Lab in June 2024, after completing the 3rd year of his integrated masters degree in biology at York. His summer project involves using TCGA WGS data to determine the transcriptomic impact of non-coding mutations in muscle invasive bladder cancer. Charlie hopes to develop both his bioinformatic skills and understanding of cancer biology prior to starting a 1 year placement with the GSK Genomics R&D team.