Jez Swann
Research Software Engineer
Jez is a Research Software Engineer who joined the group in 2016 after completing his PhD at the University of Leeds. He currently works on the HPC infrastructure, metadata databases and web interfaces that support the group’s Nanopore sequencing. He has also developed a variety of containers and bioinformatics pipelines for the group. Before joining the group, he has worked at the University of Leeds and Linköping University developing tools to allow interactive registration of 3D pathology and MRI volumes.
Recent publications
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ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
Journal article
Hunt M. et al, (2022), Bioinformatics, 38, 3291 - 3293
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Enhancing epidemiological investigation of nosocomial SARS-CoV-2 infection with whole genome sequencing: A retrospective cohort study across four hospitals in the UK
Lumley SF. et al, (2021)
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Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK
Journal article
Auguet OT. et al, (2021), EClinicalMedicine, 36, 100910 - 100910
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Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
Journal article
Shaw LP. et al, (2021), Science Advances, 7, eabe3868 - eabe3868
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Optimized use of Oxford Nanopore flowcells for hybrid assemblies
Journal article
Lipworth S. et al, (2020), Microbial Genomics