📅 22 July
🕑 12:00 – 13:00 UTC
Speaker: Matthew Bashton
Designation: Vice Chancellors Senior Fellow
Affiliation : The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
Dr Matthew Bashton is the lead bioinformatician of the COVID-19 Genomics UK Consortium (COG-UK) team at Northumbria University. His talk will describe the software set-up and environment used at Northumbria for delivering their COVID-19 genomics solution, variant, and lineage classification, including pipelines developed as well as other tools in use within COG-UK. The team at Northumbria have successfully sequenced over 16,000 COVID-19 genomes contributing to both genomic surveillance nationally and participating in local outbreak investigations where genomics helped to track the spread of the virus amongst people and inform infection control efforts. Matthew will talk about the challenge of building and maintaining a production software environment, as you use it, in a rapidly developing and constantly evolving landscape.
Dr Matthew Bashton is a Computational Biologist, with extensive bio-, chemo- and clinical informatics experience, with specific expertise in the areas of protein domains, protein structure and function, ligand protein interactions, high-throughput sequence analysis, genome analysis, and biomarker discovery.
Matthew did an undergraduate degree in Biochemistry at Newcastle University; his PhD was in the area of structural genomics at the MRC Laboratory of Molecular Biology in Cambridge in the group of Dr Cyrus Cothia FRS. His PhD focused on how different families of protein domain come together geometrically and grammatically to realise functions at a whole protein level.
Matthew worked as a Research Fellow in the Group of Professor Dame Janet Thornton FRS at the European Bioinformatics Institute (EBI); here he was part of the US DOE funded Midwest Centre for Structural Genomics (MCSG) Consortium. Whilst at the EBI Matthew developed the PROCOGNATE database which relates protein domain families to the range of cognate ligands they bind. He also worked on the Small Molecular Subgraph Detector (SMSD) which enables rapid and accurate 2D graph based chemical similarly and fragment matching. Following his time at the EBI Matthew went to work in the Bioinformatics Support Unit at Newcastle University where he gained a breadth of experience working with high-throughput sequencing (HTS) data on a range of omic projects with many different PIs in the medical school. He then moved into cancer genomics research working at the Northern Institute for Cancer Research (NICR) in Newcastle, where he developed a variety of HPC analysis pipelines for somatic genome and exome analysis, alongside biomarker based risk and subgroup classification projects on paediatric brain tumours and leukaemia.
Matthew is now working within the multidisciplinary Hub for Biotechnology in the Built Environment (HBBE), working with a range of designers, architects, engineers and synthetic and molecular biologists to enhance building construction, sustainability, and environmental health of the built environment using biology.
In 2020-2021 Matthew became a member of the UKs COVID-19 genomics effort working alongside a team at Northumbria University to sequence of 16,000 COVID-19 genomes from 7 different hospital Trusts across the North East and Cumbria.