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Dr Matthew Bashton

VC Senior Fellow

Department: Applied Sciences

Matthew Bashton

PGR Supervision

Matthew Crown Novel artificial intelligence and functional annotation approaches to the microbiome of the built environment Start Date: 01/10/2020

Research Themes and Scholarly Interests

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.

Within the Hub for Biotechnology in the Built Environment (HBBE) at Northumbria, Matthew will be contributing his informatics expertise to a range of research projects and developing novel infrastructure for microbiome analysis, annotation and exploitation.

Qualifications

Bioinformatics PhD October 16 2004

Key Publications

  • Please visit the Pure Research Information Portal for further information
  • Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK, Du Plessis, L., Mccrone, J., Zarebski, A., Hill, V., Ruis, C., Gutierrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T., Faria, N., Jackson, B., Loman, N., O’toole, Á., Nicholls, S., Parag, K., Scher, E., Vasylyeva, T., Volz, E., Watts, A., Bogoch, I., Khan, K., Aanensen, D., Kraemer, M., Rambaut, A., Pybus, O., Bashton, M., Smith, D., Young, G., Nelson, A. 12 Feb 2021, In: Science
  • Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity, Volz, E., Hill, V., McCrone, J., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F., Rey, S., Nicholls, S., Colquhoun, R., da Silva Filipe, A., Shepherd, J., Pascall, D., Shah, R., Jesudason, N., Li, K., Jarrett, R., Pacchiarini, N., Bull, M., Geidelberg, L., Siveroni, I., Goodfellow, I., Loman, N., Pybus, O., Robertson, D., Thomson, E., Rambaut, A., Connor, T., Bashton, M., Young, G., Smith, D. 7 Jan 2021, In: Cell
  • An integrated national scale SARS-CoV-2 genomic surveillance network, Smith, D., Bashton, M. 1 Jul 2020, In: The Lancet Microbe
  • Concordance of copy number abnormality detection using SNP arrays and Multiplex Ligation-dependent Probe Amplification (MLPA) in acute lymphoblastic leukaemia, Bashton, M., Hollis, R., Ryan, S., Schwab, C., Moppett, J., Harrison, C., Moorman, A., Enshaei, A. Dec 2020, In: Scientific Reports
  • Dynamic clonal progression in xenografts of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21, Sinclair, P., Blair, H., Ryan, S., Buechler, L., Cheng, J., Clayton, J., Hanna, R., Hollern, S., Hawking, Z., Bashton, M., Schwab, C., Jones, L., Russell, L., Marr, H., Carey, P., Halsey, C., Heidenreich, O., Moorman, A., Harrison, C. 15 Feb 2018, In: Haematologica
  • The role of the RAS pathway in iAMP21-ALL, Ryan, S., Matheson, E., Grossmann, V., Sinclair, P., Bashton, M., Schwab, C., Towers, W., Partington, M., Elliott, A., Minto, L., Richardson, S., Rahman, T., Keavney, B., Skinner, R., Bown, N., Haferlach, T., Vandenberghe, P., Haferlach, C., Santibanez-Koref, M., Moorman, A., Kohlmann, A., Irving, J., Harrison, C. Sep 2016, In: Leukemia
  • Critical roles of arginine in growth and biofilm development by Streptococcus gordonii, Jakubovics, N., Robinson, J., Samarian, D., Kolderman, E., Yassin, S., Bettampadi, D., Bashton, M., Rickard, A. Jul 2015, In: Molecular Microbiology
  • Crowdsourcing genomic analyses of ash and ash dieback - power to the people, Maclean, D., Yoshida, K., Edwards, A., Crossman, L., Clavijo, B., Clark, M., Swarbreck, D., Bashton, M., Chapman, P., Gijzen, M., Caccamo, M., Downie, A., Kamoun, S., Saunders, D. 12 Feb 2013, In: GigaScience
  • Domain-ligand mapping for enzymes, Bashton, M., Thornton, J. 1 Mar 2010, In: Journal of Molecular Recognition
  • Small Molecule Subgraph Detector (SMSD) toolkit, Rahman, S., Bashton, M., Holliday, G., Schrader, R., Thornton, J. 10 Aug 2009, In: Journal of Cheminformatics


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