Tom Connor | Bioinformatics Lead, Public Health Wales Pathogen Genomics Unit, Professor
Cardiff University

Tom Connor, Bioinformatics Lead, Public Health Wales Pathogen Genomics Unit, Professor, Cardiff University

Roles

  • Biocomputing Research Hub lead
  • Member of College of Biomedical and Life Sciences Data Strategy Group
  • Member of Supercomputing Wales Infrastructure Committee
  • Member of Cardiff Supercomputing Facility Oversight Group
  • Wales regional lead and technical lead for the Cloud Infrastructure for Microbial Bioinformatics
  • Bioinformatics Lead for the Public Health Wales Pathogen Genomics Unit.
Bio
The research that is undertaken in my lab seeks to understand pathogen variation in order to answer a range of questions from how pathogens evolve, to how and why they spread in local and global outbreaks. This work has a number of labels, but broadly speaking we use genomic epidemiology, phylogenomics and population genetics approaches to answer our research questions.  Historically we have examined questions on a range of pathogens, including gastrointestinal pathogens (E. coliSalmonellaShigellaC. difficile) which collectively account for over a billion cases of disease around the world every year, pathogens which are particularly associated with antimicrobial resistance and viruses including HIV and Influenza.  My research is underpinned by whole genome sequencing, using the data from organisms genomes to work out how they are related to, and different from, other organisms of interest. This work is heavily computational, and we use and develop mathematical and computational approaches to analyse and interpret the "Big Biological Data" that we and our collaborators generate. This work is also readily translatable, and I have spent the past few years working closely with colleagues in the NHS to translate the approaches we develop into diagnostic and surveillance tools that can be used at a local and national level. In a practical sense this has seen us take approaches we use in our resarch, and build clinical diagnostic and surveillance services in the NHS in Wales for HIV, TB and other Mycobacteria, C. difficile and Influenza. Our Pathogen Genomics work is undertaken with the Public Health Wales Pathogen Genomics Unit and Genomics Partnership Wales. In addition to my research team, I also lead the Bioinformatics team within the Pathogen Genomics Unit. Our HIV work was highlighted in the 2020 Cardiff University Innovation Awards: https://www.cardiff.ac.uk/business/why-work-with-us/who-we-work-with/healthcare-innovation  As part of the COVID-19 pandemic, almost all of my time has been spent supporting the pandemic response in Wales. We have taken our expertise in other pathogens to develop the capacity to sequence and analyse COVID-19 from Welsh patients, sequencing more than 7,500 SARS-CoV-2 genomes since the start of the pandemic. We use this data to understand the spread of the pandemic over time, and to support outbreak response and national surveillance efforts. This work is undertaken as part of the COVID-19 Genomics UK Consortium. In addition to my pathogen research activities, I have an additional focus on the development and design of research infrastructures to support the analysis of the genomic datasets that we produce. This work has included the design and development of national computational resources in the UK, as well as the design of computational resources used in translational settings in the NHS and Industry. The largest of these infrastructures, MRC CLIMB, which I helped design and play a role in leading supports over 1,000 microbiology researchers from across the UK, and has been the key peice of UK infrastructure that has underpinned the COG-UK sequencing effort to date. The CLIMB-COVID system has provided a core infrastructure for the collation and analysis of over 70,000 SARS-CoV-2 genomes sequenced across the UK.  Microbiomes, Microbes and Informatics The Connor group is part of the recently formed Microbiomes, Microbes and Informatics (MMI) group (webpage underdevelopment). The MMI group currently comprises the research groups of Thomas Connor, Esh Mahenthiralingam, Julian Marchesi and Andrew Weightman, and has over 25 active research staff and postgraduate students. The MMI group are highly research active generating over £3.5 million in grant income between 2010 and 2017, and publishing extensively in top journals (cumulative h index > 150, > 400 publications, and > 25,000 citations; source Scopus.com). The four current MMI staff recently moved (June 2017) to a single shared location within a new £1.6 million refurbished area of the Sir Martin Evans Building. This comprises a large class II certified research laboratory, equipment and tissue culture rooms, a group office area and academic offices. The MMI group welcomes approaches by potential fellowship applicants and funded PhD students to host their research and expand our strategic research on Microbiomes, Microbes and Informatics.  

Appearances:



BioData World Congress Day 1 @ 09:40

The Diagnostic Drive in Health Systems – How COVID-19 has driven a future of novel diagnostics into standard care

  • What are the impacts?
  • What are the economic costs for this transition?
  • What are the challenges to rolling out across large health systems?

BioData World Congress Day 1 @ 16:00

Cloud Infrastructure for Microbial Bioinformatics (Climb) – Evolving the largest compute and storage system for microbiology to enable COVID analysis

  • The current system in place
  • Developing a national pathogen surveillance system
  • Sequencing and analysing over 70,000 COVID-19 samples
  • Future adaptability of the system post-pandemic
last published: 21/Sep/21 15:25 GMT
last published: 21/Sep/21 15:25 GMT

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