Dr Richard Orton
- Research Associate (Centre for Virus Research)
- Intra and inter-host viral diversity and evolution: using high-throughput sequencing to monitor viral evolution both within and between hosts: FMDV, Rabies, West Nile Virus, Ebola, Classical Swine Fever. As part of this I develop computational tools to aid in the visualisation and analysis of viral high-throughput sequence data: DiversiTools, VALVS, vNvS.
- Viral host adaptation: using Synthetical Attenuated Viral Engineering (SAVE) aproaches to deoptimise viral sequences relative to their host (using codon-pair and dinucleotide biases) to generate candidate vaccines, and using viral sequence data and biases to predict their hosts, evaluating host adaptation, and determine zoonotic risk.
- Metagenomics: using metagenomics approaches for virus discovery in a range of environments from vampire bats and mosquioties in South America to honeybees and ticks in the UK.
- Epidemic modelling: using computational methods to model the spatial spread of bovine tuberculosis, FMDV and bluetongue virus in the UK and evaluate how best to control them
- Systems biology of cell signalling: computational modelling of the EGFR and MAPK pathways, where I investigated the drug resistance properties of different cancerous mutations to identify the best targets for drug intervention, focussing on the role of negative feedback loops.
I spend 50% of my time working for the International Committee on the Taxonomy of Viruses (ICTV) on a Wellcome Trust bioresource grant (WT108418AIA) entitled "A database for the universal classification of viruses: development of an open access model for the dissemination of classification information and virus descriptions" with Andrew Davison, Peter Simmonds and Stuart Siddell. As part of this, I am the Technical Editor of the ICTV Report, and am also a member of the ICTV Herpesviridae Study Group.
Grants and Awards listed are those received whilst working with the University of Glasgow.
- Comparing the fitness and patient landscapes of HIV-1 (ISSF Catalyst)
2014 - 2015
MSc Bioinformatics project students:
2018. Eilidh Greig
AllmondViz a GUI for Heatmap based Visualisation of Viral Metagenomics Diversity
2017. Zack Boyd
A pipeline for low frequency variant calling from viral high throughput sequencing & benchmarking of variant callers and aligners
2017. Ng Kai
Visualisation of viral quasispecies populations from next generation sequencing data using Circos
2015. Ewan Straiton
CircReads: a bioinformatics pipeline for processing circular NGS reads and characterisation of sequence errors
2014-2018. Laura Bergner (with Daniel Streicker and Roman Biek)
Viral Communities in Vampire Bats: Geographic Variation and Ecological Drivers
2015-Present. Michael Oade (with Erica Bickerton, John Hammond and Daniel Haydon)
Towards in silico IBV vaccine design: defining the role of polymorphism in viral attenuation
2017-Present. Kathy Li (with Andrew Davison)
Third-generation sequencing of whole human cytomegalovirus genomes from clinical material
2018-Present. Sejal Modha (with David Robertson and Sreenu Vattipally)
Data mining and characterisation of dark metagenomic sequence data
I have taught on the following viral bioinformatics courses:
- 2015. 1st Viral Bioinformatics and Genomics training course, CVR, Glasgow, UK
- 2016. EPIZONE Workshop on Next Generation Sequencing applications and Bioinformatics, CODA-CERVA, Brussels, Belgium
- 2016. 2nd Viral Bioinformatics and Genomics training course, CVR, Glasgow, UK
- 2017. 3rd Viral Bioinformatics and Genomics training course, CVR, Glasgow, UK
- 2018. Genomics and Clinical Virology, Wellcome Genome Campus, Cambridge, UK
- 2018. 4th Viral Bioinformatics and Genomics training course, CVR, Glasgow, UK
- 2018. Viral Bioinformatics and Genomics, OUCRU, Ho Chi Minh City, Vietnam
- 2019. Genomics and Clinical Virology, Wellcome Genome Campus, Cambridge, UK
- 2019. Viral Bioinformatics and Genomics, Makerere University, Kampala, Uganda