Dr Richard Orton

Research Scientist (Virology)

telephone: 01413304019
email: Richard.Orton@glasgow.ac.uk

Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1qh

Biography

I am a bioinformatician working in CVR Bioinformatics at the MRC-University of Glasgow Centre for Virus (CVR), focussing on viral intra and inter-host diversity, metagenomics, taxonomy and computational tool development. My previous positions include:

Research Associate, Dan Haydon, IBAHCM, University of Glasgow
Scientific Programmer, Rowland Kao, IBAHCM, University of Glasgow
Smalltalk programmer, J.P. Morgan, Glasgow
Research Associate, David Gilbert, Department of Computing Science, University of Glasgow
Bioinformatics PhD, Dietlind Gerloff, University of Edinburgh
Biochemsitry with Biotechnology BSc (Hons), University of Birmingham

Research interests

I am a bioinformatician working in CVR Bioinformatics at the MRC-University of Glasgow Centre for Virus (CVR). My current research focuses on:

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.

Google Scholar - Publication Profile

CVR Bioinformatics

Publications

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Jump to: 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2010 | 2009 | 2008 | 2006 | 2005 | 2004

Number of items: 75.

2023

Li, K. K., Lau, B. , Suárez, N. M., Camiolo, S. , Gunson, R., Davison, A. J. and Orton, R. J. (2023) Direct nanopore sequencing of human cytomegalovirus genomes from high-viral-load clinical samples. Viruses, 15(6), 1248. (doi: 10.3390/v15061248) (PMID:37376548) (PMCID:PMC10303703)

Ho, A. et al. (2023) Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature, 617(7961), pp. 555-563. (doi: 10.1038/s41586-023-05948-2) (PMID:36996873)

Viana, M. et al. (2023) Effects of culling vampire bats on the spatial spread and spillover of rabies virus. Science Advances, 9(10), eadd7437. (doi: 10.1126/sciadv.add7437) (PMID:36897949) (PMCID:PMC10005164)

Manali, M. et al. (2023) SARS-CoV-2 evolution and patient immunological history shape the breadth and potency of antibody-mediated immunity. Journal of Infectious Diseases, 227(1), pp. 40-49. (doi: 10.1093/infdis/jiac332) (PMID:35920058) (PMCID:PMC9384671)

2022

Johnson, P. C. D. , Hägglund, S., Näslund, K., Meyer, G., Taylor, G., Orton, R. J. , Zohari, S., Haydon, D. T. and Valarcher, J. F. (2022) Evaluating the potential of whole-genome sequencing for tracing transmission routes in experimental infections and natural outbreaks of bovine respiratory syncytial virus. Veterinary Research, 53, 107. (doi: 10.1186/s13567-022-01127-9)

Lista, M. J. et al. (2022) The P681H mutation in the spike glycoprotein of the alpha variant of SARS-CoV-2 escapes IFITM restriction and is necessary for type I interferon resistance. Journal of Virology, 96(23), e0125022. (doi: 10.1128/jvi.01250-22) (PMID:36350154) (PMCID:PMC9749455)

Walker, P. J. et al. (2022) Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Archives of Virology, 167(11), pp. 2429-2440. (doi: 10.1007/s00705-022-05516-5) (PMID:35999326)

Willett, B. J. et al. (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(8), pp. 1161-1179. (doi: 10.1038/s41564-022-01143-7) (PMID:35798890) (PMCID:PMC9352574)

Nickbakhsh, S. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)

Modha, S. , Robertson, D. L. , Hughes, J. and Orton, R. J. (2022) Quantifying and cataloguing unknown sequences within human microbiomes. mSystems, 7(2), e01468-21. (doi: 10.1128/msystems.01468-21) (PMID:35258340) (PMCID:PMC9052204)

Martin, D. P. et al. (2022) Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function. Molecular Biology and Evolution, 39(4), msac061. (doi: 10.1093/molbev/msac061) (PMID:35325204) (PMCID:PMC9037384)

Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z)

Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)

Twohig, K. A. et al. (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infectious Diseases, 22(1), pp. 35-42. (doi: 10.1016/S1473-3099(21)00475-8) (PMID:34461056) (PMCID:PMC8397301)

Gömer, A. et al. (2022) Intra-host analysis of hepaciviral glycoprotein evolution reveals signatures associated with viral persistence and clearance. Virus Evolution, 8(1), veac007. (doi: 10.1093/ve/veac007) (PMID:35242360) (PMCID:PMC8887644)

Wright, D. W. et al. (2022) Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus Evolution, 8(1), veac023. (doi: 10.1093/ve/veac023) (PMID:35502202) (PMCID:PMC9037374)

2021

Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)

Davis, C. et al. (2021) Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLoS Pathogens, 17(12), e1010022. (doi: 10.1371/journal.ppat.1010022) (PMID:34855916) (PMCID:PMC8639073)

Shaw, A. E. et al. (2021) The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. PLoS Biology, 19(9), e3001352. (doi: 10.1371/journal.pbio.3001352) (PMID:34491982) (PMCID:PMC8423302)

Szemiel, A. M. et al. (2021) In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. PLoS Pathogens, 17(9), e1009929. (doi: 10.1371/journal.ppat.1009929) (PMID:34534263) (PMCID:PMC8496873)

Walker, P. J. et al. (2021) Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Archives of Virology, 166(9), pp. 2633-2648. (doi: 10.1007/s00705-021-05156-1) (PMID:34231026)

Graham, M. S. et al. (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health, 6(5), e335-e345. (doi: 10.1016/S2468-2667(21)00055-4)

Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)

Hosie, M. J. et al. (2021) Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission. Veterinary Record, 188(8), e247. (doi: 10.1002/vetr.247) (PMID:33890314) (PMCID:PMC8251078)

Bergner, L. M. , Mollentze, N. , Orton, R. J. , Tello, C., Broos, A. , Biek, R. and Streicker, D. G. (2021) Characterizing and evaluating the zoonotic potential of novel viruses discovered in vampire bats. Viruses, 13(2), 252. (doi: 10.3390/v13020252) (PMID:33562073) (PMCID:PMC7914986)

Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831) (PMCID:PMC7906417)

Bergner, L. M. , Orton, R. J. , Broos, A. , Tello, C., Becker, D. J., Carrera, J. E., Patel, A. H. , Biek, R. and Streicker, D. G. (2021) Diversification of mammalian deltaviruses by host shifting. Proceedings of the National Academy of Sciences of the United States of America, 118(3), e201990711. (doi: 10.1073/pnas.2019907118) (PMID:33397804) (PMCID:PMC7826387)

Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)

2020

Walker, P. J. et al. (2020) Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020). Archives of Virology, 165(11), pp. 2737-2748. (doi: 10.1007/s00705-020-04752-x) (PMID:32816125)

Clark, J. J., Gilray, J., Orton, R. J. , Baird, M., Wilkie, G., da Silva Filipe, A. , Johnson, N., McInnes, C. J., Kohl, A. and Biek, R. (2020) Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses. PLoS Neglected Tropical Diseases, 14(9), e0008133. (doi: 10.1371/journal.pntd.0008133) (PMID:32925939) (PMCID:PMC7515184)

Bergner, L. M. , Orton, R. J. and Streicker, D. G. (2020) Complete Alphacoronavirus genome sequence from common vampire bats in Peru. Microbiology Resource Announcements, 9(34), e00742- 2. (doi: 10.1128/MRA.00742-20) (PMID:32816981) (PMCID:PMC7441239)

Howson, E. L.A., Orton, R. J. , Mioulet, V., Lembo, T. , King, D. P. and Fowler, V. L. (2020) GoPrime: development of an in silico framework to predict the performance of real-time PCR primers and probes using foot-and-mouth disease virus as a model. Pathogens, 9(4), e303. (doi: 10.3390/pathogens9040303) (PMID:32326039) (PMCID:PMC7238122)

Orton, R. J. , Wright, C. F., King, D. P. and Haydon, D. T. (2020) Estimating viral bottleneck sizes for FMDV transmission within and between hosts and implications for the rate of viral evolution. Interface Focus, 10, 20190066. (doi: 10.1098/rsfs.2019.0066) (PMID:31897294) (PMCID:PMC6936012)

Bergner, L. M. , Orton, R. J. , Benavides, J. A., Becker, D. J., Tello, C., Biek, R. and Streicker, D. G. (2020) Demographic and environmental drivers of metagenomic viral diversity in vampire bats. Molecular Ecology, 29(1), pp. 26-39. (doi: 10.1111/mec.15250) (PMID:31561274) (PMCID:PMC7004108)

MacLean, O. A. , Orton, R. J. , Singer, J. B. and Robertson, D. L. (2020) No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution, 6(1), veaa034. (doi: 10.1093/ve/veaa034) (PMID:32817804) (PMCID:PMC7197565)

2019

Fahnøe, U., Pedersen, A. G., Johnston, C. M., Orton, R. J. , Höper, D., Beer, M., Bukh, J., Belsham, G. J. and Rasmussen, T. B. (2019) Virus adaptation and selection following challenge of animals vaccinated against classical swine fever virus. Viruses, 11(10), e932. (doi: 10.3390/v11100932)

Oade, M. S., Keep, S., Freimanis, G. L., Orton, R. J. , Britton, P., Hammond, J. A. and Bickerton, E. (2019) Attenuation of infectious bronchitis virus in eggs results in different patterns of genomic variation across multiple replicates. Journal of Virology, 93(14), e00492-19. (doi: 10.1128/JVI.00492-19) (PMID:31043525) (PMCID:PMC6600199)

Bergner, L. M. , Orton, R. J. , da Silva Filipe, A. , Shaw, A. E., Becker, D. J., Tello, C., Biek, R. and Streicker, D. G. (2019) Using noninvasive metagenomics to characterize viral communities from wildlife. Molecular Ecology Resources, 19(1), pp. 128-143. (doi: 10.1111/1755-0998.12946) (PMID:30240114) (PMCID:PMC6378809)

2018

Babayan, S. A. , Orton, R. J. and Streicker, D. G. (2018) Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes. Science, 362(6414), pp. 577-580. (doi: 10.1126/science.aap9072) (PMID:30385576) (PMCID:PMC6536379)

Dagleish, M.P., Clark, J.J., Robson, C., Tucker, M., Orton, R.J. and Rocchi, M.S. (2018) A fatal case of louping-ill in a dog: immunolocalization and full genome sequencing of the virus. Journal of Comparative Pathology, 165, pp. 23-32. (doi: 10.1016/j.jcpa.2018.09.004) (PMID:30502792) (PMCID:PMC6302148)

Becker, D. J., Bergner, L. M. , Bentz, A. B., Orton, R. J. , Altizer, S. and Streicker, D. (2018) Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats. PLoS Neglected Tropical Diseases, 12(9), e0006786. (doi: 10.1371/journal.pntd.0006786) (PMID:30260954) (PMCID:PMC6159870)

Orton, R.J. , Deason, M., Bessell, P.R., Green, D.M., Kao, R.R. and Salvador, L.C.M. (2018) Identifying genotype specific elevated-risk areas and associated herd risk factors for bovine tuberculosis spread in British cattle. Epidemics, 24, pp. 34-42. (doi: 10.1016/j.epidem.2018.02.004) (PMID:29548927) (PMCID:PMC6105618)

Lefkowitz, E. J., Dempsey, D. M., Hendrickson, R. C., Orton, R. J. , Siddell, S. G. and Smith, D. B. (2018) Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Research, 46(D1), D708-D717. (doi: 10.1093/nar/gkx932) (PMID:29040670) (PMCID:PMC5753373)

2017

Shaw, A. E. et al. (2017) Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biology, 15(12), e2004086. (doi: 10.1371/journal.pbio.2004086) (PMID:29253856) (PMCID:PMC574750)

Volokhov, D.V., Becker, D.J., Bergner, L.M. , Camus, M.S., Orton, R.J. , Chizhikov, V.E., Altizer, S.M. and Streicker, D.G. (2017) Novel hemotropic mycoplasmas are widespread and genetically diverse in vampire bats. Epidemiology and Infection, 145(15), pp. 3154-3167. (doi: 10.1017/S095026881700231X) (PMID:29061202)

Marston, D. A. et al. (2017) Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host. Virus Evolution, 3(2), vex038. (doi: 10.1093/ve/vex038) (PMID:29255631) (PMCID:PMC5729694)

Adams, M. J. et al. (2017) 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Archives of Virology, 162(5), pp. 1441-1446. (doi: 10.1007/s00705-016-3215-y) (PMID:28078475)

Sumner, T., Orton, R. J. , Green, D. M., Kao, R. R. and Gubbins, S. (2017) Quantifying the roles of host movement and vector dispersal in the transmission of vector-borne diseases of livestock. PLoS Computational Biology, 13(4), e1005470. (doi: 10.1371/journal.pcbi.1005470) (PMID:28369082) (PMCID:PMC5393902)

Simmonds, P. et al. (2017) Consensus statement: virus taxonomy in the age of metagenomics. Nature Reviews Microbiology, (doi: 10.1038/nrmicro.2016.177) (PMID:28134265)

Conley, M. , Emmott, E., Orton, R. , Taylor, D., Carneiro, D. G., Murata, K., Goodfellow, I. G., Hansman, G. S. and Bhella, D. (2017) Vesivirus 2117 capsids more closely resemble sapovirus and lagovirus particles than other known vesivirus structures. Journal of General Virology, 98(1), pp. 68-76. (doi: 10.1099/jgv.0.000658) (PMID:27902397) (PMCID:PMC537039)

2016

King, D. J., Freimanis, G. L., Orton, R. , Waters, R. A., Haydon, D. T. and King, D. P. (2016) Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus. Infection, Genetics and Evolution, 44, pp. 286-292. (doi: 10.1016/j.meegid.2016.07.010) (PMID:27421209)

Jacobs, M. et al. (2016) Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet, 388(10043), pp. 498-503. (doi: 10.1016/S0140-6736(16)30386-5) (PMID:27209148) (PMCID:PMC4967715)

Orton, R.J. , Gu, Q. , Hughes, J. , Maabar, M., Modha, S. , Vattipally, S. , Wilkie, G.S. and Davison, A. (2016) Bioinformatics tools for analysing viral genomic data. Revue scientifique et technique (International Office of Epizootics), 35(1), pp. 241-285. (doi: 10.20506/rst.35.1.2432) (PMID:27217183)

Trewby, H. et al. (2016) Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis. Epidemics, 14, pp. 26-35. (doi: 10.1016/j.epidem.2015.08.003) (PMID:26972511) (PMCID:PMC4773590)

2015

Fahnøe, U., Pedersen, A. G., Dräger, C., Orton, R. J. , Blome, S., Höper, D., Beer, M. and Rasmussen, T. B. (2015) Creation of functional viruses from non-functional cDNA clones obtained from an RNA virus population by the use of ancestral reconstruction. PLoS ONE, 10(10), e0140912. (doi: 10.1371/journal.pone.0140912) (PMID:26485566) (PMCID:PMC4613144)

Dridi, M., Lecollinet, S., Orton, R. , Johnson, P. , Rosseel, T., van Borm, S., Lambrecht, B. and Muylkens, B. (2015) Next generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model. Journal of General Virology, 96, p. 2999. (doi: 10.1099/jgv.0.000231) (PMID:26297666)

Orton, R. J. , Wright, C. F., Morelli, M. J., King, D. J., Paton, D., King, D. and Haydon, D. T. (2015) Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC Genomics, 16, 229. (doi: 10.1186/s12864-015-1456-x) (PMID:25886445) (PMCID:PMC4425905)

Van Borm, S., Belák, S., Freimanis, G., Fusaro, A., Granberg, F., Höper, D., King, D. P., Monne, I., Orton, R. and Rosseel, T. (2015) Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Methods in Molecular Biology, 1247, pp. 415-436. (doi: 10.1007/978-1-4939-2004-4_30)

2014

O'Hare, A., Orton, R. J. , Bessell, P. R. and Kao, R. R. (2014) Estimating epidemiological parameters for bovine tuberculosis in British cattle using a Bayesian partial-likelihood approach. Proceedings of the Royal Society of London Series B: Biological Sciences, 281(1783), p. 20140248. (doi: 10.1098/rspb.2014.0248)

2013

Orton, R.J. , Wright, C.F., Morelli, M.J., Juleff, N., Thebaud, G., Knowles, N.J., Valdazo-Gonzalez, B., Paton, D.J., King, D.P. and Haydon, D.T. (2013) Observing micro-evolutionary processes of viral populations at multiple scales. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1614), (doi: 10.1098/rstb.2012.0203) (PMID:23382425) (PMCID:PMC3678327)

Bessell, P.R., Orton, R. , O'Hare, A., Mellor, D.J. , Logue, D. and Kao, R.R. (2013) Developing a framework for risk-based surveillance of tuberculosis in cattle: a case study of its application in Scotland. Epidemiology and Infection, 141(02), pp. 314-323. (doi: 10.1017/S0950268812000635)

2012

Bessell, P., Orton, R. and Kao, R. (2012) Risk factors for bovine Tuberculosis at the national level in Great Britain. BMC Veterinary Research, 8(51), (doi: 10.1186/1746-6148-8-51)

Orton, R. , Bessell, P., O'Hare, A. and Kao, R. (2012) Risk of foot-and-mouth disease spread due to sole occupancy authorities and linked cattle holdings. PLoS ONE, 7(4), e35089. (doi: 10.1371/journal.pone.0035089) (PMID:22532841) (PMCID:PMC3331861)

Biek, R. , O'Hare, A., Wright, D., Mallon, T., McCormick, C., Orton, R.J. , McDowell, S., Trewby, H., Skuce, R.A. and Kao, R.R. (2012) Whole genome sequencing reveals local transmission patterns of mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathogens, 8(11), e1003008. (doi: 10.1371/journal.ppat.1003008)

2010

Sturm, O. E., Orton, R. , Grindlay, J., Birtwistle, M., Vyshemirsky, V. , Gilbert, D., Calder, M. , Pitt, A.R., Kholodenko, B. and Kolch, W. (2010) The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. Science Signaling, 3(153), ra90. (doi: 10.1126/scisignal.2001212)

2009

von Kriegsheim, A. et al. (2009) Cell fate decisions are specified by the dynamic ERK interactome. Nature Cell Biology, 11(12), pp. 1458-1464. (doi: 10.1038/ncb1994)

Orton, R.J. , Adriaens, M.E., Gormand, A., Sturm, O.E., Kolch, W. and Gilbert, D.R. (2009) Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Systems Biology, 3, p. 100. (doi: 10.1186/1752-0509-3-100)

Saffrey, P. and Orton, R. (2009) Version control of pathway models using XML patches. BMC Systems Biology, 3(34), (doi: 10.1186/1752-0509-3-34)

2008

Breitling, R., Gilbert, D., Heiner, M. and Orton, R. (2008) A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings in Bioinformatics, 9(5), pp. 404-421. (doi: 10.1093/bib/bbn026)

Orton, R.J. , Sturm, O.E., Gormand, A., Kolch, W. and Gilbert, D.R. (2008) Computational modelling reveals feedback redundancy within the epidermal growth factor receptor/extracellular-signal regulated kinase signalling pathway. Systems Biology, 2(4), pp. 173-183. (doi: 10.1049/iet-syb:20070066)

2006

Calder, M., Vyshemirsky, V., Gilbert, D. and Orton, R. (2006) Analysis of signalling pathways using continuous time Markov chains. Lecture Notes in Computer Science, 4220, pp. 44-67. (doi: 10.1007/11880646_3)

Gilbert, D., Fuss, H., Gu, X., Orton, R. , Robinson, S., Vyshemirsky, V., Kurth, M.J., Downes, C.S. and Dubitzky, W. (2006) Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings in Bioinformatics, 7(4), pp. 339-353. (doi: 10.1093/bib/bbl043)

2005

Calder, M. , Vyshemirsky, V. , Gilbert, D. and Orton, R. (2005) Analysis of Signalling Pathways Using the PRISM Model Checker. In: Computational Methods in Systems Biology (CMSB'05), Edinburgh, United Kingdom, 03-05 Apr 2005, pp. 179-190.

Orton, R.J. , Sturm, O.E., Vyshemirsky, V., Calder, M., Gilbert, D.R. and Kolch, W. (2005) Computational modelling of the receptor-tyrosine-kinase-activated MAR pathway. Biochemical Journal, 392, pp. 249-261. (doi: 10.1042/BJ20050908)

2004

Orton, R.J. , Sellers, W.I. and Gerloff, D.L. (2004) YETI: yeast exploration tool integrator. Bioinformatics, 20(2), pp. 284-285. (doi: 10.1093/bioinformatics/btg408)

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Articles

Ho, A. et al. (2023) Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature, 617(7961), pp. 555-563. (doi: 10.1038/s41586-023-05948-2) (PMID:36996873)

Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z)

Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)

Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)

Simmonds, P. et al. (2017) Consensus statement: virus taxonomy in the age of metagenomics. Nature Reviews Microbiology, (doi: 10.1038/nrmicro.2016.177) (PMID:28134265)

Bessell, P., Orton, R. and Kao, R. (2012) Risk factors for bovine Tuberculosis at the national level in Great Britain. BMC Veterinary Research, 8(51), (doi: 10.1186/1746-6148-8-51)

von Kriegsheim, A. et al. (2009) Cell fate decisions are specified by the dynamic ERK interactome. Nature Cell Biology, 11(12), pp. 1458-1464. (doi: 10.1038/ncb1994)

Saffrey, P. and Orton, R. (2009) Version control of pathway models using XML patches. BMC Systems Biology, 3(34), (doi: 10.1186/1752-0509-3-34)

Orton, R.J. , Sellers, W.I. and Gerloff, D.L. (2004) YETI: yeast exploration tool integrator. Bioinformatics, 20(2), pp. 284-285. (doi: 10.1093/bioinformatics/btg408)

Conference Proceedings

This list was generated on Thu Sep 28 17:50:10 2023 BST.

Grants

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)
Wellcome Trust
2014 - 2015

Supervision

Current PhD students:

2017-Present. Kathy Li (with Andrew Davison)

Third-generation sequencing of whole human cytomegalovirus genomes from clinical material

2020-Present. Jordan Bone (with Pablo Murcia, Willy Weir and Roman Biek)

Tracing equine influenza virus spread using next generation sequencing data

Completed MSc Bioinformatics project students:

2022. Chang Yan

Bioinformatics pipeline to identify Illumina errors from overlapping read pairs

2022. Hong Chen

Mind the Gap: exploring influenza A viruses defective-interfering RNAs

2022. Janhavi Rajendra Prasad Mada

Discovery of Cryptic Gene Products in Segmented Negative-Stranded RNA Viruses

2020. Gesthimani Kakavouli

Dynamic heatmap visualisation of mutations from the viral epidemics: SARS-CoV-2

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

Completed PhD students:

2014-2018. Laura Bergner (with Daniel Streicker and Roman Biek)

Viral Communities in Vampire Bats: Geographic Variation and Ecological Drivers

2015-2019. Michael Oade (with Erica Bickerton, John Hammond and Daniel Haydon)

Towards in silico IBV vaccine design: defining the role of polymorphism in viral attenuation

2018-2022. Sejal Modha (with David Robertson and Joseph Hughes)

Data mining and characterisation of dark metagenomic sequence data

Teaching

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
2017. CVR Phd Students Basic Virology Course - Bioinformatics, 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
2018. CVR PhD Students Basic Virology Course - Bioinformatics, Glasgow, UK
2019. Genomics and Clinical Virology, Wellcome Genome Campus, Cambridge, UK
2019. Viral Bioinformatics and Genomics, Makerere University, Kampala, Uganda
2019. 5th Viral Bioinformatics and Genomics training course, Glasgow, UK
2019. CVR PhD Students Basic Virology Course - Bioinformatics, CVR, Glasgow, UK
2020. Genomics and Clinical Virology, Wellcome Genome Campus, Cambridge, UK
2021. Viral Bioinformatics and Genomics, Institute of Hygiene, Montevideo, Uruguay [Virtual Course]
2022. Genomics and Clinical Virology, Wellcome Genome Campus, Cambridge, UK
2022. Viral Genomics and Bioinformatics - Latin America and the Caribbean, Wellcome Connecting Science & COG-Train
2022. Viral Genomics and Bioinformatics, Wellcome Connecting Science & COG-Train
2022. A practical guide for SARS-CoV-2 whole-genome sequencing, COG-Train & FutureLearn

Research datasets

Jump to: 2022 | 2021 | 2018

Number of items: 4.

2022

Johnson, P. , Orton, R. and Haydon, D. (2022) Evaluating the potential of whole-genome sequencing for tracing transmission routes in experimental infections and natural outbreaks of bovine respiratory syncytial virus. [Data Collection]

2021

Szemiel, A., Orton, R. , MacLean, O. , Furnon, W. and Stewart, M. (2021) In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. [Data Collection]

Shaw, A., Rihn, S. , Mollentze, N. , Wickenhagen, A., Stewart, D., Orton, R. , Kuchi, S., Bakshi, S., Collados Rodriguez, M. , Turnbull, M. , Busby, J., Gu, Q. , Smollett, K., Bamford, C., Sugrue, E. , Johnson, P. , Da Silva Filipe, A. , Castello, A. , Streicker, D. , Robertson, D. , Palmarini, M. and Wilson, S. (2021) The 'antiviral state' has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. [Data Collection] (Unpublished)

2018

Becker, D. J., Bergner, L., Bentz, A. B., Orton, R. , Altizer, S. and Streicker, D. (2018) Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats. [Data Collection]

This list was generated on Fri Sep 29 18:43:31 2023 BST.

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Dr Richard Orton

Biography

Research interests

Publications

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2010

2009

2008

2006

2005

2004

Articles

Conference Proceedings

Grants

Supervision

Teaching

Research datasets

2022

2021

2018