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
Publications
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)
Articles
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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
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.
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
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]