Dr Richard Orton

  • Research Associate (Centre for Virus Research)

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

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

ORCID iDhttps://orcid.org/0000-0002-3389-4325

Research interests

CVR logo

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

 

Viral genomics & bioinformatics programme

Publications

List by: Type | Date

Jump to: 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2010 | 2009 | 2008 | 2006 | 2005 | 2004
Number of items: 44.

2020

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)

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)

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)

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)

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

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)

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)

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)

This list was generated on Thu Sep 24 17:42:20 2020 BST.
Number of items: 44.

Articles

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)

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)

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)

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)

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)

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)

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)

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.

This list was generated on Thu Sep 24 17:42:20 2020 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
     

Teaching

I have taught on the following viral bioinformatics courses:

Research datasets

Jump to: 2018
Number of items: 1.

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 Thu Sep 24 17:41:53 2020 BST.