Dr Richard Orton

  • Research Associate (Centre for Virus Research)

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: 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2010 | 2009 | 2008 | 2006 | 2005 | 2004
Number of items: 40.

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., Orton, R. , Benavides, J., Becker, D. J., Tello, C., Biek, R. and Streicker, D. G. (2019) Demographic and environmental drivers of metagenomic viral diversity in vampire bats. Molecular Ecology, (doi:10.1111/mec.15250) (Early Online Publication)

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)

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)

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:https://doi.org/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)

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 Tue Oct 22 06:33:28 2019 BST.
Number of items: 40.

Articles

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., Orton, R. , Benavides, J., Becker, D. J., Tello, C., Biek, R. and Streicker, D. G. (2019) Demographic and environmental drivers of metagenomic viral diversity in vampire bats. Molecular Ecology, (doi:10.1111/mec.15250) (Early Online Publication)

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)

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)

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:https://doi.org/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)

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 Tue Oct 22 06:33:28 2019 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

    MSc Bioinformatics project students:

    2018. Eilidh Greig

    AllmondViz a GUI for Heatmap based Visualisation of Viral Metagenomics Diversity

    2017. Zack Boyd

    A pipeline for low frequency variant calling from viral high throughput sequencing & benchmarking of variant callers and aligners

    2017. Ng Kai

    Visualisation of viral quasispecies populations from next generation sequencing data using Circos

    2015. Ewan Straiton

    CircReads: a bioinformatics pipeline for processing circular NGS reads and characterisation of sequence errors

    PhD students:

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

    Viral Communities in Vampire Bats: Geographic Variation and Ecological Drivers

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

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

    2017-Present. Kathy Li (with Andrew Davison)

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

    2018-Present. Sejal Modha (with David Robertson and Sreenu Vattipally)

    Data mining and characterisation of dark metagenomic sequence data

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 Tue Oct 22 09:22:54 2019 BST.