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Number of items: 84.

2026

Buddle, S. et al. (2026)Contaminating plasmid sequences and disrupted vector genomes in the liver following adeno-associated virus gene therapy. Nature Medicine, (doi: 10.1038/s41591-025-04073-z) (PMID:41545588) (Early Online Publication)

2025

Li, Kathy K., Suarez, Nicolas M., Camiolo, Salvatore ORCID: https://orcid.org/0000-0002-8874-9993, Davison, Andrew J. ORCID: https://orcid.org/0000-0002-4991-9128 and Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325(2025)DNA sequencing of whole human cytomegalovirus genomes from formalin-fixed, paraffin-embedded tissues from congenital cytomegalovirus disease cases. PLoS ONE, 20(5), e0318897. (doi: 10.1371/journal.pone.0318897) (PMID:40446191) (PMCID:PMC12124853)

Modha, Sejal ORCID: https://orcid.org/0000-0002-8440-885X, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325 and Lytras, Spyros(2025)Expanding the genomic diversity of human anelloviruses. Virus Evolution, 11(1), veaf002. (doi: 10.1093/ve/veaf002) (PMID:39839678) (PMCID:PMC11749082)

Furnon, W. et al. (2025)Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic. Nature Microbiology, 10, pp. 77-93. (doi: 10.1038/s41564-024-01878-5) (PMID:39753670) (PMCID:PMC11726466)

2024

Kamel, W. et al. (2024)Alphavirus infection triggers selective cytoplasmic translocation of nuclear RBPs with moonlighting antiviral roles. Molecular Cell, 84(24), 4896-4911.e7. (doi: 10.1016/j.molcel.2024.11.015) (PMID:39642884)

Ranum, J. N. et al. (2024)Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome. Nucleic Acids Research, 52(6), pp. 3199-3212. (doi: 10.1093/nar/gkae133) (PMID:38407436) (PMCID:PMC11014358)

Lamb, Kieran D., Luka, Martha M., Saathoff, Megan, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Phan, My V.T., Cotten, Matthew ORCID: https://orcid.org/0000-0002-3361-3351, Yuan, Ke ORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221(2024)Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Computational Biology, 20(1), e1011795. (doi: 10.1371/journal.pcbi.1011795) (PMID:38271457) (PMCID:PMC10868779)

2023

Willett, B. J. et al. (2023)Omicron BA.2.86 cross-neutralising activity in community sera from the UK. Lancet, 402(10417), pp. 2075-2076. (doi: 10.1016/s0140-6736(23)02397-8) (PMID:37952549)

Li, Kathy K., Lau, Betty ORCID: https://orcid.org/0000-0003-1382-9830, Suárez, Nicolás M., Camiolo, Salvatore ORCID: https://orcid.org/0000-0002-8874-9993, Gunson, Rory, Davison, Andrew J. ORCID: https://orcid.org/0000-0002-4991-9128 and Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325(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)

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, Paul C. D. ORCID: https://orcid.org/0000-0001-6663-7520, Hägglund, Sara, Näslund, Katarina, Meyer, Gilles, Taylor, Geraldine, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Zohari, Siamak, Haydon, Daniel T. ORCID: https://orcid.org/0000-0002-1240-1886 and Valarcher, Jean François(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) (PMID:36510312) (PMCID:PMC9746130)

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)

Ho, A. et al. (2022)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)

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)Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1709. (doi: 10.1038/s41564-022-01241-6) (PMID:36114232) (PMCID:PMC9483304)

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, Sejal ORCID: https://orcid.org/0000-0002-8440-885X, Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563 and Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325(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) (PMID:35197443) (PMCID:PMC8866425)

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, Laura M. ORCID: https://orcid.org/0000-0003-4169-7169, Mollentze, Nardus ORCID: https://orcid.org/0000-0002-2452-6416, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Tello, Carlos, Broos, Alice ORCID: https://orcid.org/0000-0001-7593-1000, Biek, Roman ORCID: https://orcid.org/0000-0003-3471-5357 and Streicker, Daniel G. ORCID: https://orcid.org/0000-0001-7475-2705(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, Laura M. ORCID: https://orcid.org/0000-0003-4169-7169, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Broos, Alice ORCID: https://orcid.org/0000-0001-7593-1000, Tello, Carlos, Becker, Daniel J., Carrera, Jorge E., Patel, Arvind H. ORCID: https://orcid.org/0000-0003-4600-2047, Biek, Roman ORCID: https://orcid.org/0000-0003-3471-5357 and Streicker, Daniel G. ORCID: https://orcid.org/0000-0001-7475-2705(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, Jordan J., Gilray, Janice, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Baird, Margaret, Wilkie, Gavin, da Silva Filipe, Ana ORCID: https://orcid.org/0000-0002-9442-2903, Johnson, Nicholas, McInnes, Colin J., Kohl, Alain ORCID: https://orcid.org/0000-0002-1523-9458 and Biek, Roman ORCID: https://orcid.org/0000-0003-3471-5357(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, Laura M. ORCID: https://orcid.org/0000-0003-4169-7169, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325 and Streicker, Daniel G. ORCID: https://orcid.org/0000-0001-7475-2705(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, Emma L.A., Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Mioulet, Valerie, Lembo, Tiziana ORCID: https://orcid.org/0000-0002-6405-1849, King, Donald P. and Fowler, Veronica 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, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Wright, Caroline F., King, Donald P. and Haydon, Daniel T. ORCID: https://orcid.org/0000-0002-1240-1886(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, Laura M. ORCID: https://orcid.org/0000-0003-4169-7169, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Benavides, Julio A., Becker, Daniel J., Tello, Carlos, Biek, Roman ORCID: https://orcid.org/0000-0003-3471-5357 and Streicker, Daniel G. ORCID: https://orcid.org/0000-0001-7475-2705(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, Oscar A. ORCID: https://orcid.org/0000-0003-4919-4697, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Singer, Joshua B. and Robertson, David L. ORCID: https://orcid.org/0000-0001-6338-0221(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, Ulrik, Pedersen, Anders Gorm, Johnston, Camille Melissa, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Höper, Dirk, Beer, Martin, Bukh, Jens, Belsham, Graham J. and Rasmussen, Thomas Bruun(2019)Virus adaptation and selection following challenge of animals vaccinated against classical swine fever virus. Viruses, 11(10), e932. (doi: 10.3390/v11100932)

Oade, Michael S., Keep, Sarah, Freimanis, Graham L., Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Britton, Paul, Hammond, John A. and Bickerton, Erica(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, Laura M. ORCID: https://orcid.org/0000-0003-4169-7169, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, da Silva Filipe, Ana ORCID: https://orcid.org/0000-0002-9442-2903, Shaw, Andrew E., Becker, Daniel J., Tello, Carlos, Biek, Roman ORCID: https://orcid.org/0000-0003-3471-5357 and Streicker, Daniel G. ORCID: https://orcid.org/0000-0001-7475-2705(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, Simon A. ORCID: https://orcid.org/0000-0002-4949-1117, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325 and Streicker, Daniel G. ORCID: https://orcid.org/0000-0001-7475-2705(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. ORCID: https://orcid.org/0000-0002-3389-4325 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, Daniel J., Bergner, Laura M. ORCID: https://orcid.org/0000-0003-4169-7169, Bentz, Alexandra B., Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Altizer, Sonia and Streicker, Daniel ORCID: https://orcid.org/0000-0001-7475-2705(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. ORCID: https://orcid.org/0000-0002-3389-4325, Deason, M., Bessell, P.R., Green, D.M., Kao, R.R. and Salvador, L.C.M. ORCID: https://orcid.org/0000-0001-8472-1179(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, Elliot J., Dempsey, Donald M., Hendrickson, Robert Curtis, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Siddell, Stuart G. and Smith, Donald 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. ORCID: https://orcid.org/0000-0003-4169-7169, Camus, M.S., Orton, R.J. ORCID: https://orcid.org/0000-0002-3389-4325, Chizhikov, V.E., Altizer, S.M. and Streicker, D.G. ORCID: https://orcid.org/0000-0001-7475-2705(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, Tom, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Green, Darren M., Kao, Rowland R. and Gubbins, Simon(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, Michaela ORCID: https://orcid.org/0000-0002-3457-1149, Emmott, Edward, Orton, Richard ORCID: https://orcid.org/0000-0002-3389-4325, Taylor, David, Carneiro, Daniel G., Murata, Kazuyoshi, Goodfellow, Ian G., Hansman, Grant S. and Bhella, David ORCID: https://orcid.org/0000-0003-2096-8310(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, David J., Freimanis, Graham L., Orton, Richard ORCID: https://orcid.org/0000-0002-3389-4325, Waters, Ryan A., Haydon, Daniel T. ORCID: https://orcid.org/0000-0002-1240-1886 and King, Donald 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. ORCID: https://orcid.org/0000-0002-3389-4325, Gu, Q. ORCID: https://orcid.org/0000-0002-1201-6734, Hughes, J. ORCID: https://orcid.org/0000-0003-2556-2563, Maabar, M., Modha, S. ORCID: https://orcid.org/0000-0002-8440-885X, Vattipally, Sreenu ORCID: https://orcid.org/0000-0001-6673-4697, Wilkie, G.S. and Davison, A. ORCID: https://orcid.org/0000-0002-4991-9128(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, Ulrik, Pedersen, Anders Gorm, Dräger, Carolin, Orton, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Blome, Sandra, Höper, Dirk, Beer, Martin and Rasmussen, Thomas Bruun(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, Maha, Lecollinet, Sylvie, Orton, Richard ORCID: https://orcid.org/0000-0002-3389-4325, Johnson, Paul ORCID: https://orcid.org/0000-0001-6663-7520, Rosseel, Toon, van Borm, Steven, Lambrecht, Bénédicte and Muylkens, Benoît(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, Richard J. ORCID: https://orcid.org/0000-0002-3389-4325, Wright, Caroline F., Morelli, Marco J., King, David J., Paton, David, King, Donald and Haydon, Daniel T. ORCID: https://orcid.org/0000-0002-1240-1886(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, Steven, Belák, Sándor, Freimanis, Graham, Fusaro, Alice, Granberg, Fredrik, Höper, Dirk, King, Donald P., Monne, Isabella, Orton, Richard ORCID: https://orcid.org/0000-0002-3389-4325 and Rosseel, Toon(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. ORCID: https://orcid.org/0000-0002-3389-4325, 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. ORCID: https://orcid.org/0000-0002-3389-4325, 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. ORCID: https://orcid.org/0000-0002-1240-1886(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. ORCID: https://orcid.org/0000-0002-3389-4325, O'Hare, A., Mellor, D.J. ORCID: https://orcid.org/0000-0001-7141-652X, 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. ORCID: https://orcid.org/0000-0002-3389-4325 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. ORCID: https://orcid.org/0000-0002-3389-4325, 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. ORCID: https://orcid.org/0000-0003-3471-5357, O'Hare, A., Wright, D., Mallon, T., McCormick, C., Orton, R.J. ORCID: https://orcid.org/0000-0002-3389-4325, 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. ORCID: https://orcid.org/0000-0002-3389-4325, Grindlay, J., Birtwistle, M., Vyshemirsky, V. ORCID: https://orcid.org/0000-0003-1984-0053, Gilbert, D., Calder, M. ORCID: https://orcid.org/0000-0001-5033-7232, 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. ORCID: https://orcid.org/0000-0002-3389-4325, 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. ORCID: https://orcid.org/0000-0002-3389-4325(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. ORCID: https://orcid.org/0000-0002-3389-4325, 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. ORCID: https://orcid.org/0000-0002-3389-4325(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. ORCID: https://orcid.org/0000-0002-3389-4325, 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, Muffy ORCID: https://orcid.org/0000-0001-5033-7232, Vyshemirsky, Vladislav ORCID: https://orcid.org/0000-0003-1984-0053, Gilbert, David and Orton, Richard ORCID: https://orcid.org/0000-0002-3389-4325(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. ORCID: https://orcid.org/0000-0002-3389-4325, 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. ORCID: https://orcid.org/0000-0002-3389-4325, 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 Feb 17 02:42:30 2026 GMT.